Download or read book Structure and Property of Polymers and Biopolymers from Molecular Dynamic Simulations written by Xiaoquan Sun and published by . This book was released on 2018 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt: Natural and synthetic polymers and biopolymers have been studied for a variety of applications in food emulsion, biopharmaceutical purification, tissue engineering, and biosensor. The structure and property of polymers and biopolymers are critically important to determine their functions. Molecular dynamics (MD) simulations have a unique advantage to explore the structure and property of polymers and biopolymers from the molecular level. In the dissertation, MD simulations were conducted to study the mechanisms of various biological and chemical processes controlled by polymers and biopolymers based on real-world experimental results. Seven heptapeptides have been screened from a peptide library in our earlier study of the antibody purification. They have substantial binding affinities to the Fc fragment of IgG. In Chapter 2, the binding mechanisms between seven heptapeptides and the Fc fragment have been investigated by protein-ligand docking, free energy calculation and MD simulations. It is the first time that glycan residues are found to be the binding pocket for small ligands. The novel binding pocket is different from the CBS binding site for protein A and protein G. We also found out that, the results of free energy calculations are in good agreement with the ELISA experiments. The thermos-responsive polymer, PVCL (poly(N-vinylcaprolactam)) was grafted on the surface of a membrane as the responsive hydrophobic chromatography for the protein purification in our earlier study. In Chapter 3, significant efforts have been devoted to develop the force field parameters for PVCL. The coil-to-globule conformational transition of PVCL has been successfully observed in MD simulation for the first time. The water dynamics analysis provides significant insights into the interaction between PVCL and water molecules. The novel statistical analysis of VCL ring conformations and the distribution along backbone also elucidate the steric requirement in the coil-to-globule transition. In Chapter 4, MD simulations were conducted to investigate the biocompatibility, energetics and interaction mechanisms between the PVCL polymer chains and bovine serum albumin (BSA) in 1M NaCl and aqueous solutions. Water structures surrounding the polymer chains and BSA as well as their hydrogen bonding, electrostatic and van der Waals interactions were determined. Significant insights were obtained on the effects of polymer hydration state, polymer chain length as well as the presence of salt ions on the proteinligand interactions. A novel polymeric solid acid catalyst consisting of two polymer chains grafted on a substrate for biomass hydrolysis was successfully synthesized. A poly (styrene sulfonic acid) (PSSA) polymer chain is immobilized on a substrate and used to catalyze biomass hydrolysis. A neighboring poly (vinyl imidazolium chloride) ionic liquid (PIL) polymer chain is grafted to help solubilize lignocellulosic biomass and enhance the catalytic activity. To elucidate mechanistically the catalytic actions and further optimize its performance, interactions among the PSSA, PIL, and cellulose chains were investigated using MD simulations in Chapter 5. Moreover, the free energies surfaces for the interactions between polymer chains and cellulose substrate were determined using combined MD and Metadynamics (MTD) simulations. The research clearly demonstrate that the solvent plays a critical role in the cellulose hydrolysis reaction catalyzed by novel enzyme mimic polymeric catalysts PSSA and PIL. It is found that PSSA chain is likely to form partially dehydrated interaction with cellulose in both aqueous and [EMIM]Cl solutions. PIL plays an important role to prevent the completely dehydrated interactions and facilitate partially dehydrated interaction between PSSA and cellulose chains.
Download or read book Molecular Dynamic Modeling and Simulation for Polymers written by Anthony F. Harrell and published by . This book was released on 2003-09 with total page 67 pages. Available in PDF, EPUB and Kindle. Book excerpt: Polymers have been widely used in various engineering applications. For more than a quarter century, the materials have been utilized intensively for the binding materials for composites. The material properties of the binding materials called matrix materials play an important role for the composite material behaviors, As a result, the objective of this study was to understand the mechanical properties of polymers. In particular, the goal was to develop insights as to how a molecular level structure is connected to the bulk properties of materials assuming homogeneity. To this end, molecular dynamics was used to model and simulate the polymeric behaviors. Polymeric chains were modeled using the bead and spring model along with interacting potentials. The study examined the effects of different sizes, densities, and numbers of molecules per chain on the shear moduli of the polymers. Furthermore, some preliminary study was also conducted for metallic particle reinforced polymer composites.
Download or read book Molecular Interfacial Phenomena of Polymers and Biopolymers written by P Chen and published by Elsevier. This book was released on 2005-07-22 with total page 709 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the most exciting areas of polymer research is the study of interfacial phenomena and their practical applications. This major work reviews the key research in this important area and is used in such areas as biomaterials.Part one looks at the thermodynamics, kinetics and other fundamental properties of polymer surfaces and interfaces. The second part of the book reviews ways of characterising and manipulating interfacial phenomena. It includes examples of practical applications such as vaccine delivery, tissue engineering and the development of therapeutic lung surfactants.With its distinguished editor and international team of contributors, Molecular interfacial phenomena of polymers and biopolymers is a standard work on understanding polymeric interfacial properties and their medical and other practical applications. Reviews key research in this hot area including biomaterials Examines polymeric interfacial properties and reviews medical and other practical applications Edited by a leading authority with contributions from distinguished experts worldwide
Download or read book Multiscale Modeling of Structure property Relationships in Polymers with Heterogenous Structure written by Yiyang Li and published by . This book was released on 2017 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The exceptional mechanical properties of polymers with heterogeneous structure, such as the high toughness of polyethylene and the excellent blast-protection capability of polyurea, are strongly related to their morphology and nanoscale structure. Different polymer microstructures, such as semicrystalline morphology and segregated nanophases, lead to coordinated molecular motions during deformation in order to preserve compatibility between the different material phases. To study molecular relaxation in polyethylene, a coarse-grained model of polyethylene was calibrated to match the local structural variable distributions sampled from supercooled atomistic melts. The coarse-grained model accurately reproduces structural properties, e.g., the local structure of both the amorphous and crystalline phases, and thermal properties, e.g., glass transition and melt temperatures, and dynamic properties: including the vastly different relaxation time scales of the amorphous and crystalline phases. A hybrid Monte Carlo routine was developed to generate realistic semicrystalline configurations of polyethylene. The generated systems accurately predict the activation energy of the alpha relaxation process within the crystalline phase. Furthermore, the models show that connectivity to long chain segments in the amorphous phase increases the energy barrier for chain slip within crystalline phase. This prediction can guide the development of tougher semicrystalline polymers by providing a fundamental understanding of how nanoscale morphology contributes to chain mobility. In a different study, the macroscopic shock response of polyurea, a phase segregated copolymer, was analyzed using density functional theory (DFT) molecular dynamics (MD) simulations and classical MD simulations. The two models predict the shock response consistently up to shock pressures of 15 GPa, beyond which the DFT-based simulations predict a softer response. From the DFT simulations, an analysis of bond scission was performed as a first step in developing a more fundamental understanding of how shock induced material transformations effect the shock response and pressure dependent strength of polyurea subjected to extreme shocks.
Download or read book Simulation Methods for Polymers written by Michael Kotelyanskii and published by CRC Press. This book was released on 2004-03-01 with total page 572 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Computer Simulation of Polymers written by Elizabeth A. Colbourn and published by Longman Publishing Group. This book was released on 1994 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: For chemists, physicists, and students of computer simulation, provides a detailed examination of the complex problems of time and size scaling in molecular modeling and simulation. It includes not only atomistic modeling but also coarse-grained models, which allow longer time scales and therefore larger systems to be studied. Monte Carlo methods are also discussed, and have proven to be particularly powerful tools for examining a range of polymer problems. Assumes a background knowledge of synthetic polymer properties and simulation. Annotation copyright by Book News, Inc., Portland, OR
Download or read book Structure and Dynamics of Confined Polymers written by John J. Kasianowicz and published by Springer Science & Business Media. This book was released on 2002-07-31 with total page 46 pages. Available in PDF, EPUB and Kindle. Book excerpt: Polymers are essential to biology because they can have enough stable degrees of freedom to store the molecular code of heredity and to express the sequences needed to manufacture new molecules. Through these they perform or control virtually every function in life. Although some biopolymers are created and spend their entire career in the relatively large free space inside cells or organelles, many biopolymers must migrate through a narrow passageway to get to their targeted destination. This suggests the questions: How does confining a polymer affect its behavior and function? What does that tell us about the interactions between the monomers that comprise the polymer and the molecules that confine it? Can we design and build devices that mimic the functions of these nanoscale systems? The NATO Advanced Research Workshop brought together for four days in Bikal, Hungary over forty experts in experimental and theoretical biophysics, molecular biology, biophysical chemistry, and biochemistry interested in these questions. Their papers collected in this book provide insight on biological processes involving confinement and form a basis for new biotechnological applications using polymers. In his paper Edmund DiMarzio asks: What is so special about polymers? Why are polymers so prevalent in living things? The chemist says the reason is that a protein made of N amino acids can have any of 20 different kinds at each position along the chain, resulting in 20 N different polymers, and that the complexity of life lies in this variety.
Download or read book Biopolymer Research Trends written by Tamás S. Németh and published by Nova Publishers. This book was released on 2007 with total page 240 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biopolymers are a special class of polymers produced by living organisms. Starch, proteins and peptides, DNA, and RNA are all examples of biopolymers, in which the monomer units, respectively, are sugars, amino acids, and nucleic acids.A major but defining difference between polymers and biopolymers can be found in their structures. Polymers, including biopolymers, are made of repetitive units called monomers. Biopolymers inherently have a well defined structure: The exact chemical composition and the sequence in which these units are arranged is called the primary structure. Many biopolymers spontaneously fold into characteristic compact shapes (see also "protein folding" as well as secondary structure and tertiary structure), which determine their biological functions and depend in a complicated way on their primary structures. Structural biology is the study of the structural properties of the biopolymers. In contrast most synthetic polymers have much simpler and more random (or statistic) structures. This book presents leading-edge research from around the world in this dynamic field.
Download or read book Molecular Modeling of Polymers written by Gregory C. Rutledge and published by John Wiley & Sons. This book was released on 1998 with total page 134 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Structure and Dynamics of Biopolymers written by C. Nicolini and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 275 pages. Available in PDF, EPUB and Kindle. Book excerpt: This NATO-ASI on BIOPOLYMERS STRUCTURE AND DYNAMICS held between 22nd June 4th July 1986 at Erice (Italy) has brought together scientists from a broad variety of biophysical disciplines - polymer physics, biophysics and physical chemistry, structure and dynamics of polynucleotides, proteins, and polysaccharides - to present the current state of knowledge in their fields, both experimental and theoretical. This Advanced Study Institute was indeed a successfull attempt to enhance the possibility of intersection of a number of research lines that currently are progressing well but are still running largely in parallel with one another: protein folding, single-polymer phase transitions, DNA condensation into liquid crystalline-like arrays, packaging in viruses, and polysaccharide gel formation. Although each phenomenon is distinctive, an awareness of similarities may lead to new ic;leas. The program has emphasized "condensed" forms of biopolymers. We are universally confronted in biology by chain polymers folded on themselves or interlinked in gel-like assemblies, whether we look at the native structure of proteins, the role of polysaccharides in connective tissue, or the genetic apparatus. A number of lectures have been devoted to condensed forms of DNA - closed circular supercoils, toruses, chromatin.
Download or read book Modern Methods for Theoretical Physical Chemistry of Biopolymers written by Evgeni Starikov and published by Elsevier. This book was released on 2011-08-11 with total page 605 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modern Methods for Theoretical Physical Chemistry of Biopolymers provides an interesting selection of contributions from an international team of researchers in theoretical chemistry. This book is extremely useful for tackling the complicated scientific problems connected with biopolymers' physics and chemistry. The applications of both the classical molecular-mechanical and molecular-dynamical methods and the quantum chemical methods needed for bridging the gap to structural and dynamical properties dependent on electron dynamics are explained. Also included are ways to deal with complex problems when all three approaches need to be considered at the same time. The book gives a rich spectrum of applications: from theoretical considerations of how ATP is produced and used as ‘energy currency’ in the living cell, to the effects of subtle solvent influence on properties of biopolymers and how structural changes in DNA during single-molecule manipulation may be interpreted. · Presents modern successes and trends in theoretical physical chemistry/chemical physics of biopolymers · Topics covered are of relevant importance to rapidly developing areas in science such as nanotechnology and molecular medicine · Quality selection of contributions from renowned scientists in the field
Download or read book Molecular Dynamics of Additives in Polymers written by Aleksandr Lʹvovich Kovarskiĭ and published by CRC Press. This book was released on 1997 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume focuses on the dynamical behaviour of low-molecular additives in solid polymer matrixes. It covers: types and models of molecular motion in condensed media; dependence of motional frequency on particle structure and size, temperature, volume and stress; and polymer properties and polymeric structures. Extensive analysis of common regularities of rotational and translational dynamics of molecules introduced into polymers are given. The book also includes experimental techniques for molecular mobility evaluation, and features detailed data on rotational dynamics of additives. It should be of interest to specialists in various fields of polymer physical chemistry and materials science.
Download or read book Monte Carlo and Molecular Dynamics Simulations in Polymer Science written by Kurt Binder and published by Oxford University Press. This book was released on 1995-08-03 with total page 602 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by leading experts from around the world, Monte Carlo and Molecular Dynamics Simulations in Polymer Science comprehensively reviews the latest simulation techniques for macromolecular materials. Focusing in particular on numerous new techniques, the book offers authoritative introductions to solutions of neutral polymers and polyelectrolytes; dynamics of polymer melts, rubbers and gels, and glassy materials; thermodynamics of polymer mixing and mesophase formation, and polymers confined at interfaces and grafted to walls. Throughout, contributors offer practical advice on how to overcome the unique challenges posed by the large size and slow relaxation of polymer coils. Students and researchers in polymer chemistry, polymer physics, chemical engineering, and materials and computational science will all benefit from the cogent, step-by-step introductions contained in this important new book.
Download or read book Predicting Structure property Relationships in Polymers Through the Development of Thermodynamically Consistent Coarse grained Molecular Models written by Vipin Agrawal and published by . This book was released on 2016 with total page 120 pages. Available in PDF, EPUB and Kindle. Book excerpt: Improved knowledge connecting the chemistry, structure, and properties of polymers is necessary to develop advanced materials in a materials-by-design approach. Molecular dynamics (MD) simulations can provide tremendous insight into how the fine details of chemistry, molecular architecture, and microstructure affect many physical properties; however, they face well-known restrictions in their applicable temporal and spatial scales. These limitations have motivated the development of computationally-efficient, coarse-grained methods to investigate how microstructural details affect thermophysical properties. In this dissertation, I summarize my research work in structure-based coarse-graining methods to establish the link between molecular-scale structure and macroscopic properties of two different polymers. Systematically coarse-grained models were developed to study the viscoelastic stress response of polyurea, a copolymer that segregates into rigid and viscous phases, at time scales characteristic of blast and impact loading. With the application of appropriate scaling parameters, the coarse-grained models can predict viscoelastic properties with a speed up of 5-6 orders of magnitude relative to the atomistic MD models. Coarse-grained models of polyethylene were also created to investigate the thermomechanical material response under shock loading. As structure-based coarse-grained methods are generally not transferable to states different from which they were calibrated at, their applicability for modeling non-equilibrium processes such as shock and impact is highly limited. To address this problem, a new model is developed that incorporates many-body interactions and is calibrated across a range of different thermodynamic states using a least square minimization scheme. The new model is validated by comparing shock Hugoniot properties with atomistic and experimental data for polyethylene. Lastly, a high fidelity coarse-grained model of polyethylene was constructed that reproduces the joint-probability distributions of structural variables such as the distributions of bond lengths and bond angles between sequential coarse-grained sites along polymer chains. This new model accurately represents the structure of both the amorphous and crystal phases of polyethylene and enabling investigation of how polymer processing such as cold-drawing and bulk crystallization affect material structure at significantly larger time and length scales than traditional molecular simulations.
Download or read book Molecular Modeling of Polymer Structures and Properties written by Bruce R. Gelin and published by Hanser Gardner Publications. This book was released on 1994-01-01 with total page 168 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an introduction to the techniques of molecular modeling and simulation with practical examples.
Download or read book Structure and Dynamics of Biopolymers written by C Nicolini and published by . This book was released on 1987-06-30 with total page 284 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Structure and Properties of Polymers written by Robert W. Cahn and published by Wiley-VCH. This book was released on 1993 with total page 812 pages. Available in PDF, EPUB and Kindle. Book excerpt: V. 12. Structure and properties of polymers.
