Books on the topic 'Complex systems- Molecular dynamics study'

This text provides a uniform and consistent approach to diversified problems encountered in the study of dynamical processes in condensed phase molecular systems. Given the broad interdisciplinary aspect of this subject, the book focuses on three themes: coverage of needed background material, in-depth introduction of methodologies, and analysis of several key applications. The uniform approach and common language used in all discussions help to develop general understanding and insight on condensed phases chemical dynamics. The applications discussed are among the most fundamental processes that underlie physical, chemical and biological phenomena in complex systems. The first part of the book starts with a general review of basic mathematical and physical methods (Chapter 1) and a few introductory chapters on quantum dynamics (Chapter 2), interaction of radiation and matter (Chapter 3) and basic properties of solids (chapter 4) and liquids (Chapter 5). In the second part the text embarks on a broad coverage of the main methodological approaches. The central role of classical and quantum time correlation functions is emphasized in Chapter 6. The presentation of dynamical phenomena in complex systems as stochastic processes is discussed in Chapters 7 and 8. The basic theory of quantum relaxation phenomena is developed in Chapter 9, and carried on in Chapter 10 which introduces the density operator, its quantum evolution in Liouville space, and the concept of reduced equation of motions. The methodological part concludes with a discussion of linear response theory in Chapter 11, and of the spin-boson model in chapter 12. The third part of the book applies the methodologies introduced earlier to several fundamental processes that underlie much of the dynamical behaviour of condensed phase molecular systems. Vibrational relaxation and vibrational energy transfer (Chapter 13), Barrier crossing and diffusion controlled reactions (Chapter 14), solvation dynamics (Chapter 15), electron transfer in bulk solvents (Chapter 16) and at electrodes/electrolyte and metal/molecule/metal junctions (Chapter 17), and several processes pertaining to molecular spectroscopy in condensed phases (Chapter 18) are the main subjects discussed in this part.

This chapter explains some of the fundamental issues associated with applying perturbations to a molecular dynamics simulation, along with practical details of methods for studying systems out of equilibrium. The main emphasis is on fluid flow and viscosity measurements. Spatially homogeneous perturbations are described to study shear and extensional flow. Non-equilibrium methods are applied to the study of heat flow and the calculation of the thermal conductivity. Issues of thermostatting, and the modelling of surface-fluid interactions for inhomogeneous systems, are discussed. The measurement of free energy changes through non-equilibrium work expressions such as those of Jarzynski and Crooks is also explained.

Earthquakes are a huge global threat. In thirty-six countries, severe seismic risks threaten populations and their increasingly interdependent systems of transportation, communication, energy, and finance. This book provides an examination of how twelve communities in nine countries responded to destructive earthquakes between 1999 and 2015. And many of the book's lessons can also be applied to other large-scale risks. The book sets the global problem of seismic risk in the framework of complex adaptive systems to explore how the consequences of such events ripple across jurisdictions, communities, and organizations in complex societies, triggering unexpected alliances but also exposing social, economic, and legal gaps. It assesses how the networks of organizations involved in response and recovery adapted and acted collectively after the twelve earthquakes it examines. It describes how advances in information technology enabled some communities to anticipate seismic risk better and to manage response and recovery operations more effectively, decreasing losses. Finally, the book shows why investing substantively in global information infrastructure would create shared awareness of seismic risk and make post-disaster relief more effective and less expensive. The result is a landmark study of how to improve the way we prepare for and respond to earthquakes and other disasters in our ever-more-complex world.

Dynamics of Skill Acquisition, Second Edition, provides an analysis of the processes underlying human skill acquisition. As the first text to outline the multidisciplinary ecological dynamics framework for understanding movement behavior, this heavily updated edition stays on the cutting edge, with principles of nonlinear pedagogy and methodologies from the constraints-led approach. Students and practitioners across a variety of professions—including coaches, physical educators, trainers, and rehabilitation specialists—will appreciate the applied focus of this second edition. Movement models throughout the text provide examples for visualizing task constraints and enhancing the study and understanding of movement behavior. Athletes and sports teams are presented as specific complex adaptive systems, with information on designing learning environments and adapting programs to foster skill development. Readers will learn the historical evolution of dynamical systems theory and the ecological dynamics framework. These foundational concepts illustrate the integration between intentional action, cognition, and decision making and their effects on performance and behavior. Complex theoretical concepts are explained in simple terms and related to practice, focusing on the implications of the work of pioneering researchers such as Nikolai Bernstein, Egon Brunswik, James Gibson, Scott Kelso, and Karl Newell. Case studies written by practitioners contain specific examples of the ecological dynamics framework in action, bringing theory to life. By learning how to identify and manipulate key constraints that influence learning skilled behavior, readers will gain insight into practice designs for creating positive learning experiences that enable individuals to develop and learn functional movements. Throughout the book, learning features guide readers through material with clear direction and focus to improve understanding. Spotlight on Research sidebars provide detailed descriptions of important studies to connect theory, research, and application. Lab activities teach application skills beyond the content, ensuring reader understanding. In addition, chapter objectives, self-test questions, and Key Concept sidebars highlight important concepts in each chapter. With the study of human movement now bridging many disciplines, including motor development, psychology, biology, and physical therapy, Dynamics of Skill Acquisition, Second Edition, provides a timely analysis of the ecological dynamics framework and presents a comprehensive model for understanding how coordination patterns are assembled, controlled, and acquired. The theoretical roots and development of the ecological dynamics framework provide application strategies for all people with an interest in movement coordination and control. AUDIENCE An upper-level undergraduate or graduate textbook for courses in human movement and skill acquisition. A professional reference for movement practitioners and scientists, including teachers, coaches, trainers, physical educators, physical therapists, rehabilitation specialists, sport scientists, psychologists, biomechanists, sport analysts and physiologists.

The preceding chapters established the central role played by families of trajectories in phase space to explain the time evolution of complex systems. This chapter, in turn, uses these ideas to explore the history and development of the theory of natural evolution by Charles Darwin and others. Darwin had many influences, including ideas from Thomas Malthus in the context of economic dynamics. After Darwin, the ideas of evolution matured to encompass broad topics in evolutionary dynamics and the emergence of the idea of fitness landscapes and game theory driving the origin of new species. This chapter shows how the rise of genetics with Gregor Mendel supplied a firm foundation for molecular evolution, leading to the molecular clock of Linus Pauling and the replicator dynamics of Richard Dawkins.

This book provides a practical guide to molecular dynamics and Monte Carlo simulation techniques used in the modelling of simple and complex liquids. Computer simulation is an essential tool in studying the chemistry and physics of condensed matter, complementing and reinforcing both experiment and theory. Simulations provide detailed information about structure and dynamics, essential to understand the many fluid systems that play a key role in our daily lives: polymers, gels, colloidal suspensions, liquid crystals, biological membranes, and glasses. The second edition of this pioneering book aims to explain how simulation programs work, how to use them, and how to interpret the results, with examples of the latest research in this rapidly evolving field. Accompanying programs in Fortran and Python provide practical, hands-on, illustrations of the ideas in the text.

While Darwinism has successfully resisted reduction to physics, the authors point out that it has from the outset developed and applied its core explanatory concept, natural selection, by borrowing models from dynamics, a branch of physics. The recent development of complex systems dynamics may afford Darwinism yet another occasion to expand its explanatory power. Darwinism's use of dynamical models has received insufficient attention from biologists, historians, and philosophers who have concentrated instead on how evolutionary biology has maintained its autonomy from physics. Yet, as Depew and Weber observe, it is only by recovering Darwin's own relationship to Newtonian models of systems dynamics, and genetical Darwinism's relationship to statistical mechanics and probability theory, that insight can be gained into how Darwinism can successfully meet the challenges it is currently facing. Drawing on recent scholarship in the history of biology, Depew and Weber bring the dynamical perspective to bear on a number of important episodes in the history of the Darwinian research tradition: Darwin's "Newtonian" Darwinism, the rise of "developmentalist" evolutionary theories and the eclipse of Darwinism at the turn of the century, Darwinism's struggles to incorporate genetics, its eventual regeneration in the modern evolutionary synthesis, challenges to that synthesis that have been posed in recent decades by molecular genetics, and recent proposals for meeting those challenges. Bradford Books imprint

The book provides a new conceptual framework to explain the interaction of complex systems, specifically humans and their environment. It proposes that human physiology and the environment do not “connect” with each other in a direct, unidirectional manner, like a beaker pouring water into a cup. Rather, the authors propose the Biodynamic Interface Conjecture with the central axiom that complex systems cannot interact directly or exist in isolation due to temporally embedded functional interdependencies within and between systems. The authors propose that human physiology and the environment contribute to the formation of an interface, and by doing so they give rise to an intermediary that guides the interaction by letting some influences pass between the systems while restricting others. This proposition counters many structural approaches that assume that complex systems, such as the environment and humans, can transfer information directly between them while remaining discrete entities. Although developed for environmental health sciences, the conjecture has broader implications for the study of complex system interactions across various levels of organization, and the central role of time and temporal dynamics in system-to-system information exchange. This conjecture also argues against causal paradigms that (incorrectly) assume that systems are distinct entities interacting directly and ignore boundary conditions, and organizational levels, and complexity inherent in biological and environmental systems.

Self-organization describes a dynamic in a system whereby local interactions between individuals collectively yield global order, i.e. spatial patterns unobservable in their entirety to the individuals. By this working definition, self-organization is intimately related to chaos, i.e. global order in the dynamics of deterministic systems that are locally unpredictable. A useful distinction is that a small perturbation to a chaotic system causes a large deviation in its trajectory, i.e. the butterfly effect, whereas self-organizing patterns are robust to noise and perturbation. For many, self-organization is as important to the understanding of biological processes as natural selection. For some, self-organization explains where the complex forms that compete for survival in the natural world originate from. This chapter outlines some fundamental ideas from the study of simulated self-organizing systems, before suggesting how self-organizing principles could be applied through biohybrid societies to establish new theories of living systems.

Parasites are ubiquitous and shape almost every aspect of their hosts, including physiology, behaviour, life histories, the structure of the microbiota, and entire communities. Hence, parasitism is one of the most potent forces in nature and, without parasites, the world would look very different. The book gives an overview over the parasite groups and the diversity of defences that hosts have evolved, such as immune systems. Principles of evolutionary biology and ecology analyse major elements of host–parasite interactions, including virulence, infection processes, tolerance, resistance, specificity, memory, polymorphisms, within-host dynamics, diseases spaces, and many other aspects. Genetics is always one of the key elements in these topics. Modelling, furthermore, can predict best strategies for host and parasites. Similarly, the spread of an infectious disease in epidemiology combines with molecular data and genomics. Furthermore, parasites have evolved ways to overcome defences and to manipulate their hosts. Hosts and parasites, therefore, continuously co-evolve, with changes sometimes occurring very rapidly, and sometimes requiring geological times. Many infectious diseases of humans have emerged from a zoonotic origin, in processes governed by the basic principles discussed in the different sections. Hence, this book integrates different fields to study the diversity of host–parasite processes and phenomena. It summarizes the essential topics for the study of evolutionary parasitology and will be useful for a broad audience.

The main milestones of the formation and development of astronomical science in Kharkiv during 1883–1945 are reconstructed on the example of the activities of the astronomical observatory of Kharkiv University. During this period, the outstanding worldview science in Kharkiv has achieved significant success: the works of Kharkiv astronomers have received world recognition; a well-known scientific planetary school has been established at the Observatory; the scientific community highly appreciated the research on the physics and chemistry of the Moon, the giant and small planets of the Solar System. The primary goal of the research is to inscribe the history of the university Observatory into the European and world context. Its purpose is to summarize the results of a comprehensive historical ad scientific study of the development of astronomical research in Kharkiv at the end of the 19th century – the first half of the 20th century and identification of ways of further scientific research. The completed research, which continues the problems of works devoted to the study of the history of astronomical science in Ukraine, focuses on expanding the well-known source base by attracting new retro-information resources. In particular, the monograph used a significant array of archival primary sources from almost twenty archival and library institutions of different countries. Most of them were introduced into scientific circulation for the first time, which allowed to determine and specify the sequence of stages of development of astronomical science in Kharkiv during the research period, to clarify and identify the little-known circumstances of the observatory life. The methodological basis of the study is the principles of historism, objectivity and a systematic approach to studying the problem. To solve specific problematic tasks in the monograph, general scientific and specially historical methods were used which allowed to study, analyze and summarize the presented factual material in a complex manner. The main sections of the monograph represent the dynamics of replenishment of the instrumental base of the university observatory, the chronology of the construction of the observatory complex of buildings at the location of the modern Scientific Research Institute of Astronomy of the V. N. Karazin Kharkiv National University. According to the author’s periodization, the stages of formation of subjects and directions of scientific work of university astronomers have been analyzed, including: seismic observations with the help of horizontal Rebeur-Paschwitz pendulums, research of the activity of the Sun, astrometric observations on the Repsold meridian circle of for the purpose of compiling a catalog of zodiac stars, studying lunar eclipses and meteor showers. The participation of university astronomers in the creation of the plan of the city of Kharkiv and its connection with the general network of precise geometric leveling of the Military Topographic Department of the General Staff; the organization of observations by an expedition of Kharkiv astronomers of the total Solar eclipse of 1914 in Henichesk; the creation of the School-workshop of precision mechanics at the Faculty of Physics and Mathematics of Kharkiv University were considered; information on the participation of Kharkiv astronomers in the events of the civil war during the Ukrainian Revolution was documented. The scientific research activity of Kharkiv astronomers during 1920-1930-s which was devoted to carrying out important astrometric works on meridian observations of star declinations by absolute methods and observations of Kopf-Rentz stars according to the programs of the International Astronomical Union; the initiation of the creation of the Catalog of faint stars; research in astrophysics aimed at studying the physical conditions on the Moon and the Sun, planets and the interstellar environment; performing long series of spectrophotometric observations of the Moon, Jupiter, Mars and Saturn under different conditions of observation; study of the kinematics of stellar systems of different order, the physical parameters and evolution of stars, the morphology of the Galaxy, the nature of the stellar subsurfaces and atmospheres, dust and gas nebulae, new stars and the variability of stars have been considered; the directions of solid works carried out in the field of celestial mechanics, devoted to the dynamics of the minor planets of the Jupiter group, the definition and improvement of the orbits of minor planets have been clarified. The development of amateur astronomy in Kharkiv, in particular, the functioning of circles and societies that directed their activities to the dissemination of astronomical knowledge, was highlighted; the participation of their representatives in astronomical observations at the Kharkiv Astronomical Observatory was emphasized. Reconstructed the development of historical events in the 1930s related to the involvement of Soviet and Western astronomers in the processes of political confrontation between the USSR and the Western world; investigated the course of circumstances that prevented the implementation of the project of creating a new modern astronomical center of national importance – the central Ukrainian observatory in Kharkiv; the participation of an expedition of Kharkiv astronomers in the observation of the «great Soviet eclipse» – the total solar eclipse of 1936 – in the North Caucasus is highlighted; established the facts of political «purges» and repressions by the People’s Commissariat for Internal Affairs ( the NKVD) in the Kharkiv Astronomical Observatory. The activity of the Kharkiv Astronomical Observatory has been documented and authentic biographical information about its representatives during the Nazi occupation of 1941–1943, the period of the German-Soviet war, has been presented; the unpopular facts of the forced collaboration of some scientists are highlighted; the process of recovery and reconstruction of the Kharkiv Astronomical Observatory after the liberation of the city is characterized. With the aim of researching the personal history of Kharkiv astronomy of the studied period, the monograph presents the results of a historical and biographical study of facts of life and scientific heritage of scientists who fully devoted themselves to Science, laid the foundations for the future development of many directions of modern astronomical research, made a significant contribution to the treasury of the national and European astronomical science, whose activities were connected with the Kharkiv Astronomical Observatory, in particular: Grigory Levytsky, Ludwig Struve, Mykola Evdokymov, Otto Struve, Mykola Barabashov, Boris Gerasimovich, Vasil Fesenkov, Oleksiy Razdolsky, Boris Ostashchenko-Kudryavtsev, Nicholas Bobrovnikov, Paraskovia Parkhomenko, Mstislav Savron, Boris Semeykin, Kostyantyn Savchenko and others (25 biographical essays are presented). A significant part of the mentioned factual material was also introduced into scientific circulation for the first time. A separate section of the monograph provides chronologically structured information that reflects the sequence of research work of the Kharkiv Astronomical Observatory employees during the period under study: from astrometric observations of stars and seismic research to spectrohelioscopic and spectroheliographic observations of the Sun and the initiation of the Kharkiv school of planetary science. It is assumed that the materials of the monograph will be used in research work devoted to the study of the process of institutionalization of astronomical research in Kharkiv at the end of the 19th century – the first half of the 20th century.