Understanding the EF-hand closing pathway using non-biased interatomic potentials

L. Dupuis and Normand Mousseau

The authors simulated the folding pathway, from Ca²⁺-unbound open holo conformations to closed apo states, of two well-studied EF-hand: the NT domains of calmodulin and Troponin C. Trajectories were generated using an activated algorithm, ART nouveau, along with the multi-scale holographic method, which lead to an unbiased sampling of the conformation space with a focus on the flexible regions.

J. Chem. Phys. 136, 035101 (2012)

The effects of shape and flexibility on bio-engineered fd-virus suspensions

M. Dennison, M. Dijkstra, and R. van Roij

The authors present a theoretical model to describe binary mixtures of semi-flexible colloidal rods applying it to fd-virus systems with different diameter (thick-thin) and length (long-short) ratios. The authors find the behavior of fd-virus systems to be very sensitive to the stiffness of the constituent particles, with only small changes in particle stiffness required to give dramatic changes in the observed phase behavior.

J. Chem. Phys. 135, 144106 (2011)

Communication: Spectroscopic phase and lineshapes in high-resolution broadband sum frequency vibrational spectroscopy: Resolving interfacial inhomogeneities of “identical” molecular groups

Luis Velarde, Xian-yi Zhang, Zhou Lu, Alan G. Joly, Zheming Wang, and Hong-fei Wang

The authors utilize high-resolution broadband sum-frequency generation vibrational spectroscopy to probe structural spectroscopic phase and lineshapes. They observe an unexpected spectral splitting between two methyl groups at the vapor/dimethyl sulfoxide (DMSO) liquid interface and determine their orientational angles.

J. Chem. Phys. 135, 241102 (2011)

Milestoning with transition memory

Alexander T. Hawk and Dmitrii E. Makarov

Milestoning is used to calculate the kinetics and thermodynamics of molecular processes occurring in long time scale computer simulations. The authors introduce a generalized procedure, accounting for memory of previous transitions made by the system, and demonstrate its applicability for a polymer chain undergoing Langevin dynamics.

J. Chem. Phys. 135, 224109 (2011)

State-dependent doubly weighted stochastic simulation algorithm for automatic characterization of stochastic biochemical rare events

Min K. Roh, Bernie J. Daigle, Jr., Dan T. Gillespie, and Linda R. Petzold

Rare events in stochastic biochemical systems are modeled using a novel modification of the state-dependent doubly weighted stochastic simulation algorithm. The state-dependent importance sampling parameters are computed via a multilevel cross-entropy method. Applications show improved accuracy and efficiency.

J. Chem. Phys. 135, 234108 (2011)