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Rui Huang's picture

EPN - E-print Network

I was notified today that my Web site (http://www.ae.utexas.edu/~ruihuang/) has been included in the E-print Network (EPN). EPN is a fast-growing searchable scientific network of over 20,000 Web sites containing research conducted by researchers - from Nobel Laureates to post-doctoral students - who are offering e-prints of their work via the Internet.

Developed by the Office of Scientific and Technical Information (OSTI) to facilitate the needs of the Department of Energy (DOE) research community, E-print Network enhances dissemination of important research and helps to create opportunities for productive professional contacts.

E-print Network indexes over 900,000 e-prints. Most documents included in the network are recent scientific literature. Functions available to users include conducting full-text searches, searching for documents by contributing author, establishing a personalized alert service to keep abreast of new e-prints, and exploring laboratory Web sites for further details about selected research programs.

Once users find a paper of interest, they can download it from the site hosting the paper. This way you control distribution of your e-prints and can more readily track Web interest in your papers.

My page is listed under both Engineering and Materials Science.

Rui Huang's picture

Modeling Place

Starting from January 2006, my group has been posting in Modeling Place as a blogspot to share research experience and ideas. We will gradually migrate to iMechanica for better publicity and more web functions.

Xi Chen's picture

Why is molecular mechanics simulation at 0K useful?

Although it is more realistic to study the mechanical properties of nanostructures such as the carbon nanotubes (CNTs) at room temperature, atomistic simulations at finite temperature (such as molecular dynamics, MD) may cause the following problems: (1) Due to the limitation of the time scale achievable in MD (typically at the nanosecond scale), the loading rate in MD simulation at any finite temperature is not realistic. Very often, the loading rate used in MD simulations may well exceed 10m/s at 300K and thus many orders of magnitude higher than the real loading rate used in experiments. (2) A great advantage of simulation is to be able to turn on and turn off certain features and explore their effects, which is otherwise impossible in experiments. For example, the buckling behavior of CNTs is very sensitive to geometrical perturbations, which is prominent at room temperature and such perturbations causes severe uncertainties and makes it difficult to explore the intrinsic buckling behaviors. Therefore, by removing the temperature effect, we could better evaluate other key factors affecting the intrinsic buckling behavior, such as tube chirality, radius, and length, which could be otherwise covered by the thermal fluctuation effect. (3) Due to both time and length scale limitations, the MD simulations of large system are not yet possible, and thus the effective continuum models must be developed which need to be calibrated by atomistic simulations. At present, the temperature factor is still absent in most continuum models. Therefore, atomistic simulations at 0K or near 0K may provide a useful benchmark for the development of parallel continuum models, focusing on the most intrinsic and basic mechanical properties of nanostructures. Based on the above analysis, atomistic simulations at 0K by using the molecular mechanics (MM) method are still very useful, especially to us as mechanicians.

Xi Chen's picture

A molecular dynamics-decorated finite element framework for simulating the mechanical behaviors of biomolecules

Cover of Biophysical JournalOur first paper in biomechanics is featured as the cover of the Biophysical Journal. The paper is attached. Several freelance writers in biophysics have reported this paper in magazines and websites/blogs. This framework is very versatile and powerful, and we are now implementing more details/atomistic features into this phenomenological approach, and the follow-up paper will be submitted soon.

Abstract: The gating pathways of mechanosensitive channels of large conductance (MscL) in two bacteria (Mycobacterium tuberculosis and Escherichia coli) are studied using the finite element method. The phenomenological model treats transmembrane helices as elastic rods and the lipid membrane as an elastic sheet of finite thickness; the model is inspired by the crystal structure of MscL. The interactions between various continuum components are derived from molecular-mechanics energy calculations using the CHARMM all-atom force field. Both bacterial MscLs open fully upon in-plane tension in the membrane and the variation of pore diameter with membrane tension is found to be essentially linear. The estimated gating tension is close to the experimental value. The structural variations along the gating pathway are consistent with previous analyses based on structural models with experimental constraints and biased atomistic molecular-dynamics simulations. Upon membrane bending, neither MscL opens substantially, although there is notable and nonmonotonic variation in the pore radius. This emphasizes that the gating behavior of MscL depends critically on the form of the mechanical perturbation and reinforces the idea that the crucial gating parameter is lateral tension in the membrane rather than the curvature of the

Xi Chen's picture

Appropriate range of materials used in indentation analysis

The conventional indentation analysis uses finite element simulations on a wide range of materials and studies their indentation responses, which is known as the forward analysis; then, from the reverse analysis it may be possible to extract material properties from the indentation responses on a particular specimen. In doing so, it is important to selecte a wide yet appropriate range of materials during the forward analysis. Often times when I read or review papers, I found some authors "randomly" select a large range of materials without really knowing what does that mean and whether it is practical; in many cases the materials employed in their forward/reverse analyses do not exist in reality or are actually not suitable for conventional indentation analysis.

In indentation analysis the constitutive elastoplastic properties of the specimen is often expressed by the power-law form. It is important to note that most brittle ceramic or glass materials crack upon indentation, and polymers creep during indentation experiment, moreover the tension and compression behaviors of polymers are often very different; thus, they typically cannot be well-described by the power-law form and their mechanical properties cannot be obtained from the conventional indentation analysis. Thus, ceramics and polymers should be excluded from the present analysis, as well as the highly anisotropic woods. In addition, composite materials, nanocomposites and other nano-structured materials, as well as thin films also need to be excluded from the continuum analysis because the underlying micro/nanostructures play a key role in their mechanical responses. Therefore, only the more ductile and "plastic" polycrystalline bulk metals and alloys are suitable for conventional indentation analysis at room temperature since large strain will occur beneath the indenter during indentation, and also because the conventional plasticity theory is developed for metals which is the foundation of the elastoplastic finite element analysis. The indentation depth also has to be sufficient large on the bulk specimen so as to overcome the strain gradient effect.

The material selection chart taken from page 425 of the famous handbook"Materials selection in mechanical design" by Mike Ashby can be used as a guide. In general, for most engineering metals and alloys suitable for conventional indentation study, the Young's modulus is from about 10 to 600GPa, and the yield strength is from roughly 10MPa to 2GPa, and the inverse of yield strain is in the range roughly from 100 to about 5000 (some pure metals may have even higher inverse yield strain, but should not far exceed such bound). Note that since the specimen must undergo relatively large strain during indentation without cracking, thus the material must be sufficiently ductile (i.e. plastic or soft).

In forward analysis, however, the material range chosen in finite element simulation needs to be moderately larger than the aforementioned bound, so as to avoid possible numerical ill conditions at the boundaries. The reverse analysis, however, should focus on the more practical materials, i.e. the range of metals and alloys listed above.

Xi Chen's picture

use NMA to get the elastic properties of loop

(originally written by Yuye Tang) A key procedure of the molecular-dynamics decorated finite element method (MDeFEM) is to determine the effective properties of components of a macromolecule. Here I illustrate how could one use the NMA computed from MD to estimate the elastic properties of loops in mechanosensitive channels, which is related with my research.

Split singularities and the competition between crack penetration and debond at a bimaterial interface

Zhen Zhang and Zhigang Suo

For a crack impinging upon a bimaterial interface at an angle, the singular stress field is a linear superposition of two modes, usually of unequal exponents, either a pair of complex conjugates, or two unequal real numbers. In the latter case, a stronger and a weaker singularity coexist (known as split singularities). We define a dimensionless parameter, called the local mode mixity, to characterize the proportion of the two modes at the length scale where the processes of fracture occur. We show that the weaker singularity can readily affect whether the crack will penetrate, or debond, the interface.

Zhigang Suo's picture

How to make long distance phone calls for free

Like many other communities, we mechanicians are scattered all over the world, often separated from families and colleagues. The Internet has promised for years to make long dstances irrelevant: anybody anywhere is just a click away. While nothing will ever be the same as being together in person, many Internet services can facilitate distant communication and collaboration. For example, Skype, an Internet phone service, allows you make free phone calls around the world. The sound quality is excellent.

Zhigang Suo's picture

Pay per paper (P3)

(Originally published on Applied Mechanics News on 22 July 2006, where many comments provided remarkable insight)

I’ve just stopped subscribing to Science. The magazine is great, but few papers in it interest me. The signal-to-noise ratio of Science, I guess, is just too low to most individuals. Instead, I’ve now subscribed to the RSS feed of Science. If any paper looks interesting, I can access to the full paper online through Harvard Libraries. Outside my office, a color printer is free to use for everyone. A library of an institution seems to be an ideal home for a journal like Science. Nearly every individual paper in Science is of high enough quality to appeal to someone in the institution.

Few journals can make that claim, however. Most journals are only relevant to several people in an institution. Furthermore, few researchers read any scholarly journal from cover to cover. Rather, we all read individual papers. However, libraries subscribe to journals, or even bundles of journals. As a result, the libraries pay for many papers that nobody reads, and miss other papers that someone would like to read.

This business model is bad for authors and readers, and possibly even bad for publishers. Technology now exists to distribute information far more efficiently, in a unit consistent with how people consume the information. For example, many people now prefer buying individual songs to albums. See a recent book, The Long Tail, by Chris Anderson, the editor-in-chief of Wired, for a remarkably perceptive analysis of media industries.

The same business model may apply to scholarly papers. One may argue that journals, like albums, were invented as a packaging technology to suit the old economics of delivery. As scholarly papers are all online, the name of a journal becomes simply a tag to the papers published in that journal. Maybe a powerful tag, but a tag nonetheless. So far as how papers should be distributed, the name of a journal should serve the same function as all other tag-like entities: keywords, names of authors, etc: the tags help readers to sort papers and set priorities. It makes no sense for anyone to insist that papers with any particular tag be delivered as a bundle.

Many publishers already offer individual papers for sale online; for example, the cost is at $30 per paper for many Elsevier journals. Once a reader buys a paper, it seems reasonable to share this paper with his close colleagues, and it also seems reasonable to store the paper for future use. Perhaps we can formalize this practice.

How about we treat a paper just like a book? With one click, a reader will have the paper, and his library will automatically pay for it. Once bought, the paper is accessible to every user of the library. We can also collect statistics. If the users of a library buy many papers in a journal, the library should subscribe to the journal. Libraries will set up an algorithm to minimize the total cost. Publishers will set up their algorithms to maximize profits. However, libraries and publishers do have a common ground: they both want to help people to find papers.

To support such a business model, a third party may provide a web service. It seems to be too wasteful to make every individual library and every individual publisher maintain a separate web service. Something like Amazon.com or Last.fm for papers might do. The service can also be an extension of services like EZproxy or CiteULike.

Zhigang Suo's picture

The LibraryLookup Bookmarklet

(Opriginally posted on Applied Mechanics News on 8 July 2006)

Quick link added on 12 July 2006. Here is a list of LibraryLookup Bookmarklets for many libraries, along with an instruction to use them.

Zhigang Suo's picture

Libraries and Amazon

(Originally posted on Applied Mechanics News on 25 June 2006)

Libraries take premium spaces, which will not grow and will likely shrink. As more and more books are stored in off-campus depositories, people miss the serendipity of browsing among shelves and discovering books that they don’t know they’d like to read. They can browse the catalogues of the libraries. However, a typical catalogue of a library contains meager information: the online catalogue is a clone of its ancestor on cards. Creating an information-rich and user-friendly online catalogue is too expensive for a library.

These problems have a solution. The primary source of data on books is Amazon. It contains publisher-supplied data such as cover images, table of contents, index, and sample material. Searchable full texts are within reach. Perhaps even more valuable, Amazon contains comments of users on books. Based on collective behavior of users, Amazon also recommends books to users. Amazon will no doubt continue relentless innovation.

In an ideal world, a user should not waste his time on the catalog of a library, nor should the library waste its resources on maintaining a stand-alone catalog. The user should simply browse on Amazon. Once he finds an interesting book, a single click should tell him if the book is in any of the libraries accessible to him. In this ideal world, to enter a book into the catalog of a library, a librarian only needs to enter a single number: the call number of the book. All other data of the book are not library-specific and are already in Amazon. What if the library owns a book not in Amazon? The librarian should enter a detailed description of the book, as if she were the publisher of the book.

This ideal world may not be far different from our world. The LibraryLookup Project allows a user to generate a bookmarklet, so that with one click he can look up a book in a library, while surfing on Amazon. The creator of the Project, Jon Udell, has developed a screencast to guide you through the process of generating your own bookmarklet.

A deeper integration of Amazon and libraries would harness more power. The statistics of borrowing books could be aggregated from all libraries and be used to recommend books to users. Amazon, libraries and some third party could collaborate on the business of print on demand. Libraries could send even more books to depositories and greatly simplify efforts in cataloging books. Users would have a seamless experience with books. Oh, if a book is not in a library, users could suggest, with a single click, that the library order the book.

Ending added on 26 June 2006, after reading a message from Zak Stone. Amazon.com is named after the Amazon River, the largest river in the world, carrying more water than the next six largest rivers combined. May the rivers of libraries and the streams of users contribute to the River of All Books. May Amazon.com nurture the civilization without drowning us with commercialism.

Note added on 10 July 2006. An entry describes my experience with LibraryLookup Bookmarklets.

Note added on 15 July 2006. Wall Street Journal (13 July 2006) on Rice University's Press on line and print on demand (POD). For an example of comercial POD, see lulu.com. Also see a recent product annoucement of e-reader.

Note added on 17 July 2006. OCLC and Amazon: A Connection Revealed.

Note added on 27 July 2006. Springer will offer all new titles in e-book form.

Note added on 20 August 2006. Amazon introduces library processing.

Note added on 31 August 2006. Google offers free download of books.

Note added on 31 August 2006. Stanford's vision for library.

Zhigang Suo's picture

What's wrong with Applied Mechanics?

(Originally posted on Applied Mechanics News in 16 May 2006)

Zhigang Suo's picture

Connexions: knowledge as commodities

(Originally posted on Applied Mechanics News on 2 May 2006)

A twelve-year old found a blueprint to assemble a computer in a magazine, and ordered parts on newegg.com, a website that listed parts from all vendors and comments on each part by customers. Both features were reassuring. When the parts arrived in mail a week or two later, the boy assembled the computer himself. In the process, he saved a substantial amount of money. He also learned a lot about computers, and about dealing with his parents.

The boy could do all these because computer parts are commodities, products that are produced by different companies but conforming to the same standards: all parts fit. Websites like newegg bring the parts from the companies directly to boys and girls of all ages, skipping middlemen like Dell.

Commoditization has also occurred in the software industry, largely due to the open-source movement that has produced the Linux operating system, as well as a large number of other software systems.

Can we also commoditize knowledge? This is precisely the mission of the Connexions Project, founded by the electrical engineer Richard Baraniuk, of Rice University, in 1999. The Project has been funded by the National Science Foundation and private donors, and has produced a system of software to enable anyone to author parts of knowledge (called modules). It also enables anyone to assemble parts into a functional product of knowledge (called a course), free of charge, under a Creative Commons open license. By January 2006, Connexions hosted over 2900 modules and 138 courses.

Connexions will likely have tremendous impact on the textbook industry, which has an annual revenue of 10 billion dollars in the US alone. The Project is also bringing free, up-to-date knowledge to developing countries, including North Karea.

Connexions will also likely to change the practice of scholarship. If you'd like to learn how Connexions works, you may visit the website of Connexions, or look at a course, or read a white paper written by the Connexions staff, or simply enjoy a video of an inspiring talk given by Professor Baraniuk to Google engineers.

Notes added on 15 July 2006. Wall Street Journal (13 July 2006) reported on Rice University's Press on line and print on demand.

Zhigang Suo's picture

Wikipedia and Applied Mechanics

(Originally posted on Applied Mechanics News on 25 February 2006)

Zhigang Suo's picture

Plan activities of the Applied Mechanics Division at 2007 ASME Congress

The ASME International Mechanical Engineering Congress and Exposition (IMECE) will be held in 11-16 November 2007, in Seattle, Washington. As the 2007 Program Chair of the Applied Mechanics Division (AMD), I hope to get you involved in planning activities at the Congress.

IMECE is a place where you can meet people and attend talks in Applied Mechanics, as well as in other fields, such as Materials, Electronic Packaging, Tribology, and Heat Transfer. For many mechanicians, a highlight of the Congress is the Applied Mechanics Annual Dinner, where old acquaintances are resumed, new friends made, awards announced, and the Timoshenko lectures delivered.

Teng Li's picture

What can mechanics community learn from the success of Google?

A cartoon in The New Yorker magazine shows a boy asking his dad a question. The dad, reading a book, replies, “Go ask your search engine.” The cartoon was published in Feb. 2000, three months before Google officially became the world's largest search engine with its introduction of a billion-page index — the first time so much of the web's content was made searchable. If the boy asks again today, his dad will say, “Go ask Google.”

At $6 billion a year in revenue and $7.6 billion in cash, Google is a success. What’s more important to the rest of us, Google is running its business in a way that may change the world. Through its never-about-average products (i.e., Google search, Google Earth (and Mars too), Google Map, and more recently, Writely), Google is radically redefining the ways we obtain, organize, use, store, and share information.

Teng Li's picture

Review Articles on Flexible Electronics

[img_assist|nid=46|title=|desc=|link=url,http://www.materialstoday.com/2006_issues/april.htm|align=right|width=75|height=100]The cover story of the April 2006 issue of Materials Today features Flexible Electronics. This issue also includes two review articles in this emerging field of research. Access to full text articles is free of charge at http://www.materialstoday.com.

Review Article:

Material challenge for flexible organic devices, by Jay Lewis

Review Article:

Organic and polymer transistors for electronics, by Ananth Dodabalapur

Cover Story:

Jet printing flexible displays, by R.A. Street et al.

Zhigang Suo's picture

Applied Mechanics in the Age of Web 2.0

The ASME International Applied Mechanics Division has about 5000 members. The number is too large for us to know each other individually, but too small for CNN to cover us in the Situation Room.

Then came the Internet. We have since been in touch through emails, and looked up each other on the Web. Many web pages created in 1990s, however, are static. For such a web page, the bottleneck is often the webmaster. He or she gets a request each time anyone wants to post anything. It is more like a broadcast than a web.

In recent years, there have been waves of new internet phenomena, such as Wikipedia, Real Simple Syndicates (RSS), open-source movement, and web logs (blogs). They are collectively known as Web 2.0.

A new home for mechanics researchers

Zhigang is really a master of good ideas. He learned the new technology from his son months ago, and then so many good ideas have been popping up in the mechanics community. Google group was the first trial, then google blog, wikepedia, etc. Now even fancier, iMech. I dreamed before, if I had money, I would buy a series of products by Apple. Now and in the future, I wish I can obtain iMech for free. I wish it has the quality as other products of i*** by Apple, but not as expensive as those. Good news is that the iMech is made by Zhigang, not Apple.

Zhigang Suo's picture

Let us seize the greatest opportunity of our time

We've been hearing rumors that print is dead, killed by the Internet. What is the reality then? For example, how are newspapers doing? Not too badly, according to the numbers cited by James Surowiecki, of The New Yorker. He also made the following remarks, however.

"The popular conviction that papers are doomed may cause owners and shareholders to prefer the cash-cow approach, accepting eventual oblivion while continuing to harvest billions of dollars in profits. Settling for a tolerable short-term future, newspapers could end up writing themselves out of the long-term one. Yet it’s also clear that this moment of supposed doom represents a sizable opportunity for newspapers, a chance to reinvigorate their product and, eventually, improve the economics of their business."

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