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Model Systems In Biology
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Book Synopsis Model Systems in Biology by : Georg Striedter
Download or read book Model Systems in Biology written by Georg Striedter and published by MIT Press. This book was released on 2022-08-02 with total page 303 pages. Available in PDF, EPUB and Kindle. Book excerpt: How biomedical research using various animal species and in vitro cellular systems has resulted in both major successes and translational failure. In Model Systems in Biology, comparative neurobiologist Georg Striedter examines how biomedical researchers have used animal species and in vitro cellular systems to understand and develop treatments for human diseases ranging from cancer and polio to Alzheimer’s disease and schizophrenia. Although there have been some major successes, much of this “translational” research on model systems has failed to generalize to humans. Striedter explores the history of such research, focusing on the models used and considering the question of model selection from a variety of perspectives—the philosophical, the historical, and that of practicing biologists. Striedter reviews some philosophical concepts and ethical issues, including concerns over animal suffering and the compromises that result. He traces the history of the most widely used animal and in vitro models, describing how they compete with one another in a changing ecosystem of models. He examines how therapies for bacterial and viral infections, cancer, cardiovascular diseases, and neurological disorders have been developed using animal and cell culture models—and how research into these diseases has both taken advantage of and been hindered by model system differences. Finally, Striedter argues for a “big tent” biology, in which a diverse set of models and research strategies can coexist productively.
Book Synopsis Mathematical Modeling in Systems Biology by : Brian P. Ingalls
Download or read book Mathematical Modeling in Systems Biology written by Brian P. Ingalls and published by MIT Press. This book was released on 2022-06-07 with total page 423 pages. Available in PDF, EPUB and Kindle. Book excerpt: An introduction to the mathematical concepts and techniques needed for the construction and analysis of models in molecular systems biology. Systems techniques are integral to current research in molecular cell biology, and system-level investigations are often accompanied by mathematical models. These models serve as working hypotheses: they help us to understand and predict the behavior of complex systems. This book offers an introduction to mathematical concepts and techniques needed for the construction and interpretation of models in molecular systems biology. It is accessible to upper-level undergraduate or graduate students in life science or engineering who have some familiarity with calculus, and will be a useful reference for researchers at all levels. The first four chapters cover the basics of mathematical modeling in molecular systems biology. The last four chapters address specific biological domains, treating modeling of metabolic networks, of signal transduction pathways, of gene regulatory networks, and of electrophysiology and neuronal action potentials. Chapters 3–8 end with optional sections that address more specialized modeling topics. Exercises, solvable with pen-and-paper calculations, appear throughout the text to encourage interaction with the mathematical techniques. More involved end-of-chapter problem sets require computational software. Appendixes provide a review of basic concepts of molecular biology, additional mathematical background material, and tutorials for two computational software packages (XPPAUT and MATLAB) that can be used for model simulation and analysis.
Download or read book C. Elegans II written by Donald L. Riddle and published by Firefly Books. This book was released on 1997 with total page 1252 pages. Available in PDF, EPUB and Kindle. Book excerpt: Defines the current status of research in the genetics, anatomy, and development of the nematode C. elegans, providing a detailed molecular explanation of how development is regulated and how the nervous system specifies varied aspects of behavior. Contains sections on the genome, development, neural networks and behavior, and life history and evolution. Appendices offer genetic nomenclature, a list of laboratory strain and allele designations, skeleton genetic maps, a list of characterized genes, a table of neurotransmitter assignments for specific neurons, and information on codon usage. Includes bandw photos. For researchers in worm studies, as well as the wider community of researchers in cell and molecular biology. Annotation copyrighted by Book News, Inc., Portland, OR
Book Synopsis Scientific Frontiers in Developmental Toxicology and Risk Assessment by : National Research Council
Download or read book Scientific Frontiers in Developmental Toxicology and Risk Assessment written by National Research Council and published by National Academies Press. This book was released on 2000-12-21 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: Scientific Frontiers in Developmental Toxicology and Risk Assessment reviews advances made during the last 10-15 years in fields such as developmental biology, molecular biology, and genetics. It describes a novel approach for how these advances might be used in combination with existing methodologies to further the understanding of mechanisms of developmental toxicity, to improve the assessment of chemicals for their ability to cause developmental toxicity, and to improve risk assessment for developmental defects. For example, based on the recent advances, even the smallest, simplest laboratory animals such as the fruit fly, roundworm, and zebrafish might be able to serve as developmental toxicological models for human biological systems. Use of such organisms might allow for rapid and inexpensive testing of large numbers of chemicals for their potential to cause developmental toxicity; presently, there are little or no developmental toxicity data available for the majority of natural and manufactured chemicals in use. This new approach to developmental toxicology and risk assessment will require simultaneous research on several fronts by experts from multiple scientific disciplines, including developmental toxicologists, developmental biologists, geneticists, epidemiologists, and biostatisticians.
Book Synopsis A Guide to Numerical Modelling in Systems Biology by : Peter Deuflhard
Download or read book A Guide to Numerical Modelling in Systems Biology written by Peter Deuflhard and published by Springer. This book was released on 2015-07-06 with total page 185 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is intended for students of computational systems biology with only a limited background in mathematics. Typical books on systems biology merely mention algorithmic approaches, but without offering a deeper understanding. On the other hand, mathematical books are typically unreadable for computational biologists. The authors of the present book have worked hard to fill this gap. The result is not a book on systems biology, but on computational methods in systems biology. This book originated from courses taught by the authors at Freie Universität Berlin. The guiding idea of the courses was to convey those mathematical insights that are indispensable for systems biology, teaching the necessary mathematical prerequisites by means of many illustrative examples and without any theorems. The three chapters cover the mathematical modelling of biochemical and physiological processes, numerical simulation of the dynamics of biological networks and identification of model parameters by means of comparisons with real data. Throughout the text, the strengths and weaknesses of numerical algorithms with respect to various systems biological issues are discussed. Web addresses for downloading the corresponding software are also included.
Book Synopsis Systems Biology by : Andreas Kremling
Download or read book Systems Biology written by Andreas Kremling and published by CRC Press. This book was released on 2013-11-12 with total page 382 pages. Available in PDF, EPUB and Kindle. Book excerpt: Drawing on the latest research in the field, Systems Biology: Mathematical Modeling and Model Analysis presents many methods for modeling and analyzing biological systems, in particular cellular systems. It shows how to use predictive mathematical models to acquire and analyze knowledge about cellular systems. It also explores how the models are systematically applied in biotechnology. The first part of the book introduces biological basics, such as metabolism, signaling, gene expression, and control as well as mathematical modeling fundamentals, including deterministic models and thermodynamics. The text also discusses linear regression methods, explains the differences between linear and nonlinear regression, and illustrates how to determine input variables to improve estimation accuracy during experimental design. The second part covers intracellular processes, including enzymatic reactions, polymerization processes, and signal transduction. The author highlights the process–function–behavior sequence in cells and shows how modeling and analysis of signal transduction units play a mediating role between process and function. The third part presents theoretical methods that address the dynamics of subsystems and the behavior near a steady state. It covers techniques for determining different time scales, sensitivity analysis, structural kinetic modeling, and theoretical control engineering aspects, including a method for robust control. It also explores frequent patterns (motifs) in biochemical networks, such as the feed-forward loop in the transcriptional network of E. coli. Moving on to models that describe a large number of individual reactions, the last part looks at how these cellular models are used in biotechnology. The book also explains how graphs can illustrate the link between two components in large networks with several interactions.
Book Synopsis Modeling Dynamic Biological Systems by : Bruce Hannon
Download or read book Modeling Dynamic Biological Systems written by Bruce Hannon and published by Springer. This book was released on 2014-07-05 with total page 419 pages. Available in PDF, EPUB and Kindle. Book excerpt: Many biologists and ecologists have developed models that find widespread use in theoretical investigations and in applications to organism behavior, disease control, population and metapopulation theory, ecosystem dynamics, and environmental management. This book captures and extends the process of model development by concentrating on the dynamic aspects of these processes and by providing the tools such that virtually anyone with basic knowledge in the Life Sciences can develop meaningful dynamic models. Examples of the systems modeled in the book range from models of cell development, the beating heart, the growth and spread of insects, spatial competition and extinction, to the spread and control of epidemics, including the conditions for the development of chaos. Key features: - easy-to-learn and easy-to-use software - examples from many subdisciplines of biology, covering models of cells, organisms, populations, and metapopulations - no prior computer or programming experience required Key benefits: - learn how to develop modeling skills and system thinking on your own rather than use models developed by others - be able to easily run models under alternative assumptions and investigate the implications of these assumptions for the dynamics of the biological system being modeled - develop skills to assess the dynamics of biological systems
Book Synopsis Model Organisms in Drug Discovery by : Pamela M. Carroll
Download or read book Model Organisms in Drug Discovery written by Pamela M. Carroll and published by John Wiley & Sons. This book was released on 2004-04-21 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fruit flies are "little people with wings" goes the saying in the scientific community, ever since the completion of the Human Genome Project and its revelations about the similarity amongst the genomes of different organisms. It is humbling that most signalling pathways which "define" humans are conserved in Drosophila, the common fruit fly. Feed a fruit fly caffeine and it has trouble falling asleep; feed it antihistamines and it cannot stay awake. A C. elegans worm placed on the antidepressant flouxetine has increased serotonin levels in its tiny brain. Yeast treated with chemotherapeutics stop their cell division. Removal of a single gene from a mouse or zebrafish can cause the animals to develop Alzheimer’s disease or heart disease. These organisms are utilized as surrogates to investigate the function and design of complex human biological systems. Advances in bioinformatics, proteomics, automation technologies and their application to model organism systems now occur on an industrial scale. The integration of model systems into the drug discovery process, the speed of the tools, and the in vivo validation data that these models can provide, will clearly help definition of disease biology and high-quality target validation. Enhanced target selection will lead to the more efficacious and less toxic therapeutic compounds of the future. Leading experts in the field provide detailed accounts of model organism research that have impacted on specific therapeutic areas and they examine state-of-the-art applications of model systems, describing real life applications and their possible impact in the future. This book will be of interest to geneticists, bioinformaticians, pharmacologists, molecular biologists and people working in the pharmaceutical industry, particularly genomics.
Book Synopsis Modeling Methods for Medical Systems Biology by : María Elena Álvarez-Buylla Roces
Download or read book Modeling Methods for Medical Systems Biology written by María Elena Álvarez-Buylla Roces and published by Springer. This book was released on 2018-08-03 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book contributes to better understand how lifestyle modulations can effectively halt the emergence and progression of human diseases. The book will allow the reader to gain a better understanding of the mechanisms by which the environment interferes with the bio-molecular regulatory processes underlying the emergence and progression of complex diseases, such as cancer. Focusing on key and early cellular bio-molecular events giving rise to the emergence of degenerative chronic disease, it builds on previous experience on the development of multi-cellular organisms, to propose a mathematical and computer based framework that allows the reader to analyze the complex interplay between bio-molecular processes and the (micro)-environment from an integrative, mechanistic, quantitative and dynamical perspective. Taking the wealth of empirical evidence that exists it will show how to build and analyze models of core regulatory networks involved in the emergence and progression of chronic degenerative diseases, using a bottom-up approach.
Book Synopsis Networks in Systems Biology by : Fabricio Alves Barbosa da Silva
Download or read book Networks in Systems Biology written by Fabricio Alves Barbosa da Silva and published by Springer Nature. This book was released on 2020-10-03 with total page 381 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a range of current research topics in biological network modeling, as well as its application in studies on human hosts, pathogens, and diseases. Systems biology is a rapidly expanding field that involves the study of biological systems through the mathematical modeling and analysis of large volumes of biological data. Gathering contributions from renowned experts in the field, some of the topics discussed in depth here include networks in systems biology, the computational modeling of multidrug-resistant bacteria, and systems biology of cancer. Given its scope, the book is intended for researchers, advanced students, and practitioners of systems biology. The chapters are research-oriented, and present some of the latest findings on their respective topics.
Book Synopsis Model Systems in Biology by : Georg F. Striedter
Download or read book Model Systems in Biology written by Georg F. Striedter and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Instead of arguing for a specific animal model, Striedter will review the history and philosophy of animal models in biomedical research, examining their various advantages and limitations"--
Book Synopsis The Microbial Models of Molecular Biology by : Rowland H. Davis
Download or read book The Microbial Models of Molecular Biology written by Rowland H. Davis and published by Oxford University Press. This book was released on 2003-09-11 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book explains the role of simple biological model systems in the growth of molecular biology. Essentially the whole history of molecular biology is presented here, tracing the work in bacteriophages in E. coli, the role of other prokaryotic systems, and also the protozoan and algal models - Paramecium and Chlamydomonas, primarily - and the move into eukaryotes with the fungal systems - Neurospora, Aspergillus and yeast. Each model was selected for its appropriateness for asking a given class of questions, and each spawned its own community of investigators. Some individuals made the transition to a new model over time, and remnant communities of investigators continue to pursue questions in all these models, as the cutting edge of molecular biological research flowed onward from model to model, and onward into higher organisms and, ultimately, mouse and man.
Book Synopsis Model-Based Hypothesis Testing in Biomedicine by : Rikard Johansson
Download or read book Model-Based Hypothesis Testing in Biomedicine written by Rikard Johansson and published by Linköping University Electronic Press. This book was released on 2017-10-03 with total page 102 pages. Available in PDF, EPUB and Kindle. Book excerpt: The utilization of mathematical tools within biology and medicine has traditionally been less widespread compared to other hard sciences, such as physics and chemistry. However, an increased need for tools such as data processing, bioinformatics, statistics, and mathematical modeling, have emerged due to advancements during the last decades. These advancements are partly due to the development of high-throughput experimental procedures and techniques, which produce ever increasing amounts of data. For all aspects of biology and medicine, these data reveal a high level of inter-connectivity between components, which operate on many levels of control, and with multiple feedbacks both between and within each level of control. However, the availability of these large-scale data is not synonymous to a detailed mechanistic understanding of the underlying system. Rather, a mechanistic understanding is gained first when we construct a hypothesis, and test its predictions experimentally. Identifying interesting predictions that are quantitative in nature, generally requires mathematical modeling. This, in turn, requires that the studied system can be formulated into a mathematical model, such as a series of ordinary differential equations, where different hypotheses can be expressed as precise mathematical expressions that influence the output of the model. Within specific sub-domains of biology, the utilization of mathematical models have had a long tradition, such as the modeling done on electrophysiology by Hodgkin and Huxley in the 1950s. However, it is only in recent years, with the arrival of the field known as systems biology that mathematical modeling has become more commonplace. The somewhat slow adaptation of mathematical modeling in biology is partly due to historical differences in training and terminology, as well as in a lack of awareness of showcases illustrating how modeling can make a difference, or even be required, for a correct analysis of the experimental data. In this work, I provide such showcases by demonstrating the universality and applicability of mathematical modeling and hypothesis testing in three disparate biological systems. In Paper II, we demonstrate how mathematical modeling is necessary for the correct interpretation and analysis of dominant negative inhibition data in insulin signaling in primary human adipocytes. In Paper III, we use modeling to determine transport rates across the nuclear membrane in yeast cells, and we show how this technique is superior to traditional curve-fitting methods. We also demonstrate the issue of population heterogeneity and the need to account for individual differences between cells and the population at large. In Paper IV, we use mathematical modeling to reject three hypotheses concerning the phenomenon of facilitation in pyramidal nerve cells in rats and mice. We also show how one surviving hypothesis can explain all data and adequately describe independent validation data. Finally, in Paper I, we develop a method for model selection and discrimination using parametric bootstrapping and the combination of several different empirical distributions of traditional statistical tests. We show how the empirical log-likelihood ratio test is the best combination of two tests and how this can be used, not only for model selection, but also for model discrimination. In conclusion, mathematical modeling is a valuable tool for analyzing data and testing biological hypotheses, regardless of the underlying biological system. Further development of modeling methods and applications are therefore important since these will in all likelihood play a crucial role in all future aspects of biology and medicine, especially in dealing with the burden of increasing amounts of data that is made available with new experimental techniques. Användandet av matematiska verktyg har inom biologi och medicin traditionellt sett varit mindre utbredd jämfört med andra ämnen inom naturvetenskapen, såsom fysik och kemi. Ett ökat behov av verktyg som databehandling, bioinformatik, statistik och matematisk modellering har trätt fram tack vare framsteg under de senaste decennierna. Dessa framsteg är delvis ett resultat av utvecklingen av storskaliga datainsamlingstekniker. Inom alla områden av biologi och medicin så har dessa data avslöjat en hög nivå av interkonnektivitet mellan komponenter, verksamma på många kontrollnivåer och med flera återkopplingar både mellan och inom varje nivå av kontroll. Tillgång till storskaliga data är emellertid inte synonymt med en detaljerad mekanistisk förståelse för det underliggande systemet. Snarare uppnås en mekanisk förståelse först när vi bygger en hypotes vars prediktioner vi kan testa experimentellt. Att identifiera intressanta prediktioner som är av kvantitativ natur, kräver generellt sett matematisk modellering. Detta kräver i sin tur att det studerade systemet kan formuleras till en matematisk modell, såsom en serie ordinära differentialekvationer, där olika hypoteser kan uttryckas som precisa matematiska uttryck som påverkar modellens output. Inom vissa delområden av biologin har utnyttjandet av matematiska modeller haft en lång tradition, såsom den modellering gjord inom elektrofysiologi av Hodgkin och Huxley på 1950?talet. Det är emellertid just på senare år, med ankomsten av fältet systembiologi, som matematisk modellering har blivit ett vanligt inslag. Den något långsamma adapteringen av matematisk modellering inom biologi är bl.a. grundad i historiska skillnader i träning och terminologi, samt brist på medvetenhet om exempel som illustrerar hur modellering kan göra skillnad och faktiskt ofta är ett krav för en korrekt analys av experimentella data. I detta arbete tillhandahåller jag sådana exempel och demonstrerar den matematiska modelleringens och hypotestestningens allmängiltighet och tillämpbarhet i tre olika biologiska system. I Arbete II visar vi hur matematisk modellering är nödvändig för en korrekt tolkning och analys av dominant-negativ-inhiberingsdata vid insulinsignalering i primära humana adipocyter. I Arbete III använder vi modellering för att bestämma transporthastigheter över cellkärnmembranet i jästceller, och vi visar hur denna teknik är överlägsen traditionella kurvpassningsmetoder. Vi demonstrerar också frågan om populationsheterogenitet och behovet av att ta hänsyn till individuella skillnader mellan celler och befolkningen som helhet. I Arbete IV använder vi matematisk modellering för att förkasta tre hypoteser om hur fenomenet facilitering uppstår i pyramidala nervceller hos råttor och möss. Vi visar också hur en överlevande hypotes kan beskriva all data, inklusive oberoende valideringsdata. Slutligen utvecklar vi i Arbete I en metod för modellselektion och modelldiskriminering med hjälp av parametrisk ”bootstrapping” samt kombinationen av olika empiriska fördelningar av traditionella statistiska tester. Vi visar hur det empiriska ”log-likelihood-ratio-testet” är den bästa kombinationen av två tester och hur testet är applicerbart, inte bara för modellselektion, utan också för modelldiskriminering. Sammanfattningsvis är matematisk modellering ett värdefullt verktyg för att analysera data och testa biologiska hypoteser, oavsett underliggande biologiskt system. Vidare utveckling av modelleringsmetoder och tillämpningar är därför viktigt eftersom dessa sannolikt kommer att spela en avgörande roll i framtiden för biologi och medicin, särskilt när det gäller att hantera belastningen från ökande datamängder som blir tillgänglig med nya experimentella tekniker.
Book Synopsis Fundamentals of Systems Biology by : Markus W. Covert
Download or read book Fundamentals of Systems Biology written by Markus W. Covert and published by CRC Press. This book was released on 2017-10-19 with total page 367 pages. Available in PDF, EPUB and Kindle. Book excerpt: For decades biology has focused on decoding cellular processes one gene at a time, but many of the most pressing biological questions, as well as diseases such as cancer and heart disease, are related to complex systems involving the interaction of hundreds, or even thousands, of gene products and other factors. How do we begin to understand this complexity? Fundamentals of Systems Biology: From Synthetic Circuits to Whole-cell Models introduces students to methods they can use to tackle complex systems head-on, carefully walking them through studies that comprise the foundation and frontier of systems biology. The first section of the book focuses on bringing students quickly up to speed with a variety of modeling methods in the context of a synthetic biological circuit. This innovative approach builds intuition about the strengths and weaknesses of each method and becomes critical in the book’s second half, where much more complicated network models are addressed—including transcriptional, signaling, metabolic, and even integrated multi-network models. The approach makes the work much more accessible to novices (undergraduates, medical students, and biologists new to mathematical modeling) while still having much to offer experienced modelers--whether their interests are microbes, organs, whole organisms, diseases, synthetic biology, or just about any field that investigates living systems.
Book Synopsis Dynamic Systems Biology Modeling and Simulation by : Joseph DiStefano III
Download or read book Dynamic Systems Biology Modeling and Simulation written by Joseph DiStefano III and published by Academic Press. This book was released on 2015-01-10 with total page 886 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dynamic Systems Biology Modeling and Simuation consolidates and unifies classical and contemporary multiscale methodologies for mathematical modeling and computer simulation of dynamic biological systems – from molecular/cellular, organ-system, on up to population levels. The book pedagogy is developed as a well-annotated, systematic tutorial – with clearly spelled-out and unified nomenclature – derived from the author’s own modeling efforts, publications and teaching over half a century. Ambiguities in some concepts and tools are clarified and others are rendered more accessible and practical. The latter include novel qualitative theory and methodologies for recognizing dynamical signatures in data using structural (multicompartmental and network) models and graph theory; and analyzing structural and measurement (data) models for quantification feasibility. The level is basic-to-intermediate, with much emphasis on biomodeling from real biodata, for use in real applications. Introductory coverage of core mathematical concepts such as linear and nonlinear differential and difference equations, Laplace transforms, linear algebra, probability, statistics and stochastics topics The pertinent biology, biochemistry, biophysics or pharmacology for modeling are provided, to support understanding the amalgam of “math modeling” with life sciences Strong emphasis on quantifying as well as building and analyzing biomodels: includes methodology and computational tools for parameter identifiability and sensitivity analysis; parameter estimation from real data; model distinguishability and simplification; and practical bioexperiment design and optimization Companion website provides solutions and program code for examples and exercises using Matlab, Simulink, VisSim, SimBiology, SAAMII, AMIGO, Copasi and SBML-coded models A full set of PowerPoint slides are available from the author for teaching from his textbook. He uses them to teach a 10 week quarter upper division course at UCLA, which meets twice a week, so there are 20 lectures. They can easily be augmented or stretched for a 15 week semester course Importantly, the slides are editable, so they can be readily adapted to a lecturer’s personal style and course content needs. The lectures are based on excerpts from 12 of the first 13 chapters of DSBMS. They are designed to highlight the key course material, as a study guide and structure for students following the full text content The complete PowerPoint slide package (~25 MB) can be obtained by instructors (or prospective instructors) by emailing the author directly, at: [email protected]
Book Synopsis Dynamical Systems for Biological Modeling by : Fred Brauer
Download or read book Dynamical Systems for Biological Modeling written by Fred Brauer and published by CRC Press. This book was released on 2015-12-23 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dynamical Systems for Biological Modeling: An Introduction prepares both biology and mathematics students with the understanding and techniques necessary to undertake basic modeling of biological systems. It achieves this through the development and analysis of dynamical systems.The approach emphasizes qualitative ideas rather than explicit computa
Book Synopsis Kinetic Modelling in Systems Biology by : Oleg Demin
Download or read book Kinetic Modelling in Systems Biology written by Oleg Demin and published by CRC Press. This book was released on 2008-10-24 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: With more and more interest in how components of biological systems interact, it is important to understand the various aspects of systems biology. Kinetic Modelling in Systems Biology focuses on one of the main pillars in the future development of systems biology. It explores both the methods and applications of kinetic modeling in this emerging f