Kilho Eom's blog
https://imechanica.org/blog/93
enWCCM 2016, Mini-symposium on "Computational Mechanics of Biological Materials at Small Scales" (Call for Abstracts)
https://imechanica.org/node/18949
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/74">conference</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/10786">WCCM 2016</a></div><div class="field-item odd"><a href="/taxonomy/term/8046">computational simulations</a></div><div class="field-item even"><a href="/taxonomy/term/321">biological materials</a></div><div class="field-item odd"><a href="/taxonomy/term/2276">self-assembly</a></div><div class="field-item even"><a href="/taxonomy/term/10787">Small-Scale Biomechanics</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p class="MsoNoSpacing" align="center"><span><strong><span lang="EN-US" xml:lang="EN-US">World Congress on Computational Mechanics (WCCM XII) &</span></strong></span></p>
<p class="MsoNoSpacing" align="center"><strong><span lang="EN-US" xml:lang="EN-US"><span>6th Asia-Pacific Congress on Computational Mechanics (APCOM VI)</span></span></strong></p>
<p class="MsoNoSpacing" align="center"><strong><span lang="EN-US" xml:lang="EN-US"> </span></strong></p>
<p class="MsoNoSpacing" align="center"><span><strong><em><span lang="EN-US" xml:lang="EN-US">Mini-symposium on “Computational Mechanics of Biological Materials at Small Scales”</span></em></strong></span></p>
<p class="MsoNoSpacing" align="center"><span lang="EN-US" xml:lang="EN-US"> </span></p>
<p class="MsoNoSpacing" align="center"><span><strong><span lang="EN-US" xml:lang="EN-US">Call For Abstracts</span></strong></span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US">Biological materials at small scales have recently received attention from the community due to their important role in not only biology but also material sciences and engineering. In particular, the last decade has witnessed the development of novel biological materials such as protein fibrils, which are formed by the self-assembly of biological building blocks such as biomolecules (e.g. protein molecule, DNA, etc.). They are an interesting material as they exhibit the unique material properties such as mechanical properties. This observation suggests the necessity of studying the structures and properties of biological materials at small scales.</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"><span> </span>For the last two decades, with advances in computational simulation techniques, the structures and properties of biological materials at small scale have been extensively studied. Since the late 1990s, when the mechanical behavior of muscle protein domain was characterized using molecular dynamics simulations, the computational simulation technique has become an important toolkit for not only understanding the structures and properties of biological materials ranging from a single-molecule to self-assembled biological structures but also designing a bio-inspired or biomimetic materials that can perform unique mechanical functions.</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"><span> </span>With recent explosive expansion of the area of computational biological material science as described above, this mini-symposium is aimed towards presenting the current state-of-arts in computational research works on biological materials at small scales. This mini-symposium invites the contributions from the computational simulations of small-scale biological materials.</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"> </span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US">Potential topics include but are not limited to:</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"><span>o<span> </span></span></span><span lang="EN-US" xml:lang="EN-US">Computational design of protein materials</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"><span>o<span> </span></span></span><span lang="EN-US" xml:lang="EN-US">Computational design of DNA-based materials</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"><span>o<span> </span></span></span><span lang="EN-US" xml:lang="EN-US">Computational design of interface between biological materials and nano-materials</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"><span>o<span> </span></span></span><span lang="EN-US" xml:lang="EN-US">Single-molecule manipulation <em>in silico</em></span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"><span>o<span> </span></span></span><span lang="EN-US" xml:lang="EN-US">Protein unfolding mechanics</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"><span>o<span> </span></span></span><span lang="EN-US" xml:lang="EN-US">Mechanical characterization of biological materials</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"><span>o<span> </span></span></span><span lang="EN-US" xml:lang="EN-US">Protein self-assembly (e.g. protein fibril, etc.)</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"><span>o<span> </span></span></span><span lang="EN-US" xml:lang="EN-US">DNA self-assembly (e.g. origami, etc.)</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"><span>o<span> </span></span></span><span lang="EN-US" xml:lang="EN-US">Atomistic simulations / Multi-scale simulations / Coarse-grained simulations</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"> </span><span lang="EN-US" xml:lang="EN-US"> </span></p>
<p class="MsoNoSpacing"><strong><span lang="EN-US" xml:lang="EN-US">Organizing Committee</span></strong></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US">Prof. Kilho Eom, Ph.D. (E-mail: </span><span lang="EN-US" xml:lang="EN-US"><a href="mailto:kilhoeom@skku.edu"><span>kilhoeom@skku.edu</span></a></span><span lang="EN-US" xml:lang="EN-US">), Sungkyunkwan University (SKKU), Republic of Korea</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"> </span></p>
<p class="MsoNoSpacing"><strong><span lang="EN-US" xml:lang="EN-US">Important Date</span></strong></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US">November 30, 2015<span> </span>Deadline for abstract submission</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US">January 30, 2015<span> </span><span> </span>Notification of acceptance</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US">March 31, 2016<span> </span>Deadline for pre-registration</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US">July 24-29, 2015<span> </span>Congress</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"> </span><span lang="EN-US" xml:lang="EN-US"> </span></p>
<p> Normal<br />
0</p>
<p> false<br />
false<br />
false</p>
<p> EN-US<br />
JA<br />
X-NONE</p>
<p> /* Style Definitions */<br />
table.MsoNormalTable<br />
{mso-style-name:"Table Normal";<br />
mso-tstyle-rowband-size:0;<br />
mso-tstyle-colband-size:0;<br />
mso-style-noshow:yes;<br />
mso-style-priority:99;<br />
mso-style-parent:"";<br />
mso-padding-alt:0cm 5.4pt 0cm 5.4pt;<br />
mso-para-margin-top:0cm;<br />
mso-para-margin-right:0cm;<br />
mso-para-margin-bottom:10.0pt;<br />
mso-para-margin-left:0cm;<br />
mso-pagination:widow-orphan;<br />
font-size:12.0pt;<br />
font-family:Cambria;<br />
mso-ascii-font-family:Cambria;<br />
mso-ascii-theme-font:minor-latin;<br />
mso-hansi-font-family:Cambria;<br />
mso-hansi-theme-font:minor-latin;<br />
mso-fareast-language:JA;}</p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US">Additional information can be found at </span><span lang="EN-US" xml:lang="EN-US"><a href="http://www.wccm2016.org"><span>http://www.wccm2016.org</span></a></span><span lang="EN-US" xml:lang="EN-US">. </span></p>
</div></div></div><div class="field field-name-upload field-type-file field-label-hidden"><div class="field-items"><div class="field-item even"><table class="sticky-enabled">
<thead><tr><th>Attachment</th><th>Size</th> </tr></thead>
<tbody>
<tr class="odd"><td><span class="file"><img class="file-icon" alt="PDF icon" title="application/pdf" src="/modules/file/icons/application-pdf.png" /> <a href="https://imechanica.org/files/Session-call-for-abstracts_0.pdf" type="application/pdf; length=96077">Session-call-for-abstracts.pdf</a></span></td><td>93.83 KB</td> </tr>
</tbody>
</table>
</div></div></div>Wed, 07 Oct 2015 01:21:03 +0000Kilho Eom18949 at https://imechanica.orghttps://imechanica.org/node/18949#commentshttps://imechanica.org/crss/node/18949Call for Papers: Special Issue of "Nanoscale Biological Materials" for Journal of Nanomaterials
https://imechanica.org/node/18510
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/10618">Journal of Nanomaterials</a></div><div class="field-item odd"><a href="/taxonomy/term/3236">Special issue</a></div><div class="field-item even"><a href="/taxonomy/term/10619">Nanoscale Biological Materials</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>Special Issue on <span><strong>Nanoscale Biological Materials</strong></span> <strong><span> </span></strong>
</p><p><strong><span>Call for Papers</span></strong></p>
<p>Biological materials at nanoscale such as proteins, antibodies, lipids, and nucleic acids have recently received significant attention due to their importance in understanding biology as well as engineering and materials science. In particular, it is necessary to characterize the microstructures and material properties of nanoscale biological materials at nanoscale not only for understanding in depth their biological role but also for providing design methodologies and techniques to optimize engineering products and systems.</p>
<p>Over the past 20 years, with technological advance in single-molecule experiments and multiscale computer simulations, the function of biological materials has been significantly unveiled. Their functions are found to be related to their microstructures and material properties. Meanwhile, as inspired by some biological materials (e.g., muscle protein, water, and ion channel) that perform excellent mechanical functions, there are notable efforts to develop biomimetic and bioinspired materials with controllable performance.</p>
<p>With recent advancements in the area of nanoscale biological materials as described above, this special issue is aimed towards presenting the current state of arts in understanding the structures, material properties, and functions of nanoscale biological materials including DNA, RNA, protein, lipid, and self-assembled structures made of these building blocks. This special issue is aimed to publish high-quality research articles and review articles addressing the aforementioned aspects of nanoscale biological materials.</p>
<p>Potential topics include, but are not limited to:</p>
<ul class="li_special"><li>Nanoscale biomimetics and bioinspired applications</li>
<li>Biosensors</li>
<li>Biomolecular assembly</li>
<li>Biomechanical response</li>
<li>Bioinspired materials</li>
<li>Self-assembled biological structures (e.g., protein fibrils, protein films, DNA condensation, and DNA origami) and their characterization</li>
<li>Multiscale modeling of structure, dynamics, and assembly of biomaterials</li>
<li>Single-molecule techniques for biological material characterization</li>
<li>Mechanical tests of biological materials at nanoscale</li>
<li>Material properties of biological materials</li>
<li>Transport properties of biological molecules</li>
<li>Mechanical tests of biological materials at nanoscale</li>
<li>Interface between biological molecules and nanomaterials </li>
</ul><p>Authors can submit their manuscripts via the Manuscript Tracking System at <a href="http://mts.hindawi.com/submit/journals/jnm/nbm/">http://mts.hindawi.com/submit/journals/jnm/nbm/</a>.</p>
<p><span><strong>Manuscript Due:</strong> Friday, 1 January, 2016<br /><strong>1st Round of Review:</strong> Friday, 25 March, 2016<br /><strong>Publication Due:</strong> Friday, 20 May, 2016</span></p>
<p>Lead Guest Editor
</p><ul><li><a href="mailto:kilhoeom@skku.edu">Kilho Eom</a>, Sungkyunkwan University, Seoul, Republic of Korea</li>
</ul><p>Guest Editors
</p><ul><li><a href="mailto:serdal@nyu.edu">Serdal Kirmizialtin</a>, New York University, Abu Dhabi, UAE</li>
<li><a href="mailto:yal310@lehigh.edu">Yaling Liu</a>, Lehigh University, Bethlehem, USA</li>
<li><a href="mailto:xuzp@tsinghua.edu.cn">Zhiping Xu</a>, Tsinghua University, Beijing, China</li>
</ul></div></div></div><div class="field field-name-upload field-type-file field-label-hidden"><div class="field-items"><div class="field-item even"><table class="sticky-enabled">
<thead><tr><th>Attachment</th><th>Size</th> </tr></thead>
<tbody>
<tr class="odd"><td><span class="file"><img class="file-icon" alt="PDF icon" title="application/pdf" src="/modules/file/icons/application-pdf.png" /> <a href="https://imechanica.org/files/Call-for-Papers_639798.pdf" type="application/pdf; length=128158">Call-for-Papers_639798.pdf</a></span></td><td>125.15 KB</td> </tr>
</tbody>
</table>
</div></div></div>Mon, 29 Jun 2015 05:27:08 +0000Kilho Eom18510 at https://imechanica.orghttps://imechanica.org/node/18510#commentshttps://imechanica.org/crss/node/18510Call for abstracts for session "Small-Scale, and Multiiscale Biomechanics" in 2015 World Congress on Advances in Structural Engineering and Mechanics (ASEM)
https://imechanica.org/node/18263
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/74">conference</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/10461">ASEM (Advances in Structural Engineering and Mechanics)</a></div><div class="field-item odd"><a href="/taxonomy/term/297">multiscale mechanics</a></div><div class="field-item even"><a href="/taxonomy/term/10462">small-scale mechanics</a></div><div class="field-item odd"><a href="/taxonomy/term/19">biomechanics</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p class="MsoNoSpacing"><strong><span lang="EN-US" xml:lang="EN-US">Call for Abstracts (2015 World Congress on Advances in Structural Engineering and Mechanics)</span></strong></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"> </span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US">Program: MS566 (in Conference of Multiscale and Multiphysics Mechanics)</span></p>
<p class="MsoNoSpacing"><strong><span lang="EN-US" xml:lang="EN-US">Session: “Small-Scale, and Multiscale Biomechanics”</span></strong></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"> </span></p>
<p class="MsoNoSpacing"><span><span lang="EN-US" xml:lang="EN-US">Organizer: Prof. Kilho Eom (E-mail: </span><span lang="EN-US" xml:lang="EN-US"><a href="mailto:kilhoeom@skku.edu">kilhoeom@skku.edu</a></span><span lang="EN-US" xml:lang="EN-US"> or </span><span lang="EN-US" xml:lang="EN-US"><a href="mailto:kilhoeom@gmail.com">kilhoeom@gmail.com</a></span></span><span lang="EN-US" xml:lang="EN-US"><span>)</span></span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"> </span></p>
<p class="MsoNoSpacing"><span><strong><span lang="EN-US" xml:lang="EN-US">THEME</span></strong></span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"><span>This session is aimed towards presenting the current state-of-art in multiscale and/or small-scale mechanics of biological systems at multiple spatial scales ranging from atomistic scale to mesoscale and macroscopic scales. This session is suitable for not only computational researchers but also experimental researchers, who have been studying the mechanics of biological systems at multiple spatial scales. The topics of this session may include but not limited to atomistic/multiscale simulation and single-molecule studies of biological systems ranging from single protein molecule to macromolecular protein assemblies and bulk-scale biological components (e.g. muscle).</span></span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"> </span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"> </span></p>
<p class="MsoNoSpacing"><strong><span lang="EN-US" xml:lang="EN-US">Important Dates</span></strong></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US">May 11, 2015<span> </span>Submission of abstract</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US">June 15, 2015<span> </span>Submission of conference paper (Optional)</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US">June 30, 2015<span> </span>Last day for early registration</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US">July 31, 2015<span> </span>Last day for pre-registration</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US">August 25-19, 2015<span> </span>Congress</span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"> </span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US"> </span></p>
<p class="MsoNoSpacing"><span lang="EN-US" xml:lang="EN-US">For more information, please visit the official website of the congress: </span><span lang="EN-US" xml:lang="EN-US"><a href="http://asem.cti3.com/asem15.htm"><span>http://asem.cti3.com/asem15.htm</span></a></span></p>
</div></div></div><div class="field field-name-upload field-type-file field-label-hidden"><div class="field-items"><div class="field-item even"><table class="sticky-enabled">
<thead><tr><th>Attachment</th><th>Size</th> </tr></thead>
<tbody>
<tr class="odd"><td><span class="file"><img class="file-icon" alt="PDF icon" title="application/pdf" src="/modules/file/icons/application-pdf.png" /> <a href="https://imechanica.org/files/Call%20for%20Abstracts.pdf" type="application/pdf; length=231590">Call for Abstracts.pdf</a></span></td><td>226.16 KB</td> </tr>
</tbody>
</table>
</div></div></div>Mon, 04 May 2015 03:28:37 +0000Kilho Eom18263 at https://imechanica.orghttps://imechanica.org/node/18263#commentshttps://imechanica.org/crss/node/18263Controllable viscoelastic behavior of vertically aligned carbon nanotube arrays
https://imechanica.org/node/15507
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/678">Energy dissipation</a></div><div class="field-item odd"><a href="/taxonomy/term/795">viscoelasticity</a></div><div class="field-item even"><a href="/taxonomy/term/4643">Nano-indentation</a></div><div class="field-item odd"><a href="/taxonomy/term/9239">carbon nanotube array</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>
<strong>Controllable viscoelastic behavior of vertically aligned carbon nanotube arrays</strong>
</p>
<p>
</p>
<p>
Kilho Eom, Kihwan Nam, Huihun Jung, Pilhan Kim, Michael S. Strano, Jae-Hee Han, Taeyun Kwon
</p>
<p>
</p>
<p>
<strong>Abstract</strong>
</p>
<p>
<span>We have characterized the mechanical behavior of aligned carbon nanotube (CNT) arrays that serve as foam-like energy absorbing materials, by using atomic force microscope indentation. It is shown that the mechanical properties (e.g. elastic modulus, adhesion force, and energy dissipation) of aligned CNT arrays are dependent on the length of CNTs as well as chemical environment that surrounds CNT arrays. More remarkably, it is found that CNT array made of CNTs with their length of 10 μm exhibits the excellent damping property (i.e. energy dissipation) higher than that of a conventional composite such as Kevlar. It is also shown that the energy dissipation of CNT arrays during loading–unloading process can be reduced by the solution surrounding CNT array, and that the decrease of energy dissipation for CNT array due to solution depends on the solution type, which mediates the interaction between individual nanotubes. Our study sheds light on the design principles for CNT array-based foam-like materials.</span>
</p>
<p>
</p>
<p>
This paper was published at <em>Carbon</em>, and attached in pdf format.
</p>
</div></div></div><div class="field field-name-upload field-type-file field-label-hidden"><div class="field-items"><div class="field-item even"><table class="sticky-enabled">
<thead><tr><th>Attachment</th><th>Size</th> </tr></thead>
<tbody>
<tr class="odd"><td><span class="file"><img class="file-icon" alt="PDF icon" title="application/pdf" src="/modules/file/icons/application-pdf.png" /> <a href="https://imechanica.org/files/Carbon%20%282013%29%20Eom%20j.carbon.2013.08.030%20Controllable%20viscoelastic%20behavior%20of%20vertically%20aligned%20carbon%20nanotube%20arrays.pdf" type="application/pdf; length=2362061" title="Carbon (2013) Eom j.carbon.2013.08.030 Controllable viscoelastic behavior of vertically aligned carbon nanotube arrays.pdf">Carbon (2013) Eom j.carbon.2013.08.030 Controllable viscoelastic behavior of vertically aligned carbon nanotube arrays.pdf</a></span></td><td>2.25 MB</td> </tr>
</tbody>
</table>
</div></div></div>Tue, 22 Oct 2013 05:30:03 +0000Kilho Eom15507 at https://imechanica.orghttps://imechanica.org/node/15507#commentshttps://imechanica.org/crss/node/15507Relationship between disease-specific structures of amyloid fibrils and their mechanical properties
https://imechanica.org/node/14078
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/1759">normal mode analysis</a></div><div class="field-item odd"><a href="/taxonomy/term/1760">elastic network model</a></div><div class="field-item even"><a href="/taxonomy/term/4862">Coarse-Grained Modeling</a></div><div class="field-item odd"><a href="/taxonomy/term/6261">amyloid fibril</a></div><div class="field-item even"><a href="/taxonomy/term/8378">beam model</a></div><div class="field-item odd"><a href="/taxonomy/term/8379">disease specificity</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>
<strong>Relationship between disease-specific structures of amyloid fibrils and their mechanical properties</strong>
</p>
<p>
Gwonchan Yoon, Young Gab Kim, Kilho Eom*, Sungsoo Na*
</p>
<p>
</p>
<p>
<strong>ABSTRACT</strong>
</p>
<p>
<span>It has recently been reported that the mechanical behavior of prion nanofibrils may play a critical role in expression of neurodegenerative diseases. In this work, we have studied the mechanical behavior of HET-s prion nanofibrils using an elastic network model. We have shown that the mechanical properties of prion nanofibrils formed as left-handed β-helices are different from those of non-prion nanofibrils formed as right-handed β-helices. In particular, the bending behavior of prion nanofibrils depends on the length of the nanofibril and that the bending rigidity of the prion nanofibril is larger than that of the non-prion nanofibril.</span>
</p>
<p>
</p>
<p>
This paper was published at Applied Physics Letters, and you may read the full text of an article linked <a href="https://docs.google.com/file/d/0BxbHuVN5A0X1elkyU1lRU3FqRjA/preview">here</a> .
</p>
</div></div></div>Thu, 24 Jan 2013 20:25:33 +0000Kilho Eom14078 at https://imechanica.orghttps://imechanica.org/node/14078#commentshttps://imechanica.org/crss/node/14078Continuum Modeling of Nonlinear Vibration of Graphene Resonators and Graphene-Based Mass Detection
https://imechanica.org/node/13359
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/8020">von Karman plate model</a></div><div class="field-item odd"><a href="/taxonomy/term/8021">graphene resonator</a></div><div class="field-item even"><a href="/taxonomy/term/8022">mass sensing</a></div><div class="field-item odd"><a href="/taxonomy/term/8023">nonlinear vibration</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>
We have employed continuum elastic model such as plate model for understanding the nonlinear vibration behavior of monolayer graphene and graphene resonator-based mass sensing. This work was published in Nanoscale Research Letters (Vol. <strong>7</strong>, Art No. 499, 2012).
</p>
<p>
</p>
<p>
<strong>Abstract</strong>
</p>
<p><span class="Apple-style-span"></span></p>
<p>
Graphene has received significant attention due to its excellent mechanical properties, which has resulted in the emergence of graphene-based nano-electro-mechanical system such as nanoresonators. The nonlinear vibration of a graphene resonator and its application to mass sensing (based on nonlinear oscillation) have been poorly studied, although a graphene resonator is able to easily reach the nonlinear vibration. In this work, we have studied the nonlinear vibration of a graphene resonator driven by a geometric nonlinear effect due to an edge-clamped boundary condition using a continuum elastic model such as a plate model. We have shown that an in-plane tension can play a role in modulating the nonlinearity of a resonance for a graphene. It has been found that the detection sensitivity of a graphene resonator can be improved by using nonlinear vibration induced by an actuation force-driven geometric nonlinear effect. It is also shown that an in-plane tension can control the detection sensitivity of a graphene resonator that operates both harmonic and nonlinear oscillation regimes. Our study suggests the design principles of a graphene resonator as a mass sensor for developing a novel detection scheme using graphene-based nonlinear oscillators.
</p>
<p></p>
<p>
</p>
<p>Keywords: Graphene resonator; Mass sensing; Nonlinear oscillation; NEMS </p>
<p>
</p>
</div></div></div><div class="field field-name-upload field-type-file field-label-hidden"><div class="field-items"><div class="field-item even"><table class="sticky-enabled">
<thead><tr><th>Attachment</th><th>Size</th> </tr></thead>
<tbody>
<tr class="odd"><td><span class="file"><img class="file-icon" alt="PDF icon" title="application/pdf" src="/modules/file/icons/application-pdf.png" /> <a href="https://imechanica.org/files/Nanoscale%20Res%20Lett%207%20%282012%29%20Eom%20499%20Nonlinear%20vibration%20behavior%20of%20graphene%20resonators%20and%20their%20applications%20in%20sensitive%20mass%20detection.pdf" type="application/pdf; length=406973" title="Nanoscale Res Lett 7 (2012) Eom 499 Nonlinear vibration behavior of graphene resonators and their applications in sensitive mass detection.pdf">Nanoscale Res Lett 7 (2012) Eom 499 Nonlinear vibration behavior of graphene resonators and their applications in sensitive mass detection.pdf</a></span></td><td>397.43 KB</td> </tr>
</tbody>
</table>
</div></div></div>Wed, 03 Oct 2012 16:51:52 +0000Kilho Eom13359 at https://imechanica.orghttps://imechanica.org/node/13359#commentshttps://imechanica.org/crss/node/13359Loading device effect on protein unfolding mechanics
https://imechanica.org/node/12770
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/6491">free energy landscape</a></div><div class="field-item odd"><a href="/taxonomy/term/7707">protein unfolding mechanics</a></div><div class="field-item even"><a href="/taxonomy/term/7708">unfolding pathway</a></div><div class="field-item odd"><a href="/taxonomy/term/7709">single-molecule manipulation</a></div><div class="field-item even"><a href="/taxonomy/term/7710">coarse-grained simulation</a></div><div class="field-item odd"><a href="/taxonomy/term/7711">bond rupture</a></div><div class="field-item even"><a href="/taxonomy/term/7712">loading device effect</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>
We have studied the effect of loading device such as its stiffness on the mechanical force-driven protein unfolding based on coarse-grained simulation (i.e. Brownian dynamics simulation with coarse-grained model). We have shown that loading device effect has played a vital role on not only the unfolding force but also the unfolding pathway of a protein. Moreover, the loading device effect on protein unfolding force has been elucidated by a theoretical model such as Kramers theory with appropriate free energy landscape. This work was published at <em>Journal of Chemical Physics</em> (for link, click <a href="http://link.aip.org/link/?JCP/137/025102">http://link.aip.org/link/?JCP/137/025102</a>).
</p>
<p>
</p>
<p>
<img src="http://jcp.aip.org/FEWebservices/ImagesWebservice?id=JCPSA6000137000002025102000001&type=online&fid=2" alt="Loading device effect on protein unfolding pathway" title="Loading device effect on protein unfolding pathway" width="700" height="979" /> <strong>Figure.</strong> The unfolding pathway of a ubiquitin is shown when it is pulled with a soft loading device (a) or a stiff force probe (b).
</p>
</div></div></div>Fri, 13 Jul 2012 07:52:37 +0000Kilho Eom12770 at https://imechanica.orghttps://imechanica.org/node/12770#commentshttps://imechanica.org/crss/node/12770Good Vibration for Cancer Diagnosis
https://imechanica.org/node/12453
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/188">Microcantilever</a></div><div class="field-item odd"><a href="/taxonomy/term/1879">resonance</a></div><div class="field-item even"><a href="/taxonomy/term/7479">Cancer Diagnosis</a></div><div class="field-item odd"><a href="/taxonomy/term/7480">Enzymatic Activity</a></div><div class="field-item even"><a href="/taxonomy/term/7481">Frequency Shift</a></div><div class="field-item odd"><a href="/taxonomy/term/7482">Membrane Type 1-Matrix Metalloproteinase</a></div><div class="field-item even"><a href="/taxonomy/term/7483">Peptide Cleavage</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>
We have reported a cantilever-based diagnosis of cancer by measuring the proteolytic activity of proteinases (i.e. membrane type 1-matrix metalloproteinase [MT1-MMP]) expressed on live cancer cells based on the resonant cantilevers. The detection principle is the direct transduction of MT1-MMP-driven peptide cleavage on a cantilever surface into the shifts of the resonance of the cantilever. It is shown that cantilever-based bioassay enables the quantification of the expression level of MT1-MMP on cancer cells (or genetically engineered cells) as well as the proteolytic activity of MT1-MMP (or mutant MT1-MMP) extracted from live cancer cells and genetically engineered cells. Our study sheds light on cantilever bioassay for its potential in quantifying the metastasis state of cancer cells.
</p>
<p>
Our work was published online at <em>Angewandte Chemie</em>. For our article, please click the <a href="http://onlinelibrary.wiley.com/doi/10.1002/anie.201108830/abstract">link</a> (<a href="http://onlinelibrary.wiley.com/doi/10.1002/anie.201108830/abstract">http://onlinelibrary.wiley.com/doi/10.1002/anie.201108830/abstract</a>)
</p>
<p>
</p>
<p>
</p>
<p>
<img src="http://onlinelibrary.wiley.com/store/10.1002/anie.201108830/asset/image_n/ncontent.gif?v=1&s=e6ac6534cc345d1215e5ce7ae6c1dc2a16d25725" alt="Detection Principles of Cantilever Assay for Cancer Diagnosis" title="Detection principles of cantilever assay for cancer diagnosis" width="346" height="98" />
</p>
<p>
Schematics: Detection principles of cantilever-based assay for quantifying the expression level of MT1-MMP as well as the proteolytic activity of MT1-MMP extracted from cancer cells.
</p>
<p>
This article is selected as an Inside Back Cover Article at <em>Angewandte Chemie</em>. Cover Art is shown as below:
</p>
<p>
<img src="http://onlinelibrary.wiley.com/store/10.1002/anie.201203359/asset/image_n/ncontent.gif?v=1&s=491f55dca26f247ddae36b29cefeecd959fdc9a0" alt=" " width="197" height="280" /></p>
<p>
<span class="Apple-style-span"><strong>Cover Descriptions:</strong> Active matrix metalloproteinases (MMPs; green missiles in the picture) expressed on a cancer cell surface can be sensed by a resonant cantilever device (satellite arm in the picture) as D. S. Yoon, T. Kwon, and co-workers report in their Communication (DOI:10.1002/anie.201108830). Active MMPs attack the peptide sequence immobilized on the cantilever surface, and the peptide cleavage leads to an increase in the resonant frequency of the cantilever owing to a decrease in the mass of immobilized peptide.</span>
</p>
</div></div></div>Wed, 16 May 2012 15:01:35 +0000Kilho Eom12453 at https://imechanica.orghttps://imechanica.org/node/12453#commentshttps://imechanica.org/crss/node/12453Book "Simulations in Nanobiotechnology"
https://imechanica.org/node/11280
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/128">education</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/188">Microcantilever</a></div><div class="field-item odd"><a href="/taxonomy/term/258">NEMS</a></div><div class="field-item even"><a href="/taxonomy/term/278">nanotechnology</a></div><div class="field-item odd"><a href="/taxonomy/term/387">biomimetics</a></div><div class="field-item even"><a href="/taxonomy/term/671">graphene</a></div><div class="field-item odd"><a href="/taxonomy/term/1188">atomistic simulation</a></div><div class="field-item even"><a href="/taxonomy/term/1284">Protein</a></div><div class="field-item odd"><a href="/taxonomy/term/4862">Coarse-Grained Modeling</a></div><div class="field-item even"><a href="/taxonomy/term/4864">Protein Mechanics</a></div><div class="field-item odd"><a href="/taxonomy/term/6257">nanoresonator</a></div><div class="field-item even"><a href="/taxonomy/term/6747">Biotechnology</a></div><div class="field-item odd"><a href="/taxonomy/term/6748">Nanopore</a></div><div class="field-item even"><a href="/taxonomy/term/6749">DNA Sequencing</a></div><div class="field-item odd"><a href="/taxonomy/term/6750">Continuum Model</a></div><div class="field-item even"><a href="/taxonomy/term/6751">Nanoparticle</a></div><div class="field-item odd"><a href="/taxonomy/term/6752">Membrane Protein</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>
I am happy to announce the publication of a book <a href="http://www.crcpress.com/product/isbn/9781439835043;jsessionid=7zAUWEac9DKUcTVr6el3Bg**">"Simulations in Nanobiotechnology"</a>, which was contributed from researchers (including iMechanicians) who have expertise in the area of nanobiotechnology. The book is aimed at presenting the current state-of-arts in computational simulations of biological objects such as proteins as well as nanomaterials such as graphene, and also bio-nano-hybrid system such as nanopore-biomolecule interactions. This book provides the insight into the simulation-based characterization in nanobiotechnology.
</p>
<p>
</p>
<p>
</p>
<p>
<img src="http://www.crcpress.com/coverimage/?isbn=9781439835043&size=medium&flat=false" alt=" " width="180" height="255" />
</p>
<p>
Editor: Kilho Eom
</p>
<p>
Publisher: CRC Press (Oct. 17, 2011)
</p>
<p>
ISBN: <span class="Apple-style-span">9781439835043</span>
</p>
<p>
</p>
<p>
Presenting the simulation-based nanoscale characterizations in biological science, <em>Part 1</em>:
</p>
<ul><li>Describes recent efforts in MD simulation-based characterization and CG modeling of DNA and protein transport dynamics in the nanopore and nanochannel</li>
<li>Presents recent advances made in continuum mechanics-based modeling of membrane proteins</li>
<li>Summarizes theoretical frameworks along with atomistic simulations in single-molecule mechanics</li>
<li>Provides the computational simulation-based mechanical characterization of protein materials</li>
<p>
</p>
</ul><p>
Discussing advances in modeling techniques and their applications, <em>Part 2</em>:
</p>
<ul><li>Describes advances in nature-inspired material design; atomistic simulation-based characterization of nanoparticles’ optical properties; and nanoparticle-based applications in therapeutics</li>
<li>Overviews of the recent advances made in experiment and simulation-based characterizations of nanoscale adhesive properties</li>
<li>Suggests theoretical frameworks with experimental efforts in the development of nanoresonators for future nanoscale device designs</li>
<li>Delineates advances in theoretical and computational methods for understanding the mechanical behavior of a graphene monolayer</li>
</ul><p>
</p>
<p>
<strong>Table of Contents</strong>
</p>
<p>
Chapter 1. Introduction to Simulations in Nanobiotechnology (<a href="user/93">Kilho Eom</a>)
</p>
<p>
Chapter 2. Modeling the Interface between Biological and Synthetic Components in Hybrid Nanosystems (<a href="http://bionano.physics.illinois.edu/People/rogan.html">Rogan Carr</a>, <a href="http://bionano.physics.illinois.edu/People/jeff.html">Jeffrey Comer</a>, and <a href="http://bionano.physics.illinois.edu/People/alek.html">Aleksei Aksimentiev</a>)
</p>
<p>
Chapter 3. Coarse-Grained Modeling of Large Protein Complexes for Understanding Their Conformational Dynamics (<a href="user/93">Kilho Eom</a>, Gwonchan Yoon, Jae In Kim, and Sungsoo Na)
</p>
<p>
Chapter 4. Continuum Modeling and Simulation of Membrane Proteins (<a href="user/15">Xi Chen</a>)
</p>
<p>
Chapter 5. Exploring the Energy Landscape of Biopolymers Using Single-Molecule Force Spectroscopy and Molecular Simulations (<a href="http://newton.kias.re.kr/~hyeoncb/">Changbong Hyeon</a>)
</p>
<p>
Chapter 6. Coarse-Grained Modeling of Deoxyribonucleic Acid-Nanopore Interactions (<a href="http://www.lehigh.edu/~yal310/people.html">Yaling Liu, Abhijit Ramachandra, and Qingjiang Guo</a>)
</p>
<p>
Chapter 7. Mechanical Characterization of Protein Materials (<a href="user/93">Kilho Eom</a>)
</p>
<p>
Chapter 8. Nature's Flexible and Tough Armor: Geometric and Size Effects on Diatom-Inspired Nanoscale Glass (<a href="user/24957">Andre P. Garcia</a>, <a href="http://web.mit.edu/mbuehler/www/group/sen.html">Dipanjan Sen</a>, and <a href="user/74">Markus J. Buehler</a>)
</p>
<p>
Chapter 9. Resonant Theranostics: A New Nanotechnological Method for Cancer Treatment Using X-ray Spectroscopy of Nanoparticles (<a href="http://www.astronomy.ohio-state.edu/~nahar/">Sultana N. Nahar</a>, <a href="http://www.astronomy.ohio-state.edu/~pradhan/">Anil K. Pradhan</a>, and Maximiliano Montenegro)
</p>
<p>
Chapter 10. Nanomechanical In Vitro Molecular Recognitions: Mechanical Resonance-Based Detections (<a href="user/93">Kilho Eom</a>, and <a href="http://www.molecularscience.org/bbs/board.php?bo_table=member_01&wr_id=2">Taeyun Kwon</a>)
</p>
<p>
Chapter 11. Surface-Enhanced Microcantilever Sensors with Novel Structures (<a href="http://www.coe.pku.edu.cn/faculty/duanhuiling/web/home.html">H.L. Duan</a>)
</p>
<p>
Chapter 12. Nanoscale Adhesion Interactions in 1D and 2D Nanostructure-Based Material Systems (<a href="http://bingweb.binghamton.edu/~cke/Members.html">Changhong Ke, and Meng Zheng</a>)
</p>
<p>
Chapter 13. Advances in Nanoresonators: Towards Ultimate Mass, Force, and Molecule Sensing (<a href="http://bingweb.binghamton.edu/~cke/Members.html">Changhong Ke, and Qing Wei</a>)
</p>
<p>
Chapter 14. Mechanical Behavior of Monolayer Graphene by Continuum and Atomistic Modeling (<a href="user/4585">Qiang Lu</a>, and <a href="user/22">Rui Huang</a>)
</p>
<p>
</p>
</div></div></div>Wed, 19 Oct 2011 07:18:35 +0000Kilho Eom11280 at https://imechanica.orghttps://imechanica.org/node/11280#commentshttps://imechanica.org/crss/node/11280Actuation of Microcantilever Using Light-Driven DNA Conformational Changes
https://imechanica.org/node/11262
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/95">nanomechanics</a></div><div class="field-item odd"><a href="/taxonomy/term/188">Microcantilever</a></div><div class="field-item even"><a href="/taxonomy/term/5717">actuation</a></div><div class="field-item odd"><a href="/taxonomy/term/6737">DNA Motor</a></div><div class="field-item even"><a href="/taxonomy/term/6738">i-motif DNA</a></div><div class="field-item odd"><a href="/taxonomy/term/6739">Conformational Change</a></div><div class="field-item even"><a href="/taxonomy/term/6740">Light Irradiation</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>
<strong>Nanomechanical Actuation Driven by Light-Induced DNA Fuel</strong>
</p>
<p>
Kilho Eom, Huihun Jung, Gyudo Lee, Jinsung Park, Kihwan Nam, Sang Woo Lee, Dae Sung Yoon, Jaemoon Yang, and Taeyun Kwon
</p>
<p>
<strong>Abstract</strong>
</p>
<p>
We report the reversible nanomechanical actuation of a microcantilever driven by the light irradiation-induced conformational changes of i-motif DNA chains, which are functionalized on the cantilever's surface. It is shown that light irradiation-driven nanomechanical actuation can be manipulated using DNA hybridization and/or ionic concentrations.
</p>
<p>
</p>
<p>
This work was published online at Chemmical Communications. You can read the paper by clicking the <a href="http://pubs.rsc.org/en/Content/ArticleLanding/2011/CC/C1CC12893K">official website of our paper</a> .
</p>
</div></div></div>Fri, 14 Oct 2011 10:45:13 +0000Kilho Eom11262 at https://imechanica.orghttps://imechanica.org/node/11262#commentshttps://imechanica.org/crss/node/11262AFM Imaging of Single Biomolecules and Their Interactions with Small Molecules
https://imechanica.org/node/10729
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/526">atomic force microscopy</a></div><div class="field-item odd"><a href="/taxonomy/term/6489">Kelvin probe force microscopy</a></div><div class="field-item even"><a href="/taxonomy/term/6490">single-molecule imaging</a></div><div class="field-item odd"><a href="/taxonomy/term/6491">free energy landscape</a></div><div class="field-item even"><a href="/taxonomy/term/6492">binding affinity</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>
<strong>Single-Molecule Recognition of Biomolecular Interaction via Kelvin Probe Force Microscopy</strong>
</p>
<p>
<em>Jinsung Park, Jaemoon Yang, Gyudo Lee, Chang Young Lee, Sungsoo Na, Sang Woo Lee, Seungjoo Haam, Yong-Min Huh, Dae Sung Yoon, Kilho Eom*, Taeyun Kwon*</em>
</p>
<p>
</p>
<p class="articleBody_abstractText">
We report the scanning probe microscope (SPM)-based single-molecule recognition of biomolecular interactions between protein kinase and small ligands (<em>i.e.</em>, ATP and Imatinib). In general, it is difficult to sense and detect the small ligands bound to protein kinase (at single-molecule resolution) using a conventional atomic force microscope (AFM) due to the limited resolution of conventional AFM for detecting the miniscule changes in molecular size driven by ligand binding. In this study, we have demonstrated that Kelvin probe force microscopy (KPFM) is able to articulate the surface potential of biomolecules interacting with ligands (<em>i.e.</em>, the protein kinase–ATP interactions and inhibition phenomena induced by antagonistic molecules) in a label-free manner. Furthermore, measured surface potentials for biomolecular interactions enable quantitative descriptions on the ability of protein kinase to interact with small ligands such as ATP or antagonistic molecules. Our study sheds light on KPFM that allows the precise recognition of single-molecule interactions, which opens a new avenue for the design and development of novel molecular therapeutics.
</p>
<p>Keywords: single molecule; biomolecular interactions; protein kinase; Kelvin probe force microscopy; label-free; surface potential</p>
<p>
</p>
<p>
<img src="http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/ancac3/0/ancac3.ahead-of-print/nn201540c/aop/images/medium/nn-2011-01540c_0004.gif" alt=" " width="500" height="472" />
</p>
<p>
For the full text of the article, you may click <a href="http://pubs.acs.org/doi/abs/10.1021/nn201540c">here</a>. This work was published at <em>ACS Nano</em>.
</p>
<p>
</p>
</div></div></div>Mon, 01 Aug 2011 23:42:57 +0000Kilho Eom10729 at https://imechanica.orghttps://imechanica.org/node/10729#commentshttps://imechanica.org/crss/node/10729Mechanical Characterization of Amyloid Fibrils Using Coarse-Grained Normal Mode Analysis
https://imechanica.org/node/10257
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/1759">normal mode analysis</a></div><div class="field-item odd"><a href="/taxonomy/term/1760">elastic network model</a></div><div class="field-item even"><a href="/taxonomy/term/2936">Elastic properties</a></div><div class="field-item odd"><a href="/taxonomy/term/6261">amyloid fibril</a></div><div class="field-item even"><a href="/taxonomy/term/6262">structure-property relation</a></div><div class="field-item odd"><a href="/taxonomy/term/6263">shear effect</a></div><div class="field-item even"><a href="/taxonomy/term/6264">Timoshenko beam model</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p><span class="Apple-style-span"><strong>Mechanical Characterization of Amyloid Fibrils Using Coarse-Grained Normal Mode Analysis</strong></span></p>
<p><span class="Apple-style-span">Gwonchan Yoon, Jinhak Kwak, Jae In Kim, Sungsoo Na, and Kilho Eom</span></p>
<p><span class="Apple-style-span">Abstract</span></p>
<p><span class="Apple-style-span">Recentexperimental studies have shown that amyloid fibril formed by aggregation of βpeptide exhibits excellent mechanical properties comparable to other proteinmaterials such as actin filaments and microtubules. These excellent mechanicalproperties of amyloid fibrils are related to their functional role in diseaseexpression. This indicates the necessity to understand how an amyloid fibrilachieves the remarkable mechanical properties through self-aggregation withstructural hierarchy, highlighting the structure-property-function relationshipfor amyloids, whereas such relationship still remains elusive. In this work, wehave studied the mechanical properties of human islet amyloid polypeptide(hIAPP) with respect to its structural hierarchies and structural shapes bycoarse-grained normal mode analysis. Our simulation shows that hIAPP fibril canachieve the excellent bending rigidity via specific aggregation pattern such asantiparallel stacking of β peptides. Moreover, we have found thelength-dependent mechanical properties of amyloids. This length-dependentproperty has been elucidated from Timoshenko beam model that takes into accountthe shear effect on the bending of amyloids. In summary, our study sheds lighton the importance of not only the molecular architecture, which encodes themechanical properties of the fibril, but also the shear effect on themechanical (bending) behavior of the fibril.</span></p>
<p> </p>
<p><span class="Apple-style-span">This manuscript will appear at <em>Advanced Functional Materials</em>.</span> </p>
</div></div></div><div class="field field-name-upload field-type-file field-label-hidden"><div class="field-items"><div class="field-item even"><table class="sticky-enabled">
<thead><tr><th>Attachment</th><th>Size</th> </tr></thead>
<tbody>
<tr class="odd"><td><span class="file"><img class="file-icon" alt="PDF icon" title="application/pdf" src="/modules/file/icons/application-pdf.png" /> <a href="https://imechanica.org/files/manuscript_Final_AdvFunctMater.pdf" type="application/pdf; length=4054102" title="manuscript_Final_AdvFunctMater.pdf">manuscript_Final_AdvFunctMater.pdf</a></span></td><td>3.87 MB</td> </tr>
</tbody>
</table>
</div></div></div>Wed, 11 May 2011 03:33:07 +0000Kilho Eom10257 at https://imechanica.orghttps://imechanica.org/node/10257#commentshttps://imechanica.org/crss/node/10257Finite Size Effect on Nanomechanical Mass Detection: Role of Surface Elasticity
https://imechanica.org/node/10256
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/2904">surface effect</a></div><div class="field-item odd"><a href="/taxonomy/term/6099">nonlinear oscillation</a></div><div class="field-item even"><a href="/taxonomy/term/6257">nanoresonator</a></div><div class="field-item odd"><a href="/taxonomy/term/6258">surface elasticity</a></div><div class="field-item even"><a href="/taxonomy/term/6259">detection sensitivity</a></div><div class="field-item odd"><a href="/taxonomy/term/6260">sensing performance</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p><span class="Apple-style-span"><strong>Finite Size Effect on Nanomechanical Mass Detection: Role of Surface Elasticity</strong></span></p>
<p><span class="Apple-style-span">Mai Duc Dai, Chang-Wan Kim, and Kilho Eom</span> </p>
<p><span class="Apple-style-span">Abstract</span></p>
<p><span class="Apple-style-span">Nanomechanical resonators have recently been highlighted because of their remarkable ability to perform the sensing and detection. Since the nanomechanical resonators arecharacterized by large surface-to-volume ratio, it is implied that the surfaceeffect plays a substantial role on not only the resonance but also the sensing performance of nanomechanical resonators. In this work, we have studied therole of surface effect on the detection sensitivity of a nanoresonator that undergoes either harmonic vibration or nonlinear oscillation based on the continuum elastic model such as an elastic beam model. It is shown that surface effect makes an impact on both harmonic resonance and nonlinear oscillations, and that the sensing performance is dependent on the surface effect. Moreover,we have also investigated the surface effect on the mechanical tuning of resonance and sensing performance. It is interestingly found that the mechanical tuning of resonance is independent of surface effect, while the mechanical tuning of sensing performance is determined by surface effect. Our study shedslight on the importance of surface effect on the sensing performance of nanoresonators.</span> </p>
<p> </p>
<p><span class="Apple-style-span">This manuscript will appear in <em>Nanotechnology</em>.</span> </p>
</div></div></div><div class="field field-name-upload field-type-file field-label-hidden"><div class="field-items"><div class="field-item even"><table class="sticky-enabled">
<thead><tr><th>Attachment</th><th>Size</th> </tr></thead>
<tbody>
<tr class="odd"><td><span class="file"><img class="file-icon" alt="PDF icon" title="application/pdf" src="/modules/file/icons/application-pdf.png" /> <a href="https://imechanica.org/files/Manuscript_Final_Nanotechnol.pdf" type="application/pdf; length=2426598" title="Manuscript_Final_Nanotechnol.pdf">Manuscript_Final_Nanotechnol.pdf</a></span></td><td>2.31 MB</td> </tr>
</tbody>
</table>
</div></div></div>Wed, 11 May 2011 03:28:17 +0000Kilho Eom10256 at https://imechanica.orghttps://imechanica.org/node/10256#commentshttps://imechanica.org/crss/node/10256Nanomechanical Resonators and Their Applications in Biological/Chemical Detection: Nanomechanics Principles
https://imechanica.org/node/9970
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/95">nanomechanics</a></div><div class="field-item odd"><a href="/taxonomy/term/139">Carbon nanotube</a></div><div class="field-item even"><a href="/taxonomy/term/186">Review</a></div><div class="field-item odd"><a href="/taxonomy/term/671">graphene</a></div><div class="field-item even"><a href="/taxonomy/term/1744">nanowire</a></div><div class="field-item odd"><a href="/taxonomy/term/1910">multiscale modeling</a></div><div class="field-item even"><a href="/taxonomy/term/3762">atomistic modeling</a></div><div class="field-item odd"><a href="/taxonomy/term/4416">surface effects</a></div><div class="field-item even"><a href="/taxonomy/term/4862">Coarse-Grained Modeling</a></div><div class="field-item odd"><a href="/taxonomy/term/5163">cantilever</a></div><div class="field-item even"><a href="/taxonomy/term/6098">resonator</a></div><div class="field-item odd"><a href="/taxonomy/term/6099">nonlinear oscillation</a></div><div class="field-item even"><a href="/taxonomy/term/6100">coupled resonance</a></div><div class="field-item odd"><a href="/taxonomy/term/6101">detection</a></div><div class="field-item even"><a href="/taxonomy/term/6102">Q-factor</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p><span class="Apple-style-span">Nanomechanical Resonators and Their Applications in Biological/Chemical Detection: Nanomechanics Principles</span></p>
<p><span class="Apple-style-span">Kilho Eom, Harold S. Park, Dae Sung Yoon, Taeyun Kwon</span> </p>
<p> </p>
<p><strong><span class="Apple-style-span">Abstract</span></strong></p>
<p><span class="Apple-style-span"><span class="Apple-style-span">Recent advances in nanotechnology have led to the development of nano-electro-mechanical systems (NEMS) such as nanomechanical resonators, which have recently received significant attention from the scientific community. This has not only been for their capability for the label-free detection of bio/chemical-molecules at single-molecule (or atomic) resolution for future applications such as the early diagnostics of diseases such as cancer, but also for their unprecedented ability to detect physical quantities such as molecular weight, elastic stiffness, surface stress, and surface elastic stiffness for adsorbed molecules on the surface. Most experimental works on resonator-based molecular detection have been based on the principle that molecular adsorption onto a resonator surface increases the effective mass, and consequently decreases the resonant frequencies of the nanomechanical resonator. However, this principle is insufficient to provide fundamental insights into resonator-based molecular detection at the nanoscale; this is due to recently proposed novel nanoscale detection principles including various effects such as surface effects, nonlinear oscillations, coupled resonance, and stiffness effects. Furthermore, these effects have only recently been incorporated into existing physical models for resonators, and therefore the universal physical principles governing nanoresonator-based detection have not been completely described. Therefore, our objective in this review is to overview the current attempts to understand the underlying mechanisms in nanoresonator-based detection using physical models coupled to computational simulations and/or experiments. Specifically, we will focus on issues of special relevance to the dynamic behavior of nanoresonators and their applications in biological/chemical detection: the resonance behavior of micro/nano-resonators; resonator-based chemical/biological detection; physical models of various nanoresonators such as nanowires, carbon nanotubes, and graphene. We pay particular attention to experimental and computational approaches that have been useful in elucidating the mechanisms underlying the dynamic behavior of resonators across multiple and disparate spatial/length scales, and the resulting insight into resonator-based detection that has been obtained. We additionally provide extensive discussion regarding potentially fruitful future research directions coupling experiments and simulations in order to develop a fundamental understanding of the basic physical principles that govern NEMS and NEMS-based sensing and detection applications.</span></span></p>
<p><span class="Apple-style-span">This review is published in Physics Reports. For the preprint of an article, please click the following link: </span><a href="http://dx.doi.org/10.1016/j.physrep.2011.03.002"><span class="Apple-style-span">doi:10.1016/j.physrep.2011.03.002</span></a><span class="Apple-style-span">. </span></p>
</div></div></div>Sun, 20 Mar 2011 06:11:04 +0000Kilho Eom9970 at https://imechanica.orghttps://imechanica.org/node/9970#commentshttps://imechanica.org/crss/node/9970Domain decomposition-based structural condensation of large protein structures for understanding their conformational dynamics
https://imechanica.org/node/8876
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/1759">normal mode analysis</a></div><div class="field-item odd"><a href="/taxonomy/term/1760">elastic network model</a></div><div class="field-item even"><a href="/taxonomy/term/5554">coarse-grained model</a></div><div class="field-item odd"><a href="/taxonomy/term/5555">large protein structure</a></div><div class="field-item even"><a href="/taxonomy/term/5556">conformational dynamics</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>
<strong>Abstract</strong>
</p>
<p>
Normal mode analysis (NMA) with coarse-grained model, such as elastic network model (ENM), has allowed the quantitative understanding of protein dynamics. As the protein size is increased, there emerges the expensive computational process to find the dynamically important low-frequency normal modes due to diagonalization of massive Hessian matrix. In this study, we have provided the domain decomposition-based structural condensation method that enables the efficient computations on low-frequency motions. Specifically, our coarse-graining method is established by coupling between model condensation (MC; Eom et al., J Comput Chem 2007, <strong>28</strong>, 1400) and component mode synthesis (Kim et al., J Chem Theor Comput 2009, <strong>5</strong>, 1931). A protein structure is first decomposed into substructural units, and then each substructural unit is coarse-grained by MC. Once the NMA is implemented to coarse-grained substructural units, normal modes and natural frequencies for each coarse-grained substructural unit are assembled by using geometric constraints to provide the normal modes and natural frequencies for whole protein structure. It is shown that our coarse-graining method enhances the computational efficiency for analysis of large protein complexes. It is clearly suggested that our coarse-graining method provides the B-factors of 100 large proteins, quantitatively comparable with those obtained from original NMA, with computational efficiency. Moreover, the collective behaviors and/or the correlated motions for model proteins are well delineated by our suggested coarse-grained models, quantitatively comparable with those computed from original NMA. It is implied that our coarse-grained method enables the computationally efficient studies on conformational dynamics of large protein complex.
</p>
<p>
This work was published online in Journal of Computational Chemistry
</p>
</div></div></div><div class="field field-name-upload field-type-file field-label-hidden"><div class="field-items"><div class="field-item even"><table class="sticky-enabled">
<thead><tr><th>Attachment</th><th>Size</th> </tr></thead>
<tbody>
<tr class="odd"><td><span class="file"><img class="file-icon" alt="PDF icon" title="application/pdf" src="/modules/file/icons/application-pdf.png" /> <a href="https://imechanica.org/files/J%20Comput%20Chem%20%282010%29%20Eom%20jcc21613%20Domain%20decomposition-based%20structural%20condensation%20of%20large%20protein%20structures.pdf" type="application/pdf; length=1513497" title="J Comput Chem (2010) Eom jcc21613 Domain decomposition-based structural condensation of large protein structures.pdf">J Comput Chem (2010) Eom jcc21613 Domain decomposition-based structural condensation of large protein structures.pdf</a></span></td><td>1.44 MB</td> </tr>
<tr class="even"><td><span class="file"><img class="file-icon" alt="PDF icon" title="application/pdf" src="/modules/file/icons/application-pdf.png" /> <a href="https://imechanica.org/files/JCC_21613_sm_suppinfo.pdf" type="application/pdf; length=772543" title="JCC_21613_sm_suppinfo.pdf">JCC_21613_sm_suppinfo.pdf</a></span></td><td>754.44 KB</td> </tr>
</tbody>
</table>
</div></div></div>Sat, 11 Sep 2010 08:27:55 +0000Kilho Eom8876 at https://imechanica.orghttps://imechanica.org/node/8876#commentshttps://imechanica.org/crss/node/8876Call for Abstract in Track 5.6. of the World Congress on Biomehanics 2010 (WCB 2010)
https://imechanica.org/node/7652
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/74">conference</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/366">Protein dynamics</a></div><div class="field-item odd"><a href="/taxonomy/term/452">molecular mechanics</a></div><div class="field-item even"><a href="/taxonomy/term/1910">multiscale modeling</a></div><div class="field-item odd"><a href="/taxonomy/term/4861">Protein Modeling</a></div><div class="field-item even"><a href="/taxonomy/term/4862">Coarse-Grained Modeling</a></div><div class="field-item odd"><a href="/taxonomy/term/4863">Molecular Modeling</a></div><div class="field-item even"><a href="/taxonomy/term/4864">Protein Mechanics</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>
Dear. Collegue
</p>
<p>
I would like to introduce the conference of <a href="http://www.wcb2010.net">World Congress on Biomechanics 2010 (WCB 2010)</a>, which may be of interest to some of iMechanicians. Especially, I as a track chair would like to announce the call for abstract for <strong>Track 5.6. "Multiscale Modeling and Simulation of Molecular and Supramolecular Structures"</strong> under <a href="http://www.wcb2010.net/programme/theme-chairs">Theme 5. Molecular Mechanics</a> organized by <a href="user/74">Markus Buehler</a>. The objective of the track 5.6 is to discuss the current state-of-art in novel coarse-grained and/or multiscale modelings of biological supramolecules such as proteins, ribosome, etc. for gaining insight into the dynamics and/or mechanics of such supramolecules.
</p>
<p>
<strong>The deadline for abstract submission is March 1, 2010 via online submission (click <a href="http://www.wcb2010.net/abstracts/abstracts-submission">here</a>). The conference will be held between August 1, 2010 and August 6, 2010 at Singapore. For more details, please look at <a href="http://www.wcb2010.net/main-menu/about-the-congress">here</a>.</strong>
</p>
<p>
For more information, please refer to the pdf announcement. If you have any inquiries related to Track 5.6., you can feel free to contact me.
</p>
<p>
</p>
</div></div></div><div class="field field-name-upload field-type-file field-label-hidden"><div class="field-items"><div class="field-item even"><table class="sticky-enabled">
<thead><tr><th>Attachment</th><th>Size</th> </tr></thead>
<tbody>
<tr class="odd"><td><span class="file"><img class="file-icon" alt="PDF icon" title="application/pdf" src="/modules/file/icons/application-pdf.png" /> <a href="https://imechanica.org/files/Letter.pdf" type="application/pdf; length=16887" title="Letter.pdf">Letter.pdf</a></span></td><td>16.49 KB</td> </tr>
</tbody>
</table>
</div></div></div>Tue, 23 Feb 2010 17:28:54 +0000Kilho Eom7652 at https://imechanica.orghttps://imechanica.org/node/7652#commentshttps://imechanica.org/crss/node/7652Micromechanical observation of the kinetics of biomolecular interactions in liquid
https://imechanica.org/node/4390
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/188">Microcantilever</a></div><div class="field-item odd"><a href="/taxonomy/term/897">biosensor</a></div><div class="field-item even"><a href="/taxonomy/term/3120">kinetics</a></div><div class="field-item odd"><a href="/taxonomy/term/3121">biomolecular interaction</a></div><div class="field-item even"><a href="/taxonomy/term/3122">resonant frequency shift</a></div><div class="field-item odd"><a href="/taxonomy/term/3123">Langmuir kinetics</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>
We have recently suggested the potential of resonant microcantilever for quantitative study on the kinetics of biomolecular interactions such as protein-protein interaction and DNA hybridization. We have employed the Langmuir kinetic model for describing the molecular interactions on the surface, which leads to change of overall mass of cantilever responsible for resonant frequency shift. Such Langmuir kinetic model dictates the <em>in situ</em> resonant frequency shift due to biomolecular interaction in liquid. This indicates that resonant cantilever is able to provide the information of biochemical reaction. This work was published in <em>Applied Physics Letters</em> in Oct 31, 2008.
</p>
<p>
<strong>ABSTRACT</strong><br />
Resonant microcantilevers have recently enabled the label-free detection of biomolecules. Here, we observed the kinetics of biomolecular interactions such as antigen-antibody interactions and/or DNA hybridization based on a resonant frequency shift, obeying Langmuir kinetics, measured in a buffer solution. It is shown that the kinetics of DNA adsorptions on the surface is governed by intermolecular interactions between adsorbed DNA molecules. It is also shown that the kinetics of DNA hybridization is determined by the intermolecular interaction. It is implied that resonant microcantilever in buffer solution may allow for gaining insights into the kinetics of various molecular interactions. [link: <a href="http://link.aip.org/link/?APPLAB/93/173901/1">http://link.aip.org/link/?APPLAB/93/173901/1</a>]
</p>
</div></div></div>Fri, 28 Nov 2008 09:04:24 +0000Kilho Eom4390 at https://imechanica.orghttps://imechanica.org/node/4390#commentshttps://imechanica.org/crss/node/4390Mesoscopic model for mechanical characterization of protein materials
https://imechanica.org/node/3520
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/1760">elastic network model</a></div><div class="field-item odd"><a href="/taxonomy/term/2623">mesoscopic model</a></div><div class="field-item even"><a href="/taxonomy/term/2624">protein crystal</a></div><div class="field-item odd"><a href="/taxonomy/term/2625">Go potential</a></div><div class="field-item even"><a href="/taxonomy/term/2626">mechanical property</a></div><div class="field-item odd"><a href="/taxonomy/term/2627">structure-property relationship</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>
We consider the mesoscopic model of protein materials composed of protein crystals with given space group for understanding the mechanical properties of protein materials with respect to their structures. This preprint was accepted for publication at Journal of Computational Chemistry.
</p>
<p>
<strong>Abstract</strong><br />
Mechanical characterization of protein molecules has played a role on gaining insight into the biological functions of proteins, since some proteins perform the mechanical function. Here, we present the mesoscopic model of biological protein materials composed of protein crystals prescribed by Go potential for characterization of elastic behavior of protein materials. Specifically, we consider the representative volume element (RVE) containing the protein crystals represented by alpha-carbon atoms, prescribed by Go potential, with application of constant normal strain to RVE. The stress-strain relationship computed from virial stress theory provides the nonlinear elastic behavior of protein materials and their mechanical properties such as Young's modulus, quantitatively and/or qualitatively comparable to mechanical properties of biological protein materials obtained from experiments and/or atomistic simulations. Further, we discuss the role of native topology on the mechanical properties of protein crystals. It is shown that parallel strands (hydrogen bonds in parallel) enhances the mechanical resilience of protein materials.
</p>
</div></div></div><div class="field field-name-upload field-type-file field-label-hidden"><div class="field-items"><div class="field-item even"><table class="sticky-enabled">
<thead><tr><th>Attachment</th><th>Size</th> </tr></thead>
<tbody>
<tr class="odd"><td><span class="file"><img class="file-icon" alt="PDF icon" title="application/pdf" src="/modules/file/icons/application-pdf.png" /> <a href="https://imechanica.org/files/Manuscript_JCC_final.pdf" type="application/pdf; length=495084" title="Manuscript_JCC_final.pdf">Manuscript_JCC_final.pdf</a></span></td><td>483.48 KB</td> </tr>
</tbody>
</table>
</div></div></div>Thu, 17 Jul 2008 05:09:21 +0000Kilho Eom3520 at https://imechanica.orghttps://imechanica.org/node/3520#commentshttps://imechanica.org/crss/node/3520Review: Coarse-grained model for normal mode analysis of proteins
https://imechanica.org/node/2643
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/366">Protein dynamics</a></div><div class="field-item odd"><a href="/taxonomy/term/412">coarse-graining</a></div><div class="field-item even"><a href="/taxonomy/term/1759">normal mode analysis</a></div><div class="field-item odd"><a href="/taxonomy/term/1760">elastic network model</a></div><div class="field-item even"><a href="/taxonomy/term/1761">Go model</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>
The preprint provides the summary and/or review of current state-of-art in coarse-grained modeling of protein structures for normal mode analysis. This review summarizes the quasiharmonic analysis, Go model, elastic network model, and recently suggested coarse-grained models for protein structures.
</p>
<p>
<strong>Abstract</strong>
</p>
<p>
Understanding the protein mechanics is <em>a priori</em> requisite for gaining insight into protein's biological function, since most protein performs its function through the structural deformation renowned as conformational change. Such conformational change has been computationally delineated by atomistic simulations, albeit the mechanics of large protein structure is computationally inaccessible with atomistic simulation such as molecular dynamics simulation. In a recent decade, normal mode analysis with coarse-grained modeling of protein structures has been a computational alternative to atomistic simulations for understanding large protein mechanics. In this review, we delineate the current state-of-art in coarse-grained modeling of proteins for normal mode analysis. Specifically, the pioneered coarse-grained models such as Go model and elastic network model as well as recently developed coarse-grained elastic network models are summarized and discussed for understanding large protein mechanics.
</p>
<p>
</p>
</div></div></div><div class="field field-name-upload field-type-file field-label-hidden"><div class="field-items"><div class="field-item even"><table class="sticky-enabled">
<thead><tr><th>Attachment</th><th>Size</th> </tr></thead>
<tbody>
<tr class="odd"><td><span class="file"><img class="file-icon" alt="PDF icon" title="application/pdf" src="/modules/file/icons/application-pdf.png" /> <a href="https://imechanica.org/files/review_protein_0128.pdf" type="application/pdf; length=700958" title="review_protein_0128.pdf">review_protein_0128.pdf</a></span></td><td>684.53 KB</td> </tr>
</tbody>
</table>
</div></div></div>Tue, 29 Jan 2008 15:27:12 +0000Kilho Eom2643 at https://imechanica.orghttps://imechanica.org/node/2643#commentshttps://imechanica.org/crss/node/2643P. G. de Gennes: described as "Issac Newton of our times" (Perspective published at Science on July 27, 2007)
https://imechanica.org/node/1734
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/75">mechanician</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/1148">chemist</a></div><div class="field-item odd"><a href="/taxonomy/term/1149">physicist</a></div><div class="field-item even"><a href="/taxonomy/term/1150">Perspective</a></div><div class="field-item odd"><a href="/taxonomy/term/1151">P.G. de Gennes</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>
Today morning (July 27, 2007), I read through Science published today. Among many interesting articles, I found the very interesting article about perspectives in the memory of Pierre-Gilles de Gennes, who won the Nobel Prize in Physics and died this year. I was very impressed to his contributions to various research areas - superconductivity, granular materials, fracture mechanics, polymer chemistry, magnetism, cell mechanics, brain functions, and so on. His contributions have inspired many people in different research areas from mechanics to biology, and even to chemistry and physics. If you are interested in his life and contributions to various communities, then you may read the article published today (<a href="http://www.sciencemag.org/cgi/content/summary/317/5837/466">click here to link</a>).
</p>
</div></div></div>Fri, 27 Jul 2007 17:26:14 +0000Kilho Eom1734 at https://imechanica.orghttps://imechanica.org/node/1734#commentshttps://imechanica.org/crss/node/1734Dynamical Response of Nanomechanical Resonators to Biomolecular Interactions
https://imechanica.org/node/1620
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/893">In-vitro biomolecular detection</a></div><div class="field-item odd"><a href="/taxonomy/term/1077">Nanomechanical Resonator</a></div><div class="field-item even"><a href="/taxonomy/term/1078">DNA-DNA interaction</a></div><div class="field-item odd"><a href="/taxonomy/term/1079">Theoretical Model</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>
We made a simple model for understanding the dynamic behavior of nanomechanical resonator in response to biomolecular interactions. Specifically, in our model, we considered the nanomechanical resonator, on whose surface the biomolecules (dsDNA) are adsorbed, such that Hamiltonian of the system consists of elastic bending energy of nanomechanical resonator and potential energy for biomolecular interaction (i.e. DNA-DNA interaction). It was shown that DNA-DNA interaction plays a role on the resonant frequency shift for nano-scale resonators. This work was accepted for publications at Physical Review B.
</p>
<p>
<strong>Dynamical Response of Nanomechanical Resonators to Biomolecular Interactions</strong>
</p>
<p><strong>ABSTRACT<br /></strong><span>We studied the dynamical response of a nanomechanical resonator to biomolecular (e.g. DNA) adsorptions on a resonator’s surface by using theoretical model, which considers the Hamiltonian <em>H</em> such that the potential energy consists of elastic bending energy of a resonator and the potential energy for biomolecular interactions. It was shown that the resonant frequency shift for a resonator due to biomolecular adsorption depends on not only the mass of adsorbed biomolecules but also the biomolecular interactions. Specifically, for dsDNA adsorption on a resonator’s surface, the resonant frequency shift is also dependent on the ionic strength of a solvent, implying the role of biomolecular interactions on the dynamic behavior of a resonator. This indicates that nanomechanical resonators may enable one to quantify the biomolecular mass, implying the enumeration of biomolecules, as well as gain insight into intermolecular interactions between adsorbed biomolecules on the surface.</span></p>
</div></div></div><div class="field field-name-upload field-type-file field-label-hidden"><div class="field-items"><div class="field-item even"><table class="sticky-enabled">
<thead><tr><th>Attachment</th><th>Size</th> </tr></thead>
<tbody>
<tr class="odd"><td><span class="file"><img class="file-icon" alt="PDF icon" title="application/pdf" src="/modules/file/icons/application-pdf.png" /> <a href="https://imechanica.org/files/manuscript_revised_PRB_0817.pdf" type="application/pdf; length=260808" title="manuscript_revised_PRB_0817.pdf">manuscript_revised_PRB_0817.pdf</a></span></td><td>254.7 KB</td> </tr>
</tbody>
</table>
</div></div></div>Tue, 26 Jun 2007 15:02:22 +0000Kilho Eom1620 at https://imechanica.orghttps://imechanica.org/node/1620#commentshttps://imechanica.org/crss/node/1620Biomolecular detection by a cantilever functionalized by RNA aptamers as receptor molecules
https://imechanica.org/node/1467
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/188">Microcantilever</a></div><div class="field-item odd"><a href="/taxonomy/term/897">biosensor</a></div><div class="field-item even"><a href="/taxonomy/term/1000">HCV helicase</a></div><div class="field-item odd"><a href="/taxonomy/term/1001">RNA aptamer</a></div><div class="field-item even"><a href="/taxonomy/term/1002">label-free detection</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>
We have recently reported the label-free detection of HCV (Hepatitis C Virus) helicase by using a resonating microcantilever whose surface is functionalized by RNA aptamers as receptor molecules. This work was accepted for publication at Biosensors & Bioelectronics.
</p>
<p>
<strong>Abstract</strong>
</p>
<p>
We report the nanomechanical microcantilevers operated in vibration modes with use of RNA aptamers as receptor molecules for label-free detection of hepatitis C virus (HCV) helicase. The nanomechanical detection principle is that ligand-receptor binding on the microcantilever surface induces the dynamic response change of a microcantilevers. We implemented the label-free detection of HCV helicase in the low concentration as much as 100 pg/ml from measuring the dynamic response change of microcantilevers. Moreover, from the recent studies showing that the ligand-receptor binding generates the surface stress on the microcantilever, we estimate the surface stress, on the oscillating microcantilever surface, induced by ligand-receptor binding, i.e. binding between HCV helicase and RNA aptamer. In this article, it is suggested that the oscillating microcantilevers with use of RNA aptamers as receptor molecules may enable one to implement the sensitive label-free detection of very small amount of small-scale proteins.
</p>
</div></div></div><div class="field field-name-upload field-type-file field-label-hidden"><div class="field-items"><div class="field-item even"><table class="sticky-enabled">
<thead><tr><th>Attachment</th><th>Size</th> </tr></thead>
<tbody>
<tr class="odd"><td><span class="file"><img class="file-icon" alt="PDF icon" title="application/pdf" src="/modules/file/icons/application-pdf.png" /> <a href="https://imechanica.org/files/manuscript_BSBE_0502.pdf" type="application/pdf; length=443836" title="manuscript_BSBE_0502.pdf">manuscript_BSBE_0502.pdf</a></span></td><td>433.43 KB</td> </tr>
</tbody>
</table>
</div></div></div>Fri, 25 May 2007 07:07:50 +0000Kilho Eom1467 at https://imechanica.orghttps://imechanica.org/node/1467#commentshttps://imechanica.org/crss/node/1467Microcantilever operated in liquid environment for in-vitro biomolecular detection
https://imechanica.org/node/1297
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/188">Microcantilever</a></div><div class="field-item odd"><a href="/taxonomy/term/893">In-vitro biomolecular detection</a></div><div class="field-item even"><a href="/taxonomy/term/894">quality factor</a></div><div class="field-item odd"><a href="/taxonomy/term/895">C reactive protein</a></div><div class="field-item even"><a href="/taxonomy/term/897">biosensor</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>
We have recently reported the piezoelectric thick film microcantilever, which enables the in-situ real-time detection of the protein related to disease (e.g. C reactive protein) in liquid environment. This work was published at APL (click <a href="http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=APPLAB000090000022223903000001&idtype=cvips&gifs=Yes">here</a>).
</p>
<p>
<strong>"<em>In-situ</em> real-time monitoring of biomolecular interactions based on resonating microcantilevers immersed in a viscous fluid"</strong>
</p>
<p><span>We report the precise (noise-free) <em>in-situ</em> real-time monitoring of a specific protein antigen-antibody interaction by using a resonating microcantilever immersed in a viscous fluid. In this work, we utilized a resonating piezoelectric thick film microcantilever, which exhibits the high quality factor (e.g. <em>Q</em> = 15) in a viscous liquid at a viscosity comparable to that of human blood serum. This implies a great potential of our resonating microcantilever to <em>in-situ</em> biosensor applications. It is shown that our microcantilever enables us to monitor the C reactive protein (CRP) antigen-antibody interactions in real-time, providing an insight into the protein binding kinetics.</span></p>
</div></div></div><div class="field field-name-upload field-type-file field-label-hidden"><div class="field-items"><div class="field-item even"><table class="sticky-enabled">
<thead><tr><th>Attachment</th><th>Size</th> </tr></thead>
<tbody>
<tr class="odd"><td><span class="file"><img class="file-icon" alt="PDF icon" title="application/pdf" src="/modules/file/icons/application-pdf.png" /> <a href="https://imechanica.org/files/manuscript_APL_revised_0424.pdf" type="application/pdf; length=1681859" title="manuscript_APL_revised_0424.pdf">manuscript_APL_revised_0424.pdf</a></span></td><td>1.6 MB</td> </tr>
</tbody>
</table>
</div></div></div>Thu, 26 Apr 2007 03:17:25 +0000Kilho Eom1297 at https://imechanica.orghttps://imechanica.org/node/1297#commentshttps://imechanica.org/crss/node/1297Mass sensing by using a resonating microcantilever
https://imechanica.org/node/550
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/188">Microcantilever</a></div><div class="field-item odd"><a href="/taxonomy/term/414">Micromechanical mass sensing</a></div><div class="field-item even"><a href="/taxonomy/term/415">Sensitivity</a></div><div class="field-item odd"><a href="/taxonomy/term/416">Resonance behavior</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>We recently reported the mass sensing by using resonating microcantilevers. The characterization of mass-sensing and its related sensitivity was suggested on the basis of elasticity theory. This work was published online at Sensors and Actuators A (click <a href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6THG-4M9H3M4-1&_user=88858&_coverDate=11%2F09%2F2006&_rdoc=160&_fmt=full&_orig=browse&_srch=doc-info(%23toc%235282%239999%23999999999%2399999%23FLA%23display%23Articles)&_cdi=5282&_sort=d&_docanchor=&view=c&_ct=310&_acct=C000007018&_version=1&_urlVersion=0&_userid=88858&md5=f9f7c8149a535679ffb326813c104d52">here</a>).</p>
<p>Abstract
</p><p>Through the use of oscillating microcantilevers, a micromechanical mass detection with a resolution of a Hz per picogram regime is reported. Through MEMS processes, piezoelectric microcantilevers that are simultaneously capable of self-actuation and the electrical measurement of resonant frequencies were fabricated. Mass detection in the Hz per picogram regime is demonstrated with a deposition of an Au thin-layer, of which the thickness is precisely controlled. In addition, it is shown that a scaling down of the microcantilevers enhances the sensitivity during the micromechanical mass detection. </p>
<p><strong>Keywords: </strong>Microcantilever; Micromechanical mass detection; Analytical sensitivity; Resonant frequency </p>
</div></div></div><div class="field field-name-upload field-type-file field-label-hidden"><div class="field-items"><div class="field-item even"><table class="sticky-enabled">
<thead><tr><th>Attachment</th><th>Size</th> </tr></thead>
<tbody>
<tr class="odd"><td><span class="file"><img class="file-icon" alt="PDF icon" title="application/pdf" src="/modules/file/icons/application-pdf.png" /> <a href="https://imechanica.org/files/Sens%20Actuat%20A%20%282007%29%20Eom%20K.pdf" type="application/pdf; length=682651" title="Sens Actuat A (2007) Eom K.pdf">Sens Actuat A (2007) Eom K.pdf</a></span></td><td>666.65 KB</td> </tr>
</tbody>
</table>
</div></div></div>Mon, 11 Dec 2006 02:23:12 +0000Kilho Eom550 at https://imechanica.orghttps://imechanica.org/node/550#commentshttps://imechanica.org/crss/node/550Model Reduction of Large Proteins for Normal Mode Studies
https://imechanica.org/node/549
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/365">Quasi-harmonic model</a></div><div class="field-item odd"><a href="/taxonomy/term/366">Protein dynamics</a></div><div class="field-item even"><a href="/taxonomy/term/412">coarse-graining</a></div><div class="field-item odd"><a href="/taxonomy/term/413">low-frequency normal modes</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>
Recently, I reported the model reduction method for large proteins for understanding large protein dynamics based on low-frequency normal modes. This work was pubslihed at Journal of Computational Chemistry (click <a href="http://www3.interscience.wiley.com/cgi-bin/abstract/114131990/ABSTRACT">here</a>).
</p>
<p>
<strong>Coarse-Graining of protein structures for the normal mode studies</strong>
</p>
<p>
<strong>Abstracts</strong>
</p>
<p>
<span>The coarse-grained structural model such as Gaussian network has played a vital role in the normal mode studies for understanding protein dynamics related to biological functions. However, for the large proteins, the Gaussian network model is computationally unfavorable for diagonalization of Hessian (stiffness) matrix for the normal mode studies. In this article, we provide the coarse-graining method, referred to as “dynamic model condensation,” which enables the further coarse-graining of protein structures consisting of small number of residues. It is shown that the coarser-grained structures reconstructed by dynamic model condensation exhibit the dynamic characteristics, such as low-frequency normal modes, qualitatively comparable to original structures. This sheds light on that dynamic model condensation may enable one to study the large protein dynamics for gaining insight into biological functions of proteins.</span><span> </span>
</p>
<p>
<strong><span>Key words:</span></strong><span><span> </span>coarse-graining; normal mode analysis; protein dynamics; low-frequency normal modes; Gaussian network model</span><span> </span>
</p>
</div></div></div><div class="field field-name-upload field-type-file field-label-hidden"><div class="field-items"><div class="field-item even"><table class="sticky-enabled">
<thead><tr><th>Attachment</th><th>Size</th> </tr></thead>
<tbody>
<tr class="odd"><td><span class="file"><img class="file-icon" alt="PDF icon" title="application/pdf" src="/modules/file/icons/application-pdf.png" /> <a href="https://imechanica.org/files/manuscript_J_Comput_Chem_accepted.pdf" type="application/pdf; length=6371867" title="manuscript_J_Comput_Chem_accepted.pdf">manuscript_J_Comput_Chem_accepted.pdf</a></span></td><td>6.08 MB</td> </tr>
</tbody>
</table>
</div></div></div>Mon, 11 Dec 2006 00:05:29 +0000Kilho Eom549 at https://imechanica.orghttps://imechanica.org/node/549#commentshttps://imechanica.org/crss/node/549Elastic model for proteins (polymers)
https://imechanica.org/node/474
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/186">Review</a></div><div class="field-item odd"><a href="/taxonomy/term/242">protein unfolding</a></div><div class="field-item even"><a href="/taxonomy/term/365">Quasi-harmonic model</a></div><div class="field-item odd"><a href="/taxonomy/term/366">Protein dynamics</a></div><div class="field-item even"><a href="/taxonomy/term/367">Cross-linked single molecule</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>There has been a lot of attention on the study of mechanics of proteins and/or single molecules. Such study was typically implemented by using classical molecular dynamics (MD) simulation. In spite of ability to describe the dynamics of biological macromolecules (e.g. proteins), MD simulation exhibits the computational restriction in the spatial and temporal scale. In order to overcome such computational limitation, the coarse-grained model has recently been taken into account. In this review, I would take a look at a couple of coarse-grained models of protein molecules.</p>
<p>Proteins perform the biological functions through conformational changes that are well described by low-frequency normal modes of protein structures. For low-frequency normal modes, the normal mode analysis (NMA) for molecular structure of proteins was typically utilized. However, such NMA possesses the computational difficulties, because of anharmonic potential field prescribed to whole atoms of protein structures. Recently, M.M. Tirion (<a href="http://prola.aps.org/abstract/PRL/v77/i9/p1905_1">Phys. Rev. Lett., 1996</a>) provided the coarse-grained model, which revolutionize the protein dynamics studies [for details, see <a href="http://prola.aps.org/abstract/PRL/v77/i9/p1905_1">Ref</a>]. In her work, the alpha carbon atoms (dominant carbon atom in backbone chain) were prescribed by a harmonic potential field in such a way that alpha carbons in neighborhood (defined by a cut-off distance) were connected by elastic harmonic springs (with only one single stiffness parameter). One may regard this simple model as mass-spring model to protein structures. This simple model was surprisingly able to describe the conformational fluctuation of protein structures. Moreover, this simple model (referred to as Tirion's model) allows one to describe the conformational transition of protein structures by using low-frequency normal modes from Tirion's model. For instance, several researchers (<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=15571723">C.L. Brooks</a>, <a href="http://www.pnas.org/cgi/content-nw/full/102/52/18908/">I. Bahar</a>, <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?itool=abstractplus&db=pubmed&cmd=Retrieve&dopt=abstractplus&list_uids=12972347">R.L. Jernigan</a>, M. Karplus, <a href="http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=PRLTAO000094000007078102000001&idtype=cvips&gifs=yes">A. Kidera</a>, et al.) have successfully described the biological function of viruses, motor proteins, and protein kinase, and protein folding core predictions based on the Tirion's model. Recently, I have deveoped the coarse-graining scheme of protein structures, that is, the model reduction of elastic network model (for details, click <a href="/node/549">here</a>). It was reported that reduced elastic model is sufficient for Normal Mode studies of proteins for understanding the protein dynamics related to biological functions.</p>
<p>Proteins are renowned as a strong molecule that exhibits the remarkable mechanical strength. For instance, spider silk protein exhibits the high mechanical strength upon mechanical loading. Such remarkable mechanical strength is ascribed to protein structures, that is, the folded structure of proteins is unfolded upon mechanical loading. For computational experiment of protein unfolding, the protein structural change upon mechanical loading was well described by <a href="http://www.ks.uiuc.edu/Research/smd_imd/">steered MD simulation</a> developed by Schulten and coworkers. For computational tractability for study of correlation between folding topology and mechanical response, I and my former advisors developed the coarse-grained model of cross-linked polymer molecules, which reveals the relationship between folding topology (cross-link topology) and mechanical unfolding behavior (mechanical strength) of proteins (For details, see <a href="http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=PLEEE8000071000002021904000001&idtype=cvips&gifs=yes">here</a>). In this work, it is shown that specific folding topology such as parallel strand is responsible for remarkable mechanical strength of proteins.</p>
</div></div></div><div class="field field-name-upload field-type-file field-label-hidden"><div class="field-items"><div class="field-item even"><table class="sticky-enabled">
<thead><tr><th>Attachment</th><th>Size</th> </tr></thead>
<tbody>
<tr class="odd"><td><span class="file"><img class="file-icon" alt="PDF icon" title="application/pdf" src="/modules/file/icons/application-pdf.png" /> <a href="https://imechanica.org/files/Phys%20Rev%20Lett%2077-9%20%281996%29%20Tirion%20MM%20p1905%20Large%20amplitude%20el.pdf" type="application/pdf; length=183107" title="Phys Rev Lett 77-9 (1996) Tirion MM p1905 Large amplitude el.pdf">Phys Rev Lett 77-9 (1996) Tirion MM p1905 Large amplitude el.pdf</a></span></td><td>178.82 KB</td> </tr>
<tr class="even"><td><span class="file"><img class="file-icon" alt="PDF icon" title="application/pdf" src="/modules/file/icons/application-pdf.png" /> <a href="https://imechanica.org/files/J%20Phys%20Chem%20B%20107%20%282003%29%20Eom%20p8730%20Relationship%20between%20mechanical%20properties%20and%20topology%20of%20cross-linked%20polymer%20molecules.pdf" type="application/pdf; length=124141" title="J Phys Chem B 107 (2003) Eom p8730 Relationship between mechanical properties and topology of cross-linked polymer molecules.pdf">J Phys Chem B 107 (2003) Eom p8730 Relationship between mechanical properties and topology of cross-linked polymer molecules.pdf</a></span></td><td>121.23 KB</td> </tr>
<tr class="odd"><td><span class="file"><img class="file-icon" alt="PDF icon" title="application/pdf" src="/modules/file/icons/application-pdf.png" /> <a href="https://imechanica.org/files/Phys%20Rev%20E%2071%20%282005%29%20Eom%20K%20021904%20Theoretical%20studies%20of%20kin.pdf" type="application/pdf; length=174238" title="Phys Rev E 71 (2005) Eom K 021904 Theoretical studies of kin.pdf">Phys Rev E 71 (2005) Eom K 021904 Theoretical studies of kin.pdf</a></span></td><td>170.15 KB</td> </tr>
</tbody>
</table>
</div></div></div>Tue, 21 Nov 2006 14:37:23 +0000Kilho Eom474 at https://imechanica.orghttps://imechanica.org/node/474#commentshttps://imechanica.org/crss/node/474Microcantilever for biomolecular detections
https://imechanica.org/node/219
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/76">research</a></div></div></div><div class="field field-name-taxonomy-vocabulary-8 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/186">Review</a></div><div class="field-item odd"><a href="/taxonomy/term/187">Bio-MEMS/NEMS</a></div><div class="field-item even"><a href="/taxonomy/term/188">Microcantilever</a></div><div class="field-item odd"><a href="/taxonomy/term/189">Biomolecular detection</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>Microcantilevers have taken much attention as devices for label-free detection of molecules and/or their conformations in solutions and air. Recently, microcantilevers have allowed the nanomechanical mass detection of thin film [1-3], small molecules [4, 5], and biological components such as viruses [6] and vesicles [7] in the order of a pico-gram to a zepto-gram. The great potential of microcantilevers is the sensitive, reliable, fast label-free detection of proteins and/or protein conformations. Specifically, microcantilevers are capable of label-free detection of marker proteins related to diseases, even at a low concentration in solution [8-17]. Microcantilevers, operated in a viscous fluid, have also enabled the real-time monitoring of protein-protein interactions [8, 12-15]. Furthermore, microcantilevers are able to recognize the specific protein conformations [18] and/or reversible conformation changes of proteins/polymers [19, 20].</p>
<p>The fundamental principle for label-free detection of molecules is the transduction of molecular adsorption and/or molecular interactions on a cantilever surface into the mechanical response change of a cantilever (e.g. deflection change, resonant frequency shift). Understanding the role of added mass and/or molecular interactions, due to binding events of target molecules to functionalized cantilever, in the mechanical response change is central to quantification of mass of target molecules and/or molecular interactions.</p>
<p>Many recent studies provide that the deflection change of a static microcantilever is induced by molecular interactions. From the classical elasticity (Gurtin, Stoney), the deflection change of a cantilever is ascribed to the surface stress driven by molecular interactions during the binding events. Microcantilevers operated in static mode have allowed many researchers to detect the specific proteins as well as to observe the conformation changes of biological molecules (e.g. DNA). Nevertheless, static microcantilevers exhibit the limitations such that the deflection change is minuscule for a miniaturized (in a micron size) cantilever, leading to error-proneness to measure deflection.</p>
<p>Recently, microcantilevers in vibration (oscillation) mode has been taken account because miniaturization broadens the dynamical range, resulting in increasing the sensitivity of a cantilever. The dynamic behavior of a cantilever for protein-protein interactions on a cantilever surface has been quantitatively understood. We provided the basic principles for dynamical response of a cantilever to biomolecular interactions. It is shown that the surface stress driven by protein-protein interactions play a significant role on the dynamical response of a cantilever. For details, you may refer to my papers, one of which will be published in Applied Physics Letters in the near future [21].</p>
<p>References</p>
<p>[1] Park, J.H., Kwon, T.Y., Kim, H.J., Kim, S.R., Yoon, D.S., Chun, C.-I., Kim, H., & Kim, T.S<em>. J. Electrocram. in press</em></p>
<p>[2] Chun, D.W., Hwang, K.S., Eom, K., Lee, J.H., Cha, B.H., Lee, W.Y., Yoon, D.S., & Kim, T.S<em>. submitted to Sens. Actuat. A</em>.</p>
<p>[3] Lavrik, N.V., & Datskos, P.G. (2003).<em> Appl. Phys. Lett</em><strong>. 82</strong>, 2697-2699.</p>
<p>[4] Berger, R., Delamarche, E., Lang, H.P., Gerber, C., Gimzewski, J.K., Meyer, E., & Guntherodt, H.-J. (1997) <em>Science</em><strong>. 276</strong>. 2021-2024.</p>
<p>[5] Yang, Y.T., Callergari, C., Feng, X.L., Ekinci, K.L., & Roukes, M.L. (2006). <em>Nano Lett</em><strong>. 6</strong>. 583-586.</p>
<p>[6] Illic, B., & Craighead, H.G. (2004). <em>Appl. Phys. Lett</em><strong>. 85</strong>. 2604-2606.</p>
<p>[7] Ghatnekar-Nilsson, S., Lindahl, J., Dahlin, A., Stjernholm, T., Jeppensen, S., Hook, F., & Montelius, L. (2005). <em>Nanotechnology</em><strong>. 16</strong>. 1512-1516.</p>
<p>[8] Arntz, Y., Seelig, J.D., Lang, H.P., Zhang, J., Hunziker, P., Ramseyer, J.P., Meyer, E., Hegner, M., & Gerber, C. (2003). <em>Nanotechnology</em><strong>. 14</strong>. 86-90.</p>
<p>[9] Wu, W., Datar, R.H., Hansen, K.M., Thundat, T., Cote, R.J., & Majumdar, A. (2001). <em>Nat. Biotechnol</em><strong>. 19</strong>. 856-860.</p>
<p>[10] Lee, J.H., Yoon, K.H., Hwang, K.S., Park, J., Ahn, S., & Kim, T.S. (2004). <em>Biosens. Bioelectron</em><strong>. 20</strong>. 269-275.</p>
<p>[11] Lee, J.H., Hwang, K.S., Park, J., Yoon, K.H., Yoon, D.S., & Kim, T.S. (2005). <em>Biosens. Bioelectron</em><strong>. 20</strong>. 2157-2162.</p>
<p>[12] Braun, T., Barwich, V., Ghatkesar, M.K., Bredekamp, A.H., Gerber, C., Hegner, M., & Lang, H.P. (2005). <em>Phys. Rev. E</em><strong>. 72</strong>. 031907.</p>
<p>[13] McKendry, R., Zhang, J., Arntz, Y., Strunz, T., Hegner, M., Lang, H.P., Baller, M.K., Certa, U., Meyer, E., Guntherodt, H.-J., & Geber, C. (2002) <em>Proc. Natl. Acad. Sci. USA</em><strong>. 99</strong>. 9783-9788.</p>
<p>[14] Hwang, K.S., Lee, J.H., Park, J., Yoon, D.S., Park, J.H., & Kim, T.S. (2004) <em>Lab Chip</em><strong>. 4</strong>. 9783-9788.</p>
<p>[15] Backmann, N., Zahnd, C., Huber, F., Bietsch, A., Pluckthun, A., Lang, H.-P., Guntherodt, H.-J., Hegner, M., & Gerber, C. (2005) <em>Proc. Natl. Acad. Sci. USA</em><strong>. 102</strong>. 14587-14592.</p>
<p>[16] Wu, G., Ji, H., Hansen, K., Thundat, T., Datar, R., Cote, R., Hagan, M.F., Chakraborty, A.K., & Majumdar, A. (2001) <em>Proc. Natl. Acad. Sci. USA</em><strong>. 98</strong>. 1560-1564.</p>
<p>[17] Savran, C.A., Knudsen, S.M., Ellington, A.D., & Manalis, S.R. (2004) <em>Anal. Chem</em><strong>. 76</strong>. 3194-3198.</p>
<p>[18] Mukhopadhyay, R., Sumbayev, V.V., Lorentzen, M., Kjems, J., Andreasen, P.A., & Besenbacher, F. (2005) <em>Nano. Lett</em><strong>. 5</strong>. 2385-2388.</p>
<p>[19] Shu, W., Liu, D., Watari, M., Riener, C.K., Strunz, T., Welland, M.E., Balasubramanian, S., & McKendry, R. (2005). <em>J. Am. Chem. Soc</em><strong>. 127</strong>. 17054-17060.</p>
<p>[20] Zhou, F., Shu, W., Welland, M.E., & Hucks, W.T.S. (2006) <em>J. Am. Chem. Soc</em><strong>. 128</strong>. 5326-5327. </p>
<p>[21] <a href="http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=APPLAB000089000017173905000001&idtype=cvips&gifs=yes">Hwang, K.S., Eom, K., Lee, J.H., Chun, D.W., Cha, B.H., Park, J.H., Yoon, D.S., & Kim, T.S. <em>Appl. Phys. Lett.</em> 89, 173905, 2006<em>.</em></a></p>
</div></div></div><div class="field field-name-upload field-type-file field-label-hidden"><div class="field-items"><div class="field-item even"><table class="sticky-enabled">
<thead><tr><th>Attachment</th><th>Size</th> </tr></thead>
<tbody>
<tr class="odd"><td><span class="file"><img class="file-icon" alt="PDF icon" title="application/pdf" src="/modules/file/icons/application-pdf.png" /> <a href="https://imechanica.org/files/Appl%20Phys%20Lett%2089%20%282006%29%20Eom%20K%20173905%20Dominant%20surface%20stress.pdf" type="application/pdf; length=254644" title="Appl Phys Lett 89 (2006) Eom K 173905 Dominant surface stress.pdf">Appl Phys Lett 89 (2006) Eom K 173905 Dominant surface stress.pdf</a></span></td><td>248.68 KB</td> </tr>
</tbody>
</table>
</div></div></div>Wed, 20 Sep 2006 11:45:49 +0000Kilho Eom219 at https://imechanica.orghttps://imechanica.org/node/219#commentshttps://imechanica.org/crss/node/219Interesting Conference: "micro-TAS 2006"
https://imechanica.org/node/209
<div class="field field-name-taxonomy-vocabulary-6 field-type-taxonomy-term-reference field-label-hidden"><div class="field-items"><div class="field-item even"><a href="/taxonomy/term/74">conference</a></div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>The conference "micro-TAS" may be interesting to researchers in engineering and science, especially involving Bio-MEMS/NEMS, biophysics, and biochemistry. See <a href="http://www.conferences.jp/microtas2006/">details of this conference</a>. </p>
</div></div></div>Tue, 19 Sep 2006 11:21:41 +0000Kilho Eom209 at https://imechanica.orghttps://imechanica.org/node/209#commentshttps://imechanica.org/crss/node/209Error | iMechanica