Lactate dehydrogenase A (LDHA) is an important enzyme in fermentative glycolysis, generating most energy for cancer cells that rely on anaerobic respiration even under normal oxygen concentrations. This renders LDHA a promising molecular target for the treatment of various cancers. Several efforts have been made recently to develop LDHA inhibitors with nanomolar inhibition and cellular activity...

Serum Albumin is the most aboundant protein in blood plasma. Its two major roles aremaintaining osmotic pressure and depositing and transporting compounds. In this paper,Albumin-methanol solution simulation is carried out by three techniques including MonteCarlo (MC), Molecular Dynamic (MD) and Langevin Dynamic (LD) simulations. Byinvestigating energy changes by time and temperature (between 27...

Methods for Molecular Dynamics(MD) simulations are investigated. MD simulation is the widely used computer simulation approach to study the properties of molecular system. Force calculation in MD is computationally intensive. Paral-lel programming techniques can be applied to improve those calculations. The major aim of this paper is to speed up the MD simulation calculations by/using General P...

Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analysing multi-scale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD) simulations in the remainder of the domain. The first MD model is formulated in one spatial dimension. It is based on elastic collisions of heavy molecules (e.g. ...

Molecular dynamics (MD) simulations provide a molecular-resolution physical description of the folding and assembly processes, but the size and the timescales of simulations are limited because the underlying algorithm is computationally demanding. We recently introduced a parallel neighbor list algorithm that was specifically optimized for MD simulations on GPUs. In our present study, we analy...

Two-dimensional (2D) pressure field estimation in molecular dynamics (MD) simulations has been done using three-dimensional (3D) pressure field calculations followed by averaging, which is computationally expensive due to 3D convolutions. In this work, we develop a direct 2D pressure field estimation method which is much faster than 3D methods without losing accuracy. The method is validated wi...

Static and molecular dynamics (MD) calculations based on density-functional theory (DFT) are emerging as a valuable means for simulations in the field of biology, especially when coupled with classical simulations. In this contribution, we point out the strengths as well as the limitations of the DFT–MD method, and its possible use to complement existing approaches. Recent applications to syste...

Graphene single layers grown by chemical vapor deposition on single crystal Cu substrates are subject to nonuniform physisorption strains that depend on the orientation of the Cu surface. The strains are revealed in Raman spectra and quantitatively interpreted by molecular dynamics (MD) simulations. An average compressive strain on the order of 0.5% is determined in graphene on Cu(111). In grap...

NMR spectroscopy and molecular dynamics (MD) simulation analyses of the chiral molecular micelles poly-(sodium undecyl-(L,L)-leucine-valine) (poly-SULV) and poly-(sodium undecyl-(L,L)- valine-leucine) (poly-(SUVL)) are reported. Both molecular micelles are used as chiral selectors in electrokinetic chromatography and each consists of covalently linked surfactant chains with chiral dipeptide hea...