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  1. 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 α-spectrin and β-spectrin polypeptides consist primarily of triple coiled-coil modular repeat units, and two important factors that determine spec...
  2. Development and use of an atomistic CHARMM-based forcefield for peptoid simulation.

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

    We present a first-generation atomistic forcefield for peptoids. Our forcefield is based on the peptide forcefield CHARMM22, with key parameters tuned to match both experimental data and quantum mechanical calculations for two model peptoids (dimethylacetamide and a sarcosine dipeptoid). We used thi...
  3. A new perspective on the coarse-grained dynamics of fluids.

    The 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 of c...
  4. 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 orientation-de...
  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 α-helical linker was constructed by employing periodic boundary conditions, allowing a novel scheme for evaluating the thermodynamic force as a function of...
  6. 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 found...