Equilibrium Born-Oppenheimer molecular dynamics simulations have been performed in the canonical ensemble to investigate the structural properties of liquid water and ice Ih (hexagonal ice) at 298 and 273 K, respectively, using a state-of-the-art non-local correlation functional, whilst size effects have been examined explicitly in the case of liquid water. This has led to improved agreement wi...

This short commentary presents the result of long molecular dynamics simulation calculations of the shear viscosity of liquid n-decane and n-hexadecane using the Green± Kubo integration method. The relaxation time of the stress± stress correlation function is compared with those of rotation and di€ usion. The rotational and di€ usional relaxation times, which are easy to calculate, provide usef...

A variety of experimental evidence suggests that rapid, long-range propagation of conformational changes through the core of proteins plays a vital role in allosteric communication. Here, we describe a non-equilibrium molecular dynamics simulation method, anisotropic thermal diffusion (ATD), which allowed us to observe a dominant intramolecular signaling pathway in PSD-95, a member of the PDZ d...

molecular dynamic simulation is a powerful method that monitors all variations in the atomic level in explicit solvent. by this method we can calculate many chemical and biochemical properties of large scale biological systems. in this work all-atom molecular dynamics simulation of polyalanine (pa) was investigated in the presence of 0.224, 0.448, 0.673, 0.897 and 1.122 m of guanidinium chlorid...

Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-­‐based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication fidelity through the non-­‐equilibrium enzymatic ...