In the field of biology, MD simulations are continuously used to investigate biological studies. A Molecular Dynamics (MD) system is defined by the position and momentum of particles and their interactions. The dynamics of a system can be evaluated by an N-body problem and the simulation is continued until the energy reaches equilibrium. Thus, solving the dynamics numerically and evaluating the...

although carbon nanotubes (cnt) have been employed as reinforcements in nanocomposites, presence of nano scale defects such as stone-wales and vacancy defects in carbon nanotubes (cnt) weakens the mechanical properties of these materials. in this paper the effects of defects in cnts on nanocomposite elastic behavior are investigated using molecular dynamics. stiffness matrices of cnt and nanoco...

In this paper, we propose coarse-grained single-site (CGSS), wall-CO(2), and CO(2)-CO(2) interaction potential models to study the structure of carbon dioxide under confinement. The CGSS potentials are used in an empirical potential based quasi-continuum theory, EQT, to compute the center-of-mass density and potential profiles of CO(2) confined inside different size graphite slit pores. Results...

A new QM/MM molecular dynamics approach that can deal with the dynamics of large real systems involving several simultaneous active zones is presented. Multiple, unconnected but interacting quantum regions are treated independently in an ordinary QM/MM approach but in a manner which converges to a unique simulation. The multiple active zones in the hybrid QM/MM molecular dynamics methodology (m...

In this paper, the stability characteristics of single-walled carbon nanotubes (SWCNTs) under the action of axial load are investigated. To this end, a nonlocal Flügge shell model is developed to accommodate the small length scale effects. The analytical Rayleigh-Ritz method with beam functions is applied to the variational statement derived from the Flügge-type buckling equations. Molecular dy...

The fundamental problems in drug discovery are based on the process of molecular recognition by small molecules. The binding specificity of DNA-small molecule is identified mainly by studying the hydrogen bonding and polar interactions. Majority of the minor groove binders and their mechanism of action at the molecular level are not well studied. As these small molecules can act as effective th...

A general statistical approach is described to couple the continuum with molecular dynamics in fluid simulation. Arbitrary thermodynamic field boundary conditions can be imposed on an MD system while minimally disturbing the particle dynamics of the system. The importance of incorporating a higher order single-particle distribution function in light of the Chapman–Enskog development is demonstr...

Functionally relevant slow conformational motions of proteins are, at present, in most cases inaccessible to molecular dynamics (MD) simulations. The main reason is that the major part of the computational effort is spend for the accurate description of a huge number of high frequency motions of the protein and the surrounding solvent. The accumulated influence of these fluctuations is crucial ...

Understanding the distance distribution and dynamics between moieties attached to the walls of a resorcin[4]arene cavitand, which is switchable between an expanded kite and a contracted vase form, might enable the use of this molecular system for the study of fundamental distance-dependent interactions. Toward this goal, a combined experimental and molecular dynamics (MD) simulation study on do...

The replica exchange molecular dynamics ~REMD! approach is applied to a 20-residue three-stranded antiparallel b-sheet peptide. At physiologically relevant temperature REMD samples conformational space much more efficiently than constant temperature molecular dynamics ~MD! and allows reversible folding ~312 folding events during a total simulation time of 32 ms!. The energetic and structural pr...