Shake, rattle, and roll: Impact of the dynamics of flavivirus particles on their interactions with the host.

SHAKE, rattle, and roll: Efficient constraint algorithms for linked rigid bodies

We present an iterative constraint algorithm, QSHAKE, for use with semirigid molecules in molecular dynamics simulations. The algorithm is based on ‘‘SHAKE-ing’’ bond constraints between rigid bodies, whose equations of motion are solved in the quaternion framework. The algorithm is derived and its performance compared with SHAKE for liquid octane. QSHAKE is Ž . significantly more efficient whe...

Rigid-body dynamics in the isothermal-isobaric ensemble: A test on the accuracy and computational efficiency

We have developed a time-reversible rigid-body (rRB) molecular dynamics algorithm in the isothermal-isobaric (NPT) ensemble. The algorithm is an extension of rigid-body dynamics [Matubayasi and Nakahara, J Chem Phys 1999, 110, 3291] to the NPT ensemble on the basis of non-Hamiltonian statistical mechanics [Martyna, G. J. et al., J Chem Phys 1994, 101, 4177]. A series of MD simulations of water ...

Shake, rattle, and roll . . . preventing platelets from turning into Golden Oldies.

Human Virome

Viruses are dominant entities in the biosphere and parasitize all cellular life forms. The relative abundances of different classes of viruses are dramatically different between prokaryotes and eukaryotes. In marine, soil and animal-associated environments, virus particles consistently outnumber cells by one to two orders of magnitude. It is estimated that 10 quintillion (1030) viral particles ...

Molecular Insight into the Mutual Interactions of Two Transmembrane Domains of Human Glycine Receptor (TM23-GlyR), with the Lipid Bilayers

Appearing as a computational microscope, MD simulation can ‘zoom in’ to atomic resolution to assess detailed interactions of a membrane protein with its surrounding lipids, which play important roles in the stability and function of such proteins. This study has employed the molecular dynamics (MD) simulations, to determine the effect of added DMPC or DMTAP molecules on the structure of D...