Coarse Grained Modelling Of Dna And Dna Self Assembly
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Coarse Grained Modelling Of Dna And Dna Self Assembly
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Author : Thomas E. Ouldridge
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-07-09
Coarse Grained Modelling Of Dna And Dna Self Assembly written by Thomas E. Ouldridge and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-07-09 with Science categories.
This thesis presents a novel coarse-grained model of DNA, in which bases are represented as rigid nucleotides. The model is shown to quantitatively reproduce many phenomena, including elastic properties of the double-stranded state, hairpin formation in single strands and hybridization of pairs of strands to form duplexes, the first time such a wide range of properties has been captured by a coarse-grained model. The scope and potential of the model is demonstrated by simulating DNA tweezers, an iconic nanodevice, and a two-footed DNA walker — the first time that coarse-grained modelling has been applied to dynamic DNA nanotechnology.
Dna Systems Under Internal And External Forcing
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Author : Megan Clare Engel
language : en
Publisher: Springer Nature
Release Date : 2019-09-17
Dna Systems Under Internal And External Forcing written by Megan Clare Engel and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-09-17 with Science categories.
The interactions of DNA with force are central to manifold fields of inquiry, including the de novo design of DNA nanostructures, the use of DNA to probe the principles of biological self-assembly, and the operation of cellular nanomachines. This work presents a survey of three distinct ways coarse-grained simulations can help characterize these interactions. A non-equilibrium energy landscape reconstruction technique is validated for use with the oxDNA model and a practical framework to guide future applications is established. A novel method for calculating entropic forces in DNA molecules is outlined and contrasted with existing, flawed approaches. Finally, a joint experimental-simulation study of large DNA origami nanostructures under force sheds light on design principles and, through vivid illustrations, their unfolding process. This text provides an accessible and exciting launching point for any student interested in the computational study of DNA mechanics and force interactions.
Coarse Grained Modeling Of Biomolecules
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Author : Garegin A. Papoian
language : en
Publisher: CRC Press
Release Date : 2017-10-30
Coarse Grained Modeling Of Biomolecules written by Garegin A. Papoian and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-10-30 with Science categories.
"The chapters in this book survey the progress in simulating biomolecular dynamics.... The images conjured up by this work are not yet universally loved, but are beginning to bring new insights into the study of biological structure and function. The future will decide whether this scientific movement can bring forth its Picasso or Modigliani." –from the Foreword by Peter G. Wolynes, Bullard-Welch Foundation Professor of Science, Rice University This book highlights the state-of-art in coarse-grained modeling of biomolecules, covering both fundamentals as well as various cutting edge applications. Coarse-graining of biomolecules is an area of rapid advances, with numerous new force fields having appeared recently and significant progress made in developing a systematic theory of coarse-graining. The contents start with first fundamental principles based on physics, then survey specific state-of-art coarse-grained force fields of proteins and nucleic acids, and provide examples of exciting biological problems that are at large scale, and hence, only amenable to coarse-grained modeling. Introduces coarse-grained models of proteins and nucleic acids. Showcases applications such as genome packaging in nuclei and understanding ribosome dynamics Gives the physical foundations of coarse-graining Demonstrates use of models for large-scale assemblies in modern studies Garegin A. Papoian is the first Monroe Martin Associate Professor with appointments in the Department of Chemistry and Biochemistry and the Institute for Physical Science and Technology at the University of Maryland.
Self Assembly Of Nano And Micro Structured Materials Using Colloidal Engineering
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Author : Dwaipayan Chakrabarti
language : en
Publisher: Elsevier
Release Date : 2019-04-25
Self Assembly Of Nano And Micro Structured Materials Using Colloidal Engineering written by Dwaipayan Chakrabarti and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-04-25 with Science categories.
Self-assembly of Nano- and Micro-structured Materials Using Colloidal Engineering, Volume 12, covers the recent breakthroughs in the design and manufacture of functional colloids at the micro- and nanoscale level. In addition, it provides analyses on how these functionalities can be exploited to develop self-assembly pathways towards nano- and micro-structured materials. As we seek increasingly complex functions for colloidal superstructures, in silico design will play a critical role in guiding experimental fabrication by reducing the element of trial-and-error that would otherwise be involved. In addition to novel experimental approaches, recent developments in computational modelling are also presented, along with an overview of the arsenal of designing tools that are available to the modern materials scientist. Focuses on promoting feedback between experiment, theory and computation in this cross-disciplinary research area Shows how colloid science plays a crucial role in the bottom-up fabrication of nanostructured materials Presents recent developments in computational modelling
Self Assembly
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Author : Ramanathan Nagarajan
language : en
Publisher: John Wiley & Sons
Release Date : 2019-01-07
Self Assembly written by Ramanathan Nagarajan 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 2019-01-07 with Science categories.
An introduction to the state-of-the-art of the diverse self-assembly systems Self-Assembly: From Surfactants to Nanoparticles provides an effective entry for new researchers into this exciting field while also giving the state of the art assessment of the diverse self-assembling systems for those already engaged in this research. Over the last twenty years, self-assembly has emerged as a distinct science/technology field, going well beyond the classical surfactant and block copolymer molecules, and encompassing much larger and complex molecular, biomolecular and nanoparticle systems. Within its ten chapters, each contributed by pioneers of the respective research topics, the book: Discusses the fundamental physical chemical principles that govern the formation and properties of self-assembled systems Describes important experimental techniques to characterize the properties of self-assembled systems, particularly the nature of molecular organization and structure at the nano, meso or micro scales. Provides the first exhaustive accounting of self-assembly derived from various kinds of biomolecules including peptides, DNA and proteins. Outlines methods of synthesis and functionalization of self-assembled nanoparticles and the further self-assembly of the nanoparticles into one, two or three dimensional materials. Explores numerous potential applications of self-assembled structures including nanomedicine applications of drug delivery, imaging, molecular diagnostics and theranostics, and design of materials to specification such as smart responsive materials and self-healing materials. Highlights the unifying as well as contrasting features of self-assembly, as we move from surfactant molecules to nanoparticles. Written for students and academic and industrial scientists and engineers, by pioneers of the research field, Self-Assembly: From Surfactants to Nanoparticles is a comprehensive resource on diverse self-assembly systems, that is simultaneously introductory as well as the state of the art.
The 15th International Conference On Biomedical Engineering
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Author : James Goh
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-11-18
The 15th International Conference On Biomedical Engineering written by James Goh and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-11-18 with Technology & Engineering categories.
This volume presents the processing of the 15th ICMBE held from 4th to 7th December 2013, Singapore. Biomedical engineering is applied in most aspects of our healthcare ecosystem. From electronic health records to diagnostic tools to therapeutic, rehabilitative and regenerative treatments, the work of biomedical engineers is evident. Biomedical engineers work at the intersection of engineering, life sciences and healthcare. The engineers would use principles from applied science including mechanical, electrical, chemical and computer engineering together with physical sciences including physics, chemistry and mathematics to apply them to biology and medicine. Applying such concepts to the human body is very much the same concepts that go into building and programming a machine. The goal is to better understand, replace or fix a target system to ultimately improve the quality of healthcare. With this understanding, the conference proceedings offer a single platform for individuals and organizations working in the biomedical engineering related field to gather and network with each other in so doing create the catalyst for future development of biomedical engineering in Asia.
Foundations Of Molecular Modeling And Simulation
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Author : Edward J. Maginn
language : en
Publisher: Springer Nature
Release Date : 2021-03-25
Foundations Of Molecular Modeling And Simulation written by Edward J. Maginn and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-03-25 with Science categories.
This highly informative and carefully presented book comprises select proceedings of Foundation for Molecular Modelling and Simulation (FOMMS 2018). The contents are written by invited speakers centered on the theme Innovation for Complex Systems. It showcases new developments and applications of computational quantum chemistry, statistical mechanics, molecular simulation and theory, and continuum and engineering process simulation. This volume will serve as a useful reference to researchers, academicians and practitioners alike.
Dna Computing And Molecular Programming
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Author : Darko Stefanovic
language : en
Publisher: Springer
Release Date : 2012-07-25
Dna Computing And Molecular Programming written by Darko Stefanovic and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-07-25 with Computers categories.
This book constitutes the refereed proceedings of the 18th International Conference on DNA Computing and Molecular Programming, DNA 18, held in Aarhus, Denmark, in August 2012. The 11 full papers presented were carefully selected from 37 submissions. The papers are organized in topical sections on advancing the engineering and science of biology and chemistry from the point of view of computer science, physics, and mathematics.
Dna And Rna Origami
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Author : Julián Valero
language : en
Publisher: Springer Nature
Release Date : 2023-05-11
Dna And Rna Origami written by Julián Valero and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-05-11 with Medical categories.
This volume detials diverse methodological approaches on the assembly and applications of DNA origami assemblies. Chapters guide readers through different synthetic and computational methods, isolation and structural characterization of 2D and 3D DNA origami nanoarchitectures, nanophotonics, drug delivery, biophysics, and synthetic biology.Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, DNA and RNA Origami: Methods and Protocols aims to serve as a guideline describing the current state-of-the-art assembly methodologies and applications of DNA origami nanostructures.
Dna Origami
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Author : Masayuki Endo
language : en
Publisher: John Wiley & Sons
Release Date : 2022-05-05
Dna Origami written by Masayuki Endo 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 2022-05-05 with Technology & Engineering categories.
DNA ORIGAMI Discover the impact and multidisciplinary applications of this subfield of DNA nanotechnology DNA origami refers to the technique of assembling single-stranded DNA template molecules into target two- and three-dimensional shapes at the nanoscale. This is accomplished by annealing templates with hundreds of DNA strands and then binding them through the specific base-pairing of complementary bases. The inherent properties of these DNA molecules—molecular recognition, self-assembly, programmability, and structural predictability—has given rise to intriguing applications from drug delivery systems to uses in circuitry in plasmonic devices. The first book to examine this important subfield, DNA Origami brings together leading experts from all fields to explain the current state and future directions of this cutting-edge avenue of study. The book begins by providing a detailed examination of structural design and assembly systems and their applications. As DNA origami technology is growing in popularity in the disciplines of chemistry, materials science, physics, biophysics, biology, and medicine, interdisciplinary studies are classified and discussed in detail. In particular, the book focuses on DNA origami used for creating new functional materials (combining chemistry and materials science; DNA origami for single-molecule analysis and measurements (as applied in physics and biophysics); and DNA origami for biological detection, diagnosis and therapeutics (medical and biological applications). DNA Origami readers will also find: A complete guide for newcomers that brings together fundamental and developmental aspects of DNA origami technology Contributions by a leading team of experts that bring expert views from different angles of the structural developments and applications of DNA origami An emerging and impactful research topic that will be of interest in numerous multidisciplinary areas A helpful list of references provided at the end of each chapter to give avenues for further study Given the wide scope found in this groundbreaking work, DNA Origami is a perfect resource for nanotechnologists, biologists, biophysicists, chemists, materials scientists, medical scientists, and pharmaceutical researchers.