Molecular Dynamics (MD) delivers dynamical information for large biomolecular systems using enormous CPU-resources. Consequently, several implementations of parallel MD programs have been presented. 1-13 We will analyse the characteristics of MD simulations of real-live biomolecular systems, summarise the serial algorithms tha t have been developed to significantly speed up these simulations an...

This data article contains the results of molecular dynamics (MD) simulations performed to assess the stability of the previously computed complex between the hCES1 structure and the Amplex Red (AR) substrate (Miwa et al., 2015) [1] and to compare the dynamic behavior of this complex with that of the corresponding hCES1-deacetylAR product. The study involves both standard molecular dynamics (MD...

We study the onset of patterns in vertically oscillated layers of frictionless dissipative particles. Using both numerical solutions of continuum equations to Navier-Stokes order and molecular dynamics (MD) simulations, we find that standing waves form stripe patterns above a critical acceleration of the cell. Changing the frequency of oscillation of the cell changes the wavelength of the resul...

Recent advances in molecular dynamics (MD) simulation methods and in available computational resources have allowed for more reliable simulations of biological phenomena. From all-atom MD simulations, we are now able to visualize in detail the interactions between antimicrobial peptides (AMPs) and a variety of membrane mimics. This helps us to understand the molecular mechanisms of antimicrobia...

We study the onset of patterns in vertically oscillated layers of frictionless dissipative particles. Using both numerical solutions of continuum equations to Navier-Stokes order and molecular dynamics (MD) simulations, we find that standing waves form stripe patterns above a critical acceleration of the cell. Changing the frequency of oscillation of the cell changes the wavelength of the resul...

We present here a quantitative study of dislocation cross-slip, an essential thermally activated process in deformation metals, discrete dynamics (DDD) simulations. implemented stress-dependent line-tension model DDD simulations, with minimal information from molecular (MD) This allows reproducing simulations the probabilistic cross-slip rate calculated MD for Cu large range stresses and temper...

A Molecular Dynamics (MD) study of static and dynamic properties of molten and glassy germanium dioxide is presented. The interactions between the atoms are modelled by the classical pair potential proposed by Oeffner and Elliott (OE) [Oeffner R D and Elliott S R 1998 Phys. Rev. B 58 14791]. We compare our results to experiments and previous simulations. In addition, an “ab initio” method, the ...

in this paper, we use molecular dynamics and finite element simulations to determine the mechanical properties of single-crystal metal of silver (ag) with nano-holes. the lattice transition method from 3-dimensions into 2-dimentions in molecular dynamics simulation as well as plane stress model in finite element method, is used to lessen the simulation time consuming. elasticity module reductio...

During the last four decades Molecular Dynamics (MD) simulations have developed to a powerful discipline and finally very close to the early vision from early 80’s that it would mature and become a computer laboratory to study molecular systems in conditions similar to that valid in experimental studies using instruments giving information about molecular structure, interactions and dynamics in...

Density functional theory (DFT) calculations were performed on tripeptide arginyl-glycyl-aspartic acid (RGD) as an efficient drug carrier to deliver the commercially famous cyclophosphamide (CP) anticancer drug within ethanol solution. The most negative binding energy (-5.22 kcal/mol) was measured for the CP-RGD-7 created through the H-bond interaction between the P=O (phosphoryl) oxygen atom o...