Molecular Dynamics Studies of Peptide, Nanoparticle, and Lipid Interactions Using Multiscale Simulations PDF Download
Are you looking for read ebook online? Search for your book and save it on your Kindle device, PC, phones or tablets. Download Molecular Dynamics Studies of Peptide, Nanoparticle, and Lipid Interactions Using Multiscale Simulations PDF full book. Access full book title Molecular Dynamics Studies of Peptide, Nanoparticle, and Lipid Interactions Using Multiscale Simulations by Hwan Kyu Lee. Download full books in PDF and EPUB format.
Author: Hwan Kyu Lee
Publisher:
ISBN:
Category :
Languages : en
Pages : 358
Get Book Here
Book Description
Author: Hwan Kyu Lee
Publisher:
ISBN:
Category :
Languages : en
Pages : 358
Get Book Here
Book Description
Author: Lichang Wang
Publisher: BoD – Books on Demand
ISBN: 9535104438
Category : Mathematics
Languages : en
Pages : 440
Get Book Here
Book Description
Molecular Dynamics is a two-volume compendium of the ever-growing applications of molecular dynamics simulations to solve a wider range of scientific and engineering challenges. The contents illustrate the rapid progress on molecular dynamics simulations in many fields of science and technology, such as nanotechnology, energy research, and biology, due to the advances of new dynamics theories and the extraordinary power of today's computers. This first book begins with a general description of underlying theories of molecular dynamics simulations and provides extensive coverage of molecular dynamics simulations in nanotechnology and energy. Coverage of this book includes: Recent advances of molecular dynamics theory Formation and evolution of nanoparticles of up to 106 atoms Diffusion and dissociation of gas and liquid molecules on silicon, metal, or metal organic frameworks Conductivity of ionic species in solid oxides Ion solvation in liquid mixtures Nuclear structures
Author: Michael King
Publisher: John Wiley & Sons
ISBN: 047057982X
Category : Science
Languages : en
Pages : 398
Get Book Here
Book Description
Discover how the latest computational tools are building our understanding of particle interactions and leading to new applications With this book as their guide, readers will gain a new appreciation of the critical role that particle interactions play in advancing research and developing new applications in the biological sciences, chemical engineering, toxicology, medicine, and manufacturing technology The book explores particles ranging in size from cations to whole cells to tissues and processed materials. A focus on recreating complex, real-world dynamical systems helps readers gain a deeper understanding of cell and tissue mechanics, theoretical aspects of multiscale modeling, and the latest applications in biology and nanotechnology. Following an introductory chapter, Multiscale Modeling of Particle Interactions is divided into two parts: Part I, Applications in Nanotechnology, covers: Multiscale modeling of nanoscale aggregation phenomena: applications in semiconductor materials processing Multiscale modeling of rare events in self-assembled systems Continuum description of atomic sheets Coulombic dragging and mechanical propelling of molecules in nanofluidic systems Molecular dynamics modeling of nanodroplets and nanoparticles Modeling the interactions between compliant microcapsules and patterned surfaces Part II, Applications in Biology, covers: Coarse-grained and multiscale simulations of lipid bilayers Stochastic approach to biochemical kinetics In silico modeling of angiogenesis at multiple scales Large-scale simulation of blood flow in microvessels Molecular to multicellular deformation during adhesion of immune cells under flow Each article was contributed by one or more leading experts and pioneers in the field. All readers, from chemists and biologists to engineers and students, will gain new insights into how the latest tools in computational science can improve our understanding of particle interactions and support the development of novel applications across the broad spectrum of disciplines in biology and nanotechnology.
Author: Lichang Wang
Publisher: BoD – Books on Demand
ISBN: 9535104446
Category : Computers
Languages : en
Pages : 448
Get Book Here
Book Description
Molecular Dynamics is a two-volume compendium of the ever-growing applications of molecular dynamics simulations to solve a wider range of scientific and engineering challenges. The contents illustrate the rapid progress on molecular dynamics simulations in many fields of science and technology, such as nanotechnology, energy research, and biology, due to the advances of new dynamics theories and the extraordinary power of today's computers. This second book begins with an introduction of molecular dynamics simulations to macromolecules and then illustrates the computer experiments using molecular dynamics simulations in the studies of synthetic and biological macromolecules, plasmas, and nanomachines. Coverage of this book includes: Complex formation and dynamics of polymers Dynamics of lipid bilayers, peptides, DNA, RNA, and proteins Complex liquids and plasmas Dynamics of molecules on surfaces Nanofluidics and nanomachines
Author: Vivek Raut
Publisher:
ISBN:
Category :
Languages : en
Pages : 256
Get Book Here
Book Description
Author: Brian Andrews
Publisher:
ISBN:
Category : Biophysics
Languages : en
Pages : 0
Get Book Here
Book Description
The prevalence of Intrinsically Disordered Proteins (IDPs) in the eukaryotic genome, associated with both physiological function and diseases, provides motivation to effectively characterize these systems. Experimental methods can be limited in their ability to characterize IDPs. Molecular dynamics (MD) simulations can provide details of these systems with atomistic detail. However, the performance of MD simulations is always based on approximations and assumptions of some extent. The reliability of MD simulation results largely depends on the correctness and precision of these assumptions. There are known issues in MD regarding the simulation of IDPs and many of the force fields commonly used for MD simulations are not typically validated for many small, unfolded peptides or IDPs. To this end, Chapter 3 assesses multiple state-of-the-art MD force fields in their capacity to produce the intrinsic backbone dynamics, as characterized by Ramachandran distributions, of 14 of the 20 amino acids as the central amino acid resiude of GxG tripeptides with respect to a comprehensive set of experimental data. An additional study was performed for a select tetra- and pentapeptide, GRRG and GRRRG. Generally, MD force fields do not reproduce amino acid-specific conformational properties or nearest neighbor interactions. A model Ramachandran distribution, constructed using a linear combination of Gaussian subdistributions, were shown to produce experimental results better than MD by at least an order of magnitude. Errors of the dynamics of amino acid residues in short peptides likely proliferates in larger IDPs, effectively limiting the effectiveness of MD for studying disease-related IDPs. Chapter 4 extends the assessment of Chapter 3 to protein-protein interactions. First, the effect of mixed solvent of ethanol and water on GAG peptide aggregates, which surpringly form gels in experiments, is investigated. Then, the ability for MD force fields to capture the solubility of a short, natively folded protein is assessed. Finally, based on the analyses throughout the thesis, the potential physiological function of an IDP associated with Alzheimer's Disease is explored via protein-soluble lipid interactions.
Author: Michael King
Publisher: Wiley
ISBN: 9780470242353
Category : Science
Languages : en
Pages : 388
Get Book Here
Book Description
Discover how the latest computational tools are building our understanding of particle interactions and leading to new applications With this book as their guide, readers will gain a new appreciation of the critical role that particle interactions play in advancing research and developing new applications in the biological sciences, chemical engineering, toxicology, medicine, and manufacturing technology The book explores particles ranging in size from cations to whole cells to tissues and processed materials. A focus on recreating complex, real-world dynamical systems helps readers gain a deeper understanding of cell and tissue mechanics, theoretical aspects of multiscale modeling, and the latest applications in biology and nanotechnology. Following an introductory chapter, Multiscale Modeling of Particle Interactions is divided into two parts: Part I, Applications in Nanotechnology, covers: Multiscale modeling of nanoscale aggregation phenomena: applications in semiconductor materials processing Multiscale modeling of rare events in self-assembled systems Continuum description of atomic sheets Coulombic dragging and mechanical propelling of molecules in nanofluidic systems Molecular dynamics modeling of nanodroplets and nanoparticles Modeling the interactions between compliant microcapsules and patterned surfaces Part II, Applications in Biology, covers: Coarse-grained and multiscale simulations of lipid bilayers Stochastic approach to biochemical kinetics In silico modeling of angiogenesis at multiple scales Large-scale simulation of blood flow in microvessels Molecular to multicellular deformation during adhesion of immune cells under flow Each article was contributed by one or more leading experts and pioneers in the field. All readers, from chemists and biologists to engineers and students, will gain new insights into how the latest tools in computational science can improve our understanding of particle interactions and support the development of novel applications across the broad spectrum of disciplines in biology and nanotechnology.
Author: Lichang Wang
Publisher: IntechOpen
ISBN: 9789535104445
Category : Computers
Languages : en
Pages : 446
Get Book Here
Book Description
Molecular Dynamics is a two-volume compendium of the ever-growing applications of molecular dynamics simulations to solve a wider range of scientific and engineering challenges. The contents illustrate the rapid progress on molecular dynamics simulations in many fields of science and technology, such as nanotechnology, energy research, and biology, due to the advances of new dynamics theories and the extraordinary power of today's computers. This second book begins with an introduction of molecular dynamics simulations to macromolecules and then illustrates the computer experiments using molecular dynamics simulations in the studies of synthetic and biological macromolecules, plasmas, and nanomachines. Coverage of this book includes: Complex formation and dynamics of polymers Dynamics of lipid bilayers, peptides, DNA, RNA, and proteins Complex liquids and plasmas Dynamics of molecules on surfaces Nanofluidics and nanomachines
Author: Paraskevi Gkeka
Publisher:
ISBN:
Category :
Languages : en
Pages : 193
Get Book Here
Book Description
Peptide-membrane interactions play an important role in a number of biological processes, such as antimicrobial defence mechanisms, viral translocation, membrane fusion and functions ofmembrane proteins. In particular, amphipathic [alpha]-helical peptides comprise a large family of membrane-active peptides that could exhibit a broad range of biological activities. A membrane, interacting with an amphipathic [alpha]-helical peptide, may experience a number of possible structural transitions, including stretching, reorganization of lipid molecules, formation of defects, transient and stable pores, formation of vesicles, endo- and pinocytosis and other phenomena. Naturally, theoretical and experimental studies of these interactions have been an intense on-going area of research. However, complete understanding of the relationship between the structure of the peptide and themechanismof interaction it induces, as well asmolecular details of this process, still remain elusive. Lack of this knowledge is a key challenge in our efforts to elucidate some of the biological functions of membrane active peptides or to design peptides with tailored functionalities that can be exploited in drug delivery or antimicrobial strategies. In principle,molecular dynamics is a powerful research tool to study peptide-membrane interactions, which can provide a detailed description of these processes on molecular level. However, a model operating on the appropriate time and length scale is imperative in this description. In this study, we adopt a coarse-grained approach where the accessible simulation time and length scales reach microseconds and tens of nanometers, respectively. Thus, the two key objectives of this study are to validate the applicability of the adopted coarse-grained approach to the study of peptide-membrane interactions and to provide a systematic description of these interactions as a function of peptide structure and surface chemistry. We applied the adopted strategy to a range of peptide systems, whose behaviour has been well established in either experiments or detailed atomistic simulations and outlined the scope and applicability of the coarse-grained model. We generated some useful insights on the relationship between the structure of the peptides and themechanism of peptide-membrane interactions. Particularly interesting results have been obtained for LS3, a membrane spanning peptide, with a propensity to self-assembly into ion-conducting channels. Firstly, we captured, for the first time, the complete process of self-assembly of LS3 into a hexameric ion-conducting channel and explored its properties. The channel has structure of a barrel-stave pore with peptides aligned along the lipid tails. However, we discovered that a shorter version of the peptide leads to a more disordered, less stable structure often classified as a toroidal pore. This link between two types of pores has been established for the first time and opens interesting opportunities in tuning peptide structures for a particular pore-inducing mechanism. We also established that different classes of peptides can be uniquely characterized by the distinct energy profile as they cross the membrane. Finally, we extended this investigation to the internalization mechanisms of more complex entities such as peptide complexes and nanoparticles. Coarse-grained steered molecular dynamics simulations of these model systems are performed and some preliminary results are presented in this thesis. To summarize, in this thesis, we demonstrate that coarse-grained models can be successfully used to underpin peptide interaction and self-assembly processes in the presence of membranes in their full complexity. We believe that these simulations can be used to guide the design of peptides with tailored functionalities for applications such as drug delivery vectors and antimicrobial systems. This study also suggests that coarse-grained simulations can be used as an efficient way to generate initial configurations for more detailed atomistic simulations. These multiscale simulation ideas will be a natural future extension of this work.
Author: Troy Wayne Wymore
Publisher:
ISBN:
Category : Molecular dynamics
Languages : en
Pages : 314
Get Book Here
Book Description
The peptides Substance P and Substance P(Tyr-8) were studied by molecular dynamics (MD) simulations in two membrane mimetic environments, (1) a biphasic solvent cell made up of carbon tetrachloride molecules and water molecules, and (2) an explicit sodium dodecylsulfate (SDS) micelle. MD simulations of adrenocorticotropin (ACTH[1-10]) were also performed in an SDS micelle. It was proposed that these peptides interact with their receptors via a membrane-mediated mechanism. The analysis of the MD simulation includes (1) the peptide's orientation with respect to the membrane mimetic surface, (2) the peptide backbone hydration, hydrogen bonding and secondary structures, (3) sidechain hydrophobicity and location from the micelle center-of-mass, (4) interaction of the peptides with the micelle headgroups, and (5) the dynamics of the peptide backbone. Comparison to experiments carried out in our lab and others is also presented. The MD simulation of a solvated dodecylphosphocholine (DPC) micelle, a commonly used membrane mimetic, was performed. The analysis includes the micelle shape and shape fluctuations, conformational properties of the lipid chains, interaction of the lipids with water molecules, and the dynamics of the lipid chains.
