We describe a versatile method to enforce the rotation of subsets of atoms, e.g., a protein subunit, in molecular dynamics (MD) simulations. In particular, we introduce a "flexible axis" technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation. A variety of useful rotation potentials were implemented for the GROMACS 4...

the aim of this research is to calculate the elastic constants and bulk modulus of cu-20 wt% ni random nanoalloy. the molecular dynamics simulation technique was used to calculate the mechanical properties in npt ensemble. the interaction between atoms as well as cohesive energy in the nanoalloy modeled systems was calculated by morse et al. two body potential. also the temperature of the syste...

the overall aim of this study is to calculate some water properties in the single wall carbon naotubes (swcnt) and compare them to the bulk water properties to investigate the deviation of water properties inside the swcnt from those in the bulk. here some physical and transport properties of water molecules in the single wall carbon nanotube were reported by performing molecular dynamics (md) ...

the aim of this study is investigating the transport mechanism of ibuprofen chiral isomers inside singlewall carbon nano tube (swcnt) using mathematical modeling. to achieve this goal, molecular dynamicssimulation has been performed to evaluate the interactions of ibuprofen isomers with swcnt in an aqueoussolution. results show that both chiral forms of ibuprofen molecules enter and remain insi...

in this work the conduction of ion-water solution through two discrete bundles of armchair carbon and silicon carbide nanotubes, as useful membranes for water desalination, is studied. in order that studies on different types of nanotubes be comparable, the chiral vectors of c and si-c nanotubes are selected as (7,7) and (5,5), respectively, so that    a similar volume of fluid is investigated ...

We present a molecular dynamics simulation scheme which allows to speed up molecular dynamics simulations by linear prediction of force time series. The explicit calculation of nonbonding forces is periodically replaced by linear prediction from past values. Applying our method to liquid oxygen consisting of flexible molecules we obtained real speedups between 5.4 and 6.5, compared to conventio...

Efficient computational techniques can aid to study of the protein structure allowing diverse applications in many scientific research fields [1]. The knowledge of their 3D structure can be very important in order to know their function and to find other macromolecular partners with whom they may interact. [1][2]. Combining GA, Rotamer Library , Molecular Dynamics and Molecular Dynamics (MD) ca...

Two-body interatomic potentials in the Morse potential form have been developed for bismuth telluride, and the potentials are used in molecular dynamics simulations to predict the thermal conductivity. The densityfunctional theory with local-density approximations is first used to calculate the total energies for many artificially distorted Bi2Te3 configurations to produce the energy surface. T...

This paper is concerned with the problem of design and implementation a robust adaptive control strategy for flexible joint electrically driven robots (FJEDR), while considering to the constraints on the actuator voltage input. The control design procedure is based on function approximation technique, to avoid saturation besides being robust against both structured and unstructured uncertaintie...

The work of molecular machines such as the ribosome is accompanied by conformational changes, often characterized by relative motions of their domains. The method we have developed seeks to quantify these motions in a general way, facilitating comparisons of results obtained by different researchers. Typically there are multiple snapshots of a structure in the form of pdb coordinates resulting ...