iMechanica

We recently reported the mass sensing by using resonating microcantilevers. The characterization of mass-sensing and its related sensitivity was suggested on the basis of elasticity theory.

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

Abstracts 

Lambert 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.

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)).

Phys. Rev. Lett. 97, 075501 (2006) 

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.

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:

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.

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.

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.

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.

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.

This is a model of a single semiflexible polymer chain under sustained tension. The model captures two key features of the cytoskeletal rheology: a) the power-law behavior; and b) the dependence of the power-law on mechanical prestress. The model also reveals the underlying mechanisms.

The essence of mechanobiology is, probably, the interrelation between mechanical and biochemical factors.  An exciting example of such phenomenon is signaling associated with the interaction between the cell and extracellular matrix (EM).  While some purely biochemical pathways initiated in the area of contact of the cell and EM are known, there are interesting ideas how the mechanical forces, stresses and strains can be involved too. This view goes back to works of Donald Ingber's group in the 90s that showed how perturbations of the adhesion area as a whole and of an individual integrin result in deformation of the cell nucleus. Interestingly, a distinguished oncologist at Johns Hopkins, Donald Coffey, published similar experimental results about the same time, and he also demonstrated that the observed cytoskeleton/nucleus interaction is different in tumor cells. There are several separate pieces of the puzzle that have been resolved: mechanical forces are generated at focal adhesions, the cytoskeleton is involved, nucleus deforms, gene expression changes as a result of perturbation of the adhesions, however, the whole picture of the interrelated mechanical and biochemical factors has yet to be understood. We recently published some results on this topic in the Journal of Biomechanical Engineering (Jean et al., 2004 and 2005). I was glad to find an interest in the same problem from some participants of this website (e.g., N. Wang, Z. Suo,   Long-distance propagation of forces in a cell, 2005 and P.R. LeDuc and R.M. Bellin, Nanoscale Intracellular Organization and Functional Architecture Mediating Cellular Behavior, 2006). This aspect of mechanotransduction is important for many areas beyond mechanics such as cancer, wound healing, cell adhesion and motility, effect of surface micro- and nanopatterning, etc.

Listed below is a recent publication of mine in Science for your possible interest and critics. This is a review article focusing on the multiscale simulation issues in strucutral composites. I will be more than happy to discuss with those of you who are interested. The following is the abstract.

The difficult challenge of simulating diffuse and complex fracture patterns in tough structural composites is at last beginning to yield to conceptual and computational advances in fracture modeling. Contributing successes include the refinement of cohesive models of fracture and the formulation of hybrid stress-strain and traction-displacement models that combine continuum (spatially averaged) and discrete damage representations in a single calculation. Emerging hierarchical formulations add the potential of tracing the damage mechanisms down through all scales to the atomic. As the models near the fidelity required for their use as virtual experiments, opportunities arise for reducing the number of costly tests needed to certify safety and extending the design space to include material configurations that are too complex to certify by purely empirical methods.

I am at Boston for MRS 2006 Fall meeting this week, where I met a real "spiderman" at the poster session tonight. I'd like to share with you the following videos which were posted at YouTube by the "spiderman" himself, Mr. Jose Berengueres at Tokyo Instititute of Technology.

Mr. "Spiderman" also has posted a video on fasting climbing robot.

A variable core model of a moving crystal dislocation is proposed and used to derive an expression for the Peierls stress. The dislocation width varies periodically as a dislocation moves through the lattice, which leads to an expression for the Peierls stress in terms of the difference of the total energies in the crystal corresponding to stable and unstable equilibrium configurations of the dislocation, rather than the difference in the misfit energies alone. Results for both edge and mixed dislocations are given and proposed to be used in conjunction with ab initio calculations.

Mechanics of Solids and Materials intends to provide a modern and integrated treatment of the foundations of solid mechanics as applied to the mathematical description of material behavior. The book blends both innovative (e.g., large strain, strain rate, temperature, time-dependent deformation and localized plastic deformation in crystalline solids, and deformation of biological networks) and traditional topics (e.g., elastic theory of torsion, elastic beam and plate theories, and contact mechanics) in a coherent theoretical framework. This, and the extensive use of transform methods to generate solutions, makes the book of interest to structural, mechanical, and aerospace engineers.

The German Academic Exchange Service (DAAD) - in cooperation with science organizations in North America and Germany— is to invite undergraduate students from the US and Canada in the fields of biology, chemistry, physics, earth Sciences and engineering to apply for a summer research internship in Germany. RISE summer placements take place with research groups at universities and top research institutions across Germany. The RISE interns are matched with a doctoral student whom they assist and who will also serve as their mentor. This program is funded by the Federal Ministry of Economics and Technology as part of the European Recovery Program (ERP).

More details at http://www.daad.de/rise/en/1.html.

Please look at this low cost alternative CO2 Sequestration system.The integrated energy strategy offered by Terra Preta Soil technology may
provide the only path to sustain our agricultural and fossil fueled power
structure without climate degradation, other than nuclear power.

I feel we should push for this Terra Preta Soils CO2 sequestration strategy as not only a global warming remedy for the first world, but to solve fertilization and transport issues for the third world. This information needs to be shared with all the state programs.
 
The economics look good, and truly great if we had CO2 cap & trade in place: 
 
These are processes where you can have your Bio-fuel and fertility too.Terra Preta' soils I feel has great possibilities to revolutionize sustainable agriculture into a major CO2 sequestration strategy.

Nature 439, 281 (2006)

The theoretical maximum tensile strain — that is, elongation — of a single-walled carbon nanotube is almost 20%, but in practice only 6% is achieved. Here we show that, at high temperatures, individual single-walled carbon nanotubes can undergo superplastic deformation, becoming nearly 280% longer and 15 times narrower before breaking. This superplastic deformation is the result of the nucleation and motion of kinks in the structure, and could prove useful in helping to strengthen and toughen ceramics and other nanocomposites at high temperatures.