Mechanism of smell: Electrochemistry,receptors and cell signaling

This report presents in four main parts a novel approach based on electrochemistry, receptors and cell signaling. In Part A, there is limited correlation between dipole moments (DMs), associated electrostatic fields (EFs), and odor. For Part B, binding of the odorant to the receptor results in interaction of the ligand EF with those of the protein receptor, resulting in alteration. Part C addresses passage of the message by the altered EF to the olfactory neurons. Part D represents the final step in which the electrical signal is converted to perceived odor in the cerebral olfactory cortex.     

Collisionless plasma expansion and fast ion generation at plasma-vacuum boundary

Collisionless plasma expansion into a vacuum is investigated by computational treatment of a system of Vlasov equations for both ions and electrons coupled by a selfconsistent field. High-velocity low-density mass expansion is observed as a result of an electrostatic acceleration of ions.     

On Solving Three-Dimensional Electrostatic Field Distribution by Multigrid Method

A highly efficient numerical algorithm using the multigrid method (MGM) is introduced to solve a three-dimensional (3-D)field distribution. Taking advantage of the restriction and prolongation in MGM computation, a more accurate field distribution can be acquired rapidly. According to the MGM algorithm, a 3-D program is accomplished, which can solve the field distributions in electron optical systems for various electrostatic lenses. The 3-D field distribution in an electrostatic concentric spherical model is tested with the MGM algorithm and with an algorithm based on the finite difference method (FDM). Comparing these two results in terms of computational efficiency and computational accuracy, it appears that MGM is superior to FDM, which is now used the most in field computations. This paper shows that the 3-D field computation using MGM greatly improves the computational efficiency of field distributions in electron optical systems and shortens the computational time.     

Computation of effective resistivity in materials with microinclusions by a heterogeneous multiscale finite element method

In this paper, we propose a numerical method to obtain an effective electrical resistivity of heterogeneous media under the influence of a direct current. The heterogeneous multiscale finite element method is used to solve the direct problem of simulation of an electrostatic field. The computational experiments using the developed software complex showed that even the small inclusion concentrations define the effective resistivity of the media. In addition, the change in the localization, orientation, and geometrical shape of inclusions also leads to a significant change of the effective properties of the media.     

Novel formulation of nonlocal electrostatics

The accurate modeling of the dielectric properties of water is crucial for many applications in physics, computational chemistry, and molecular biology. This becomes possible in the framework of nonlocal electrostatics, for which we propose a novel formulation allowing for numerical solutions for the nontrivial molecular geometries arising in the applications mentioned before. Our approach is based on the introduction of a secondary field psi, which acts as the potential for the rotation free part of the dielectric displacement field D. For many relevant models, the dielectric function of the medium can be expressed as the Green's function of a local differential operator. In this case, the resulting coupled Poisson (-Boltzmann) equations for psi and the electrostatic potential phi reduce to a system of coupled partial differential equations. The approach is illustrated by its application to simple geometries.     

Microrheological consequences of attractive colloid-colloid potentials in a two-dimensional Brownian fluid

By using microrheological methods commonly employed in videomicroscopy experiments, we study the rheology of a two-dimensional computational fluid formed by Brownian disks with the aim of exploring the influence of some effective colloid-colloid attractive interactions. The model of fluid is developed by Brownian dynamics simulations without hydrodynamical interactions, and it is characterized by calculating its equation of state from the pair distribution function. Micromechanical properties, relative and intrinsic viscosity and freezing are discussed. Then, we include attractive forces such a Asakura-Oosawa depletion force or an empiric expression proposed by Grier and Hal (GH) for an anomalous electrostatic potential observed in confined and charged colloids. By using both potentials, viscosity is clearly increased, but when the GH potential is included, viscoelastic gel state is reached for intermediate values of surface concentration. Finally, we analyse the influence of the attractive potentials in the breaking-up by thermal fluctuations of linear chains formed by 2D particles, finding that the GH potential reduces the characteristical time at which the disks can be considered as disaggregated. In this work, we employ an experimental-like methodology for the study of a Brownian hard-disk fluid, providing a very useful link with experimental procedures.     

基于MATLAB的静电场模拟

在静电场中引入电位和电场强度后,通过等电位线图和场强分布图可以具体的描述静电场这种抽象的物质场。传统的静电场模拟实验直观地展现出了静电场的分布从而形象地描述了静电场,由于这种方法属于类比模拟,所以存在一定的缺陷(比如不直接,不能描述立体规律等等)。随着计算机技术的发展,利用计算机技术来模拟静电场等物质场逐渐成为趋势。通过借鉴大量资料简要地介绍了如何利用计算机模拟静电场,如何利用MATLAB软件模拟静电场的问题。     

Computer analysis of the source image structure in 3D electron-optic systems: I. An electrostatic system

Computer analysis of the arbitrary source image obtained in 3D electron-optic systems is performed. The systems involve electrostatic fields focusing and deflecting electron beams. Specifically, the structure of a net electron beam from an extended source at the crossover is examined. It is shown that the spread function of the source, which characterizes the imaging quality of the system most fully, may serve as a primary computational criterion.     

MLIMCL：基于机器学习的隐式溶剂蒙特卡罗方法

对于分子结构的优化和预测,蒙特卡罗(MC)是很重要的计算工具. 当溶剂效应被显式的考虑时,由于水分子和电离子的自由度很大,蒙特卡罗方法变得非常昂贵. 相对而言,基于隐式溶剂的蒙特卡罗方法可以通过对溶剂效应平均场的近似来大大降低计算成本,同时还能保持目标分子在原子水平上的细节. 目前两种最流行的隐式溶剂模型是泊松-波兹曼模型和通用化波恩模型. 通用化波恩模型是泊松-波兹曼模型的近似,但在模拟计算时间上要快得多. 本文通过结合两种隐式溶剂模型在准确性和效率方面的优势,开发了一种基于机器学习的隐式溶剂蒙特卡罗方法. 具体而言,蒙特卡罗方法通过机器学习既保留了泊松-波兹曼模型的精度,又达到了通用化波恩模型的速度,从而能快速准确地获取模拟计算中每一步的静电溶解自由能. 本文采用苯-水系统和蛋白质-水系统来验证我们的蒙特卡罗方法. 实验证明蒙特卡罗方法在分子结构优化和预测的速度和准确性方面具有很大优势.     

New developments in the multiscale hybrid energy density computational method

Further developments in the hybrid multiscale energy density method are proposed on the basis of our previous papers. The key points are as follows.(i) The theoretical method for the determination of the weight parameter in the energy coupling equation of transition region in multiscale model is given via constructing underdetermined equations.(ii)By applying the developed mathematical method, the weight parameters have been given and used to treat some problems in homogeneous charge density systems, which are directly related with multiscale science.(iii) A theoretical algorithm has also been presented for treating non-homogeneous systems of charge density. The key to the theoretical computational methods is the decomposition of the electrostatic energy in the total energy of density functional theory for probing the spanning characteristic at atomic scale, layer by layer, by which the choice of chemical elements and the defect complex effect can be understood deeply.(iv) The numerical computational program and design have also been presented.     

Closed-form solution of mid-potential between two parallel charged plates with more extensive application

Efficient calculation of the electrostatic interactions including repulsive force between charged molecules in a biomolecule system or charged particles in a colloidal system is necessary for the molecular scale or particle scale mechanical analyses of these systems. The electrostatic repulsive force depends on the mid-plane potential between two charged particles. Previous analytical solutions of the mid-plane potential, including those based on simplified assumptions and modern mathematic methods, are reviewed. It is shown that none of these solutions applies to wide ranges of interparticle distance from 0 to 10 and surface potential from 1 to 10. Three previous analytical solutions are chosen to develop a semi-analytical solution which is proven to have more extensive applications. Furthermore, an empirical closed-form expression of mid-plane potential is proposed based on plenty of numerical solutions. This empirical solution has extensive applications, as well as high computational efficiency.     

Capacitance and surface charge distribution computations for a satellite modeled as a rectangular cuboid and two plates

This paper presents a method to evaluate the capacitance and the surface charge distributions of a satellite modeled as a structure consisting of a rectangular cuboid with two coplanar rectangular plates. The Charges accumulate on the satellite surfaces result destructive electrostatic discharges (ESD). Integral equations are formed by relating the unknown charge density on the metallic cuboid and the two rectangular plates to the potential on the surface of these bodies. The integral equations are solved using the Method of Moments (MoM) based on pulse function as basis functions and delta functions as testing functions. In order to apply MoM, the surfaces of the metallic bodies are discretized by using non-uniform rectangular subsections. The numerical data on capacitance of this structure have been presented. The key results are that the computational method is validated by computing the capacitance of a cuboid to be 73.46 pF/m, which is consistent with previous works. Faster convergence and shorter computational time are achieved using non-uniform subsections. And, as expected, the surface charge density diminishes at joints where the plates connect to the cuboid.     

Differential geometry based solvation model I: Eulerian formulation

This paper presents a differential geometry based model for the analysis and computation of the equilibrium property of solvation. Differential geometry theory of surfaces is utilized to define and construct smooth interfaces with good stability and differentiability for use in characterizing the solvent-solute boundaries and in generating continuous dielectric functions across the computational domain. A total free energy functional is constructed to couple polar and nonpolar contributions to the salvation process. Geometric measure theory is employed to rigorously convert a Lagrangian formulation of the surface energy into an Eulerian formulation so as to bring all energy terms into an equal footing. By minimizing the total free energy functional, we derive coupled generalized Poisson-Boltzmann equation (GPBE) and generalized geometric flow equation (GGFE) for the electrostatic potential and the construction of realistic solvent-solute boundaries, respectively. By solving the coupled GPBE and GGFE, we obtain the electrostatic potential, the solvent-solute boundary profile, and the smooth dielectric function, and thereby improve the accuracy and stability of implicit solvation calculations. We also design efficient second order numerical schemes for the solution of the GPBE and GGFE. Matrix resulted from the discretization of the GPBE is accelerated with appropriate preconditioners. An alternative direct implicit (ADI) scheme is designed to improve the stability of solving the GGFE. Two iterative approaches are designed to solve the coupled system of nonlinear partial differential equations. Extensive numerical experiments are designed to validate the present theoretical model, test computational methods, and optimize numerical algorithms. Example solvation analysis of both small compounds and proteins are carried out to further demonstrate the accuracy, stability, efficiency and robustness of the present new model and numerical approaches. Comparison is given to both experimental and theoretical results in the literature.     

"New-version-fast-multipole-method" accelerated electrostatic interactions in biomolecular systems

In this paper, we present an efficient and accurate numerical algorithm for calculating the electrostatic interactions in biomolecular systems. In our scheme, a boundary integral equation (BIE) approach is applied to discretize the linearized Poisson-Boltzmann (PB) equation. The resulting integral formulas are well conditioned for single molecule cases as well as for systems with more than one macromolecule, and are solved efficiently using Krylov subspace based iterative methods such as generalized minimal residual (GMRES) or bi-conjugate gradients stabilized (BiCGStab) methods. In each iteration, the convolution type matrix-vector multiplications are accelerated by a new version of the fast multipole method (FMM). The implemented algorithm is asymptotically optimal O(N) both in CPU time and memory usage with optimized prefactors. Our approach enhances the present computational ability to treat electrostatics of large scale systems in protein-protein interactions and nano particle assembly processes. Applications including calculating the electrostatics of the nicotinic acetylcholine receptor (nAChR) and interactions between protein Sso7d and DNA are presented.     

Electrostatic lenses

The various types of electrostatic lenses that are used to control beams of ions or electrons are briefly described, together with the computational techniques for evaluating their properties. Particular emphasis is placed on the calculation and minimization of the aberrations of these lenses. In computer-aided designs of lens systems it is convenient to have lens properties available in the form of numerical approximations, and the achievement of this is discussed. Special types of lens, such as the zoom lens, are also discussed.     

A study of growth mechanism of KDP and ADP crystals by means of quantum chemistry

Impurity adsorption, crystal growth by adsorption of growth unit and step-pinning mechanism of metal ion adsorption were investigated for potassium dihydrogen phosphate (KDP; KH₂PO₄) and ammonium dihydrogen phosphate (ADP; NH₄H₂PO₄) by quantum chemistry. In this study, the ideal crystal morphologies, the growth unit and the crystal surface with and without metal ions were calculated and analyzed by using electrostatic property. It is found that the computational results based on electrostatic potential distribution can account for the observed behaviours on KDP and ADP crystal growth.     

Computer analysis of the source image structure in 3D electron-optic systems: II. A stationary electromagnetic system

Computer analysis of the image of an arbitrary (point or extended) source obtained in 3D electron-optic systems is performed. The systems involve magnetostatic and electrostatic fields, which, respectively, focus and deflect the electron beams. Two approaches to image scanning are considered where the scan potentials are applied in two (symmetric and asymmetric) modes. It is shown that the spread function of the source, which characterizes the imaging quality of the system most fully, may serve as a primary computational criterion.