Search results for "molecular modeling"

BANΔIT: B’‐factor Analysis for Drug Design and Structural Biology

2020

The analysis of B‐factor profiles from X‐ray protein structures can be utilized for structure‐based drug design since protein mobility changes have been associated with the quality of protein‐ligand interactions. With the BANΔIT (B’‐factor analysis and ΔB’ interpretation toolkit), we have developed a JavaScript‐based browser application that provides a graphical user interface for the normalization and analysis of B’‐factor profiles. To emphasize the usability for rational drug design applications, we have analyzed a selection of crystallographic protein‐ligand complexes and have given exemplary conclusions for further drug optimization including the development of a B’‐factor‐supported pha…

H−ZSM-5 Modified Zeolite:  Quantum Chemical Models of Acidic Sites

2007

A ZSM-5 fragment, containing 52 tetrahedral moieties, each of them formed by one silicon or one aluminum atom surrounded by four oxygen atoms, was employed to model (52T systems) by quantum chemical calculations (i) the influence of the positions of the acidic sites on the energetics of 22 aluminum monosubstituted and bisubstituted 52T acidic zeolite (H-ZSM-5) systems and (ii) the local adsorption properties and acidic strength of the corresponding -OH sites. The energetics and the structural properties of simpler acid H-ZSM-5 systems containing only five Tetrahedral moieties (5T systems) were also modeled for comparison. B3LYP/6-31G(d,p) partial geometry optimization routines were performe…

Statistical characterization of self-assembled charged nanoparticle structures

2013

We propose a novel approach for description of dynamics of nanostructure formation for a system consisting of oppositely charged particles. The combination of numerical solution of analytical Bogolyubov–Born–Green–Kirkwood–Yvon (BBGKY) type equation set with reverse Monte Carlo (RMC) method allows us to overcome difficulties of standard approaches, such as kinetic Monte Carlo or Molecular Dynamics, to describe effects of long-range Coulomb interactions. Moreover, this allows one to study the system dynamics on realistic time and length scales. We applied this method to a simple short-range Lenard–Jones (LJ)-like three- (3D) and two-dimensional (2D) system combining the long-range Coulomb an…

IDEA: interface dynamics and energetics algorithm.

2007

IDEA, interface dynamics and energetics algorithm, was implemented, in FORTRAN, under different operating systems to mimic dynamics and energetics of elementary events involved in interfacial processes. The code included a parallel elaboration scheme in which both the stochastic and the deterministic components, involved in the developed physical model, worked simultaneously. IDEA also embodied an optionally running VISUAL subroutine, showing the dynamic energy changes caused by the surface events, e.g., occurring at the gas-solid interface. Monte Carlo and ordinary differential equation system subroutines were employed in a synergistic way to drive the occurrence of the elementary events a…

Equation of State for Macromolecules of Variable Flexibility in Good Solvents: A Comparison of Techniques for Monte Carlo Simulations of Lattice Mode…

2007

The osmotic equation of state for the athermal bond fluctuation model on the simple cubic lattice is obtained from extensive Monte Carlo simulations. For short macromolecules (chain length N=20) we study the influence of various choices for the chain stiffness on the equation of state. Three techniques are applied and compared in order to critically assess their efficiency and accuracy: the repulsive wall method, the thermodynamic integration method (which rests on the feasibility of simulations in the grand canonical ensemble), and the recently advocated sedimentation equilibrium method, which records the density profile in an external (e.g. gravitation-like) field and infers, via a local …

Simple sampling Monte Carlo methods

2005

Single-cluster Monte Carlo study of the Ising model on two-dimensional random lattices.

1994

We use the single-cluster Monte Carlo update algorithm to simulate the Ising model on two-dimensional Poissonian random lattices with up to 80,000 sites which are linked together according to the Voronoi/Delaunay prescription. In one set of simulations we use reweighting techniques and finite-size scaling analysis to investigate the critical properties of the model in the very vicinity of the phase transition. In the other set of simulations we study the approach to criticality in the disordered phase, making use of improved estimators for measurements. From both sets of simulations we obtain clear evidence that the critical exponents agree with the exactly known exponents for regular latti…

Application of the Monte Carlo coherent-anomaly method to two-dimensional lattice-gas systems with further-neighbor interactions

1990

A Monte Carlo version of the coherent-anomaly method has been used to determine critical properties of a two-dimensional Ising ferromagnet with nearest- and next-nearest-neighbor interactions and of a series of two-dimensional lattice-gas systems of particles interacting via 6-12 Lennard-Jones potential. It has demonstrated that the method leads to quite accurate determination of critical temperature but is less successful when used to determine the values of critical exponents \ensuremath{\gamma} and \ensuremath{\nu}.

Monte Carlo simulation of correlated electrons in disordered systems

1992

Abstract The properties of many-electron states in disordered systems with long-range electron-eletron interaction are investigated by means of a Monte Carlo simulation. Using the Metropolis algorithm, three-dimensional systems up to 512 sites are systematically analysed. The low-lying excitations are investigated in order to distinguish between one-particle and many-particle hopping. In the interesting regime in which disorder and correlation effects are equally important we find that variable-range hopping is insignificant for electron transfer when compared with the contribution from nearest-neighbour one-electron hopping processes as well as variable-number hopping.

Quantum Monte Carlo methods

2005

Introduction In most of the discussion presented so far in this book, the quantum character of atoms and electrons has been ignored. The Ising spin models have been an exception, but since the Ising Hamiltonian is diagonal (in the absence of a transverse magnetic field), all energy eigenvalues are known and the Monte Carlo sampling can be carried out just as in the case of classical statistical mechanics. Furthermore, the physical properties are in accord with the third law of thermodynamics for Ising-type Hamiltonians (e.g. entropy S and specific heat vanish for temperature T → 0, etc.) in contrast to the other truly classical models dealt with in previous chapters (e.g. classical Heisenbe…