Development and use of an atomistic CHARMM-based forcefield for peptoid simulation.
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...
Atomistic and Coarse-grained Analysis of Double Spectrin Repeat Units: The Molecular Origins of Flexibility
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...
A new perspective on the coarse-grained dynamics of fluids.
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...
Path integral molecular dynamics simulation of solidpara-hydrogen with an aluminum impurity
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...
Extending a Spectrin Repeat Unit. I: Linear Force-Extension Response
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...
Unique elastic properties of the spectrin tetramer as revealed by multiscale coarse-grained modeling.
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...