in this report, we describe a procedure for in-silico design of a novel haloalkane dehalogenase protein that exhibits luciferase property which can be potentially used in biosensor applications. from a pdb blast search, the selected haloalkane dehalogenase (pdb code: 1ede) had a close structural homology with a lucifearse (pdb code: 2psj chain a) sharing an identity of 33%. initially, the amino...

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...

The mechanisms of pressure-driven water infiltration into single walled carbon nanotubes are explored using molecular dynamics simulations. Both quasi-static and dynamic loading conditions are investigated, and the influence of tube size is examined. Under quasi-static loading, the water molecules flow into the tube via surface diffusion at a low pressure and when the external pressure reaches ...

   In this paper we propose a simulation study to carry out dynamic analysis of CNTFET-based digital circuit, introducing in the semi-empirical compact model for CNTFETs, already proposed by us, both the quantum capacitance effects and the sub-threshold currents. To verify the validity of the obtained results, a comparison with Wong model was carried out. Our mode...

The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures and currently holds the world record for the largest molecular simulation with over four trillion particles. It enables the application of pair potentials to length and time scales that were previously out of scope for molecular...

Abstract Membrane technology is extensively used for water treatment including desalination to cope with the present demands. The membrane performance can be analyzed and improved by various methods. A deep understanding of molecular-level interaction occurring during achieved molecular dynamic simulations as it helps develop a thorough knowledge systems processes that occur in an experiment, w...

The dynamic simulation of macromolecular systems with biologically relevant sizes and time scales is critical for understanding macromolecular function. In this context, normal mode analysis (NMA) approximates the complex dynamicalbehaviourofa macromoleculeas a simple setof harmonic oscillators vibrating around a given equilibrium conformation. This technique, originated from classical mechanic...