arXiv: Biomolecules最新文献_第2页

A Review of Mathematical Modeling, Simulation and Analysis of Membrane Channel Charge Transport 膜通道电荷输运的数学建模、仿真与分析综述

arXiv: Biomolecules Pub Date : 2016-09-29 DOI: 10.1016/B978-0-12-809633-8.12044-8

Duan Chen, G. Wei

引用次数: 8

Statistical Mechanics and Kinetics of Amyloid Fibrillation 淀粉样蛋白颤动的统计力学和动力学

arXiv: Biomolecules Pub Date : 2016-09-06 DOI: 10.1142/9789813202382_0004

Liu Hong, Chiu Fan Lee, Yafei Huang

引用次数: 7

Cisplatin coordination chemistry determination at hen egg white lysozyme His15 with ligand distances and angles, and their standard uncertainties, and also reporting a split occupancy effect 顺铂配位化学在蛋清溶菌酶His15的配体距离和角度的测定，以及它们的标准不确定度，也报道了分裂占用效应

arXiv: Biomolecules Pub Date : 2016-06-04 DOI: 10.2210/pdb5l3h/pdb

J. Helliwell, S.W.M. Tanley, A. Schreurs, L. Kroon-Batenburg

引用次数: 1

Investigating the Selectivity of KcsA Channel by an Image Charge Solvation Method (ICSM) in Molecular Dynamics Simulations 分子动力学模拟中像电荷溶剂化法(ICSM)研究KcsA通道的选择性

arXiv: Biomolecules Pub Date : 2015-10-15 DOI: 10.4208/CICP.130315.310815A

Katherine Baker, Duan Chen, W. Cai

引用次数: 7

Geometric combinatorics and computational molecular biology: Branching polytopes for RNA sequences 几何组合学与计算分子生物学:RNA序列的分支多面体

arXiv: Biomolecules Pub Date : 2015-09-14 DOI: 10.1090/conm/685/13754

Elizabeth Drellich, Andrew Gainer-Dewar, H. Harrington, Qijun He, Christine E. Heitsch, Svetlana Poznanovi'c

引用次数: 4

Superparamagnetism of tryptophan and walk memory of proteins 色氨酸的超顺磁性和蛋白质的行走记忆

arXiv: Biomolecules Pub Date : 2015-08-27 DOI: 10.19185/MATTERS.201602000027

S. Raja, A. Dasgupta, N. Jain

引用次数: 2

Structuring of counterions around dna double helix: a molecular dynamics study dna双螺旋反离子结构:分子动力学研究

arXiv: Biomolecules Pub Date : 2015-03-18 DOI: 10.15407/UJPE60.05.0433

O. O. Liubysh, A. Vlasiuk, S. Perepelytsya, T. Shevchenko

{"title":"Structuring of counterions around dna double helix: a molecular dynamics study","authors":"O. O. Liubysh, A. Vlasiuk, S. Perepelytsya, T. Shevchenko","doi":"10.15407/UJPE60.05.0433","DOIUrl":"https://doi.org/10.15407/UJPE60.05.0433","url":null,"abstract":"Structuring of DNA counterions around the double helix has been studied by the molecular dynamics method. A DNA dodecamer d(CGCGAATTCGCG) in water solution with the alkali metal counterions Na$^{+}$, K$^{+}$, and Cs$^{+}$ has been simulated. The systems have been considered in the regimes without excess salt and with different salts (0.5 M of NaCl, KCl or CsCl) added. The results have showed that the Na$^{+}$ counterions interact with the phosphate groups directly from outside of the double helix and via water molecules at the top edge of DNA minor groove. The potassium ions are mostly localized in the grooves of the double helix, and the cesium ions penetrate deeply inside the minor groove being bonded directly to the atoms of nucleic bases. Due to the electrostatic repulsion the chlorine ions tend to be localized at large distances from the DNA polyanion, but some Cl$^{-}$ anions have been detected near atomic groups of the double helix forming electrically neutral pairs with counterions already condensed on DNA. The DNA sites, where counterions are incorporated, are characterized by local changes of double helix structure. The lifetime of Na$^{+}$ and K$^{+}$ in complex with DNA atomic groups is less than 0.5 ns, while in the case of the cesium ions it may reach several nanoseconds. In this time scale, the Cs$^{+}$ counterions form a structured system of charges in the DNA minor groove that can be considered as ionic lattice.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":"4 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2015-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91505555","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: 7

Towards de novo RNA 3D structure prediction 迈向从头RNA三维结构预测

arXiv: Biomolecules Pub Date : 2015-01-27 DOI: 10.14800/rd.544

Sandro Bottaro, Francesco Di Palma, G. Bussi

引用次数: 2

Relaxing the Hypotheses of Symmetry and Time-Reversibility in Genome Evolutionary Models 放宽基因组进化模型中的对称性和时间可逆性假设

arXiv: Biomolecules Pub Date : 2015-01-10 DOI: 10.9734/BJMCS/2015/14280

J. Bahi, C. Guyeux, A. Perasso

引用次数: 1

Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: A review 生物分子建模中基于微分几何的溶剂化和电解质传输模型:综述

arXiv: Biomolecules Pub Date : 2014-11-30 DOI: 10.1201/b21343-15

G. Wei, Nathan A. Baker

{"title":"Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: A review","authors":"G. Wei, Nathan A. Baker","doi":"10.1201/b21343-15","DOIUrl":"https://doi.org/10.1201/b21343-15","url":null,"abstract":"This chapter reviews the differential geometry-based solvation and electrolyte transport for biomolecular solvation that have been developed over the past decade. A key component of these methods is the differential geometry of surfaces theory, as applied to the solvent-solute boundary. In these approaches, the solvent-solute boundary is determined by a variational principle that determines the major physical observables of interest, for example, biomolecular surface area, enclosed volume, electrostatic potential, ion density, electron density, etc. Recently, differential geometry theory has been used to define the surfaces that separate the microscopic (solute) domains for biomolecules from the macroscopic (solvent) domains. In these approaches, the microscopic domains are modeled with atomistic or quantum mechanical descriptions, while continuum mechanics models (including fluid mechanics, elastic mechanics, and continuum electrostatics) are applied to the macroscopic domains. This multiphysics description is integrated through an energy functional formalism and the resulting Euler-Lagrange equation is employed to derive a variety of governing partial differential equations for different solvation and transport processes; e.g., the Laplace-Beltrami equation for the solvent-solute interface, Poisson or Poisson-Boltzmann equations for electrostatic potentials, the Nernst-Planck equation for ion densities, and the Kohn-Sham equation for solute electron density. Extensive validation of these models has been carried out over hundreds of molecules, including proteins and ion channels, and the experimental data have been compared in terms of solvation energies, voltage-current curves, and density distributions. We also propose a new quantum model for electrolyte transport.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2014-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91065051","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