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  1. 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...
  2. 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...
  3. 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...
  4. 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...
  5. 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 ...
  6. 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...