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EPN - E-print Network

Submitted by Rui Huang on
research
Huang Group
web sites
searchable scientific network
e-prints

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.

Why is molecular mechanics simulation at 0K useful?

Submitted by Xi Chen on
chen group
molecular dynamics
nanomechanics
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.

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

Submitted by Xi Chen on
research
biomechanics
chen group

Our 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

Appropriate range of materials used in indentation analysis

Submitted by Xi Chen on
chen group
indentation
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.

use NMA to get the elastic properties of loop

Submitted by Xi Chen on
biomechanics
chen group
molecular dynamics
(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

Submitted by Zhen Zhang on
research
suo group research
singularity
crack
penetration
deflection
debond
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.

How to make long distance phone calls for free

Submitted by Zhigang Suo on
Internet
collaboration
p2p

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.

Pay per paper (P3)

Submitted by Zhigang Suo on
publishing
Internet
library

(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.

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