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Model Reduction of Large Proteins for Normal Mode Studies

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 here).

Coarse-Graining of protein structures for the normal mode studies


Researcher Spotlight: Professor Lambert Ben Freund (LBF)

L. Ben FreundLambert Ben Freund (LBF) was born on November 23, 1942, in Johnsburg, Illinois, a tiny rural community of a few hundred people in the northeast corner of the state. This part of the Midwest was opened to European settlement by the Black Hawk War of the 1830s. A small delegation of his ancestors arrived in the area in 1841.

Quantum Stability of Metallic Thin Films and Nanostructures

When a metal system shrinks its dimension(s), the conduction electrons inside the metal feel the squeezing, and are forced into (discrete) quantum states. Such confined motion of the conduction electrons may influence the global or local stability of the low dimensional systems, and in the case of a thin film on a foreign substrate this "quantum energy" of electronic origin can easily overwhelm the strain effects in definging the film stability, thereby severely influencing the preferred growth mode (see, e.g., Suo and Zhang, Phys. Rev. B 58, 5116 (1998)).

Juil Yoon's picture

Spacing effect on dislocation injection from sharp features in strained silicon structures

In practice, the SiN stripes or pads are periodically patterned on silicon, so the spacing effect on dislocation injection from sharp features deserves attention. As in Figure 1, the SiN stripes with residue stress, of width L and thickness h, are periodically patterned with spacing S. In the numerical calculation, we take shear modulus and Poisson’s ratio of Si3N4 to be 54.3 GPa and 0.27, and those of silicon 68.1GPa and 0.22, the same as in Ref.[1].

Symposium on Characterization and Modeling of Time-Dependent Materials and Processes at the 2007 ASME M&M Conference

The Symposium on Characterization and Modeling of Time-Dependent Materials and Processes at the 2007 ASME Mechanics and Materials conference will be held June 3-7, 2007, at the University of Texas at Austin. Additional information about the conference can be found at the conference website.

Papers dealing with modeling and experimental aspects of the subject area, involving all materials, are sought. The mechanical response should be non-negligable in cases involving non-mechanical fields. Possible topics include, but are not limited to: characterization and modeling of behavior at multiple scales; viscoelasticity, viscoplasticity; transport, chemically and electronically active processes; multiphase and biomaterial systems; thermodynamics; shape memory; mechanics of testing; micro/nanoindentation on time-dependent materials; dynamic behavior of polymers and composites; large deformations; residual stresses; time-dependent damage and failure; polycrystalline and single crystal behaviors; multifunctional materials; mechanics of processing.

Leon Mishnaevsky's picture

Postdoctoral Position in Micromechanics and Fatigue of Natural Composites, at Risø National Laboratory, Denmark

Applications are invited from suitably qualified candidates for a Postdoc/Research Scientist position in the framework of a Danish/Nepalese collaborative research project, in the Materials Research Department of Risø National Laboratory, Denmark 

Job description: As a postdoc/scientist, you will carry out numerical micromechanical modelling of fatigue processes in wood. The theme of the project is the computational analysis of the effect of microstructures of natural materials (wood), coatings and other microscale parameters on their fatigue resistance and lifetime under cyclic loading. The experiments and verification of results will be carried out in collaboration with project partners in Kathmandu, Nepal. The deliverables of the project should include the development of recommendations for the improvement of the reliability of wind turbine blades, produced from coated wood in Nepal, as well as extracting “lessons from nature” to be used in the improvement of polymer matrix fiber reinforced composites for wind energy applications.  

Ashkan Vaziri's picture

Mechanics and deformation of the nucleus in micropipette aspiration experiment

Robust biomechanical models are essential for studying the nuclear mechanics and can help shed light on the underlying mechanisms of stress transition in nuclear elements. Here, we develop a computational model for an isolated nucleus undergoing micropipette aspiration. Our model includes distinct components representing the nucleoplasm and the nuclear envelope. The nuclear envelope itself comprises three layers: inner and outer nuclear membranes and one thicker layer representing the nuclear lamina.

Xiaoyan Li's picture

Atomistic simulations for the evolution of a U-shaped dislocation in fcc Al

We show, through MD simulations, a new evolution pattern of the U-shaped dislocation in fcc Al that would enrich the FR mechanism. Direct atomistic investigation indicates that a U-shaped dislocation may behave in different manners when it emits the first dislocation loop by bowing out of an extended dislocation. One manner is that the glissile dislocation segment always bows in the original glide plane, as the conventional FR mechanism. Another is that non-coplanar composite dislocations appear owing to conservative motion of polar dislocation segments, and then bow out along each slip plane, creating a closed helical loop. The motion of these segments involves a cross-slip mechanism by which a dislocation with screw component moves from one slip plane into another. Ultimately, such non-coplanar evolution results in the formation of a FR source.


I am writing to you to bring to your attention a new Master Course on Computational Mechanics, which has been awarded the Erasmus Mundus label.

It is an international Master course given jointly in English by the Universidad Politécnica de Cataluña (Barcelona), University of Wales Swansea), Ecole Centrale Nantes and Universität Stuttgart with the collaboration of CIMNE International Centre for Numerical Methods in Engineering, Barcelona). The Erasmus Mundus program:

Prototype for a journal in iMechanica

Hi fellow mechanicians,

Professor Suo and I have devised a model for creating a journal on iMechanica. It is a simple model which doesn’t require installing any additional modules or features.

Alexander A. Spector's picture

Back to the Mechanics vs. Biochemistry in Cellular Mechanotransduction

In his interesting response to our comment posted on 11/28, Ning Wang focused on the transmission of a local force generated at the adhesion site(s). We agree that this is a question important to our understanding of the signaling to the nucleus. The question is not only about the range of the force transmission but also about the magnitude of such force because the nucleus is several times stiffer than the cytoskeleton.

A Model for Superplasticity not Controlled By Grain Boundary Sliding

It is commonly assumed that grain boundary sliding can control plastic deformation in fine grained crystalline solids.  Superplasticity is often considered to be controlled by grain boundary sliding, for example.  I have never accepted that view, though my own opinion is very much at odds with the commonly accepted picture.  When I was asked to write a paper in honor of Professor F.R.N. Nabarro's 90th birthday (Prof.

Mechanical Properties of Thin Films (class notes for a graduate class at Stanford University)

The attached file is a set of class notes developed by W.D. Nix of Stanford University and used in a graduate course on Mechanical Properties of Thin Films. These notes have been used in the graduate course MSE 353 since the late 1980's. That course has been taught every year or so since that time. The notes were last updated in January of 2005. The reader will see a note to the effect that many of the figures and illustrations in the file have been taken from the work of students and colleagues at Stanford without proper attribution.

Hanqing Jiang's picture

Symposium: Multiscale Multiphysics Modeling and Simulation of Nanomaterials and Nanostructures

McMat 2007, June 3-7, 2007, University of Texas at Austin


Call for paper

Symposium: Multiscale Multiphysics Modeling and Simulation of Nanomaterials and Nanostructures

Zhigang Suo's picture

What Is Mechanics?

So, What is Mechanics? It seems that useful answers ought to depend on who you are talking to. If you are persuading your dean to hire a new faculty member in Mechanics, perhaps you’d like to point out promising research in one area or another, and how foundational mechanics is to the education of future scientists and technologists in (almost) all fields.

How to Make a Free Web Site

In the present time the internet craze has swept the nation and these days everything and everyone is online. Everyone having fun on internet and get knowledge from the web site.

If you want to know how to make a free web site, the good news is that you've set an easy goal for yourself. Learning how to make a free web site is about more than just getting your web domain for free - you need to know how to put information on that site as well. Many domains offering free web sites also feature free online tutorials that will help you write your web pages. Some sites are so user-friendly; you don't have to write any of your own web code at all! You can select colors and font sizes from the domain's own page editing service. When the domain is willing to write your pages for you, it's very easy to learn how to make a free web site.

Michael H. Suo's picture

Who Owns Your Content? [draft]

Who owns your content? Is it you or the copyright holder? If it isn't you, then why did you pay for it? All these questions are at the heart of the current war for the rights to music, movies, and everything in between.

The first shots of this war were fired with the start of the digital age. Before, the best you could was make physical copies of media. Technically possible, yes, but the equipment and manpower needed to run an operation on a scale large enough to threaten publishers was nearly impossible to obtain without being noticed.

Mogadalai Gururajan's picture

Some numerical mechanics software

Recently, during one of my net searches, I came across this page of RPI, where I learnt about a couple of numerical mechanics software which might be of interest to some of you.


As for the effort toward the scalable engineering simulations on distributed environements, we addressed this challenge by developing a distributed mesh data management infrastructure that satisfies the needs of distributed domain of applications.

A structure-based sliding-rebinding mechanism for catch bonds

This is a paper by Jizhong Lou and myself, which is in press in Biophysical Journal.

Abstract.  Catch bonds, whose lifetimes are prolonged by force, have been observed in selectin-ligand interactions and other systems. Several biophysical models have been proposed to explain this counter-intuitive phenomenon, but none was based on the structure of the interacting molecules and the noncovalent interactions at the binding interface. Here we used molecular dynamics simulations to study changes in structure and atomic-level interactions during forced unbinding of P-selectin from P-selectin glycoprotein ligand-1. A mechanistic model for catch bonds was developed based on these observations. In the model, "catch" results from forced opening of an interdomain hinge that tilts the binding interface to allow two sides of the contact to slide against each other. Sliding promotes formation of new interactions and even rebinding to the original state, thereby slowing dissociation and prolonging bond lifetimes. Properties of this sliding-rebinding mechanism were explored using a pseudo-atom representation and Monte Carlo simulations. The model has been supported by its ability to fit experimental data and can be related to previously proposed two-pathway models.

How can we obtain more information from protein structure?

We know - or believe - protein function is determined by structure. Crystallographic and NMR studies can provide protein structures with atomic-level details at equilibrium. MD simulations can follow protein conformational changes in time with fs temporal resolution in the absence or presence of a bias mechanism, e.g., applied force, used to induce such changes.

Dhirendra Kubair's picture

Mode-3 spontaneous crack propagation along functionally graded bimaterial interfaces

This is a paper that has been accepted for publication in the Journal of the Mechanics and Physics of Solids from our group. The paper describes the combined effect of material inertia and inhomogeneous material property variation on spontaneous cohesive-crack propagation in functionally graded materials. The preprint is attached as a PDF.

Abstract- The effects of combining functionally graded materials of different inhomogeneous property gradients on the mode-3 propagation characteristics of an interfacial crack are numerically investigated. Spontaneous interfacial crack propagation simulations were performed using the newly developed spectral scheme. The numerical scheme derived and implemented in the present work can efficiently simulate planar crack propagation along functionally graded bimaterial interfaces. The material property inhomogeneity was assumed to be in the direction normal to the interface. Various bimaterial combinations were simulated by varying the material property inhomogeneity length scale. Our parametric study showed that the inclusion of a softening type functionally graded material in the bimaterial system leads to a reduction in the fracture resistance indicated by the increase in crack propagation velocity and power absorbed. An opposite trend of increased fracture resistance was predicted when a hardening material was included in the bimaterial system. The cohesive tractions and crack opening displacements were altered due to the material property inhomogeneity, but the stresses ahead of the cohesive zone remained unaffected.


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