MDSIMAID: automatic parameter optimization in fast electrostatic algorithms

MDSIMAID is a recommender system that optimizes parallel Particle Mesh Ewald (PME) and both sequential and parallel multigrid (MG) summation fast electrostatic solvers. MDSIMAID optimizes the running time or parallel scalability of these methods within a given error tolerance. MDSIMAID performs a run time constrained search on the parameter space of each method starting from semiempirical performance models. Recommended parameters are presented to the user. MDSIMAID's optimization of MG leads to configurations that are up to 14 times faster or 17 times more accurate than published recommendations. Optimization of PME can improve its parallel scalability, making it run twice as fast in parallel in our tests. MDSIMAID and its Python source code are accessible through a Web portal located at http://mdsimaid.cse.nd.edu.     

Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities

The development and implementation of a tree code (TC) and fast multipole method (FMM) for the efficient, linear-scaling calculation of long-range electrostatic interactions of particle distributions with variable shape and multipole character are described. The target application of these methods are stochastic boundary molecular simulations with polarizable force fields and/or combined quantum mechanical/molecular mechanical potentials. Linear-scaling is accomplished through the adaptive decomposition of the system into a hierarchy of interacting particle sets. Two methods for effecting this decomposition are evaluated: fluc-splitting and box-splitting, for which the latter is demonstrated to be generally more accurate. In addition, a generalized termination criterion is developed that delivers optimal performance at fixed error tolerance that, in the case of quadrupole-represented Drude water, effects a speed-up by a factor of 2-3 relative to a multipole-independent termination criteria. The FMM is shown to be approximately 2-3 times faster than the TC, independent of the system size and multipole order of the particles. The TC and FMM are tested for a variety of static and polarizable water systems, and for the the 70S ribosome functional complex containing an assembly of transfer and messenger RNAs.     

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

This study compares generalized Born (GB) and Poisson (PB) methods for calculating electrostatic solvation energies of proteins. A large set of GB and PB implementations from our own laboratories as well as others is applied to a series of protein structure test sets for evaluating the performance of these methods. The test sets cover a significant range of native protein structures of varying size, fold topology, and amino acid composition as well as nonnative extended and misfolded structures that may be found during structure prediction and folding/unfolding studies. We find that the methods tested here span a wide range from highly accurate and computationally demanding PB-based methods to somewhat less accurate but more affordable GB-based approaches and a few fast, approximate PB solvers. Compared with PB solvation energies, the latest, most accurate GB implementations were found to achieve errors of 1% for relative solvation energies between different proteins and 0.4% between different conformations of the same protein. This compares to accurate PB solvers that produce results with deviations of less than 0.25% between each other for both native and nonnative structures. The performance of the best GB methods is discussed in more detail for the application for force field-based minimizations or molecular dynamics simulations.     

Oxidation‐Induced C—H Functionalization: A Formal Way for C—H Activation

Cross‐coupling reactions have developed widely and provided a powerful means to synthesize a variety of compounds in each chemical field. The compounds which have C—H bonds are widespread in fossil fuels, chemical raw materials, biologically active molecules, etc. Using these readily‐ available substances as substrates is high atom‐ and step‐economy for cross‐coupling reactions. Over the past decades, our research group focused on finding and developing new strategies for C—H functionalization. Compared with classical C—H activation methods, for example, C—H bonds are deprotonated by strong base or converted into C—M bonds, oxidation‐induced C—H functionalization would be another pathway for C—H bond activation. This perspective shows a brief introduction of our recent works in this oxidation‐induced C—H functionalization. We categorized this approach of these C—H bond activations by the key intermediates, radical cations, radicals and cations.     

Current status of gross alpha/beta activity analysis in water samples: a short overview of methods

Gross alpha/beta measurement is one of the simplest radioanalytical procedures which are applied widely as a screening technique in the field of radioecology, environmental monitoring and industrial applications as well. Due to the uncertainties of gross alpha/beta measurements this method is often the subject of discussions and debates. The aim of this work is to collect information about recently used standard and routine methods concerning gross alpha/beta activity determination in drinking waters in order to get an overview about the current situation and evaluate their possibilities. Sample preparation methods—e.g. evaporation, co-precipitation—and detection systems—e.g. gas flow proportional counting, liquid scintillation counting and scintillation counting—are compared on the ground of literature data. In the course of our work, the following parameters were analyzed and discussed: background, counting efficiency, interferences, sample capacity, minimal detectable activity, typical counting time, time demand of sample preparation.     

烯丙位化学键均裂离解能及其取代基效应

使用复合从头算方法系统地获得了一批精确的烯丙位化学键的均裂裂解能(BDE). 取代基效应的研究表明, C—H与Si—H的BDE表现出差的Hammett关系, 而N—H, O—H, P—H与S—H的BDE表现出好的Hammett关系. 进一步分析表明烯丙位BDE受共轭效应比诱导/场效应的影响更为明显. 并且还讨论了BDE的基态效应和自由基效应, 其结果与最近报道的有关苄位BDE的结果基本一致.     

Assessment of linear finite‐difference Poisson–Boltzmann solvers

CPU time and memory usage are two vital issues that any numerical solvers for the Poisson–Boltzmann equation have to face in biomolecular applications. In this study, we systematically analyzed the CPU time and memory usage of five commonly used finite‐difference solvers with a large and diversified set of biomolecular structures. Our comparative analysis shows that modified incomplete Cholesky conjugate gradient and geometric multigrid are the most efficient in the diversified test set. For the two efficient solvers, our test shows that their CPU times increase approximately linearly with the numbers of grids. Their CPU times also increase almost linearly with the negative logarithm of the convergence criterion at very similar rate. Our comparison further shows that geometric multigrid performs better in the large set of tested biomolecules. However, modified incomplete Cholesky conjugate gradient is superior to geometric multigrid in molecular dynamics simulations of tested molecules. We also investigated other significant components in numerical solutions of the Poisson–Boltzmann equation. It turns out that the time‐limiting step is the free boundary condition setup for the linear systems for the selected proteins if the electrostatic focusing is not used. Thus, development of future numerical solvers for the Poisson–Boltzmann equation should balance all aspects of the numerical procedures in realistic biomolecular applications. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

An alignment-free measure based on physicochemical properties of amino acids for protein sequence comparison

Sequence comparison is an important topic in bioinformatics. With the exponential increase of biological sequences, the traditional protein sequence comparison methods — the alignment methods become limited, so the alignment-free methods are widely proposed in the past two decades. In this paper, we considered not only the six typical physicochemical properties of amino acids, but also their frequency and positional distribution. A 51-dimensional vector was obtained to describe the protein sequence. We got a pairwise distance matrix by computing the standardized Euclidean distance, and discriminant analysis and phylogenetic analysis can be made. The results on the Influenza A virus and ND5 datasets indicate that our method is accurate and efficient for classifying proteins and inferring the phylogeny of species.     

XO: An extended ONIOM method for accurate and efficient modeling of large systems

Calculation of large complex systems remains to be a great challenge, where there is always a trade‐off between accuracy and efficiency. Recently, we proposed the extended our own n‐layered integrated molecular orbital (ONIOM) method (XO) (Guo, Wu, Xu, Chem. Phys. Lett. 2010 , 498, 203) which surmounts some inherited limitations of the popular ONIOM method by introducing the inclusion‐exclusion principle used in the fragmentation methods. The present work sets up general guidelines for the construction of a good XO scheme. In particular, force‐error test is proposed to quantitatively validate the usefulness of an XO scheme, taking accuracy, efficiency and scalability all into account. Representative studies on zeolites, polypeptides and cyclodextrins have been carried out to demonstrate how to strive for high accuracy without sacrificing efficiency. As a natural extension, XO is applied to calculate the total energy, fully optimized geometry and vibrational spectra of the whole system, where ONIOM becomes inapplicable. © 2012 Wiley Periodicals, Inc.     

非晶氮化铁薄膜的生长机制——传统动力学生长标度方法的适用性

采用动力学标度方法研究了磁控溅射沉积的非晶氮化铁薄膜的动力学生长机制, 结果表明, 具有连续类柱状岛形貌的非晶氮化铁薄膜具有标度不变的自仿射分形特点, 其粗糙度指数α=0.82±0.21, 生长指数β=0.44±0.07, 动力学标度指数1/z=0.54±0.07. 薄膜生长符合提出的热重新发射生长模型.     

Multiple grid methods for classical molecular dynamics

Presented in the context of classical molecular mechanics and dynamics are multilevel summation methods for the fast calculation of energies/forces for pairwise interactions, which are based on the hierarchical interpolation of interaction potentials on multiple grids. The concepts and details underlying multigrid interpolation are described. For integration of molecular dynamics the use of different time steps for different interactions allows longer time steps for many of the interactions, and this can be combined with multiple grids in space. Comparison is made to the fast multipole method, and evidence is presented suggesting that for molecular simulations multigrid methods may be superior to the fast multipole method and other tree methods.     

MIBPB: A software package for electrostatic analysis

The Poisson–Boltzmann equation (PBE) is an established model for the electrostatic analysis of biomolecules. The development of advanced computational techniques for the solution of the PBE has been an important topic in the past two decades. This article presents a matched interface and boundary (MIB)‐based PBE software package, the MIBPB solver, for electrostatic analysis. The MIBPB has a unique feature that it is the first interface technique‐based PBE solver that rigorously enforces the solution and flux continuity conditions at the dielectric interface between the biomolecule and the solvent. For protein molecular surfaces, which may possess troublesome geometrical singularities, the MIB scheme makes the MIBPB by far the only existing PBE solver that is able to deliver the second‐order convergence, that is, the accuracy increases four times when the mesh size is halved. The MIBPB method is also equipped with a Dirichlet‐to‐Neumann mapping technique that builds a Green's function approach to analytically resolve the singular charge distribution in biomolecules in order to obtain reliable solutions at meshes as coarse as 1 Å — whereas it usually takes other traditional PB solvers 0.25 Å to reach similar level of reliability. This work further accelerates the rate of convergence of linear equation systems resulting from the MIBPB by using the Krylov subspace (KS) techniques. Condition numbers of the MIBPB matrices are significantly reduced by using appropriate KS solver and preconditioner combinations. Both linear and nonlinear PBE solvers in the MIBPB package are tested by protein–solvent solvation energy calculations and analysis of salt effects on protein–protein binding energies, respectively. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Dynamical mean-field theory from a quantum chemical perspective

We investigate the dynamical mean-field theory (DMFT) from a quantum chemical perspective. Dynamical mean-field theory offers a formalism to extend quantum chemical methods for finite systems to infinite periodic problems within a local correlation approximation. In addition, quantum chemical techniques can be used to construct new ab initio Hamiltonians and impurity solvers for DMFT. Here, we explore some ways in which these things may be achieved. First, we present an informal overview of dynamical mean-field theory to connect to quantum chemical language. Next, we describe an implementation of dynamical mean-field theory where we start from an ab initio Hartree-Fock Hamiltonian that avoids double counting issues present in many applications of DMFT. We then explore the use of the configuration interaction hierarchy in DMFT as an approximate solver for the impurity problem. We also investigate some numerical issues of convergence within DMFT. Our studies are carried out in the context of the cubic hydrogen model, a simple but challenging test for correlation methods. Finally, we finish with some conclusions for future directions.     

Summary of ISO/TC 201 Standard: ISO 29081: 2010, surface chemical analysis—Auger electron spectroscopy—reporting of methods used for charge control and charge correction

This international standard specifies the minimum amount of information required for describing the methods of charge control and charge correction in measurements of Auger electron transitions from insulating specimens by electron‐stimulated AES to be reported with the analytical results. Information is provided in an Annex on methods that have been found useful for charge control prior to or during AES analysis. The Annex also includes a summary table of methods or approaches, ordered by simplicity of approach. A similar international standard has been published for XPS (ISO 19318: 2003(E), Surface chemical analysis—XPS—reporting of methods used for charge control and charge correction. Copyright © 2010 John Wiley & Sons, Ltd.     

A new outer boundary formulation and energy corrections for the nonlinear Poisson-Boltzmann equation

The nonlinear Poisson-Boltzmann equation (PBE) has been successfully used for the prediction of numerous electrostatic properties of highly charged biopolyelectrolytes immersed in aqueous salt solutions. While numerous numerical solvers for the 3D PBE have been developed, the formulation of the outer boundary treatments used in these methods has only been loosely addressed, especially in the nonlinear case. The de facto standard in current nonlinear PBE implementations is to either set the potential at the outer boundaries to zero or estimate it using the (linear) Debye-Hückel (DH) approximation. However, an assessment of how these outer boundary treatments affect the overall solution accuracy does not appear to have been previously made. As will be demonstrated here, both approximations can, under certain conditions, produce completely erroneous estimates of the potential and energy salt dependencies. A related concern for calculations carried out on grids of finite extent (e.g., all current finite difference and finite element implementations) is the contribution to the energy and salt dependence from the exterior region outside the computational grid. This too is shown to be significant, especially at low salt concentration where essentially all of the contributions to the excess osmotic pressure and ion stress energies originate from this exterior region. In this paper the authors introduce a new outer boundary treatment that is valid for both the linear and nonlinear PBE. The authors also formulate energy corrections to account for contributions from outside the computational domain. Finally, the authors also consider the effects of general ion exclusion layers upon biomolecular electrostatics. It is shown that while these layers tend to increase the surface electrostatic potential, under physiological salt conditions and high net charges their effect on the excess osmotic pressure term, which is a measure of the salt dependence of the total electrostatic free energy, is weak. To facilitate presentation and allow very fine resolutions and/or large computational domains to be considered, attention is restricted to the 1D spherically symmetric nonlinear PBE. Though geometrically limited, the modeling principles nevertheless extend to general PBE solvers as discussed in the Appendix. The 1D model can also be used to benchmark and validate the salt effect prediction capabilities of existing PBE solvers.     

Gaussian split Ewald: A fast Ewald mesh method for molecular simulation

Gaussian split Ewald (GSE) is a versatile Ewald mesh method that is fast and accurate when used with both real-space and k-space Poisson solvers. While real-space methods are known to be asymptotically superior to k-space methods in terms of both computational cost and parallelization efficiency, k-space methods such as smooth particle-mesh Ewald (SPME) have thus far remained dominant because they have been more efficient than existing real-space methods for simulations of typical systems in the size range of current practical interest. Real-space GSE, however, is approximately a factor of 2 faster than previously described real-space Ewald methods for the level of force accuracy typically required in biomolecular simulations, and is competitive with leading k-space methods even for systems of moderate size. Alternatively, GSE may be combined with a k-space Poisson solver, providing a conveniently tunable k-space method that performs comparably to SPME. The GSE method follows naturally from a uniform framework that we introduce to concisely describe the differences between existing Ewald mesh methods.     

Sparse matrix multiplications for linear scaling electronic structure calculations in an atom-centered basis set using multiatom blocks

A sparse matrix multiplication scheme with multiatom blocks is reported, a tool that can be very useful for developing linear-scaling methods with atom-centered basis functions. Compared to conventional element-by-element sparse matrix multiplication schemes, efficiency is gained by the use of the highly optimized basic linear algebra subroutines (BLAS). However, some sparsity is lost in the multiatom blocking scheme because these matrix blocks will in general contain negligible elements. As a result, an optimal block size that minimizes the CPU time by balancing these two effects is recovered. In calculations on linear alkanes, polyglycines, estane polymers, and water clusters the optimal block size is found to be between 40 and 100 basis functions, where about 55-75% of the machine peak performance was achieved on an IBM RS6000 workstation. In these calculations, the blocked sparse matrix multiplications can be 10 times faster than a standard element-by-element sparse matrix package.     

Fast and reliable numerical methods to simulate complex chemical kinetic mechanisms

Models that simulate atmospheric photochemistry require the use of a stiff ordinary differential equations (ODEs) solver. Since the simulation of the chemical transformations taking place in the system takes up to 80 percent of the CPU time, the numerical solver must be computationally fast. Also, the residual error from the solver must be small. Because most accurate solvers are relatively slow, modelers continue to search for timely, yet accurate integration methods. Over the past years an extensive number of articles have been dedicated to this subject. One of the highly debated questions is whether one should construct specialized algorithms or instead use general methods for stiff ODEs. In the present article we use the second alternative. We apply three linearly (semi-)implicit methods from the classical stiff ODE literature which we modified to implement the sparse routines to solve the system of equations describing a complex kinetic mechanism. © 1998 John Wiley & Sons, Inc. Int J Chem Kinet 30: 349–358, 1998     

Long range interactions on wires: a reciprocal space based formalism

There are many atomic scale systems in materials, chemistry, and biology that can be effectively modeled as finite in two of the physical spatial dimensions and periodically replicated in the third including nanoscale metallic and semiconducting wires, carbon nanotubes, and DNA. However, it is difficult to design techniques to treat long range forces in these systems without truncation or recourse to slowly convergent supercells or computationally inefficient Poisson solvers. In this paper, a rigorous reciprocal space based formalism which permits long range forces on wires to be evaluated simply and easily via a small modification of existing methods for three dimensional periodicity is derived. The formalism is applied to determine long range interactions both between point particles using an Ewald-like approach and the continuous charge distributions that appear in electronic structure calculations. In this way, both empirical force field calculations and, for example, plane-wave based density functional theory computations on wires can be performed easily. The methodology is tested on model and realistic systems including a lithium doped carbon nanotube.     

FAMUSAMM: An algorithm for rapid evaluation of electrostatic interactions in molecular dynamics simulations

Within molecular dynamics simulations of protein–solvent systems the exact evaluation of long-range Coulomb interactions is computationally demanding and becomes prohibitive for large systems. Conventional truncation methods circumvent that computational problem, but are hampered by serious artifacts concerning structure and dynamics of the simulated systems. To avoid these artifacts we have developed an efficient and yet sufficiently accurate approximation scheme which combines the structure-adapted multipole method (SAMM) [C. Niedermeier and P. Tavan, J. Chem. Phys., 101 , 734 (1994)] with a multiple-time-step method. The computational effort for MD simulations required within our fast multiple-time-step structure-adapted multipole method (FAMUSAMM) scales linearly with the number of particles. For a system with 36,000 atoms we achieve a computational speed-up by a factor of 60 as compared with the exact evaluation of the Coulomb forces. Extended test simulations show that the applied approximations do not seriously affect structural or dynamical properties of the simulated systems. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1729–1749, 1997