Validation of molecular dynamics simulation

How the results obtained by computer simulation of molecular systems can be validated is considered. The overall quality of the simulated properties of a molecular system will depend on (i) the quality of the theory or model, (ii) the accuracy of the interatomic interaction function or force field, (iii) the degree of sampling, statistics and convergence reached in the simulation, (iv) the quality of the simulation software, and (v) how competently the simulation software is used. These five validation issues are discussed and illustrated with examples. Guidelines for different members of the scientific community are formulated which are aimed at enabling and improving the validation of simulation results in the literature. © 1998 American Institute of Physics

NMscatt: a program for calculating inelastic scattering from large biomolecular systems using classical force-field simulations

Computational tools for normal mode analysis, which are widely used in physics and materials science problems, are designed here in a single package called NMscatt (Normal Modes & scattering) that allows arbitrarily large systems to be handled. The package allows inelastic neutron and X-ray scattering observables to be calculated, allowing comparison with experimental data produced at large scale facilities. Various simplification schemes are presented for analysing displacement vectors, which are otherwise too complicated to understand in very large systems.Comment: 13 pages, 5 figures, preprint submitted to Computer Physics Communication

Structure–activity exploration of a small-molecule Lipid II inhibitor

We have recently identified low-molecular weight compounds that act as inhibitors of Lipid II, an essential precursor of bacterial cell wall biosynthesis. Lipid II comprises specialized lipid (bactoprenol) linked to a hydrophilic head group consisting of a peptidoglycan subunit (N-acetyl glucosamine [GlcNAc]–N-acetyl muramic acid [MurNAc] disaccharide coupled to a short pentapeptide moiety) via a pyrophosphate. One of our lead compounds, a diphenyl-trimethyl indolene pyrylium, termed BAS00127538, interacts with the MurNAc moiety and the isoprenyl tail of Lipid II. Here, we report on the structure–activity relationship of BAS00127538 derivatives obtained by in silico analyses and de novo chemical synthesis. Our results indicate that Lipid II binding and bacterial killing are related to three features: the diphenyl moiety, the indolene moiety, and the positive charge of the pyrylium. Replacement of the pyrylium moiety with an N-methyl pyridinium, which may have importance in stability of the molecule, did not alter Lipid II binding or antibacterial potency

Influence of Finite Amplitude Disturbances on the Nonstationary Modes of a Compressible Boundary Layer Flow

A weakly nonlinear stability analysis is performed to search for the effects of compressibility on a mode of instability of the three-dimensional boundary layer flow due to a rotating disk. The motivation is to extend the stationary work of [ 1] ( hereafter referred to as S90) to incorporate into the nonstationary mode so that it will be investigated whether the finite amplitude destabilization of the boundary layer is owing to this mode or the mode of S90. Therefore, the basic compressible flow obtained in the large Reynolds number limit is perturbed by disturbances that are nonlinear and also time dependent. In this connection, the effects of nonlinearity are explored allowing the finite amplitude growth of a disturbance close to the neutral location and thus, a finite amplitude equation governing the evolution of the nonlinear lower branch modes is obtained. The coefficients of this evolution equation clearly demonstrate that the nonlinearity is destabilizing for all the modes, the effect of which is higher for the nonstationary waves as compared to the stationary waves. Some modes particularly having positive frequency, regardless of the adiabatic or wall heating/cooling conditions, are always found to be unstable, which are apparently more important than those stationary modes determined in S90. The solution of the asymptotic amplitude equation reveals that compressibility as the local Mach number increases, has the influence of stabilization by requiring smaller initial amplitude of the disturbance for the laminar rotating disk boundary layer flow to become unstable. Apart from the already unstable positive frequency waves, perturbations with positive frequency are always seen to compete to lead the solution to unstable state before the negative frequency waves do. Also, cooling the surface of the disk will be apparently ineffective to suppress the instability mechanisms operating in this boundary layer flow

An asymptotic investigation into the stabilization effect of suction in the rotating-disk boundary layer flow

AbstractThe suction effects in the three-dimensional boundary layer flow due to a rotating disk are analyzed from the linear stability point of view making use of the asymptotic structure of the suction mean velocity profiles of the boundary layer. The primary interest of the current work is in giving an explanation to the well-known stabilization influence of the suction from an easy to implement asymptotic means. As a consequence of the analysis, the shapes of the linear amplitude functions are derived analytically. There also results a dispersion relation for the eigenvalues existing in the limit of large suction. A comparison is then made between the perturbations obtained from the present work and also from the direct numerical solution of the linear stability equations. The asymptotic approach pursued provides a good indication as to why the large suction in the specific three-dimensional boundary layer should act in favor of the stabilization of the flow by strongly damping the external disturbances received into the suction boundary layer