research

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 

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)).

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.

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.