Publications

Crozier, Paul C.; Grest, Gary S.; Ismail, Ahmed I.; Lehoucq, Richard B.; Plimpton, Steven J.; Stevens, Mark J.

We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

Holdych, David J.; Stevens, Mark J.; In 't Veld, Pieter J.

The purpose of this project is to develop tools to model and simulate the processes of self-assembly and growth in biological systems from the molecular to the continuum length scales. The model biological system chosen for the study is the tendon fiber which is composed mainly of Type I collagen fibrils. The macroscopic processes of self-assembly and growth at the fiber scale arise from microscopic processes at the fibrillar and molecular length scales. At these nano-scopic length scales, we employed molecular modeling and simulation method to characterize the mechanical behavior and stability of the collagen triple helix and the collagen fibril. To obtain the physical parameters governing mass transport in the tendon fiber we performed direct numerical simulations of fluid flow and solute transport through an idealized fibrillar microstructure. At the continuum scale, we developed a mixture theory approach for modeling the coupled processes of mechanical deformation, transport, and species inter-conversion involved in growth. In the mixture theory approach, the microstructure of the tissue is represented by the species concentration and transport and material parameters, obtained from fibril and molecular scale calculations, while the mechanical deformation, transport, and growth processes are governed by balance laws and constitutive relations developed within a thermodynamically consistent framework.

Crozier, Paul C.; Plimpton, Steven J.; Stevens, Mark J.; Lehoucq, Richard B.

Abstract not provided.

Journal of Polymer Science, Part B: Polymer Physics

Sides, Scott W.; Grest, Gary S.; Stevens, Mark J.; Plimpton, Steven J.

The adhesion between a glassy polymer melt and substrate is studied in the presence of end-grafted chains chemically attached to the substrate surface. Extensive molecular dynamics simulations have been carried out to study the effect of the areal density Σ of tethered chains and tensile pull velocity v on the adhesive failure mechanisms. The initial configurations are generated using a double-bridging algorithm in which new bonds are formed across a pair of monomers equidistant from their respective free ends. This generates new chain configurations that are substantially different than the original two chains such that the systems can be equilibrated in a reasonable amount of cpu time. At the slowest tensile pull velocity studied, a crossover from chain scission to crazing is observed as the coverage increases, while for very large pull velocity, only chain scission is observed. As the coverage increases, the sections of the tethered chains pulled out from the interface form the fibrils of a craze that are strong enough to suppress chain scission, resulting in cohesive rather than adhesive failure. © 2003 Wiley Periodicals, Inc.

Frink, Laura J.; Rempe, Susan R.; Means, Shawn A.; Stevens, Mark J.; Crozier, Paul C.; Martin, Marcus G.; Sears, Mark P.; Hjalmarson, Harold P.

This LDRD project has involved the development and application of Sandia's massively parallel materials modeling software to several significant biophysical systems. They have been successful in applying the molecular dynamics code LAMMPS to modeling DNA, unstructured proteins, and lipid membranes. They have developed and applied a coupled transport-molecular theory code (Tramonto) to study ion channel proteins with gramicidin A as a prototype. they have used the Towhee configurational bias Monte-Carlo code to perform rigorous tests of biological force fields. they have also applied the MP-Sala reacting-diffusion code to model cellular systems. Electroporation of cell membranes has also been studied, and detailed quantum mechanical studies of ion solvation have been performed. In addition, new molecular theory algorithms have been developed (in FasTram) that may ultimately make protein solvation calculations feasible on workstations. Finally, they have begun implementation of a combined molecular theory and configurational bias Monte-Carlo code. They note that this LDRD has provided a basis for several new internal (e.g. several new LDRD) and external (e.g. 4 NIH proposals and a DOE/Genomes to Life) proposals.