A network dynamics approach to chemical reaction networks
NASA Astrophysics Data System (ADS)
van der Schaft, A. J.; Rao, S.; Jayawardhana, B.
2016-04-01
A treatment of a chemical reaction network theory is given from the perspective of nonlinear network dynamics, in particular of consensus dynamics. By starting from the complex-balanced assumption, the reaction dynamics governed by mass action kinetics can be rewritten into a form which allows for a very simple derivation of a number of key results in the chemical reaction network theory, and which directly relates to the thermodynamics and port-Hamiltonian formulation of the system. Central in this formulation is the definition of a balanced Laplacian matrix on the graph of chemical complexes together with a resulting fundamental inequality. This immediately leads to the characterisation of the set of equilibria and their stability. Furthermore, the assumption of complex balancedness is revisited from the point of view of Kirchhoff's matrix tree theorem. Both the form of the dynamics and the deduced behaviour are very similar to consensus dynamics, and provide additional perspectives to the latter. Finally, using the classical idea of extending the graph of chemical complexes by a 'zero' complex, a complete steady-state stability analysis of mass action kinetics reaction networks with constant inflows and mass action kinetics outflows is given, and a unified framework is provided for structure-preserving model reduction of this important class of open reaction networks.
Identification of dynamical models of chemical reaction networks
NASA Astrophysics Data System (ADS)
Haber, Aleksandar
Current first-principles models of complex chemistry, such as combustion reaction networks, often give inaccurate predictions of the time variation of chemical species. Moreover, the high complexity and dimensionality of these models render them impractical for real-time prediction and control of chemical network processes. These limitations have motivated us to search for an alternative paradigm that is able to both identify the correct model from the observed dynamical data and reduce complexity while preserving the underlying network structure. In this talk, I will present one such modeling paradigm under the scenarios of complete and incomplete observability of the dynamics. The proposed approach is applicable to combustion chemistry and a range of other chemical reaction networks. Research supported by ARO Grant W911NF-14-1-0359.
Reduction of dynamical biochemical reactions networks in computational biology
Radulescu, O.; Gorban, A. N.; Zinovyev, A.; Noel, V.
2012-01-01
Biochemical networks are used in computational biology, to model mechanistic details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as combinatorial explosion are strong obstacles against analyzing the dynamics of large models of this type. Multiscaleness, an important property of these networks, can be used to get past some of these obstacles. Networks with many well separated time scales, can be reduced to simpler models, in a way that depends only on the orders of magnitude and not on the exact values of the kinetic parameters. The main idea used for such robust simplifications of networks is the concept of dominance among model elements, allowing hierarchical organization of these elements according to their effects on the network dynamics. This concept finds a natural formulation in tropical geometry. We revisit, in the light of these new ideas, the main approaches to model reduction of reaction networks, such as quasi-steady state (QSS) and quasi-equilibrium approximations (QE), and provide practical recipes for model reduction of linear and non-linear networks. We also discuss the application of model reduction to the problem of parameter identification, via backward pruning machine learning techniques. PMID:22833754
Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement
NASA Astrophysics Data System (ADS)
Srinivas, Niranjan
Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry. In this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive. Abstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the "device physics" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for
Catalysis in reaction networks.
Gopalkrishnan, Manoj
2011-12-01
We define catalytic networks as chemical reaction networks with an essentially catalytic reaction pathway: one which is "on" in the presence of certain catalysts and "off" in their absence. We show that examples of catalytic networks include synthetic DNA molecular circuits that have been shown to perform signal amplification and molecular logic. Recall that a critical siphon is a subset of the species in a chemical reaction network whose absence is forward invariant and stoichiometrically compatible with a positive point. Our main theorem is that all weakly-reversible networks with critical siphons are catalytic. Consequently, we obtain new proofs for the persistence of atomic event-systems of Adleman et al., and normal networks of Gnacadja. We define autocatalytic networks, and conjecture that a weakly-reversible reaction network has critical siphons if and only if it is autocatalytic. PMID:21503834
Autocatalysis in reaction networks.
Deshpande, Abhishek; Gopalkrishnan, Manoj
2014-10-01
The persistence conjecture is a long-standing open problem in chemical reaction network theory. It concerns the behavior of solutions to coupled ODE systems that arise from applying mass-action kinetics to a network of chemical reactions. The idea is that if all reactions are reversible in a weak sense, then no species can go extinct. A notion that has been found useful in thinking about persistence is that of "critical siphon." We explore the combinatorics of critical siphons, with a view toward the persistence conjecture. We introduce the notions of "drainable" and "self-replicable" (or autocatalytic) siphons. We show that: Every minimal critical siphon is either drainable or self-replicable; reaction networks without drainable siphons are persistent; and nonautocatalytic weakly reversible networks are persistent. Our results clarify that the difficulties in proving the persistence conjecture are essentially due to competition between drainable and self-replicable siphons. PMID:25245394
Liang, Xiao; Wang, Linshan; Wang, Yangfan; Wang, Ruili
2016-09-01
In this paper, we focus on the long time behavior of the mild solution to delayed reaction-diffusion Hopfield neural networks (DRDHNNs) driven by infinite dimensional Wiener processes. We analyze the existence, uniqueness, and stability of this system under the local Lipschitz function by constructing an appropriate Lyapunov-Krasovskii function and utilizing the semigroup theory. Some easy-to-test criteria affecting the well-posedness and stability of the networks, such as infinite dimensional noise and diffusion effect, are obtained. The criteria can be used as theoretic guidance to stabilize DRDHNNs in practical applications when infinite dimensional noise is taken into consideration. Meanwhile, considering the fact that the standard Brownian motion is a special case of infinite dimensional Wiener process, we undertake an analysis of the local Lipschitz condition, which has a wider range than the global Lipschitz condition. Two samples are given to examine the availability of the results in this paper. Simulations are also given using the MATLAB. PMID:26259224
NASA Astrophysics Data System (ADS)
Agrawal, Paras M.; Samadh, Abdul N. A.; Raff, Lionel M.; Hagan, Martin T.; Bukkapatnam, Satish T.; Komanduri, Ranga
2005-12-01
A new approach involving neural networks combined with molecular dynamics has been used for the determination of reaction probabilities as a function of various input parameters for the reactions associated with the chemical-vapor deposition of carbon dimers on a diamond (100) surface. The data generated by the simulations have been used to train and test neural networks. The probabilities of chemisorption, scattering, and desorption as a function of input parameters, such as rotational energy, translational energy, and direction of the incident velocity vector of the carbon dimer, have been considered. The very good agreement obtained between the predictions of neural networks and those provided by molecular dynamics and the fact that, after training the network, the determination of the interpolated probabilities as a function of various input parameters involves only the evaluation of simple analytical expressions rather than computationally intensive algorithms show that neural networks are extremely powerful tools for interpolating the probabilities and rates of chemical reactions. We also find that a neural network fits the underlying trends in the data rather than the statistical variations present in the molecular-dynamics results. Consequently, neural networks can also provide a computationally convenient means of averaging the statistical variations inherent in molecular-dynamics calculations. In the present case the application of this method is found to reduce the statistical uncertainty in the molecular-dynamics results by about a factor of 3.5.
Photochemical reaction dynamics
Moore, B.C.
1993-12-01
The purpose of the program is to develop a fundamental understanding of unimolecular and bimolecular reaction dynamics with application in combustion and energy systems. The energy dependence in ketene isomerization, ketene dissociation dynamics, and carbonyl substitution on organometallic rhodium complexes in liquid xenon have been studied. Future studies concerning unimolecular processes in ketene as well as energy transfer and kinetic studies of methylene radicals are discussed.
Ubiquitous ``glassy'' relaxation in catalytic reaction networks
NASA Astrophysics Data System (ADS)
Awazu, Akinori; Kaneko, Kunihiko
2009-10-01
Study of reversible catalytic reaction networks is important not only as an issue for chemical thermodynamics but also for protocells. From extensive numerical simulations and theoretical analysis, slow relaxation dynamics to sustain nonequlibrium states are commonly observed. These dynamics show two types of salient behaviors that are reminiscent of glassy behavior: slow relaxation along with the logarithmic time dependence of the correlation function and the emergence of plateaus in the relaxation-time course. The former behavior is explained by the eigenvalue distribution of a Jacobian matrix around the equilibrium state that depends on the distribution of kinetic coefficients of reactions. The latter behavior is associated with kinetic constraints rather than metastable states and is due to the absence of catalysts for chemicals in excess and the negative correlation between two chemical species. Examples are given and generality is discussed with relevance to bottleneck-type dynamics in biochemical reactions as well.
Deciphering Time Scale Hierarchy in Reaction Networks.
Nagahata, Yutaka; Maeda, Satoshi; Teramoto, Hiroshi; Horiyama, Takashi; Taketsugu, Tetsuya; Komatsuzaki, Tamiki
2016-03-01
Markovian dynamics on complex reaction networks are one of the most intriguing subjects in a wide range of research fields including chemical reactions, biological physics, and ecology. To represent the global kinetics from one node (corresponding to a basin on an energy landscape) to another requires information on multiple pathways that directly or indirectly connect these two nodes through the entire network. In this paper we present a scheme to extract a hierarchical set of global transition states (TSs) over a discrete-time Markov chain derived from first-order rate equations. The TSs can naturally take into account the multiple pathways connecting any pair of nodes. We also propose a new type of disconnectivity graph (DG) to capture the hierarchical organization of different time scales of reactions that can capture changes in the network due to changes in the time scale of observation. The crux is the introduction of the minimum conductance cut (MCC) in graph clustering, corresponding to the dividing surface across the network having the "smallest" transition probability between two disjoint subnetworks (superbasins on the energy landscape) in the network. We present a new combinatorial search algorithm for finding this MCC. We apply our method to a reaction network of Claisen rearrangement of allyl vinyl ether that consists of 23 nodes and 66 links (saddles on the energy landscape) connecting them. We compare the kinetic properties of our DG to those of the transition matrix of the rate equations and show that our graph can properly reveal the hierarchical organization of time scales in a network. PMID:26641663
From Catalytic Reaction Networks to Protocells
NASA Astrophysics Data System (ADS)
Kaneko, Kunihiko
2013-12-01
In spite of recent advances, there still remains a large gape between a set of chemical reactions and a biological cell. Here we discuss several theoretical efforts to fill in the gap. The topics cover (i) slow relaxation to equilibrium due to glassy behavior in catalytic reaction networks (ii) consistency between molecule replication and cell growth, as well as energy metabolism (iii) control of a system by minority molecules in mutually catalytic system, which work as a carrier of genetic information, and leading to evolvability (iv) generation of a compartmentalized structure as a cluster of molecules centered around the minority molecule, and division of the cluster accompanied by the replication of minority molecule (v) sequential, logical process over several states from concurrent reaction dynamics, by taking advantage of discreteness in molecule number.
Programmability of Chemical Reaction Networks
NASA Astrophysics Data System (ADS)
Cook, Matthew; Soloveichik, David; Winfree, Erik; Bruck, Jehoshua
Motivated by the intriguing complexity of biochemical circuitry within individual cells we study Stochastic Chemical Reaction Networks (SCRNs), a formal model that considers a set of chemical reactions acting on a finite number of molecules in a well-stirred solution according to standard chemical kinetics equations. SCRNs have been widely used for describing naturally occurring (bio)chemical systems, and with the advent of synthetic biology they become a promising language for the design of artificial biochemical circuits. Our interest here is the computational power of SCRNs and how they relate to more conventional models of computation. We survey known connections and give new connections between SCRNs and Boolean Logic Circuits, Vector Addition Systems, Petri nets, Gate Implementability, Primitive Recursive Functions, Register Machines, Fractran, and Turing Machines. A theme to these investigations is the thin line between decidable and undecidable questions about SCRN behavior.
Boolean constraint satisfaction problems for reaction networks
NASA Astrophysics Data System (ADS)
Seganti, A.; De Martino, A.; Ricci-Tersenghi, F.
2013-09-01
We define and study a class of (random) Boolean constraint satisfaction problems representing minimal feasibility constraints for networks of chemical reactions. The constraints we consider encode, respectively, for hard mass-balance conditions (where the consumption and production fluxes of each chemical species are matched) and for soft mass-balance conditions (where a net production of compounds is in principle allowed). We solve these constraint satisfaction problems under the Bethe approximation and derive the corresponding belief propagation equations, which involve eight different messages. The statistical properties of ensembles of random problems are studied via the population dynamics methods. By varying a chemical potential attached to the activity of reactions, we find first-order transitions and strong hysteresis, suggesting a non-trivial structure in the space of feasible solutions.
Some Concepts in Reaction Dynamics
NASA Astrophysics Data System (ADS)
Polanyi, John C.
1987-05-01
The objective in this work has been one which I have shared with the two other 1986 Nobel lecturers in chemistry, D. R. Herschbach and Y. T. Lee, as well as with a wide group of colleagues and co-workers who have been responsible for bringing this field to its current state. That state is summarized in the title; we now have some concepts relevant to the motions of atoms and molecules in simple reactions, and some examples of the application of these concepts. We are, however, richer in vocabulary than in literature. The great epics of reaction dynamics remain to be written. I shall confine myself to some simple stories.
Modeling the Dynamics of Compromised Networks
Soper, B; Merl, D M
2011-09-12
Accurate predictive models of compromised networks would contribute greatly to improving the effectiveness and efficiency of the detection and control of network attacks. Compartmental epidemiological models have been applied to modeling attack vectors such as viruses and worms. We extend the application of these models to capture a wider class of dynamics applicable to cyber security. By making basic assumptions regarding network topology we use multi-group epidemiological models and reaction rate kinetics to model the stochastic evolution of a compromised network. The Gillespie Algorithm is used to run simulations under a worst case scenario in which the intruder follows the basic connection rates of network traffic as a method of obfuscation.
A Networks Approach to Modeling Enzymatic Reactions.
Imhof, P
2016-01-01
Modeling enzymatic reactions is a demanding task due to the complexity of the system, the many degrees of freedom involved and the complex, chemical, and conformational transitions associated with the reaction. Consequently, enzymatic reactions are not determined by precisely one reaction pathway. Hence, it is beneficial to obtain a comprehensive picture of possible reaction paths and competing mechanisms. By combining individually generated intermediate states and chemical transition steps a network of such pathways can be constructed. Transition networks are a discretized representation of a potential energy landscape consisting of a multitude of reaction pathways connecting the end states of the reaction. The graph structure of the network allows an easy identification of the energetically most favorable pathways as well as a number of alternative routes. PMID:27497170
Combining molecular dynamics with mesoscopic Green's function reaction dynamics simulations
NASA Astrophysics Data System (ADS)
Vijaykumar, Adithya; Bolhuis, Peter G.; ten Wolde, Pieter Rein
2015-12-01
In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.
Minimal Increase Network Coding for Dynamic Networks
Wu, Yanxia
2016-01-01
Because of the mobility, computing power and changeable topology of dynamic networks, it is difficult for random linear network coding (RLNC) in static networks to satisfy the requirements of dynamic networks. To alleviate this problem, a minimal increase network coding (MINC) algorithm is proposed. By identifying the nonzero elements of an encoding vector, it selects blocks to be encoded on the basis of relationship between the nonzero elements that the controls changes in the degrees of the blocks; then, the encoding time is shortened in a dynamic network. The results of simulations show that, compared with existing encoding algorithms, the MINC algorithm provides reduced computational complexity of encoding and an increased probability of delivery. PMID:26867211
Minimal Increase Network Coding for Dynamic Networks.
Zhang, Guoyin; Fan, Xu; Wu, Yanxia
2016-01-01
Because of the mobility, computing power and changeable topology of dynamic networks, it is difficult for random linear network coding (RLNC) in static networks to satisfy the requirements of dynamic networks. To alleviate this problem, a minimal increase network coding (MINC) algorithm is proposed. By identifying the nonzero elements of an encoding vector, it selects blocks to be encoded on the basis of relationship between the nonzero elements that the controls changes in the degrees of the blocks; then, the encoding time is shortened in a dynamic network. The results of simulations show that, compared with existing encoding algorithms, the MINC algorithm provides reduced computational complexity of encoding and an increased probability of delivery. PMID:26867211
Adaptive Dynamic Bayesian Networks
Ng, B M
2007-10-26
A discrete-time Markov process can be compactly modeled as a dynamic Bayesian network (DBN)--a graphical model with nodes representing random variables and directed edges indicating causality between variables. Each node has a probability distribution, conditional on the variables represented by the parent nodes. A DBN's graphical structure encodes fixed conditional dependencies between variables. But in real-world systems, conditional dependencies between variables may be unknown a priori or may vary over time. Model errors can result if the DBN fails to capture all possible interactions between variables. Thus, we explore the representational framework of adaptive DBNs, whose structure and parameters can change from one time step to the next: a distribution's parameters and its set of conditional variables are dynamic. This work builds on recent work in nonparametric Bayesian modeling, such as hierarchical Dirichlet processes, infinite-state hidden Markov networks and structured priors for Bayes net learning. In this paper, we will explain the motivation for our interest in adaptive DBNs, show how popular nonparametric methods are combined to formulate the foundations for adaptive DBNs, and present preliminary results.
Stochastic flux analysis of chemical reaction networks
2013-01-01
Background Chemical reaction networks provide an abstraction scheme for a broad range of models in biology and ecology. The two common means for simulating these networks are the deterministic and the stochastic approaches. The traditional deterministic approach, based on differential equations, enjoys a rich set of analysis techniques, including a treatment of reaction fluxes. However, the discrete stochastic simulations, which provide advantages in some cases, lack a quantitative treatment of network fluxes. Results We describe a method for flux analysis of chemical reaction networks, where flux is given by the flow of species between reactions in stochastic simulations of the network. Extending discrete event simulation algorithms, our method constructs several data structures, and thereby reveals a variety of statistics about resource creation and consumption during the simulation. We use these structures to quantify the causal interdependence and relative importance of the reactions at arbitrary time intervals with respect to the network fluxes. This allows us to construct reduced networks that have the same flux-behavior, and compare these networks, also with respect to their time series. We demonstrate our approach on an extended example based on a published ODE model of the same network, that is, Rho GTP-binding proteins, and on other models from biology and ecology. Conclusions We provide a fully stochastic treatment of flux analysis. As in deterministic analysis, our method delivers the network behavior in terms of species transformations. Moreover, our stochastic analysis can be applied, not only at steady state, but at arbitrary time intervals, and used to identify the flow of specific species between specific reactions. Our cases study of Rho GTP-binding proteins reveals the role played by the cyclic reverse fluxes in tuning the behavior of this network. PMID:24314153
Multilayer Network Analysis of Nuclear Reactions.
Zhu, Liang; Ma, Yu-Gang; Chen, Qu; Han, Ding-Ding
2016-01-01
The nuclear reaction network is usually studied via precise calculation of differential equation sets, and much research interest has been focused on the characteristics of nuclides, such as half-life and size limit. In this paper, however, we adopt the methods from both multilayer and reaction networks, and obtain a distinctive view by mapping all the nuclear reactions in JINA REACLIB database into a directed network with 4 layers: neutron, proton, (4)He and the remainder. The layer names correspond to reaction types decided by the currency particles consumed. This combined approach reveals that, in the remainder layer, the β-stability has high correlation with node degree difference and overlapping coefficient. Moreover, when reaction rates are considered as node strength, we find that, at lower temperatures, nuclide half-life scales reciprocally with its out-strength. The connection between physical properties and topological characteristics may help to explore the boundary of the nuclide chart. PMID:27558995
Multilayer Network Analysis of Nuclear Reactions
Zhu, Liang; Ma, Yu-Gang; Chen, Qu; Han, Ding-Ding
2016-01-01
The nuclear reaction network is usually studied via precise calculation of differential equation sets, and much research interest has been focused on the characteristics of nuclides, such as half-life and size limit. In this paper, however, we adopt the methods from both multilayer and reaction networks, and obtain a distinctive view by mapping all the nuclear reactions in JINA REACLIB database into a directed network with 4 layers: neutron, proton, 4He and the remainder. The layer names correspond to reaction types decided by the currency particles consumed. This combined approach reveals that, in the remainder layer, the β-stability has high correlation with node degree difference and overlapping coefficient. Moreover, when reaction rates are considered as node strength, we find that, at lower temperatures, nuclide half-life scales reciprocally with its out-strength. The connection between physical properties and topological characteristics may help to explore the boundary of the nuclide chart. PMID:27558995
Law of Localization in Chemical Reaction Networks
NASA Astrophysics Data System (ADS)
Okada, Takashi; Mochizuki, Atsushi
2016-07-01
In living cells, chemical reactions are connected by sharing their products and substrates, and form complex networks, e.g., metabolic pathways. Here we developed a theory to predict the sensitivity, i.e., the responses of concentrations and fluxes to perturbations of enzymes, from network structure alone. Nonzero response patterns turn out to exhibit two characteristic features, localization and hierarchy. We present a general theorem connecting sensitivity with network topology that explains these characteristic patterns. Our results imply that network topology is an origin of biological robustness. Finally, we suggest a strategy to determine real networks from experimental measurements.
Disease dynamics in a dynamic social network
NASA Astrophysics Data System (ADS)
Christensen, Claire; Albert, István; Grenfell, Bryan; Albert, Réka
2010-07-01
We develop a framework for simulating a realistic, evolving social network (a city) into which a disease is introduced. We compare our results to prevaccine era measles data for England and Wales, and find that they capture the quantitative and qualitative features of epidemics in populations spanning two orders of magnitude. Our results provide unique insight into how and why the social topology of the contact network influences the propagation of the disease through the population. We argue that network simulation is suitable for concurrently probing contact network dynamics and disease dynamics in ways that prior modeling approaches cannot and it can be extended to the study of less well-documented diseases.
Computational functions in biochemical reaction networks.
Arkin, A; Ross, J
1994-01-01
In prior work we demonstrated the implementation of logic gates, sequential computers (universal Turing machines), and parallel computers by means of the kinetics of chemical reaction mechanisms. In the present article we develop this subject further by first investigating the computational properties of several enzymatic (single and multiple) reaction mechanisms: we show their steady states are analogous to either Boolean or fuzzy logic gates. Nearly perfect digital function is obtained only in the regime in which the enzymes are saturated with their substrates. With these enzymatic gates, we construct combinational chemical networks that execute a given truth-table. The dynamic range of a network's output is strongly affected by "input/output matching" conditions among the internal gate elements. We find a simple mechanism, similar to the interconversion of fructose-6-phosphate between its two bisphosphate forms (fructose-1,6-bisphosphate and fructose-2,6-bisphosphate), that functions analogously to an AND gate. When the simple model is supplanted with one in which the enzyme rate laws are derived from experimental data, the steady state of the mechanism functions as an asymmetric fuzzy aggregation operator with properties akin to a fuzzy AND gate. The qualitative behavior of the mechanism does not change when situated within a large model of glycolysis/gluconeogenesis and the TCA cycle. The mechanism, in this case, switches the pathway's mode from glycolysis to gluconeogenesis in response to chemical signals of low blood glucose (cAMP) and abundant fuel for the TCA cycle (acetyl coenzyme A). Images FIGURE 3 FIGURE 4 FIGURE 5 FIGURE 7 FIGURE 10 FIGURE 12 FIGURE 13 FIGURE 14 FIGURE 15 FIGURE 16 PMID:7948674
Li, Jun; Guo, Hua E-mail: hguo@unm.edu; Chen, Jun; Zhang, Dong H. E-mail: hguo@unm.edu
2014-01-28
A permutationally invariant global potential energy surface for the HOCO system is reported by fitting a larger number of high-level ab initio points using the newly proposed permutation invariant polynomial-neural network method. The small fitting error (∼5 meV) indicates a faithful representation of the potential energy surface over a large configuration space. Full-dimensional quantum and quasi-classical trajectory studies of the title reaction were performed on this potential energy surface. While the results suggest that the differences between this and an earlier neural network fits are small, discrepancies with state-to-state experimental data remain significant.
Timescale analysis of rule-based biochemical reaction networks
Klinke, David J.; Finley, Stacey D.
2012-01-01
The flow of information within a cell is governed by a series of protein-protein interactions that can be described as a reaction network. Mathematical models of biochemical reaction networks can be constructed by repetitively applying specific rules that define how reactants interact and what new species are formed upon reaction. To aid in understanding the underlying biochemistry, timescale analysis is one method developed to prune the size of the reaction network. In this work, we extend the methods associated with timescale analysis to reaction rules instead of the species contained within the network. To illustrate this approach, we applied timescale analysis to a simple receptor-ligand binding model and a rule-based model of Interleukin-12 (IL-12) signaling in näive CD4+ T cells. The IL-12 signaling pathway includes multiple protein-protein interactions that collectively transmit information; however, the level of mechanistic detail sufficient to capture the observed dynamics has not been justified based upon the available data. The analysis correctly predicted that reactions associated with JAK2 and TYK2 binding to their corresponding receptor exist at a pseudo-equilibrium. In contrast, reactions associated with ligand binding and receptor turnover regulate cellular response to IL-12. An empirical Bayesian approach was used to estimate the uncertainty in the timescales. This approach complements existing rank- and flux-based methods that can be used to interrogate complex reaction networks. Ultimately, timescale analysis of rule-based models is a computational tool that can be used to reveal the biochemical steps that regulate signaling dynamics. PMID:21954150
Orthogonal gradient networks via post polymerization reaction
NASA Astrophysics Data System (ADS)
Chinnayan Kannan, Pandiyarajan; Genzer, Jan
2015-03-01
We report a novel synthetic route to generate orthogonal gradient networks through post polymerization reaction using pentaflurophenylmethacrylate (PFPMAc) active ester chemistry. These chemoselective monomers were successfully copolymerized with 5 mole% of the photo (methacryloyloxybenzophenone) and thermal (styrenesulfonylazide) crosslinkers. Subsequently, the copolymers were modified by a series of amines having various alkyl chain lengths. The conversion of post polymerization reaction was monitored using Fourier Transform Infrared Spectroscopy (FT-IR) and noticed that almost all pentaflurophenyl moieties are substituted by amines within in an hour without affecting the crosslinkers. In addition, the incorporation of photo and thermal crosslinkers in the polymer enabled us to achieve stable and covalently surface-bound polymer gradient networks (PGN) in an orthogonal manner, i.e. complete control over the crosslink density of the network in two opposite directions (i.e. heat vs photo). The network properties such as wettability, swelling and tensile modulus of the gradient coatings are studied and revealed in the paper.
Entropy of dynamical social networks
NASA Astrophysics Data System (ADS)
Zhao, Kun; Karsai, Marton; Bianconi, Ginestra
2012-02-01
Dynamical social networks are evolving rapidly and are highly adaptive. Characterizing the information encoded in social networks is essential to gain insight into the structure, evolution, adaptability and dynamics. Recently entropy measures have been used to quantify the information in email correspondence, static networks and mobility patterns. Nevertheless, we still lack methods to quantify the information encoded in time-varying dynamical social networks. In this talk we present a model to quantify the entropy of dynamical social networks and use this model to analyze the data of phone-call communication. We show evidence that the entropy of the phone-call interaction network changes according to circadian rhythms. Moreover we show that social networks are extremely adaptive and are modified by the use of technologies such as mobile phone communication. Indeed the statistics of duration of phone-call is described by a Weibull distribution and is significantly different from the distribution of duration of face-to-face interactions in a conference. Finally we investigate how much the entropy of dynamical social networks changes in realistic models of phone-call or face-to face interactions characterizing in this way different type human social behavior.
Dynamic Reaction Figures: An Integrative Vehicle for Understanding Chemical Reactions
ERIC Educational Resources Information Center
Schultz, Emeric
2008-01-01
A highly flexible learning tool, referred to as a dynamic reaction figure, is described. Application of these figures can (i) yield the correct chemical equation by simply following a set of menu driven directions; (ii) present the underlying "mechanism" in chemical reactions; and (iii) help to solve quantitative problems in a number of different…
Nonlinear Dynamics on Interconnected Networks
NASA Astrophysics Data System (ADS)
Arenas, Alex; De Domenico, Manlio
2016-06-01
Networks of dynamical interacting units can represent many complex systems, from the human brain to transportation systems and societies. The study of these complex networks, when accounting for different types of interactions has become a subject of interest in the last few years, especially because its representational power in the description of users' interactions in diverse online social platforms (Facebook, Twitter, Instagram, etc.) [1], or in representing different transportation modes in urban networks [2,3]. The general name coined for these networks is multilayer networks, where each layer accounts for a type of interaction (see Fig. 1).
Structurally Dynamic Spin Market Networks
NASA Astrophysics Data System (ADS)
Horváth, Denis; Kuscsik, Zoltán
The agent-based model of stock price dynamics on a directed evolving complex network is suggested and studied by direct simulation. The stationary regime is maintained as a result of the balance between the extremal dynamics, adaptivity of strategic variables and reconnection rules. The inherent structure of node agent "brain" is modeled by a recursive neural network with local and global inputs and feedback connections. For specific parametric combination the complex network displays small-world phenomenon combined with scale-free behavior. The identification of a local leader (network hub, agent whose strategies are frequently adapted by its neighbors) is carried out by repeated random walk process through network. The simulations show empirically relevant dynamics of price returns and volatility clustering. The additional emerging aspects of stylized market statistics are Zipfian distributions of fitness.
Some Concepts in Reaction Dynamics
NASA Technical Reports Server (NTRS)
Polannyi, John C.
1972-01-01
In 1929 London 1 published a very approximate solution of the Schroedinger equation for a system of chemical interest: H3. To the extent that chemistry can be regarded as existing separately from physics, this was a landmark in the history of chemistry, comparable in importance to the landmark in the history of physics marked by the appearance of the Heitler-London equation for H2. The expression for H3, was, of necessity, even less accurate than that for H2, but chemists, like the habitual poor, were accustomed to this sort of misfortune. Together with the physicists they enjoyed the sensation of living in a renaissance. The physicists still could not calculate a great deal that was of interest to them, and the chemists could calculate less, but both could now dream. It would be too easy to say that their dreams were dreams of unlimited computer time. Their dreams were a lot more productive than that. Two years after London published his equation, H. Eyring and M. Polanyi obtained the first numerical energy surface for H3. They infused the London equation with a measure of empiricism to produce an energy surface which, whether or not it was correct in its details, provided a basis for further speculations of an important sort. The existence of a tangible energy surface in 1931 stimulated speculation along two different lines. The following year Pelzer and Wigner used this London-Eyring-Polanyi (LEP) energy surface for a thermodynamic treatment of the reaction rate in H + H2. This important development reached its full flowering a few years later. In these remarks I shall be concerned with another line of development. A second more-or-less distinct category of speculation that began with (and, indeed, in) the 1931 paper has to do with the dynamics of individual reactive encounters under the influence of specified interaction potentials.
Dynamic and interacting complex networks
NASA Astrophysics Data System (ADS)
Dickison, Mark E.
This thesis employs methods of statistical mechanics and numerical simulations to study some aspects of dynamic and interacting complex networks. The mapping of various social and physical phenomena to complex networks has been a rich field in the past few decades. Subjects as broad as petroleum engineering, scientific collaborations, and the structure of the internet have all been analyzed in a network physics context, with useful and universal results. In the first chapter we introduce basic concepts in networks, including the two types of network configurations that are studied and the statistical physics and epidemiological models that form the framework of the network research, as well as covering various previously-derived results in network theory that are used in the work in the following chapters. In the second chapter we introduce a model for dynamic networks, where the links or the strengths of the links change over time. We solve the model by mapping dynamic networks to the problem of directed percolation, where the direction corresponds to the time evolution of the network. We show that the dynamic network undergoes a percolation phase transition at a critical concentration pc, that decreases with the rate r at which the network links are changed. The behavior near criticality is universal and independent of r. We find that for dynamic random networks fundamental laws are changed: i) The size of the giant component at criticality scales with the network size N for all values of r, rather than as N2/3 in static network, ii) In the presence of a broad distribution of disorder, the optimal path length between two nodes in a dynamic network scales as N1/2, compared to N1/3 in a static network. The third chapter consists of a study of the effect of quarantine on the propagation of epidemics on an adaptive network of social contacts. For this purpose, we analyze the susceptible-infected-recovered model in the presence of quarantine, where susceptible
Disease Dynamics in a Dynamic Social Network
Christensen, Claire; Albert, István; Grenfell, Bryan; Albert, Réka
2010-01-01
We develop a framework for simulating a realistic, evolving social network (a city) into which a disease is introduced. We compare our results to prevaccine era measles data for England and Wales, and find that they capture the quantitative and qualitative features of epidemics in populations spanning two orders of magnitude. Our results provide unique insight into how and why the social topology of the contact network influences the propagation of the disease through the population. We argue that network simulation is suitable for concurrently probing contact network dynamics and disease dynamics in ways that prior modeling approaches cannot and it can be extended to the study of less well-documented diseases. PMID:20563303
Infering Networks From Collective Dynamics
NASA Astrophysics Data System (ADS)
Timme, Marc
How can we infer direct physical interactions between pairs of units from only knowing the units' time series? Here we present a dynamical systems' view on collective network dynamics, and propose the concept of a dynamics' space to reveal interaction networks from time series. We present two examples: one, where the time series stem from standard ordinary differential equations, and a second, more abstract, where the time series exhibits only partial information about the units' states. We apply the latter to neural circuit dynamics where the observables are spike timing data, i.e. only a discrete, state-dependent outputs of the neurons. These results may help revealing network structure for systems where direct access to dynamics is simpler than to connectivity, cf.. This is work with Jose Casadiego, Srinivas Gorur Shandilya, Mor Nitzan, Hauke Haehne and Dimitra Maoutsa. Supported by Grants of the BMBF (Future Compliant Power Grids - CoNDyNet) and by the Max Planck Society to MT.
Anomalous subdiffusion with multispecies linear reaction dynamics.
Langlands, T A M; Henry, B I; Wearne, S L
2008-02-01
We have introduced a set of coupled fractional reaction-diffusion equations to model a multispecies system undergoing anomalous subdiffusion with linear reaction dynamics. The model equations are derived from a mesoscopic continuous time random walk formulation of anomalously diffusing species with linear mean field reaction kinetics. The effect of reactions is manifest in reaction modified spatiotemporal diffusion operators as well as in additive mean field reaction terms. One consequence of the nonseparability of reaction and subdiffusion terms is that the governing evolution equation for the concentration of one particular species may include both reactive and diffusive contributions from other species. The general solution is derived for the multispecies system and some particular special cases involving both irreversible and reversible reaction dynamics are analyzed in detail. We have carried out Monte Carlo simulations corresponding to these special cases and we find excellent agreement with theory. PMID:18351991
Realistic Control of Network Dynamics
Cornelius, Sean P.; Kath, William L.; Motter, Adilson E.
2014-01-01
The control of complex networks is of paramount importance in areas as diverse as ecosystem management, emergency response, and cell reprogramming. A fundamental property of networks is that perturbations to one node can affect other nodes, potentially causing the entire system to change behavior or fail. Here, we show that it is possible to exploit the same principle to control network behavior. Our approach accounts for the nonlinear dynamics inherent to real systems, and allows bringing the system to a desired target state even when this state is not directly accessible due to constraints that limit the allowed interventions. Applications show that this framework permits reprogramming a network to a desired task as well as rescuing networks from the brink of failure—which we illustrate through the mitigation of cascading failures in a power-grid network and the identification of potential drug targets in a signaling network of human cancer. PMID:23803966
Transient spatiotemporal chaos in reaction-diffusion networks
NASA Astrophysics Data System (ADS)
Wackerbauer, Renate
2010-03-01
Complex transient dynamics is reported in various extended systems, including transient turbulence in shear flows, transient spatiotemporal chaos in reaction- diffusion models, and non-chaotic irregular transient dynamics in neural networks. The asymptotic stability is difficult to determine since the transient lifetime typically increases exponentially with the system size. Our studies show that transient spatiotemporal chaos is extensive in various reaction- diffusion systems; the Lyapunov dimension increases linearly with the network size. A master stability analysis provides insight into the asymptotic stability in the Baer- Eiswirth and the Gray-Scott systems. The asymptotic state is characterized by negative transverse Lyapunov exponents on the attractor of the invariant synchronization manifold. The average lifetime depends on the number of transverse directions that are unstable along a typical excitation cycle.
Solution of Chemical Master Equations for Nonlinear Stochastic Reaction Networks
Smadbeck, Patrick; Kaznessis, Yiannis N.
2014-01-01
Stochasticity in the dynamics of small reacting systems requires discrete-probabilistic models of reaction kinetics instead of traditional continuous-deterministic ones. The master probability equation is a complete model of randomly evolving molecular populations. Because of its ambitious character, the master equation remained unsolved for all but the simplest of molecular interaction networks. With the first solution of chemical master equations, a wide range of experimental observations of small-system interactions may be mathematically conceptualized. PMID:25215268
Interfacial welding of dynamic covalent network polymers
NASA Astrophysics Data System (ADS)
Yu, Kai; Shi, Qian; Li, Hao; Jabour, John; Yang, Hua; Dunn, Martin L.; Wang, Tiejun; Qi, H. Jerry
2016-09-01
Dynamic covalent network (or covalent adaptable network) polymers can rearrange their macromolecular chain network by bond exchange reactions (BERs) where an active unit replaces a unit in an existing bond to form a new bond. Such macromolecular events, when they occur in large amounts, can attribute to unusual properties that are not seen in conventional covalent network polymers, such as shape reforming and surface welding; the latter further enables the important attributes of material malleability and powder-based reprocessing. In this paper, a multiscale modeling framework is developed to study the surface welding of thermally induced dynamic covalent network polymers. At the macromolecular network level, a lattice model is developed to describe the chain density evolution across the interface and its connection to bulk stress relaxation due to BERs. The chain density evolution rule is then fed into a continuum level interfacial model that takes into account surface roughness and applied pressure to predict the effective elastic modulus and interfacial fracture energy of welded polymers. The model yields particularly accessible results where the moduli and interfacial strength of the welded samples as a function of temperature and pressure can be predicted with four parameters, three of which can be measured directly. The model identifies the dependency of surface welding efficiency on the applied thermal and mechanical fields: the pressure will affect the real contact area under the consideration of surface roughness of dynamic covalent network polymers; the chain density increment on the real contact area of interface is only dependent on the welding time and temperature. The modeling approach shows good agreement with experiments and can be extended to other types of dynamic covalent network polymers using different stimuli for BERs, such as light and moisture etc.
A model reduction method for biochemical reaction networks
2014-01-01
Background In this paper we propose a model reduction method for biochemical reaction networks governed by a variety of reversible and irreversible enzyme kinetic rate laws, including reversible Michaelis-Menten and Hill kinetics. The method proceeds by a stepwise reduction in the number of complexes, defined as the left and right-hand sides of the reactions in the network. It is based on the Kron reduction of the weighted Laplacian matrix, which describes the graph structure of the complexes and reactions in the network. It does not rely on prior knowledge of the dynamic behaviour of the network and hence can be automated, as we demonstrate. The reduced network has fewer complexes, reactions, variables and parameters as compared to the original network, and yet the behaviour of a preselected set of significant metabolites in the reduced network resembles that of the original network. Moreover the reduced network largely retains the structure and kinetics of the original model. Results We apply our method to a yeast glycolysis model and a rat liver fatty acid beta-oxidation model. When the number of state variables in the yeast model is reduced from 12 to 7, the difference between metabolite concentrations in the reduced and the full model, averaged over time and species, is only 8%. Likewise, when the number of state variables in the rat-liver beta-oxidation model is reduced from 42 to 29, the difference between the reduced model and the full model is 7.5%. Conclusions The method has improved our understanding of the dynamics of the two networks. We found that, contrary to the general disposition, the first few metabolites which were deleted from the network during our stepwise reduction approach, are not those with the shortest convergence times. It shows that our reduction approach performs differently from other approaches that are based on time-scale separation. The method can be used to facilitate fitting of the parameters or to embed a detailed model of
Wong, Albert S Y; Postma, Sjoerd G J; Vialshin, Ilia N; Semenov, Sergey N; Huck, Wilhelm T S
2015-09-30
Our knowledge of the properties and dynamics of complex molecular reaction networks, for example those found in living systems, considerably lags behind the understanding of elementary chemical reactions. In part, this is because chemical reactions networks are nonlinear systems that operate under conditions far from equilibrium. Of particular interest is the role of individual reaction rates on the stability of the network output. In this research we use a rational approach combined with computational methods, to produce complex behavior (in our case oscillations) and show that small changes in molecular structure are sufficient to impart large changes in network behavior. PMID:26352485
Dynamical dipole mode in fusion reactions
Pierroutsakou, D.; Boiano, A.; Romoli, M.; Martin, B.; Inglima, G.; La Commara, M.; Sandoli, M.; Agodi, C.; Alba, R.; Coniglione, R.; Zoppo, A. Del; Maiolino, C.; Piattelli, P.; Santonocito, D.; Sapienza, P.; Baran, V.; Glodariu, T.; Cardella, G.; De Filippo, E.; Pagano, A.
2009-05-04
We investigated the dynamical dipole mode, related with entrance channel charge asymmetry effects, in the {sup 40}Ar+{sup 92}Zr and {sup 36}Ar+{sup 96}Zr fusion reactions at E{sub lab} = 15.1 A and 16 A MeV, respectively. These reactions populate, through entrance channels having different charge asymmetries, a compound nucleus in the A = 126 mass energy region, identical spin distribution at an average excitation energy of about 280 MeV. The compound nucleus average excitation energy and average mass were deduced by the analysis of the light charged particle energy spectra. By studying the {gamma}-ray energy spectra and the {gamma}-ray angular distributions of the considered reactions, the dynamical nature of the prompt radiation related to the dynamical dipole mode was evidenced. The data are compared with calculations based on a collective bremsstrahlung analysis of the reaction dynamics.
Dynamical detection of network communities
NASA Astrophysics Data System (ADS)
Quiles, Marcos G.; Macau, Elbert E. N.; Rubido, Nicolás
2016-05-01
A prominent feature of complex networks is the appearance of communities, also known as modular structures. Specifically, communities are groups of nodes that are densely connected among each other but connect sparsely with others. However, detecting communities in networks is so far a major challenge, in particular, when networks evolve in time. Here, we propose a change in the community detection approach. It underlies in defining an intrinsic dynamic for the nodes of the network as interacting particles (based on diffusive equations of motion and on the topological properties of the network) that results in a fast convergence of the particle system into clustered patterns. The resulting patterns correspond to the communities of the network. Since our detection of communities is constructed from a dynamical process, it is able to analyse time-varying networks straightforwardly. Moreover, for static networks, our numerical experiments show that our approach achieves similar results as the methodologies currently recognized as the most efficient ones. Also, since our approach defines an N-body problem, it allows for efficient numerical implementations using parallel computations that increase its speed performance.
Dynamical detection of network communities
Quiles, Marcos G.; Macau, Elbert E. N.; Rubido, Nicolás
2016-01-01
A prominent feature of complex networks is the appearance of communities, also known as modular structures. Specifically, communities are groups of nodes that are densely connected among each other but connect sparsely with others. However, detecting communities in networks is so far a major challenge, in particular, when networks evolve in time. Here, we propose a change in the community detection approach. It underlies in defining an intrinsic dynamic for the nodes of the network as interacting particles (based on diffusive equations of motion and on the topological properties of the network) that results in a fast convergence of the particle system into clustered patterns. The resulting patterns correspond to the communities of the network. Since our detection of communities is constructed from a dynamical process, it is able to analyse time-varying networks straightforwardly. Moreover, for static networks, our numerical experiments show that our approach achieves similar results as the methodologies currently recognized as the most efficient ones. Also, since our approach defines an N-body problem, it allows for efficient numerical implementations using parallel computations that increase its speed performance. PMID:27158092
Dynamical detection of network communities.
Quiles, Marcos G; Macau, Elbert E N; Rubido, Nicolás
2016-01-01
A prominent feature of complex networks is the appearance of communities, also known as modular structures. Specifically, communities are groups of nodes that are densely connected among each other but connect sparsely with others. However, detecting communities in networks is so far a major challenge, in particular, when networks evolve in time. Here, we propose a change in the community detection approach. It underlies in defining an intrinsic dynamic for the nodes of the network as interacting particles (based on diffusive equations of motion and on the topological properties of the network) that results in a fast convergence of the particle system into clustered patterns. The resulting patterns correspond to the communities of the network. Since our detection of communities is constructed from a dynamical process, it is able to analyse time-varying networks straightforwardly. Moreover, for static networks, our numerical experiments show that our approach achieves similar results as the methodologies currently recognized as the most efficient ones. Also, since our approach defines an N-body problem, it allows for efficient numerical implementations using parallel computations that increase its speed performance. PMID:27158092
Cellular automata modelling of biomolecular networks dynamics.
Bonchev, D; Thomas, S; Apte, A; Kier, L B
2010-01-01
The modelling of biological systems dynamics is traditionally performed by ordinary differential equations (ODEs). When dealing with intracellular networks of genes, proteins and metabolites, however, this approach is hindered by network complexity and the lack of experimental kinetic parameters. This opened the field for other modelling techniques, such as cellular automata (CA) and agent-based modelling (ABM). This article reviews this emerging field of studies on network dynamics in molecular biology. The basics of the CA technique are discussed along with an extensive list of related software and websites. The application of CA to networks of biochemical reactions is exemplified in detail by the case studies of the mitogen-activated protein kinase (MAPK) signalling pathway, the FAS-ligand (FASL)-induced and Bcl-2-related apoptosis. The potential of the CA method to model basic pathways patterns, to identify ways to control pathway dynamics and to help in generating strategies to fight with cancer is demonstrated. The different line of CA applications presented includes the search for the best-performing network motifs, an analysis of importance for effective intracellular signalling and pathway cross-talk. PMID:20373215
Stochastic dynamics of macromolecular-assembly networks.
NASA Astrophysics Data System (ADS)
Saiz, Leonor; Vilar, Jose
2006-03-01
The formation and regulation of macromolecular complexes provides the backbone of most cellular processes, including gene regulation and signal transduction. The inherent complexity of assembling macromolecular structures makes current computational methods strongly limited for understanding how the physical interactions between cellular components give rise to systemic properties of cells. Here we present a stochastic approach to study the dynamics of networks formed by macromolecular complexes in terms of the molecular interactions of their components [1]. Exploiting key thermodynamic concepts, this approach makes it possible to both estimate reaction rates and incorporate the resulting assembly dynamics into the stochastic kinetics of cellular networks. As prototype systems, we consider the lac operon and phage λ induction switches, which rely on the formation of DNA loops by proteins [2] and on the integration of these protein-DNA complexes into intracellular networks. This cross-scale approach offers an effective starting point to move forward from network diagrams, such as those of protein-protein and DNA-protein interaction networks, to the actual dynamics of cellular processes. [1] L. Saiz and J.M.G. Vilar, submitted (2005). [2] J.M.G. Vilar and L. Saiz, Current Opinion in Genetics & Development, 15, 136-144 (2005).
Dynamics of associating networks
NASA Astrophysics Data System (ADS)
Tang, Shengchang; Habicht, Axel; Wang, Muzhou; Li, Shuaili; Seiffert, Sebastian; Olsen, Bradley
Associating polymers offer important technological solutions to renewable and self-healing materials, conducting electrolytes for energy storage and transport, and vehicles for cell and protein deliveries. The interplay between polymer topologies and association chemistries warrants new interesting physics from associating networks, yet poses significant challenges to study these systems over a wide range of time and length scales. In a series of studies, we explored self-diffusion mechanisms of associating polymers above the percolation threshold, by combining experimental measurements using forced Rayleigh scattering and analytical insights from a two-state model. Despite the differences in molecular structures, a universal super-diffusion phenomenon is observed when diffusion of molecular species is hindered by dissociation kinetics. The molecular dissociation rate can be used to renormalize shear rheology data, which yields an unprecedented time-temperature-concentration superposition. The obtained shear rheology master curves provide experimental evidence of the relaxation hierarchy in associating networks.
Spontaneous recovery in dynamical networks
NASA Astrophysics Data System (ADS)
Majdandzic, Antonio; Podobnik, Boris; Buldyrev, Sergey V.; Kenett, Dror Y.; Havlin, Shlomo; Eugene Stanley, H.
2014-01-01
Much research has been carried out to explore the structural properties and vulnerability of complex networks. Of particular interest are abrupt dynamic events that cause networks to irreversibly fail. However, in many real-world phenomena, such as brain seizures in neuroscience or sudden market crashes in finance, after an inactive period of time a significant part of the damaged network is capable of spontaneously becoming active again. The process often occurs repeatedly. To model this marked network recovery, we examine the effect of local node recoveries and stochastic contiguous spreading, and find that they can lead to the spontaneous emergence of macroscopic `phase-flipping' phenomena. As the network is of finite size and is stochastic, the fraction of active nodes z switches back and forth between the two network collective modes characterized by high network activity and low network activity. Furthermore, the system exhibits a strong hysteresis behaviour analogous to phase transitions near a critical point. We present real-world network data exhibiting phase switching behaviour in accord with the predictions of the model.
Dynamic interactions in neural networks
Arbib, M.A. ); Amari, S. )
1989-01-01
The study of neural networks is enjoying a great renaissance, both in computational neuroscience, the development of information processing models of living brains, and in neural computing, the use of neurally inspired concepts in the construction of intelligent machines. This volume presents models and data on the dynamic interactions occurring in the brain, and exhibits the dynamic interactions between research in computational neuroscience and in neural computing. The authors present current research, future trends and open problems.
Recent advances in symmetric and network dynamics
NASA Astrophysics Data System (ADS)
Golubitsky, Martin; Stewart, Ian
2015-09-01
We summarize some of the main results discovered over the past three decades concerning symmetric dynamical systems and networks of dynamical systems, with a focus on pattern formation. In both of these contexts, extra constraints on the dynamical system are imposed, and the generic phenomena can change. The main areas discussed are time-periodic states, mode interactions, and non-compact symmetry groups such as the Euclidean group. We consider both dynamics and bifurcations. We summarize applications of these ideas to pattern formation in a variety of physical and biological systems, and explain how the methods were motivated by transferring to new contexts René Thom's general viewpoint, one version of which became known as "catastrophe theory." We emphasize the role of symmetry-breaking in the creation of patterns. Topics include equivariant Hopf bifurcation, which gives conditions for a periodic state to bifurcate from an equilibrium, and the H/K theorem, which classifies the pairs of setwise and pointwise symmetries of periodic states in equivariant dynamics. We discuss mode interactions, which organize multiple bifurcations into a single degenerate bifurcation, and systems with non-compact symmetry groups, where new technical issues arise. We transfer many of the ideas to the context of networks of coupled dynamical systems, and interpret synchrony and phase relations in network dynamics as a type of pattern, in which space is discretized into finitely many nodes, while time remains continuous. We also describe a variety of applications including animal locomotion, Couette-Taylor flow, flames, the Belousov-Zhabotinskii reaction, binocular rivalry, and a nonlinear filter based on anomalous growth rates for the amplitude of periodic oscillations in a feed-forward network.
Recent advances in symmetric and network dynamics.
Golubitsky, Martin; Stewart, Ian
2015-09-01
We summarize some of the main results discovered over the past three decades concerning symmetric dynamical systems and networks of dynamical systems, with a focus on pattern formation. In both of these contexts, extra constraints on the dynamical system are imposed, and the generic phenomena can change. The main areas discussed are time-periodic states, mode interactions, and non-compact symmetry groups such as the Euclidean group. We consider both dynamics and bifurcations. We summarize applications of these ideas to pattern formation in a variety of physical and biological systems, and explain how the methods were motivated by transferring to new contexts René Thom's general viewpoint, one version of which became known as "catastrophe theory." We emphasize the role of symmetry-breaking in the creation of patterns. Topics include equivariant Hopf bifurcation, which gives conditions for a periodic state to bifurcate from an equilibrium, and the H/K theorem, which classifies the pairs of setwise and pointwise symmetries of periodic states in equivariant dynamics. We discuss mode interactions, which organize multiple bifurcations into a single degenerate bifurcation, and systems with non-compact symmetry groups, where new technical issues arise. We transfer many of the ideas to the context of networks of coupled dynamical systems, and interpret synchrony and phase relations in network dynamics as a type of pattern, in which space is discretized into finitely many nodes, while time remains continuous. We also describe a variety of applications including animal locomotion, Couette-Taylor flow, flames, the Belousov-Zhabotinskii reaction, binocular rivalry, and a nonlinear filter based on anomalous growth rates for the amplitude of periodic oscillations in a feed-forward network. PMID:26428565
Time-Dependent Molecular Reaction Dynamics
Oehrn, Yngve
2007-11-29
This paper is a brief review of a time-dependent, direct, nonadiabatic theory of molecular processes called Electron Nuclear Dynamics (END). This approach to the study of molecular reaction dynamics is a hierarchical theory that can be applied at various levels of approximation. The simplest level of END uses classical nuclei and represents all electrons by a single, complex, determinantal wave function. The wave function parameters such as average nuclear positions and momenta, and molecular orbital coefcients carry the time dependence and serve as dynamical variables. Examples of application are given of the simplest level of END to ion-atom and ion-molecule reactions.
Adaptive hybrid simulations for multiscale stochastic reaction networks
NASA Astrophysics Data System (ADS)
Hepp, Benjamin; Gupta, Ankit; Khammash, Mustafa
2015-01-01
The probability distribution describing the state of a Stochastic Reaction Network (SRN) evolves according to the Chemical Master Equation (CME). It is common to estimate its solution using Monte Carlo methods such as the Stochastic Simulation Algorithm (SSA). In many cases, these simulations can take an impractical amount of computational time. Therefore, many methods have been developed that approximate sample paths of the underlying stochastic process and estimate the solution of the CME. A prominent class of these methods include hybrid methods that partition the set of species and the set of reactions into discrete and continuous subsets. Such a partition separates the dynamics into a discrete and a continuous part. Simulating such a stochastic process can be computationally much easier than simulating the exact discrete stochastic process with SSA. Moreover, the quasi-stationary assumption to approximate the dynamics of fast subnetworks can be applied for certain classes of networks. However, as the dynamics of a SRN evolves, these partitions may have to be adapted during the simulation. We develop a hybrid method that approximates the solution of a CME by automatically partitioning the reactions and species sets into discrete and continuous components and applying the quasi-stationary assumption on identifiable fast subnetworks. Our method does not require any user intervention and it adapts to exploit the changing timescale separation between reactions and/or changing magnitudes of copy-numbers of constituent species. We demonstrate the efficiency of the proposed method by considering examples from systems biology and showing that very good approximations to the exact probability distributions can be achieved in significantly less computational time. This is especially the case for systems with oscillatory dynamics, where the system dynamics change considerably throughout the time-period of interest.
Adaptive hybrid simulations for multiscale stochastic reaction networks
Hepp, Benjamin; Gupta, Ankit; Khammash, Mustafa
2015-01-21
The probability distribution describing the state of a Stochastic Reaction Network (SRN) evolves according to the Chemical Master Equation (CME). It is common to estimate its solution using Monte Carlo methods such as the Stochastic Simulation Algorithm (SSA). In many cases, these simulations can take an impractical amount of computational time. Therefore, many methods have been developed that approximate sample paths of the underlying stochastic process and estimate the solution of the CME. A prominent class of these methods include hybrid methods that partition the set of species and the set of reactions into discrete and continuous subsets. Such a partition separates the dynamics into a discrete and a continuous part. Simulating such a stochastic process can be computationally much easier than simulating the exact discrete stochastic process with SSA. Moreover, the quasi-stationary assumption to approximate the dynamics of fast subnetworks can be applied for certain classes of networks. However, as the dynamics of a SRN evolves, these partitions may have to be adapted during the simulation. We develop a hybrid method that approximates the solution of a CME by automatically partitioning the reactions and species sets into discrete and continuous components and applying the quasi-stationary assumption on identifiable fast subnetworks. Our method does not require any user intervention and it adapts to exploit the changing timescale separation between reactions and/or changing magnitudes of copy-numbers of constituent species. We demonstrate the efficiency of the proposed method by considering examples from systems biology and showing that very good approximations to the exact probability distributions can be achieved in significantly less computational time. This is especially the case for systems with oscillatory dynamics, where the system dynamics change considerably throughout the time-period of interest.
Competitive dynamics on complex networks.
Zhao, Jiuhua; Liu, Qipeng; 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 most likely to be the winner. These findings may shed new light on the role of network structure in competition and to what extent could competitors adjust network structure so as to win the competition. PMID:25068622
Competitive Dynamics on Complex Networks
NASA Astrophysics Data System (ADS)
Zhao, Jiuhua; Liu, Qipeng; Wang, Xiaofan
2014-07-01
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 most likely to be the winner. These findings may shed new light on the role of network structure in competition and to what extent could competitors adjust network structure so as to win the competition.
A chemical reaction network solver for the astrophysics code NIRVANA
NASA Astrophysics Data System (ADS)
Ziegler, U.
2016-02-01
Context. Chemistry often plays an important role in astrophysical gases. It regulates thermal properties by changing species abundances and via ionization processes. This way, time-dependent cooling mechanisms and other chemistry-related energy sources can have a profound influence on the dynamical evolution of an astrophysical system. Modeling those effects with the underlying chemical kinetics in realistic magneto-gasdynamical simulations provide the basis for a better link to observations. Aims: The present work describes the implementation of a chemical reaction network solver into the magneto-gasdynamical code NIRVANA. For this purpose a multispecies structure is installed, and a new module for evolving the rate equations of chemical kinetics is developed and coupled to the dynamical part of the code. A small chemical network for a hydrogen-helium plasma was constructed including associated thermal processes which is used in test problems. Methods: Evolving a chemical network within time-dependent simulations requires the additional solution of a set of coupled advection-reaction equations for species and gas temperature. Second-order Strang-splitting is used to separate the advection part from the reaction part. The ordinary differential equation (ODE) system representing the reaction part is solved with a fourth-order generalized Runge-Kutta method applicable for stiff systems inherent to astrochemistry. Results: A series of tests was performed in order to check the correctness of numerical and technical implementation. Tests include well-known stiff ODE problems from the mathematical literature in order to confirm accuracy properties of the solver used as well as problems combining gasdynamics and chemistry. Overall, very satisfactory results are achieved. Conclusions: The NIRVANA code is now ready to handle astrochemical processes in time-dependent simulations. An easy-to-use interface allows implementation of complex networks including thermal processes
Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks
Ziaul Huque
2007-08-31
This is the final technical report for the project titled 'Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks'. The aim of the project was to develop an efficient chemistry model for combustion simulations. The reduced chemistry model was developed mathematically without the need of having extensive knowledge of the chemistry involved. To aid in the development of the model, Neural Networks (NN) was used via a new network topology known as Non-linear Principal Components Analysis (NPCA). A commonly used Multilayer Perceptron Neural Network (MLP-NN) was modified to implement NPCA-NN. The training rate of NPCA-NN was improved with the GEneralized Regression Neural Network (GRNN) based on kernel smoothing techniques. Kernel smoothing provides a simple way of finding structure in data set without the imposition of a parametric model. The trajectory data of the reaction mechanism was generated based on the optimization techniques of genetic algorithm (GA). The NPCA-NN algorithm was then used for the reduction of Dimethyl Ether (DME) mechanism. DME is a recently discovered fuel made from natural gas, (and other feedstock such as coal, biomass, and urban wastes) which can be used in compression ignition engines as a substitute for diesel. An in-house two-dimensional Computational Fluid Dynamics (CFD) code was developed based on Meshfree technique and time marching solution algorithm. The project also provided valuable research experience to two graduate students.
Morphisms of reaction networks that couple structure to function
2014-01-01
Background The mechanisms underlying complex biological systems are routinely represented as networks. Network kinetics is widely studied, and so is the connection between network structure and behavior. However, similarity of mechanism is better revealed by relationships between network structures. Results We define morphisms (mappings) between reaction networks that establish structural connections between them. Some morphisms imply kinetic similarity, and yet their properties can be checked statically on the structure of the networks. In particular we can determine statically that a complex network will emulate a simpler network: it will reproduce its kinetics for all corresponding choices of reaction rates and initial conditions. We use this property to relate the kinetics of many common biological networks of different sizes, also relating them to a fundamental population algorithm. Conclusions Structural similarity between reaction networks can be revealed by network morphisms, elucidating mechanistic and functional aspects of complex networks in terms of simpler networks. PMID:25128194
Stochastic analysis of complex reaction networks using binomial moment equations.
Barzel, Baruch; Biham, Ofer
2012-09-01
The stochastic analysis of complex reaction networks is a difficult problem because the number of microscopic states in such systems increases exponentially with the number of reactive species. Direct integration of the master equation is thus infeasible and is most often replaced by Monte Carlo simulations. While Monte Carlo simulations are a highly effective tool, equation-based formulations are more amenable to analytical treatment and may provide deeper insight into the dynamics of the network. Here, we present a highly efficient equation-based method for the analysis of stochastic reaction networks. The method is based on the recently introduced binomial moment equations [Barzel and Biham, Phys. Rev. Lett. 106, 150602 (2011)]. The binomial moments are linear combinations of the ordinary moments of the probability distribution function of the population sizes of the interacting species. They capture the essential combinatorics of the reaction processes reflecting their stoichiometric structure. This leads to a simple and transparent form of the equations, and allows a highly efficient and surprisingly simple truncation scheme. Unlike ordinary moment equations, in which the inclusion of high order moments is prohibitively complicated, the binomial moment equations can be easily constructed up to any desired order. The result is a set of equations that enables the stochastic analysis of complex reaction networks under a broad range of conditions. The number of equations is dramatically reduced from the exponential proliferation of the master equation to a polynomial (and often quadratic) dependence on the number of reactive species in the binomial moment equations. The aim of this paper is twofold: to present a complete derivation of the binomial moment equations; to demonstrate the applicability of the moment equations for a representative set of example networks, in which stochastic effects play an important role. PMID:23030885
Partition signed social networks via clustering dynamics
NASA Astrophysics Data System (ADS)
Wu, Jianshe; Zhang, Long; Li, Yong; Jiao, Yang
2016-02-01
Inspired by the dynamics phenomenon occurred in social networks, the WJJLGS model is modified to imitate the clustering dynamics of signed social networks. Analyses show that the clustering dynamics of the model can be applied to partition signed social networks. Traditionally, blockmodel is applied to partition signed networks. In this paper, a detailed dynamics-based algorithm for signed social networks (DBAS) is presented. Simulations on several typical real-world and illustrative networks that have been analyzed by the blockmodel verify the correctness of the proposed algorithm. The efficiency of the algorithm is verified on large scale synthetic networks.
Probing reaction dynamics with GDR decay
Beene, J.R.
1994-10-01
The giant dipole resonance (GDR) has been a prolific source of information on the physics of the nucleus. Mostly it has taught us about nuclear structure, but recently experiments have utilized the GDR as a probe of nuclear reaction dynamics. In this report two examples of such investigations are discussed involving very different reactions and probing time scales that differ by a factor of {approximately}10{sup 3}.
Reaction dynamics and the interstellar environment
NASA Technical Reports Server (NTRS)
Polanyi, J. C.
1973-01-01
Following a brief outline of the 'normal' equilibrium reaction rate laws, the theme of thermal disequilibrium in interstellar space and the related topic of detailed rate constants are more extensively discussed. Comment is made concerning the two principal techniques that are currently being used to explore the dynamical details of an increasing range of chemical reactions in the laboratory, since it is considered that these techniques suggest ways in which the understanding of the chemistry of interstellar space may be extended.
Clustering under the line graph transformation: application to reaction network
Nacher, Jose C; Ueda, Nobuhisa; Yamada, Takuji; Kanehisa, Minoru; Akutsu, Tatsuya
2004-01-01
Background Many real networks can be understood as two complementary networks with two kind of nodes. This is the case of metabolic networks where the first network has chemical compounds as nodes and the second one has nodes as reactions. In general, the second network may be related to the first one by a technique called line graph transformation (i.e., edges in an initial network are transformed into nodes). Recently, the main topological properties of the metabolic networks have been properly described by means of a hierarchical model. While the chemical compound network has been classified as hierarchical network, a detailed study of the chemical reaction network had not been carried out. Results We have applied the line graph transformation to a hierarchical network and the degree-dependent clustering coefficient C(k) is calculated for the transformed network. C(k) indicates the probability that two nearest neighbours of a vertex of degree k are connected to each other. While C(k) follows the scaling law C(k) ~ k-1.1 for the initial hierarchical network, C(k) scales weakly as k0.08 for the transformed network. This theoretical prediction was compared with the experimental data of chemical reactions from the KEGG database finding a good agreement. Conclusions The weak scaling found for the transformed network indicates that the reaction network can be identified as a degree-independent clustering network. By using this result, the hierarchical classification of the reaction network is discussed. PMID:15617578
Complex reaction networks in high temperature hydrocarbon chemistry.
Mutlay, İbrahim; Restrepo, Albeiro
2015-03-28
Complex chemical reaction mechanisms of high temperature hydrocarbon decomposition are represented as networks and their underlying graph topologies are analyzed as a dynamic system. As model reactants, 1,3-butadiene, acetylene, benzene, ethane, ethylene, methane, methyl isobutyl ketone (MIBK) and toluene are chosen in view of their importance for the global environment, energy technologies as well as their quantum chemical properties. Accurate kinetic mechanisms are computationally simulated and converted to bipartite graphs for the incremental conversion steps of the main reactant. Topological analysis of the resulting temporal networks reveals novel features unknown to classical chemical kinetics theory. The time-dependent percolation behavior of the chemical reaction networks shows infinite order phase transition and a unique correlation between the percolation thresholds and electron distribution of the reactants. These observations are expected to yield important applications in the development of a new theoretical perspective to chemical reactions and technological processes e.g. inhibition of greenhouse gases, efficient utilization of fossil fuels, and large scale carbon nanomaterial production. PMID:25720589
Bosonic reaction-diffusion processes on scale-free networks
NASA Astrophysics Data System (ADS)
Baronchelli, Andrea; Catanzaro, Michele; Pastor-Satorras, Romualdo
2008-07-01
Reaction-diffusion processes can be adopted to model a large number of dynamics on complex networks, such as transport processes or epidemic outbreaks. In most cases, however, they have been studied from a fermionic perspective, in which each vertex can be occupied by at most one particle. While still useful, this approach suffers from some drawbacks, the most important probably being the difficulty to implement reactions involving more than two particles simultaneously. Here we develop a general framework for the study of bosonic reaction-diffusion processes on complex networks, in which there is no restriction on the number of interacting particles that a vertex can host. We describe these processes theoretically by means of continuous-time heterogeneous mean-field theory and divide them into two main classes: steady-state and monotonously decaying processes. We analyze specific examples of both behaviors within the class of one-species processes, comparing the results (whenever possible) with the corresponding fermionic counterparts. We find that the time evolution and critical properties of the particle density are independent of the fermionic or bosonic nature of the process, while differences exist in the functional form of the density of occupied vertices in a given degree class k . We implement a continuous-time Monte Carlo algorithm, well suited for general bosonic simulations, which allows us to confirm the analytical predictions formulated within mean-field theory. Our results, at both the theoretical and numerical levels, can be easily generalized to tackle more complex, multispecies, reaction-diffusion processes and open a promising path for a general study and classification of this kind of dynamical systems on complex networks.
Data modeling of network dynamics
NASA Astrophysics Data System (ADS)
Jaenisch, Holger M.; Handley, James W.; Faucheux, Jeffery P.; Harris, Brad
2004-01-01
This paper highlights Data Modeling theory and its use for text data mining as a graphical network search engine. Data Modeling is then used to create a real-time filter capable of monitoring network traffic down to the port level for unusual dynamics and changes in business as usual. This is accomplished in an unsupervised fashion without a priori knowledge of abnormal characteristics. Two novel methods for converting streaming binary data into a form amenable to graphics based search and change detection are introduced. These techniques are then successfully applied to 1999 KDD Cup network attack data log-on sessions to demonstrate that Data Modeling can detect attacks without prior training on any form of attack behavior. Finally, two new methods for data encryption using these ideas are proposed.
Nonlinear Opinion Dynamics on Networks
NASA Astrophysics Data System (ADS)
Gabbay, Michael; Das, Arindam
2013-03-01
A model which treats group decision making as nonlinear opinion dynamics occurring over a network is presented. The model makes predictions regarding the interaction of network structure and initial disagreement level upon decision outcomes and consensus formation. The model displays bifurcations at high disagreement levels which lead to behaviors that are qualitatively distinct from those at low disagreement. For example, at high disagreement, the model exhibits asymmetric, majority rule outcomes that arise even when the system is symmetric with respect to the distribution of initial opinions and network structure. Analytical approximations for the bifurcation boundaries agree well with numerically-determined boundaries. An ongoing experimental effort involving the use of online discussion groups to test the model predictions is briefly described. We acknowledge the support of the Defense Threat Reduction Agency and the Office of Naval Research under grant HDTRA1-10-1-0075
Chemical Reaction Dynamics in Nanoscle Environments
Evelyn M. Goldfield
2006-09-26
The major focus of the research in this program is the study of the behavior of molecular systems confined in nanoscale environments. The goal is to develop a theoretical framework for predicting how chemical reactions occur in nanoscale environments. To achieve this goal we have employed ab initio quantum chemistry, classical dynamics and quantum dynamics methods. Much of the research has focused on the behavior of molecules confined within single-walled carbon nanotubes (SWCNTs). We have also studied interactions of small molecules with the exterior surface of SWCNTs. Nonequilibrium molecular dynamics of interfaces of sliding surface interfaces have also been performed.
Reaction dynamics in polyatomic molecular systems
Miller, W.H.
1993-12-01
The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.
Hierarchical Feedback Modules and Reaction Hubs in Cell Signaling Networks
Xu, Jianfeng; Lan, Yueheng
2015-01-01
Despite much effort, identification of modular structures and study of their organizing and functional roles remain a formidable challenge in molecular systems biology, which, however, is essential in reaching a systematic understanding of large-scale cell regulation networks and hence gaining capacity of exerting effective interference to cell activity. Combining graph theoretic methods with available dynamics information, we successfully retrieved multiple feedback modules of three important signaling networks. These feedbacks are structurally arranged in a hierarchical way and dynamically produce layered temporal profiles of output signals. We found that global and local feedbacks act in very different ways and on distinct features of the information flow conveyed by signal transduction but work highly coordinately to implement specific biological functions. The redundancy embodied with multiple signal-relaying channels and feedback controls bestow great robustness and the reaction hubs seated at junctions of different paths announce their paramount importance through exquisite parameter management. The current investigation reveals intriguing general features of the organization of cell signaling networks and their relevance to biological function, which may find interesting applications in analysis, design and control of bio-networks. PMID:25951347
Dynamics of the Ethanolamine Glycerophospholipid Remodeling Network
Hermansson, Martin; Somerharju, Pentti; Chuang, Jeffrey
2012-01-01
Acyl chain remodeling in lipids is a critical biochemical process that plays a central role in disease. However, remodeling remains poorly understood, despite massive increases in lipidomic data. In this work, we determine the dynamic network of ethanolamine glycerophospholipid (PE) remodeling, using data from pulse-chase experiments and a novel bioinformatic network inference approach. The model uses a set of ordinary differential equations based on the assumptions that (1) sn1 and sn2 acyl positions are independently remodeled; (2) remodeling reaction rates are constant over time; and (3) acyl donor concentrations are constant. We use a novel fast and accurate two-step algorithm to automatically infer model parameters and their values. This is the first such method applicable to dynamic phospholipid lipidomic data. Our inference procedure closely fits experimental measurements and shows strong cross-validation across six independent experiments with distinct deuterium-labeled PE precursors, demonstrating the validity of our assumptions. In constrast, fits of randomized data or fits using random model parameters are worse. A key outcome is that we are able to robustly distinguish deacylation and reacylation kinetics of individual acyl chain types at the sn1 and sn2 positions, explaining the established prevalence of saturated and unsaturated chains in the respective positions. The present study thus demonstrates that dynamic acyl chain remodeling processes can be reliably determined from dynamic lipidomic data. PMID:23251394
Anomaly Detection in Dynamic Networks
Turcotte, Melissa
2014-10-14
Anomaly detection in dynamic communication networks has many important security applications. These networks can be extremely large and so detecting any changes in their structure can be computationally challenging; hence, computationally fast, parallelisable methods for monitoring the network are paramount. For this reason the methods presented here use independent node and edge based models to detect locally anomalous substructures within communication networks. As a first stage, the aim is to detect changes in the data streams arising from node or edge communications. Throughout the thesis simple, conjugate Bayesian models for counting processes are used to model these data streams. A second stage of analysis can then be performed on a much reduced subset of the network comprising nodes and edges which have been identified as potentially anomalous in the first stage. The first method assumes communications in a network arise from an inhomogeneous Poisson process with piecewise constant intensity. Anomaly detection is then treated as a changepoint problem on the intensities. The changepoint model is extended to incorporate seasonal behavior inherent in communication networks. This seasonal behavior is also viewed as a changepoint problem acting on a piecewise constant Poisson process. In a static time frame, inference is made on this extended model via a Gibbs sampling strategy. In a sequential time frame, where the data arrive as a stream, a novel, fast Sequential Monte Carlo (SMC) algorithm is introduced to sample from the sequence of posterior distributions of the change points over time. A second method is considered for monitoring communications in a large scale computer network. The usage patterns in these types of networks are very bursty in nature and don’t fit a Poisson process model. For tractable inference, discrete time models are considered, where the data are aggregated into discrete time periods and probability models are fitted to the
Deconvolution of dynamic mechanical networks
Hinczewski, Michael; von Hansen, Yann; Netz, Roland R.
2010-01-01
Time-resolved single-molecule biophysical experiments yield data that contain a wealth of dynamic information, in addition to the equilibrium distributions derived from histograms of the time series. In typical force spectroscopic setups the molecule is connected via linkers to a readout device, forming a mechanically coupled dynamic network. Deconvolution of equilibrium distributions, filtering out the influence of the linkers, is a straightforward and common practice. We have developed an analogous dynamic deconvolution theory for the more challenging task of extracting kinetic properties of individual components in networks of arbitrary complexity and topology. Our method determines the intrinsic linear response functions of a given object in the network, describing the power spectrum of conformational fluctuations. The practicality of our approach is demonstrated for the particular case of a protein linked via DNA handles to two optically trapped beads at constant stretching force, which we mimic through Brownian dynamics simulations. Each well in the protein free energy landscape (corresponding to folded, unfolded, or possibly intermediate states) will have its own characteristic equilibrium fluctuations. The associated linear response function is rich in physical content, because it depends both on the shape of the well and its diffusivity—a measure of the internal friction arising from such processes as the transient breaking and reformation of bonds in the protein structure. Starting from the autocorrelation functions of the equilibrium bead fluctuations measured in this force clamp setup, we show how an experimentalist can accurately extract the state-dependent protein diffusivity using a straightforward two-step procedure. PMID:21118989
Modeling stochasticity in biochemical reaction networks
NASA Astrophysics Data System (ADS)
Constantino, P. H.; Vlysidis, M.; Smadbeck, P.; Kaznessis, Y. N.
2016-03-01
Small biomolecular systems are inherently stochastic. Indeed, fluctuations of molecular species are substantial in living organisms and may result in significant variation in cellular phenotypes. The chemical master equation (CME) is the most detailed mathematical model that can describe stochastic behaviors. However, because of its complexity the CME has been solved for only few, very small reaction networks. As a result, the contribution of CME-based approaches to biology has been very limited. In this review we discuss the approach of solving CME by a set of differential equations of probability moments, called moment equations. We present different approaches to produce and to solve these equations, emphasizing the use of factorial moments and the zero information entropy closure scheme. We also provide information on the stability analysis of stochastic systems. Finally, we speculate on the utility of CME-based modeling formalisms, especially in the context of synthetic biology efforts.
Unimolecular reaction dynamics of free radicals
Terry A. Miller
2006-09-01
Free radical reactions are of crucial importance in combustion and in atmospheric chemistry. Reliable theoretical models for predicting the rates and products of these reactions are required for modeling combustion and atmospheric chemistry systems. Unimolecular reactions frequently play a crucial role in determining final products. The dissociations of vinyl, CH2= CH, and methoxy, CH3O, have low barriers, about 13,000 cm-1 and 8,000 cm-1, respectively. Since barriers of this magnitude are typical of free radicals these molecules should serve as benchmarks for this important class of reactions. To achieve this goal, a detailed understanding of the vinyl and methoxy radicals is required. Results for dissociation dynamics of vinyl and selectively deuterated vinyl radical are reported. Significantly, H-atom scrambling is shown not to occur in this reaction. A large number of spectroscopic experiments for CH3O and CHD2O have been performed. Spectra recorded include laser induced fluorescence (LIF), laser excited dispersed fluorescence (LEDF), fluorescence dip infrared (FDIR) and stimulated emission pumping (SEP). Such results are critical for implementing dynamics experiments involving the dissociation of methoxy.
Network dynamics in nanofilled polymers
Baeza, Guilhem P.; Dessi, Claudia; Costanzo, Salvatore; Zhao, Dan; Gong, Shushan; Alegria, Angel; Colby, Ralph H.; Rubinstein, Michael; Vlassopoulos, Dimitris; Kumar, Sanat K.
2016-01-01
It is well accepted that adding nanoparticles (NPs) to polymer melts can result in significant property improvements. Here we focus on the causes of mechanical reinforcement and present rheological measurements on favourably interacting mixtures of spherical silica NPs and poly(2-vinylpyridine), complemented by several dynamic and structural probes. While the system dynamics are polymer-like with increased friction for low silica loadings, they turn network-like when the mean face-to-face separation between NPs becomes smaller than the entanglement tube diameter. Gel-like dynamics with a Williams–Landel–Ferry temperature dependence then result. This dependence turns particle dominated, that is, Arrhenius-like, when the silica loading increases to ∼31 vol%, namely, when the average nearest distance between NP faces becomes comparable to the polymer's Kuhn length. Our results demonstrate that the flow properties of nanocomposites are complex and can be tuned via changes in filler loading, that is, the character of polymer bridges which ‘tie' NPs together into a network. PMID:27109062
Network dynamics in nanofilled polymers.
Baeza, Guilhem P; Dessi, Claudia; Costanzo, Salvatore; Zhao, Dan; Gong, Shushan; Alegria, Angel; Colby, Ralph H; Rubinstein, Michael; Vlassopoulos, Dimitris; Kumar, Sanat K
2016-01-01
It is well accepted that adding nanoparticles (NPs) to polymer melts can result in significant property improvements. Here we focus on the causes of mechanical reinforcement and present rheological measurements on favourably interacting mixtures of spherical silica NPs and poly(2-vinylpyridine), complemented by several dynamic and structural probes. While the system dynamics are polymer-like with increased friction for low silica loadings, they turn network-like when the mean face-to-face separation between NPs becomes smaller than the entanglement tube diameter. Gel-like dynamics with a Williams-Landel-Ferry temperature dependence then result. This dependence turns particle dominated, that is, Arrhenius-like, when the silica loading increases to ∼31 vol%, namely, when the average nearest distance between NP faces becomes comparable to the polymer's Kuhn length. Our results demonstrate that the flow properties of nanocomposites are complex and can be tuned via changes in filler loading, that is, the character of polymer bridges which 'tie' NPs together into a network. PMID:27109062
Network dynamics in nanofilled polymers
NASA Astrophysics Data System (ADS)
Baeza, Guilhem P.; Dessi, Claudia; Costanzo, Salvatore; Zhao, Dan; Gong, Shushan; Alegria, Angel; Colby, Ralph H.; Rubinstein, Michael; Vlassopoulos, Dimitris; Kumar, Sanat K.
2016-04-01
It is well accepted that adding nanoparticles (NPs) to polymer melts can result in significant property improvements. Here we focus on the causes of mechanical reinforcement and present rheological measurements on favourably interacting mixtures of spherical silica NPs and poly(2-vinylpyridine), complemented by several dynamic and structural probes. While the system dynamics are polymer-like with increased friction for low silica loadings, they turn network-like when the mean face-to-face separation between NPs becomes smaller than the entanglement tube diameter. Gel-like dynamics with a Williams-Landel-Ferry temperature dependence then result. This dependence turns particle dominated, that is, Arrhenius-like, when the silica loading increases to ~31 vol%, namely, when the average nearest distance between NP faces becomes comparable to the polymer's Kuhn length. Our results demonstrate that the flow properties of nanocomposites are complex and can be tuned via changes in filler loading, that is, the character of polymer bridges which `tie' NPs together into a network.
Dynamics of active actin networks
NASA Astrophysics Data System (ADS)
Koehler, Simone
2014-03-01
Local mechanical and structural properties of a eukaryotic cell are determined by its cytoskeleton. To adapt to their environment, cells rely on constant self-organized rearrangement processes of their actin cytoskeleton. To shed light on the principles underlying these dynamic self-organization processes we investigate a minimal reconstituted active system consisting of actin filaments, crosslinking molecules and molecular motor filaments. Using quantitative fluorescence microscopy and image analysis, we show, that these minimal model systems exhibit a generic structure formation mechanism. The competition between force generation by molecular motors and the stabilization of the network by crosslinking proteins results in a highly dynamic reorganization process which is characterized by anomalous transport dynamics with a superdiffusive behavior also found in intracellular dynamics. In vitro, these dynamics are governed by chemical and physical parameters that alter the balance of motor and crosslinking proteins, such as pH. These findings can be expected to have broad implications in our understanding of cytoskeletal regulation in vivo.
Quantum effects in unimolecular reaction dynamics
Gezelter, J.D.
1995-12-01
This work is primarily concerned with the development of models for the quantum dynamics of unimolecular isomerization and photodissociation reactions. We apply the rigorous quantum methodology of a Discrete Variable Representation (DVR) with Absorbing Boundary Conditions (ABC) to these models in an attempt to explain some very surprising results from a series of experiments on vibrationally excited ketene. Within the framework of these models, we are able to identify the experimental signatures of tunneling and dynamical resonances in the energy dependence of the rate of ketene isomerization. Additionally, we investigate the step-like features in the energy dependence of the rate of dissociation of triplet ketene to form {sup 3}B{sub 1} CH{sub 2} + {sup 1}{sigma}{sup +} CO that have been observed experimentally. These calculations provide a link between ab initio calculations of the potential energy surfaces and the experimentally observed dynamics on these surfaces. Additionally, we develop an approximate model for the partitioning of energy in the products of photodissociation reactions of large molecules with appreciable barriers to recombination. In simple bond cleavage reactions like CH{sub 3}COCl {yields} CH{sub 3}CO + Cl, the model does considerably better than other impulsive and statistical models in predicting the energy distribution in the products. We also investigate ways of correcting classical mechanics to include the important quantum mechanical aspects of zero-point energy. The method we investigate is found to introduce a number of undesirable dynamical artifacts including a reduction in the above-threshold rates for simple reactions, and a strong mixing of the chaotic and regular energy domains for some model problems. We conclude by discussing some of the directions for future research in the field of theoretical chemical dynamics.
Theoretical studies of chemical reaction dynamics
Schatz, G.C.
1993-12-01
This collaborative program with the Theoretical Chemistry Group at Argonne involves theoretical studies of gas phase chemical reactions and related energy transfer and photodissociation processes. Many of the reactions studied are of direct relevance to combustion; others are selected they provide important examples of special dynamical processes, or are of relevance to experimental measurements. Both classical trajectory and quantum reactive scattering methods are used for these studies, and the types of information determined range from thermal rate constants to state to state differential cross sections.
Molecular beam studies of reaction dynamics
Lee, Y.T.
1987-03-01
Purpose of this research project is two-fold: (1) to elucidate detailed dynamics of simple elementary reactions which are theoretically important and to unravel the mechanism of complex chemical reactions or photo chemical processes which play an important role in many macroscopic processes and (2) to determine the energetics of polyatomic free radicals using microscopic experimental methods. Most of the information is derived from measurement of the product fragment translational energy and angular distributions using unique molecular beam apparati designed for these purposes.
Yildirim, Necmettin; Kazanci, Caner
2011-01-01
A brief introduction to mathematical modeling of biochemical regulatory reaction networks is presented. Both deterministic and stochastic modeling techniques are covered with examples from enzyme kinetics, coupled reaction networks with oscillatory dynamics and bistability. The Yildirim-Mackey model for lactose operon is used as an example to discuss and show how deterministic and stochastic methods can be used to investigate various aspects of this bacterial circuit. PMID:21187231
Spiralling dynamics near heteroclinic networks
NASA Astrophysics Data System (ADS)
Rodrigues, Alexandre A. P.; Labouriau, Isabel S.
2014-02-01
There are few explicit examples in the literature of vector fields exhibiting complex dynamics that may be proved analytically. We construct explicitly a two parameter family of vector fields on the three-dimensional sphere S, whose flow has a spiralling attractor containing the following: two hyperbolic equilibria, heteroclinic trajectories connecting them transversely and a non-trivial hyperbolic, invariant and transitive set. The spiralling set unfolds a heteroclinic network between two symmetric saddle-foci and contains a sequence of topological horseshoes semiconjugate to full shifts over an alphabet with more and more symbols, coexisting with Newhouse phenomena. The vector field is the restriction to S of a polynomial vector field in R. In this article, we also identify global bifurcations that induce chaotic dynamics of different types.
Dynamics and pattern formation in a cancer network with diffusion
NASA Astrophysics Data System (ADS)
Zheng, Qianqian; Shen, Jianwei
2015-10-01
Diffusion is ubiquitous inside cells, and it is capable of inducing spontaneous pattern formation in reaction-diffusion systems on a spatially homogeneous domain. In this paper, we investigate the dynamics of a diffusive cancer network regulated by microRNA and obtain the condition that the network undergoes a Hopf bifurcation and a Turing pattern bifurcation. In addition, we also develop the amplitude equation of the network model by using Taylor series expansion, multi-scaling and further expansion in powers of a small parameter. As a result of these analyses, we obtain the explicit condition on how the dynamics of the diffusive cancer network evolve. These results reveal that this system has rich dynamics, such as spotted stripe and hexagon patterns. The bifurcation diagram helps us understand the biological mechanism in the cancer network. Finally, numerical simulations confirm our analytical results.
Reduction of chemical reaction networks through delay distributions
NASA Astrophysics Data System (ADS)
Barrio, Manuel; Leier, André; Marquez-Lago, Tatiana T.
2013-03-01
Accurate modelling and simulation of dynamic cellular events require two main ingredients: an adequate description of key chemical reactions and simulation of such chemical events in reasonable time spans. Quite logically, posing the right model is a crucial step for any endeavour in Computational Biology. However, more often than not, it is the associated computational costs which actually limit our capabilities of representing complex cellular behaviour. In this paper, we propose a methodology aimed at representing chains of chemical reactions by much simpler, reduced models. The abridgement is achieved by generation of model-specific delay distribution functions, consecutively fed to a delay stochastic simulation algorithm. We show how such delay distributions can be analytically described whenever the system is solely composed of consecutive first-order reactions, with or without additional "backward" bypass reactions, yielding an exact reduction. For models including other types of monomolecular reactions (constitutive synthesis, degradation, or "forward" bypass reactions), we discuss why one must adopt a numerical approach for its accurate stochastic representation, and propose two alternatives for this. In these cases, the accuracy depends on the respective numerical sample size. Our model reduction methodology yields significantly lower computational costs while retaining accuracy. Quite naturally, computational costs increase alongside network size and separation of time scales. Thus, we expect our model reduction methodologies to significantly decrease computational costs in these instances. We anticipate the use of delays in model reduction will greatly alleviate some of the current restrictions in simulating large sets of chemical reactions, largely applicable in pharmaceutical and biological research.
Molecular beam studies of reaction dynamics
Lee, Y.T.
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.
Molecular beam studies of reaction dynamics
Lee, Yuan T.
1991-03-01
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.
Deterministic Function Computation with Chemical Reaction Networks*
Chen, Ho-Lin; Doty, David; Soloveichik, David
2013-01-01
Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. CRNs are widely used to describe information processing occurring in natural cellular regulatory networks, and with upcoming advances in synthetic biology, CRNs are a promising language for the design of artificial molecular control circuitry. Nonetheless, despite the widespread use of CRNs in the natural sciences, the range of computational behaviors exhibited by CRNs is not well understood. CRNs have been shown to be efficiently Turing-universal (i.e., able to simulate arbitrary algorithms) when allowing for a small probability of error. CRNs that are guaranteed to converge on a correct answer, on the other hand, have been shown to decide only the semilinear predicates (a multi-dimensional generalization of “eventually periodic” sets). We introduce the notion of function, rather than predicate, computation by representing the output of a function f : ℕk → ℕl by a count of some molecular species, i.e., if the CRN starts with x1, …, xk molecules of some “input” species X1, …, Xk, the CRN is guaranteed to converge to having f(x1, …, xk) molecules of the “output” species Y1, …, Yl. We show that a function f : ℕk → ℕl is deterministically computed by a CRN if and only if its graph {(x, y) ∈ ℕk × ℕl ∣ f(x) = y} is a semilinear set. Finally, we show that each semilinear function f (a function whose graph is a semilinear set) can be computed by a CRN on input x in expected time O(polylog ∥x∥1). PMID:25383068
Neural dynamics in superconducting networks
NASA Astrophysics Data System (ADS)
Segall, Kenneth; Schult, Dan; Crotty, Patrick; Miller, Max
2012-02-01
We discuss the use of Josephson junction networks as analog models for simulating neuron behaviors. A single unit called a ``Josephson Junction neuron'' composed of two Josephson junctions [1] displays behavior that shows characteristics of single neurons such as action potentials, thresholds and refractory periods. Synapses can be modeled as passive filters and can be used to connect neurons together. The sign of the bias current to the Josephson neuron can be used to determine if the neuron is excitatory or inhibitory. Due to the intrinsic speed of Josephson junctions and their scaling properties as analog models, a large network of Josephson neurons measured over typical lab times contains dynamics which would essentially be impossible to calculate on a computer We discuss the operating principle of the Josephson neuron, coupling Josephson neurons together to make large networks, and the Kuramoto-like synchronization of a system of disordered junctions.[4pt] [1] ``Josephson junction simulation of neurons,'' P. Crotty, D. Schult and K. Segall, Physical Review E 82, 011914 (2010).
Lattice based Kinetic Monte Carlo Simulations of a complex chemical reaction network
NASA Astrophysics Data System (ADS)
Danielson, Thomas; Savara, Aditya; Hin, Celine
Lattice Kinetic Monte Carlo (KMC) simulations offer a powerful alternative to using ordinary differential equations for the simulation of complex chemical reaction networks. Lattice KMC provides the ability to account for local spatial configurations of species in the reaction network, resulting in a more detailed description of the reaction pathway. In KMC simulations with a large number of reactions, the range of transition probabilities can span many orders of magnitude, creating subsets of processes that occur more frequently or more rarely. Consequently, processes that have a high probability of occurring may be selected repeatedly without actually progressing the system (i.e. the forward and reverse process for the same reaction). In order to avoid the repeated occurrence of fast frivolous processes, it is necessary to throttle the transition probabilities in such a way that avoids altering the overall selectivity. Likewise, as the reaction progresses, new frequently occurring species and reactions may be introduced, making a dynamic throttling algorithm a necessity. We present a dynamic steady-state detection scheme with the goal of accurately throttling rate constants in order to optimize the KMC run time without compromising the selectivity of the reaction network. The algorithm has been applied to a large catalytic chemical reaction network, specifically that of methanol oxidative dehydrogenation, as well as additional pathways on CeO2(111) resulting in formaldehyde, CO, methanol, CO2, H2 and H2O as gas products.
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
2016-01-01
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
NASA Astrophysics Data System (ADS)
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.
Robustness Analysis and Behavior Discrimination in Enzymatic Reaction Networks
Donzé, Alexandre; Fanchon, Eric; Gattepaille, Lucie Martine; Maler, Oded; Tracqui, Philippe
2011-01-01
Characterizing the behavior and robustness of enzymatic networks with numerous variables and unknown parameter values is a major challenge in biology, especially when some enzymes have counter-intuitive properties or switch-like behavior between activation and inhibition. In this paper, we propose new methodological and tool-supported contributions, based on the intuitive formalism of temporal logic, to express in a rigorous manner arbitrarily complex dynamical properties. Our multi-step analysis allows efficient sampling of the parameter space in order to define feasible regions in which the model exhibits imposed or experimentally observed behaviors. In a first step, an algorithmic methodology involving sensitivity analysis is conducted to determine bifurcation thresholds for a limited number of model parameters or initial conditions. In a second step, this boundary detection is supplemented by a global robustness analysis, based on quasi-Monte Carlo approach that takes into account all model parameters. We apply this method to a well-documented enzymatic reaction network describing collagen proteolysis by matrix metalloproteinase MMP2 and membrane type 1 metalloproteinase (MT1-MMP) in the presence of tissue inhibitor of metalloproteinase TIMP2. For this model, our method provides an extended analysis and quantification of network robustness toward paradoxical TIMP2 switching activity between activation or inhibition of MMP2 production. Further implication of our approach is illustrated by demonstrating and analyzing the possible existence of oscillatory behaviors when considering an extended open configuration of the enzymatic network. Notably, we construct bifurcation diagrams that specify key parameters values controlling the co-existence of stable steady and non-steady oscillatory proteolytic dynamics. PMID:21980344
Robustness analysis and behavior discrimination in enzymatic reaction networks.
Donzé, Alexandre; Fanchon, Eric; Gattepaille, Lucie Martine; Maler, Oded; Tracqui, Philippe
2011-01-01
Characterizing the behavior and robustness of enzymatic networks with numerous variables and unknown parameter values is a major challenge in biology, especially when some enzymes have counter-intuitive properties or switch-like behavior between activation and inhibition. In this paper, we propose new methodological and tool-supported contributions, based on the intuitive formalism of temporal logic, to express in a rigorous manner arbitrarily complex dynamical properties. Our multi-step analysis allows efficient sampling of the parameter space in order to define feasible regions in which the model exhibits imposed or experimentally observed behaviors. In a first step, an algorithmic methodology involving sensitivity analysis is conducted to determine bifurcation thresholds for a limited number of model parameters or initial conditions. In a second step, this boundary detection is supplemented by a global robustness analysis, based on quasi-Monte Carlo approach that takes into account all model parameters. We apply this method to a well-documented enzymatic reaction network describing collagen proteolysis by matrix metalloproteinase MMP2 and membrane type 1 metalloproteinase (MT1-MMP) in the presence of tissue inhibitor of metalloproteinase TIMP2. For this model, our method provides an extended analysis and quantification of network robustness toward paradoxical TIMP2 switching activity between activation or inhibition of MMP2 production. Further implication of our approach is illustrated by demonstrating and analyzing the possible existence of oscillatory behaviors when considering an extended open configuration of the enzymatic network. Notably, we construct bifurcation diagrams that specify key parameters values controlling the co-existence of stable steady and non-steady oscillatory proteolytic dynamics. PMID:21980344
Flux-concentration duality in dynamic nonequilibrium biological networks.
Jamshidi, Neema; Palsson, Bernhard Ø
2009-09-01
The structure of dynamic states in biological networks is of fundamental importance in understanding their function. Considering the elementary reaction structure of reconstructed metabolic networks, we show how appreciation of a gradient matrix, G =dv/dx (where v is the vector of fluxes and x is the vector of concentrations), enables the formulation of dual Jacobian matrices. One is for concentrations, J(x) =S x G, and the other is for fluxes, J(v) =G x S. The fundamental properties of these two Jacobians and the underlying duality that relates them are delineated. We describe a generalized approach to decomposing reaction networks in terms of the thermodynamic and kinetic components in the context of the network structure. The thermodynamic and kinetic influences can be viewed in terms of direction-driver relationships in the network. PMID:19720010
Quantum dynamics of fast chemical reactions
Light, J.C.
1993-12-01
The aims of this research are to explore, develop, and apply theoretical methods for the evaluation of the dynamics of gas phase collision processes, primarily chemical reactions. The primary theoretical tools developed for this work have been quantum scattering theory, both in time dependent and time independent forms. Over the past several years, the authors have developed and applied methods for the direct quantum evaluation of thermal rate constants, applying these to the evaluation of the hydrogen isotopic exchange reactions, applied wave packet propagation techniques to the dissociation of Rydberg H{sub 3}, incorporated optical potentials into the evaluation of thermal rate constants, evaluated the use of optical potentials for state-to-state reaction probability evaluations, and, most recently, have developed quantum approaches for electronically non-adiabatic reactions which may be applied to simplify calculations of reactive, but electronically adiabatic systems. Evaluation of the thermal rate constants and the dissociation of H{sub 3} were reported last year, and have now been published.
Community dynamics in social networks
NASA Astrophysics Data System (ADS)
Palla, Gergely; Barabási, Albert-László; Vicsek, Tamás
2007-06-01
We study the statistical properties of community dynamics in large social networks, where the evolving communities are obtained from subsequent snapshots of the modular structure. Such cohesive groups of people can grow by recruiting new members, or contract by loosing members; two (or more) groups may merge into a single community, while a large enough social group can split into several smaller ones; new communities are born and old ones may disappear. We find significant difference between the behaviour of smaller collaborative or friendship circles and larger communities, eg. institutions. Social groups containing only a few members persist longer on average when the fluctuations of the members is small. In contrast, we find that the condition for stability for large communities is continuous changes in their membership, allowing for the possibility that after some time practically all members are exchanged.
Mode specificity in unimolecular reaction dynamics
Waite, B.A.
1982-07-01
Theoretical studies on mode specificity in unimolecular reaction dynamics are presented, based on essentially exact quantum mechanical methods, a semi-classical multichannel branching model, and classical trajectory methods. The principal aim is to discover the relevant factors governing whether a unimolecular system exhibits mode specificity in its individual state rate constants, i.e., whether quasi-degenerate metastable states decay with significantly different rates. Model studies of two nonlinearly coupled oscillators (one of which can dissociate) demonstrate the effects of various features of potential energy surfaces on the character of the rates (e.g., degeneracy of modes, reaction path curvature, frequency modulation, etc.). These results and those obtained for the Henon-Heiles potential energy surface indicate and apparent absence of correlation between the quasi-periodic/ergodic motion of classical mechanics and the mode specific/statistical behavior of the unimolecular rate constants.
New methods for quantum mechanical reaction dynamics
Thompson, W.H. |
1996-12-01
Quantum mechanical methods are developed to describe the dynamics of bimolecular chemical reactions. We focus on developing approaches for directly calculating the desired quantity of interest. Methods for the calculation of single matrix elements of the scattering matrix (S-matrix) and initial state-selected reaction probabilities are presented. This is accomplished by the use of absorbing boundary conditions (ABC) to obtain a localized (L{sup 2}) representation of the outgoing wave scattering Green`s function. This approach enables the efficient calculation of only a single column of the S-matrix with a proportionate savings in effort over the calculation of the entire S-matrix. Applying this method to the calculation of the initial (or final) state-selected reaction probability, a more averaged quantity, requires even less effort than the state-to-state S-matrix elements. It is shown how the same representation of the Green`s function can be effectively applied to the calculation of negative ion photodetachment intensities. Photodetachment spectroscopy of the anion ABC{sup -} can be a very useful method for obtaining detailed information about the neutral ABC potential energy surface, particularly if the ABC{sup -} geometry is similar to the transition state of the neutral ABC. Total and arrangement-selected photodetachment spectra are calculated for the H{sub 3}O{sup -} system, providing information about the potential energy surface for the OH + H{sub 2} reaction when compared with experimental results. Finally, we present methods for the direct calculation of the thermal rate constant from the flux-position and flux-flux correlation functions. The spirit of transition state theory is invoked by concentrating on the short time dynamics in the area around the transition state that determine reactivity. These methods are made efficient by evaluating the required quantum mechanical trace in the basis of eigenstates of the Boltzmannized flux operator.
Controlling the rates of biochemical reactions and signaling networks by shape and volume changes.
Lizana, L; Bauer, B; Orwar, O
2008-03-18
In biological systems, chemical activity takes place in micrometer- and nanometer-sized compartments that constantly change in shape and volume. These ever-changing cellular compartments embed chemical reactions, and we demonstrate that the rates of such incorporated reactions are directly affected by the ongoing shape reconfigurations. First, we show that the rate of product formation in an enzymatic reaction can be regulated by simple volume contraction-dilation transitions. The results suggest that mitochondria may regulate the dynamics of interior reaction pathways (e.g., the Krebs cycle) by volume changes. We then show the effect of shape changes on reactions occurring in more complex and structured systems by using biomimetic networks composed of micrometer-sized compartments joined together by nanotubes. Chemical activity was measured by implementing an enzymatic reaction-diffusion system. During ongoing reactions, the network connectivity is changed suddenly (similar to the dynamic tube formations found inside Golgi stacks, for example), and the effect on the reaction is registered. We show that spatiotemporal properties of the reaction-diffusion system are extremely sensitive to sudden changes in network topology and that chemical reactions can be initiated, or boosted, in certain nodes as a function of connectivity. PMID:18337513
NASA Astrophysics Data System (ADS)
Pal, Krishnendu; Das, Biswajit; Banerjee, Kinshuk; Gangopadhyay, Gautam
2015-09-01
We have introduced an approach to nonequilibrium thermodynamics of an open chemical reaction network in terms of the propensities of the individual elementary reactions and the corresponding reverse reactions. The method is a microscopic formulation of the dissipation function in terms of the relative entropy or Kullback-Leibler distance which is based on the analogy of phase space trajectory with the path of elementary reactions in a network of chemical process. We have introduced here a fluctuation theorem valid for each opposite pair of elementary reactions which is useful in determining the contribution of each sub-reaction on the nonequilibrium thermodynamics of overall reaction. The methodology is applied to an oligomeric enzyme kinetics at a chemiostatic condition that leads the reaction to a nonequilibrium steady state for which we have estimated how each step of the reaction is energy driven or entropy driven to contribute to the overall reaction.
Networked Dynamic Systems: Identification, Controllability, and Randomness
NASA Astrophysics Data System (ADS)
Nabi-Abdolyousefi, Marzieh
The presented dissertation aims to develop a graph-centric framework for the analysis and synthesis of networked dynamic systems (NDS) consisting of multiple dynamic units that interact via an interconnection topology. We examined three categories of network problems, namely, identification, controllability, and randomness. In network identification, as a subclass of inverse problems, we made an explicit relation between the input-output behavior of an NDS and the underlying interacting network. In network controllability, we provided structural and algebraic insights into features of the network that enable external signal(s) to control the state of the nodes in the network for certain classes of interconnections, namely, path, circulant, and Cartesian networks. We also examined the relation between network controllability and the symmetry structure of the graph. Motivated by the analysis results for the controllability and observability of deterministic networks, a natural question is whether randomness in the network layer or in the layer of inputs and outputs generically leads to favorable system theoretic properties. In this direction, we examined system theoretic properties of random networks including controllability, observability, and performance of optimal feedback controllers and estimators. We explored some of the ramifications of such an analysis framework in opinion dynamics over social networks and sensor networks in estimating the real-time position of a Seaglider from experimental data.
Toward cell circuitry: Topological analysis of enzyme reaction networks via reaction route graphs
NASA Astrophysics Data System (ADS)
Datta, Ravindra; Vilekar, Saurabh A.; Fishtik, Ilie; Dittami, James P.
2008-05-01
The first step toward developing complete cell circuitry is to build quantitative networks for enzyme reactions. The conventional King-Altman-Hill (KAH) algorithm for topological analysis of enzyme networks, adapted from electrical networks, is based on “Reaction Graphs” that, unlike electrical circuits, are not quantitative, being straightforward renderings of conventional schematics of reaction mechanisms. Therefore, we propose the use of “Reaction Route (RR) Graphs” instead, as a more suitable graph-theoretical representation for topological analysis of enzyme reaction networks. The RR Graphs are drawn such that they are not only useful for visualizing the various reaction routes or pathways, but unlike Reaction Graphs possess network properties consistent with requisite kinetic, mass balance, and thermodynamic constraints. Therefore, they are better than the conventional Reaction Graphs for topological representation and analysis of enzyme reactions, both via the KAH methodology as well as via numerical matrix inversion. The difference between the two is highlighted based on the example of a single enzyme reaction network for the conversion of 7,8-dihydrofolate and NADPH into 5,6,7,8-tetrahydrofolate and NADP +, catalyzed by the enzyme dihydrofolate reductase.
Model Of Neural Network With Creative Dynamics
NASA Technical Reports Server (NTRS)
Zak, Michail; Barhen, Jacob
1993-01-01
Paper presents analysis of mathematical model of one-neuron/one-synapse neural network featuring coupled activation and learning dynamics and parametrical periodic excitation. Demonstrates self-programming, partly random behavior of suitable designed neural network; believed to be related to spontaneity and creativity of biological neural networks.
Structure, dynamics, and surface reactions of bioactive glasses
NASA Astrophysics Data System (ADS)
Zeitler, Todd R.
Three bioactive glasses (45S5, 55S4.3, and 60S3.8) have been investigated using atomic-scale molecular dynamics simulations in attempt to explain differences in observed macroscopic bioactivity. Bulk and surface structures and bulk dynamics have been characterized. Ion exchange and hydrolysis reactions, the first two stages in Hench's model describing the reactions of bioactive glass surfaces in vivo, have been investigated in detail. The 45S5 composition shows a much greater network fragmentation: it is suggested that this fragmentation can play a role in at least the first two stages of Hench's model for HCA formation on the surfaces of bioactive glasses. In terms of dynamic behavior, long-range diffusion was only observed for sodium. Calcium showed only jumps between adjacent sites, while phosphorus showed only local vibrations. Surface simulations show the distinct accumulation of sodium at the immediate surface for each composition. Surface channels are also shown to exist and are most evident for 45S5 glass. Results for a single ion exchange showed that the ion-exchange reaction is preferred (more exothermic) for Na+ ions near Si, rather than P. A range of reaction energies were found, due to a range of local environments, as expected for a glass surface. The average reaction energies are not significantly different among the three glass compositions. The results for bond hydrolysis on as-created surfaces show no significant differences among the three compositions for simulations involving Si-O-Si or Si-O-P. All average values are greater than zero, indicating endothermic reactions that are not favorable by themselves. However, it is shown that the hydrolysis reactions became more favorable (in fact, exothermic for 45S5 and 55S4.3) when simulated on surfaces that had already been ion-exchanged. This is significant because it gives evidence supporting Hench's proposed reaction sequence. Perhaps even more significantly, the reaction energies for hydrolysis
Forced synchronization of autonomous dynamical Boolean networks
Rivera-Durón, R. R. Campos-Cantón, E.; Campos-Cantón, I.; Gauthier, Daniel J.
2015-08-15
We present the design of an autonomous time-delay Boolean network realized with readily available electronic components. Through simulations and experiments that account for the detailed nonlinear response of each circuit element, we demonstrate that a network with five Boolean nodes displays complex behavior. Furthermore, we show that the dynamics of two identical networks display near-instantaneous synchronization to a periodic state when forced by a common periodic Boolean signal. A theoretical analysis of the network reveals the conditions under which complex behavior is expected in an individual network and the occurrence of synchronization in the forced networks. This research will enable future experiments on autonomous time-delay networks using readily available electronic components with dynamics on a slow enough time-scale so that inexpensive data collection systems can faithfully record the dynamics.
Using Network Dynamical Influence to Drive Consensus
NASA Astrophysics Data System (ADS)
Punzo, Giuliano; Young, George F.; MacDonald, Malcolm; Leonard, Naomi E.
2016-05-01
Consensus and decision-making are often analysed in the context of networks, with many studies focusing attention on ranking the nodes of a network depending on their relative importance to information routing. Dynamical influence ranks the nodes with respect to their ability to influence the evolution of the associated network dynamical system. In this study it is shown that dynamical influence not only ranks the nodes, but also provides a naturally optimised distribution of effort to steer a network from one state to another. An example is provided where the “steering” refers to the physical change in velocity of self-propelled agents interacting through a network. Distinct from other works on this subject, this study looks at directed and hence more general graphs. The findings are presented with a theoretical angle, without targeting particular applications or networked systems; however, the framework and results offer parallels with biological flocks and swarms and opportunities for design of technological networks.
Using Network Dynamical Influence to Drive Consensus.
Punzo, Giuliano; Young, George F; Macdonald, Malcolm; Leonard, Naomi E
2016-01-01
Consensus and decision-making are often analysed in the context of networks, with many studies focusing attention on ranking the nodes of a network depending on their relative importance to information routing. Dynamical influence ranks the nodes with respect to their ability to influence the evolution of the associated network dynamical system. In this study it is shown that dynamical influence not only ranks the nodes, but also provides a naturally optimised distribution of effort to steer a network from one state to another. An example is provided where the "steering" refers to the physical change in velocity of self-propelled agents interacting through a network. Distinct from other works on this subject, this study looks at directed and hence more general graphs. The findings are presented with a theoretical angle, without targeting particular applications or networked systems; however, the framework and results offer parallels with biological flocks and swarms and opportunities for design of technological networks. PMID:27210291
Using Network Dynamical Influence to Drive Consensus
Punzo, Giuliano; Young, George F.; Macdonald, Malcolm; Leonard, Naomi E.
2016-01-01
Consensus and decision-making are often analysed in the context of networks, with many studies focusing attention on ranking the nodes of a network depending on their relative importance to information routing. Dynamical influence ranks the nodes with respect to their ability to influence the evolution of the associated network dynamical system. In this study it is shown that dynamical influence not only ranks the nodes, but also provides a naturally optimised distribution of effort to steer a network from one state to another. An example is provided where the “steering” refers to the physical change in velocity of self-propelled agents interacting through a network. Distinct from other works on this subject, this study looks at directed and hence more general graphs. The findings are presented with a theoretical angle, without targeting particular applications or networked systems; however, the framework and results offer parallels with biological flocks and swarms and opportunities for design of technological networks. PMID:27210291
Reaction dynamics and photochemistry of divalent systems
Davis, H.F.
1992-05-01
Results are presented of molecular beam studies of bimolecular and unimolecular reactions of Ba. Chapter 1 discusses the reaction Ba + NO{sub 2}. Formation of the dominant BaO({sup 1}{Sigma}) + NO products resulted primarily from decay of long-lived Ba{sup +}NO{sub 2}{sup {minus}} collision complexes. Secondary mechanisms led to formation of forward scattered, internally excited BaO, and BaNO + O. D{sub o}(Ba-NO) = 65{plus_minus}20 kcal/mol. Reactions of ground state and electronically excited Ba with water and alcohols are examined in Chapter 2. Reaction of Ba({sup 1}S) + H{sup 2}O led to BaO + H{sub 2}, whereas excited state Ba({sup 1}D) + H{sub 2}O reacted to form BaOH + H. Collisions between Ba and CH{sub 3}OH led to BaOCH{sub 3} + H. Radical channels involve H-atom migration and are promoted by excitation of the incident Ba atom. In Chapter 3, reactions of Ba({sup 1}S) with ClO{sub 2}2 and O{sub 3} are discussed. Again, direct and complex mechanisms were observed. Formation of BaCl + O{sub 2} from decomposition of Ba{sup +}ClO{sub 2}{sup {minus}} accounted for 10% of total reaction crass section. Although Ba + O{sub 3} {yields} BaO + 0{sub 2} occurs primarily by direct reaction mechanisms, the secondary channel Ba + 0{sub 3} {yields} BaO{sub 2} + 0 involved decay of long lived Ba{sup +}O{sub 3}{sup {minus}} intermediates. D{sub o}(Ba{minus}O{sub 2}) = 120 {plus_minus}20 kcal/mol. Photodissociation dynamics of NO{sub 3} is explored in chapter 4. Visible excitation leads to formation of NO + 0{sub 2} and NO{sub 2} + O. Wavelength dependence of branching ratios is investigated. D{sub o}(O-NO{sub 2}) = 48.55 kcal/mole ;and calculate {Delta}H{sub f}(NO{sub 3}) = 17.75 kcal/mole (298K). Chapter 5 discusses the photodissociation of OClO in a molecular beam. Although ClO({sup 2}II) + O({sup 3}P) is dominant, Cl({sup 2}P) + O{sub 2} also forms, with a max yield of 3.9{plus_minus}0.8% near 404nm.
Dynamics on Complex Networks and Applications
NASA Astrophysics Data System (ADS)
Motter, Adilson E.; Matías, Manuel A.; Kurths, Jürgen; Ott, Edward
2006-12-01
At the eight-year anniversary of Watts and Strogatz’s work on the collective dynamics of small-world networks and seven years after Barabási and Albert’s discovery of scale-free networks, the area of dynamical processes on complex networks is at the forefront of the current research on nonlinear dynamics and complex systems. This volume brings together a selection of original contributions in complementary topics of statistical physics, nonlinear dynamics and biological sciences, and is expected to provide the reader with a comprehensive up-to-date representation of this rapidly developing area.
Charge transport network dynamics in molecular aggregates.
Jackson, Nicholas E; Chen, Lin X; Ratner, Mark A
2016-08-01
Due to the nonperiodic nature of charge transport in disordered systems, generating insight into static charge transport networks, as well as analyzing the network dynamics, can be challenging. Here, we apply time-dependent network analysis to scrutinize the charge transport networks of two representative molecular semiconductors: a rigid n-type molecule, perylenediimide, and a flexible p-type molecule, [Formula: see text] Simulations reveal the relevant timescale for local transfer integral decorrelation to be [Formula: see text]100 fs, which is shown to be faster than that of a crystalline morphology of the same molecule. Using a simple graph metric, global network changes are observed over timescales competitive with charge carrier lifetimes. These insights demonstrate that static charge transport networks are qualitatively inadequate, whereas average networks often overestimate network connectivity. Finally, a simple methodology for tracking dynamic charge transport properties is proposed. PMID:27439871
Using Visualizations to Explore Network Dynamics
Chu, Kar-Hai; Wipfli, Heather; Valente, Thomas W.
2014-01-01
Network analysis has become a popular tool to examine data from online social networks to politics to ecological systems. As more computing power has become available, new technology-driven methods and tools are being developed that can support larger and richer network data, including dynamic network analysis. This timely merger of abundant data and cutting edge techniques affords researchers the ability to better understand networks over time, accurately show how they evolve, find patterns of growth, or study models such as the diffusion of innovation. We combine traditional methods in social network analysis with new innovative visualizations and methods in dynamic network studies to explore an online tobacco-control community called GLOBALink, using almost twenty years of longitudinal data. We describe the methods used for the study, and perform an exploratory network study that links empirical results to real-world events. PMID:25285051
Mélykúti, Bence; Hespanha, João P.; Khammash, Mustafa
2014-01-01
Many biochemical reaction networks are inherently multiscale in time and in the counts of participating molecular species. A standard technique to treat different time scales in the stochastic kinetics framework is averaging or quasi-steady-state analysis: it is assumed that the fast dynamics reaches its equilibrium (stationary) distribution on a time scale where the slowly varying molecular counts are unlikely to have changed. We derive analytic equilibrium distributions for various simple biochemical systems, such as enzymatic reactions and gene regulation models. These can be directly inserted into simulations of the slow time-scale dynamics. They also provide insight into the stimulus–response of these systems. An important model for which we derive the analytic equilibrium distribution is the binding of dimer transcription factors (TFs) that first have to form from monomers. This gene regulation mechanism is compared to the cases of the binding of simple monomer TFs to one gene or to multiple copies of a gene, and to the cases of the cooperative binding of two or multiple TFs to a gene. The results apply equally to ligands binding to enzyme molecules. PMID:24920118
Mélykúti, Bence; Hespanha, João P; Khammash, Mustafa
2014-08-01
Many biochemical reaction networks are inherently multiscale in time and in the counts of participating molecular species. A standard technique to treat different time scales in the stochastic kinetics framework is averaging or quasi-steady-state analysis: it is assumed that the fast dynamics reaches its equilibrium (stationary) distribution on a time scale where the slowly varying molecular counts are unlikely to have changed. We derive analytic equilibrium distributions for various simple biochemical systems, such as enzymatic reactions and gene regulation models. These can be directly inserted into simulations of the slow time-scale dynamics. They also provide insight into the stimulus-response of these systems. An important model for which we derive the analytic equilibrium distribution is the binding of dimer transcription factors (TFs) that first have to form from monomers. This gene regulation mechanism is compared to the cases of the binding of simple monomer TFs to one gene or to multiple copies of a gene, and to the cases of the cooperative binding of two or multiple TFs to a gene. The results apply equally to ligands binding to enzyme molecules. PMID:24920118
Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks
Nelson Butuk
2006-09-21
This is an annual technical report for the work done over the last year (period ending 9/30/2005) on the project titled ''Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks''. The aim of the project is to develop an efficient chemistry model for combustion simulations. The reduced chemistry model will be developed mathematically without the need of having extensive knowledge of the chemistry involved. To aid in the development of the model, Neural Networks (NN) will be used via a new network topology know as Non-linear Principal Components Analysis (NPCA). We report on the significant development made in developing a truly meshfree computational fluid dynamics (CFD) flow solver to be coupled to NPCA. First, the procedure of obtaining nearly analytic accurate first order derivatives using the complex step method (CSM) is extended to include computation of accurate meshfree second order derivatives via a theorem described in this report. Next, boosted generalized regression neural network (BGRNN), described in our previous report is combined with CSM and used to obtain complete solution of a hard to solve wave dominated sample second order partial differential equation (PDE): the cubic Schrodinger equation. The resulting algorithm is a significant improvement of the meshfree technique of smooth particle hydrodynamics method (SPH). It is suggested that the demonstrated meshfree technique be termed boosted smooth particle hydrodynamics method (BSPH). Some of the advantages of BSPH over other meshfree methods include; it is of higher order accuracy than SPH; compared to other meshfree methods, it is completely meshfree and does not require any background meshes; It does not involve any construction of shape function with their associated solution of possibly ill conditioned matrix equations; compared to some SPH techniques, no equation for the smoothing parameter is required; finally it is easy to program.
Psychology and social networks: a dynamic network theory perspective.
Westaby, James D; Pfaff, Danielle L; Redding, Nicholas
2014-04-01
Research on social networks has grown exponentially in recent years. However, despite its relevance, the field of psychology has been relatively slow to explain the underlying goal pursuit and resistance processes influencing social networks in the first place. In this vein, this article aims to demonstrate how a dynamic network theory perspective explains the way in which social networks influence these processes and related outcomes, such as goal achievement, performance, learning, and emotional contagion at the interpersonal level of analysis. The theory integrates goal pursuit, motivation, and conflict conceptualizations from psychology with social network concepts from sociology and organizational science to provide a taxonomy of social network role behaviors, such as goal striving, system supporting, goal preventing, system negating, and observing. This theoretical perspective provides psychologists with new tools to map social networks (e.g., dynamic network charts), which can help inform the development of change interventions. Implications for social, industrial-organizational, and counseling psychology as well as conflict resolution are discussed, and new opportunities for research are highlighted, such as those related to dynamic network intelligence (also known as cognitive accuracy), levels of analysis, methodological/ethical issues, and the need to theoretically broaden the study of social networking and social media behavior. (PsycINFO Database Record (c) 2014 APA, all rights reserved). PMID:24750076
Embedding dynamical networks into distributed models
NASA Astrophysics Data System (ADS)
Innocenti, Giacomo; Paoletti, Paolo
2015-07-01
Large networks of interacting dynamical systems are well-known for the complex behaviours they are able to display, even when each node features a quite simple dynamics. Despite examples of such networks being widespread both in nature and in technological applications, the interplay between the local and the macroscopic behaviour, through the interconnection topology, is still not completely understood. Moreover, traditional analytical methods for dynamical response analysis fail because of the intrinsically large dimension of the phase space of the network which makes the general problem intractable. Therefore, in this paper we develop an approach aiming to condense all the information in a compact description based on partial differential equations. By focusing on propagative phenomena, rigorous conditions under which the original network dynamical properties can be successfully analysed within the proposed framework are derived as well. A network of Fitzhugh-Nagumo systems is finally used to illustrate the effectiveness of the proposed method.
Temporal fidelity in dynamic social networks
NASA Astrophysics Data System (ADS)
Stopczynski, Arkadiusz; Sapiezynski, Piotr; Pentland, Alex `Sandy'; Lehmann, Sune
2015-10-01
It has recently become possible to record detailed social interactions in large social systems with high resolution. As we study these datasets, human social interactions display patterns that emerge at multiple time scales, from minutes to months. On a fundamental level, understanding of the network dynamics can be used to inform the process of measuring social networks. The details of measurement are of particular importance when considering dynamic processes where minute-to-minute details are important, because collection of physical proximity interactions with high temporal resolution is difficult and expensive. Here, we consider the dynamic network of proximity-interactions between approximately 500 individuals participating in the Copenhagen Networks Study. We show that in order to accurately model spreading processes in the network, the dynamic processes that occur on the order of minutes are essential and must be included in the analysis.
Reaction-Diffusion Processes on Random and Scale-Free Networks
NASA Astrophysics Data System (ADS)
Banerjee, Subhasis; Mallick, Shrestha Basu; Bose, Indrani
We study the discrete Gierer-Meinhardt model of reaction-diffusion on three different types of networks: regular, random and scale-free. The model dynamics lead to the formation of stationary Turing patterns in the steady state in certain parameter regions. Some general features of the patterns are studied through numerical simulation. The results for the random and scale-free networks show a marked difference from those in the case of the regular network. The difference may be ascribed to the small world character of the first two types of networks.
Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations
Vijaykumar, Adithya; Bolhuis, Peter G.; Rein ten Wolde, Pieter
2015-12-07
In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.
Computational fluid dynamics of reaction injection moulding
NASA Astrophysics Data System (ADS)
Mateus, Artur; Mitchell, Geoffrey; Bártolo, Paulo
2012-09-01
The modern approach to the development of moulds for injection moulding (Reaction Injection Moulding - RIM, Thermoplastic Injection Moulding - TIM and others) differs from the conventional approach based exclusively on the designer's experience and hypotheses. The increasingly complexityof moulds and the requirement by the clients for the improvement of their quality, shorter delivery times, and lower prices, demand the development of novel approaches to developed optimal moulds and moulded parts. The development of more accurate computational tools is fundamental to optimize both, the injection mouldingprocesses and the design, quality and durability of the moulds. This paper focuses on the RIM process proposing a novel thermo-rheo-kinetic model. The proposed model was implemented in generalpurpose Computational Fluid Dynamics (CFD) software. The model enables to accurately describe both flow and curing stages. Simulation results were validated against experimental results.
Reconstructing Directed Networks From Noisy Dynamics
NASA Astrophysics Data System (ADS)
Tam, Hiu Ching; Ching, Emily Sc
Complex systems can be fruitfully studied as networks of many elementary units, known as nodes, interacting with one another with the interactions being the links between the nodes. The overall behavior of the systems depends crucially on the network structure depicting how the nodes are linked with each other. It is usually possible to measure the dynamics of the individual nodes but difficult, if not impossible, to directly measure the interactions or links between the nodes. For most systems of interest, the links are directional in that one node affects the dynamics of the other but not vice versa. Moreover, the strength of interaction can vary for different links. Reconstructing directed and weighted networks from dynamics is one of the biggest challenges in network research. We have studied directed and weighted networks modelled by noisy dynamical systems with nonlinear dynamics and developed a method that reconstructs the links and their directions using only the dynamics of the nodes as input. Our method is motivated by a mathematical result derived for dynamical systems that approach a fixed point in the noise-free limit. We show that our method gives good reconstruction results for several directed and weighted networks with different nonlinear dynamics. Supported by Hong Kong Research Grants Council under Grant No. CUHK 14300914.
Dynamic network analysis of protein interactions
NASA Astrophysics Data System (ADS)
Almaas, Eivind; Deri, Joya
2007-03-01
Network approaches have recently become a popular tool to study complex systems such as cellular metabolism and protein interactions. A substantial number of analyses of the protein interaction network (PIN) of the yeast Saccharomyces cerevisiae have considered this network as a static entity, not taking the network's dynamic nature into account. Here, we examine the time-variation of gene regulation superimposed on the PIN by defining mRNA expression profiles throughout the cell cycle as node weights. To characterize these network dynamics, we have both developed a set of novel network measures as well as studied previously published measures for weighted networks. We expect that our approach will provide a deeper understanding of protein regulation during the cell cycle.
Dynamical robustness analysis of weighted complex networks
NASA Astrophysics Data System (ADS)
He, Zhiwei; Liu, Shuai; Zhan, Meng
2013-09-01
Robustness of weighted complex networks is analyzed from nonlinear dynamical point of view and with focus on different roles of high-degree and low-degree nodes. We find that the phenomenon for the low-degree nodes being the key nodes in the heterogeneous networks only appears in weakly weighted networks and for weak coupling. For all other parameters, the heterogeneous networks are always highly vulnerable to the failure of high-degree nodes; this point is the same as in the structural robustness analysis. We also find that with random inactivation, heterogeneous networks are always more robust than the corresponding homogeneous networks with the same average degree except for one special parameter. Thus our findings give an integrated picture for the dynamical robustness analysis on complex networks.
Impulsive synchronization of networked nonlinear dynamical systems
NASA Astrophysics Data System (ADS)
Jiang, Haibo; Bi, Qinsheng
2010-06-01
In this Letter, we investigate the problem of impulsive synchronization of networked multi-agent systems, where each agent can be modeled as an identical nonlinear dynamical system. Firstly, an impulsive control protocol is designed for network with fixed topology based on the local information of agents. Then sufficient conditions are given to guarantee the synchronization of the networked nonlinear dynamical system by using algebraic graph theory and impulsive control theory. Furthermore, how to select the discrete instants and impulsive constants is discussed. The case that the topologies of the networks are switching is also considered. Numerical simulations show the effectiveness of our theoretical results.
Reaction dynamics of photochromic dithienylethene derivatives
NASA Astrophysics Data System (ADS)
Ern, J.; Bens, A. T.; Martin, H.-D.; Mukamel, S.; Schmid, D.; Tretiak, S.; Tsiper, E.; Kryschi, C.
1999-07-01
The reaction dynamics of the photochromic ring-opening reaction of 1,2-bis(5-formyl-2-methyl-thien-3-yl)perfluorocyclopentene (CHO-BMTFP) in dichloromethane solution was investigated using femtosecond transient absorption spectroscopy. The data were analyzed in terms of a model potential and single-electron density matrices, which were calculated using the collective electronic oscillator (CEO) approach and the INDO/S semiempirical Hamiltonian. The S 0-S 1 and S 0-S 2 transitions of the closed isomer were resonantly excited using 120 fs pump pulses at 610 and 410 nm, respectively. A temporally delayed white light continuum probe pulse monitors the decay of the S 1 or S 2 state as well as the recovery of the S 0 state. Within the first picosecond after excitation, CHO-BMTFP was observed to undergo a fast structural relaxation along the S 1 potential energy surface into a minimum constituting a precursor of the ring-opening process. The rather long lifetime of the precursor, τ2=13 ps, was consistent with the calculated potential barrier in front of the conical intersection with the S 0 potential energy surface, which may arise from stabilization of the nearly planar closed isomer by an efficiently delocalized π-electron system.
Stochastic Generator of Chemical Structure. 3. Reaction Network Generation
FAULON,JEAN-LOUP; SAULT,ALLEN G.
2000-07-15
A new method to generate chemical reaction network is proposed. The particularity of the method is that network generation and mechanism reduction are performed simultaneously using sampling techniques. Our method is tested for hydrocarbon thermal cracking. Results and theoretical arguments demonstrate that our method scales in polynomial time while other deterministic network generator scale in exponential time. This finding offers the possibility to investigate complex reacting systems such as those studied in petroleum refining and combustion.
Exploring Collective Dynamics in Communication Networks
Yuan, Jian; Mills, Kevin
2002-01-01
A communication network, such as the Internet, comprises a complex system where cooperative phenomena may emerge from interactions among various traffic flows generated and forwarded by individual nodes. To identify and understand such phenomena, we model a network as a two-dimensional cellular automaton. We suspect such models can promote better understanding of the spatial-temporal evolution of network congestion, and other emergent phenomena in communication networks. To search the behavior space of the model, we study dynamic patterns arising from interactions among traffic flows routed across shared network nodes, as we employ various configurations of parameters and two different congestion-control algorithms. In this paper, we characterize correlation in congestion behavior within the model at different system sizes and time granularities. As expected, we find that long-range dependence (LRD) appears at some time granularities, and that for a given network size LRD decays as time granularity increases. As network size increases, we find that long-range dependence exists at larger time scales. To distinguish effects due to network size from effects due to collective phenomena, we compare congestion behavior within networks of selected sizes to congestion behavior within comparably sized sub-areas in a larger network. We find stronger long-range dependence for sub-areas within the larger network. This suggests the importance of modeling networks of sufficiently large size when studying the effects of collective dynamics.
The Dynamics of Network Topology
NASA Astrophysics Data System (ADS)
Voicu, Ramiro; Legrand, Iosif; Newman, Harvey; Barczyk, Artur; Grigoras, Costin; Dobre, Ciprian
2011-12-01
Network monitoring is vital to ensure proper network operation over time, and is tightly integrated with all the data intensive processing tasks used by the LHC experiments. In order to build a coherent set of network management services it is very important to collect in near real-time information about the network topology, the main data flows, traffic volume and the quality of connectivity. A set of dedicated modules were developed in the MonALISA framework to periodically perform network measurements tests between all sites. We developed global services to present in near real-time the entire network topology used by a community. For any LHC experiment such a network topology includes several hundred of routers and tens of Autonomous Systems. Any changes in the global topology are recorded and this information is can be easily correlated with traffic patterns. The evolution in time of global network topology is shown a dedicated GUI. Changes in the global topology at this level occur quite frequently and even small modifications in the connectivity map may significantly affect the network performance. The global topology graphs are correlated with active end to end network performance measurements, done with the Fast Data Transfer application, between all sites. Access to both real-time and historical data, as provided by MonALISA, is also important for developing services able to predict the usage pattern, to aid in efficiently allocating resources globally.
Dynamical Adaptation in Terrorist Cells/Networks
NASA Astrophysics Data System (ADS)
Hussain, D. M. Akbar; Ahmed, Zaki
Typical terrorist cells/networks have dynamical structure as they evolve or adapt to changes which may occur due to capturing or killing of a member of the cell/network. Analytical measures in graph theory like degree centrality, betweenness and closeness centralities are very common and have long history of their successful use in revealing the importance of various members of the network. However, modeling of covert, terrorist or criminal networks through social graph dose not really provide the hierarchical structure which exist in these networks as these networks are composed of leaders and followers etc. In this research we analyze and predict the most likely role a particular node can adapt once a member of the network is either killed or caught. The adaptation is based on computing Bayes posteriori probability of each node and the level of the said node in the network structure.
Optimal dynamic bandwidth allocation for complex networks
NASA Astrophysics Data System (ADS)
Jiang, Zhong-Yuan; Liang, Man-Gui; Li, Qian; Guo, Dong-Chao
2013-03-01
Traffic capacity of one network strongly depends on the link’s bandwidth allocation strategy. In previous bandwidth allocation mechanisms, once one link’s bandwidth is allocated, it will be fixed throughout the overall traffic transmission process. However, the traffic load of every link changes from time to time. In this paper, with finite total bandwidth resource of the network, we propose to dynamically allocate the total bandwidth resource in which each link’s bandwidth is proportional to the queue length of the output buffer of the link per time step. With plenty of data packets in the network, the traffic handling ability of all links of the network achieves full utilization. The theoretical analysis and the extensive simulation results on complex networks are consistent. This work is valuable for network service providers to improve network performance or to do reasonable network design efficiently.
Functional Motifs in Biochemical Reaction Networks
Tyson, John J.; Novák, Béla
2013-01-01
The signal-response characteristics of a living cell are determined by complex networks of interacting genes, proteins, and metabolites. Understanding how cells respond to specific challenges, how these responses are contravened in diseased cells, and how to intervene pharmacologically in the decision-making processes of cells requires an accurate theory of the information-processing capabilities of macromolecular regulatory networks. Adopting an engineer’s approach to control systems, we ask whether realistic cellular control networks can be decomposed into simple regulatory motifs that carry out specific functions in a cell. We show that such functional motifs exist and review the experimental evidence that they control cellular responses as expected. PMID:20055671
Dynamics of comb-of-comb networks
NASA Astrophysics Data System (ADS)
Liu, Hongxiao; Lin, Yuan; Dolgushev, Maxim; Zhang, Zhongzhi
2016-03-01
The dynamics of complex networks, a current hot topic in many scientific fields, is often coded through the corresponding Laplacian matrix. The spectrum of this matrix carries the main features of the networks' dynamics. Here we consider the deterministic networks which can be viewed as "comb-of-comb" iterative structures. For their Laplacian spectra we find analytical equations involving Chebyshev polynomials whose properties allow one to analyze the spectra in deep. Here, in particular, we find that in the infinite size limit the corresponding spectral dimension goes as ds→2 . The ds leaves its fingerprint on many dynamical processes, as we exemplarily show by considering the dynamical properties of polymer networks, including single monomer displacement under a constant force, mechanical relaxation, and fluorescence depolarization.
Accelerated Sensitivity Analysis in High-Dimensional Stochastic Reaction Networks
Arampatzis, Georgios; Katsoulakis, Markos A.; Pantazis, Yannis
2015-01-01
Existing sensitivity analysis approaches are not able to handle efficiently stochastic reaction networks with a large number of parameters and species, which are typical in the modeling and simulation of complex biochemical phenomena. In this paper, a two-step strategy for parametric sensitivity analysis for such systems is proposed, exploiting advantages and synergies between two recently proposed sensitivity analysis methodologies for stochastic dynamics. The first method performs sensitivity analysis of the stochastic dynamics by means of the Fisher Information Matrix on the underlying distribution of the trajectories; the second method is a reduced-variance, finite-difference, gradient-type sensitivity approach relying on stochastic coupling techniques for variance reduction. Here we demonstrate that these two methods can be combined and deployed together by means of a new sensitivity bound which incorporates the variance of the quantity of interest as well as the Fisher Information Matrix estimated from the first method. The first step of the proposed strategy labels sensitivities using the bound and screens out the insensitive parameters in a controlled manner. In the second step of the proposed strategy, a finite-difference method is applied only for the sensitivity estimation of the (potentially) sensitive parameters that have not been screened out in the first step. Results on an epidermal growth factor network with fifty parameters and on a protein homeostasis with eighty parameters demonstrate that the proposed strategy is able to quickly discover and discard the insensitive parameters and in the remaining potentially sensitive parameters it accurately estimates the sensitivities. The new sensitivity strategy can be several times faster than current state-of-the-art approaches that test all parameters, especially in “sloppy” systems. In particular, the computational acceleration is quantified by the ratio between the total number of parameters over
Restoration of rhythmicity in diffusively coupled dynamical networks
Zou, Wei; Senthilkumar, D. V.; Nagao, Raphael; Kiss, István Z.; Tang, Yang; Koseska, Aneta; Duan, Jinqiao; Kurths, Jürgen
2015-01-01
Oscillatory behaviour is essential for proper functioning of various physical and biological processes. However, diffusive coupling is capable of suppressing intrinsic oscillations due to the manifestation of the phenomena of amplitude and oscillation deaths. Here we present a scheme to revoke these quenching states in diffusively coupled dynamical networks, and demonstrate the approach in experiments with an oscillatory chemical reaction. By introducing a simple feedback factor in the diffusive coupling, we show that the stable (in)homogeneous steady states can be effectively destabilized to restore dynamic behaviours of coupled systems. Even a feeble deviation from the normal diffusive coupling drastically shrinks the death regions in the parameter space. The generality of our method is corroborated in diverse non-linear systems of diffusively coupled paradigmatic models with various death scenarios. Our study provides a general framework to strengthen the robustness of dynamic activity in diffusively coupled dynamical networks. PMID:26173555
Restoration of rhythmicity in diffusively coupled dynamical networks.
Zou, Wei; Senthilkumar, D V; Nagao, Raphael; Kiss, István Z; Tang, Yang; Koseska, Aneta; Duan, Jinqiao; Kurths, Jürgen
2015-01-01
Oscillatory behaviour is essential for proper functioning of various physical and biological processes. However, diffusive coupling is capable of suppressing intrinsic oscillations due to the manifestation of the phenomena of amplitude and oscillation deaths. Here we present a scheme to revoke these quenching states in diffusively coupled dynamical networks, and demonstrate the approach in experiments with an oscillatory chemical reaction. By introducing a simple feedback factor in the diffusive coupling, we show that the stable (in)homogeneous steady states can be effectively destabilized to restore dynamic behaviours of coupled systems. Even a feeble deviation from the normal diffusive coupling drastically shrinks the death regions in the parameter space. The generality of our method is corroborated in diverse non-linear systems of diffusively coupled paradigmatic models with various death scenarios. Our study provides a general framework to strengthen the robustness of dynamic activity in diffusively coupled dynamical networks. PMID:26173555
Restoration of rhythmicity in diffusively coupled dynamical networks
NASA Astrophysics Data System (ADS)
Zou, Wei; Senthilkumar, D. V.; Nagao, Raphael; Kiss, István Z.; Tang, Yang; Koseska, Aneta; Duan, Jinqiao; Kurths, Jürgen
2015-07-01
Oscillatory behaviour is essential for proper functioning of various physical and biological processes. However, diffusive coupling is capable of suppressing intrinsic oscillations due to the manifestation of the phenomena of amplitude and oscillation deaths. Here we present a scheme to revoke these quenching states in diffusively coupled dynamical networks, and demonstrate the approach in experiments with an oscillatory chemical reaction. By introducing a simple feedback factor in the diffusive coupling, we show that the stable (in)homogeneous steady states can be effectively destabilized to restore dynamic behaviours of coupled systems. Even a feeble deviation from the normal diffusive coupling drastically shrinks the death regions in the parameter space. The generality of our method is corroborated in diverse non-linear systems of diffusively coupled paradigmatic models with various death scenarios. Our study provides a general framework to strengthen the robustness of dynamic activity in diffusively coupled dynamical networks.
A Dynamic Navigation Algorithm Considering Network Disruptions
NASA Astrophysics Data System (ADS)
Jiang, J.; Wu, L.
2014-04-01
In traffic network, link disruptions or recoveries caused by sudden accidents, bad weather and traffic congestion, lead to significant increase or decrease in travel times on some network links. Similar situation also occurs in real-time emergency evacuation plan in indoor areas. As the dynamic nature of real-time network information generates better navigation solutions than the static one, a real-time dynamic navigation algorithm for emergency evacuation with stochastic disruptions or recoveries in the network is presented in this paper. Compared with traditional existing algorithms, this new algorithm adjusts pre-existing path to a new optimal one according to the changing link travel time. With real-time network information, it can provide the optional path quickly to adapt to the rapid changing network properties. Theoretical analysis and experimental results demonstrate that this proposed algorithm performs a high time efficiency to get exact solution and indirect information can be calculated in spare time.
Krumholz, Elias W.; Libourel, Igor G. L.
2015-01-01
Genome-scale metabolic models are central in connecting genotypes to metabolic phenotypes. However, even for well studied organisms, such as Escherichia coli, draft networks do not contain a complete biochemical network. Missing reactions are referred to as gaps. These gaps need to be filled to enable functional analysis, and gap-filling choices influence model predictions. To investigate whether functional networks existed where all gap-filling reactions were supported by sequence similarity to annotated enzymes, four draft networks were supplemented with all reactions from the Model SEED database for which minimal sequence similarity was found in their genomes. Quadratic programming revealed that the number of reactions that could partake in a gap-filling solution was vast: 3,270 in the case of E. coli, where 72% of the metabolites in the draft network could connect a gap-filling solution. Nonetheless, no network could be completed without the inclusion of orphaned enzymes, suggesting that parts of the biochemistry integral to biomass precursor formation are uncharacterized. However, many gap-filling reactions were well determined, and the resulting networks showed improved prediction of gene essentiality compared with networks generated through canonical gap filling. In addition, gene essentiality predictions that were sensitive to poorly determined gap-filling reactions were of poor quality, suggesting that damage to the network structure resulting from the inclusion of erroneous gap-filling reactions may be predictable. PMID:26041773
DNA reaction networks: Providing a panoramic view
NASA Astrophysics Data System (ADS)
Wang, Fei; Fan, Chunhai
2016-08-01
A quantitative understanding of the functional landscape of a biochemical circuit can reveal the design rules required to optimize the circuit. Now, a high-throughput droplet-based microfluidic platform has been developed which enables high-resolution mapping of bifurcation diagrams for two nonlinear DNA networks.
Recent Advances in Quantum Dynamics of Bimolecular Reactions
NASA Astrophysics Data System (ADS)
Zhang, Dong H.; Guo, Hua
2016-05-01
In this review, we survey the latest advances in theoretical understanding of bimolecular reaction dynamics in the past decade. The remarkable recent progress in this field has been driven by more accurate and efficient ab initio electronic structure theory, effective potential-energy surface fitting techniques, and novel quantum scattering algorithms. Quantum mechanical characterization of bimolecular reactions continues to uncover interesting dynamical phenomena in atom-diatom reactions and beyond, reaching an unprecedented level of sophistication. In tandem with experimental explorations, these theoretical developments have greatly advanced our understanding of key issues in reaction dynamics, such as microscopic reaction mechanisms, mode specificity, product energy disposal, influence of reactive resonances, and nonadiabatic effects.
Network analysis of human heartbeat dynamics
NASA Astrophysics Data System (ADS)
Shao, Zhi-Gang
2010-02-01
We construct the complex networks of human heartbeat dynamics and investigate their statistical properties, using the visibility algorithm proposed by Lacasa and co-workers [Proc. Natl. Acad. Sci. U.S.A. 105, 4972 (2008)]. Our results show that the associated networks for the time series of heartbeat interval are always scale-free, high clustering, hierarchy, and assortative mixing. In particular, the assortative coefficient of associated networks could distinguish between healthy subjects and patients with congestive heart failure.
Amplitude dynamics favors synchronization in complex networks
Gambuzza, Lucia Valentina; Gómez-Gardeñes, Jesus; Frasca, Mattia
2016-01-01
In this paper we study phase synchronization in random complex networks of coupled periodic oscillators. In particular, we show that, when amplitude dynamics is not negligible, phase synchronization may be enhanced. To illustrate this, we compare the behavior of heterogeneous units with both amplitude and phase dynamics and pure (Kuramoto) phase oscillators. We find that in small network motifs the behavior crucially depends on the topology and on the node frequency distribution. Surprisingly, the microscopic structures for which the amplitude dynamics improves synchronization are those that are statistically more abundant in random complex networks. Thus, amplitude dynamics leads to a general lowering of the synchronization threshold in arbitrary random topologies. Finally, we show that this synchronization enhancement is generic of oscillators close to Hopf bifurcations. To this aim we consider coupled FitzHugh-Nagumo units modeling neuron dynamics. PMID:27108847
Network Physiology: How Organ Systems Dynamically Interact
Bartsch, Ronny P.; Liu, Kang K. L.; Bashan, Amir; Ivanov, Plamen Ch.
2015-01-01
We systematically study how diverse physiologic systems in the human organism dynamically interact and collectively behave to produce distinct physiologic states and functions. This is a fundamental question in the new interdisciplinary field of Network Physiology, and has not been previously explored. Introducing the novel concept of Time Delay Stability (TDS), we develop a computational approach to identify and quantify networks of physiologic interactions from long-term continuous, multi-channel physiological recordings. We also develop a physiologically-motivated visualization framework to map networks of dynamical organ interactions to graphical objects encoded with information about the coupling strength of network links quantified using the TDS measure. Applying a system-wide integrative approach, we identify distinct patterns in the network structure of organ interactions, as well as the frequency bands through which these interactions are mediated. We establish first maps representing physiologic organ network interactions and discover basic rules underlying the complex hierarchical reorganization in physiologic networks with transitions across physiologic states. Our findings demonstrate a direct association between network topology and physiologic function, and provide new insights into understanding how health and distinct physiologic states emerge from networked interactions among nonlinear multi-component complex systems. The presented here investigations are initial steps in building a first atlas of dynamic interactions among organ systems. PMID:26555073
Network Physiology: How Organ Systems Dynamically Interact.
Bartsch, Ronny P; Liu, Kang K L; Bashan, Amir; Ivanov, Plamen Ch
2015-01-01
We systematically study how diverse physiologic systems in the human organism dynamically interact and collectively behave to produce distinct physiologic states and functions. This is a fundamental question in the new interdisciplinary field of Network Physiology, and has not been previously explored. Introducing the novel concept of Time Delay Stability (TDS), we develop a computational approach to identify and quantify networks of physiologic interactions from long-term continuous, multi-channel physiological recordings. We also develop a physiologically-motivated visualization framework to map networks of dynamical organ interactions to graphical objects encoded with information about the coupling strength of network links quantified using the TDS measure. Applying a system-wide integrative approach, we identify distinct patterns in the network structure of organ interactions, as well as the frequency bands through which these interactions are mediated. We establish first maps representing physiologic organ network interactions and discover basic rules underlying the complex hierarchical reorganization in physiologic networks with transitions across physiologic states. Our findings demonstrate a direct association between network topology and physiologic function, and provide new insights into understanding how health and distinct physiologic states emerge from networked interactions among nonlinear multi-component complex systems. The presented here investigations are initial steps in building a first atlas of dynamic interactions among organ systems. PMID:26555073
Dynamic Random Networks in Dynamic Populations
NASA Astrophysics Data System (ADS)
Britton, Tom; Lindholm, Mathias
2010-05-01
We consider a random network evolving in continuous time in which new nodes are born and old may die, and where undirected edges between nodes are created randomly and may also disappear. The node population is Markovian and so is the creation and deletion of edges, given the node population. Each node is equipped with a random social index and the intensity at which a node creates new edges is proportional to the social index, and the neighbour is either chosen uniformly or proportional to its social index in a modification of the model. We derive properties of the network as time and the node population tends to infinity. In particular, the degree-distribution is shown to be a mixed Poisson distribution which may exhibit a heavy tail (e.g. power-law) if the social index distribution has a heavy tail. The limiting results are verified by means of simulations, and the model is fitted to a network of sexual contacts.
Cellular Metabolic Network Analysis: Discovering Important Reactions in Treponema pallidum
Chen, Xueying; Zhao, Min; Qu, Hong
2015-01-01
T. pallidum, the syphilis-causing pathogen, performs very differently in metabolism compared with other bacterial pathogens. The desire for safe and effective vaccine of syphilis requests identification of important steps in T. pallidum's metabolism. Here, we apply Flux Balance Analysis to represent the reactions quantitatively. Thus, it is possible to cluster all reactions in T. pallidum. By calculating minimal cut sets and analyzing topological structure for the metabolic network of T. pallidum, critical reactions are identified. As a comparison, we also apply the analytical approaches to the metabolic network of H. pylori to find coregulated drug targets and unique drug targets for different microorganisms. Based on the clustering results, all reactions are further classified into various roles. Therefore, the general picture of their metabolic network is obtained and two types of reactions, both of which are involved in nucleic acid metabolism, are found to be essential for T. pallidum. It is also discovered that both hubs of reactions and the isolated reactions in purine and pyrimidine metabolisms play important roles in T. pallidum. These reactions could be potential drug targets for treating syphilis. PMID:26495292
Cellular metabolic network analysis: discovering important reactions in Treponema pallidum.
Chen, Xueying; Zhao, Min; Qu, Hong
2015-01-01
T. pallidum, the syphilis-causing pathogen, performs very differently in metabolism compared with other bacterial pathogens. The desire for safe and effective vaccine of syphilis requests identification of important steps in T. pallidum's metabolism. Here, we apply Flux Balance Analysis to represent the reactions quantitatively. Thus, it is possible to cluster all reactions in T. pallidum. By calculating minimal cut sets and analyzing topological structure for the metabolic network of T. pallidum, critical reactions are identified. As a comparison, we also apply the analytical approaches to the metabolic network of H. pylori to find coregulated drug targets and unique drug targets for different microorganisms. Based on the clustering results, all reactions are further classified into various roles. Therefore, the general picture of their metabolic network is obtained and two types of reactions, both of which are involved in nucleic acid metabolism, are found to be essential for T. pallidum. It is also discovered that both hubs of reactions and the isolated reactions in purine and pyrimidine metabolisms play important roles in T. pallidum. These reactions could be potential drug targets for treating syphilis. PMID:26495292
Mapping dynamical systems onto complex networks
NASA Astrophysics Data System (ADS)
Borges, E. P.; Cajueiro, D. O.; Andrade, R. F. S.
2007-08-01
The objective of this study is to design a procedure to characterize chaotic dynamical systems, in which they are mapped onto a complex network. The nodes represent the regions of space visited by the system, while the edges represent the transitions between these regions. Parameters developed to quantify the properties of complex networks, including those related to higher order neighbourhoods, are used in the analysis. The methodology is tested on the logistic map, focusing on the onset of chaos and chaotic regimes. The corresponding networks were found to have distinct features that are associated with the particular type of dynamics that generated them.
Metric projection for dynamic multiplex networks.
Jurman, Giuseppe
2016-08-01
Evolving multiplex networks are a powerful model for representing the dynamics along time of different phenomena, such as social networks, power grids, biological pathways. However, exploring the structure of the multiplex network time series is still an open problem. Here we propose a two-step strategy to tackle this problem based on the concept of distance (metric) between networks. Given a multiplex graph, first a network of networks is built for each time step, and then a real valued time series is obtained by the sequence of (simple) networks by evaluating the distance from the first element of the series. The effectiveness of this approach in detecting the occurring changes along the original time series is shown on a synthetic example first, and then on the Gulf dataset of political events. PMID:27626089
Collective dynamics of `small-world' networks
NASA Astrophysics Data System (ADS)
Watts, Duncan J.; Strogatz, Steven H.
1998-06-01
Networks of coupled dynamical systems have been used to model biological oscillators, Josephson junction arrays,, excitable media, neural networks, spatial games, genetic control networks and many other self-organizing systems. Ordinarily, the connection topology is assumed to be either completely regular or completely random. But many biological, technological and social networks lie somewhere between these two extremes. Here we explore simple models of networks that can be tuned through this middle ground: regular networks `rewired' to introduce increasing amounts of disorder. We find that these systems can be highly clustered, like regular lattices, yet have small characteristic path lengths, like random graphs. We call them `small-world' networks, by analogy with the small-world phenomenon, (popularly known as six degrees of separation). The neural network of the worm Caenorhabditis elegans, the power grid of the western United States, and the collaboration graph of film actors are shown to be small-world networks. Models of dynamical systems with small-world coupling display enhanced signal-propagation speed, computational power, and synchronizability. In particular, infectious diseases spread more easily in small-world networks than in regular lattices.
The molecular dynamics of atmospheric reaction
NASA Technical Reports Server (NTRS)
Polanyi, J. C.
1971-01-01
Detailed information about the chemistry of the upper atmosphere took the form of quantitative data concerning the rate of reaction into specified states of product vibration, rotation and translation for exothermic reaction, as well as concerning the rate of reaction from specified states of reagent vibration, rotation and translation for endothermic reaction. The techniques used were variants on the infrared chemiluminescence method. Emphasis was placed on reactions that formed, and that removed, vibrationally-excited hydroxyl radicals. Fundamental studies were also performed on exothermic reactions involving hydrogen halides.
Memory Dynamics in Attractor Networks
Li, Guoqi; Ramanathan, Kiruthika; Ning, Ning; Shi, Luping; Wen, Changyun
2015-01-01
As can be represented by neurons and their synaptic connections, attractor networks are widely believed to underlie biological memory systems and have been used extensively in recent years to model the storage and retrieval process of memory. In this paper, we propose a new energy function, which is nonnegative and attains zero values only at the desired memory patterns. An attractor network is designed based on the proposed energy function. It is shown that the desired memory patterns are stored as the stable equilibrium points of the attractor network. To retrieve a memory pattern, an initial stimulus input is presented to the network, and its states converge to one of stable equilibrium points. Consequently, the existence of the spurious points, that is, local maxima, saddle points, or other local minima which are undesired memory patterns, can be avoided. The simulation results show the effectiveness of the proposed method. PMID:25960737
Memory dynamics in attractor networks.
Li, Guoqi; Ramanathan, Kiruthika; Ning, Ning; Shi, Luping; Wen, Changyun
2015-01-01
As can be represented by neurons and their synaptic connections, attractor networks are widely believed to underlie biological memory systems and have been used extensively in recent years to model the storage and retrieval process of memory. In this paper, we propose a new energy function, which is nonnegative and attains zero values only at the desired memory patterns. An attractor network is designed based on the proposed energy function. It is shown that the desired memory patterns are stored as the stable equilibrium points of the attractor network. To retrieve a memory pattern, an initial stimulus input is presented to the network, and its states converge to one of stable equilibrium points. Consequently, the existence of the spurious points, that is, local maxima, saddle points, or other local minima which are undesired memory patterns, can be avoided. The simulation results show the effectiveness of the proposed method. PMID:25960737
Competing dynamic phases of active polymer networks
NASA Astrophysics Data System (ADS)
Freedman, Simon; Banerjee, Shiladitya; Dinner, Aaron R.
Recent experiments on in-vitro reconstituted assemblies of F-actin, myosin-II motors, and cross-linking proteins show that tuning local network properties can changes the fundamental biomechanical behavior of the system. For example, by varying cross-linker density and actin bundle rigidity, one can switch between contractile networks useful for reshaping cells, polarity sorted networks ideal for directed molecular transport, and frustrated networks with robust structural properties. To efficiently investigate the dynamic phases of actomyosin networks, we developed a coarse grained non-equilibrium molecular dynamics simulation of model semiflexible filaments, molecular motors, and cross-linkers with phenomenologically defined interactions. The simulation's accuracy was verified by benchmarking the mechanical properties of its individual components and collective behavior against experimental results at the molecular and network scales. By adjusting the model's parameters, we can reproduce the qualitative phases observed in experiment and predict the protein characteristics where phase crossovers could occur in collective network dynamics. Our model provides a framework for understanding cells' multiple uses of actomyosin networks and their applicability in materials research. Supported by the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program.
Origin and Structure of Dynamic Cooperative Networks
Wardil, Lucas; Hauert, Christoph
2014-01-01
Societies are built on social interactions among individuals. Cooperation represents the simplest form of a social interaction: one individual provides a benefit to another one at a cost to itself. Social networks represent a dynamical abstraction of social interactions in a society. The behaviour of an individual towards others and of others towards the individual shape the individual's neighbourhood and hence the local structure of the social network. Here we propose a simple theoretical framework to model dynamic social networks by focussing on each individual's actions instead of interactions between individuals. This eliminates the traditional dichotomy between the strategy of individuals and the structure of the population and easily complements empirical studies. As a consequence, altruists, egoists and fair types are naturally determined by the local social structures, while globally egalitarian networks or stratified structures arise. Cooperative interactions drive the emergence and shape the structure of social networks. PMID:25030202
Origin and Structure of Dynamic Cooperative Networks
NASA Astrophysics Data System (ADS)
Wardil, Lucas; Hauert, Christoph
2014-07-01
Societies are built on social interactions among individuals. Cooperation represents the simplest form of a social interaction: one individual provides a benefit to another one at a cost to itself. Social networks represent a dynamical abstraction of social interactions in a society. The behaviour of an individual towards others and of others towards the individual shape the individual's neighbourhood and hence the local structure of the social network. Here we propose a simple theoretical framework to model dynamic social networks by focussing on each individual's actions instead of interactions between individuals. This eliminates the traditional dichotomy between the strategy of individuals and the structure of the population and easily complements empirical studies. As a consequence, altruists, egoists and fair types are naturally determined by the local social structures, while globally egalitarian networks or stratified structures arise. Cooperative interactions drive the emergence and shape the structure of social networks.
The structure and dynamics of multilayer networks
NASA Astrophysics Data System (ADS)
Boccaletti, S.; Bianconi, G.; Criado, R.; del Genio, C. I.; Gómez-Gardeñes, J.; Romance, M.; Sendiña-Nadal, I.; Wang, Z.; Zanin, M.
2014-11-01
In the past years, network theory has successfully characterized the interaction among the constituents of a variety of complex systems, ranging from biological to technological, and social systems. However, up until recently, attention was almost exclusively given to networks in which all components were treated on equivalent footing, while neglecting all the extra information about the temporal- or context-related properties of the interactions under study. Only in the last years, taking advantage of the enhanced resolution in real data sets, network scientists have directed their interest to the multiplex character of real-world systems, and explicitly considered the time-varying and multilayer nature of networks. We offer here a comprehensive review on both structural and dynamical organization of graphs made of diverse relationships (layers) between its constituents, and cover several relevant issues, from a full redefinition of the basic structural measures, to understanding how the multilayer nature of the network affects processes and dynamics.
Gupta, Ankit; Briat, Corentin; Khammash, Mustafa
2014-06-01
Reaction networks are systems in which the populations of a finite number of species evolve through predefined interactions. Such networks are found as modeling tools in many biological disciplines such as biochemistry, ecology, epidemiology, immunology, systems biology and synthetic biology. It is now well-established that, for small population sizes, stochastic models for biochemical reaction networks are necessary to capture randomness in the interactions. The tools for analyzing such models, however, still lag far behind their deterministic counterparts. In this paper, we bridge this gap by developing a constructive framework for examining the long-term behavior and stability properties of the reaction dynamics in a stochastic setting. In particular, we address the problems of determining ergodicity of the reaction dynamics, which is analogous to having a globally attracting fixed point for deterministic dynamics. We also examine when the statistical moments of the underlying process remain bounded with time and when they converge to their steady state values. The framework we develop relies on a blend of ideas from probability theory, linear algebra and optimization theory. We demonstrate that the stability properties of a wide class of biological networks can be assessed from our sufficient theoretical conditions that can be recast as efficient and scalable linear programs, well-known for their tractability. It is notably shown that the computational complexity is often linear in the number of species. We illustrate the validity, the efficiency and the wide applicability of our results on several reaction networks arising in biochemistry, systems biology, epidemiology and ecology. The biological implications of the results as well as an example of a non-ergodic biological network are also discussed. PMID:24968191
Khammash, Mustafa
2014-01-01
Reaction networks are systems in which the populations of a finite number of species evolve through predefined interactions. Such networks are found as modeling tools in many biological disciplines such as biochemistry, ecology, epidemiology, immunology, systems biology and synthetic biology. It is now well-established that, for small population sizes, stochastic models for biochemical reaction networks are necessary to capture randomness in the interactions. The tools for analyzing such models, however, still lag far behind their deterministic counterparts. In this paper, we bridge this gap by developing a constructive framework for examining the long-term behavior and stability properties of the reaction dynamics in a stochastic setting. In particular, we address the problems of determining ergodicity of the reaction dynamics, which is analogous to having a globally attracting fixed point for deterministic dynamics. We also examine when the statistical moments of the underlying process remain bounded with time and when they converge to their steady state values. The framework we develop relies on a blend of ideas from probability theory, linear algebra and optimization theory. We demonstrate that the stability properties of a wide class of biological networks can be assessed from our sufficient theoretical conditions that can be recast as efficient and scalable linear programs, well-known for their tractability. It is notably shown that the computational complexity is often linear in the number of species. We illustrate the validity, the efficiency and the wide applicability of our results on several reaction networks arising in biochemistry, systems biology, epidemiology and ecology. The biological implications of the results as well as an example of a non-ergodic biological network are also discussed. PMID:24968191
Efficient stochastic simulations of complex reaction networks on surfaces.
Barzel, Baruch; Biham, Ofer
2007-10-14
Surfaces serve as highly efficient catalysts for a vast variety of chemical reactions. Typically, such surface reactions involve billions of molecules which diffuse and react over macroscopic areas. Therefore, stochastic fluctuations are negligible and the reaction rates can be evaluated using rate equations, which are based on the mean-field approximation. However, in case that the surface is partitioned into a large number of disconnected microscopic domains, the number of reactants in each domain becomes small and it strongly fluctuates. This is, in fact, the situation in the interstellar medium, where some crucial reactions take place on the surfaces of microscopic dust grains. In this case rate equations fail and the simulation of surface reactions requires stochastic methods such as the master equation. However, in the case of complex reaction networks, the master equation becomes infeasible because the number of equations proliferates exponentially. To solve this problem, we introduce a stochastic method based on moment equations. In this method the number of equations is dramatically reduced to just one equation for each reactive species and one equation for each reaction. Moreover, the equations can be easily constructed using a diagrammatic approach. We demonstrate the method for a set of astrophysically relevant networks of increasing complexity. It is expected to be applicable in many other contexts in which problems that exhibit analogous structure appear, such as surface catalysis in nanoscale systems, aerosol chemistry in stratospheric clouds, and genetic networks in cells. PMID:17935419
Turing instability in reaction-diffusion models on complex networks
NASA Astrophysics Data System (ADS)
Ide, Yusuke; Izuhara, Hirofumi; Machida, Takuya
2016-09-01
In this paper, the Turing instability in reaction-diffusion models defined on complex networks is studied. Here, we focus on three types of models which generate complex networks, i.e. the Erdős-Rényi, the Watts-Strogatz, and the threshold network models. From analysis of the Laplacian matrices of graphs generated by these models, we numerically reveal that stable and unstable regions of a homogeneous steady state on the parameter space of two diffusion coefficients completely differ, depending on the network architecture. In addition, we theoretically discuss the stable and unstable regions in the cases of regular enhanced ring lattices which include regular circles, and networks generated by the threshold network model when the number of vertices is large enough.
Stochastic Simulation of Biomolecular Networks in Dynamic Environments.
Voliotis, Margaritis; Thomas, Philipp; Grima, Ramon; Bowsher, Clive G
2016-06-01
Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the dynamic environment of the cell and its surroundings. We thus sample trajectories of the stochastic process described by the chemical master equation with time-varying propensities. A comparative analysis shows that existing approaches can either fail dramatically, or else can impose impractical computational burdens due to numerical integration of reaction propensities, especially when cell ensembles are studied. Here we introduce the Extrande method which, given a simulated time course of dynamic network inputs, provides a conditionally exact and several orders-of-magnitude faster simulation solution. The new approach makes it feasible to demonstrate-using decision-making by a large population of quorum sensing bacteria-that robustness to fluctuations from upstream signaling places strong constraints on the design of networks determining cell fate. Our approach has the potential to significantly advance both understanding of molecular systems biology and design of synthetic circuits. PMID:27248512
Stochastic Simulation of Biomolecular Networks in Dynamic Environments
Voliotis, Margaritis; Thomas, Philipp; Grima, Ramon; Bowsher, Clive G.
2016-01-01
Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the dynamic environment of the cell and its surroundings. We thus sample trajectories of the stochastic process described by the chemical master equation with time-varying propensities. A comparative analysis shows that existing approaches can either fail dramatically, or else can impose impractical computational burdens due to numerical integration of reaction propensities, especially when cell ensembles are studied. Here we introduce the Extrande method which, given a simulated time course of dynamic network inputs, provides a conditionally exact and several orders-of-magnitude faster simulation solution. The new approach makes it feasible to demonstrate—using decision-making by a large population of quorum sensing bacteria—that robustness to fluctuations from upstream signaling places strong constraints on the design of networks determining cell fate. Our approach has the potential to significantly advance both understanding of molecular systems biology and design of synthetic circuits. PMID:27248512
Semiclassical methods in chemical reaction dynamics
Keshavamurthy, S.
1994-12-01
Semiclassical approximations, simple as well as rigorous, are formulated in order to be able to describe gas phase chemical reactions in large systems. We formulate a simple but accurate semiclassical model for incorporating multidimensional tunneling in classical trajectory simulations. This model is based on the existence of locally conserved actions around the saddle point region on a multidimensional potential energy surface. Using classical perturbation theory and monitoring the imaginary action as a function of time along a classical trajectory we calculate state-specific unimolecular decay rates for a model two dimensional potential with coupling. Results are in good comparison with exact quantum results for the potential over a wide range of coupling constants. We propose a new semiclassical hybrid method to calculate state-to-state S-matrix elements for bimolecular reactive scattering. The accuracy of the Van Vleck-Gutzwiller propagator and the short time dynamics of the system make this method self-consistent and accurate. We also go beyond the stationary phase approximation by doing the resulting integrals exactly (numerically). As a result, classically forbidden probabilties are calculated with purely real time classical trajectories within this approach. Application to the one dimensional Eckart barrier demonstrates the accuracy of this approach. Successful application of the semiclassical hybrid approach to collinear reactive scattering is prevented by the phenomenon of chaotic scattering. The modified Filinov approach to evaluating the integrals is discussed, but application to collinear systems requires a more careful analysis. In three and higher dimensional scattering systems, chaotic scattering is suppressed and hence the accuracy and usefulness of the semiclassical method should be tested for such systems.
Controlling statistical moments of stochastic dynamical networks
NASA Astrophysics Data System (ADS)
Bielievtsov, Dmytro; Ladenbauer, Josef; Obermayer, Klaus
2016-07-01
We consider a general class of stochastic networks and ask which network nodes need to be controlled, and how, to stabilize and switch between desired metastable (target) states in terms of the first and second statistical moments of the system. We first show that it is sufficient to directly interfere with a subset of nodes which can be identified using information about the graph of the network only. Then we develop a suitable method for feedback control which acts on that subset of nodes and preserves the covariance structure of the desired target state. Finally, we demonstrate our theoretical results using a stochastic Hopfield network and a global brain model. Our results are applicable to a variety of (model) networks and further our understanding of the relationship between network structure and collective dynamics for the benefit of effective control.
Controlling statistical moments of stochastic dynamical networks.
Bielievtsov, Dmytro; Ladenbauer, Josef; Obermayer, Klaus
2016-07-01
We consider a general class of stochastic networks and ask which network nodes need to be controlled, and how, to stabilize and switch between desired metastable (target) states in terms of the first and second statistical moments of the system. We first show that it is sufficient to directly interfere with a subset of nodes which can be identified using information about the graph of the network only. Then we develop a suitable method for feedback control which acts on that subset of nodes and preserves the covariance structure of the desired target state. Finally, we demonstrate our theoretical results using a stochastic Hopfield network and a global brain model. Our results are applicable to a variety of (model) networks and further our understanding of the relationship between network structure and collective dynamics for the benefit of effective control. PMID:27575147
Reaction-diffusion processes on interconnected scale-free networks
NASA Astrophysics Data System (ADS)
Garas, Antonios
2015-08-01
We study the two-particle annihilation reaction A +B →∅ on interconnected scale-free networks, using different interconnecting strategies. We explore how the mixing of particles and the process evolution are influenced by the number of interconnecting links, by their functional properties, and by the interconnectivity strategies in use. We show that the reaction rates on this system are faster than what was observed in other topologies, due to the better particle mixing that suppresses the segregation effect, in line with previous studies performed on single scale-free networks.
Dynamics of Bottlebrush Networks: A Computational Study
NASA Astrophysics Data System (ADS)
Dobrynin, Andrey; Cao, Zhen; Sheiko, Sergei
We study dynamics of deformation of bottlebrush networks using molecular dynamics simulations and theoretical calculations. Analysis of our simulation results show that the dynamics of bottlebrush network deformation can be described by a Rouse model for polydisperse networks with effective Rouse time of the bottlebrush network strand, τR =τ0Ns2 (Nsc + 1) where, Ns is the number-average degree of polymerization of the bottlebrush backbone strands between crosslinks, Nsc is the degree of polymerization of the side chains and τ0is a characteristic monomeric relaxation time. At time scales t smaller than the Rouse time, t <τR , the time dependent network shear modulus decays with time as G (t) ~ ρkB T(τ0 / t) 1 / 2 , where ρis the monomer number density. However, at the time scale t larger than the Rouse time of the bottlebrush strands between crosslinks, the network response is pure elastic with shear modulus G (t) =G0 , where G0 is the equilibrium shear modulus at small deformation. The stress evolution in the bottlebrush networks can be described by a universal function of t /τR . NSF DMR-1409710.
Dynamics-based centrality for directed networks
NASA Astrophysics Data System (ADS)
Masuda, Naoki; Kori, Hiroshi
2010-11-01
Determining the relative importance of nodes in directed networks is important in, for example, ranking websites, publications, and sports teams, and for understanding signal flows in systems biology. A prevailing centrality measure in this respect is the PageRank. In this work, we focus on another class of centrality derived from the Laplacian of the network. We extend the Laplacian-based centrality, which has mainly been applied to strongly connected networks, to the case of general directed networks such that we can quantitatively compare arbitrary nodes. Toward this end, we adopt the idea used in the PageRank to introduce global connectivity between all the pairs of nodes with a certain strength. Numerical simulations are carried out on some networks. We also offer interpretations of the Laplacian-based centrality for general directed networks in terms of various dynamical and structural properties of networks. Importantly, the Laplacian-based centrality defined as the stationary density of the continuous-time random walk with random jumps is shown to be equivalent to the absorption probability of the random walk with sinks at each node but without random jumps. Similarly, the proposed centrality represents the importance of nodes in dynamics on the original network supplied with sinks but not with random jumps.
Traffic Dynamics of Computer Networks
NASA Astrophysics Data System (ADS)
Fekete, Attila
2008-10-01
Two important aspects of the Internet, namely the properties of its topology and the characteristics of its data traffic, have attracted growing attention of the physics community. My thesis has considered problems of both aspects. First I studied the stochastic behavior of TCP, the primary algorithm governing traffic in the current Internet, in an elementary network scenario consisting of a standalone infinite-sized buffer and an access link. The effect of the fast recovery and fast retransmission (FR/FR) algorithms is also considered. I showed that my model can be extended further to involve the effect of link propagation delay, characteristic of WAN. I continued my thesis with the investigation of finite-sized semi-bottleneck buffers, where packets can be dropped not only at the link, but also at the buffer. I demonstrated that the behavior of the system depends only on a certain combination of the parameters. Moreover, an analytic formula was derived that gives the ratio of packet loss rate at the buffer to the total packet loss rate. This formula makes it possible to treat buffer-losses as if they were link-losses. Finally, I studied computer networks from a structural perspective. I demonstrated through fluid simulations that the distribution of resources, specifically the link bandwidth, has a serious impact on the global performance of the network. Then I analyzed the distribution of edge betweenness in a growing scale-free tree under the condition that a local property, the in-degree of the "younger" node of an arbitrary edge, is known in order to find an optimum distribution of link capacity. The derived formula is exact even for finite-sized networks. I also calculated the conditional expectation of edge betweenness, rescaled for infinite networks.
Mathematics of small stochastic reaction networks: A boundary layer theory for eigenstate analysis
Mjolsness, Eric; Prasad, Upendra
2013-01-01
We study and analyze the stochastic dynamics of a reversible bimolecular reaction A + B ↔ C called the “trivalent reaction.” This reaction is of a fundamental nature and is part of many biochemical reaction networks. The stochastic dynamics is given by the stochastic master equation, which is difficult to solve except when the equilibrium state solution is desired. We present a novel way of finding the eigenstates of this system of difference-differential equations, using perturbation analysis of ordinary differential equations arising from approximation of the difference equations. The time evolution of the state probabilities can then be expressed in terms of the eigenvalues and the eigenvectors. PMID:23514469
Communication Dynamics in Finite Capacity Social Networks
NASA Astrophysics Data System (ADS)
Haerter, Jan O.; Jamtveit, Bjørn; Mathiesen, Joachim
2012-10-01
In communication networks, structure and dynamics are tightly coupled. The structure controls the flow of information and is itself shaped by the dynamical process of information exchanged between nodes. In order to reconcile structure and dynamics, a generic model, based on the local interaction between nodes, is considered for the communication in large social networks. In agreement with data from a large human organization, we show that the flow is non-Markovian and controlled by the temporal limitations of individuals. We confirm the versatility of our model by predicting simultaneously the degree-dependent node activity, the balance between information input and output of nodes, and the degree distribution. Finally, we quantify the limitations to network analysis when it is based on data sampled over a finite period of time.
Dynamic fracture toughnesses of reaction-bonded silicon nitride
NASA Technical Reports Server (NTRS)
Kobayashi, A. S.; Emery, A. F.; Liaw, B. M.
1983-01-01
The room-temperature dynamic fracture response of reaction-bonded silicon nitride is investigated using a hybrid experimental-numerical procedure. In this procedure, experimentally determined crack velocities are utilized to drive a dynamic finite-element code or dynamic finite-difference code in its generation mode in order to extract numerically the dynamic stress intensity factor of the fracturing specimen. Results show that the dynamic fracture toughness vs crack velocity relations of the two reaction-bonded silicon nitrides do not follow the general trend in those relations of brittle polymers and steel. A definite slow crack velocity during the initial phase of dynamic crack propagation is observed in reaction-bonded silicon nitride, which results in a nonunique dynamic fracture toughness vs crack velocity relation. In addition, it is found that a propagating crack will continue to propagate under a static stress intensity factor substantially lower than K(IC).
Targeting the dynamics of complex networks
Gutiérrez, Ricardo; Sendiña-Nadal, Irene; Zanin, Massimiliano; Papo, David; Boccaletti, Stefano
2012-01-01
We report on a generic procedure to steer (target) a network's dynamics towards a given, desired evolution. The problem is here tackled through a Master Stability Function approach, assessing the stability of the aimed dynamics, and through a selection of nodes to be targeted. We show that the degree of a node is a crucial element in this selection process, and that the targeting mechanism is most effective in heterogeneous scale-free architectures. This makes the proposed approach applicable to the large majority of natural and man-made networked systems. PMID:22563525
The cost and capacity of signaling in the Escherichia coli protein reaction network
NASA Astrophysics Data System (ADS)
Axelsen, Jacob Bock; Krishna, Sandeep; Sneppen, Kim
2008-01-01
In systems biology new ways are required to analyze the large amount of existing data on regulation of cellular processes. Recent work can be roughly classified into either dynamical models of well-described subsystems, or coarse-grained descriptions of the topology of the molecular networks at the scale of the whole organism. In order to bridge these two disparate approaches one needs to develop simplified descriptions of dynamics and topological measures which address the propagation of signals in molecular networks. Transmission of a signal across a reaction node depends on the presence of other reactants. It will typically be more demanding to transmit a signal across a reaction node with more input links. Sending signals along a path with several subsequent reaction nodes also increases the constraints on the presence of other proteins in the overall network. Therefore counting in and out links along reactions of a potential pathway can give insight into the signaling properties of a particular molecular network. Here, we consider the directed network of protein regulation in E. coli, characterizing its modularity in terms of its potential to transmit signals. We demonstrate that the simplest measure based on identifying subnetworks of strong components, within which each node could send a signal to every other node, does indeed partition the network into functional modules. We suggest that the total number of reactants needed to send a signal between two nodes in the network can be considered as the cost associated with transmitting this signal. Similarly we define spread as the number of reaction products that could be influenced by transmission of a successful signal. Our considerations open for a new class of network measures that implicitly utilize the constrained repertoire of chemical modifications of any biological molecule. The counting of cost and spread connects the topology of networks to the specificity of signaling across the network. Thereby, we
Neural network with formed dynamics of activity
Dunin-Barkovskii, V.L.; Osovets, N.B.
1995-03-01
The problem of developing a neural network with a given pattern of the state sequence is considered. A neural network structure and an algorithm, of forming its bond matrix which lead to an approximate but robust solution of the problem are proposed and discussed. Limiting characteristics of the serviceability of the proposed structure are studied. Various methods of visualizing dynamic processes in a neural network are compared. Possible applications of the results obtained for interpretation of neurophysiological data and in neuroinformatics systems are discussed.
Dynamics of overlapping structures in modular networks.
Almendral, J A; Leyva, I; Li, D; Sendiña-Nadal, I; Havlin, S; Boccaletti, S
2010-07-01
Modularity is a fundamental feature of real networks, being intimately bounded to their functionality, i.e., to their capability of performing parallel tasks in a coordinated way. Although the modular structure of real graphs has been intensively studied, very little is known on the interactions between functional modules of a graph. Here, we present a general method based on synchronization of networking oscillators, that is able to detect overlapping structures in multimodular environments. We furthermore report the full analytical and theoretical description on the relationship between the overlapping dynamics and the underlying network topology. The method is illustrated by means of a series of applications. PMID:20866697
Cytoskeletal Network Morphology Regulates Intracellular Transport Dynamics.
Ando, David; Korabel, Nickolay; Huang, Kerwyn Casey; Gopinathan, Ajay
2015-10-20
Intracellular transport is essential for maintaining proper cellular function in most eukaryotic cells, with perturbations in active transport resulting in several types of disease. Efficient delivery of critical cargos to specific locations is accomplished through a combination of passive diffusion and active transport by molecular motors that ballistically move along a network of cytoskeletal filaments. Although motor-based transport is known to be necessary to overcome cytoplasmic crowding and the limited range of diffusion within reasonable timescales, the topological features of the cytoskeletal network that regulate transport efficiency and robustness have not been established. Using a continuum diffusion model, we observed that the time required for cellular transport was minimized when the network was localized near the nucleus. In simulations that explicitly incorporated network spatial architectures, total filament mass was the primary driver of network transit times. However, filament traps that redirect cargo back to the nucleus caused large variations in network transport. Filament polarity was more important than filament orientation in reducing average transit times, and transport properties were optimized in networks with intermediate motor on and off rates. Our results provide important insights into the functional constraints on intracellular transport under which cells have evolved cytoskeletal structures, and have potential applications for enhancing reactions in biomimetic systems through rational transport network design. PMID:26488648
Structural and dynamical properties of complex networks
NASA Astrophysics Data System (ADS)
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
NASA Astrophysics Data System (ADS)
Zañudo, Jorge G. T.; Albert, Réka
2013-06-01
Discrete dynamic models are a powerful tool for the understanding and modeling of large biological networks. Although a lot of progress has been made in developing analysis tools for these models, there is still a need to find approaches that can directly relate the network structure to its dynamics. Of special interest is identifying the stable patterns of activity, i.e., the attractors of the system. This is a problem for large networks, because the state space of the system increases exponentially with network size. In this work, we present a novel network reduction approach that is based on finding network motifs that stabilize in a fixed state. Notably, we use a topological criterion to identify these motifs. Specifically, we find certain types of strongly connected components in a suitably expanded representation of the network. To test our method, we apply it to a dynamic network model for a type of cytotoxic T cell cancer and to an ensemble of random Boolean networks of size up to 200. Our results show that our method goes beyond reducing the network and in most cases can actually predict the dynamical repertoire of the nodes (fixed states or oscillations) in the attractors of the system.
Fundamental structures of dynamic social networks.
Sekara, Vedran; Stopczynski, Arkadiusz; Lehmann, Sune
2016-09-01
Social systems are in a constant state of flux, with dynamics spanning from minute-by-minute changes to patterns present on the timescale of years. Accurate models of social dynamics are important for understanding the spreading of influence or diseases, formation of friendships, and the productivity of teams. Although there has been much progress on understanding complex networks over the past decade, little is known about the regularities governing the microdynamics of social networks. Here, we explore the dynamic social network of a densely-connected population of ∼1,000 individuals and their interactions in the network of real-world person-to-person proximity measured via Bluetooth, as well as their telecommunication networks, online social media contacts, geolocation, and demographic data. These high-resolution data allow us to observe social groups directly, rendering community detection unnecessary. Starting from 5-min time slices, we uncover dynamic social structures expressed on multiple timescales. On the hourly timescale, we find that gatherings are fluid, with members coming and going, but organized via a stable core of individuals. Each core represents a social context. Cores exhibit a pattern of recurring meetings across weeks and months, each with varying degrees of regularity. Taken together, these findings provide a powerful simplification of the social network, where cores represent fundamental structures expressed with strong temporal and spatial regularity. Using this framework, we explore the complex interplay between social and geospatial behavior, documenting how the formation of cores is preceded by coordination behavior in the communication networks and demonstrating that social behavior can be predicted with high precision. PMID:27555584
NASA Astrophysics Data System (ADS)
Brennan, John K.; Lísal, Martin; Gubbins, Keith E.; Rice, Betsy M.
2004-12-01
A molecular simulation method to study the dynamics of chemically reacting mixtures is presented. The method uses a combination of stochastic and dynamic simulation steps, allowing for the simulation of both thermodynamic and transport properties. The method couples a molecular dynamics simulation cell (termed dynamic cell) to a reaction mixture simulation cell (termed control cell) that is formulated upon the reaction ensemble Monte Carlo (RxMC) method, hence the term reaction ensemble molecular dynamics. Thermodynamic and transport properties are calculated in the dynamic cell by using a constant-temperature molecular dynamics simulation method. RxMC forward and reverse reaction steps are performed in the control cell only, while molecular dynamics steps are performed in both the dynamic cell and the control cell. The control cell, which acts as a sink and source reservoir, is maintained at reaction equilibrium conditions via the RxMC algorithm. The reaction ensemble molecular dynamics method is analogous to the grand canonical ensemble molecular dynamics technique, while using some elements of the osmotic molecular dynamics method, and so simulates conditions that directly relate to real, open systems. The accuracy and stability of the method is assessed by considering the ammonia synthesis reaction N2+3H2⇔2NH3 . It is shown to be a viable method for predicting the effects of nonideal environments on the dynamic properties (particularly diffusion) as well as reaction equilibria for chemically reacting mixtures.
Spreading dynamics in complex networks
NASA Astrophysics Data System (ADS)
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.
Dynamic regimes of random fuzzy logic networks
NASA Astrophysics Data System (ADS)
Wittmann, Dominik M.; Theis, Fabian J.
2011-01-01
Random multistate networks, generalizations of the Boolean Kauffman networks, are generic models for complex systems of interacting agents. Depending on their mean connectivity, these networks exhibit ordered as well as chaotic behavior with a critical boundary separating both regimes. Typically, the nodes of these networks are assigned single discrete states. Here, we describe nodes by fuzzy numbers, i.e. vectors of degree-of-membership (DOM) functions specifying the degree to which the nodes are in each of their discrete states. This allows our models to deal with imprecision and uncertainties. Compatible update rules are constructed by expressing the update rules of the multistate network in terms of Boolean operators and generalizing them to fuzzy logic (FL) operators. The standard choice for these generalizations is the Gödel FL, where AND and OR are replaced by the minimum and maximum of two DOMs, respectively. In mean-field approximations we are able to analytically describe the percolation and asymptotic distribution of DOMs in random Gödel FL networks. This allows us to characterize the different dynamic regimes of random multistate networks in terms of FL. In a low-dimensional example, we provide explicit computations and validate our mean-field results by showing that they agree well with network simulations.
On a theory of stability for nonlinear stochastic chemical reaction networks
NASA Astrophysics Data System (ADS)
Smadbeck, Patrick; Kaznessis, Yiannis N.
2015-05-01
We present elements of a stability theory for small, stochastic, nonlinear chemical reaction networks. Steady state probability distributions are computed with zero-information (ZI) closure, a closure algorithm that solves chemical master equations of small arbitrary nonlinear reactions. Stochastic models can be linearized around the steady state with ZI-closure, and the eigenvalues of the Jacobian matrix can be readily computed. Eigenvalues govern the relaxation of fluctuation autocorrelation functions at steady state. Autocorrelation functions reveal the time scales of phenomena underlying the dynamics of nonlinear reaction networks. In accord with the fluctuation-dissipation theorem, these functions are found to be congruent to response functions to small perturbations. Significant differences are observed in the stability of nonlinear reacting systems between deterministic and stochastic modeling formalisms.
On a theory of stability for nonlinear stochastic chemical reaction networks
Smadbeck, Patrick; Kaznessis, Yiannis N.
2015-05-14
We present elements of a stability theory for small, stochastic, nonlinear chemical reaction networks. Steady state probability distributions are computed with zero-information (ZI) closure, a closure algorithm that solves chemical master equations of small arbitrary nonlinear reactions. Stochastic models can be linearized around the steady state with ZI-closure, and the eigenvalues of the Jacobian matrix can be readily computed. Eigenvalues govern the relaxation of fluctuation autocorrelation functions at steady state. Autocorrelation functions reveal the time scales of phenomena underlying the dynamics of nonlinear reaction networks. In accord with the fluctuation-dissipation theorem, these functions are found to be congruent to response functions to small perturbations. Significant differences are observed in the stability of nonlinear reacting systems between deterministic and stochastic modeling formalisms.
Solvable non-Markovian dynamic network
NASA Astrophysics Data System (ADS)
Georgiou, Nicos; Kiss, Istvan Z.; Scalas, Enrico
2015-10-01
Non-Markovian processes are widespread in natural and human-made systems, yet explicit modeling and analysis of such systems is underdeveloped. We consider a non-Markovian dynamic network with random link activation and deletion (RLAD) and heavy-tailed Mittag-Leffler distribution for the interevent times. We derive an analytically and computationally tractable system of Kolmogorov-like forward equations utilizing the Caputo derivative for the probability of having a given number of active links in the network and solve them. Simulations for the RLAD are also studied for power-law interevent times and we show excellent agreement with the Mittag-Leffler model. This agreement holds even when the RLAD network dynamics is coupled with the susceptible-infected-susceptible spreading dynamics. Thus, the analytically solvable Mittag-Leffler model provides an excellent approximation to the case when the network dynamics is characterized by power-law-distributed interevent times. We further discuss possible generalizations of our result.
Dynamical networks with topological self-organization
NASA Technical Reports Server (NTRS)
Zak, M.
2001-01-01
Coupled evolution of state and topology of dynamical networks is introduced. Due to the well organized tensor structure, the governing equations are presented in a canonical form, and required attractors as well as their basins can be easily implanted and controlled.
Limit-cycle oscillations and chaos in reaction networks subject to conservation of mass.
Di Cera, E; Phillipson, P E; Wyman, J
1989-01-01
A cyclic network of autocatalytic reactions involving an unbuffered cofactor and a number of components subject to conservation of mass displays a surprising richness of dynamical behaviors. Limit-cycle oscillations are possible over a wide range of parameter values. Additionally, a cascade of period-doubling bifurcations leading to chaos can coexist with a multiplicity of stable steady states. These results draw attention to the role of unbuffering as a feedback in biochemical systems. PMID:2911564
Dynamic salt effect on intramolecular charge-transfer reactions
Zhu Jianjun; Ma Rong; Lu Yan; Stell, George
2005-12-08
The dynamic salt effect in charge-transfer reactions is investigated theoretically in this paper. Free-energy surfaces are derived based on a nonequilibrium free-energy functional. Reaction coordinates are clearly defined. The solution of the reaction-diffusion equation leads to a rate constant depending on the time correlation function of the reaction coordinates. The time correlation function of the ion-atmosphere coordinate is derived from the solution of the Debye-Falkenhagen equation. It is shown that the dynamic salt effect plays an important role in controlling the rate of charge-transfer reactions in the narrow-window limit but is balanced by the energetics and the dynamics of the polar-solvent coordinate. The simplest version of the theory is compared with an experiment, and the agreement is fairly good. The theory can also be extended to charge-transfer in the class of electrolytes that has come to be called 'ionic fluids'.
Recent Advances in Quantum Dynamics of Bimolecular Reactions.
Zhang, Dong H; Guo, Hua
2016-05-27
In this review, we survey the latest advances in theoretical understanding of bimolecular reaction dynamics in the past decade. The remarkable recent progress in this field has been driven by more accurate and efficient ab initio electronic structure theory, effective potential-energy surface fitting techniques, and novel quantum scattering algorithms. Quantum mechanical characterization of bimolecular reactions continues to uncover interesting dynamical phenomena in atom-diatom reactions and beyond, reaching an unprecedented level of sophistication. In tandem with experimental explorations, these theoretical developments have greatly advanced our understanding of key issues in reaction dynamics, such as microscopic reaction mechanisms, mode specificity, product energy disposal, influence of reactive resonances, and nonadiabatic effects. PMID:26980305
Chemical reaction network approaches to Biochemical Systems Theory.
Arceo, Carlene Perpetua P; Jose, Editha C; Marin-Sanguino, Alberto; Mendoza, Eduardo R
2015-11-01
This paper provides a framework to represent a Biochemical Systems Theory (BST) model (in either GMA or S-system form) as a chemical reaction network with power law kinetics. Using this representation, some basic properties and the application of recent results of Chemical Reaction Network Theory regarding steady states of such systems are shown. In particular, Injectivity Theory, including network concordance [36] and the Jacobian Determinant Criterion [43], a "Lifting Theorem" for steady states [26] and the comprehensive results of Müller and Regensburger [31] on complex balanced equilibria are discussed. A partial extension of a recent Emulation Theorem of Cardelli for mass action systems [3] is derived for a subclass of power law kinetic systems. However, it is also shown that the GMA and S-system models of human purine metabolism [10] do not display the reactant-determined kinetics assumed by Müller and Regensburger and hence only a subset of BST models can be handled with their approach. Moreover, since the reaction networks underlying many BST models are not weakly reversible, results for non-complex balanced equilibria are also needed. PMID:26363083
A dynamical systems view of network centrality.
Grindrod, Peter; Higham, Desmond J
2014-05-01
To gain insights about dynamic networks, the dominant paradigm is to study discrete snapshots, or timeslices, as the interactions evolve. Here, we develop and test a new mathematical framework where network evolution is handled over continuous time, giving an elegant dynamical systems representation for the important concept of node centrality. The resulting system allows us to track the relative influence of each individual. This new setting is natural in many digital applications, offering both conceptual and computational advantages. The novel differential equations approach is convenient for modelling and analysis of network evolution and gives rise to an interesting application of the matrix logarithm function. From a computational perspective, it avoids the awkward up-front compromises between accuracy, efficiency and redundancy required in the prevalent discrete-time setting. Instead, we can rely on state-of-the-art ODE software, where discretization takes place adaptively in response to the prevailing system dynamics. The new centrality system generalizes the widely used Katz measure, and allows us to identify and track, at any resolution, the most influential nodes in terms of broadcasting and receiving information through time-dependent links. In addition to the classical static network notion of attenuation across edges, the new ODE also allows for attenuation over time, as information becomes stale. This allows 'running measures' to be computed, so that networks can be monitored in real time over arbitrarily long intervals. With regard to computational efficiency, we explain why it is cheaper to track good receivers of information than good broadcasters. An important consequence is that the overall broadcast activity in the network can also be monitored efficiently. We use two synthetic examples to validate the relevance of the new measures. We then illustrate the ideas on a large-scale voice call network, where key features are discovered that are not
On correlated reaction sets and coupled reaction sets in metabolic networks.
Marashi, Sayed-Amir; Hosseini, Zhaleh
2015-08-01
Two reactions are in the same "correlated reaction set" (or "Co-Set") if their fluxes are linearly correlated. On the other hand, two reactions are "coupled" if nonzero flux through one reaction implies nonzero flux through the other reaction. Flux correlation analysis has been previously used in the analysis of enzyme dysregulation and enzymopathy, while flux coupling analysis has been used to predict co-expression of genes and to model network evolution. The goal of this paper is to emphasize, through a few examples, that these two concepts are inherently different. In other words, except for the case of full coupling, which implies perfect correlation between two fluxes (R(2) = 1), there are no constraints on Pearson correlation coefficients (CC) in case of any other type of (un)coupling relations. In other words, Pearson CC can take any value between 0 and 1 in other cases. Furthermore, by analyzing genome-scale metabolic networks, we confirm that there are some examples in real networks of bacteria, yeast and human, which approve that flux coupling and flux correlation cannot be used interchangeably. PMID:25747383
Complex Dynamics in Information Sharing Networks
NASA Astrophysics Data System (ADS)
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.
Coevolutionary dynamics on scale-free networks
NASA Astrophysics Data System (ADS)
Lee, Sungmin; Kim, Yup
2005-05-01
We investigate Bak-Sneppen coevolution models on scale-free networks with various degree exponents γ including random networks. For γ>3 , the critical fitness value fc approaches a nonzero finite value in the limit N→∞ , whereas fc approaches zero as 2<γ⩽3 . These results are explained by showing analytically fc(N)≃A/⟨(k+1)2⟩N on the networks with size N . The avalanche size distribution P(s) shows the normal power-law behavior for γ>3 . In contrast, P(s) for 2<γ⩽3 has two power-law regimes. One is a short regime for small s with a large exponent τ1 and the other is a long regime for large s with a small exponent τ2(τ1>τ2) . The origin of the two power regimes is explained by the dynamics on an artificially made star-linked network.
Dynamics on modular networks with heterogeneous correlations
Melnik, Sergey; Porter, Mason A.; Mucha, Peter J.; Gleeson, James P.
2014-06-15
We develop a new ensemble of modular random graphs in which degree-degree correlations can be different in each module, and the inter-module connections are defined by the joint degree-degree distribution of nodes for each pair of modules. We present an analytical approach that allows one to analyze several types of binary dynamics operating on such networks, and we illustrate our approach using bond percolation, site percolation, and the Watts threshold model. The new network ensemble generalizes existing models (e.g., the well-known configuration model and Lancichinetti-Fortunato-Radicchi networks) by allowing a heterogeneous distribution of degree-degree correlations across modules, which is important for the consideration of nonidentical interacting networks.
Roaming dynamics in radical addition-elimination reactions
NASA Astrophysics Data System (ADS)
Joalland, Baptiste; Shi, Yuanyuan; Kamasah, Alexander; Suits, Arthur G.; Mebel, Alexander M.
2014-06-01
Radical addition-elimination reactions are a major pathway for transformation of unsaturated hydrocarbons. In the gas phase, these reactions involve formation of a transient strongly bound intermediate. However, the detailed mechanism and dynamics for these reactions remain unclear. Here we show, for reaction of chlorine atoms with butenes, that the Cl addition-HCl elimination pathway occurs from an abstraction-like Cl-H-C geometry rather than a conventional three-centre or four-centre transition state. Furthermore, access to this geometry is attained by roaming excursions of the Cl atom from the initially formed adduct. In effect, the alkene π cloud serves to capture the Cl atom and hold it, allowing many subsequent opportunities for the energized intermediate to find a suitable approach to the abstraction geometry. These bimolecular roaming reactions are closely related to the roaming radical dynamics recently discovered to play an important role in unimolecular reactions.
Nonparametric inference of network structure and dynamics
NASA Astrophysics Data System (ADS)
Peixoto, Tiago P.
The network structure of complex systems determine their function and serve as evidence for the evolutionary mechanisms that lie behind them. Despite considerable effort in recent years, it remains an open challenge to formulate general descriptions of the large-scale structure of network systems, and how to reliably extract such information from data. Although many approaches have been proposed, few methods attempt to gauge the statistical significance of the uncovered structures, and hence the majority cannot reliably separate actual structure from stochastic fluctuations. Due to the sheer size and high-dimensionality of many networks, this represents a major limitation that prevents meaningful interpretations of the results obtained with such nonstatistical methods. In this talk, I will show how these issues can be tackled in a principled and efficient fashion by formulating appropriate generative models of network structure that can have their parameters inferred from data. By employing a Bayesian description of such models, the inference can be performed in a nonparametric fashion, that does not require any a priori knowledge or ad hoc assumptions about the data. I will show how this approach can be used to perform model comparison, and how hierarchical models yield the most appropriate trade-off between model complexity and quality of fit based on the statistical evidence present in the data. I will also show how this general approach can be elegantly extended to networks with edge attributes, that are embedded in latent spaces, and that change in time. The latter is obtained via a fully dynamic generative network model, based on arbitrary-order Markov chains, that can also be inferred in a nonparametric fashion. Throughout the talk I will illustrate the application of the methods with many empirical networks such as the internet at the autonomous systems level, the global airport network, the network of actors and films, social networks, citations among
Dynamic functional network connectivity using distance correlation
NASA Astrophysics Data System (ADS)
Rudas, Jorge; Guaje, Javier; Demertzi, Athena; Heine, Lizette; Tshibanda, Luaba; Soddu, Andrea; Laureys, Steven; Gómez, Francisco
2015-01-01
Investigations about the intrinsic brain organization in resting-state are critical for the understanding of healthy, pathological and pharmacological cerebral states. Recent studies on fMRI suggest that resting state activity is organized on large scale networks of coordinated activity, in the so called, Resting State Networks (RSNs). The assessment of the interactions among these functional networks plays an important role for the understanding of different brain pathologies. Current methods to quantify these interactions commonly assume that the underlying coordination mechanisms are stationary and linear through the whole recording of the resting state phenomena. Nevertheless, recent evidence suggests that rather than stationary, these mechanisms may exhibit a rich set of time-varying repertoires. In addition, these approaches do not consider possible non-linear relationships maybe linked to feed-back communication mechanisms between RSNs. In this work, we introduce a novel approach for dynamical functional network connectivity for functional magnetic resonance imaging (fMRI) resting activity, which accounts for non-linear dynamic relationships between RSNs. The proposed method is based on a windowed distance correlations computed on resting state time-courses extracted at single subject level. We showed that this strategy is complementary to the current approaches for dynamic functional connectivity and will help to enhance the discrimination capacity of patients with disorder of consciousness.
Dynamic protoneural networks in plants
Debono, Marc-Williams
2013-01-01
Taking as a basis of discussion Kalanchoe’s spontaneous and evoked extracellular activities recorded at the whole plant level, we put the challenging questions: do these low-voltage variations, together with endocellular events, reflect integrative properties and complex behavior in plants? Does it reflect common perceptive systems in animal and plant species? Is the ability of plants to treat short-term variations and information transfer without nervous system relevant? Is a protoneural construction of the world by lower organisms possible? More generally, the aim of this paper is to reevaluate the probably underestimated role of plant surface potentials in the plant relation life, carefully comparing the biogenesis of both animal and plant organisms in the era of plant neurobiology. Knowing that surface potentials participate at least to morphogenesis, cell to cell coupling, long distance transmission and transduction of stimuli, some hypothesis are given indicating that plants have to be studied as environmental biosensors and non linear dynamic systems able to detect transitional states between perception and response to stimuli. This study is conducted in the frame of the “plasticity paradigm,” which gives a theoretical model of evolutionary processes and suggests some hypothesis about the nature of complexity, information and behavior. PMID:23603975
Population Dynamics of Genetic Regulatory Networks
NASA Astrophysics Data System (ADS)
Braun, Erez
2005-03-01
Unlike common objects in physics, a biological cell processes information. The cell interprets its genome and transforms the genomic information content, through the action of genetic regulatory networks, into proteins which in turn dictate its metabolism, functionality and morphology. Understanding the dynamics of a population of biological cells presents a unique challenge. It requires to link the intracellular dynamics of gene regulation, through the mechanism of cell division, to the level of the population. We present experiments studying adaptive dynamics of populations of genetically homogeneous microorganisms (yeast), grown for long durations under steady conditions. We focus on population dynamics that do not involve random genetic mutations. Our experiments follow the long-term dynamics of the population distributions and allow to quantify the correlations among generations. We focus on three interconnected issues: adaptation of genetically homogeneous populations following environmental changes, selection processes on the population and population variability and expression distributions. We show that while the population exhibits specific short-term responses to environmental inputs, it eventually adapts to a robust steady-state, largely independent of external conditions. Cycles of medium-switch show that the adapted state is imprinted in the population and that this memory is maintained for many generations. To further study population adaptation, we utilize the process of gene recruitment whereby a gene naturally regulated by a specific promoter is placed under a different regulatory system. This naturally occurring process has been recognized as a major driving force in evolution. We have recruited an essential gene to a foreign regulatory network and followed the population long-term dynamics. Rewiring of the regulatory network allows us to expose their complex dynamics and phase space structure.
Modeling Insurgent Network Structure and Dynamics
NASA Astrophysics Data System (ADS)
Gabbay, Michael; Thirkill-Mackelprang, Ashley
2010-03-01
We present a methodology for mapping insurgent network structure based on their public rhetoric. Indicators of cooperative links between insurgent groups at both the leadership and rank-and-file levels are used, such as joint policy statements or joint operations claims. In addition, a targeting policy measure is constructed on the basis of insurgent targeting claims. Network diagrams which integrate these measures of insurgent cooperation and ideology are generated for different periods of the Iraqi and Afghan insurgencies. The network diagrams exhibit meaningful changes which track the evolution of the strategic environment faced by insurgent groups. Correlations between targeting policy and network structure indicate that insurgent targeting claims are aimed at establishing a group identity among the spectrum of rank-and-file insurgency supporters. A dynamical systems model of insurgent alliance formation and factionalism is presented which evolves the relationship between insurgent group dyads as a function of their ideological differences and their current relationships. The ability of the model to qualitatively and quantitatively capture insurgent network dynamics observed in the data is discussed.
Dynamic motifs in socio-economic networks
NASA Astrophysics Data System (ADS)
Zhang, Xin; Shao, Shuai; Stanley, H. Eugene; Havlin, Shlomo
2014-12-01
Socio-economic networks are of central importance in economic life. We develop a method of identifying and studying motifs in socio-economic networks by focusing on “dynamic motifs,” i.e., evolutionary connection patterns that, because of “node acquaintances” in the network, occur much more frequently than random patterns. We examine two evolving bi-partite networks: i) the world-wide commercial ship chartering market and ii) the ship build-to-order market. We find similar dynamic motifs in both bipartite networks, even though they describe different economic activities. We also find that “influence” and “persistence” are strong factors in the interaction behavior of organizations. When two companies are doing business with the same customer, it is highly probable that another customer who currently only has business relationship with one of these two companies, will become customer of the second in the future. This is the effect of influence. Persistence means that companies with close business ties to customers tend to maintain their relationships over a long period of time.
Motion detection based on recurrent network dynamics
Joukes, Jeroen; Hartmann, Till S.; Krekelberg, Bart
2014-01-01
The detection of visual motion requires temporal delays to compare current with earlier visual input. Models of motion detection assume that these delays reside in separate classes of slow and fast thalamic cells, or slow and fast synaptic transmission. We used a data-driven modeling approach to generate a model that instead uses recurrent network dynamics with a single, fixed temporal integration window to implement the velocity computation. This model successfully reproduced the temporal response dynamics of a population of motion sensitive neurons in macaque middle temporal area (MT) and its constituent parts matched many of the properties found in the motion processing pathway (e.g., Gabor-like receptive fields (RFs), simple and complex cells, spatially asymmetric excitation and inhibition). Reverse correlation analysis revealed that a simplified network based on first and second order space-time correlations of the recurrent model behaved much like a feedforward motion energy (ME) model. The feedforward model, however, failed to capture the full speed tuning and direction selectivity properties based on higher than second order space-time correlations typically found in MT. These findings support the idea that recurrent network connectivity can create temporal delays to compute velocity. Moreover, the model explains why the motion detection system often behaves like a feedforward ME network, even though the anatomical evidence strongly suggests that this network should be dominated by recurrent feedback. PMID:25565992
Dynamic network mechanisms of relational integration.
Parkin, Beth L; Hellyer, Peter J; Leech, Robert; Hampshire, Adam
2015-05-20
A prominent hypothesis states that specialized neural modules within the human lateral frontopolar cortices (LFPCs) support "relational integration" (RI), the solving of complex problems using inter-related rules. However, it has been proposed that LFPC activity during RI could reflect the recruitment of additional "domain-general" resources when processing more difficult problems in general as opposed to RI specifically. Moreover, theoretical research with computational models has demonstrated that RI may be supported by dynamic processes that occur throughout distributed networks of brain regions as opposed to within a discrete computational module. Here, we present fMRI findings from a novel deductive reasoning paradigm that controls for general difficulty while manipulating RI demands. In accordance with the domain-general perspective, we observe an increase in frontoparietal activation during challenging problems in general as opposed to RI specifically. Nonetheless, when examining frontoparietal activity using analyses of phase synchrony and psychophysiological interactions, we observe increased network connectivity during RI alone. Moreover, dynamic causal modeling with Bayesian model selection identifies the LFPC as the effective connectivity source. Based on these results, we propose that during RI an increase in network connectivity and a decrease in network metastability allows rules that are coded throughout working memory systems to be dynamically bound. This change in connectivity state is top-down propagated via a hierarchical system of domain-general networks with the LFPC at the apex. In this manner, the functional network perspective reconciles key propositions of the globalist, modular, and computational accounts of RI within a single unified framework. PMID:25995457
Dynamic Network Mechanisms of Relational Integration
Parkin, Beth L.; Hellyer, Peter J.; Leech, Robert
2015-01-01
A prominent hypothesis states that specialized neural modules within the human lateral frontopolar cortices (LFPCs) support “relational integration” (RI), the solving of complex problems using inter-related rules. However, it has been proposed that LFPC activity during RI could reflect the recruitment of additional “domain-general” resources when processing more difficult problems in general as opposed to RI specifically. Moreover, theoretical research with computational models has demonstrated that RI may be supported by dynamic processes that occur throughout distributed networks of brain regions as opposed to within a discrete computational module. Here, we present fMRI findings from a novel deductive reasoning paradigm that controls for general difficulty while manipulating RI demands. In accordance with the domain-general perspective, we observe an increase in frontoparietal activation during challenging problems in general as opposed to RI specifically. Nonetheless, when examining frontoparietal activity using analyses of phase synchrony and psychophysiological interactions, we observe increased network connectivity during RI alone. Moreover, dynamic causal modeling with Bayesian model selection identifies the LFPC as the effective connectivity source. Based on these results, we propose that during RI an increase in network connectivity and a decrease in network metastability allows rules that are coded throughout working memory systems to be dynamically bound. This change in connectivity state is top-down propagated via a hierarchical system of domain-general networks with the LFPC at the apex. In this manner, the functional network perspective reconciles key propositions of the globalist, modular, and computational accounts of RI within a single unified framework. PMID:25995457
Testing string dynamics in lepton nucleus reactions
Gyulassy, M.; Pluemer, M.
1989-10-01
The sensitivity of nuclear attenuation of 10-100 GeV lepton nucleus ({ell}A) reactions to space-time aspects of hadronization is investigated within the context of the Lund string model. We consider two mechanisms for attenuation in a nucleus: final state cascading and string flip excitations. Implications for the evolution of the energy density in nuclear collisions are discussed. 16 refs., 10 figs.
trans-Symmetric Dynamic Covalent Systems: Connected Transamination and Transimination Reactions
Schaufelberger, Fredrik; Hu, Lei; Ramström, Olof
2015-01-01
The development of chemical transaminations as a new type of dynamic covalent reaction is described. The key 1,3-proton shift is under complete catalytic control and can be conducted orthogonally to, or simultaneous with, transimination in the presence of an amine to rapidly yield two-dimensional dynamic systems with a high degree of complexity evolution. The transamination–transimination systems are proven to be fully reversible, stable over several days, compatible with a range of functional groups, and highly tunable. Kinetic studies show transamination to be the rate-limiting reaction in the network. Furthermore, it was discovered that readily available quinuclidine is a highly potent catalyst for aldimine transaminations. This study demonstrates how connected dynamic reactions give rise to significantly larger systems than the unconnected counterparts, and shows how reversible isomerizations can be utilized as an effective diversity-generating element. PMID:26044061
NASA Astrophysics Data System (ADS)
Marchetti, Luca; Priami, Corrado; Thanh, Vo Hong
2016-07-01
This paper introduces HRSSA (Hybrid Rejection-based Stochastic Simulation Algorithm), a new efficient hybrid stochastic simulation algorithm for spatially homogeneous biochemical reaction networks. HRSSA is built on top of RSSA, an exact stochastic simulation algorithm which relies on propensity bounds to select next reaction firings and to reduce the average number of reaction propensity updates needed during the simulation. HRSSA exploits the computational advantage of propensity bounds to manage time-varying transition propensities and to apply dynamic partitioning of reactions, which constitute the two most significant bottlenecks of hybrid simulation. A comprehensive set of simulation benchmarks is provided for evaluating performance and accuracy of HRSSA against other state of the art algorithms.
Nuclear Reactions and Stellar Evolution: Unified Dynamics
Bauer, W.; Strother, T.
2007-10-26
Motivated by the success of kinetic theory in the description of observables in intermediate and high energy heavy ion collisions, we use kinetic theory to model the dynamics of collapsing iron cores in type II supernova explosions. The algorithms employed to model the collapse, some preliminary results and predictions, and the future of the code are discussed.
MONOMIALS AND BASIN CYLINDERS FOR NETWORK DYNAMICS
AUSTIN, DANIEL; DINWOODIE, IAN H
2014-01-01
We describe methods to identify cylinder sets inside a basin of attraction for Boolean dynamics of biological networks. Such sets are used for designing regulatory interventions that make the system evolve towards a chosen attractor, for example initiating apoptosis in a cancer cell. We describe two algebraic methods for identifying cylinders inside a basin of attraction, one based on the Groebner fan that finds monomials that define cylinders and the other on primary decomposition. Both methods are applied to current examples of gene networks. PMID:25620893
Spreading out of perturbations in reversible reaction networks.
Maslov, Sergei; Sneppen, Kim; Ispolatov, I
2007-08-17
Using an example of physical interactions between proteins, we study how a perturbation propagates in the equilibrium of a network of reversible reactions governed by the law of mass action. We introduce a matrix formalism to describe the linear response of all equilibrium concentrations to shifts in total abundances of individual reactants, and reveal its heuristic analogy to the flow of electric current in a network of resistors. Our main conclusion is that, on average, the induced changes in equilibrium concentrations decay exponentially as a function of network distance from the source of perturbation. We analyze how this decay is influenced by such factors as the topology of a network, binding strength, and correlations between concentrations of neighboring nodes. We find that the minimal branching of the network, small values of dissociation constants, and low equilibrium free (unbound) concentrations of reacting substances all decrease the decay constant and thus increase the range of propagation. Exact analytic expressions for the decay constant are obtained for the case of equally strong interactions and uniform as well as oscillating concentrations on the Bethe lattice. Our general findings are illustrated using a real network of protein-protein interactions in baker's yeast with experimentally determined protein concentrations. PMID:18046464
Spreading out of perturbations in reversible reaction networks
NASA Astrophysics Data System (ADS)
Maslov, Sergei; Sneppen, Kim; Ispolatov, I.
2007-08-01
Using an example of physical interactions between proteins, we study how a perturbation propagates in the equilibrium of a network of reversible reactions governed by the law of mass action. We introduce a matrix formalism to describe the linear response of all equilibrium concentrations to shifts in total abundances of individual reactants, and reveal its heuristic analogy to the flow of electric current in a network of resistors. Our main conclusion is that, on average, the induced changes in equilibrium concentrations decay exponentially as a function of network distance from the source of perturbation. We analyze how this decay is influenced by such factors as the topology of a network, binding strength, and correlations between concentrations of neighboring nodes. We find that the minimal branching of the network, small values of dissociation constants, and low equilibrium free (unbound) concentrations of reacting substances all decrease the decay constant and thus increase the range of propagation. Exact analytic expressions for the decay constant are obtained for the case of equally strong interactions and uniform as well as oscillating concentrations on the Bethe lattice. Our general findings are illustrated using a real network of protein-protein interactions in baker's yeast with experimentally determined protein concentrations.
Traffic chaotic dynamics modeling and analysis of deterministic network
NASA Astrophysics Data System (ADS)
Wu, Weiqiang; Huang, Ning; Wu, Zhitao
2016-07-01
Network traffic is an important and direct acting factor of network reliability and performance. To understand the behaviors of network traffic, chaotic dynamics models were proposed and helped to analyze nondeterministic network a lot. The previous research thought that the chaotic dynamics behavior was caused by random factors, and the deterministic networks would not exhibit chaotic dynamics behavior because of lacking of random factors. In this paper, we first adopted chaos theory to analyze traffic data collected from a typical deterministic network testbed — avionics full duplex switched Ethernet (AFDX, a typical deterministic network) testbed, and found that the chaotic dynamics behavior also existed in deterministic network. Then in order to explore the chaos generating mechanism, we applied the mean field theory to construct the traffic dynamics equation (TDE) for deterministic network traffic modeling without any network random factors. Through studying the derived TDE, we proposed that chaotic dynamics was one of the nature properties of network traffic, and it also could be looked as the action effect of TDE control parameters. A network simulation was performed and the results verified that the network congestion resulted in the chaotic dynamics for a deterministic network, which was identical with expectation of TDE. Our research will be helpful to analyze the traffic complicated dynamics behavior for deterministic network and contribute to network reliability designing and analysis.
Dynamic Trust Management for Mobile Networks and Its Applications
ERIC Educational Resources Information Center
Bao, Fenye
2013-01-01
Trust management in mobile networks is challenging due to dynamically changing network environments and the lack of a centralized trusted authority. In this dissertation research, we "design" and "validate" a class of dynamic trust management protocols for mobile networks, and demonstrate the utility of dynamic trust management…
Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks
Eddy, James A.; Papin, Jason A.
2008-01-01
Extracellular cues affect signaling, metabolic, and regulatory processes to elicit cellular responses. Although intracellular signaling, metabolic, and regulatory networks are highly integrated, previous analyses have largely focused on independent processes (e.g., metabolism) without considering the interplay that exists among them. However, there is evidence that many diseases arise from multifunctional components with roles throughout signaling, metabolic, and regulatory networks. Therefore, in this study, we propose a flux balance analysis (FBA)–based strategy, referred to as integrated dynamic FBA (idFBA), that dynamically simulates cellular phenotypes arising from integrated networks. The idFBA framework requires an integrated stoichiometric reconstruction of signaling, metabolic, and regulatory processes. It assumes quasi-steady-state conditions for “fast” reactions and incorporates “slow” reactions into the stoichiometric formalism in a time-delayed manner. To assess the efficacy of idFBA, we developed a prototypic integrated system comprising signaling, metabolic, and regulatory processes with network features characteristic of actual systems and incorporating kinetic parameters based on typical time scales observed in literature. idFBA was applied to the prototypic system, which was evaluated for different environments and gene regulatory rules. In addition, we applied the idFBA framework in a similar manner to a representative module of the single-cell eukaryotic organism Saccharomyces cerevisiae. Ultimately, idFBA facilitated quantitative, dynamic analysis of systemic effects of extracellular cues on cellular phenotypes and generated comparable time-course predictions when contrasted with an equivalent kinetic model. Since idFBA solves a linear programming problem and does not require an exhaustive list of detailed kinetic parameters, it may be efficiently scaled to integrated intracellular systems that incorporate signaling, metabolic, and
Hybrid discrete/continuum algorithms for stochastic reaction networks
Safta, Cosmin Sargsyan, Khachik Debusschere, Bert Najm, Habib N.
2015-01-15
Direct solutions of the Chemical Master Equation (CME) governing Stochastic Reaction Networks (SRNs) are generally prohibitively expensive due to excessive numbers of possible discrete states in such systems. To enhance computational efficiency we develop a hybrid approach where the evolution of states with low molecule counts is treated with the discrete CME model while that of states with large molecule counts is modeled by the continuum Fokker–Planck equation. The Fokker–Planck equation is discretized using a 2nd order finite volume approach with appropriate treatment of flux components. The numerical construction at the interface between the discrete and continuum regions implements the transfer of probability reaction by reaction according to the stoichiometry of the system. The performance of this novel hybrid approach is explored for a two-species circadian model with computational efficiency gains of about one order of magnitude.
Hybrid discrete/continuum algorithms for stochastic reaction networks
NASA Astrophysics Data System (ADS)
Safta, Cosmin; Sargsyan, Khachik; Debusschere, Bert; Najm, Habib N.
2015-01-01
Direct solutions of the Chemical Master Equation (CME) governing Stochastic Reaction Networks (SRNs) are generally prohibitively expensive due to excessive numbers of possible discrete states in such systems. To enhance computational efficiency we develop a hybrid approach where the evolution of states with low molecule counts is treated with the discrete CME model while that of states with large molecule counts is modeled by the continuum Fokker-Planck equation. The Fokker-Planck equation is discretized using a 2nd order finite volume approach with appropriate treatment of flux components. The numerical construction at the interface between the discrete and continuum regions implements the transfer of probability reaction by reaction according to the stoichiometry of the system. The performance of this novel hybrid approach is explored for a two-species circadian model with computational efficiency gains of about one order of magnitude.
Hybrid discrete/continuum algorithms for stochastic reaction networks
Safta, Cosmin; Sargsyan, Khachik; Debusschere, Bert; Najm, Habib N.
2014-10-22
Direct solutions of the Chemical Master Equation (CME) governing Stochastic Reaction Networks (SRNs) are generally prohibitively expensive due to excessive numbers of possible discrete states in such systems. To enhance computational efficiency we develop a hybrid approach where the evolution of states with low molecule counts is treated with the discrete CME model while that of states with large molecule counts is modeled by the continuum Fokker-Planck equation. The Fokker-Planck equation is discretized using a 2nd order finite volume approach with appropriate treatment of flux components to avoid negative probability values. The numerical construction at the interface between the discrete and continuum regions implements the transfer of probability reaction by reaction according to the stoichiometry of the system. As a result, the performance of this novel hybrid approach is explored for a two-species circadian model with computational efficiency gains of about one order of magnitude.
Hybrid discrete/continuum algorithms for stochastic reaction networks
Safta, Cosmin; Sargsyan, Khachik; Debusschere, Bert; Najm, Habib N.
2014-10-22
Direct solutions of the Chemical Master Equation (CME) governing Stochastic Reaction Networks (SRNs) are generally prohibitively expensive due to excessive numbers of possible discrete states in such systems. To enhance computational efficiency we develop a hybrid approach where the evolution of states with low molecule counts is treated with the discrete CME model while that of states with large molecule counts is modeled by the continuum Fokker-Planck equation. The Fokker-Planck equation is discretized using a 2nd order finite volume approach with appropriate treatment of flux components to avoid negative probability values. The numerical construction at the interface between the discretemore » and continuum regions implements the transfer of probability reaction by reaction according to the stoichiometry of the system. As a result, the performance of this novel hybrid approach is explored for a two-species circadian model with computational efficiency gains of about one order of magnitude.« less
Transverse flow reactor studies of the dynamics of radical reactions
Macdonald, R.G.
1993-12-01
Radical reactions are in important in combustion chemistry; however, little state-specific information is available for these reactions. A new apparatus has been constructed to measure the dynamics of radical reactions. The unique feature of this apparatus is a transverse flow reactor in which an atom or radical of known concentration will be produced by pulsed laser photolysis of an appropriate precursor molecule. The time dependence of individual quantum states or products and/or reactants will be followed by rapid infrared laser absorption spectroscopy. The reaction H + O{sub 2} {yields} OH + O will be studied.
Nonlinear Network Dynamics on Earthquake Fault Systems
NASA Astrophysics Data System (ADS)
Rundle, P. B.; Rundle, J. B.; Tiampo, K. F.
2001-12-01
Understanding the physics of earthquakes is essential if large events are ever to be forecast. Real faults occur in topologically complex networks that exhibit cooperative, emergent space-time behavior that includes precursory quiescence or activation, and clustering of events. The purpose of this work is to investigate the sensitivity of emergent behavior of fault networks to changes in the physics on the scale of single faults or smaller. In order to investigate the effect of changes at small scales on the behavior of the network, we need to construct models of earthquake fault systems that contain the essential physics. A network topology is therefore defined in an elastic medium, the stress Green's functions (i.e. the stress transfer coefficients) are computed, frictional properties are defined and the system is driven via the slip deficit as defined below. The long-range elastic interactions produce mean-field dynamics in the simulations. We focus in this work on the major strike-slip faults in Southern California that produce the most frequent and largest magnitude events. To determine the topology and properties of the network, we used the tabulation of fault properties published in the literature. We have found that the statistical distribution of large earthquakes on a model of a topologically complex, strongly correlated real fault network is highly sensitive to the precise nature of the stress dissipation properties of the friction laws associated with individual faults. These emergent, self-organizing space-time modes of behavior are properties of the network as a whole, rather than of the individual fault segments of which the network is comprised (ref: PBR et al., Physical Review Letters, in press, 2001).
Eigenvector dynamics under perturbation of modular networks
NASA Astrophysics Data System (ADS)
Sarkar, Somwrita; Chawla, Sanjay; Robinson, P. A.; Fortunato, Santo
2016-06-01
Rotation dynamics of eigenvectors of modular network adjacency matrices under random perturbations are presented. In the presence of q communities, the number of eigenvectors corresponding to the q largest eigenvalues form a "community" eigenspace and rotate together, but separately from that of the "bulk" eigenspace spanned by all the other eigenvectors. Using this property, the number of modules or clusters in a network can be estimated in an algorithm-independent way. A general argument and derivation for the theoretical detectability limit for sparse modular networks with q communities is presented, beyond which modularity persists in the system but cannot be detected. It is shown that for detecting the clusters or modules using the adjacency matrix, there is a "band" in which it is hard to detect the clusters even before the theoretical detectability limit is reached, and for which the theoretically predicted detectability limit forms the sufficient upper bound. Analytic estimations of these bounds are presented and empirically demonstrated.
Failure dynamics of the global risk network
Szymanski, Boleslaw K.; Lin, Xin; Asztalos, Andrea; Sreenivasan, Sameet
2015-01-01
Risks threatening modern societies form an intricately interconnected network that often underlies crisis situations. Yet, little is known about how risk materializations in distinct domains influence each other. Here we present an approach in which expert assessments of likelihoods and influence of risks underlie a quantitative model of the global risk network dynamics. The modeled risks range from environmental to economic and technological, and include difficult to quantify risks, such as geo-political and social. Using the maximum likelihood estimation, we find the optimal model parameters and demonstrate that the model including network effects significantly outperforms the others, uncovering full value of the expert collected data. We analyze the model dynamics and study its resilience and stability. Our findings include such risk properties as contagion potential, persistence, roles in cascades of failures and the identity of risks most detrimental to system stability. The model provides quantitative means for measuring the adverse effects of risk interdependencies and the materialization of risks in the network. PMID:26087020
Dynamic congestion control mechanisms for MPLS networks
NASA Astrophysics Data System (ADS)
Holness, Felicia; Phillips, Chris I.
2001-02-01
Considerable interest has arisen in congestion control through traffic engineering from the knowledge that although sensible provisioning of the network infrastructure is needed, together with sufficient underlying capacity, these are not sufficient to deliver the Quality of Service required for new applications. This is due to dynamic variations in load. In operational Internet Protocol (IP) networks, it has been difficult to incorporate effective traffic engineering due to the limited capabilities of the IP technology. In principle, Multiprotocol Label Switching (MPLS), which is a connection-oriented label swapping technology, offers new possibilities in addressing the limitations by allowing the operator to use sophisticated traffic control mechanisms. This paper presents a novel scheme to dynamically manage traffic flows through the network by re-balancing streams during periods of congestion. It proposes management-based algorithms that will allow label switched routers within the network to utilize mechanisms within MPLS to indicate when flows are starting to experience frame/packet loss and then to react accordingly. Based upon knowledge of the customer's Service Level Agreement, together with instantaneous flow information, the label edge routers can then instigate changes to the LSP route and circumvent congestion that would hitherto violate the customer contacts.
Failure dynamics of the global risk network.
Szymanski, Boleslaw K; Lin, Xin; Asztalos, Andrea; Sreenivasan, Sameet
2015-01-01
Risks threatening modern societies form an intricately interconnected network that often underlies crisis situations. Yet, little is known about how risk materializations in distinct domains influence each other. Here we present an approach in which expert assessments of likelihoods and influence of risks underlie a quantitative model of the global risk network dynamics. The modeled risks range from environmental to economic and technological, and include difficult to quantify risks, such as geo-political and social. Using the maximum likelihood estimation, we find the optimal model parameters and demonstrate that the model including network effects significantly outperforms the others, uncovering full value of the expert collected data. We analyze the model dynamics and study its resilience and stability. Our findings include such risk properties as contagion potential, persistence, roles in cascades of failures and the identity of risks most detrimental to system stability. The model provides quantitative means for measuring the adverse effects of risk interdependencies and the materialization of risks in the network. PMID:26087020
Failure dynamics of the global risk network
NASA Astrophysics Data System (ADS)
Szymanski, Boleslaw K.; Lin, Xin; Asztalos, Andrea; Sreenivasan, Sameet
2015-06-01
Risks threatening modern societies form an intricately interconnected network that often underlies crisis situations. Yet, little is known about how risk materializations in distinct domains influence each other. Here we present an approach in which expert assessments of likelihoods and influence of risks underlie a quantitative model of the global risk network dynamics. The modeled risks range from environmental to economic and technological, and include difficult to quantify risks, such as geo-political and social. Using the maximum likelihood estimation, we find the optimal model parameters and demonstrate that the model including network effects significantly outperforms the others, uncovering full value of the expert collected data. We analyze the model dynamics and study its resilience and stability. Our findings include such risk properties as contagion potential, persistence, roles in cascades of failures and the identity of risks most detrimental to system stability. The model provides quantitative means for measuring the adverse effects of risk interdependencies and the materialization of risks in the network.
Information spreading on dynamic social networks
NASA Astrophysics Data System (ADS)
Liu, Chuang; Zhang, Zi-Ke
2014-04-01
Nowadays, information spreading on social networks has triggered an explosive attention in various disciplines. Most of previous works in this area mainly focus on discussing the effects of spreading probability or immunization strategy on static networks. However, in real systems, the peer-to-peer network structure changes constantly according to frequently social activities of users. In order to capture this dynamical property and study its impact on information spreading, in this paper, a link rewiring strategy based on the Fermi function is introduced. In the present model, the informed individuals tend to break old links and reconnect to their second-order friends with more uninformed neighbors. Simulation results on the susceptible-infected-recovered (SIR) model with fixed recovery time T=1 indicate that the information would spread more faster and broader with the proposed rewiring strategy. Extensive analyses of the information cascade size distribution show that the spreading process of the initial steps plays a very important role, that is to say, the information will spread out if it is still survival at the beginning time. The proposed model may shed some light on the in-depth understanding of information spreading on dynamical social networks.
Dynamics of domain wall networks with junctions
Avelino, P. P.; Oliveira, J. C. R. E.; Martins, C. J. A. P.; Menezes, J.; Menezes, R.
2008-11-15
We use a combination of analytic tools and an extensive set of the largest and most accurate three-dimensional field theory numerical simulations to study the dynamics of domain wall networks with junctions. We build upon our previous work and consider a class of models which, in the limit of large number N of coupled scalar fields, approaches the so-called ''ideal'' model (in terms of its potential to lead to network frustration). We consider values of N between N=2 and N=20, and a range of cosmological epochs, and we also compare this class of models with other toy models used in the past. In all cases we find compelling evidence for a gradual approach to scaling, strongly supporting our no-frustration conjecture. We also discuss the various possible types of junctions (including cases where there is a hierarchy of them) and their roles in the dynamics of the network. Finally, we provide a cosmological Zel'dovich-type bound on the energy scale of this kind of defect network: it must be lower than 10 keV.
Vehicle dynamic analysis using neuronal network algorithms
NASA Astrophysics Data System (ADS)
Oloeriu, Florin; Mocian, Oana
2014-06-01
Theoretical developments of certain engineering areas, the emergence of new investigation tools, which are better and more precise and their implementation on-board the everyday vehicles, all these represent main influence factors that impact the theoretical and experimental study of vehicle's dynamic behavior. Once the implementation of these new technologies onto the vehicle's construction had been achieved, it had led to more and more complex systems. Some of the most important, such as the electronic control of engine, transmission, suspension, steering, braking and traction had a positive impact onto the vehicle's dynamic behavior. The existence of CPU on-board vehicles allows data acquisition and storage and it leads to a more accurate and better experimental and theoretical study of vehicle dynamics. It uses the information offered directly by the already on-board built-in elements of electronic control systems. The technical literature that studies vehicle dynamics is entirely focused onto parametric analysis. This kind of approach adopts two simplifying assumptions. Functional parameters obey certain distribution laws, which are known in classical statistics theory. The second assumption states that the mathematical models are previously known and have coefficients that are not time-dependent. Both the mentioned assumptions are not confirmed in real situations: the functional parameters do not follow any known statistical repartition laws and the mathematical laws aren't previously known and contain families of parameters and are mostly time-dependent. The purpose of the paper is to present a more accurate analysis methodology that can be applied when studying vehicle's dynamic behavior. A method that provides the setting of non-parametrical mathematical models for vehicle's dynamic behavior is relying on neuronal networks. This method contains coefficients that are time-dependent. Neuronal networks are mostly used in various types' system controls, thus
Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks
Nelson Butuk
2004-12-01
This is an annual technical report for the work done over the last year (period ending 9/30/2004) on the project titled ''Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks''. The aim of the project is to develop an efficient chemistry model for combustion simulations. The reduced chemistry model will be developed mathematically without the need of having extensive knowledge of the chemistry involved. To aid in the development of the model, Neural Networks (NN) will be used via a new network topology know as Non-linear Principal Components Analysis (NPCA). We report on the development of a procedure to speed up the training of NPCA. The developed procedure is based on the non-parametric statistical technique of kernel smoothing. When this smoothing technique is implemented as a Neural Network, It is know as Generalized Regression Neural Network (GRNN). We present results of implementing GRNN on a test problem. In addition, we present results of an in house developed 2-D CFD code that will be used through out the project period.
State-to-state reaction dynamics: A selective review
NASA Astrophysics Data System (ADS)
Teslja, Alexey; Valentini, James J.
2006-10-01
A selective review of state-to-state reaction dynamics experiments is presented. The review focuses on three classes of reactions that exemplify the rich history and illustrate the current state of the art in such work. These three reactions are (1) the hydrogen exchange reaction, H +H2→H2+H and its isotopomers; (2) the H +RH→H2+R reactions, where RH is an alkane, beginning with H +CH4→H2+CH3 and extending to much larger alkanes; and (3) the Cl +RH→HCl+R reactions, principally Cl +CH4→HCl+CH3. We describe the experiments, discuss their results, present comparisons with theory, and introduce heuristic models.
Hybrid function projective synchronization in complex dynamical networks
Wei, Qiang; Wang, Xing-yuan Hu, Xiao-peng
2014-02-15
This paper investigates hybrid function projective synchronization in complex dynamical networks. When the complex dynamical networks could be synchronized up to an equilibrium or periodic orbit, a hybrid feedback controller is designed to realize the different component of vector of node could be synchronized up to different desired scaling function in complex dynamical networks with time delay. Hybrid function projective synchronization (HFPS) in complex dynamical networks with constant delay and HFPS in complex dynamical networks with time-varying coupling delay are researched, respectively. Finally, the numerical simulations show the effectiveness of theoretical analysis.
Interdisciplinary applications of network dynamics: From microscopic to Macroscopic
NASA Astrophysics Data System (ADS)
Jeong, Hawoong
``Everything touches everything.'' We are living in a connected world, which has been modeled successfully by complex networks. Ever since, network science becomes new paradigm for understanding our connected yet complex world. After investigating network structure itself, our focus naturally moved to dynamics of/on the network because our connected world is not static but dynamic. In this presentation, we will briefly review the historical development of network science and show some applications of network dynamics ranging from microscopic (metabolic engineering, PNAS, 104 13638) to macroscopic scale (price of anarchy in transportation network, Phys.Rev.Lett. 101 128701). Supported by National Research Foundation of Korea through Grant No. 2011-0028908.
Propagation dynamics on networks featuring complex topologies
NASA Astrophysics Data System (ADS)
Hébert-Dufresne, Laurent; Noël, Pierre-André; Marceau, Vincent; Allard, Antoine; Dubé, Louis J.
2010-09-01
Analytical description of propagation phenomena on random networks has flourished in recent years, yet more complex systems have mainly been studied through numerical means. In this paper, a mean-field description is used to coherently couple the dynamics of the network elements (such as nodes, vertices, individuals, etc.) on the one hand and their recurrent topological patterns (such as subgraphs, groups, etc.) on the other hand. In a susceptible-infectious-susceptible (SIS) model of epidemic spread on social networks with community structure, this approach yields a set of ordinary differential equations for the time evolution of the system, as well as analytical solutions for the epidemic threshold and equilibria. The results obtained are in good agreement with numerical simulations and reproduce the behavior of random networks in the appropriate limits which highlights the influence of topology on the processes. Finally, it is demonstrated that our model predicts higher epidemic thresholds for clustered structures than for equivalent random topologies in the case of networks with zero degree correlation.
Dynamic traffic grooming in survivable WDM networks
NASA Astrophysics Data System (ADS)
Zhu, Yonghua; Lin, Rujian
2005-11-01
This paper investigates the survivable traffic grooming problem for optical mesh networks employing wavelength-division multiplexing (WDM). While the transmission rate of a wavelength channel is high, the bandwidth requirement of a typical connection request can vary from the full wavelength capacity down to subwavelength. To efficiently utilize network resources, subwavelength-granularity connections can be groomed onto direct optical transmission channels, or lightpaths. Meanwhile, the failure of a network element can cause the failure of several lightpaths, thereby leading to large data and revenue loss. Fault-management schemes such as protection are essential to survive such failures. Different low-speed connections may request different bandwidth granularities as well as different protection schemes. How to efficiently groom such low-speed connections while satisfying their protection requirements is the main focus of our investigation. The paper tackles the dynamic survivable traffic grooming problems in multifiber wavelength-routed optical networks by representing the network as a layered graph model. This graph multi layers, where each layer represents a specific wavelength. Each link in the layered graph has more than one fibers and an associated cost. We use a modified Dijkstra algorithm that has a reduced complexity due to the structure of the layered graph. Heuristic algorithms for fiber selection based on a well-designed link-cost metrics are proposed. The performance of various routing algorithms is evaluated through simulation studies.
NASA Astrophysics Data System (ADS)
Jablonski, Piotr; Poe, Gina; Zochowski, Michal
2007-03-01
The hippocampus has the capacity for reactivating recently acquired memories and it is hypothesized that one of the functions of sleep reactivation is the facilitation of consolidation of novel memory traces. The dynamic and network processes underlying such a reactivation remain, however, unknown. We show that such a reactivation characterized by local, self-sustained activity of a network region may be an inherent property of the recurrent excitatory-inhibitory network with a heterogeneous structure. The entry into the reactivation phase is mediated through a physiologically feasible regulation of global excitability and external input sources, while the reactivated component of the network is formed through induced network heterogeneities during learning. We show that structural changes needed for robust reactivation of a given network region are well within known physiological parameters.
NASA Astrophysics Data System (ADS)
Jablonski, Piotr; Poe, Gina R.; Zochowski, Michal
2007-01-01
The hippocampus has the capacity for reactivating recently acquired memories and it is hypothesized that one of the functions of sleep reactivation is the facilitation of consolidation of novel memory traces. The dynamic and network processes underlying such a reactivation remain, however, unknown. We show that such a reactivation characterized by local, self-sustained activity of a network region may be an inherent property of the recurrent excitatory-inhibitory network with a heterogeneous structure. The entry into the reactivation phase is mediated through a physiologically feasible regulation of global excitability and external input sources, while the reactivated component of the network is formed through induced network heterogeneities during learning. We show that structural changes needed for robust reactivation of a given network region are well within known physiological parameters.
Cortical attractor network dynamics with diluted connectivity.
Rolls, Edmund T; Webb, Tristan J
2012-01-24
The connectivity of the cerebral cortex is diluted, with the probability of excitatory connections between even nearby pyramidal cells rarely more than 0.1, and in the hippocampus 0.04. To investigate the extent to which this diluted connectivity affects the dynamics of attractor networks in the cerebral cortex, we simulated an integrate-and-fire attractor network taking decisions between competing inputs with diluted connectivity of 0.25 or 0.1, and with the same number of synaptic connections per neuron for the recurrent collateral synapses within an attractor population as for full connectivity. The results indicated that there was less spiking-related noise with the diluted connectivity in that the stability of the network when in the spontaneous state of firing increased, and the accuracy of the correct decisions increased. The decision times were a little slower with diluted than with complete connectivity. Given that the capacity of the network is set by the number of recurrent collateral synaptic connections per neuron, on which there is a biological limit, the findings indicate that the stability of cortical networks, and the accuracy of their correct decisions or memory recall operations, can be increased by utilizing diluted connectivity and correspondingly increasing the number of neurons in the network, with little impact on the speed of processing of the cortex. Thus diluted connectivity can decrease cortical spiking-related noise. In addition, we show that the Fano factor for the trial-to-trial variability of the neuronal firing decreases from the spontaneous firing state value when the attractor network makes a decision. This article is part of a Special Issue entitled "Neural Coding". PMID:21875702
Roaming dynamics in the MgH + H→Mg + H 2 reaction: Quantum dynamics calculations
NASA Astrophysics Data System (ADS)
Takayanagi, Toshiyuki; Tanaka, Tomokazu
2011-03-01
Reaction mechanisms of the MgH + H→Mg + H 2 reaction have been investigated using quantum reactive scattering methods on a global ab initio potential energy surface. There exist two microscopic mechanisms in the dynamics of this reaction. One is a direct hydrogen abstraction reaction and the other proceeds via initial formation of a HMgH complex in the deep potential well. The result of the present quantum dynamics calculations suggests that the HMgH complex formed in the reaction mainly decays into the Mg + H 2 channel via a 'roaming mechanism' without going through the saddle point region.
On lateral competition in dynamic neural networks
Bellyustin, N.S.
1995-02-01
Artificial neural networks connected homogeneously, which use retinal image processing methods, are considered. We point out that there are probably two different types of lateral inhibition for each neural element by the neighboring ones-due to the negative connection coefficients between elements and due to the decreasing neuron`s response to a too high input signal. The first case characterized by stable dynamics, which is given by the Lyapunov function, while in the second case, stability is absent and two-dimensional dynamic chaos occurs if the time step in the integration of model equations is large enough. The continuous neural medium approximation is used for analytical estimation in both cases. The result is the partition of the parameter space into domains with qualitatively different dynamic modes. Computer simulations confirm the estimates and show that joining two-dimensional chaos with symmetries provided by the initial and boundary conditions may produce patterns which are genuine pieces of art.
Bootstrapping least-squares estimates in biochemical reaction networks.
Linder, Daniel F; Rempała, Grzegorz A
2015-01-01
The paper proposes new computational methods of computing confidence bounds for the least-squares estimates (LSEs) of rate constants in mass action biochemical reaction network and stochastic epidemic models. Such LSEs are obtained by fitting the set of deterministic ordinary differential equations (ODEs), corresponding to the large-volume limit of a reaction network, to network's partially observed trajectory treated as a continuous-time, pure jump Markov process. In the large-volume limit the LSEs are asymptotically Gaussian, but their limiting covariance structure is complicated since it is described by a set of nonlinear ODEs which are often ill-conditioned and numerically unstable. The current paper considers two bootstrap Monte-Carlo procedures, based on the diffusion and linear noise approximations for pure jump processes, which allow one to avoid solving the limiting covariance ODEs. The results are illustrated with both in-silico and real data examples from the LINE 1 gene retrotranscription model and compared with those obtained using other methods. PMID:25898769
Theoretical Chemical Dynamics Studies of Elementary Combustion Reactions
Donald L. Thompson
2006-04-27
The purpose of this research was the development and application of theoretical/computational methods for accurate predictions of the rates of reactions in many-atom systems. The specific aim was to improve computational methods for studying the chemical dynamics of large, complex systems and to obtain a better understanding of the chemical reactions involving large polyatomic molecules and radicals. The focus was on the development an automatic potential energy surface generation algorithm that takes advantage of high-performance computing environments; e.g., software for rate calculations that direct quantum chemistry codes to produce ab initio predictions of reaction rates and related dynamics quantities. Specifically, we developed interpolative moving least-squares (IMLS) methods for accurately fitting ab initio energies to provide global PESs and for use in direct dynamics simulations.
Network biomarkers, interaction networks and dynamical network biomarkers in respiratory diseases.
Wu, Xiaodan; Chen, Luonan; Wang, Xiangdong
2014-01-01
Identification and validation of interaction networks and network biomarkers have become more critical and important in the development of disease-specific biomarkers, which are functionally changed during disease development, progression or treatment. The present review headlined the definition, significance, research and potential application for network biomarkers, interaction networks and dynamical network biomarkers (DNB). Disease-specific interaction networks, network biomarkers, or DNB have great significance in the understanding of molecular pathogenesis, risk assessment, disease classification and monitoring, or evaluations of therapeutic responses and toxicities. Protein-based DNB will provide more information to define the differences between the normal and pre-disease stages, which might point to early diagnosis for patients. Clinical bioinformatics should be a key approach to the identification and validation of disease-specific biomarkers. PMID:24995123
Dynamical features of reaction-diffusion fronts in fractals.
Méndez, Vicenç; Campos, Daniel; Fort, Joaquim
2004-01-01
The speed of front propagation in fractals is studied by using (i) the reduction of the reaction-transport equation into a Hamilton-Jacobi equation and (ii) the local-equilibrium approach. Different equations proposed for describing transport in fractal media, together with logistic reaction kinetics, are considered. Finally, we analyze the main features of wave fronts resulting from this dynamic process, i.e., why they are accelerated and what is the exact form of this acceleration. PMID:14995742
Dynamical Effects and Product Distributions in Simulated CN + Methane Reactions.
Preston, Thomas J; Hornung, Balázs; Pandit, Shubhrangshu; Harvey, Jeremy N; Orr-Ewing, Andrew J
2016-07-14
Dynamics of collisions between structured molecular species quickly become complex as molecules become large. Reactions of methane with halogen and oxygen atoms serve as model systems for polyatomic molecule chemical dynamics, and replacing the atomic reagent with a diatomic radical affords further insights. A new, full-dimensional potential energy surface for collisions between CN + CH4 to form HCN + CH3 is developed and then used to perform quasi-classical simulations of the reaction. Coupled-cluster energies serve as input to an empirical valence bonding (EVB) model, which provides an analytical function for the surface. Efficient sampling permits simulation of velocity-map ion images and exploration of dynamics over a range of collision energies. Reaction populates HCN vibration, and energy partitioning changes with collision energy. The reaction cross-section depends on the orientation of the diatomic CN radical. A two-dimensional extension of the cone of acceptance for an atom in the line-of-centers model appropriately describes its reactivity. The simulation results foster future experiments and diatomic extensions to existing atomic models of chemical collisions and reaction dynamics. PMID:26812395
Comparing artificial and biological dynamical neural networks
NASA Astrophysics Data System (ADS)
McAulay, Alastair D.
2006-05-01
Modern computers can be made more friendly and otherwise improved by making them behave more like humans. Perhaps we can learn how to do this from biology in which human brains evolved over a long period of time. Therefore, we first explain a commonly used biological neural network (BNN) model, the Wilson-Cowan neural oscillator, that has cross-coupled excitatory (positive) and inhibitory (negative) neurons. The two types of neurons are used for frequency modulation communication between neurons which provides immunity to electromagnetic interference. We then evolve, for the first time, an artificial neural network (ANN) to perform the same task. Two dynamical feed-forward artificial neural networks use cross-coupling feedback (like that in a flip-flop) to form an ANN nonlinear dynamic neural oscillator with the same equations as the Wilson-Cowan neural oscillator. Finally we show, through simulation, that the equations perform the basic neural threshold function, switching between stable zero output and a stable oscillation, that is a stable limit cycle. Optical implementation with an injected laser diode and future research are discussed.
Indirect dynamics in a highly exoergic substitution reaction
Mikosch, Jochen; Zhang, Jiaxu; Trippel, Sebastian; Eichhorn, Christoph; Otto, Rico; Sun, Rui; De Jong, Wibe A.; Weidemuller, Matthias; Hase, William L.; Wester, Roland
2013-01-16
The highly exoergic nucleophilic substitution reaction F^{−} + CH_{3}I shows strikingly different reaction dynamics than substitution reactions of larger halogen ions. Over a wide range of collision energies, a large fraction of indirect scattering via a long-lived hydrogen-bonded complex is found both in crossed-beam imaging experiments and in direct chemical dynamics simulations. Our measured differential scattering cross sections show dominant large-angle scattering and low product velocities for all collision energies, resulting from efficient transfer of the collision energy to internal energy of the CH_{3}F reaction product. Both findings are in strong contrast to the previously studied substitution reaction of Cl^{−} + CH_{3}I [Science 2008, 319, 183] at all but the lowest collision energies, a discrepancy that was not captured in a subsequent study at only a low collision energy [J. Phys. Chem. Lett. 2010, 1, 2747]. Our direct chemical dynamics simulations at the DFT/B97-1 level of theory show that the reaction is dominated by three atomic-level mechanisms, an indirect reaction proceeding via an F−–HCH2I hydrogen-bonded complex, a direct rebound and a direct stripping reaction. The indirect mechanism is found to contribute ∼ 60% of the overall substitution reaction at both low and high collision energies. This large fraction of indirect scattering at high collision energy is particularly surprising, since the barrier for the F^{−}–HCH_{2}I complex to form products is only 0.10 eV. Overall, experiment and simulation agree very favorably in both the scattering angle and the product internal energy distributions.
Explicit Integration of Extremely Stiff Reaction Networks: Partial Equilibrium Methods
Guidry, Mike W; Billings, J. J.; Hix, William Raphael
2013-01-01
In two preceding papers [1,2] we have shown that, when reaction networks are well removed from equilibrium, explicit asymptotic and quasi-steady-state approximations can give algebraically stabilized integration schemes that rival standard implicit methods in accuracy and speed for extremely stiff systems. However, we also showed that these explicit methods remain accurate but are no longer competitive in speed as the network approaches equilibrium. In this paper we analyze this failure and show that it is associated with the presence of fast equilibration timescales that neither asymptotic nor quasi-steady-state approximations are able to remove efficiently from the numerical integration. Based on this understanding, we develop a partial equilibrium method to deal effectively with the new partial equilibrium methods, give an integration scheme that plausibly can deal with the stiffest networks, even in the approach to equilibrium, with accuracy and speed competitive with that of implicit methods. Thus we demonstrate that algebraically stabilized explicit methods may offer alternatives to implicit integration of even extremely stiff systems, and that these methods may permit integration of much larger networks than have been feasible previously in a variety of fields.
Dynamics of synchrotron VUV-induced intracluster reactions
Grover, J.R.
1993-12-01
Photoionization mass spectrometry (PIMS) using the tunable vacuum ultraviolet radiation available at the National Synchrotron Light Source is being exploited to study photoionization-induced reactions in small van der Waals mixed complexes. The information gained includes the observation and classification of reaction paths, the measurement of onsets, and the determination of relative yields of competing reactions. Additional information is obtained by comparison of the properties of different reacting systems. Special attention is given to finding unexpected features, and most of the reactions investigated to date display such features. However, understanding these reactions demands dynamical information, in addition to what is provided by PIMS. Therefore the program has been expanded to include the measurement of kinetic energy release distributions.
Opinion dynamics on an adaptive random network
NASA Astrophysics Data System (ADS)
Benczik, I. J.; Benczik, S. Z.; Schmittmann, B.; Zia, R. K. P.
2009-04-01
We revisit the classical model for voter dynamics in a two-party system with two basic modifications. In contrast to the original voter model studied in regular lattices, we implement the opinion formation process in a random network of agents in which interactions are no longer restricted by geographical distance. In addition, we incorporate the rapidly changing nature of the interpersonal relations in the model. At each time step, agents can update their relationships. This update is determined by their own opinion, and by their preference to make connections with individuals sharing the same opinion, or rather with opponents. In this way, the network is built in an adaptive manner, in the sense that its structure is correlated and evolves with the dynamics of the agents. The simplicity of the model allows us to examine several issues analytically. We establish criteria to determine whether consensus or polarization will be the outcome of the dynamics and on what time scales these states will be reached. In finite systems consensus is typical, while in infinite systems a disordered metastable state can emerge and persist for infinitely long time before consensus is reached.
Lumping evolutionary game dynamics on networks.
Iacobelli, G; Madeo, D; Mocenni, C
2016-10-21
We study evolutionary game dynamics on networks (EGN), where players reside in the vertices of a graph, and games are played between neighboring vertices. The model is described by a system of ordinary differential equations which depends on players payoff functions, as well as on the adjacency matrix of the underlying graph. Since the number of differential equations increases with the number of vertices in the graph, the analysis of EGN becomes hard for large graphs. Building on the notion of lumpability for Markov chains, we identify conditions on the network structure allowing to reduce the original graph. In particular, we identify a partition of the vertex set of the graph and show that players in the same block of a lumpable partition have equivalent dynamical behaviors, whenever their payoff functions and initial conditions are equivalent. Therefore, vertices belonging to the same partition block can be merged into a single vertex, giving rise to a reduced graph and consequently to a simplified system of equations. We also introduce a tighter condition, called strong lumpability, which can be used to identify dynamical symmetries in EGN which are related to the interchangeability of players in the system. PMID:27475842
A dynamic evidential network for fall detection.
Aguilar, Paulo Armando Cavalcante; Boudy, Jerome; Istrate, Dan; Dorizzi, Bernadette; Mota, Joao Cesar Moura
2014-07-01
This study is part of the development of a remote home healthcare monitoring application designed to detect distress situations through several types of sensors. The multisensor fusion can provide more accurate and reliable information compared to information provided by each sensor separately. Furthermore, data from multiple heterogeneous sensors present in the remote home healthcare monitoring systems have different degrees of imperfection and trust. Among the multisensor fusion methods, Dempster-Shafer theory (DST) is currently considered the most appropriate for representing and processing the imperfect information. Based on a graphical representation of the DST called evidential networks, a structure of heterogeneous data fusion from multiple sensors for fall detection has been proposed. The evidential networks, implemented on our remote medical monitoring platform, are also proposed in this paper to maximize the performance of automatic fall detection and thus make the system more reliable. However, the presence of noise, the variability of recorded signals by the sensors, and the failing or unreliable sensors may thwart the evidential networks performance. In addition, the sensors signals nonstationary nature may degrade the experimental conditions. To compensate the nonstationary effect, the time evolution is considered by introducing the dynamic evidential network which was evaluated by the simulated fall scenarios corresponding to various use cases. PMID:24235255
Optimizing Dynamical Network Structure for Pinning Control
Orouskhani, Yasin; Jalili, Mahdi; Yu, Xinghuo
2016-01-01
Controlling dynamics of a network from any initial state to a final desired state has many applications in different disciplines from engineering to biology and social sciences. In this work, we optimize the network structure for pinning control. The problem is formulated as four optimization tasks: i) optimizing the locations of driver nodes, ii) optimizing the feedback gains, iii) optimizing simultaneously the locations of driver nodes and feedback gains, and iv) optimizing the connection weights. A newly developed population-based optimization technique (cat swarm optimization) is used as the optimization method. In order to verify the methods, we use both real-world networks, and model scale-free and small-world networks. Extensive simulation results show that the optimal placement of driver nodes significantly outperforms heuristic methods including placing drivers based on various centrality measures (degree, betweenness, closeness and clustering coefficient). The pinning controllability is further improved by optimizing the feedback gains. We also show that one can significantly improve the controllability by optimizing the connection weights. PMID:27067020
Optimizing Dynamical Network Structure for Pinning Control.
Orouskhani, Yasin; Jalili, Mahdi; Yu, Xinghuo
2016-01-01
Controlling dynamics of a network from any initial state to a final desired state has many applications in different disciplines from engineering to biology and social sciences. In this work, we optimize the network structure for pinning control. The problem is formulated as four optimization tasks: i) optimizing the locations of driver nodes, ii) optimizing the feedback gains, iii) optimizing simultaneously the locations of driver nodes and feedback gains, and iv) optimizing the connection weights. A newly developed population-based optimization technique (cat swarm optimization) is used as the optimization method. In order to verify the methods, we use both real-world networks, and model scale-free and small-world networks. Extensive simulation results show that the optimal placement of driver nodes significantly outperforms heuristic methods including placing drivers based on various centrality measures (degree, betweenness, closeness and clustering coefficient). The pinning controllability is further improved by optimizing the feedback gains. We also show that one can significantly improve the controllability by optimizing the connection weights. PMID:27067020
Optimizing Dynamical Network Structure for Pinning Control
NASA Astrophysics Data System (ADS)
Orouskhani, Yasin; Jalili, Mahdi; Yu, Xinghuo
2016-04-01
Controlling dynamics of a network from any initial state to a final desired state has many applications in different disciplines from engineering to biology and social sciences. In this work, we optimize the network structure for pinning control. The problem is formulated as four optimization tasks: i) optimizing the locations of driver nodes, ii) optimizing the feedback gains, iii) optimizing simultaneously the locations of driver nodes and feedback gains, and iv) optimizing the connection weights. A newly developed population-based optimization technique (cat swarm optimization) is used as the optimization method. In order to verify the methods, we use both real-world networks, and model scale-free and small-world networks. Extensive simulation results show that the optimal placement of driver nodes significantly outperforms heuristic methods including placing drivers based on various centrality measures (degree, betweenness, closeness and clustering coefficient). The pinning controllability is further improved by optimizing the feedback gains. We also show that one can significantly improve the controllability by optimizing the connection weights.
Dynamic Privacy Management in Pervasive Sensor Networks
NASA Astrophysics Data System (ADS)
Gong, Nan-Wei; Laibowitz, Mathew; Paradiso, Joseph A.
This paper describes the design and implementation of a dynamic privacy management system aimed at enabling tangible privacy control and feedback in a pervasive sensor network. Our work began with the development of a potentially invasive sensor network (with high resolution video, audio, and motion tracking capabilities) featuring different interactive applications that created incentive for accepting this network as an extension of people's daily social space. A user study was then conducted to evaluate several privacy management approaches - an active badge system for both online and on-site control, on/off power switches for physically disabling the hardware, and touch screen input control. Results from a user study indicated that an active badge for on-site privacy control is the most preferable method among all provided options. We present a set of results that yield insight into the privacy/benefit tradeoff from various sensing capabilities in pervasive sensor networks and how privacy settings and user behavior relate in these environments.
Creative Cognition and Brain Network Dynamics.
Beaty, Roger E; Benedek, Mathias; Silvia, Paul J; Schacter, Daniel L
2016-02-01
Creative thinking is central to the arts, sciences, and everyday life. How does the brain produce creative thought? A series of recently published papers has begun to provide insight into this question, reporting a strikingly similar pattern of brain activity and connectivity across a range of creative tasks and domains, from divergent thinking to poetry composition to musical improvisation. This research suggests that creative thought involves dynamic interactions of large-scale brain systems, with the most compelling finding being that the default and executive control networks, which can show an antagonistic relation, tend to cooperate during creative cognition and artistic performance. These findings have implications for understanding how brain networks interact to support complex cognitive processes, particularly those involving goal-directed, self-generated thought. PMID:26553223
Stochastic dynamics for idiotypic immune networks
NASA Astrophysics Data System (ADS)
Barra, Adriano; Agliari, Elena
2010-12-01
In this work we introduce and analyze the stochastic dynamics obeyed by a model of an immune network recently introduced by the authors. We develop Fokker-Planck equations for the single lymphocyte behavior and coarse grained Langevin schemes for the averaged clone behavior. After showing agreement with real systems (as a short path Jerne cascade), we suggest, both with analytical and numerical arguments, explanations for the generation of (metastable) memory cells, improvement of the secondary response (both in the quality and quantity) and bell shaped modulation against infections as a natural behavior. The whole emerges from the model without being postulated a-priori as it often occurs in second generation immune networks: so the aim of the work is to present some out-of-equilibrium features of this model and to highlight mechanisms which can replace a-priori assumptions in view of further detailed analysis in theoretical systemic immunology.
Unfolding Dynamic Networks for Visual Exploration.
Bach, Benjamin
2016-01-01
Visualization builds on the human capacity to quickly process parallel visual inputs and to offload cognitive processes. Interactive visualizations can become interfaces between humans, their data, and the phenomena represented by the data. Such interfaces can allow for exploration, enable serendipitous discoveries, and serve as a mental metaphor to help us remember and reason about the data. This article gives a brief overview of the author's dissertation research, which is concerned with creating and evaluating novel interfaces to explore dynamic networks, supporting analysts in formulating hypotheses, and discussing proper analysis methods. PMID:26960029
Reaction Dynamics and Spectroscopy of Hydrocarbons in Plasma
Braams, Bastiaan J.
2014-03-24
This grant supported research in theoretical and computational Chemical Physics that resulted in numerous publications on fitting ab initio potential energy surfaces and dipole moment surfaces of polyatomic molecules and cations. This work made use of novel fitting methods that ensures that these surfaces are invariant with respect to all permutations of like atoms. The surfaces were used in various dynamics calculations, ranging from quantum vibrational dynamics to(quasi)classical trajectory calculations of reaction dynamics. A number of these studies were done in collaboration with experimental groups where the theoretical analyses turned out to be essential to give a proper understanding of the experimental results.
Bootstrapping Least Squares Estimates in Biochemical Reaction Networks
Linder, Daniel F.
2015-01-01
The paper proposes new computational methods of computing confidence bounds for the least squares estimates (LSEs) of rate constants in mass-action biochemical reaction network and stochastic epidemic models. Such LSEs are obtained by fitting the set of deterministic ordinary differential equations (ODEs), corresponding to the large volume limit of a reaction network, to network’s partially observed trajectory treated as a continuous-time, pure jump Markov process. In the large volume limit the LSEs are asymptotically Gaussian, but their limiting covariance structure is complicated since it is described by a set of nonlinear ODEs which are often ill-conditioned and numerically unstable. The current paper considers two bootstrap Monte-Carlo procedures, based on the diffusion and linear noise approximations for pure jump processes, which allow one to avoid solving the limiting covariance ODEs. The results are illustrated with both in-silico and real data examples from the LINE 1 gene retrotranscription model and compared with those obtained using other methods. PMID:25898769
Quantum Molecular Dynamics Simulations of Nanotube Tip Assisted Reactions
NASA Technical Reports Server (NTRS)
Menon, Madhu
1998-01-01
In this report we detail the development and application of an efficient quantum molecular dynamics computational algorithm and its application to the nanotube-tip assisted reactions on silicon and diamond surfaces. The calculations shed interesting insights into the microscopic picture of tip surface interactions.
Quantum dynamics study for D{sub 2} + OH reaction
Zhang, Y.; Zhang, D.; Li, W.; Zhang, Q.; Wang, D.; Zhang, D.H.; Zhang, J.Z.H.
1995-11-16
A PA5D (potential averaged 5D) TD (time-dependent) quantum wave-packet calculation is reported for the reaction D{sub 2} + OH {yields} D + DOH on the Schatz-Elgersma potential energy surface. The dynamics calculation is carried out on a workstation with a modest memory, which is made possible by using a normalized angular quadrature scheme to minimize the requirement for computer memory during wave-packet propagation. Reaction probabilities, cross sections, and rate constants are presented for the title reaction, and the comparison of the present result with those of the isotopic reactions, H{sub 2} + OH and HD + OH, is given. Consistent with its isotopic reactions, the rotational orientation of D{sub 2} has a stronger effect than that of OH and, in particular, the D{sub 2} (j=1) reactant produces the largest reaction probability, which is attributed to a general steric effect. The comparison of all three isotopic reactions shows that the reactivity (reaction probability and cross section) of the HH(D) + OH system is in the order of P{sub H(2)} > P{sub HD} > P{sub D(2)}. This trend is in good agreement with reduced dimensionality calculations. 27 refs., 8 figs., 4 tabs.
Potential energy surfaces and reaction dynamics of polyatomic molecules
Chang, Yan-Tyng.
1991-11-01
A simple empirical valence bond (EVB) model approach is suggested for constructing global potential energy surfaces for reactions of polyatomic molecular systems. This approach produces smooth and continuous potential surfaces which can be directly utilized in a dynamical study. Two types of reactions are of special interest, the unimolecular dissociation and the unimolecular isomerization. For the first type, the molecular dissociation dynamics of formaldehyde on the ground electronic surface is investigated through classical trajectory calculations on EVB surfaces. The product state distributions and vector correlations obtained from this study suggest very similar behaviors seen in the experiments. The intramolecular hydrogen atom transfer in the formic acid dimer is an example of the isomerization reaction. High level ab initio quantum chemistry calculations are performed to obtain optimized equilibrium and transition state dimer geometries and also the harmonic frequencies.
Morrison, Erin S; Badyaev, Alexander V
2016-08-01
The network of the interactions among genes, proteins, and metabolites delineates a range of potential phenotypic diversifications in a lineage, and realized phenotypic changes are the result of differences in the dynamics of the expression of the elements and interactions in this deterministic network. Regulatory mechanisms, such as hormones, mediate the relationship between the structural and dynamic properties of networks by determining how and when the elements are expressed and form a functional unit or state. Changes in regulatory mechanisms lead to variable expression of functional states of a network within and among generations. Functional properties of network elements, and the magnitude and direction of evolutionary change they determine, depend on their location within a network. Here, we examine the relationship between network structure and the dynamic mechanisms that regulate flux through a metabolic network. We review the mechanisms that control metabolic flux in enzymatic reactions and examine structural properties of the network locations that are targets of flux control. We aim to establish a predictive framework to test the contributions of structural and dynamic properties of deterministic networks to evolutionary diversifications. PMID:27252203
Dynamic Processes in Network Goods: Modeling, Analysis and Applications
ERIC Educational Resources Information Center
Paothong, Arnut
2013-01-01
The network externality function plays a very important role in the study of economic network industries. Moreover, the consumer group dynamic interactions coupled with network externality concept is going to play a dominant role in the network goods in the 21st century. The existing literature is stemmed on a choice of externality function with…
NASA Astrophysics Data System (ADS)
Ozasa, Kazunari; Aono, Masashi; Maeda, Mizuo; Hara, Masahiko
In order to develop an adaptive computing system, we investigate microscopic optical feedback to a group of microbes (Euglena gracilis in this study) with a neural network algorithm, expecting that the unique characteristics of microbes, especially their strategies to survive/adapt against unfavorable environmental stimuli, will explicitly determine the temporal evolution of the microbe-based feedback system. The photophobic reactions of Euglena are extracted from experiments, and built in the Monte-Carlo simulation of a microbe-based neurocomputing. The simulation revealed a good performance of Euglena-based neurocomputing. Dynamic transition among the solutions is discussed from the viewpoint of feedback instability.
Nonlinear Dynamics and Control in Microfluidic Networks
NASA Astrophysics Data System (ADS)
Case, Daniel; Angilella, Jean-Regis; Motter, Adilson
2015-03-01
Researchers currently use abundant external devices (e.g., pumps and computers) to achieve precise flow dynamics in microfluidic systems. Here, I show our use of network concepts and computational methods to design microfluidic systems that do not depend on external devices yet still exhibit a diverse range of flow dynamics. I present an example of a microfluidic channel described by a nonlinear pressure-flow relation and show that complex flow behavior can emerge in systems designed around this channel. By controlling the pressure at only a single terminal in such a system, I demonstrate the ability to switch the direction of fluid flow through intermediate channels not directly connected to the controlled terminal. I also show that adding (or removing) flow channels to a system can result in unexpected changes in the total mass flow rate, depending on the network structure of the system. We expect this work to both expand the applicability of microfluidics and promote scaling up of current experiments. This research was funded by the National Science Foundation.
Dynamic Social Networks in Recovery Homes
Jason, Leonard A.; Light, John M.; Stevens, Edward B.; Beers, Kimberly
2013-01-01
Acute treatment aftercare in the form of sober living environments—i.e., recovery houses—provide an inexpensive and effective medium-term treatment alternative for many with substance use disorders. Limited evidence suggests that house-situated social relationships and associated social support are critical determinants of how successful these residential experiences are for their members, but little is known about the mechanisms underlying these relationships. This study explored the feasibility of using dynamic social network modeling to understand house-situated longitudinal associations among individual Alcoholics Anonymous (AA) related recovery behaviors, length of residence, dyadic interpersonal trust, and dyadic confidant relationship formation processes. Trust and confidant relationships were measured 3 months apart in U.S. urban-area recovery houses, all of which were part of a network of substance use recovery homes. A stochastic actor-based model was successfully estimated from this data set. Results suggest that confidant relationships are predicted by trust, while trust is affected by recovery behaviors and length of residence. Conceptualizing recovery houses as a set of independent, evolving social networks that can be modeled jointly appears to be a promising direction for research. PMID:24217855
Dynamics of interacting information waves in networks.
Mirshahvalad, A; Esquivel, A V; Lizana, L; Rosvall, M
2014-01-01
To better understand the inner workings of information spreading, network researchers often use simple models to capture the spreading dynamics. But most models only highlight the effect of local interactions on the global spreading of a single information wave, and ignore the effects of interactions between multiple waves. Here we take into account the effect of multiple interacting waves by using an agent-based model in which the interaction between information waves is based on their novelty. We analyzed the global effects of such interactions and found that information that actually reaches nodes reaches them faster. This effect is caused by selection between information waves: lagging waves die out and only leading waves survive. As a result, and in contrast to models with noninteracting information dynamics, the access to information decays with the distance from the source. Moreover, when we analyzed the model on various synthetic and real spatial road networks, we found that the decay rate also depends on the path redundancy and the effective dimension of the system. In general, the decay of the information wave frequency as a function of distance from the source follows a power-law distribution with an exponent between -0.2 for a two-dimensional system with high path redundancy and -0.5 for a tree-like system with no path redundancy. We found that the real spatial networks provide an infrastructure for information spreading that lies in between these two extremes. Finally, to better understand the mechanics behind the scaling results, we provide analytical calculations of the scaling for a one-dimensional system. PMID:24580283
Foetal ECG recovery using dynamic neural networks.
Camps-Valls, Gustavo; Martínez-Sober, Marcelino; Soria-Olivas, Emilio; Magdalena-Benedito, Rafael; Calpe-Maravilla, Javier; Guerrero-Martínez, Juan
2004-07-01
Non-invasive electrocardiography has proven to be a very interesting method for obtaining information about the foetus state and thus to assure its well-being during pregnancy. One of the main applications in this field is foetal electrocardiogram (ECG) recovery by means of automatic methods. Evident problems found in the literature are the limited number of available registers, the lack of performance indicators, and the limited use of non-linear adaptive methods. In order to circumvent these problems, we first introduce the generation of synthetic registers and discuss the influence of different kinds of noise to the modelling. Second, a method which is based on numerical (correlation coefficient) and statistical (analysis of variance, ANOVA) measures allows us to select the best recovery model. Finally, finite impulse response (FIR) and gamma neural networks are included in the adaptive noise cancellation (ANC) scheme in order to provide highly non-linear, dynamic capabilities to the recovery model. Neural networks are benchmarked with classical adaptive methods such as the least mean squares (LMS) and the normalized LMS (NLMS) algorithms in simulated and real registers and some conclusions are drawn. For synthetic registers, the most determinant factor in the identification of the models is the foetal-maternal signal-to-noise ratio (SNR). In addition, as the electromyogram contribution becomes more relevant, neural networks clearly outperform the LMS-based algorithm. From the ANOVA test, we found statistical differences between LMS-based models and neural models when complex situations (high foetal-maternal and foetal-noise SNRs) were present. These conclusions were confirmed after doing robustness tests on synthetic registers, visual inspection of the recovered signals and calculation of the recognition rates of foetal R-peaks for real situations. Finally, the best compromise between model complexity and outcomes was provided by the FIR neural network. Both
Synchronization in complex dynamical networks coupled with complex chaotic system
NASA Astrophysics Data System (ADS)
Wei, Qiang; Xie, Cheng-Jun; Wang, Bo
2015-11-01
This paper investigates synchronization in complex dynamical networks with time delay and perturbation. The node of complex dynamical networks is composed of complex chaotic system. A complex feedback controller is designed to realize different component of complex state variable synchronize up to different scaling complex function when complex dynamical networks realize synchronization. The synchronization scaling function is changed from real field to complex field. Synchronization in complex dynamical networks with constant delay and time-varying coupling delay are investigated, respectively. Numerical simulations show the effectiveness of the proposed method.
Coherent reaction dynamics in a bacterial cytochrome c oxidase.
Liebl, U; Lipowski, G; Négrerie, M; Lambry, J C; Martin, J L; Vos, M H
1999-09-01
Biological reactions in protein complexes involve structural dynamics spanning many orders of magnitude in time. In standard descriptions of catalysis by enzymes, the transition state between reactant and product is reached by thermal, stochastic motion. In the ultrashort time domain, however, the protein moiety and cofactor motions leading to altered conformations can be coherent rather than stochastic in nature. Such coherent motions may play a key role in controlling the accessibility of the transition state and explain the high efficiency of the reaction. Here we present evidence for coherent population transfer to the product state during an ultrafast reaction catalysed by a key enzyme in aerobic organisms. Using the enzyme cytochrome c oxidase aa3 from the bacterium Paracoccus denitrificans, we have studied haem dynamics during the photo-initiated ultrafast transfer of carbon monoxide from haem a3 to CuB by femtosecond spectroscopy. The ground state of the unliganded a3 species is populated in a stepwise manner in time, indicating that the reaction is mainly governed by coherent vibrations (47cm(-1)). The reaction coordinate involves conformational relaxation of the haem group and we suggest that ligand transfer also contributes. PMID:10490029
Self-organization of complex networks as a dynamical system
NASA Astrophysics Data System (ADS)
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.
Chemical Accelerator Studies of Ion-Molecule Reaction Dynamics
NASA Astrophysics Data System (ADS)
Zhang, Jingfeng
1995-01-01
A chemical accelerator instrument has been used to study the dynamics of ion-molecule reaction processes in the gas phase. Specifically, the following reactions are investigated: eqalign{rm CO^+ + H_2&longrightarrowrm HCO ^+ + Hcrrm CO^+ + D_2& longrightarrowrm DCO^+ + Dcrrm CO^+ + HDlongrightarrow &rm HCO ^+ (DCO^+) + D (H)cr} . Both angular and velocity distributions of reactively scattered product ions are measured, as well as reaction cross sections as a function of reactant relative translational energy. Formation of HCO^+ ion from rm CO^+ + H_2 over the collision energy range from 0.35 to 3.02 eV (c.m.) follows closely the predictions of the spectator stripping model, and results in highly excited HCO^+ product ions. This reaction is found to proceed via a direct impulsive mechanism, without any long-lived intermediate complexes involved. The reaction cross section is proportional to E_{T} ^{-1/2}, where E_ {rm T} is the reactant ion relative translational energy. Deuterium atom transfer from D_2 to CO^+ over the collision energy range from 0.41 to 5.14 eV (c.m.) occurs also in a direct process. Reaction cross section is proportional to rm E_{T}^{ -1/2}. The results are very similar to those of the reaction rm CO^+ + H_2. The reaction CO^+ + HD has two product channels, leading to the formation of HCO ^+ and DCO^+, respectively. The reaction is studied over the energy range from 0.88 to 5.00 eV (c.m.). It is found that the production of HCO^+ is consistently the slightly favored reaction channel, which is attributed to the orientation isotope effect. The translational exoergicity for both reaction channels follows closely the prediction of spectator stripping model. Product DCO^+ ions are in higher excited states than HCO ^+ ions. Product velocity distribution contour maps indicate that, at the lowest energies, the DCO ^+ production channel has a longer reaction duration than the HCO^+ production channel, but both reaction channels are dominated by direct
Crossed molecular beam studies of atmospheric chemical reaction dynamics
Zhang, Jingsong
1993-04-01
The dynamics of several elementary chemical reactions that are important in atmospheric chemistry are investigated. The reactive scattering of ground state chlorine or bromine atoms with ozone molecules and ground state chlorine atoms with nitrogen dioxide molecules is studied using a crossed molecular beams apparatus with a rotatable mass spectrometer detector. The Cl + O{sub 3} {yields} ClO + O{sub 2} reaction has been studied at four collision energies ranging from 6 kcal/mole to 32 kcal/mole. The derived product center-of-mass angular and translational energy distributions show that the reaction has a direct reaction mechanism and that there is a strong repulsion on the exit channel. The ClO product is sideways and forward scattered with respect to the Cl atom, and the translational energy release is large. The Cl atom is most likely to attack the terminal oxygen atom of the ozone molecule. The Br + O{sub 3} {yields} ClO + O{sub 2} reaction has been studied at five collision energies ranging from 5 kcal/mole to 26 kcal/mole. The derived product center-of-mass angular and translational energy distributions are quite similar to those in the Cl + O{sub 3} reaction. The Br + O{sub 3} reaction has a direct reaction mechanism similar to that of the Cl + O{sub 3} reaction. The electronic structure of the ozone molecule seems to play the central role in determining the reaction mechanism in atomic radical reactions with the ozone molecule. The Cl + NO{sub 2} {yields} ClO + NO reaction has been studied at three collision energies ranging from 10.6 kcal/mole to 22.4 kcal/mole. The center-of-mass angular distribution has some forward-backward symmetry, and the product translational energy release is quite large. The reaction proceeds through a short-lived complex whose lifetime is less than one rotational period. The experimental results seem to show that the Cl atom mainly attacks the oxygen atom instead of the nitrogen atom of the NO{sub 2} molecule.
NASA Astrophysics Data System (ADS)
Grytskyy, Dmytro; Diesmann, Markus; Helias, Moritz
2016-06-01
Self-organized structures in networks with spike-timing dependent synaptic plasticity (STDP) are likely to play a central role for information processing in the brain. In the present study we derive a reaction-diffusion-like formalism for plastic feed-forward networks of nonlinear rate-based model neurons with a correlation sensitive learning rule inspired by and being qualitatively similar to STDP. After obtaining equations that describe the change of the spatial shape of the signal from layer to layer, we derive a criterion for the nonlinearity necessary to obtain stable dynamics for arbitrary input. We classify the possible scenarios of signal evolution and find that close to the transition to the unstable regime metastable solutions appear. The form of these dissipative solitons is determined analytically and the evolution and interaction of several such coexistent objects is investigated.
In silico evolution of oscillatory dynamics in biochemical networks
NASA Astrophysics Data System (ADS)
Ali, Md Zulfikar; Wingreen, Ned S.; Mukhopadhyay, Ranjan
2015-03-01
We are studying in silico evolution of complex, oscillatory network dynamics within the framework of a minimal mutational model of protein-protein interactions. In our model we consider two different types of proteins, kinase (activator) and phosphatase(inhibitor). In our model. each protein can either be phosphorylated(active) or unphospphorylated (inactive), represented by binary strings. Active proteins can modify their target based on the Michaelis-Menten kinetics of chemical equation. Reaction rate constants are directly related to sequence dependent protein-protein interaction energies. This model can be stuided for non-trivial behavior e.g. oscillations, chaos, multiple stable states. We focus here on biochemical oscillators; some questions we will address within our framework include how the oscillatory dynamics depends on number of protein species, connectivity of the network, whether evolution can readily converge on a stable oscillator if we start with random intitial parameters, neutral evolution with additional protein components and general questions of robustness and evolavability.
The photodissociation and reaction dynamics of vibrationally excited molecules
Crim, F.F.
1993-12-01
This research determines the nature of highly vibrationally excited molecules, their unimolecular reactions, and their photodissociation dynamics. The goal is to characterize vibrationally excited molecules and to exploit that understanding to discover and control their chemical pathways. Most recently the author has used a combination of vibrational overtone excitation and laser induced fluorescence both to characterize vibrationally excited molecules and to study their photodissociation dynamics. The author has also begun laser induced grating spectroscopy experiments designed to obtain the electronic absorption spectra of highly vibrationally excited molecules.
Dynamics of Coupled Cell Networks: Synchrony, Heteroclinic Cycles and Inflation
NASA Astrophysics Data System (ADS)
Aguiar, M.; Ashwin, P.; Dias, A.; Field, M.
2011-04-01
We consider the dynamics of small networks of coupled cells. We usually assume asymmetric inputs and no global or local symmetries in the network and consider equivalence of networks in this setting; that is, when two networks with different architectures give rise to the same set of possible dynamics. Focussing on transitive (strongly connected) networks that have only one type of cell (identical cell networks) we address three questions relating the network structure to dynamics. The first question is how the structure of the network may force the existence of invariant subspaces (synchrony subspaces). The second question is how these invariant subspaces can support robust heteroclinic attractors. Finally, we investigate how the dynamics of coupled cell networks with different structures and numbers of cells can be related; in particular we consider the sets of possible "inflations" of a coupled cell network that are obtained by replacing one cell by many of the same type, in such a way that the original network dynamics is still present within a synchrony subspace. We illustrate the results with a number of examples of networks of up to six cells.
Motif analysis for small-number effects in chemical reaction dynamics.
Saito, Nen; Sughiyama, Yuki; Kaneko, Kunihiko
2016-09-01
The number of molecules involved in a cell or subcellular structure is sometimes rather small. In this situation, ordinary macroscopic-level fluctuations can be overwhelmed by non-negligible large fluctuations, which results in drastic changes in chemical-reaction dynamics and statistics compared to those observed under a macroscopic system (i.e., with a large number of molecules). In order to understand how salient changes emerge from fluctuations in molecular number, we here quantitatively define small-number effect by focusing on a "mesoscopic" level, in which the concentration distribution is distinguishable both from micro- and macroscopic ones and propose a criterion for determining whether or not such an effect can emerge in a given chemical reaction network. Using the proposed criterion, we systematically derive a list of motifs of chemical reaction networks that can show small-number effects, which includes motifs showing emergence of the power law and the bimodal distribution observable in a mesoscopic regime with respect to molecule number. The list of motifs provided herein is helpful in the search for candidates of biochemical reactions with a small-number effect for possible biological functions, as well as for designing a reaction system whose behavior can change drastically depending on molecule number, rather than concentration. PMID:27608993
Attractor dynamics in local neuronal networks
Thivierge, Jean-Philippe; Comas, Rosa; Longtin, André
2014-01-01
Patterns of synaptic connectivity in various regions of the brain are characterized by the presence of synaptic motifs, defined as unidirectional and bidirectional synaptic contacts that follow a particular configuration and link together small groups of neurons. Recent computational work proposes that a relay network (two populations communicating via a third, relay population of neurons) can generate precise patterns of neural synchronization. Here, we employ two distinct models of neuronal dynamics and show that simulated neural circuits designed in this way are caught in a global attractor of activity that prevents neurons from modulating their response on the basis of incoming stimuli. To circumvent the emergence of a fixed global attractor, we propose a mechanism of selective gain inhibition that promotes flexible responses to external stimuli. We suggest that local neuronal circuits may employ this mechanism to generate precise patterns of neural synchronization whose transient nature delimits the occurrence of a brief stimulus. PMID:24688457
Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings.
Maucher, Fabian; Sutcliffe, Paul
2016-04-29
We introduce and illustrate a new approach to the unknotting problem via the dynamics of vortex strings in a nonlinear partial differential equation of reaction-diffusion type. To untangle a given knot, a Biot-Savart construction is used to initialize the knot as a vortex string in the FitzHugh-Nagumo equation. Remarkably, we find that the subsequent evolution preserves the topology of the knot and can untangle an unknot into a circle. Illustrative test case examples are presented, including the untangling of a hard unknot known as the culprit. Our approach to the unknotting problem has two novel features, in that it applies field theory rather than particle mechanics and uses reaction-diffusion dynamics in place of energy minimization. PMID:27176541
Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings
NASA Astrophysics Data System (ADS)
Maucher, Fabian; Sutcliffe, Paul
2016-04-01
We introduce and illustrate a new approach to the unknotting problem via the dynamics of vortex strings in a nonlinear partial differential equation of reaction-diffusion type. To untangle a given knot, a Biot-Savart construction is used to initialize the knot as a vortex string in the FitzHugh-Nagumo equation. Remarkably, we find that the subsequent evolution preserves the topology of the knot and can untangle an unknot into a circle. Illustrative test case examples are presented, including the untangling of a hard unknot known as the culprit. Our approach to the unknotting problem has two novel features, in that it applies field theory rather than particle mechanics and uses reaction-diffusion dynamics in place of energy minimization.
Polarization dynamics in optical ground wire network.
Leeson, Jesse; Bao, Xiaoyi; Côté, Alain
2009-04-20
We report the polarization dynamics in an optical ground wire (OPGW) network for a summer period and a fall period for what is believed to be the first time. To better observe the surrounding magnetic fields contribution to modulating the state of polarization (SOP) we installed a Faraday rotating mirror to correct reciprocal birefringence from quasi-static changes. We also monitored the OPGW while no electrical current was present in the towers' electrical conductors. The spectral analysis, the arc length mapped out over a given time interval on a Poincaré sphere, histograms of the arc length, and the SOP autocorrelation function are calculated to analyze the SOP changes. Ambient temperature changes, wind, Sun-induced temperature gradients, and electrical current all have a significant impact on the SOP drift in an OPGW network. Wind-generated cable oscillations and Sun-induced temperature gradients are shown to be the dominant slow SOP modulations, while Aeolian vibrations and electrical current are shown to be the dominant fast SOP modulations. The spectral analysis revealed that the electrical current gives the fastest SOP modulation to be 300 Hz for the sampling frequency of 1 KHz. This has set the upper speed limit for real-time polarization mode dispersion compensation devices. PMID:19381169
The Dynamics of Initiative in Communication Networks
Mollgaard, Anders; Mathiesen, Joachim
2016-01-01
Human social interaction is often intermittent. Two acquainted persons can have extended periods without social interaction punctuated by periods of repeated interaction. In this case, the repeated interaction can be characterized by a seed initiative by either of the persons and a number of follow-up interactions. The tendency to initiate social interaction plays an important role in the formation of social networks and is in general not symmetric between persons. In this paper, we study the dynamics of initiative by analysing and modeling a detailed call and text message network sampled from a group of 700 individuals. We show that in an average relationship between two individuals, one part is almost twice as likely to initiate communication compared to the other part. The asymmetry has social consequences and ultimately might lead to the discontinuation of a relationship. We explain the observed asymmetry by a positive feedback mechanism where individuals already taking initiative are more likely to take initiative in the future. In general, people with many initiatives receive attention from a broader spectrum of friends than people with few initiatives. Lastly, we compare the likelihood of taking initiative with the basic personality traits of the five factor model. PMID:27124493
Filtering in Hybrid Dynamic Bayesian Networks
NASA Technical Reports Server (NTRS)
Andersen, Morten Nonboe; Andersen, Rasmus Orum; Wheeler, Kevin
2000-01-01
We implement a 2-time slice dynamic Bayesian network (2T-DBN) framework and make a 1-D state estimation simulation, an extension of the experiment in (v.d. Merwe et al., 2000) and compare different filtering techniques. Furthermore, we demonstrate experimentally that inference in a complex hybrid DBN is possible by simulating fault detection in a watertank system, an extension of the experiment in (Koller & Lerner, 2000) using a hybrid 2T-DBN. In both experiments, we perform approximate inference using standard filtering techniques, Monte Carlo methods and combinations of these. In the watertank simulation, we also demonstrate the use of 'non-strict' Rao-Blackwellisation. We show that the unscented Kalman filter (UKF) and UKF in a particle filtering framework outperform the generic particle filter, the extended Kalman filter (EKF) and EKF in a particle filtering framework with respect to accuracy in terms of estimation RMSE and sensitivity with respect to choice of network structure. Especially we demonstrate the superiority of UKF in a PF framework when our beliefs of how data was generated are wrong. Furthermore, we investigate the influence of data noise in the watertank simulation using UKF and PFUKD and show that the algorithms are more sensitive to changes in the measurement noise level that the process noise level. Theory and implementation is based on (v.d. Merwe et al., 2000).
Choice Shift in Opinion Network Dynamics
NASA Astrophysics Data System (ADS)
Gabbay, Michael
Choice shift is a phenomenon associated with small group dynamics whereby group discussion causes group members to shift their opinions in a more extreme direction so that the mean post-discussion opinion exceeds the mean pre-discussion opinion. Also known as group polarization, choice shift is a robust experimental phenomenon and has been well-studied within social psychology. In opinion network models, shifts toward extremism are typically produced by the presence of stubborn agents at the extremes of the opinion axis, whose opinions are much more resistant to change than moderate agents. However, we present a model in which choice shift can arise without the assumption of stubborn agents; the model evolves member opinions and uncertainties using coupled nonlinear differential equations. In addition, we briefly describe the results of a recent experiment conducted involving online group discussion concerning the outcome of National Football League games are described. The model predictions concerning the effects of network structure, disagreement level, and team choice (favorite or underdog) are in accord with the experimental results. This research was funded by the Office of Naval Research and the Defense Threat Reduction Agency.
Memory and burstiness in dynamic networks.
Colman, Ewan R; Vukadinović Greetham, Danica
2015-07-01
A discrete-time random process is described, which can generate bursty sequences of events. A Bernoulli process, where the probability of an event occurring at time t is given by a fixed probability x, is modified to include a memory effect where the event probability is increased proportionally to the number of events that occurred within a given amount of time preceding t. For small values of x the interevent time distribution follows a power law with exponent -2-x. We consider a dynamic network where each node forms, and breaks connections according to this process. The value of x for each node depends on the fitness distribution, ρ(x), from which it is drawn; we find exact solutions for the expectation of the degree distribution for a variety of possible fitness distributions, and for both cases where the memory effect either is, or is not present. This work can potentially lead to methods to uncover hidden fitness distributions from fast changing, temporal network data, such as online social communications and fMRI scans. PMID:26274235
The Dynamics of Initiative in Communication Networks.
Mollgaard, Anders; Mathiesen, Joachim
2016-01-01
Human social interaction is often intermittent. Two acquainted persons can have extended periods without social interaction punctuated by periods of repeated interaction. In this case, the repeated interaction can be characterized by a seed initiative by either of the persons and a number of follow-up interactions. The tendency to initiate social interaction plays an important role in the formation of social networks and is in general not symmetric between persons. In this paper, we study the dynamics of initiative by analysing and modeling a detailed call and text message network sampled from a group of 700 individuals. We show that in an average relationship between two individuals, one part is almost twice as likely to initiate communication compared to the other part. The asymmetry has social consequences and ultimately might lead to the discontinuation of a relationship. We explain the observed asymmetry by a positive feedback mechanism where individuals already taking initiative are more likely to take initiative in the future. In general, people with many initiatives receive attention from a broader spectrum of friends than people with few initiatives. Lastly, we compare the likelihood of taking initiative with the basic personality traits of the five factor model. PMID:27124493
Filtering in Hybrid Dynamic Bayesian Networks
NASA Technical Reports Server (NTRS)
Andersen, Morten Nonboe; Andersen, Rasmus Orum; Wheeler, Kevin
2004-01-01
We demonstrate experimentally that inference in a complex hybrid Dynamic Bayesian Network (DBN) is possible using the 2 - T i e Slice DBN (2T-DBN) from [Koller & Lerner, 20001 to model fault detection in a watertank system. In [Koller & Lerner, 20001 a generic Particle Filter (PF) is used for inference. We extend the experiment and perform approximate inference using The Extended Kalman Filter (EKF) and the Unscented Kalman Filter (UKF). Furthermore, we combine these techniques in a 'non-strict' Rao-Blackwellisation framework and apply it to the watertank system. We show that UKF and UKF in a PF framework outperfom the generic PF, EKF and EKF in a PF framework with respect to accuracy and robustness in terms of estimation RMSE. Especially we demonstrate the superiority of UKF in a PF framework when our beliefs of how data was generated are wrong. We also show that the choice of network structure is very important for the performance of the generic PF and the EKF algorithms, but not for the UKF algorithms. Furthermore, we investigate the influence of data noise in the water[ank simulation. Theory and implementation is based on the theory presented.
Breakup locations: Intertwining effects of nuclear structure and reaction dynamics
NASA Astrophysics Data System (ADS)
Dasgupta, M.; Simpson, E. C.; Luong, D. H.; Kalkal, Sunil; Cook, K. J.; Carter, I. P.; Hinde, D. J.; Williams, E.
2016-05-01
Studies at the Australian National University aim to distinguish breakup of the projectile like-nucleus that occurs when approaching the target from that when receding from the target. Helped by breakup simulations, observables have been found that are sensitive to the breakup location, and thus to the mean-lives of unbound states; sensitivity to even sub-zeptosecond lifetime is found. These results provide insights to understand the reaction dynamics of weakly bound nuclei at near barrier energies.
Fluid dynamic modeling of nano-thermite reactions
NASA Astrophysics Data System (ADS)
Martirosyan, Karen S.; Zyskin, Maxim; Jenkins, Charles M.; Yuki Horie, Yasuyuki
2014-03-01
This paper presents a direct numerical method based on gas dynamic equations to predict pressure evolution during the discharge of nanoenergetic materials. The direct numerical method provides for modeling reflections of the shock waves from the reactor walls that generates pressure-time fluctuations. The results of gas pressure prediction are consistent with the experimental evidence and estimates based on the self-similar solution. Artificial viscosity provides sufficient smoothing of shock wave discontinuity for the numerical procedure. The direct numerical method is more computationally demanding and flexible than self-similar solution, in particular it allows study of a shock wave in its early stage of reaction and allows the investigation of "slower" reactions, which may produce weaker shock waves. Moreover, numerical results indicate that peak pressure is not very sensitive to initial density and reaction time, providing that all the material reacts well before the shock wave arrives at the end of the reactor.
Reaction dynamics studies for the system 7Be+58Ni
NASA Astrophysics Data System (ADS)
Torresi, D.; Mazzocco, M.; Acosta, L.; Boiano, A.; Boiano, C.; Diaz-Torres, A.; Fierro, N.; Glodariu, T.; Grilj, L.; Guglielmetti, A.; Keeley, N.; La Commara, M.; Martel, I.; Mazzocchi, C.; Molini, P.; Pakou, A.; Parascandolo, C.; Parkar, V. V.; Patronis, N.; Pierroutsakou, D.; Romoli, M.; Rusek, K.; Sanchez-Benitez, A. M.; Sandoli, M.; Signorini, C.; Silvestri, R.; Soramel, F.; Stiliaris, E.; Strano, E.; Stroe, L.; Zerva, K.
2015-04-01
The study of reactions induced by exotic weakly bound nuclei at energies around the Coulomb barrier had attracted a large interest in the last decade, since the features of these nuclei can deeply affect the reaction dynamics. The discrimination between different reaction mechanisms is, in general, a rather difficult task. It can be achieved by using detector arrays covering high solid angle and with high granularity that allow to measure the reaction products and, possibly, coincidences between them, as, for example, recently done for stable weakly bound nuclei [1, 2]. We investigated the collision of the weakly bound nucleus 7Be on a 58Ni target at the beam energy of 1.1 times the Coulomb barrier, measuring the elastic scattering angular distribution and the energy and angular distributions of 3He and 4He. The 7Be radioactive ion beam was produced by the facility EXOTIC at INFN-LNL with an energy of 22 MeV and an intensity of ~3×105 pps. Results showed that the 4He yeld is about 4 times larger than 3He yield, suggesting that reaction mechanisms other than the break-up mostly produce the He isotopes. Theoretical calculations for transfer channels and compound nucleus reactions suggest that complete fusion accounts for (41±5%) of the total reaction cross section extracted from optical model analysis of the elastic scattering data, and that 3He and 4He stripping are the most populated reaction channels among direct processes. Eventually estimation of incomplete fusion contributions to the 3,4He production cross sections was performed through semi-classical calculations with the code PLATYPUS [3].
Topological effects of network structure on long-term social network dynamics in a wild mammal
Ilany, Amiyaal; Booms, Andrew S.; Holekamp, Kay E.
2015-01-01
Social structure influences ecological processes such as dispersal and invasion, and affects survival and reproductive success. Recent studies have used static snapshots of social networks, thus neglecting their temporal dynamics, and focused primarily on a limited number of variables that might be affecting social structure. Here, instead we modelled effects of multiple predictors of social network dynamics in the spotted hyena, using observational data collected during 20 years of continuous field research in Kenya. We tested the hypothesis that the current state of the social network affects its long-term dynamics. We employed stochastic agent-based models that allowed us to estimate the contribution of multiple factors to network changes. After controlling for environmental and individual effects, we found that network density and individual centrality affected network dynamics, but that social bond transitivity consistently had the strongest effects. Our results emphasise the significance of structural properties of networks in shaping social dynamics. PMID:25975663
Topological effects of network structure on long-term social network dynamics in a wild mammal.
Ilany, Amiyaal; Booms, Andrew S; Holekamp, Kay E
2015-07-01
Social structure influences ecological processes such as dispersal and invasion, and affects survival and reproductive success. Recent studies have used static snapshots of social networks, thus neglecting their temporal dynamics, and focused primarily on a limited number of variables that might be affecting social structure. Here, instead we modelled effects of multiple predictors of social network dynamics in the spotted hyena, using observational data collected during 20 years of continuous field research in Kenya. We tested the hypothesis that the current state of the social network affects its long-term dynamics. We employed stochastic agent-based models that allowed us to estimate the contribution of multiple factors to network changes. After controlling for environmental and individual effects, we found that network density and individual centrality affected network dynamics, but that social bond transitivity consistently had the strongest effects. Our results emphasise the significance of structural properties of networks in shaping social dynamics. PMID:25975663
Dynamic treatment of invariant and univariant reactions in metamorphic systems
Lasaga, A.C.; Luettge, A.; Rye, D.M.; Bolton, E.W.
2000-03-01
A simple model is presented that incorporates the essential dynamics of metamorphic processes leading to reactions along univariant curves and up to and beyond the invariant point. The model includes both heat flow by conduction and convection as well as fluid flow in and out of a representative volume. Overall mineral reactions can then take place within this rock volume in response to internal and external factors. The paper derives a simple back-of-the-envelope expression for the steady state reached by the system. The steady state composition of the fluid and the steady state temperature are then compared with the composition and temperature predicted by the assumption of thermodynamic equilibrium. Expressions for the amount of fluid passing through the system based on the kinetic model are compared with previous calculations of the mass of fluid added to the system using the equilibrium assumptions. The approach to this steady state is also analyzed and an analytical solution is obtained for the time evolution up to the steady state. Both the steady state and the time evolution solution are then applied to an understanding of the dynamics involved in obtaining T-X-t paths in nature. The results of the kinetic approach lead to major revisions in many of the previously held concepts used in petrologic fluid flow models. These include the expected reaction pathway, the role of metastable reactions, the calculation of fluid flux, the role of the invariant point, and the interpretation of mineral textures and modal abundances of minerals.
Rumor diffusion in an interests-based dynamic social network.
Tang, Mingsheng; Mao, Xinjun; Guessoum, Zahia; Zhou, Huiping
2013-01-01
To research rumor diffusion in social friend network, based on interests, a dynamic friend network is proposed, which has the characteristics of clustering and community, and a diffusion model is also proposed. With this friend network and rumor diffusion model, based on the zombie-city model, some simulation experiments to analyze the characteristics of rumor diffusion in social friend networks have been conducted. The results show some interesting observations: (1) positive information may evolve to become a rumor through the diffusion process that people may modify the information by word of mouth; (2) with the same average degree, a random social network has a smaller clustering coefficient and is more beneficial for rumor diffusion than the dynamic friend network; (3) a rumor is spread more widely in a social network with a smaller global clustering coefficient than in a social network with a larger global clustering coefficient; and (4) a network with a smaller clustering coefficient has a larger efficiency. PMID:24453911
Rumor Diffusion in an Interests-Based Dynamic Social Network
Mao, Xinjun; Guessoum, Zahia; Zhou, Huiping
2013-01-01
To research rumor diffusion in social friend network, based on interests, a dynamic friend network is proposed, which has the characteristics of clustering and community, and a diffusion model is also proposed. With this friend network and rumor diffusion model, based on the zombie-city model, some simulation experiments to analyze the characteristics of rumor diffusion in social friend networks have been conducted. The results show some interesting observations: (1) positive information may evolve to become a rumor through the diffusion process that people may modify the information by word of mouth; (2) with the same average degree, a random social network has a smaller clustering coefficient and is more beneficial for rumor diffusion than the dynamic friend network; (3) a rumor is spread more widely in a social network with a smaller global clustering coefficient than in a social network with a larger global clustering coefficient; and (4) a network with a smaller clustering coefficient has a larger efficiency. PMID:24453911
Dynamics of Actively Driven Crosslinked Microtubule Networks
NASA Astrophysics Data System (ADS)
Yadav, Vikrant; Stanhope, Kasimira; Evans, Arthur A.; Ross, Jennifer L.
We have designed a model experiment to explore dynamics of crosslinked active microtubule clusters crosslinked with MAP65. Microtubule clusters are allowed to settle on a slide coated with kinesin-1 molecular motors, which move microtubules. We systematically tune either concentration of cross linkers bound to microtubule (ρc) or the global concentration of microtubules (ρMT) . We quantified the shape of the cluster by measuring the standard deviation (σ) of the cluster outline. At low ρMTor ρc the network is in an expanding state. At higher ρMTor ρc expansion slows down, reaches zero at a critical density, and become negative indicating contraction. Further increase of ρMTor ρc halts any kind of dynamics. The ρMT-ρc phase space shows distinct regions of extensile, contractile and static regimes. We model these results using active hydrodynamic theory. Microtubules are modeled as active rods whereas effect of crosslinkers is modeled using a collision term that prefers anti-parallel alignment of microtubules. A linearized analysis of hydrodynamic equation predicts existence of density driven expanding, contracting, and static phases for microtubule clusters.
Dynamic tubulation of mitochondria drives mitochondrial network formation
Wang, Chong; Du, Wanqing; Su, Qian Peter; Zhu, Mingli; Feng, Peiyuan; Li, Ying; Zhou, Yichen; Mi, Na; Zhu, Yueyao; Jiang, Dong; Zhang, Senyan; Zhang, Zerui; Sun, Yujie; Yu, Li
2015-01-01
Mitochondria form networks. Formation of mitochondrial networks is important for maintaining mitochondrial DNA integrity and interchanging mitochondrial material, whereas disruption of the mitochondrial network affects mitochondrial functions. According to the current view, mitochondrial networks are formed by fusion of individual mitochondria. Here, we report a new mechanism for formation of mitochondrial networks through KIF5B-mediated dynamic tubulation of mitochondria. We found that KIF5B pulls thin, highly dynamic tubules out of mitochondria. Fusion of these dynamic tubules, which is mediated by mitofusins, gives rise to the mitochondrial network. We further demonstrated that dynamic tubulation and fusion is sufficient for mitochondrial network formation, by reconstituting mitochondrial networks in vitro using purified fusion-competent mitochondria, recombinant KIF5B, and polymerized microtubules. Interestingly, KIF5B only controls network formation in the peripheral zone of the cell, indicating that the mitochondrial network is divided into subzones, which may be constructed by different mechanisms. Our data not only uncover an essential mechanism for mitochondrial network formation, but also reveal that different parts of the mitochondrial network are formed by different mechanisms. PMID:26206315
Quantum dynamics of tunneling dominated reactions at low temperatures
NASA Astrophysics Data System (ADS)
Hazra, Jisha; Balakrishnan, N.
2015-05-01
We report a quantum dynamics study of the Li + HF → LiF + H reaction at low temperatures of interest to cooling and trapping experiments. Contributions from non-zero partial waves are analyzed and results show narrow resonances in the energy dependence of the cross section that survive partial wave summation. The computations are performed using the ABC code and a simple modification of the ABC code that enables separate energy cutoffs for the reactant and product rovibrational energy levels is found to dramatically reduce the basis set size and computational expense. Results obtained using two ab initio electronic potential energy surfaces for the LiHF system show strong sensitivity to the choice of the potential. In particular, small differences in the barrier heights of the two potential surfaces are found to dramatically influence the reaction cross sections at low energies. Comparison with recent measurements of the reaction cross section (Bobbenkamp et al 2011 J. Chem. Phys. 135 204306) shows similar energy dependence in the threshold regime and an overall good agreement with experimental data compared to previous theoretical results. Also, usefulness of a recently introduced method for ultracold reactions that employ the quantum close-coupling method at short-range and the multichannel quantum defect theory at long-range, is demonstrated in accurately evaluating product state-resolved cross sections for D + H2 and H + D2 reactions.
Gender, Friendship Networks, and Delinquency: A Dynamic Network Approach**
Haynie, Dana L.; Doogan, Nathan J.; Soller, Brian
2014-01-01
Researchers have examined selection and influence processes in shaping delinquency similarity among friends, but little is known about the role of gender in moderating these relationships. Our objective is to examine differences between adolescent boys and girls regarding delinquency-based selection and influence processes. Using longitudinal network data from adolescents attending two large schools in AddHealth (N = 1,857) and stochastic actor-oriented models, we evaluate whether girls are influenced to a greater degree by friends' violence or delinquency than boys (influence hypothesis) and whether girls are more likely to select friends based on violent or delinquent behavior than boys (selection hypothesis). The results indicate that girls are more likely than boys to be influenced by their friends' involvement in violence. Although a similar pattern emerges for nonviolent delinquency, the gender differences are not significant. Some evidence shows that boys are influenced toward increasing their violence or delinquency when exposed to more delinquent or violent friends but are immune to reducing their violence or delinquency when associating with less violent or delinquent friends. In terms of selection dynamics, although both boys and girls have a tendency to select friends based on friends' behavior, girls have a stronger tendency to do so, suggesting that among girls, friends' involvement in violence or delinquency is an especially decisive factor for determining friendship ties. PMID:26097241
Model framework for describing the dynamics of evolving networks
NASA Astrophysics Data System (ADS)
Tobochnik, Jan; Strandburg, Katherine; Csardi, Gabor; Erdi, Peter
2007-03-01
We present a model framework for describing the dynamics of evolving networks. In this framework the addition of edges is stochastically governed by some important intrinsic and structural properties of network vertices through an attractiveness function. We discuss the solution of the inverse problem: determining the attractiveness function from the network evolution data. We also present a number of example applications: the description of the US patent citation network using vertex degree, patent age and patent category variables, and we show how the time-dependent version of the method can be used to find and describe important changes in the internal dynamics. We also compare our results to scientific citation networks.
Dynamic Evolution Model Based on Social Network Services
NASA Astrophysics Data System (ADS)
Xiong, Xi; Gou, Zhi-Jian; Zhang, Shi-Bin; Zhao, Wen
2013-11-01
Based on the analysis of evolutionary characteristics of public opinion in social networking services (SNS), in the paper we propose a dynamic evolution model, in which opinions are coupled with topology. This model shows the clustering phenomenon of opinions in dynamic network evolution. The simulation results show that the model can fit the data from a social network site. The dynamic evolution of networks accelerates the opinion, separation and aggregation. The scale and the number of clusters are influenced by confidence limit and rewiring probability. Dynamic changes of the topology reduce the number of isolated nodes, while the increased confidence limit allows nodes to communicate more sufficiently. The two effects make the distribution of opinion more neutral. The dynamic evolution of networks generates central clusters with high connectivity and high betweenness, which make it difficult to control public opinions in SNS.
Major component analysis of dynamic networks of physiologic organ interactions
NASA Astrophysics Data System (ADS)
Liu, Kang K. L.; Bartsch, Ronny P.; Ma, Qianli D. Y.; Ivanov, Plamen Ch
2015-09-01
The human organism is a complex network of interconnected organ systems, where the behavior of one system affects the dynamics of other systems. Identifying and quantifying dynamical networks of diverse physiologic systems under varied conditions is a challenge due to the complexity in the output dynamics of the individual systems and the transient and nonlinear characteristics of their coupling. We introduce a novel computational method based on the concept of time delay stability and major component analysis to investigate how organ systems interact as a network to coordinate their functions. We analyze a large database of continuously recorded multi-channel physiologic signals from healthy young subjects during night-time sleep. We identify a network of dynamic interactions between key physiologic systems in the human organism. Further, we find that each physiologic state is characterized by a distinct network structure with different relative contribution from individual organ systems to the global network dynamics. Specifically, we observe a gradual decrease in the strength of coupling of heart and respiration to the rest of the network with transition from wake to deep sleep, and in contrast, an increased relative contribution to network dynamics from chin and leg muscle tone and eye movement, demonstrating a robust association between network topology and physiologic function.
Identify Dynamic Network Modules with Temporal and Spatial Constraints
Jin, R; McCallen, S; Liu, C; Almaas, E; Zhou, X J
2007-09-24
Despite the rapid accumulation of systems-level biological data, understanding the dynamic nature of cellular activity remains a difficult task. The reason is that most biological data are static, or only correspond to snapshots of cellular activity. In this study, we explicitly attempt to detangle the temporal complexity of biological networks by using compilations of time-series gene expression profiling data.We define a dynamic network module to be a set of proteins satisfying two conditions: (1) they form a connected component in the protein-protein interaction (PPI) network; and (2) their expression profiles form certain structures in the temporal domain. We develop the first efficient mining algorithm to discover dynamic modules in a temporal network, as well as frequently occurring dynamic modules across many temporal networks. Using yeast as a model system, we demonstrate that the majority of the identified dynamic modules are functionally homogeneous. Additionally, many of them provide insight into the sequential ordering of molecular events in cellular systems. We further demonstrate that identifying frequent dynamic network modules can significantly increase the signal to noise separation, despite the fact that most dynamic network modules are highly condition-specific. Finally, we note that the applicability of our algorithm is not limited to the study of PPI systems, instead it is generally applicable to the combination of any type of network and time-series data.
Common and Unique Network Dynamics in Football Games
Yamamoto, Yuji; Yokoyama, Keiko
2011-01-01
The sport of football is played between two teams of eleven players each using a spherical ball. Each team strives to score by driving the ball into the opposing goal as the result of skillful interactions among players. Football can be regarded from the network perspective as a competitive relationship between two cooperative networks with a dynamic network topology and dynamic network node. Many complex large-scale networks have been shown to have topological properties in common, based on a small-world network and scale-free network models. However, the human dynamic movement pattern of this network has never been investigated in a real-world setting. Here, we show that the power law in degree distribution emerged in the passing behavior in the 2006 FIFA World Cup Final and an international “A” match in Japan, by describing players as vertices connected by links representing passes. The exponent values are similar to the typical values that occur in many real-world networks, which are in the range of , and are larger than that of a gene transcription network, . Furthermore, we reveal the stochastically switched dynamics of the hub player throughout the game as a unique feature in football games. It suggests that this feature could result not only in securing vulnerability against intentional attack, but also in a power law for self-organization. Our results suggest common and unique network dynamics of two competitive networks, compared with the large-scale networks that have previously been investigated in numerous works. Our findings may lead to improved resilience and survivability not only in biological networks, but also in communication networks. PMID:22216336
NASA Astrophysics Data System (ADS)
Mauguière, Frédéric A. L.; Collins, Peter; Ezra, Gregory S.; Farantos, Stavros C.; Wiggins, Stephen
2014-04-01
A model Hamiltonian for the reaction CH_4^+ rArr CH_3^+ + H, parametrized to exhibit either early or late inner transition states, is employed to investigate the dynamical characteristics of the roaming mechanism. Tight/loose transition states and conventional/roaming reaction pathways are identified in terms of time-invariant objects in phase space. These are dividing surfaces associated with normally hyperbolic invariant manifolds (NHIMs). For systems with two degrees of freedom NHIMS are unstable periodic orbits which, in conjunction with their stable and unstable manifolds, unambiguously define the (locally) non-recrossing dividing surfaces assumed in statistical theories of reaction rates. By constructing periodic orbit continuation/bifurcation diagrams for two values of the potential function parameter corresponding to late and early transition states, respectively, and using the total energy as another parameter, we dynamically assign different regions of phase space to reactants and products as well as to conventional and roaming reaction pathways. The classical dynamics of the system are investigated by uniformly sampling trajectory initial conditions on the dividing surfaces. Trajectories are classified into four different categories: direct reactive and non-reactive trajectories, which lead to the formation of molecular and radical products respectively, and roaming reactive and non-reactive orbiting trajectories, which represent alternative pathways to form molecular and radical products. By analysing gap time distributions at several energies, we demonstrate that the phase space structure of the roaming region, which is strongly influenced by nonlinear resonances between the two degrees of freedom, results in nonexponential (nonstatistical) decay.
Defect reaction network in Si-doped InAs. Numerical predictions.
Schultz, Peter A.
2015-05-01
This Report characterizes the defects in the def ect reaction network in silicon - doped, n - type InAs predicted with first principles density functional theory. The reaction network is deduced by following exothermic defect reactions starting with the initially mobile interstitial defects reacting with common displacement damage defects in Si - doped InAs , until culminating in immobile reaction p roducts. The defect reactions and reaction energies are tabulated, along with the properties of all the silicon - related defects in the reaction network. This Report serves to extend the results for the properties of intrinsic defects in bulk InAs as colla ted in SAND 2013 - 2477 : Simple intrinsic defects in InAs : Numerical predictions to include Si - containing simple defects likely to be present in a radiation - induced defect reaction sequence . This page intentionally left blank
Defect reaction network in Si-doped InP : numerical predictions.
Schultz, Peter Andrew
2013-10-01
This Report characterizes the defects in the defect reaction network in silicon-doped, n-type InP deduced from first principles density functional theory. The reaction network is deduced by following exothermic defect reactions starting with the initially mobile interstitial defects reacting with common displacement damage defects in Si-doped InP until culminating in immobile reaction products. The defect reactions and reaction energies are tabulated, along with the properties of all the silicon-related defects in the reaction network. This Report serves to extend the results for intrinsic defects in SAND 2012-3313: %E2%80%9CSimple intrinsic defects in InP: Numerical predictions%E2%80%9D to include Si-containing simple defects likely to be present in a radiation-induced defect reaction sequence.
NASA Astrophysics Data System (ADS)
Born, Benjamin; Heyden, Matthias; Grossman, Moran; Sagi, Irit; Havenith, Martina
2013-02-01
For long, the contribution of water network motions to enzymatic reactions was enigmatic due to the complexity of biological systems and to experimental limitations. Thanks to the development of new powerful THz emitters and detectors in the last decades, it is now possible to probe dynamics on the timescale of the fast hydrogen bond rearrangements during biochemical reactions. For this purpose, we developed a kinetic terahertz absorption (KITA) spectrometer which combines the strength of THz radiation (~1012 Hz = 1 ps) to directly probe collective picosecond protein-water dynamics with the fast mixing properties of a stopped-flow apparatus which initializes a biochemical reaction within milliseconds. With KITA, we analyzed the collective water dynamics during substrate hydrolyses by a human matrix-metalloproteinase. In addition, we studied the reorganization and electrostatic changes at the catalytic zinc-ion from the enzyme active site and performed molecular dynamics simulations of the enzyme-substrate-water system. Our results revealed a systematic gradient of water network motions: From the active site to the bulk water hydrogen bond dynamics increased from 7 ps (active site) to 1ps (bulk water) prior to substrate binding and hydrolysis. The approaching substrate perturbs the dynamic water gradient resulting in an overshoot of KITA signal which then relaxes back during onset of substrate hydrolyses. Our findings suggest that collective water dynamics may contribute to effective substrate binding to enzyme active sites and could be induced by the charge of the catalytic zinc-ion residing at the active site.
An Adaptive QSE-reduced Nuclear Reaction Network for Silicon Burning
NASA Astrophysics Data System (ADS)
Parete-Koon, Suzanne; Hix, W.; Thielemann, F.
2008-03-01
The nuclei of the "iron peak" are formed in massive stars shortly before core collapse and during their supernova outbursts as well as during thermonuclear supernovae. Complete and incomplete silicon burning during these events are responsible for the production of a wide range of nuclei with atomic mass numbers from 28 to 64. Because of the large number of nuclei involved, accurate modeling of silicon burning is computationally expensive. However, examination of the physics of silicon burning has revealed that the nuclear evolution is dominated by large groups of nuclei in mutual equilibrium. We present an improvement on our hybrid equilibrium-network scheme which takes advantage of this quasi-equilibrium in order to reduce the number of independent variables calculated. Because the size and membership of these groups vary as the temperature, density and electron faction change, achieving maximal efficiency requires dynamic adjustment of group number and membership. Toward this end, we are implementing a scheme beginning with a single QSE (NSE) group at appropriately high temperature, then progressing through 2, 3 and 4 group stages (with successively more independent variables) as temperature declines. This combination allows accurate prediction of the nuclear abundance evolution, deleptonization and energy generation at a further reduced computational cost when compared to a conventional nuclear reaction network or our previous 3 fixed group QSE-reduced network. During silicon burning, the resultant QSE-reduced network is up to 20 times faster than the full network it replaces without significant loss of accuracy. These reductions in computational cost and the number of species evolved make QSE-reduced networks well suited for inclusion within hydrodynamic simulations, particularly in multi-dimensional applications. This work has been supported by the National Science Foundation, by the Department of Energy's Scientic Discovery through Advanced Computing
Modelling non-Markovian dynamics in biochemical reactions
2015-01-01
Background Biochemical reactions are often modelled as discrete-state continuous-time stochastic processes evolving as memoryless Markov processes. However, in some cases, biochemical systems exhibit non-Markovian dynamics. We propose here a methodology for building stochastic simulation algorithms which model more precisely non-Markovian processes in some specific situations. Our methodology is based on Constraint Programming and is implemented by using Gecode, a state-of-the-art framework for constraint solving. Results Our technique allows us to randomly sample waiting times from probability density functions that not necessarily are distributed according to a negative exponential function. In this context, we discuss an important case-study in which the probability density function is inferred from single-molecule experiments that describe the distribution of the time intervals between two consecutive enzymatically catalysed reactions. Noticeably, this feature allows some types of enzyme reactions to be modelled as non-Markovian processes. Conclusions We show that our methodology makes it possible to obtain accurate models of enzymatic reactions that, in specific cases, fit experimental data better than the corresponding Markovian models. PMID:26051249
Molecular-dynamics study of detonation. II. The reaction mechanism
NASA Astrophysics Data System (ADS)
Rice, Betsy M.; Mattson, William; Grosh, John; Trevino, S. F.
1996-01-01
In this work, we investigate mechanisms of chemical reactions that sustain an unsupported detonation. The chemical model of an energetic crystal used in this study consists of heteronuclear diatomic molecules that, at ambient pressure, dissociate endothermically. Subsequent association of the products to form homonuclear diatomic molecules provides the energy release that sustains the detonation. A many-body interaction is used to simulate changes in the electronic bonding as a function of local atomic environment. The consequence of the many-body interaction in this model is that the intramolecular bond is weakened with increasing density. The mechanism of the reaction for this model was extracted by investigating the details of the molecular properties in the reaction zone with two-dimensional molecular dynamics. The mechanism for the initiation of the reaction in this model is pressure-induced atomization. There was no evidence of excitation of vibrational modes to dissociative states. This particular result is directly attributable to the functional form and choice of parameters for this model, but might also have more general applicability.
Crossed-beam studies of the dynamics of radical reactions
Liu, K.
1993-12-01
The objective of this program is to characterize the detailed dynamics of elementary radical reactions and to provide a better understanding of radical reactivity in general. The radical beam is typically generated by a laser photolysis method. After colliding with the reacting molecule in a crossed-beam apparatus, the reaction product state distribution is interrogated by laser spectroscopic techniques. Several radicals of combustion significance, such as O, CH, OH, CN and NCO have been successfully generated and their collisional behavior at the state-to-state integral cross section level of detail has been studied in this manner. During the past year, the detection system has been converted from LIF to REMPI schemes, and the emphasis of this program shifted to investigate the product angular distributions. Both inelastic and reactive processes have been studied.
Research on dynamic routing mechanisms in wireless sensor networks.
Zhao, A Q; Weng, Y N; Lu, Y; Liu, C Y
2014-01-01
WirelessHART is the most widely applied standard in wireless sensor networks nowadays. However, it does not provide any dynamic routing mechanism, which is important for the reliability and robustness of the wireless network applications. In this paper, a collection tree protocol based, dynamic routing mechanism was proposed for WirelessHART network. The dynamic routing mechanism was evaluated through several simulation experiments in three aspects: time for generating the topology, link quality, and stability of network. Besides, the data transmission efficiency of this routing mechanism was analyzed. The simulation and evaluation results show that this mechanism can act as a dynamic routing mechanism for the TDMA-based wireless sensor network. PMID:24982927
Synthesis of recurrent neural networks for dynamical system simulation.
Trischler, Adam P; D'Eleuterio, Gabriele M T
2016-08-01
We review several of the most widely used techniques for training recurrent neural networks to approximate dynamical systems, then describe a novel algorithm for this task. The algorithm is based on an earlier theoretical result that guarantees the quality of the network approximation. We show that a feedforward neural network can be trained on the vector-field representation of a given dynamical system using backpropagation, then recast it as a recurrent network that replicates the original system's dynamics. After detailing this algorithm and its relation to earlier approaches, we present numerical examples that demonstrate its capabilities. One of the distinguishing features of our approach is that both the original dynamical systems and the recurrent networks that simulate them operate in continuous time. PMID:27182811
Perspective: network-guided pattern formation of neural dynamics.
Hütt, Marc-Thorsten; Kaiser, Marcus; Hilgetag, Claus C
2014-10-01
The understanding of neural activity patterns is fundamentally linked to an understanding of how the brain's network architecture shapes dynamical processes. Established approaches rely mostly on deviations of a given network from certain classes of random graphs. Hypotheses about the supposed role of prominent topological features (for instance, the roles of modularity, network motifs or hierarchical network organization) are derived from these deviations. An alternative strategy could be to study deviations of network architectures from regular graphs (rings and lattices) and consider the implications of such deviations for self-organized dynamic patterns on the network. Following this strategy, we draw on the theory of spatio-temporal pattern formation and propose a novel perspective for analysing dynamics on networks, by evaluating how the self-organized dynamics are confined by network architecture to a small set of permissible collective states. In particular, we discuss the role of prominent topological features of brain connectivity, such as hubs, modules and hierarchy, in shaping activity patterns. We illustrate the notion of network-guided pattern formation with numerical simulations and outline how it can facilitate the understanding of neural dynamics. PMID:25180302
Cascading failures in interconnected networks with dynamical redistribution of loads
NASA Astrophysics Data System (ADS)
Zhao, Zhuang; Zhang, Peng; Yang, Hujiang
2015-09-01
Cascading failures of loads in isolated networks and coupled networks have been studied in the past few years. In most of the corresponding results, the topologies of the networks are destroyed. Here, we present an interconnected network model considering cascading failures based on the dynamic redistribution of flow in the networks. Compared with the results of single scale-free networks, we find that interconnected scale-free networks have higher vulnerability. Additionally, the network heterogeneity plays an important role in the robustness of interconnected networks under intentional attacks. Considering the effects of various coupling preferences, the results show that there are almost no differences. Finally, the application of our model to the Beijing interconnected traffic network, which consists of a subway network and a bus network, shows that the subway network suffers more damage under the attack. Moreover, the interconnected traffic network may be more exposed to damage after initial attacks on the bus network. These discussions are important for the design and optimization of interconnected networks.
The quantum dynamics of electronically nonadiabatic chemical reactions
NASA Technical Reports Server (NTRS)
Truhlar, Donald G.
1993-01-01
Considerable progress was achieved on the quantum mechanical treatment of electronically nonadiabatic collisions involving energy transfer and chemical reaction in the collision of an electronically excited atom with a molecule. In the first step, a new diabatic representation for the coupled potential energy surfaces was created. A two-state diabatic representation was developed which was designed to realistically reproduce the two lowest adiabatic states of the valence bond model and also to have the following three desirable features: (1) it is more economical to evaluate; (2) it is more portable; and (3) all spline fits are replaced by analytic functions. The new representation consists of a set of two coupled diabatic potential energy surfaces plus a coupling surface. It is suitable for dynamics calculations on both the electronic quenching and reaction processes in collisions of Na(3p2p) with H2. The new two-state representation was obtained by a three-step process from a modified eight-state diatomics-in-molecules (DIM) representation of Blais. The second step required the development of new dynamical methods. A formalism was developed for treating reactions with very general basis functions including electronically excited states. Our formalism is based on the generalized Newton, scattered wave, and outgoing wave variational principles that were used previously for reactive collisions on a single potential energy surface, and it incorporates three new features: (1) the basis functions include electronic degrees of freedom, as required to treat reactions involving electronic excitation and two or more coupled potential energy surfaces; (2) the primitive electronic basis is assumed to be diabatic, and it is not assumed that it diagonalizes the electronic Hamiltonian even asymptotically; and (3) contracted basis functions for vibrational-rotational-orbital degrees of freedom are included in a very general way, similar to previous prescriptions for locally
The quantum dynamics of electronically nonadiabatic chemical reactions
NASA Astrophysics Data System (ADS)
Truhlar, Donald G.
1993-04-01
Considerable progress was achieved on the quantum mechanical treatment of electronically nonadiabatic collisions involving energy transfer and chemical reaction in the collision of an electronically excited atom with a molecule. In the first step, a new diabatic representation for the coupled potential energy surfaces was created. A two-state diabatic representation was developed which was designed to realistically reproduce the two lowest adiabatic states of the valence bond model and also to have the following three desirable features: (1) it is more economical to evaluate; (2) it is more portable; and (3) all spline fits are replaced by analytic functions. The new representation consists of a set of two coupled diabatic potential energy surfaces plus a coupling surface. It is suitable for dynamics calculations on both the electronic quenching and reaction processes in collisions of Na(3p2p) with H2. The new two-state representation was obtained by a three-step process from a modified eight-state diatomics-in-molecules (DIM) representation of Blais. The second step required the development of new dynamical methods. A formalism was developed for treating reactions with very general basis functions including electronically excited states. Our formalism is based on the generalized Newton, scattered wave, and outgoing wave variational principles that were used previously for reactive collisions on a single potential energy surface, and it incorporates three new features: (1) the basis functions include electronic degrees of freedom, as required to treat reactions involving electronic excitation and two or more coupled potential energy surfaces; (2) the primitive electronic basis is assumed to be diabatic, and it is not assumed that it diagonalizes the electronic Hamiltonian even asymptotically; and (3) contracted basis functions for vibrational-rotational-orbital degrees of freedom are included in a very general way, similar to previous prescriptions for locally
NASA Astrophysics Data System (ADS)
Fitz, Benjamin David
Segmental dynamics are investigated in model compounds, polymers, and network-forming polymers. Two aspects of these materials are investigated: (1) the role of molecular structure and connectivity on determining the characteristics of the segmental relaxation, and (2) monitoring the variations in the segmental dynamics during network-forming chemical reactions. We quantify the most important aspects of the dynamics: the relaxation shape, the relaxation strength, the relaxation time, and the temperature dependencies of these properties. Additionally, two general segmental dynamics issues of interest are the length-scale and the homogeneous/heterogeneous aspects. A judicious choice of network-forming polymer provides for the determination of an upper bound on the length-scale. A comparison of relaxation characteristics between dynamic light scattering (measuring density fluctuations) and dielectric relaxation spectroscopy (measuring segmental dipolar reorientation) provides one evaluation of the heterogeneity issue. Dipole dynamics in small molecule model compounds show the influence of molecular connectivity on the cooperative molecular response associated with the glass transition. A rigid, nonpolar, cyanate ester network is shown to develop an anomalous relaxation process during crosslinking. A specific local mode of motion is assigned. Additionally, the main relaxation becomes extraordinarily broad during the course of the network formation, due to markedly increased segmental rigidity and loss of configurational entropy.
Dynamic social networks promote cooperation in experiments with humans.
Rand, David G; Arbesman, Samuel; Christakis, Nicholas A
2011-11-29
Human populations are both highly cooperative and highly organized. Human interactions are not random but rather are structured in social networks. Importantly, ties in these networks often are dynamic, changing in response to the behavior of one's social partners. This dynamic structure permits an important form of conditional action that has been explored theoretically but has received little empirical attention: People can respond to the cooperation and defection of those around them by making or breaking network links. Here, we present experimental evidence of the power of using strategic link formation and dissolution, and the network modification it entails, to stabilize cooperation in sizable groups. Our experiments explore large-scale cooperation, where subjects' cooperative actions are equally beneficial to all those with whom they interact. Consistent with previous research, we find that cooperation decays over time when social networks are shuffled randomly every round or are fixed across all rounds. We also find that, when networks are dynamic but are updated only infrequently, cooperation again fails. However, when subjects can update their network connections frequently, we see a qualitatively different outcome: Cooperation is maintained at a high level through network rewiring. Subjects preferentially break links with defectors and form new links with cooperators, creating an incentive to cooperate and leading to substantial changes in network structure. Our experiments confirm the predictions of a set of evolutionary game theoretic models and demonstrate the important role that dynamic social networks can play in supporting large-scale human cooperation. PMID:22084103
Dynamic simulation of multicomponent reaction transport in water distribution systems.
Munavalli, G R; Mohan Kumar, M S M S
2004-04-01
Given the presence of nutrients, regrowth of bacteria within a distribution system is possible. The bacterial growth phenomena, which can be studied by developing a multicomponent (substrate, biomass and disinfectant) reaction transport model, is governed by its relationship with the substrate (organic carbon) and disinfectant (chlorine). The multicomponent reaction transport model developed in the present study utilizes the simplified expressions for the basic processes (in bulk flow and at pipe wall) such as bacterial growth and decay, attachment to and detachment from the surface, substrate utilization and disinfectant action involved in the model. The usefulness of the model is further enhanced by the incorporation of an expression for bulk reaction parameter relating it with the organic carbon. The model is validated and applied to study the sensitive behavior of the components using a hypothetical network. The developed model is able to simulate the biodegradable organic carbon threshold in accordance with the values reported in the literature. The spread of contaminant intruded into the system at any location can also be simulated by the model. The multicomponent model developed is useful for water supply authorities in identifying the locations with high substrate concentrations, bacterial growth and lower chlorine residuals. PMID:15087178
Bimolecular reaction dynamics from photoelectron spectroscopy of negative ions
Bradforth, S.E.
1992-11-01
The transition state region of a neutral bimolecular reaction may be experimentally investigated by photoelectron spectroscopy of an appropriate negative ion. The photoelectron spectrum provides information on the spectroscopy and dynamics of the short lived transition state and may be used to develop model potential energy surfaces that are semi-quantitative in this important region. The principles of bound [yields] bound negative ion photoelectron spectroscopy are illustrated by way of an example: a full analysis of the photoelectron bands of CN[sup [minus
Feedback between node and network dynamics can produce real-world network properties
NASA Astrophysics Data System (ADS)
Brot, Hilla; Muchnik, Lev; Goldenberg, Jacob; Louzoun, Yoram
2012-12-01
Real-world networks are characterized by common features, including among others a scale-free degree distribution, a high clustering coefficient and a short typical distance between nodes. These properties are usually explained by the dynamics of edge and node addition and deletion. In a different context, the dynamics of node content within a network has been often explained via the interaction between nodes in static networks, ignoring the dynamic aspect of edge addition and deletion. We here propose to combine the dynamics of the node content and of edge addition and deletion, using a threshold automata framework. Within this framework, we show that the typical properties of real-world networks can be reproduced with a Hebbian approach, in which nodes with similar internal dynamics have a high probability of being connected. The proper network properties emerge only if an imbalance exists between excitatory and inhibitory connections, as is indeed observed in real networks. We further check the plausibility of the suggested mechanism by observing an evolving social network and measuring the probability of edge addition as a function of the similarity between the contents of the corresponding nodes. We indeed find that similarity between nodes increases the emergence probability of a new link between them. The current work bridges between multiple important domains in network analysis, including network formation processes, Kaufmann Boolean networks and Hebbian learning. It suggests that the properties of nodes and the network convolve and can be seen as complementary parts of the same process.
A User Driven Dynamic Circuit Network Implementation
Guok, Chin; Robertson, David; Chaniotakis, Evangelos; Thompson, Mary; Johnston, William; Tierney, Brian
2008-10-01
The requirements for network predictability are becoming increasingly critical to the DoE science community where resources are widely distributed and collaborations are world-wide. To accommodate these emerging requirements, the Energy Sciences Network has established a Science Data Network to provide user driven guaranteed bandwidth allocations. In this paper we outline the design, implementation, and secure coordinated use of such a network, as well as some lessons learned.
Design and implementation of dynamic hybrid Honeypot network
NASA Astrophysics Data System (ADS)
Qiao, Peili; Hu, Shan-Shan; Zhai, Ji-Qiang
2013-05-01
The method of constructing a dynamic and self-adaptive virtual network is suggested to puzzle adversaries, delay and divert attacks, exhaust attacker resources and collect attacking information. The concepts of Honeypot and Honeyd, which is the frame of virtual Honeypot are introduced. The techniques of network scanning including active fingerprint recognition are analyzed. Dynamic virtual network system is designed and implemented. A virtual network similar to real network topology is built according to the collected messages from real environments in this system. By doing this, the system can perplex the attackers when Hackers attack and can further analyze and research the attacks. The tests to this system prove that this design can successfully simulate real network environment and can be used in network security analysis.
Pinning impulsive directed coupled delayed dynamical network and its applications
NASA Astrophysics Data System (ADS)
Lin, Chunnan; Wu, Quanjun; Xiang, Lan; Zhou, Jin
2015-01-01
The main objective of the present paper is to further investigate pinning synchronisation of a complex delayed dynamical network with directionally coupling by a single impulsive controller. By developing the analysis procedure of pinning impulsive stability for undirected coupled dynamical network previously, some simple yet general criteria of pinning impulsive synchronisation for such directed coupled network are derived analytically. It is shown that a single impulsive controller can always pin a given directed coupled network to a desired homogenous solution, including an equilibrium point, a periodic orbit, or a chaotic orbit. Subsequently, the theoretical results are illustrated by a directed small-world complex network which is a cellular neural network (CNN) and a directed scale-free complex network with the well-known Hodgkin-Huxley neuron oscillators. Numerical simulations are finally given to demonstrate the effectiveness of the proposed control methodology.
Predicting the Lifetime of Dynamic Networks Experiencing Persistent Random Attacks
Podobnik, Boris; Lipic, Tomislav; Horvatic, Davor; Majdandzic, Antonio; Bishop, Steven R.; Eugene Stanley, H.
2015-01-01
Estimating the critical points at which complex systems abruptly flip from one state to another is one of the remaining challenges in network science. Due to lack of knowledge about the underlying stochastic processes controlling critical transitions, it is widely considered difficult to determine the location of critical points for real-world networks, and it is even more difficult to predict the time at which these potentially catastrophic failures occur. We analyse a class of decaying dynamic networks experiencing persistent failures in which the magnitude of the overall failure is quantified by the probability that a potentially permanent internal failure will occur. When the fraction of active neighbours is reduced to a critical threshold, cascading failures can trigger a total network failure. For this class of network we find that the time to network failure, which is equivalent to network lifetime, is inversely dependent upon the magnitude of the failure and logarithmically dependent on the threshold. We analyse how permanent failures affect network robustness using network lifetime as a measure. These findings provide new methodological insight into system dynamics and, in particular, of the dynamic processes of networks. We illustrate the network model by selected examples from biology, and social science. PMID:26387609
Predicting the Lifetime of Dynamic Networks Experiencing Persistent Random Attacks
NASA Astrophysics Data System (ADS)
Podobnik, Boris; Lipic, Tomislav; Horvatic, Davor; Majdandzic, Antonio; Bishop, Steven R.; Eugene Stanley, H.
2015-09-01
Estimating the critical points at which complex systems abruptly flip from one state to another is one of the remaining challenges in network science. Due to lack of knowledge about the underlying stochastic processes controlling critical transitions, it is widely considered difficult to determine the location of critical points for real-world networks, and it is even more difficult to predict the time at which these potentially catastrophic failures occur. We analyse a class of decaying dynamic networks experiencing persistent failures in which the magnitude of the overall failure is quantified by the probability that a potentially permanent internal failure will occur. When the fraction of active neighbours is reduced to a critical threshold, cascading failures can trigger a total network failure. For this class of network we find that the time to network failure, which is equivalent to network lifetime, is inversely dependent upon the magnitude of the failure and logarithmically dependent on the threshold. We analyse how permanent failures affect network robustness using network lifetime as a measure. These findings provide new methodological insight into system dynamics and, in particular, of the dynamic processes of networks. We illustrate the network model by selected examples from biology, and social science.
Minimal model for dynamic bonding in colloidal transient networks
NASA Astrophysics Data System (ADS)
Krinninger, Philip; Fortini, Andrea; Schmidt, Matthias
2016-04-01
We investigate a model for colloidal network formation using Brownian dynamics computer simulations. Hysteretic springs establish transient bonds between particles with repulsive cores. If a bonded pair of particles is separated by a cutoff distance, the spring vanishes and reappears only if the two particles contact each other. We present results for the bond lifetime distribution and investigate the properties of the van Hove dynamical two-body correlation function. The model displays crossover from fluidlike dynamics, via transient network formation, to arrested quasistatic network behavior.
Bauß, Anna; Langenmaier, Michael; Strittmatter, Eric; Plattner, Dietmar A; Koslowski, Thorsten
2016-06-01
We present a computer simulation study of the thermodynamics and kinetics of charge transfer reactions within the fungal peroxidase AauDyPI from Auricularia auriculae-judae. Driving forces and reorganization energies are obtained from a thermodynamic integration scheme based upon molecular dynamics simulations. To enhance the numerical accuracy, the free energies are analyzed within a least-squares scheme of a closely knit thermodynamic network. We identify Tyr147, Tyr229, and Trp105 as oxidative agents, and find Trp377 to be a long-lived reaction intermediate. The results are compared to recent experimental findings. PMID:27182684
Growth states of catalytic reaction networks exhibiting energy metabolism
NASA Astrophysics Data System (ADS)
Kondo, Yohei; Kaneko, Kunihiko
2011-07-01
All cells derive nutrition by absorbing some chemical and energy resources from the environment; these resources are used by the cells to reproduce the chemicals within them, which in turn leads to an increase in their volume. In this study we introduce a protocell model exhibiting catalytic reaction dynamics, energy metabolism, and cell growth. Results of extensive simulations of this model show the existence of four phases with regard to the rates of both the influx of resources and cell growth. These phases include an active phase with high influx and high growth rates, an inefficient phase with high influx but low growth rates, a quasistatic phase with low influx and low growth rates, and a death phase with negative growth rate. A mean field model well explains the transition among these phases as bifurcations. The statistical distribution of the active phase is characterized by a power law, and that of the inefficient phase is characterized by a nearly equilibrium distribution. We also discuss the relevance of the results of this study to distinct states in the existing cells.
Growth states of catalytic reaction networks exhibiting energy metabolism.
Kondo, Yohei; Kaneko, Kunihiko
2011-07-01
All cells derive nutrition by absorbing some chemical and energy resources from the environment; these resources are used by the cells to reproduce the chemicals within them, which in turn leads to an increase in their volume. In this study we introduce a protocell model exhibiting catalytic reaction dynamics, energy metabolism, and cell growth. Results of extensive simulations of this model show the existence of four phases with regard to the rates of both the influx of resources and cell growth. These phases include an active phase with high influx and high growth rates, an inefficient phase with high influx but low growth rates, a quasistatic phase with low influx and low growth rates, and a death phase with negative growth rate. A mean field model well explains the transition among these phases as bifurcations. The statistical distribution of the active phase is characterized by a power law, and that of the inefficient phase is characterized by a nearly equilibrium distribution. We also discuss the relevance of the results of this study to distinct states in the existing cells. PMID:21867233
2D pattern evolution constrained by complex network dynamics
NASA Astrophysics Data System (ADS)
da Rocha, L. E. C.; Costa, L. da F.
2007-03-01
Complex networks have established themselves in recent years as being particularly suitable and flexible for representing and modelling several complex natural and artificial systems. In 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, less attention has been focused on hybrid systems, i.e. involving more than one type of network and/or dynamics. Several real systems present such an organization, e.g. the dynamics of a disease coexisting with the dynamics of the immune system. The current paper investigates a specific system involving diffusive (linear and nonlinear) dynamics taking place in a regular network while interacting with a complex network of defensive agents following Erdös Rényi (ER) and Barabási Albert (BA) graph models with moveable nodes. More specifically, the complex network is expected to control, and if possible, to extinguish the diffusion of some given unwanted process (e.g. fire, oil spilling, pest dissemination, and virus or bacteria reproduction during an infection). Two types of pattern evolution are considered: Fick and Gray Scott. The nodes of the defensive network then interact with the diffusing patterns and communicate between themselves in order to control the diffusion. The main findings include the identification of higher efficiency for the BA control networks and the presence of relapses in the case of the ER model.
Theoretical Chemical Dynamics Studies of Elementary Combustion Reactions
Donald L. Thompson
2009-09-30
The objective of this research was to develop and apply methods for more accurate predictions of reaction rates based on high-level quantum chemistry. We have developed and applied efficient, robust methods for fitting global ab initio potential energy surfaces (PESs) for both spectroscopy and dynamics calculations and for performing direct dynamics simulations. Our approach addresses the problem that high-level quantum calculations are often too costly in computer time for practical applications resulting in the use of levels of theory that are often inadequate for reactions. A critical objective was to develop practical methods that require the minimum number of electronic structure calculations for acceptable fidelity to the ab initio PES. Our method does this by a procedure that determines the optimal configurations at which ab initio points are computed, and that ensures that the final fitted PES is uniformly accurate to a prescribed tolerance. Our fitting methods can be done automatically, with little or no human intervention, and with no prior knowledge of the topology of the PES. The methods are based on local fitting schemes using interpolating moving least-squares (IMLS). IMLS has advantages over the very effective modified-Shepard methods developed by Collins and others in that higher-order polynomials can be used and does not require derivatives but can benefit from them if available.
Network cloning unfolds the effect of clustering on dynamical processes
NASA Astrophysics Data System (ADS)
Faqeeh, Ali; Melnik, Sergey; Gleeson, James P.
2015-05-01
We introduce network L -cloning, a technique for creating ensembles of random networks from any given real-world or artificial network. Each member of the ensemble is an L -cloned network constructed from L copies of the original network. The degree distribution of an L -cloned network and, more importantly, the degree-degree correlation between and beyond nearest neighbors are identical to those of the original network. The density of triangles in an L -cloned network, and hence its clustering coefficient, is reduced by a factor of L compared to those of the original network. Furthermore, the density of loops of any fixed length approaches zero for sufficiently large values of L . Other variants of L -cloning allow us to keep intact the short loops of certain lengths. As an application, we employ these network cloning methods to investigate the effect of short loops on dynamical processes running on networks and to inspect the accuracy of corresponding tree-based theories. We demonstrate that dynamics on L -cloned networks (with sufficiently large L ) are accurately described by the so-called adjacency tree-based theories, examples of which include the message passing technique, some pair approximation methods, and the belief propagation algorithm used respectively to study bond percolation, SI epidemics, and the Ising model.
Multistage neural network model for dynamic scene analysis
Ajjimarangsee, P.
1989-01-01
This research is concerned with dynamic scene analysis. The goal of scene analysis is to recognize objects and have a meaningful interpretation of the scene from which images are obtained. The task of the dynamic scene analysis process generally consists of region identification, motion analysis and object recognition. The objective of this research is to develop clustering algorithms using neural network approach and to investigate a multi-stage neural network model for region identification and motion analysis. The research is separated into three parts. First, a clustering algorithm using Kohonens' self-organizing feature map network is developed to be capable of generating continuous membership valued outputs. A newly developed version of the updating algorithm of the network is introduced to achieve a high degree of parallelism. A neural network model for the fuzzy c-means algorithm is proposed. In the second part, the parallel algorithms of a neural network model for clustering using the self-organizing feature maps approach and a neural network that models the fuzzy c-means algorithm are modified for implementation on a distributed memory parallel architecture. In the third part, supervised and unsupervised neural network models for motion analysis are investigated. For a supervised neural network, a three layer perceptron network is trained by a series of images to recognize the movement of the objects. For the unsupervised neural network, a self-organizing feature mapping network will learn to recognize the movement of the objects without an explicit training phase.
A unique transformation from ordinary differential equations to reaction networks.
Soliman, Sylvain; Heiner, Monika
2010-01-01
Many models in Systems Biology are described as a system of Ordinary Differential Equations, which allows for transient, steady-state or bifurcation analysis when kinetic information is available. Complementary structure-related qualitative analysis techniques have become increasingly popular in recent years, like qualitative model checking or pathway analysis (elementary modes, invariants, flux balance analysis, graph-based analyses, chemical organization theory, etc.). They do not rely on kinetic information but require a well-defined structure as stochastic analysis techniques equally do. In this article, we look into the structure inference problem for a model described by a system of Ordinary Differential Equations and provide conditions for the uniqueness of its solution. We describe a method to extract a structured reaction network model, represented as a bipartite multigraph, for example, a continuous Petri net (CPN), from a system of Ordinary Differential Equations (ODEs). A CPN uniquely defines an ODE, and each ODE can be transformed into a CPN. However, it is not obvious under which conditions the transformation of an ODE into a CPN is unique, that is, when a given ODE defines exactly one CPN. We provide biochemically relevant sufficient conditions under which the derived structure is unique and counterexamples showing the necessity of each condition. Our method is implemented and available; we illustrate it on some signal transduction models from the BioModels database. A prototype implementation of the method is made available to modellers at http://contraintes.inria.fr/~soliman/ode2pn.html, and the data mentioned in the "Results" section at http://contraintes.inria.fr/~soliman/ode2pn_data/. Our results yield a new recommendation for the import/export feature of tools supporting the SBML exchange format. PMID:21203560
Bimolecular reaction dynamics from photoelectron spectroscopy of negative ions
Bradforth, S.E.
1992-11-01
The transition state region of a neutral bimolecular reaction may be experimentally investigated by photoelectron spectroscopy of an appropriate negative ion. The photoelectron spectrum provides information on the spectroscopy and dynamics of the short lived transition state and may be used to develop model potential energy surfaces that are semi-quantitative in this important region. The principles of bound {yields} bound negative ion photoelectron spectroscopy are illustrated by way of an example: a full analysis of the photoelectron bands of CN{sup {minus}}, NCO{sup {minus}} and NCS{sup {minus}}. Transition state photoelectron spectra are presented for the following systems Br + HI, Cl + HI, F + HI, F + CH{sub 3}0H,F + C{sub 2}H{sub 5}OH,F + OH and F + H{sub 2}. A time dependent framework for the simulation and interpretation of the bound {yields} free transition state photoelectron spectra is subsequently developed and applied to the hydrogen transfer reactions Br + HI, F + OH {yields} O({sup 3}P, {sup 1}D) + HF and F + H{sub 2}. The theoretical approach for the simulations is a fully quantum-mechanical wave packet propagation on a collinear model reaction potential surface. The connection between the wavepacket time evolution and the photoelectron spectrum is given by the time autocorrelation function. For the benchmark F + H{sub 2} system, comparisons with three-dimensional quantum calculations are made.
Systematic development of reduced reaction mechanisms for dynamic modeling
NASA Technical Reports Server (NTRS)
Frenklach, M.; Kailasanath, K.; Oran, E. S.
1986-01-01
A method for systematically developing a reduced chemical reaction mechanism for dynamic modeling of chemically reactive flows is presented. The method is based on the postulate that if a reduced reaction mechanism faithfully describes the time evolution of both thermal and chain reaction processes characteristic of a more complete mechanism, then the reduced mechanism will describe the chemical processes in a chemically reacting flow with approximately the same degree of accuracy. Here this postulate is tested by producing a series of mechanisms of reduced accuracy, which are derived from a full detailed mechanism for methane-oxygen combustion. These mechanisms were then tested in a series of reactive flow calculations in which a large-amplitude sinusoidal perturbation is applied to a system that is initially quiescent and whose temperature is high enough to start ignition processes. Comparison of the results for systems with and without convective flow show that this approach produces reduced mechanisms that are useful for calculations of explosions and detonations. Extensions and applicability to flames are discussed.
RPMDRATE: Bimolecular chemical reaction rates from ring polymer molecular dynamics
NASA Astrophysics Data System (ADS)
Suleimanov, Yu. V.; Allen, J. W.; Green, W. H.
2013-03-01
We present RPMDRATE, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH4, OH+CH4 and H+C2H6 reactions. Catalogue identifier: AENW_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AENW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: MIT license No. of lines in distributed program, including test data, etc.: 94512 No. of bytes in distributed program, including test data, etc.: 1395674 Distribution format: tar.gz Programming language: Fortran 90/95, Python (version 2.6.x or later, including any version of Python 3, is recommended). Computer: Not computer specific. Operating system: Any for which Python, Fortran 90/95 compiler and the required external routines are available. Has the code been vectorized or parallelized?: The program can efficiently utilize 4096+ processors, depending on problem and available computer. At low temperatures, 110 processors are reasonable for a typical umbrella integration run with an analytic potential energy function and gradients on the latest x86-64 machines.
The Graph Laplacian and the Dynamics of Complex Networks
Thulasidasan, Sunil
2012-06-11
In this talk, we explore the structure of networks from a spectral graph-theoretic perspective by analyzing the properties of the Laplacian matrix associated with the graph induced by a network. We will see how the eigenvalues of the graph Laplacian relate to the underlying network structure and dynamics and provides insight into a phenomenon frequently observed in real world networks - the emergence of collective behavior from purely local interactions seen in the coordinated motion of animals and phase transitions in biological networks, to name a few.
Epidemic dynamics and endemic states in complex networks
Pastor-Satorras, Romualdo; Vespignani, Alessandro
2001-06-01
We study by analytical methods and large scale simulations a dynamical model for the spreading of epidemics in complex networks. In networks with exponentially bounded connectivity we recover the usual epidemic behavior with a threshold defining a critical point below that the infection prevalence is null. On the contrary, on a wide range of scale-free networks we observe the absence of an epidemic threshold and its associated critical behavior. This implies that scale-free networks are prone to the spreading and the persistence of infections whatever spreading rate the epidemic agents might possess. These results can help understanding computer virus epidemics and other spreading phenomena on communication and social networks.
Dynamic structure evolution of time-dependent network
NASA Astrophysics Data System (ADS)
Zhang, Beibei; Zhou, Yadong; Xu, Xiaoyan; Wang, Dai; Guan, Xiaohong
2016-08-01
In this paper, we research the long-voided problem of formulating the time-dependent network structure evolution scheme, it focus not only on finding new emerging vertices in evolving communities and new emerging communities over the specified time range but also formulating the complex network structure evolution schematic. Previous approaches basically applied to community detection on time static networks and thus failed to consider the potentially crucial and useful information latently embedded in the dynamic structure evolution process of time-dependent network. To address these problems and to tackle the network non-scalability dilemma, we propose the dynamic hierarchical method for detecting and revealing structure evolution schematic of the time-dependent network. In practice and specificity, we propose an explicit hierarchical network evolution uncovering algorithm framework originated from and widely expanded from time-dependent and dynamic spectral optimization theory. Our method yields preferable results compared with previous approaches on a vast variety of test network data, including both real on-line networks and computer generated complex networks.
Interplay between collective behavior and spreading dynamics on complex networks
NASA Astrophysics Data System (ADS)
Li, Kezan; Ma, Zhongjun; Jia, Zhen; Small, Michael; Fu, Xinchu
2012-12-01
There are certain correlations between collective behavior and spreading dynamics on some real complex networks. Based on the dynamical characteristics and traditional physical models, we construct several new bidirectional network models of spreading phenomena. By theoretical and numerical analysis of these models, we find that the collective behavior can inhibit spreading behavior, but, conversely, this spreading behavior can accelerate collective behavior. The spread threshold of spreading network is obtained by using the Lyapunov function method. The results show that an effective spreading control method is to enhance the individual awareness to collective behavior. Many real-world complex networks can be thought of in terms of both collective behavior and spreading dynamics and therefore to better understand and control such complex networks systems, our work may provide a basic framework.
An efficient neural network approach to dynamic robot motion planning.
Yang, S X; Meng, M
2000-03-01
In this paper, a biologically inspired neural network approach to real-time collision-free motion planning of mobile robots or robot manipulators in a nonstationary environment is proposed. Each neuron in the topologically organized neural network has only local connections, whose neural dynamics is characterized by a shunting equation. Thus the computational complexity linearly depends on the neural network size. The real-time robot motion is planned through the dynamic activity landscape of the neural network without any prior knowledge of the dynamic environment, without explicitly searching over the free workspace or the collision paths, and without any learning procedures. Therefore it is computationally efficient. The global stability of the neural network is guaranteed by qualitative analysis and the Lyapunov stability theory. The effectiveness and efficiency of the proposed approach are demonstrated through simulation studies. PMID:10935758
Mathematical Frameworks for Oscillatory Network Dynamics in Neuroscience.
Ashwin, Peter; Coombes, Stephen; Nicks, Rachel
2016-12-01
The tools of weakly coupled phase oscillator theory have had a profound impact on the neuroscience community, providing insight into a variety of network behaviours ranging from central pattern generation to synchronisation, as well as predicting novel network states such as chimeras. However, there are many instances where this theory is expected to break down, say in the presence of strong coupling, or must be carefully interpreted, as in the presence of stochastic forcing. There are also surprises in the dynamical complexity of the attractors that can robustly appear-for example, heteroclinic network attractors. In this review we present a set of mathematical tools that are suitable for addressing the dynamics of oscillatory neural networks, broadening from a standard phase oscillator perspective to provide a practical framework for further successful applications of mathematics to understanding network dynamics in neuroscience. PMID:26739133
Dynamics of brain networks in the aesthetic appreciation
Cela-Conde, Camilo J.; García-Prieto, Juan; Ramasco, José J.; Mirasso, Claudio R.; Bajo, Ricardo; Munar, Enric; Flexas, Albert; del-Pozo, Francisco; Maestú, Fernando
2013-01-01
Neuroimage experiments have been essential for identifying active brain networks. During cognitive tasks as in, e.g., aesthetic appreciation, such networks include regions that belong to the default mode network (DMN). Theoretically, DMN activity should be interrupted during cognitive tasks demanding attention, as is the case for aesthetic appreciation. Analyzing the functional connectivity dynamics along three temporal windows and two conditions, beautiful and not beautiful stimuli, here we report experimental support for the hypothesis that aesthetic appreciation relies on the activation of two different networks, an initial aesthetic network and a delayed aesthetic network, engaged within distinct time frames. Activation of the DMN might correspond mainly to the delayed aesthetic network. We discuss adaptive and evolutionary explanations for the relationships existing between the DMN and aesthetic networks and offer unique inputs to debates on the mind/brain interaction. PMID:23754437
Sriyudthsak, Kansuporn; Shiraishi, Fumihide; Hirai, Masami Yokota
2016-01-01
The high-throughput acquisition of metabolome data is greatly anticipated for the complete understanding of cellular metabolism in living organisms. A variety of analytical technologies have been developed to acquire large-scale metabolic profiles under different biological or environmental conditions. Time series data are useful for predicting the most likely metabolic pathways because they provide important information regarding the accumulation of metabolites, which implies causal relationships in the metabolic reaction network. Considerable effort has been undertaken to utilize these data for constructing a mathematical model merging system properties and quantitatively characterizing a whole metabolic system in toto. However, there are technical difficulties between benchmarking the provision and utilization of data. Although, hundreds of metabolites can be measured, which provide information on the metabolic reaction system, simultaneous measurement of thousands of metabolites is still challenging. In addition, it is nontrivial to logically predict the dynamic behaviors of unmeasurable metabolite concentrations without sufficient information on the metabolic reaction network. Yet, consolidating the advantages of advancements in both metabolomics and mathematical modeling remain to be accomplished. This review outlines the conceptual basis of and recent advances in technologies in both the research fields. It also highlights the potential for constructing a large-scale mathematical model by estimating model parameters from time series metabolome data in order to comprehensively understand metabolism at the systems level. PMID:27200361
Sriyudthsak, Kansuporn; Shiraishi, Fumihide; Hirai, Masami Yokota
2016-01-01
The high-throughput acquisition of metabolome data is greatly anticipated for the complete understanding of cellular metabolism in living organisms. A variety of analytical technologies have been developed to acquire large-scale metabolic profiles under different biological or environmental conditions. Time series data are useful for predicting the most likely metabolic pathways because they provide important information regarding the accumulation of metabolites, which implies causal relationships in the metabolic reaction network. Considerable effort has been undertaken to utilize these data for constructing a mathematical model merging system properties and quantitatively characterizing a whole metabolic system in toto. However, there are technical difficulties between benchmarking the provision and utilization of data. Although, hundreds of metabolites can be measured, which provide information on the metabolic reaction system, simultaneous measurement of thousands of metabolites is still challenging. In addition, it is nontrivial to logically predict the dynamic behaviors of unmeasurable metabolite concentrations without sufficient information on the metabolic reaction network. Yet, consolidating the advantages of advancements in both metabolomics and mathematical modeling remain to be accomplished. This review outlines the conceptual basis of and recent advances in technologies in both the research fields. It also highlights the potential for constructing a large-scale mathematical model by estimating model parameters from time series metabolome data in order to comprehensively understand metabolism at the systems level. PMID:27200361
Generating functionals for autonomous latching dynamics in attractor relict networks
Linkerhand, Mathias; Gros, Claudius
2013-01-01
Coupling local, slowly adapting variables to an attractor network allows to destabilize all attractors, turning them into attractor ruins. The resulting attractor relict network may show ongoing autonomous latching dynamics. We propose to use two generating functionals for the construction of attractor relict networks, a Hopfield energy functional generating a neural attractor network and a functional based on information-theoretical principles, encoding the information content of the neural firing statistics, which induces latching transition from one transiently stable attractor ruin to the next. We investigate the influence of stress, in terms of conflicting optimization targets, on the resulting dynamics. Objective function stress is absent when the target level for the mean of neural activities is identical for the two generating functionals and the resulting latching dynamics is then found to be regular. Objective function stress is present when the respective target activity levels differ, inducing intermittent bursting latching dynamics. PMID:23784373
Modeling the dynamical interaction between epidemics on overlay networks
NASA Astrophysics Data System (ADS)
Marceau, Vincent; Noël, Pierre-André; Hébert-Dufresne, Laurent; Allard, Antoine; Dubé, Louis J.
2011-08-01
Epidemics seldom occur as isolated phenomena. Typically, two or more viral agents spread within the same host population and may interact dynamically with each other. We present a general model where two viral agents interact via an immunity mechanism as they propagate simultaneously on two networks connecting the same set of nodes. By exploiting a correspondence between the propagation dynamics and a dynamical process performing progressive network generation, we develop an analytical approach that accurately captures the dynamical interaction between epidemics on overlay networks. The formalism allows for overlay networks with arbitrary joint degree distribution and overlap. To illustrate the versatility of our approach, we consider a hypothetical delayed intervention scenario in which an immunizing agent is disseminated in a host population to hinder the propagation of an undesirable agent (e.g., the spread of preventive information in the context of an emerging infectious disease).
Analysis of weblike network structures of directed graphs for chemical reactions in methane plasmas
NASA Astrophysics Data System (ADS)
Sakai, Osamu; Nobuto, Kyosuke; Miyagi, Shigeyuki; Tachibana, Kunihide
2015-10-01
Chemical reactions of molecular gases like methane are so complicated that a chart of decomposed and/or synthesized species originating from molecules in plasma resembles a weblike network in which we write down species and reactions among them. Here we consider properties of the network structures of chemical reactions in methane plasmas. In the network, atoms/molecules/radical species are assumed to form nodes and chemical reactions correspond to directed edges in the terminology of graph theory. Investigation of the centrality index reveals importance of CH3 in the global chemical reaction, and difference of an index for each radical species between cases with and without electrons clarifies that the electrons are at an influential position to tighten the network structure.
Analysis of weblike network structures of directed graphs for chemical reactions in methane plasmas
Sakai, Osamu Nobuto, Kyosuke; Miyagi, Shigeyuki; Tachibana, Kunihide
2015-10-15
Chemical reactions of molecular gases like methane are so complicated that a chart of decomposed and/or synthesized species originating from molecules in plasma resembles a weblike network in which we write down species and reactions among them. Here we consider properties of the network structures of chemical reactions in methane plasmas. In the network, atoms/molecules/radical species are assumed to form nodes and chemical reactions correspond to directed edges in the terminology of graph theory. Investigation of the centrality index reveals importance of CH{sub 3} in the global chemical reaction, and difference of an index for each radical species between cases with and without electrons clarifies that the electrons are at an influential position to tighten the network structure.
Nonlinear Network Dynamics on Earthquake Fault Systems
Rundle, Paul B.; Rundle, John B.; Tiampo, Kristy F.; Sa Martins, Jorge S.; McGinnis, Seth; Klein, W.
2001-10-01
Earthquake faults occur in interacting networks having emergent space-time modes of behavior not displayed by isolated faults. Using simulations of the major faults in southern California, we find that the physics depends on the elastic interactions among the faults defined by network topology, as well as on the nonlinear physics of stress dissipation arising from friction on the faults. Our results have broad applications to other leaky threshold systems such as integrate-and-fire neural networks.
Dynamics of rumor-like information dissemination in complex networks
NASA Astrophysics Data System (ADS)
Nekovee, Maziar; Moreno, Yamir; Bianconi, Ginestra
2005-03-01
An important dynamic process that takes place in complex networks is the spreading of information via rumor-like mechanisms. In addition to their relevance to propagation of rumors and fads in human society, such mechanism are also the basis of an important class of collective communication protocols in complex computer networks, such as the Internet and the peer-to-peer systems. In this talk we present results of our analytical, numerical and large-scale Monte Carlo simulation studies of this process on several classes of complex networks, including random graphs, scale-free networks, and random and small-world topological graphs. Our studies point out to important differences between the dynamics of rumor spreading and that of virus spreading in such networks, and provide new insights into the complex interplay between the spreading phenomena and network topology.
Practical synchronization on complex dynamical networks via optimal pinning control.
Li, Kezan; Sun, Weigang; Small, Michael; Fu, Xinchu
2015-07-01
We consider practical synchronization on complex dynamical networks under linear feedback control designed by optimal control theory. The control goal is to minimize global synchronization error and control strength over a given finite time interval, and synchronization error at terminal time. By utilizing the Pontryagin's minimum principle, and based on a general complex dynamical network, we obtain an optimal system to achieve the control goal. The result is verified by performing some numerical simulations on Star networks, Watts-Strogatz networks, and Barabási-Albert networks. Moreover, by combining optimal control and traditional pinning control, we propose an optimal pinning control strategy which depends on the network's topological structure. Obtained results show that optimal pinning control is very effective for synchronization control in real applications. PMID:26274112
Computer Simulations of Mechano-Chemical Networks Choreographing Actin Dynamics in Cell Motility
NASA Astrophysics Data System (ADS)
Zhuravlev, Pavel I.; Hu, Longhua; Papoian, Garegin A.
In eukaryotic cells, cell motility is largely driven by self-assembly and growth of filamentous networks comprised of actin. Numerous proteins regulate actin network dynamics either biochemically, or through mechanical interactions. This regulation is rather complex, intricately coordinated both spatially and temporally. Although experiments in vivo and in vitro have provided a trove of structural and biochemical information about actin-based cell motility processes, experimental data is not always easy to interpret unambiguously, sometimes various interpretations being in contradiction with each other. Hence, mathematical modeling approaches are necessary for providing a physical foundation for interpreting and guiding experiments. In particular, computer simulations based on physicochemical interactions provide a systems-level description of protrusion dynamics. In this contribution, we review recent progress in modeling actin-based cell motility using detailed computer simulations. We elaborate on the way actin network dynamics is determined by the interplay between chemical reactions, mechanical feedbacks, and transport bottlenecks. We also discuss the role of inherent randomness of elementary chemical reactions in determining the dynamical behavior of the mechano-chemical network controlling actin polymerization and growth.
Information processing in neural networks with the complex dynamic thresholds
NASA Astrophysics Data System (ADS)
Kirillov, S. Yu.; Nekorkin, V. I.
2016-06-01
A control mechanism of the information processing in neural networks is investigated, based on the complex dynamic threshold of the neural excitation. The threshold properties are controlled by the slowly varying synaptic current. The dynamic threshold shows high sensitivity to the rate of the synaptic current variation. It allows both to realize flexible selective tuning of the network elements and to provide nontrivial regimes of neural coding.
Control and management of large and dynamic networks
Tsai, W.T.
1986-01-01
Dynamic networks are computer networks whose links and nodes could fail and recover frequently. The nodes may also be mobile. Large dynamic networks are dynamic networks of large size and they are clustered as hierarchical networks. The objective of this research task is to design a mechanism to support nodes to communicate with each other. To communicate with each other, the nodes would first have to know the names of other nodes, then their addresses, and finally the routes. Thus, the network should provide two mechanisms to supports the communications: binding of names of nodes with their addresses, and binding of address of nodes to the routes dynamically. The first problem, i.e., bind the names of nodes with their addresses, is usually called the naming or addressing problem. The second problem, i.e., binding the addresses with the corresponding routes, is conventionally called the routing problem. This dissertation discusses techniques to handle both problems. The author first discusses techniques for the routing problem. As the network is assumed to be very large and dynamic, he concentrates on developing hierarchical routing algorithms. A new adaptive hierarchical routing algorithm is proposed. The algorithm is based on the new Arpanet algorithm. The algorithm is good for both updating and initialization the routing tables.
Quantifying dynamical spillover in co-evolving multiplex networks
Vijayaraghavan, Vikram S.; Noël, Pierre-André; Maoz, Zeev; D’Souza, Raissa M.
2015-01-01
Multiplex networks (a system of multiple networks that have different types of links but share a common set of nodes) arise naturally in a wide spectrum of fields. Theoretical studies show that in such multiplex networks, correlated edge dynamics between the layers can have a profound effect on dynamical processes. However, how to extract the correlations from real-world systems is an outstanding challenge. Here we introduce the Multiplex Markov chain to quantify correlations in edge dynamics found in longitudinal data of multiplex networks. By comparing the results obtained from the multiplex perspective to a null model which assumes layers in a network are independent, we can identify real correlations as distinct from simultaneous changes that occur due to random chance. We use this approach on two different data sets: the network of trade and alliances between nation states, and the email and co-commit networks between developers of open source software. We establish the existence of “dynamical spillover” showing the correlated formation (or deletion) of edges of different types as the system evolves. The details of the dynamics over time provide insight into potential causal pathways. PMID:26459949
Quantifying dynamical spillover in co-evolving multiplex networks
NASA Astrophysics Data System (ADS)
Vijayaraghavan, Vikram S.; Noël, Pierre-André; Maoz, Zeev; D'Souza, Raissa M.
2015-10-01
Multiplex networks (a system of multiple networks that have different types of links but share a common set of nodes) arise naturally in a wide spectrum of fields. Theoretical studies show that in such multiplex networks, correlated edge dynamics between the layers can have a profound effect on dynamical processes. However, how to extract the correlations from real-world systems is an outstanding challenge. Here we introduce the Multiplex Markov chain to quantify correlations in edge dynamics found in longitudinal data of multiplex networks. By comparing the results obtained from the multiplex perspective to a null model which assumes layers in a network are independent, we can identify real correlations as distinct from simultaneous changes that occur due to random chance. We use this approach on two different data sets: the network of trade and alliances between nation states, and the email and co-commit networks between developers of open source software. We establish the existence of “dynamical spillover” showing the correlated formation (or deletion) of edges of different types as the system evolves. The details of the dynamics over time provide insight into potential causal pathways.
Dynamic recruitment of resting state sub-networks
O'Neill, George C.; Bauer, Markus; Woolrich, Mark W.; Morris, Peter G.; Barnes, Gareth R.; Brookes, Matthew J.
2015-01-01
Resting state networks (RSNs) are of fundamental importance in human systems neuroscience with evidence suggesting that they are integral to healthy brain function and perturbed in pathology. Despite rapid progress in this area, the temporal dynamics governing the functional connectivities that underlie RSN structure remain poorly understood. Here, we present a framework to help further our understanding of RSN dynamics. We describe a methodology which exploits the direct nature and high temporal resolution of magnetoencephalography (MEG). This technique, which builds on previous work, extends from solving fundamental confounds in MEG (source leakage) to multivariate modelling of transient connectivity. The resulting processing pipeline facilitates direct (electrophysiological) measurement of dynamic functional networks. Our results show that, when functional connectivity is assessed in small time windows, the canonical sensorimotor network can be decomposed into a number of transiently synchronising sub-networks, recruitment of which depends on current mental state. These rapidly changing sub-networks are spatially focal with, for example, bilateral primary sensory and motor areas resolved into two separate sub-networks. The likely interpretation is that the larger canonical sensorimotor network most often seen in neuroimaging studies reflects only a temporal aggregate of these transient sub-networks. Our approach opens new frontiers to study RSN dynamics, showing that MEG is capable of revealing the spatial, temporal and spectral signature of the human connectome in health and disease. PMID:25899137
Popularity and Adolescent Friendship Networks: Selection and Influence Dynamics
ERIC Educational Resources Information Center
Dijkstra, Jan Kornelis; Cillessen, Antonius H. N.; Borch, Casey
2013-01-01
This study examined the dynamics of popularity in adolescent friendship networks across 3 years in middle school. Longitudinal social network modeling was used to identify selection and influence in the similarity of popularity among friends. It was argued that lower status adolescents strive to enhance their status through befriending higher…
Network Strength Theory of Storage and Retrieval Dynamics
ERIC Educational Resources Information Center
Wickelgren, Wayne A.
1976-01-01
The notion of strength is defined in several alternative ways for chains of associations connected in series and in parallel. Network strength theory is extended to handle retrieval dynamics for a network of associations, in a manner that permits various degrees of serial versus parallel manner that permits various degrees of serial versus…
Random Evolution of Idiotypic Networks: Dynamics and Architecture
NASA Astrophysics Data System (ADS)
Brede, Markus; Behn, Ulrich
The paper deals with modelling a subsystem of the immune system, the so-called idiotypic network (INW). INWs, conceived by N.K. Jerne in 1974, are functional networks of interacting antibodies and B cells. In principle, Jernes' framework provides solutions to many issues in immunology, such as immunological memory, mechanisms for antigen recognition and self/non-self discrimination. Explaining the interconnection between the elementary components, local dynamics, network formation and architecture, and possible modes of global system function appears to be an ideal playground of statistical mechanics. We present a simple cellular automaton model, based on a graph representation of the system. From a simplified description of idiotypic interactions, rules for the random evolution of networks of occupied and empty sites on these graphs are derived. In certain biologically relevant parameter ranges the resultant dynamics leads to stationary states. A stationary state is found to correspond to a specific pattern of network organization. It turns out that even these very simple rules give rise to a multitude of different kinds of patterns. We characterize these networks by classifying `static' and `dynamic' network-patterns. A type of `dynamic' network is found to display many features of real INWs.
Converting PSO dynamics into complex network - Initial study
NASA Astrophysics Data System (ADS)
Pluhacek, Michal; Janostik, Jakub; Senkerik, Roman; Zelinka, Ivan
2016-06-01
In this paper it is presented the initial study on the possibility of capturing the inner dynamic of Particle Swarm Optimization algorithm into a complex network structure. Inspired in previous works there are two different approaches for creating the complex network presented in this paper. Visualizations of the networks are presented and commented. The possibilities for future applications of the proposed design are given in detail.
Simulating market dynamics: interactions between consumer psychology and social networks.
Janssen, Marco A; Jager, Wander
2003-01-01
Markets can show different types of dynamics, from quiet markets dominated by one or a few products, to markets with continual penetration of new and reintroduced products. In a previous article we explored the dynamics of markets from a psychological perspective using a multi-agent simulation model. The main results indicated that the behavioral rules dominating the artificial consumer's decision making determine the resulting market dynamics, such as fashions, lock-in, and unstable renewal. Results also show the importance of psychological variables like social networks, preferences, and the need for identity to explain the dynamics of markets. In this article we extend this work in two directions. First, we will focus on a more systematic investigation of the effects of different network structures. The previous article was based on Watts and Strogatz's approach, which describes the small-world and clustering characteristics in networks. More recent research demonstrated that many large networks display a scale-free power-law distribution for node connectivity. In terms of market dynamics this may imply that a small proportion of consumers may have an exceptional influence on the consumptive behavior of others (hubs, or early adapters). We show that market dynamics is a self-organized property depending on the interaction between the agents' decision-making process (heuristics), the product characteristics (degree of satisfaction of unit of consumption, visibility), and the structure of interactions between agents (size of network and hubs in a social network). PMID:14761255
Adaptive control of nonlinear systems using multistage dynamic neural networks
NASA Astrophysics Data System (ADS)
Gupta, Madan M.; Rao, Dandina H.
1992-11-01
In this paper we present a new architecture of neuron, called the dynamic neural unit (DNU). The topology of the proposed neuronal model embodies delay elements, feedforward and feedback signals weighted by the synaptic weights and a time-varying nonlinear activation function, and is thus different from the conventionally and assumed architecture of neurons. The learning algorithm for the proposed neuronal structure and the corresponding implementation scheme are presented. A multi-stage dynamic neural network is developed using the DNU as the basic processing element. The performance evaluation of the dynamic neural network is presented for nonlinear dynamic systems under various situations. The capabilities of the proposed neural network model not only account for the learning and control actions emulating some of the biological control functions, but also provide a promising parallel-distributed intelligent control scheme for large-scale complex dynamic systems.
Dynamic changes in network synchrony reveal resting-state functional networks
NASA Astrophysics Data System (ADS)
Vuksanović, Vesna; Hövel, Philipp
2015-02-01
Experimental functional magnetic resonance imaging studies have shown that spontaneous brain activity, i.e., in the absence of any external input, exhibit complex spatial and temporal patterns of co-activity between segregated brain regions. These so-called large-scale resting-state functional connectivity networks represent dynamically organized neural assemblies interacting with each other in a complex way. It has been suggested that looking at the dynamical properties of complex patterns of brain functional co-activity may reveal neural mechanisms underlying the dynamic changes in functional interactions. Here, we examine how global network dynamics is shaped by different network configurations, derived from realistic brain functional interactions. We focus on two main dynamics measures: synchrony and variations in synchrony. Neural activity and the inferred hemodynamic response of the network nodes are simulated using a system of 90 FitzHugh-Nagumo neural models subject to system noise and time-delayed interactions. These models are embedded into the topology of the complex brain functional interactions, whose architecture is additionally reduced to its main structural pathways. In the simulated functional networks, patterns of correlated regional activity clearly arise from dynamical properties that maximize synchrony and variations in synchrony. Our results on the fast changes of the level of the network synchrony also show how flexible changes in the large-scale network dynamics could be.
Bifurcation dynamics of natural drainage networks.
Petroff, Alexander P; Devauchelle, Olivier; Seybold, Hansjörg; Rothman, Daniel H
2013-01-01
As water erodes a landscape, streams form and channellize the surficial flow. In time, streams become highly ramified networks that can extend over a continent. Here, we combine physical reasoning, mathematical analysis and field observations to understand a basic feature of network growth: the bifurcation of a growing stream. We suggest a deterministic bifurcation rule arising from a relationship between the position of the tip in the network and the local shape of the water table. Next, we show that, when a stream bifurcates, competition between the stream and branches selects a special bifurcation angle α=2π/5. We confirm this prediction by measuring several thousand bifurcation angles in a kilometre-scale network fed by groundwater. In addition to providing insight into the growth of river networks, this result presents river networks as a physical manifestation of a classical mathematical problem: interface growth in a harmonic field. In the final sections, we combine these results to develop and explore a one-parameter model of network growth. The model predicts the development of logarithmic spirals. We find similar features in the kilometre-scale network. PMID:24191117
Functional clustering in hippocampal cultures: relating network structure and dynamics
NASA Astrophysics Data System (ADS)
Feldt, S.; Wang, J. X.; Shtrahman, E.; Dzakpasu, R.; Olariu, E.; Żochowski, M.
2010-12-01
In this work we investigate the relationship between gross anatomic structural network properties, neuronal dynamics and the resultant functional structure in dissociated rat hippocampal cultures. Specifically, we studied cultures as they developed under two conditions: the first supporting glial cell growth (high glial group), and the second one inhibiting it (low glial group). We then compared structural network properties and the spatio-temporal activity patterns of the neurons. Differences in dynamics between the two groups could be linked to the impact of the glial network on the neuronal network as the cultures developed. We also implemented a recently developed algorithm called the functional clustering algorithm (FCA) to obtain the resulting functional network structure. We show that this new algorithm is useful for capturing changes in functional network structure as the networks evolve over time. The FCA detects changes in functional structure that are consistent with expected dynamical differences due to the impact of the glial network. Cultures in the high glial group show an increase in global synchronization as the cultures age, while those in the low glial group remain locally synchronized. We additionally use the FCA to quantify the amount of synchronization present in the cultures and show that the total level of synchronization in the high glial group is stronger than in the low glial group. These results indicate an interdependence between the glial and neuronal networks present in dissociated cultures.
The role of dimensionality in neuronal network dynamics.
Ulloa Severino, Francesco Paolo; Ban, Jelena; Song, Qin; Tang, Mingliang; Bianconi, Ginestra; Cheng, Guosheng; Torre, Vincent
2016-01-01
Recent results from network theory show that complexity affects several dynamical properties of networks that favor synchronization. Here we show that synchronization in 2D and 3D neuronal networks is significantly different. Using dissociated hippocampal neurons we compared properties of cultures grown on a flat 2D substrates with those formed on 3D graphene foam scaffolds. Both 2D and 3D cultures had comparable glia to neuron ratio and the percentage of GABAergic inhibitory neurons. 3D cultures because of their dimension have many connections among distant neurons leading to small-world networks and their characteristic dynamics. After one week, calcium imaging revealed moderately synchronous activity in 2D networks, but the degree of synchrony of 3D networks was higher and had two regimes: a highly synchronized (HS) and a moderately synchronized (MS) regime. The HS regime was never observed in 2D networks. During the MS regime, neuronal assemblies in synchrony changed with time as observed in mammalian brains. After two weeks, the degree of synchrony in 3D networks decreased, as observed in vivo. These results show that dimensionality determines properties of neuronal networks and that several features of brain dynamics are a consequence of its 3D topology. PMID:27404281
Recovery processes and dynamics in single and interdependent networks
NASA Astrophysics Data System (ADS)
Majdandzic, Antonio
Systems composed of dynamical networks --- such as the human body with its biological networks or the global economic network consisting of regional clusters --- often exhibit complicated collective dynamics. Three fundamental processes that are typically present are failure, damage spread, and recovery. Here we develop a model for such systems and find phase diagrams for single and interacting networks. By investigating networks with a small number of nodes, where finite-size effects are pronounced, we describe the spontaneous recovery phenomenon present in these systems. In the case of interacting networks the phase diagram is very rich and becomes increasingly more complex as the number of interacting networks increases. In the simplest example of two interacting networks we find two critical points, four triple points, ten allowed transitions, and two forbidden transitions, as well as complex hysteresis loops. Remarkably, we find that triple points play the dominant role in constructing the optimal repairing strategy in damaged interacting systems. To test our model, we analyze an example of real interacting financial networks and find evidence of rapid dynamical transitions between well-defined states, in agreement with the predictions of our model.
The role of dimensionality in neuronal network dynamics
Ulloa Severino, Francesco Paolo; Ban, Jelena; Song, Qin; Tang, Mingliang; Bianconi, Ginestra; Cheng, Guosheng; Torre, Vincent
2016-01-01
Recent results from network theory show that complexity affects several dynamical properties of networks that favor synchronization. Here we show that synchronization in 2D and 3D neuronal networks is significantly different. Using dissociated hippocampal neurons we compared properties of cultures grown on a flat 2D substrates with those formed on 3D graphene foam scaffolds. Both 2D and 3D cultures had comparable glia to neuron ratio and the percentage of GABAergic inhibitory neurons. 3D cultures because of their dimension have many connections among distant neurons leading to small-world networks and their characteristic dynamics. After one week, calcium imaging revealed moderately synchronous activity in 2D networks, but the degree of synchrony of 3D networks was higher and had two regimes: a highly synchronized (HS) and a moderately synchronized (MS) regime. The HS regime was never observed in 2D networks. During the MS regime, neuronal assemblies in synchrony changed with time as observed in mammalian brains. After two weeks, the degree of synchrony in 3D networks decreased, as observed in vivo. These results show that dimensionality determines properties of neuronal networks and that several features of brain dynamics are a consequence of its 3D topology. PMID:27404281
Enabling direct nanoscale observations of biological reactions with dynamic TEM
Evans, James E.; Browning, Nigel D.
2013-01-01
Biological processes occur on a wide range of spatial and temporal scales: from femtoseconds to hours and from angstroms to meters. Many new biological insights can be expected from a better understanding of the processes that occur on these very fast and very small scales. In this regard, new instruments that use fast X-ray or electron pulses are expected to reveal novel mechanistic details for macromolecular protein dynamics. To ensure that any observed conformational change is physiologically relevant and not constrained by 3D crystal packing, it would be preferable for experiments to utilize small protein samples such as single particles or 2D crystals that mimic the target protein's native environment. These samples are not typically amenable to X-ray analysis, but transmission electron microscopy has imaged such sample geometries for over 40 years using both direct imaging and diffraction modes. While conventional transmission electron microscopes (TEM) have visualized biological samples with atomic resolution in an arrested or frozen state, the recent development of the dynamic TEM (DTEM) extends electron microscopy into a dynamic regime using pump-probe imaging. A new second-generation DTEM, which is currently being constructed, has the potential to observe live biological processes with unprecedented spatiotemporal resolution by using pulsed electron packets to probe the sample on micro- and nanosecond timescales. This article reviews the experimental parameters necessary for coupling DTEM with in situ liquid microscopy to enable direct imaging of protein conformational dynamics in a fully hydrated environment and visualize reactions propagating in real time. PMID:23315566
Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape
Wales, D. J.
2015-04-07
This perspective focuses on conceptual and computational aspects of the potential energy landscape framework. It has two objectives: first to summarise some key developments of the approach and second to illustrate how such techniques can be applied using a specific example that exploits knowledge of pathways. Recent developments in theory and simulation within the landscape framework are first outlined, including methods for structure prediction, analysis of global thermodynamic properties, and treatment of rare event dynamics. We then develop a connection between the kinetic transition network treatment of dynamics and a potential of mean force defined by a reaction coordinate. The effect of projection from the full configuration space to low dimensionality is illustrated for an atomic cluster. In this example, where a relatively successful structural order parameter is available, the principal change in cluster morphology is reproduced, but some details are not faithfully represented. In contrast, a profile based on configurations that correspond to the discrete path defined geometrically retains all the barriers and minima. This comparison provides insight into the physical origins of “friction” effects in low-dimensionality descriptions of dynamics based upon a reaction coordinate.
Dynamic interactions of proteins in complex networks
Appella, E.; Anderson, C.
2009-10-01
Recent advances in techniques such as NMR and EPR spectroscopy have enabled the elucidation of how proteins undergo structural changes to act in concert in complex networks. The three minireviews in this series highlight current findings and the capabilities of new methodologies for unraveling the dynamic changes controlling diverse cellular functions. They represent a sampling of the cutting-edge research presented at the 17th Meeting of Methods in Protein Structure Analysis, MPSA2008, in Sapporo, Japan, 26-29 August, 2008 (http://www.iapsap.bnl.gov). The first minireview, by Christensen and Klevit, reports on a structure-based yeast two-hybrid method for identifying E2 ubiquitin-conjugating enzymes that interact with the E3 BRCA1/BARD1 heterodimer ligase to generate either mono- or polyubiquitinated products. This method demonstrated for the first time that the BRCA1/BARD1 E3 can interact with 10 different E2 enzymes. Interestingly, the interaction with multiple E2 enzymes displayed unique ubiquitin-transfer properties, a feature expected to be common among other RING and U-box E3s. Further characterization of new E3 ligases and the E2 enzymes that interact with them will greatly enhance our understanding of ubiquitin transfer and facilitate studies of roles of ubiquitin and ubiquitin-like proteins in protein processing and trafficking. Stein et al., in the second minireview, describe recent progress in defining the binding specificity of different peptide-binding domains. The authors clearly point out that transient peptide interactions mediated by both post-translational modifications and disordered regions ensure a high level of specificity. They postulate that a regulatory code may dictate the number of combinations of domains and post-translational modifications needed to achieve the required level of interaction specificity. Moreover, recognition alone is not enough to obtain a stable complex, especially in a complex cellular environment. Increasing
Understanding intramembrane proteolysis: from protein dynamics to reaction kinetics.
Langosch, D; Scharnagl, C; Steiner, H; Lemberg, M K
2015-06-01
Intramembrane proteolysis - cleavage of proteins within the plane of a membrane - is a widespread phenomenon that can contribute to the functional activation of substrates and is involved in several diseases. Although different families of intramembrane proteases have been discovered and characterized, we currently do not know how these enzymes discriminate between substrates and non-substrates, how site-specific cleavage is achieved, or which factors determine the rate of proteolysis. Focusing on γ-secretase and rhomboid proteases, we argue that answers to these questions may emerge from connecting experimental readouts, such as reaction kinetics and the determination of cleavage sites, to the structures and the conformational dynamics of substrates and enzymes. PMID:25941170
Role of Substrate Dynamics in Protein Prenylation Reactions
2015-01-01
Conspectus The role dynamics plays in proteins is of intense contemporary interest. Fundamental insights into how dynamics affects reactivity and product distributions will facilitate the design of novel catalysts that can produce high quality compounds that can be employed, for example, as fuels and life saving drugs. We have used molecular dynamics (MD) methods and combined quantum mechanical/molecular mechanical (QM/MM) methods to study a series of proteins either whose substrates are too far away from the catalytic center or whose experimentally resolved substrate binding modes cannot explain the observed product distribution. In particular, we describe studies of farnesyl transferase (FTase) where the farnesyl pyrophosphate (FPP) substrate is ∼8 Å from the zinc-bound peptide in the active site of FTase. Using MD and QM/MM studies, we explain how the FPP substrate spans the gulf between it and the active site, and we have elucidated the nature of the transition state (TS) and offered an alternate explanation of experimentally observed kinetic isotope effects (KIEs). Our second story focuses on the nature of substrate dynamics in the aromatic prenyltransferase (APTase) protein NphB and how substrate dynamics affects the observed product distribution. Through the examples chosen we show the power of MD and QM/MM methods to provide unique insights into how protein substrate dynamics affects catalytic efficiency. We also illustrate how complex these reactions are and highlight the challenges faced when attempting to design de novo catalysts. While the methods used in our previous studies provided useful insights, several clear challenges still remain. In particular, we have utilized a semiempirical QM model (self-consistent charge density functional tight binding, SCC-DFTB) in our QM/MM studies since the problems we were addressing required extensive sampling. For the problems illustrated, this approach performed admirably (we estimate for these systems an
The architecture of dynamic reservoir in the echo state network
NASA Astrophysics Data System (ADS)
Cui, Hongyan; Liu, Xiang; Li, Lixiang
2012-09-01
Echo state network (ESN) has recently attracted increasing interests because of its superior capability in modeling nonlinear dynamic systems. In the conventional echo state network model, its dynamic reservoir (DR) has a random and sparse topology, which is far from the real biological neural networks from both structural and functional perspectives. We hereby propose three novel types of echo state networks with new dynamic reservoir topologies based on complex network theory, i.e., with a small-world topology, a scale-free topology, and a mixture of small-world and scale-free topologies, respectively. We then analyze the relationship between the dynamic reservoir structure and its prediction capability. We utilize two commonly used time series to evaluate the prediction performance of the three proposed echo state networks and compare them to the conventional model. We also use independent and identically distributed time series to analyze the short-term memory and prediction precision of these echo state networks. Furthermore, we study the ratio of scale-free topology and the small-world topology in the mixed-topology network, and examine its influence on the performance of the echo state networks. Our simulation results show that the proposed echo state network models have better prediction capabilities, a wider spectral radius, but retain almost the same short-term memory capacity as compared to the conventional echo state network model. We also find that the smaller the ratio of the scale-free topology over the small-world topology, the better the memory capacities.
The architecture of dynamic reservoir in the echo state network.
Cui, Hongyan; Liu, Xiang; Li, Lixiang
2012-09-01
Echo state network (ESN) has recently attracted increasing interests because of its superior capability in modeling nonlinear dynamic systems. In the conventional echo state network model, its dynamic reservoir (DR) has a random and sparse topology, which is far from the real biological neural networks from both structural and functional perspectives. We hereby propose three novel types of echo state networks with new dynamic reservoir topologies based on complex network theory, i.e., with a small-world topology, a scale-free topology, and a mixture of small-world and scale-free topologies, respectively. We then analyze the relationship between the dynamic reservoir structure and its prediction capability. We utilize two commonly used time series to evaluate the prediction performance of the three proposed echo state networks and compare them to the conventional model. We also use independent and identically distributed time series to analyze the short-term memory and prediction precision of these echo state networks. Furthermore, we study the ratio of scale-free topology and the small-world topology in the mixed-topology network, and examine its influence on the performance of the echo state networks. Our simulation results show that the proposed echo state network models have better prediction capabilities, a wider spectral radius, but retain almost the same short-term memory capacity as compared to the conventional echo state network model. We also find that the smaller the ratio of the scale-free topology over the small-world topology, the better the memory capacities. PMID:23020466
Network analysis of the state space of discrete dynamical systems.
Shreim, Amer; Grassberger, Peter; Nadler, Walter; Samuelsson, Björn; Socolar, Joshua E S; Paczuski, Maya
2007-05-11
We study networks representing the dynamics of elementary 1D cellular automata (CA) on finite lattices. We analyze scaling behaviors of both local and global network properties as a function of system size. The scaling of the largest node in-degree is obtained analytically for a variety of CA including rules 22, 54, and 110. We further define the path diversity as a global network measure. The coappearance of nontrivial scaling in both the hub size and the path diversity separates simple dynamics from the more complex behaviors typically found in Wolfram's class IV and some class III CA. PMID:17677672
Network Analysis of the State Space of Discrete Dynamical Systems
NASA Astrophysics Data System (ADS)
Shreim, Amer; Grassberger, Peter; Nadler, Walter; Samuelsson, Björn; Socolar, Joshua E. S.; Paczuski, Maya
2007-05-01
We study networks representing the dynamics of elementary 1D cellular automata (CA) on finite lattices. We analyze scaling behaviors of both local and global network properties as a function of system size. The scaling of the largest node in-degree is obtained analytically for a variety of CA including rules 22, 54, and 110. We further define the path diversity as a global network measure. The coappearance of nontrivial scaling in both the hub size and the path diversity separates simple dynamics from the more complex behaviors typically found in Wolfram’s class IV and some class III CA.
Dynamics and processing in finite self-similar networks
DeDeo, Simon; Krakauer, David C.
2012-01-01
A common feature of biological networks is the geometrical property of self-similarity. Molecular regulatory networks through to circulatory systems, nervous systems, social systems and ecological trophic networks show self-similar connectivity at multiple scales. We analyse the relationship between topology and signalling in contrasting classes of such topologies. We find that networks differ in their ability to contain or propagate signals between arbitrary nodes in a network depending on whether they possess branching or loop-like features. Networks also differ in how they respond to noise, such that one allows for greater integration at high noise, and this performance is reversed at low noise. Surprisingly, small-world topologies, with diameters logarithmic in system size, have slower dynamical time scales, and may be less integrated (more modular) than networks with longer path lengths. All of these phenomena are essentially mesoscopic, vanishing in the infinite limit but producing strong effects at sizes and time scales relevant to biology. PMID:22378750
Network structure, topology, and dynamics in generalized models of synchronization
NASA Astrophysics Data System (ADS)
Lerman, Kristina; Ghosh, Rumi
2012-08-01
Network structure is a product of both its topology and interactions between its nodes. We explore this claim using the paradigm of distributed synchronization in a network of coupled oscillators. As the network evolves to a global steady state, nodes synchronize in stages, revealing the network's underlying community structure. Traditional models of synchronization assume that interactions between nodes are mediated by a conservative process similar to diffusion. However, social and biological processes are often nonconservative. We propose a model of synchronization in a network of oscillators coupled via nonconservative processes. We study the dynamics of synchronization of a synthetic and real-world networks and show that the traditional and nonconservative models of synchronization reveal different structures within the same network.
Binary dynamics on star networks under external perturbations.
Moreira, Carolina A; Schneider, David M; de Aguiar, Marcus A M
2015-10-01
We study a binary dynamical process that is a representation of the voter model with two candidates and opinion makers. The voters are represented by nodes of a network of social contacts with internal states labeled 0 or 1 and nodes that are connected can influence each other. The network is also perturbed by opinion makers, a set of external nodes whose states are frozen in 0 or 1 and that can influence all nodes of the network. The quantity of interest is the probability of finding m nodes in state 1 at time t. Here we study this process on star networks, which are simple representations of hubs found in complex systems, and compare the results with those obtained for networks that are fully connected. In both cases a transition from disordered to ordered equilibrium states is observed as the number of external nodes becomes small. For fully connected networks the probability distribution becomes uniform at the critical point. For star networks, on the other hand, we show that the equilibrium distribution splits in two peaks, reflecting the two possible states of the central node. We obtain approximate analytical solutions for the equilibrium distribution that clarify the role of the central node in the process. We show that the network topology also affects the time scale of oscillations in single realizations of the dynamics, which are much faster for the star network. Finally, extending the analysis to two stars we compare our results with simulations in simple scale-free networks. PMID:26565294
Binary dynamics on star networks under external perturbations
NASA Astrophysics Data System (ADS)
Moreira, Carolina A.; Schneider, David M.; de Aguiar, Marcus A. M.
2015-10-01
We study a binary dynamical process that is a representation of the voter model with two candidates and opinion makers. The voters are represented by nodes of a network of social contacts with internal states labeled 0 or 1 and nodes that are connected can influence each other. The network is also perturbed by opinion makers, a set of external nodes whose states are frozen in 0 or 1 and that can influence all nodes of the network. The quantity of interest is the probability of finding m nodes in state 1 at time t . Here we study this process on star networks, which are simple representations of hubs found in complex systems, and compare the results with those obtained for networks that are fully connected. In both cases a transition from disordered to ordered equilibrium states is observed as the number of external nodes becomes small. For fully connected networks the probability distribution becomes uniform at the critical point. For star networks, on the other hand, we show that the equilibrium distribution splits in two peaks, reflecting the two possible states of the central node. We obtain approximate analytical solutions for the equilibrium distribution that clarify the role of the central node in the process. We show that the network topology also affects the time scale of oscillations in single realizations of the dynamics, which are much faster for the star network. Finally, extending the analysis to two stars we compare our results with simulations in simple scale-free networks.
Dynamic three-dimensional pore-scale imaging of reaction in a carbonate at reservoir conditions.
Menke, Hannah P; Bijeljic, Branko; Andrew, Matthew G; Blunt, Martin J
2015-04-01
Quantifying CO2 transport and average effective reaction rates in the subsurface is essential to assess the risks associated with underground carbon capture and storage. We use X-ray microtomography to investigate dynamic pore structure evolution in situ at temperatures and pressures representative of underground reservoirs and aquifers. A 4 mm diameter Ketton carbonate core is injected with CO2-saturated brine at 50 °C and 10 MPa while tomographic images are taken at 15 min intervals with a 3.8 μm spatial resolution over a period of 2(1/2) h. An approximate doubling of porosity with only a 3.6% increase in surface area to volume ratio is measured from the images. Pore-scale direct simulation and network modeling on the images quantify an order of magnitude increase in permeability and an appreciable alteration of the velocity field. We study the uniform reaction regime, with dissolution throughout the core. However, at the pore scale, we see variations in the degree of dissolution with an overall reaction rate which is approximately 14 times lower than estimated from batch measurements. This work implies that in heterogeneous rocks, pore-scale transport of reactants limits dissolution and can reduce the average effective reaction rate by an order of magnitude. PMID:25738415
Reaction dynamics of the UV-B photosensor UVR8.
Miyamori, Takaaki; Nakasone, Yusuke; Hitomi, Kenichi; Christie, John M; Getzoff, Elizabeth D; Terazima, Masahide
2015-05-01
UVR8 is a recently discovered ultraviolet-B (UV-B) photoreceptor protein identified in plants and algae. In the dark state, UVR8 exists as a homodimer, whereas UV-B irradiation induces UVR8 monomerization and initiation of signaling. Although the biological functions of UVR8 have been studied, the fundamental reaction mechanism and associated kinetics have not yet been fully elucidated. Here, we used the transient grating method to determine the reaction dynamics of UVR8 monomerization based on its diffusion coefficient. We found that the UVR8 photodissociation reaction proceeds in three stages: (i) photoexcitation of cross-dimer tryptophan (Trp) pyramids; (ii) an initial conformational change with a time constant of 50 ms; and (iii) dimer dissociation with a time constant of 200 ms. We identified W285 as the key Trp residue responsible for initiating this photoreaction. Although the C-terminus of UVR8 is essential for biological interactions and signaling via downstream components such as COP1, no obvious differences were detected between the photoreactions of wild-type UVR8 (amino acids 1-440) and a mutant lacking the C-terminus (amino acids 1-383). This similarity indicates that the conformational change associated with stage ii cannot primarily be attributed to this region. A UV-B-driven conformational change with a time constant of 50 ms was also detected in the monomeric mutants of UVR8. Dimer recovery following monomerization, as measured by circular dichroism spectroscopy, was decreased under oxygen-purged conditions, suggesting that redox reactivity is a key factor contributing to the UVR8 oligomeric state. PMID:25811405
Temporal dynamics of connectivity and epidemic properties of growing networks
NASA Astrophysics Data System (ADS)
Fotouhi, Babak; Shirkoohi, Mehrdad Khani
2016-01-01
Traditional mathematical models of epidemic disease had for decades conventionally considered static structure for contacts. Recently, an upsurge of theoretical inquiry has strived towards rendering the models more realistic by incorporating the temporal aspects of networks of contacts, societal and online, that are of interest in the study of epidemics (and other similar diffusion processes). However, temporal dynamics have predominantly focused on link fluctuations and nodal activities, and less attention has been paid to the growth of the underlying network. Many real networks grow: Online networks are evidently in constant growth, and societal networks can grow due to migration flux and reproduction. The effect of network growth on the epidemic properties of networks is hitherto unknown, mainly due to the predominant focus of the network growth literature on the so-called steady state. This paper takes a step towards alleviating this gap. We analytically study the degree dynamics of a given arbitrary network that is subject to growth. We use the theoretical findings to predict the epidemic properties of the network as a function of time. We observe that the introduction of new individuals into the network can enhance or diminish its resilience against endemic outbreaks and investigate how this regime shift depends upon the connectivity of newcomers and on how they establish connections to existing nodes. Throughout, theoretical findings are corroborated with Monte Carlo simulations over synthetic and real networks. The results shed light on the effects of network growth on the future epidemic properties of networks and offers insights for devising a priori immunization strategies.
Temporal dynamics of connectivity and epidemic properties of growing networks.
Fotouhi, Babak; Shirkoohi, Mehrdad Khani
2016-01-01
Traditional mathematical models of epidemic disease had for decades conventionally considered static structure for contacts. Recently, an upsurge of theoretical inquiry has strived towards rendering the models more realistic by incorporating the temporal aspects of networks of contacts, societal and online, that are of interest in the study of epidemics (and other similar diffusion processes). However, temporal dynamics have predominantly focused on link fluctuations and nodal activities, and less attention has been paid to the growth of the underlying network. Many real networks grow: Online networks are evidently in constant growth, and societal networks can grow due to migration flux and reproduction. The effect of network growth on the epidemic properties of networks is hitherto unknown, mainly due to the predominant focus of the network growth literature on the so-called steady state. This paper takes a step towards alleviating this gap. We analytically study the degree dynamics of a given arbitrary network that is subject to growth. We use the theoretical findings to predict the epidemic properties of the network as a function of time. We observe that the introduction of new individuals into the network can enhance or diminish its resilience against endemic outbreaks and investigate how this regime shift depends upon the connectivity of newcomers and on how they establish connections to existing nodes. Throughout, theoretical findings are corroborated with Monte Carlo simulations over synthetic and real networks. The results shed light on the effects of network growth on the future epidemic properties of networks and offers insights for devising a priori immunization strategies. PMID:26871086
Collective relaxation dynamics of small-world networks
NASA Astrophysics Data System (ADS)
Grabow, Carsten; Grosskinsky, Stefan; Kurths, Jürgen; Timme, Marc
2015-05-01
Complex networks exhibit a wide range of collective dynamic phenomena, including synchronization, diffusion, relaxation, and coordination processes. Their asymptotic dynamics is generically characterized by the local Jacobian, graph Laplacian, or a similar linear operator. The structure of networks with regular, small-world, and random connectivities are reasonably well understood, but their collective dynamical properties remain largely unknown. Here we present a two-stage mean-field theory to derive analytic expressions for network spectra. A single formula covers the spectrum from regular via small-world to strongly randomized topologies in Watts-Strogatz networks, explaining the simultaneous dependencies on network size N , average degree k , and topological randomness q . We present simplified analytic predictions for the second-largest and smallest eigenvalue, and numerical checks confirm our theoretical predictions for zero, small, and moderate topological randomness q , including the entire small-world regime. For large q of the order of one, we apply standard random matrix theory, thereby overarching the full range from regular to randomized network topologies. These results may contribute to our analytic and mechanistic understanding of collective relaxation phenomena of network dynamical systems.
Simulating Timescale Dynamics of Network Traffic Using Homogeneous Modeling
Yuan, Jian; Mills, Kevin L.
2006-01-01
Simulating and understanding traffic dynamics in large networks are difficult and challenging due to the complexity of such networks and the limitations inherent in simulation modeling. Typically, simulation models used to study traffic dynamics include substantial detail representing protocol mechanisms across several layers of functionality. Such models must be restricted in space and time in order to be computationally tractable. We propose an alternative simulation approach that uses homogeneous modeling with an increased level of abstraction, in order to explore networks at larger space-time scales than otherwise feasible and to develop intuition and insight about the space-time dynamics of large networks. To illustrate the utility of our approach, we examine some current understandings of the timescale dynamics of network traffic, and we discuss some speculative results obtained with homogeneous modeling. Using a wavelet-based technique, we show correlation structures, and changes in correlation structures, of network traffic under variations in traffic sources, transport mechanisms, and network structure. Our simulation results justify further investigation of our approach, which might benefit from cross-verifications against more detailed simulation models. PMID:27274931
Dynamics of Opinion Forming in Structurally Balanced Social Networks
Altafini, Claudio
2012-01-01
A structurally balanced social network is a social community that splits into two antagonistic factions (typical example being a two-party political system). The process of opinion forming on such a community is most often highly predictable, with polarized opinions reflecting the bipartition of the network. The aim of this paper is to suggest a class of dynamical systems, called monotone systems, as natural models for the dynamics of opinion forming on structurally balanced social networks. The high predictability of the outcome of a decision process is explained in terms of the order-preserving character of the solutions of this class of dynamical systems. If we represent a social network as a signed graph in which individuals are the nodes and the signs of the edges represent friendly or hostile relationships, then the property of structural balance corresponds to the social community being splittable into two antagonistic factions, each containing only friends. PMID:22761667
Dynamic structural network evolution in compressed granular systems
NASA Astrophysics Data System (ADS)
Papadopoulos, Lia; Puckett, James; Daniels, Karen; Bassett, Danielle
The heterogeneous dynamic behavior of granular packings under shear or compression is not well-understood. In this study, we use novel techniques from network science to investigate the structural evolution that occurs in compressed granular systems. Specifically, we treat particles as network nodes, and pressure-dependent forces between particles as layer-specific network edges. Then, we use a generalization of community detection methods to multilayer networks, and develop quantitative measures that characterize changes in the architecture of the force network as a function of pressure. We observe that branchlike domains reminiscent of force chains evolve differentially as pressure is applied: topological characteristics of these domains at rest predict their coalescence or dispersion under pressure. Our methods allow us to study the dynamics of mesoscale structure in granular systems, and provide a direct way to compare data from systems under different external conditions or with different physical makeup.
An Architecture for Dynamic Trust Monitoring in Mobile Networks
NASA Astrophysics Data System (ADS)
Onolaja, Olufunmilola; Bahsoon, Rami; Theodoropoulos, Georgios
Collusion attacks remain a major problem of reputation and trust models, in mobile ad hoc networks. By covering up malicious behaviour of one another from the remaining part of the network, two or more malicious nodes may collaborate to cause damage to or disrupt the network. A number of models exist, which have been proposed to address this issue. Despite these however, the assurance of trusted communication still remains a challenge in these networks. We present a dynamic trust model that detects malicious behaviour at runtime and prevents collusion attacks. Our proposed model employs a novel approach that has the advantage of predicting the future trustworthiness of nodes, based on historical and online behaviour of nodes. This is achieved by an architecture that applies the paradigm of Dynamic Data Driven Application Systems, in solving the problem of collusion attacks in mobile networks.
Task-Based Cohesive Evolution of Dynamic Brain Networks
NASA Astrophysics Data System (ADS)
Davison, Elizabeth
2014-03-01
Applications of graph theory to neuroscience have resulted in significant progress towards a mechanistic understanding of the brain. Functional network representation of the brain has linked efficient network structure to psychometric intelligence and altered configurations with disease. Dynamic graphs provide us with tools to further study integral properties of the brain; specifically, the mathematical convention of hyperedges has allowed us to study the brain's cross-linked structure. Hyperedges capture the changes in network structure by identifying groups of brain regions with correlation patterns that change cohesively through time. We performed a hyperedge analysis on functional MRI data from 86 subjects and explored the cohesive evolution properties of their functional brain networks as they performed a series of tasks. Our results establish the hypergraph as a useful measure in understanding functional brain dynamics over tasks and reveal characteristic differences in the co-evolution structure of task-specific networks.
Slow dynamics in features of synchronized neural network responses
Haroush, Netta; Marom, Shimon
2015-01-01
In this report trial-to-trial variations in the synchronized responses of neural networks are explored over time scales of minutes, in ex-vivo large scale cortical networks. We show that sub-second measures of the individual synchronous response, namely—its latency and decay duration, are related to minutes-scale network response dynamics. Network responsiveness is reflected as residency in, or shifting amongst, areas of the latency-decay plane. The different sensitivities of latency and decay durations to synaptic blockers imply that these two measures reflect aspects of inhibitory and excitatory activities. Taken together, the data suggest that trial-to-trial variations in the synchronized responses of neural networks might be related to effective excitation-inhibition ratio being a dynamic variable over time scales of minutes. PMID:25926787
Identifying and tracking dynamic processes in social networks
NASA Astrophysics Data System (ADS)
Chung, Wayne; Savell, Robert; Schütt, Jan-Peter; Cybenko, George
2006-05-01
The detection and tracking of embedded malicious subnets in an active social network can be computationally daunting due to the quantity of transactional data generated in the natural interaction of large numbers of actors comprising a network. In addition, detection of illicit behavior may be further complicated by evasive strategies designed to camouflage the activities of the covert subnet. In this work, we move beyond traditional static methods of social network analysis to develop a set of dynamic process models which encode various modes of behavior in active social networks. These models will serve as the basis for a new application of the Process Query System (PQS) to the identification and tracking of covert dynamic processes in social networks. We present a preliminary result from application of our technique in a real-world data stream-- the Enron email corpus.
Pattern Analysis in Social Networks with Dynamic Connections
NASA Astrophysics Data System (ADS)
Wu, Yu; Zhang, Yu
In this paper, we explore how decentralized local interactions of autonomous agents in a network relate to collective behaviors. Most existing work in this area models social network in which agent relations are fixed; instead, we focus on dynamic social networks where agents can rationally adjust their neighborhoods based on their individual interests. We propose a new connection evaluation rule called the Highest Weighted Reward (HWR) rule, with which agents dynamically choose their neighbors in order to maximize their own utilities based on the rewards from previous interactions. Our experiments show that in the 2-action pure coordination game, our system will stabilize to a clustering state where all relationships in the network are rewarded with the optimal payoff. Our experiments also reveal additional interesting patterns in the network.
Latino social network dynamics and the Hurricane Katrina disaster.
Hilfinger Messias, DeAnne K; Barrington, Clare; Lacy, Elaine
2012-01-01
The aim of this qualitative research was to examine the dynamics of existing and emerging social networks among Latino survivors of Hurricane Katrina. Data were generated through individual, in-depth interviews conducted with 65 Latinos within six months of the storm striking the Gulf Coast of the United States in August 2005. The findings illustrated both the role of social networks in gathering information, making decisions and accessing resources, and how these existing social networks were disrupted and strained by overwhelming needs. Broader structural issues, including poverty and a lack of transportation, combined with marginalised status as immigrants, further constrained access to essential information and resources. In response, new, if temporary, social networks emerged, based primarily on shared nationality, language, and a sense of collective commitment. Practice implications include the need to consider the social network dynamics of marginalised groups in developing innovative strategies to overcome structural barriers to accessing resources essential for disaster preparedness and survival. PMID:21623889
Toward a systems-level view of dynamic phosphorylation networks
Newman, Robert H.; Zhang, Jin; Zhu, Heng
2014-01-01
To better understand how cells sense and respond to their environment, it is important to understand the organization and regulation of the phosphorylation networks that underlie most cellular signal transduction pathways. These networks, which are composed of protein kinases, protein phosphatases and their respective cellular targets, are highly dynamic. Importantly, to achieve signaling specificity, phosphorylation networks must be regulated at several levels, including at the level of protein expression, substrate recognition, and spatiotemporal modulation of enzymatic activity. Here, we briefly summarize some of the traditional methods used to study the phosphorylation status of cellular proteins before focusing our attention on several recent technological advances, such as protein microarrays, quantitative mass spectrometry, and genetically-targetable fluorescent biosensors, that are offering new insights into the organization and regulation of cellular phosphorylation networks. Together, these approaches promise to lead to a systems-level view of dynamic phosphorylation networks. PMID:25177341
Dynamical Monte Carlo methods for plasma-surface reactions
NASA Astrophysics Data System (ADS)
Guerra, Vasco; Marinov, Daniil
2016-08-01
Different dynamical Monte Carlo algorithms to investigate molecule formation on surfaces are developed, evaluated and compared with the deterministic approach based on reaction-rate equations. These include a null event algorithm, the n-fold way/BKL algorithm and an ‘hybrid’ variant of the latter. NO2 formation by NO oxidation on Pyrex and O recombination on silica with the formation of O2 are taken as case studies. The influence of the grid size on the CPU calculation time and the accuracy of the results is analysed. The role of Langmuir–Hinsehlwood recombination involving two physisorbed atoms and the effect of back diffusion and its inclusion in a deterministic formulation are investigated and discussed. It is shown that dynamical Monte Carlo schemes are flexible, simple to implement, describe easily elementary processes that are not straightforward to include in deterministic simulations, can run very efficiently if appropriately chosen and give highly reliable results. Moreover, the present approach provides a relatively simple procedure to describe fully coupled surface and gas phase chemistries.
Selection on Network Dynamics Drives Differential Rates of Protein Domain Evolution
Mannakee, Brian K.; Gutenkunst, Ryan N.
2016-01-01
The long-held principle that functionally important proteins evolve slowly has recently been challenged by studies in mice and yeast showing that the severity of a protein knockout only weakly predicts that protein’s rate of evolution. However, the relevance of these studies to evolutionary changes within proteins is unknown, because amino acid substitutions, unlike knockouts, often only slightly perturb protein activity. To quantify the phenotypic effect of small biochemical perturbations, we developed an approach to use computational systems biology models to measure the influence of individual reaction rate constants on network dynamics. We show that this dynamical influence is predictive of protein domain evolutionary rate within networks in vertebrates and yeast, even after controlling for expression level and breadth, network topology, and knockout effect. Thus, our results not only demonstrate the importance of protein domain function in determining evolutionary rate, but also the power of systems biology modeling to uncover unanticipated evolutionary forces. PMID:27380265
Dynamic Network-Based Epistasis Analysis: Boolean Examples
Azpeitia, Eugenio; Benítez, Mariana; Padilla-Longoria, Pablo; Espinosa-Soto, Carlos; Alvarez-Buylla, Elena R.
2011-01-01
In this article we focus on how the hierarchical and single-path assumptions of epistasis analysis can bias the inference of gene regulatory networks. Here we emphasize the critical importance of dynamic analyses, and specifically illustrate the use of Boolean network models. Epistasis in a broad sense refers to gene interactions, however, as originally proposed by Bateson, epistasis is defined as the blocking of a particular allelic effect due to the effect of another allele at a different locus (herein, classical epistasis). Classical epistasis analysis has proven powerful and useful, allowing researchers to infer and assign directionality to gene interactions. As larger data sets are becoming available, the analysis of classical epistasis is being complemented with computer science tools and system biology approaches. We show that when the hierarchical and single-path assumptions are not met in classical epistasis analysis, the access to relevant information and the correct inference of gene interaction topologies is hindered, and it becomes necessary to consider the temporal dynamics of gene interactions. The use of dynamical networks can overcome these limitations. We particularly focus on the use of Boolean networks that, like classical epistasis analysis, relies on logical formalisms, and hence can complement classical epistasis analysis and relax its assumptions. We develop a couple of theoretical examples and analyze them from a dynamic Boolean network model perspective. Boolean networks could help to guide additional experiments and discern among alternative regulatory schemes that would be impossible or difficult to infer without the elimination of these assumption from the classical epistasis analysis. We also use examples from the literature to show how a Boolean network-based approach has resolved ambiguities and guided epistasis analysis. Our article complements previous accounts, not only by focusing on the implications of the hierarchical and
The relevance of network micro-structure for neural dynamics.
Pernice, Volker; Deger, Moritz; Cardanobile, Stefano; Rotter, Stefan
2013-01-01
The activity of cortical neurons is determined by the input they receive from presynaptic neurons. Many previous studies have investigated how specific aspects of the statistics of the input affect the spike trains of single neurons and neurons in recurrent networks. However, typically very simple random network models are considered in such studies. Here we use a recently developed algorithm to construct networks based on a quasi-fractal probability measure which are much more variable than commonly used network models, and which therefore promise to sample the space of recurrent networks in a more exhaustive fashion than previously possible. We use the generated graphs as the underlying network topology in simulations of networks of integrate-and-fire neurons in an asynchronous and irregular state. Based on an extensive dataset of networks and neuronal simulations we assess statistical relations between features of the network structure and the spiking activity. Our results highlight the strong influence that some details of the network structure have on the activity dynamics of both single neurons and populations, even if some global network parameters are kept fixed. We observe specific and consistent relations between activity characteristics like spike-train irregularity or correlations and network properties, for example the distributions of the numbers of in- and outgoing connections or clustering. Exploiting these relations, we demonstrate that it is possible to estimate structural characteristics of the network from activity data. We also assess higher order correlations of spiking activity in the various networks considered here, and find that their occurrence strongly depends on the network structure. These results provide directions for further theoretical studies on recurrent networks, as well as new ways to interpret spike train recordings from neural circuits. PMID:23761758
NASA Astrophysics Data System (ADS)
Gan, Qintao; Lv, Tianshi; Fu, Zhenhua
2016-04-01
In this paper, the synchronization problem for a class of generalized neural networks with time-varying delays and reaction-diffusion terms is investigated concerning Neumann boundary conditions in terms of p-norm. The proposed generalized neural networks model includes reaction-diffusion local field neural networks and reaction-diffusion static neural networks as its special cases. By establishing a new inequality, some simple and useful conditions are obtained analytically to guarantee the global exponential synchronization of the addressed neural networks under the periodically intermittent control. According to the theoretical results, the influences of diffusion coefficients, diffusion space, and control rate on synchronization are analyzed. Finally, the feasibility and effectiveness of the proposed methods are shown by simulation examples, and by choosing different diffusion coefficients, diffusion spaces, and control rates, different controlled synchronization states can be obtained.
Gan, Qintao; Lv, Tianshi; Fu, Zhenhua
2016-04-01
In this paper, the synchronization problem for a class of generalized neural networks with time-varying delays and reaction-diffusion terms is investigated concerning Neumann boundary conditions in terms of p-norm. The proposed generalized neural networks model includes reaction-diffusion local field neural networks and reaction-diffusion static neural networks as its special cases. By establishing a new inequality, some simple and useful conditions are obtained analytically to guarantee the global exponential synchronization of the addressed neural networks under the periodically intermittent control. According to the theoretical results, the influences of diffusion coefficients, diffusion space, and control rate on synchronization are analyzed. Finally, the feasibility and effectiveness of the proposed methods are shown by simulation examples, and by choosing different diffusion coefficients, diffusion spaces, and control rates, different controlled synchronization states can be obtained. PMID:27131492
Critical dynamics of randomly assembled and diluted threshold networks
NASA Astrophysics Data System (ADS)
Kürten, Karl E.; Clark, John W.
2008-04-01
The dynamical behavior of a class of randomly assembled networks of binary threshold units subject to random deletion of connections is studied based on the annealed approximation suitable in the thermodynamic limit. The dynamical phase diagram is constructed for several forms of the probability density distribution of nonvanishing connection strengths. The family of power-law distribution functions ρ0(x)=(1-α)/(2|x|α) is found to play a special role in expanding the domain of stable, ordered dynamics at the expense of the disordered, “chaotic” phase. Relationships with other recent studies of the dynamics of complex networks allowing for variable in-degree of the units are explored. The relevance of the pruning of network connections to neural modeling and developmental neurobiology is discussed.
Distal gap junctions and active dendrites can tune network dynamics.
Saraga, Fernanda; Ng, Leo; Skinner, Frances K
2006-03-01
Gap junctions allow direct electrical communication between CNS neurons. From theoretical and modeling studies, it is well known that although gap junctions can act to synchronize network output, they can also give rise to many other dynamic patterns including antiphase and other phase-locked states. The particular network pattern that arises depends on cellular, intrinsic properties that affect firing frequencies as well as the strength and location of the gap junctions. Interneurons or GABAergic neurons in hippocampus are diverse in their cellular characteristics and have been shown to have active dendrites. Furthermore, parvalbumin-positive GABAergic neurons, also known as basket cells, can contact one another via gap junctions on their distal dendrites. Using two-cell network models, we explore how distal electrical connections affect network output. We build multi-compartment models of hippocampal basket cells using NEURON and endow them with varying amounts of active dendrites. Two-cell networks of these model cells as well as reduced versions are explored. The relationship between intrinsic frequency and the level of active dendrites allows us to define three regions based on what sort of network dynamics occur with distal gap junction coupling. Weak coupling theory is used to predict the delineation of these regions as well as examination of phase response curves and distal dendritic polarization levels. We find that a nonmonotonic dependence of network dynamic characteristics (phase lags) on gap junction conductance occurs. This suggests that distal electrical coupling and active dendrite levels can control how sensitive network dynamics are to gap junction modulation. With the extended geometry, gap junctions located at more distal locations must have larger conductances for pure synchrony to occur. Furthermore, based on simulations with heterogeneous networks, it may be that one requires active dendrites if phase-locking is to occur in networks formed
Lin, Pan; Yang, Yong; Jovicich, Jorge; De Pisapia, Nicola; Wang, Xiang; Zuo, Chun S; Levitt, James Jonathan
2016-03-01
Characterization of the default mode network (DMN) as a complex network of functionally interacting dynamic systems has received great interest for the study of DMN neural mechanisms. In particular, understanding the relationship of intrinsic resting-state DMN brain network with cognitive behaviors is an important issue in healthy cognition and mental disorders. However, it is still unclear how DMN functional connectivity links to cognitive behaviors during resting-state. In this study, we hypothesize that static and dynamic DMN nodal topology is associated with upcoming cognitive task performance. We used graph theory analysis in order to understand better the relationship between the DMN functional connectivity and cognitive behavior during resting-state and task performance. Nodal degree of the DMN was calculated as a metric of network topology. We found that the static and dynamic posterior cingulate cortex (PCC) nodal degree within the DMN was associated with task performance (Reaction Time). Our results show that the core node PCC nodal degree within the DMN was significantly correlated with reaction time, which suggests that the PCC plays a key role in supporting cognitive function. PMID:25904156
Irrelevant stimulus processing in ADHD: catecholamine dynamics and attentional networks
Aboitiz, Francisco; Ossandón, Tomás; Zamorano, Francisco; Palma, Bárbara; Carrasco, Ximena
2014-01-01
A cardinal symptom of attention deficit and hyperactivity disorder (ADHD) is a general distractibility where children and adults shift their attentional focus to stimuli that are irrelevant to the ongoing behavior. This has been attributed to a deficit in dopaminergic signaling in cortico-striatal networks that regulate goal-directed behavior. Furthermore, recent imaging evidence points to an impairment of large scale, antagonistic brain networks that normally contribute to attentional engagement and disengagement, such as the task-positive networks and the default mode network (DMN). Related networks are the ventral attentional network (VAN) involved in attentional shifting, and the salience network (SN) related to task expectancy. Here we discuss the tonic–phasic dynamics of catecholaminergic signaling in the brain, and attempt to provide a link between this and the activities of the large-scale cortical networks that regulate behavior. More specifically, we propose that a disbalance of tonic catecholamine levels during task performance produces an emphasis of phasic signaling and increased excitability of the VAN, yielding distractibility symptoms. Likewise, immaturity of the SN may relate to abnormal tonic signaling and an incapacity to build up a proper executive system during task performance. We discuss different lines of evidence including pharmacology, brain imaging and electrophysiology, that are consistent with our proposal. Finally, restoring the pharmacodynamics of catecholaminergic signaling seems crucial to alleviate ADHD symptoms; however, the possibility is open to explore cognitive rehabilitation strategies to top-down modulate network dynamics compensating the pharmacological deficits. PMID:24723897
Social Insects: A Model System for Network Dynamics
NASA Astrophysics Data System (ADS)
Charbonneau, Daniel; Blonder, Benjamin; Dornhaus, Anna
Social insect colonies (ants, bees, wasps, and termites) show sophisticated collective problem-solving in the face of variable constraints. Individuals exchange information and materials such as food. The resulting network structure and dynamics can inform us about the mechanisms by which the insects achieve particular collective behaviors and these can be transposed to man-made and social networks. We discuss how network analysis can answer important questions about social insects, such as how effective task allocation or information flow is realized. We put forward the idea that network analysis methods are under-utilized in social insect research, and that they can provide novel ways to view the complexity of collective behavior, particularly if network dynamics are taken into account. To illustrate this, we present an example of network tasks performed by ant workers, linked by instances of workers switching from one task to another. We show how temporal network analysis can propose and test new hypotheses on mechanisms of task allocation, and how adding temporal elements to static networks can drastically change results. We discuss the benefits of using social insects as models for complex systems in general. There are multiple opportunities emergent technologies and analysis methods in facilitating research on social insect network. The potential for interdisciplinary work could significantly advance diverse fields such as behavioral ecology, computer sciences, and engineering.
Modeling Scalable Pattern Generation in DNA Reaction Networks
Allen, Peter B.; Chen, Xi; Simpson, Zack B.; Ellington, Andrew D.
2013-01-01
We have developed a theoretical framework for developing patterns in multiple dimensions using controllable diffusion and designed reactions implemented in DNA. This includes so-called strand displacement reactions in which one single-stranded DNA hybridizes to a hemi-duplex DNA and displaces another single-stranded DNA, reversibly or irreversibly. These reactions can be designed to proceed with designed rate and molecular specificity. By also controlling diffusion by partial complementarity to a stationary, cross-linked DNA, we can generate predictable patterns. We demonstrate this with several simulations showing deterministic, predictable shapes in space. PMID:25506295
Cytoskeleton dynamics: Fluctuations within the network
Bursac, Predrag; Fabry, Ben; Trepat, Xavier; Lenormand, Guillaume; Butler, James P.; Wang, Ning; Fredberg, Jeffrey J.; An, Steven S.; E-mail: san@jhsph.edu
2007-04-06
Out-of-equilibrium systems, such as the dynamics of a living cytoskeleton (CSK), are inherently noisy with fluctuations arising from the stochastic nature of the underlying biochemical and molecular events. Recently, such fluctuations within the cell were characterized by observing spontaneous nano-scale motions of an RGD-coated microbead bound to the cell surface [Bursac et al., Nat. Mater. 4 (2005) 557-561]. While these reported anomalous bead motions represent a molecular level reorganization (remodeling) of microstructures in contact with the bead, a precise nature of these cytoskeletal constituents and forces that drive their remodeling dynamics are largely unclear. Here, we focused upon spontaneous motions of an RGD-coated bead and, in particular, assessed to what extent these motions are attributable to (i) bulk cell movement (cell crawling), (ii) dynamics of focal adhesions, (iii) dynamics of lipid membrane, and/or (iv) dynamics of the underlying actin CSK driven by myosin motors.
Inferring slowly-changing dynamic gene-regulatory networks
2015-01-01
Dynamic gene-regulatory networks are complex since the interaction patterns between their components mean that it is impossible to study parts of the network in separation. This holistic character of gene-regulatory networks poses a real challenge to any type of modelling. Graphical models are a class of models that connect the network with a conditional independence relationships between random variables. By interpreting these random variables as gene activities and the conditional independence relationships as functional non-relatedness, graphical models have been used to describe gene-regulatory networks. Whereas the literature has been focused on static networks, most time-course experiments are designed in order to tease out temporal changes in the underlying network. It is typically reasonable to assume that changes in genomic networks are few, because biological systems tend to be stable. We introduce a new model for estimating slow changes in dynamic gene-regulatory networks, which is suitable for high-dimensional data, e.g. time-course microarray data. Our aim is to estimate a dynamically changing genomic network based on temporal activity measurements of the genes in the network. Our method is based on the penalized likelihood with ℓ1-norm, that penalizes conditional dependencies between genes as well as differences between conditional independence elements across time points. We also present a heuristic search strategy to find optimal tuning parameters. We re-write the penalized maximum likelihood problem into a standard convex optimization problem subject to linear equality constraints. We show that our method performs well in simulation studies. Finally, we apply the proposed model to a time-course T-cell dataset. PMID:25917062
A moment-convergence method for stochastic analysis of biochemical reaction networks
NASA Astrophysics Data System (ADS)
Zhang, Jiajun; Nie, Qing; Zhou, Tianshou
2016-05-01
Traditional moment-closure methods need to assume that high-order cumulants of a probability distribution approximate to zero. However, this strong assumption is not satisfied for many biochemical reaction networks. Here, we introduce convergent moments (defined in mathematics as the coefficients in the Taylor expansion of the probability-generating function at some point) to overcome this drawback of the moment-closure methods. As such, we develop a new analysis method for stochastic chemical kinetics. This method provides an accurate approximation for the master probability equation (MPE). In particular, the connection between low-order convergent moments and rate constants can be more easily derived in terms of explicit and analytical forms, allowing insights that would be difficult to obtain through direct simulation or manipulation of the MPE. In addition, it provides an accurate and efficient way to compute steady-state or transient probability distribution, avoiding the algorithmic difficulty associated with stiffness of the MPE due to large differences in sizes of rate constants. Applications of the method to several systems reveal nontrivial stochastic mechanisms of gene expression dynamics, e.g., intrinsic fluctuations can induce transient bimodality and amplify transient signals, and slow switching between promoter states can increase fluctuations in spatially heterogeneous signals. The overall approach has broad applications in modeling, analysis, and computation of complex biochemical networks with intrinsic noise.
A moment-convergence method for stochastic analysis of biochemical reaction networks.
Zhang, Jiajun; Nie, Qing; Zhou, Tianshou
2016-05-21
Traditional moment-closure methods need to assume that high-order cumulants of a probability distribution approximate to zero. However, this strong assumption is not satisfied for many biochemical reaction networks. Here, we introduce convergent moments (defined in mathematics as the coefficients in the Taylor expansion of the probability-generating function at some point) to overcome this drawback of the moment-closure methods. As such, we develop a new analysis method for stochastic chemical kinetics. This method provides an accurate approximation for the master probability equation (MPE). In particular, the connection between low-order convergent moments and rate constants can be more easily derived in terms of explicit and analytical forms, allowing insights that would be difficult to obtain through direct simulation or manipulation of the MPE. In addition, it provides an accurate and efficient way to compute steady-state or transient probability distribution, avoiding the algorithmic difficulty associated with stiffness of the MPE due to large differences in sizes of rate constants. Applications of the method to several systems reveal nontrivial stochastic mechanisms of gene expression dynamics, e.g., intrinsic fluctuations can induce transient bimodality and amplify transient signals, and slow switching between promoter states can increase fluctuations in spatially heterogeneous signals. The overall approach has broad applications in modeling, analysis, and computation of complex biochemical networks with intrinsic noise. PMID:27208938
A single-ended IP roaming solution for dynamic network reconstruction
NASA Astrophysics Data System (ADS)
White, Joshua S.; Pilbeam, Adam W.; McCoy, Joe R.
2011-06-01
Today's networks must maintain functionality in an ever increasing threat environment. To date, many of the PDR (Protection, Detection, Reaction) mechanisms have focused on technologies to defend systems while maintaining consistent network presence. In this paper we discuss a dynamic network schema wherein system protection is accomplished through a unique implementation of IP roaming. This method is shown to mask a system on a network undergoing various types of attacks while maintaining connectivity with trusted clients. Additionally, this method allows for new clients to associate without heavy authentication or knowledge of the remote systems IP Roaming status. This paper will show the advantages of implementing this unique method of IP roaming with the goal of minimizing system overhead and maximizing sustained connectivity.
Recruitment dynamics in adaptive social networks.
Shkarayev, Maxim S; Schwartz, Ira B; Shaw, Leah B
2013-01-01
We model recruitment in adaptive social networks in the presence of birth and death processes. Recruitment is characterized by nodes changing their status to that of the recruiting class as a result of contact with recruiting nodes. Only a susceptible subset of nodes can be recruited. The recruiting individuals may adapt their connections in order to improve recruitment capabilities, thus changing the network structure adaptively. We derive a mean field theory to predict the dependence of the growth threshold of the recruiting class on the adaptation parameter. Furthermore, we investigate the effect of adaptation on the recruitment level, as well as on network topology. The theoretical predictions are compared with direct simulations of the full system. We identify two parameter regimes with qualitatively different bifurcation diagrams depending on whether nodes become susceptible frequently (multiple times in their lifetime) or rarely (much less than once per lifetime). PMID:25395989
Dynamics of TCP traffic over ATM networks
NASA Astrophysics Data System (ADS)
Romanow, Allyn; Floyd, Sally
1995-05-01
We investigate the performance of TCP connections over ATM networks without ATM-level congestion control and compare it to the performance of TCP over packet-based networks. For simulations of congested networks, the effective throughput of TCP over ATM can be quite low when cells are dropped at the congested ATM switch. The low throughput is due to wasted bandwidth as the congested link transmits cells from 'corrupted' packets, i.e., packets in which at least one cell is dropped by the switch. We investigate two packet-discard strategies that alleviate the effects of fragmentation. Partial packet discard, in which remaining cells are discarded after one cell has been dropped from a packet, somewhat improves throughput. We introduce early packet discard, a strategy in which the switch drops whole packets prior to buffer overflow. This mechanism prevents fragmentation and restores throughput to maximal levels.
Reducing Neuronal Networks to Discrete Dynamics
Terman, David; Ahn, Sungwoo; Wang, Xueying; Just, Winfried
2008-01-01
We consider a general class of purely inhibitory and excitatory-inhibitory neuronal networks, with a general class of network architectures, and characterize the complex firing patterns that emerge. Our strategy for studying these networks is to first reduce them to a discrete model. In the discrete model, each neuron is represented as a finite number of states and there are rules for how a neuron transitions from one state to another. In this paper, we rigorously demonstrate that the continuous neuronal model can be reduced to the discrete model if the intrinsic and synaptic properties of the cells are chosen appropriately. In a companion paper [1], we analyze the discrete model. PMID:18443649
Dynamic Artificial Neural Networks with Affective Systems
Schuman, Catherine D.; Birdwell, J. Douglas
2013-01-01
Artificial neural networks (ANNs) are processors that are trained to perform particular tasks. We couple a computational ANN with a simulated affective system in order to explore the interaction between the two. In particular, we design a simple affective system that adjusts the threshold values in the neurons of our ANN. The aim of this paper is to demonstrate that this simple affective system can control the firing rate of the ensemble of neurons in the ANN, as well as to explore the coupling between the affective system and the processes of long term potentiation (LTP) and long term depression (LTD), and the effect of the parameters of the affective system on its performance. We apply our networks with affective systems to a simple pole balancing example and briefly discuss the effect of affective systems on network performance. PMID:24303015
Effects of substrate network topologies on competition dynamics
NASA Astrophysics Data System (ADS)
Lee, Sang Hoon; Jeong, Hawoong
2006-08-01
We study a competition dynamics, based on the minority game, endowed with various substrate network structures. We observe the effects of the network topologies by investigating the volatility of the system and the structure of follower networks. The topology of substrate structures significantly influences the system efficiency represented by the volatility and such substrate networks are shown to amplify the herding effect and cause inefficiency in most cases. The follower networks emerging from the leadership structure show a power-law incoming degree distribution. This study shows the emergence of scale-free structures of leadership in the minority game and the effects of the interaction among players on the networked version of the game.
ERIC Educational Resources Information Center
Turock, Betty J.; Turock, David L.
1987-01-01
A Public Library Association (PLA) survey compiled information on public libraries in bibliographic networks. Aspects identified and measured were perceptions of participation, reasons for non-participation, reactions to services, and suggestions for increasing participation. Recommendations are made for actions by PLA and the networks to ensure…
Dynamic hydro-climatic networks in pristine and regulated rivers
NASA Astrophysics Data System (ADS)
Botter, G.; Basso, S.; Lazzaro, G.; Doulatyari, B.; Biswal, B.; Schirmer, M.; Rinaldo, A.
2014-12-01
Flow patterns observed at-a-station are the dynamical byproduct of a cascade of processes involving different compartments of the hydro-climatic network (e.g., climate, rainfall, soil, vegetation) that regulates the transformation of rainfall into streamflows. In complex branching rivers, flow regimes result from the heterogeneous arrangement around the stream network of multiple hydrologic cascades that simultaneously occur within distinct contributing areas. As such, flow regimes are seen as the integrated output of a complex "network of networks", which can be properly characterized by its degree of temporal variability and spatial heterogeneity. Hydrologic networks that generate river flow regimes are dynamic in nature. In pristine rivers, the time-variance naturally emerges at multiple timescales from climate variability (namely, seasonality and inter-annual fluctuations), implying that the magnitude (and the features) of the water flow between two nodes may be highly variable across different seasons and years. Conversely, the spatial distribution of river flow regimes within pristine rivers involves scale-dependent transport features, as well as regional climatic and soil use gradients, which in small and meso-scale catchments (A < 103 km2) are usually mild enough to guarantee quite uniform flow regimes and high spatial correlations. Human-impacted rivers, instead, constitute hybrid networks where observed spatio-temporal patterns are dominated by anthropogenic shifts, such as landscape alterations and river regulation. In regulated rivers, the magnitude and the features of water flows from node to node may change significantly through time due to damming and withdrawals. However, regulation may impact river regimes in a spatially heterogeneous manner (e.g. in localized river reaches), with a significant decrease of spatial correlations and network connectivity. Provided that the spatial and temporal dynamics of flow regimes in complex rivers may strongly
Detecting complex network modularity by dynamical clustering
NASA Astrophysics Data System (ADS)
Boccaletti, S.; Ivanchenko, M.; Latora, V.; Pluchino, A.; Rapisarda, A.
2007-04-01
Based on cluster desynchronization properties of phase oscillators, we introduce an efficient method for the detection and identification of modules in complex networks. The performance of the algorithm is tested on computer generated and real-world networks whose modular structure is already known or has been studied by means of other methods. The algorithm attains a high level of precision, especially when the modular units are very mixed and hardly detectable by the other methods, with a computational effort O(KN) on a generic graph with N nodes and K links.
Dynamic functional tuning of nonlinear cortical networks
NASA Astrophysics Data System (ADS)
Stetter, Martin
2006-03-01
The mammalian neocortex is a highly complex and nonlinear dynamic system. One of its most prominent features is an omnipresent spontaneous neuronal activity. Here the possible functional role of this global background for cognitive flexibility is studied in a prototypic mean-field model area. It is demonstrated that the level of global background current efficiently controls the stimulus-response threshold and the stability and properties of short-term memory states. Moreover, it can dynamically gate arbitrary cortical subnetworks, when applied to parts of the area as a weak bias signal. These results suggest a central functional role of the level of background activation: the dynamic functional tuning of neocortical circuits.
Infinite dimensional variational inequalities and dynamic network disequilibrium modeling
Friesz, T.; Bernstein, D.
1994-12-31
In this paper we explain the importance of modeling disequilibrium flow patterns occurring on networks, with special emphasis on automobile networks and the role of information technology. We show how elementary notions of disequilibrium, whether abstract, physical or economic in nature, give rise to an adjustment process expressible as a dynamical system. We comment that when such a system is autonomous its steady states can be given the traditional finite dimensional variational inequality/fixed point representations common to static network equilibria. Beyond this, and unique to our work, we show that if the disequilibrium dynamical system is nonautonomous it may tend toward moving or dynamic (instead of static) network equilibria expressible as infinite dimensional variational inequalities. Using concepts of fast and slow dynamic systems, we show how day-to-day and within-day aspects of automobile travel decision making can be combined to yield a nonautonomous dynamical system with the mathematical properties reviewed previously. We introduce axioms for a proper predictive model of urban network flows which integrates both day-to-day and within-day considerations and postulate one such model for further study.
Self-organized network evolution coupled to extremal dynamics
NASA Astrophysics Data System (ADS)
Garlaschelli, Diego; Capocci, Andrea; Caldarelli, Guido
2007-11-01
The interplay between topology and dynamics in complex networks is a fundamental but widely unexplored problem. Here, we study this phenomenon on a prototype model in which the network is shaped by a dynamical variable. We couple the dynamics of the Bak-Sneppen evolution model with the rules of the so-called fitness network model for establishing the topology of a network; each vertex is assigned a `fitness', and the vertex with minimum fitness and its neighbours are updated in each iteration. At the same time, the links between the updated vertices and all other vertices are drawn anew with a fitness-dependent connection probability. We show analytically and numerically that the system self-organizes to a non-trivial state that differs from what is obtained when the two processes are decoupled. A power-law decay of dynamical and topological quantities above a threshold emerges spontaneously, as well as a feedback between different dynamical regimes and the underlying correlation and percolation properties of the network.
Cell fate reprogramming by control of intracellular network dynamics
NASA Astrophysics Data System (ADS)
Zanudo, Jorge G. T.; Albert, Reka
Identifying control strategies for biological networks is paramount for practical applications that involve reprogramming a cell's fate, such as disease therapeutics and stem cell reprogramming. Although the topic of controlling the dynamics of a system has a long history in control theory, most of this work is not directly applicable to intracellular networks. Here we present a network control method that integrates the structural and functional information available for intracellular networks to predict control targets. Formulated in a logical dynamic scheme, our control method takes advantage of certain function-dependent network components and their relation to steady states in order to identify control targets, which are guaranteed to drive any initial state to the target state with 100% effectiveness and need to be applied only transiently for the system to reach and stay in the desired state. We illustrate our method's potential to find intervention targets for cancer treatment and cell differentiation by applying it to a leukemia signaling network and to the network controlling the differentiation of T cells. We find that the predicted control targets are effective in a broad dynamic framework. Moreover, several of the predicted interventions are supported by experiments. This work was supported by NSF Grant PHY 1205840.
Agreement dynamics of finite-memory language games on networks
NASA Astrophysics Data System (ADS)
Wang, W. X.; Lin, B. Y.; Tang, C. L.; Chen, G. R.
2007-12-01
We propose a Finite-Memory Naming Game (FMNG) model with respect to the bounded rationality of agents or finite resources for information storage in communication systems. We study its dynamics on several kinds of complex networks, including random networks, small-world networks and scale-free networks. We focus on the dynamics of the FMNG affected by the memory restriction as well as the topological properties of the networks. Interestingly, we found that the most important quantity, the convergence time of reaching the consensus, shows some non-monotonic behaviors by varying the average degrees of the networks with the existence of the fastest convergence at some specific average degrees. We also investigate other main quantities, such as the success rate in negotiation, the total number of words in the system and the correlations between agents of full memory and the total number of words, which clearly explain the nontrivial behaviors of the convergence. We provide some analytical results which help better understand the dynamics of the FMNG. We finally report a robust scaling property of the convergence time, which is regardless of the network structure and the memory restriction.
Statistical dynamics of early river networks
NASA Astrophysics Data System (ADS)
Wang, Xu-Ming; Wang, Peng; Zhang, Ping; Hao, Rui; Huo, Jie
2012-10-01
Based on local erosion rule and fluctuations in rainfall, geology and parameters of a river channel, a generalized Langevin equation is proposed to describe the random prolongation of a river channel. This equation is transformed into the Fokker-Plank equation to follow the early evolution of a river network and the variation of probability distribution of channel lengths. The general solution of the equation is in the product form of two terms. One term is in power form and the other is in exponent form. This distribution shows a complete history of a river network evolving from its infancy to “adulthood”). The infancy is characterized by the Gaussian distribution of the channel lengths, while the adulthood is marked by a power law distribution of the channel lengths. The variation of the distribution from the Gaussian to the power law displays a gradual developing progress of the river network. The distribution of basin areas is obtained by means of Hack's law. These provide us with new understandings towards river networks.
Dynamic Optical Networks for Future Internet Environments
NASA Astrophysics Data System (ADS)
Matera, Francesco
2014-05-01
This article reports an overview on the evolution of the optical network scenario taking into account the exponential growth of connected devices, big data, and cloud computing that is driving a concrete transformation impacting the information and communication technology world. This hyper-connected scenario is deeply affecting relationships between individuals, enterprises, citizens, and public administrations, fostering innovative use cases in practically any environment and market, and introducing new opportunities and new challenges. The successful realization of this hyper-connected scenario depends on different elements of the ecosystem. In particular, it builds on connectivity and functionalities allowed by converged next-generation networks and their capacity to support and integrate with the Internet of Things, machine-to-machine, and cloud computing. This article aims at providing some hints of this scenario to contribute to analyze impacts on optical system and network issues and requirements. In particular, the role of the software-defined network is investigated by taking into account all scenarios regarding data centers, cloud computing, and machine-to-machine and trying to illustrate all the advantages that could be introduced by advanced optical communications.
Social Dynamics within Electronic Networks of Practice
ERIC Educational Resources Information Center
Mattson, Thomas A., Jr.
2013-01-01
Electronic networks of practice (eNoP) are special types of electronic social structures focused on discussing domain-specific problems related to a skill-based craft or profession in question and answer style forums. eNoP have implemented peer-to-peer feedback systems in order to motivate future contributions and to distinguish contribution…
Genomic analysis of regulatory network dynamics reveals large topological changes
NASA Astrophysics Data System (ADS)
Luscombe, Nicholas M.; Madan Babu, M.; Yu, Haiyuan; Snyder, Michael; Teichmann, Sarah A.; Gerstein, Mark
2004-09-01
Network analysis has been applied widely, providing a unifying language to describe disparate systems ranging from social interactions to power grids. It has recently been used in molecular biology, but so far the resulting networks have only been analysed statically. Here we present the dynamics of a biological network on a genomic scale, by integrating transcriptional regulatory information and gene-expression data for multiple conditions in Saccharomyces cerevisiae. We develop an approach for the statistical analysis of network dynamics, called SANDY, combining well-known global topological measures, local motifs and newly derived statistics. We uncover large changes in underlying network architecture that are unexpected given current viewpoints and random simulations. In response to diverse stimuli, transcription factors alter their interactions to varying degrees, thereby rewiring the network. A few transcription factors serve as permanent hubs, but most act transiently only during certain conditions. By studying sub-network structures, we show that environmental responses facilitate fast signal propagation (for example, with short regulatory cascades), whereas the cell cycle and sporulation direct temporal progression through multiple stages (for example, with highly inter-connected transcription factors). Indeed, to drive the latter processes forward, phase-specific transcription factors inter-regulate serially, and ubiquitously active transcription factors layer above them in a two-tiered hierarchy. We anticipate that many of the concepts presented here-particularly the large-scale topological changes and hub transience-will apply to other biological networks, including complex sub-systems in higher eukaryotes.
A mathematical programming approach for sequential clustering of dynamic networks
NASA Astrophysics Data System (ADS)
Silva, Jonathan C.; Bennett, Laura; Papageorgiou, Lazaros G.; Tsoka, Sophia
2016-02-01
A common analysis performed on dynamic networks is community structure detection, a challenging problem that aims to track the temporal evolution of network modules. An emerging area in this field is evolutionary clustering, where the community structure of a network snapshot is identified by taking into account both its current state as well as previous time points. Based on this concept, we have developed a mixed integer non-linear programming (MINLP) model, SeqMod, that sequentially clusters each snapshot of a dynamic network. The modularity metric is used to determine the quality of community structure of the current snapshot and the historical cost is accounted for by optimising the number of node pairs co-clustered at the previous time point that remain so in the current snapshot partition. Our method is tested on social networks of interactions among high school students, college students and members of the Brazilian Congress. We show that, for an adequate parameter setting, our algorithm detects the classes that these students belong more accurately than partitioning each time step individually or by partitioning the aggregated snapshots. Our method also detects drastic discontinuities in interaction patterns across network snapshots. Finally, we present comparative results with similar community detection methods for time-dependent networks from the literature. Overall, we illustrate the applicability of mathematical programming as a flexible, adaptable and systematic approach for these community detection problems. Contribution to the Topical Issue "Temporal Network Theory and Applications", edited by Petter Holme.
LOGISTIC NETWORK REGRESSION FOR SCALABLE ANALYSIS OF NETWORKS WITH JOINT EDGE/VERTEX DYNAMICS
Almquist, Zack W.; Butts, Carter T.
2015-01-01
Change in group size and composition has long been an important area of research in the social sciences. Similarly, interest in interaction dynamics has a long history in sociology and social psychology. However, the effects of endogenous group change on interaction dynamics are a surprisingly understudied area. One way to explore these relationships is through social network models. Network dynamics may be viewed as a process of change in the edge structure of a network, in the vertex set on which edges are defined, or in both simultaneously. Although early studies of such processes were primarily descriptive, recent work on this topic has increasingly turned to formal statistical models. Although showing great promise, many of these modern dynamic models are computationally intensive and scale very poorly in the size of the network under study and/or the number of time points considered. Likewise, currently used models focus on edge dynamics, with little support for endogenously changing vertex sets. Here, the authors show how an existing approach based on logistic network regression can be extended to serve as a highly scalable framework for modeling large networks with dynamic vertex sets. The authors place this approach within a general dynamic exponential family (exponential-family random graph modeling) context, clarifying the assumptions underlying the framework (and providing a clear path for extensions), and they show how model assessment methods for cross-sectional networks can be extended to the dynamic case. Finally, the authors illustrate this approach on a classic data set involving interactions among windsurfers on a California beach. PMID:26120218
A biologically inspired neural network for dynamic programming.
Francelin Romero, R A; Kacpryzk, J; Gomide, F
2001-12-01
An artificial neural network with a two-layer feedback topology and generalized recurrent neurons, for solving nonlinear discrete dynamic optimization problems, is developed. A direct method to assign the weights of neural networks is presented. The method is based on Bellmann's Optimality Principle and on the interchange of information which occurs during the synaptic chemical processing among neurons. The neural network based algorithm is an advantageous approach for dynamic programming due to the inherent parallelism of the neural networks; further it reduces the severity of computational problems that can occur in methods like conventional methods. Some illustrative application examples are presented to show how this approach works out including the shortest path and fuzzy decision making problems. PMID:11852439
Triadic closure dynamics drives scaling laws in social multiplex networks
NASA Astrophysics Data System (ADS)
Klimek, Peter; Thurner, Stefan
2013-06-01
Social networks exhibit scaling laws for several structural characteristics, such as degree distribution, scaling of the attachment kernel and clustering coefficients as a function of node degree. A detailed understanding if and how these scaling laws are inter-related is missing so far, let alone whether they can be understood through a common, dynamical principle. We propose a simple model for stationary network formation and show that the three mentioned scaling relations follow as natural consequences of triadic closure. The validity of the model is tested on multiplex data from a well-studied massive multiplayer online game. We find that the three scaling exponents observed in the multiplex data for the friendship, communication and trading networks can simultaneously be explained by the model. These results suggest that triadic closure could be identified as one of the fundamental dynamical principles in social multiplex network formation.
Zhang, Fan; Chen, Nanhao; Wu, Ruibo
2016-05-23
The Mg-dependent 5-epi-aristolochene synthase from Nicotiana tabacum (called TEAS) could catalyze the linear farnesyl pyrophosphate (FPP) substrate to form bicyclic hydrocarbon 5-epi-aristolochene. The cyclization reaction mechanism of TEAS was proposed based on static crystal structures and quantum chemistry calculations in a few previous studies, but substrate FPP binding kinetics and protein conformational dynamics responsible for the enzymatic catalysis are still unclear. Herein, by elaborative and extensive molecular dynamics simulations, the loop conformation change and several crucial residues promoting the cyclization reaction in TEAS are elucidated. It is found that the unusual noncatalytic NH2-terminal domain is essential to stabilize Helix-K and the adjoining J-K loop of the catalytic COOH-terminal domain. It is also illuminated that the induce-fit J-K/A-C loop dynamics is triggered by Y527 and the optimum substrate binding mode in a "U-shape" conformation. The U-shaped ligand binding pose is maintained well with the cooperative interaction of the three Mg(2+)-containing coordination shell and conserved residue W273. Furthermore, the conserved Arg residue pair R264/R266 and aromatic residue pair Y527/W273, whose spatial orientations are also crucial to promote the closure of the active site to a hydrophobic pocket, as well as to form π-stacking interactions with the ligand, would facilitate the carbocation migration and electrophilic attack involving the catalytic reaction. Our investigation more convincingly proves the greater roles of the protein local conformational dynamics than do hints from the static crystal structure observations. Thus, these findings can act as a guide to new protein engineering strategies on diversifying the sesquiterpene products for drug discovery. PMID:27082764
Modeling Human Dynamics of Face-to-Face Interaction Networks
NASA Astrophysics Data System (ADS)
Starnini, Michele; Baronchelli, Andrea; Pastor-Satorras, Romualdo
2013-04-01
Face-to-face interaction networks describe social interactions in human gatherings, and are the substrate for processes such as epidemic spreading and gossip propagation. The bursty nature of human behavior characterizes many aspects of empirical data, such as the distribution of conversation lengths, of conversations per person, or of interconversation times. Despite several recent attempts, a general theoretical understanding of the global picture emerging from data is still lacking. Here we present a simple model that reproduces quantitatively most of the relevant features of empirical face-to-face interaction networks. The model describes agents that perform a random walk in a two-dimensional space and are characterized by an attractiveness whose effect is to slow down the motion of people around them. The proposed framework sheds light on the dynamics of human interactions and can improve the modeling of dynamical processes taking place on the ensuing dynamical social networks.
Turing-Hopf instability in biochemical reaction networks arising from pairs of subnetworks.
Mincheva, Maya; Roussel, Marc R
2012-11-01
Network conditions for Turing instability in biochemical systems with two biochemical species are well known and involve autocatalysis or self-activation. On the other hand general network conditions for potential Turing instabilities in large biochemical reaction networks are not well developed. A biochemical reaction network with any number of species where only one species moves is represented by a simple digraph and is modeled by a reaction-diffusion system with non-mass action kinetics. A graph-theoretic condition for potential Turing-Hopf instability that arises when a spatially homogeneous equilibrium loses its stability via a single pair of complex eigenvalues is obtained. This novel graph-theoretic condition is closely related to the negative cycle condition for oscillations in ordinary differential equation models and its generalizations, and requires the existence of a pair of subnetworks, each containing an even number of positive cycles. The technique is illustrated with a double-cycle Goodwin type model. PMID:22698892
Ab initio dynamics of the cytochrome P450 hydroxylation reaction
Elenewski, Justin E.; Hackett, John C
2015-01-01
The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis. PMID:25681906
Ab initio dynamics of the cytochrome P450 hydroxylation reaction
NASA Astrophysics Data System (ADS)
Elenewski, Justin E.; Hackett, John C.
2015-02-01
The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis.
Ab initio dynamics of the cytochrome P450 hydroxylation reaction
Elenewski, Justin E.; Hackett, John C
2015-02-14
The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis.
Reaction Diffusion Modeling of Calcium Dynamics with Realistic ER Geometry
Means, Shawn; Smith, Alexander J.; Shepherd, Jason; Shadid, John; Fowler, John; Wojcikiewicz, Richard J. H.; Mazel, Tomas; Smith, Gregory D.; Wilson, Bridget S.
2006-01-01
We describe a finite-element model of mast cell calcium dynamics that incorporates the endoplasmic reticulum's complex geometry. The model is built upon a three-dimensional reconstruction of the endoplasmic reticulum (ER) from an electron tomographic tilt series. Tetrahedral meshes provide volumetric representations of the ER lumen, ER membrane, cytoplasm, and plasma membrane. The reaction-diffusion model simultaneously tracks changes in cytoplasmic and ER intraluminal calcium concentrations and includes luminal and cytoplasmic protein buffers. Transport fluxes via PMCA, SERCA, ER leakage, and Type II IP3 receptors are also represented. Unique features of the model include stochastic behavior of IP3 receptor calcium channels and comparisons of channel open times when diffusely distributed or aggregated in clusters on the ER surface. Simulations show that IP3R channels in close proximity modulate activity of their neighbors through local Ca2+ feedback effects. Cytoplasmic calcium levels rise higher, and ER luminal calcium concentrations drop lower, after IP3-mediated release from receptors in the diffuse configuration. Simulation results also suggest that the buffering capacity of the ER, and not restricted diffusion, is the predominant factor influencing average luminal calcium concentrations. PMID:16617072
Toward modeling a dynamic biological neural network.
Ross, M D; Dayhoff, J E; Mugler, D H
1990-01-01
Mammalian macular endorgans are linear bioaccelerometers located in the vestibular membranous labyrinth of the inner ear. In this paper, the organization of the endorgan is interpreted on physical and engineering principles. This is a necessary prerequisite to mathematical and symbolic modeling of information processing by the macular neural network. Mathematical notations that describe the functioning system were used to produce a novel, symbolic model. The model is six-tiered and is constructed to mimic the neural system. Initial simulations show that the network functions best when some of the detecting elements (type I hair cells) are excitatory and others (type II hair cells) are weakly inhibitory. The simulations also illustrate the importance of disinhibition of receptors located in the third tier in shaping nerve discharge patterns at the sixth tier in the model system. PMID:11538873
A self-organized model for network evolution. Coupling network evolution and extremal dynamics
NASA Astrophysics Data System (ADS)
Caldarelli, G.; Capocci, A.; Garlaschelli, D.
2008-08-01
Here we provide a detailed analysis, along with some extensions and additonal investigations, of a recently proposed [1] self-organized model for the evolution of complex networks. Vertices of the network are characterized by a fitness variable evolving through an extremal dynamics process, as in the Bak-Sneppen [2] model representing a prototype of Self-Organized Criticality. The network topology is in turn shaped by the fitness variable itself, as in the fitness network model [3]. The system self-organizes to a nontrivial state, characterized by a power-law decay of dynamical and topological quantities above a critical threshold. The interplay between topology and dynamics in the system is the key ingredient leading to an unexpected behaviour of these quantities.
Neural network with dynamically adaptable neurons
NASA Technical Reports Server (NTRS)
Tawel, Raoul (Inventor)
1994-01-01
This invention is an adaptive neuron for use in neural network processors. The adaptive neuron participates in the supervised learning phase of operation on a co-equal basis with the synapse matrix elements by adaptively changing its gain in a similar manner to the change of weights in the synapse IO elements. In this manner, training time is decreased by as much as three orders of magnitude.
Min, Wei; Xie, X Sunney; Bagchi, Biman
2008-01-17
We introduce a two-dimensional (2D) multisurface reaction free energy description of the catalytic cycle that explicitly connects the recently observed multi-time-scale conformational dynamics as well as dispersed enzymatic kinetics to the classical Michaelis-Menten equation. A slow conformational motion on a collective enzyme coordinate Q facilitates the catalytic reaction along the intrinsic reaction coordinate X, providing a dynamic realization of Pauling's well-known idea of transition-state stabilization. The catalytic cycle is modeled as transitions between multiple displaced harmonic wells in the XQ space representing different states of the cycle, which is constructed according to the free energy driving force of the cycle. Subsequent to substrate association with the enzyme, the enzyme-substrate complex under strain exhibits a nonequilibrium relaxation toward a new conformation that lowers the activation energy of the reaction, as first proposed by Haldane. The chemical reaction in X is thus enslaved to the down hill slow motion on the Q surface. One consequence of the present theory is that, in spite of the existence of dispersive kinetics, the Michaelis-Menten expression of the catalysis rate remains valid under certain conditions, as observed in recent single-molecule experiments. This dynamic theory builds the relationship between the protein conformational dynamics and the enzymatic reaction kinetics and offers a unified description of enzyme fluctuation-assisted catalysis. PMID:18085768
Dynamics of the mitochondrial network during mitosis.
Kanfer, Gil; Kornmann, Benoît
2016-04-15
During mitosis, cells undergo massive deformation and reorganization, impacting on all cellular structures. Mitochondria, in particular, are highly dynamic organelles, which constantly undergo events of fission, fusion and cytoskeleton-based transport. This plasticity ensures the proper distribution of the metabolism, and the proper inheritance of functional organelles. During cell cycle, mitochondria undergo dramatic changes in distribution. In this review, we focus on the dynamic events that target mitochondria during mitosis. We describe how the cell-cycle-dependent microtubule-associated protein centromeric protein F (Cenp-F) is recruited to mitochondria by the mitochondrial Rho GTPase (Miro) to promote mitochondrial transport and re-distribution following cell division. PMID:27068963
Replicator dynamics with diffusion on multiplex networks
NASA Astrophysics Data System (ADS)
Requejo, R. J.; Díaz-Guilera, A.
2016-08-01
In this study we present an extension of the dynamics of diffusion in multiplex graphs, which makes the equations compatible with the replicator equation with mutations. We derive an exact formula for the diffusion term, which shows that, while diffusion is linear for numbers of agents, it is necessary to account for nonlinear terms when working with fractions of individuals. We also derive the transition probabilities that give rise to such macroscopic behavior, completing the bottom-up description. Finally, it is shown that the usual assumption of constant population sizes induces a hidden selective pressure due to the diffusive dynamics, which favors the increase of fast diffusing strategies.
How memory generates heterogeneous dynamics in temporal networks.
Vestergaard, Christian L; Génois, Mathieu; Barrat, Alain
2014-10-01
Empirical temporal networks display strong heterogeneities in their dynamics, which profoundly affect processes taking place on these networks, such as rumor and epidemic spreading. Despite the recent wealth of data on temporal networks, little work has been devoted to the understanding of how such heterogeneities can emerge from microscopic mechanisms at the level of nodes and links. Here we show that long-term memory effects are present in the creation and disappearance of links in empirical networks. We thus consider a simple generative modeling framework for temporal networks able to incorporate these memory mechanisms. This allows us to study separately the role of each of these mechanisms in the emergence of heterogeneous network dynamics. In particular, we show analytically and numerically how heterogeneous distributions of contact durations, of intercontact durations, and of numbers of contacts per link emerge. We also study the individual effect of heterogeneities on dynamical processes, such as the paradigmatic susceptible-infected epidemic spreading model. Our results confirm in particular the crucial role of the distributions of intercontact durations and of the numbers of contacts per link. PMID:25375547
Applications of flow-networks to opinion-dynamics
NASA Astrophysics Data System (ADS)
Tupikina, Liubov; Kurths, Jürgen
2015-04-01
Networks were successfully applied to describe complex systems, such as brain, climate, processes in society. Recently a socio-physical problem of opinion-dynamics was studied using network techniques. We present the toy-model of opinion-formation based on the physical model of advection-diffusion. We consider spreading of the opinion on the fixed subject, assuming that opinion on society is binary: if person has opinion then the state of the node in the society-network equals 1, if the person doesn't have opinion state of the node equals 0. Opinion can be spread from one person to another if they know each other, or in the network-terminology, if the nodes are connected. We include into the system governed by advection-diffusion equation the external field to model such effects as for instance influence from media. The assumptions for our model can be formulated as the following: 1.the node-states are influenced by the network structure in such a way, that opinion can be spread only between adjacent nodes (the advective term of the opinion-dynamics), 2.the network evolution can have two scenarios: -network topology is not changing with time; -additional links can appear or disappear each time-step with fixed probability which requires adaptive networks properties. Considering these assumptions for our system we obtain the system of equations describing our model-dynamics which corresponds well to other socio-physics models, for instance, the model of the social cohesion and the famous voter-model. We investigate the behavior of the suggested model studying "waiting time" of the system, time to get to the stable state, stability of the model regimes for different values of model parameters and network topology.
Noninvasive brain stimulation: from physiology to network dynamics and back
Dayan, Eran; Censor, Nitzan; Buch, Ethan R; Sandrini, Marco; Cohen, Leonardo G
2016-01-01
Noninvasive brain stimulation techniques have been widely used for studying the physiology of the CNS, identifying the functional role of specific brain structures and, more recently, exploring large-scale network dynamics. Here we review key findings that contribute to our understanding of the mechanisms underlying the physiological and behavioral effects of these techniques. We highlight recent innovations using noninvasive stimulation to investigate global brain network dynamics and organization. New combinations of these techniques, in conjunction with neuroimaging, will further advance the utility of their application. PMID:23799477
A dynamical network model for frailty-induced mortality
NASA Astrophysics Data System (ADS)
Taneja, Swadhin; Rutenberg, Andrew; Mitnitski, Arnold; Rockwood, Kenneth
2014-03-01
Age-related clinical and biological deficits can be used to build a frailty index that is a simple fraction of observed to possible deficits. As a proxy measure of aging, such a frailty index is empirically a better predictor of human mortality than chronological age. We present a network dynamical model of deficits that allows us to naturally consider causal interactions between deficits, deficit formation and repair, and mortality. We investigate the information provided by various model frailty indices, how they reflect the underlying dynamics of the network, and how well they predict mortality.
Dynamic model of neural networks with asymmetric diluted couplings
NASA Astrophysics Data System (ADS)
Choi, M. Y.; Choi, Meekyoung
1990-06-01
We study an asymmetric diluted version of the dynamic model for neural networks proposed recently, which explicitly takes into account the existence of several time scales without discretizing the time. The dynamics is neither totally synchronous nor totally asynchronous, and the couplings in the neural networks are asymmetric. These considerations may be regarded as more biologically realistic. We obtain the phase diagram as a function of the temperature ɛ-1, the capacity α, and the ratio a of the refractory period to the action potential duration.
Collective Dynamics for Heterogeneous Networks of Theta Neurons
NASA Astrophysics Data System (ADS)
Luke, Tanushree
Collective behavior in neural networks has often been used as an indicator of communication between different brain areas. These collective synchronization and desynchronization patterns are also considered an important feature in understanding normal and abnormal brain function. To understand the emergence of these collective patterns, I create an analytic model that identifies all such macroscopic steady-states attainable by a network of Type-I neurons. This network, whose basic unit is the model "theta'' neuron, contains a mixture of excitable and spiking neurons coupled via a smooth pulse-like synapse. Applying the Ott-Antonsen reduction method in the thermodynamic limit, I obtain a low-dimensional evolution equation that describes the asymptotic dynamics of the macroscopic mean field of the network. This model can be used as the basis in understanding more complicated neuronal networks when additional dynamical features are included. From this reduced dynamical equation for the mean field, I show that the network exhibits three collective attracting steady-states. The first two are equilibrium states that both reflect partial synchronization in the network, whereas the third is a limit cycle in which the degree of network synchronization oscillates in time. In addition to a comprehensive identification of all possible attracting macro-states, this analytic model permits a complete bifurcation analysis of the collective behavior of the network with respect to three key network features: the degree of excitability of the neurons, the heterogeneity of the population, and the overall coupling strength. The network typically tends towards the two macroscopic equilibrium states when the neuron's intrinsic dynamics and the network interactions reinforce each other. In contrast, the limit cycle state, bifurcations, and multistability tend to occur when there is competition between these network features. I also outline here an extension of the above model where the
Brandt, Josef; Guimard, Nathalie K; Barner-Kowollik, Christopher; Schmidt, Friedrich G; Lederer, Albena
2013-11-01
Polymers capable of dynamic bonding/debonding reactions are of great interest in modern day research. Potential applications can be found in the fields of self-healing materials or printable networks. Since temperature is often used as a stimulus for triggering reversible bonding reactions, an analysis operating at elevated temperatures is very useful for the in situ investigation of the reaction mechanism, as unwanted side effects can be minimized when performing the analyses at the same temperature at which the reactions occur. A temperature-dependent size exclusion chromatographic system (TD SEC) has been optimized for investigating the kinetics of retro Diels-Alder-based depolymerization of Diels-Alder polymers. The changing molecular weight distribution of the analyzed polymers during depolymerization gives valuable quantitative information on the kinetics of the reactions. Adequate data interpretation methods were developed for the correct evaluation of the chromatograms. The results are confirmed by high-temperature dynamic light scattering, thermogravimetric analysis, and time-resolved nuclear magnetic resonance spectroscopy at high temperatures. In addition, the SEC system and column material stability under application conditions were assessed using thermoanalysis methods, infrared spectroscopy, nitrogen physisorption, and scanning electron microscopy. The findings demonstrate that the system is stable and, thus, we can reliably characterize such dynamically bonding/debonding systems with TD SEC. PMID:23877179
Higher-Order Synaptic Interactions Coordinate Dynamics in Recurrent Networks
Chambers, Brendan; MacLean, Jason N.
2016-01-01
Linking synaptic connectivity to dynamics is key to understanding information processing in neocortex. Circuit dynamics emerge from complex interactions of interconnected neurons, necessitating that links between connectivity and dynamics be evaluated at the network level. Here we map propagating activity in large neuronal ensembles from mouse neocortex and compare it to a recurrent network model, where connectivity can be precisely measured and manipulated. We find that a dynamical feature dominates statistical descriptions of propagating activity for both neocortex and the model: convergent clusters comprised of fan-in triangle motifs, where two input neurons are themselves connected. Fan-in triangles coordinate the timing of presynaptic inputs during ongoing activity to effectively generate postsynaptic spiking. As a result, paradoxically, fan-in triangles dominate the statistics of spike propagation even in randomly connected recurrent networks. Interplay between higher-order synaptic connectivity and the integrative properties of neurons constrains the structure of network dynamics and shapes the routing of information in neocortex. PMID:27542093
Control of complex networks requires both structure and dynamics.
Gates, Alexander J; Rocha, Luis M
2016-01-01
The study of network structure has uncovered signatures of the organization of complex systems. However, there is also a need to understand how to control them; for example, identifying strategies to revert a diseased cell to a healthy state, or a mature cell to a pluripotent state. Two recent methodologies suggest that the controllability of complex systems can be predicted solely from the graph of interactions between variables, without considering their dynamics: structural controllability and minimum dominating sets. We demonstrate that such structure-only methods fail to characterize controllability when dynamics are introduced. We study Boolean network ensembles of network motifs as well as three models of biochemical regulation: the segment polarity network in Drosophila melanogaster, the cell cycle of budding yeast Saccharomyces cerevisiae, and the floral organ arrangement in Arabidopsis thaliana. We demonstrate that structure-only methods both undershoot and overshoot the number and which sets of critical variables best control the dynamics of these models, highlighting the importance of the actual system dynamics in determining control. Our analysis further shows that the logic of automata transition functions, namely how canalizing they are, plays an important role in the extent to which structure predicts dynamics. PMID:27087469
Higher-Order Synaptic Interactions Coordinate Dynamics in Recurrent Networks.
Chambers, Brendan; MacLean, Jason N
2016-08-01
Linking synaptic connectivity to dynamics is key to understanding information processing in neocortex. Circuit dynamics emerge from complex interactions of interconnected neurons, necessitating that links between connectivity and dynamics be evaluated at the network level. Here we map propagating activity in large neuronal ensembles from mouse neocortex and compare it to a recurrent network model, where connectivity can be precisely measured and manipulated. We find that a dynamical feature dominates statistical descriptions of propagating activity for both neocortex and the model: convergent clusters comprised of fan-in triangle motifs, where two input neurons are themselves connected. Fan-in triangles coordinate the timing of presynaptic inputs during ongoing activity to effectively generate postsynaptic spiking. As a result, paradoxically, fan-in triangles dominate the statistics of spike propagation even in randomly connected recurrent networks. Interplay between higher-order synaptic connectivity and the integrative properties of neurons constrains the structure of network dynamics and shapes the routing of information in neocortex. PMID:27542093
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. PMID:26211717
Coupled disease-behavior dynamics on complex networks: A review
NASA Astrophysics Data System (ADS)
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.
Control of complex networks requires both structure and dynamics
Gates, Alexander J.; Rocha, Luis M.
2016-01-01
The study of network structure has uncovered signatures of the organization of complex systems. However, there is also a need to understand how to control them; for example, identifying strategies to revert a diseased cell to a healthy state, or a mature cell to a pluripotent state. Two recent methodologies suggest that the controllability of complex systems can be predicted solely from the graph of interactions between variables, without considering their dynamics: structural controllability and minimum dominating sets. We demonstrate that such structure-only methods fail to characterize controllability when dynamics are introduced. We study Boolean network ensembles of network motifs as well as three models of biochemical regulation: the segment polarity network in Drosophila melanogaster, the cell cycle of budding yeast Saccharomyces cerevisiae, and the floral organ arrangement in Arabidopsis thaliana. We demonstrate that structure-only methods both undershoot and overshoot the number and which sets of critical variables best control the dynamics of these models, highlighting the importance of the actual system dynamics in determining control. Our analysis further shows that the logic of automata transition functions, namely how canalizing they are, plays an important role in the extent to which structure predicts dynamics. PMID:27087469
Phase multistability in a dynamical small world network.
Shabunin, A V
2015-01-01
The effect of phase multistability is explored in a small world network of periodic oscillators with diffusive couplings. The structure of the network represents a ring with additional non-local links, which spontaneously arise and vanish between arbitrary nodes. The dynamics of random couplings is modeled by "birth" and "death" stochastic processes by means of the cellular automate approach. The evolution of the network under gradual increasing of the number of random couplings goes through stages of phases fluctuations and spatial cluster formation. Finally, in the presence of non-local couplings the phase multistability "dies" and only the in-phase regime survives. PMID:25637920
Phase multistability in a dynamical small world network
Shabunin, A. V.
2015-01-15
The effect of phase multistability is explored in a small world network of periodic oscillators with diffusive couplings. The structure of the network represents a ring with additional non-local links, which spontaneously arise and vanish between arbitrary nodes. The dynamics of random couplings is modeled by “birth” and “death” stochastic processes by means of the cellular automate approach. The evolution of the network under gradual increasing of the number of random couplings goes through stages of phases fluctuations and spatial cluster formation. Finally, in the presence of non-local couplings the phase multistability “dies” and only the in-phase regime survives.
Enhancing synchronizability of weighted dynamical networks using betweenness centrality
NASA Astrophysics Data System (ADS)
Jalili, Mahdi; Rad, Ali Ajdari; Hasler, Martin
2008-07-01
By considering the eigenratio of the Laplacian of the connection graph as a synchronizability measure, we propose a procedure for weighting dynamical networks to enhance their synchronizability. The method is based on node and edge betweenness centrality measures and is tested on artificially constructed scale-free, Watts-Strogatz, and random networks as well as on some real-world graphs. It is also numerically shown that the same procedure could be used to enhance the phase synchronizability of networks of nonidentical oscillators.
Prosperity is associated with instability in dynamical networks
Cavaliere, Matteo; Sedwards, Sean; Tarnita, Corina E.; Nowak, Martin A.; Csikász-Nagy, Attila
2011-01-01
Social, biological and economic networks grow and decline with occasional fragmentation and re-formation, often explained in terms of external perturbations. We show that these phenomena can be a direct consequence of simple imitation and internal conflicts between ‘cooperators’ and ‘defectors’. We employ a game-theoretic model of dynamic network formation where successful individuals are more likely to be imitated by newcomers who adopt their strategies and copy their social network. We find that, despite using the same mechanism, cooperators promote well-connected highly prosperous networks and defectors cause the network to fragment and lose its prosperity; defectors are unable to maintain the highly connected networks they invade. Once the network is fragmented it can be reconstructed by a new invasion of cooperators, leading to the cycle of formation and fragmentation seen, for example, in bacterial communities and socio-economic networks. In this endless struggle between cooperators and defectors we observe that cooperation leads to prosperity, but prosperity is associated with instability. Cooperation is prosperous when the network has frequent formation and fragmentation. PMID:21983567
A network-based dynamical ranking system for competitive sports
NASA Astrophysics Data System (ADS)
Motegi, Shun; Masuda, Naoki
2012-12-01
From the viewpoint of networks, a ranking system for players or teams in sports is equivalent to a centrality measure for sports networks, whereby a directed link represents the result of a single game. Previously proposed network-based ranking systems are derived from static networks, i.e., aggregation of the results of games over time. However, the score of a player (or team) fluctuates over time. Defeating a renowned player in the peak performance is intuitively more rewarding than defeating the same player in other periods. To account for this factor, we propose a dynamic variant of such a network-based ranking system and apply it to professional men's tennis data. We derive a set of linear online update equations for the score of each player. The proposed ranking system predicts the outcome of the future games with a higher accuracy than the static counterparts.
A network-based dynamical ranking system for competitive sports
Motegi, Shun; Masuda, Naoki
2012-01-01
From the viewpoint of networks, a ranking system for players or teams in sports is equivalent to a centrality measure for sports networks, whereby a directed link represents the result of a single game. Previously proposed network-based ranking systems are derived from static networks, i.e., aggregation of the results of games over time. However, the score of a player (or team) fluctuates over time. Defeating a renowned player in the peak performance is intuitively more rewarding than defeating the same player in other periods. To account for this factor, we propose a dynamic variant of such a network-based ranking system and apply it to professional men's tennis data. We derive a set of linear online update equations for the score of each player. The proposed ranking system predicts the outcome of the future games with a higher accuracy than the static counterparts. PMID:23226590
Pietrucci, Fabio; Saitta, Antonino Marco
2015-12-01
Increasing experimental and theoretical evidence points to formamide as a possible hub in the complex network of prebiotic chemical reactions leading from simple precursors like H2, H2O, N2, NH3, CO, and CO2 to key biological molecules like proteins, nucleic acids, and sugars. We present an in-depth computational study of the formation and decomposition reaction channels of formamide by means of ab initio molecular dynamics. To this aim we introduce a new theoretical method combining the metadynamics sampling scheme with a general purpose topological formulation of collective variables able to track a wide range of different reaction mechanisms. Our approach is flexible enough to discover multiple pathways and intermediates starting from minimal insight on the systems, and it allows passing in a seamless way from reactions in gas phase to reactions in liquid phase, with the solvent active role fully taken into account. We obtain crucial new insight into the interplay of the different formamide reaction channels and into environment effects on pathways and barriers. In particular, our results indicate a similar stability of formamide and hydrogen cyanide in solution as well as their relatively facile interconversion, thus reconciling experiments and theory and, possibly, two different and competing prebiotic scenarios. Moreover, although not explicitly sought, formic acid/ammonium formate is produced as an important formamide decomposition byproduct in solution. PMID:26598679
Pietrucci, Fabio; Saitta, Antonino Marco
2015-01-01
Increasing experimental and theoretical evidence points to formamide as a possible hub in the complex network of prebiotic chemical reactions leading from simple precursors like H2, H2O, N2, NH3, CO, and CO2 to key biological molecules like proteins, nucleic acids, and sugars. We present an in-depth computational study of the formation and decomposition reaction channels of formamide by means of ab initio molecular dynamics. To this aim we introduce a new theoretical method combining the metadynamics sampling scheme with a general purpose topological formulation of collective variables able to track a wide range of different reaction mechanisms. Our approach is flexible enough to discover multiple pathways and intermediates starting from minimal insight on the systems, and it allows passing in a seamless way from reactions in gas phase to reactions in liquid phase, with the solvent active role fully taken into account. We obtain crucial new insight into the interplay of the different formamide reaction channels and into environment effects on pathways and barriers. In particular, our results indicate a similar stability of formamide and hydrogen cyanide in solution as well as their relatively facile interconversion, thus reconciling experiments and theory and, possibly, two different and competing prebiotic scenarios. Moreover, although not explicitly sought, formic acid/ammonium formate is produced as an important formamide decomposition byproduct in solution. PMID:26598679
Circuitry and dynamics of human transcription factor regulatory networks
Neph, Shane; Stergachis, Andrew B.; Reynolds, Alex; Sandstrom, Richard; Borenstein, Elhanan; Stamatoyannopoulos, John A.
2012-01-01
SUMMARY The combinatorial cross-regulation of hundreds of sequence-specific transcription factors defines a regulatory network that underlies cellular identity and function. Here we use genome-wide maps of in vivo DNaseI footprints to assemble an extensive core human regulatory network comprising connections among 475 sequence-specific transcription factors, and to analyze the dynamics of these connections across 41 diverse cell and tissue types. We find that human transcription factor networks are highly cell-selective and are driven by cohorts of factors that include regulators with previously unrecognized roles in control of cellular identity. Moreover, we identify many widely expressed factors that impact transcriptional regulatory networks in a cell-selective manner. Strikingly, in spite of their inherent diversity, all cell type regulatory networks independently converge on a common architecture that closely resembles the topology of living neuronal networks. Together, our results provide the first description of the circuitry, dynamics, and organizing principles of the human transcription factor regulatory network. PMID:22959076
Dynamic pattern evolution on scale-free networks
Zhou, Haijun; Lipowsky, Reinhard
2005-01-01
A general class of dynamic models on scale-free networks is studied by analytical methods and computer simulations. Each network consists of N vertices and is characterized by its degree distribution, P(k), which represents the probability that a randomly chosen vertex is connected to k nearest neighbors. Each vertex can attain two internal states described by binary variables or Ising-like spins that evolve in time according to local majority rules. Scale-free networks, for which the degree distribution has a power law tail P(k) ∼ k-γ, are shown to exhibit qualitatively different dynamic behavior for γ < 5/2 and γ > 5/2, shedding light on the empirical observation that many real-world networks are scale-free with 2 < γ < 5/2. For 2 < γ < 5/2, strongly disordered patterns decay within a finite decay time even in the limit of infinite networks. For γ > 5/2, on the other hand, this decay time diverges as ln(N) with the network size N. An analogous distinction is found for a variety of more complex models including Hopfield models for associative memory networks. In the latter case, the storage capacity is found, within mean field theory, to be independent of N in the limit of large N for γ > 5/2 but to grow as Nα with α = (5 - 2γ)/(γ - 1) for 2 < γ < 5/2. PMID:16006533
Molecular Dynamics Simulations of Chemical Reactions for Use in Education
ERIC Educational Resources Information Center
Qian Xie; Tinker, Robert
2006-01-01
One of the simulation engines of an open-source program called the Molecular Workbench, which can simulate thermodynamics of chemical reactions, is described. This type of real-time, interactive simulation and visualization of chemical reactions at the atomic scale could help students understand the connections between chemical reaction equations…
Glucans monomer-exchange dynamics as an open chemical network
NASA Astrophysics Data System (ADS)
Rao, Riccardo; Lacoste, David; Esposito, Massimiliano
2015-12-01
We describe the oligosaccharides-exchange dynamics performed by the so-called D-enzymes on polysaccharides. To mimic physiological conditions, we treat this process as an open chemical network by assuming some of the polymer concentrations fixed (chemostatting). We show that three different long-time behaviors may ensue: equilibrium states, nonequilibrium steady states, and continuous growth states. We dynamically and thermodynamically characterize these states and emphasize the crucial role of conservation laws in identifying the chemostatting conditions inducing them.
Glucans monomer-exchange dynamics as an open chemical network
Rao, Riccardo Esposito, Massimiliano; Lacoste, David
2015-12-28
We describe the oligosaccharides-exchange dynamics performed by the so-called D-enzymes on polysaccharides. To mimic physiological conditions, we treat this process as an open chemical network by assuming some of the polymer concentrations fixed (chemostatting). We show that three different long-time behaviors may ensue: equilibrium states, nonequilibrium steady states, and continuous growth states. We dynamically and thermodynamically characterize these states and emphasize the crucial role of conservation laws in identifying the chemostatting conditions inducing them.
Chimera states in population dynamics: Networks with fragmented and hierarchical connectivities
NASA Astrophysics Data System (ADS)
Hizanidis, Johanne; Panagakou, Evangelia; Omelchenko, Iryna; Schöll, Eckehard; Hövel, Philipp; Provata, Astero
2015-07-01
We study numerically the development of chimera states in networks of nonlocally coupled oscillators whose limit cycles emerge from a Hopf bifurcation. This dynamical system is inspired from population dynamics and consists of three interacting species in cyclic reactions. The complexity of the dynamics arises from the presence of a limit cycle and four fixed points. When the bifurcation parameter increases away from the Hopf bifurcation the trajectory approaches the heteroclinic invariant manifolds of the fixed points producing spikes, followed by long resting periods. We observe chimera states in this spiking regime as a coexistence of coherence (synchronization) and incoherence (desynchronization) in a one-dimensional ring with nonlocal coupling and demonstrate that their multiplicity depends on both the system and the coupling parameters. We also show that hierarchical (fractal) coupling topologies induce traveling multichimera states. The speed of motion of the coherent and incoherent parts along the ring is computed through the Fourier spectra of the corresponding dynamics.
Computer-assisted design for scaling up systems based on DNA reaction networks.
Aubert, Nathanaël; Mosca, Clément; Fujii, Teruo; Hagiya, Masami; Rondelez, Yannick
2014-04-01
In the past few years, there have been many exciting advances in the field of molecular programming, reaching a point where implementation of non-trivial systems, such as neural networks or switchable bistable networks, is a reality. Such systems require nonlinearity, be it through signal amplification, digitalization or the generation of autonomous dynamics such as oscillations. The biochemistry of DNA systems provides such mechanisms, but assembling them in a constructive manner is still a difficult and sometimes counterintuitive process. Moreover, realistic prediction of the actual evolution of concentrations over time requires a number of side reactions, such as leaks, cross-talks or competitive interactions, to be taken into account. In this case, the design of a system targeting a given function takes much trial and error before the correct architecture can be found. To speed up this process, we have created DNA Artificial Circuits Computer-Assisted Design (DACCAD), a computer-assisted design software that supports the construction of systems for the DNA toolbox. DACCAD is ultimately aimed to design actual in vitro implementations, which is made possible by building on the experimental knowledge available on the DNA toolbox. We illustrate its effectiveness by designing various systems, from Montagne et al.'s Oligator or Padirac et al.'s bistable system to new and complex networks, including a two-bit counter or a frequency divider as well as an example of very large system encoding the game Mastermind. In the process, we highlight a variety of behaviours, such as enzymatic saturation and load effect, which would be hard to handle or even predict with a simpler model. We also show that those mechanisms, while generally seen as detrimental, can be used in a positive way, as functional part of a design. Additionally, the number of parameters included in these simulations can be large, especially in the case of complex systems. For this reason, we included the
Gas-Dynamic Transients Flow Networks
1987-09-01
TVENT1P predicts flows and pressures in a ventilation system or other air pathway caused by pressure transients, such as a tornado. For an analytical model to simulate an actual system, it must have (1) the same arrangement of components in a network of flow paths; (2) the same friction characteristics; (3) the same boundary pressures; (4) the same capacitance; and (5) the same forces that drive the air. A specific set of components used formore » constructing the analytical model includes filters, dampers, ducts, blowers, rooms, or volume connected at nodal points to form networks. The effects of a number of similar components can be lumped into a single one. TVENT1P contains a material transport algorithm and features for turning blowers off and on, changing blower speeds, changing the resistance of dampers and filters, and providing a filter model to handle very high flows. These features make it possible to depict a sequence of events during a single run. Component properties are varied using time functions. The filter model is not used by the code unless it is specified by the user. The basic results of a TVENT1P solution are flows in branches and pressures at nodes. A postprocessor program, PLTTEX, is included to produce the plots specified in the TVENT1P input. PLTTEX uses the proprietary CA-DISSPLA graphics software.« less
Femtosecond stimulated Raman spectroscopy of ultrafast biophysical reaction dynamics
NASA Astrophysics Data System (ADS)
McCamant, David William
2004-12-01
that the excited population moves away from the ground-state geometry in 250 fs. Spectral changes between 1.5 to 100 ps reveal that a significant fraction of the isomerization occurs on the ground state photoproduct surface. The many benefits FSRS will make it a valuable tool for vibrational spectroscopy of reaction dynamics in ultrafast photochemical and photophysical processes.
The US nuclear reaction data network. Summary of the first meeting, March 13 & 14 1996
1996-03-01
The first meeting of the US Nuclear Reaction Data Network (USNRDN) was held at the Colorado School of Mines, March 13-14, 1996 chaired by F. Edward Cecil. The Agenda of the meeting is attached. The Network, its mission, products and services; related nuclear data and data networks, members, and organization are described in Attachment 1. The following progress reports from the members of the USNRDN were distributed prior to the meeting and are given as Attachment 2. (1) Measurements and Development of Analytic Techniques for Basic Nuclear Physics and Nuclear Applications; (2) Nuclear Reaction Data Activities at the National Nuclear Data Center; (3) Studies of nuclear reactions at very low energies; (4) Nuclear Reaction Data Activities, Nuclear Data Group; (5) Progress in Neutron Physics at Los Alamos - Experiments; (6) Nuclear Reaction Data Activities in Group T2; (7) Progress Report for the US Nuclear Reaction Data Network Meeting; (8) Nuclear Astrophysics Research Group (ORNL); (9) Progress Report from Ohio University; (10) Exciton Model Phenomenology; and (11) Progress Report for Coordination Meeting USNRDN.