research

Computational models of the cell nucleus, along with experimental observations, can help in understanding the biomechanics of force-induced nuclear deformation and mechanisms of stress transition throughout the nucleus. Here, we develop a computational model for an isolated nucleus undergoing indentation, which includes separate components representing the nucleoplasm and the nuclear envelope. The nuclear envelope itself is composed of three separate layers: two thin elastic layers representing the inner and outer nuclear membranes and one thicker layer representing the nuclear lamina. The proposed model is capable of separating the structural role of major nuclear components in the force-induced biological response of the nucleus (and ultimately the cell). A systematic analysis is carried out to explore the role of major individual nuclear elements, namely inner and outer membranes, nuclear lamina, and nucleoplasm, as well as the loading and experimental factors such as indentation rate and probe angle, on the biomechanical response of an isolated nucleus in atomic force microscopy indentation experiment.

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].

Cellular and Molecular Mechanics I was invited by Dr. Zhigang Suo to write a short piece on “Cellular and Molecular Mechanics”. I am writing this informally to introduce this subject matter rather than talk in vernacular such as mechanotransduction, phosphorylation, etc. I have more formal papers if someone is interested in more detailed discussions on this subject area. This is a field in which I have been working for over a decade now and I find it more exciting every day. The question always is how does mechanics affect biological processes. This is a very interdisciplinary subject matter as mechanists, engineers, physicists, chemists, and biologists have been investigating this process from various perspectives. I am obviously not the first to study this process. For most of us, it is realized from an empirical perspective that mechanics matters to biology, but exactly how mechanics specifically alters biochemistry continues to be highly debated today. Mechanics of course matters in many physiological areas. Your blood flows, your heart pumps, your bone and muscle feel mechanics. Not only does the body experience mechanical stimulation, but it reacts biochemically to it. A wonderful example is when people go into space (NASA) for long periods of time. The bone in one’s body begins to resorb in a similar response mode to what one experiences in aging (osteoporosis). This is primarily due to just the change in the gravity (mechanics). Other diseases are related to these issues including the two biggest killers: heart disease and cancer. While biomechanics on this scale has been studied for awhile (Leonardo Da Vinci, who was interested in mechanics, also wrote one of the first texts on anatomy), the movement to the cellular and molecular scales has brought a tremendous amount of excitement. I consider the cell as one of the ultimate smart materials exhibiting these characteristics. The cell has evolved over millions of years and is designed better than almost any system that we can personally build. Just as the biological eye provides a beautiful template for optics based lenses, much can be learned about building technology (“nanotechnology” and “microtechnology”) through examining the behavior of cells and molecules.

by S. Yip (Editor), 2005

Book Review
"A new guide to materials modeling largely succeeds in its aim to be the defining reference for the field of computational materials science and represents a huge undertaking..." -- by James Elliott | University of Cambridge, Materials Today, Volume 9, Issues 7-8, July-Aug 2006, Pages 51-52.

Book Description
The first reference of its kind in the rapidly emerging field of computational approachs to materials research, this is a compendium of perspective-providing and topical articles written to inform students and non-specialists of the current status and capabilities of modelling and simulation. From the standpoint of methodology, the development follows a multiscale approach with emphasis on electronic-structure, atomistic, and mesoscale methods, as well as mathematical analysis and rate processes. Basic models are treated across traditional disciplines, not only in the discussion of methods but also in chapters on crystal defects, microstructure, fluids, polymers and soft matter. Written by authors who are actively participating in the current development, this collection of 150 articles has the breadth and depth to be a major contributor toward defining the field of computational materials. In addition, there are 40 commentaries by highly respected researchers, presenting various views that should interest the future generations of the community. Subject Editors: Martin Bazant, MIT; Bruce Boghosian, Tufts University; Richard Catlow, Royal Institution; Long-Qing Chen, Pennsylvania State University; William Curtin, Brown University; Tomas Diaz de la Rubia, Lawrence Livermore National Laboratory; Nicolas Hadjiconstantinou, MIT; Mark F. Horstemeyer, Mississippi State University; Efthimios Kaxiras, Harvard University; L. Mahadevan, Harvard University; Dimitrios Maroudas, University of Massachusetts; Nicola Marzari, MIT; Horia Metiu, University of California Santa Barbara; Gregory C. Rutledge, MIT; David J. Srolovitz, Princeton University; Bernhardt L. Trout, MIT; Dieter Wolf, Argonne National Laboratory.

Nanocomposite performance fundamentally relies on reproducible dispersion and arrangement of nanoparticles, such that the dominate morphology across macroscopic dimensions is also nanoscopic. To facilitate dispersion, chemical approaches, including surfactant or macromolecular stabilization are usually employed to modify the surface of nanoparticles. However, the approach depends on the material system and usually involves trial-and-error to identify the best practice. Much less quantitative information is available on the coupling between the surface modification and external processing factors, including shear, electric or magnetic fields. In a recent work, we considered electric field on the interaction of nano-plates. For ideal dielectrics an electric field may assist (or retard) exfoliation depending on the angle between a collection of plates and the field. A critical electric field strength to promote exfoliation is predicted when the field is parallel to the surface of the plates. Structural refinement is predicted to occur by cleavage through the center of the stack. For lossy dielectrics, frequency can be tuned to cause exfoliation in all plate orientations.

Professor Rodney Ruoff and colleagues at Northwestern University and Purdue University have developed a process that promises to lead to the creation of a new class of composite materials - graphene-based materials. They reported the results of their research in Nature, 442 (2006) 282-286. This team has overcome the difficulties of yielding a uniform distribution of graphene-based sheets in a polymer matrix. Such composites can be readily processed using standard industrial technologies such as moulding and hot-pressing. The technique should be applicable to a wide variety of polymers. The graphene composites may compete with carbon nanotube-based materials in terms of mechanical properties. This new class of composites may stimulate the applied mechanics community to study the fundamental reinforcing mechanisms of graphene sheets from both experimental and theoretical approaches.

A vicinal Si (001) surface may form stripes of terraces, separated by monatomic-layer-high steps of two kinds, SA and SB. As adatoms diffuse on the terraces and attach to or detach from the steps, the steps move. In equilibrium, the steps are equally spaced due to elastic interaction. During deposition, however, SA is less mobile than SB. We model the interplay between the elastic and kinetic effects that drives step motion, and show that during homoepitaxy all the steps may move in a steady state, such that alternating terraces have time-independent, but unequal, widths. The ratio between the widths of neighboring terraces is tunable by the deposition flux and substrate temperature. We study the stability of the steady state mode of growth using both linear perturbation analysis and numerical simulations. We elucidate the delicate roles played by the standard Ehrlich-Schwoebel (ES) barriers and inverse ES barriers in influencing growth stability in the complex system containing (SA+SB) step pairs.

Preprint available in the attachment.

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

[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.