Studies of Transition Metal Complexes Using Dynamic NMR Techniques.
Coston, Timothy Peter John
Available from UMI in association with The British Library. This Thesis is primarily concerned with the quantitative study of fluxional processes in, predominantly platinum(IV) complexes, with the ligands 1,1,2,2-tetrakis(methylthio)ethane (MeS)_2CHCH(SMe)_2 , and 1,1,2,2-tetrakis(methylthio)ethene (MeS) _2C=C(SMe)_2. Quantitative information relating to the energetics of these processes has been obtained by a combination of one- and two-dimensional NMR techniques. Chapter One provides an introduction to the background of fluxional processes in transition metal complexes together with data concerning the energetics of the processes that have already been studied by NMR techniques. Chapter Two provides a thorough grounding in NMR techniques, in particular those concerned with the quantitative measurement of rates involved in chemical exchange processes. A description of the use of 2D EXSY NMR spectroscopy in obtaining rate data is given. The properties of the magnetic isotope of platinum are given in Chapter Three. A general survey is also given of some additional compounds that have already been studied by platinum-195 spectroscopy. Chapter Four is concerned with the quantitative study of low temperature (complexes (PtXMe_3 (MeS)_2CHCH(SMe) _2) (X = Cl, Br, I). These complexes were studied by dynamic nuclear magnetic resonance and the information regarding the rates of sulphur inversion was obtained by complete band-shape analysis. Chapter Five is concerned with high temperature (>333 K) fluxionality, of the previous complexes, as studied by a combination of one- and two -dimensional NMR techniques. Aside from obtaining thermodynamic parameters for all the processes, a new novel mechanism is proposed. Chapter Six is primarily concerned with the NMR investigation of the new dinuclear complexes ((PtXMe _3)_2(MeS) _2CHCH(SMe)_2) (X = Cl, Br, I). The solution properties have been established and thermo-dynamic parameters obtained for low and high temperature
Carleson, Lennart
1993-01-01
Complex dynamics is today very much a focus of interest. Though several fine expository articles were available, by P. Blanchard and by M. Yu. Lyubich in particular, until recently there was no single source where students could find the material with proofs. For anyone in our position, gathering and organizing the material required a great deal of work going through preprints and papers and in some cases even finding a proof. We hope that the results of our efforts will be of help to others who plan to learn about complex dynamics and perhaps even lecture. Meanwhile books in the field a. re beginning to appear. The Stony Brook course notes of J. Milnor were particularly welcome and useful. Still we hope that our special emphasis on the analytic side will satisfy a need. This book is a revised and expanded version of notes based on lectures of the first author at UCLA over several \\Vinter Quarters, particularly 1986 and 1990. We owe Chris Bishop a great deal of gratitude for supervising the production of cour...
Large scale molecular dynamics study of polymer-surfactant complex
Goswami, Monojoy; Sumpter, Bobby
2012-02-01
In this work, we study the self-assembly of cationic polyelectrolytes mediated by anionic surfactants in dilute or semi-dilute and gel states. The understanding of the dilute system is a requirement for the understanding of gel states. The importance of polyelectrolyte with oppositely charged colloidal particles can be found in biological systems, such as immobilization of enzymes in polyelectrolyte complexes or nonspecific association of DNA with protein. With the same understanding, interaction of surfactants with polyelectrolytes shows intriguing phenomena that are important for both in academic research as well as industrial applications. Many useful properties of PE surfactant complexes come from the highly ordered structures of surfactant self-assembly inside the PE aggregate. We do large scale molecular dynamics simulation using LAMMPS to understand the structure and dynamics of PE-surfactant systems. Our investigation shows highly ordered ring-string structures that have been observed experimentally in biological systems. We will investigate many different properties of PE-surfactant complexation which will be helpful for pharmaceutical, engineering and biological applications.
Studying microstructural dynamics of complex fluids with particle tracking microrheology
Breedveld, Victor
2004-11-01
Over the last decade, particle tracking microrheology has matured as a new tool for complex fluids research. The main advantages of microrheology over traditional macroscopic rheometry are: the required sample size is extremely small ( ˜ 1 microliter); local viscoelastic properties in a sample can be probed with high spatial resolution ( ˜1-10 micrometer); and the sample is not disturbed by moving rheometer parts. I will present two examples of recent work in my group that highlight how these characteristics can be exploited to acquire unique information about the microstructure of complex fluids. First, we have studied protein unfolding. Traditionally, protein unfolding is studied with spectroscopic techniques (circular dichroism, NMR, fluorescence). Although viscosity has been listed in textbooks as a suitable technique, few -if any- quantitative rheological studies of unfolding have been reported, mainly due to technical difficulties. With microrheology, we have been able to quantify the size of the folded and unfolded protein, as well as the Gibbs free energy of unfolding, for aqueous bovine serum albumine solutions upon addition of urea as a denaturant. The results are in excellent agreement with literature data. Secondly, we have developed new technology for studying the microstructural dynamics of solvent-responsive complex fluids. In macroscopic rheometry it is virtually impossible to change solvent composition and measure the rheological response of a sample. By integrating microfluidics and microrheology we have been able to overcome this barrier: due to the micrometer lengthscales in microfluidiv devices, diffusive timescales in a dialysis set-up become short enough to achieve rapid and reversible changes in sample composition, without affecting the concentration of macromolecular components. Our dialysis cell for microrheology is a unique tool for studying the dynamics of structural and rheological changes induced by solvent composition. I will
Study of the structure and dynamics of complex biological networks
Samal, Areejit
2008-12-01
In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large scale metabolic networks inside three organisms, Escherichia coli, Saccharomyces cerevisiae and Staphylococcus aureus. We also study the dynamics of the large scale genetic network controlling E. coli metabolism. We have tried to explain the observed system level dynamical properties of these networks in terms of their underlying structure. Our studies of the system level dynamics of these large scale biological networks provide a different perspective on their functioning compared to that obtained from purely structural studies. Our study also leads to some new insights on features such as robustness, fragility and modularity of these large scale biological networks. We also shed light on how different networks inside the cell such as metabolic networks and genetic networks are interrelated to each other.
Molecular Dynamic Studies of the Complex Polyethylenimine and Glucose Oxidase
Directory of Open Access Journals (Sweden)
Beata Szefler
2016-10-01
Full Text Available Glucose oxidase (GOx is an enzyme produced by Aspergillus, Penicillium and other fungi species. It catalyzes the oxidation of β-d-glucose (by the molecular oxygen or other molecules, like quinones, in a higher oxidation state to form d-glucono-1,5-lactone, which hydrolyses spontaneously to produce gluconic acid. A coproduct of this enzymatic reaction is hydrogen peroxide (H2O2. GOx has found several commercial applications in chemical and pharmaceutical industries including novel biosensors that use the immobilized enzyme on different nanomaterials and/or polymers such as polyethylenimine (PEI. The problem of GOx immobilization on PEI is retaining the enzyme native activity despite its immobilization onto the polymer surface. Therefore, the molecular dynamic (MD study of the PEI ligand (C14N8_07_B22 and the GOx enzyme (3QVR was performed to examine the final complex PEI-GOx stabilization and the affinity of the PEI ligand to the docking sites of the GOx enzyme. The docking procedure showed two places/regions of major interaction of the protein with the polymer PEI: (LIG1 of −5.8 kcal/mol and (LIG2 of −4.5 kcal/mol located inside the enzyme and on its surface, respectively. The values of enthalpy for the PEI-enzyme complex, located inside of the protein (LIG1 and on its surface (LIG2 were computed. Docking also discovered domains of the GOx protein that exhibit no interactions with the ligand or have even repulsive characteristics. The structural data clearly indicate some differences in the ligand PEI behavior bound at the two places/regions of glucose oxidase.
Molecular Dynamic Studies of the Complex Polyethylenimine and Glucose Oxidase
Szefler, Beata; Diudea, Mircea V.; Putz, Mihai V.; Grudzinski, Ireneusz P.
2016-01-01
Glucose oxidase (GOx) is an enzyme produced by Aspergillus, Penicillium and other fungi species. It catalyzes the oxidation of β-d-glucose (by the molecular oxygen or other molecules, like quinones, in a higher oxidation state) to form d-glucono-1,5-lactone, which hydrolyses spontaneously to produce gluconic acid. A coproduct of this enzymatic reaction is hydrogen peroxide (H2O2). GOx has found several commercial applications in chemical and pharmaceutical industries including novel biosensors that use the immobilized enzyme on different nanomaterials and/or polymers such as polyethylenimine (PEI). The problem of GOx immobilization on PEI is retaining the enzyme native activity despite its immobilization onto the polymer surface. Therefore, the molecular dynamic (MD) study of the PEI ligand (C14N8_07_B22) and the GOx enzyme (3QVR) was performed to examine the final complex PEI-GOx stabilization and the affinity of the PEI ligand to the docking sites of the GOx enzyme. The docking procedure showed two places/regions of major interaction of the protein with the polymer PEI: (LIG1) of −5.8 kcal/mol and (LIG2) of −4.5 kcal/mol located inside the enzyme and on its surface, respectively. The values of enthalpy for the PEI-enzyme complex, located inside of the protein (LIG1) and on its surface (LIG2) were computed. Docking also discovered domains of the GOx protein that exhibit no interactions with the ligand or have even repulsive characteristics. The structural data clearly indicate some differences in the ligand PEI behavior bound at the two places/regions of glucose oxidase. PMID:27801788
Molecular Dynamic Studies of the Complex Polyethylenimine and Glucose Oxidase.
Szefler, Beata; Diudea, Mircea V; Putz, Mihai V; Grudzinski, Ireneusz P
2016-10-27
Glucose oxidase (GOx) is an enzyme produced by Aspergillus, Penicillium and other fungi species. It catalyzes the oxidation of β-d-glucose (by the molecular oxygen or other molecules, like quinones, in a higher oxidation state) to form d-glucono-1,5-lactone, which hydrolyses spontaneously to produce gluconic acid. A coproduct of this enzymatic reaction is hydrogen peroxide (H₂O₂). GOx has found several commercial applications in chemical and pharmaceutical industries including novel biosensors that use the immobilized enzyme on different nanomaterials and/or polymers such as polyethylenimine (PEI). The problem of GOx immobilization on PEI is retaining the enzyme native activity despite its immobilization onto the polymer surface. Therefore, the molecular dynamic (MD) study of the PEI ligand (C14N8_07_B22) and the GOx enzyme (3QVR) was performed to examine the final complex PEI-GOx stabilization and the affinity of the PEI ligand to the docking sites of the GOx enzyme. The docking procedure showed two places/regions of major interaction of the protein with the polymer PEI: (LIG1) of -5.8 kcal/mol and (LIG2) of -4.5 kcal/mol located inside the enzyme and on its surface, respectively. The values of enthalpy for the PEI-enzyme complex, located inside of the protein (LIG1) and on its surface (LIG2) were computed. Docking also discovered domains of the GOx protein that exhibit no interactions with the ligand or have even repulsive characteristics. The structural data clearly indicate some differences in the ligand PEI behavior bound at the two places/regions of glucose oxidase.
Inelastic neutron scattering and lattice dynamics studies in complex solids
Indian Academy of Sciences (India)
Mala N Rao; R Mittal; Narayani Choudhury; S L Chaplot
2004-07-01
At Trombay, lattice dynamics studies employing coherent inelastic neutron scattering (INS) experiments have been carried out at the two research reactors, CIRUS and Dhruva. While the early work at CIRUS involved many elemental solids and ionic molecular solids, recent experiments at Dhruva have focussed on certain superconductors (cuprates and intermetallics), geophysically important minerals (Al2SiO5, ZrSiO4, MnCO3) and layered halides (BaFCl, ZnCl2). In most of the studies, theoretical modelling of lattice dynamics has played a significant role in the interpretation and analysis of the results from experiments. This talk summarises the developments and current activities in the field of inelastic neutron scattering and lattice dynamics at Trombay.
Structural dynamics in complex liquids studied with multidimensional vibrational spectroscopy
Energy Technology Data Exchange (ETDEWEB)
Tokmakoff, Andrei [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
2013-08-31
The development of new sustainable energy sources is linked to our understanding of the molecular properties of water and aqueous solutions. Energy conversion, storage, and transduction processes, particularly those that occur in biology, fuel cells, and batteries, make use of water for the purpose of moving energy in the form of charges and mediating the redox chemistry that allows this energy to be stored as and released from chemical bonds. To build our fundamental knowledge in this area, this project supports work in the Tokmakoff group to investigate the molecular dynamics of water’s hydrogen bond network, and how these dynamics influence its solutes and the mechanism of proton transport in water. To reach the goals of this grant, we developed experiments to observe molecular dynamics in water as directly as possible, using ultrafast multidimensional vibrational spectroscopy. We excite and probe broad vibrational resonances of water, molecular solutes, and protons in water. By correlating how molecules evolve from an initial excitation frequency to a final frequency, we can describe the underlying molecular dynamics. Theoretical modeling of the data with the help of computational spectroscopy coupled with molecular dynamics simulations provided the atomistic insight in these studies.
Complexity of gold nanoparticle formation disclosed by dynamics study
DEFF Research Database (Denmark)
Engelbrekt, Christian; Jensen, Palle Skovhus; Sørensen, Karsten
2013-01-01
Although chemically synthesized gold nanoparticles (AuNPs) from gold salt (HAuCl4) are among the most studied nanomaterials, understanding the formation mechanisms is a challenge mainly due to limited dynamics information. A range of in situ methods with down to millisecond (ms) time resolution...... have been employed in the present report to monitor time-dependent physical and chemical properties in aqueous solution during the chemical synthesis. Chemical synthesis of AuNPs is a reduction process accompanied by release of ions and protons, and formation of solid particles. Dynamic information......]- to form Au atoms during the early stage of the synthesis process. pH- and conductivity-dynamics point further clearly to formation of coating layers on AuNPs and adsorbate exchange between MES and starch. © 2013 American Chemical Society....
Valenza, Gaetano; Citi, Luca; Barbieri, Riccardo
2014-01-01
Measures of nonlinearity and complexity, and in particular the study of Lyapunov exponents, have been increasingly used to characterize dynamical properties of a wide range of biological nonlinear systems, including cardiovascular control. In this work, we present a novel methodology able to effectively estimate the Lyapunov spectrum of a series of stochastic events in an instantaneous fashion. The paradigm relies on a novel point-process high-order nonlinear model of the event series dynamics. The long-term information is taken into account by expanding the linear, quadratic, and cubic Wiener-Volterra kernels with the orthonormal Laguerre basis functions. Applications to synthetic data such as the Hénon map and Rössler attractor, as well as two experimental heartbeat interval datasets (i.e., healthy subjects undergoing postural changes and patients with severe cardiac heart failure), focus on estimation and tracking of the Instantaneous Dominant Lyapunov Exponent (IDLE). The novel cardiovascular assessment demonstrates that our method is able to effectively and instantaneously track the nonlinear autonomic control dynamics, allowing for complexity variability estimations.
On the study of nonlinear dynamics of complex chemical reaction systems
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
With ever-increasing attentions being paid to complex systems such as the life system, soft matter, and nano-systems, theoretical studies of non-equilibrium nonlinear problems involved in chemical dynamics are now of general interest. In this mini-review, we mainly give a brief introduction to some frontier topics in this field, namely, nonlinear state-state dynamics, nonlinear chemical dynamics on complex networks, and nonlinear dynamics in mesoscopic chemical reaction systems. Deep study of these topics will make great contribution to discovering new laws of chemical dynamics, to exploring new control methods of complex chemical processes, to figuring out the very roles of chemical processes in the life system, and to crosslinking the scientific study of chemistry, physics and biology.
Dynamics in photosynthetic transient complexes studied by paramagnetic NMR spectroscopy
Scanu, Sandra
2013-01-01
This PhD thesis focuses on fundamental aspects of protein-protein interactions. A multidisciplinary methodology for the detection and visualization of transient, lowly-populated encounter protein complexes is described. The new methodology combined paramagnetic NMR spectroscopy with computational
Complexity in Dynamical Systems
Moore, Cristopher David
The study of chaos has shown us that deterministic systems can have a kind of unpredictability, based on a limited knowledge of their initial conditions; after a finite time, the motion appears essentially random. This observation has inspired a general interest in the subject of unpredictability, and more generally, complexity; how can we characterize how "complex" a dynamical system is?. In this thesis, we attempt to answer this question with a paradigm of complexity that comes from computer science, we extract sets of symbol sequences, or languages, from a dynamical system using standard methods of symbolic dynamics; we then ask what kinds of grammars or automata are needed a generate these languages. This places them in the Chomsky heirarchy, which in turn tells us something about how subtle and complex the dynamical system's behavior is. This gives us insight into the question of unpredictability, since these automata can also be thought of as computers attempting to predict the system. In the culmination of the thesis, we find a class of smooth, two-dimensional maps which are equivalent to the highest class in the Chomsky heirarchy, the turning machine; they are capable of universal computation. Therefore, these systems possess a kind of unpredictability qualitatively different from the usual "chaos": even if the initial conditions are known exactly, questions about the system's long-term dynamics are undecidable. No algorithm exists to answer them. Although this kind of unpredictability has been discussed in the context of distributed, many-degree-of -freedom systems (for instance, cellular automata) we believe this is the first example of such phenomena in a smooth, finite-degree-of-freedom system.
Complex dynamics in nanosystems.
Ni, Xuan; Ying, Lei; Lai, Ying-Cheng; Do, Younghae; Grebogi, Celso
2013-05-01
Complex dynamics associated with multistability have been studied extensively in the past but mostly for low-dimensional nonlinear dynamical systems. A question of fundamental interest is whether multistability can arise in high-dimensional physical systems. Motivated by the ever increasing widespread use of nanoscale systems, we investigate a prototypical class of nanoelectromechanical systems: electrostatically driven Si nanowires, mathematically described by a set of driven, nonlinear partial differential equations. We develop a computationally efficient algorithm to solve the equations. Our finding is that multistability and complicated structures of basins of attraction are common types of dynamics, and the latter can be attributed to extensive transient chaos. Implications of these phenomena to device operations are discussed.
Complexity and Dynamical Depth
Directory of Open Access Journals (Sweden)
Terrence Deacon
2014-07-01
Full Text Available We argue that a critical difference distinguishing machines from organisms and computers from brains is not complexity in a structural sense, but a difference in dynamical organization that is not well accounted for by current complexity measures. We propose a measure of the complexity of a system that is largely orthogonal to computational, information theoretic, or thermodynamic conceptions of structural complexity. What we call a system’s dynamical depth is a separate dimension of system complexity that measures the degree to which it exhibits discrete levels of nonlinear dynamical organization in which successive levels are distinguished by local entropy reduction and constraint generation. A system with greater dynamical depth than another consists of a greater number of such nested dynamical levels. Thus, a mechanical or linear thermodynamic system has less dynamical depth than an inorganic self-organized system, which has less dynamical depth than a living system. Including an assessment of dynamical depth can provide a more precise and systematic account of the fundamental difference between inorganic systems (low dynamical depth and living systems (high dynamical depth, irrespective of the number of their parts and the causal relations between them.
Nonlinear dynamics and complexity
Luo, Albert; Fu, Xilin
2014-01-01
This important collection presents recent advances in nonlinear dynamics including analytical solutions, chaos in Hamiltonian systems, time-delay, uncertainty, and bio-network dynamics. Nonlinear Dynamics and Complexity equips readers to appreciate this increasingly main-stream approach to understanding complex phenomena in nonlinear systems as they are examined in a broad array of disciplines. The book facilitates a better understanding of the mechanisms and phenomena in nonlinear dynamics and develops the corresponding mathematical theory to apply nonlinear design to practical engineering.
SYNCHRONIZATION IN COMPLEX DYNAMICAL NETWORKS
Institute of Scientific and Technical Information of China (English)
WANG Xiaofan; CHEN Guanrong
2003-01-01
In the past few years, the discovery of small-world and scale-free properties of many natural and artificial complex networks has stimulated increasing interest in further studying the underlying organizing principles of various complex networks. This has led to significant advances in understanding the relationship between the topology and the dynamics of such complex networks. This paper reviews some recent research works on the synchronization phenomenon in various dynamical networks with small-world and scalefree connections.
Transformations, Dynamics and Complexity
Glazunov, Nikolaj
2011-01-01
We review and investigate some new problems and results in the field of dynamical systems generated by iteration of maps, {\\beta}-transformations, partitions, group actions, bundle dynamical systems, Hasse-Kloosterman maps, and some aspects of complexity of the systems.
Bountis, Tassos
2012-01-01
This book introduces and explores modern developments in the well established field of Hamiltonian dynamical systems. It focuses on high degree-of-freedom systems and the transitional regimes between regular and chaotic motion. The role of nonlinear normal modes is highlighted and the importance of low-dimensional tori in the resolution of the famous FPU paradox is emphasized. Novel powerful numerical methods are used to study localization phenomena and distinguish order from strongly and weakly chaotic regimes. The emerging hierarchy of complex structures in such regimes gives rise to particularly long-lived patterns and phenomena called quasi-stationary states, which are explored in particular in the concrete setting of one-dimensional Hamiltonian lattices and physical applications in condensed matter systems. The self-contained and pedagogical approach is blended with a unique balance between mathematical rigor, physics insights and concrete applications. End of chapter exercises and (more demanding) res...
Energy Technology Data Exchange (ETDEWEB)
Satoshi Matsuzaki
2002-08-01
This thesis contains the candidate's original work on excitonic structure and energy transfer dynamics of two bacterial antenna complexes as studied using spectral hole-burning spectroscopy. The general introduction is divided into two chapters (1 and 2). Chapter 1 provides background material on photosynthesis and bacterial antenna complexes with emphasis on the two bacterial antenna systems related to the thesis research. Chapter 2 reviews the underlying principles and mechanism of persistent nonphotochemical hole-burning (NPHB) spectroscopy. Relevant energy transfer theories are also discussed. Chapters 3 and 4 are papers by the candidate that have been published. Chapter 3 describes the application of NPHB spectroscopy to the Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Prosthecochloris aestuarii; emphasis is on determination of the low energy vibrational structure that is important for understanding the energy transfer process associated within three lowest energy Qy-states of the complex. The results are compared with those obtained earlier on the FMO complex from Chlorobium tepidum. In Chapter 4, the energy transfer dynamics of the B800 molecules of intact LH2 and B800-deficient LH2 complexes of the purple bacterium Rhodopseudomonas acidophila are compared. New insights on the additional decay channel of the B800 ring of bacteriochlorophyll a (BChl a) molecules are provided. General conclusions are given in Chapter 5.
Study on dynamic anti-sliding stability of a high gravity dam considering complex dam foundation
Deng-hong CHEN; Cheng-bin DU
2011-01-01
There existed some limitations when analyzing the anti-sliding seismic stability of dam-foundation system by traditional pseudo-static method and response spectrum method. The dynamic strength reduction method was used to study on the deep anti-sliding stability of a high gravity dam considering complex dam foundation under strong earthquake-induced ground action. The static analysis was firstly carried out by reducing the shear strength parameters of the dam foundation’s rock mass with equal...
Energy Technology Data Exchange (ETDEWEB)
Matsuzaki, Satoshi [Iowa State Univ., Ames, IA (United States)
2001-01-01
This thesis contains the candidate's original work on excitonic structure and energy transfer dynamics of two bacterial antenna complexes as studied using spectral hole-burning spectroscopy. The general introduction is divided into two chapters (1 and 2). Chapter 1 provides background material on photosynthesis and bacterial antenna complexes with emphasis on the two bacterial antenna systems related to the thesis research. Chapter 2 reviews the underlying principles and mechanism of persistent nonphotochemical hole-burning (NPHB) spectroscopy. Relevant energy transfer theories are also discussed. Chapters 3 and 4 are papers by the candidate that have been published. Chapter 3 describes the application of NPHB spectroscopy to the Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Prosthecochloris aestuarii; emphasis is on determination of the low energy vibrational structure that is important for understanding the energy transfer process associated within three lowest energy Q_{y}-states of the complex. The results are compared with those obtained earlier on the FMO complex from Chlorobium tepidum. In Chapter 4, the energy transfer dynamics of the B800 molecules of intact LH2 and B800-deficient LH2 complexes of the purple bacterium Rhodopseudomonas acidophila are compared. New insights on the additional decay channel of the B800 ring of bacteriochlorophyll_{a} (BChl_{a}) molecules are provided. General conclusions are given in Chapter 5. A version of the hole spectrum simulation program written by the candidate for the FMO complex study (Chapter 3) is included as an appendix. The references for each chapter are given at the end of each chapter.
Energy Technology Data Exchange (ETDEWEB)
Satoshi Matsuzaki
2002-06-27
This thesis contains the candidate's original work on excitonic structure and energy transfer dynamics of two bacterial antenna complexes as studied using spectral hole-burning spectroscopy. The general introduction is divided into two chapters (1 and 2). Chapter 1 provides background material on photosynthesis and bacterial antenna complexes with emphasis on the two bacterial antenna systems related to the thesis research. Chapter 2 reviews the underlying principles and mechanism of persistent nonphotochemical hole-burning (NPHB) spectroscopy. Relevant energy transfer theories are also discussed. Chapters 3 and 4 are papers by the candidate that have been published. Chapter 3 describes the application of NPHB spectroscopy to the Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Prosthecochloris aestuarii; emphasis is on determination of the low energy vibrational structure that is important for understanding the energy transfer process associated within three lowest energy Q{sub y}-states of the complex. The results are compared with those obtained earlier on the FMO complex from Chlorobium tepidum. In Chapter 4, the energy transfer dynamics of the B800 molecules of intact LH2 and B800-deficient LH2 complexes of the purple bacterium Rhodopseudomonas acidophila are compared. New insights on the additional decay channel of the B800 ring of bacteriochlorophyll{sub a} (BChl{sub a}) molecules are provided. General conclusions are given in Chapter 5. A version of the hole spectrum simulation program written by the candidate for the FMO complex study (Chapter 3) is included as an appendix. The references for each chapter are given at the end of each chapter.
Complex and Fractional Dynamics
Directory of Open Access Journals (Sweden)
J. A. Tenreiro Machado
2017-02-01
Full Text Available Complex systems (CS are pervasive in many areas, namely financial markets; highway transportation; telecommunication networks; world and country economies; social networks; immunological systems; living organisms; computational systems; and electrical and mechanical structures. CS are often composed of a large number of interconnected and interacting entities exhibiting much richer global scale dynamics than could be inferred from the properties and behavior of individual elements. [...
Theoretical Studies on Docking Dynamics and Electronic Structure in Metalloprotein Complexes
Sugiyama, Ayumu; Nishikawa, Keigo; Yamamoto, Tetsunori; Purqon, Acep; Nishikawa, Kiyoshi; Nagao, Hidemi
2007-12-01
An investigating of docking structure and dynamics between metalloprotein is interested from the viewpoint of searching the function of protein. We investigate the cytochrome c551 and azurin complexes by three computational methods, quantum mechanical calculation, docking searching algorism and molecular dynamics simulation. At first we present the docking structure of the cytochrome c551-azurin complexes expected by ZDOCK searching algorism. Quantum chemical calculation is tools to estimate the charge distrubution around the active site for each protein and force field parameters. From these parameters, we reproduce the protein docking dynamics by molecular dynamics simulation. We analyze some physical properties of complex system such as binding free energy, dynamical cross correlation map, and so on. We discuss the docking stability and dynamical effect of the cytochrome c551-azurin complexes.
Permutation Complexity in Dynamical Systems
Amigo, Jose
2010-01-01
The study of permutation complexity can be envisioned as a new kind of symbolic dynamics whose basic blocks are ordinal patterns, that is, permutations defined by the order relations among points in the orbits of dynamical systems. Since its inception in 2002 the concept of permutation entropy has sparked a new branch of research in particular regarding the time series analysis of dynamical systems that capitalizes on the order structure of the state space. Indeed, on one hand ordinal patterns and periodic points are closely related, yet ordinal patterns are amenable to numerical methods, while periodicity is not. Another interesting feature is that since it can be shown that random (unconstrained) dynamics has no forbidden patterns with probability one, their existence can be used as a fingerprint to identify any deterministic origin of orbit generation. This book is primarily addressed to researchers working in the field of nonlinear dynamics and complex systems, yet will also be suitable for graduate stude...
Study on dynamic anti-sliding stability of a high gravity dam considering complex dam foundation
Directory of Open Access Journals (Sweden)
Deng-hong CHEN
2011-06-01
Full Text Available There existed some limitations when analyzing the anti-sliding seismic stability of dam-foundation system by traditional pseudo-static method and response spectrum method. The dynamic strength reduction method was used to study on the deep anti-sliding stability of a high gravity dam considering complex dam foundation under strong earthquake-induced ground action. The static analysis was firstly carried out by reducing the shear strength parameters of the dam foundation’s rock mass with equal proportion. Then, the time-history seismic analysis was carried out based on the static analysis. It was proposed as one of dynamic instability criterions that the peak values of the dynamic displacements and plastic strain energy change suddenly with increasing strength reduction coefficient. The elasto-plastic behavior of the dam foundation was idealized using Drucker–Prager yield criterion based on associated flow rule assumption. Through the static, dynamic strength reduction analysis and dynamic linear elastic analysis of the overflow dam monolith of a high gravity dam, the results’ reliability of elastic-plastic time history analysis was confirmed. The results also showed that the rock mass strength of the high gravity dam foundation has higher strength reserve coefficient. The instability criterions of dynamic strength reduction method proposed were feasible. Although the static anti-slide analysis methods and standards of gravity dam based on the numerical methods are being discussed at present, the dynamic calculation method and instability criterions proposed in this paper would provide some meaningful suggestions for the dynamic analysis of the similar projects.
Epidemic dynamics on complex networks
Institute of Scientific and Technical Information of China (English)
ZHOU Tao; FU Zhongqian; WANG Binghong
2006-01-01
Recently, motivated by the pioneer work in revealing the small-world effect and scale-free property of various real-life networks, many scientists devote themselves to studying complex networks. One of the ultimate goals is to understand how the topological structures affect the dynamics upon networks. In this paper, we give a brief review on the studies of epidemic dynamics on complex networks, including the description of classical epidemic models, the epidemic spread on small-world and scale-free networks, and network immunization. Finally, perspectives and some interesting problems are proposed.
Coordination mode of nitrate in uranyl(VI) complexes: a first-principles molecular dynamics study.
Bühl, Michael; Diss, Romain; Wipff, Georges
2007-06-25
According to Car-Parrinello molecular dynamics simulations for [UO(2)(NO(3))(3)](-), [UO(2)(NO(3))(4)](2-), and [UO(2)(OH(2))(4-)(NO(3))](+) complexes in the gas phase and in aqueous solution, the nitrate coordination mode to uranyl depends on the interplay between ligand-metal attractions, interligand repulsions, and solvation. In the trinitrate, the eta(2)-coordination is clearly favored in water and in the gas phase, leading to a coordination number (CN) of 6. According to pointwise thermodynamic integration involving constrained molecular dynamics simulations, a change in free energy of +6 kcal/mol is predicted for eta(2)- to eta(1)-transition of one of the three nitrate ligands in the gas phase. In the gas phase, the mononitrate-hydrate complex also prefers a eta(2)-binding mode but with a CN of 5, one H(2)O molecule being in the second shell. This contrasts with the aqueous solution where the nitrate binds in a eta(1)-fashion and uranyl coordinates to four H2O ligands. A driving force of ca. -3 kcal/mol is predicted for the eta(2)- to eta(1)- transition in water. This structural preference is interpreted in terms of steric arguments and differential solvation of terminal vs uranyl-coordinated O atoms of the nitrate ligands. The [UO(2)(NO(3))(4)](2-) complex with two eta(2)- and two eta(1)- coordinated nitrates, observed in the solid state, is stable for 1-2 ps in the gas phase and in solution. In the studied series, the modulation of uranyl-ligand distances upon immersion of the complex in water is found to depend on the nature of the ligand and the composition of the complex.
Devleesschauwer, Brecht; Aryal, Arjun; Tharmalingam, Jayaraman; Joshi, Durga Datt; Rijal, Suman; Speybroeck, Niko; Gabriël, Sarah; Victor, Bjorn; Dorny, Pierre
2013-03-31
The transmission dynamics of the pork tapeworm, Taenia solium, remain a matter of research and debate. In a longitudinal field study performed in southeastern Nepal, 18 sentinel pigs were serologically monitored to study the field kinetics of Taenia antigens and anti-T. solium antibodies. At the end of the twelve months' study period, necropsy was performed and suspected lesions were subjected to molecular identification of the Taenia species. The study generated new hypotheses on the transmission dynamics of Taenia spp. and exposed crucial complexities in the use of sentinel pigs in longitudinal field studies. Sentinel pigs can be useful epidemiological tools, but their use should be thoroughly planned before initiating a study and carefully monitored throughout the course of the study. Important aspects to be considered are those affecting the pig's susceptibility to infection, such as passive immunity, age, hormonal levels, and infection with competing Taenia species. In addition, serological test results should be interpreted considering possible cross-reactions and with proper understanding of the significance of a positive test result.
Theoretical research progress in complexity of complex dynamical networks
Institute of Scientific and Technical Information of China (English)
Fang Jinqing
2007-01-01
This article reviews the main progress in dynamical complexity of theoretical models for nonlinear complex networks proposed by our Joint Complex Network Research Group (JCNRG). The topological and dynamical properties of these theoretical models are numerically and analytically studied. Several findings are useful for understanding and deeply studying complex networks from macroscopic to microscopic levels and have a potential of applications in real-world networks.
First principles molecular dynamics study of nitrogen vacancy complexes in boronitrene.
Ukpong, A M; Chetty, N
2012-07-04
We present the results of first principles molecular dynamics simulations of nitrogen vacancy complexes in monolayer hexagonal boron nitride. The threshold for local structure reconstruction is found to be sensitive to the presence of a substitutional carbon impurity. We show that activated nitrogen dynamics triggers the annihilation of defects in the layer through formation of Stone-Wales-type structures. The lowest energy state of nitrogen vacancy complexes is negatively charged and spin polarized. Using the divacancy complex, we show that their formation induces spontaneous magnetic moments, which is tunable by electron or hole injection. The Fermi level s-resonant defect state is identified as a unique signature of the ground state of the divacancy complex. Due to their ability to enhance structural cohesion, only the divacancy and the nitrogen vacancy carbon-antisite complexes are able to suppress the Fermi level resonant defect state to open a gap between the conduction and valence bands.
Sala, Adrien; Shoaib, Muhammad; Anufrieva, Olga; Mutharasu, Gnanavel; Jahan Hoque, Rawnak; Yli-Harja, Olli; Kandhavelu, Meenakshisundaram
2015-05-19
In E. coli, promoter closed and open complexes are key steps in transcription initiation, where magnesium-dependent RNA polymerase catalyzes RNA synthesis. However, the exact mechanism of initiation remains to be fully elucidated. Here, using single mRNA detection and dual reporter studies, we show that increased intracellular magnesium concentration affects Plac initiation complex formation resulting in a highly dynamic process over the cell growth phases. Mg2+ regulates transcription transition, which modulates bimodality of mRNA distribution in the exponential phase. We reveal that Mg2+ regulates the size and frequency of the mRNA burst by changing the open complex duration. Moreover, increasing magnesium concentration leads to higher intrinsic and extrinsic noise in the exponential phase. RNAP-Mg2+ interaction simulation reveals critical movements creating a shorter contact distance between aspartic acid residues and Nucleotide Triphosphate residues and increasing electrostatic charges in the active site. Our findings provide unique biophysical insights into the balanced mechanism of genetic determinants and magnesium ion in transcription initiation regulation during cell growth.
JIDT: An information-theoretic toolkit for studying the dynamics of complex systems
Lizier, Joseph T
2014-01-01
Complex systems are increasingly being viewed as distributed information processing systems, particularly in the domains of computational neuroscience, bioinformatics and Artificial Life. This trend has resulted in a strong uptake in the use of (Shannon) information-theoretic measures to analyse the dynamics of complex systems in these fields. We introduce the Java Information Dynamics Toolkit (JIDT): a Google code project which provides a standalone, (GNU GPL v3 licensed) open-source code implementation for empirical estimation of information-theoretic measures from time-series data. While the toolkit provides classic information-theoretic measures (e.g. entropy, mutual information, conditional mutual information), it ultimately focusses on implementing higher-level measures for information dynamics. That is, JIDT focusses on quantifying information storage, transfer and modification, and the dynamics of these operations in space and time. For this purpose, it includes implementations of the transfer entropy...
Project Dynamics and Emergent Complexity
Schlick, Christopher M
2011-01-01
The present paper presents theoretical and empirical analyses of project dynamics and emergent complexity in new product development (NPD) projects. A model-driven approach was taken and a vector autoregression (VAR) model of cooperative task processing was formulated. The model is explained and validated based on an empirical study carried out in a industrial company. Furthermore, concepts and measures of complex systems science were reviewed and applied to project management. To evaluate emergent complexity in NPD projects, an information-theory quantity -termed "effective measure complexity" (EMC)- was selected, because it can be derived from first principles and therefore has high construct validity. Furthermore, EMC can be calculated efficiently from generative models of task processing or purely from historical data, without intervening models. EMC measures the mutual information between the infinite past and future histories of a stochastic process. According to this principle, it is particularly inter...
Complex dynamics of epileptic EEG.
Kannathal, N; Puthusserypady, Sadasivan K; Choo Min, Lim
2004-01-01
Electroencephalogram (EEG) - the recorded representation of electrical activity of the brain contain useful information about the state of the brain. Recent studies indicate that nonlinear methods can extract valuable information from neuronal dynamics. We compare the dynamical properties of EEG signals of healthy subjects with epileptic subjects using nonlinear time series analysis techniques. Chaotic invariants like correlation dimension (D2) , largest Lyapunov exponent (lambda1), Hurst exponent (H) and Kolmogorov entropy (K) are used to characterize the signal. Our study showed clear differences in dynamical properties of brain electrical activity of the normal and epileptic subjects with a confidence level of more than 90%. Furthermore to support this claim fractal dimension (FD) analysis is performed. The results indicate reduction in value of FD for epileptic EEG indicating reduction in system complexity.
Energy Technology Data Exchange (ETDEWEB)
Fani, N. [Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111 (Iran, Islamic Republic of); Bordbar, A.K., E-mail: bordbar@chem.ui.ac.ir [Department of Chemistry, University of Isfahan, Isfahan 81746-73441 (Iran, Islamic Republic of); Ghayeb, Y. [Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111 (Iran, Islamic Republic of)
2013-09-15
This study was designed to examine the interaction of two Schiff base complexes with human serum albumin (HSA), by different kinds of spectroscopic and molecular modeling techniques. Fluorescence quenching and absorption spectra were investigated in order to estimate the binding parameters. The analysis of absorption data at different temperatures were done in order to estimate the thermodynamics parameters of interactions between Schiff base complexes and HSA. The experimental data suggested that both complexes demonstrated a significant binding affinity to HSA and the process is enthalpy driven. Molecular docking study indicated that both Schiff base complexes bind to polar and apolar residues located in the subdomain IB of HSA. Molecular dynamics (MD) simulations were also performed with the GROMACS program package to study the characters of HSA in binding states. Molecular dynamics results suggested that both Schiff base complexes can interact with HSA, without affecting the secondary structure of HSA but probably with a slight modification of its tertiary structure. All the molecular docking and molecular dynamics results kept in good consistence with experimental data. -- Highlights: • The fluorescence of HSA quenched due to reacting with Schiff base complexes. • The absorbance of Schiff base complexes in the presence of HSA changed. • Binding parameters and the pose of the molecules in the binding site were estimated. • Both complexes can interact with HSA, without affecting the secondary structure. • Simulation results predicted slight compactness of tertiary structure for HSA.
Butkus, Vytautas; Augulis, Ramūnas; Gall, Andrew; Büchel, Claudia; Robert, Bruno; Zigmantas, Donatas; Valkunas, Leonas; Abramavicius, Darius
2015-01-01
The energy transfer processes and coherent phenomena in the fucoxanthin-chlorophyll protein complex, which is responsible for the light harvesting function in marine algae diatoms, were investigated at 77 K by using two-dimensional electronic spectroscopy. Experiments performed on the femtosecond and picosecond timescales led to separation of spectral dynamics, witnessing evolutions of coherence and population states of the system in the spectral region of ${\\rm Q}_{y}$ transitions of chlorophylls $a$ and $c$. Analysis of the coherence dynamics allowed us to identify chlorophyll (Chl) $a$ and fucoxanthin intramolecular vibrations dominating over the first few picoseconds. Closer inspection of the spectral region of the ${\\rm Q}_{y}$ transition of Chl $c$ revealed previously not identified mutually non-interacting chlorophyll $c$ states participating in femtosecond or picosecond energy transfer to the Chl $a$ molecules. Consideration of separated coherent and incoherent dynamics allowed us to hypothesize the v...
Butkus, Vytautas; Gelzinis, Andrius; Augulis, Ramūnas; Gall, Andrew; Büchel, Claudia; Robert, Bruno; Zigmantas, Donatas; Valkunas, Leonas; Abramavicius, Darius
2015-06-07
Energy transfer processes and coherent phenomena in the fucoxanthin-chlorophyll protein complex, which is responsible for the light harvesting function in marine algae diatoms, were investigated at 77 K by using two-dimensional electronic spectroscopy. Experiments performed on femtosecond and picosecond timescales led to separation of spectral dynamics, witnessing evolutions of coherence and population states of the system in the spectral region of Qy transitions of chlorophylls a and c. Analysis of the coherence dynamics allowed us to identify chlorophyll (Chl) a and fucoxanthin intramolecular vibrations dominating over the first few picoseconds. Closer inspection of the spectral region of the Qy transition of Chl c revealed previously not identified, mutually non-interacting chlorophyll c states participating in femtosecond or picosecond energy transfer to the Chl a molecules. Consideration of separated coherent and incoherent dynamics allowed us to hypothesize the vibrations-assisted coherent energy transfer between Chl c and Chl a and the overall spatial arrangement of chlorophyll molecules.
JIDT: An information-theoretic toolkit for studying the dynamics of complex systems
Directory of Open Access Journals (Sweden)
Joseph Troy Lizier
2014-12-01
Full Text Available Complex systems are increasingly being viewed as distributed information processing systems, particularly in the domains of computational neuroscience, bioinformatics and Artificial Life. This trend has resulted in a strong uptake in the use of (Shannon information-theoretic measures to analyse the dynamics of complex systems in these fields. We introduce the Java Information Dynamics Toolkit (JIDT: a Google code project which provides a standalone, (GNU GPL v3 licensed open-source code implementation for empirical estimation of information-theoretic measures from time-series data. While the toolkit provides classic information-theoretic measures (e.g. entropy, mutual information, conditional mutual information, it ultimately focusses on implementing higher-level measures for information dynamics. That is, JIDT focusses on quantifying information storage, transfer and modification, and the dynamics of these operations in space and time. For this purpose, it includes implementations of the transfer entropy and active information storage, their multivariate extensions and local or pointwise variants. JIDT provides implementations for both discrete and continuous-valued data for each measure, including various types of estimator for continuous data (e.g. Gaussian, box-kernel and Kraskov-Stoegbauer-Grassberger which can be swapped at run-time due to Java's object-oriented polymorphism. Furthermore, while written in Java, the toolkit can be used directly in MATLAB, GNU Octave, Python and other environments. We present the principles behind the code design, and provide several examples to guide users.
Dynamic Development of Complexity and Accuracy: A Case Study in Second Language Academic Writing
Rosmawati
2014-01-01
This paper reports on the development of complexity and accuracy in English as a Second Language (ESL) academic writing. Although research into complexity and accuracy development in second language (L2) writing has been well established, few studies have assumed the multidimensionality of these two constructs (Norris & Ortega, 2009) or…
Dynamic Development of Complexity and Accuracy: A Case Study in Second Language Academic Writing
Rosmawati
2014-01-01
This paper reports on the development of complexity and accuracy in English as a Second Language (ESL) academic writing. Although research into complexity and accuracy development in second language (L2) writing has been well established, few studies have assumed the multidimensionality of these two constructs (Norris & Ortega, 2009) or…
Studies of Structure and Dynamics of Light Harvesting Complex 1 of R. Sphaeroides by Solid State NMR
Energy Technology Data Exchange (ETDEWEB)
McDermott, Ann E [Columbia Univ., New York, NY (United States)
2014-11-14
Studies of the structure and dynamics of a light harvesting complex from photosynthetic bacteria are described. Using Nuclear Magnetic Resonance methods, we explored the idea that optical properties are modulated via a conformational switch in the BChl chromophores, in a way that provides benefits for the efficiency of energy conversion.
Complex dynamical invariants for two-dimensional complex potentials
Indian Academy of Sciences (India)
J S Virdi; F Chand; C N Kumar; S C Mishra
2012-08-01
Complex dynamical invariants are searched out for two-dimensional complex potentials using rationalization method within the framework of an extended complex phase space characterized by $x = x_{1} + ip_{3}. y = x_{2} + ip_{4}, p_{x} = p_{1} + ix_{3}, p_{y} = p_{2} + ix_{4}$. It is found that the cubic oscillator and shifted harmonic oscillator admit quadratic complex invariants. THe obtained invariants may be useful for studying non-Hermitian Hamiltonian systems.
Managing Complex Dynamical Systems
Cox, John C.; Webster, Robert L.; Curry, Jeanie A.; Hammond, Kevin L.
2011-01-01
Management commonly engages in a variety of research designed to provide insight into the motivation and relationships of individuals, departments, organizations, etc. This paper demonstrates how the application of concepts associated with the analysis of complex systems applied to such data sets can yield enhanced insights for managerial action.
Molecular dynamics studies of the HIV-1 TAR and its complex with argininamide
Nifosì, Riccardo; Reyes, Carolina M.; Kollman, Peter A.
2000-01-01
The dynamic behavior of HIV-1 TAR and its complex with argininamide is investigated by means of molecular dynamics simulations starting from NMR structures, with explicit inclusion of water and periodic boundary conditions particle mesh Ewald representation of the electrostatic energy. During simulations of free and argininamide-bound TAR, local structural patterns, as determined by NMR experiments, were reproduced. An interdomain motion was observed in the simulations of free TAR, which is absent in the case of bound TAR, leading to the conclusion that the free conformation of TAR is intrinsically more flexible than the bound conformation. In particular, in the bound conformation the TAR–argininamide interface is very well ordered, as a result of the formation of a U·A·U base triple, which imposes structural constraints on the global conformation of the molecule. Free energy analysis, which includes solvation contributions, was used to evaluate the influence of van der Waals and electrostatic terms on formation of the complex and on the conformational rearrangement from free to bound TAR. PMID:11121486
Coarse-graining complex dynamics
DEFF Research Database (Denmark)
Sibani, Paolo
2013-01-01
Continuous Time Random Walks (CTRW) are widely used to coarse-grain the evolution of systems jumping from a metastable sub-set of their configuration space, or trap, to another via rare intermittent events. The multi-scaled behavior typical of complex dynamics is provided by a fat-tailed distribu......Continuous Time Random Walks (CTRW) are widely used to coarse-grain the evolution of systems jumping from a metastable sub-set of their configuration space, or trap, to another via rare intermittent events. The multi-scaled behavior typical of complex dynamics is provided by a fat......-law and logarithmic relaxation behaviors ubiquitous in complex dynamics, together with the sub-diffusive time dependence of the Mean Square Displacement characteristic of single particles moving in a complex environment....
Energy Technology Data Exchange (ETDEWEB)
Butkus, Vytautas; Gelzinis, Andrius; Valkunas, Leonas [Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio Ave. 9-III, 10222 Vilnius (Lithuania); Center for Physical Sciences and Technology, Savanoriu Ave. 231, 02300 Vilnius (Lithuania); Augulis, Ramūnas [Center for Physical Sciences and Technology, Savanoriu Ave. 231, 02300 Vilnius (Lithuania); Gall, Andrew; Robert, Bruno [Institut de Biologie et Technologies de Saclay, Bât 532, Commissariat à l’Energie Atomique Saclay, 91191 Gif sur Yvette (France); Büchel, Claudia [Institut für Molekulare Biowissenschaften, Universität Frankfurt, Max-von-Laue-Straße 9, Frankfurt (Germany); Zigmantas, Donatas [Department of Chemical Physics, Lund University, P.O. Box 124, 22100 Lund (Sweden); Abramavicius, Darius, E-mail: darius.abramavicius@ff.vu.lt [Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio Ave. 9-III, 10222 Vilnius (Lithuania)
2015-06-07
Energy transfer processes and coherent phenomena in the fucoxanthin–chlorophyll protein complex, which is responsible for the light harvesting function in marine algae diatoms, were investigated at 77 K by using two-dimensional electronic spectroscopy. Experiments performed on femtosecond and picosecond timescales led to separation of spectral dynamics, witnessing evolutions of coherence and population states of the system in the spectral region of Q{sub y} transitions of chlorophylls a and c. Analysis of the coherence dynamics allowed us to identify chlorophyll (Chl) a and fucoxanthin intramolecular vibrations dominating over the first few picoseconds. Closer inspection of the spectral region of the Q{sub y} transition of Chl c revealed previously not identified, mutually non-interacting chlorophyll c states participating in femtosecond or picosecond energy transfer to the Chl a molecules. Consideration of separated coherent and incoherent dynamics allowed us to hypothesize the vibrations-assisted coherent energy transfer between Chl c and Chl a and the overall spatial arrangement of chlorophyll molecules.
Complex networks: Dynamics and security
Indian Academy of Sciences (India)
Ying-Cheng Lai; Adilson Motter; Takashi Nishikawa; Kwangho Park; Liang Zhao
2005-04-01
This paper presents a perspective in the study of complex networks by focusing on how dynamics may affect network security under attacks. In particular, we review two related problems: attack-induced cascading breakdown and range-based attacks on links. A cascade in a network means the failure of a substantial fraction of the entire network in a cascading manner, which can be induced by the failure of or attacks on only a few nodes. These have been reported for the internet and for the power grid (e.g., the August 10, 1996 failure of the western United States power grid). We study a mechanism for cascades in complex networks by constructing a model incorporating the flows of information and physical quantities in the network. Using this model we can also show that the cascading phenomenon can be understood as a phase transition in terms of the key parameter characterizing the node capacity. For a parameter value below the phase-transition point, cascading failures can cause the network to disintegrate almost entirely. We will show how to obtain a theoretical estimate for the phase-transition point. The second problem is motivated by the fact that most existing works on the security of complex networks consider attacks on nodes rather than on links. We address attacks on links. Our investigation leads to the finding that many scale-free networks are more sensitive to attacks on short-range than on long-range links. Considering that the small-world phenomenon in complex networks has been identified as being due to the presence of long-range links, i.e., links connecting nodes that would otherwise be separated by a long node-to-node distance, our result, besides its importance concerning network efficiency and security, has the striking implication that the small-world property of scale-free networks is mainly due to short-range links.
Keaveny, Eric E; Pivkin, Igor V; Maxey, Martin; Em Karniadakis, George
2005-09-08
The purpose of this study is to compare the results from molecular-dynamics and dissipative particle dynamics (DPD) simulations of Lennard-Jones (LJ) fluid and determine the quantitative effects of DPD coarse graining on flow parameters. We illustrate how to select the conservative force coefficient, the cut-off radius, and the DPD time scale in order to simulate a LJ fluid. To show the effects of coarse graining and establish accuracy in the DPD simulations, we conduct equilibrium simulations, Couette flow simulations, Poiseuille flow simulations, and simulations of flow around a periodic array of square cylinders. For the last flow problem, additional comparisons are performed against continuum simulations based on the spectral/hp element method.
Wealth dynamics on complex networks
Garlaschelli, Diego; Loffredo, Maria I.
2004-07-01
We study a model of wealth dynamics (Physica A 282 (2000) 536) which mimics transactions among economic agents. The outcomes of the model are shown to depend strongly on the topological properties of the underlying transaction network. The extreme cases of a fully connected and a fully disconnected network yield power-law and log-normal forms of the wealth distribution, respectively. We perform numerical simulations in order to test the model on more complex network topologies. We show that the mixed form of most empirical distributions (displaying a non-smooth transition from a log-normal to a power-law form) can be traced back to a heterogeneous topology with varying link density, which on the other hand is a recently observed property of real networks.
Khlebtsov, Boris N.; Burygin, Gennadii L.; Matora, Larisa Y.; Shchyogolev, Sergei Y.; Khlebtsov, Nikolai G.
2004-07-01
We describe two variants of a method for determining the average composition of insoluble immune complex particles (IICP). The first variant is based on measuring the specific turbidity (the turbidity per unit mass concentration of the dispersed substance) and the average size of IICP determined from dynamic light scattering (DLS). In the second variant, the wavelength exponent (i.e., the slope of the logarithmic turbidity spectrum) is used in combination with specific turbidity measurements. Both variants allow the average biopolymer volume fraction to be determined in terms of the average refractive index of IICP. The method is exemplified by two experimental antigen+antibody systems: (i) lipopolysaccharide-protein complex (LPPC) of Azospirillum brasilense Sp245+rabbit anti-LPPC; and (ii) human IgG (hIgG)+sheep anti-hIgG. Our measurements by the two methods for both types of systems gave, on the average, the same result: the volume fraction of the IICP biopolymers is about 30%; accordingly, the volume fraction of buffer solvent is 70%.
Complex Dynamics in Communication Networks
Kocarev, Ljupco
2005-01-01
Computer and communication networks are among society's most important infrastructures. The internet, in particular, is a giant global network of networks without central control or administration. It is a paradigm of a complex system, where complexity may arise from different sources: topological structure, network evolution, connection and node diversity, or dynamical evolution. The present volume is the first book entirely devoted to the new and emerging field of nonlinear dynamics of TCP/IP networks. It addresses both scientists and engineers working in the general field of communication networks.
ON COMPLEX DYNAMIC CONTROL SYSTEMS
Institute of Scientific and Technical Information of China (English)
CHENG Daizhan
2003-01-01
This paper presents some recent works on the control of dynamic systems, which have certain complex properties caused by singularity of the nonlinear structures, structure-varyings, or evolution process etc. First, we consider the structure singularity of nonlinear control systems. It was revealed that the focus of researches on nonlinear control theory is shifting from regular systems to singular systems. The singularity of nonlinear systems causes certain complexity. Secondly, the switched systems are considered. For such systems the complexity is caused by the structure varying. We show that the switched systems have significant characteristics of complex systems. Finally, we investigate the evolution systems. The evolution structure makes complexity, and itself is a proper model for complex systems.
Controlling edge dynamics in complex networks
Nepusz, Tamás; Vicsek, Tamás
2012-01-01
The interaction of distinct units in physical, social, biological and technological systems naturally gives rise to complex network structures. Networks have constantly been in the focus of research for the last decade, with considerable advances in the description of their structural and dynamical properties. However, much less effort has been devoted to studying the controllability of the dynamics taking place on them. Here we introduce and evaluate a dynamical process defined on the edges ...
Pinning Synchronization of Switched Complex Dynamical Networks
Directory of Open Access Journals (Sweden)
Liming Du
2015-01-01
Full Text Available Network topology and node dynamics play a key role in forming synchronization of complex networks. Unfortunately there is no effective synchronization criterion for pinning synchronization of complex dynamical networks with switching topology. In this paper, pinning synchronization of complex dynamical networks with switching topology is studied. Two basic problems are considered: one is pinning synchronization of switched complex networks under arbitrary switching; the other is pinning synchronization of switched complex networks by design of switching when synchronization cannot achieved by using any individual connection topology alone. For the two problems, common Lyapunov function method and single Lyapunov function method are used respectively, some global synchronization criteria are proposed and the designed switching law is given. Finally, simulation results verify the validity of the results.
Energy Technology Data Exchange (ETDEWEB)
Thomassin-Naggara, Isabelle [Hopital Tenon, Assistance Publique-Hopitaux de Paris, Department of Radiology, Paris (France); Laboratoire de recherche en imagerie - UMR 970 INSERM - Universite Rene Descartes, Paris (France); Service de Radiologie, Hopital Tenon, Paris (France); Balvay, Daniel [Laboratoire de recherche en imagerie - UMR 970 INSERM - Universite Rene Descartes, Paris (France); Aubert, Emilie; Bazot, Marc [Hopital Tenon, Assistance Publique-Hopitaux de Paris, Department of Radiology, Paris (France); Darai, Emile; Rouzier, Roman [Hopital Tenon, Assistance Publique-Hopitaux de Paris, Department of Gynaecology-Obstetrics, Paris (France); Cuenod, Charles A. [Laboratoire de recherche en imagerie - UMR 970 INSERM - Universite Rene Descartes, Paris (France); Hopital Europeen Georges Pompidou (HEGP), Department of Radiology, Paris (France)
2012-04-15
To evaluate the ability of quantitative dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) to differentiate malignant from benign adnexal tumours. Fifty-six women with 38 malignant and 18 benign tumours underwent MR imaging before surgery for complex adnexal masses. Microvascular parameters were extracted from high temporal resolution DCE-MRI series, using a pharmacokinetic model in the solid tissue of adnexal tumours. These parameters were tissue blood flow (F{sub T}), blood volume fraction (Vb), permeability-surface area product (PS), interstitial volume fraction (Ve), lag time (Dt) and area under the enhancing curve (rAUC). Area under the receiver operating curve (AUROC) was calculated as a descriptive tool to assess the overall discrimination of parameters. Malignant tumours displayed higher F{sub T}, Vb, rAUC and lower Ve than benign tumours (P < 0.0001, P = 0.0006, P = 0.04 and P = 0.0002, respectively). F{sub T} was the most relevant factor for discriminating malignant from benign tumours (AUROC = 0.86). Primary ovarian invasive tumours displayed higher F{sub T} and shorter Dt than borderline tumours. Malignant adnexal tumours with associated peritoneal carcinomatosis at surgery displayed a shorter Dt than those without peritoneal carcinomatosis at surgery (P = 0.01). Quantitative DCE-MRI is a feasible and accurate technique to differentiate malignant from benign adnexal tumours and could potentially help oncologists with management decisions. (orig.)
Complex networks for streamflow dynamics
Directory of Open Access Journals (Sweden)
B. Sivakumar
2014-07-01
Full Text Available Streamflow modeling is an enormously challenging problem, due to the complex and nonlinear interactions between climate inputs and landscape characteristics over a wide range of spatial and temporal scales. A basic idea in streamflow studies is to establish connections that generally exist, but attempts to identify such connections are largely dictated by the problem at hand and the system components in place. While numerous approaches have been proposed in the literature, our understanding of these connections remains far from adequate. The present study introduces the theory of networks, and in particular complex networks, to examine the connections in streamflow dynamics, with a particular focus on spatial connections. Monthly streamflow data observed over a period of 52 years from a large network of 639 monitoring stations in the contiguous United States are studied. The connections in this streamflow network are examined using the concept of clustering coefficient, which is a measure of local density and quantifies the network's tendency to cluster. The clustering coefficient analysis is performed with several different threshold levels, which are based on correlations in streamflow data between the stations. The clustering coefficient values of the 639 stations are used to obtain important information about the connections in the network and their extent, similarity and differences between stations/regions, and the influence of thresholds. The relationship of the clustering coefficient with the number of links/actual links in the network and the number of neighbors is also addressed. The results clearly indicate the usefulness of the network-based approach for examining connections in streamflow, with important implications for interpolation and extrapolation, classification of catchments, and predictions in ungaged basins.
Díaz-Rodríguez, Miguel; Valera, Angel; Page, Alvaro; Besa, Antonio; Mata, Vicente
2016-05-01
Accurate knowledge of body segment inertia parameters (BSIP) improves the assessment of dynamic analysis based on biomechanical models, which is of paramount importance in fields such as sport activities or impact crash test. Early approaches for BSIP identification rely on the experiments conducted on cadavers or through imaging techniques conducted on living subjects. Recent approaches for BSIP identification rely on inverse dynamic modeling. However, most of the approaches are focused on the entire body, and verification of BSIP for dynamic analysis for distal segment or chain of segments, which has proven to be of significant importance in impact test studies, is rarely established. Previous studies have suggested that BSIP should be obtained by using subject-specific identification techniques. To this end, our paper develops a novel approach for estimating subject-specific BSIP based on static and dynamics identification models (SIM, DIM). We test the validity of SIM and DIM by comparing the results using parameters obtained from a regression model proposed by De Leva (1996, "Adjustments to Zatsiorsky-Seluyanov's Segment Inertia Parameters," J. Biomech., 29(9), pp. 1223-1230). Both SIM and DIM are developed considering robotics formalism. First, the static model allows the mass and center of gravity (COG) to be estimated. Second, the results from the static model are included in the dynamics equation allowing us to estimate the moment of inertia (MOI). As a case study, we applied the approach to evaluate the dynamics modeling of the head complex. Findings provide some insight into the validity not only of the proposed method but also of the application proposed by De Leva (1996, "Adjustments to Zatsiorsky-Seluyanov's Segment Inertia Parameters," J. Biomech., 29(9), pp. 1223-1230) for dynamic modeling of body segments.
Thomassin-Naggara, Isabelle; Balvay, Daniel; Aubert, Emilie; Daraï, Emile; Rouzier, Roman; Cuenod, Charles A; Bazot, Marc
2012-04-01
To evaluate the ability of quantitative dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) to differentiate malignant from benign adnexal tumours. Fifty-six women with 38 malignant and 18 benign tumours underwent MR imaging before surgery for complex adnexal masses. Microvascular parameters were extracted from high temporal resolution DCE-MRI series, using a pharmacokinetic model in the solid tissue of adnexal tumours. These parameters were tissue blood flow (F(T)), blood volume fraction (Vb), permeability-surface area product (PS), interstitial volume fraction (Ve), lag time (Dt) and area under the enhancing curve (rAUC). Area under the receiver operating curve (AUROC) was calculated as a descriptive tool to assess the overall discrimination of parameters. Malignant tumours displayed higher F(T), Vb, rAUC and lower Ve than benign tumours (P < 0.0001, P = 0.0006, P = 0.04 and P = 0.0002, respectively). F(T) was the most relevant factor for discriminating malignant from benign tumours (AUROC = 0.86). Primary ovarian invasive tumours displayed higher F(T) and shorter Dt than borderline tumours. Malignant adnexal tumours with associated peritoneal carcinomatosis at surgery displayed a shorter Dt than those without peritoneal carcinomatosis at surgery (P = 0.01). Quantitative DCE-MRI is a feasible and accurate technique to differentiate malignant from benign adnexal tumours and could potentially help oncologists with management decisions. Quantitative DCE MR imaging allows accurate differentiation between malignant and benign tumours. Quantitative DCE MRI may help predict peritoneal carcinomatosis associated with ovarian tumors. Quantitative DCE MRI helps distinguish between invasive and borderline primary ovarian tumours.
Complex Dynamics of Equatorial Scintillation
Piersanti, Mirko; Materassi, Massimo; Forte, Biagio; Cicone, Antonio
2017-04-01
Radio power scintillation, namely highly irregular fluctuations of the power of trans-ionospheric GNSS signals, is the effect of ionospheric plasma turbulence. The scintillation patterns on radio signals crossing the medium inherit the ionospheric turbulence characteristics of inter-scale coupling, local randomness and large time variability. On this basis, the remote sensing of local features of the turbulent plasma is feasible by studying radio scintillation induced by the ionosphere. The distinctive character of intermittent turbulent media depends on the fluctuations on the space- and time-scale statistical properties of the medium. Hence, assessing how the signal fluctuation properties vary under different Helio-Geophysical conditions will help to understand the corresponding dynamics of the turbulent medium crossed by the signal. Data analysis tools, provided by complex system science, appear to be best fitting to study the response of a turbulent medium, as the Earth's equatorial ionosphere, to the non-linear forcing exerted by the Solar Wind (SW). In particular we used the Adaptive Local Iterative Filtering, the Wavelet analysis and the Information theory data analysis tool. We have analysed the radio scintillation and ionospheric fluctuation data at low latitude focusing on the time and space multi-scale variability and on the causal relationship between forcing factors from the SW environment and the ionospheric response.
Badrinarayanan, Anjana
2016-01-01
The SMC complex, MukBEF, is important for chromosome organization and segregation in Escherichia coli. Fluorescently tagged MukBEF forms distinct spots (or 'foci') in the cell, where it is thought to carry out most of its chromosome associated activities. This chapter outlines the technique of Fluorescence Recovery After Photobleaching (FRAP) as a method to study the properties of YFP-tagged MukB in fluorescent foci. This method can provide important insight into the dynamics of MukB on DNA and be used to study its biochemical properties in vivo.
Gate complexity using Dynamic Programming
Sridharan, Srinivas; Gu, Mile; James, Matthew R.
2008-01-01
The relationship between efficient quantum gate synthesis and control theory has been a topic of interest in the quantum control literature. Motivated by this work, we describe in the present article how the dynamic programming technique from optimal control may be used for the optimal synthesis of quantum circuits. We demonstrate simulation results on an example system on SU(2), to obtain plots related to the gate complexity and sample paths for different logic gates.
Directory of Open Access Journals (Sweden)
Samantha C W Chan
Full Text Available The spine is routinely subjected to repetitive complex loading consisting of axial compression, torsion, flexion and extension. Mechanical loading is one of the important causes of spinal diseases, including disc herniation and disc degeneration. It is known that static and dynamic compression can lead to progressive disc degeneration, but little is known about the mechanobiology of the disc subjected to combined dynamic compression and torsion. Therefore, the purpose of this study was to compare the mechanobiology of the intervertebral disc when subjected to combined dynamic compression and axial torsion or pure dynamic compression or axial torsion using organ culture. We applied four different loading modalities [1. control: no loading (NL, 2. cyclic compression (CC, 3. cyclic torsion (CT, and 4. combined cyclic compression and torsion (CCT] on bovine caudal disc explants using our custom made dynamic loading bioreactor for disc organ culture. Loads were applied for 8 h/day and continued for 14 days, all at a physiological magnitude and frequency. Our results provided strong evidence that complex loading induced a stronger degree of disc degeneration compared to one degree of freedom loading. In the CCT group, less than 10% nucleus pulposus (NP cells survived the 14 days of loading, while cell viabilities were maintained above 70% in the NP of all the other three groups and in the annulus fibrosus (AF of all the groups. Gene expression analysis revealed a strong up-regulation in matrix genes and matrix remodeling genes in the AF of the CCT group. Cell apoptotic activity and glycosaminoglycan content were also quantified but there were no statistically significant differences found. Cell morphology in the NP of the CCT was changed, as shown by histological evaluation. Our results stress the importance of complex loading on the initiation and progression of disc degeneration.
Kong, Wei; Yang, Fang; Liu, Songfen; Shi, Feng
2016-10-01
A Langevin dynamics simulation method is used to study the two-dimensional (2D) equilibrium structure of complex plasmas while considering an external magnetic field. The traditional Yukawa potential and a modified Yukawa potential according to Shukla et al. [Phys. Lett. A 291, 413 (2001); Shukla and Mendonca, Phys. Scr. T113 82 (2004)] and Salimullah et al. [Phys. Plasmas 10, 3047 (2003)] respectively, are employed to account for the interaction of the charged dust particles. It is found that the collisions between neutral gas and charged dust particles have minor effects on the 2D equilibrium structure of the system. Based on the modified Yukawa potential, studies on the 2D equilibrium structure show that the traditional Yukawa potential is still suitable for describing the magnetized complex plasmas, even if the shielding distance of charged dust particles is affected by the strong external magnetic field.
Chaumont, Alain; Wipff, Georges
2012-05-14
We report a molecular dynamics study on the EuBr(n)(3-n) complexes (n=0 to 6) formed upon complexation of Br(-) by Eu(3+) in the [BMI][PF(6)], [BMI][Tf(2)N] and [MeBu(3)N][Tf(2)N] ionic liquids (ILs), to compare the effect of the IL anion (PF(6)(-) versus Tf(2)N(-)), the IL cation (BMI(+) versus MeBu(3)N(+)) and the "IL humidity" on their solvation and stability. In "dry" solutions all complexes remain stable and the first coordination shell of Eu(3+) is purely anionic (Br(-) and IL anions), surrounded by IL cations (BMI(+) or MeBu(3)N(+) ions). Long range "onion type" solvation features (up to 20 Å from Eu(3+)), with alternating cation-rich and anion-rich solvent shells, are observed around the different complexes. The comparison of gas phase-optimized structures of EuBr(n)(3-n) complexes (that are unstable for n=5 and 6) with those observed in solution points to the importance of solvation forces on the nature of the complex, with a higher stabilization by imidazolium- than by ammonium-based dry ILs. Adding water to the IL has different effects, depending on the IL. In the highly hygroscopic [BMI][PF(6)] IL, Br(-) ligands are displaced by water, to finally form Eu(H(2)O)(9)(3+). In the less "humid" [BMI][Tf(2)N], the EuBr(n)(3-n) complexes do not dissociate and coordinate at most 1-2 H(2)O molecules. We also calculated the free-energy profiles (Potential of Mean Force calculations) for the stepwise complexation of Br(-), and found significant solvent effects. EuBr(6)(3-) is predicted to form in both [BMI][PF(6)] and [BMI][Tf(2)N], but not in [MeBu(3)N][Tf(2)N], mainly due to weaker interactions with the cationic solvation shell. First steps are found to be more exergonic in the PF(6)(-)- than in the Tf(2)N(-)-based IL. Molecular dynamics (MD) comparisons between ILs and classical solvents (acetonitrile and water) are also reported, affording good agreement with the experimental observations of Br(-) complexation by trivalent lanthanides in these classical
Synchronization of fractional order complex dynamical networks
Wang, Yu; Li, Tianzeng
2015-06-01
In this letter the synchronization of complex dynamical networks with fractional order chaotic nodes is studied. A fractional order controller for synchronization of complex network is presented. Some new sufficient synchronization criteria are proposed based on the Lyapunov stability theory and the LaSalle invariance principle. These synchronization criteria can apply to an arbitrary fractional order complex network in which the coupling-configuration matrix and the inner-coupling matrix are not assumed to be symmetric or irreducible. It means that this method is more general and effective. Numerical simulations of two fractional order complex networks demonstrate the universality and the effectiveness of the proposed method.
Energy Technology Data Exchange (ETDEWEB)
Tokmakoff, Andrei [Univ. of Chicago, IL (United States); Fiechtner, Gregory J. [Univ. of Chicago, IL (United States)
2015-12-10
This grant supported work in the Tokmakoff lab at the University of Chicago aimed at understanding the fundamental properties of water at a molecular level, and how water participates in proton transport in aqueous media. The physical properties of water and aqueous solutions are inextricably linked with efforts to develop new sustainable energy sources. Energy conversion, storage, and transduction processes, particularly those that occur in biology and soft matter, make use of water for the purpose of storing and moving charge. Water’s unique physical and chemical properties depend on the ability of water molecules to participate in up to four hydrogen bonds, and the rapid fluctuations and ultrafast energy dissipation of its hydrogenbonded networks. Our work during the grant period led to advances in four areas: (1) the generation of short pulses of broadband infrared light (BBIR) for use in time-resolved twodimensional spectroscopy (2D IR), (2) the investigation of the spectroscopy and transport of excess protons in water, (3) the study of aqueous hydroxide to describe the interaction of the ion and water and the dynamics of proton transfer, and (4) the coupled motion of water and its hydrogen-bonding solutes.
Molecular dynamics study of ionic liquids complexation within β-cyclodextrins.
Semino, Rocío; Rodríguez, Javier
2015-04-09
We have studied 1:1 inclusion complexes of two imidazole-based ionic liquids within β-cyclodextrin: 1-dodecyl-3-methylimidazolium and 1-butyl-3-methylimidazolium. By means of an adaptive biasing force scheme, we obtained the free energy profile along two different pathways, differing in the orientations of the head-to-tail vector with respect to the primary-secondary rim axis. Regarding 1-dodecyl-3-methylimidazolium, we found one minimum energy structure for each pathway, in which the hydrophobic tail remains embedded within the cyclodextrin, while the headgroup lies ∼11-12 Å from one of the rims; the structure where the polar head lies near the primary rim is the most stable. The analysis of the free energy of encapsulation of 1-butyl-3-methylimidazolium shows two minima for each insertion pathway, each of them associated with configurations where the imidazolium head lies close to one of the polar rims. As such, the most stable structure corresponds to one where the hydrophobic tail lies embedded within the cyclodextrin, while its head is localized near the secondary rim. The results are interpreted in terms of a simple model which captures the essential features that control the encapsulation process. A comparison with available experimental data is presented.
Controlling complex Langevin dynamics at finite density
Energy Technology Data Exchange (ETDEWEB)
Aarts, Gert; Bongiovanni, Lorenzo [Swansea University, Department of Physics, College of Science, Swansea (United Kingdom); Seiler, Erhard [Max-Planck-Institut fuer Physik (Werner-Heisenberg-Institut), Muenchen (Germany); Sexty, Denes [Universitaet Heidelberg, Institut fuer Theoretische Physik, Heidelberg (Germany); Stamatescu, Ion-Olimpiu [Universitaet Heidelberg, Institut fuer Theoretische Physik, Heidelberg (Germany); FEST, Heidelberg (Germany)
2013-07-15
At nonzero chemical potential the numerical sign problem in lattice field theory limits the use of standard algorithms based on importance sampling. Complex Langevin dynamics provides a possible solution, but it has to be applied with care. In this review, we first summarise our current understanding of the approach, combining analytical and numerical insight. In the second part we study SL(N,C) gauge cooling, which was introduced recently as a tool to control complex Langevin dynamics in nonabelian gauge theories. We present new results in Polyakov chain models and in QCD with heavy quarks and compare various adaptive cooling implementations. (orig.)
Claesson, E.M.; Erne, B.H.; Philipse, A.P.
2007-01-01
The weak permanent magnetic dipole moment of cobalt ferrite-doped colloidal silica spheres was increased by exposure to a saturating magnetic field. The resulting change of the rotational dynamics of the magnetic microspheres in a weak alternating field was measured from low to high volume fraction
Gao, Jiao; Seifert, Nathan A.; Thomas, Javix; Xu, Yunjie; Jäger, Wolfgang
2016-12-01
The microwave spectra of the van der Waals complexes acetone-20Ne and acetone-22Ne were measured using a cavity-based supersonic jet Fourier-transform microwave spectrometer in the region from 5 to 18 GHz. For these two isotopologues, both c- and weaker a-type transitions were observed. The transitions are split into multiplets due to the internal rotation of the two methyl groups in acetone. Initial electronic structure calculations were performed at the MP2/6-311++g (2d, p) level of theory and the internal rotation barrier height of the methyl groups was calculated to be ∼2.8 kJ/mol. The ab initio rotational constants were the basis for the spectroscopic searches, but the multiplet structures and floppiness of the complex made the quantum number assignment very difficult. The assignment was finally achieved with the aid of constructing closed frequency loops and predicting internal rotation splittings using the XIAM internal rotation program. The acetone methyl group tunneling barrier height was determined experimentally to be 3.10(6) kJ mol-1 [259(5) cm-1] in the acetone-Ne complex, which is lower than in the acetone monomer but comparable to the acetone-Ar complex (Kang et al., 2002). Experimental data and high-level CCSD(T)/aug-cc-pVTZ calculations suggest that the Ne atom lies directly above the plane formed by the carbonyl group and the two carbon-carbon bonds, which is different than the slightly offset position found previously in the acetone-Ar complex. Additionally, ab initio calculations and Quantum Theory of Atoms in Molecules analyses were used to analyze the methyl internal rotation motions in acetone and acetone-Ne.
Controlling Complex Systems and Developing Dynamic Technology
Avizienis, Audrius Victor
In complex systems, control and understanding become intertwined. Following Ilya Prigogine, we define complex systems as having control parameters which mediate transitions between distinct modes of dynamical behavior. From this perspective, determining the nature of control parameters and demonstrating the associated dynamical phase transitions are practically equivalent and fundamental to engaging with complexity. In the first part of this work, a control parameter is determined for a non-equilibrium electrochemical system by studying a transition in the morphology of structures produced by an electroless deposition reaction. Specifically, changing the size of copper posts used as the substrate for growing metallic silver structures by the reduction of Ag+ from solution under diffusion-limited reaction conditions causes a dynamical phase transition in the crystal growth process. For Cu posts with edge lengths on the order of one micron, local forces promoting anisotropic growth predominate, and the reaction produces interconnected networks of Ag nanowires. As the post size is increased above 10 microns, the local interfacial growth reaction dynamics couple with the macroscopic diffusion field, leading to spatially propagating instabilities in the electrochemical potential which induce periodic branching during crystal growth, producing dendritic deposits. This result is interesting both as an example of control and understanding in a complex system, and as a useful combination of top-down lithography with bottom-up electrochemical self-assembly. The second part of this work focuses on the technological development of devices fabricated using this non-equilibrium electrochemical process, towards a goal of integrating a complex network as a dynamic functional component in a neuromorphic computing device. Self-assembled networks of silver nanowires were reacted with sulfur to produce interfacial "atomic switches": silver-silver sulfide junctions, which exhibit
The self as a complex dynamic system
Directory of Open Access Journals (Sweden)
Sarah Mercer
2011-04-01
Full Text Available This article explores the potential offered by complexity theories for understanding language learners’ sense of self and attempts to show how the self might usefully be conceived of as a complex dynamic system. Rather than presenting empirical findings, the article discusses existent research on the self and aims at outlining a conceptual perspective that may inform future studies into the self and possibly other individual learner differences. The article concludes by critically considering the merits of a complexity perspective but also reflecting on the challenges it poses for research.
Lippold, Holger; Eidner, Sascha; Kumke, Michael U.; Lippmann-Pipke, Johanna
2017-01-01
Complexation with dissolved humic matter can be crucial in controlling the mobility of toxic or radioactive contaminant metals. For speciation and transport modelling, a dynamic equilibrium process is commonly assumed, where association and dissociation run permanently. This is, however, questionable in view of reported observations of a growing resistance to dissociation over time. In this study, the isotope exchange principle was employed to gain direct insight into the dynamics of the complexation equilibrium, including kinetic inertisation phenomena. Terbium(III), an analogue of trivalent actinides, was used as a representative of higher-valent metals. Isotherms of binding to (flocculated) humic acid, determined by means of 160Tb as a radiotracer, were found to be identical regardless of whether the radioisotope was introduced together with the bulk of stable 159Tb or subsequently after pre-equilibration for up to 3 months. Consequently, there is a permanent exchange of free and humic-bound Tb since all available binding sites are occupied in the plateau region of the isotherm. The existence of a dynamic equilibrium was thus evidenced. There was no indication of an inertisation under these experimental conditions. If the small amount of 160Tb was introduced prior to saturation with 159Tb, the expected partial desorption of 160Tb occurred at much lower rates than observed for the equilibration process in the reverse procedure. In addition, the rates decreased with time of pre-equilibration. Inertisation phenomena are thus confined to the stronger sites of humic molecules (occupied at low metal concentrations). Analysing the time-dependent course of isotope exchange according to first-order kinetics indicated that up to 3 years are needed to attain equilibrium. Since, however, metal-humic interaction remains reversible, exchange of metals between humic carriers and mineral surfaces cannot be neglected on the long time scale to be considered in predictive
Blessy, J Jino; Sharmila, D Jeya Sundara
2015-01-01
Cholera toxin (CT) is an AB5 protein complex secreted by the pathogen Vibrio cholera, which is responsible for cholera infection. N-acetylneuraminic acid (NeuNAc) is a derivative of neuraminic acid with nine-carbon backbone. NeuNAc is distributed on the cell surface mainly located in the terminal components of glycoconjugates, and also plays an important role in cell-cell interaction. In our current study, molecular docking and molecular dynamic (MD) simulations were implemented to identify the potent NeuNAc analogs with high-inhibitory activity against CT protein. Thirty-four NeuNAc analogs, modified in different positions C-1/C-2/C-4/C-5/C-7/C-8/C-9, were modeled and docked against the active site of CT protein. Among the 34 NeuNAc analogs, the analog Neu5Gc shows the least extra precision glide score of -9.52 and glide energy of -44.71 kcal/mol. NeuNAc analogs block the CT active site residues HIS:13, ASN:90, LYS:91, GLN:56, GLN:61, and TRP:88 through intermolecular hydrogen bonding. The MD simulation for CT-Neu5Gc docking complex was performed using Desmond. MD simulation of CT-Neu5Gc complex reveals the stable nature of docking interaction.
Studies on femtosecond fluorescence dynamics of photosystem II Particle complex at low temperature
Liu Xiao; He, Jun Fang; Cai, Xia; Peng Jun Fang; Kuang Ting Yun
2004-01-01
In order to understanding the diversity of energy transfer in PS II at different temperatures, PS II particle complex purified from spinach was investigated with femtosecond time-resolved fluorescence spectroscopy in the case of excitation 507 nm at 83 K, 160 K, 273 K. The data were analyzed by Gauss analysis and fluorescence decay time- fitting. Some results were achieved. (1) Increase of the temperature results in a broadening of the fluorescence emission spectra due to the temperature-dependent expressions for nonradiative transitions between two electronic states. (2) There are at least several characteristic Chl molecules exist in PS II particle complex, i.e. Chl b/sub 639//sup 640/, Chl b/sub 640//sup 645/, Chl a/sub 660//sup 663/, Chl a/sub 667//sup 668/, Chl a/sub 673//sup 676/, Chl a/sub 680 //sup 681/, Chl a/sub 680/681//sup 682/, Chl a/sub 684,685//sup 668 /689/, Chl a/sub 688//sup 698/, (Chl a/b/sub a//sup e/: a represents the peak of absorption, e represents the peak of emission). (3) Though the ...
Improving the Complexity of the Lorenz Dynamics
Directory of Open Access Journals (Sweden)
María Pilar Mareca
2017-01-01
Full Text Available A new four-dimensional, hyperchaotic dynamic system, based on Lorenz dynamics, is presented. Besides, the most representative dynamics which may be found in this new system are located in the phase space and are analyzed here. The new system is especially designed to improve the complexity of Lorenz dynamics, which, despite being a paradigm to understand the chaotic dissipative flows, is a very simple example and shows great vulnerability when used in secure communications. Here, we demonstrate the vulnerability of the Lorenz system in a general way. The proposed 4D system increases the complexity of the Lorenz dynamics. The trajectories of the novel system include structures going from chaos to hyperchaos and chaotic-transient solutions. The symmetry and the stability of the proposed system are also studied. First return maps, Poincaré sections, and bifurcation diagrams allow characterizing the global system behavior and locating some coexisting structures. Numerical results about the first return maps, Poincaré cross sections, Lyapunov spectrum, and Kaplan-Yorke dimension demonstrate the complexity of the proposed equations.
Finding order in complexity: A study of the fluid dynamics in a three-dimensional branching network
Guha, Abhijit; Pradhan, Kaustav; Halder, Prodosh Kumar
2016-12-01
The complex fluid dynamics associated with the flow in three-dimensional dichotomously branching networks is investigated. The flow physics described here is generic, though the particular flow geometry employed represents a model human bronchial tree. Up to six generations of branches (involving 63 straight portions and 31 bifurcation modules) are computed in one go; such computational challenges are rarely taken in the literature. In the present study, two branching configurations are considered side by side: the most widely studied in-plane configuration in which the centrelines of all generations lie on the same plane, and the 90∘ out-of-plane configuration in which the centreline of each generation is rotated with respect to its grandmother generation following a systematic methodology to form a space-filling three-dimensional structure. The paper develops a physical understanding of the fluid dynamics of branching networks and its dependence on the configuration (in-plane versus out-of-plane) and the extent (four, five, or six generations) of the network under consideration. The study of co-planar vis-à-vis non-planar configurations establishes a quantitative evaluation of the dependence of the fluid dynamics on the three-dimensional arrangement of the same individual branches. It is shown that apparent symmetry in the geometry of any two branches does not automatically imply symmetry in the flow field in those two branches. With the help of velocity contours, pressure contours, and distribution of mass flow in each branch, a qualitative and quantitative study is performed on the nature and evolution of flow asymmetry. The computations show that the degree of mass-flow asymmetry is smaller for the out-of-plane configuration (which is a more realistic model of a human bronchial tree) as compared to that for the in-plane configuration. The mass-flow asymmetry grows in each successive generation (starting from generation G2 for in-plane and G3 for out
Controlling edge dynamics in complex networks
Nepusz, Tamás
2011-01-01
The interaction of distinct units in physical, social, biological and technological systems naturally gives rise to complex network structures. Networks have constantly been in the focus of research for the last decade, with considerable advances in the description of their structural and dynamical properties. However, much less effort has been devoted to studying the controllability of the dynamics taking place on them. Here we introduce and evaluate a dynamical process defined on the edges of a network, and demonstrate that the controllability properties of this process significantly differ from simple nodal dynamics. Evaluation of real-world networks indicates that most of them are more controllable than their randomized counterparts. We also find that transcriptional regulatory networks are particularly easy to control. Analytic calculations show that networks with scale-free degree distributions have better controllability properties than uncorrelated networks, and positively correlated in- and out-degre...
Dynamics of a complex mass movement triggered by heavy rainfall: a case study from NW Turkey
Ocakoglu, Faruk; Gokceoglu, Candan; Ercanoglu, Murat
2002-01-01
Following a period of heavy precipitation, a large and complex mass movement, namely the Dagkoy landslide, occurred in the West Black Sea Region of Turkey on May 21, 1998. This paper describes the conditioning factors of the landslide and interprets the mass transport processes in terms of a movement scenario. Geology, geomorphology and vegetation cover were considered as the conditioning factors of the failure. Observations showed that the gently sloping (about 10°) area is mostly covered by dense forest trees at the crown where the motion initiated. Significant intersection of the collapsed slope with dip of the local marls seems to have contributed to the formation and geometry of the landslide. The distance from the crown down to the toe of the landslide measured more than 600 m, with about 0.6 km 3 total earth material displaced. The landslide has both a block sliding characteristics in the upper portions and a debris flow/soil flow component around the margins of the sliding blocks in the middle parts and at the toe. The proposed scenario for the landslide reveals that the movement was initiated near crown as a result of the excess water content in the marls at the end of 3 days of heavy rainfall. The early perturbations (transverse cracks, ridges, etc.) lasted for 6-7 h, after which the central part of the zone started to move as a soil flow in which very large intact blocks were transported. Even though the movement was very rapid (1.2 m/min), there was no loss of life. However, the movement destroyed 38 houses, one mosque and a considerable amount of farmland.
Cognitive dynamics: complexity and creativity
Energy Technology Data Exchange (ETDEWEB)
Arecchi, F Tito [Dipartimento di Fisica, Universita di Firenze (Italy); Istituto Nazionale di Ottica Applicata, Florence (Italy)
2007-05-15
A scientific problem described within a given code is mapped by a corresponding computational problem. We call (algorithmic) complexity the bit length of the shortest instruction which solves the problem. Deterministic chaos in general affects a dynamical system making the corresponding problem experimentally and computationally heavy, since one must reset the initial conditions at a rate higher than that of information loss (Kolmogorov entropy). One can control chaos by adding to the system new degrees of freedom (information swapping: information lost by chaos is replaced by that arising from the new degrees of freedom). This implies a change of code, or a new augmented model. Within a single code, changing hypotheses is equivalent to fixing different sets of control parameters, each with a different a-priori probability, to be then confirmed and transformed to an a-posteriori probability via Bayes theorem. Sequential application of Bayes rule is nothing else than the Darwinian strategy in evolutionary biology. The sequence is a steepest ascent algorithm, which stops once maximum probability has been reached. At this point the hypothesis exploration stops. By changing code (and hence the set of relevant variables) one can start again to formulate new classes of hypotheses. We call creativity the action of code changing, which is guided by hints not formalized within the previous code, whence not accessible to a computer. We call semantic complexity the number of different scientific codes, or models, that describe a situation. It is however a fuzzy concept, in so far as this number changes due to interaction of the operator with the context. These considerations are illustrated with reference to a cognitive task, starting from synchronization of neuron arrays in a perceptual area and tracing the putative path towards a model building. Since this is a report on work in progress, we skip technicalities in order to stress the gist of the question, and provide
Dynamics of complex interconnected systems: Networks and bioprocesses[A NATO study seminary
Energy Technology Data Exchange (ETDEWEB)
Wilhelmsen, Line K.
2005-07-01
Rapid detection of chemical and biological agents and weapons, and rapid diagnosis of their effects on people will require molecular recognition as well as signal discrimination, i.e. avoiding false positives and negatives, and signal transduction. It will be important to have reagentless, cheap, easily manufactured sensors that can be field deployed in large numbers. While this problem is urgent it is not yet solved. This ASI brought together researchers with various interests and background including theoretical physicists, soft condensed matter experimentalists, biological physicists, and molecular biologists to identify and discuss areas where synergism between modem physics and biology may be most fruitfully applied to the study of bioprocesses for molecular recognition and of networks for converting molecular reactions into usable signals and appropriate responses. (Author)
Tachikawa, Hiroto
2006-01-12
Ionization processes of chlorobenzene-ammonia 1:1 complex (PhCl-NH3) have been investigated by means of full dimensional direct ab initio molecular dynamics (MD) method, static ab initio calculations, and density functional theory (DFT) calculations. The static ab initio and DFT calculations of neutral PhCl-NH3 complex showed that one of the hydrogen atoms of NH3 orients toward a carbon atom in the para-position of PhCl. The dynamics calculation for ionization of PhCl-NH3 indicated that two reaction channels are competitive with each other as product channels: one is an intramolecular SN2 reaction expressed by a reaction scheme [PhCl-NH3]+-->SN2 intermediate complex-->PhNH3++Cl, and the other is ortho-NH3 addition complex (ortho complex) in which NH3 attacks the ortho-carbon of PhCl+ and the trajectory leads to a bound complex expressed by (PhCl-NH3)+. The mechanism of the ionization of PhCl-NH3 is discussed on the basis of the theoretical results.
DEFF Research Database (Denmark)
Dohn, Asmus Ougaard; Jónsson, Elvar Örn; Kjær, Kasper Skov
2014-01-01
By using a newly implemented QM/MM multiscale MD method to simulate the excited state dynamics of the Ir2(dimen)42+ (dimen = 1,8-diisocyano-p-menthane) complex, we not only report on results that support the two experimentally observed coherent dynamical modes in the molecule but also reveal...... a third mode, not distinguishable by spectroscopic methods. We directly follow the channels of energy dissipation to the solvent and report that the main cause for coherence decay is the initial wide range of configurations in the excited state population. We observe that the solvent can actually extend...
Drolle, E.; Bennett, W. F. D.; Hammond, K.; Lyman, E.; Karttunen, M.; Leonenko, Z.
The molecular arrangement of lipids and proteins within biomembranes and monolayers gives rise to complex film morphologies as well as regions of distinct electrical surface potential, topographical and electrostatic nanoscale domains. To probe these nanodomains in soft matter is a challenging task both experimentally and theoretically. This work addresses the effects of cholesterol, lipid composition, lipid charge, and lipid phase on the monolayer structure and the electrical surface potential distribution. Atomic Force Microscopy (AFM) was used to resolve topographical nanodomains and Kelvin Probe Force Microscopy (KPFM) to resolve electrical surface potential of these nanodomains in lipid monolayers. Model monolayers composed of dipalmitoylphosphatidylcholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2-dioleoyl-sn-glycero-3-[phospho-rac-(3-lysyl(1-glycerol))] (DOPG), sphingomyelin, and cholesterol were studied. It is shown that cholesterol changes nanoscale domain formation, affecting both topography and electrical surface potential. The molecular basis for differences in electrical surface potential was addressed with atomistic molecular dynamics (MD). MD simulations qualitatively match the experimental results, with 100s of mV difference in electrostatic potential between liquid-disordered bilayer (Ld, less cholesterol and lower chain order) and a liquid-ordered bilayer (Lo, more cholesterol and higher chain order). Importantly, the difference in electrostatic properties between Lo and Ld phases suggests a new mechanism by which membrane composition couples to membrane function.
Nonlinear Dynamics, Chaotic and Complex Systems
Infeld, E.; Zelazny, R.; Galkowski, A.
2011-04-01
Part I. Dynamic Systems Bifurcation Theory and Chaos: 1. Chaos in random dynamical systems V. M. Gunldach; 2. Controlling chaos using embedded unstable periodic orbits: the problem of optimal periodic orbits B. R. Hunt and E. Ott; 3. Chaotic tracer dynamics in open hydrodynamical flows G. Karolyi, A. Pentek, T. Tel and Z. Toroczkai; 4. Homoclinic chaos L. P. Shilnikov; Part II. Spatially Extended Systems: 5. Hydrodynamics of relativistic probability flows I. Bialynicki-Birula; 6. Waves in ionic reaction-diffusion-migration systems P. Hasal, V. Nevoral, I. Schreiber, H. Sevcikova, D. Snita, and M. Marek; 7. Anomalous scaling in turbulence: a field theoretical approach V. Lvov and I. Procaccia; 8. Abelian sandpile cellular automata M. Markosova; 9. Transport in an incompletely chaotic magnetic field F. Spineanu; Part III. Dynamical Chaos Quantum Physics and Foundations Of Statistical Mechanics: 10. Non-equilibrium statistical mechanics and ergodic theory L. A. Bunimovich; 11. Pseudochaos in statistical physics B. Chirikov; 12. Foundations of non-equilibrium statistical mechanics J. P. Dougherty; 13. Thermomechanical particle simulations W. G. Hoover, H. A. Posch, C. H. Dellago, O. Kum, C. G. Hoover, A. J. De Groot and B. L. Holian; 14. Quantum dynamics on a Markov background and irreversibility B. Pavlov; 15. Time chaos and the laws of nature I. Prigogine and D. J. Driebe; 16. Evolutionary Q and cognitive systems: dynamic entropies and predictability of evolutionary processes W. Ebeling; 17. Spatiotemporal chaos information processing in neural networks H. Szu; 18. Phase transitions and learning in neural networks C. Van den Broeck; 19. Synthesis of chaos A. Vanecek and S. Celikovsky; 20. Computational complexity of continuous problems H. Wozniakowski; Part IV. Complex Systems As An Interface Between Natural Sciences and Environmental Social and Economic Sciences: 21. Stochastic differential geometry in finance studies V. G. Makhankov; Part V. Conference Banquet
Complex Dynamics in Information Sharing Networks
Cronin, Bruce
This study examines the roll-out of an electronic knowledge base in a medium-sized professional services firm over a six year period. The efficiency of such implementation is a key business problem in IT systems of this type. Data from usage logs provides the basis for analysis of the dynamic evolution of social networks around the depository during this time. The adoption pattern follows an "s-curve" and usage exhibits something of a power law distribution, both attributable to network effects, and network position is associated with organisational performance on a number of indicators. But periodicity in usage is evident and the usage distribution displays an exponential cut-off. Further analysis provides some evidence of mathematical complexity in the periodicity. Some implications of complex patterns in social network data for research and management are discussed. The study provides a case study demonstrating the utility of the broad methodological approach.
Odoux, Anne; Jindal, Darren; Tamas, Tamara C; Lim, Benjamin W H; Pollard, Drake; Xu, Wu
2016-06-01
The coactivators CBP (CREBBP) and its paralog p300 (EP300), two conserved multi-domain proteins in eukaryotic organisms, regulate gene expression in part by binding DNA-binding transcription factors. It was previously reported that the CBP/p300 KIX domain mutant (Y650A, A654Q, and Y658A) altered both c-Myb-dependent gene activation and repression, and that mice with these three point mutations had reduced numbers of platelets, B cells, T cells, and red blood cells. Here, our transient transfection assays demonstrated that mouse embryonic fibroblast cells containing the same mutations in the KIX domain and without a wild-type allele of either CBP or p300, showed decreased c-Myb-mediated transcription. Dr. Wright's group solved a 3-D structure of the mouse CBP:c-Myb complex using NMR. To take advantage of the experimental structure and function data and improved theoretical calculation methods, we performed MD simulations of CBP KIX, CBP KIX with the mutations, and c-Myb, as well as binding energy analysis for both the wild-type and mutant complexes. The binding between CBP and c-Myb is mainly mediated by a shallow hydrophobic groove in the center where the side-chain of Leu302 of c-Myb plays an essential role and two salt bridges at the two ends. We found that the KIX mutations slightly decreased stability of the CBP:c-Myb complex as demonstrated by higher binding energy calculated using either MM/PBSA or MM/GBSA methods. More specifically, the KIX mutations affected the two salt bridges between CBP and c-Myb (CBP-R646 and c-Myb-E306; CBP-E665 and c-Myb-R294). Our studies also revealed differing dynamics of the hydrogen bonds between CBP-R646 and c-Myb-E306 and between CBP-E665 and c-Myb-R294 caused by the CBP KIX mutations. In the wild-type CBP:c-Myb complex, both of the hydrogen bonds stayed relatively stable. In contrast, in the mutant CBP:c-Myb complex, hydrogen bonds between R646 and E306 showed an increasing trend followed by a decreasing trend, and hydrogen
Team dynamics in complex projects
Oeij, P.; Vroome, E.E.M. de; Dhondt, S.; Gaspersz, J.B.R.
2012-01-01
Complexity of projects is hotly debated and a factor which affects innovativeness of team performance. Much attention in the past is paid to technical complexity and many issues are related to natural and physical sciences. A growing awareness of the importance of socioorganisational issues is annou
Team dynamics in complex projects
Oeij, P.; Vroome, E.E.M. de; Dhondt, S.; Gaspersz, J.B.R.
2012-01-01
Complexity of projects is hotly debated and a factor which affects innovativeness of team performance. Much attention in the past is paid to technical complexity and many issues are related to natural and physical sciences. A growing awareness of the importance of socioorganisational issues is
Automated design of complex dynamic systems.
Directory of Open Access Journals (Sweden)
Michiel Hermans
Full Text Available Several fields of study are concerned with uniting the concept of computation with that of the design of physical systems. For example, a recent trend in robotics is to design robots in such a way that they require a minimal control effort. Another example is found in the domain of photonics, where recent efforts try to benefit directly from the complex nonlinear dynamics to achieve more efficient signal processing. The underlying goal of these and similar research efforts is to internalize a large part of the necessary computations within the physical system itself by exploiting its inherent non-linear dynamics. This, however, often requires the optimization of large numbers of system parameters, related to both the system's structure as well as its material properties. In addition, many of these parameters are subject to fabrication variability or to variations through time. In this paper we apply a machine learning algorithm to optimize physical dynamic systems. We show that such algorithms, which are normally applied on abstract computational entities, can be extended to the field of differential equations and used to optimize an associated set of parameters which determine their behavior. We show that machine learning training methodologies are highly useful in designing robust systems, and we provide a set of both simple and complex examples using models of physical dynamical systems. Interestingly, the derived optimization method is intimately related to direct collocation a method known in the field of optimal control. Our work suggests that the application domains of both machine learning and optimal control have a largely unexplored overlapping area which envelopes a novel design methodology of smart and highly complex physical systems.
Automated design of complex dynamic systems.
Hermans, Michiel; Schrauwen, Benjamin; Bienstman, Peter; Dambre, Joni
2014-01-01
Several fields of study are concerned with uniting the concept of computation with that of the design of physical systems. For example, a recent trend in robotics is to design robots in such a way that they require a minimal control effort. Another example is found in the domain of photonics, where recent efforts try to benefit directly from the complex nonlinear dynamics to achieve more efficient signal processing. The underlying goal of these and similar research efforts is to internalize a large part of the necessary computations within the physical system itself by exploiting its inherent non-linear dynamics. This, however, often requires the optimization of large numbers of system parameters, related to both the system's structure as well as its material properties. In addition, many of these parameters are subject to fabrication variability or to variations through time. In this paper we apply a machine learning algorithm to optimize physical dynamic systems. We show that such algorithms, which are normally applied on abstract computational entities, can be extended to the field of differential equations and used to optimize an associated set of parameters which determine their behavior. We show that machine learning training methodologies are highly useful in designing robust systems, and we provide a set of both simple and complex examples using models of physical dynamical systems. Interestingly, the derived optimization method is intimately related to direct collocation a method known in the field of optimal control. Our work suggests that the application domains of both machine learning and optimal control have a largely unexplored overlapping area which envelopes a novel design methodology of smart and highly complex physical systems.
Taming Dynamical Complexity and Managing High Technology
Institute of Scientific and Technical Information of China (English)
FANGJin-qing; CHENGuan-rong; ZHAOGeng
2003-01-01
Variability is one of the most important features of complexity m complex networks anu systems,which usually depends sensitively on small perturbations. Various possible competing behaviours in a system may provide great flexibility in regulating or taming dynamical complexity, through which the designer may be able to better select and manage a desired behaviour for a specific application. In many high-tech fields, how to regulate or manage complexity is a very important but challenge issue.
Symbolic Dynamics and Grammatical Complexity
Hao, Bai-Lin; Zheng, Wei-Mou
The following sections are included: * Formal Languages and Their Complexity * Formal Language * Chomsky Hierarchy of Grammatical Complexity * The L-System * Regular Language and Finite Automaton * Finite Automaton * Regular Language * Stefan Matrix as Transfer Function for Automaton * Beyond Regular Languages * Feigenbaum and Generalized Feigenbaum Limiting Sets * Even and Odd Fibonacci Sequences * Odd Maximal Primitive Prefixes and Kneading Map * Even Maximal Primitive Prefixes and Distinct Excluded Blocks * Summary of Results
The study of photo-induced ultrafast dynamics in light-harvesting complex LH2 of purple bacteria
Institute of Scientific and Technical Information of China (English)
LIU Wei-min; YAN Yong-li; LIU Kang-jun; XU Chun-he; QIAN Shi-xiong
2006-01-01
In this paper,we introduce the photo-induced ultrafast dynamics taking place in the peripheral light harvesting antenna LH2 from purple bacteria Rhodobacter sphaeroides by using absorption,fluorescence emission and ultrafast spectroscopic techniques.Three kinds of LH2 sampies,pH treated LH2 (complete removal of B800 pigments),carotenoid mutated LH2 (GM 309) and electrochemical oxidation treated LH2 were used in comparison with native LH2 to investigate the mechanism of photo-induced ultrafast energy transfer within the LH2 complex.
Institute of Scientific and Technical Information of China (English)
无
2009-01-01
In this paper,a series of major policy decisions used to improve the power grid reliability,reduce the risk and losses of major power outages,and realize the modernization of 21st century power grid are discussed. These decisions were adopted by American government and would also be helpful for the strategic development of Chinese power grid. It is proposed that China should take precaution,carry out security research on the overall dynamic behaviour characteristics of the UHV grid using the complexity theo...
Adaptive learning and complex dynamics
Energy Technology Data Exchange (ETDEWEB)
Gomes, Orlando [Escola Superior de Comunicacao Social, Instituto Politecnico de Lisboa, Unidade de Investigacao em Desenvolvimento Empresarial Economics Research Center - UNIDE/ISCTE - ERC, Campus de Benfica do IPL, 1549-014 Lisbon (Portugal)], E-mail: ogomes@escs.ipl.pt
2009-10-30
In this paper, we explore the dynamic properties of a group of simple deterministic difference equation systems in which the conventional perfect foresight assumption gives place to a mechanism of adaptive learning. These systems have a common feature: under perfect foresight (or rational expectations) they all possess a unique fixed point steady state. This long-term outcome is obtained also under learning if the quality underlying the learning process is high. Otherwise, when the degree of inefficiency of the learning process is relatively strong, nonlinear dynamics (periodic and a-periodic cycles) arise. The specific properties of each one of the proposed systems is explored both in terms of local and global dynamics. One macroeconomic model is used to illustrate how the formation of expectations through learning may eventually lead to awkward long-term outcomes.
Markovian dynamics on complex reaction networks
Energy Technology Data Exchange (ETDEWEB)
Goutsias, J., E-mail: goutsias@jhu.edu; Jenkinson, G., E-mail: jenkinson@jhu.edu
2013-08-10
Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological, ecological, social, neural, and multi-agent networks. A common approach to modeling such networks is by a master equation that governs the dynamic evolution of the joint probability mass function of the underlying population process and naturally leads to Markovian dynamics for such process. Due however to the nonlinear nature of most reactions and the large size of the underlying state-spaces, computation and analysis of the resulting stochastic population dynamics is a difficult task. This review article provides a coherent and comprehensive coverage of recently developed approaches and methods to tackle this problem. After reviewing a general framework for modeling Markovian reaction networks and giving specific examples, the authors present numerical and computational techniques capable of evaluating or approximating the solution of the master equation, discuss a recently developed approach for studying the stationary behavior of Markovian reaction networks using a potential energy landscape perspective, and provide an introduction to the emerging theory of thermodynamic analysis of such networks. Three representative problems of opinion formation, transcription regulation, and neural network dynamics are used as illustrative examples.
Directory of Open Access Journals (Sweden)
Amit Kumar
Full Text Available Sardinia is a major Island in the Mediterranean with a high incidence of multiple sclerosis, a chronic autoimmune inflammatory disease of the central nervous system. Disease susceptibility in Sardinian population has been associated with five alleles of major histocompatibility complex (MHC class II DRB1 gene. We performed 120 ns of molecular dynamics simulation on one predisposing and one protective alleles, unbound and in complex with the two relevant peptides: Myelin Basic Protein and Epstein Barr Virus derived peptide. In particular we focused on the MHC peptide binding groove dynamics. The predisposing allele was found to form a stable complex with both the peptides, while the protective allele displayed stability only when bound with myelin peptide. The local flexibility of the MHC was probed dividing the binding groove into four compartments covering the well known peptide anchoring pockets. The predisposing allele in the first half cleft exhibits a narrower and more rigid groove conformation in the presence of myelin peptide. The protective allele shows a similar behavior, while in the second half cleft it displays a narrower and more flexible groove conformation in the presence of viral peptide. We further characterized these dynamical differences by evaluating H-bonds, hydrophobic and stacking interaction networks, finding striking similarities with super-type patterns emerging in other autoimmune diseases. The protective allele shows a defined preferential binding to myelin peptide, as confirmed by binding free energy calculations. All together, we believe the presented molecular analysis could help to design experimental assays, supports the molecular mimicry hypothesis and suggests that propensity to multiple sclerosis in Sardinia could be partly linked to distinct peptide-MHC interaction and binding characteristics of the antigen presentation mechanism.
Kumar, Amit; Cocco, Eleonora; Atzori, Luigi; Marrosu, Maria Giovanna; Pieroni, Enrico
2013-01-01
Sardinia is a major Island in the Mediterranean with a high incidence of multiple sclerosis, a chronic autoimmune inflammatory disease of the central nervous system. Disease susceptibility in Sardinian population has been associated with five alleles of major histocompatibility complex (MHC) class II DRB1 gene. We performed 120 ns of molecular dynamics simulation on one predisposing and one protective alleles, unbound and in complex with the two relevant peptides: Myelin Basic Protein and Epstein Barr Virus derived peptide. In particular we focused on the MHC peptide binding groove dynamics. The predisposing allele was found to form a stable complex with both the peptides, while the protective allele displayed stability only when bound with myelin peptide. The local flexibility of the MHC was probed dividing the binding groove into four compartments covering the well known peptide anchoring pockets. The predisposing allele in the first half cleft exhibits a narrower and more rigid groove conformation in the presence of myelin peptide. The protective allele shows a similar behavior, while in the second half cleft it displays a narrower and more flexible groove conformation in the presence of viral peptide. We further characterized these dynamical differences by evaluating H-bonds, hydrophobic and stacking interaction networks, finding striking similarities with super-type patterns emerging in other autoimmune diseases. The protective allele shows a defined preferential binding to myelin peptide, as confirmed by binding free energy calculations. All together, we believe the presented molecular analysis could help to design experimental assays, supports the molecular mimicry hypothesis and suggests that propensity to multiple sclerosis in Sardinia could be partly linked to distinct peptide-MHC interaction and binding characteristics of the antigen presentation mechanism. PMID:23555757
Energy Technology Data Exchange (ETDEWEB)
Orzechowski, Marek [Faculty of Chemistry, Warsaw University, 1 Pasteura Street, Warsaw, 02-093 (Poland); Cieplak, Piotr [Accelrys Incorporated, 9685 Scranton Road, San Diego, CA 92121 (United States)
2005-05-11
We present the preliminary results of two computer experiments involving the application of an external force to molecular systems. In the first experiment we simulated the process of pulling out a simple intercalator, the 9-aminoacridine molecule, from its complex with a short DNA oligonucleotide in aqueous solution. Removing a drug from the DNA is assumed to be an opposite process to the complex formation. The force and energy profiles suggest that formation of the DNA-9-aminoacridine complex is preferred when the acridine approaches the DNA from the minor groove rather than the major groove side. For a given mode of pulling the intercalation process is also shown to be nucleotide sequence dependent. In another computer experiment we performed a series of molecular dynamics simulations for stretching short, containing 15 amino acids, helical polypeptides in aqueous solution using an external force. The purpose of these simulations is to check whether this type of approach is sensitive enough to probe the sequence dependent helical propensity of short polypeptides.
Product development projects dynamics and emergent complexity
Schlick, Christopher
2016-01-01
This book primarily explores two topics: the representation of simultaneous, cooperative work processes in product development projects with the help of statistical models, and the assessment of their emergent complexity using a metric from theoretical physics (Effective Measure Complexity, EMC). It is intended to promote more effective management of development projects by shifting the focus from the structural complexity of the product being developed to the dynamic complexity of the development processes involved. The book is divided into four main parts, the first of which provides an introduction to vector autoregression models, periodic vector autoregression models and linear dynamical systems for modeling cooperative work in product development projects. The second part presents theoretical approaches for assessing complexity in the product development environment, while the third highlights and explains closed-form solutions for the complexity metric EMC for vector autoregression models and linear dyn...
Dynamics of complex quantum systems
Akulin, Vladimir M
2014-01-01
This book gathers together a range of similar problems that can be encountered in different fields of modern quantum physics and that have common features with regard to multilevel quantum systems. The main motivation was to examine from a uniform standpoint various models and approaches that have been developed in atomic, molecular, condensed matter, chemical, laser and nuclear physics in various contexts. The book should help senior-level undergraduate, graduate students and researchers putting particular problems in these fields into a broader scientific context and thereby taking advantage of well-established techniques used in adjacent fields. This second edition has been expanded to include substantial new material (e.g. new sections on Dynamic Localization and on Euclidean Random Matrices and new chapters on Entanglement, Open Quantum Systems, and Coherence Protection). It is based on the author’s lectures at the Moscow Institute of Physics and Technology, at the CNRS Aimé Cotton Laboratory, and on ...
Complex networks repair strategies: Dynamic models
Fu, Chaoqi; Wang, Ying; Gao, Yangjun; Wang, Xiaoyang
2017-09-01
Network repair strategies are tactical methods that restore the efficiency of damaged networks; however, unreasonable repair strategies not only waste resources, they are also ineffective for network recovery. Most extant research on network repair focuses on static networks, but results and findings on static networks cannot be applied to evolutionary dynamic networks because, in dynamic models, complex network repair has completely different characteristics. For instance, repaired nodes face more severe challenges, and require strategic repair methods in order to have a significant effect. In this study, we propose the Shell Repair Strategy (SRS) to minimize the risk of secondary node failures due to the cascading effect. Our proposed method includes the identification of a set of vital nodes that have a significant impact on network repair and defense. Our identification of these vital nodes reduces the number of switching nodes that face the risk of secondary failures during the dynamic repair process. This is positively correlated with the size of the average degree and enhances network invulnerability.
Spreading dynamics in complex networks
Pei, Sen
2013-01-01
Searching for influential spreaders in complex networks is an issue of great significance for applications across various domains, ranging from the epidemic control, innovation diffusion, viral marketing, social movement to idea propagation. In this paper, we first display some of the most important theoretical models that describe spreading processes, and then discuss the problem of locating both the individual and multiple influential spreaders respectively. Recent approaches in these two topics are presented. For the identification of privileged single spreaders, we summarize several widely used centralities, such as degree, betweenness centrality, PageRank, k-shell, etc. We investigate the empirical diffusion data in a large scale online social community -- LiveJournal. With this extensive dataset, we find that various measures can convey very distinct information of nodes. Of all the users in LiveJournal social network, only a small fraction of them involve in spreading. For the spreading processes in Li...
Directory of Open Access Journals (Sweden)
Thomas Homer-Dixon
2013-12-01
Full Text Available We propose a complex systems approach to the study of political belief systems, to overcome some of the fragmentation in the current scholarship on ideology. We review relevant work in psychology, sociology, and political science and identify major cleavages in the literature: the spatial vs. non-spatial divide (ideologies as reducible to a spatially organized set of dimensions vs. as complex conceptual structures and the person-group problem (ideologies as driven by psychological needs of individuals vs. by institutional and power structures of society. We argue that construing ideologies as conceptual networks of cognitive-affective representations embedded in social networks of people may provide a path for bridging these existing gaps and epistemological disputes. Tools from cognitive science and computational social science such as cognitive-affective mapping, connectionist simulations, and agent-based modeling are appropriate methods for a new research program that substantiates our complex systems perspective on ideology.
Competitive Dynamics on Complex Networks
Zhao, Jiuhua; Wang, Xiaofan
2014-01-01
We consider a dynamical network model in which two competitors have fixed and different states, and each normal agent adjusts its state according to a distributed consensus protocol. The state of each normal agent converges to a steady value which is a convex combination of the competitors' states, and is independent of the initial states of agents. This implies that the competition result is fully determined by the network structure and positions of competitors in the network. We compute an Influence Matrix (IM) in which each element characterizing the influence of an agent on another agent in the network. We use the IM to predict the bias of each normal agent and thus predict which competitor will win. Furthermore, we compare the IM criterion with seven node centrality measures to predict the winner. We find that the competitor with higher Katz Centrality in an undirected network or higher PageRank in a directed network is much more likely to be the winner. These findings may shed new light on the role of n...
Complexity, dynamic cellular network, and tumorigenesis.
Waliszewski, P
1997-01-01
A holistic approach to tumorigenesis is proposed. The main element of the model is the existence of dynamic cellular network. This network comprises a molecular and an energetistic structure of a cell connected through the multidirectional flow of information. The interactions within dynamic cellular network are complex, stochastic, nonlinear, and also involve quantum effects. From this non-reductionist perspective, neither tumorigenesis can be limited to the genetic aspect, nor the initial event must be of molecular nature, nor mutations and epigenetic factors are mutually exclusive, nor a link between cause and effect can be established. Due to complexity, an unstable stationary state of dynamic cellular network rather than a group of unrelated genes determines the phenotype of normal and transformed cells. This implies relativity of tumor suppressor genes and oncogenes. A bifurcation point is defined as an unstable state of dynamic cellular network leading to the other phenotype-stationary state. In particular, the bifurcation point may be determined by a change of expression of a single gene. Then, the gene is called bifurcation point gene. The unstable stationary state facilitates the chaotic dynamics. This may result in a fractal dimension of both normal and tumor tissues. The co-existence of chaotic dynamics and complexity is the essence of cellular processes and shapes differentiation, morphogenesis, and tumorigenesis. In consequence, tumorigenesis is a complex, unpredictable process driven by the interplay between self-organisation and selection.
Spreading dynamics in complex networks
Pei, Sen; Makse, Hernán A.
2013-12-01
Searching for influential spreaders in complex networks is an issue of great significance for applications across various domains, ranging from epidemic control, innovation diffusion, viral marketing, and social movement to idea propagation. In this paper, we first display some of the most important theoretical models that describe spreading processes, and then discuss the problem of locating both the individual and multiple influential spreaders respectively. Recent approaches in these two topics are presented. For the identification of privileged single spreaders, we summarize several widely used centralities, such as degree, betweenness centrality, PageRank, k-shell, etc. We investigate the empirical diffusion data in a large scale online social community—LiveJournal. With this extensive dataset, we find that various measures can convey very distinct information of nodes. Of all the users in the LiveJournal social network, only a small fraction of them are involved in spreading. For the spreading processes in LiveJournal, while degree can locate nodes participating in information diffusion with higher probability, k-shell is more effective in finding nodes with a large influence. Our results should provide useful information for designing efficient spreading strategies in reality.
Ontology of Earth's nonlinear dynamic complex systems
Babaie, Hassan; Davarpanah, Armita
2017-04-01
As a complex system, Earth and its major integrated and dynamically interacting subsystems (e.g., hydrosphere, atmosphere) display nonlinear behavior in response to internal and external influences. The Earth Nonlinear Dynamic Complex Systems (ENDCS) ontology formally represents the semantics of the knowledge about the nonlinear system element (agent) behavior, function, and structure, inter-agent and agent-environment feedback loops, and the emergent collective properties of the whole complex system as the result of interaction of the agents with other agents and their environment. It also models nonlinear concepts such as aperiodic, random chaotic behavior, sensitivity to initial conditions, bifurcation of dynamic processes, levels of organization, self-organization, aggregated and isolated functionality, and emergence of collective complex behavior at the system level. By incorporating several existing ontologies, the ENDCS ontology represents the dynamic system variables and the rules of transformation of their state, emergent state, and other features of complex systems such as the trajectories in state (phase) space (attractor and strange attractor), basins of attractions, basin divide (separatrix), fractal dimension, and system's interface to its environment. The ontology also defines different object properties that change the system behavior, function, and structure and trigger instability. ENDCS will help to integrate the data and knowledge related to the five complex subsystems of Earth by annotating common data types, unifying the semantics of shared terminology, and facilitating interoperability among different fields of Earth science.
Complexity and dynamics of topological and community structure in complex networks
Berec, Vesna
2017-07-01
Complexity is highly susceptible to variations in the network dynamics, reflected on its underlying architecture where topological organization of cohesive subsets into clusters, system's modular structure and resulting hierarchical patterns, are cross-linked with functional dynamics of the system. Here we study connection between hierarchical topological scales of the simplicial complexes and the organization of functional clusters - communities in complex networks. The analysis reveals the full dynamics of different combinatorial structures of q-th-dimensional simplicial complexes and their Laplacian spectra, presenting spectral properties of resulting symmetric and positive semidefinite matrices. The emergence of system's collective behavior from inhomogeneous statistical distribution is induced by hierarchically ordered topological structure, which is mapped to simplicial complex where local interactions between the nodes clustered into subcomplexes generate flow of information that characterizes complexity and dynamics of the full system.
Testing dynamic stabilisation in complex Langevin simulations
Attanasio, Felipe
2016-01-01
Complex Langevin methods have been successfully applied in theories that suffer from a sign problem such as QCD with a chemical potential. We present and illustrate a novel method (dynamic stabilisation) that ensures that Complex Langevin simulations stay close to the SU(3) manifold, which lead to correct and improved results in the framework of pure Yang-Mills simulations and QCD in the limit of heavy quarks.
Imura, Jun-ichi; Ueta, Tetsushi
2015-01-01
This book is the first to report on theoretical breakthroughs on control of complex dynamical systems developed by collaborative researchers in the two fields of dynamical systems theory and control theory. As well, its basic point of view is of three kinds of complexity: bifurcation phenomena subject to model uncertainty, complex behavior including periodic/quasi-periodic orbits as well as chaotic orbits, and network complexity emerging from dynamical interactions between subsystems. Analysis and Control of Complex Dynamical Systems offers a valuable resource for mathematicians, physicists, and biophysicists, as well as for researchers in nonlinear science and control engineering, allowing them to develop a better fundamental understanding of the analysis and control synthesis of such complex systems.
Complex systems and networks dynamics, controls and applications
Yu, Xinghuo; Chen, Guanrong; Yu, Wenwu
2016-01-01
This elementary book provides some state-of-the-art research results on broad disciplinary sciences on complex networks. It presents an in-depth study with detailed description of dynamics, controls and applications of complex networks. The contents of this book can be summarized as follows. First, the dynamics of complex networks, for example, the cluster dynamic analysis by using kernel spectral methods, community detection algorithms in bipartite networks, epidemiological modeling with demographics and epidemic spreading on multi-layer networks, are studied. Second, the controls of complex networks are investigated including topics like distributed finite-time cooperative control of multi-agent systems by applying homogenous-degree and Lyapunov methods, composite finite-time containment control for disturbed second-order multi-agent systems, fractional-order observer design of multi-agent systems, chaos control and anticontrol of complex systems via Parrondos game and many more. Third, the applications of ...
Dynamic information routing in complex networks
Kirst, Christoph; Timme, Marc; Battaglia, Demian
2016-01-01
Flexible information routing fundamentally underlies the function of many biological and artificial networks. Yet, how such systems may specifically communicate and dynamically route information is not well understood. Here we identify a generic mechanism to route information on top of collective dynamical reference states in complex networks. Switching between collective dynamics induces flexible reorganization of information sharing and routing patterns, as quantified by delayed mutual information and transfer entropy measures between activities of a network's units. We demonstrate the power of this mechanism specifically for oscillatory dynamics and analyse how individual unit properties, the network topology and external inputs co-act to systematically organize information routing. For multi-scale, modular architectures, we resolve routing patterns at all levels. Interestingly, local interventions within one sub-network may remotely determine nonlocal network-wide communication. These results help understanding and designing information routing patterns across systems where collective dynamics co-occurs with a communication function. PMID:27067257
Dynamic information routing in complex networks
Kirst, Christoph; Timme, Marc; Battaglia, Demian
2016-04-01
Flexible information routing fundamentally underlies the function of many biological and artificial networks. Yet, how such systems may specifically communicate and dynamically route information is not well understood. Here we identify a generic mechanism to route information on top of collective dynamical reference states in complex networks. Switching between collective dynamics induces flexible reorganization of information sharing and routing patterns, as quantified by delayed mutual information and transfer entropy measures between activities of a network's units. We demonstrate the power of this mechanism specifically for oscillatory dynamics and analyse how individual unit properties, the network topology and external inputs co-act to systematically organize information routing. For multi-scale, modular architectures, we resolve routing patterns at all levels. Interestingly, local interventions within one sub-network may remotely determine nonlocal network-wide communication. These results help understanding and designing information routing patterns across systems where collective dynamics co-occurs with a communication function.
Energy Technology Data Exchange (ETDEWEB)
Lebedev, V. M., E-mail: lebedev@pnpi.spb.ru; Lebedev, V. T.; Ivanova, I. N.; Orlova, D. N. [Russian Academy of Sciences, St. Petersburg Nuclear Physics Institute (Russian Federation)
2011-12-15
A project of the center for studying reactor materials and solving problems of materials science is presented which will be equipped with the following neutron instruments: a small-angle Membrana diffractometer, a spin-echo spectrometer, and a time-of-flight spectrometer. It is proposed to irradiate materials in the PIK reactor core and use neutron-scattering tools to analyze the structure and dynamics of these materials and investigate radiative defects in the complete experimental cycle (initial material-irradiation-strength tests, thermal loads, and other effects) using materials science techniques.
Understanding Learner Agency as a Complex Dynamic System
Mercer, Sarah
2011-01-01
This paper attempts to contribute to a fuller understanding of the nature of language learner agency by considering it as a complex dynamic system. The purpose of the study was to explore detailed situated data to examine to what extent it is feasible to view learner agency through the lens of complexity theory. Data were generated through a…
Major depression as a complex dynamic system
Cramer, A.O.J.; van Borkulo, C.D.; Giltay, E.J.; van der Maas, H.L.J.; Kendler, K.S.; Scheffer, M.; Borsboom, D.
2016-01-01
In this paper, we characterize major depression (MD) as a complex dynamic system in which symptoms (e.g., insomnia and fatigue) are directly connected to one another in a network structure. We hypothesize that individuals can be characterized by their own network with unique architecture and resulti
Coherent Dynamics of Complex Quantum Systems
Akulin, Vladimir M
2006-01-01
A large number of modern problems in physics, chemistry, and quantum electronics require a consideration of population dynamics in complex multilevel quantum systems. The purpose of this book is to provide a systematic treatment of these questions and to present a number of exactly solvable problems. It considers the different dynamical problems frequently encountered in different areas of physics from the same perspective, based mainly on the fundamental ideas of group theory and on the idea of ensemble average. Also treated are concepts of complete quantum control and correction of decoherence induced errors that are complementary to the idea of ensemble average. "Coherent Dynamics of Complex Quantum Systems" is aimed at senior-level undergraduate students in the areas of Atomic, Molecular, and Laser Physics, Physical Chemistry, Quantum Optics and Quantum Informatics. It should help them put particular problems in these fields into a broader scientific context and thereby take advantage of the well-elabora...
Complex and Adaptive Dynamical Systems A Primer
Gros, Claudius
2011-01-01
We are living in an ever more complex world, an epoch where human actions can accordingly acquire far-reaching potentialities. Complex and adaptive dynamical systems are ubiquitous in the world surrounding us and require us to adapt to new realities and the way of dealing with them. This primer has been developed with the aim of conveying a wide range of "commons-sense" knowledge in the field of quantitative complex system science at an introductory level, providing an entry point to this both fascinating and vitally important subject. The approach is modular and phenomenology driven. Examples of emerging phenomena of generic importance treated in this book are: -- The small world phenomenon in social and scale-free networks. -- Phase transitions and self-organized criticality in adaptive systems. -- Life at the edge of chaos and coevolutionary avalanches resulting from the unfolding of all living. -- The concept of living dynamical systems and emotional diffusive control within cognitive system theory. Techn...
Complex and adaptive dynamical systems a primer
Gros, Claudius
2007-01-01
We are living in an ever more complex world, an epoch where human actions can accordingly acquire far-reaching potentialities. Complex and adaptive dynamical systems are ubiquitous in the world surrounding us and require us to adapt to new realities and the way of dealing with them. This primer has been developed with the aim of conveying a wide range of "commons-sense" knowledge in the field of quantitative complex system science at an introductory level, providing an entry point to this both fascinating and vitally important subject. The approach is modular and phenomenology driven. Examples of emerging phenomena of generic importance treated in this book are: -- The small world phenomenon in social and scale-free networks. -- Phase transitions and self-organized criticality in adaptive systems. -- Life at the edge of chaos and coevolutionary avalanches resulting from the unfolding of all living. -- The concept of living dynamical systems and emotional diffusive control within cognitive system theory. Techn...
Design tools for complex dynamic security systems.
Energy Technology Data Exchange (ETDEWEB)
Byrne, Raymond Harry; Rigdon, James Brian; Rohrer, Brandon Robinson; Laguna, Glenn A.; Robinett, Rush D. III (.; ); Groom, Kenneth Neal; Wilson, David Gerald; Bickerstaff, Robert J.; Harrington, John J.
2007-01-01
The development of tools for complex dynamic security systems is not a straight forward engineering task but, rather, a scientific task where discovery of new scientific principles and math is necessary. For years, scientists have observed complex behavior but have had difficulty understanding it. Prominent examples include: insect colony organization, the stock market, molecular interactions, fractals, and emergent behavior. Engineering such systems will be an even greater challenge. This report explores four tools for engineered complex dynamic security systems: Partially Observable Markov Decision Process, Percolation Theory, Graph Theory, and Exergy/Entropy Theory. Additionally, enabling hardware technology for next generation security systems are described: a 100 node wireless sensor network, unmanned ground vehicle and unmanned aerial vehicle.
Dynamic information routing in complex networks
Kirst, Christoph; Battaglia, Demian
2015-01-01
Flexible information routing fundamentally underlies the function of many biological and artificial networks. Yet, how such systems may specifically communicate and dynamically route information is not well understood. Here we identify a generic mechanism to route information on top of collective dynamical reference states in complex networks. Switching between collective dynamics induces flexible reorganization of information sharing and routing patterns, as quantified by delayed mutual information and transfer entropy measures between activities of a network's units. We demonstrate the power of this generic mechanism specifically for oscillatory dynamics and analyze how individual unit properties, the network topology and external inputs coact to systematically organize information routing. For multi-scale, modular architectures, we resolve routing patterns at all levels. Interestingly, local interventions within one sub-network may remotely determine non-local network-wide communication. These results help...
Complexity of software trustworthiness and its dynamical statistical analysis methods
Institute of Scientific and Technical Information of China (English)
ZHENG ZhiMing; MA ShiLong; LI Wei; JIANG Xin; WEI Wei; MA LiLi; TANG ShaoTing
2009-01-01
Developing trusted softwares has become an important trend and a natural choice in the development of software technology and applications.At present,the method of measurement and assessment of software trustworthiness cannot guarantee safe and reliable operations of software systems completely and effectively.Based on the dynamical system study,this paper interprets the characteristics of behaviors of software systems and the basic scientific problems of software trustworthiness complexity,analyzes the characteristics of complexity of software trustworthiness,and proposes to study the software trustworthiness measurement in terms of the complexity of software trustworthiness.Using the dynamical statistical analysis methods,the paper advances an invariant-measure based assessment method of software trustworthiness by statistical indices,and hereby provides a dynamical criterion for the untrustworthiness of software systems.By an example,the feasibility of the proposed dynamical statistical analysis method in software trustworthiness measurement is demonstrated using numerical simulations and theoretical analysis.
Advances in dynamics, patterns, cognition challenges in complexity
Pikovsky, Arkady; Rulkov, Nikolai; Tsimring, Lev
2017-01-01
This book focuses on recent progress in complexity research based on the fundamental nonlinear dynamical and statistical theory of oscillations, waves, chaos, and structures far from equilibrium. Celebrating seminal contributions to the field by Prof. M. I. Rabinovich of the University of California at San Diego, this volume brings together perspectives on both the fundamental aspects of complexity studies, as well as in applications in different fields ranging from granular patterns to understanding of the cognitive brain and mind dynamics. The slate of world-class authors review recent achievements that together present a broad and coherent coverage of modern research in complexity greater than the sum of its parts. Presents the most up-to-date developments in the studies of complexity Combines basic and applied aspects Links background nonlinear theory of oscillations and waves with modern approaches Allows readers to recognize general dynamical principles across the applications fields.
Zhao, Yan; Yang, Fan; Wang, Jianru; Yu, Pengyun; Pan, Huifen; Wang, Hongfei; Wang, Jianping
2016-09-01
The characteristic nitrosyl stretching (NO) in the region of 1800-1900 cm- 1 was used to study the geometric and ligand effect on two nitrosylruthenium complexes, namely [Ru(OAc)(2QN)2NO] (QN = 2-chloro-8-quinolinol (H2cqn) or QN = 2-methyl-8-quinolinol (H2mqn)). The NO stretching frequency (νNO) was found in the following order: νcis-1 (2cqn) > νcis-2 (2cqn) > νcis-1 (2mqn) > νtrans (2mqn). The results exhibited a spectral sensitivity of the NO mode to both charge distribution and ligand arrangement, which was supported by ab initio computations and natural bond orbital (NBO) analyses. Further, the vibrational population of the vibrationally excited NO stretching mode was found to relax on the order of 7-10 ps, showing less than 30% variation from one isomer to another, which were explained on the basis of NO local structures and solute-solvent interactions in these isomeric nitrosylruthenium complexes.
The Complex Dynamics of Sponsored Search Markets
Robu, Valentin; La Poutré, Han; Bohte, Sander
This paper provides a comprehensive study of the structure and dynamics of online advertising markets, mostly based on techniques from the emergent discipline of complex systems analysis. First, we look at how the display rank of a URL link influences its click frequency, for both sponsored search and organic search. Second, we study the market structure that emerges from these queries, especially the market share distribution of different advertisers. We show that the sponsored search market is highly concentrated, with less than 5% of all advertisers receiving over 2/3 of the clicks in the market. Furthermore, we show that both the number of ad impressions and the number of clicks follow power law distributions of approximately the same coefficient. However, we find this result does not hold when studying the same distribution of clicks per rank position, which shows considerable variance, most likely due to the way advertisers divide their budget on different keywords. Finally, we turn our attention to how such sponsored search data could be used to provide decision support tools for bidding for combinations of keywords. We provide a method to visualize keywords of interest in graphical form, as well as a method to partition these graphs to obtain desirable subsets of search terms.
Banerjee, Tanmay; Biswas, Abul Kalam; Sahu, Tuhin Subhra; Ganguly, Bishwajit; Das, Amitava; Ghosh, Hirendra Nath
2014-09-28
New Ru(ii)- and Os(ii)-polypyridyl complexes have been synthesized with pendant acetylacetone (acac) functionality for anchoring on nanoparticulate TiO2 surfaces with a goal of developing an alternate sensitizer that could be utilized for designing an efficient dye-sensitized solar cell (DSSC). Time-resolved transient absorption spectroscopic studies in the femtosecond time domain have been carried out. The charge recombination rates are observed to be very slow, compared with those for strongly coupled dye molecules having catechol as the anchoring functionality. The results of such studies reveal that electron-injection rates from the metal complex-based LUMO to the conduction band of TiO2 are faster than one would expect for an analogous complex in which the chromophoric core and the anchoring moiety are separated with multiple saturated C-C linkages. Such an observation is rationalized based on computational studies, and a relatively smaller spatial distance between the dye LUMO and the TiO2 surface accounted for this. Results of this study are compared with those for analogous complexes having a gem-dicarboxy group as the anchoring functionality for covalent binding to the TiO2 surface to compare the role of binding functionalities on electron-transfer dynamics.
Drolle, Elizabeth; Bennett, W F D; Lyman, Edward; Karttunen, Mikko; Leonenko, Zoya
2016-01-01
The molecular arrangement of lipids and proteins within biomembranes and monolayers gives rise to complex film morphologies as well as regions of distinct electrical surface potential, topographical and electrostatic nanoscale domains. To probe these nanodomains in soft matter is a challenging task both experimentally and theoretically. This work addresses the effects of cholesterol, lipid composition, lipid charge, and lipid phase on the monolayer structure and the electrical surface potential distribution. Atomic Force Microscopy (AFM) was used to resolve topographical nanodomains and Kelvin Probe Force Microscopy (KPFM) to resolve electrical surface potential of these nanodomains in lipid monolayers. Model monolayers composed of dipalmitoylphosphatidylcholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2-dioleoyl-sn-glycero-3-[phospho-rac-(3-lysyl(1-glycerol))] (DOPG), sphingomyelin, and cholesterol were studied. It is shown that chole...
Gholami, Samira; Bordbar, Abdol-Khalegh; Akvan, Nadia
2016-09-01
UV-Vis absorption data of β-lactoglobulin (BLG) and arachidonoyl serotonin (AA-5HT) in BLG complex were examined and analyzed using chemometrics method. Analysis of the spectral data matrices by using the multivariate curve resolution-alternating least squares (MCR-ALS) algorithm resulted to the pure concentration calculation and spectral profiles resolution of the chemical constituents and the values of (6.433±0.019)×10(4)M(-1), (4.532±0.007)×10(4)M(-1), (3.364±0.010)×10(4)M(-1) and (2.977±0.013)×10(4)M(-1) as estimated equilibrium constants at 288, 293, 298 and 303K, respectively. The number of chemical constituents involved in the interaction which was extracted by PCA method were free and bound BLG. The spontaneity of the binding process and critical role of hydrogen bonding and van der Waals interactions in stabilizing protein-ligand complex have been designated by negative values of Gibbs free energy, entropy and enthalpy changes. Molecular docking study showed that AA-5HT binds to Val(41), Leu(39), Leu(54), Ile(71), Phe(82), Asn(90), Val(92), Phe(105), Met(107), Glu(108) with the free binding energy of -37.478kJ/mol. Computational studies predicted that in spite of serotonin (5HT) which anchors to the outer surface of BLG by hydrogen bonds, AA-5HT is situated in the calyx pose and stayed there during the entire time of simulation. This binding is accompanying with no apparent influence on secondary structure and partially destabilization of tertiary structure of BLG which pointed the suitability of this protein as drug carrier for AA-5HT.
Xie, Yu; Zheng, Jie; Lan, Zhenggang
2015-02-28
Electron transfer at the donor-acceptor heterojunctions plays a critical role in the photoinduced process during the solar energy conversion in organic photovoltaic materials. We theoretically investigate the electron transfer process in the anthracene/C60 donor-acceptor complex by using quantum dynamics calculations. The electron-transfer model Hamiltonian with full dimensionality was built by quantum-chemical calculations. The quantum dynamics calculations were performed using the multiconfigurational time-dependent Hartree (MCTDH) theory and multilayer (ML) MCTDH methods. The latter approach (ML-MCTDH) allows us to conduct the comprehensive study on the quantum evolution of the full-dimensional electron-transfer model including 4 electronic states and 246 vibrational degrees of freedom. Our quantum dynamics calculations exhibit the ultrafast anthracene → C60 charge transfer process because of the strong coupling between excitonic and charge transfer states. This work demonstrates that the ML-MCTDH is a very powerful method to treat the quantum evolution of complex systems.
Energy Technology Data Exchange (ETDEWEB)
Xie, Yu; Zheng, Jie; Lan, Zhenggang, E-mail: lanzg@qibebt.ac.cn [CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101 (China); University of Chinese Academy of Sciences, Beijing 100049 (China)
2015-02-28
Electron transfer at the donor-acceptor heterojunctions plays a critical role in the photoinduced process during the solar energy conversion in organic photovoltaic materials. We theoretically investigate the electron transfer process in the anthracene/C60 donor-acceptor complex by using quantum dynamics calculations. The electron-transfer model Hamiltonian with full dimensionality was built by quantum-chemical calculations. The quantum dynamics calculations were performed using the multiconfigurational time-dependent Hartree (MCTDH) theory and multilayer (ML) MCTDH methods. The latter approach (ML-MCTDH) allows us to conduct the comprehensive study on the quantum evolution of the full-dimensional electron-transfer model including 4 electronic states and 246 vibrational degrees of freedom. Our quantum dynamics calculations exhibit the ultrafast anthracene → C60 charge transfer process because of the strong coupling between excitonic and charge transfer states. This work demonstrates that the ML-MCTDH is a very powerful method to treat the quantum evolution of complex systems.
Complex Human Dynamics From Mind to Societies
Winkowska-Nowak, Katarzyna; Brée, David
2013-01-01
This book, edited and authored by a closely collaborating network of social scientists and psychologists, recasts typical research topics in these fields into the language of nonlinear, dynamic and complex systems. The aim is to provide scientists with different backgrounds - physics, applied mathematics and computer sciences - with the opportunity to apply the tools of their trade to an altogether new range of possible applications. At the same time, this book will serve as a first reference for a new generation of social scientists and psychologists wishing to familiarize themselves with the new methodology and the "thinking in complexity".
Guiding locomotion in complex dynamic environments
Directory of Open Access Journals (Sweden)
Brett R Fajen
2013-07-01
Full Text Available Locomotion in complex dynamic environments is an integral part of many daily activities, including walking in crowded spaces, driving on busy roadways, and playing sports. Many of the tasks that humans perform in such environments involve interactions with moving objects -- that is, they require people to coordinate their own movement with the movements of other objects. A widely adopted framework for research on the detection, avoidance, and interception of moving objects is the bearing angle model, according to which observers move so as to keep the bearing angle of the object constant for interception and varying for obstacle avoidance. The bearing angle model offers a simple, parsimonious account of visual control but has several significant limitations and does not easily scale up to more complex tasks. In this paper, I introduce an alternative account of how humans choose actions and guide locomotion in the presence of moving objects. I show how the new approach addresses the limitations of the bearing angle model and accounts for a variety of behaviors involving moving objects, including (1 choosing whether to pass in front of or behind a moving obstacle, (2 perceiving whether a gap between a pair of moving obstacles is passable, (3 avoiding a collision while passing through single or multiple lanes of traffic, (4 coordinating speed and direction of locomotion during interception, (5 simultaneously intercepting a moving target while avoiding a stationary or moving obstacle, and (6 knowing whether to abandon the chase of a moving target. I also summarize data from recent studies that support the new approach.
Markovian Dynamics on Complex Reaction Networks
Goutsias, John
2012-01-01
Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological, ecological, social, neural, and multi-agent networks. A common approach to modeling such networks is by a master equation that governs the dynamic evolution of the joint probability mass function of the underling population process and naturally leads to Markovian dynamics for such process. Due however to the nonlinear nature of most reactions, the computation and analysis of the resulting stochastic population dynamics is a difficult task. This review article provides a coherent and comprehensive coverage of recently developed approaches and methods to tackle this problem. After reviewing a general framework for modeling Markovian reaction networks and giving specific examples, the authors present numerical and computational techniques capable of evaluating or approximating...
Early days in complex dynamics a history of complex dynamics in one variable during 1906-1942
Alexander, Daniel S; Rosa, Alessandro
2011-01-01
The theory of complex dynamics, whose roots lie in 19th-century studies of the iteration of complex function conducted by Kœnigs, Schröder, and others, flourished remarkably during the first half of the 20th century, when many of the central ideas and techniques of the subject developed. This book by Alexander, Iavernaro, and Rosa paints a robust picture of the field of complex dynamics between 1906 and 1942 through detailed discussions of the work of Fatou, Julia, Siegel, and several others. A recurrent theme of the authors' treatment is the center problem in complex dynamics. They present its complete history during this period and, in so doing, bring out analogies between complex dynamics and the study of differential equations, in particular, the problem of stability in Hamiltonian systems. Among these analogies are the use of iteration and problems involving small divisors which the authors examine in the work of Poincaré and others, linking them to complex dynamics, principally via the work of Samuel...
Junaid, Muhammad; Muhseen, Ziyad Tariq; Ullah, Ata; Wadood, Abdul; Liu, Junjun; Zhang, Houjin
2014-01-01
Rab9 is required for the transport of mannose 6-phosphate receptors to the trans-Golgi network from late endosomes through the interaction with its effector: RhoBTB3. Earlier research indicates the C-terminus of RhoBTB3 (Rho_Cterm) is used for the interaction with Rab9. We used the homology modeling along with the molecular dynamics (MD) simulation to study the binding pattern of Rho_Cterm and Rab9 at atomic level. Both modeled structures, Rab9 and Rho_Cterm, are of high quality as suggested by the Ramachandran plot and ProCheck. The complex of Rab9-Rho_Cterm was generated by unrestrained pairwise docking using ZDOCK server. The interface of complex is consistent with the previous experimental data. The results of MD simulation indicate that the binding interface is stable along the simulation process. PMID:25670879
Dynamical characteristics of software trustworthiness and their evolutionary complexity
Institute of Scientific and Technical Information of China (English)
ZHENG ZhiMing; MA ShiLong; LI Wei; WEI Wei; JIANG Xin; ZHANG ZhanLi; GUO BingHui
2009-01-01
Developing trusted $oftwares has become an important trend and a natural choice In the development of software technology and applications, and software trustworthiness modeling has become a prerequisite and necessary means. To discuss and explain the basic scientific problems in software trustworthiness and to establish theoretical foundations for software trustworthiness measurement, combining the Ideas of dynamical system study, this paper studies evolutionary laws of software trustworthiness and the dynamical mechanism under the effect of various internal and external factors, and proposes dynamical models for software trustworthiness, thus, software trustworthiness can be considered as the statistical characteristics of behaviors of software systems in the dynamical and open environment. By analyzing two simple examples, the paper explains the relationship between the limit evolutionary behaviors of software trustworthiness attributes and dynamical system characteristics, and interprets the dynamical characteristics of software trustworthiness and their evolutionary complexity.
Complex and adaptive dynamical systems a primer
Gros, Claudius
2013-01-01
Complex system theory is rapidly developing and gaining importance, providing tools and concepts central to our modern understanding of emergent phenomena. This primer offers an introduction to this area together with detailed coverage of the mathematics involved. All calculations are presented step by step and are straightforward to follow. This new third edition comes with new material, figures and exercises. Network theory, dynamical systems and information theory, the core of modern complex system sciences, are developed in the first three chapters, covering basic concepts and phenomena like small-world networks, bifurcation theory and information entropy. Further chapters use a modular approach to address the most important concepts in complex system sciences, with the emergence and self-organization playing a central role. Prominent examples are self-organized criticality in adaptive systems, life at the edge of chaos, hypercycles and coevolutionary avalanches, synchronization phenomena, absorbing phase...
Dynamics in electron transfer protein complexes
Bashir, Qamar
2010-01-01
Recent studies have provided experimental evidence for the existence of an encounter complex, a transient intermediate in the formation of protein complexes. We have used paramagnetic relaxation enhancement NMR spectroscopy in combination with Monte Carlo simulations to characterize and visualize th
Energy Technology Data Exchange (ETDEWEB)
Sibener, Steven J. [University of Chicago, IL (United States)
2014-03-11
This research program explored the efficacy of using molecular-level manipulation, imaging and scanning tunneling spectroscopy in conjunction with supersonic molecular beam gas-surface scattering to significantly enhance our understanding of chemical processes occurring on well-characterized interfaces. One program focus was on the spatially-resolved emergent behavior of complex reaction systems as a function of the local geometry and density of adsorbate-substrate systems under reaction conditions. Another focus was on elucidating the emergent electronic and related reactivity characteristics of intentionally constructed single and multicomponent atom- and nanoparticle-based materials. We also examined emergent chirality and self-organization in adsorbed molecular systems where collective interactions between adsorbates and the supporting interface lead to spatial symmetry breaking. In many of these studies we combined the advantages of scanning tunneling (STM) and atomic force (AFM) imaging, scanning tunneling local electronic spectroscopy (STS), and reactive supersonic molecular beams to elucidate precise details of interfacial reactivity that had not been observed by more traditional surface science methods. Using these methods, it was possible to examine, for example, the differential reactivity of molecules adsorbed at different bonding sites in conjunction with how reactivity is modified by the local configuration of nearby adsorbates. At the core of this effort was the goal of significantly extending our understanding of interfacial atomic-scale interactions to create, with intent, molecular assemblies and materials with advanced chemical and physical properties. This ambitious program addressed several key topics in DOE Grand Challenge Science, including emergent chemical and physical properties in condensed phase systems, novel uses of chemical imaging, and the development of advanced reactivity concepts in combustion and catalysis including carbon
The study of basis sets for the calculation of the structure and dynamics of the benzene-Kr complex
Energy Technology Data Exchange (ETDEWEB)
Shirkov, Leonid; Makarewicz, Jan, E-mail: jama@amu.edu.pl [Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań (Poland)
2015-05-28
An ab initio intermolecular potential energy surface (PES) has been constructed for the benzene-krypton (BKr) van der Waals (vdW) complex. The interaction energy has been calculated at the coupled cluster level of theory with single, double, and perturbatively included triple excitations using different basis sets. As a result, a few analytical PESs of the complex have been determined. They allowed a prediction of the complex structure and its vibrational vdW states. The vibrational energy level pattern exhibits a distinct polyad structure. Comparison of the equilibrium structure, the dipole moment, and vibrational levels of BKr with their experimental counterparts has allowed us to design an optimal basis set composed of a small Dunning’s basis set for the benzene monomer, a larger effective core potential adapted basis set for Kr and additional midbond functions. Such a basis set yields vibrational energy levels that agree very well with the experimental ones as well as with those calculated from the available empirical PES derived from the microwave spectra of the BKr complex. The basis proposed can be applied to larger complexes including Kr because of a reasonable computational cost and accurate results.
The study of basis sets for the calculation of the structure and dynamics of the benzene-Kr complex.
Shirkov, Leonid; Makarewicz, Jan
2015-05-28
An ab initio intermolecular potential energy surface (PES) has been constructed for the benzene-krypton (BKr) van der Waals (vdW) complex. The interaction energy has been calculated at the coupled cluster level of theory with single, double, and perturbatively included triple excitations using different basis sets. As a result, a few analytical PESs of the complex have been determined. They allowed a prediction of the complex structure and its vibrational vdW states. The vibrational energy level pattern exhibits a distinct polyad structure. Comparison of the equilibrium structure, the dipole moment, and vibrational levels of BKr with their experimental counterparts has allowed us to design an optimal basis set composed of a small Dunning's basis set for the benzene monomer, a larger effective core potential adapted basis set for Kr and additional midbond functions. Such a basis set yields vibrational energy levels that agree very well with the experimental ones as well as with those calculated from the available empirical PES derived from the microwave spectra of the BKr complex. The basis proposed can be applied to larger complexes including Kr because of a reasonable computational cost and accurate results.
Tozan, Yesim; Ompad, Danielle C
2015-06-01
In a variety of urban health frameworks, cities are conceptualized as complex and dynamic yet commonly used epidemiological methods have failed to address this complexity and dynamism head on due to their narrow problem definitions and linear analytical representations. Scholars from a variety of disciplines have also long conceptualized cities as systems, but few have modeled urban health issues as problems within a system. Systems thinking in general and system dynamics in particular are relatively new approaches in public health, but ones that hold immense promise as methodologies to model and analyze the complexity underlying urban processes to effectively inform policy actions in dynamic environments. This conceptual essay reviews the utility of applying the concepts, principles, and methods of systems thinking to the study of complex urban health phenomena as a complementary approach to standard epidemiological methods using specific examples and provides recommendations on how to better incorporate systems thinking methods in urban health research and practice.
Dynamical systems examples of complex behaviour
Jost, Jürgen
2005-01-01
Our aim is to introduce, explain, and discuss the fundamental problems, ideas, concepts, results, and methods of the theory of dynamical systems and to show how they can be used in speci?c examples. We do not intend to give a comprehensive overview of the present state of research in the theory of dynamical systems, nor a detailed historical account of its development. We try to explain the important results, often neglecting technical re?nements 1 and, usually, we do not provide proofs. One of the basic questions in studying dynamical systems, i.e. systems that evolve in time, is the construction of invariants that allow us to classify qualitative types of dynamical evolution, to distinguish between qualitatively di?erent dynamics, and to studytransitions between di?erent types. Itis also important to ?nd out when a certain dynamic behavior is stable under small perturbations, as well as to understand the various scenarios of instability. Finally, an essential aspect of a dynamic evolution is the transformat...
Stochastic synchronization for time-varying complex dynamical networks
Institute of Scientific and Technical Information of China (English)
Guo Xiao-Yong; Li Jun-Min
2012-01-01
This paper studies the stochastic synchronization problem for time-varying complex dynamical networks. This model is totally different from some existing network models. Based on the Lyapunov stability theory, inequality techniques, and the properties of the Weiner process, some controllers and adaptive laws are designed to ensure achieving stochastic synchronization of a complex dynamical network model. A sufficient synchronization condition is given to ensure that the proposed network model is mean-square stable. Theoretical analysis and numerical simulation fully verify the main results.
Complex and adaptive dynamical systems a primer
Gros, Claudius
2015-01-01
This primer offers readers an introduction to the central concepts that form our modern understanding of complex and emergent behavior, together with detailed coverage of accompanying mathematical methods. All calculations are presented step by step and are easy to follow. This new fourth edition has been fully reorganized and includes new chapters, figures and exercises. The core aspects of modern complex system sciences are presented in the first chapters, covering network theory, dynamical systems, bifurcation and catastrophe theory, chaos and adaptive processes, together with the principle of self-organization in reaction-diffusion systems and social animals. Modern information theoretical principles are treated in further chapters, together with the concept of self-organized criticality, gene regulation networks, hypercycles and coevolutionary avalanches, synchronization phenomena, absorbing phase transitions and the cognitive system approach to the brain. Technical course prerequisites are the standard ...
Simulating the dynamics of complex plasmas
Schwabe, Mierk
2014-01-01
Complex plasmas are low-temperature plasmas that contain micrometer-size particles in addition to the neutral gas particles and the ions and electrons that make up the plasma. The microparticles interact strongly and display a wealth of collective effects. Here we report on linked numerical simulations that reproduce many of the experimental results of complex plasmas. We model a capacitively coupled plasma with a fluid code written for the commercial package comsol. The output of this model is used to calculate forces on microparticles. The microparticles are modeled using the molecular dynamics package lammps, which we extended to include the forces from the plasma. Using this method, we are able to reproduce void formation, the separation of particles of different sizes into layers, lane formation, vortex formation, and other effects.
Synchronization in Complex Networks of Nonlinear Dynamical Systems
Wu, Chai Wah
2007-01-01
This book brings together two emerging research areas: synchronization in coupled nonlinear systems and complex networks, and study conditions under which a complex network of dynamical systems synchronizes. While there are many texts that study synchronization in chaotic systems or properties of complex networks, there are few texts that consider the intersection of these two very active and interdisciplinary research areas. The main theme of this book is that synchronization conditions can be related to graph theoretical properties of the underlying coupling topology. The book introduces ide
Directory of Open Access Journals (Sweden)
Olchawa Ryszard
2015-07-01
Full Text Available Penetration of the liposome membranes doped with vanadium complex formed in the liquid-crystalline phase from egg yolk lecithin (EYL by the TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl spin probes has been investigated. The penetration process was followed by 360 hours at 24°C, using the electron spin resonance (EPR method. The spectroscopic parameter of the partition (F of this probe indicated that a maximum rigidity of the membrane was at 3% concentration of the vanadium complex. Computer simulations showed that the increase in the rigidity of the membrane corresponds to the closure of gaps in the surface layer of the membrane, and indicates the essential role of the membrane surface in transport processes.
Eslami Moghadam, Mahboube; Saidifar, Maryam; Divsalar, Adeleh; Mansouri-Torshizi, Hassan; Saboury, Ali Akbar; Farhangian, Hossein; Ghadamgahi, Maryam
2016-01-01
Some amino acid derivatives, such as R-glycine, have been synthesized together with their full spectroscopic characterization. The sodium salts of these bidentate amino acid ligands have been interacted with [M(bpy)(H2O)2](NO3)2 giving the corresponding some new complexes with formula [M(bpy)(R-gly)]NO3 (where M is Pt(II) or Pd(II), bpy is 2,2'-bipyridine and R-gly is butyl-, hexyl- and octyl-glycine). Due to less solubility of octyl derivatives, the biological activities of butyl and hexyl derivatives have been tested against chronic myelogenous leukemia cell line, K562. The interaction of these complexes with highly polymerized calf thymus DNA has been extensively studied by means of electronic absorption, fluorescence and other measurements. The experimental results suggest that these complexes positive cooperatively bind to DNA presumably via groove binding. Molecular dynamic results show that the DNA structure is largely maintained its native structure in hexylglycine derivative-water mixtures and at lower temperatures. The simulation data indicates that the more destabilizing effect of butylglycine is induced by preferential accumulation of these molecules around the DNA and due to their more negative free energy of binding via groove binding.
Soliton-Complex Dynamics in Strongly Dispersive Medium
Bogdan, M M; Maugin, G A; Bogdan, Mikhail M.; Kosevich, Arnold M.; Maugin, Gerard A.
1999-01-01
The concept of soliton complex in a nonlinear dispersive medium is proposed. It is shown that strongly interacting identical topological solitons in the medium can form bound soliton complexes which move without radiation. This phenomenon is considered to be universal and applicable to various physical systems. The soliton complex and its "excited" states are described analytically and numerically as solutions of nonlinear dispersive equations with the fourth and higher spatial or mixed derivatives. The dispersive sine-Gordon, double and triple sine-Gordon, and piecewise-linear models are studied in detail. Mechanisms and conditions of the formation of soliton complexes, and peculiarities of their stationary dynamics are investigated. A phenomenological approach to the description of the complexes and the classification of all the possible complex states are proposed. Some examples of physical systems, where the phenomenon can be experimentally observed, are briefly discussed.
Dynamics of lane formation in driven binary complex plasmas
Sutterlin, K. R.; Wysocki, A.; Ivlev, A. V.; Rath, C.; Thomas, H. M.; Rubin-Zuzic, M.; W. J. Goedheer,; Fortov, V. E.; Lipaev, A. M.; Molotkov, V. I.; Petrov, O. F.; Morfill, G. E.; Lowen, H.
2009-01-01
The dynamical onset of lane formation is studied in experiments with binary complex plasmas under microgravity conditions. Small microparticles are driven and penetrate into a cloud of big particles, revealing a strong tendency towards lane formation. The observed time-resolved lane-formation proces
Coupled disease-behavior dynamics on complex networks: A review
Wang, Zhen; Andrews, Michael A.; Wu, Zhi-Xi; Wang, Lin; Bauch, Chris T.
2015-12-01
It is increasingly recognized that a key component of successful infection control efforts is understanding the complex, two-way interaction between disease dynamics and human behavioral and social dynamics. Human behavior such as contact precautions and social distancing clearly influence disease prevalence, but disease prevalence can in turn alter human behavior, forming a coupled, nonlinear system. Moreover, in many cases, the spatial structure of the population cannot be ignored, such that social and behavioral processes and/or transmission of infection must be represented with complex networks. Research on studying coupled disease-behavior dynamics in complex networks in particular is growing rapidly, and frequently makes use of analysis methods and concepts from statistical physics. Here, we review some of the growing literature in this area. We contrast network-based approaches to homogeneous-mixing approaches, point out how their predictions differ, and describe the rich and often surprising behavior of disease-behavior dynamics on complex networks, and compare them to processes in statistical physics. We discuss how these models can capture the dynamics that characterize many real-world scenarios, thereby suggesting ways that policy makers can better design effective prevention strategies. We also describe the growing sources of digital data that are facilitating research in this area. Finally, we suggest pitfalls which might be faced by researchers in the field, and we suggest several ways in which the field could move forward in the coming years.
STUDYING COMPLEX ADAPTIVE SYSTEMS
Institute of Scientific and Technical Information of China (English)
John H. Holland
2006-01-01
Complex adaptive systems (cas) - systems that involve many components that adapt or learn as they interact - are at the heart of important contemporary problems. The study of cas poses unique challenges: Some of our most powerful mathematical tools, particularly methods involving fixed points, attractors, and the like, are of limited help in understanding the development of cas. This paper suggests ways to modify research methods and tools, with an emphasis on the role of computer-based models, to increase our understanding of cas.
Complex Granular Flow Dynamics in Fruit Powder Production Lines
Bakhshinejad, Ali, 1984-
2013-01-01
One of the most important parts in every industry, is packaging which is located at the last part of the product line. In fruit powder product line lots of studies applied to study the complex dynamics of the powders in response to the vertical vibration. In this study cyclone collector condition was simulate with a rectangular throw out bin and the dynamics of the powders in response to the horizontal vibration studied. An ADXL345 accelerometer does employed in order to observe the accel...
The heterogeneous dynamics of economic complexity.
Directory of Open Access Journals (Sweden)
Matthieu Cristelli
Full Text Available What will be the growth of the Gross Domestic Product (GDP or the competitiveness of China, United States, and Vietnam in the next 3, 5 or 10 years? Despite this kind of questions has a large societal impact and an extreme value for economic policy making, providing a scientific basis for economic predictability is still a very challenging problem. Recent results of a new branch--Economic Complexity--have set the basis for a framework to approach such a challenge and to provide new perspectives to cast economic prediction into the conceptual scheme of forecasting the evolution of a dynamical system as in the case of weather dynamics. We argue that a recently introduced non-monetary metrics for country competitiveness (fitness allows for quantifying the hidden growth potential of countries by the means of the comparison of this measure for intangible assets with monetary figures, such as GDP per capita. This comparison defines the fitness-income plane where we observe that country dynamics presents strongly heterogeneous patterns of evolution. The flow in some zones is found to be laminar while in others a chaotic behavior is instead observed. These two regimes correspond to very different predictability features for the evolution of countries: in the former regime, we find strong predictable pattern while the latter scenario exhibits a very low predictability. In such a framework, regressions, the usual tool used in economics, are no more the appropriate strategy to deal with such a heterogeneous scenario and new concepts, borrowed from dynamical systems theory, are mandatory. We therefore propose a data-driven method--the selective predictability scheme--in which we adopt a strategy similar to the methods of analogues, firstly introduced by Lorenz, to assess future evolution of countries.
The heterogeneous dynamics of economic complexity.
Cristelli, Matthieu; Tacchella, Andrea; Pietronero, Luciano
2015-01-01
What will be the growth of the Gross Domestic Product (GDP) or the competitiveness of China, United States, and Vietnam in the next 3, 5 or 10 years? Despite this kind of questions has a large societal impact and an extreme value for economic policy making, providing a scientific basis for economic predictability is still a very challenging problem. Recent results of a new branch--Economic Complexity--have set the basis for a framework to approach such a challenge and to provide new perspectives to cast economic prediction into the conceptual scheme of forecasting the evolution of a dynamical system as in the case of weather dynamics. We argue that a recently introduced non-monetary metrics for country competitiveness (fitness) allows for quantifying the hidden growth potential of countries by the means of the comparison of this measure for intangible assets with monetary figures, such as GDP per capita. This comparison defines the fitness-income plane where we observe that country dynamics presents strongly heterogeneous patterns of evolution. The flow in some zones is found to be laminar while in others a chaotic behavior is instead observed. These two regimes correspond to very different predictability features for the evolution of countries: in the former regime, we find strong predictable pattern while the latter scenario exhibits a very low predictability. In such a framework, regressions, the usual tool used in economics, are no more the appropriate strategy to deal with such a heterogeneous scenario and new concepts, borrowed from dynamical systems theory, are mandatory. We therefore propose a data-driven method--the selective predictability scheme--in which we adopt a strategy similar to the methods of analogues, firstly introduced by Lorenz, to assess future evolution of countries.
Complex Dynamics Caused by Torus Bifurcation in Power Systems
Institute of Scientific and Technical Information of China (English)
YU Xiaodan; JIA Hongjie; DONG Cun
2006-01-01
Torus bifurcation is a relatively complicated bifurcation caused by a pair of complex conjuployed to reveal the relationship between torus bifurcation and some complex dynamics.Based on theoretical analysis and simulation studies, it is found that torus bifurcation is a typical route to chaos in power system.Some complex dynamics usually occur after a torus bifurcation, such as self-organization, deep bifurcations, exquisite structure, coexistence of chaos and divergence.It is also found that chaos has close relationship with various instability scenarios of power systems.Studies of this paper are helpful to understand the mechanism of torus bifurcation in power system and relationship of chaos and power system instabilities.
Lewis, Kenneth T; Naik, Akshata R; Laha, Suvra S; Wang, Sunxi; Mao, Guangzhao; Kuhn, Eric; Jena, Bhanu P
2017-08-03
A wide range of cellular activities including protein folding and cell secretion, such as neurotransmission or insulin release, are all governed by intracellular pH homeostasis, underscoring the importance of pH on critical life processes. Nano- scale pH measurements of cells and biomolecules therefore hold great promise in understanding a plethora of cellular functions, in addition to disease detection and therapy. In the current study, a novel approach using cadmium telluride quantum dots (CdTeQDs) as pH sensors, combined with fluorescent imaging, spectrofluorimetry, atomic force microscopy (AFM), and Western blot analysis, enabled the study of intracellular pH dynamics at 1 milli-pH sensitivity and 80nm pixel resolution, during insulin secretion. Additionally, the pH-dependent interaction between membrane fusion proteins, also called the soluble N-ethylmaleimide-sensitive factor activating protein receptor (SNARE), was determined. Glucose stimulation of CdTeQD-loaded insulin secreting Min-6 mouse insulinoma cell line demonstrated the initial (5-6min) intracellular acidification reflected as a loss in QD fluorescence, followed by alkalization and a return to resting pH in 10min. Analysis of the SNARE complex in insulin secreting Min-6 cells demonstrated an initial gain followed by loss of complexed SNAREs in 10min. Stabilization of the SNARE complex at low intracellular pH is further supported by results from studies utilizing both native and AFM measurements of liposome-reconstituted recombinant neuronal SNAREs, providing a molecular understanding of the role of pH during cell secretion. Copyright © 2017 Elsevier Ltd. All rights reserved.
Complex systems dynamics in aging: new evidence, continuing questions.
Cohen, Alan A
2016-02-01
There have long been suggestions that aging is tightly linked to the complex dynamics of the physiological systems that maintain homeostasis, and in particular to dysregulation of regulatory networks of molecules. This review synthesizes recent work that is starting to provide evidence for the importance of such complex systems dynamics in aging. There is now clear evidence that physiological dysregulation--the gradual breakdown in the capacity of complex regulatory networks to maintain homeostasis--is an emergent property of these regulatory networks, and that it plays an important role in aging. It can be measured simply using small numbers of biomarkers. Additionally, there are indications of the importance during aging of emergent physiological processes, functional processes that cannot be easily understood through clear metabolic pathways, but can nonetheless be precisely quantified and studied. The overall role of such complex systems dynamics in aging remains an important open question, and to understand it future studies will need to distinguish and integrate related aspects of aging research, including multi-factorial theories of aging, systems biology, bioinformatics, network approaches, robustness, and loss of complexity.
Thangsunan, Patcharapong; Tateing, Suriya; Hannongbua, Supa; Suree, Nuttee
2016-07-01
Protein kinase C (PKC) isozymes are important regulatory enzymes that have been implicated in many diseases, including cancer, Alzheimer's disease, and in the eradication of HIV/AIDS. Given their potential clinical ramifications, PKC modulators, e.g. phorbol esters and bryostatin, are also of great interest in the drug development. However, structural details on the binding between PKC and its modulators, especially bryostatin - the highly potent and non-tumor promoting activator for PKCs, are still lacking. Here, we report the first comparative molecular dynamics study aimed at gaining structural insight into the mechanisms by which the PKC delta cys2 activator domain is used in its binding to phorbol ester and bryostatin-1. As anticipated in the phorbol ester binding, hydrogen bonds are formed through the backbone atoms of Thr242, Leu251, and Gly253 of PKC. However, the opposition of H-bond formation between Thr242 and Gly253 may cause the phorbol ester complex to become less stable when compared with the bryostatin binding. For the PKC delta-bryostatin complex, hydrogen bonds are formed between the Gly253 backbone carbonyl and the C30 carbomethoxy substituent of the ligand. Additionally, the indole Nε1 of the highly homologous Trp252 also forms an H-bond to the C20 ester group on bryostatin. Backbone fluctuations also suggest that this latter H-bond formation may abrogate the transient interaction between Trp252 and His269, thus dampening the fluctuations observed on the nearby Zn(2+)-coordinating residues. This new dynamic fluctuation dampening model can potentially benefit future design of new PKC modulators.
Dynamics of swimming bacteria at complex interfaces
Lopez, Diego
2014-01-01
Flagellated bacteria exploiting helical propulsion are known to swim along circular trajectories near surfaces. Fluid dynamics predicts this circular motion to be clockwise (CW) above a rigid surface (when viewed from inside the fluid) and counter-clockwise (CCW) below a free surface. Recent experimental investigations showed that complex physicochemical processes at the nearby surface could lead to a change in the direction of rotation, both at solid surfaces absorbing slip-inducing polymers and interfaces covered with surfactants. Motivated by these results, we use a far-field hydrodynamic model to predict the kinematics of swimming near three types of interfaces: clean fluid-fluid interface, slipping rigid wall, and a fluid interface covered by incompressible surfactants. Representing the helical swimmer by a superposition of hydrodynamic singularities, we first show that in all cases the surfaces reorient the swimmer parallel to the surface and attract it, both of which are a consequence of the Stokes dip...
On the complexity of Nash dynamics and Sink Equilibria
Mirrokni, Vahab
2009-01-01
Studying Nash dynamics is an important approach for analyzing the outcome of games with repeated selfish behavior of self-interested agents. Sink equilibria has been introduced by Goemans, Mirrokni, and Vetta for studying social cost on Nash dynamics over pure strategies in games. However, they do not address the complexity of sink equilibria in these games. Recently, Fabrikant and Papadimitriou initiated the study of the complexity of Nash dynamics in two classes of games. In order to completely understand the complexity of Nash dynamics in a variety of games, we study the following three questions for various games: (i) given a state in game, can we verify if this state is in a sink equilibrium or not? (ii) given an instance of a game, can we verify if there exists any sink equilibrium other than pure Nash equilibria? and (iii) given an instance of a game, can we verify if there exists a pure Nash equilibrium (i.e, a sink equilibrium with one state)? In this paper, we almost answer all of the above question...
Applications of dynamical complexity theory in traditional Chinese medicine.
Ma, Yan; Sun, Shuchen; Peng, Chung-Kang
2014-09-01
Traditional Chinese medicine (TCM) has been gradually accepted by the world. Despite its widespread use in clinical settings, a major challenge in TCM is to study it scientifically. This difficulty arises from the fact that TCM views human body as a complex dynamical system, and focuses on the balance of the human body, both internally and with its external environment. As a result, conventional tools that are based on reductionist approach are not adequate. Methods that can quantify the dynamics of complex integrative systems may bring new insights and utilities about the clinical practice and evaluation of efficacy of TCM. The dynamical complexity theory recently proposed and its computational algorithm, Multiscale Entropy (MSE) analysis, are consistent with TCM concepts. This new system level analysis has been successfully applied to many health and disease related topics in medicine. We believe that there could be many promising applications of this dynamical complexity concept in TCM. In this article, we propose some promising applications and research areas that TCM practitioners and researchers can pursue.
Entropy and enthalpy of polyelectrolyte complexation: Langevin dynamics simulations.
Ou, Zhaoyang; Muthukumar, M
2006-04-21
We report a systematic study by Langevin dynamics simulation on the energetics of complexation between two oppositely charged polyelectrolytes of same charge density in dilute solutions of a good solvent with counterions and salt ions explicitly included. The enthalpy of polyelectrolyte complexation is quantified by comparisons of the Coulomb energy before and after complexation. The entropy of polyelectrolyte complexation is determined directly from simulations and compared with that from a mean-field lattice model explicitly accounting for counterion adsorption. At weak Coulomb interaction strengths, e.g., in solvents of high dielectric constant or with weakly charged polyelectrolytes, complexation is driven by a negative enthalpy due to electrostatic attraction between two oppositely charged chains, with counterion release entropy playing only a subsidiary role. In the strong interaction regime, complexation is driven by a large counterion release entropy and opposed by a positive enthalpy change. The addition of salt reduces the enthalpy of polyelectrolyte complexation by screening electrostatic interaction at all Coulomb interaction strengths. The counterion release entropy also decreases in the presence of salt, but the reduction only becomes significant at higher Coulomb interaction strengths. More significantly, in the range of Coulomb interaction strengths appropriate for highly charged polymers in aqueous solutions, complexation enthalpy depends weakly on salt concentration and counterion release entropy exhibits a large variation as a function of salt concentration. Our study quantitatively establishes that polyelectrolyte complexation in highly charged Coulomb systems is of entropic origin.
Major depression as a complex dynamical system
Cramer, Angélique O J; Giltay, Erik J; van der Maas, Han L J; Kendler, Kenneth S; Scheffer, Marten; Borsboom, Denny
2016-01-01
In this paper, we characterize major depression (MD) as a complex dynamical system in which symptoms (e.g., insomnia and fatigue) are directly connected to one another in a network structure. We hypothesize that individuals can be characterized by their own network with unique architecture and resulting dynamics. With respect to architecture, we show that individuals vulnerable to developing MD are those with strong connections between symptoms: e.g., only one night of poor sleep suffices to make a particular person feel tired. Such vulnerable networks, when pushed by forces external to the system such as stress, are more likely to end up in a depressed state; whereas networks with weaker connections tend to remain in or return to a healthy state. We show this with a simulation in which we model the probability of a symptom becoming active as a logistic function of the activity of its neighboring symptoms. Additionally, we show that this model potentially explains some well-known empirical phenomena such as s...
Forest microbiome: diversity, complexity and dynamics.
Baldrian, Petr
2016-11-16
Globally, forests represent highly productive ecosystems that act as carbon sinks where soil organic matter is formed from residuals after biomass decomposition as well as from rhizodeposited carbon. Forests exhibit a high level of spatial heterogeneity and the importance of trees, the dominant primary producers, for their structure and functioning. Fungi, bacteria and archaea inhabit various forest habitats: foliage, the wood of living trees, the bark surface, ground vegetation, roots and the rhizosphere, litter, soil, deadwood, rock surfaces, invertebrates, wetlands or the atmosphere, each of which has its own specific features, such as nutrient availability or temporal dynamicy and specific drivers that affect microbial abundance, the level of dominance of bacteria or fungi as well as the composition of their communities. However, several microorganisms, and in particular fungi, inhabit or even connect multiple habitats, and most ecosystem processes affect multiple habitats. Forests are dynamic on a broad temporal scale with processes ranging from short-term events over seasonal ecosystem dynamics to long-term stand development after disturbances such as fires or insect outbreaks. The understanding of these processes can be only achieved by the exploration of the complex 'ecosystem microbiome' and its functioning using focused, integrative microbiological and ecological research performed across multiple habitats.
H. Buncherd
2013-01-01
In the cell, most proteins carry out their functions as subunits of larger assemblies. Knowledge about the folding and mutual interactions of composing subunits is crucial to comprehend the dynamics and structures of such protein complexes and the molecular mechanisms underlying biological processes
Robustness of pinning a general complex dynamical network
Energy Technology Data Exchange (ETDEWEB)
Wang Lei, E-mail: lwang@buaa.edu.c [Laboratory of Mathematics, Information and Behavior of the Ministry of Education, Department of Systems and Control, Beihang University, Beijing 100191 (China); Sun Youxian [State Key Laboratory of Industrial Control Technology, Institute of Industrial Process Control, Zhejiang University, Hangzhou 310027 (China)
2010-04-05
This Letter studies the robustness problem of pinning a general complex dynamical network toward an assigned synchronous evolution. Several synchronization criteria are presented to guarantee the convergence of the pinning process locally and globally by construction of Lyapunov functions. In particular, if a pinning strategy has been designed for synchronization of a given complex dynamical network, then no matter what uncertainties occur among the pinned nodes, synchronization can still be guaranteed through the pinning. The analytical results show that pinning control has a certain robustness against perturbations on network architecture: adding, deleting and changing the weights of edges. Numerical simulations illustrated by scale-free complex networks verify the theoretical results above-acquired.
Localised distributions and criteria for correctness in complex Langevin dynamics
Energy Technology Data Exchange (ETDEWEB)
Aarts, Gert, E-mail: g.aarts@swan.ac.uk [Department of Physics, College of Science, Swansea University, Swansea (United Kingdom); Giudice, Pietro, E-mail: p.giudice@uni-muenster.de [Department of Physics, College of Science, Swansea University, Swansea (United Kingdom); Seiler, Erhard, E-mail: ehs@mppmu.mpg.de [Max-Planck-Institut für Physik (Werner-Heisenberg-Institut), München (Germany)
2013-10-15
Complex Langevin dynamics can solve the sign problem appearing in numerical simulations of theories with a complex action. In order to justify the procedure, it is important to understand the properties of the real and positive distribution, which is effectively sampled during the stochastic process. In the context of a simple model, we study this distribution by solving the Fokker–Planck equation as well as by brute force and relate the results to the recently derived criteria for correctness. We demonstrate analytically that it is possible that the distribution has support in a strip in the complexified configuration space only, in which case correct results are expected. -- Highlights: •Characterisation of the equilibrium distribution sampled in complex Langevin dynamics. •Connection between criteria for correctness and breakdown. •Solution of the Fokker–Planck equation in the case of real noise. •Analytical determination of support in complexified space.
Lyapunov exponents a tool to explore complex dynamics
Pikovsky, Arkady
2016-01-01
Lyapunov exponents lie at the heart of chaos theory, and are widely used in studies of complex dynamics. Utilising a pragmatic, physical approach, this self-contained book provides a comprehensive description of the concept. Beginning with the basic properties and numerical methods, it then guides readers through to the most recent advances in applications to complex systems. Practical algorithms are thoroughly reviewed and their performance is discussed, while a broad set of examples illustrate the wide range of potential applications. The description of various numerical and analytical techniques for the computation of Lyapunov exponents offers an extensive array of tools for the characterization of phenomena such as synchronization, weak and global chaos in low and high-dimensional set-ups, and localization. This text equips readers with all the investigative expertise needed to fully explore the dynamical properties of complex systems, making it ideal for both graduate students and experienced researchers...
Topology identification of complex dynamical networks
Zhao, Junchan; Li, Qin; Lu, Jun-An; Jiang, Zhong-Ping
2010-06-01
Recently, some researchers investigated the topology identification for complex networks via LaSalle's invariance principle. The principle cannot be directly applied to time-varying systems since the positive limit sets are generally not invariant. In this paper, we study the topology identification problem for a class of weighted complex networks with time-varying node systems. Adaptive identification laws are proposed to estimate the coupling parameters of the networks with and without communication delays. We prove that the asymptotic identification is ensured by a persistently exciting condition. Numerical simulations are given to demonstrate the effectiveness of the proposed approach.
Sun, He; Steinkrauss, Rasmus; van der Steen, Steffie; Cox, Ralf; de Bot, Kees
2016-01-01
The current study focuses on one child's (male, 3 years old) learning behaviors in an English as a Foreign Language classroom, and explores the coordination and developmental patterns of his nonverbal (gestures and body language) and verbal (verbal repetition and verbal responses) learning behaviors
Sun, He; Steinkrauss, Rasmus; van der Steen, Steffie; Cox, Ralf; de Bot, Kees
2016-01-01
The current study focuses on one child's (male, 3 years old) learning behaviors in an English as a Foreign Language classroom, and explores the coordination and developmental patterns of his nonverbal (gestures and body language) and verbal (verbal repetition and verbal responses) learning behaviors
Rhythm dynamics of complex neuronal networks with mixed bursting neurons
Institute of Scientific and Technical Information of China (English)
Lü Yong-Bing; Shi Xia; Zheng Yan-Hong
2013-01-01
The spatiotemporal order and rhythm dynamics of a complex neuronal network with mixed bursting neurons are studied in this paper.A quantitative characteristic,the width factor,is introduced to describe the rhythm dynamics of an individual neuron,and the average width factor is used to characterize the rhythm dynamics of a neuronal network.An r parameter is introduced to denote the ratio of the short bursting neurons in the network.Then we investigate the effect of the ratio on the rhythm dynamics of the neuronal network.The critical value of r is derived,and the neurons in the network always remain short bursting when the r ratio is larger than the critical value.
Advances in dynamic network modeling in complex transportation systems
Ukkusuri, Satish V
2013-01-01
This book focuses on the latest in dynamic network modeling, including route guidance and traffic control in transportation systems and other complex infrastructure networks. Covers dynamic traffic assignment, flow modeling, mobile sensor deployment and more.
On Complex Langevin Dynamics and the Evaluation of Observables
Durakovic, Amel; Tranberg, Anders
2014-01-01
In stochastic quantisation, quantum mechanical expectation values are computed as averages over the time history of a stochastic process described by a Langevin equation. Complex stochastic quantisation, though theoretically not rigorously established, extends this idea to cases where the action is complex-valued by complexifying the basic degrees of freedom, all observables and allowing the stochastic process to probe the complexified configuration space. We review the method for a previously studied one-dimensional toy model, the U(1) one link model. We confirm that complex Langevin dynamics only works for a certain range of parameters, misestimating observables otherwise. A curious effect is observed where all moments of the basic stochastic variable are misestimated, although these misestimated moments may be used to construct, by a Taylor series, other observables that are reproduced correctly. This suggests a subtle but not completely resolved relationship between the original complex integration measur...
Dynamics of DNA/intercalator complexes
Schurr, J. M.; Wu, Pengguang; Fujimoto, Bryant S.
1990-05-01
Complexes of linear and supercoiled DNAs with different intercalating dyes are studied by time-resolved fluorescence polarization anisotropy using intercalated ethidium as the probe. Existing theory is generalized to take account of excitation transfer between intercalated ethidiums, and Forster theory is shown to be valid in this context. The effects of intercalated ethidium, 9-aminoacridine, and proflavine on the torsional rigidity of linear and supercoiled DNAs are studied up to rather high binding ratios. Evidence is presented that metastable secondary structure persists in dye-relaxed supercoiled DNAs, which contradicts the standard model of supercoiled DNAs.
Theoretical studies of combustion dynamics
Energy Technology Data Exchange (ETDEWEB)
Bowman, J.M. [Emory Univ., Atlanta, GA (United States)
1993-12-01
The basic objectives of this research program are to develop and apply theoretical techniques to fundamental dynamical processes of importance in gas-phase combustion. There are two major areas currently supported by this grant. One is reactive scattering of diatom-diatom systems, and the other is the dynamics of complex formation and decay based on L{sup 2} methods. In all of these studies, the authors focus on systems that are of interest experimentally, and for which potential energy surfaces based, at least in part, on ab initio calculations are available.
Directory of Open Access Journals (Sweden)
Vineetha Mandlik
2016-09-01
Full Text Available Inositol phosphorylceramide synthase (IPCS has emerged as an important, interesting and attractive target in the sphingolipid metabolism of Leishmania. IPCS catalyzes the conversion of ceramide to IPC which forms the most predominant sphingolipid in Leishmania. IPCS has no mammalian equivalent and also plays an important role in maintaining the infectivity and viability of the parasite. The present study explores the possibility of targeting IPCS; development of suitable inhibitors for the same would serve as a treatment strategy for the infectious disease leishmaniasis. Five coumarin derivatives were developed as inhibitors of IPCS protein. Molecular dynamics simulations of the complexes of IPCS with these inhibitors were performed which provided insights into the binding modes of the inhibitors. In vitro screening of the top three compounds has resulted in the identification of one of the compounds (compound 3 which shows little cytotoxic effects. This compound therefore represents a good starting point for further in vivo experimentation and could possibly serve as an important drug candidate for the treatment of leishmaniasis.
Das, Kiranmoy
2015-06-01
The revolution in the genetic research in our time is mainly due to (i) the successful completion of human genome project (2003) and its derivative hapmap project (2005), (ii) advanced statistical methodologies for analyzing ultrahigh dimensional data and (iii) the availability of statistical softwares (R, SAS etc.) to analyze large datasets. When complex traits are to be modeled as dynamic systems, the statistical issues regarding the complexity in the model, predictive power of the model, computational cost etc. are to be addressed adequately for powerful inferences. I will mention two additional considerations (statistical) which make dynamic models more meaningful and the results from GWAS more reliable.
Molecular dynamics simulations of a membrane protein/amphipol complex.
Perlmutter, Jason D; Popot, Jean-Luc; Sachs, Jonathan N
2014-10-01
Amphipathic polymers known as "amphipols" provide a highly stabilizing environment for handling membrane proteins in aqueous solutions. A8-35, an amphipol with a polyacrylate backbone and hydrophobic grafts, has been extensively characterized and widely employed for structural and functional studies of membrane proteins using biochemical and biophysical approaches. Given the sensitivity of membrane proteins to their environment, it is important to examine what effects amphipols may have on the structure and dynamics of the proteins they complex. Here we present the first molecular dynamics study of an amphipol-stabilized membrane protein, using Escherichia coli OmpX as a model. We begin by describing the structure of the complexes formed by supplementing OmpX with increasing amounts of A8-35, in order to determine how the amphipol interacts with the transmembrane and extramembrane surfaces of the protein. We then compare the dynamics of the protein in either A8-35, a detergent, or a lipid bilayer. We find that protein dynamics on all accessible length scales is restrained by A8-35, which provides a basis to understanding some of the stabilizing and functional effects of amphipols that have been experimentally observed.
Complex dynamics in learning complicated games
Galla, Tobias
2011-01-01
Game theory is the standard tool used to model strategic interactions in evolutionary biology and social science. Traditional game theory studies the equilibria of simple games. But is traditional game theory applicable if the game is complicated, and if not, what is? We investigate this question here, defining a complicated game as one with many possible moves, and therefore many possible payoffs conditional on those moves. We investigate two-person games in which the players learn based on experience. By generating games at random we show that under some circumstances the strategies of the two players converge to fixed points, but under others they follow limit cycles or chaotic attractors. The dimension of the chaotic attractors can be very high, implying that the dynamics of the strategies are effectively random. In the chaotic regime the payoffs fluctuate intermittently, showing bursts of rapid change punctuated by periods of quiescence, similar to what is observed in fluid turbulence and financial marke...
Structural and dynamical properties of complex networks
Ghoshal, Gourab
Recent years have witnessed a substantial amount of interest within the physics community in the properties of networks. Techniques from statistical physics coupled with the widespread availability of computing resources have facilitated studies ranging from large scale empirical analysis of the worldwide web, social networks, biological systems, to the development of theoretical models and tools to explore the various properties of these systems. Following these developments, in this dissertation, we present and solve for a diverse set of new problems, investigating the structural and dynamical properties of both model and real world networks. We start by defining a new metric to measure the stability of network structure to disruptions, and then using a combination of theory and simulation study its properties in detail on artificially generated networks; we then compare our results to a selection of networks from the real world and find good agreement in most cases. In the following chapter, we propose a mathematical model that mimics the structure of popular file-sharing websites such as Flickr and CiteULike and demonstrate that many of its properties can solved exactly in the limit of large network size. The remaining part of the dissertation primarily focuses on the dynamical properties of networks. We first formulate a model of a network that evolves under the addition and deletion of vertices and edges, and solve for the equilibrium degree distribution for a variety of cases of interest. We then consider networks whose structure can be manipulated by adjusting the rules by which vertices enter and leave the network. We focus in particular on degree distributions and show that, with some mild constraints, it is possible by a suitable choice of rules to arrange for the network to have any degree distribution we desire. In addition we define a simple local algorithm by which appropriate rules can be implemented in practice. Finally, we conclude our
Ab initio lattice dynamics of complex structures
DEFF Research Database (Denmark)
Voss, Johannes
2008-01-01
systems in particular. A more detailed analysis of the phonon spectrum has been performed for the compound Mg(BH4)2, where several crystal symmetries have been proposed theoretically and experimentally. By means of an analysis of the instabilities of these structures, a new, stable phase has been......In this thesis, density functional theory is applied in a study of thermodynamic properties of so-called complex metal hydrides, which are promising materials for hydrogen storage applications. Since the unit cells of these crystals can be relatively large with many symmetrically inequivalent...... determined. Aiming at finding scaling relationships between alloy stabilities and computationally inexpensive properties, the stabilities of cation-alloyed metal aluminum hexahydrides have been studied. The analysis shows that charge density symmetries are correlated to the stability. In addition...
Double symbolic joint entropy in nonlinear dynamic complexity analysis
Yao, Wenpo; Wang, Jun
2017-07-01
Symbolizations, the base of symbolic dynamic analysis, are classified as global static and local dynamic approaches which are combined by joint entropy in our works for nonlinear dynamic complexity analysis. Two global static methods, symbolic transformations of Wessel N. symbolic entropy and base-scale entropy, and two local ones, namely symbolizations of permutation and differential entropy, constitute four double symbolic joint entropies that have accurate complexity detections in chaotic models, logistic and Henon map series. In nonlinear dynamical analysis of different kinds of heart rate variability, heartbeats of healthy young have higher complexity than those of the healthy elderly, and congestive heart failure (CHF) patients are lowest in heartbeats' joint entropy values. Each individual symbolic entropy is improved by double symbolic joint entropy among which the combination of base-scale and differential symbolizations have best complexity analysis. Test results prove that double symbolic joint entropy is feasible in nonlinear dynamic complexity analysis.
An introduction to complex systems society, ecology, and nonlinear dynamics
Fieguth, Paul
2017-01-01
This undergraduate text explores a variety of large-scale phenomena - global warming, ice ages, water, poverty - and uses these case studies as a motivation to explore nonlinear dynamics, power-law statistics, and complex systems. Although the detailed mathematical descriptions of these topics can be challenging, the consequences of a system being nonlinear, power-law, or complex are in fact quite accessible. This book blends a tutorial approach to the mathematical aspects of complex systems together with a complementary narrative on the global/ecological/societal implications of such systems. Nearly all engineering undergraduate courses focus on mathematics and systems which are small scale, linear, and Gaussian. Unfortunately there is not a single large-scale ecological or social phenomenon that is scalar, linear, and Gaussian. This book offers students insights to better understand the large-scale problems facing the world and to realize that these cannot be solved by a single, narrow academic field or per...
Vo, Uybach; Vajpai, Navratna; Embrey, Kevin J; Golovanov, Alexander P
2016-07-14
The cycling between GDP- and GTP- bound forms of the Ras protein is partly regulated by the binding of Sos. The structural/dynamic behavior of the complex formed between activated Sos and Ras at the point of the functional cycle where the nucleotide exchange is completed has not been described to date. Here we show that solution NMR spectra of H-Ras∙GTPγS mixed with a functional fragment of Sos (Sos(Cat)) at a 2:1 ratio are consistent with the formation of a rather dynamic assembly. H-Ras∙GTPγS binding was in fast exchange on the NMR timescale and retained a significant degree of molecular tumbling independent of Sos(Cat), while Sos(Cat) also tumbled largely independently of H-Ras. Estimates of apparent molecular weight from both NMR data and SEC-MALS revealed that, at most, only one H-Ras∙GTPγS molecule appears stably bound to Sos. The weak transient interaction between Sos and the second H-Ras∙GTPγS may provide a necessary mechanism for complex dissociation upon the completion of the native GDP → GTP exchange reaction, but also explains measurable GTP → GTP exchange activity of Sos routinely observed in in vitro assays that use fluorescently-labelled analogs of GTP. Overall, the data presents the first dynamic snapshot of Ras functional cycle as controlled by Sos.
Hamiltonian dynamics for complex food webs.
Kozlov, Vladimir; Vakulenko, Sergey; Wennergren, Uno
2016-03-01
We investigate stability and dynamics of large ecological networks by introducing classical methods of dynamical system theory from physics, including Hamiltonian and averaging methods. Our analysis exploits the topological structure of the network, namely the existence of strongly connected nodes (hubs) in the networks. We reveal new relations between topology, interaction structure, and network dynamics. We describe mechanisms of catastrophic phenomena leading to sharp changes of dynamics and hence completely altering the ecosystem. We also show how these phenomena depend on the structure of interaction between species. We can conclude that a Hamiltonian structure of biological interactions leads to stability and large biodiversity.
Universal structural estimator and dynamics approximator for complex networks
Chen, Yu-Zhong
2016-01-01
Revealing the structure and dynamics of complex networked systems from observed data is of fundamental importance to science, engineering, and society. Is it possible to develop a universal, completely data driven framework to decipher the network structure and different types of dynamical processes on complex networks, regardless of their details? We develop a Markov network based model, sparse dynamical Boltzmann machine (SDBM), as a universal network structural estimator and dynamics approximator. The SDBM attains its topology according to that of the original system and is capable of simulating the original dynamical process. We develop a fully automated method based on compressive sensing and machine learning to find the SDBM. We demonstrate, for a large variety of representative dynamical processes on model and real world complex networks, that the equivalent SDBM can recover the network structure of the original system and predicts its dynamical behavior with high precision.
Melchior, Andrea; Gaillard, Clotilde; Gràcia Lanas, Sara; Tolazzi, Marilena; Billard, Isabelle; Georg, Sylvia; Sarrasin, Lola; Boltoeva, Maria
2016-04-04
The complex formation of nitrate ions with nickel(II) in dry [C4mim][Tf2N] ionic liquid (IL) was investigated by means of UV-visible spectrophotometry, isothermal titration calorimetry (ITC), extended X-ray absorption fine structure spectroscopy (EXAFS), and molecular dynamics (MD) simulations. EXAFS spectroscopy and MD simulations show that the solvated Ni(II) cation is initially coordinated by the oxygens of the [Tf2N](-) anion of IL, which can behave either as mono- or bidentate. Spectroscopic and thermodynamic data show that Ni(II) is able to form up to three stable mononuclear complexes with nitrate in this solvent. The stability constants for Ni(NO3)j complexes (j = 1-3) calculated from spectrophotometry and ITC experiments decrease in the order log K1 > log K2 > log K3. The formation of the first two species is enthalpy-driven, while the third species is entropy-stabilized. The UV-vis spectra of solutions containing different nitrate/Ni(II) ratios show that the metal ion retains the six-coordinate geometry. Furthermore, the EXAFS evidences that nitrate is always bidentate. Molecular dynamics simulations show that the [Tf2N](-) anions bind Ni(II) through the sulfonyl oxygen atoms and can coordinate either as monodentate or chelate. The analysis of the MD data shows that introduction of nitrates in the first coordination sphere of the metal ion results in remarkable structural rearrangement of the ionic liquid.
Imaging complex nutrient dynamics in mycelial networks.
Fricker, M D; Lee, J A; Bebber, D P; Tlalka, M; Hynes, J; Darrah, P R; Watkinson, S C; Boddy, L
2008-08-01
Transport networks are vital components of multi-cellular organisms, distributing nutrients and removing waste products. Animal cardiovascular and respiratory systems, and plant vasculature, are branching trees whose architecture is thought to determine universal scaling laws in these organisms. In contrast, the transport systems of many multi-cellular fungi do not fit into this conceptual framework, as they have evolved to explore a patchy environment in search of new resources, rather than ramify through a three-dimensional organism. These fungi grow as a foraging mycelium, formed by the branching and fusion of threadlike hyphae, that gives rise to a complex network. To function efficiently, the mycelial network must both transport nutrients between spatially separated source and sink regions and also maintain its integrity in the face of continuous attack by mycophagous insects or random damage. Here we review the development of novel imaging approaches and software tools that we have used to characterise nutrient transport and network formation in foraging mycelia over a range of spatial scales. On a millimetre scale, we have used a combination of time-lapse confocal imaging and fluorescence recovery after photobleaching to quantify the rate of diffusive transport through the unique vacuole system in individual hyphae. These data then form the basis of a simulation model to predict the impact of such diffusion-based movement on a scale of several millimetres. On a centimetre scale, we have used novel photon-counting scintillation imaging techniques to visualize radiolabel movement in small microcosms. This approach has revealed novel N-transport phenomena, including rapid, preferential N-resource allocation to C-rich sinks, induction of simultaneous bi-directional transport, abrupt switching between different pre-existing transport routes, and a strong pulsatile component to transport in some species. Analysis of the pulsatile transport component using Fourier
Rajamanikandan, Sundaraj; Srinivasan, Pappu
2017-03-01
Bacteria communicate with one another using extracellular signaling molecules called auto-inducers (AHLs), a process termed as quorum sensing. The quorum sensing process allows bacteria to regulate various physiological activities. In this regard, quorum sensing master regulator LuxR from Vibrio harveyi represents an attractive therapeutic target for the development of novel anti-quorum sensing agents. Eventhough the binding of AHL complex with LuxR is evidenced in earlier reports, but their mode of binding is not clearly determined. Therefore, in the present work, molecular docking, in silico mutational studies, molecular dynamics simulations and free energy calculations were performed to understand the selectivity of AHL into the binding site of LuxR. The results revealed that Asn133 and Gln137 residues play a crucial role in recognizing AHL more effectively into the binding site of LuxR with good binding free energy. In addition to that, the carbonyl group presents in the lactone ring and amide group of AHL plays a vital role in the formation of hydrogen bond interactions with the protein. Further, structure based virtual screening was performed using ChemBridge database to screen potent lead molecules against LuxR. 4-benzyl-2-pyrrolidinone and N-[2(1-cyclohexen-1-yl) enthyl]-N'(2-ethoxyphenyl) were selected based on dock score, binding affinity and mode of interactions with the receptor. Furthermore, binding free energy, density functional theory and ADME prediction were performed to rank the lead molecules. Thus, the identified lead molecules can be used for the development of anti-quorum sensing drugs.
Shirokikh, Nikolay E; Archer, Stuart K; Beilharz, Traude H; Powell, David; Preiss, Thomas
2017-04-01
Messenger RNA (mRNA) translation is a tightly controlled process that is integral to gene expression. It features intricate and dynamic interactions of the small and large subunits of the ribosome with mRNAs, aided by multiple auxiliary factors during distinct initiation, elongation and termination phases. The recently developed ribosome profiling method can generate transcriptome-wide surveys of translation and its regulation. Ribosome profiling records the footprints of fully assembled ribosomes along mRNAs and thus primarily interrogates the elongation phase of translation. Importantly, it does not monitor multiple substeps of initiation and termination that involve complexes between the small ribosomal subunit (SSU) and mRNA. Here we describe a related method, termed 'translation complex profile sequencing' (TCP-seq), that is uniquely capable of recording positions of any type of ribosome-mRNA complex transcriptome-wide. It uses fast covalent fixation of translation complexes in live cells, followed by RNase footprinting of translation intermediates and their separation into complexes involving either the full ribosome or the SSU. The footprints derived from each type of complex are then deep-sequenced separately, generating native distribution profiles during the elongation, as well as the initiation and termination stages of translation. We provide the full TCP-seq protocol for Saccharomyces cerevisiae liquid suspension culture, including a data analysis pipeline. The protocol takes ∼3 weeks to complete by a researcher who is well acquainted with standard molecular biology techniques and who has some experience in ultracentrifugation and the preparation of RNA sequencing (RNA-seq) libraries. Basic Bash and UNIX/Linux command skills are required to use the bioinformatics tools provided.
Emergence of dynamical complexity related to human heart rate variability
Chang, Mei-Chu; Peng, C.-K.; Stanley, H. Eugene
2014-12-01
We apply the refined composite multiscale entropy (MSE) method to a one-dimensional directed small-world network composed of nodes whose states are binary and whose dynamics obey the majority rule. We find that the resulting fluctuating signal becomes dynamically complex. This dynamical complexity is caused (i) by the presence of both short-range connections and long-range shortcuts and (ii) by how well the system can adapt to the noisy environment. By tuning the adaptability of the environment and the long-range shortcuts we can increase or decrease the dynamical complexity, thereby modeling trends found in the MSE of a healthy human heart rate in different physiological states. When the shortcut and adaptability values increase, the complexity in the system dynamics becomes uncorrelated.
Exponential rise of dynamical complexity in quantum computing through projections.
Burgarth, Daniel Klaus; Facchi, Paolo; Giovannetti, Vittorio; Nakazato, Hiromichi; Pascazio, Saverio; Yuasa, Kazuya
2014-10-10
The ability of quantum systems to host exponentially complex dynamics has the potential to revolutionize science and technology. Therefore, much effort has been devoted to developing of protocols for computation, communication and metrology, which exploit this scaling, despite formidable technical difficulties. Here we show that the mere frequent observation of a small part of a quantum system can turn its dynamics from a very simple one into an exponentially complex one, capable of universal quantum computation. After discussing examples, we go on to show that this effect is generally to be expected: almost any quantum dynamics becomes universal once 'observed' as outlined above. Conversely, we show that any complex quantum dynamics can be 'purified' into a simpler one in larger dimensions. We conclude by demonstrating that even local noise can lead to an exponentially complex dynamics.
Dynamics of complex fluids in rotary atomization
Keshavarz, Bavand; McKinley, Gareth; MIT, Mechanical Engineering Department Team
2016-11-01
We study the dynamics of fragmentation for different Newtonian and viscoelastic liquids in rotary atomization. In this process, at the rim of a spinning cup, the centripetal acceleration destabilizes the formed liquid torus due to the Rayleigh-Taylor instability. The resulting ligaments leave the liquid torus with a remarkably repeatable spacing that scales linearly with the inverse of the rotation rate. Filaments then follow a well-defined geometrical path-line that is described by the involute of the circle. Knowing the geometry of this phenomenon we derive the detailed kinematics of this process and compare it with the experimental observations. We show that the ligaments elongate tangentially to the involute of the circle and thin radially as they separate from the cup. A theoretical form is derived for the spatial variation of the filament deformation rate. Once the ligaments are far from the cup they breakup into droplets since they are not stretched fast enough (compared to the critical rate of capillary thinning). We couple these derivations with the known properties of Newtonian and viscoelastic liquids to provide a physical analysis for this fragmentation process that is compared in detail with our experiments.
The Dynamics of Coalition Formation on Complex Networks
Auer, S.; Heitzig, J.; Kornek, U.; Schöll, E.; Kurths, J.
2015-08-01
Complex networks describe the structure of many socio-economic systems. However, in studies of decision-making processes the evolution of the underlying social relations are disregarded. In this report, we aim to understand the formation of self-organizing domains of cooperation (“coalitions”) on an acquaintance network. We include both the network’s influence on the formation of coalitions and vice versa how the network adapts to the current coalition structure, thus forming a social feedback loop. We increase complexity from simple opinion adaptation processes studied in earlier research to more complex decision-making determined by costs and benefits, and from bilateral to multilateral cooperation. We show how phase transitions emerge from such coevolutionary dynamics, which can be interpreted as processes of great transformations. If the network adaptation rate is high, the social dynamics prevent the formation of a grand coalition and therefore full cooperation. We find some empirical support for our main results: Our model develops a bimodal coalition size distribution over time similar to those found in social structures. Our detection and distinguishing of phase transitions may be exemplary for other models of socio-economic systems with low agent numbers and therefore strong finite-size effects.
Dynamical complexity changes during two forms of meditation
Li, Jin; Hu, Jing; Zhang, Yinhong; Zhang, Xiaofeng
2011-06-01
Detection of dynamical complexity changes in natural and man-made systems has deep scientific and practical meaning. We use the base-scale entropy method to analyze dynamical complexity changes for heart rate variability (HRV) series during specific traditional forms of Chinese Chi and Kundalini Yoga meditation techniques in healthy young adults. The results show that dynamical complexity decreases in meditation states for two forms of meditation. Meanwhile, we detected changes in probability distribution of m-words during meditation and explained this changes using probability distribution of sine function. The base-scale entropy method may be used on a wider range of physiologic signals.
Chaos and complexity in a simple model of production dynamics
Directory of Open Access Journals (Sweden)
I. Katzorke
2000-01-01
Full Text Available We consider complex dynamical behavior in a simple model of production dynamics, based on the Wiendahl’s funnel approach. In the case of continuous order flow a model of three parallel funnels reduces to the one-dimensional Bernoulli-type map, and demonstrates strong chaotic properties. The optimization of production costs is possible with the OGY method of chaos control. The dynamics changes drastically in the case of discrete order flow. We discuss different dynamical behaviors, the complexity and the stability of this discrete system.
Dynamics Control of the Complex Systems via Nondifferentiability
Directory of Open Access Journals (Sweden)
Carmen Nejneru
2013-01-01
Full Text Available A new topic in the analyses of complex systems dynamics, considering that the movements of complex system entities take place on continuum but nondifferentiable curves, is proposed. In this way, some properties of complex systems (barotropic-type behaviour, self-similarity behaviour, chaoticity through turbulence and stochasticization, etc. are controlled through nondifferentiability of motion curves. These behaviours can simulate the standard properties of the complex systems (emergence, self-organization, adaptability, etc..
Dynamics Control of the Complex Systems via Nondifferentiability
Carmen Nejneru; Anca Nicuţă; Boris Constantin; Liliana Rozemarie Manea; Mirela Teodorescu; Maricel Agop
2013-01-01
A new topic in the analyses of complex systems dynamics, considering that the movements of complex system entities take place on continuum but nondifferentiable curves, is proposed. In this way, some properties of complex systems (barotropic-type behaviour, self-similarity behaviour, chaoticity through turbulence and stochasticization, etc.) are controlled through nondifferentiability of motion curves. These behaviours can simulate the standard properties of the complex systems (emergence, se...
Complex phase dynamics in coupled bursters
DEFF Research Database (Denmark)
Postnov, D.E.; Sosnovtseva, Olga; Malova, S.Y.;
2003-01-01
The phenomenon of phase multistability in the synchronization of two coupled oscillatory systems typically arises when the systems individually display complex wave forms associated, for instance, with the presence of subharmonic components. Alternatively, phase multistability can be caused...
Dynamic analysis of biochemical network using complex network method
Directory of Open Access Journals (Sweden)
Wang Shuqiang
2015-01-01
Full Text Available In this study, the stochastic biochemical reaction model is proposed based on the law of mass action and complex network theory. The dynamics of biochemical reaction system is presented as a set of non-linear differential equations and analyzed at the molecular-scale. Given the initial state and the evolution rules of the biochemical reaction system, the system can achieve homeostasis. Compared with random graph, the biochemical reaction network has larger information capacity and is more efficient in information transmission. This is consistent with theory of evolution.
Universal nonexponential relaxation: Complex dynamics in simple liquids.
Turton, David A; Wynne, Klaas
2009-11-28
The dynamics of the noble-gas liquids underlies that of all liquids making them an important prototypical model system. Using optical Kerr-effect spectroscopy we show that for argon, krypton, and xenon, both the librational and diffusional contributions to the spectrum are surprisingly complex. The diffusional relaxation appears as a stretched-exponential, such as widely found in studies of structured (e.g., glass-forming) liquids and as predicted by mode-coupling theory. We show that this behavior is remarkably similar to that measured in water and suggest that it is a fundamental or universal property.
Complex Dynamics of an Adnascent-Type Game Model
Directory of Open Access Journals (Sweden)
Baogui Xin
2008-01-01
Full Text Available The paper presents a nonlinear discrete game model for two oligopolistic firms whose products are adnascent. (In biology, the term adnascent has only one sense, “growing to or on something else,” e.g., “moss is an adnascent plant.” See Webster's Revised Unabridged Dictionary published in 1913 by C. & G. Merriam Co., edited by Noah Porter. The bifurcation of its Nash equilibrium is analyzed with Schwarzian derivative and normal form theory. Its complex dynamics is demonstrated by means of the largest Lyapunov exponents, fractal dimensions, bifurcation diagrams, and phase portraits. At last, bifurcation and chaos anticontrol of this system are studied.
Young Children's Knowledge About the Moon: A Complex Dynamic System
Venville, Grady J.; Louisell, Robert D.; Wilhelm, Jennifer A.
2012-08-01
The purpose of this research was to use a multidimensional theoretical framework to examine young children's knowledge about the Moon. The research was conducted in the interpretive paradigm and the design was a multiple case study of ten children between the ages of three and eight from the USA and Australia. A detailed, semi-structured interview was conducted with each child. In addition, each child's parents were interviewed to determine possible social and cultural influences on the child's knowledge. We sought evidence about how the social and cultural experiences of the children might have influenced the development of their ideas. From a cognitive perspective we were interested in whether the children's ideas were constructed in a theory like form or whether the knowledge was the result of gradual accumulation of fragments of isolated cultural information. Findings reflected the strong and complex relationship between individual children, their social and cultural milieu, and the way they construct ideas about the Moon and astronomy. Findings are presented around four themes including ontology, creatures and artefacts, animism, and permanence. The findings support a complex dynamic system view of students' knowledge that integrates the framework theory perspective and the knowledge in fragments perspective. An initial model of a complex dynamic system of young children's knowledge about the Moon is presented.
Entropy Rate Maps of Complex Excitable Dynamics in Cardiac Monolayers
Directory of Open Access Journals (Sweden)
Alexander Schlemmer
2015-02-01
Full Text Available The characterization of spatiotemporal complexity remains a challenging task. This holds in particular for the analysis of data from fluorescence imaging (optical mapping, which allows for the measurement of membrane potential and intracellular calcium at high spatial and temporal resolutions and, therefore, allows for an investigation of cardiac dynamics. Dominant frequency maps and the analysis of phase singularities are frequently used for this type of excitable media. These methods address some important aspects of cardiac dynamics; however, they only consider very specific properties of excitable media. To extend the scope of the analysis, we present a measure based on entropy rates for determining spatiotemporal complexity patterns of excitable media. Simulated data generated by the Aliev–Panfilov model and the cubic Barkley model are used to validate this method. Then, we apply it to optical mapping data from monolayers of cardiac cells from chicken embryos and compare our findings with dominant frequency maps and the analysis of phase singularities. The studies indicate that entropy rate maps provide additional information about local complexity, the origins of wave breakup and the development of patterns governing unstable wave propagation.
Vibrational energy transfer dynamics in ruthenium polypyridine transition metal complexes.
Fedoseeva, Marina; Delor, Milan; Parker, Simon C; Sazanovich, Igor V; Towrie, Michael; Parker, Anthony W; Weinstein, Julia A
2015-01-21
Understanding the dynamics of the initial stages of vibrational energy transfer in transition metal complexes is a challenging fundamental question which is also of crucial importance for many applications, such as improving the performance of solar devices or photocatalysis. The present study investigates vibrational energy transport in the ground and the electronic excited state of Ru(4,4'-(COOEt)2-2,2-bpy)2(NCS)2, a close relative of the efficient "N3" dye used in dye-sensitized solar cells. Using the emerging technique of ultrafast two-dimensional infrared spectroscopy, we show that, similarly to other transition-metal complexes, the central Ru heavy atom acts as a "bottleneck" making the energy transfer from small ligands with high energy vibrational stretching frequencies less favorable and thereby affecting the efficiency of vibrational energy flow in the complex. Comparison of the vibrational relaxation times in the electronic ground and excited state of Ru(4,4'-(COOEt)2-2,2-bpy)2(NCS)2 shows that it is dramatically faster in the latter. We propose to explain this observation by the intramolecular electrostatic interactions between the thiocyanate group and partially oxidised Ru metal center, which increase the degree of vibrational coupling between CN and Ru-N modes in the excited state thus reducing structural and thermodynamic barriers that slow down vibrational relaxation and energy transport in the electronic ground state. As a very similar behavior was earlier observed in another transition-metal complex, Re(4,4'-(COOEt)2-2,2'-bpy)(CO)3Cl, we suggest that this effect in vibrational energy dynamics might be common for transition-metal complexes with heavy central atoms.
Slow dynamics of the contact process on complex networks
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Ódor Géza
2013-03-01
Full Text Available The Contact Process has been studied on complex networks exhibiting different kinds of quenched disorder. Numerical evidence is found for Griffiths phases and other rare region effects, in Erdős Rényi networks, leading rather generically to anomalously slow (algebraic, logarithmic,… relaxation. More surprisingly, it turns out that Griffiths phases can also emerge in the absence of quenched disorder, as a consequence of sole topological heterogeneity in networks with finite topological dimension. In case of scalefree networks, exhibiting infinite topological dimension, slow dynamics can be observed on tree-like structures and a superimposed weight pattern. In the infinite size limit the correlated subspaces of vertices seem to cause a smeared phase transition. These results have a broad spectrum of implications for propagation phenomena and other dynamical process on networks and are relevant for the analysis of both models and empirical data.
Dynamics of Dust Aggregates in a Complex Plasma
Davis, Allen; Carmona Reyes, Jorge; Matthews, Lorin; Hyde, Truell
2012-10-01
Charged dust aggregates play an important role in many astrophysical phenomena, such as early stages of protostellar and protoplanetary growth, the dynamics of planetary rings and cometary tails, and the formation of noctilucent clouds in earth's upper atmosphere. Dust is also expected to be an unwanted byproduct in the operation of plasma fusion devices, such as ITER. In all of these environments, direct study of the dust aggregates in their in situ environment is extremely difficult, if not impossible. As a model for these complex plasma environments, dust aggregates are formed in a laboratory plasma as monodisperse spheres are accelerated in a self-excited dust density wave. Individual dust particles are perturbed using a diode pumped solid state laser (Coherent VERDI) with their motions recorded by a high-speed camera at 1000 fps. Analysis of the particle motion allows determination of the aggregate characteristics which determine the grain dynamics, such as charge, mass, and gas drag.
Dynamics of nanoparticles in complex fluids
Omari, Rami A.
Soft matter is a subfield of condensed matter including polymers, colloidal dispersions, surfactants, and liquid crystals. These materials are familiar from our everyday life- glues, paints, soaps, and plastics are examples of soft materials. Many phenomena in these systems have the same underlying physical mechanics. Moreover, it has been recognized that combinations of these systems, like for example polymers and colloids, exhibit new properties which are not found in each system separately. These mixed systems have a higher degree of complexity than the separate systems. In order to understand their behavior, knowledge from each subfields of soft matter has to be put together. One of these complex systems is the mixture of nanoparticles with macromolecules such as polymers, proteins, etc. Understanding the interactions in these systems is essential for solving various problems in technological and medical fields, such as developing high performance polymeric materials, chromatography, and drug delivery vehicles. The author of this dissertation investigates fundemental soft matter systems, including colloid dispersions in polymer solutions and binary mixture. The diffusion of gold nanoparticles in semidilute and entangled solutions of polystyrene (PS) in toluene were studied using fluorescence correlation spectroscopy (FCS). In our experiments, the particle radius (R ≈ 2.5 nm) was much smaller compared to the radius of gyration of the chain but comparable to the average mesh size of the fluctuating polymer network. The diffusion coefficient (D) of the particles decreased monotonically with polymer concentration and it can be fitted with a stretched exponential function. At high concentration of the polymer, a clear subdiffusive motion of the particles was observed. The results were compared with the diffusion of free dyes, which showed normal diffusive behavior for all concentrations. In another polymer solution, poly ethylene glycol (PEG) in water, the
Jamshidi, Shirin; Jalili, Seifollah; Rafii-Tabar, Hashem
2015-01-01
Catalytic mechanism of orotidine 5'-monophosphate decarboxylase (OMPDC), one of the nature most proficient enzymes which provides large rate enhancement, has not been fully understood yet. A series of 30 ns molecular dynamics (MD) simulations were run on X-ray structure of the OMPDC from Saccharomyces cerevisiae in its free form as well as in complex with different ligands, namely 1-(5'-phospho-D-ribofuranosyl) barbituric acid (BMP), orotidine 5'-monophosphate (OMP), and 6-phosphonouridine 5'-monophosphate (PMP). The importance of this biological system is justified both by its high rate enhancement and its potential use as a target in chemotherapy. This work focuses on comparing two physicochemical states of the enzyme (protonated and deprotonated Asp91) and three ligands (substrate OMP, inhibitor, and transition state analog BMP and substrate analog PMP). Detailed analysis of the active site geometry and its interactions is properly put in context by extensive comparison with relevant experimental works. Our overall results show that in terms of hydrogen bond occupancy, electrostatic interactions, dihedral angles, active site configuration, and movement of loops, notable differences among different complexes are observed. Comparison of the results obtained from these simulations provides some detailed structural data for the complexes, the enzyme, and the ligands, as well as useful insights into the inhibition mechanism of the OMPDC enzyme. Furthermore, these simulations are applied to clarify the ambiguous mechanism of the OMPDC enzyme, and imply that the substrate destabilization and transition state stabilization contribute to the mechanism of action of the most proficient enzyme, OMPDC.
Applications of Nonlinear Dynamics Model and Design of Complex Systems
In, Visarath; Palacios, Antonio
2009-01-01
This edited book is aimed at interdisciplinary, device-oriented, applications of nonlinear science theory and methods in complex systems. In particular, applications directed to nonlinear phenomena with space and time characteristics. Examples include: complex networks of magnetic sensor systems, coupled nano-mechanical oscillators, nano-detectors, microscale devices, stochastic resonance in multi-dimensional chaotic systems, biosensors, and stochastic signal quantization. "applications of nonlinear dynamics: model and design of complex systems" brings together the work of scientists and engineers that are applying ideas and methods from nonlinear dynamics to design and fabricate complex systems.
Mörl, Falk; Siebert, Tobias; Häufle, Daniel
2016-02-01
Experimental studies show different muscle-tendon complex (MTC) functions (e.g. motor or spring) depending on the muscle fibre-tendon length ratio. Comparing different MTC of different animals examined experimentally, the extracted MTC functions are biased by, for example, MTC-specific pennation angle and fibre-type distribution or divergent experimental protocols (e.g. influence of temperature or stimulation on MTC force). Thus, a thorough understanding of variation of these inner muscle fibre-tendon length ratios on MTC function is difficult. In this study, we used a hill-type muscle model to simulate MTC. The model consists of a contractile element (CE) simulating muscle fibres, a serial element (SE) as a model for tendon, and a parallel elastic element (PEE) modelling tissue in parallel to the muscle fibres. The simulation examines the impact of length variations of these components on contraction dynamics and MTC function. Ensuring a constant overall length of the MTC by L(MTC) = L(SE) + L(CE), the SE rest length was varied over a broad physiological range from 0.1 to 0.9 MTC length. Five different MTC functions were investigated by simulating typical physiological experiments: the stabilising function with isometric contractions, the motor function with contractions against a weight, the capability of acceleration with contractions against a small inertial mass, the braking function by decelerating a mass, and the spring function with stretch-shortening cycles. The ratio of SE and CE mainly determines the MTC function. MTC with comparably short tendon generates high force and maximal shortening velocity and is able to produce maximal work and power. MTC with long tendon is suitable to store and release a maximum amount of energy. Variation of muscle fibre-tendon ratio yielded two peaks for MTC's force response for short and long SE lengths. Further, maximum work storage capacity of the SE is at long relL(SE,0). Impact of fibre-tendon length ratio on MTC
Nonlinear Dynamics of the Perceived Pitch of Complex Sounds
Cartwright, J H E; Piro, O; Cartwright, Julyan H. E.; Gonzalez, Diego L.; Piro, Oreste
1999-01-01
We apply results from nonlinear dynamics to an old problem in acoustical physics: the mechanism of the perception of the pitch of sounds, especially the sounds known as complex tones that are important for music and speech intelligibility.
Non-equilibrium dynamics of language games on complex networks
Dall'Asta, L; Barrat, A; Loreto, V; Asta, Luca Dall'; Baronchelli, Andrea; Barrat, Alain; Loreto, Vittorio
2006-01-01
The Naming Game is a model of non-equilibrium dynamics for the self-organized emergence of a linguistic convention or a communication system in a population of agents with pairwise local interactions. We present an extensive study of its dynamics on complex networks, that can be considered as the most natural topological embedding for agents involved in language games and opinion dynamics. Except for some community structured networks on which metastable phases can be observed, agents playing the Naming Game always manage to reach a global consensus. This convergence is obtained after a time generically scaling with the population's size $N$ as $t\\_{conv} \\sim N^{1.4 \\pm 0.1}$, i.e. much faster than for agents embedded on regular lattices. Moreover, the memory capacity required by the system scales only linearly with its size. Particular attention is given to heterogenous networks, in which the dynamical activity pattern of a node depends on its degree. High degree nodes have a fundamental role, but require l...
Dynamics of Complex Fluid-Fluid Interfaces
Sagis, L.M.C.
2016-01-01
This chapter presents an overview of recent progress in modelling the behaviour of complex fluid–fluid interfaces with non-equilibrium thermodynamics. We will limit ourselves to frameworks employing the Gibbs dividing surface model, and start with a general discussion of the surface excess variables
Complex phase dynamics in coupled bursters
DEFF Research Database (Denmark)
Postnov, D E; Sosnovtseva, Olga; Malova, S Y
2003-01-01
The phenomenon of phase multistability in the synchronization of two coupled oscillatory systems typically arises when the systems individually display complex wave forms associated, for instance, with the presence of subharmonic components. Alternatively, phase multistability can be caused...... the number of spikes per train and the proximity of a neighboring equilibrium point can influence the formation of coexisting regimes....
Complex dynamics in supervised work groups
Dal Forno, Arianna; Merlone, Ugo
2013-07-01
In supervised work groups many factors concur to determine productivity. Some of them may be economical and some psychological. According to the literature, the heterogeneity in terms of individual capacity seems to be one of the principal causes for chaotic dynamics in a work group. May sorting groups of people with same capacity for effort be a solution? In the organizational psychology literature an important factor is the engagement in the task, while expectations are central in the economics literature. Therefore, we propose a dynamical model which takes into account both engagement in the task and expectations. An important lesson emerges. The intolerance deriving from the exposure to inequity may not be only caused by differences in individual capacities, but also by these factors combined. Consequently, solutions have to be found in this new direction.
Ferrofluids, complex particle dynamics and braid description
Energy Technology Data Exchange (ETDEWEB)
Skjeltorp, A.T. E-mail: arne.skjeltorp@ife.no; Clausen, Sigmund; Helgesen, Geir
2001-05-01
Finely divided magnetic matter is important in many areas of science and technology. A special sub-class of systems are made up of freely moving particles suspended in a carrier liquid where the magnetic interactions play an important role in the actual structure formation and dynamical behaviour. These include ferrofluids, which are colloids of magnetic particles dispersed in carrier fluids, magnetic micro-beads, which are micrometer sized plastic beads loaded with iron oxide, and nonmagnetic particles dispersed in ferrofluids, forming the so-called 'magnetic holes'. How, in a simple and forceful way, is it possible to characterise the dynamics of systems with several moving components like dispersed magnetic particles subjected to external magnetic fields? The methods based on the theory of braids may provide the answer. Braid theory is a sub-field of mathematics known as topology. It involves classifying different ways of tracing curves in space. The topological description of braids thus provides a simple and concise language for describing the dynamics of a system of moving particles as if they perform a complicated dance as they move about one another, and the braid encodes the choreography of this dance.
Emergence of dynamical order synchronization phenomena in complex systems
Manrubia, Susanna C; Zanette, Damián H
2004-01-01
Synchronization processes bring about dynamical order and lead tospontaneous development of structural organization in complex systemsof various origins, from chemical oscillators and biological cells tohuman societies and the brain. This book provides a review and adetailed theoretical analysis of synchronization phenomena in complexsystems with different architectures, composed of elements withperiodic or chaotic individual dynamics. Special attention is paid tostatistical concepts, such as nonequilibrium phase transitions, orderparameters and dynamical glasses.
Dynamic analysis of the human brain with complex cerebral sulci.
Tseng, Jung-Ge; Huang, Bo-Wun; Ou, Yi-Wen; Yen, Ke-Tien; Wu, Yi-Te
2016-07-03
The brain is one of the most vulnerable organs inside the human body. Head accidents often appear in daily life and are easy to cause different level of brain damage inside the skull. Once the brain suffered intense locomotive impact, external injuries, falls, or other accidents, it will result in different degrees of concussion. This study employs finite element analysis to compare the dynamic characteristics between the geometric models of an assumed simple brain tissue and a brain tissue with complex cerebral sulci. It is aimed to understand the free vibration of the internal brain tissue and then to protect the brain from injury caused by external influences. Reverse engineering method is used for a Classic 5-Part Brain (C18) model produced by 3B Scientific Corporation. 3D optical scanner is employed to scan the human brain structure model with complex cerebral sulci and imported into 3D graphics software to construct a solid brain model to simulate the real complex brain tissue. Obtaining the normal mode analysis by inputting the material properties of the true human brain into finite element analysis software, and then to compare the simplified and the complex of brain models.
Yun, Yonghyeon; Hwang, Minki; Park, Jae Hyung; Shin, Hangsik; Shim, Eun Bo; Pak, Hui-Nam
2014-03-01
Although complex fractionated electrogram (CFE) is known to be a target for catheter ablation of fibrillation, its physiological meaning in fibrillation wave-dynamics remains to be clarified. We evaluated the spatiotemporal relationships among the parameters of fibrillation wave-dynamics by simulation modeling. We generated maps of CFE-cycle length (CFE-CL), local dominant frequency (LDF), wave break (WB), and phase singularity (PS) of fibrillation in 2-dimensional homogeneous bidomain cardiac modeling (1,000 × 1,000 cells ten Tusscher model). We compared spatiotemporal correlations by dichotomizing each maps into 10 × 10 lattice zones. In spatial distribution, WB and PS showed excellent correlation (R = 0.963, P CFE-CL had weak correlations with WB (R = 0.288, P CFE-CL area. Virtual ablation (5% of critical mass) of CFE-CL CFE-CL was weakly correlated with WB, PS, and LDF, spatiotemporally. PSs are mostly positioned at the periphery of low CFE-CL areas, and virtual ablation targeting low CFE-CL regions terminated fibrillation successfully.
Complex Dynamical Network Control for Trajectory Tracking Using Delayed Recurrent Neural Networks
Directory of Open Access Journals (Sweden)
Jose P. Perez
2014-01-01
Full Text Available In this paper, the problem of trajectory tracking is studied. Based on the V-stability and Lyapunov theory, a control law that achieves the global asymptotic stability of the tracking error between a delayed recurrent neural network and a complex dynamical network is obtained. To illustrate the analytic results, we present a tracking simulation of a dynamical network with each node being just one Lorenz’s dynamical system and three identical Chen’s dynamical systems.
Universal properties of dynamically complex systems - The organization of chaos
Procaccia, Itamar
1988-06-01
The complex dynamic behavior of natural systems far from equilibrium is discussed. Progress that has been made in understanding universal aspects of the paths to such behavior, of the trajectories at the borderline of chaos, and of the nature of the complexity in the chaotic regime, is reviewed. The emerging grammar of chaos is examined.
Complex, Dynamic Systems: A New Transdisciplinary Theme for Applied Linguistics?
Larsen-Freeman, Diane
2012-01-01
In this plenary address, I suggest that Complexity Theory has the potential to contribute a transdisciplinary theme to applied linguistics. Transdisciplinary themes supersede disciplines and spur new kinds of creative activity (Halliday 2001 [1990]). Investigating complex systems requires researchers to pay attention to system dynamics. Since…
Complex, Dynamic Systems: A New Transdisciplinary Theme for Applied Linguistics?
Larsen-Freeman, Diane
2012-01-01
In this plenary address, I suggest that Complexity Theory has the potential to contribute a transdisciplinary theme to applied linguistics. Transdisciplinary themes supersede disciplines and spur new kinds of creative activity (Halliday 2001 [1990]). Investigating complex systems requires researchers to pay attention to system dynamics. Since…
Parameter Estimation in Epidemiology: from Simple to Complex Dynamics
Aguiar, Maíra; Ballesteros, Sebastién; Boto, João Pedro; Kooi, Bob W.; Mateus, Luís; Stollenwerk, Nico
2011-09-01
We revisit the parameter estimation framework for population biological dynamical systems, and apply it to calibrate various models in epidemiology with empirical time series, namely influenza and dengue fever. When it comes to more complex models like multi-strain dynamics to describe the virus-host interaction in dengue fever, even most recently developed parameter estimation techniques, like maximum likelihood iterated filtering, come to their computational limits. However, the first results of parameter estimation with data on dengue fever from Thailand indicate a subtle interplay between stochasticity and deterministic skeleton. The deterministic system on its own already displays complex dynamics up to deterministic chaos and coexistence of multiple attractors.
Functional Loop Dynamics of the Streptavidin-Biotin Complex
Song, Jianing; Li, Yongle; Ji, Changge; Zhang, John Z. H.
2015-01-01
Accelerated molecular dynamics (aMD) simulation is employed to study the functional dynamics of the flexible loop3-4 in the strong-binding streptavidin-biotin complex system. Conventional molecular (cMD) simulation is also performed for comparison. The present study reveals the following important properties of the loop dynamics: (1) The transition of loop3-4 from open to closed state is observed in 200 ns aMD simulation. (2) In the absence of biotin binding, the open-state streptavidin is more stable, which is consistent with experimental evidences. The free energy (ΔG) difference is about 5 kcal/mol between two states. But with biotin binding, the closed state is more stable due to electrostatic and hydrophobic interactions between the loop3-4 and biotin. (3) The closure of loop3-4 is concerted to the stable binding of biotin to streptavidin. When the loop3-4 is in its open-state, biotin moves out of the binding pocket, indicating that the interactions between the loop3-4 and biotin are essential in trapping biotin in the binding pocket. (4) In the tetrameric streptavidin system, the conformational change of the loop3-4 in each monomer is independent of each other. That is, there is no cooperative binding for biotin bound to the four subunits of the tetramer.
Path planning for complex terrain navigation via dynamic programming
Energy Technology Data Exchange (ETDEWEB)
Kwok, K.S.; Driessen, B.J.
1998-12-31
This work considers the problem of planning optimal paths for a mobile robot traversing complex terrain. In addition to the existing obstacles, locations in the terrain where the slope is too steep for the mobile robot to navigate safely without tipping over become mathematically equivalent to extra obstacles. To solve the optimal path problem, the authors use a dynamic programming approach. The dynamic programming approach utilized herein does not suffer the difficulties associated with spurious local minima that the artificial potential field approaches do. In fact, a globally optimal solution is guaranteed to be found if a feasible solution exists. The method is demonstrated on several complex examples including very complex terrains.
Complex Langevin dynamics for chiral random matrix theory
Mollgaard, A.; Splittorff, K.
2013-12-01
We apply complex Langevin dynamics to chiral random matrix theory at nonzero chemical potential. At large quark mass, the simulations agree with the analytical results while incorrect convergence is found for small quark masses. The region of quark masses for which the complex Langevin dynamics converges incorrectly is identified as the region where the fermion determinant frequently traces out a path surrounding the origin of the complex plane during the Langevin flow. This links the incorrect convergence to an ambiguity in the Langevin force due to the presence of the logarithm of the fermion determinant in the action.
Complex Langevin Dynamics for chiral Random Matrix Theory
Mollgaard, A
2013-01-01
We apply complex Langevin dynamics to chiral random matrix theory at nonzero chemical potential. At large quark mass the simulations agree with the analytical results while incorrect convergence is found for small quark masses. The region of quark masses for which the complex Langevin dynamics converges incorrectly is identified as the region where the fermion determinant frequently traces out a path surrounding the origin of the complex plane during the Langevin flow. This links the incorrect convergence to an ambiguity in the Langevin force due to the presence of the logarithm of the fermion determinant in the action.
Spatial price dynamics: From complex network perspective
Li, Y. L.; Bi, J. T.; Sun, H. J.
2008-10-01
The spatial price problem means that if the supply price plus the transportation cost is less than the demand price, there exists a trade. Thus, after an amount of exchange, the demand price will decrease. This process is continuous until an equilibrium state is obtained. However, how the trade network structure affects this process has received little attention. In this paper, we give a evolving model to describe the levels of spatial price on different complex network structures. The simulation results show that the network with shorter path length is sensitive to the variation of prices.
Identifying Changes of Complex Flood Dynamics with Recurrence Analysis
Wendi, D.; Merz, B.; Marwan, N.
2016-12-01
Temporal changes in flood hazard system are known to be difficult to detect and attribute due to multiple drivers that include complex processes that are non-stationary and highly variable. These drivers, such as human-induced climate change, natural climate variability, implementation of flood defense, river training, or land use change, could impact variably on space-time scales and influence or mask each other. Flood time series may show complex behavior that vary at a range of time scales and may cluster in time. Moreover hydrological time series (i.e. discharge) are often subject to measurement errors, such as rating curve error especially in the case of extremes where observation are actually derived through extrapolation. This study focuses on the application of recurrence based data analysis techniques (recurrence plot) for understanding and quantifying spatio-temporal changes in flood hazard in Germany. The recurrence plot is known as an effective tool to visualize the dynamics of phase space trajectories i.e. constructed from a time series by using an embedding dimension and a time delay, and it is known to be effective in analyzing non-stationary and non-linear time series. Sensitivity of the common measurement errors and noise on recurrence analysis will also be analyzed and evaluated against conventional methods. The emphasis will be on the identification of characteristic recurrence properties that could associate typical dynamic to certain flood events.
Micro-Level Affect Dynamics in Psychopathology Viewed From Complex Dynamical System Theory
Wichers, M.; Wigman, J. T. W.; Myin-Germeys, I.
2015-01-01
This article discusses the role of moment-to-moment affect dynamics in mental disorder and aims to integrate recent literature on this topic in the context of complex dynamical system theory. First, we will review the relevance of temporal and contextual aspects of affect dynamics in relation to psy
Modeling and Analysis of Complex Equipment Maintenance Dynamics
Institute of Scientific and Technical Information of China (English)
无
2007-01-01
An equipment maintenance system is naturally a complex dynamical system. The effective maintenance management must be based on the knowledge of the system's intrinsic dynamics. And the structure of the maintenance system determines its behavior. This paper analyzes the basic structures and elements of a maintenance system for complex multi-components equipment. The maintenance system is considered as a dynamic system whose behavior is influenced by its structure's feedback and interaction, and the system's available resources. Building the dynamical model with Simulink, we show some results about the maintenance system's nonlinear dynamics, which are never given by stochastic process methods. The model can be used for understanding and determining maintenance system behavior, towards which operational adjustments of maintenance infrastructure, precise prediction of maintenance requirements and timely supply of maintenance resources can be made in a more informed way.
Untangling complex dynamical systems via derivative-variable correlations
Levnaji, Zoran; Pikovsky, Arkady
2014-05-01
Inferring the internal interaction patterns of a complex dynamical system is a challenging problem. Traditional methods often rely on examining the correlations among the dynamical units. However, in systems such as transcription networks, one unit's variable is also correlated with the rate of change of another unit's variable. Inspired by this, we introduce the concept of derivative-variable correlation, and use it to design a new method of reconstructing complex systems (networks) from dynamical time series. Using a tunable observable as a parameter, the reconstruction of any system with known interaction functions is formulated via a simple matrix equation. We suggest a procedure aimed at optimizing the reconstruction from the time series of length comparable to the characteristic dynamical time scale. Our method also provides a reliable precision estimate. We illustrate the method's implementation via elementary dynamical models, and demonstrate its robustness to both model error and observation error.
Dynamics of ranking processes in complex systems.
Blumm, Nicholas; Ghoshal, Gourab; Forró, Zalán; Schich, Maximilian; Bianconi, Ginestra; Bouchaud, Jean-Philippe; Barabási, Albert-László
2012-09-21
The world is addicted to ranking: everything, from the reputation of scientists, journals, and universities to purchasing decisions is driven by measured or perceived differences between them. Here, we analyze empirical data capturing real time ranking in a number of systems, helping to identify the universal characteristics of ranking dynamics. We develop a continuum theory that not only predicts the stability of the ranking process, but shows that a noise-induced phase transition is at the heart of the observed differences in ranking regimes. The key parameters of the continuum theory can be explicitly measured from data, allowing us to predict and experimentally document the existence of three phases that govern ranking stability.
Cleave to Leave : Structural Insights into the Dynamic Organization of the Nuclear Pore Complex
Dokudovskaya, Svetlana; Veenhoff, Liesbeth M.; Rout, Michael P.
2002-01-01
A detailed understanding of the fine structure of the nuclear pore complex has remained elusive. Now, studies on a small protein domain have shed light on the dynamic organization of this massive assembly.
Energy Technology Data Exchange (ETDEWEB)
Wu, Xiaokun; Han, Min; Ming, Dengming, E-mail: dming@fudan.edu.cn [Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai (China)
2015-10-07
Membrane proteins play critically important roles in many cellular activities such as ions and small molecule transportation, signal recognition, and transduction. In order to fulfill their functions, these proteins must be placed in different membrane environments and a variety of protein-lipid interactions may affect the behavior of these proteins. One of the key effects of protein-lipid interactions is their ability to change the dynamics status of membrane proteins, thus adjusting their functions. Here, we present a multi-scaled normal mode analysis (mNMA) method to study the dynamics perturbation to the membrane proteins imposed by lipid bi-layer membrane fluctuations. In mNMA, channel proteins are simulated at all-atom level while the membrane is described with a coarse-grained model. mNMA calculations clearly show that channel gating motion can tightly couple with a variety of membrane deformations, including bending and twisting. We then examined bi-channel systems where two channels were separated with different distances. From mNMA calculations, we observed both positive and negative gating correlations between two neighboring channels, and the correlation has a maximum as the channel center-to-center distance is close to 2.5 times of their diameter. This distance is larger than recently found maximum attraction distance between two proteins embedded in membrane which is 1.5 times of the protein size, indicating that membrane fluctuation might impose collective motions among proteins within a larger area. The hybrid resolution feature in mNMA provides atomic dynamics information for key components in the system without costing much computer resource. We expect it to be a conventional simulation tool for ordinary laboratories to study the dynamics of very complicated biological assemblies. The source code is available upon request to the authors.
Wu, Xiaokun; Han, Min; Ming, Dengming
2015-10-01
Membrane proteins play critically important roles in many cellular activities such as ions and small molecule transportation, signal recognition, and transduction. In order to fulfill their functions, these proteins must be placed in different membrane environments and a variety of protein-lipid interactions may affect the behavior of these proteins. One of the key effects of protein-lipid interactions is their ability to change the dynamics status of membrane proteins, thus adjusting their functions. Here, we present a multi-scaled normal mode analysis (mNMA) method to study the dynamics perturbation to the membrane proteins imposed by lipid bi-layer membrane fluctuations. In mNMA, channel proteins are simulated at all-atom level while the membrane is described with a coarse-grained model. mNMA calculations clearly show that channel gating motion can tightly couple with a variety of membrane deformations, including bending and twisting. We then examined bi-channel systems where two channels were separated with different distances. From mNMA calculations, we observed both positive and negative gating correlations between two neighboring channels, and the correlation has a maximum as the channel center-to-center distance is close to 2.5 times of their diameter. This distance is larger than recently found maximum attraction distance between two proteins embedded in membrane which is 1.5 times of the protein size, indicating that membrane fluctuation might impose collective motions among proteins within a larger area. The hybrid resolution feature in mNMA provides atomic dynamics information for key components in the system without costing much computer resource. We expect it to be a conventional simulation tool for ordinary laboratories to study the dynamics of very complicated biological assemblies. The source code is available upon request to the authors.
The Influence of Information Acquisition on the Complex Dynamics of Market Competition
Guo, Zhanbing; Ma, Junhai
In this paper, we build a dynamical game model with three bounded rational players (firms) to study the influence of information on the complex dynamics of market competition, where useful information is about rival’s real decision. In this dynamical game model, one information-sharing team is composed of two firms, they acquire and share the information about their common competitor, however, they make their own decisions separately, where the amount of information acquired by this information-sharing team will determine the estimation accuracy about the rival’s real decision. Based on this dynamical game model and some creative 3D diagrams, the influence of the amount of information on the complex dynamics of market competition such as local dynamics, global dynamics and profits is studied. These results have significant theoretical and practical values to realize the influence of information.
The dynamical complexity of work-hardening: a large-scale molecular dynamics simulation
Institute of Scientific and Technical Information of China (English)
Markus J. Buehler; Alexander Hartmaier; Mark A. Duchaineau; Farid F. Abraham; Huajian Gao
2005-01-01
We analyze a large-scale molecular dynamics simulation of work hardening in a model system of a ductile solid.With tensile loading, we observe emission of thousands of dislocations from two sharp cracks. The dislocations interact in a complex way, revealing three fundamental mechanisms of work-hardening in this ductile material. These are (1) dislocation cutting processes, jog formation and generation of trails of point defects; (2) activation of secondary slip systems by Frank-Read and cross-slip mechanisms; and (3) formation of sessile dislocations such as Lomer-Cottrell locks.We report the discovery of a new class of point defects referred to as trail of partial point defects, which could play an important role in situations when partial dislocations dominate plasticity. Another important result of the present work is the rediscovery of the Fleischer-mechanism of cross-slip of partial dislocations that was theoretically proposed more than 50 years ago, and is now, for the first time, confirmed by atomistic simulation. On the typical time scale of molecular dynamics simulations, the dislocations self-organize into a complex sessile defect topology. Our analysis illustrates numerous mechanisms formerly only conjectured in textbooks and observed indirectly in experiments. It is the first time that such a rich set of fundamental phenomena have been revealed in a single computer simulation, and its dynamical evolution has been studied. The present study exemplifies the simulation and analysis of the complex nonlinear dynamics of a many-particle system during failure using ultra-large scale computing.
Computational complexity of symbolic dynamics at the onset of chaos
Lakdawala, Porus
1996-05-01
In a variety of studies of dynamical systems, the edge of order and chaos has been singled out as a region of complexity. It was suggested by Wolfram, on the basis of qualitative behavior of cellular automata, that the computational basis for modeling this region is the universal Turing machine. In this paper, following a suggestion of Crutchfield, we try to show that the Turing machine model may often be too powerful as a computational model to describe the boundary of order and chaos. In particular we study the region of the first accumulation of period doubling in unimodal and bimodal maps of the interval, from the point of view of language theory. We show that in relation to the ``extended'' Chomsky hierarchy, the relevant computational model in the unimodal case is the nested stack automaton or the related indexed languages, while the bimodal case is modeled by the linear bounded automaton or the related context-sensitive languages.
New Concept of Dynamic Complexity in Quantum Mechanics and Beyond
Kirilyuk, A P
1996-01-01
The qualitatively new concept of dynamic complexity in quantum mechanics is based on a new paradigm appearing within a nonperturbational analysis of the Schroedinger equation for a generic Hamiltonian system. The unreduced analysis explicitly provides the complete, consistent solution as a set of many incompatible components ('realisations') which should permanently and probabilistically replace one another, since each of them is 'complete' in the ordinary sense. This discovery leads to the universally applicable concept of dynamic complexity and self-consistent, realistic resolution of the stagnating problems of quantum chaos, quantum measurement, indeterminacy and wave reduction. The peculiar, 'mysterious' character of quantum behaviour itself is seen now as a result of a dynamically complex, intrinsically multivalued behaviour of interacting fields at the corresponding lowest levels of the (now completely causal) structure of reality. Incorporating the results of the canonical theories as an over-simplifie...
Some remarks on Lefschetz thimbles and complex Langevin dynamics
Aarts, Gert; Seiler, Erhard; Sexty, Denes
2014-01-01
Lefschetz thimbles and complex Langevin dynamics both provide a means to tackle the numerical sign problem prevalent in theories with a complex weight in the partition function, e.g. due to nonzero chemical potential. Here we collect some findings for the quartic model, and for U(1) and SU(2) models in the presence of a determinant, which have some features not discussed before, due to a singular drift. We find evidence for a relation between classical runaways and stable thimbles, and give an example of a degenerate fixed point. We typically find that the distributions sampled in complex Langevin dynamics are related to the thimble(s), but with some important caveats, for instance due to the presence of unstable fixed points in the Langevin dynamics.
Newtonian Nonlinear Dynamics for Complex Linear and Optimization Problems
Vázquez, Luis
2013-01-01
Newtonian Nonlinear Dynamics for Complex Linear and Optimization Problems explores how Newton's equation for the motion of one particle in classical mechanics combined with finite difference methods allows creation of a mechanical scenario to solve basic problems in linear algebra and programming. The authors present a novel, unified numerical and mechanical approach and an important analysis method of optimization. This book also: Presents mechanical method for determining matrix singularity or non-independence of dimension and complexity Illustrates novel mathematical applications of classical Newton’s law Offers a new approach and insight to basic, standard problems Includes numerous examples and applications Newtonian Nonlinear Dynamics for Complex Linear and Optimization Problems is an ideal book for undergraduate and graduate students as well as researchers interested in linear problems and optimization, and nonlinear dynamics.
The Dynamic Checking of Complex Real Time System
Institute of Scientific and Technical Information of China (English)
YU Chao; HUANG Benwen; WU Guoqing
2006-01-01
The paper presents an dynamic execution model of complex real-time software based on requirement description model RTRSM, and then propose a checking method based on configuration covering and its corresponding algorithm. This checking method can check the execution situations between parallel elements in a dynamic execution step of real-time software systems. It also can check all the states and transitions which assure the completeness of checking. In the end, related theorem is proofed.
Dynamics of competing ideas in complex social systems
Wang, Yubo; Liu, Jian
2011-01-01
Individuals accepting an idea may intentionally or unintentionally impose influences in a certain neighborhood area, making other individuals within the area less likely or even impossible to accept other competing ideas. Depending on whether such influences strictly prohibit neighborhood individuals from accepting other ideas or not, we classify them into exclusive and non-exclusive influences, respectively. Our study reveals for the first time the rich and complex dynamics of two competing ideas with neighborhood influences in scale-free social networks: depending on whether they have exclusive or non-exclusive influences, the final state varies from multiple coexistence to founder control to exclusion, with different sizes of population accepting each of the ideas respectively. Such results provide insights helpful for better understanding the spread (and the control of spread) of ideas in human society.
Dynamic inclusion complexes of metal nanoparticles inside nanocups.
Alarcón-Correa, Mariana; Lee, Tung-Chun; Fischer, Peer
2015-06-01
Host-guest inclusion complexes are abundant in molecular systems and of fundamental importance in living organisms. Realizing a colloidal analogue of a molecular dynamic inclusion complex is challenging because inorganic nanoparticles (NPs) with a well-defined cavity and portal are difficult to synthesize in high yield and with good structural fidelity. Herein, a generic strategy towards the fabrication of dynamic 1:1 inclusion complexes of metal nanoparticles inside oxide nanocups with high yield (>70%) and regiospecificity (>90%) by means of a reactive double Janus nanoparticle intermediate is reported. Experimental evidence confirms that the inclusion complexes are formed by a kinetically controlled mechanism involving a delicate interplay between bipolar galvanic corrosion and alloying-dealloying oxidation. Release of the NP guest from the nanocups can be efficiently triggered by an external stimulus. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Reconstructing complex networks with binary-state dynamics
Li, Jingwen; Lai, Ying-Cheng; Grebogi, Celso
2015-01-01
The prerequisite for our understanding of many complex networked systems lies in the reconstruction of network structure from measurable data. Although binary-state dynamics occurring in a broad class of complex networked systems in nature and society and has been intensively investigated, a general framework for reconstructing complex networks from binary states, the inverse problem, is lacking. Here we offer a general solution to the reconstruction problem by developing a data-based linearization approach for binary-state dynamics with linear, nonlinear, discrete and stochastic switching functions. The linearization allows us to convert the network reconstruction problem into a sparse signal reconstruction problem that can be resolved efficiently and credibly by convex optimization based on compressed sensing. The completely data-based linearization method and the sparse signal reconstruction constitutes a general framework for reconstructing complex networks without any knowledge of the binary-state dynami...
Structure, dynamics, assembly, and evolution of protein complexes.
Marsh, Joseph A; Teichmann, Sarah A
2015-01-01
The assembly of individual proteins into functional complexes is fundamental to nearly all biological processes. In recent decades, many thousands of homomeric and heteromeric protein complex structures have been determined, greatly improving our understanding of the fundamental principles that control symmetric and asymmetric quaternary structure organization. Furthermore, our conception of protein complexes has moved beyond static representations to include dynamic aspects of quaternary structure, including conformational changes upon binding, multistep ordered assembly pathways, and structural fluctuations occurring within fully assembled complexes. Finally, major advances have been made in our understanding of protein complex evolution, both in reconstructing evolutionary histories of specific complexes and in elucidating general mechanisms that explain how quaternary structure tends to evolve. The evolution of quaternary structure occurs via changes in self-assembly state or through the gain or loss of protein subunits, and these processes can be driven by both adaptive and nonadaptive influences.
Energy Technology Data Exchange (ETDEWEB)
Agieienko, Vira N.; Kolesnik, Yaroslav V.; Kalugin, Oleg N., E-mail: onkalugin@gmail.com [Department of Inorganic Chemistry, V. N. Karazin Kharkiv National University, Kharkiv 61022 (Ukraine)
2014-05-21
Molecular dynamics simulations of complexes of Mg{sup 2+}, Ca{sup 2+}, Sr{sup 2+}, and Ba{sup 2+} with 3-hydroxyflavone (flavonol, 3HF) and ClO {sub 4}{sup −} in acetonitrile were performed. The united atoms force field model was proposed for the 3HF molecule using the results of DFT quantum chemical calculations. 3HF was interpreted as a rigid molecule with two internal degrees of freedom, i.e., rotation of the phenyl ring and of the OH group with respect to the chromone moiety. The interatomic radial distribution functions showed that interaction of the cations with flavonol occurs via the carbonyl group of 3HF and it is accompanied with substitution of one of the acetonitrile molecules in the cations’ first solvation shells. Formation of the cation–3HF complexes does not have significant impact on the rotation of the phenyl ring with respect to the chromone moiety. However, the orientation of the flavonol's OH-group is more sensitive to the interaction with doubly charged cations. When complex with Mg{sup 2+} is formed, the OH-group turns out of the plane of the chromone moiety that leads to rupture of intramolecular H-bond in the ligand molecule. Complexation of Ca{sup 2+}, Sr{sup 2+}, and BaClO {sub 4}{sup +} with 3HF produces two structures with different OH-positions, as in the free flavonol with the intramolecular H-bond and as in the complex with Mg{sup 2+} with disrupted H-bonding. It was shown that additional stabilization of the [MgClO{sub 4}(3HF)]{sup +} and [BaClO{sub 4}(3HF)]{sup +} complexes is determined by strong affinity of perchlorate anion to interact with flavonol via intracomplex hydrogen bond between an oxygen atom of the anion and the hydrogen atom of the 3-hydroxyl group. Noticeable difference in the values of the self-diffusion coefficients for Kt{sup 2+} from one side and ClO {sub 4}{sup −}, 3HF, and AN in the cations’ coordination shell from another side implies quite weak interaction between cation, anion, and ligands in
Agieienko, Vira N.; Kolesnik, Yaroslav V.; Kalugin, Oleg N.
2014-05-01
Molecular dynamics simulations of complexes of Mg2+, Ca2+, Sr2+, and Ba2+ with 3-hydroxyflavone (flavonol, 3HF) and ClO_4 ^ - in acetonitrile were performed. The united atoms force field model was proposed for the 3HF molecule using the results of DFT quantum chemical calculations. 3HF was interpreted as a rigid molecule with two internal degrees of freedom, i.e., rotation of the phenyl ring and of the OH group with respect to the chromone moiety. The interatomic radial distribution functions showed that interaction of the cations with flavonol occurs via the carbonyl group of 3HF and it is accompanied with substitution of one of the acetonitrile molecules in the cations' first solvation shells. Formation of the cation-3HF complexes does not have significant impact on the rotation of the phenyl ring with respect to the chromone moiety. However, the orientation of the flavonol's OH-group is more sensitive to the interaction with doubly charged cations. When complex with Mg2+ is formed, the OH-group turns out of the plane of the chromone moiety that leads to rupture of intramolecular H-bond in the ligand molecule. Complexation of Ca2+, Sr2+, and BaClO_4 ^ + with 3HF produces two structures with different OH-positions, as in the free flavonol with the intramolecular H-bond and as in the complex with Mg2+ with disrupted H-bonding. It was shown that additional stabilization of the [MgClO4(3HF)]+ and [BaClO4(3HF)]+ complexes is determined by strong affinity of perchlorate anion to interact with flavonol via intracomplex hydrogen bond between an oxygen atom of the anion and the hydrogen atom of the 3-hydroxyl group. Noticeable difference in the values of the self-diffusion coefficients for Kt2+ from one side and ClO_4 ^ -, 3HF, and AN in the cations' coordination shell from another side implies quite weak interaction between cation, anion, and ligands in the investigated complexes.
Minimal model for complex dynamics in cellular processes.
Suguna, C; Chowdhury, K K; Sinha, S
1999-11-01
Cellular functions are controlled and coordinated by the complex circuitry of biochemical pathways regulated by genetic and metabolic feedback processes. This paper aims to show, with the help of a minimal model of a regulated biochemical pathway, that the common nonlinearities and control structures present in biomolecular interactions are capable of eliciting a variety of functional dynamics, such as homeostasis, periodic, complex, and chaotic oscillations, including transients, that are observed in various cellular processes.
Dynamic control of the lumbopelvic complex; lack of reliability of established test procedures
DEFF Research Database (Denmark)
Henriksen, Marius; Lund, Hans; Bliddal, Henning
2007-01-01
Impairment of the dynamic control of the lumbopelvic complex in LBP has gained increased focus both clinically and experimentally. The objectives of this study were to determine the reliability of inclinometry as a measure of dynamic lumbopelvic control. Lumbopelvic reposition accuracy during pel...
Complex Dynamics of Discrete SEIS Models with Simple Demography
Directory of Open Access Journals (Sweden)
Hui Cao
2011-01-01
Full Text Available We investigate bifurcations and dynamical behaviors of discrete SEIS models with exogenous reinfections and a variety of treatment strategies. Bifurcations identified from the models include period doubling, backward, forward-backward, and multiple backward bifurcations. Multiple attractors, such as bistability and tristability, are observed. We also estimate the ultimate boundary of the infected regardless of initial status. Our rigorously mathematical analysis together with numerical simulations show that epidemiological factors alone can generate complex dynamics, though demographic factors only support simple equilibrium dynamics. Our model analysis supports and urges to treat a fixed percentage of exposed individuals.
Nonlinear dynamics in the study of birdsong
Mindlin, Gabriel B.
2017-09-01
Birdsong, a rich and complex behavior, is a stellar model to understand a variety of biological problems, from motor control to learning. It also enables us to study how behavior emerges when a nervous system, a biomechanical device and the environment interact. In this review, I will show that many questions in the field can benefit from the approach of nonlinear dynamics, and how birdsong can inspire new directions for research in dynamics.
Proceedings of "Optical Probes of Dynamics in Complex Environments"
Energy Technology Data Exchange (ETDEWEB)
Sension, R; Tokmakoff, A
2008-04-01
This document contains the proceedings from the symposium on Optical Probes of Dynamics in Complex Environments, which organized as part of the 235th National Meeting of the American Chemical Society in New Orleans, LA from April 6 to 10, 2008. The study of molecular dynamics in chemical reaction and biological processes using time ÃÂÃÂÃÂÃÂÃÂÃÂÃÂÃÂresolved spectroscopy plays an important role in our understanding of energy conversion, storage, and utilization problems. Fundamental studies of chemical reactivity, molecular rearrangements, and charge transport are broadly supported by the DOE Office of Science because of their role in the development of alternative energy sources, the understanding of biological energy conversion processes, the efficient utilization of existing energy resources, and the mitigation of reactive intermediates in radiation chemistry. In addition, time resolved spectroscopy is central to all of DOEs grand challenges for fundamental energy science. This symposium brought together leaders in the field of ultrafast spectroscopy, including experimentalists, theoretical chemists, and simulators, to discuss the most recent scientific and technological advances. DOE support for this conference was used to help young US and international scientists travel to the meeting. The latest technology in ultrafast infrared, optical, and xray spectroscopy and the scientific advances that these methods enable were covered. Particular emphasis was placed on new experimental methods used to probe molecular dynamics in liquids, solids, interfaces, nanostructured materials, and biomolecules.
Structure-based control of complex networks with nonlinear dynamics
Zañudo, Jorge G T; Albert, Réka
2016-01-01
Given the network of interactions underlying a complex system, what can we learn about controlling such a system solely from its structure? Over a century of research in control theory has given us tools to answer this question, which were widely applied in science and engineering. Yet the current tools do not always consider the inherently nonlinear dynamics of real systems and the naturally occurring system states in their definition of "control", a term whose interpretation varies across disciplines. Here we use a new mathematical framework for structure-based control of networks governed by a broad class of nonlinear dynamics that includes the major dynamic models of biological, technological, and social processes. This framework provides realizable node overrides that steer a system towards any of its natural long term dynamic behaviors and which are guaranteed to be effective regardless of the dynamic details and parameters of the underlying system. We use this framework on several real networks, compar...
Dynamical complexity in the perception-based network formation model
Jo, Hang-Hyun; Moon, Eunyoung
2016-12-01
Many link formation mechanisms for the evolution of social networks have been successful to reproduce various empirical findings in social networks. However, they have largely ignored the fact that individuals make decisions on whether to create links to other individuals based on cost and benefit of linking, and the fact that individuals may use perception of the network in their decision making. In this paper, we study the evolution of social networks in terms of perception-based strategic link formation. Here each individual has her own perception of the actual network, and uses it to decide whether to create a link to another individual. An individual with the least perception accuracy can benefit from updating her perception using that of the most accurate individual via a new link. This benefit is compared to the cost of linking in decision making. Once a new link is created, it affects the accuracies of other individuals' perceptions, leading to a further evolution of the actual network. As for initial actual networks, we consider both homogeneous and heterogeneous cases. The homogeneous initial actual network is modeled by Erdős-Rényi (ER) random networks, while we take a star network for the heterogeneous case. In any cases, individual perceptions of the actual network are modeled by ER random networks with controllable linking probability. Then the stable link density of the actual network is found to show discontinuous transitions or jumps according to the cost of linking. As the number of jumps is the consequence of the dynamical complexity, we discuss the effect of initial conditions on the number of jumps to find that the dynamical complexity strongly depends on how much individuals initially overestimate or underestimate the link density of the actual network. For the heterogeneous case, the role of the highly connected individual as an information spreader is also discussed.
Copper dynamics in doped metal-bis(histidine) complexes.
Colaneri, Michael J; Vitali, Jacqueline
2014-07-03
Electron paramagnetic resonance (EPR) temperature-dependent measurements were undertaken on three Cu(II)-doped metal-histidine complexes to assess copper site dynamic behavior. Previous single-crystal EPR analysis on two of these, zinc d,l-histidine pentahydrate (ZnDLH) and bis(l-histidinato)cadmium dihydrate (CdLH), found that doped Cu(2+) can be modeled as hopping between two neighboring conformational states, with a temperature-dependent rate becoming large enough at room temperature to produce an "averaged" spectrum. By comparing spectra from their powdered form, we show that Cu(2+) doped into a third system, Cd(2+)-d,l-histidine (CdDLH), also exhibits temperature-dependent EPR with features indicating a similar motional-averaging process. In addition, the change of g and copper hyperfine parameters from low to high temperature for CdDLH resembles that in ZnDLH, whereas the change in these parameters for CdLH is like that found in a fourth copper-doped system, zinc l-histidine dihydrate (ZnLH). Taken together, these results suggest that averaging motion between neighboring copper sites is common in metal-bis(histidine) compounds. More detailed studies on biological models are thus warranted, especially because they reveal unique relationships between structure, dynamic processes, and stability and can lead to a better understanding of the role played by site flexibility in copper proteins.
Early signatures of regime shifts in complex dynamical systems
Indian Academy of Sciences (India)
Indrani Bose; Mainak Pal
2015-02-01
A large number of studies have recently been carried out on the early signatures of regime shifts in a number of dynamical systems, e.g., ecosystems, the climate, fish and wildlife populations, financial markets, complex diseases and gene circuits. The underlying model in most cases is that of the fold-bifurcation in which a sudden regime shift occurs at a bifurcation point. The shift involves a discontinuous jump from one type of stable steady state to another. The dynamics of natural systems have both deterministic and stochastic components. The early signatures of abrupt regime shifts include the critical slowing down as a transition point is approached, rising variance and the lag-1 autocorrelation function, increased skewness of the steady-state probability distribution and the ratio of two mean first passage times for the exits from the stable steady states as the bifurcation point is approached. Noise-induced regime shifts are also possible for which the vicinity of the bifurcation point is not essential. In this paper, we review examples of regime shifts in natural systems and the associated early signatures. We further discuss how such approaches provide useful insights on a cell biological process involving the fold-bifurcation.
Dynamic hysteresis in the rheology of complex fluids.
Puisto, Antti; Mohtaschemi, Mikael; Alava, Mikko J; Illa, Xavier
2015-04-01
Recently, rheological hysteresis has been studied systematically in a wide range of complex fluids combining global rheology and time-resolved velocimetry. In this paper we present an analysis of the roles of the three most fundamental mechanisms in simple-yield-stress fluids: structure dynamics, viscoelastic response, and spatial flow heterogeneities, i.e., time-dependent shear bands. Dynamical hysteresis simulations are done analogously to rheological ramp-up and -down experiments on a coupled model which incorporates viscoelasticity and time-dependent structure evolution. Based on experimental data, a coupling between hysteresis measured from the local velocity profiles and that measured from the global flow curve has been suggested. According to the present model, even if transient shear banding appears during the shear ramps, in typical narrow-gap devices, only a small part of the hysteretic response can be attributed to heterogeneous flow. This results in decoupling of the hysteresis measured from the local velocity profiles and the global flow curve, demonstrating that for an arbitrary time-dependent rheological response this proposed coupling can be very weak.
New Approach to Cluster Synchronization in Complex Dynamical Networks
Institute of Scientific and Technical Information of China (English)
LU Xin-Biao; QIN Bu-Zhi; LU Xin-Yu
2009-01-01
In this paper, a distributed control strategy is proposed to make a complex dynamical network achieve cluster synchronization, which means that nodes in the same group achieve the same synchronization state, while nodes in different groups achieve different synchronization states. The local and global stability of the cluster synchronization state are analyzed. Moreover, simulation results verify the effectiveness of the new approach
Stochastic simulation of HIV population dynamics through complex network modelling
Sloot, P.M.A.; Ivanov, S.V.; Boukhanovsky, A.V.; van de Vijver, D.A.M.C.; Boucher, C.A.B.
2008-01-01
We propose a new way to model HIV infection spreading through the use of dynamic complex networks. The heterogeneous population of HIV exposure groups is described through a unique network degree probability distribution. The time evolution of the network nodes is modelled by a Markov process and
Stochastic simulation of HIV population dynamics through complex network modelling
Sloot, P. M. A.; Ivanov, S. V.; Boukhanovsky, A. V.; van de Vijver, D. A. M. C.; Boucher, C. A. B.
We propose a new way to model HIV infection spreading through the use of dynamic complex networks. The heterogeneous population of HIV exposure groups is described through a unique network degree probability distribution. The time evolution of the network nodes is modelled by a Markov process and
2D pattern evolution constrained by complex network dynamics
Rocha, L E C; Costa, Luciano da Fontoura; Rocha, Luis Enrique Correa da
2006-01-01
Complex networks have established themselves along the last years as being particularly suitable and flexible for representing and modeling several complex natural and human-made systems. At the same time in which the structural intricacies of such networks are being revealed and understood, efforts have also been directed at investigating how such connectivity properties define and constrain the dynamics of systems unfolding on such structures. However, lesser attention has been focused on hybrid systems, \\textit{i.e.} involving more than one type of network and/or dynamics. Because several real systems present such an organization (\\textit{e.g.} the dynamics of a disease coexisting with the dynamics of the immune system), it becomes important to address such hybrid systems. The current paper investigates a specific system involving a diffusive (linear and non-linear) dynamics taking place in a regular network while interacting with a complex network of defensive agents following Erd\\"os-R\\'enyi and Barab\\'a...
Coslovich, Daniele; Kahl, Gerhard; Krakoviack, Vincent
2011-06-01
Over the past two decades, the dynamics of fluids under nanoscale confinement has attracted much attention. Motivation for this rapidly increasing interest is based on both practical and fundamental reasons. On the practical and rather applied side, problems in a wide range of scientific topics, such as polymer and colloidal sciences, rheology, geology, or biophysics, benefit from a profound understanding of the dynamical behaviour of confined fluids. Further, effects similar to those observed in confinement are expected in fluids whose constituents have strong size or mass asymmetry, and in biological systems where crowding and obstruction phenomena in the cytosol are responsible for clear separations of time scales for macromolecular transport in the cell. In fundamental research, on the other hand, the interest focuses on the complex interplay between confinement and structural relaxation, which is responsible for the emergence of new phenomena in the dynamics of the system: in confinement, geometric constraints associated with the pore shape are imposed to the adsorbed fluids and an additional characteristic length scale, i.e. the pore size, comes into play. For many years, the topic has been mostly experimentally driven. Indeed, a broad spectrum of systems has been investigated by sophisticated experimental techniques, while theoretical and simulation studies were rather scarce due to conceptual and computational issues. In the past few years, however, theory and simulations could largely catch up with experiments. On one side, new theories have been put forward that duly take into account the porosity, the connectivity, and the randomness of the confinement. On the other side, the ever increasing available computational power now allows investigations that were far out of reach a few years ago. Nowadays, instead of isolated state points, systematic investigations on the dynamics of confined fluids, covering a wide range of system parameters, can be realized
Nonlinear Dynamics of Complex Coevolutionary Systems in Historical Times
Perdigão, Rui A. P.
2016-04-01
A new theoretical paradigm for statistical-dynamical modeling of complex coevolutionary systems is introduced, with the aim to provide historical geoscientists with a practical tool to analyse historical data and its underlying phenomenology. Historical data is assumed to represent the history of dynamical processes of physical and socio-economic nature. If processes and their governing laws are well understood, they are often treated with traditional dynamical equations: deterministic approach. If the governing laws are unknown or impracticable, the process is often treated as if being random (even if it is not): statistical approach. Although single eventful details - such as the exact spatiotemporal structure of a particular hydro-meteorological incident - may often be elusive to a detailed analysis, the overall dynamics exhibit group properties summarized by a simple set of categories or dynamical regimes at multiple scales - from local short-lived convection patterns to large-scale hydro-climatic regimes. The overwhelming microscale complexity is thus conveniently wrapped into a manageable group entity, such as a statistical distribution. In a stationary setting whereby the distribution is assumed to be invariant, alternating regimes are approachable as dynamical intermittence. For instance, in the context of bimodal climatic oscillations such as NAO and ENSO, each mode corresponds to a dynamical regime or phase. However, given external forcings or longer-term internal variability and multiscale coevolution, the structural properties of the system may change. These changes in the dynamical structure bring about a new distribution and associated regimes. The modes of yesteryear may no longer exist as such in the new structural order of the system. In this context, aside from regime intermittence, the system exhibits structural regime change. New oscillations may emerge whilst others fade into the annals of history, e.g. particular climate fluctuations during
Directory of Open Access Journals (Sweden)
Benjamin eCowley
2016-02-01
Full Text Available BackgroundRecognition of objects and their context relies heavily on the integrated functioning of global and local visual processing. In a realistic setting such as work, this processing becomes a sustained activity, implying a consequent interaction with executive functions.MotivationThere have been many studies of either global-local attention or executive functions; however it is relatively novel to combine these processes to study a more ecological form of attention. We aim to explore the phenomenon of global-local processing during a task requiring sustained attention and working memory.MethodsWe develop and test a novel protocol for global-local dissociation, with task structure including phases of divided ('rule search' and selective ('rule found' attention, based on the Wisconsin Card Sorting Task.We test it in a laboratory study with 25 participants, and report on behaviour measures (physiological data was also gathered, but not reported here. We develop novel stimuli with more naturalistic levels of information and noise, based primarily on face photographs, with consequently more ecological validity.ResultsWe report behavioural results indicating that sustained difficulty when participants test their hypotheses impacts matching-task performance, and diminishes the global precedence effect. Results also show a dissociation between subjectively experienced difficulty and objective dimension of performance, and establish the internal validity of the protocol.ContributionWe contribute an advance in the state of the art for testing global-local attention processes in concert with complex cognition. With three results we establish a connection between global-local dissociation and aspects of complex cognition. Our protocol also improves ecological validity and opens options for testing additional interactions in future work.
Synchronization criteria based on a general complex dynamical network model
Institute of Scientific and Technical Information of China (English)
ZHANG Jian-lin; WANG Chang-jian; XU Cong-fu
2008-01-01
Many complex dynamical networks display synchronization phenomena. We introduce a general complex dynamical network model. The model is equivalent to a simple vector model of adopting the Kronecker product. Some synchronization criteria, including time-variant networks and time-varying networks, are deduced based on Lyapunov's stability theory, and they are proven on the condition of obtaining a certain synchronous solution of an isolated cell. In particular, the inner-coupling matrix directly determines the synchronization of the time-invariant network; while for a time-varying periodic dynamical network, the asymptotic stability of a synchronous solution is determined by a constant matrix which is related to the fundamental solution matrices of the linearization system. Finally, illustrative examples are given to validate the results.
Dynamic properties of epidemic spreading on finite size complex networks
Institute of Scientific and Technical Information of China (English)
Li Ying; Liu Yang; Shan Xiu-Ming; Ren Yong; Jiao Jian; Qiu Ben
2005-01-01
The Internet presents a complex topological structure, on which computer viruses can easily spread. By using theoretical analysis and computer simulation methods, the dynamic process of disease spreading on finite size networks with complex topological structure is investigated. On the finite size networks, the spreading process of SIS (susceptibleinfected-susceptible) model is a finite Markov chain with an absorbing state. Two parameters, the survival probability and the conditional infecting probability, are introduced to describe the dynamic properties of disease spreading on finite size networks. Our results can help understanding computer virus epidemics and other spreading phenomena on communication and social networks. Also, knowledge about the dynamic character of virus spreading is helpful for adopting immunity policy.
Decentralized adaptive synchronization of an uncertain complex delayed dynamical network
Institute of Scientific and Technical Information of China (English)
Weisong ZHONG; Jun ZHAO; Georgi M.DIMIROVSKI
2009-01-01
In this paper,we investigate the locally and globally adaptive synchronization problem for an uncertain complex dynamical network with time-varying coupling delays based on the decentralized control.The coupling terms here are bounded by high-order polynomials with known gains that are ubiquitous in a large class of complex dynamical networks.We generalize the usual technology of searching for an appropriate coordinates transformation to change the network dynamics into a series of decoupled lower-dimensional systems.Several adaptive synchronization criteria are derived by constructing the Lyapunov-Krasovskii functional and Barbalat lemma,and the proposed criteria are simple in form and convenient for the practical engineering design.Numerical simulations illustrated by a nearest-neighbor coupling network verify the effectiveness of the proposed synchronization scheme.
Experimental study on dynamic parameters of red mud loess complex%赤泥黄土复合体的动参数试验研究
Institute of Scientific and Technical Information of China (English)
董晓强; 张强; 寇晓辉; 刘彦忠; 张军
2016-01-01
Sample red mud,loess and red mud loess composite samples were tested by GDS dynamic triaxial apparatus to study some dynamic parameters of red mud,loess and red mud loess composite samples,and analyze the impact of red mud content and confining pressure,aiming to explore the en-gineering properties of red mud loess composite material for roadbed. The results show that the red mud, red mud loess composite sample curves of stress-strain σd-εd,strain-dynamic elastic modulus Ed-εd,strain-damping ratioλ-εd have similar characteristic variation with loess,but difference in val-ue. The incorporation of red mud enhances the composite sample strength and stiffness,and is propor-tional to the incorporation of m. And with the increasing incorporation of red mud,dynamic elastic modulus Ed and maximum dynamic modulus Edmax significantly increase, but increased degrees are different in different confining pressures. The corresponding damping ratioλof composite sample de-creases with the increase of the red mud content,but with the increase of the confining pressure,the impact on the red mud content is smaller. The impact of confining pressure on dynamic parameters:in the same strain, the stress σd increases with increase of the confining pressure, the dynamic elastic modulus Ed increases with increase of the confining pressure,the damping ratio λ increases with in-crease of the confining pressure in previous period, but it decreases with increase of the confining pressure in the latter. Thus,the best ratio of red mud loess composite sample of red mud:loess is 3∶7.%本试验使用GDS动三轴仪，对赤泥黄土复合试样、赤泥试样、黄土试样进行了动三轴试验，研究了赤泥、黄土及赤泥黄土复合试样的部分动参数，分析了赤泥含量、围压的影响，旨在探索赤泥黄土复合体用于路基材料的工程性能.试验结果表明：赤泥、赤泥黄土复合试样的应力应变σd~εd、应变动弹模Ed~εd、应变阻
Directory of Open Access Journals (Sweden)
Rayevsky A. V.
2016-02-01
Full Text Available Aim. To investigate the structural bases for the amino acid selectivity of the Thermus thermophilus leucyl-tRNA synthetase (LeuRSTT aminoacylation site and to disclose the binding pattern of pre-transfer editing substrates. Methods. Eight amino acids proposed as semi-cognate substrates for aminoacylation and eight aminoacyl-adenylates (formed from AMP and eight amino acids were prepared in zwitterions form. The protein structure with a co-crystallized substrate in the aminoacylation site [PDBID: 1OBH] was taken from RCSB. Docking settings and evaluation of substrate efficiency were followed by twofold docking function analysis for each conformation with Gold CCDC. The molecular dynamics simulation was performed using Gromacs. The procedures of relaxation and binding study were separated in two different subsequent simulations for 50ns and 5ns. Results. The evaluation of substrate efficiency for 8 amino acids by twofold docking function analysis, based on score values,has shown that the ligands of LeuRSTT can be positioned in the following order: Leu>Nva>Hcy>Nle>Met>Cys>Ile >Val. MD simulation has revealed lower electrostatic interactions of isoleucine with the active site of the enzyme compared with those for norvaline and leucine. In the case of aminoacyl-adenylates no significant differences were found based on score values for both GoldScore and Asp functions. Molecular dynamics of leucyl-, isoleucyl- and norvalyl-adenylates showed that the most stable and conformationally favorable is leucine, then follow norvaline and isoleucine. It has been also found that the TYR43 of the active site covers carboxyl group of leucine and norvaline like a shield and deflected towards isoleucine, allowing water molecules to come closer. Conclusions. In this study we revealed some structural basis for screening unfavorable substrates by shape, size and flexibility of a radical. The results obtained for different amino acids by molecular docking and MD studies
Universality classes of fluctuation dynamics in hierarchical complex systems
Macêdo, A. M. S.; González, Iván R. Roa; Salazar, D. S. P.; Vasconcelos, G. L.
2017-03-01
A unified approach is proposed to describe the statistics of the short-time dynamics of multiscale complex systems. The probability density function of the relevant time series (signal) is represented as a statistical superposition of a large time-scale distribution weighted by the distribution of certain internal variables that characterize the slowly changing background. The dynamics of the background is formulated as a hierarchical stochastic model whose form is derived from simple physical constraints, which in turn restrict the dynamics to only two possible classes. The probability distributions of both the signal and the background have simple representations in terms of Meijer G functions. The two universality classes for the background dynamics manifest themselves in the signal distribution as two types of tails: power law and stretched exponential, respectively. A detailed analysis of empirical data from classical turbulence and financial markets shows excellent agreement with the theory.
Architecture and dynamics of proteins and aqueous solvation complexes
Lotze, S.M.
2015-01-01
For this thesis, the molecular dynamics of water and biological (model) systems have been studied with advanced nonlinear optical techniques. In chapters 4-5, the technique of femtosecond mid-infrared pump probe spectroscopy has been used to study the energy transfer and the reorientational dynamics
Complex systems approach to fire dynamics and climate change impacts
Pueyo, S.
2012-04-01
I present some recent advances in complex systems theory as a contribution to understanding fire regimes and forecasting their response to a changing climate, qualitatively and quantitatively. In many regions of the world, fire sizes have been found to follow, approximately, a power-law frequency distribution. As noted by several authors, this distribution also arises in the "forest fire" model used by physicists to study mechanisms that give rise to scale invariance (the power law is a scale-invariant distribution). However, this model does not give and does not pretend to give a realistic description of fire dynamics. For example, it gives no role to weather and climate. Pueyo (2007) developed a variant of the "forest fire" model that is also simple but attempts to be more realistic. It also results into a power law, but the parameters of this distribution change through time as a function of weather and climate. Pueyo (2007) observed similar patterns of response to weather in data from boreal forest fires, and used the fitted response functions to forecast fire size distributions in a possible climate change scenario, including the upper extreme of the distribution. For some parameter values, the model in Pueyo (2007) displays a qualitatively different behavior, consisting of simple percolation. In this case, fire is virtually absent, but megafires sweep through the ecosystem a soon as environmental forcings exceed a critical threshold. Evidence gathered by Pueyo et al. (2010) suggests that this is realistic for tropical rainforests (specifically, well-conserved upland rainforests). Some climate models suggest that major tropical rainforest regions are going to become hotter and drier if climate change goes ahead unchecked, which could cause such abrupt shifts. Not all fire regimes are well described by this model. Using data from a tropical savanna region, Pueyo et al. (2010) found that the dynamics in this area do not match its assumptions, even though fire
Conte, Marco; Hippler, Michael
2016-09-01
The stereochemistry and dynamics of MoO2(acac)2 in benzene, chloroform, and toluene were investigated by variable temperature (1)H NMR, density functional theory (SOGGA11-X, B3LYP), and ab initio (MP2) methods. In solution, an equilibrium between two chiral enantiomers with C2 symmetry was identified, Λ-cis-MoO2(acac)2 and Δ-cis-MoO2(acac)2. The two enantiomers are connected via achiral cis transition states that switch the enantiomeric conformations via a Ray-Dutt, Bailar, and a newly described racemization twisting mechanism. All three mechanisms have similar calculated activation energies. Activation parameters Ea, ΔH(‡), and ΔS(‡) were experimentally determined for the exchange process, with a small, negative ΔS(‡), and a positive ΔH(‡) of 68.1 kJ mol(-1) in benzene, 54.9 kJ mol(-1) in chloroform, and 60.6 kJ mol(-1) in toluene, in reasonable general agreement with the calculations. Trans configurations of MoO2(acac)2 are very much higher in energy than cis and are not relevant in the temperature range experimentally studied, 243-340 K. The enantiomers interconvert within seconds near room temperature and much faster at elevated temperatures. Racemization will thus prevent the use of enantiomerically pure MoO2(acac)2 for chiral catalysis under practical conditions.
Ganguly, Niloy; Mukherjee, Animesh
2009-01-01
This self-contained book systematically explores the statistical dynamics on and of complex networks having relevance across a large number of scientific disciplines. The theories related to complex networks are increasingly being used by researchers for their usefulness in harnessing the most difficult problems of a particular discipline. The book is a collection of surveys and cutting-edge research contributions exploring the interdisciplinary relationship of dynamics on and of complex networks. Towards this goal, the work is thematically organized into three main sections: Part I studies th
Directory of Open Access Journals (Sweden)
Mihailović Dragutin T.
2015-01-01
Full Text Available We propose novel metrics based on the Kolmogorov complexity for use in complex system behavior studies and time series analysis. We consider the origins of the Kolmogorov complexity and discuss its physical meaning. To get better insights into the nature of complex systems and time series analysis we introduce three novel measures based on the Kolmogorov complexity: (i the Kolmogorov complexity spectrum, (ii the Kolmogorov complexity spectrum highest value and (iii the overall Kolmogorov complexity. The characteristics of these measures have been tested using a generalized logistic equation. Finally, the proposed measures have been applied to different time series originating from: a model output (the biochemical substance exchange in a multi-cell system, four different geophysical phenomena (dynamics of: river flow, long term precipitation, indoor 222Rn concentration and UV radiation dose and the economy (stock price dynamics. The results obtained offer deeper insights into the complexity of system dynamics and time series analysis with the proposed complexity measures.
Oliveira, A Sofia F; Baptista, António M; Soares, Cláudio M
2011-08-01
ATP-Binding Cassette transporters are ubiquitous membrane proteins that convert the energy from ATP-binding and hydrolysis into conformational changes of the transmembrane region to allow the translocation of substrates against their concentration gradient. Despite the large amount of structural and biochemical data available for this family, it is still not clear how the energy obtained from ATP hydrolysis in the ATPase domains is "transmitted" to the transmembrane domains. In this work, we focus our attention on the consequences of hydrolysis and inorganic phosphate exit in the maltose uptake system (MalFGK(2)E) from Escherichia coli. The prime goal is to identify and map the structural changes occurring during an ATP-hydrolytic cycle. For that, we use extensive molecular dynamics simulations to study three potential intermediate states (with 10 replicates each): an ATP-bound, an ADP plus inorganic phosphate-bound and an ADP-bound state. Our results show that the residues presenting major rearrangements are located in the A-loop, in the helical sub-domain, and in the "EAA motif" (especially in the "coupling helices" region). Additionally, in one of the simulations with ADP we were able to observe the opening of the NBD dimer accompanied by the dissociation of ADP from the ABC signature motif, but not from its corresponding P-loop motif. This work, together with several other MD studies, suggests a common communication mechanism both for importers and exporters, in which ATP-hydrolysis induces conformational changes in the helical sub-domain region, in turn transferred to the transmembrane domains via the "coupling helices".
Directory of Open Access Journals (Sweden)
A Sofia F Oliveira
2011-08-01
Full Text Available ATP-Binding Cassette transporters are ubiquitous membrane proteins that convert the energy from ATP-binding and hydrolysis into conformational changes of the transmembrane region to allow the translocation of substrates against their concentration gradient. Despite the large amount of structural and biochemical data available for this family, it is still not clear how the energy obtained from ATP hydrolysis in the ATPase domains is "transmitted" to the transmembrane domains. In this work, we focus our attention on the consequences of hydrolysis and inorganic phosphate exit in the maltose uptake system (MalFGK(2E from Escherichia coli. The prime goal is to identify and map the structural changes occurring during an ATP-hydrolytic cycle. For that, we use extensive molecular dynamics simulations to study three potential intermediate states (with 10 replicates each: an ATP-bound, an ADP plus inorganic phosphate-bound and an ADP-bound state. Our results show that the residues presenting major rearrangements are located in the A-loop, in the helical sub-domain, and in the "EAA motif" (especially in the "coupling helices" region. Additionally, in one of the simulations with ADP we were able to observe the opening of the NBD dimer accompanied by the dissociation of ADP from the ABC signature motif, but not from its corresponding P-loop motif. This work, together with several other MD studies, suggests a common communication mechanism both for importers and exporters, in which ATP-hydrolysis induces conformational changes in the helical sub-domain region, in turn transferred to the transmembrane domains via the "coupling helices".
Structural Dynamics of the MecA-ClpC Complex
Liu, Jing; Mei, Ziqing; Li, Ningning; Qi, Yutao; Xu, Yanji; Shi, Yigong; Wang, Feng; Lei, Jianlin; Gao, Ning
2013-01-01
The MecA-ClpC complex is a bacterial type II AAA+ molecular machine responsible for regulated unfolding of substrates, such as transcription factors ComK and ComS, and targeting them to ClpP for degradation. The six subunits of the MecA-ClpC complex form a closed barrel-like structure, featured with three stacked rings and a hollow passage, where substrates are threaded and translocated through successive pores. Although the general concepts of how polypeptides are unfolded and translocated by internal pore loops of AAA+ proteins have long been conceived, the detailed mechanistic model remains elusive. With cryoelectron microscopy, we captured four different structures of the MecA-ClpC complexes. These complexes differ in the nucleotide binding states of the two AAA+ rings and therefore might presumably reflect distinctive, representative snapshots from a dynamic unfolding cycle of this hexameric complex. Structural analysis reveals that nucleotide binding and hydrolysis modulate the hexameric complex in a number of ways, including the opening of the N-terminal ring, the axial and radial positions of pore loops, the compactness of the C-terminal ring, as well as the relative rotation between the two nucleotide-binding domain rings. More importantly, our structural and biochemical data indicate there is an active allosteric communication between the two AAA+ rings and suggest that concerted actions of the two AAA+ rings are required for the efficiency of the substrate unfolding and translocation. These findings provide important mechanistic insights into the dynamic cycle of the MecA-ClpC unfoldase and especially lay a foundation toward the complete understanding of the structural dynamics of the general type II AAA+ hexamers. PMID:23595989
Wake Dynamics in the Atmospheric Boundary Layer Over Complex Terrain
Markfort, Corey D.
The goal of this research is to advance our understanding of atmospheric boundary layer processes over heterogeneous landscapes and complex terrain. The atmospheric boundary layer (ABL) is a relatively thin (˜ 1 km) turbulent layer of air near the earth's surface, in which most human activities and engineered systems are concentrated. Its dynamics are crucially important for biosphere-atmosphere couplings and for global atmospheric dynamics, with significant implications on our ability to predict and mitigate adverse impacts of land use and climate change. In models of the ABL, land surface heterogeneity is typically represented, in the context of Monin-Obukhov similarity theory, as changes in aerodynamic roughness length and surface heat and moisture fluxes. However, many real landscapes are more complex, often leading to massive boundary layer separation and wake turbulence, for which standard models fail. Trees, building clusters, and steep topography produce extensive wake regions currently not accounted for in models of the ABL. Wind turbines and wind farms also generate wakes that combine in complex ways to modify the ABL. Wind farms are covering an increasingly significant area of the globe and the effects of large wind farms must be included in regional and global scale models. Research presented in this thesis demonstrates that wakes caused by landscape heterogeneity must be included in flux parameterizations for momentum, heat, and mass (water vapor and trace gases, e.g. CO2 and CH4) in ABL simulation and prediction models in order to accurately represent land-atmosphere interactions. Accurate representation of these processes is crucial for the predictions of weather, air quality, lake processes, and ecosystems response to climate change. Objectives of the research reported in this thesis are: 1) to investigate turbulent boundary layer adjustment, turbulent transport and scalar flux in wind farms of varying configurations and develop an improved
Life as Complex Systems Viewpoint from Intra-Inter Dynamics
Kaneko, K
1998-01-01
Basic problems in complex systems are surveyed in connection with Life. As a key issue for complex systems, complementarity between syntax/rule/parts and semantics/behavior/whole is stressed. To address the issue, a constructive approach for a biological system is proposed. As a construction in a computer, intra-inter dynamics is presented for cell biology, where the following five general features are drawn from our model experiments; intrinsic diversification, recursive type formation, rule generation, formation of internal representation, and macroscopic robustness. Significance of the constructed logic to the biology of existing organisms is also discussed.
Epitope flexibility and dynamic footprint revealed by molecular dynamics of a pMHC-TCR complex.
Reboul, Cyril F; Meyer, Grischa R; Porebski, Benjamin T; Borg, Natalie A; Buckle, Ashley M
2012-01-01
The crystal structures of unliganded and liganded pMHC molecules provide a structural basis for TCR recognition yet they represent 'snapshots' and offer limited insight into dynamics that may be important for interaction and T cell activation. MHC molecules HLA-B*3501 and HLA-B*3508 both bind a 13 mer viral peptide (LPEP) yet only HLA-B*3508-LPEP induces a CTL response characterised by the dominant TCR clonetype SB27. HLA-B*3508-LPEP forms a tight and long-lived complex with SB27, but the relatively weak interaction between HLA-B*3501-LPEP and SB27 fails to trigger an immune response. HLA-B*3501 and HLA-B*3508 differ by only one amino acid (L/R156) located on α2-helix, but this does not alter the MHC or peptide structure nor does this polymorphic residue interact with the peptide or SB27. In the absence of a structural rationalisation for the differences in TCR engagement we performed a molecular dynamics study of both pMHC complexes and HLA-B*3508-LPEP in complex with SB27. This reveals that the high flexibility of the peptide in HLA-B*3501 compared to HLA-B*3508, which was not apparent in the crystal structure alone, may have an under-appreciated role in SB27 recognition. The TCR pivots atop peptide residues 6-9 and makes transient MHC contacts that extend those observed in the crystal structure. Thus MD offers an insight into 'scanning' mechanism of SB27 that extends the role of the germline encoded CDR2α and CDR2β loops. Our data are consistent with the vast body of experimental observations for the pMHC-LPEP-SB27 interaction and provide additional insights not accessible using crystallography.
Epitope flexibility and dynamic footprint revealed by molecular dynamics of a pMHC-TCR complex.
Directory of Open Access Journals (Sweden)
Cyril F Reboul
Full Text Available The crystal structures of unliganded and liganded pMHC molecules provide a structural basis for TCR recognition yet they represent 'snapshots' and offer limited insight into dynamics that may be important for interaction and T cell activation. MHC molecules HLA-B*3501 and HLA-B*3508 both bind a 13 mer viral peptide (LPEP yet only HLA-B*3508-LPEP induces a CTL response characterised by the dominant TCR clonetype SB27. HLA-B*3508-LPEP forms a tight and long-lived complex with SB27, but the relatively weak interaction between HLA-B*3501-LPEP and SB27 fails to trigger an immune response. HLA-B*3501 and HLA-B*3508 differ by only one amino acid (L/R156 located on α2-helix, but this does not alter the MHC or peptide structure nor does this polymorphic residue interact with the peptide or SB27. In the absence of a structural rationalisation for the differences in TCR engagement we performed a molecular dynamics study of both pMHC complexes and HLA-B*3508-LPEP in complex with SB27. This reveals that the high flexibility of the peptide in HLA-B*3501 compared to HLA-B*3508, which was not apparent in the crystal structure alone, may have an under-appreciated role in SB27 recognition. The TCR pivots atop peptide residues 6-9 and makes transient MHC contacts that extend those observed in the crystal structure. Thus MD offers an insight into 'scanning' mechanism of SB27 that extends the role of the germline encoded CDR2α and CDR2β loops. Our data are consistent with the vast body of experimental observations for the pMHC-LPEP-SB27 interaction and provide additional insights not accessible using crystallography.
Complex chaos in the conditional dynamics of qubits
Kiss, T; Jex, I; Vymetal, S
2005-01-01
We analyse the consequences of measurement induced non-linearity for the dynamical behaviour of qubits. We present a one-qubit scheme where the equation governing the time evolution is a complex nonlinear map with one complex parameter. The map is a rational function of degree two leading to chaotic dynamics of the quantum state, in contrast to the usual notion of quantum chaos. The set of initial values with irregular behavior, the Julia set, has a nontrivial structure depending crucially on the parameter of the map. The family of maps labeled by the parameter can be characterized by the attractive fixed points. Each map with a fixed parameter can have at most two attractive cycles. This type of instability is also present in purification protocols based on conditional non-linear transformations of qubits.
A dynamic epidemic control model on uncorrelated complex networks
Institute of Scientific and Technical Information of China (English)
Pei Wei-Dong; Chen Zeng-Qiang; Yuan Zhu-Zhi
2008-01-01
In this paper,a dynamic epidemic control model on the uncorrelated complex networks is proposed.By means of theoretical analysis,we found that the new model has a similar epidemic threshold as that of the susceptible-infectedrecovered (SIR) model on the above networks,but it can reduce the prevalence of the infected individuals remarkably.This result may help us understand epidemic spreading phenomena on real networks and design appropriate strategies to control infections.
Coupled dark energy: a dynamical analysis with complex scalar field
Energy Technology Data Exchange (ETDEWEB)
Landim, Ricardo C.G. [Universidade de Sao Paulo, Instituto de Fisica, Caixa Postal 66318, Sao Paulo, SP (Brazil)
2016-01-15
The dynamical analysis for coupled dark energy with dark matter is presented, where a complex scalar field is taken into account and it is considered in the presence of a barothropic fluid. We consider three dark-energy candidates: quintessence, phantom, and tachyon. The critical points are found and their stabilities analyzed, leading to the three cosmological eras (radiation, matter, and dark energy), for a generic potential. The results presented here extend the previous analyses found in the literature. (orig.)
Structure and dynamics of small van der Waals complexes
Energy Technology Data Exchange (ETDEWEB)
Loreau, J. [Service de Chimie Quantique et Photophysique, Université Libre de Bruxelles (ULB) CP 160/09, 1050 Brussels (Belgium)
2014-10-06
We illustrate computational aspects of the calculation of the potential energy surfaces of small (up to five atoms) van der Waals complexes with high-level quantum chemistry techniques such as the CCSD(T) method with extended basis sets. We discuss the compromise between the required accuracy and the computational time. Further, we show how these potential energy surfaces can be fitted and used in dynamical calculations such as non-reactive inelastic scattering.
Quantum Sensing of Noisy and Complex Systems under Dynamical Control
Directory of Open Access Journals (Sweden)
Gershon Kurizki
2016-12-01
Full Text Available We review our unified optimized approach to the dynamical control of quantum-probe interactions with noisy and complex systems viewed as thermal baths. We show that this control, in conjunction with tools of quantum estimation theory, may be used for inferring the spectral and spatial characteristics of such baths with high precision. This approach constitutes a new avenue in quantum sensing, dubbed quantum noise spectroscopy.
Dynamic Coherence in Excitonic Molecular Complexes under Various Excitation Conditions
Chenu, Aurélia; Mancal, Tomáš
2013-01-01
In this paper, we investigate the relevance of dynamic electronic coherence under conditions natural to light-harvesting systems. We formulate the results of a quantum mechanical treatment of a weak light-matter interaction in terms of experimental observable, such as the incident light spectrum and the absorption spectrum of the material, and we derive the description of the incoherent F\\"orster type energy transfer fully from the wave function formalism. We demonstrate that excitation of a coherent superposition of electronic eigenstates of natural light-harvesting complexes by sunlight or by excitation transfer from a neighboring antenna is unlikely and that dynamical coherence therefore cannot play any significant role in natural photosynthesis, regardless of their life time. Dynamical coherence as a transient phenomenon must be strictly distinguished from the effect of excited state delocalization (also termed quantum coherence in the literature) which is established by interaction between the pigments a...
Dynamical complexity in the C.elegans neural network
Antonopoulos, C. G.; Fokas, A. S.; Bountis, T. C.
2016-09-01
We model the neuronal circuit of the C.elegans soil worm in terms of a Hindmarsh-Rose system of ordinary differential equations, dividing its circuit into six communities which are determined via the Walktrap and Louvain methods. Using the numerical solution of these equations, we analyze important measures of dynamical complexity, namely synchronicity, the largest Lyapunov exponent, and the ΦAR auto-regressive integrated information theory measure. We show that ΦAR provides a useful measure of the information contained in the C.elegans brain dynamic network. Our analysis reveals that the C.elegans brain dynamic network generates more information than the sum of its constituent parts, and that attains higher levels of integrated information for couplings for which either all its communities are highly synchronized, or there is a mixed state of highly synchronized and desynchronized communities.
Topics in Complexity: Dynamical Patterns in the Cyberworld
Qi, Hong
Quantitative understanding of mechanism in complex systems is a common "difficult" problem across many fields such as physical, biological, social and economic sciences. Investigation on underlying dynamics of complex systems and building individual-based models have recently been fueled by big data resulted from advancing information technology. This thesis investigates complex systems in social science, focusing on civil unrests on streets and relevant activities online. Investigation consists of collecting data of unrests from open digital source, featuring dynamical patterns underlying, making predictions and constructing models. A simple law governing the progress of two-sided confrontations is proposed with data of activities at micro-level. Unraveling the connections between activity of organizing online and outburst of unrests on streets gives rise to a further meso-level pattern of human behavior, through which adversarial groups evolve online and hyper-escalate ahead of real-world uprisings. Based on the patterns found, noticeable improvement of prediction of civil unrests is achieved. Meanwhile, novel model created from combination of mobility dynamics in the cyberworld and a traditional contagion model can better capture the characteristics of modern civil unrests and other contagion-like phenomena than the original one.
Kularathna, M.D.U.P.
1992-01-01
The technique of Stochastic Dynamic Programming (SDP) is ideally suited for operation policy analyses of water resources systems. However SDP has a major drawback which is appropriately termed as its "curse of dimensionality".Aggregation/Disaggregation techniques based on SDP and simulation are pres
Chen, Jinfan; Sit, Patrick H-L
2017-05-11
The catalytic hydrogen-producing processes of two prototypical cobaloxime catalysts, Co(dmgBF2)2 (dmgBF2 = difluoroboryl-dimethylglyoxime) and Co(dmgH)2 (dmgH = dimethylglyoxime), were studied by density functional theory (DFT) and Car-Parrinello molecular dynamics (CPMD) simulations in the explicit acetonitrile-water solvent. Our study demonstrates the key role of water molecules as shuttles to deliver protons to the cobalt active centers of these catalysts. However, the transfer of protons to the cobalt centers also competes with the diffusion of the proton away from the complex via the hydrogen bond network of water. Protons were found to react with the oxygen of the side group of Co(dmgH)2, while a similar reaction was not observed for Co(dmgBF2)2. This explains the experimentally observed relative instability of Co(dmgH)2 in the acidic medium. The rate-limiting step of the hydrogen-producing process was found to be the first proton transfer to the cobalt center for both cobaloxime complexes. Structural and electron population analysis was carried out to provide insight into the origin of the difference of the proton transfer free-energy barriers of these two cobalt complexes. Our study has contributed to the key microscopic understanding of the hydrogen-producing process by this class of catalysts.
VUV studies of molecular photofragmentation dynamics
Energy Technology Data Exchange (ETDEWEB)
White, M.G. [Brookhaven National Laboratory, Upton, NY (United States)
1993-12-01
State-resolved, photoion and photoelectron methods are used to study the neutral fragmentation and ionization dynamics of small molecules relevant to atmospheric and combustion chemistry. Photodissociation and ionization are initiated by coherent VUV radiation and the fragmentation dynamics are extracted from measurements of product rovibronic state distributions, kinetic energies and angular distributions. The general aim of these studies is to investigate the multichannel interactions between the electronic and nuclear motions which determine the evolution of the photoexcited {open_quotes}complex{close_quotes} into the observed asymptotic channels.
Universality of flux-fluctuation law in complex dynamical systems
Zhou, Zhao; Huang, Zi-Gang; Huang, Liang; Lai, Ying-Cheng; Yang, Lei; Xue, De-Sheng
2013-01-01
Recent work has revealed a law governing flux fluctuation and the average flux in complex dynamical systems. We establish the universality of this flux-fluctuation law through the following steps: (i) We derive the law in a more general setting, showing that it depends on a single parameter characterizing the external driving; (ii) we conduct extensive numerical computations using distinct external driving, different network topologies, and multiple traffic routing strategies; and (iii) we analyze data from an actual vehicle traffic system in a major city in China to lend more credence to the universality of the flux-fluctuation law. Additional factors considered include flux fluctuation on links, window size effect, and hidden topological structures such as nodal degree correlation. Besides its fundamental importance in complex systems, the flux-fluctuation law can be used to infer certain intrinsic property of the system for potential applications such as control of complex systems for improved performance.
Proofreading of Peptide-MHC Complexes through Dynamic Multivalent Interactions.
Thomas, Christoph; Tampé, Robert
2017-01-01
The adaptive immune system is able to detect and destroy cells that are malignantly transformed or infected by intracellular pathogens. Specific immune responses against these cells are elicited by antigenic peptides that are presented on major histocompatibility complex class I (MHC I) molecules and recognized by cytotoxic T lymphocytes at the cell surface. Since these MHC I-presented peptides are generated in the cytosol by proteasomal protein degradation, they can be metaphorically described as a window providing immune cells with insights into the state of the cellular proteome. A crucial element of MHC I antigen presentation is the peptide-loading complex (PLC), a multisubunit machinery, which contains as key constituents the transporter associated with antigen processing (TAP) and the MHC I-specific chaperone tapasin (Tsn). While TAP recognizes and shuttles the cytosolic antigenic peptides into the endoplasmic reticulum (ER), Tsn samples peptides in the ER for their ability to form stable complexes with MHC I, a process called peptide proofreading or peptide editing. Through its selection of peptides that improve MHC I stability, Tsn contributes to the hierarchy of immunodominant peptide epitopes. Despite the fact that it concerns a key event in adaptive immunity, insights into the catalytic mechanism of peptide proofreading carried out by Tsn have only lately been gained via biochemical, biophysical, and structural studies. Furthermore, a Tsn homolog called TAP-binding protein-related (TAPBPR) has only recently been demonstrated to function as a second MHC I-specific chaperone and peptide proofreader. Although TAPBPR is PLC-independent and has a distinct allomorph specificity, it is likely to share a common catalytic mechanism with Tsn. This review focuses on the current knowledge of the multivalent protein-protein interactions and the concomitant dynamic molecular processes underlying peptide-proofreading catalysis. We do not only derive a model that
Proofreading of Peptide—MHC Complexes through Dynamic Multivalent Interactions
Thomas, Christoph; Tampé, Robert
2017-01-01
The adaptive immune system is able to detect and destroy cells that are malignantly transformed or infected by intracellular pathogens. Specific immune responses against these cells are elicited by antigenic peptides that are presented on major histocompatibility complex class I (MHC I) molecules and recognized by cytotoxic T lymphocytes at the cell surface. Since these MHC I-presented peptides are generated in the cytosol by proteasomal protein degradation, they can be metaphorically described as a window providing immune cells with insights into the state of the cellular proteome. A crucial element of MHC I antigen presentation is the peptide-loading complex (PLC), a multisubunit machinery, which contains as key constituents the transporter associated with antigen processing (TAP) and the MHC I-specific chaperone tapasin (Tsn). While TAP recognizes and shuttles the cytosolic antigenic peptides into the endoplasmic reticulum (ER), Tsn samples peptides in the ER for their ability to form stable complexes with MHC I, a process called peptide proofreading or peptide editing. Through its selection of peptides that improve MHC I stability, Tsn contributes to the hierarchy of immunodominant peptide epitopes. Despite the fact that it concerns a key event in adaptive immunity, insights into the catalytic mechanism of peptide proofreading carried out by Tsn have only lately been gained via biochemical, biophysical, and structural studies. Furthermore, a Tsn homolog called TAP-binding protein-related (TAPBPR) has only recently been demonstrated to function as a second MHC I-specific chaperone and peptide proofreader. Although TAPBPR is PLC-independent and has a distinct allomorph specificity, it is likely to share a common catalytic mechanism with Tsn. This review focuses on the current knowledge of the multivalent protein–protein interactions and the concomitant dynamic molecular processes underlying peptide-proofreading catalysis. We do not only derive a model that
Directory of Open Access Journals (Sweden)
Anand Swadha
2012-05-01
Full Text Available Abstract Background Modular polyketide synthases are multifunctional megasynthases which biosynthesize a variety of secondary metabolites using various combinations of dehydratase (DH, ketoreductase (KR and enoyl-reductase (ER domains. During the catalysis of various reductive steps these domains act on a substrate moiety which is covalently attached to the phosphopantetheine (P-pant group of the holo-Acyl Carrier Protein (holo-ACP domain, thus necessitating the formation of holo-ACP:DH and holo-ACP:KR complexes. Even though three dimensional structures are available for DH, KR and ACP domains, no structures are available for DH or KR domains in complex with ACP or substrate moieties. Since Ser of holo-ACP is covalently attached to a large phosphopantetheine group, obtaining complexes involving holo-ACP by standard protein-protein docking has been a difficult task. Results We have modeled the holo-ACP:DH and holo-ACP:KR complexes for identifying specific residues on DH and KR domains which are involved in interaction with ACP, phosphopantetheine and substrate moiety. A novel combination of protein-protein and protein-ligand docking has been used to first model complexes involving apo-ACP and then dock the phosphopantetheine and substrate moieties using covalent connectivity between ACP, phosphopantetheine and substrate moiety as constraints. The holo-ACP:DH and holo-ACP:KR complexes obtained from docking have been further refined by restraint free explicit solvent MD simulations to incorporate effects of ligand and receptor flexibilities. The results from 50 ns MD simulations reveal that substrate enters into a deep tunnel in DH domain while in case of KR domain the substrate binds a shallow surface exposed cavity. Interestingly, in case of DH domain the predicted binding site overlapped with the binding site in the inhibitor bound crystal structure of FabZ, the DH domain from E.Coli FAS. In case of KR domain, the substrate binding site
Modularity and the spread of perturbations in complex dynamical systems
Kolchinsky, Artemy; Gates, Alexander J.; Rocha, Luis M.
2015-12-01
We propose a method to decompose dynamical systems based on the idea that modules constrain the spread of perturbations. We find partitions of system variables that maximize "perturbation modularity," defined as the autocovariance of coarse-grained perturbed trajectories. The measure effectively separates the fast intramodular from the slow intermodular dynamics of perturbation spreading (in this respect, it is a generalization of the "Markov stability" method of network community detection). Our approach captures variation of modular organization across different system states, time scales, and in response to different kinds of perturbations: aspects of modularity which are all relevant to real-world dynamical systems. It offers a principled alternative to detecting communities in networks of statistical dependencies between system variables (e.g., "relevance networks" or "functional networks"). Using coupled logistic maps, we demonstrate that the method uncovers hierarchical modular organization planted in a system's coupling matrix. Additionally, in homogeneously coupled map lattices, it identifies the presence of self-organized modularity that depends on the initial state, dynamical parameters, and type of perturbations. Our approach offers a powerful tool for exploring the modular organization of complex dynamical systems.
Self-organization of complex networks as a dynamical system
Aoki, Takaaki; Yawata, Koichiro; Aoyagi, Toshio
2015-01-01
To understand the dynamics of real-world networks, we investigate a mathematical model of the interplay between the dynamics of random walkers on a weighted network and the link weights driven by a resource carried by the walkers. Our numerical studies reveal that, under suitable conditions, the co-evolving dynamics lead to the emergence of stationary power-law distributions of the resource and link weights, while the resource quantity at each node ceaselessly changes with time. We analyze the network organization as a deterministic dynamical system and find that the system exhibits multistability, with numerous fixed points, limit cycles, and chaotic states. The chaotic behavior of the system leads to the continual changes in the microscopic network dynamics in the absence of any external random noises. We conclude that the intrinsic interplay between the states of the nodes and network reformation constitutes a major factor in the vicissitudes of real-world networks.
Slow dynamics in a quasi-two-dimensional binary complex plasma
Du, Cheng-Ran; Thomas, Hubertus M; Morfill, Gregor E; Ivlev, Alexei V
2016-01-01
Slow dynamics in an amorphous quasi-two-dimensional complex plasma, comprised of microparticles of two different sizes, was studied experimentally. The motion of individual particles was observed using video microscopy, and the self part of the intermediate scattering function as well as the mean-squared particle displacement was calculated. The long-time structural relaxation reveals the characteristic behavior near the glass transition. Our results suggest that binary complex plasmas can be an excellent model system to study slow dynamics in classical supercooled fluids.
Thinking in complexity the complex dynamics of matter, mind, and mankind
Mainzer, Klaus
1994-01-01
The theory of nonlinear complex systems has become a successful and widely used problem-solving approach in the natural sciences - from laser physics, quantum chaos and meteorology to molecular modeling in chemistry and computer simulations of cell growth in biology In recent times it has been recognized that many of the social, ecological and political problems of mankind are also of a global, complex and nonlinear nature And one of the most exciting topics of present scientific and public interest is the idea that even the human mind is governed largely by the nonlinear dynamics of complex systems In this wide-ranging but concise treatment Prof Mainzer discusses, in nontechnical language, the common framework behind these endeavours Special emphasis is given to the evolution of new structures in natural and cultural systems and it is seen clearly how the new integrative approach of complexity theory can give new insights that were not available using traditional reductionistic methods
Macroscopic description of complex adaptive networks co-evolving with dynamic node states
Wiedermann, Marc; Heitzig, Jobst; Lucht, Wolfgang; Kurths, Jürgen
2015-01-01
In many real-world complex systems, the time-evolution of the network's structure and the dynamic state of its nodes are closely entangled. Here, we study opinion formation and imitation on an adaptive complex network which is dependent on the individual dynamic state of each node and vice versa to model the co-evolution of renewable resources with the dynamics of harvesting agents on a social network. The adaptive voter model is coupled to a set of identical logistic growth models and we show that in such systems, the rate of interactions between nodes as well as the adaptive rewiring probability play a crucial role for the sustainability of the system's equilibrium state. We derive a macroscopic description of the system which provides a general framework to model and quantify the influence of single node dynamics on the macroscopic state of the network and is applicable to many fields of study, such as epidemic spreading or social modeling.
Studying Dynamics in Business Networks
DEFF Research Database (Denmark)
Andersen, Poul Houman; Anderson, Helen; Havila, Virpi;
1998-01-01
This paper develops a theory on network dynamics using the concepts of role and position from sociological theory. Moreover, the theory is further tested using case studies from Denmark and Finland...
Outlier-resilient complexity analysis of heartbeat dynamics
Lo, Men-Tzung; Chang, Yi-Chung; Lin, Chen; Young, Hsu-Wen Vincent; Lin, Yen-Hung; Ho, Yi-Lwun; Peng, Chung-Kang; Hu, Kun
2015-03-01
Complexity in physiological outputs is believed to be a hallmark of healthy physiological control. How to accurately quantify the degree of complexity in physiological signals with outliers remains a major barrier for translating this novel concept of nonlinear dynamic theory to clinical practice. Here we propose a new approach to estimate the complexity in a signal by analyzing the irregularity of the sign time series of its coarse-grained time series at different time scales. Using surrogate data, we show that the method can reliably assess the complexity in noisy data while being highly resilient to outliers. We further apply this method to the analysis of human heartbeat recordings. Without removing any outliers due to ectopic beats, the method is able to detect a degradation of cardiac control in patients with congestive heart failure and a more degradation in critically ill patients whose life continuation relies on extracorporeal membrane oxygenator (ECMO). Moreover, the derived complexity measures can predict the mortality of ECMO patients. These results indicate that the proposed method may serve as a promising tool for monitoring cardiac function of patients in clinical settings.
Precise regulation of gene expression dynamics favors complex promoter architectures.
Directory of Open Access Journals (Sweden)
Dirk Müller
2009-01-01
Full Text Available Promoters process signals through recruitment of transcription factors and RNA polymerase, and dynamic changes in promoter activity constitute a major noise source in gene expression. However, it is barely understood how complex promoter architectures determine key features of promoter dynamics. Here, we employ prototypical promoters of yeast ribosomal protein genes as well as simplified versions thereof to analyze the relations among promoter design, complexity, and function. These promoters combine the action of a general regulatory factor with that of specific transcription factors, a common motif of many eukaryotic promoters. By comprehensively analyzing stationary and dynamic promoter properties, this model-based approach enables us to pinpoint the structural characteristics underlying the observed behavior. Functional tradeoffs impose constraints on the promoter architecture of ribosomal protein genes. We find that a stable scaffold in the natural design results in low transcriptional noise and strong co-regulation of target genes in the presence of gene silencing. This configuration also exhibits superior shut-off properties, and it can serve as a tunable switch in living cells. Model validation with independent experimental data suggests that the models are sufficiently realistic. When combined, our results offer a mechanistic explanation for why specific factors are associated with low protein noise in vivo. Many of these findings hold for a broad range of model parameters and likely apply to other eukaryotic promoters of similar structure.
Clustering determines the dynamics of complex contagions in multiplex networks
Zhuang, Yong; Arenas, Alex; Yaǧan, Osman
2017-01-01
We present the mathematical analysis of generalized complex contagions in a class of clustered multiplex networks. The model is intended to understand spread of influence, or any other spreading process implying a threshold dynamics, in setups of interconnected networks with significant clustering. The contagion is assumed to be general enough to account for a content-dependent linear threshold model, where each link type has a different weight (for spreading influence) that may depend on the content (e.g., product, rumor, political view) that is being spread. Using the generating functions formalism, we determine the conditions, probability, and expected size of the emergent global cascades. This analysis provides a generalization of previous approaches and is especially useful in problems related to spreading and percolation. The results present nontrivial dependencies between the clustering coefficient of the networks and its average degree. In particular, several phase transitions are shown to occur depending on these descriptors. Generally speaking, our findings reveal that increasing clustering decreases the probability of having global cascades and their size, however, this tendency changes with the average degree. There exists a certain average degree from which on clustering favors the probability and size of the contagion. By comparing the dynamics of complex contagions over multiplex networks and their monoplex projections, we demonstrate that ignoring link types and aggregating network layers may lead to inaccurate conclusions about contagion dynamics, particularly when the correlation of degrees between layers is high.
Complex coacervation: A field theoretic simulation study of polyelectrolyte complexation
Lee, Jonghoon; Popov, Yuri O.; Fredrickson, Glenn H.
2008-06-01
Using the complex Langevin sampling strategy, field theoretic simulations are performed to study the equilibrium phase behavior and structure of symmetric polycation-polyanion mixtures without salt in good solvents. Static structure factors for the segment density and charge density are calculated and used to study the role of fluctuations in the electrostatic and chemical potential fields beyond the random phase approximation. We specifically focus on the role of charge density and molecular weight on the structure and complexation behavior of polycation-polyanion solutions. A demixing phase transition to form a ``complex coacervate'' is observed in strongly charged systems, and the corresponding spinodal and binodal boundaries of the phase diagram are investigated.
Chiu, Chih-Chung; Hung, Chih-Chang; Cheng, Po-Yuan
2016-12-08
The charge-transfer (CT) state relaxation dynamics of the binary (1:1) and ternary (2:1) benzene/tetracyanoethylene (BZ/TCNE) complexes are reported. Steady-state and ultrafast time-resolved broadband fluorescence (TRFL) spectra of TCNE dissolved in a series of BZ/CCl4 mixed solvents are measured to elucidate the spectroscopic properties of the BZ/TCNE complexes and their CT-state relaxation dynamics. Both steady-state and TRFL spectra exhibit marked BZ concentration dependences, which can be attributed to the formation of two types of 2:1 complexes in the ground and excited states. By combining with the density functional theory (DFT) calculations, it was concluded that the BZ concentration dependence of the absorption spectra is mainly due to the formation and excitation of the sandwich-type 2:1 ternary complexes, whereas the changes in fluorescence spectra at high BZ concentrations are due to the formation of the asymmetric-type 2:1 ternary complex CT1 state. A unified mechanism involving both direct excitation and secondary formation of the 2:1 complexes CT states are proposed to account for the observations. The equilibrium charge recombination (CR) time constant of the 1:1 CT1 state is determined to be ∼150 ps in CCl4, whereas that of the 2:1 DDA-type CT1 state becomes ∼70 ps in 10% BZ/CCl4 and ∼34 ps in pure BZ. The CR rates and the CT1-S0 energy gap of these complexes in different solvents exhibit a correlation conforming to the Marcus inverted region. It is concluded that partial charge resonance occurring between the two adjacent BZs in the asymmetric-type 2:1 CT1-state reduces the CR reaction exothermicity and increases the CR rate.
Without bounds a scientific canvas of nonlinearity and complex dynamics
Ryazantsev, Yuri; Starov, Victor; Huang, Guo-Xiang; Chetverikov, Alexander; Arena, Paolo; Nepomnyashchy, Alex; Ferrus, Alberto; Morozov, Eugene
2013-01-01
Bringing together over fifty contributions on all aspects of nonlinear and complex dynamics, this impressive topical collection is both a scientific and personal tribute, on the occasion of his 70th birthday, by many outstanding colleagues in the broad fields of research pursued by Prof. Manuel G Velarde. The topics selected reflect the research areas covered by the famous Instituto Pluridisciplinar at the Universidad Complutense of Madrid, which he co-founded over two decades ago, and include: fluid physics and related nonlinear phenomena at interfaces and in other geometries, wetting and spreading dynamics, geophysical and astrophysical flows, and novel aspects of electronic transport in anharmonic lattices, as well as topics in neurodynamics and robotics.
Complex-Dynamical Approach to Cosmological Problem Solution
Kirilyuk, A P
2005-01-01
Universe structure emerges in the unreduced, complex-dynamic interaction process with the simplest initial configuration (two attracting homogeneous fields). The unreduced interaction analysis, avoiding any perturbative model, gives intrinsically creative cosmology describing the real, explicitly emerging world structure with dynamic randomness on each scale. Without imposing any postulates or additional entities, we obtain physically real, three-dimensional space, irreversibly flowing time, elementary particles with their detailed structure and intrinsic properties, causally complete and unified version of quantum and relativistic behaviour, the origin and number of naturally unified fundamental forces, classical behaviour emergence in a closed system, and true quantum chaos. Major problems of standard cosmology and astrophysics are consistently solved in this extended picture, including those of quantum cosmology and gravity, entropy growth and time arrow, "hierarchy" of elementary particles (Planckian unit...
Hash function construction using weighted complex dynamical networks
Institute of Scientific and Technical Information of China (English)
Song Yu-Rong; Jiang Guo-Ping
2013-01-01
A novel scheme to construct a hash function based on a weighted complex dynamical network (WCDN) generated from an original message is proposed in this paper.First,the original message is divided into blocks.Then,each block is divided into components,and the nodes and weighted edges are well defined from these components and their relations.Namely,the WCDN closely related to the original message is established.Furthermore,the node dynamics of the WCDN are chosen as a chaotic map.After chaotic iterations,quantization and exclusive-or operations,the fixed-length hash value is obtained.This scheme has the property that any tiny change in message can be diffused rapidly through the WCDN,leading to very different hash values.Analysis and simulation show that the scheme possesses good statistical properties,excellent confusion and diffusion,strong collision resistance and high efficiency.
Clustering determines the dynamics of complex contagions in multiplex networks
Zhuang, Yong; Yağan, Osman
2016-01-01
We present the mathematical analysis of generalized complex contagions in clustered multiplex networks for susceptible-infected-recovered (SIR)-like dynamics. The model is intended to understand diffusion of influence, or any other spreading process implying a threshold dynamics, in setups of interconnected networks with significant clustering. The contagion is assumed to be general enough to account for a content-dependent linear threshold model, where each link type has a different weight (for spreading influence) that may depend on the content (e.g., product, rumor, political view) that is being spread. Using the generating functions formalism, we determine the conditions, probability, and expected size of the emergent global cascades. This analysis provides a generalization of previous approaches and is specially useful in problems related to spreading and percolation. The results present non trivial dependencies between the clustering coefficient of the networks and its average degree. In particular, sev...
Klemm, Konstantin; Eguiluz, Victor M; Miguel, Maxi San
2010-01-01
Identifying key players in complex networks remains a challenge affecting a great variety of research fields, from the efficient dissemination of ideas to drug target discovery in biomedical problems. The difficulty lies at several levels: how to single out the role of individual elements in such intermingled systems, or which is the best way to quantify their importance. Centrality measures aim at capturing the influence of a node from its position in a network. The key issue obviated is that the contribution of a node to the collective behaviour is not uniquely determined by the structure of the system but a result of both dynamics and network structure. Here we define dynamical influence as an explicit measure of how strongly a node's dynamical state affects collective behavior. Influence is derived analytically for dissipative processes in complex networks, directed or undirected. We show that it quantifies precisely how efficiently real systems may be driven by manipulating the state of single nodes. It ...
Mihailovic, Dragutin T; Nikolic-Djoric, Emilija; Arsenic, Ilija
2013-01-01
We have proposed novel measures based on the Kolmogorov complexity for use in complex system behavior studies and time series analysis. We have considered background of the Kolmogorov complexity and also we have discussed meaning of the physical as well as other complexities. To get better insights into the complexity of complex systems and time series analysis we have introduced the three novel measures based on the Kolmogorov complexity: (i) the Kolmogorov complexity spectrum, (ii) the Kolmogorov complexity spectrum highest value and (iii) the overall Kolmogorov complexity. The characteristics of these measures have been tested using a generalized logistic equation. Finally, the proposed measures have been applied on different time series originating from: the model output (the biochemical substance exchange in a multi-cell system), four different geophysical phenomena (dynamics of: river flow, long term precipitation, indoor 222Rn concentration and UV radiation dose) and economy (stock prices dynamics). Re...
Dynamic behavior and complexity of modulated optical micro ring resonator
Institute of Scientific and Technical Information of China (English)
Lei Yang; Wei Pan; Bin Luo; ShuiYing Xiang; Ning Jiang
2011-01-01
@@ The dynamic behavior of an optical micro ring resonator (OMRR) with an amplitude modulator positioned in the micro ring is investigated quantitatively by adopting a recently introduced quantifier, the permutation entropy (PE).The effects of modulation depth are focused on, and the roles of input power are considered.The two-dimensional (2D) maps of PE showing dependence on both modulation depth and input power are presented as well.PE values nearly increase with modulation depth.On the other hand, the optimal value of input power is achieved when the PE reaches its maximum.Thus, PE can successfully quantify the dynamics of modulated OMRR.Selecting the parameters in the region with high PE values would contribute to the complexity-enhanced OMRR-based chaotic communication systems.%The dynamic behavior of an optical micro ring resonator (OMRR) with an amplitude modulator positioned in the micro ring is investigated quantitatively by adopting a recently introduced quantifier, the permutation entropy (PE). The effects of modulation depth are focused on, and the roles of input power are considered. The two-dimensional (2D) maps of PE showing dependence on both modulation depth and input power are presented as well. PE values nearly increase with modulation depth. On the other hand, the optimal value of input power is achieved when the PE reaches its maximum. Thus, PE can successfully quantify the dynamics of modulated OMRR. Selecting the parameters in the region with high PE values would contribute to the complexity-enhanced OMRR-based chaotic communication systems.
WATERWAVES: wave particles dynamics on a complex triatomic potential
Taioli, Simone; Tennyson, Jonathan
2006-07-01
The WATERWAVES program suite performs complex scattering calculations by propagating a wave packet in a complex, full-dimensional potential for non-rotating ( J=0) but vibrating triatomic molecules. Potential energy and decay probability surfaces must be provided. Expectation values of geometric quantities can be calculated, which are useful for following the wave packet motion. The programs use a local complex potential approximation (LCP) for the Hamiltonian and Jacobi coordinates. The bottleneck of the calculation is the application of each term of the Hamiltonian to the wave packet. To solve this problem the programs use a different representation for each term: normalized associated Legendre polynomials PjK(x) as a functional basis for the angular kinetic term and an evenly spaced grid for the radial kinetic term yielding a fully point-wise representation of the wave functions. The potential term is treated using an efficient Discrete Variable Representation (DVR) being diagonal in the coordinate representation. The radial kinetic term uses a fast Fourier transform (FFT) to obtain an operator which is diagonal in the momentum space. To avoid artificial reflection at the boundaries of the grid a complex absorbing potential is included for calculating continuum quantities. Asymptotic analysis is performed to obtain scattering observables such as cross sections and other dynamical properties. Program summaryProgram title: WATERWAVES Catalogue identifier:ADXT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXT_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: Freely available from CPC Programming language: Fortran 77 Computer(s) for which the program has been designed: PC Operating system(s) for which the program has been designed: Linux RAM required to execute with typical data: case dependent: test run requires 976 024 kB No. of bytes in distributed program, including test data, etc.:11
Synchronization and Bifurcation of General Complex Dynamical Networks
Institute of Scientific and Technical Information of China (English)
SUN Wei-Gang; XU Cong-Xiang; LI Chang-Pin; FANG Jin-Qing
2007-01-01
In the present paper, synchronization and bifurcation of general complex dynamical networks are investigated. We mainly focus on networks with a somewhat general coupling matrix, i.e., the sum of each row equals a nonzero constant u. We derive a result that the networks can reach a new synchronous state, which is not the asymptotic limit set determined by the node equation. At the synchronous state, the networks appear bifurcation if we regard the constant u as a bifurcation parameter. Numerical examples are given to illustrate our derived conclusions.
Metcalf, K.; Kapp, P. A.; Orme, D. A.
2015-12-01
Intra-continental sutures are the geologic record of ancient subduction zones. Subduction complexes are a useful record of ancient continental collisions because they preserve sediments and/or blocks from units which have since eroded and are the first point of contact during collision. The India-Asia collision is one of the most-studied collisional orogens, but how much of the original subduction complex is preserved and what we can determine about the dynamics of the ancient subduction zone along the southern margin of Asia is poorly understood. Compared to other subduction complexes around the world, the complex preserved in the Indus Yarlung Suture Zone (IYSZ) of southern Tibet is anomalous. Blueschist facies metamorphism, a prominent mineral assemblage along intra-continental suture zones, is common in the northwest Himalaya, but not found along the central segment of the IYSZ. Most of the subduction complex is greenschist facies, inconsistent with the geotherm for a subduction zone. We present a metamorphic history for the greenschist facies rocks to reconcile this contradiction. A deep forearc basin (~5-8 km) developed during the Cretaceous, requiring an accretionary subduction zone, a topographic or structural outer forearc high behind which to trap sediment, and/or basal subduction erosion. The preserved subduction complex is almost entirely tectonic sedimentary-matrix mélange with minor outcrops of overlying turbidites. We present evidence from detrital zircon U-Pb geochronology of sandstones that indicate along-strike variability in the provenance of the sedimentary-matrix mélange. For example, both lower and upper plate material are present near the town of Ngamring, while regions along-strike to the west contain little to no upper plate material. The blocks in the sedimentary-matrix mélange are well-mixed throughout kilometers of exposed width. Sandstone blocks of Tethyan affinity, which could have entered the trench only at the onset of collision
Pinning control of a generalized complex dynamical network model
Institute of Scientific and Technical Information of China (English)
Huizhong YANG; Li SHENG
2009-01-01
This paper investigates the local and global synchronization of a generalized complex dynamical network model with constant and delayed coupling.Without assuming symmetry of the couplings,we proved that a single controller can pin the generalized complex network to a homogenous solution.Some previous synchronization results are generalized.In this paper,we first discuss how to pin an array of delayed neural networks to the synchronous solution by adding only one controller.Next,by using the Lyapunov functional method,some sufficient conditions are derived for the local and global synchronization of the coupled systems.The obtained results are expressed in terms of LMIs,which can be efficiently checked by the Matlab LMI toolbox.Finally,an example is given to illustrate the theoretical results.
Dynamic of astrophysical jets in the complex octonion space
Weng, Zi-Hua
2015-01-01
The paper aims to consider the strength gradient force as the dynamic of astrophysical jets, explaining the movement phenomena of astrophysical jets. J. C. Maxwell applied the quaternion analysis to describe the electromagnetic theory. This encourages others to adopt the complex quaternion and octonion to depict the electromagnetic and gravitational theories. In the complex octonion space, it is capable of deducing the field potential, field strength, field source, angular momentum, torque, force and so forth. As one component of the force, the strength gradient force relates to the gradient of the norm of field strength only, and is independent of not only the direction of field strength but also the mass and electric charge for the test particle. When the strength gradient force is considered as the thrust of the astrophysical jets, one can deduce some movement features of astrophysical jets, including the bipolarity, matter ingredient, precession, symmetric distribution, emitting, collimation, stability, c...
Control of complex dynamics and chaos in distributed parameter systems
Energy Technology Data Exchange (ETDEWEB)
Chakravarti, S.; Marek, M.; Ray, W.H. [Univ. of Wisconsin, Madison, WI (United States)
1995-12-31
This paper discusses a methodology for controlling complex dynamics and chaos in distributed parameter systems. The reaction-diffusion system with Brusselator kinetics, where the torus-doubling or quasi-periodic (two characteristic incommensurate frequencies) route to chaos exists in a defined range of parameter values, is used as an example. Poincare maps are used for characterization of quasi-periodic and chaotic attractors. The dominant modes or topos, which are inherent properties of the system, are identified by means of the Singular Value Decomposition. Tested modal feedback control schemas based on identified dominant spatial modes confirm the possibility of stabilization of simple quasi-periodic trajectories in the complex quasi-periodic or chaotic spatiotemporal patterns.
Institute of Scientific and Technical Information of China (English)
刘赟
2013-01-01
本文立足于动态视角对组织复杂性的管理展开研究，进而提出了包括动态要素、实施模型和成功要素的组织复杂性动态管理的逻辑框架。以格力电器为案例，基于逻辑框架，阶段性地描述格力电器组织复杂性动态管理的过程，分析动态要素、实施模型以评价其组织复杂性管理的有效性。%The study on the management of organizational complexity in this paper is carried out from the dynamic perspective, and the logic framework of dynamically managing organizational complexity which includes the dynamic factors, executive models and successful factors is put forward. Taking GREE ELECTRIC APPLIANCES as the case and based on the logic framework, a deep analysis by period is made on the process of GREE's dynamic management of organizational complexity, the dynamic factors and executive models. The effectiveness of GREE's managing organizational complexity is also evaluated.
Investigation of Plasmas Having Complex, Dynamic Evolving Morphology
Energy Technology Data Exchange (ETDEWEB)
Bellan, Paul M. [California Inst. of Technology (CalTech), Pasadena, CA (United States)
2017-01-03
Three different types of plasmas have been investigated using both experimental and theoretical methods. The first type of plasma is dense, highly ionized, governed by magnetohydrodynamics, and highly dynamic. This plasma is relevant to solar coronal loops, astrophysical jets, and other situations where strong magnetic forces act on the plasma. A well-diagnosed laboratory experiment creates a magnetohydrodynamically driven highly collimated plasma jet. This jet undergoes a kink instability such that it rapidly develops a corkscrew shape. The kink causes lateral acceleration of the jet, and this lateral acceleration drives a Rayleigh-Taylor instability that in turn chokes the current flowing in the jet and causes a magnetic reconnection. The magnetic reconnection causes electron and ion heating as well as emission of whistler waves. This entire sequence of events has been observed, measured in detail, and related to theoretical models. The second type of plasma is a transient rf-produced plasma used as a seed plasma for the magnetohydrodynamic experiments described above. Detailed atomic physics ionization processes have been investigated and modeled. The third type of plasma that has been studied is a dusty plasma where the dust particles are spontaneously growing ice grains. The rapid growth of the ice grains to large size and their highly ordered alignment has been investigated as well as collective motion of the ice grains, including well-defined flows on the surface of nested toroids. In addition to the experimental work described above, several related theoretical models have been developed, most notably a model showing how a complex interaction between gravity and magnetic fields on extremely weakly ionized plasma in an accretion disk provides an electric power source that can drive astrophysical jets associated with the accretion disk. Eighteen papers reporting this work have been published in a wide variety of journals.
Enhanced dynamic complexity in the human EEG during creative thinking.
Mölle, M; Marshall, L; Lutzenberger, W; Pietrowsky, R; Fehm, H L; Born, J
1996-04-12
This study shows that divergent thinking, considered the general process underlying creative production, can be distinguished from convergent, analytical thought based on the dimensional complexity of ongoing electroencephalographic (EEG) activity. EEG complexity over the central and posterior cortex was higher while subjects solved tasks of divergent than convergent thinking, and also higher than during mental relaxation. Over the frontal cortex, EEG complexity was comparable during divergent thinking and mental relaxation, but reduced during convergent thinking. Results indicate that the basic process underlying the generation of novel ideas expresses itself in a strong increase in the EEG's complexity, reflecting higher degrees of freedom in the competitive interactions among cortical neuron assemblies. Frontocortical EEG complexity being comparable with that during mental relaxation, speaks for a loosened attentional control during creative thinking.
Computational complexity of ecological and evolutionary spatial dynamics.
Ibsen-Jensen, Rasmus; Chatterjee, Krishnendu; Nowak, Martin A
2015-12-22
There are deep, yet largely unexplored, connections between computer science and biology. Both disciplines examine how information proliferates in time and space. Central results in computer science describe the complexity of algorithms that solve certain classes of problems. An algorithm is deemed efficient if it can solve a problem in polynomial time, which means the running time of the algorithm is a polynomial function of the length of the input. There are classes of harder problems for which the fastest possible algorithm requires exponential time. Another criterion is the space requirement of the algorithm. There is a crucial distinction between algorithms that can find a solution, verify a solution, or list several distinct solutions in given time and space. The complexity hierarchy that is generated in this way is the foundation of theoretical computer science. Precise complexity results can be notoriously difficult. The famous question whether polynomial time equals nondeterministic polynomial time (i.e., P = NP) is one of the hardest open problems in computer science and all of mathematics. Here, we consider simple processes of ecological and evolutionary spatial dynamics. The basic question is: What is the probability that a new invader (or a new mutant) will take over a resident population? We derive precise complexity results for a variety of scenarios. We therefore show that some fundamental questions in this area cannot be answered by simple equations (assuming that P is not equal to NP).
Thresholds and Complex Dynamics of Interdependent Cascading Infrastructure Systems
Carreras, B. A.; Newman, D. E.; Dobson, I.; Lynch, V. E.; Gradney, Paul
Critical infrastructures have a number of the characteristic properties of complex systems. Among these are infrequent large failures through cascading events. These events, though infrequent, often obey a power law distribution in their probability versus size which suggests that conventional risk analysis does not apply to these systems. Real infrastructure systems typically have an additional layer of complexity, namely the heterogeneous coupling to other infrastructure systems that can allow a failure in one system to propagate to the other system. Here, we model the infrastructure systems through a network with complex system dynamics. We use both mean field theory to get analytic results and a numerical complex systems model, Demon, for computational results. An isolated system has bifurcated fixed points and a cascading threshold which is the same as the bifurcation point. When systems are coupled, this is no longer true and the cascading threshold is different from the bifurcation point of the fixed point solutions. This change in the cascading threshold caused by the interdependence of the system can have an impact on the "safe operation" of interdependent infrastructure systems by changing the critical point and even the power law exponent.
Bagdasaryan, Armen
2008-01-01
We present a method of discrete modeling and analysis of multilevel dynamics of complex large-scale hierarchical dynamic systems subject to external dynamic control mechanism. Architectural model of information system supporting simulation and analysis of dynamic processes and development scenarios (strategies) of complex large-scale hierarchical systems is also proposed.
NATO Advanced Research Workshop on Dynamics of Polyatomic Van der Waals Complexes
Janda, Kenneth
1991-01-01
This publication is the Proceedings of the NATO Advanced Research Workshop (ARW) on the Dynamics of Polyatomic Van der Waals Molecules held at the Chateau de Bonas, Castera-Verduzan, France, from August 21 through August 26, 1989. Van der Waals complexes provide important model problems for understanding energy transfer and dissipation. These processes can be described in great detail for Van der Waals complexes, and the insight gained from such studies can be applied to more complicated chemical problems that are not amenable to detailed study. The workshop concentrated on the current questions and future prospects for extend ing our highly detailed knowledge of triatomic Van der Waals molecule dynamics to polyatomic molecules and clusters (one molecule surrounded by several, or up to sev eral tens of, atoms). Both experimental and theoretical studies were discussed, with particular emphasis on the dynamical behavior of dissociation as observed in the dis tributions of quantum states of the dissociatio...
Taramopoulos, A.; Psillos, D.
2017-01-01
The present study investigates the impact of utilizing virtual laboratory environments combining dynamically linked concrete and abstract representations in investigative activities on the ability of students to comprehend simple and complex phenomena in the field of electric circuits. Forty-two 16- to 17-year-old high school students participated…
Cameron, Lynne
2015-01-01
Complex dynamic systems (CDS) theory offers a powerful metaphorical model of applied linguistic processes, allowing holistic descriptions of situated phenomena, and addressing the connectedness and change that often characterise issues in our field. A recent study of Kenyan conflict transformation illustrates application of a CDS perspective. Key…
Perdigão, Rui A. P.
2016-04-01
The fundamental stochastic-dynamic coevolution laws governing complex coevolutionary systems are introduced in a mathematical physics framework formally unifying nonlinear stochastic physics with fundamental deterministic interaction laws among spatiotemporally distributed processes. The methodological developments are then used to shed light onto fundamental interactions underlying complex spatiotemporal behaviour and emergence in multiscale hydroclimate dynamics. For this purpose, a mathematical physics framework is presented predicting evolving distributions of hydrologic quantities under nonlinearly coevolving geophysical processes. The functional formulation is grounded on first principles regulating the dynamics of each system constituent and their interactions, therefore its applicability is general and data-independent, not requiring local calibrations. Moreover, it enables the dynamical estimation of hydroclimatic variations in space and time from knowledge at different spatiotemporal conditions, along with the associated uncertainties. This paves the way for a robust physically based prediction of hydroclimatic changes in unsupervised areas (e.g. ungauged basins). Validation is achieved by producing, with the mathematical physics framework, a comprehensive spatiotemporal legacy consistent with the observed distributions along with their statistic-dynamic relations. The similarity between simulated and observed distributions is further assessed with novel robust nonlinear information-theoretic diagnostics. The present study brings to light emerging signatures of structural change in hydroclimate dynamics arising from nonlinear synergies across multiple spatiotemporal scales, and contributes to a better dynamical understanding and prediction of spatiotemporal regimes, transitions, structural changes and extremes in complex coevolutionary systems. This study further sheds light onto a diversity of emerging properties from harmonic to hyper-chaotic in general
Directory of Open Access Journals (Sweden)
Hai-Xiao Jin
Full Text Available The current paradigm of cyclin-dependent kinase (CDK regulation based on the well-established CDK2 has been recently expanded. The determination of CDK9 crystal structures suggests the requirement of an additional regulatory protein, such as human immunodeficiency virus type 1 (HIV-1 Tat, to exert its physiological functions. In most kinases, the exact number and roles of the cofactor metal ions remain unappreciated, and the repertoire has thus gained increasing attention recently. Here, molecular dynamics (MD simulations were implemented on CDK9 to explore the functional roles of HIV-1 Tat and the second Mg2+ ion at site 1 (Mg12+. The simulations unveiled that binding of HIV-1 Tat to CDK9 not only stabilized hydrogen bonds (H-bonds between ATP and hinge residues Asp104 and Cys106, as well as between ATP and invariant Lys48, but also facilitated the salt bridge network pertaining to the phosphorylated Thr186 at the activation loop. By contrast, these H-bonds cannot be formed in CDK9 owing to the absence of HIV-1 Tat. MD simulations further revealed that the Mg12+ ion, coupled with the Mg22+ ion, anchored to the triphosphate moiety of ATP in its catalytic competent conformation. This observation indicates the requirement of the Mg12+ ion for CDK9 to realize its function. Overall, the introduction of HIV-1 Tat and Mg12+ ion resulted in the active site architectural characteristics of phosphorylated CDK9. These data highlighted the functional roles of HIV-1 Tat and Mg12+ ion in the regulation of CDK9 activity, which contributes an important complementary understanding of CDK molecular underpinnings.
The topology and dynamics of protein complexes: insights from intra- molecular network theory.
Hu, Guang; Zhou, Jianhong; Yan, Wenying; Chen, Jiajia; Shen, Bairong
2013-03-01
Intra-molecular interactions within complex systems play a pivotal role in the biological function. They form a major challenge to computational structural proteomics. The network paradigm treats any system as a set of nodes linked by edges corresponding to the relations existing between the nodes. It offers a computationally efficient tool to meet this challenge. Here, we review the recent advances in the use of network theory to study the topology and dynamics of protein- ligand and protein-nucleic acid complexes. The study of protein complexes networks not only involves the topological classification in term of network parameters, but also reveals the consistent picture of intrinsic functional dynamics. Current dynamical analysis focuses on a plethora of functional phenomena: the process of allosteric communication, the binding induced conformational changes, prediction and identification of binding sites of protein complexes, which will give insights into intra-protein complexes interactions. Furthermore, such computational results may elucidate a variety of known biological processes and experimental data, and thereby demonstrate a huge potential for applications such as drug design and functional genomics. Finally we describe some web-based resources for protein complexes, as well as protein network servers and related bioinformatics tools.
Complex processes from dynamical architectures with time-scale hierarchy.
Directory of Open Access Journals (Sweden)
Dionysios Perdikis
Full Text Available The idea that complex motor, perceptual, and cognitive behaviors are composed of smaller units, which are somehow brought into a meaningful relation, permeates the biological and life sciences. However, no principled framework defining the constituent elementary processes has been developed to this date. Consequently, functional configurations (or architectures relating elementary processes and external influences are mostly piecemeal formulations suitable to particular instances only. Here, we develop a general dynamical framework for distinct functional architectures characterized by the time-scale separation of their constituents and evaluate their efficiency. Thereto, we build on the (phase flow of a system, which prescribes the temporal evolution of its state variables. The phase flow topology allows for the unambiguous classification of qualitatively distinct processes, which we consider to represent the functional units or modes within the dynamical architecture. Using the example of a composite movement we illustrate how different architectures can be characterized by their degree of time scale separation between the internal elements of the architecture (i.e. the functional modes and external interventions. We reveal a tradeoff of the interactions between internal and external influences, which offers a theoretical justification for the efficient composition of complex processes out of non-trivial elementary processes or functional modes.
Complex processes from dynamical architectures with time-scale hierarchy.
Perdikis, Dionysios; Huys, Raoul; Jirsa, Viktor
2011-02-10
The idea that complex motor, perceptual, and cognitive behaviors are composed of smaller units, which are somehow brought into a meaningful relation, permeates the biological and life sciences. However, no principled framework defining the constituent elementary processes has been developed to this date. Consequently, functional configurations (or architectures) relating elementary processes and external influences are mostly piecemeal formulations suitable to particular instances only. Here, we develop a general dynamical framework for distinct functional architectures characterized by the time-scale separation of their constituents and evaluate their efficiency. Thereto, we build on the (phase) flow of a system, which prescribes the temporal evolution of its state variables. The phase flow topology allows for the unambiguous classification of qualitatively distinct processes, which we consider to represent the functional units or modes within the dynamical architecture. Using the example of a composite movement we illustrate how different architectures can be characterized by their degree of time scale separation between the internal elements of the architecture (i.e. the functional modes) and external interventions. We reveal a tradeoff of the interactions between internal and external influences, which offers a theoretical justification for the efficient composition of complex processes out of non-trivial elementary processes or functional modes.
Tear Film Dynamics: the roles of complex structure and rheology
Dey, Mohar; Feng, James; Vivek, Atul S.; Dixit, Harish N.; Richhariya, Ashutosh
2016-11-01
Ocular surface infections such as microbial and fungal keratitis are among leading causes of blindness in the world. A thorough understanding of the pre-corneal tear film dynamics is essential to comprehend the role of various tear layer components in the escalation of such ocular infections. The pre-corneal tear film comprises of three layers of complex fluids, viz. the innermost mucin layer, a hydrophilic protective cover over the sensitive corneal epithelium, the intermediate aqueous layer that forms the bulk of the tear film and is often embedded with large number of bio-polymers either in the form of soluble mucins or pathogens, and finally the outermost lipid layer that stabilizes the film by decreasing the air/tear film interfacial tension. We have developed a comprehensive mathematical model to describe such a film by incorporating the effects of the non-uniform mucin distribution along with the complex rheology of the aqueous layer with/without pathogens, Marangoni effects from the lipid layer and the slip effects at the base of the tear film. A detailed linear stability analysis and a fully non-linear solution determine the break up time (BUT) of such a tear film. We also probe the role of the various components of the pre-corneal tear film in the dynamics of rupture.
Complexity, Sustainability, Justice, and Meaning: Chronological Versus Dynamical Time
Directory of Open Access Journals (Sweden)
Horacio Velasco
2009-11-01
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When nonlinear dynamics came to be complemented with semiotic modulation through the implement of symbol-mediated language (a complementation subsequently termed semantic closure as first instantiated through the communicating (as opposed to merely dynamically interacting molecular complexes of the cell, what can be termed semiotic hysteresis was born. The paper attempts to show that indefinitely evolving complexity, sustainability, justice, and meaning are indissolubly bound with chronological time in the sense of semiotic hysteresis (as afforded initially by non-cognitive semantic closure and subsequently, at least one hopes, by cognitive semantic closure: This semiotic hysteresis yields the indefinite evolutionary time of the living condition—including culture.
Energy Technology Data Exchange (ETDEWEB)
Wu, H.M.; Savikhin, S.; Reddy, N.R.S.; Jankowiak, R.; Struve, W.S.; Small, G.J. [Ames Lab., IA (United States)]|[Iowa State Univ., Ames, IA (United States); Cogdell, R.J. [Univ. of Glasgow (United Kingdom)
1996-07-18
One- and two-color pump/probe femtosecond and hole-burning data are reported for the isolated B800-850 (LH2) antenna complex of Rhodopseudomonas acidophila (strain 10050). The two-color profiles are interpretable in terms of essentially monophasic B800{yields}B850 energy transfer with kinetics ranging from 1.6 to 1.1 ps between 19 and 130 K for excitation at or to the red of the B800 absorption maximum. The B800 zero-phonon hole profiles obtained at 4.2 K with burn frequencies located near or to the red of this maximum yielded a transfer time of 1.8 ps. B800 hole-burning data (4.2 K) are also reported for chromatophores at ambient pressure and pressures of 270 and 375 MPa. At ambient pressure the B800-B850 energy gap is 950 cm{sup -1}, while at 270 and 375 MPa it is close to 1000 and 1050 cm{sup -1}, respectively. However, no dependence of the B800{yields}B850 transfer time on pressure was observed. The resilience of the transfer rate to pressure-induced changes in the energy gap and the weak temperature dependence of the rate are consistent with the model that has the spectral overlap (of Foerster theory) provided by the B800 fluorescence origin band and weak vibronic absorption bands of B850. However, both the time domain and hole-burning data establish that there is an additional relaxation channel for B800, which is observed when excitation is located to the blue of the B800 absorption maximum. 40 refs., 11 figs., 6 tabs.
The Nonrandom Brain: Efficiency, Economy, and Complex Dynamics
Directory of Open Access Journals (Sweden)
Olaf eSporns
2011-02-01
Full Text Available Modern anatomical tracing and imaging techniques are beginning to reveal the structural anatomy of neural circuits at small and large scales in unprecedented detail. When examined with analytic tools from graph theory and network science, neural connectivity exhibits highly nonrandom features, including high clustering and short path length, as well as modules and highly central hub nodes. These characteristic topological features of neural connections shape nonrandom dynamic interactions that occur during spontaneous activity or in response to external stimulation. Disturbances of connectivity and thus of neural dynamics are thought to underlie a number of disease states of the brain, and some evidence suggests that degraded functional performance of brain networks may be the outcome of a process of randomization affecting their nodes and edges. This article provides a survey of the nonrandom structure of neural connectivity, primarily at the large-scale of regions and pathways in the mammalian cerebral cortex. In addition, we will discuss how nonrandom connections can give rise to differentiated and complex patterns of dynamics and information flow. Finally, we will explore the idea that at least some disorders of the nervous system are associated with increased randomness of neural connections.
On Impact Dynamics under Complex or Extreme Conditions
Kouraytem, Nadia
2016-11-01
The impact of a spherical object onto a surface of a liquid, solid or granular material, is a configuration which occurs in numerous industrial and natural phenomena. The resulting dynamics can produce complex outcomes and often occur on very short time-scales. Their study thereby requires high-speed video imaging, as is done herein. This three-part dissertation investigates widely disparate but kindred impact configurations, where the impacting object is a solid steel sphere, or a molten metal droplet. The substrate, on the other hand, is either granular material, a liquid, or solid ice. Therefore both fluid mechanics and thermodynamics play a key role in some of these dynamics. Part I, investigates the penetration depth of a steel sphere which impacts onto a granular bed containing a mixture of grains of two different sizes. The addition of smaller grains within a bed of larger grains can promote a “lubrication” effect and deeper penetration of the sphere. However, there needs to be enough mass fraction of the smaller grains so that they get lodged between the larger grains and are not simply like isolated rattlers inside the voids between the larger grains. This lubrication occurs even though the addition of the small grains increases the overall packing fraction of the bed. We compare the enhanced penetration for the mixtures to a simple interpolative model based on the results for monodispersed media of the constitutive sizes. The strongest lubrication is observed for large irregular shaped Ottawa sand grains, which are seeded with small spherical glass beads. Part II, tackles the topic of a molten metal drop impacting onto a pool of water. When the drop temperature is far above the boiling temperature of water, a continuous vapor layer can form at the interface between the metal and water, in what is called the Leidenfrost phenomenon. This vapor layer can become unstable forming what is called a vapor explosion, which can break up the molten metal drop
LZ complexity in chaotic dynamical systems and the quasiperiodic Fibonacci sequence
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D. Arasteh
1998-04-01
Full Text Available The origin the concept of LZ compexity is in information science. Here we use this notion to characterize chaotic dynamical systems. We make contact with the usual characteristics of chaos, such as Lyapunov exponent and K-entropy. It is shown that for a two-dimensional system LZ complexity is as powerful as other characteristics. We also apply LZ complexity to the study of the quasiperiodic Fibonacci sequence. We prove a theorem about its LZ complexity and based upon it conclude its long range order.
Ultrafast Laser Dynamics and Interactions in Complex Materials
Patz, Aaron Edward
The work described in this thesis underscores specific examples of using an ultrafast laser as a materials research tool for studying condensed matter physics in complex materials. The majority of materials studied fall into the iron-pnictide class of unconventional superconductors, which exhibit a multitude of phases that appear to be dependent on each other, or the magnetic semiconductor, GaMnAs. In my work I show various ultrafast laser techniques for studying these complex materials in order to decouple the different properties in the time-domain and gain information about the underlying physics governing the material properties.
Cui, Yiqian; Shi, Junyou; Wang, Zili
2015-11-01
Quantum Neural Networks (QNN) models have attracted great attention since it innovates a new neural computing manner based on quantum entanglement. However, the existing QNN models are mainly based on the real quantum operations, and the potential of quantum entanglement is not fully exploited. In this paper, we proposes a novel quantum neuron model called Complex Quantum Neuron (CQN) that realizes a deep quantum entanglement. Also, a novel hybrid networks model Complex Rotation Quantum Dynamic Neural Networks (CRQDNN) is proposed based on Complex Quantum Neuron (CQN). CRQDNN is a three layer model with both CQN and classical neurons. An infinite impulse response (IIR) filter is embedded in the Networks model to enable the memory function to process time series inputs. The Levenberg-Marquardt (LM) algorithm is used for fast parameter learning. The networks model is developed to conduct time series predictions. Two application studies are done in this paper, including the chaotic time series prediction and electronic remaining useful life (RUL) prediction.
Chou, Chia-Chun
2014-03-14
The complex quantum Hamilton-Jacobi equation-Bohmian trajectories (CQHJE-BT) method is introduced as a synthetic trajectory method for integrating the complex quantum Hamilton-Jacobi equation for the complex action function by propagating an ensemble of real-valued correlated Bohmian trajectories. Substituting the wave function expressed in exponential form in terms of the complex action into the time-dependent Schrödinger equation yields the complex quantum Hamilton-Jacobi equation. We transform this equation into the arbitrary Lagrangian-Eulerian version with the grid velocity matching the flow velocity of the probability fluid. The resulting equation describing the rate of change in the complex action transported along Bohmian trajectories is simultaneously integrated with the guidance equation for Bohmian trajectories, and the time-dependent wave function is readily synthesized. The spatial derivatives of the complex action required for the integration scheme are obtained by solving one moving least squares matrix equation. In addition, the method is applied to the photodissociation of NOCl. The photodissociation dynamics of NOCl can be accurately described by propagating a small ensemble of trajectories. This study demonstrates that the CQHJE-BT method combines the considerable advantages of both the real and the complex quantum trajectory methods previously developed for wave packet dynamics.
Multiple-node basin stability in complex dynamical networks
Mitra, Chiranjit; Choudhary, Anshul; Sinha, Sudeshna; Kurths, Jürgen; Donner, Reik V.
2017-03-01
Dynamical entities interacting with each other on complex networks often exhibit multistability. The stability of a desired steady regime (e.g., a synchronized state) to large perturbations is critical in the operation of many real-world networked dynamical systems such as ecosystems, power grids, the human brain, etc. This necessitates the development of appropriate quantifiers of stability of multiple stable states of such systems. Motivated by the concept of basin stability (BS) [P. J. Menck et al., Nat. Phys. 9, 89 (2013), 10.1038/nphys2516], we propose here the general framework of multiple-node basin stability for gauging the global stability and robustness of networked dynamical systems in response to nonlocal perturbations simultaneously affecting multiple nodes of a system. The framework of multiple-node BS provides an estimate of the critical number of nodes that, when simultaneously perturbed, significantly reduce the capacity of the system to return to the desired stable state. Further, this methodology can be applied to estimate the minimum number of nodes of the network to be controlled or safeguarded from external perturbations to ensure proper operation of the system. Multiple-node BS can also be utilized for probing the influence of spatially localized perturbations or targeted attacks to specific parts of a network. We demonstrate the potential of multiple-node BS in assessing the stability of the synchronized state in a deterministic scale-free network of Rössler oscillators and a conceptual model of the power grid of the United Kingdom with second-order Kuramoto-type nodal dynamics.
Li, Yuanyuan; Jin, Suoqin; Lei, Lei; Pan, Zishu; Zou, Xiufen
2015-03-01
The early diagnosis and investigation of the pathogenic mechanisms of complex diseases are the most challenging problems in the fields of biology and medicine. Network-based systems biology is an important technique for the study of complex diseases. The present study constructed dynamic protein-protein interaction (PPI) networks to identify dynamical network biomarkers (DNBs) and analyze the underlying mechanisms of complex diseases from a systems level. We developed a model-based framework for the construction of a series of time-sequenced networks by integrating high-throughput gene expression data into PPI data. By combining the dynamic networks and molecular modules, we identified significant DNBs for four complex diseases, including influenza caused by either H3N2 or H1N1, acute lung injury and type 2 diabetes mellitus, which can serve as warning signals for disease deterioration. Function and pathway analyses revealed that the identified DNBs were significantly enriched during key events in early disease development. Correlation and information flow analyses revealed that DNBs effectively discriminated between different disease processes and that dysfunctional regulation and disproportional information flow may contribute to the increased disease severity. This study provides a general paradigm for revealing the deterioration mechanisms of complex diseases and offers new insights into their early diagnoses.
Predicting the evolution of complex networks via similarity dynamics
Wu, Tao; Chen, Leiting; Zhong, Linfeng; Xian, Xingping
2017-01-01
Almost all real-world networks are subject to constant evolution, and plenty of them have been investigated empirically to uncover the underlying evolution mechanism. However, the evolution prediction of dynamic networks still remains a challenging problem. The crux of this matter is to estimate the future network links of dynamic networks. This paper studies the evolution prediction of dynamic networks with link prediction paradigm. To estimate the likelihood of the existence of links more accurate, an effective and robust similarity index is presented by exploiting network structure adaptively. Moreover, most of the existing link prediction methods do not make a clear distinction between future links and missing links. In order to predict the future links, the networks are regarded as dynamic systems in this paper, and a similarity updating method, spatial-temporal position drift model, is developed to simulate the evolutionary dynamics of node similarity. Then the updated similarities are used as input information for the future links' likelihood estimation. Extensive experiments on real-world networks suggest that the proposed similarity index performs better than baseline methods and the position drift model performs well for evolution prediction in real-world evolving networks.
National Research Council Canada - National Science Library
QIAN Hong
2014-01-01
The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra...
Complex dynamics in planar two-electron quantum dots
Energy Technology Data Exchange (ETDEWEB)
Schroeter, Sebastian Josef Arthur
2013-06-25
Quantum dots play an important role in a wide range of recent experimental and technological developments. In particular they are promising candidates for realisations of quantum bits and further applications in quantum information theory. The harmonically confined Hooke's atom model is experimentally verified and separates in centre-of-mass and relative coordinates. Findings that are contradictory to this separability call for an extension of the model, in particular changing the confinement potential. In order to study effects of an anharmonic confinement potential on spectral properties of planar two-electron quantum dots a sophisticated numerical approach is developed. Comparison between the Helium atom, Hooke's atom and an anharmonic potential model are undertaken in order to improve the description of quantum dots. Classical and quantum features of complexity and chaos are investigated and used to characterise the dynamics of the system to be mixed regular-chaotic. Influence of decoherence can be described by quantum fidelity, which measures the effect of a perturbation on the time evolution. The quantum fidelity of eigenstates of the system depends strongly on the properties of the perturbation. Several methods for solving the time-dependent Schrödinger equation are implemented and a high level of accuracy for long time evolutions is achieved. The concept of offset entanglement, the entanglement of harmonic models in the noninteracting limit, is introduced. This concept explains different questions raised in the literature for harmonic quantum dot models, recently. It shows that only in the groundstate the electrons are not entangled in the fermionic sense. The applicability, validity, and origin of Hund's first rule in general quantum dot models is further addressed. In fact Hund's first rule is only applicable, and in this case also valid, for one pair of singlet and triplet states in Hooke's atom. For more realistic models of two
A single-molecule view of DNA replication : the dynamic nature of multi-protein complexes revealed
Geertsema, Hylkje J.; van Oijen, Antoine M.; Chiu, Wah; Wagner, Gerhard
2013-01-01
Recent advances in the development of single-molecule approaches have made it possible to study the dynamics of biomolecular systems in great detail. More recently, such tools have been applied to study the dynamic nature of large multiprotein complexes that support multiple enzymatic activities. In
Energy Technology Data Exchange (ETDEWEB)
Rundle, John B. [Univ. of California, Davis, CA (United States); Klein, William [Boston Univ., MA (United States)
2015-09-29
We have carried out research to determine the dynamics of failure in complex geomaterials, specifically focusing on the role of defects, damage and asperities in the catastrophic failure processes (now popularly termed “Black Swan events”). We have examined fracture branching and flow processes using models for invasion percolation, focusing particularly on the dynamics of bursts in the branching process. We have achieved a fundamental understanding of the dynamics of nucleation in complex geomaterials, specifically in the presence of inhomogeneous structures.
Balance between noise and information flow maximizes set complexity of network dynamics.
Directory of Open Access Journals (Sweden)
Tuomo Mäki-Marttunen
Full Text Available Boolean networks have been used as a discrete model for several biological systems, including metabolic and genetic regulatory networks. Due to their simplicity they offer a firm foundation for generic studies of physical systems. In this work we show, using a measure of context-dependent information, set complexity, that prior to reaching an attractor, random Boolean networks pass through a transient state characterized by high complexity. We justify this finding with a use of another measure of complexity, namely, the statistical complexity. We show that the networks can be tuned to the regime of maximal complexity by adding a suitable amount of noise to the deterministic Boolean dynamics. In fact, we show that for networks with Poisson degree distributions, all networks ranging from subcritical to slightly supercritical can be tuned with noise to reach maximal set complexity in their dynamics. For networks with a fixed number of inputs this is true for near-to-critical networks. This increase in complexity is obtained at the expense of disruption in information flow. For a large ensemble of networks showing maximal complexity, there exists a balance between noise and contracting dynamics in the state space. In networks that are close to critical the intrinsic noise required for the tuning is smaller and thus also has the smallest effect in terms of the information processing in the system. Our results suggest that the maximization of complexity near to the state transition might be a more general phenomenon in physical systems, and that noise present in a system may in fact be useful in retaining the system in a state with high information content.
Complex dynamical behaviors of daily data series in stock exchange
Wang, Hongchun; Chen, Guanrong; Lü, Jinhu
2004-12-01
It is well known that many economic data series show chaotic behaviors. In this Letter, we further investigate the complex dynamical behaviors of the daily data series, including opening quotation, closing quotation, maximum price, minimum price, and total exchange quantum, in Shenzhen stock exchange and Shanghai stock exchange, which are two representative stock exchanges in mainland China. The maximum Lyapunov exponents, correlation dimensions, and frequency spectra are calculated for these time series. Our results indicate that some daily data series of stock exchanges display low-dimensional chaotic behaviors, and some other daily data series do not show any chaotic behavior. Moreover, we introduce a weighted one-rank local-region approach for predicting short-term daily data series of stock exchange.
Complex Ion Dynamics in Carbonate Lithium-Ion Battery Electrolytes
Energy Technology Data Exchange (ETDEWEB)
Ong, Mitchell T.; Bhatia, Harsh; Gyulassy, Attila G.; Draeger, Erik W.; Pascucci, Valerio; Bremer, Peer-Timo; Lordi, Vincenzo; Pask, John E.
2017-03-16
Li-ion battery performance is strongly influenced by ionic conductivity, which depends on the mobility of the Li ions in solution, and is related to their solvation structure. In this work, we have performed first-principles molecular dynamics (FPMD) simulations of a LiPF6 salt solvated in different Li-ion battery organic electrolytes. We employ an analytical method using relative angles from successive time intervals to characterize complex ionic motion in multiple dimensions from our FPMD simulations. We find different characteristics of ionic motion on different time scales. We find that the Li ion exhibits a strong caging effect due to its strong solvation structure, while the counterion, PF6– undergoes more Brownian-like motion. Our results show that ionic motion can be far from purely diffusive and provide a quantitative characterization of the microscopic motion of ions over different time scales.
Reduced complexity turbo equalization using a dynamic Bayesian network
Myburgh, Hermanus C.; Olivier, Jan C.; van Zyl, Augustinus J.
2012-12-01
It is proposed that a dynamic Bayesian network (DBN) is used to perform turbo equalization in a system transmitting information over a Rayleigh fading multipath channel. The DBN turbo equalizer (DBN-TE) is modeled on a single directed acyclic graph by relaxing the Markov assumption and allowing weak connections to past and future states. Its complexity is exponential in encoder constraint length and approximately linear in the channel memory length. Results show that the performance of the DBN-TE closely matches that of a traditional turbo equalizer that uses a maximum a posteriori equalizer and decoder pair. The DBN-TE achieves full convergence and near-optimal performance after small number of iterations.
Complex Dynamic Flows in Solar Flare Sheet Structures
McKenzie, David E.; Reeves, Katharine K.; Savage, Sabrina
2012-01-01
Observations of high-energy emission from solar flares often reveal the presence of large sheet-like structures, sometimes extending over a space comparable to the Sun's radius. Given that these structures are found between a departing coronal mass ejection and the post-eruption flare arcade, it is natural to associate the structure with a current sheet; though the relationship is unclear. Moreover, recent high-resolution observations have begun to reveal that the motions in this region are highly complex, including reconnection outflows, oscillations, and apparent wakes and eddies. We present a detailed first look at the complicated dynamics within this supra-arcade plasma, and consider implications for the interrelationship between the plasma and its embedded magnetic field.
Self-Avoiding Random Dynamics on Integer Complex Systems
Hamze, Firas; de Freitas, Nando
2011-01-01
This paper introduces a new specialized algorithm for equilibrium Monte Carlo sampling of binary-valued systems, which allows for large moves in the state space. This is achieved by constructing self-avoiding walks (SAWs) in the state space. As a consequence, many bits are flipped in a single MCMC step. We name the algorithm SARDONICS, an acronym for Self-Avoiding Random Dynamics on Integer Complex Systems. The algorithm has several free parameters, but we show that Bayesian optimization can be used to automatically tune them. SARDONICS performs remarkably well in a broad number of sampling tasks: toroidal ferromagnetic and frustrated Ising models, 3D Ising models, restricted Boltzmann machines and chimera graphs arising in the design of quantum computers.
Universal relation between skewness and kurtosis in complex dynamics.
Cristelli, Matthieu; Zaccaria, Andrea; Pietronero, Luciano
2012-06-01
We identify an important correlation between skewness and kurtosis for a broad class of complex dynamic systems and present a specific analysis of earthquake and financial time series. Two regimes of non-Gaussianity can be identified: a parabolic one, which is common in various fields of physics, and a power law one, with exponent 4/3, which at the moment appears to be specific of earthquakes and financial markets. For this property we propose a model and an interpretation in terms of very rare events dominating the statistics independently on the nature of the events considered. The predicted scaling relation between skewness and kurtosis matches very well the experimental pattern of the second regime. Regarding price fluctuations, this situation characterizes a universal stylized fact.
Nonlinear problems of complex natural systems: Sun and climate dynamics.
Bershadskii, A
2013-01-13
The universal role of the nonlinear one-third subharmonic resonance mechanism in generation of strong fluctuations in complex natural dynamical systems related to global climate is discussed using wavelet regression detrended data. The role of the oceanic Rossby waves in the year-scale global temperature fluctuations and the nonlinear resonance contribution to the El Niño phenomenon have been discussed in detail. The large fluctuations in the reconstructed temperature on millennial time scales (Antarctic ice core data for the past 400,000 years) are also shown to be dominated by the one-third subharmonic resonance, presumably related to the Earth's precession effect on the energy that the intertropical regions receive from the Sun. The effects of galactic turbulence on the temperature fluctuations are also discussed.
Dynamics of Complex Interconnected Systems: Networks and Bioprocesses
Skjeltorp, Arne T
2006-01-01
The book reviews the synergism between various fields of research that are confronted with networks, such as genetic and metabolic networks, social networks, the Internet and ecological systems. In many cases, the interacting networks manifest so-called emergent properties that are not possessed by any of the individual components. This means that the detailed knowledge of the components is insufficient to describe the whole system. Recent work has indicated that networks in nature have so-called scale-free characteristics, and the associated dynamic network modelling shows unexpected results such as an amazing robustness against accidental failures. Modelling the signal transduction networks in bioprocesses as in living cells is a challenging interdisciplinary research area. It is now realized that the many features of molecular interaction networks within a cell are shared to a large degree by the other complex systems mentioned above, such as the Internet, computer chips and society. Thus knowledge gained ...
Modeling complex spatial dynamics of two-population interaction in urbanization process
Chen, Yanguang
2013-01-01
This paper is mainly devoted to lay an empirical foundation for further research on complex spatial dynamics of two-population interaction. Based on the US population census data, a rural and urban population interaction model is developed. Subsequently a logistic equation on percentage urban is derived from the urbanization model so that spatial interaction can be connected mathematically with logistic growth. The numerical experiment by using the discretized urban-rural population interaction model of urbanization shows a period-doubling bifurcation and chaotic behavior, which is identical in patterns to those from the simple mathematical models of logistic growth in ecology. This suggests that the complicated dynamics of logistic growth may come from some kind of the nonlinear interaction. The results from this study help to understand urbanization, urban-rural population interaction, chaotic dynamics, and spatial complexity of geographical systems.
Trend Motif: A Graph Mining Approach for Analysis of Dynamic Complex Networks
Energy Technology Data Exchange (ETDEWEB)
Jin, R; McCallen, S; Almaas, E
2007-05-28
Complex networks have been used successfully in scientific disciplines ranging from sociology to microbiology to describe systems of interacting units. Until recently, studies of complex networks have mainly focused on their network topology. However, in many real world applications, the edges and vertices have associated attributes that are frequently represented as vertex or edge weights. Furthermore, these weights are often not static, instead changing with time and forming a time series. Hence, to fully understand the dynamics of the complex network, we have to consider both network topology and related time series data. In this work, we propose a motif mining approach to identify trend motifs for such purposes. Simply stated, a trend motif describes a recurring subgraph where each of its vertices or edges displays similar dynamics over a userdefined period. Given this, each trend motif occurrence can help reveal significant events in a complex system; frequent trend motifs may aid in uncovering dynamic rules of change for the system, and the distribution of trend motifs may characterize the global dynamics of the system. Here, we have developed efficient mining algorithms to extract trend motifs. Our experimental validation using three disparate empirical datasets, ranging from the stock market, world trade, to a protein interaction network, has demonstrated the efficiency and effectiveness of our approach.
Dynamics around solutes and solute-solvent complexes in mixed solvents.
Kwak, Kyungwon; Park, Sungnam; Fayer, M D
2007-09-04
Ultrafast 2D-IR vibrational echo experiments, IR pump-probe experiments, and FT-IR spectroscopy of the hydroxyl stretch of phenol-OD in three solvents, CCl4, mesitylene (1, 3, 5 trimethylbenzene), and the mixed solvent of mesitylene and CCl4 (0.83 mole fraction CCl4), are used to study solute-solvent dynamics via observation of spectral diffusion. Phenol forms a complex with Mesitylene. In the mesitylene solution, there is only complexed phenol; in the CCl4 solution, there is only uncomplexed phenol; and in the mixed solvent, both phenol species are present. Dynamics of the free phenol in CCl4 or the mixed solvent are very similar, and dynamics of the complex in mesitylene and in the mixed solvent are very similar. However, there are differences in the slowest time scale dynamics between the pure solvents and the mixed solvents. The mixed solvent produces slower dynamics that are attributed to first solvent shell solvent composition variations. The composition variations require a longer time to randomize than is required in the pure solvents, where only density variations occur. The experimental results and recent MD simulations indicate that the solvent structure around the solute may be different from the mixed solvent's mole fraction.
MADS-complexes regulate transcriptome dynamics during pollen maturation
Verelst, J.S.; Twell, D.; Folter, de S.; Immink, G.H.
2007-01-01
Background - Differentiation processes are responsible for the diversity and functional specialization of the cell types that compose an organism. The outcome of these processes can be studied at molecular, physiologic, and biochemical levels by comparing different cell types, but the complexity and
Arbona, A.; Bona, C.; Miñano, B.; Plastino, A.
2014-09-01
The definition of complexity through Statistical Complexity Measures (SCM) has recently seen major improvements. Mostly, the effort is concentrated in measures on time series. We propose a SCM definition for spatial dynamical systems. Our definition is in line with the trend to combine entropy with measures of structure (such as disequilibrium). We study the behaviour of our definition against the vectorial noise model of Collective Motion. From a global perspective, we show how our SCM is minimal at both the microscale and macroscale, while it reaches a maximum at the ranges that define the mesoscale in this model. From a local perspective, the SCM is minimum both in highly ordered and disordered areas, while it reaches a maximum at the edges between such areas. These characteristics suggest this is a good candidate for detecting the mesoscale of arbitrary dynamical systems as well as regions where the complexity is maximal in such systems.
Dynamics of Crowd Behaviors: From Complex Plane to Quantum Random Fields
Ivancevic, Vladimir G.; Reid, Darryn J.
2015-11-01
The following sections are included: * Complex Plane Dynamics of Crowds and Groups * Introduction * Complex-Valued Dynamics of Crowd and Group Behaviors * Kähler Geometry of Crowd and Group Dynamics * Computer Simulations of Crowds and Croups Dynamics * Braids of Agents' Behaviors in the Complex Plane * Hilbert-Space Control of Crowds and Groups Dynamics * Quantum Random Fields: A Unique Framework for Simulation, Optimization, Control and Learning * Introduction * Adaptive Quantum Oscillator * Optimization and Learning on Banach and Hilbert Spaces * Appendix * Complex-Valued Image Processing * Linear Integral Equations * Riemann-Liouville Fractional Calculus * Rigorous Geometric Quantization * Supervised Machine-Learning Methods * First-Order Logic and Quantum Random Fields
Iyer, Swami; Killingback, Timothy
2014-10-01
The traveler's dilemma game and the minimum-effort coordination game are social dilemmas that have received significant attention resulting from the fact that the predictions of classical game theory are inconsistent with the results found when the games are studied experimentally. Moreover, both the traveler's dilemma and the minimum-effort coordination games have potentially important applications in evolutionary biology. Interestingly, standard deterministic evolutionary game theory, as represented by the replicator dynamics in a well-mixed population, is also inadequate to account for the behavior observed in these games. Here we study the evolutionary dynamics of both these games in populations with interaction patterns described by a variety of complex network topologies. We investigate the evolutionary dynamics of these games through agent-based simulations on both model and empirical networks. In particular, we study the effects of network clustering and assortativity on the evolutionary dynamics of both games. In general, we show that the evolutionary behavior of the traveler's dilemma and minimum-effort coordination games on complex networks is in good agreement with that observed experimentally. Thus, formulating the traveler's dilemma and the minimum-effort coordination games on complex networks neatly resolves the paradoxical aspects of these games.
De Wispelaere, Kristof; Ensing, Bernd; Ghysels, An; Meijer, Evert Jan; Van Speybroeck, Veronique
2015-06-22
The methanol-to-olefin process is a showcase example of complex zeolite-catalyzed chemistry. At real operating conditions, many factors affect the reactivity, such as framework flexibility, adsorption of various guest molecules, and competitive reaction pathways. In this study, the strength of first principle molecular dynamics techniques to capture this complexity is shown by means of two case studies. Firstly, the adsorption behavior of methanol and water in H-SAPO-34 at 350 °C is investigated. Hereby an important degree of framework flexibility and proton mobility was observed. Secondly, the methylation of benzene by methanol through a competitive direct and stepwise pathway in the AFI topology was studied. Both case studies clearly show that a first-principle molecular dynamics approach enables unprecedented insights into zeolite-catalyzed reactions at the nanometer scale to be obtained.
Hana Koorehdavoudi; Paul Bogdan
2016-01-01
Biological systems are frequently categorized as complex systems due to their capabilities of generating spatio-temporal structures from apparent random decisions. In spite of research on analyzing biological systems, we lack a quantifiable framework for measuring their complexity. To fill this gap, in this paper, we develop a new paradigm to study a collective group of N agents moving and interacting in a three-dimensional space. Our paradigm helps to identify the spatio-temporal states of t...
Dynamics and regulation of nuclear import and nuclear movements of HIV-1 complexes
Burdick, Ryan C.; Chen, Jianbo; Sastri, Jaya; Hu, Wei-Shau
2017-01-01
The dynamics and regulation of HIV-1 nuclear import and its intranuclear movements after import have not been studied. To elucidate these essential HIV-1 post-entry events, we labeled viral complexes with two fluorescently tagged virion-incorporated proteins (APOBEC3F or integrase), and analyzed the HIV-1 dynamics of nuclear envelope (NE) docking, nuclear import, and intranuclear movements in living cells. We observed that HIV-1 complexes exhibit unusually long NE residence times (1.5±1.6 hrs) compared to most cellular cargos, which are imported into the nuclei within milliseconds. Furthermore, nuclear import requires HIV-1 capsid (CA) and nuclear pore protein Nup358, and results in significant loss of CA, indicating that one of the viral core uncoating steps occurs during nuclear import. Our results showed that the CA-Cyclophilin A interaction regulates the dynamics of nuclear import by delaying the time of NE docking as well as transport through the nuclear pore, but blocking reverse transcription has no effect on the kinetics of nuclear import. We also visualized the translocation of viral complexes docked at the NE into the nucleus and analyzed their nuclear movements and determined that viral complexes exhibited a brief fast phase (HIV-1 complexes quickly tether to chromatin at or near their sites of integration in both wild-type cells and cells in which LEDGF/p75 was deleted using CRISPR/cas9, indicating that the tethering interactions do not require LEDGF/p75. These studies provide novel insights into the dynamics of viral complex-NE association, regulation of nuclear import, viral core uncoating, and intranuclear movements that precede integration site selection. PMID:28827840
A complex-valued neural dynamical optimization approach and its stability analysis.
Zhang, Songchuan; Xia, Youshen; Zheng, Weixing
2015-01-01
In this paper, we propose a complex-valued neural dynamical method for solving a complex-valued nonlinear convex programming problem. Theoretically, we prove that the proposed complex-valued neural dynamical approach is globally stable and convergent to the optimal solution. The proposed neural dynamical approach significantly generalizes the real-valued nonlinear Lagrange network completely in the complex domain. Compared with existing real-valued neural networks and numerical optimization methods for solving complex-valued quadratic convex programming problems, the proposed complex-valued neural dynamical approach can avoid redundant computation in a double real-valued space and thus has a low model complexity and storage capacity. Numerical simulations are presented to show the effectiveness of the proposed complex-valued neural dynamical approach.
Construction of exact complex dynamical invariant of a two-dimensional classical system
Indian Academy of Sciences (India)
Fakir Chand; S C Mishra
2006-12-01
We present the construction of exact complex dynamical invariant of a two-dimensional classical dynamical system on an extended complex space utilizing Lie algebraic approach. These invariants are expected to play a vital role in understanding the complex trajectories of both classical and quantum systems.
Identification of Complex Dynamical Systems with Neural Networks (2/2)
CERN. Geneva
2016-01-01
The identification and analysis of high dimensional nonlinear systems is obviously a challenging task. Neural networks have been proven to be universal approximators but this still leaves the identification task a hard one. To do it efficiently, we have to violate some of the rules of classical regression theory. Furthermore we should focus on the interpretation of the resulting model to overcome its black box character. First, we will discuss function approximation with 3 layer feedforward neural networks up to new developments in deep neural networks and deep learning. These nets are not only of interest in connection with image analysis but are a center point of the current artificial intelligence developments. Second, we will focus on the analysis of complex dynamical system in the form of state space models realized as recurrent neural networks. After the introduction of small open dynamical systems we will study dynamical systems on manifolds. Here manifold and dynamics have to be identified in parall...
Identification of Complex Dynamical Systems with Neural Networks (1/2)
CERN. Geneva
2016-01-01
The identification and analysis of high dimensional nonlinear systems is obviously a challenging task. Neural networks have been proven to be universal approximators but this still leaves the identification task a hard one. To do it efficiently, we have to violate some of the rules of classical regression theory. Furthermore we should focus on the interpretation of the resulting model to overcome its black box character. First, we will discuss function approximation with 3 layer feedforward neural networks up to new developments in deep neural networks and deep learning. These nets are not only of interest in connection with image analysis but are a center point of the current artificial intelligence developments. Second, we will focus on the analysis of complex dynamical system in the form of state space models realized as recurrent neural networks. After the introduction of small open dynamical systems we will study dynamical systems on manifolds. Here manifold and dynamics have to be identified in parall...
Manor, Brad; Costa, Madalena D; Hu, Kun; Newton, Elizabeth; Starobinets, Olga; Kang, Hyun Gu; Peng, C K; Novak, Vera; Lipsitz, Lewis A
2010-12-01
The degree of multiscale complexity in human behavioral regulation, such as that required for postural control, appears to decrease with advanced aging or disease. To help delineate causes and functional consequences of complexity loss, we examined the effects of visual and somatosensory impairment on the complexity of postural sway during quiet standing and its relationship to postural adaptation to cognitive dual tasking. Participants of the MOBILIZE Boston Study were classified into mutually exclusive groups: controls [intact vision and foot somatosensation, n = 299, 76 ± 5 (SD) yr old], visual impairment only (Postural sway (i.e., center-of-pressure) dynamics were assessed during quiet standing and cognitive dual tasking, and a complexity index was quantified using multiscale entropy analysis. Postural sway speed and area, which did not correlate with complexity, were also computed. During quiet standing, the complexity index (mean ± SD) was highest in controls (9.5 ± 1.2) and successively lower in the visual (9.1 ± 1.1), somatosensory (8.6 ± 1.6), and combined (7.8 ± 1.3) impairment groups (P = 0.001). Dual tasking resulted in increased sway speed and area but reduced complexity (P postural sway speed from quiet standing to dual-tasking conditions. Sensory impairments contributed to decreased postural sway complexity, which reflected reduced adaptive capacity of the postural control system. Relatively low baseline complexity may, therefore, indicate control systems that are more vulnerable to cognitive and other stressors.
Kresh, J Y; Izrailtyan, I
1998-09-01
The capacity of self-organized systems to adapt is embodied in the functional organization of intrinsic control mechanisms. Evolution in functional complexity of heart rate variability (HRV) was used as measure of the capacity of the transplanted heart to express newly emergent regulatory order. In a cross-sectional study of 100 patients after (0-10 yr) heart transplantation (HTX), heart rate dynamics were assessed using pointwise correlation dimension (PD2) analysis. A new observation is that, commencing with the acute event of allograft transplantation, the dynamics of rhythm formation proceed through complex phase transitions. At implantation, the donor heart manifested metronome-like chronotropic behavior (PD2 approximately 1.0). At 11-100 days, dimensional complexity of HRV reached a peak (PD2 approximately 2.0) associated with resurgence in the high-frequency component (0.15-0.5 Hz) of the power spectral density. Subsequent dimensional loss to PD2 approximately 1.0 at 20-30 mo after HTX was followed by a progressive near-linear gain in system complexity, reaching PD2 approximately 3.0 7-10 yr after HTX. The "dynamic reorganization" in the allograft rhythm-generating system, seen in the first 100 days, is a manifestation of the adaptive capacity of intrinsic control mechanisms. The loss of HRV 2 yr after HTX implies a withdrawal of intrinsic autonomic control and/or development of an entrained dynamic pattern characteristic of extrinsic sympathetic input. The subsequent long-term progressive rise in dimensional complexity of HRV can be attributed to the restoration of a functional order patterning parasympathetic control. The recognition that the decentralized heart can restitute the multidimensional state space of HR generator dynamics independent of external autonomic signaling may provide a new perspective on principles that constitute homeodynamic regulation.
Yang, Ge; Wang, Jun
2016-11-01
A random agent-based financial model is developed and investigated by the finite-range multitype contact dynamic system, in an attempt to reproduce and study the dynamics of financial markets. And an analysis method of detecting duration and intensity relationship in volatility series is introduced, called the volatility duration analysis. Then the auto-correlation analysis suggests that there exists evident volatility clustering feature in absolute volatility durations for the simulation data and the real data. Besides, the Lempel-Ziv complexity analysis is applied to study the complexity of the returns, the corresponding absolute returns and the volatility duration returns, which can reflect the fluctuation behaviors, the volatility behaviors and the volatility duration behaviors. At last, the multifractal phenomena of volatility durations of returns are comparatively studied for Shanghai Composite Index and the proposed model by multifractal detrended fluctuation analysis.
Kwac, Kijeong; Lee, Chewook; Jung, Yousung; Han, Jaebeom; Kwak, Kyungwon; Zheng, Junrong; Fayer, M D; Cho, Minhaeng
2006-12-28
Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol's first solvent shell.
Complex dynamics of a particle in an oscillating potential field
Indian Academy of Sciences (India)
BARNALI PAL; DEBJIT DUTTA; SWARUP PORIA
2017-08-01
In this paper, the classical problem of the motion of a particle in one dimension with an external time dependent field is studied from the point of view of the dynamical system. The dynamical equations of motion of the particle are formulated. Equilibrium points of the non-oscillating systems are found and their local stability natures are analysed. Effect of oscillating potential barrier is analysed through numerical simulations. Phase diagrams,bifurcation diagrams and variations of largest Lyapunov exponents are presented to show the existence of a wide range of nonlinear phenomena such as limit cycle, quasiperiodic and chaotic oscillations in the system. Effects ofnonlinear damping in the model are also reported. Analysis of the physically interesting cases where damping is proportional to higher powers of velocity are presented for the sake of generalizing our findings and establishingfirm conclusion.
Multi-ethnic studies in complex traits
Fu, Jingyuan; Festen, Eleonora A. M.; Wijmenga, Cisca
2011-01-01
The successes of genome-wide association (GWA) studies have mainly come from studies performed in populations of European descent. Since complex traits are characterized by marked genetic heterogeneity, the findings so far may provide an incomplete picture of the genetic architecture of complex trai
Quantum Dynamical Behaviour in Complex Systems - A Semiclassical Approach
Energy Technology Data Exchange (ETDEWEB)
Ananth, Nandini [Univ. of California, Berkeley, CA (United States)
2008-01-01
One of the biggest challenges in Chemical Dynamics is describing the behavior of complex systems accurately. Classical MD simulations have evolved to a point where calculations involving thousands of atoms are routinely carried out. Capturing coherence, tunneling and other such quantum effects for these systems, however, has proven considerably harder. Semiclassical methods such as the Initial Value Representation (SC-IVR) provide a practical way to include quantum effects while still utilizing only classical trajectory information. For smaller systems, this method has been proven to be most effective, encouraging the hope that it can be extended to deal with a large number of degrees of freedom. Several variations upon the original idea of the SCIVR have been developed to help make these larger calculations more tractable; these range from the simplest, classical limit form, the Linearized IVR (LSC-IVR) to the quantum limit form, the Exact Forward-Backward version (EFB-IVR). In this thesis a method to tune between these limits is described which allows us to choose exactly which degrees of freedom we wish to treat in a more quantum mechanical fashion and to what extent. This formulation is called the Tuning IVR (TIVR). We further describe methodology being developed to evaluate the prefactor term that appears in the IVR formalism. The regular prefactor is composed of the Monodromy matrices (jacobians of the transformation from initial to finial coordinates and momenta) which are time evolved using the Hessian. Standard MD simulations require the potential surfaces and their gradients, but very rarely is there any information on the second derivative. We would like to be able to carry out the SC-IVR calculation without this information too. With this in mind a finite difference scheme to obtain the Hessian on-the-fly is proposed. Wealso apply the IVR formalism to a few problems of current interest. A method to obtain energy eigenvalues accurately for complex
When do perturbative approaches accurately capture the dynamics of complex quantum systems?
Fruchtman, Amir; Lambert, Neill; Gauger, Erik M.
2016-06-01
Understanding the dynamics of higher-dimensional quantum systems embedded in a complex environment remains a significant theoretical challenge. While several approaches yielding numerically converged solutions exist, these are computationally expensive and often provide only limited physical insight. Here we address the question: when do more intuitive and simpler-to-compute second-order perturbative approaches provide adequate accuracy? We develop a simple analytical criterion and verify its validity for the case of the much-studied FMO dynamics as well as the canonical spin-boson model.
Dynamics of Symmetric Conserved Mass Aggregation Model on Complex Networks
Institute of Scientific and Technical Information of China (English)
HUA Da-Yin
2009-01-01
We investigate the dynamical behaviour of the aggregation process in the symmetric conserved mass aggregation model under three different topological structures. The dispersion σ(t, L) = (∑i(mi - ρ0)2/L)1/2 is defined to describe the dynamical behaviour where ρ0 is the density of particle and mi is the particle number on a site. It is found numerically that for a regular lattice and a scale-free network, σ(t, L) follows a power-law scaling σ(t, L) ～ tδ1 and σ(t, L) ～ tδ4 from a random initial condition to the stationary states, respectively. However, for a small-world network, there are two power-law scaling regimes, σ(t, L) ～ tδ2 when t＜T and a(t, L) ～ tδ3 when tT. Moreover, it is found numerically that δ2 is near to δ1 for small rewiring probability q, and δ3 hardly changes with varying q and it is almost the same as δ4. We speculate that the aggregation of the connection degree accelerates the mass aggregation in the initial relaxation stage and the existence of the long-distance interactions in the complex networks results in the acceleration of the mass aggregation when tT for the small-world networks. We also show that the relaxation time T follows a power-law scaling τ Lz and σ(t, L) in the stationary state follows a power-law σs(L) ～ Lσ for three different structures.
Efficient modelling of droplet dynamics on complex surfaces
Karapetsas, George; Chamakos, Nikolaos T.; Papathanasiou, Athanasios G.
2016-03-01
This work investigates the dynamics of droplet interaction with smooth or structured solid surfaces using a novel sharp-interface scheme which allows the efficient modelling of multiple dynamic contact lines. The liquid-gas and liquid-solid interfaces are treated in a unified context and the dynamic contact angle emerges simply due to the combined action of the disjoining and capillary pressure, and viscous stresses without the need of an explicit boundary condition or any requirement for the predefinition of the number and position of the contact lines. The latter, as it is shown, renders the model able to handle interfacial flows with topological changes, e.g. in the case of an impinging droplet on a structured surface. Then it is possible to predict, depending on the impact velocity, whether the droplet will fully or partially impregnate the structures of the solid, or will result in a ‘fakir’, i.e. suspended, state. In the case of a droplet sliding on an inclined substrate, we also demonstrate the built-in capability of our model to provide a prediction for either static or dynamic contact angle hysteresis. We focus our study on hydrophobic surfaces and examine the effect of the geometrical characteristics of the solid surface. It is shown that the presence of air inclusions trapped in the micro-structure of a hydrophobic substrate (Cassie-Baxter state) result in the decrease of contact angle hysteresis and in the increase of the droplet migration velocity in agreement with experimental observations for super-hydrophobic surfaces. Moreover, we perform 3D simulations which are in line with the 2D ones regarding the droplet mobility and also indicate that the contact angle hysteresis may be significantly affected by the directionality of the structures with respect to the droplet motion.
DEFF Research Database (Denmark)
Simonsen, Jakob Grue
2009-01-01
We consider the computational complexity of languages of symbolic dynamical systems. In particular, we study complexity hierarchies and membership of the non-uniform class P/poly. We prove: 1.For every time-constructible, non-decreasing function t(n)=@w(n), there is a symbolic dynamical system...... with language decidable in deterministic time O(n^2t(n)), but not in deterministic time o(t(n)). 2.For every space-constructible, non-decreasing function s(n)=@w(n), there is a symbolic dynamical system with language decidable in deterministic space O(s(n)), but not in deterministic space o(s(n)). 3.There...... are symbolic dynamical systems having hard and complete languages under @?"m^l^o^g^s- and @?"m^p-reduction for every complexity class above LOGSPACE in the backbone hierarchy (hence, P-complete, NP-complete, coNP-complete, PSPACE-complete, and EXPTIME-complete sets). 4.There are decidable languages of symbolic...
Complex dynamics analysis of impulsively coupled Duffing oscillators with ring structure
Institute of Scientific and Technical Information of China (English)
姜海波; 张丽萍; 于建江
2015-01-01
Impulsively coupled systems are high-dimensional non-smooth systems that can exhibit rich and complex dynamics. This paper studies the complex dynamics of a non-smooth system which is unidirectionally impulsively coupled by three Duffing oscillators in a ring structure. By constructing a proper Poincar ´e map of the non-smooth system, an analytical expression of the Jacobian matrix of Poincar´e map is given. Two-parameter Hopf bifurcation sets are obtained by combining the shooting method and the Runge–Kutta method. When the period is fixed and the coupling strength changes, the system undergoes stable, periodic, quasi-periodic, and hyper-chaotic solutions, etc. The Floquet theory is used to study the stability of the periodic solutions of the system and their bifurcations.
Li, Y; Zakharov, D; Zhao, S; Tappero, R; Jung, U; Elsen, A; Baumann, Ph; Nuzzo, R G; Stach, E A; Frenkel, A I
2015-06-29
Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction-ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. This method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes.
Li, Y.; Zakharov, D.; Zhao, S.; Tappero, R.; Jung, U.; Elsen, A.; Baumann, Ph.; Nuzzo, R. G.; Stach, E. A.; Frenkel, A. I.
2015-06-01
Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction--ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. This method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes.
Kumar, NR Shashi; Selvarani, R
2010-01-01
Software design in Software Engineering is a critical and dynamic cognitive process. Accurate and flawless system design will lead to fast coding and early completion of a software project. Blooms taxonomy classifies cognitive domain into six dynamic levels such as Knowledge at base level to Comprehension, Application, Analysis, Synthesis and Evaluation at the highest level in the order of increasing complexity. A case study indicated in this paper is a gira system, which is a gprs based Intranet Remote Administration which monitors and controls the intranet from a mobile device. This paper investigates from this case study that the System Design stage in Software Engineering uses all the six levels of Blooms Taxonomy. The application of the highest levels of Blooms Taxonomy such as Synthesis and Evaluation in the design of gira indicates that Software Design in Software Development Life Cycle is a complex and critical cognitive process.
Ding, Hang
2014-01-01
Structures in recurrence plots (RPs), preserving the rich information of nonlinear invariants and trajectory characteristics, have been increasingly analyzed in dynamic discrimination studies. The conventional analysis of RPs is mainly focused on quantifying the overall diagonal and vertical line structures through a method, called recurrence quantification analysis (RQA). This study extensively explores the information in RPs by quantifying local complex RP structures. To do this, an approach was developed to analyze the combination of three major RQA variables: determinism, laminarity, and recurrence rate (DLR) in a metawindow moving over a RP. It was then evaluated in two experiments discriminating (1) ideal nonlinear dynamic series emulated from the Lorenz system with different control parameters and (2) data sets of human heart rate regulations with normal sinus rhythms (n = 18) and congestive heart failure (n = 29). Finally, the DLR was compared with seven major RQA variables in terms of discriminatory power, measured by standardized mean difference (DSMD). In the two experiments, DLR resulted in the highest discriminatory power with DSMD = 2.53 and 0.98, respectively, which were 7.41 and 2.09 times the best performance from RQA. The study also revealed that the optimal RP structures for the discriminations were neither typical diagonal structures nor vertical structures. These findings indicate that local complex RP structures contain some rich information unexploited by RQA. Therefore, future research to extensively analyze complex RP structures would potentially improve the effectiveness of the RP analysis in dynamic discrimination studies.
Ding, Hang
2014-01-01
Structures in recurrence plots (RPs), preserving the rich information of nonlinear invariants and trajectory characteristics, have been increasingly analyzed in dynamic discrimination studies. The conventional analysis of RPs is mainly focused on quantifying the overall diagonal and vertical line structures through a method, called recurrence quantification analysis (RQA). This study extensively explores the information in RPs by quantifying local complex RP structures. To do this, an approach was developed to analyze the combination of three major RQA variables: determinism, laminarity, and recurrence rate (DLR) in a metawindow moving over a RP. It was then evaluated in two experiments discriminating (1) ideal nonlinear dynamic series emulated from the Lorenz system with different control parameters and (2) data sets of human heart rate regulations with normal sinus rhythms (n = 18) and congestive heart failure (n = 29). Finally, the DLR was compared with seven major RQA variables in terms of discriminatory power, measured by standardized mean difference (DSMD). In the two experiments, DLR resulted in the highest discriminatory power with DSMD = 2.53 and 0.98, respectively, which were 7.41 and 2.09 times the best performance from RQA. The study also revealed that the optimal RP structures for the discriminations were neither typical diagonal structures nor vertical structures. These findings indicate that local complex RP structures contain some rich information unexploited by RQA. Therefore, future research to extensively analyze complex RP structures would potentially improve the effectiveness of the RP analysis in dynamic discrimination studies.
Complexity and Control: Towards a Rigorous Behavioral Theory of Complex Dynamical Systems
Ivancevic, Vladimir G.; Reid, Darryn J.
We introduce our motive for writing this book on complexity and control with a popular "complexity myth," which seems to be quite wide spread among chaos and complexity theory fashionistas: Low-dimensional systems usually exhibit complex behaviours (which we know fromMay's studies of the Logisticmap), while high-dimensional systems usually exhibit simple behaviours (which we know from synchronisation studies of the Kuramoto model)... We admit that this naive view on complex (e.g., human) systems versus simple (e.g., physical) systems might seem compelling to various technocratic managers and politicians; indeed, the idea makes for appealing sound-bites. However, it is enough to see both in the equations and computer simulations of pendula of various degree - (i) a single pendulum, (ii) a double pendulum, and (iii) a triple pendulum - that this popular myth is plain nonsense. The only thing that we can learn from it is what every tyrant already knows: by using force as a strong means of control, it is possible to effectively synchronise even hundreds of millions of people, at least for a while.
Contributions of the complexity paradigm to the understanding of Cerrado's organization and dynamics
National Research Council Canada - National Science Library
MATTOS, SÉRGIO H.V.L. DE; VICENTE, LUIZ E; PEREZ FILHO, ARCHIMEDES; PIQUEIRA, JOSÉ R.C
2016-01-01
.... The contributions of the complexity paradigm in this context are still less exploited, despite its great potential for explanations and predictions presented in previous diverse dynamic systems...
Clewley, Richard; Stupple, Edward J N
2015-01-01
Many complex work environments rely heavily on cognitive operators using rules. Operators sometimes fail to implement rules, with catastrophic human, social and economic costs. Rule-based error is widely reported, yet the mechanisms of rule vulnerability have received less attention. This paper examines rule vulnerability in the complex setting of airline transport operations. We examined 'the stable approach criteria rule', which acts as a system defence during the approach to land. The study experimentally tested whether system state complexity influenced rule failure. The results showed increased uncertainty and dynamism led to increased likelihood of rule failure. There was also an interaction effect, indicating complexity from different sources can combine to further constrain rule-based response. We discuss the results in relation to recent aircraft accidents and suggest that 'rule-based error' could be progressed to embrace rule vulnerability, fragility and failure. This better reflects the influence that system behaviour and cognitive variety have on rule-based response. Practitioner Summary: In this study, we examined mechanisms of rule vulnerability in the complex setting of airline transport operations. The results suggest work scenarios featuring high uncertainty and dynamism constrain rule-based response, leading to rules becoming vulnerable, fragile or failing completely. This has significant implications for rule-intensive, safety critical work environments.
Molecular dynamic simulation of complex NS2B-NS3 DENV2 ...
African Journals Online (AJOL)
Usman Sumo Friend Tambunan, Irwan Kurniawan, Arli Aditya Parikesit ... The results provide conformational changes of enzyme-inhibitor complex ... These results show that dynamic behavior of the complex occurs in the presence of solvent.
Diffusion Models for Information Dissemination Dynamics in Wireless Complex Communication Networks
Shin-Ming Cheng; Vasileios Karyotis; Pin-Yu Chen; Kwang-Cheng Chen; Symeon Papavassiliou
2013-01-01
Information dissemination has become one of the most important services of communication networks. Modeling the diffusion of information through such networks is crucial for our modern information societies. In this work, novel models, segregating between useful and malicious types of information, are introduced, in order to better study Information Dissemination Dynamics (IDD) in wireless complex communication networks, and eventually allow taking into account special network features in IDD...
Zhang, A Ping; Qu, Xin; Soman, Pranav; Hribar, Kolin C; Lee, Jin W; Chen, Shaochen; He, Sailing
2012-08-16
The topographic features of the extracelluar matrix (ECM) lay the foundation for cellular behavior. A novel biofabrication method using a digital-mirror device (DMD), called dynamic optical projection stereolithography (DOPsL) is demonstrated. This robust and versatile platform can generate complex biomimetic scaffolds within seconds. Such 3D scaffolds have promising potentials for studying cell interactions with microenvironments in vitro and in vivo.
Complex dynamics and morphogenesis an introduction to nonlinear science
Misbah, Chaouqi
2017-01-01
This book offers an introduction to the physics of nonlinear phenomena through two complementary approaches: bifurcation theory and catastrophe theory. Readers will be gradually introduced to the language and formalisms of nonlinear sciences, which constitute the framework to describe complex systems. The difficulty with complex systems is that their evolution cannot be fully predicted because of the interdependence and interactions between their different components. Starting with simple examples and working toward an increasing level of universalization, the work explores diverse scenarios of bifurcations and elementary catastrophes which characterize the qualitative behavior of nonlinear systems. The study of temporal evolution is undertaken using the equations that characterize stationary or oscillatory solutions, while spatial analysis introduces the fascinating problem of morphogenesis. Accessible to undergraduate university students in any discipline concerned with nonlinear phenomena (physics, mathema...
Nonlinear problems of complex natural systems: Sun and climate dynamics
Bershadskii, A
2012-01-01
Universal role of the nonlinear one-third subharmonic resonance mechanism in generation of the strong fluctuations in such complex natural dynamical systems as global climate and global solar activity is discussed using wavelet regression detrended data. Role of the oceanic Rossby waves in the year-scale global temperature fluctuations and the nonlinear resonance contribution to the El Nino phenomenon have been discussed in detail. The large fluctuations of the reconstructed temperature on the millennial time-scales (Antarctic ice cores data for the past 400,000 years) are also shown to be dominated by the one-third subharmonic resonance, presumably related to Earth precession effect on the energy that the intertropical regions receive from the Sun. Effects of Galactic turbulence on the temperature fluctuations are discussed in this content. It is also shown that the one-third subharmonic resonance can be considered as a background for the 11-years solar cycle, and again the global (solar) rotation and chaoti...
Stochastic dynamics of complex systems: from glasses to evolution (series on complexity science)
Sibani, Paolo
2013-01-01
Dynamical evolution over long time scales is a prominent feature of all the systems we intuitively think of as complex - for example, ecosystems, the brain or the economy. In physics, the term ageing is used for this type of slow change, occurring over time scales much longer than the patience, or indeed the lifetime, of the observer. The main focus of this book is on the stochastic processes which cause ageing, and the surprising fact that the ageing dynamics of systems which are very different at the microscopic level can be treated in similar ways. The first part of this book provides the necessary mathematical and computational tools and the second part describes the intuition needed to deal with these systems. Some of the first few chapters have been covered in several other books, but the emphasis and selection of the topics reflect both the authors' interests and the overall theme of the book. The second part contains an introduction to the scientific literature and deals in some detail with the desc...
Al-Soufi, Wajih; Reija, Belén; Novo, Mercedes; Felekyan, Suren; Kühnemuth, Ralf; Seidel, Claus A M
2005-06-22
The control of supramolecular systems requires a thorough understanding of their dynamics on a molecular level. We present fluorescence correlation spectroscopy (FCS) as a powerful spectroscopic tool to study supramolecular dynamics with single molecule sensitivity. The formation of a supramolecular complex between beta-cyclodextrin (beta-CD) as host and pyronines Y (PY) and B (PB) as guests is studied by FCS. Global target analysis of full correlation curves with a newly derived theoretical model yields in a single experiment the fluorescence lifetimes and the diffusion coefficients of free and complexed guests and the rate constants describing the complexation dynamics. These data give insight into the recently published surprising fact that the association equilibrium constant of beta-CD with PY is much lower than that with the much bulkier guest PB. FCS shows that the stability of the complexes is dictated by the dissociation and not by the association process. The association rate constants are very similar for both guests and among the highest reported for this type of systems, although much lower than the diffusion-controlled collision rate constant. A two-step model including the formation of an encounter complex allows one to identify the unimolecular inclusion reaction as the rate-limiting step. Simulations indicate that this step may be controlled by geometrical and orientational requirements. These depend on critical molecular dimensions which are only weakly affected by the different alkyl substituents of PY and PB. Diffusion coefficients of PY and PB, of their complexes, and of rhodamine 110 are given and compared to those of similar molecules.
Koorehdavoudi, Hana; Bogdan, Paul
2016-06-01
Biological systems are frequently categorized as complex systems due to their capabilities of generating spatio-temporal structures from apparent random decisions. In spite of research on analyzing biological systems, we lack a quantifiable framework for measuring their complexity. To fill this gap, in this paper, we develop a new paradigm to study a collective group of N agents moving and interacting in a three-dimensional space. Our paradigm helps to identify the spatio-temporal states of the motion of the group and their associated transition probabilities. This framework enables the estimation of the free energy landscape corresponding to the identified states. Based on the energy landscape, we quantify missing information, emergence, self-organization and complexity for a collective motion. We show that the collective motion of the group of agents evolves to reach the most probable state with relatively lowest energy level and lowest missing information compared to other possible states. Our analysis demonstrates that the natural group of animals exhibit a higher degree of emergence, self-organization and complexity over time. Consequently, this algorithm can be integrated into new frameworks to engineer collective motions to achieve certain degrees of emergence, self-organization and complexity.
Studies of complexity in fluid systems
Energy Technology Data Exchange (ETDEWEB)
Nagel, Sidney R.
2000-06-12
This is the final report of Grant DE-FG02-92ER25119, ''Studies of Complexity in Fluids'', we have investigated turbulence, flow in granular materials, singularities in evolution of fluid surfaces and selective withdrawal fluid flows. We have studied numerical methods for dealing with complex phenomena, and done simulations on the formation of river networks. We have also studied contact-line deposition that occurs in a drying drop.
Kirilyuk, A P
2006-01-01
The universal symmetry, or conservation, of complexity underlies any law or principle of system dynamics and describes the unceasing transformation of dynamic information into dynamic entropy as the unique way to conserve their sum, the total dynamic complexity. Here we describe the real world structure emergence and dynamics as manifestation of the universal symmetry of complexity of initially homogeneous interaction between two protofields. It provides the unified complex-dynamic, causally complete origin of physically real, 3D space, time, elementary particles, their properties (mass, charge, spin, etc.), quantum, relativistic, and classical behaviour, as well as fundamental interaction forces, including naturally quantized gravitation. The old and new cosmological problems (including "dark" mass and energy) are basically solved for this explicitly emerging, self-tuning world structure characterised by strictly positive (and large) energy-complexity. A general relation is obtained between the numbers of wo...
Complexity multiscale asynchrony measure and behavior for interacting financial dynamics
Yang, Ge; Wang, Jun; Niu, Hongli
2016-08-01
A stochastic financial price process is proposed and investigated by the finite-range multitype contact dynamical system, in an attempt to study the nonlinear behaviors of real asset markets. The viruses spreading process in a finite-range multitype system is used to imitate the interacting behaviors of diverse investment attitudes in a financial market, and the empirical research on descriptive statistics and autocorrelation behaviors of return time series is performed for different values of propagation rates. Then the multiscale entropy analysis is adopted to study several different shuffled return series, including the original return series, the corresponding reversal series, the random shuffled series, the volatility shuffled series and the Zipf-type shuffled series. Furthermore, we propose and compare the multiscale cross-sample entropy and its modification algorithm called composite multiscale cross-sample entropy. We apply them to study the asynchrony of pairs of time series under different time scales.
Abdel-Azeim, Safwat; Chermak, Edrisse; Vangone, Anna; Oliva, Romina; Cavallo, Luigi
2014-01-01
Molecular Dynamics (MD) simulations of protein complexes suffer from the lack of specific tools in the analysis step. Analyses of MD trajectories of protein complexes indeed generally rely on classical measures, such as the RMSD, RMSF and gyration radius, conceived and developed for single macromolecules. As a matter of fact, instead, researchers engaged in simulating the dynamics of a protein complex are mainly interested in characterizing the conservation/variation of its biological interface. On these bases, herein we propose a novel approach to the analysis of MD trajectories or other conformational ensembles of protein complexes, MDcons, which uses the conservation of inter-residue contacts at the interface as a measure of the similarity between different snapshots. A "consensus contact map" is also provided, where the conservation of the different contacts is drawn in a grey scale. Finally, the interface area of the complex is monitored during the simulations. To show its utility, we used this novel approach to study two protein-protein complexes with interfaces of comparable size and both dominated by hydrophilic interactions, but having binding affinities at the extremes of the experimental range. MDcons is demonstrated to be extremely useful to analyse the MD trajectories of the investigated complexes, adding important insight into the dynamic behavior of their biological interface. MDcons specifically allows the user to highlight and characterize the dynamics of the interface in protein complexes and can thus be used as a complementary tool for the analysis of MD simulations of both experimental and predicted structures of protein complexes.
A Bayesian Algorithm for Functional Mapping of Dynamic Complex Traits
Directory of Open Access Journals (Sweden)
Rongling Wu
2009-04-01
Full Text Available Functional mapping of dynamic traits measured in a longitudinal study was originally derived within the maximum likelihood (ML context and implemented with the EM algorithm. Although ML-based functional mapping possesses many favorable statistical properties in parameter estimation, it may be computationally intractable for analyzing longitudinal data with high dimensions and high measurement errors. In this article, we derive a general functional mapping framework for quantitative trait locus mapping of dynamic traits within the Bayesian paradigm. Markov chain Monte Carlo techniques were implemented for functional mapping to estimate biologically and statistically sensible parameters that model the structures of time-dependent genetic effects and covariance matrix. The Bayesian approach is useful to handle difficulties in constructing confidence intervals as well as the identifiability problem, enhancing the statistical inference of functional mapping. We have undertaken simulation studies to investigate the statistical behavior of Bayesian-based functional mapping and used a real example with F2 mice to validate the utilization and usefulness of the model.
Regulation and controlled synchronization for complex dynamical systems
Huijberts, H.J.C.; Nijmeijer, Henk; Willems, R.M.A.
2000-01-01
In this paper we investigate the problem of controlled synchronization as a regulator problem. In controlled synchronization one is given autonomous transmitter dynamics and controlled receiver dynamics. The question is to find a (output) feedback controller that achieves matching between
Synchronization of spatiotemporal chaos in a class of complex dynamical networks
Institute of Scientific and Technical Information of China (English)
Zhang Qing-Ling; Lü Ling
2011-01-01
This paper studies the synchronization of complex dynamical networks constructed by spatiotemporal chaotic systems with unknown parameters. The state variables in the systems with uncertain parameters are used to construct the parameter recognizers, and the unknown parameters are identified. Uncertain spatiotemporal chaotic systems are taken as the nodes of complex dynamical networks, connection among the nodes of all the spatiotemporal chaotic systems is of nonlinear coupling. The structure of the coupling functions between the connected nodes and the control gain are obtained based on Lyapunov stability theory. It is seen that stable chaos synchronization exists in the whole network when the control gain is in a certain range. The Gray-Scott models which have spatiotemporal chaotic behaviour are taken as examples for simulation and the results show that the method is very effective.
Different approaches of symbolic dynamics to quantify heart rate complexity.
Cysarz, Dirk; Porta, Alberto; Montano, Nicola; Van Leeuwen, Peter; Kurths, Jürgen; Wessel, Niels
2013-01-01
The analysis of symbolic dynamics applied to physiological time series is able to retrieve information about dynamical properties of the underlying system that cannot be gained with standard methods like e.g. spectral analysis. Different approaches for the transformation of the original time series to the symbolic time series have been proposed. Yet the differences between the approaches are unknown. In this study three different transformation methods are investigated: (1) symbolization according to the deviation from the average time series, (2) symbolization according to several equidistant levels between the minimum and maximum of the time series, (3) binary symbolization of the first derivative of the time series. Each method was applied to the cardiac interbeat interval series RR(i) and its difference ΔRR(I) of 17 healthy subjects obtained during head-up tilt testing. The symbolic dynamics of each method is analyzed by means of the occurrence of short sequences ('words') of length 3. The occurrence of words is grouped according to words without variations of the symbols (0V%), words with one variation (1V%), two like variations (2LV%) and two unlike variations (2UV%). Linear regression analysis showed that for method 1 0V%, 1V%, 2LV% and 2UV% changed with increasing tilt angle. For method 2 0V%, 2LV% and 2UV% changed with increasing tilt angle and method 3 showed changes for 0V% and 1V%. In conclusion, all methods are capable of reflecting changes of the cardiac autonomic nervous system during head-up tilt. All methods show that even the analysis of very short symbolic sequences is capable of tracking changes of the cardiac autonomic regulation during head-up tilt testing.
Molecular basis for the dissociation dynamics of protein A-immunoglobulin G1 complex.
Directory of Open Access Journals (Sweden)
Fu-Feng Liu
Full Text Available Staphylococcus aureus protein A (SpA is the most popular affinity ligand for immunoglobulin G1 (IgG1. However, the molecular basis for the dissociation dynamics of SpA-IgG1 complex is unclear. Herein, coarse-grained (CG molecular dynamics (MD simulations with the Martini force field were used to study the dissociation dynamics of the complex. The CG-MD simulations were first verified by the agreement in the structural and interactional properties of SpA and human IgG1 (hIgG1 in the association process between the CG-MD and all-atom MD at different NaCl concentrations. Then, the CG-MD simulation studies focused on the molecular insight into the dissociation dynamics of SpA-hIgG1 complex at pH 3.0. It is found that there are four steps in the dissociation process of the complex. First, there is a slight conformational adjustment of helix II in SpA. This is followed by the phenomena that the electrostatic interactions provided by the three hot spots (Glu143, Arg146 and Lys154 of helix II of SpA break up, leading to the dissociation of helix II from the binding site of hIgG1. Subsequently, breakup of the hydrophobic interactions between helix I (Phe132, Tyr133 and His137 in SpA and hIgG1 occurs, resulting in the disengagement of helix I from its binding site of hIgG1. Finally, the non-specific interactions between SpA and hIgG1 decrease slowly till disappearance, leading to the complete dissociation of the SpA-hIgG1 complex. This work has revealed that CG-MD coupled with the Martini force field is an effective method for studying the dissociation dynamics of protein-protein complex.
Complex dynamics of evaporation-driven convection in liquid layers
Chauvet, F; Colinet, P
2010-01-01
The spontaneous convective patterns induced by evaporation of a pure liquid layer are studied experimentally. A volatile liquid layer placed in a cylindrical container is left free to evaporate into air at rest under ambient conditions. The liquid/gas interface of the evaporating liquid layer is visualized using an infrared (IR) camera. The phenomenology of the observed convective patterns is qualitatively analysed, showing in particular that the latter can be quite complex especially at moderate liquid thicknesses. Attention is also paid to the influence of the container diameter on the observed patterns sequence.
Liu, Rui; Wang, Xiangdong; Aihara, Kazuyuki; Chen, Luonan
2014-05-01
Many studies have been carried out for early diagnosis of complex diseases by finding accurate and robust biomarkers specific to respective diseases. In particular, recent rapid advance of high-throughput technologies provides unprecedented rich information to characterize various disease genotypes and phenotypes in a global and also dynamical manner, which significantly accelerates the study of biomarkers from both theoretical and clinical perspectives. Traditionally, molecular biomarkers that distinguish disease samples from normal samples are widely adopted in clinical practices due to their ease of data measurement. However, many of them suffer from low coverage and high false-positive rates or high false-negative rates, which seriously limit their further clinical applications. To overcome those difficulties, network biomarkers (or module biomarkers) attract much attention and also achieve better performance because a network (or subnetwork) is considered to be a more robust form to characterize diseases than individual molecules. But, both molecular biomarkers and network biomarkers mainly distinguish disease samples from normal samples, and they generally cannot ensure to identify predisease samples due to their static nature, thereby lacking ability to early diagnosis. Based on nonlinear dynamical theory and complex network theory, a new concept of dynamical network biomarkers (DNBs, or a dynamical network of biomarkers) has been developed, which is different from traditional static approaches, and the DNB is able to distinguish a predisease state from normal and disease states by even a small number of samples, and therefore has great potential to achieve "real" early diagnosis of complex diseases. In this paper, we comprehensively review the recent advances and developments on molecular biomarkers, network biomarkers, and DNBs in particular, focusing on the biomarkers for early diagnosis of complex diseases considering a small number of samples and high
Excited state dynamics in photosynthetic reaction center and light harvesting complex 1
Strümpfer, Johan; Schulten, Klaus
2012-08-01
Key to efficient harvesting of sunlight in photosynthesis is the first energy conversion process in which electronic excitation establishes a trans-membrane charge gradient. This conversion is accomplished by the photosynthetic reaction center (RC) that is, in case of the purple photosynthetic bacterium Rhodobacter sphaeroides studied here, surrounded by light harvesting complex 1 (LH1). The RC employs six pigment molecules to initiate the conversion: four bacteriochlorophylls and two bacteriopheophytins. The excited states of these pigments interact very strongly and are simultaneously influenced by the surrounding thermal protein environment. Likewise, LH1 employs 32 bacteriochlorophylls influenced in their excited state dynamics by strong interaction between the pigments and by interaction with the protein environment. Modeling the excited state dynamics in the RC as well as in LH1 requires theoretical methods, which account for both pigment-pigment interaction and pigment-environment interaction. In the present study we describe the excitation dynamics within a RC and excitation transfer between light harvesting complex 1 (LH1) and RC, employing the hierarchical equation of motion method. For this purpose a set of model parameters that reproduce RC as well as LH1 spectra and observed oscillatory excitation dynamics in the RC is suggested. We find that the environment has a significant effect on LH1-RC excitation transfer and that excitation transfers incoherently between LH1 and RC.
Macroscopic description of complex adaptive networks coevolving with dynamic node states
Wiedermann, Marc; Donges, Jonathan F.; Heitzig, Jobst; Lucht, Wolfgang; Kurths, Jürgen
2015-05-01
In many real-world complex systems, the time evolution of the network's structure and the dynamic state of its nodes are closely entangled. Here we study opinion formation and imitation on an adaptive complex network which is dependent on the individual dynamic state of each node and vice versa to model the coevolution of renewable resources with the dynamics of harvesting agents on a social network. The adaptive voter model is coupled to a set of identical logistic growth models and we mainly find that, in such systems, the rate of interactions between nodes as well as the adaptive rewiring probability are crucial parameters for controlling the sustainability of the system's equilibrium state. We derive a macroscopic description of the system in terms of ordinary differential equations which provides a general framework to model and quantify the influence of single node dynamics on the macroscopic state of the network. The thus obtained framework is applicable to many fields of study, such as epidemic spreading, opinion formation, or socioecological modeling.
Using activity theory to study cultural complexity in medical education.
Frambach, Janneke M; Driessen, Erik W; van der Vleuten, Cees P M
2014-06-01
There is a growing need for research on culture, cultural differences and cultural effects of globalization in medical education, but these are complex phenomena to investigate. Socio-cultural activity theory seems a useful framework to study cultural complexity, because it matches current views on culture as a dynamic process situated in a social context, and has been valued in diverse fields for yielding rich understandings of complex issues and key factors involved. This paper explains how activity theory can be used in (cross-)cultural medical education research. We discuss activity theory's theoretical background and principles, and we show how these can be applied to the cultural research practice by discussing the steps involved in a cross-cultural study that we conducted, from formulating research questions to drawing conclusions. We describe how the activity system, the unit of analysis in activity theory, can serve as an organizing principle to grasp cultural complexity. We end with reflections on the theoretical and practical use of activity theory for cultural research and note that it is not a shortcut to capture cultural complexity: it is a challenge for researchers to determine the boundaries of their study and to analyze and interpret the dynamics of the activity system.
Different facets of dynamical complexity in the magnetosphere - A recurrence perspective
Stolbova, Veronika; Donner, Reik V.; Donges, Jonathan F.; Georgiou, Marina; Balasis, Georgios; Potirakis, Stelios; Kurths, Jürgen
2014-05-01
Modern human civilizations rely to a great extent on the proper functioning of infrastructures such as communication and electrical power generation and supply. Natural hazards present an ongoing threat to these infrastructures. Whereas earthquakes, storms and other types of disasters associated with the Earth's internal dynamics have mostly local to regional effects, severe magnetic storms (most prominently those following strong solar eruptions) and related phenomena have the particular potential of affecting large parts of the globe at once (in case of damaging communication infrastructures relying on satellite transmissions, they even have global hazardous potential). In order to better understanding the variations between quiescence and activity phases of the Earth's magnetic field, the complex structure of fluctuations of magnetic field strength needs to be carefully analyzed. In this work, we utilize the powerful framework of recurrence analysis for studying the properties of the Earth's magnetosphere during one year of observations including several quiescence and activity phases. Specifically, we apply several measures of recurrence quantification analysis (RQA) and recurrence network analysis (RNA) to hourly values of the disturbance storm-time (Dst) index for the year 2001. Both RQA and RNA have recently shown their great potentials for tracing variations in dynamical complexity in non-stationary models as well as real-world time series, including various applications to geoscientific problems. Here, both frameworks are used for the first time to study the complex signatures of magnetospheric fluctuations during non-storm and storm conditions. Our results reveal that recurrence characteristics provide excellent tracers for changes in the dynamical complexity along non-stationary records of geomagnetic activity. In particular, trapping time (characterizing the typical length of "laminar phases" in the observed dynamics) and network transitivity
Draft dynamic student learning in design and manufacturing of complex shape parts
Directory of Open Access Journals (Sweden)
Ivana Kleinedlerová
2013-04-01
Full Text Available The contribution deals with the dynamic teaching of students through blended learning and teaching online distance teaching which can be considered nowadays to be a very effective and dynamic education of students. Content of the article is focused on the sphere of programming with CNC machines and use Cax systems for the production of a particular shape complex parts - shearing knife. The article presented also proposed effective teaching resources. The motivation for solution of this project is that dynamic education leads students to gaining experience and skills, individual identification of the issue, creativity, suggestion of problem solving variations. The achieved way of education and its confirmed and verified positive results can be applied for various target groups of students and their fields of study
GraphStream: A Tool for bridging the gap between Complex Systems and Dynamic Graphs
Pigné, Yoann; Guinand, Frédéric; Olivier, Damien
2008-01-01
The notion of complex systems is common to many domains, from Biology to Economy, Computer Science, Physics, etc. Often, these systems are made of sets of entities moving in an evolving environment. One of their major characteristics is the emergence of some global properties stemmed from local interactions between the entities themselves and between the entities and the environment. The structure of these systems as sets of interacting entities leads researchers to model them as graphs. However, their understanding requires most often to consider the dynamics of their evolution. It is indeed not relevant to study some properties out of any temporal consideration. Thus, dynamic graphs seem to be a very suitable model for investigating the emergence and the conservation of some properties. GraphStream is a Java-based library whose main purpose is to help researchers and developers in their daily tasks of dynamic problem modeling and of classical graph management tasks: creation, processing, display, etc. It ma...
Classification of time series patterns from complex dynamic systems
Energy Technology Data Exchange (ETDEWEB)
Schryver, J.C.; Rao, N.
1998-07-01
An increasing availability of high-performance computing and data storage media at decreasing cost is making possible the proliferation of large-scale numerical databases and data warehouses. Numeric warehousing enterprises on the order of hundreds of gigabytes to terabytes are a reality in many fields such as finance, retail sales, process systems monitoring, biomedical monitoring, surveillance and transportation. Large-scale databases are becoming more accessible to larger user communities through the internet, web-based applications and database connectivity. Consequently, most researchers now have access to a variety of massive datasets. This trend will probably only continue to grow over the next several years. Unfortunately, the availability of integrated tools to explore, analyze and understand the data warehoused in these archives is lagging far behind the ability to gain access to the same data. In particular, locating and identifying patterns of interest in numerical time series data is an increasingly important problem for which there are few available techniques. Temporal pattern recognition poses many interesting problems in classification, segmentation, prediction, diagnosis and anomaly detection. This research focuses on the problem of classification or characterization of numerical time series data. Highway vehicles and their drivers are examples of complex dynamic systems (CDS) which are being used by transportation agencies for field testing to generate large-scale time series datasets. Tools for effective analysis of numerical time series in databases generated by highway vehicle systems are not yet available, or have not been adapted to the target problem domain. However, analysis tools from similar domains may be adapted to the problem of classification of numerical time series data.
Physical Studies of Some Hydrazinobenzoic Acid Complexes
Institute of Scientific and Technical Information of China (English)
M.G.Abd El Wahed; S.Abd El Wanees; M. El Gamel; S.Abd El Haleem
2005-01-01
The stability constants of complexes of 2-hydrazinobenzoic acid and 4-hydrazinobenzoic acid with Ni (Ⅱ), Cu (Ⅱ),Zn (Ⅱ), Cd (Ⅱ), and Hg (Ⅱ) were determined potentiometrically at different temperatures. The thermodynamic parameters,△AG°,△AH°, and △S° were calculated and proved that the complexation process is spontaneous and endothermic. The thermodynamic functions were analyzed in terms of electrostatic and non-electrostatic components and the results reveal that ionic bonds are formed between the studied ligands and metal ions. Conductometric titration was shown that the stoichiometry of the formed complexes are M:L and M:2L. The structure of the prepared solid complexes was characterized using IR, 1H NMR, 13C NMR spectroscopies as well as X-ray diffraction technique.Finally electrical conductivity of the ligands and their copper complexes was measured and shown that the ligands have a semiconductor behaviour.
A dynamic finite element analysis of human foot complex in the sagittal plane during level walking.
Qian, Zhihui; Ren, Lei; Ding, Yun; Hutchinson, John R; Ren, Luquan
2013-01-01
The objective of this study is to develop a computational framework for investigating the dynamic behavior and the internal loading conditions of the human foot complex during locomotion. A subject-specific dynamic finite element model in the sagittal plane was constructed based on anatomical structures segmented from medical CT scan images. Three-dimensional gait measurements were conducted to support and validate the model. Ankle joint forces and moment derived from gait measurements were used to drive the model. Explicit finite element simulations were conducted, covering the entire stance phase from heel-strike impact to toe-off. The predicted ground reaction forces, center of pressure, foot bone motions and plantar surface pressure showed reasonably good agreement with the gait measurement data over most of the stance phase. The prediction discrepancies can be explained by the assumptions and limitations of the model. Our analysis showed that a dynamic FE simulation can improve the prediction accuracy in the peak plantar pressures at some parts of the foot complex by 10%-33% compared to a quasi-static FE simulation. However, to simplify the costly explicit FE simulation, the proposed model is confined only to the sagittal plane and has a simplified representation of foot structure. The dynamic finite element foot model proposed in this study would provide a useful tool for future extension to a fully muscle-driven dynamic three-dimensional model with detailed representation of all major anatomical structures, in order to investigate the structural dynamics of the human foot musculoskeletal system during normal or even pathological functioning.
A dynamic finite element analysis of human foot complex in the sagittal plane during level walking.
Directory of Open Access Journals (Sweden)
Zhihui Qian
Full Text Available The objective of this study is to develop a computational framework for investigating the dynamic behavior and the internal loading conditions of the human foot complex during locomotion. A subject-specific dynamic finite element model in the sagittal plane was constructed based on anatomical structures segmented from medical CT scan images. Three-dimensional gait measurements were conducted to support and validate the model. Ankle joint forces and moment derived from gait measurements were used to drive the model. Explicit finite element simulations were conducted, covering the entire stance phase from heel-strike impact to toe-off. The predicted ground reaction forces, center of pressure, foot bone motions and plantar surface pressure showed reasonably good agreement with the gait measurement data over most of the stance phase. The prediction discrepancies can be explained by the assumptions and limitations of the model. Our analysis showed that a dynamic FE simulation can improve the prediction accuracy in the peak plantar pressures at some parts of the foot complex by 10%-33% compared to a quasi-static FE simulation. However, to simplify the costly explicit FE simulation, the proposed model is confined only to the sagittal plane and has a simplified representation of foot structure. The dynamic finite element foot model proposed in this study would provide a useful tool for future extension to a fully muscle-driven dynamic three-dimensional model with detailed representation of all major anatomical structures, in order to investigate the structural dynamics of the human foot musculoskeletal system during normal or even pathological functioning.
Stability studies of Solar Optical Telescope dynamics
Gullapalli, Sarma N.; Pal, Parimal K.; Ruthven, Gregory P.
1987-01-01
The Solar Optical Telescope (SOT) is designed to operate as an attached payload mounted on the Instrument Pointing System (IPS) in the cargo bay of the Shuttle Orbiter. Pointing and control of SOT is accomplished by an active Articulated Primary Mirror (APM), an active Tertiary Mirror (TM), an elaborate set of optical sensors, electromechanical actuators and programmable controllers. The structural interactions of this complex control system are significant factors in the stability of the SOT. The preliminary stability study results of the SOT dynamical system are presented. Structural transfer functions obtained from the NASTRAN model of the structure were used. These studies apply to a single degree of freedom (elevation). Fully integrated model studies will be conducted in the future.
Cross-correlation markers in stochastic dynamics of complex systems
Panischev, O Yu; Bhattacharya, J; 10.1016/j.physa.2010.06.026
2010-01-01
The neuromagnetic activity (magnetoencephalogram, MEG) from healthy human brain and from an epileptic patient against chromatic flickering stimuli has been earlier analyzed on the basis of a memory functions formalism (MFF). Information measures of memory as well as relaxation parameters revealed high individuality and unique features in the neuromagnetic brain responses of each subject. The current paper demonstrates new capabilities of MFF by studying cross-correlations between MEG signals obtained from multiple and distant brain regions. It is shown that the MEG signals of healthy subjects are characterized by well-defined effects of frequency synchronization and at the same time by the domination of low-frequency processes. On the contrary, the MEG of a patient is characterized by a sharp abnormality of frequency synchronization, and also by prevalence of high-frequency quasi-periodic processes. Modification of synchronization effects and dynamics of cross-correlations offer a promising method of detectin...
Dynamical Crossover in Complex Networks near the Percolation Transition
Kawasaki, Fumiya; Yakubo, Kousuke
2011-10-01
The return probability P0(t) of random walkers is investigated numerically for several scale-free fractal networks. Our results show that P0(t) is proportional to t-ds/2 with the non-integer spectral dimension ds as in the case of non-scale free fractal networks. We also study how the diffusion process is affected by the structural crossover from a fractal to a small-world architecture in a network near the percolation transition. It is elucidated that the corresponding dynamical crossover is scaled only by the unique characteristic time tξ regardless of whether the network is scale free or not. In addition, the scaling relation ds= 2Df/dw is found to be valid even for scale-free fractal networks, where Df and dw are the fractal and the walk dimensions. These results suggest that qualitative properties of P0(t) are irrelevant to the scale-free nature of networks.
Rosenfeld, Marina; Brenner-Lavie, Hanit; Ari, Shunit Gal-Ben; Kavushansky, Alexandra; Ben-Shachar, Dorit
2011-05-15
Mitochondria have been suggested to be involved in the pathology of bipolar disorder (BD) and schizophrenia. However, the mechanism underlying mitochondrial dysfunction is unclear. Mitochondrial network dynamics, which reflects cellular metabolic state, is important for embryonic development, synapse formation, and neurodegeneration. This study aimed to investigate mitochondrial network dynamics and its plausible association with abnormal cellular oxygen consumption in schizophrenia. Viable Epstein-Barr virus (EBV)-transformed lymphocytes (lymphoblastoids) from DSM-IV diagnosed patients with schizophrenia (n = 17), BD (n = 15), and healthy control subjects (n = 15) were assessed for mitochondrial respiration, mitochondrial dynamics, and relevant protein levels by oxygraph, confocal microscopy, and immunoblotting, respectively. Respiration of schizophrenia-derived lymphoblastoids was significantly lower compared with control subjects, and was twice as sensitive to dopamine (DA)-induced inhibition. Unlike DA, haloperidol inhibited complex I-driven respiration to a similar extent in both schizophrenia and the control cells. Both drugs interact with complex I but at different sites. At the site of DA interaction, we found alterations in protein levels of three subunits of complex I in schizophrenia. In addition, we observed structural and connectivity perturbations in the mitochondrial network, associated with alterations in the profusion protein OPA1, which was similarly reduced in schizophrenia prefrontal cortex specimens. None of these alterations were observed in the BD cells, which were similar to control cells. We show impaired mitochondrial network dynamics associated with reduced cellular respiration and complex I abnormalities in schizophrenia but not in BD. If these findings represent disease-specific alterations, they may become an endophenotype biomarker for schizophrenia. Copyright © 2011 Society of Biological Psychiatry. Published by Elsevier Inc. All
Xu, Jianhua; Chen, Yaning; Li, Weihong; Liu, Zuhan; Wei, Chunmeng; Tang, Jie
2013-01-01
Based on the observed data from 51 meteorological stations during the period from 1958 to 2012 in Xinjiang, China, we investigated the complexity of temperature dynamics from the temporal and spatial perspectives by using a comprehensive approach including the correlation dimension (CD), classical statistics, and geostatistics. The main conclusions are as follows (1) The integer CD values indicate that the temperature dynamics are a complex and chaotic system, which is sensitive to the initial conditions. (2) The complexity of temperature dynamics decreases along with the increase of temporal scale. To describe the temperature dynamics, at least 3 independent variables are needed at daily scale, whereas at least 2 independent variables are needed at monthly, seasonal, and annual scales. (3) The spatial patterns of CD values at different temporal scales indicate that the complex temperature dynamics are derived from the complex landform.
Directory of Open Access Journals (Sweden)
Jianhua Xu
2013-01-01
Full Text Available Based on the observed data from 51 meteorological stations during the period from 1958 to 2012 in Xinjiang, China, we investigated the complexity of temperature dynamics from the temporal and spatial perspectives by using a comprehensive approach including the correlation dimension (CD, classical statistics, and geostatistics. The main conclusions are as follows (1 The integer CD values indicate that the temperature dynamics are a complex and chaotic system, which is sensitive to the initial conditions. (2 The complexity of temperature dynamics decreases along with the increase of temporal scale. To describe the temperature dynamics, at least 3 independent variables are needed at daily scale, whereas at least 2 independent variables are needed at monthly, seasonal, and annual scales. (3 The spatial patterns of CD values at different temporal scales indicate that the complex temperature dynamics are derived from the complex landform.
Quantum dynamics in light-harvesting complexes: Beyond the single-exciton limit
Cui, B; Yi, X X
2011-01-01
Primitive photosynthetic cells appear over three billion years prior to any other more complex life-forms, thus it is reasonable to assume that Nature has designed a photosynthetic mechanism using minimal resources but honed to perfection under the action of evolution. A number of different quantum models have been proposed to understand the high degree of efficient energy transport, most of them are limited to the scenario of single-exciton. Here we present a study on the dynamics in light-harvesting complexes beyond the single exciton limit, and show how this model describes the energy transfer in the Fenna-Matthew-Olson (FMO) complex. We find that the energy transfer efficiency above 90% under realistic conditions is achievable.
Unpacking complexities of managerial subjectivity: An analytic fixation on constitutive dynamics
DEFF Research Database (Denmark)
Plotnikof, Mie
2012-01-01
In the critical streams of organization studies managerial subjects are destabilized through different discursive approaches, and discussions are raised to advance these further. This revitalizes conceptual debates of the complex relations of organizational discourses and subjective agency......, and the analytic challenges of discourse/Discourse-distinctions and avoiding agency-structure-dualism. This paper proposes an integral conceptualization of subjectification that directs analytic attention to the complex constitutive dynamics of organizational discourses and agency normative to organizational...... practices and reality constructs. Inspired by poststructuralist theorizing in social psychology, subjectification is conceptualized as simultaneous co-productions of subjection and agency in intersecting discourses, and, hence, better unpacked with sensitivity to this complexity. The analytic potential...
Agent-oriented modeling of the dynamics of complex biological processes I: single agent models
Jonker, C.M.; Treur, J.
2008-01-01
In the pair of papers of which this is Part I, the agent-oriented modeling perspective to cope with biological complexity is discussed. Three levels of dynamics are distinguished and related to each other: dynamics of externally observable agent behavior, dynamics of internal agent processes, and dy
Leistedt, S J-J; Linkowski, P.; Lanquart, J-P; Mietus, J E; Davis, Roger B.; Goldberger, Ary Louis; Costa, Madalena Damasio
2011-01-01
Major depression affects multiple physiologic systems. Therefore, analysis of signals that reflect integrated function may be useful in probing dynamical changes in this syndrome. Increasing evidence supports the conceptual framework that complex variability is a marker of healthy, adaptive control mechanisms and that dynamical complexity decreases with aging and disease. We tested the hypothesis that heart rate (HR) dynamics in non-medicated, young to middle-aged males during an acute major ...
Optimization and dynamics of protein-protein complexes using B-splines.
Gillilan, Richard E; Lilien, Ryan H
2004-10-01
A moving-grid approach for optimization and dynamics of protein-protein complexes is introduced, which utilizes cubic B-spline interpolation for rapid energy and force evaluation. The method allows for the efficient use of full electrostatic potentials joined smoothly to multipoles at long distance so that multiprotein simulation is possible. Using a recently published benchmark of 58 protein complexes, we examine the performance and quality of the grid approximation, refining cocrystallized complexes to within 0.68 A RMSD of interface atoms, close to the optimum 0.63 A produced by the underlying MMFF94 force field. We quantify the theoretical statistical advantage of using minimization in a stochastic search in the case of two rigid bodies, and contrast it with the underlying cost of conjugate gradient minimization using B-splines. The volumes of conjugate gradient minimization basins of attraction in cocrystallized systems are generally orders of magnitude larger than well volumes based on energy thresholds needed to discriminate native from nonnative states; nonetheless, computational cost is significant. Molecular dynamics using B-splines is doubly efficient due to the combined advantages of rapid force evaluation and large simulation step sizes. Large basins localized around the native state and other possible binding sites are identifiable during simulations of protein-protein motion. In addition to providing increased modeling detail, B-splines offer new algorithmic possibilities that should be valuable in refining docking candidates and studying global complex behavior.
Complex dynamics in diatomic molecules. Part II: Quantum trajectories
Energy Technology Data Exchange (ETDEWEB)
Yang, C.-D. [Department of Aeronautics and Astronautics, National Cheng Kung University, Tainan 701, Taiwan (China)], E-mail: cdyang@mail.ncku.edu.tw; Weng, H.-J. [Department of Aeronautics and Astronautics, National Cheng Kung University, Tainan 701, Taiwan (China)], E-mail: principlex@yahoo.com.tw
2008-10-15
The second part of this paper deals with quantum trajectories in diatomic molecules, which has not been considered before in the literature. Morse potential serves as a more accurate function than a simple harmonic oscillator for illustrating a realistic picture about the vibration of diatomic molecules. However, if we determine molecular dynamics by integrating the classical force equations derived from a Morse potential, we will find that the resulting trajectories do not consist with the probabilistic prediction of quantum mechanics. On the other hand, the quantum trajectory determined by Bohmian mechanics [Bohm D. A suggested interpretation of the quantum theory in terms of hidden variable. Phys. Rev. 1952;85:166-179] leads to the conclusion that a diatomic molecule is motionless in all its vibrational eigen-states, which also contradicts probabilistic prediction of quantum mechanics. In this paper, we point out that the quantum trajectory of a diatomic molecule completely consistent with quantum mechanics does exist and can be solved from the quantum Hamilton equations of motion derived in Part I, which is based on a complex-space formulation of fractal spacetime [El Naschie MS. A review of E-Infinity theory and the mass spectrum of high energy particle physics. Chaos, Solitons and Fractals 2004;19:209-36; El Naschie MS. E-Infinity theory - some recent results and new interpretations. Chaos, Solitons and Fractals 2006;29:845-853; El Naschie MS. The concepts of E-infinity. An elementary introduction to the cantorian-fractal theory of quantum physics. Chaos, Solitons and Fractals 2004;22:495-511; El Naschie MS. SU(5) grand unification in a transfinite form. Chaos, Solitons and Fractals 2007;32:370-374; Nottale L. Fractal space-time and microphysics: towards a theory of scale relativity. Singapore: World Scientific; 1993; Ord G. Fractal space time and the statistical mechanics of random works. Chaos, Soiltons and Fractals 1996;7:821-843] approach to quantum
Lu, Gui; Wang, Xiao-Dong; Duan, Yuan-Yuan
2016-10-01
Dynamic wetting is an important interfacial phenomenon in many industrial applications. There have been many excellent reviews of dynamic wetting, especially on super-hydrophobic surfaces with physical or chemical coatings, porous layers, hybrid micro/nano structures and biomimetic structures. This review summarizes recent research on dynamic wetting from the viewpoint of the fluids rather than the solid surfaces. The reviewed fluids range from simple Newtonian fluids to non-Newtonian fluids and complex nanofluids. The fundamental physical concepts and principles involved in dynamic wetting phenomena are also reviewed. This review focus on recent investigations of dynamic wetting by non-Newtonian fluids, including the latest experimental studies with a thorough review of the best dynamic wetting models for non-Newtonian fluids, to illustrate their successes and limitations. This paper also reports on new results on the still fledgling field of nanofluid wetting kinetics. The challenges of research on nanofluid dynamic wetting is not only due to the lack of nanoscale experimental techniques to probe the complex nanoparticle random motion, but also the lack of multiscale experimental techniques or theories to describe the effects of nanoparticle motion at the nanometer scale (10(-9) m) on the dynamic wetting taking place at the macroscopic scale (10(-3) m). This paper describes the various types of nanofluid dynamic wetting behaviors. Two nanoparticle dissipation modes, the bulk dissipation mode and the local dissipation mode, are proposed to resolve the uncertainties related to the various types of dynamic wetting mechanisms reported in the literature.
Complexities of Organization Dynamics and Development: Leaders and Managers
Nderu-Boddington, Eulalee
2008-01-01
This article shows the theoretical framework for understanding organizational dynamics and development - the change theory and subordinate relationships within contemporary organizations. The emphasis is on power strategies and the relationship to organizational dynamics and development. The integrative process broadens the understanding of…
Modularity and the Spread of Perturbations in Complex Dynamical Systems
Kolchinsky, Artemy; Rocha, Luis M
2015-01-01
We propose a method to decompose a multivariate dynamical system into weakly-coupled modules based on the idea that module boundaries constrain the spread of perturbations. Using a novel quality function called 'perturbation modularity', we find system coarse-grainings that optimally separate the dynamics of perturbation spreading into fast intra-modular and slow inter-modular components. Our method is defined directly in terms of system dynamics, unlike approaches that find communities in networks (whether in structural networks or 'functional networks' of statistical dependencies) or that impose arbitrary dynamics onto graphs. Due to this, we are able to capture the variation of modular organization across states, timescales, and in response to different perturbations, aspects of modularity which are all relevant to real-world dynamical systems. However, in certain cases, mappings exist between perturbation modularity and community detection methods of `Markov stability' and Newman's modularity. Our approac...
Dynamical behaviour of an epidemic on complex networks with population mobility
Institute of Scientific and Technical Information of China (English)
Zhang Hai-Feng; Small Michael; Fu Xin-Chu; Wang Bing-Hong
2009-01-01
In this paper,we study the dynamical behaviour of an epidemic on complex networks with population mobility.In our model,the number of people on each node is unrestricted as the nodes of the network are considered as cities,communities,and so on. Because people can travel between different cities,we study the effect of a population's mobility on the epidemic spreading. In view of the population's mobility,we suppose that the usceptible individual can be infected by an infected individual in the same city or other connected cities. Simulations are presented to verify our analysis.
Parameters in dynamic models of complex traits are containers of missing heritability.
Directory of Open Access Journals (Sweden)
Yunpeng Wang
Full Text Available Polymorphisms identified in genome-wide association studies of human traits rarely explain more than a small proportion of the heritable variation, and improving this situation within the current paradigm appears daunting. Given a well-validated dynamic model of a complex physiological trait, a substantial part of the underlying genetic variation must manifest as variation in model parameters. These parameters are themselves phenotypic traits. By linking whole-cell phenotypic variation to genetic variation in a computational model of a single heart cell, incorporating genotype-to-parameter maps, we show that genome-wide association studies on parameters reveal much more genetic variation than when using higher-level cellular phenotypes. The results suggest that letting such studies be guided by computational physiology may facilitate a causal understanding of the genotype-to-phenotype map of complex traits, with strong implications for the development of phenomics technology.
Including Quantum Effects in the Dynamics of Complex (i.e., Large)Molecular Systems
Energy Technology Data Exchange (ETDEWEB)
Miller, William H.
2006-04-27
The development in the 1950's and 60's of crossed molecular beam methods for studying chemical reactions at the single-collision molecular level stimulated the need and desire for theoretical methods to describe these and other dynamical processes in molecular systems. Chemical dynamics theory has made great strides in the ensuing decades, so that methods are now available for treating the quantum dynamics of small molecular systems essentially completely. For the large molecular systems that are of so much interest nowadays (e.g. chemical reactions in solution, in clusters, in nano-structures, in biological systems, etc.), however, the only generally available theoretical approach is classical molecular dynamics (MD) simulations. Much effort is currently being devoted to the development of approaches for describing the quantum dynamics of these complex systems. This paper reviews some of these approaches, especially the use of semiclassical approximations for adding quantum effects to classical MD simulations, also showing some new versions that should make these semiclassical approaches even more practical and accurate.
Asselin, P; Goubet, M; Lewerenz, M; Soulard, P; Perchard, J P
2004-09-15
Fourier transform infrared spectra of the nu(s) (HF stretching) band of the (CH(2))(2)S-HF complex have been recorded at 0.1-0.5 cm(-1) resolution in a cooled cell, in a supersonic jet expansion seeded with argon and in a neon matrix at 4.5 K. The combination of controlled temperature effects over a range of 40-250 K and a sophisticated band contour simulation program allows the separation of homogeneous and inhomogeneous contributions and reveals significant anharmonic couplings between intramolecular and intermolecular vibrational modes similar to our previous work on (CH(2))(2)S-DF. The sign of the coupling constants is consistent with the expected strengthening of the hydrogen bond upon vibrational excitation of HF which also explains the observed small variations of the geometrical parameters in the excited state. The analysis of sum and difference combination bands involving nu(s) provides accurate values of intermolecular harmonic frequencies and anharmonicities and a good estimate of the dissociation energy of the complex. Frequencies and coupling parameters derived from gas phase spectra compare well with results from neon matrix experiments. The effective linewidth provides a lower bound for the predissociation lifetime of 10 ps. The comparison between effective linewidths and vibrational densities of states for (CH(2))(2)S-HF and -DF complexes highlights the important role of intramolecular vibrational redistribution in the vibrational dynamics of medium strength hydrogen bonds.
Liu, Y. Z.; Hao, Y. X.; Zhang, W.; Chen, J.; Li, S. B.
2015-07-01
The nonlinear vibration of a simply supported FGM cylindrical shell with small initial geometric imperfection under complex loads is studied. The effects of radial harmonic excitation, compressive in-plane force combined with supersonic aerodynamic and thermal loads are considered. The small initial geometric imperfection of the cylindrical shell is characterized in the form of the sine-type trigonometric functions. The effective material properties of this FGM cylindrical shell are graded in the radial direction according to a simple power law in terms of the volume fractions. Based on Reddy's third-order shear deformation theory, von Karman-type nonlinear kinematics and Hamilton's principle, the nonlinear partial differential equation that controls the shell dynamics is derived. Both axial symmetric and driven modes of the cylindrical shell deflection pattern are included. Furthermore, the equations of motion can be reduced into a set of coupled nonlinear ordinary differential equations by applying Galerkin's method. In the study of the nonlinear dynamics responses of small initial geometric imperfect FGM cylindrical shell under complex loads, the 4th order Runge-Kutta method is used to obtain time history, phase portraits, bifurcation diagrams and Poincare maps with different parameters. The effects of external loads, geometric imperfections and volume fractions on the nonlinear dynamics of the system are discussed.
Complex Dynamic Thresholds and Generation of the Action Potentials in the Neural-Activity Model
Kirillov, S. Yu.; Nekorkin, V. I.
2016-05-01
This work is devoted to studying the processes of activation of the neurons whose excitation thresholds are not constant and vary in time (the so-called dynamic thresholds). The neuron dynamics is described by the FitzHugh-Nagumo model with nonlinear behavior of the recovery variable. The neuron response to the external pulsed activating action in the presence of a slowly varying synaptic current is studied within the framework of this model. The structure of the dynamic threshold is studied and its properties depending on the external-action parameters are established. It is found that the formation of the "folds" in the separatrix threshold manifold in the model phase space is a typical feature of the complex dynamic threshold. High neuron sensitivity to the action of the comparatively weak slow control signals is established. This explains the capability of the neurons to perform flexible tuning of their selective properties for detecting various external signals in sufficiently short times (of the order of duration of several spikes).
Bialonski, S
2012-01-01
Understanding the dynamics of spatially extended systems represents a challenge in diverse scientific disciplines, ranging from physics and mathematics to the earth and climate sciences or the neurosciences. This challenge has stimulated the development of sophisticated data analysis approaches adopting concepts from network theory: systems are considered to be composed of subsystems (nodes) which interact with each other (represented by edges). In many studies, such complex networks of interactions have been derived from empirical time series for various spatially extended systems and have been repeatedly reported to possess the same, possibly desirable, properties (e.g. small-world characteristics and assortativity). In this thesis we study whether and how interaction networks are influenced by the analysis methodology, i.e. by the way how empirical data is acquired (the spatial and temporal sampling of the dynamics) and how nodes and edges are derived from multivariate time series. Our modeling and numeric...
Dynamics and complexity of the Schelling segregation model
Domic, Nicolás Goles; Goles, Eric; Rica, Sergio
2011-05-01
In this paper we consider the Schelling social segregation model for two different populations. In Schelling’s model, segregation appears as a consequence of discrimination, measured by the local difference between two populations. For that, the model defines a tolerance criterion on the neighborhood of an individual, indicating wether the individual is able to move to a new place or not. Next, the model chooses which of the available unhappy individuals really moves. In our work, we study the patterns generated by the dynamical evolution of the Schelling model in terms of various parameters or the initial condition, such as the size of the neighborhood of an inhabitant, the tolerance, and the initial number of individuals. As a general rule we observe that segregation patterns minimize the interface of zones of different people. In this context we introduce an energy functional associated with the configuration which is a strictly decreasing function for the tolerant people case. Moreover, as far as we know, we are the first to notice that in the case of a non-strictly-decreasing energy functional, the system may segregate very efficiently.
Kirilyuk, Andrei P
2012-01-01
We review the recently proposed unreduced, complex-dynamical solution to many-body problem with arbitrary interaction and its application to unified solution of fundamental problems, including foundations of causally complete quantum mechanics, relativity, particle properties and cosmology. We first analyse the universal properties of many-body problem solution without any perturbative reduction and show that the emerging new quality of fundamental dynamic multivaluedness (or redundance) of resulting system configuration leads to universal concept of dynamic complexity, chaoticity and fractality of any real system behaviour. We then consider unified features of this complex dynamics. Applications of that universal description to systems at various complexity levels have been performed and in this paper we review those at the lowest, fundamental complexity levels leading to causal understanding of unified origins of quantum mechanics, relativity (special and general), elementary particles, their intrinsic prop...
A Constraint Embedding Approach for Complex Vehicle Suspension Dynamics
2015-04-24
2015, Barcelona, Catalonia , Spain same number of degrees of freedom as the number of independent degrees of freedom for the loops they replace...13. SUPPLEMENTARY NOTES ECCOMAS Thematic Conference on Multibody Dynamics 2015, June 29-July 2, 2015, Barcelona, Catalonia , Spain 14. ABSTRACT See...Z39-18 ECCOMAS Thematic Conference on Multibody Dynamics June 29 - July 2, 2015, Barcelona, Catalonia , Spain A Constraint Embedding Approach for
Monte Carlo study of real time dynamics
Alexandru, Andrei; Bedaque, Paulo F; Vartak, Sohan; Warrington, Neill C
2016-01-01
Monte Carlo studies involving real time dynamics are severely restricted by the sign problem that emerges from highly oscillatory phase of the path integral. In this letter, we present a new method to compute real time quantities on the lattice using the Schwinger-Keldysh formalism via Monte Carlo simulations. The key idea is to deform the path integration domain to a complex manifold where the phase oscillations are mild and the sign problem is manageable. We use the previously introduced "contraction algorithm" to create a Markov chain on this alternative manifold. We substantiate our approach by analyzing the quantum mechanical anharmonic oscillator. Our results are in agreement with the exact ones obtained by diagonalization of the Hamiltonian. The method we introduce is generic and in principle applicable to quantum field theory albeit very slow. We discuss some possible improvements that should speed up the algorithm.
Dynamical Study of 3D Boson Stars
Choi, Dae-Il; Choptuik, M. W.
1998-10-01
We study the dynamical evolution of ``boson stars'' in 3D numerical relativity. Boson stars are equilibrium states of a self-gravitating, complex Klein-Gordon field: a resurgence of interest in scalar fields in the context of astroparticle physics and quantum cosmology has prompted investigation of their dynamics, particularly since they are possible dark matter candidates. In addition, even though any direct physical relevance has yet to be demonstrated, boson star systems provide excellent numerical laboratories in which to study strong gravitational fields. Specifically, the boson star model provides an ideal vehicle with which to implement and evaluate (1) various coordinate conditions in the context of the ADM formalism, and (2) multi-dimensional adaptive mesh refinement techniques which appear crucial for many problems in 3D numerical relativity. We first consider boson stars in the Newtonian regime, where the (numerical) stability of single stars is shown and the interaction of multiple-star-systems is simulated. We also discuss issues which hamper progress towards a stable evolution of general relativistic boson stars, and then show some preliminary results for the general relativistic case.
Liang, Jie; Qian, Hong
2010-01-01
Modern molecular biology has always been a great source of inspiration for computational science. Half a century ago, the challenge from understanding macromolecular dynamics has led the way for computations to be part of the tool set to study molecular biology. Twenty-five years ago, the demand from genome science has inspired an entire generation of computer scientists with an interest in discrete mathematics to join the field that is now called bioinformatics. In this paper, we shall lay out a new mathematical theory for dynamics of biochemical reaction systems in a small volume (i.e., mesoscopic) in terms of a stochastic, discrete-state continuous-time formulation, called the chemical master equation (CME). Similar to the wavefunction in quantum mechanics, the dynamically changing probability landscape associated with the state space provides a fundamental characterization of the biochemical reaction system. The stochastic trajectories of the dynamics are best known through the simulations using the Gillespie algorithm. In contrast to the Metropolis algorithm, this Monte Carlo sampling technique does not follow a process with detailed balance. We shall show several examples how CMEs are used to model cellular biochemical systems. We shall also illustrate the computational challenges involved: multiscale phenomena, the interplay between stochasticity and nonlinearity, and how macroscopic determinism arises from mesoscopic dynamics. We point out recent advances in computing solutions to the CME, including exact solution of the steady state landscape and stochastic differential equations that offer alternatives to the Gilespie algorithm. We argue that the CME is an ideal system from which one can learn to understand "complex behavior" and complexity theory, and from which important biological insight can be gained.
Liu, Quan-Hui; Tang, Ming; Zhang, Hai-Feng
2015-01-01
Information diffusion and disease spreading in communication-contact layered network are typically asymmetrically coupled with each other, in which how an individual being aware of disease responds to the disease can significantly affect the disease spreading. Many recent studies have demonstrated that human behavioral adoption is a complex and non-Markovian process, where the probability of adopting one behavior is dependent on the cumulative times of the received information and the social reinforcement effect of these cumulative information. We study the impact of such a non-Markovian vaccination adoption behavior on the epidemic dynamics and the control effects. We find that this complex adoption behavior caused from the communication layer can significantly increase the epidemic threshold and reduce the final infection rate. By defining the social cost as the sum of the cost of vaccination and the cost of treatment, we show that there exists an optimal social reinforcement effect or optimal information t...
Ignatova, Tetyana; Blades, Michael; Duque, Juan G; Doorn, Stephen K; Biaggio, Ivan; Rotkin, Slava V
2014-12-28
Understanding behavior of rare-earth ions (REI) in crowded environments is crucial for several nano- and bio-technological applications. Evolution of REI photoluminescence (PL) in small compartments inside a silica hydrogel, mimic to a soft matter bio-environment, has been studied and explained within a solvation model. The model uncovered the origin of high PL efficiency to be the formation of REI complexes, surrounded by bile salt (DOC) molecules. Comparative study of these REI-DOC complexes in bulk water solution and those enclosed inside the hydrogel revealed a strong correlation between an up to 5×-longer lifetime of REIs and appearance of the DOC ordered phase, further confirmed by dynamics of REI solvation shells, REI diffusion experiments and morphological characterization of microstructure of the hydrogel.
Metal speciation dynamics and bioavailability: Inert and labile complexes
Energy Technology Data Exchange (ETDEWEB)
Van Leeuwen, H.P.
1999-11-01
The free-ion activity model for the biouptake of metals from complex media is limited to cases where mass transfer is not flux-determining. This paper considers the simultaneous effects of bioconversion kinetics and metal transport in the medium coupled with metal complex dissociation kinetics. For the two kinetically limiting situations of inert and fully labile complexes, the bioavailabilities of bioinactive metal complexes are analyzed under conditions where (i) the actual biouptake follows a Michaelis-Menten type of steady-state flux and (ii) the supply of free metal is governed by diffusion of free metal or coupled diffusion of the different labile metal species. The resulting steady-site fluxes are given in terms of two fundamental quantities, i.e., the relative bioaffinity parameter (a) and the ratio between the limiting uptake flux and the limiting transport flux (b). For labile complexes, these variables are differentiated by a complexation parameter defined by the ration between the free metal on activity and the total labile metal activity. Limits of the uptake flux for extreme values of the bioaffinity parameter a and the limiting flux ratio b are easily derived from the general flux expression. The analysis precisely shows under what conditions labile complex species contribute to the biouptake process or, equivalently, under what conditions the free-ion activity model is not obeyed.
Complex spatial dynamics of oncolytic viruses in vitro: mathematical and experimental approaches.
Directory of Open Access Journals (Sweden)
Dominik Wodarz
Full Text Available Oncolytic viruses replicate selectively in tumor cells and can serve as targeted treatment agents. While promising results have been observed in clinical trials, consistent success of therapy remains elusive. The dynamics of virus spread through tumor cell populations has been studied both experimentally and computationally. However, a basic understanding of the principles underlying virus spread in spatially structured target cell populations has yet to be obtained. This paper studies such dynamics, using a newly constructed recombinant adenovirus type-5 (Ad5 that expresses enhanced jellyfish green fluorescent protein (EGFP, AdEGFPuci, and grows on human 293 embryonic kidney epithelial cells, allowing us to track cell numbers and spatial patterns over time. The cells are arranged in a two-dimensional setting and allow virus spread to occur only to target cells within the local neighborhood. Despite the simplicity of the setup, complex dynamics are observed. Experiments gave rise to three spatial patterns that we call "hollow ring structure", "filled ring structure", and "disperse pattern". An agent-based, stochastic computational model is used to simulate and interpret the experiments. The model can reproduce the experimentally observed patterns, and identifies key parameters that determine which pattern of virus growth arises. The model is further used to study the long-term outcome of the dynamics for the different growth patterns, and to investigate conditions under which the virus population eliminates the target cells. We find that both the filled ring structure and disperse pattern of initial expansion are indicative of treatment failure, where target cells persist in the long run. The hollow ring structure is associated with either target cell extinction or low-level persistence, both of which can be viewed as treatment success. Interestingly, it is found that equilibrium properties of ordinary differential equations describing the
Foundations of Complex Systems Nonlinear Dynamics, Statistical Physics, and Prediction
Nicolis, Gregoire
2007-01-01
Complexity is emerging as a post-Newtonian paradigm for approaching a large body of phenomena of concern at the crossroads of physical, engineering, environmental, life and human sciences from a unifying point of view. This book outlines the foundations of modern complexity research as it arose from the cross-fertilization of ideas and tools from nonlinear science, statistical physics and numerical simulation. It is shown how these developments lead to an understanding, both qualitative and quantitative, of the complex systems encountered in nature and in everyday experience and, conversely, h
Institute of Scientific and Technical Information of China (English)
LIU Zong-Liang; ZHAO Fang; LI Shao-Hua; ZHAO Mei-Shan; CHEN Chang-Yong
2008-01-01
This paper is concerned with the determination of a unique scaling parameter in complex scaling analysis and with accurate calculation of dynamics resonances. In the preceding paper we have presented a theoretical analysis and provided a formalism for dynamical resonance calculations. In this paper we present accurate numerical results for two non-trivial dynamical processes, namely, models of diatomie molecular predissoeiation and of barrier potential scattering for resonances. The results presented in this paper confirm our theoretical analysis, remove a theoretical ambiguity on determination of the complex scaling parameter, and provide an improved understanding for dynamical resonance calculations in rigged Hilbert space.
Nonlinear Dynamic Behavior of Functionally Graded Truncated Conical Shell Under Complex Loads
Yang, S. W.; Hao, Y. X.; Zhang, W.; Li, S. B.
Nonlinear dynamic behaviors of ceramic-metal graded truncated conical shell subjected to complex loads are investigated. The shell is modeled by first-order shear deformation theory. The nonlinear partial differential governing equation in terms of transverse displacements of the FGM truncated conical shell is derived from the Hamilton's principle. Galerkin's method is then utilized to discretize the partial governing equations to a two-degree-of-freedom nonlinear ordinary differential equation. The temperature-dependent materials properties of the constituents are graded in the radial direction in accordance with a power-law distribution. The aerodynamic pressure can be calculated by using the first-order piston theory. The temperature field is assumed to be a steady-state constant-temperature distribution. Bifurcation diagrams, the maximum Lyapunov exponents, wave forms and phase portraits are obtained by numerical simulation to demonstrate the complex nonlinear dynamics response of the FGM truncated conical shell. The influences of the semi-vertex angle, the material gradient index, in-plane and aerodynamic load on the nonlinear dynamics are studied.
Microbial Bebop: Creating Music from Complex Dynamics in Microbial Ecology
Peter Larsen; Jack Gilbert
2013-01-01
In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improv...
Study on the Supramolecular Inclusion Complex of
Institute of Scientific and Technical Information of China (English)
Liao; Kaijun
2001-01-01
Lappaconitine (Lap) is a diterpenoid akaliamide, naturally occurring in roots and rhizomes of Aconitum and delphinium. Lap reveals bradycardic, hypotensive, antinocieptive activity. However, its application is restrained owing to its poor water solubility, toxicity and side effects on humans. In a number of pharmaceutical studies,CDs have been reported to interact with many drug molecules to form inclusion complexes. These inclusion complexes have been extensively used to improve water solubility of poorly soluble drugs, to reduce their toxicity, and to increase the dissolution rate [1]. In the present work, the β-CD/Lap complex was prepared by kneading method. The products have been characterized by the solubility measurement as well as UV, FTIR, NMR spectroscopy and X-ray powder diffractometry. ……
Asymmetrically interacting spreading dynamics on complex layered networks
Wang, Wei; Yang, Hui; Do, Younghae; Lai, Ying-Cheng; Lee, GyuWon
2014-01-01
The spread of disease through a physical-contact network and the spread of information about the disease on a communication network are two intimately related dynamical processes. We investigate the asymmetrical interplay between the two types of spreading dynamics, each occurring on its own layer, by focusing on the two fundamental quantities underlying any spreading process: epidemic threshold and the final infection ratio. We find that an epidemic outbreak on the contact layer can induce an outbreak on the communication layer, and information spreading can effectively raise the epidemic threshold. When structural correlation exists between the two layers, the information threshold remains unchanged but the epidemic threshold can be enhanced, making the contact layer more resilient to epidemic outbreak. We develop a physical theory to understand the intricate interplay between the two types of spreading dynamics.
Asymmetrically interacting spreading dynamics on complex layered networks
Wang, Wei; Tang, Ming; Yang, Hui; Younghae Do; Lai, Ying-Cheng; Lee, Gyuwon
2014-05-01
The spread of disease through a physical-contact network and the spread of information about the disease on a communication network are two intimately related dynamical processes. We investigate the asymmetrical interplay between the two types of spreading dynamics, each occurring on its own layer, by focusing on the two fundamental quantities underlying any spreading process: epidemic threshold and the final infection ratio. We find that an epidemic outbreak on the contact layer can induce an outbreak on the communication layer, and information spreading can effectively raise the epidemic threshold. When structural correlation exists between the two layers, the information threshold remains unchanged but the epidemic threshold can be enhanced, making the contact layer more resilient to epidemic outbreak. We develop a physical theory to understand the intricate interplay between the two types of spreading dynamics.
Introduction to turbulent dynamical systems in complex systems
Majda, Andrew J
2016-01-01
This volume is a research expository article on the applied mathematics of turbulent dynamical systems through the paradigm of modern applied mathematics. It involves the blending of rigorous mathematical theory, qualitative and quantitative modeling, and novel numerical procedures driven by the goal of understanding physical phenomena which are of central importance to the field. The contents cover general framework, concrete examples, and instructive qualitative models. Accessible open problems are mentioned throughout. Topics covered include: · Geophysical flows with rotation, topography, deterministic and random forcing · New statistical energy principles for general turbulent dynamical systems, with applications · Linear statistical response theory combined with information theory to cope with model errors · Reduced low order models · Recent mathematical strategies for online data assimilation of turbulent dynamical systems as well as rigorous results for finite ensemble Kalman filters The volume wi...
A Review of In-Office Dynamic Image Navigation for Extraction of Complex Mandibular Third Molars.
Emery, Robert W; Korj, Oxana; Agarwal, Ravi
2017-08-01
We performed a retrospective review of in-office removal of complex mandibular third molars with a dynamic image navigation system (DINS). A retrospective review was conducted of cases completed from 2010 to 2014 by a single oral and maxillofacial surgeon. The average age of the patients was 47 years (range, 27 to 72 years). Extraction complexity was classified with Juodzbalys and Daugela's classification system. The included study cases had complexity scores of 9 or greater. Each patient received custom intraoral splints to secure the tracking array and underwent cone beam computed tomography image acquisition. All surgical procedures were performed with a precalibrated tracking straight handpiece under dynamic navigation. All 25 cases were treated successfully with the use of the DINS. Twelve of these cases were associated with pathologic lesions. Three patients were noted to have inferior alveolar nerve paresthesia. One patient sustained a pathologic fracture at week 2. Postoperative infections were noted in 7 cases, 2 of which had a pre-existing infection. One patient reported temporary limitation of mouth opening. A coronectomy was performed in 1 case. We present results using a new technology, the DINS, for removal of complex mandibular third molars. Potential advantages are 1) improved visualization and localization of anatomic structures such as the inferior alveolar nerve, lingual cortical plate, and adjacent roots; 2) improved control during osteotomy; 3) decreased surgical access requirements and reduction in overall bone removal; 4) ability to perform complex procedures successfully in an in-office setting; 5) decreased surgical time resulting from improved visualization; and 6) potential use as a teaching tool. Possible limitations of the use of an in-office DINS include increased cost, increased time attributed to presurgical planning, initial learning curve, and optical array interference by the surgeon or assistants during surgery. Copyright
Multilayer-MCTDH approach to the energy transfer dynamics in the LH2 antenna complex
Shibl, Mohamed F.; Schulze, Jan; Al-Marri, Mohammed J.; Kühn, Oliver
2017-09-01
The multilayer multiconfiguration time-dependent Hartree method is used to study the coupled exciton-vibrational dynamics in a high-dimensional nonameric model of the LH2 antenna complex of purple bacteria. The exciton-vibrational coupling is parametrized within the Huang-Rhys model according to phonon and intramolecular vibrational modes derived from an experimental bacteriochlorophyll spectral density. In contrast to reduced density matrix approaches, the Schrödinger equation is solved explicitly, giving access to the full wave function. This facilitates an unbiased analysis in terms of the coupled dynamics of excitonic and vibrational degrees of freedom. For the present system, we identify spectator modes for the B800 to B800 transfer and we find a non-additive effect of phonon and intramolecular vibrational modes on the B800 to B850 exciton transfer.
Modelling the dynamics of the health-production complex in livestock herds
DEFF Research Database (Denmark)
Sørensen, J.T.; Enevoldsen, Carsten
1992-01-01
This paper reviews how the dynamics of the health-production complex in livestock herds is mimicked by livestock herd simulation models. Twelve models simulating the dynamics of dairy, beef, sheep and sow herds were examined. All models basically included options to alter input and output...... of reproductive animals in a manner which could be related to health problems. Direct effects of diseases on growth or milk production were, however, addressed in only a few models and were confined to a few basic relations if modelled. The lack of effects on individual animal production in the models may relate...... and their interactions could be studied by applying the same standards of analysis to simulated data as to real herd data. © 1992....
Molecular beam studies of reaction dynamics
Energy Technology Data Exchange (ETDEWEB)
Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)
1993-12-01
The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.
Complex dynamic and static structures in interconnected particle systems
Energy Technology Data Exchange (ETDEWEB)
Kristiansen, Kai de Lange
2004-07-01
Observations in the magnetic hole system under different conditions have generated many different patterns and dynamical phenomena which have generated even more ideas on how to attack and analyze them on a firm physical basis. Some of these problems are described in paper 4. In this thesis we have studied the dynamics of the few body system. The braid theory provides a compact description of this motion and enables a better real-time analysis with a minimum of information needed for computation. Also the amount of data to store on disks can then be reduced. Another aspect is that braid theory provides new topological invariants which can bring new light on the phenomena under study. The world lines from the few body system can also be closed into a knot. In knot theory several invariant quantities have been developed the last two decades, where the Jones polynomial is one powerful invariant, as pointed out in Appendix B. The diffusive processes of a few body systems can take super diffusive behaviour, as shown in paper 3. Apparently intermittent states of the same system display a large variety of different modes. By analyzing these modes using rank-ordering statistics, we find that they obey the so-called Zipf-Mandelbrot relation, as discussed in papers 1, 2, 3 and 4. Numerical calculations based on Stokes' drag and magnetic dipole-dipole interactions resemble the behaviour of the experiments well. In sections 3.2 and A.1 we presented a possible derivation of the exponent {gamma} in the Zipf-Mandelbrot relation. The derived values of {gamma} are within the same order of magnitude as the values of {gamma} obtained in the experiments. However, the derived values of {gamma} have high uncertainties. These uncertainties may be reduced with a more refined definition of the work of a mode. This refinement has to take into account the correlation between the modes. The physical meaning behind the exponent {gamma} and the correction term {zeta} in the Zipf
Complex dynamic and static structures in interconnected particle systems
Energy Technology Data Exchange (ETDEWEB)
Kristiansen, Kai de Lange
2004-07-01
Observations in the magnetic hole system under different conditions have generated many different patterns and dynamical phenomena which have generated even more ideas on how to attack and analyze them on a firm physical basis. Some of these problems are described in paper 4. In this thesis we have studied the dynamics of the few body system. The braid theory provides a compact description of this motion and enables a better real-time analysis with a minimum of information needed for computation. Also the amount of data to store on disks can then be reduced. Another aspect is that braid theory provides new topological invariants which can bring new light on the phenomena under study. The world lines from the few body system can also be closed into a knot. In knot theory several invariant quantities have been developed the last two decades, where the Jones polynomial is one powerful invariant, as pointed out in Appendix B. The diffusive processes of a few body systems can take super diffusive behaviour, as shown in paper 3. Apparently intermittent states of the same system display a large variety of different modes. By analyzing these modes using rank-ordering statistics, we find that they obey the so-called Zipf-Mandelbrot relation, as discussed in papers 1, 2, 3 and 4. Numerical calculations based on Stokes' drag and magnetic dipole-dipole interactions resemble the behaviour of the experiments well. In sections 3.2 and A.1 we presented a possible derivation of the exponent {gamma} in the Zipf-Mandelbrot relation. The derived values of {gamma} are within the same order of magnitude as the values of {gamma} obtained in the experiments. However, the derived values of {gamma} have high uncertainties. These uncertainties may be reduced with a more refined definition of the work of a mode. This refinement has to take into account the correlation between the modes. The physical meaning behind the exponent {gamma} and the correction term {zeta} in the Zipf
Allosteric dynamics of SAMHD1 studied by molecular dynamics simulations
Patra, K. K.; Bhattacharya, A.; Bhattacharya, S.
2016-10-01
SAMHD1 is a human cellular enzyme that blocks HIV-1 infection in myeloid cells and non-cycling CD4+T cells. The enzyme is an allosterically regulated triphosphohydrolase that modulates the level of cellular dNTP. The virus restriction is attributed to the lowering of the pool of dNTP in the cell to a point where reverse-transcription is impaired. Mutations in SAMHD1 are also implicated in Aicardi-Goutieres syndrome. A mechanistic understanding of the allosteric activation of the enzyme is still elusive. We have performed molecular dynamics simulations to examine the allosteric site dynamics of the protein and to examine the connection between the stability of the tetrameric complex and the Allosite occupancy.
Linear systems approach to analysis of complex dynamic behaviours in biochemical networks.
Schmidt, H; Jacobsen, E W
2004-06-01
Central functions in the cell are often linked to complex dynamic behaviours, such as sustained oscillations and multistability, in a biochemical reaction network. Determination of the specific mechanisms underlying such behaviours is important, e.g. to determine sensitivity, robustness, and modelling requirements of given cell functions. In this work we adopt a systems approach to the analysis of complex behaviours in intracellular reaction networks, described by ordinary differential equations with known kinetic parameters. We propose to decompose the overall system into a number of low complexity subsystems, and consider the importance of interactions between these in generating specific behaviours. Rather than analysing the network in a state corresponding to the complex non-linear behaviour, we move the system to the underlying unstable steady state, and focus on the mechanisms causing destabilisation of this steady state. This is motivated by the fact that all complex behaviours in unforced systems can be traced to destabilisation (bifurcation) of some steady state, and hence enables us to use tools from linear system theory to qualitatively analyse the sources of given network behaviours. One important objective of the present study is to see how far one can come with a relatively simple approach to the analysis of highly complex biochemical networks. The proposed method is demonstrated by application to a model of mitotic control in Xenopus frog eggs, and to a model of circadian oscillations in Drosophila. In both examples we are able to identify the subsystems, and the related interactions, which are instrumental in generating the observed complex non-linear behaviours.
Laser altimetry reveals complex pattern of Greenland Ice Sheet dynamics
Csatho, Beata M.; Schenk, Anton F.; van der Veen, Cornelis J.; Babonis, Gregory; Duncan, Kyle; Rezvanbehbahani, Soroush; van den Broeke, Michiel R.; Simonsen, Sebastian B.; Nagarajan, Sudhagar; van Angelen, Jan H.
2014-01-01
We present a new record of ice thickness change, reconstructed at nearly 100,000 sites on the Greenland Ice Sheet (GrIS) from laser altimetry measurements spanning the period 1993-2012, partitioned into changes due to surface mass balance (SMB) and ice dynamics. We estimate a mean annual GrIS mass l
Borrowing constraints and complex dynamics in an OLG framework
Assenza, T.; Agliari, A.; Delli Gatti, D.; Santoro, E.
2009-01-01
In this paper we model an OLG economy à la Kiyotaki and Moore whose novel feature is the role of money as a store of value and of bequest as a source of funds to be "invested" in landholding. The dynamics generated by the model are generally characterized by irregular cyclical trajectories and,
Holomorphic Dynamical Systems in the Complex Plane: An Introduction
DEFF Research Database (Denmark)
Branner, Bodil
1995-01-01
The paper reviews some basic properties of Julia sets of polynomials and the Mandelbrot set. In particular we emphasize the concept of normal families, the importance of repelling periodic points. The paper is the first one in a series of three papers about Holomorphic Dynamics in the Proceedings...
Planning using dynamic epistemic logic: Correspondence and complexity
DEFF Research Database (Denmark)
Jensen, Martin Holm
2013-01-01
A growing community investigates planning using dynamic epistemic logic. Another framework based on similar ideas is knowledge-based programs as plans. Here we show how actions correspond in the two frameworks. We finally discuss fragments of DEL planning obtained by the restriction of event models...
Evolution and selection of river networks: statics, dynamics, and complexity.
Rinaldo, Andrea; Rigon, Riccardo; Banavar, Jayanth R; Maritan, Amos; Rodriguez-Iturbe, Ignacio
2014-02-18
Moving from the exact result that drainage network configurations minimizing total energy dissipation are stationary solutions of the general equation describing landscape evolution, we review the static properties and the dynamic origins of the scale-invariant structure of optimal river patterns. Optimal channel networks (OCNs) are feasible optimal configurations of a spanning network mimicking landscape evolution and network selection through imperfect searches for dynamically accessible states. OCNs are spanning loopless configurations, however, only under precise physical requirements that arise under the constraints imposed by river dynamics--every spanning tree is exactly a local minimum of total energy dissipation. It is remarkable that dynamically accessible configurations, the local optima, stabilize into diverse metastable forms that are nevertheless characterized by universal statistical features. Such universal features explain very well the statistics of, and the linkages among, the scaling features measured for fluvial landforms across a broad range of scales regardless of geology, exposed lithology, vegetation, or climate, and differ significantly from those of the ground state, known exactly. Results are provided on the emergence of criticality through adaptative evolution and on the yet-unexplored range of applications of the OCN concept.
Holomorphic Dynamical Systems in the Complex Plane: An Introduction
DEFF Research Database (Denmark)
Branner, Bodil
1995-01-01
The paper reviews some basic properties of Julia sets of polynomials and the Mandelbrot set. In particular we emphasize the concept of normal families, the importance of repelling periodic points. The paper is the first one in a series of three papers about Holomorphic Dynamics in the Proceedings...
Complex Dynamics of Autonomous Communication Networks and the Intelligent Communication Paradigm
Kirilyuk, A P
2004-01-01
Dynamics of arbitrary communication system is analysed as unreduced interaction process. The applied generalised, universally nonperturbative method of effective potential reveals the phenomenon of dynamic multivaluedness of competing system configurations forced to permanently replace each other in a causally random order, which leads to universally defined dynamical chaos, complexity, fractality, self-organisation, and adaptability (physics/9806002, physics/0211071, physics/0405063). We demonstrate the origin of huge, exponentially high efficiency of the unreduced, complex network dynamics and specify the universal symmetry of complexity (physics/0404006) as the fundamental guiding principle for creation and control of such qualitatively new kind of networks and devices. The emerging intelligent communication paradigm and its practical realisation in the form of knowledge-based networks involve the features of true, unreduced intelligence and consciousness (physics/0409140) appearing in complex (multivalued...
National Research Council Canada - National Science Library
Faubert, Jocelyn
2013-01-01
.... We trained 308 observers on a complex dynamic visual scene task void of context and motor control requirements3 and demonstrate that professionals as a group dramatically differ from high-level...
Complex transient dynamics of stage-structured populations in response to environmental changes.
Massie, Thomas M; Ryabov, Alexei; Blasius, Bernd; Weithoff, Guntram; Gaedke, Ursula
2013-07-01
Stage structures of populations can have a profound influence on their dynamics. However, not much is known about the transient dynamics that follow a disturbance in such systems. Here we combined chemostat experiments with dynamical modeling to study the response of the phytoplankton species Chlorella vulgaris to press perturbations. From an initially stable steady state, we altered either the concentration or dilution rate of a growth-limiting resource. This disturbance induced a complex transient response-characterized by the possible onset of oscillations-before population numbers relaxed to a new steady state. Thus, cell numbers could initially change in the opposite direction of the long-term change. We present quantitative indexes to characterize the transients and to show that the dynamic response is dependent on the degree of synchronization among life stages, which itself depends on the state of the population before perturbation. That is, we show how identical future steady states can be approached via different transients depending on the initial population structure. Our experimental results are supported by a size-structured model that accounts for interplay between cell-cycle and population-level processes and that includes resource-dependent variability in cell size. Our results should be relevant to other populations with a stage structure including organisms of higher order.
Atomic dynamics of alumina melt: A molecular dynamics simulation study
Directory of Open Access Journals (Sweden)
S.Jahn
2008-03-01
Full Text Available The atomic dynamics of Al2O3 melt are studied by molecular dynamics simulation. The particle interactions are described by an advanced ionic interaction model that includes polarization effects and ionic shape deformations. The model has been shown to reproduce accurately the static structure factors S(Q from neutron and x-ray diffraction and the dynamic structure factor S(Q,ω from inelastic x-ray scattering. Analysis of the partial dynamic structure factors shows inelastic features in the spectra up to momentum transfers, Q, close to the principal peaks of partial static structure factors. The broadening of the Brillouin line widths is discussed in terms of a frequency dependent viscosity η(ω.
EPR & Klein Paradoxes in Complex Hamiltonian Dynamics and Krein Space Quantization
Payandeh, Farrin
2015-07-01
Negative energy states are applied in Krein space quantization approach to achieve a naturally renormalized theory. For example, this theory by taking the full set of Dirac solutions, could be able to remove the propagator Green function's divergences and automatically without any normal ordering, to vanish the expected value for vacuum state energy. However, since it is a purely mathematical theory, the results are under debate and some efforts are devoted to include more physics in the concept. Whereas Krein quantization is a pure mathematical approach, complex quantum Hamiltonian dynamics is based on strong foundations of Hamilton-Jacobi (H-J) equations and therefore on classical dynamics. Based on complex quantum Hamilton-Jacobi theory, complex spacetime is a natural consequence of including quantum effects in the relativistic mechanics, and is a bridge connecting the causality in special relativity and the non-locality in quantum mechanics, i.e. extending special relativity to the complex domain leads to relativistic quantum mechanics. So that, considering both relativistic and quantum effects, the Klein-Gordon equation could be derived as a special form of the Hamilton-Jacobi equation. Characterizing the complex time involved in an entangled energy state and writing the general form of energy considering quantum potential, two sets of positive and negative energies will be realized. The new states enable us to study the spacetime in a relativistic entangled “space-time” state leading to 12 extra wave functions than the four solutions of Dirac equation for a free particle. Arguing the entanglement of particle and antiparticle leads to a contradiction with experiments. So, in order to correct the results, along with a previous investigation [1], we realize particles and antiparticles as physical entities with positive energy instead of considering antiparticles with negative energy. As an application of modified descriptions for entangled (space
Kant, Rik Henricus Nicolaas van der
2013-01-01
Late endosomal transport is disrupted in several diseases such as Niemann-Pick type C, ARC syndrome and Alzheimer’s disease. This thesis describes the regulation of late endosomal dynamics by cholesterol and multi-protein complexes. We find that cholesterol acts as a cellular tomtom that steers the
Unraveling the complexity of mitochondrial complex I assembly: A dynamic process.
Sánchez-Caballero, Laura; Guerrero-Castillo, Sergio; Nijtmans, Leo
2016-07-01
Mammalian complex I is composed of 44 different subunits and its assembly requires at least 13 specific assembly factors. Proper function of the mitochondrial respiratory chain enzyme is of crucial importance for cell survival due to its major participation in energy production and cell signaling. Complex I assembly depends on the coordination of several crucial processes that need to be tightly interconnected and orchestrated by a number of assembly factors. The understanding of complex I assembly evolved from simple sequential concept to the more sophisticated modular assembly model describing a convoluted process. According to this model, the different modules assemble independently and associate afterwards with each other to form the final enzyme. In this review, we aim to unravel the complexity of complex I assembly and provide the latest insights in this fundamental and fascinating process. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
Small shape deviations causes complex dynamics in large electric generators
Lundström, Niklas L. P.; Grafström, Anton; Aidanpää, Jan-Olov
2014-05-01
We prove that combinations of small eccentricity, ovality and/or triangularity in the rotor and stator can produce complex whirling motions of an unbalanced rotor in large synchronous generators. It is concluded which structures of shape deviations that are more harmful, in the sense of producing complex whirling motions, than others. For each such structure, we derive simplified equations of motions from which we conclude analytically the relation between shape deviations and mass unbalance that yield non-smooth whirling motions. Finally we discuss validity of our results in the sense of modeling of the unbalanced magnetic pull force.
Perdigão, Rui A P; Hall, Julia
2016-01-01
We formulate a nonlinear synergistic theory of coevolutionary systems, disentangling and explaining dynamic complexity in terms of fundamental processes for optimised data analysis and dynamic model design: Dynamic Source Analysis (DSA). DSA provides a nonlinear dynamical basis for spatiotemporal datasets or dynamical models, eliminating redundancies and expressing the system in terms of the smallest number of fundamental processes and interactions without loss of information. This optimises model design in dynamical systems, expressing complex coevolution in simple synergistic terms, yielding physically meaningful spatial and temporal structures. These are extracted by spatiotemporal decomposition of nonlinearly interacting subspaces via the novel concept of a Spatiotemporal Coevolution Manifold. Physical consistency is ensured and mathematical ambiguities are avoided with fundamental principles on energy minimisation and entropy production. The relevance of DSA is illustrated by retrieving a non-redundant, ...
Teachers' Beliefs and Practices: A Dynamic and Complex Relationship
Zheng, Hongying
2013-01-01
Research on teachers' beliefs has provided useful insights into understanding processes of teaching. However, no research has explored teachers' beliefs as a system nor have researchers investigated the substance of interactions between teachers' beliefs, practices and context. Therefore, the author adopts complexity theory to explore the features…