Google Scholar can localize your search to library links
Search globally, go locally. Starting from Feb. 2006, Google Scholar offers links to find papers in your local library. See here for details.
Blog posts
Online Journal Club on Flexible Electronics
For many years, people accumulate personal collections of academic publications of interest in paper form. As such collections grow with time, more file cabinets and book shelves are needed for storage. First, space becomes a problem. Second, finding a specific paper could be a headache, even if the collections are well categorized.
As more and more publications become available online in recent years, people gradually switch to collect electronic versions, e.g. PDF files of papers. These files are often stored in local hard drives. Space is not an issue anymore. But again, locating a paper from hundreds of files in tens of folders still might be a heck of efforts.
Besides the difficulty in searching, other common shortcomings include:
- Locally stored, limited access flexibility.
- Personally owned, not easy to share with other people. As a result, the scale of personal collections is often limited.
- Redundently collected. Consider this: a same gem paper is manually archived by thousands of people individually.
- Statically and passively maintained. Lack of interactions among people sharing common interests.
Any better idea? Here comes Web2.0, which is all about online collaboration. Among the numerous tools enabled by Web2.0, CiteULike could be the one able to solve the above issues for us. A previous post in AMN explored the possibility to form online journal club based on CiteULike. Here is an example.
CiteULike: Your online library of scientific literature, and more...
CiteULike is an online service to help academics to share, store, and organize the scientific literature. When you see a paper or a book on the web that interests you, you can click one button and have it added to your personal library. CiteULike automatically extracts the citation details (e.g., title, authors, abstract, and DOI). Currently, it supports more than 30 pubishing websites, many of which are of interest of mechanics community, e.g., ScienceDirect, AIP Scitation, Science, Nature, SpringerLink and Amazon.
Searching in your CiteULike library can be very easy. The surnames of all authors in your library are automatically tagged. You can also tag the papers and the books in your library as you like. All these tags appear in a tag cloud. Therefore, locating a paper in your library will be only one or two clicks away. Also, because your library is stored on the web server, you can access it from any computer.
You can also form a group, and integrate every member's own library to a group library. CiteULike also allows everyone to add note on papers or books. By combining the group and the note functions, you can easily form an online journal club among colleagues, collabarators, students, or any group with common interests, no matter how far away from each other.
Programmed by Richard Cameron and generously hosted by the University of Manchester in England, CiteULike is a free service to everyone. You just need to register to use its full functions. It all works within your web browser, no extra software is needed. So give it a try and enjoy.
Note: Nature publishing group also provides a similar service named Connotea. After experimenting both of them, I share the same feeling of many other users: while more attractive at the first sight, Connotea currently offer less flexible functions than CiteULike. I personally vote for CiteULike. You may want to share your experience with CiteULike or Connotea by commenting this entry.
Update on 4 July 2006:
Macroelectronics Journal Club, an online journal club focusing on flexible electronics and running on CiteULike platform, has been launched by www.macroelectronics.org. See a brief introduction here and detail announcement here.
Update on 14 July 2006:
By default, CiteULike stores links to papers. To get full access of a paper, you often need to locate the paper within the subscription of your institution, instead of its original link. By using a scalable bookmarklet, now localizing the paper links can be only as easy as one click away. See a recent iMechanica entry for details.
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.
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.
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.
A molecular dynamics-decorated finite element framework for simulating the mechanical behaviors of biomolecules
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
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.
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
(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.
