Computational science & discovery最新文献_第2页

Characterizing the inverses of block tridiagonal, block Toeplitz matrices 表征块三对角线，块Toeplitz矩阵的逆

Computational science & discovery Pub Date : 2014-12-04 DOI: 10.1088/1749-4680/8/1/015001

Nicholas M. Boffi, Judith C. Hill, M. Reuter

引用次数: 8

A software platform for continuum modeling of ion channels based on unstructured mesh 基于非结构网格的离子通道连续体建模软件平台

Computational science & discovery Pub Date : 2014-07-29 DOI: 10.1088/1749-4680/7/1/014002

Bin Tu, Shiyang Bai, Minxin Chen, Yan Xie, Linbo Zhang, B. Lu

{"title":"A software platform for continuum modeling of ion channels based on unstructured mesh","authors":"Bin Tu, Shiyang Bai, Minxin Chen, Yan Xie, Linbo Zhang, B. Lu","doi":"10.1088/1749-4680/7/1/014002","DOIUrl":"https://doi.org/10.1088/1749-4680/7/1/014002","url":null,"abstract":"Most traditional continuum molecular modeling adopted finite difference or finite volume methods which were based on a structured mesh (grid). Unstructured meshes were only occasionally used, but an increased number of applications emerge in molecular simulations. To facilitate the continuum modeling of biomolecular systems based on unstructured meshes, we are developing a software platform with tools which are particularly beneficial to those approaches. This work describes the software system specifically for the simulation of a typical, complex molecular procedure: ion transport through a three-dimensional channel system that consists of a protein and a membrane. The platform contains three parts: a meshing tool chain for ion channel systems, a parallel finite element solver for the Poisson–Nernst–Planck equations describing the electrodiffusion process of ion transport, and a visualization program for continuum molecular modeling. The meshing tool chain in the platform, which consists of a set of mesh generation tools, is able to generate high-quality surface and volume meshes for ion channel systems. The parallel finite element solver in our platform is based on the parallel adaptive finite element package PHG which wass developed by one of the authors [1]. As a featured component of the platform, a new visualization program, VCMM, has specifically been developed for continuum molecular modeling with an emphasis on providing useful facilities for unstructured mesh-based methods and for their output analysis and visualization. VCMM provides a graphic user interface and consists of three modules: a molecular module, a meshing module","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"7 1","pages":"014002"},"PeriodicalIF":0.0,"publicationDate":"2014-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4680/7/1/014002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60595735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Modeling of high-current devices with explosive electron emission 具有爆炸电子发射的大电流器件的建模

Computational science & discovery Pub Date : 2014-07-14 DOI: 10.1088/1749-4680/7/1/015007

S. Anishchenko, A. Gurinovich

引用次数: 5

Intramolecular cyclization of aspartic acid residues assisted by three water molecules: a density functional theory study 三个水分子辅助天冬氨酸残基的分子内环化:密度泛函理论研究

Computational science & discovery Pub Date : 2014-05-12 DOI: 10.1088/1749-4699/7/1/015005

O. Takahashi, Ryota Kirikoshi

{"title":"Intramolecular cyclization of aspartic acid residues assisted by three water molecules: a density functional theory study","authors":"O. Takahashi, Ryota Kirikoshi","doi":"10.1088/1749-4699/7/1/015005","DOIUrl":"https://doi.org/10.1088/1749-4699/7/1/015005","url":null,"abstract":"Aspartic acid (Asp) residues in peptides and proteins (l-Asp) are known to undergo spontaneous nonenzymatic reactions to form l-?-Asp, d-Asp, and d-?-Asp residues. The formation of these abnormal Asp residues in proteins may affect their three-dimensional structures and hence their properties and functions. Indeed, the reactions have been thought to contribute to aging and pathologies. Most of the above reactions of the l-Asp residues proceed via a cyclic succinimide intermediate. In this paper, a novel three-water-assisted mechanism is proposed for cyclization of an Asp residue (forming a gem-diol precursor of the succinimide) by the B3LYP/6-31?+?G(d,p) density functional theory calculations carried out for an Asp-containing model compound (Ace?Asp?Nme, where Ace?=?acetyl and Nme?=?NHCH3). The three water molecules act as catalysts by mediating 'long-range' proton transfers. In the proposed mechanism, the amide group on the C-terminal side of the Asp residue is first converted to the tautomeric iminol form (iminolization). Then, reorientation of a water molecule and a conformational change occur successively, followed by the nucleophilic attack of the iminol nitrogen on the carboxyl carbon of the Asp side chain to form the gem-diol species. A satisfactory agreement was obtained between the calculated and experimental energetics.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"7 1","pages":"015005"},"PeriodicalIF":0.0,"publicationDate":"2014-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/7/1/015005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 21

Artificial crawler model for texture analysis on silk fibroin scaffolds 用于丝素蛋白支架结构分析的人工爬行模型

Computational science & discovery Pub Date : 2014-03-28 DOI: 10.1088/1749-4699/7/1/015004

Bruno Brandoli Machado, W. Gonçalves, O. Bruno

引用次数: 1

Physicochemical signatures of nanoparticle-dependent complement activation. 纳米颗粒依赖性补体活化的物理化学特征。

Computational science & discovery Pub Date : 2014-03-21 DOI: 10.1088/1749-4699/7/1/015003

Dennis G Thomas, Satish Chikkagoudar, Alejandro Heredia-Langer, Mark F Tardiff, Zhixiang Xu, Dennis E Hourcade, Christine T N Pham, Gregory M Lanza, Kilian Q Weinberger, Nathan A Baker

{"title":"Physicochemical signatures of nanoparticle-dependent complement activation.","authors":"Dennis G Thomas, Satish Chikkagoudar, Alejandro Heredia-Langer, Mark F Tardiff, Zhixiang Xu, Dennis E Hourcade, Christine T N Pham, Gregory M Lanza, Kilian Q Weinberger, Nathan A Baker","doi":"10.1088/1749-4699/7/1/015003","DOIUrl":"https://doi.org/10.1088/1749-4699/7/1/015003","url":null,"abstract":"Nanoparticles are potentially powerful therapeutic tools that have the capacity to target drug payloads and imaging agents. However, some nanoparticles can activate complement, a branch of the innate immune system, and cause adverse side-effects. Recently, we employed an in vitro hemolysis assay to measure the serum complement activity of perfluorocarbon nanoparticles that differed by size, surface charge, and surface chemistry, quantifying the nanoparticle-dependent complement activity using a metric called Residual Hemolytic Activity (RHA). In the present work, we have used a decision tree learning algorithm to derive the rules for estimating nanoparticle-dependent complement response based on the data generated from the hemolytic assay studies. Our results indicate that physicochemical properties of nanoparticles, namely, size, polydispersity index, zeta potential, and mole percentage of the active surface ligand of a nanoparticle, can serve as good descriptors for prediction of nanoparticle-dependent complement activation in the decision tree modeling framework.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"7 1","pages":"015003"},"PeriodicalIF":0.0,"publicationDate":"2014-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/7/1/015003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32695474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 12

Hybrid symplectic integrators for relativistic particles in electric and magnetic fields 电场和磁场中相对论粒子的杂化辛积分器

Computational science & discovery Pub Date : 2014-02-11 DOI: 10.1088/1749-4699/7/1/015001

P. Channell

引用次数: 3

Considerations about the implementation of a public knowledge base regarding nanotechnology 关于建立一个有关纳米技术的公共知识库的考虑

Computational science & discovery Pub Date : 2014-01-17 DOI: 10.1088/1749-4699/7/1/014001

D. Kimmig, C. Marquardt, K. Nau, Andreas P. Schmidt, M. Dickerhof

{"title":"Considerations about the implementation of a public knowledge base regarding nanotechnology","authors":"D. Kimmig, C. Marquardt, K. Nau, Andreas P. Schmidt, M. Dickerhof","doi":"10.1088/1749-4699/7/1/014001","DOIUrl":"https://doi.org/10.1088/1749-4699/7/1/014001","url":null,"abstract":"Nanotechnology ranks among the key technologies that will bring fundamental changes to basic research, many industry sectors and daily life. However, consumers often miss reliable and understandable information on nanomaterials. To create this transparency, the DaNa project collects and evaluates the latest scientific literature before publishing these on the website www.nanoobjects.info. Though all published articles are designed to meet the needs of different recipient groups, a certain knowledge about nanomaterials is presumed due to the nanomaterial-specific structuring of the website. This poses a barrier for interested laymen who usually have a particular nano-related application in mind. These application-oriented facts on nanomaterials already exist on the website but are scattered throughout the different articles. To overcome this, we first analyzed the state of the scattered information and then assessed requirements for a new tool displaying these facts: storage of extracted knowledge in a homogenous way, visualization options and integration of the new database into the existing content management system. We therefore extended our backend to capture knowledge on a semantically higher level in a database called DaNaVis. Based on this database we can increase the accessibility of DaNa's project results by means of interactive visualization components.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"7 1","pages":"014001"},"PeriodicalIF":0.0,"publicationDate":"2014-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/7/1/014001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Application of the Firefly and Luus?Jaakola algorithms in the calculation of a double reactive azeotrope 萤火虫和Luus?双反应共沸物计算中的Jaakola算法

Computational science & discovery Pub Date : 2014-01-01 DOI: 10.1088/1749-4699/7/1/015002

G. Platt, R. Domingos, Matheus Oliveira de Andrade

{"title":"Application of the Firefly and Luus?Jaakola algorithms in the calculation of a double reactive azeotrope","authors":"G. Platt, R. Domingos, Matheus Oliveira de Andrade","doi":"10.1088/1749-4699/7/1/015002","DOIUrl":"https://doi.org/10.1088/1749-4699/7/1/015002","url":null,"abstract":"The calculation of reactive azeotropes is an important task in the preliminary design and simulation of reactive distillation columns. Classically, homogeneous nonreactive azeotropes are vapor–liquid coexistence conditions where phase compositions are equal. For homogeneous reactive azeotropes, simultaneous phase and chemical equilibria occur concomitantly with equality of compositions (in the Ung–Doherty transformed space). The modeling of reactive azeotrope calculation is represented by a nonlinear algebraic system with phase equilibrium, chemical equilibrium and azeotropy equations. This nonlinear system can exhibit more than one solution, corresponding to a double reactive azeotrope. In a previous paper (Platt et al 2013 J. Phys.: Conf. Ser. 410 012020), we investigated some numerical aspects of the calculation of reactive azeotropes in the isobutene + methanol + methyl-tert-butyl-ether (with two reactive azeotropes) system using two metaheuristics: the Luus–Jaakola adaptive random search and the Firefly algorithm. Here, we use a hybrid structure (stochastic + deterministic) in order to produce accurate results for both azeotropes. After identifying the neighborhood of the reactive azeotrope, the nonlinear algebraic system is solved using Newton's method. The results indicate that using metaheuristics and some techniques devoted to the calculation of multiple minima allows both azeotropic coordinates in this reactive system to be obtains. In this sense, we provide a comprehensive analysis of a useful framework devoted to solving nonlinear systems, particularly in phase equilibrium problems.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"7 1","pages":"015002"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/7/1/015002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Balancing efficiency and accuracy for sediment transport simulations 泥沙输运模拟的平衡效率和准确性

Computational science & discovery Pub Date : 2013-12-24 DOI: 10.1088/1749-4699/6/1/015011

Wenjie Wei, S. Clark, Huayou Su, M. Wen, X. Cai

{"title":"Balancing efficiency and accuracy for sediment transport simulations","authors":"Wenjie Wei, S. Clark, Huayou Su, M. Wen, X. Cai","doi":"10.1088/1749-4699/6/1/015011","DOIUrl":"https://doi.org/10.1088/1749-4699/6/1/015011","url":null,"abstract":"Simulating multi-lithology sediment transport requires numerically solving a fully coupled system of nonlinear partial differential equations. The most standard approach is to simultaneously update all the unknown fields. Such a fully implicit strategy can be computationally demanding due to the need for Newton–Raphson iterations to set up and solve a large system of linearized algebraic equations. Fully explicit numerical schemes that do not solve linear systems are possible to devise, but suffer from considerably lower numerical stability and accuracy. Adding to this competition, there are semi-implicit numerical schemes that lie between the two extremes. This paper presents two contributions. First, we devise a new semi-implicit scheme that has second-order accuracy in the temporal direction. Second, and more importantly, we propose a novel methodology for comparing numerical schemes by considering accuracy, stability and computing speed at the same time. This methodology is general and easy to use, based on simple prediction models for the overall computation time on multicore architectures. Our findings are accompanied by numerical experiments modeling the sediment transport in Monterey Bay.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"6 1","pages":"015011"},"PeriodicalIF":0.0,"publicationDate":"2013-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/6/1/015011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4