Effect of distortion in electron impact excitation in Coulomb-projected Born approximation

We have calculated total and differential cross-sections for 1s →ns (n = 2, 3, 4) electron impact excitation of hydrogen and hydrogenic ions at various energies in Coulomb-projected Born approximation. Distortion due to static interactions, target polarization and exchange effects has been incorporated in the initial channel. The present calculations have been compared with other theoretical and experimental results.     

Quantitative surface analysis by Auger and x-ray photoelectron spectroscopy

Recent developments in quantitative surface analysis by Auger (AES) and x-ray photoelectron (XPS) spectroscopies are reviewed and problems relating to a more accurate quantitative interpretation of AES/XPS experimental data are discussed. Special attention is paid to consideration of elementary physical processes involved and influence of multiple scattering effects on signal line intensities. In particular, the major features of core-shell ionization by electron impact, Auger transitions and photoionization are considered qualitatively and rigorous approaches used to calculate the respective transition probabilities are analysed. It is shown that, in amorphous and polycrystalline targets, incoherent scattering of primary and signal Auger and photoelectrons can be described by solving analytically a kinetic equation with appropriate boundary conditions. The analytical results for the angular and energy distribution, the mean escape depth, and the escape probability as a function of depth of origin of signal electrons as well as that for the backscattering factor in AES are in good agreement with the corresponding Mote Carlo simulation data. Methods for inelastic background subtraction, surface composition determination and depth-profile reconstructions by angle-resolved AES/XPS are discussed. Examples of novel techniques based on x-ray induced photoemission are considered.     

Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes

An essential element of implicit solvent models, such as the generalized Born method, is a knowledge of the volume associated with the individual atoms of the solute. Two approaches for determining atomic volumes for the generalized Born model are described; one is based on Voronoi polyhedra and the other, on minimizing the fluctuations in the overall volume of the solute. Volumes to be used with various parameter sets for protein and nucleic acids in the CHARMM force field are determined from a large set of known structures. The volumes resulting from the two different approaches are compared with respect to various parameters, including the size and solvent accessibility of the structures from which they are determined. The question of whether to include hydrogens in the atomic representation of the solute volume is examined. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1857-1879, 2001     

Application of torsion angle molecular dynamics for efficient sampling of protein conformations

We investigate the application of torsion angle molecular dynamics (TAMD) to augment conformational sampling of peptides and proteins. Interesting conformational changes in proteins mainly involve torsional degrees of freedom. Carrying out molecular dynamics in torsion space does not only explicitly sample the most relevant degrees of freedom, but also allows larger integration time steps with elimination of the bond and angle degrees of freedom. However, the covalent geometry needs to be fixed during internal coordinate dynamics, which can introduce severe distortions to the underlying potential surface in the extensively parameterized modern Cartesian-based protein force fields. A "projection" approach (Katritch et al. J Comput Chem 2003, 24, 254-265) is extended to construct an accurate internal coordinate force field (ICFF) from a source Cartesian force field. Torsion crossterm corrections constructed from local molecular fragments, together with softened van der Waals and electrostatic interactions, are used to recover the potential surface and incorporate implicit bond and angle flexibility. MD simulations of dipeptide models demonstrate that full flexibility in both the backbone phi/psi and side chain chi1 angles are virtually restored. The efficacy of TAMD in enhancing conformational sampling is then further examined by folding simulations of small peptides and refinement experiments of protein NMR structures. The results show that an increase of several fold in conformational sampling efficiency can be reliably achieved. The current study also reveals some complicated intrinsic properties of internal coordinate dynamics, beyond energy conservation, that can limit the maximum size of the integration time step and thus the achievable gain in sampling efficiency.     

玻恩和沃尔夫合著的《光学原理》一书写作过程

《光学原理》(Principles of Optics)一书是玻恩与沃尔夫合著的、倍受好评的光学经典名著。回顾、梳理与品味这一名著的撰写过程，会得到诸多感悟。教书育人、著书立说的物理教育家以及物理学家，都可以从中得到一把尺子，用以衡量自己的工作。这有利于中国物理学的发展。     

Behaviour of ‘free-standing’ hollow Au nanocages at finite temperatures: a BOMD study

Finite-temperature behaviour of a hollow golden cage (HGC) plays a crucialrole in its potential applications as a catalyst, drug delivery agent, contrasting agent and so on. This physico-chemical property of HGCs is not well understood so far. In that context, Born–Oppenheimer molecular dynamics (BOMD) simulations are performed on a well-known ‘free-standing’ HGC. The cluster considered in this study is the ground state Au₁₈ cluster (a cage with a diameter of about >5.5 Å). The results thus obtained are compared with the BOMD simulation results reported earlier on Au₃₂ icosahedron cage, a conformation with a diameter of nearly. The sphericity of both the clusters is studied using a shape deformation parameter as a function of time and temperature. These results are supplemented by radial distribution function at various temperatures. The observations and analysis of results indicate that, both the clusters retain an HGC conformation from 300 to 400 K, admitting structural fluxionality by the Au₁₈ cluster. Remarkably, the Au₁₈ cluster is able to maintain its hollowness and sphericity up to a high temperature of 1000 K. Underlying structural and electronic properties influencing the individualistic behaviour of cages are highlighted. Composition of the frontier molecular orbitals and the charge distribution play a crucial role in the finite-temperature behaviour of the Au cages. The conclusions are supplemented by supporting calculations on another degenerate ground state Au₁₈ hollow cage and a well-known pyramidal Au₁₈ cage at 300 and 400 K.     

FEW: A workflow tool for free energy calculations of ligand binding

In the later stages of drug design projects, accurately predicting relative binding affinities of chemically similar compounds to a biomolecular target is of utmost importance for making decisions based on the ranking of such compounds. So far, the extensive application of binding free energy approaches has been hampered by the complex and time‐consuming setup of such calculations. We introduce the free energy workflow (FEW) tool that facilitates setup and execution of binding free energy calculations with the AMBER suite for multiple ligands. FEW allows performing free energy calculations according to the implicit solvent molecular mechanics (MM‐PB(GB)SA), the linear interaction energy, and the thermodynamic integration approaches. We describe the tool's architecture and functionality and demonstrate in a show case study on Factor Xa inhibitors that the time needed for the preparation and analysis of free energy calculations is considerably reduced with FEW compared to a fully manual procedure. © 2013 Wiley Periodicals, Inc.     

Comparative assessment of computational methods for the determination of solvation free energies in alcohol‐based molecules

The determination of differences in solvation free energies between related drug molecules remains an important challenge in computational drug optimization, when fast and accurate calculation of differences in binding free energy are required. In this study, we have evaluated the performance of five commonly used polarized continuum model (PCM) methodologies in the determination of solvation free energies for 53 typical alcohol and alkane small molecules. In addition, the performance of these PCM methods, of a thermodynamic integration (TI) protocol and of the Poisson–Boltzmann (PB) and generalized Born (GB) methods, were tested in the determination of solvation free energies changes for 28 common alkane‐alcohol transformations, by the substitution of an hydrogen atom for a hydroxyl substituent. The results show that the solvation model D (SMD) performs better among the PCM‐based approaches in estimating solvation free energies for alcohol molecules, and solvation free energy changes for alkane‐alcohol transformations, with an average error below 1 kcal/mol for both quantities. However, for the determination of solvation free energy changes on alkane‐alcohol transformation, PB and TI yielded better results. TI was particularly accurate in the treatment of hydroxyl groups additions to aromatic rings (0.53 kcal/mol), a common transformation when optimizing drug‐binding in computer‐aided drug design. © 2013 Wiley Periodicals, Inc.     

Pairwise decomposition of an MMGBSA energy function for computational protein design

Computational protein design (CPD) aims at predicting new proteins or modifying existing ones. The computational challenge is huge as it requires exploring an enormous sequence and conformation space. The difficulty can be reduced by considering a fixed backbone and a discrete set of sidechain conformations. Another common strategy consists in precalculating a pairwise energy matrix, from which the energy of any sequence/conformation can be quickly obtained. In this work, we examine the pairwise decomposition of protein MMGBSA energy functions from a general theoretical perspective, and an implementation proposed earlier for CPD. It includes a Generalized Born term, whose many‐body character is overcome using an effective dielectric environment, and a Surface Area term, for which we present an improved pairwise decomposition. A detailed evaluation of the error introduced by the decomposition on the different energy components is performed. We show that the error remains reasonable, compared to other uncertainties. © 2014 Wiley Periodicals, Inc.