Multi-scale Coupling
(MSC)
With MSC, an atomistic-level (or CG-MD) simulation, under periodic boundaries, is "tricked" into behaving as if it were embedded in the larger mesoscopic system. This is done by introducing non-equilibrium perturbations on the system using the well-developed machinery of non-equilibrium molecular dynamics (NEMD). By altering the nature of the boundary conditions to, in effect, trick the atomistic-level system into bahaving as if it were not part of the periodic array, the effect of long-wavelength perturbations, orginating at the field theory level of description, can be coupled down to the atomistic-level system. Furthermore, the dynamical equations of motion remain intact and the electrostatic interactions are handled correctly via an Ewald summation, but the altered boundary conditions (which take the form of both geometrical alterations in the simulation cell geometry, as well as new locally non-equilibrium state characterized by the inclusion of long wavelength phenomena not accessible by the original system. Also, electrostatic effects orginating from mesoscopic length-scales can be handled with a Poisson-Boltzmann treatment.
Coarse-grained Modeling and Simulation of Peptides
Proteins are participants in numerous fundamental biological processes. Many of these phenomena involve large protein complexes, such as the replication of DNA by polymerases. Other phenomena, such as the folding and assembly of polypeptide chains, take place on time-scales that are currently inaccessbile to molecular simulation studies. In order to use simulations to examine such processes, it is necessary to employ methods that allow one to probe increased length- and time-scales. This project seeks to employ information from atomistically detailed dimulations to constgruct reduced representations of proteins and peptides. Such models can allow access to extended lenth- and time-scales by decreasing the complexity of simulated systems.
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Multi-scale Simulation of Actin Networks
The goal of this project is to understand the molecular mechanisms of actin growth dynamics and the associated force generation processes in the cell. Molecular origins of the dynamic behaviors of the actin filament such as tread-milling and dynamical instabilities have long been puzzles in the field of cellular mechanics. A multi-scale model of the actin filament is being developed so that these dynamical phenomena can be understood. This is also the first step in understanding how forces are generated by the self-assembly of G-actin and how these forces define the shape and size of the cell.
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