Development And Use Of Molecular Simulation Tools To Study The Structure And Function Of Biomolecules At Interfaces
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Development And Use Of Molecular Simulation Tools To Study The Structure And Function Of Biomolecules At Interfaces
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Author : Kayla G. Sprenger
language : en
Publisher:
Release Date : 2017
Development And Use Of Molecular Simulation Tools To Study The Structure And Function Of Biomolecules At Interfaces written by Kayla G. Sprenger and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017 with categories.
Predicting and controlling the biophysical chemistry of protein/host interactions remains a pressing challenge of high fundamental interest across many subfields in chemistry, engineering, and medicine. Our ability to (experimentally) probe interfacial interactions between a surface, polymer, or solvent and a biomolecule has increased due to high-resolution NMR and other spectroscopic techniques. However, new structural and mechanistic insights coming from experiments alone have been limited due to – in the case of the protein/liquid interface – the compounding challenges of simultaneously studying the protein/host interface and elucidating sequence specific interactions, and in the case of the protein/surface interface – the lack of a single unifying technique that can fully resolve the structure of an adsorbed protein. For the protein/liquid interface, the challenge is even worse in the case of synthetic frameworks such as ionic liquids (ILs) where the combinatorial design space of the solvent and protein sequence explodes beyond what could ever be feasibly considered in a laboratory. The field could be greatly advanced through the use of predictive, physics-based simulations; however, best practices of how to simulate protein interfacial adsorption and extract meaningful information about protein/host interactions from molecular simulations for direct experimental comparison, are still developing. Herein, we aim to address these challenges through the use of a variety of statistical enhanced sampling simulation techniques and novel analytical approaches. A number of systems are simulated, ranging from small model proteins adsorbing onto solid, idealized surfaces, to simulations of full proteins in complex solution environments. Ultimately, these simulations should lead to large improvements in the way we use computers to study multifaceted interfacial processes like protein adsorption, in addition to providing new fundamental insights into protein/host interactions.
Computational Methods To Study The Structure And Dynamics Of Biomolecules And Biomolecular Processes
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Author : Adam Liwo
language : en
Publisher: Springer
Release Date : 2016-09-24
Computational Methods To Study The Structure And Dynamics Of Biomolecules And Biomolecular Processes written by Adam Liwo and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-09-24 with Technology & Engineering categories.
Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over the world, address the theory and practice of computer simulation techniques in the study of biological phenomena. The chapters are grouped into four thematic sections dealing with the following topics: the methodology of molecular simulations; applications of molecular simulations; bioinformatics methods and use of experimental information in molecular simulations; and selected applications of molecular quantum mechanics. The book includes an introductory chapter written by Harold A. Scheraga, one of the true pioneers in simulation studies of biomacromolecules.
Biomolecular Simulations
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Author : Massimiliano Bonomi
language : en
Publisher: Humana
Release Date : 2020-08-14
Biomolecular Simulations written by Massimiliano Bonomi and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-08-14 with Science categories.
This volume explores the recent advancements in biomolecular simulations of proteins, small molecules, and nucleic acids, with a primary focus on classical molecular dynamics (MD) simulations at atomistic, coarse-grained, and quantum/ab-initio levels. The chapters in this book are divided into four parts: Part One looks at recent techniques used in the development of physic-chemical models of proteins, small molecules, nucleic acids, and lipids; Part Two discusses enhanced sampling and free-energy calculations; Part Three talks about integrative computational and experimental approaches for biomolecular simulations; and Part Four focuses on analyzing, visualizing, and comparing biomolecular simulations. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Biomolecular Simulations: Methods and Protocols is a valuable resource for both novice and expert researchers who are interested in studying different areas of biomolecular simulations, and discovering new tools to progress their future projects.
Computational Methods To Study The Structure And Dynamics Of Biomolecules And Biomolecular Processes
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Author : Adam Liwo
language : en
Publisher: Springer
Release Date : 2018-12-19
Computational Methods To Study The Structure And Dynamics Of Biomolecules And Biomolecular Processes written by Adam Liwo and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-12-19 with Technology & Engineering categories.
This book provides a comprehensive overview of modern computer-based techniques for analyzing the structure, properties and dynamics of biomolecules and biomolecular processes. It is organized in four main parts; the first one deals with methodology of molecular simulations; the second one with applications of molecular simulations; the third one introduces bioinformatics methods and the use of experimental information in molecular simulations; the last part reports on selected applications of molecular quantum mechanics. This second edition has been thoroughly revised and updated to include the latest progresses made in the respective field of research.
Report Of The Committee On Proposal Evaluation For Allocation Of Supercomputing Time For The Study Of Molecular Dynamics
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Author : National Academies of Sciences, Engineering, and Medicine
language : en
Publisher: National Academies Press
Release Date : 2016-10-31
Report Of The Committee On Proposal Evaluation For Allocation Of Supercomputing Time For The Study Of Molecular Dynamics written by National Academies of Sciences, Engineering, and Medicine and has been published by National Academies Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-10-31 with Science categories.
This report describes the work of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics, Seventh Round. The committee evaluated submissions received in response to a Request for Proposals (RFP) for biomolecular simulation time on Anton, a supercomputer specially designed and built by D.E. Shaw Research (DESRES). Over the past five years, DESRES has made an Anton system housed at the Pittsburgh Supercomputing Center (PSC) available to the non-commercial research community, based on the advice of previous National Research Council committees. As in prior rounds, the goal of the seventh RFP for simulation time on Anton is to continue to facilitate breakthrough research in the study of biomolecular systems by providing a massively parallel system specially designed for molecular dynamics simulations. The program seeks to continue to support research that addresses important and high impact questions demonstrating a clear need for Anton's special capabilities. Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics, Seventh Round is the report of the committee's evaluation of proposals based on scientific merit, justification for requested time allocation, and investigator qualifications and past accomplishments. This report identifies the proposals that best met the selection criteria.
Molecular Simulations To Characterize The Assembly And Transport Of Biomolecules In Solution And At Lipid Interfaces
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Author : Samarthaben Jayeshkumar Patel
language : en
Publisher:
Release Date : 2021
Molecular Simulations To Characterize The Assembly And Transport Of Biomolecules In Solution And At Lipid Interfaces written by Samarthaben Jayeshkumar Patel and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021 with categories.
Biomolecules capable of bypassing the cell membrane are of great importance for drug and gene delivery. However, there is a significant challenge in predicting the behavior of these biomolecules in biological environments. In this dissertation, we focus on two major class of biomolecules: 1) small amphiphilic bacterial signals, and 2) membrane proteins/peptides with charged residues in their loops and transmembrane helices. In the first part, we study the amphiphilic behavior of bacterial quorum sensing (QS) signal molecules which are produced by common bacteria to coordinate group behaviors. N-acyl-l-homoserine lactones (AHLs) are commonly used signals that possess a polar homoserine lactone headgroup and a nonpolar aliphatic tail. We use a combination of biophysical characterization and atomistic molecular dynamics (MD) simulations to characterize the self-assembly behaviors of 12 structurally related AHLs, and predict their thermodynamically preferred aggregate structures using alchemical free energy calculations. We then study the large-scale remodeling in model lipid membranes promoted by AHLs, and predict differences in translocation free energies are reflected in both the type and extent of reformation. We then use an implicit solvent model, called COSMOmic, to screen the water-membrane partition and translocation free energies for 50 native and non-native QS modulators at a significantly reduced computational cost compared to atomistic MD simulations. In the second part, we study the translocation of charged moieties of a peptide across a lipid bilayer. The hydrophobic core of the lipid bilayer is considered a barrier to the translocation of charged species. Despite this barrier, some peptides can interconvert between transmembrane and surface-adsorbed states by "flipping" charged flanking loops across the bilayer on a surprisingly rapid second-minute time scale. We utilize all-atom temperature accelerated molecular dynamics (TAMD) simulations to predict the likelihood of loop-flipping without predefining specific loop-flipping pathways in single-transmembrane helix peptides. Along with TAMD, we use the swarms-of-trajectories string method to analyze loop-flipping pathways and free energy barriers across lipid bilayers as a function of multiple collective variables. Overall, our results provide insights into the self-assembly and translocation of biomolecules across lipid bilayers which could prove useful in the design of synthetic drug delivery and sensing agents.
Computer Modelling In Molecular Biology
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Author : Julia M. Goodfellow
language : en
Publisher: John Wiley & Sons
Release Date : 2008-07-11
Computer Modelling In Molecular Biology written by Julia M. Goodfellow and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-07-11 with Science categories.
This book supplies an application-oriented introduction to molecular simulation techniques used to study a wide range of problems in molecular biology. Each chapter focuses in detail on one kind of application, including the scientific background, the appropriate methodology and the relationship to experimental results. The book contains many areas of interest to basic and industrial scientists, including: - flexibility of peptides - protein-peptide interactions - ion translocation across membranes - modelling protein and nucleic acid conformations - stability of mutant proteins - modelling conformational transitions Currently the only up-to-date compilation available, this book enables readers to get an overview of the methods and how they are used in various specialized applications without having to search for them in a large number of papers in different journals.
Application Of Molecular Simulations And Machine Learning Methods To Study Biological And Metallic Interfaces In Aqueous Environment
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Author : Mohammadreza Aghaaminiha
language : en
Publisher:
Release Date : 2021
Application Of Molecular Simulations And Machine Learning Methods To Study Biological And Metallic Interfaces In Aqueous Environment written by Mohammadreza Aghaaminiha and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021 with Bilayer lipid membranes categories.
Molecular dynamics (MD) simulation is a computational methodology to probe molecular-level details of physical systems. In MD, the motion of molecules is simulated and from the molecular trajectories, thermodynamic and kinetic properties are ascertained. Machine learning (ML) techniques are a set of computational tools that allow us to identify complex, non-linear relationships in data. ML methods are particularly useful when a system property of interest depends on a large number of variables, and there are no accurate physics-based models relating the property of interest to the variables. ML methods rely on the availability of large datasets to tease out the relationships between the variables. In this research, we have employed MD simulations to study the structural and thermodynamical properties of the simplified plasma membrane of eukaryotic cells, known as the lipid bilayer. We have applied ML methods to study the phase diagram of lipids. Furthermore, we have used ML methods for various corrosion-related applications. By studying asymmetric lipid bilayers using MD simulations, we have shown that in equimolar, asymmetric lipid bilayers, the two leaflets of the bilayer are in tensile and compressive mechanical stress. In response, cholesterol molecules redistribute between the leaflets to relieve these stresses. As a result, the distribution of cholesterol molecules depends on the relative ordering of lipids in the two leaflets. We show that there is a quantitative relationship between cholesterol distribution and the ordering of lipids. We have also studied the distribution of cholesterol molecules in lipid bilayers as a function of temperature and phase of the lipids. We have applied ML to study phase behavior in three-component lipid mixtures and have shown that trained ML methods are quite effective in reproducing the phase diagram of lipids. Furthermore, we have applied ML tools to model the time-dependent corrosion rate of mild steel in presence of corrosion inhibitors injected in different doses and dose schedules. We find that trained ML methods are quite effective in modeling the entire kinetics of the time-dependent corrosion rates.
Biomedical Index To Phs Supported Research Pt A Subject Access A H
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Author :
language : en
Publisher:
Release Date : 1992
Biomedical Index To Phs Supported Research Pt A Subject Access A H written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1992 with Medicine categories.
Developing A Simulation Framework For Modeling Biomolecules In Ionic Liquids
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Author : Vance W. Jaeger
language : en
Publisher:
Release Date : 2015
Developing A Simulation Framework For Modeling Biomolecules In Ionic Liquids written by Vance W. Jaeger and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015 with categories.
First, we describe the development of a protocol to quickly parameterize and validate ionic liquid force fields. Simulations that use these force fields are shown to accurately predict several thermopysical properties of ionic liquids. When compared to other solvent force fields, our force fields perform similarly well or better than many commonly used models for the prediction of solvent properties. Second, simulations containing enzymes solvated in ionic liquids and water are discussed. The mixture of ionic liquids and proteins is of interest because non-native solvents have been shown to affect the function of enzymes in both positive and negative ways. Yet, there is an incomplete understanding of the reasons why ionic liquids have such effects on proteins. The studies presented in this document focus on several different ionic liquid-enzyme systems and the ways in which the solvent affects the structure and dynamics of the solute. We also employ enhanced sampling techniques such as metadynamics to extend our understanding of the thermodynamics of ionic liquid-protein interactions. Third, we study systems that involve the self-assembly of biomolecules in ion-rich environments. One group of interesting peptides are the leucine-lysine (LK) peptides. LK peptides vary in secondary structure depending on the periodicity of their sequences, and often they have clearly separated hydrophobic and charged sides. LK peptides are known to precipitate silica bionanoparticles from silicic acid solutions. Our simulations probe the structures of LK peptide aggregates and the formation of silicic acid structures at ordered LK peptide interfaces. In addition to LK peptides, we also study the formation of metal ion-surfactant complexes in organic solvents. The morphology of these complexes can be predicted using molecular dynamics, and our simulation results compare well with experimental data. Altogether, our simulations demonstrate that molecular dynamics simulations of biomolecules in the presence of ionic liquids and other complex ions is a viable tool to understand solvent-solute interactions and that the results of such simulations compare well to available experimental data. We believe that the methods we have developed in this dissertation can be extended to study almost any commonly available solvent with almost any biomolecule.