research

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.

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.

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.

The time-dependent plastic deformation (creep) behaviors of both the as-deposited and annealed plasma-enhanced chemical vapor deposited (PECVD) silicon oxide (SiOx) films were probed by nanoindentation load relaxation tests at room temperature. Our experiments found a strong size effect in the creep responses of the as-deposited PECVD SiOx thin films, which was much reduced after rapid thermal annealing (RTA). Based on the experimental results, the deformation mechanism is depicted by the "shear transformation zone" (STZ) based amorphous plasticity theories. The physical origin of the STZ is elucidated and linked with the shear banding dynamics. It is postulated that the high strain gradient at shallow indentation depths may be responsible for the reduction in the stress exponent n=∂log(strain rate)/∂log(stress), characteristic of a more homogenous flow behavior.

Gold films on an elastomeric substrate can be stretched and relaxed reversibly by tens of percents. The films initially form in two different structures, one continuous and the other containing tri-branched microcracks. We have identified the mechanism of elastic stretchability in the films with microcracks. The metal, which is much stiffer than the elastomer, forms a percolating network.

More than fifty years ago, people realized that we can use fusion for energy, but the problem remains where and how to keep a plasma of 100 million degrees centigrade.

For TOKAMAK, one of the approaches to use the fusion power, now comes the news: "On 21 November, Ministers from the seven ITER Parties came together to sign the agreement to establish the international Organization that will implement ITER."

What might be the differences, if there is any, between mechanical signaling and chemical signaling in a living cell?

There has been a lot of attention on the study of mechanics of proteins and/or single molecules. Such study was typically implemented by using classical molecular dynamics (MD) simulation. In spite of ability to describe the dynamics of biological macromolecules (e.g. proteins), MD simulation exhibits the computational restriction in the spatial and temporal scale. In order to overcome such computational limitation, the coarse-grained model has recently been taken into account. In this review, I would take a look at a couple of coarse-grained models of protein molecules.

Questions about meshfree methods are now addressed in the forum, under the Computational Mechanics subheading.

If you click on a question below, you will be redirected to the forum. I will update this post as more questions are added. Other experts are encouraged to augment my response there.

1. If I have meshfree shape functions that satisfy Kronecker-Delta, can I satisfy essential boundary conditions?

2. Is a mesh required in meshfree methods?

As you know, the volumetric expansion by 9% during the water-to-ice transition can generate tremendous pressure in a confined space is a common sense. As a result, one may expect freezing water to also fracture rocks.

However, in a recent article in Science, Bernard Hallet explains the power of the 9% water-to-ice expansion in confined spaces is undeniable, but it may rarely be significant for rocks under natural conditions, because it requires a tight orchestration of unusual conditions. Unless the rocks are essentially saturated with water and frozen from all sides, the expansion can simply be accommodated by the flow of water into empty pores, or out of the rock through its unfrozen side.

I think it may be of interest to mechanics. Read more
I hope to hear opinions from people who know about the breaking mechanics of rocks.

This is a paper we recently published in JMPS on a study of the mechanical properties on thin films comparing experimental results with discrete dislocation simulations. It provides insight in the strengthening that occurs in thin metal films when surface or interface effects become important.

The abstract is below; the full paper can be downloaded from here

Abstract - Experimental measurements and computational results for the evolution of plastic deformation in freestanding thin films are compared. In the experiments, the stress–strain response of two sets of Cu films is determined in the plane-strain bulge test. One set of samples consists of electroplated Cu films, while the other set is sputter-deposited. Unpassivated films, films passivated on one side and films passivated on both sides are considered. The calculations are carried out within a two-dimensional plane strain framework with the dislocations modeled as line singularities in an isotropic elastic solid. The film is modeled by a unit cell consisting of eight grains, each of which has three slip systems. The film is initially free of dislocations which then nucleate from a specified distribution of Frank–Read sources. The grain boundaries and any film-passivation layer interfaces are taken to be impenetrable to dislocations. Both the experiments and the computations show: (i) a flow strength for the passivated films that is greater than for the unpassivated films and (ii) hysteresis and a Bauschinger effect that increases with increasing pre-strain for passivated films, while for unpassivated films hysteresis and a Bauschinger effect are small or absent. Furthermore, the experimental measurements and computational results for the 0.2% offset yield strength stress, and the evolution of hysteresis and of the Bauschinger effect are in good quantitative agreement.

It is well-recognized that MEMS switches, compared to their more traditional solid state counterparts, have several important advantages for wireless communications.  These include superior linearity, low insertion loss and high isolation.  Indeed, many potential applications have been investigated such as Tx/Rx antenna switching, frequency band selection, tunable matching networks for PA and antenna, tunable filters, and antenna reconfiguration. 

However, none of these applications have been materialized in high volume products to a large extent because of reliability concerns, particularly those related to the metal contacts.  The subject of the metal contact in a switch was studied extensively in the history of developing miniaturized switches, such as the reed switches for telecommunication applications.  While such studies are highly relevant, they do not address the issues encountered in the sub 100mN, low contact force regime in which most MEMS switches operate.  At such low forces, the contact resistance is extremely sensitive to even a trace amount of contamination on the contact surfaces.  Significant work was done to develop wafer cleaning processes and storage techniques for maintaining the cleanliness.  To preserve contact cleanliness over the switch service lifetime, several hermetic packaging technologies were developed and their effectiveness in protecting the contacts from contamination was examined.  

In a recent article in Physical Review Letters, Alain Goriely and Sébastien Neukirch offer a mechanical model of how the free tip of a twining plant can hold onto a smooth support, allowing the plant to grow upward. The model also explains why these vines cannot grow on supports of too large a diameter. Read more.

The mechanics involves large deflection and bifurcation of a rod. I hope to hear opinions from people who know about the mechanics of plants.

A viscous-elastic-plastic indentation model was used to assess the local variability of properties in healing porcine bone. Constant loading- and unloading-rate depth-sensing indentation tests were performed and properties were computed from nonlinear curve-fits of the unloading displacement-time data. Three properties were obtained from the fit: modulus (the coefficient of an elastic reversible process), hardness (the coefficient of a nonreversible, time-independent process) and viscosity (the coefficient of a nonreversible, time-dependent process). The region adjacent to the dental implant interface demonstrated a slightly depressed elastic modulus along with an increase in local time-dependence (lower viscosity); there was no clear trend in bone hardness with respect to the implant interface.