Pub Date : 2016-09-29DOI: 10.1016/B978-0-12-809633-8.12044-8
Duan Chen, G. Wei
{"title":"A Review of Mathematical Modeling, Simulation and Analysis of Membrane Channel Charge Transport","authors":"Duan Chen, G. Wei","doi":"10.1016/B978-0-12-809633-8.12044-8","DOIUrl":"https://doi.org/10.1016/B978-0-12-809633-8.12044-8","url":null,"abstract":"","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87854112","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}
Pub Date : 2016-09-06DOI: 10.1142/9789813202382_0004
Liu Hong, Chiu Fan Lee, Yafei Huang
Amyloid fibrillation is a protein self-assembly phenomenon that is intimately related to well-known human neurodegenerative diseases. During the past few decades, striking advances have been achieved in our understanding of the physical origin of this phenomenon and they constitute the contents of this review. Starting from a minimal model of amyloid fibrils, we explore systematically the equilibrium and kinetic aspects of amyloid fibrillation in both dilute and semi-dilute limits. We then incorporate further molecular mechanisms into the analyses. We also discuss the mathematical foundation of kinetic modeling based on chemical mass-action equations, the quantitative linkage with experimental measurements, as well as the procedure to perform global fitting.
{"title":"Statistical Mechanics and Kinetics of Amyloid Fibrillation","authors":"Liu Hong, Chiu Fan Lee, Yafei Huang","doi":"10.1142/9789813202382_0004","DOIUrl":"https://doi.org/10.1142/9789813202382_0004","url":null,"abstract":"Amyloid fibrillation is a protein self-assembly phenomenon that is intimately related to well-known human neurodegenerative diseases. During the past few decades, striking advances have been achieved in our understanding of the physical origin of this phenomenon and they constitute the contents of this review. Starting from a minimal model of amyloid fibrils, we explore systematically the equilibrium and kinetic aspects of amyloid fibrillation in both dilute and semi-dilute limits. We then incorporate further molecular mechanisms into the analyses. We also discuss the mathematical foundation of kinetic modeling based on chemical mass-action equations, the quantitative linkage with experimental measurements, as well as the procedure to perform global fitting.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78546834","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}
J. Helliwell, S.W.M. Tanley, A. Schreurs, L. Kroon-Batenburg
Following the interest of L Messori and A Merlino 2016 Coordination Chemistry Reviews in the platinum ions coordination geometries in our PDB entries 4dd4 and 4dd6 we have extended our original analyses.
{"title":"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","authors":"J. Helliwell, S.W.M. Tanley, A. Schreurs, L. Kroon-Batenburg","doi":"10.2210/pdb5l3h/pdb","DOIUrl":"https://doi.org/10.2210/pdb5l3h/pdb","url":null,"abstract":"Following the interest of L Messori and A Merlino 2016 Coordination Chemistry Reviews in the platinum ions coordination geometries in our PDB entries 4dd4 and 4dd6 we have extended our original analyses.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82448249","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}
Pub Date : 2015-10-15DOI: 10.4208/CICP.130315.310815A
Katherine Baker, Duan Chen, W. Cai
In this paper, we study the selectivity of the potassium channel KcsA by a recently developed image-charge solvation method(ICSM) combined with molecular dynamics simulations. The hybrid solvation model in the ICSM is able to demonstrate atomistically the function of the selectivity filter of the KcsA channel when potassium and sodium ions are considered and their distributions inside the filter are simulated. Our study also shows that the reaction field effect, explicitly accounted for through image charge approximation in the ICSM model, is necessary in reproducing the correct selectivity property of the potassium channels.
{"title":"Investigating the Selectivity of KcsA Channel by an Image Charge Solvation Method (ICSM) in Molecular Dynamics Simulations","authors":"Katherine Baker, Duan Chen, W. Cai","doi":"10.4208/CICP.130315.310815A","DOIUrl":"https://doi.org/10.4208/CICP.130315.310815A","url":null,"abstract":"In this paper, we study the selectivity of the potassium channel KcsA by a recently developed image-charge solvation method(ICSM) combined with molecular dynamics simulations. The hybrid solvation model in the ICSM is able to demonstrate atomistically the function of the selectivity filter of the KcsA channel when potassium and sodium ions are considered and their distributions inside the filter are simulated. Our study also shows that the reaction field effect, explicitly accounted for through image charge approximation in the ICSM model, is necessary in reproducing the correct selectivity property of the potassium channels.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80238845","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}
Elizabeth Drellich, Andrew Gainer-Dewar, H. Harrington, Qijun He, Christine E. Heitsch, Svetlana Poznanovi'c
Questions in computational molecular biology generate various discrete optimization problems, such as DNA sequence alignment and RNA secondary structure prediction. However, the optimal solutions are fundamentally dependent on the parameters used in the objective functions. The goal of a parametric analysis is to elucidate such dependencies, especially as they pertain to the accuracy and robustness of the optimal solutions. Techniques from geometric combinatorics, including polytopes and their normal fans, have been used previously to give parametric analyses of simple models for DNA sequence alignment and RNA branching configurations. Here, we present a new computational framework, and proof-of-principle results, which give the first complete parametric analysis of the branching portion of the nearest neighbor thermodynamic model for secondary structure prediction for real RNA sequences.
{"title":"Geometric combinatorics and computational molecular biology: Branching polytopes for RNA sequences","authors":"Elizabeth Drellich, Andrew Gainer-Dewar, H. Harrington, Qijun He, Christine E. Heitsch, Svetlana Poznanovi'c","doi":"10.1090/conm/685/13754","DOIUrl":"https://doi.org/10.1090/conm/685/13754","url":null,"abstract":"Questions in computational molecular biology generate various discrete optimization problems, such as DNA sequence alignment and RNA secondary structure prediction. However, the optimal solutions are fundamentally dependent on the parameters used in the objective functions. The goal of a parametric analysis is to elucidate such dependencies, especially as they pertain to the accuracy and robustness of the optimal solutions. Techniques from geometric combinatorics, including polytopes and their normal fans, have been used previously to give parametric analyses of simple models for DNA sequence alignment and RNA branching configurations. Here, we present a new computational framework, and proof-of-principle results, which give the first complete parametric analysis of the branching portion of the nearest neighbor thermodynamic model for secondary structure prediction for real RNA sequences.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86598928","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}
Pub Date : 2015-08-27DOI: 10.19185/MATTERS.201602000027
S. Raja, A. Dasgupta, N. Jain
Superparamagnetism of tryptophan implying the presence of magnetic domain is reported. The observation helps us to conceive assembly of proteins as a physical lattice gas with multidimensional Ising character, each lattice points assuming discrete spin states. When magnetic field is applied the equilibrium is lost and the population density of one spin state increases (unidirectional alignment), resulting in net magnetization. Spatial coherence between the identical spin states further imparts a ferromagnetic memory. This effect is observed using direct nanoscale video imaging. Out of the three proteins ferritin serum albumin and fibrinogen, fibrinogen showed an attenuated response, the protein being essentially one dimensional. Eventually, Ising lattice is capable of showing ferromagnetic memory only when it has a higher dimensional character. The study highlights possible presence of long range spatial coherence at physiological condition and a plausible microscopic origin of the same.
{"title":"Superparamagnetism of tryptophan and walk memory of proteins","authors":"S. Raja, A. Dasgupta, N. Jain","doi":"10.19185/MATTERS.201602000027","DOIUrl":"https://doi.org/10.19185/MATTERS.201602000027","url":null,"abstract":"Superparamagnetism of tryptophan implying the presence of magnetic domain is reported. The observation helps us to conceive assembly of proteins as a physical lattice gas with multidimensional Ising character, each lattice points assuming discrete spin states. When magnetic field is applied the equilibrium is lost and the population density of one spin state increases (unidirectional alignment), resulting in net magnetization. Spatial coherence between the identical spin states further imparts a ferromagnetic memory. This effect is observed using direct nanoscale video imaging. Out of the three proteins ferritin serum albumin and fibrinogen, fibrinogen showed an attenuated response, the protein being essentially one dimensional. Eventually, Ising lattice is capable of showing ferromagnetic memory only when it has a higher dimensional character. The study highlights possible presence of long range spatial coherence at physiological condition and a plausible microscopic origin of the same.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87219212","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}
O. O. Liubysh, A. Vlasiuk, S. Perepelytsya, T. Shevchenko
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.
用分子动力学方法研究了DNA双螺旋反离子的结构。本文模拟了DNA十二聚体d(CGCGAATTCGCG)与碱金属离子Na$^{+}$、K$^{+}$和Cs$^{+}$在水溶液中的反应。在无过量盐和添加不同盐(0.5 M NaCl、KCl或CsCl)的情况下，对体系进行了考虑。结果表明，Na$^{+}$反离子直接从双螺旋外与磷酸基相互作用，并通过DNA小槽顶部边缘的水分子与磷酸基相互作用。钾离子主要集中在双螺旋的凹槽中，而铯离子则深入到小凹槽中，直接与核酸基原子结合。由于静电斥力，氯离子倾向于定位在离DNA多阴离子较远的地方，但一些Cl$^{-}$阴离子已经在DNA上凝聚形成电中性对的双螺旋原子群附近被检测到。反离子结合的DNA位点以双螺旋结构的局部变化为特征。Na$^{+}$和K$^{+}$在与DNA原子基团配合物中的寿命小于0.5 ns，而在与铯离子配合物中的寿命可达数纳秒。在这个时间尺度上，Cs$^{+}$反离子在DNA小槽中形成了一个结构化的电荷系统，可以认为是离子晶格。
{"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":null,"pages":null},"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}
RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main challenges in this field is the development of structure-prediction algorithms, which aim at the prediction of the three-dimensional (3D) native fold from the sole knowledge of the sequence. In a recent paper, we have introduced a scoring function for RNA structure prediction. Here, we analyze in detail the performance of the method, we underline strengths and shortcomings, and we discuss the results with respect to state-of-the-art techniques. These observations provide a starting point for improving current methodologies, thus paving the way to the advances of more accurate approaches for RNA 3D structure prediction.
{"title":"Towards de novo RNA 3D structure prediction","authors":"Sandro Bottaro, Francesco Di Palma, G. Bussi","doi":"10.14800/rd.544","DOIUrl":"https://doi.org/10.14800/rd.544","url":null,"abstract":"RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main challenges in this field is the development of structure-prediction algorithms, which aim at the prediction of the three-dimensional (3D) native fold from the sole knowledge of the sequence. In a recent paper, we have introduced a scoring function for RNA structure prediction. Here, we analyze in detail the performance of the method, we underline strengths and shortcomings, and we discuss the results with respect to state-of-the-art techniques. These observations provide a starting point for improving current methodologies, thus paving the way to the advances of more accurate approaches for RNA 3D structure prediction.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76746004","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}
Pub Date : 2015-01-10DOI: 10.9734/BJMCS/2015/14280
J. Bahi, C. Guyeux, A. Perasso
Various genome evolutionary models have been proposed these last decades to predict the evolution of a DNA sequence over time, essentially described using a mutation matrix. By essence, all of these models relate the evolution of DNA sequences to the computation of the successive powers of the mutation matrix. To make this computation possible, hypotheses are assumed for the matrix, such as symmetry and time-reversibility, which are not compatible with mutation rates that have been recently obtained experimentally on genes ura3 and can1 of the Yeast Saccharomyces cerevisiae. In this work, authors investigate systematically the possibility to relax either the symmetry or the time-reversibility hypothesis of the mutation matrix, by investigating all the possible matrices of size 2*2 and 3*3. As an application example, the experimental study on the Yeast Saccharomyces cerevisiae has been used in order to deduce a simple mutation matrix, and to compute the future evolution of the rate purine/pyrimidine for $ura3$ on the one hand, and of the particular behavior of cytosines and thymines compared to purines on the other hand.
{"title":"Relaxing the Hypotheses of Symmetry and Time-Reversibility in Genome Evolutionary Models","authors":"J. Bahi, C. Guyeux, A. Perasso","doi":"10.9734/BJMCS/2015/14280","DOIUrl":"https://doi.org/10.9734/BJMCS/2015/14280","url":null,"abstract":"Various genome evolutionary models have been proposed these last decades to predict the evolution of a DNA sequence over time, essentially described using a mutation matrix. By essence, all of these models relate the evolution of DNA sequences to the computation of the successive powers of the mutation matrix. To make this computation possible, hypotheses are assumed for the matrix, such as symmetry and time-reversibility, which are not compatible with mutation rates that have been recently obtained experimentally on genes ura3 and can1 of the Yeast Saccharomyces cerevisiae. In this work, authors investigate systematically the possibility to relax either the symmetry or the time-reversibility hypothesis of the mutation matrix, by investigating all the possible matrices of size 2*2 and 3*3. As an application example, the experimental study on the Yeast Saccharomyces cerevisiae has been used in order to deduce a simple mutation matrix, and to compute the future evolution of the rate purine/pyrimidine for $ura3$ on the one hand, and of the particular behavior of cytosines and thymines compared to purines on the other hand.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74386204","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}
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.
{"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":null,"pages":null},"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}
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