An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation

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Publisher : Springer Science & Business Media
ISBN 13 : 9400776063
Total Pages : 148 pages
Book Rating : 4.4/5 (7 download)

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Book Synopsis An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation by : Gregory R. Bowman

Download or read book An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation written by Gregory R. Bowman and published by Springer Science & Business Media. This book was released on 2013-12-02 with total page 148 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim of this book volume is to explain the importance of Markov state models to molecular simulation, how they work, and how they can be applied to a range of problems. The Markov state model (MSM) approach aims to address two key challenges of molecular simulation: 1) How to reach long timescales using short simulations of detailed molecular models. 2) How to systematically gain insight from the resulting sea of data. MSMs do this by providing a compact representation of the vast conformational space available to biomolecules by decomposing it into states sets of rapidly interconverting conformations and the rates of transitioning between states. This kinetic definition allows one to easily vary the temporal and spatial resolution of an MSM from high-resolution models capable of quantitative agreement with (or prediction of) experiment to low-resolution models that facilitate understanding. Additionally, MSMs facilitate the calculation of quantities that are difficult to obtain from more direct MD analyses, such as the ensemble of transition pathways. This book introduces the mathematical foundations of Markov models, how they can be used to analyze simulations and drive efficient simulations, and some of the insights these models have yielded in a variety of applications of molecular simulation.

Molecular Biology of the Cell

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Publisher :
ISBN 13 : 9780815332183
Total Pages : 0 pages
Book Rating : 4.3/5 (321 download)

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Book Synopsis Molecular Biology of the Cell by :

Download or read book Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Nucleic Acids

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Publisher : Sterling Publishing Company
ISBN 13 : 9780935702491
Total Pages : 854 pages
Book Rating : 4.7/5 (24 download)

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Book Synopsis Nucleic Acids by : Victor A. Bloomfield

Download or read book Nucleic Acids written by Victor A. Bloomfield and published by Sterling Publishing Company. This book was released on 2000-04-17 with total page 854 pages. Available in PDF, EPUB and Kindle. Book excerpt: Providing a comprehensive account of the structures and physical chemistry properties of nucleic acids, with special emphasis on biological function, this text has been organized to meet the needs of those who have only a basic understanding of physical chemistry and molecular biology.

Biology for AP ® Courses

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Publisher :
ISBN 13 : 9781947172401
Total Pages : 1923 pages
Book Rating : 4.1/5 (724 download)

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Book Synopsis Biology for AP ® Courses by : Julianne Zedalis

Download or read book Biology for AP ® Courses written by Julianne Zedalis and published by . This book was released on 2017-10-16 with total page 1923 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biology for AP® courses covers the scope and sequence requirements of a typical two-semester Advanced Placement® biology course. The text provides comprehensive coverage of foundational research and core biology concepts through an evolutionary lens. Biology for AP® Courses was designed to meet and exceed the requirements of the College Board’s AP® Biology framework while allowing significant flexibility for instructors. Each section of the book includes an introduction based on the AP® curriculum and includes rich features that engage students in scientific practice and AP® test preparation; it also highlights careers and research opportunities in biological sciences.

RNA Exosome

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Publisher : Springer Science & Business Media
ISBN 13 : 1441978410
Total Pages : 161 pages
Book Rating : 4.4/5 (419 download)

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Book Synopsis RNA Exosome by : Torben Heick Jensen

Download or read book RNA Exosome written by Torben Heick Jensen and published by Springer Science & Business Media. This book was released on 2011-06-29 with total page 161 pages. Available in PDF, EPUB and Kindle. Book excerpt: The diversity of RNAs inside living cells is amazing. We have known of the more “classic” RNA species: mRNA, tRNA, rRNA, snRNA and snoRNA for some time now, but in a steady stream new types of molecules are being described as it is becoming clear that most of the genomic information of cells ends up in RNA. To deal with the enormous load of resulting RNA processing and degradation reactions, cells need adequate and efficient molecular machines. The RNA exosome is arising as a major facilitator to this effect. Structural and functional data gathered over the last decade have illustrated the biochemical importance of this multimeric complex and its many co-factors, revealing its enormous regulatory power. By gathering some of the most prominent researchers in the exosome field, it is the aim of this volume to introduce this fascinating protein complex as well as to give a timely and rich account of its many functions. The exosome was discovered more than a decade ago by Phil Mitchell and David Tollervey by its ability to trim the 3’end of yeast, S. cerevisiae, 5. 8S rRNA. In a historic account they laid out the events surrounding this identification and the subsequent birth of the research field. In the chapter by Kurt Januszyk and Christopher Lima the structural organization of eukaryotic exosomes and their evolutionary counterparts in bacteria and archaea are discussed in large part through presentation of structures.

The Nucleosome

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Publisher : Elsevier
ISBN 13 : 0080537847
Total Pages : 265 pages
Book Rating : 4.0/5 (85 download)

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Book Synopsis The Nucleosome by : A.P. Wolffe

Download or read book The Nucleosome written by A.P. Wolffe and published by Elsevier. This book was released on 1996-01-08 with total page 265 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the first in a series of volumes concerning the properties of the eukaryotic nucleus. Contributions from several of the most active laboratories are brought together to present a focused overview of a selected aspect of nuclear structure and function.

Transcription and Splicing

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Publisher : Oxford University Press, USA
ISBN 13 :
Total Pages : 238 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis Transcription and Splicing by : B. D. Hames

Download or read book Transcription and Splicing written by B. D. Hames and published by Oxford University Press, USA. This book was released on 1988 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book gives a co-ordinated review of our present knowledge of eukaryotic RNA synthesis.

Human Herpesviruses

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Publisher : Cambridge University Press
ISBN 13 : 1139461648
Total Pages : 1325 pages
Book Rating : 4.1/5 (394 download)

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Book Synopsis Human Herpesviruses by : Ann Arvin

Download or read book Human Herpesviruses written by Ann Arvin and published by Cambridge University Press. This book was released on 2007-08-16 with total page 1325 pages. Available in PDF, EPUB and Kindle. Book excerpt: This comprehensive account of the human herpesviruses provides an encyclopedic overview of their basic virology and clinical manifestations. This group of viruses includes human simplex type 1 and 2, Epstein–Barr virus, Kaposi's Sarcoma-associated herpesvirus, cytomegalovirus, HHV6A, 6B and 7, and varicella-zoster virus. The viral diseases and cancers they cause are significant and often recurrent. Their prevalence in the developed world accounts for a major burden of disease, and as a result there is a great deal of research into the pathophysiology of infection and immunobiology. Another important area covered within this volume concerns antiviral therapy and the development of vaccines. All these aspects are covered in depth, both scientifically and in terms of clinical guidelines for patient care. The text is illustrated generously throughout and is fully referenced to the latest research and developments.

Cell Biology by the Numbers

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Publisher : Garland Science
ISBN 13 : 1317230698
Total Pages : 400 pages
Book Rating : 4.3/5 (172 download)

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Book Synopsis Cell Biology by the Numbers by : Ron Milo

Download or read book Cell Biology by the Numbers written by Ron Milo and published by Garland Science. This book was released on 2015-12-07 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: A Top 25 CHOICE 2016 Title, and recipient of the CHOICE Outstanding Academic Title (OAT) Award. How much energy is released in ATP hydrolysis? How many mRNAs are in a cell? How genetically similar are two random people? What is faster, transcription or translation?Cell Biology by the Numbers explores these questions and dozens of others provid

Gene Quantification

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Publisher : Springer Science & Business Media
ISBN 13 : 1461241642
Total Pages : 379 pages
Book Rating : 4.4/5 (612 download)

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Book Synopsis Gene Quantification by : Francois Ferre

Download or read book Gene Quantification written by Francois Ferre and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 379 pages. Available in PDF, EPUB and Kindle. Book excerpt: Geneticists and molecular biologists have been interested in quantifying genes and their products for many years and for various reasons (Bishop, 1974). Early molecular methods were based on molecular hybridization, and were devised shortly after Marmur and Doty (1961) first showed that denaturation of the double helix could be reversed - that the process of molecular reassociation was exquisitely sequence dependent. Gillespie and Spiegelman (1965) developed a way of using the method to titrate the number of copies of a probe within a target sequence in which the target sequence was fixed to a membrane support prior to hybridization with the probe - typically a RNA. Thus, this was a precursor to many of the methods still in use, and indeed under development, today. Early examples of the application of these methods included the measurement of the copy numbers in gene families such as the ribosomal genes and the immunoglo bulin family. Amplification of genes in tumors and in response to drug treatment was discovered by this method. In the same period, methods were invented for estimating gene num bers based on the kinetics of the reassociation process - the so-called Cot analysis. This method, which exploits the dependence of the rate of reassociation on the concentration of the two strands, revealed the presence of repeated sequences in the DNA of higher eukaryotes (Britten and Kohne, 1968). An adaptation to RNA, Rot analysis (Melli and Bishop, 1969), was used to measure the abundance of RNAs in a mixed population.

Protein Conformational Dynamics

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Publisher : Springer Science & Business Media
ISBN 13 : 3319029703
Total Pages : 488 pages
Book Rating : 4.3/5 (19 download)

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Book Synopsis Protein Conformational Dynamics by : Ke-li Han

Download or read book Protein Conformational Dynamics written by Ke-li Han and published by Springer Science & Business Media. This book was released on 2014-01-20 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression. On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. These studies greatly enrich our knowledge of the interplay between structure and function. On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). New developments in computational simulations will greatly enhance our understanding of how these molecules function in various biological events.

Principles of Biology

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Publisher :
ISBN 13 : 9781636350417
Total Pages : pages
Book Rating : 4.3/5 (54 download)

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Book Synopsis Principles of Biology by : Lisa Bartee

Download or read book Principles of Biology written by Lisa Bartee and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The Principles of Biology sequence (BI 211, 212 and 213) introduces biology as a scientific discipline for students planning to major in biology and other science disciplines. Laboratories and classroom activities introduce techniques used to study biological processes and provide opportunities for students to develop their ability to conduct research.

Epigenetics: Development and Disease

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Publisher : Springer Science & Business Media
ISBN 13 : 9400745257
Total Pages : 698 pages
Book Rating : 4.4/5 (7 download)

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Book Synopsis Epigenetics: Development and Disease by : Tapas Kumar Kundu

Download or read book Epigenetics: Development and Disease written by Tapas Kumar Kundu and published by Springer Science & Business Media. This book was released on 2012-11-13 with total page 698 pages. Available in PDF, EPUB and Kindle. Book excerpt: Epigenetics fine-tunes the life processes dictated by DNA sequences, but also kick-starts pathophysiological processes including diabetes, AIDS and cancer. This volume tracks the latest research on epigenetics, including work on new-generation therapeutics.

Regulation of Alternative Splicing

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Publisher : Springer Science & Business Media
ISBN 13 : 9783540438335
Total Pages : 272 pages
Book Rating : 4.4/5 (383 download)

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Book Synopsis Regulation of Alternative Splicing by : Philippe Jeanteur

Download or read book Regulation of Alternative Splicing written by Philippe Jeanteur and published by Springer Science & Business Media. This book was released on 2002-10-21 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: The discovery in 1977 that genes are split into exons and introns has done away with the one gene - one protein dogma. Indeed, the removal of introns from the primary RNA transcript is not necessarily straightforward since there may be optional pathways leading to different messenger RNAs and consequently to different proteins. Examples of such an alternative splicing mechanism cover all fields of biology. Moreover, there are plenty of occurrences where deviant splicing can have pathological effects. Despite the high number of specific cases of alternative splicing, it was not until recently that the generality and extent of this phenomenon was fully appreciated. A superficial reading of the preliminary sequence of the human genome published in 2001 led to the surprising, and even deceiving to many scientists, low number of genes (around 32,000) which contrasted with the much higher figure around 150,000 which was previously envisioned. Attempts to make a global assessment of the use of alternative splicing are recent and rely essentially on the comparison of genomic mRNA and EST sequences as reviewed by Thanaraj and Stamm in the first chapter of this volume. Most recent estimates suggest that 40-60% of human genes might be alternatively spliced, as opposed to about 22% for C. elegans.

RNA Polymerase III Transcription

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Publisher : Springer Science & Business Media
ISBN 13 : 3662035189
Total Pages : 274 pages
Book Rating : 4.6/5 (62 download)

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Book Synopsis RNA Polymerase III Transcription by : Robert J. White

Download or read book RNA Polymerase III Transcription written by Robert J. White and published by Springer Science & Business Media. This book was released on 2013-11-11 with total page 274 pages. Available in PDF, EPUB and Kindle. Book excerpt: This monograph reviews and summarizes the substantial body of work that has been published on the transcription by polymerase III over the past 5 years. Progress in this field has been very rapid since 1993, and this new edition incorporates all the recent developments and offers the reader a highly detailed analysis of the current state of research on this largest and most complex of the eukaryotic RNA polymerases.

Gene Regulation in Eukaryotes

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Publisher : Wiley-Blackwell
ISBN 13 :
Total Pages : 452 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis Gene Regulation in Eukaryotes by : Edgar Wingender

Download or read book Gene Regulation in Eukaryotes written by Edgar Wingender and published by Wiley-Blackwell. This book was released on 1993 with total page 452 pages. Available in PDF, EPUB and Kindle. Book excerpt: A much-needed guide through the overwhelming amount of literature in the field. Comprehensive and detailed, this book combines background information with the most recentinsights. It introduces current concepts, emphasizing the transcriptional control of genetic information. Moreover, it links data on the structure of regulatory proteins with basic cellular processes. Both advanced students and experts will find answers to such intriguing questions as: - How are programs of specific gene repertoires activated and controlled? - Which genes drive and control morphogenesis? - Which genes govern tissue-specific tasks? - How do hormones control gene expression in coordinating the activities of different tissues? An abundant number of clearly presented glossary terms facilitates understanding of the biological background. Speacial feature: over 2200 (!) literature references.

Human Dna Polymerases: Biology, Medicine And Biotechnology

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Publisher : World Scientific
ISBN 13 : 9813226420
Total Pages : 398 pages
Book Rating : 4.8/5 (132 download)

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Book Synopsis Human Dna Polymerases: Biology, Medicine And Biotechnology by : Giovanni Maga

Download or read book Human Dna Polymerases: Biology, Medicine And Biotechnology written by Giovanni Maga and published by World Scientific. This book was released on 2017-11-10 with total page 398 pages. Available in PDF, EPUB and Kindle. Book excerpt: Maintenance of the information embedded in the genomic DNA sequence is essential for life. DNA polymerases play pivotal roles in the complex processes that maintain genetic integrity. Besides their tasks in vivo, DNA polymerases are the workhorses in numerous biotechnology applications such as the polymerase chain reaction (PCR), cDNA cloning, next generation sequencing, nucleic acids based diagnostics and in techniques to analyze ancient and otherwise damaged DNA (e.g. for forensic applications). Moreover, some diseases are related to DNA polymerase defects and chemotherapy through inhibition of DNA polymerases is used to fight HIV, Herpes and Hepatitis B and C infections. This book focuses on (i) biology of DNA polymerases, (ii) medical aspects of DNA polymerases and (iii) biotechnological applications of DNA polymerases. It is intended for a wide audience from basic scientists, to diagnostic laboratories, to companies and to clinicians, who seek a better understanding and the practical use of these fascinating enzymes.