1. The allosteric switching mechanism in bacteriophage MS2.

    Journal of Chemical Physics 145(3):035101 (2016) PMID 27448905 PMCID PMC4947040

    We use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopts different conformations at precise locations within the c...
  2. Development and use of an atomistic CHARMM-based forcefield for peptoid simulation.

    Journal Of Computational Chemistry 35(5):360 (2014) PMID 24293222

    Peptoids are positional isomers of peptides: peptoid sidechains are attached to backbone nitrogens rather than α-carbons. Peptoids constitute a class of sequence-specific polymers resistant to biological degradation and potentially as diverse, structurally and functionally, as proteins. While mo...
  3. Unique elastic properties of the spectrin tetramer as revealed by multiscale coarse-grained modeling.

    PNAS 105(4):1204 (2008) PMID 18202182 PMCID PMC2234116

    The force-extension profile of tetrameric spectrin is determined by using multiscale computer simulation. Fluctuation results of atomistic simulations of double spectrin repeat units (DSRU) are used to systematically build a coarse-grained (CG) model for the tetrameric form of spectrin. It is fo...
  4. Atomistic and coarse-grained analysis of double spectrin repeat units: the molecular origins of flexibility.

    Journal of Molecular Biology 365(2):523 (2007) PMID 17070548

    Spectrin is an ubiquitous protein in metazoan cells, and its flexibility is one of the keys to maintaining cellular structure and organization. Both alpha-spectrin and beta-spectrin polypeptides consist primarily of triple coiled-coil modular repeat units, and two important factors that determin...
  5. Extending a spectrin repeat unit. I: linear force-extension response.

    Biophysical Journal 90(1):92 (2006) PMID 16227506 PMCID PMC1367040

    Nonequilibrium molecular dynamics simulations were used to calculate the elastic properties of a spectrin repeat unit. A contiguous alpha-helical linker was constructed by employing periodic boundary conditions, allowing a novel scheme for evaluating the thermodynamic force as a function of exte...
  6. A new perspective on the coarse-grained dynamics of fluids.

    Journal of Chemical Physics 120(9):4074 (2004) PMID 15268574

    A computational methodology is presented that is designed to model, at a coarse-grained level, the mesoscale dynamics of fluids and potentially other forms of soft matter. Within a molecular dynamics simulation, "ghost" particles of a specific size, corresponding to the fundamental length-scale ...
  7. Path integral molecular dynamics simulation of solidpara-hydrogen with an aluminum impurity

    Chemical Physics Letters 365(5):487 (2002)

    The equilibrium properties of an aluminum impurity trapped in solid para-hydrogen have been studied. The results were compared to those of a previous study by Krumrine et al. [J. Chem. Phys. 113 (2000) 9079] with an atomic boron. In the presence of vacancy defect, when the orientatio...