The allosteric mechanism plays a key role in cellular functions of several PDZ domain proteins (PDZs) and is directly linked to pharmaceutical applications; however, it is a challenge to elaborate the nature and extent of these allosteric interactions. One solution to this problem is to explore the dynamics of PDZs, which may provide insights about how intramolecular communication occurs within...

Abbreviations: ABP, ambulatory blood pressure; ECG, electrocardiogram; HF, high frequency heart rate fluctuation; LF, low frequency heart rate fluctuation; MESOR, midline estimating statistic of rhythm; MI, mean interval; RMSSD, root mean square successive differences; RR, between two QRS complexes in ECG; %RR50, the proportion of cycles during which the RR difference is > 50 ms; SD, standard d...

In this paper we discuss the application of current ab initio computer simulation techniques to hydrogenated amorphous silicon (aSi:H). We begin by discussing thermal fluctuation in the number of coordination defects in the material, and its temperature dependence. We connect this to the ‘fluctuating bond-center detachment’ mechanism for liberating H bonded to Si atoms. Next, from extended ther...

BACKGROUND The issue of whether patients diagnosed with metastatic colorectal cancer who harbor KRAS codon 13 mutations could benefit from the addition of anti-epidermal growth factor receptor therapy remains under debate. The aim of the current study was to perform computational analysis to investigate the structural implications of the underlying mutations caused by c.38G>A (p.G13D) on protei...

A method for the calculation of elastic constants in $NVT$ ensamble using molecular dynamics (MD) simulation with a realistic many-body embedded-atom-model (EAM) potential is studied detail. It shown that, such MD simulations, evaluation robust and accurate because it gives tensor single which converges small number time steps particles. These results highlight applicability this (i) local nonh...

The ability to measure biomolecular dynamics within cells and tissues is very important to understand fundamental physiological processes including cell adhesion, signalling, movement, division or metabolism. Usually, such information is obtained using particle tracking methods or single point fluctuation spectroscopy. We show that image mean square displacement analysis, applied to single plan...

Interactions of 3,3',4,4'-tetrahydroxybiphenyl (BPT) and three isomeric 3,3",4,4"-tetrahydroxyterphenyls (OTT, MTT, PTT) with Alzheimer’s amyloid-β peptide (Aβ) were studied by molecular dynamics simulation and molecular docking. Structural parameters such as Root-mean-square derivations (RMSD), radial distribution function (RDF), helix percentage and other physical parameters were obtained. Th...

The photoisomerization reaction dynamics of a retinal chromophore in the visual receptor rhodopsin was investigated by means of hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations. The photoisomerization reaction of retinal constitutes the primary step of vision and is known as one of the fastest reactions in nature. To elucidate the molecular mechanism of...

The diffusion of small molecules in polymer matrices involves time scales (microseconds [μs] to milliseconds [ms]) far too long for routine molecular dynamics (MD) simulations. We have formulated a new method to extract coarse-grained information from short (1-2 nanoseconds [ns]) MD simulations and use this in a mesoscale simulation to calculate diffusion constants in polymer matrices. It uses ...

based on the notion of micro-structure in linear elasticity presented by mindlin, a newextended continuum mechanics (ecm) formulation is derived which can be utilized to model thematerial behavior at atomic scale. an attempt has been made to present a formulation capable ofproducing the molecular dynamics (md) simulation results with less computational effort. to thisend, some new kinematical v...