Mathematical Modeling For Transcription Of Dna With Pausing

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Mathematical Modeling for Transcription of DNA with Pausing

Author : Tamra Lindsey Heberling
Publisher :
ISBN 13 :
Total Pages : 145 pages
Book Rating : 4.:/5 (96 download)

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Book Synopsis Mathematical Modeling for Transcription of DNA with Pausing by : Tamra Lindsey Heberling

Download or read book Mathematical Modeling for Transcription of DNA with Pausing written by Tamra Lindsey Heberling and published by . This book was released on 2016 with total page 145 pages. Available in PDF, EPUB and Kindle. Book excerpt: In fast-transcribing prokaryotic genes, like an rrn gene in Escherichia coli, many RNA polymerases (RNAPs) transcribe the DNA simultaneously. Active elongation of RNAPs is often interrupted by pauses, which has been observed to cause RNAP traffic jams; yet some studies indicate that elongation seems to be faster in the presence of multiple RNAPs than elongation by a single RNAP. We propose that an interaction between RNAPs via the torque produced by RNAP on helically twisted DNA can explain this apparent paradox. We have incorporated the torque mechanism into a stochastic model and simulated transcription both with and without torque. Simulation results illustrate that the torque causes shorter pause durations and fewer collisions between polymerases. Our results suggest that the torsional interaction of RNAPs is an important mechanism in maintaining fast transcription times, and that transcription should be viewed as a cooperative group effort by multiple polymerases. In an effort to further understand transcription, we investigate the Brownian ratchet model for nucleotide translocation. We model elongation as diffusive particle transport in a tilted periodic potential. To incorporate the RNAP pauses, a second periodic potential is added to the first. We present a formula for the mean escape time from a tilted, periodic potential composed of multiple periodic functions as the product of the mean escape time from each individual periodic function. This formula is extended to an arbitrary finite number of periodic functions. Two examples using truncated Fourier series are presented and analyzed.

Multi-scale, Multi-dimension, DNA-based Mathematical Modeling of Gene Expression

Author : Jacqueline M. Dresch
Publisher :
ISBN 13 : 9781267311962
Total Pages : 171 pages
Book Rating : 4.3/5 (119 download)

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Book Synopsis Multi-scale, Multi-dimension, DNA-based Mathematical Modeling of Gene Expression by : Jacqueline M. Dresch

Download or read book Multi-scale, Multi-dimension, DNA-based Mathematical Modeling of Gene Expression written by Jacqueline M. Dresch and published by . This book was released on 2012 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Simple Mathematical Models of Gene Regulatory Dynamics

Author : Michael C. Mackey
Publisher : Springer
ISBN 13 : 3319453181
Total Pages : 128 pages
Book Rating : 4.3/5 (194 download)

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Book Synopsis Simple Mathematical Models of Gene Regulatory Dynamics by : Michael C. Mackey

Download or read book Simple Mathematical Models of Gene Regulatory Dynamics written by Michael C. Mackey and published by Springer. This book was released on 2016-11-09 with total page 128 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is a short and self-contained introduction to the field of mathematical modeling of gene-networks in bacteria. As an entry point to the field, we focus on the analysis of simple gene-network dynamics. The notes commence with an introduction to the deterministic modeling of gene-networks, with extensive reference to applicable results coming from dynamical systems theory. The second part of the notes treats extensively several approaches to the study of gene-network dynamics in the presence of noise—either arising from low numbers of molecules involved, or due to noise external to the regulatory process. The third and final part of the notes gives a detailed treatment of three well studied and concrete examples of gene-network dynamics by considering the lactose operon, the tryptophan operon, and the lysis-lysogeny switch. The notes contain an index for easy location of particular topics as well as an extensive bibliography of the current literature. The target audience of these notes are mainly graduates students and young researchers with a solid mathematical background (calculus, ordinary differential equations, and probability theory at a minimum), as well as with basic notions of biochemistry, cell biology, and molecular biology. They are meant to serve as a readable and brief entry point into a field that is currently highly active, and will allow the reader to grasp the current state of research and so prepare them for defining and tackling new research problems.

Mathematical Modeling and Analysis of Genomic Transcription Assays

Author : Chetan Jayant Gadgil
Publisher :
ISBN 13 :
Total Pages : 434 pages
Book Rating : 4.:/5 (319 download)

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Book Synopsis Mathematical Modeling and Analysis of Genomic Transcription Assays by : Chetan Jayant Gadgil

Download or read book Mathematical Modeling and Analysis of Genomic Transcription Assays written by Chetan Jayant Gadgil and published by . This book was released on 2001 with total page 434 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Stochastic Modeling of Eukaryotic Transcription at the Single Nucleotide Level

Author : Saurabh Vashishtha
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (13 download)

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Book Synopsis Stochastic Modeling of Eukaryotic Transcription at the Single Nucleotide Level by : Saurabh Vashishtha

Download or read book Stochastic Modeling of Eukaryotic Transcription at the Single Nucleotide Level written by Saurabh Vashishtha and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Discontinuous Galerkin Finite Element Method for Simulation of a Transcription Process Model

Author : Jennifer Rae Thorenson
Publisher :
ISBN 13 :
Total Pages : 220 pages
Book Rating : 4.:/5 (868 download)

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Book Synopsis Discontinuous Galerkin Finite Element Method for Simulation of a Transcription Process Model by : Jennifer Rae Thorenson

Download or read book Discontinuous Galerkin Finite Element Method for Simulation of a Transcription Process Model written by Jennifer Rae Thorenson and published by . This book was released on 2013 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt: The classical traffic flow PDE from the 1950s is used to model the biological process of transcription; the process of transferring genetic information from DNA to mRNA, in an E. coli gene. Polymerase elongating along the DNA strand encounter frequent but short pauses which are incorporated into the transcription model as several traffic lights. These pauses result in a delay in the transcription time and a delay function is defined to quantify this effect. Numerical simulations of the PDE model are conducted using a discontinuous Galerkin finite element method (DG) formulation. The entropy satisfying weak solution of the PDE model with a single pause is derived using the method of characteristics. This weak solution is used to show convergence of the DG formulation even though the flux function is not smooth. Once convergence of the DG solution is established for one pause, the numerical simulation for multiple pauses is used to calculate the delay due to the pauses and determine their effect on the overall transcription time. Preliminary parameter studies show a complex relationship between pause location and delay values. To determine the effect of pause clustering on protein production, an ongoing research goal is optimization of the delay function with respect to pause location. For preliminary work on this optimization problem, a DG formulation used to solve a sensitivity equation for a linear hyperbolic PDE with a spatial interface parameter is derived to gain insight for the more complicated nonlinear traffic flow PDE.

Biophysics of RNA-Protein Interactions

Author : Chirlmin Joo
Publisher : Springer Nature
ISBN 13 : 1493997262
Total Pages : 249 pages
Book Rating : 4.4/5 (939 download)

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Book Synopsis Biophysics of RNA-Protein Interactions by : Chirlmin Joo

Download or read book Biophysics of RNA-Protein Interactions written by Chirlmin Joo and published by Springer Nature. This book was released on 2019-09-19 with total page 249 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA molecules play key roles in all aspects of cellular life, but to do so efficiently, they must work in synergism with proteins. This book addresses how proteins and RNA interact to carry out biological functions such as protein synthesis, regulation of gene expression, genome defense, liquid phase separation and more. The topics addressed in this volume will appeal to researchers in biophysics, biochemistry and structural biology. The book is a useful resource for anybody interested in elucidating the molecular mechanisms and discrete properties of RNA-protein complexes. Included are reviews of key systems such as microRNA and CRISPR/Cas that exemplify how RNA and proteins work together to perform their biological function. Also covered are techniques ranging from single molecule fluorescence and force spectroscopy to crystallography, cryo-EM microscopy, and kinetic modeling.

DNA Computing and Molecular Programming

Author : David Doty
Publisher : Springer
ISBN 13 : 3030000303
Total Pages : 221 pages
Book Rating : 4.0/5 (3 download)

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Book Synopsis DNA Computing and Molecular Programming by : David Doty

Download or read book DNA Computing and Molecular Programming written by David Doty and published by Springer. This book was released on 2018-10-01 with total page 221 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 24th International Conference on DNA Computing and Molecular Programming, DNA 24, held in Jinan, China, in October 2018. The 12 full papers presented were carefully selected from 14 submissions. Research in DNA computing aims to draw together mathematics, computer science, physics, chemistry, biology, and nanotechnology to address the analysis, design, and synthesis of information-based molecular systems. The papers were sought in all areas related to biomolecular computing, including: algorithms and models for computation on biomolecular systems; computational processes in vitro and in vivo; molecular switches, gates, devices, and circuits; molecular folding and self-assembly of nanostructures; analysis and theoretical models of laboratory techniques; molecular motors and molecular robotics; information storage; studies of fault tolerance and error correction; software tools for analysis, simulation, and design; synthetic biology and in vitro evolution; and applications in engineering, physics, chemistry, biology, and medicine.

Algebraic and Combinatorial Computational Biology

Author : Raina Robeva
Publisher : Academic Press
ISBN 13 : 0128140690
Total Pages : 434 pages
Book Rating : 4.1/5 (281 download)

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Book Synopsis Algebraic and Combinatorial Computational Biology by : Raina Robeva

Download or read book Algebraic and Combinatorial Computational Biology written by Raina Robeva and published by Academic Press. This book was released on 2018-10-08 with total page 434 pages. Available in PDF, EPUB and Kindle. Book excerpt: Algebraic and Combinatorial Computational Biology introduces students and researchers to a panorama of powerful and current methods for mathematical problem-solving in modern computational biology. Presented in a modular format, each topic introduces the biological foundations of the field, covers specialized mathematical theory, and concludes by highlighting connections with ongoing research, particularly open questions. The work addresses problems from gene regulation, neuroscience, phylogenetics, molecular networks, assembly and folding of biomolecular structures, and the use of clustering methods in biology. A number of these chapters are surveys of new topics that have not been previously compiled into one unified source. These topics were selected because they highlight the use of technique from algebra and combinatorics that are becoming mainstream in the life sciences. Integrates a comprehensive selection of tools from computational biology into educational or research programs Emphasizes practical problem-solving through multiple exercises, projects and spinoff computational simulations Contains scalable material for use in undergraduate and graduate-level classes and research projects Introduces the reader to freely-available professional software Supported by illustrative datasets and adaptable computer code

Genomic Signal Processing

Author : Ilya Shmulevich
Publisher : Princeton University Press
ISBN 13 : 1400865263
Total Pages : 314 pages
Book Rating : 4.4/5 (8 download)

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Book Synopsis Genomic Signal Processing by : Ilya Shmulevich

Download or read book Genomic Signal Processing written by Ilya Shmulevich and published by Princeton University Press. This book was released on 2014-09-08 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genomic signal processing (GSP) can be defined as the analysis, processing, and use of genomic signals to gain biological knowledge, and the translation of that knowledge into systems-based applications that can be used to diagnose and treat genetic diseases. Situated at the crossroads of engineering, biology, mathematics, statistics, and computer science, GSP requires the development of both nonlinear dynamical models that adequately represent genomic regulation, and diagnostic and therapeutic tools based on these models. This book facilitates these developments by providing rigorous mathematical definitions and propositions for the main elements of GSP and by paying attention to the validity of models relative to the data. Ilya Shmulevich and Edward Dougherty cover real-world situations and explain their mathematical modeling in relation to systems biology and systems medicine. Genomic Signal Processing makes a major contribution to computational biology, systems biology, and translational genomics by providing a self-contained explanation of the fundamental mathematical issues facing researchers in four areas: classification, clustering, network modeling, and network intervention.

A Guide to First-Passage Processes

Author : Sidney Redner
Publisher : Cambridge University Press
ISBN 13 : 0521652480
Total Pages : 332 pages
Book Rating : 4.5/5 (216 download)

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Book Synopsis A Guide to First-Passage Processes by : Sidney Redner

Download or read book A Guide to First-Passage Processes written by Sidney Redner and published by Cambridge University Press. This book was released on 2001-08-06 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: The basic theory presented in a way which emphasizes intuition, problem-solving and the connections with other fields.

Modeling Life

Author : Alan Garfinkel
Publisher : Springer
ISBN 13 : 3319597310
Total Pages : 456 pages
Book Rating : 4.3/5 (195 download)

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Book Synopsis Modeling Life by : Alan Garfinkel

Download or read book Modeling Life written by Alan Garfinkel and published by Springer. This book was released on 2017-09-06 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book develops the mathematical tools essential for students in the life sciences to describe interacting systems and predict their behavior. From predator-prey populations in an ecosystem, to hormone regulation within the body, the natural world abounds in dynamical systems that affect us profoundly. Complex feedback relations and counter-intuitive responses are common in nature; this book develops the quantitative skills needed to explore these interactions. Differential equations are the natural mathematical tool for quantifying change, and are the driving force throughout this book. The use of Euler’s method makes nonlinear examples tractable and accessible to a broad spectrum of early-stage undergraduates, thus providing a practical alternative to the procedural approach of a traditional Calculus curriculum. Tools are developed within numerous, relevant examples, with an emphasis on the construction, evaluation, and interpretation of mathematical models throughout. Encountering these concepts in context, students learn not only quantitative techniques, but how to bridge between biological and mathematical ways of thinking. Examples range broadly, exploring the dynamics of neurons and the immune system, through to population dynamics and the Google PageRank algorithm. Each scenario relies only on an interest in the natural world; no biological expertise is assumed of student or instructor. Building on a single prerequisite of Precalculus, the book suits a two-quarter sequence for first or second year undergraduates, and meets the mathematical requirements of medical school entry. The later material provides opportunities for more advanced students in both mathematics and life sciences to revisit theoretical knowledge in a rich, real-world framework. In all cases, the focus is clear: how does the math help us understand the science?

RNA Polymerases as Molecular Motors

Author : Robert Landick
Publisher : Royal Society of Chemistry
ISBN 13 : 1839160667
Total Pages : 295 pages
Book Rating : 4.8/5 (391 download)

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Book Synopsis RNA Polymerases as Molecular Motors by : Robert Landick

Download or read book RNA Polymerases as Molecular Motors written by Robert Landick and published by Royal Society of Chemistry. This book was released on 2021-11-23 with total page 295 pages. Available in PDF, EPUB and Kindle. Book excerpt: To thrive, every living cell must continuously gauge and respond to changes in its environment. These changes are ultimately implemented by modulating gene expression, a process that relies on transcription by Nature’s most multivalent molecular machine, the RNA polymerase. This book covers progress made over the past decade understanding how this machine functions to compute the cellular state, from the atomistic structural level responsible for chemistry to the integrative level at which RNA polymerase interacts with the other key molecular machineries of the cell.

Biological Clocks, Rhythms, and Oscillations

Author : Daniel B. Forger
Publisher : MIT Press
ISBN 13 : 0262552817
Total Pages : 369 pages
Book Rating : 4.2/5 (625 download)

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Book Synopsis Biological Clocks, Rhythms, and Oscillations by : Daniel B. Forger

Download or read book Biological Clocks, Rhythms, and Oscillations written by Daniel B. Forger and published by MIT Press. This book was released on 2024-08-06 with total page 369 pages. Available in PDF, EPUB and Kindle. Book excerpt: An introduction to the mathematical, computational, and analytical techniques used for modeling biological rhythms, presenting tools from many disciplines and example applications. All areas of biology and medicine contain rhythms, and these behaviors are best understood through mathematical tools and techniques. This book offers a survey of mathematical, computational, and analytical techniques used for modeling biological rhythms, gathering these methods for the first time in one volume. Drawing on material from such disciplines as mathematical biology, nonlinear dynamics, physics, statistics, and engineering, it presents practical advice and techniques for studying biological rhythms, with a common language. The chapters proceed with increasing mathematical abstraction. Part I, on models, highlights the implicit assumptions and common pitfalls of modeling, and is accessible to readers with basic knowledge of differential equations and linear algebra. Part II, on behaviors, focuses on simpler models, describing common properties of biological rhythms that range from the firing properties of squid giant axon to human circadian rhythms. Part III, on mathematical techniques, guides readers who have specific models or goals in mind. Sections on “frontiers” present the latest research; “theory” sections present interesting mathematical results using more accessible approaches than can be found elsewhere. Each chapter offers exercises. Commented MATLAB code is provided to help readers get practical experience. The book, by an expert in the field, can be used as a textbook for undergraduate courses in mathematical biology or graduate courses in modeling biological rhythms and as a reference for researchers.

Stochastic Transport in Complex Systems

Author : Andreas Schadschneider
Publisher : Elsevier
ISBN 13 : 0080560520
Total Pages : 585 pages
Book Rating : 4.0/5 (85 download)

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Book Synopsis Stochastic Transport in Complex Systems by : Andreas Schadschneider

Download or read book Stochastic Transport in Complex Systems written by Andreas Schadschneider and published by Elsevier. This book was released on 2010-10-01 with total page 585 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first part of the book provides a pedagogical introduction to the physics of complex systems driven far from equilibrium. In this part we discuss the basic concepts and theoretical techniques which are commonly used to study classical stochastic transport in systems of interacting driven particles. The analytical techniques include mean-field theories, matrix product ansatz, renormalization group, etc. and the numerical methods are mostly based on computer simulations. In the second part of the book these concepts and techniques are applied not only to vehicular traffic but also to transport and traffic-like phenomena in living systems ranging from collective movements of social insects (for example, ants) on trails to intracellular molecular motor transport. These demonstrate the conceptual unity of the fundamental principles underlying the apparent diversity of the systems and the utility of the theoretical toolbox of non-equilibrium statistical mechanics in interdisciplinary research far beyond the traditional disciplinary boundaries of physics. Leading industry experts provide a broad overview of the interdisciplinary nature of physics Presents unified descriptions of intracellular, ant, and vehicular traffic from a physics point of view Applies theoretical methods in practical everyday situations Reference and guide for physicists, engineers and graduate students

Biomolecular Feedback Systems

Author : Domitilla Del Vecchio
Publisher : Princeton University Press
ISBN 13 : 1400850509
Total Pages : 287 pages
Book Rating : 4.4/5 (8 download)

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Book Synopsis Biomolecular Feedback Systems by : Domitilla Del Vecchio

Download or read book Biomolecular Feedback Systems written by Domitilla Del Vecchio and published by Princeton University Press. This book was released on 2014-10-26 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an accessible introduction to the principles and tools for modeling, analyzing, and synthesizing biomolecular systems. It begins with modeling tools such as reaction-rate equations, reduced-order models, stochastic models, and specific models of important core processes. It then describes in detail the control and dynamical systems tools used to analyze these models. These include tools for analyzing stability of equilibria, limit cycles, robustness, and parameter uncertainty. Modeling and analysis techniques are then applied to design examples from both natural systems and synthetic biomolecular circuits. In addition, this comprehensive book addresses the problem of modular composition of synthetic circuits, the tools for analyzing the extent of modularity, and the design techniques for ensuring modular behavior. It also looks at design trade-offs, focusing on perturbations due to noise and competition for shared cellular resources. Featuring numerous exercises and illustrations throughout, Biomolecular Feedback Systems is the ideal textbook for advanced undergraduates and graduate students. For researchers, it can also serve as a self-contained reference on the feedback control techniques that can be applied to biomolecular systems. Provides a user-friendly introduction to essential concepts, tools, and applications Covers the most commonly used modeling methods Addresses the modular design problem for biomolecular systems Uses design examples from both natural systems and synthetic circuits Solutions manual (available only to professors at press.princeton.edu) An online illustration package is available to professors at press.princeton.edu

Handbook of Computational Molecular Biology

Author : Srinivas Aluru
Publisher : CRC Press
ISBN 13 : 1420036270
Total Pages : 1108 pages
Book Rating : 4.4/5 (2 download)

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Book Synopsis Handbook of Computational Molecular Biology by : Srinivas Aluru

Download or read book Handbook of Computational Molecular Biology written by Srinivas Aluru and published by CRC Press. This book was released on 2005-12-21 with total page 1108 pages. Available in PDF, EPUB and Kindle. Book excerpt: The enormous complexity of biological systems at the molecular level must be answered with powerful computational methods. Computational biology is a young field, but has seen rapid growth and advancement over the past few decades. Surveying the progress made in this multidisciplinary field, the Handbook of Computational Molecular Biology of