Quantum dynamics modeled by interacting trajectories

Science.gov (United States)

Cruz-Rodríguez, L.; Uranga-Piña, L.; Martínez-Mesa, A.; Meier, C.

2018-03-01

We present quantum dynamical simulations based on the propagation of interacting trajectories where the effect of the quantum potential is mimicked by effective pseudo-particle interactions. The method is applied to several quantum systems, both for bound and scattering problems. For the bound systems, the quantum ground state density and zero point energy are shown to be perfectly obtained by the interacting trajectories. In the case of time-dependent quantum scattering, the Eckart barrier and uphill ramp are considered, with transmission coefficients in very good agreement with standard quantum calculations. Finally, we show that via wave function synthesis along the trajectories, correlation functions and energy spectra can be obtained based on the dynamics of interacting trajectories.

The dynamics of meaningful social interactions and the emergence of collective knowledge

Science.gov (United States)

Dankulov, Marija Mitrović; Melnik, Roderick; Tadić, Bosiljka

2015-07-01

Collective knowledge as a social value may arise in cooperation among actors whose individual expertise is limited. The process of knowledge creation requires meaningful, logically coordinated interactions, which represents a challenging problem to physics and social dynamics modeling. By combining two-scale dynamics model with empirical data analysis from a well-known Questions & Answers system Mathematics, we show that this process occurs as a collective phenomenon in an enlarged network (of actors and their artifacts) where the cognitive recognition interactions are properly encoded. The emergent behavior is quantified by the information divergence and innovation advancing of knowledge over time and the signatures of self-organization and knowledge sharing communities. These measures elucidate the impact of each cognitive element and the individual actor’s expertise in the collective dynamics. The results are relevant to stochastic processes involving smart components and to collaborative social endeavors, for instance, crowdsourcing scientific knowledge production with online games.

Quantifying Engagement: Measuring Player Involvement in Human-Avatar Interactions

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Norris, Anne E.; Weger, Harry; Bullinger, Cory; Bowers, Alyssa

2014-01-01

This research investigated the merits of using an established system for rating behavioral cues of involvement in human dyadic interactions (i.e., face-to-face conversation) to measure involvement in human-avatar interactions. Gameplay audio-video and self-report data from a Feasibility Trial and Free Choice study of an effective peer resistance skill building simulation game (DRAMA-RAMA™) were used to evaluate reliability and validity of the rating system when applied to human-avatar interactions. The Free Choice study used a revised game prototype that was altered to be more engaging. Both studies involved girls enrolled in a public middle school in Central Florida that served a predominately Hispanic (greater than 80%), low-income student population. Audio-video data were coded by two raters, trained in the rating system. Self-report data were generated using measures of perceived realism, predictability and flow administered immediately after game play. Hypotheses for reliability and validity were supported: Reliability values mirrored those found in the human dyadic interaction literature. Validity was supported by factor analysis, significantly higher levels of involvement in Free Choice as compared to Feasibility Trial players, and correlations between involvement dimension sub scores and self-report measures. Results have implications for the science of both skill-training intervention research and game design. PMID:24748718

Dynamic Soil-Structure-Interaction

DEFF Research Database (Denmark)

Kellezi, Lindita

1998-01-01

The aim of this thesis is to investigate and develop alternative methods of analyzing problems in dynamic soil-structure-interaction. The main focus is the major difficulty posed by such an analysis - the phenomenon of waves which radiate outward from the excited structures towards infinity....... In numerical calculations, only a finite region of the foundation metium is analyzed and something is done to prevent the outgoing radiating waves to reflect from the regions's boundary. The prosent work concerns itself with the study of such effects, using the finite element method, and artificial...... transmitting boundary at the edges of the computational mesh. To start with, an investigation of the main effects of the interaction phenomena is carried out employing a widely used model, considering dynamic stiffness of the unbounded soil as frequency independent. Then a complete description...

Network Physiology: How Organ Systems Dynamically Interact

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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.

Science.gov (United States)

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.

Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations

International Nuclear Information System (INIS)

Hardy, David J.; Schulten, Klaus; Wolff, Matthew A.; Skeel, Robert D.; Xia, Jianlin

2016-01-01

The multilevel summation method for calculating electrostatic interactions in molecular dynamics simulations constructs an approximation to a pairwise interaction kernel and its gradient, which can be evaluated at a cost that scales linearly with the number of atoms. The method smoothly splits the kernel into a sum of partial kernels of increasing range and decreasing variability with the longer-range parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate in the context of dynamics and minimization, because it can produce continuous gradients. This article explores the use of B-splines to increase the accuracy of the multilevel summation method (for nonperiodic boundaries) without incurring additional computation other than a preprocessing step (whose cost also scales linearly). To obtain accurate results efficiently involves technical difficulties, which are overcome by a novel preprocessing algorithm. Numerical experiments demonstrate that the resulting method offers substantial improvements in accuracy and that its performance is competitive with an implementation of the fast multipole method in general and markedly better for Hamiltonian formulations of molecular dynamics. The improvement is great enough to establish multilevel summation as a serious contender for calculating pairwise interactions in molecular dynamics simulations. In particular, the method appears to be uniquely capable for molecular dynamics in two situations, nonperiodic boundary conditions and massively parallel computation, where the fast Fourier transform employed in the particle–mesh Ewald method falls short.

Dynamic characterization of contact interactions of micro-robotic leg structures

International Nuclear Information System (INIS)

Ryou, Jeong Hoon; Oldham, Kenn Richard

2014-01-01

Contact dynamics of microelectromechanical systems (MEMS) are typically complicated and it is consequently difficult to model all dynamic characteristics observed in time-domain responses involving impact. This issue becomes worse when a device, such as a mobile micro-robot, is not clamped to a substrate and has a complex mechanical structure. To characterize such a contact interaction situation, two walking micro-robot prototypes are tested having intentionally simple structures with different dimensions (21.2 mm × 16.3 mm × 0.75 mm and 32 mm × 25.4 mm × 4.1 mm) and weights (0.16 and 2.7 g). Contact interaction behaviors are characterized by analyzing experimental data under various excitation signals. A numerical approach was used to derive a novel contact model consisting of a coefficient of restitution matrix that uses modal vibration information. Experimental validation of the simulation model shows that it captures various dynamic features of the contact interaction when simulating leg behavior more accurately than previous contact models, such as single-point coefficient of restitution or compliant ground models. In addition, this paper shows that small-scale forces can be added to the simulation to improve model accuracy, resulting in average errors across driving conditions on the order of 2–6% for bounce frequency, maximum foot height, and average foot height, although there is substantial variation from case to case. (paper)

Vortex dynamics during blade-vortex interactions

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Peng, Di; Gregory, James W.

2015-05-01

Vortex dynamics during parallel blade-vortex interactions (BVIs) were investigated in a subsonic wind tunnel using particle image velocimetry (PIV). Vortices were generated by applying a rapid pitch-up motion to an airfoil through a pneumatic system, and the subsequent interactions with a downstream, unloaded target airfoil were studied. The blade-vortex interactions may be classified into three categories in terms of vortex behavior: close interaction, very close interaction, and collision. For each type of interaction, the vortex trajectory and strength variation were obtained from phase-averaged PIV data. The PIV results revealed the mechanisms of vortex decay and the effects of several key parameters on vortex dynamics, including separation distance (h/c), Reynolds number, and vortex sense. Generally, BVI has two main stages: interaction between vortex and leading edge (vortex-LE interaction) and interaction between vortex and boundary layer (vortex-BL interaction). Vortex-LE interaction, with its small separation distance, is dominated by inviscid decay of vortex strength due to pressure gradients near the leading edge. Therefore, the decay rate is determined by separation distance and vortex strength, but it is relatively insensitive to Reynolds number. Vortex-LE interaction will become a viscous-type interaction if there is enough separation distance. Vortex-BL interaction is inherently dominated by viscous effects, so the decay rate is dependent on Reynolds number. Vortex sense also has great impact on vortex-BL interaction because it changes the velocity field and shear stress near the surface.

Reconsideration of dynamic force spectroscopy analysis of streptavidin-biotin interactions.

Science.gov (United States)

Taninaka, Atsushi; Takeuchi, Osamu; Shigekawa, Hidemi

2010-05-13

To understand and design molecular functions on the basis of molecular recognition processes, the microscopic probing of the energy landscapes of individual interactions in a molecular complex and their dependence on the surrounding conditions is of great importance. Dynamic force spectroscopy (DFS) is a technique that enables us to study the interaction between molecules at the single-molecule level. However, the obtained results differ among previous studies, which is considered to be caused by the differences in the measurement conditions. We have developed an atomic force microscopy technique that enables the precise analysis of molecular interactions on the basis of DFS. After verifying the performance of this technique, we carried out measurements to determine the landscapes of streptavidin-biotin interactions. The obtained results showed good agreement with theoretical predictions. Lifetimes were also well analyzed. Using a combination of cross-linkers and the atomic force microscope that we developed, site-selective measurement was carried out, and the steps involved in bonding due to microscopic interactions are discussed using the results obtained by site-selective analysis.

Vegetation dynamics induced by phreatophyte--aquifer interactions.

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Ridolfi, Luca; D'Odorico, Paolo; Laio, Francesco

2007-09-21

The dynamics of phreatophyte vegetation are strongly coupled to those of the shallow phreatic aquifers from which phreatophytes extract water. Vegetation is able to influence the depth of the water table, which, in turn, can induce stress in vegetation. These interactions are likely to affect the composition and structure of phreatophyte plant communities, as well as their successional dynamics. Despite the environmental and economical value of many wetland plant ecosystems around the world, the impact of vegetation-water table interactions on ecosystem succession and interspecies competition in phreatophyte plant communities remains poorly understood. This study develops a minimalistic modelling framework to investigate the dynamics of two phreatophyte species, and their interactions with the water table. In spite of its simplicity, the model exhibits a remarkable variety of dynamical behaviors, especially when the water table depth is forced by external drivers. It is shown that, even when one of the two species is dominant with respect to the other, these two species can coexist showing periodic, quasi-periodic, and chaotic dynamics. Moreover, in the presence of a random environmental forcing, noise-induced coexistence may emerge.

Model-free inference of direct network interactions from nonlinear collective dynamics.

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Casadiego, Jose; Nitzan, Mor; Hallerberg, Sarah; Timme, Marc

2017-12-19

The topology of interactions in network dynamical systems fundamentally underlies their function. Accelerating technological progress creates massively available data about collective nonlinear dynamics in physical, biological, and technological systems. Detecting direct interaction patterns from those dynamics still constitutes a major open problem. In particular, current nonlinear dynamics approaches mostly require to know a priori a model of the (often high dimensional) system dynamics. Here we develop a model-independent framework for inferring direct interactions solely from recording the nonlinear collective dynamics generated. Introducing an explicit dependency matrix in combination with a block-orthogonal regression algorithm, the approach works reliably across many dynamical regimes, including transient dynamics toward steady states, periodic and non-periodic dynamics, and chaos. Together with its capabilities to reveal network (two point) as well as hypernetwork (e.g., three point) interactions, this framework may thus open up nonlinear dynamics options of inferring direct interaction patterns across systems where no model is known.

Diet-dependent modular dynamic interactions of the equine cecal microbiota

DEFF Research Database (Denmark)

Kristoffersen, Camilla; Jensen, Rasmus Bovbjerg; Avershina, Ekaterina

2016-01-01

Knowledge on dynamic interactions in microbiota is pivotal for understanding the role of bacteria in the gut. We herein present comprehensive dynamic models of the horse cecal microbiota, which include short-chained fatty acids, carbohydrate metabolic networks, and taxonomy. Dynamic models were...... diets. We observed marked differences in the microbial dynamic interaction patterns for Fibrobacter succinogenes, Lachnospiraceae, Streptococcus, Treponema, Anaerostipes, and Anaerovibrio between the two diet groups. Fluctuations and microbiota interactions were the most pronounced for the starch rich...... sugars for the starch-rich diet and monosaccharides for the fiber-rich diet. In conclusion, diet may not only affect the composition of the cecal microbiota, but also dynamic interactions and metabolic cross-feeding....

Learning models of activities involving interacting objects

DEFF Research Database (Denmark)

Manfredotti, Cristina; Pedersen, Kim Steenstrup; Hamilton, Howard J.

2013-01-01

We propose the LEMAIO multi-layer framework, which makes use of hierarchical abstraction to learn models for activities involving multiple interacting objects from time sequences of data concerning the individual objects. Experiments in the sea navigation domain yielded learned models that were t...

Dynamical transitions in a pollination-herbivory interaction: a conflict between mutualism and antagonism.

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Tomás A Revilla

Full Text Available Plant-pollinator associations are often seen as purely mutualistic, while in reality they can be more complex. Indeed they may also display a diverse array of antagonistic interactions, such as competition and victim-exploiter interactions. In some cases mutualistic and antagonistic interactions are carried-out by the same species but at different life-stages. As a consequence, population structure affects the balance of inter-specific associations, a topic that is receiving increased attention. In this paper, we developed a model that captures the basic features of the interaction between a flowering plant and an insect with a larval stage that feeds on the plant's vegetative tissues (e.g. leaves and an adult pollinator stage. Our model is able to display a rich set of dynamics, the most remarkable of which involves victim-exploiter oscillations that allow plants to attain abundances above their carrying capacities and the periodic alternation between states dominated by mutualism or antagonism. Our study indicates that changes in the insect's life cycle can modify the balance between mutualism and antagonism, causing important qualitative changes in the interaction dynamics. These changes in the life cycle could be caused by a variety of external drivers, such as temperature, plant nutrients, pesticides and changes in the diet of adult pollinators.

Identification of genetic components involved in Lotus-endophyte interactions

DEFF Research Database (Denmark)

Zgadzaj, Rafal Lukasz

of growth hormones or nitrogen fixation. However, the genes involved in plant-endophyte interactions and bacterial accomodation within plant tissues are not known. In order to shed some light on such processes, an approach “one host-one endophyte” was chosen. The focus on a single plant species and a single......Endophytes are microorganisms capable of colonising plant tissues without inducing host defense responses. They have a large impact on plants, since they can modulate plant responses to pathogens, herbivores and environmental stress. They can also induce plant growth promotion through synthesis...... bacterial strain aimed at obtaining a reliable and easy to handle system for plant-microsymbiont interaction research. Two different methods were tested for their usefulness in identification of genetic components involved in plant-endophyte interactions. The first method was based on measuring growth...

Water-Protein Interactions: The Secret of Protein Dynamics

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Silvia Martini

2013-01-01

Full Text Available Water-protein interactions help to maintain flexible conformation conditions which are required for multifunctional protein recognition processes. The intimate relationship between the protein surface and hydration water can be analyzed by studying experimental water properties measured in protein systems in solution. In particular, proteins in solution modify the structure and the dynamics of the bulk water at the solute-solvent interface. The ordering effects of proteins on hydration water are extended for several angstroms. In this paper we propose a method for analyzing the dynamical properties of the water molecules present in the hydration shells of proteins. The approach is based on the analysis of the effects of protein-solvent interactions on water protons NMR relaxation parameters. NMR relaxation parameters, especially the nonselective (R1NS and selective (R1SE spin-lattice relaxation rates of water protons, are useful for investigating the solvent dynamics at the macromolecule-solvent interfaces as well as the perturbation effects caused by the water-macromolecule interactions on the solvent dynamical properties. In this paper we demonstrate that Nuclear Magnetic Resonance Spectroscopy can be used to determine the dynamical contributions of proteins to the water molecules belonging to their hydration shells.

Gene-environment interaction involving recently identified colorectal cancer susceptibility loci

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Kantor, Elizabeth D.; Hutter, Carolyn M.; Minnier, Jessica; Berndt, Sonja I.; Brenner, Hermann; Caan, Bette J.; Campbell, Peter T.; Carlson, Christopher S.; Casey, Graham; Chan, Andrew T.; Chang-Claude, Jenny; Chanock, Stephen J.; Cotterchio, Michelle; Du, Mengmeng; Duggan, David; Fuchs, Charles S.; Giovannucci, Edward L.; Gong, Jian; Harrison, Tabitha A.; Hayes, Richard B.; Henderson, Brian E.; Hoffmeister, Michael; Hopper, John L.; Jenkins, Mark A.; Jiao, Shuo; Kolonel, Laurence N.; Le Marchand, Loic; Lemire, Mathieu; Ma, Jing; Newcomb, Polly A.; Ochs-Balcom, Heather M.; Pflugeisen, Bethann M.; Potter, John D.; Rudolph, Anja; Schoen, Robert E.; Seminara, Daniela; Slattery, Martha L.; Stelling, Deanna L.; Thomas, Fridtjof; Thornquist, Mark; Ulrich, Cornelia M.; Warnick, Greg S.; Zanke, Brent W.; Peters, Ulrike; Hsu, Li; White, Emily

2014-01-01

BACKGROUND Genome-wide association studies have identified several single nucleotide polymorphisms (SNPs) that are associated with risk of colorectal cancer (CRC). Prior research has evaluated the presence of gene-environment interaction involving the first 10 identified susceptibility loci, but little work has been conducted on interaction involving SNPs at recently identified susceptibility loci, including: rs10911251, rs6691170, rs6687758, rs11903757, rs10936599, rs647161, rs1321311, rs719725, rs1665650, rs3824999, rs7136702, rs11169552, rs59336, rs3217810, rs4925386, and rs2423279. METHODS Data on 9160 cases and 9280 controls from the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) and Colon Cancer Family Registry (CCFR) were used to evaluate the presence of interaction involving the above-listed SNPs and sex, body mass index (BMI), alcohol consumption, smoking, aspirin use, post-menopausal hormone (PMH) use, as well as intake of dietary calcium, dietary fiber, dietary folate, red meat, processed meat, fruit, and vegetables. Interaction was evaluated using a fixed-effects meta-analysis of an efficient Empirical Bayes estimator, and permutation was used to account for multiple comparisons. RESULTS None of the permutation-adjusted p-values reached statistical significance. CONCLUSIONS The associations between recently identified genetic susceptibility loci and CRC are not strongly modified by sex, BMI, alcohol, smoking, aspirin, PMH use, and various dietary factors. IMPACT Results suggest no evidence of strong gene-environment interactions involving the recently identified 16 susceptibility loci for CRC taken one at a time. PMID:24994789

Dynamic metabolic exchange governs a marine algal-bacterial interaction.

Science.gov (United States)

Segev, Einat; Wyche, Thomas P; Kim, Ki Hyun; Petersen, Jörn; Ellebrandt, Claire; Vlamakis, Hera; Barteneva, Natasha; Paulson, Joseph N; Chai, Liraz; Clardy, Jon; Kolter, Roberto

2016-11-18

Emiliania huxleyi is a model coccolithophore micro-alga that generates vast blooms in the ocean. Bacteria are not considered among the major factors influencing coccolithophore physiology. Here we show through a laboratory model system that the bacterium Phaeobacter inhibens , a well-studied member of the Roseobacter group, intimately interacts with E. huxleyi. While attached to the algal cell, bacteria initially promote algal growth but ultimately kill their algal host. Both algal growth enhancement and algal death are driven by the bacterially-produced phytohormone indole-3-acetic acid. Bacterial production of indole-3-acetic acid and attachment to algae are significantly increased by tryptophan, which is exuded from the algal cell. Algal death triggered by bacteria involves activation of pathways unique to oxidative stress response and programmed cell death. Our observations suggest that bacteria greatly influence the physiology and metabolism of E. huxleyi. Coccolithophore-bacteria interactions should be further studied in the environment to determine whether they impact micro-algal population dynamics on a global scale.

Dynamical symmetry breaking of the electroweak interactions and the renormalization group

International Nuclear Information System (INIS)

Hill, C.T.

1990-08-01

We discuss dynamical symmetry breaking with an emphasis on the renormalization group as the key tool to obtaining reliable predictions. In particular we discuss the mechanism for breaking the electroweak interactions which relies upon the formation of condensates involving the conventional quarks and leptons. Such a scheme indicates that the top quark is heavy, greater than or of order 200 GeV, and gives further predictions for the Higgs boson mass. We also briefly describe recent attempts to incorporate a 4th generation in a more natural scheme. 13 refs., 3 figs., 1 tab

Interactions Dominate the Dynamics of Visual Cognition

Science.gov (United States)

Stephen, Damian G.; Mirman, Daniel

2010-01-01

Many cognitive theories have described behavior as the summation of independent contributions from separate components. Contrasting views have emphasized the importance of multiplicative interactions and emergent structure. We describe a statistical approach to distinguishing additive and multiplicative processes and apply it to the dynamics of eye movements during classic visual cognitive tasks. The results reveal interaction-dominant dynamics in eye movements in each of the three tasks, and that fine-grained eye movements are modulated by task constraints. These findings reveal the interactive nature of cognitive processing and are consistent with theories that view cognition as an emergent property of processes that are broadly distributed over many scales of space and time rather than a componential assembly line. PMID:20070957

Alleles versus genotypes: Genetic interactions and the dynamics of selection in sexual populations

Science.gov (United States)

Neher, Richard

2010-03-01

Physical interactions between amino-acids are essential for protein structure and activity, while protein-protein interactions and regulatory interactions are central to cellular function. As a consequence of these interactions, the combined effect of two mutations can differ from the sum of the individual effects of the mutations. This phenomenon of genetic interaction is known as epistasis. However, the importance of epistasis and its effects on evolutionary dynamics are poorly understood, especially in sexual populations where recombination breaks up existing combinations of alleles to produce new ones. Here, we present a computational model of selection dynamics involving many epistatic loci in a recombining population. We demonstrate that a large number of polymorphic interacting loci can, despite frequent recombination, exhibit cooperative behavior that locks alleles into favorable genotypes leading to a population consisting of a set of competing clones. As the recombination rate exceeds a certain critical value this ``genotype selection'' phase disappears in an abrupt transition giving way to ``allele selection'' - the phase where different loci are only weakly correlated as expected in sexually reproducing populations. Clustering of interacting sets of genes on a chromosome leads to the emergence of an intermediate regime, where localized blocks of cooperating alleles lock into genetic modules. Large populations attain highest fitness at a recombination rate just below critical, suggesting that natural selection might tune recombination rates to balance the beneficial aspect of exploration of genotype space with the breaking up of synergistic allele combinations.

Coupling functions: Universal insights into dynamical interaction mechanisms

Science.gov (United States)

Stankovski, Tomislav; Pereira, Tiago; McClintock, Peter V. E.; Stefanovska, Aneta

2017-10-01

The dynamical systems found in nature are rarely isolated. Instead they interact and influence each other. The coupling functions that connect them contain detailed information about the functional mechanisms underlying the interactions and prescribe the physical rule specifying how an interaction occurs. A coherent and comprehensive review is presented encompassing the rapid progress made recently in the analysis, understanding, and applications of coupling functions. The basic concepts and characteristics of coupling functions are presented through demonstrative examples of different domains, revealing the mechanisms and emphasizing their multivariate nature. The theory of coupling functions is discussed through gradually increasing complexity from strong and weak interactions to globally coupled systems and networks. A variety of methods that have been developed for the detection and reconstruction of coupling functions from measured data is described. These methods are based on different statistical techniques for dynamical inference. Stemming from physics, such methods are being applied in diverse areas of science and technology, including chemistry, biology, physiology, neuroscience, social sciences, mechanics, and secure communications. This breadth of application illustrates the universality of coupling functions for studying the interaction mechanisms of coupled dynamical systems.

A transmembrane polar interaction is involved in the functional regulation of integrin alpha L beta 2.

Science.gov (United States)

Vararattanavech, Ardcharaporn; Chng, Choon-Peng; Parthasarathy, Krupakar; Tang, Xiao-Yan; Torres, Jaume; Tan, Suet-Mien

2010-05-14

Integrins are heterodimeric transmembrane (TM) receptors formed by noncovalent associations of alpha and beta subunits. Each subunit contains a single alpha-helical TM domain. Inside-out activation of an integrin involves the separation of its cytoplasmic tails, leading to disruption of alphabeta TM packing. The leukocyte integrin alpha L beta 2 is required for leukocyte adhesion, migration, proliferation, cytotoxic function, and antigen presentation. In this study, we show by mutagenesis experiments that the packing of alpha L beta 2 TMs is consistent with that of the integrin alpha IIb beta 3 TMs. However, molecular dynamics simulations of alpha L beta 2 TMs in lipids predicted a polar interaction involving the side chains of alpha L Ser1071 and beta2 Thr686 in the outer-membrane association clasp (OMC). This is supported by carbonyl vibrational shifts observed in isotope-labeled alpha L beta 2 TM peptides that were incorporated into lipid bilayers. Molecular dynamics studies simulating the separation of alpha L beta 2 tails showed the presence of polar interaction during the initial perturbation of the inner-membrane association clasp. When the TMs underwent further separation, the polar interaction was disrupted. OMC polar interaction is important in regulating the functions of beta2 integrins because mutations that disrupt the OMC polar interaction generated constitutively activated alpha L beta 2, alpha M beta 2, and alpha X beta 2 in 293T transfectants. We also show that the expression of mutant beta2 Thr686Gly in beta2-deficient T cells rescued cell adhesion to intercellular adhesion molecule 1, but the cells showed overt elongated morphologies in response to chemokine stromal-cell-derived factor 1 alpha treatment as compared to wild-type beta2-expressing cells. These two TM polar residues are totally conserved in other members of the beta2 integrins in humans and across different species. Our results provide an example of the stabilizing effect of polar

Dynamic neurotransmitter interactions measured with PET

International Nuclear Information System (INIS)

Schiffer, W.K.; Dewey, S.L.

2001-01-01

Positron emission tomography (PET) has become a valuable interdisciplinary tool for understanding physiological, biochemical and pharmacological functions at a molecular level in living humans, whether in a healthy or diseased state. The utility of tracing chemical activity through the body transcends the fields of cardiology, oncology, neurology and psychiatry. In this, PET techniques span radiochemistry and radiopharmaceutical development to instrumentation, image analysis, anatomy and modeling. PET has made substantial contributions in each of these fields by providing a,venue for mapping dynamic functions of healthy and unhealthy human anatomy. As diverse as the disciplines it bridges, PET has provided insight into an equally significant variety of psychiatric disorders. Using the unique quantitative ability of PET, researchers are now better able to non-invasively characterize normally occurring neurotransmitter interactions in the brain. With the knowledge that these interactions provide the fundamental basis for brain response, many investigators have recently focused their efforts on an examination of the communication between these chemicals in both healthy volunteers and individuals suffering from diseases classically defined as neurotransmitter specific in nature. In addition, PET can measure the biochemical dynamics of acute and sustained drug abuse. Thus, PET studies of neurotransmitter interactions enable investigators to describe a multitude of specific functional interactions in the human brain. This information can then be applied to understanding side effects that occur in response to acute and chronic drug therapy, and to designing new drugs that target multiple systems as opposed to single receptor types. Knowledge derived from PET studies can be applied to drug discovery, research and development (for review, see (Fowler et al., 1999) and (Burns et al., 1999)). Here, we will cover the most substantial contributions of PET to understanding

Dynamic neurotransmitter interactions measured with PET

Energy Technology Data Exchange (ETDEWEB)

Schiffer, W.K.; Dewey, S.L.

2001-04-02

Positron emission tomography (PET) has become a valuable interdisciplinary tool for understanding physiological, biochemical and pharmacological functions at a molecular level in living humans, whether in a healthy or diseased state. The utility of tracing chemical activity through the body transcends the fields of cardiology, oncology, neurology and psychiatry. In this, PET techniques span radiochemistry and radiopharmaceutical development to instrumentation, image analysis, anatomy and modeling. PET has made substantial contributions in each of these fields by providing a,venue for mapping dynamic functions of healthy and unhealthy human anatomy. As diverse as the disciplines it bridges, PET has provided insight into an equally significant variety of psychiatric disorders. Using the unique quantitative ability of PET, researchers are now better able to non-invasively characterize normally occurring neurotransmitter interactions in the brain. With the knowledge that these interactions provide the fundamental basis for brain response, many investigators have recently focused their efforts on an examination of the communication between these chemicals in both healthy volunteers and individuals suffering from diseases classically defined as neurotransmitter specific in nature. In addition, PET can measure the biochemical dynamics of acute and sustained drug abuse. Thus, PET studies of neurotransmitter interactions enable investigators to describe a multitude of specific functional interactions in the human brain. This information can then be applied to understanding side effects that occur in response to acute and chronic drug therapy, and to designing new drugs that target multiple systems as opposed to single receptor types. Knowledge derived from PET studies can be applied to drug discovery, research and development (for review, see (Fowler et al., 1999) and (Burns et al., 1999)). Here, we will cover the most substantial contributions of PET to understanding

Structural Dynamics Investigation of Human Family 1 & 2 Cystatin-Cathepsin L1 Interaction: A Comparison of Binding Modes.

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Suman Kumar Nandy

Full Text Available Cystatin superfamily is a large group of evolutionarily related proteins involved in numerous physiological activities through their inhibitory activity towards cysteine proteases. Despite sharing the same cystatin fold, and inhibiting cysteine proteases through the same tripartite edge involving highly conserved N-terminal region, L1 and L2 loop; cystatins differ widely in their inhibitory affinity towards C1 family of cysteine proteases and molecular details of these interactions are still elusive. In this study, inhibitory interactions of human family 1 & 2 cystatins with cathepsin L1 are predicted and their stability and viability are verified through protein docking & comparative molecular dynamics. An overall stabilization effect is observed in all cystatins on complex formation. Complexes are mostly dominated by van der Waals interaction but the relative participation of the conserved regions varied extensively. While van der Waals contacts prevail in L1 and L2 loop, N-terminal segment chiefly acts as electrostatic interaction site. In fact the comparative dynamics study points towards the instrumental role of L1 loop in directing the total interaction profile of the complex either towards electrostatic or van der Waals contacts. The key amino acid residues surfaced via interaction energy, hydrogen bonding and solvent accessible surface area analysis for each cystatin-cathepsin L1 complex influence the mode of binding and thus control the diverse inhibitory affinity of cystatins towards cysteine proteases.

Dynamical equilibration in strongly-interacting parton-hadron matter

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Gorenstein M.

2011-04-01

Full Text Available We study the kinetic and chemical equilibration in 'infinite' parton-hadron matter within the Parton-Hadron-String Dynamics transport approach, which is based on a dynamical quasiparticle model for partons matched to reproduce lattice-QCD results – including the partonic equation of state – in thermodynamic equilibrium. The 'infinite' matter is simulated within a cubic box with periodic boundary conditions initialized at different baryon density (or chemical potential and energy density. The transition from initially pure partonic matter to hadronic degrees of freedom (or vice versa occurs dynamically by interactions. Different thermody-namical distributions of the strongly-interacting quark-gluon plasma (sQGP are addressed and discussed.

The role of father involvement and dyadic interactions in the development of family interactive abilities: a multilevel approach.

Directory of Open Access Journals (Sweden)

Alessandra Simonelli

2016-11-01

Full Text Available The present study aims to investigate, using multilevel analysis, the development of family interactions from pregnancy to preschool age, in a longitudinal perspective. Moreover, it intends to explore the impact of couple relationship and father involvement in childcare on the developmental trend of the quality of mother-father-child interactions.103 primiparous families were assessed at 7th month of pregnancy, 4th, 9th, 18th months of child’s life and during preschool age (36-48th, using the observational procedure named Lausanne Trilogue Play. Parents’ perception of marital satisfaction was assessed with the Dyadic Adjustment Scale at each point of measure; moreover, in the postnatal assessment parents completed the Father Involvement Questionnaire. Results showed that family interactions increase over time. Second, a decrease of marital adjustment is associated to an improvement of the quality of family interactions. Moreover, father involvement predicts the quality of family interactions from the earliest stages of child’s life.In a longitudinal perspective, family interactions and marital quality show opposite developmental trends and father’s involvement represents a particularly important feature of the family.

Unitarity, Feedback, Interactions - Dynamics Emergent from Repeated Measurements

Science.gov (United States)

Corona Ugalde, Paulina; Altamirano, Natacha; Mann, Robert; Zych, Magdalena

Modern measurement theory dispenses with the description of a measurement as a projection. Rather, the measurement is understood as an operation, whereby the system's final state is determined by an action of a completely positive trace non-increasing map and the outcomes are described by linear operators on the system, distributed according to a positive-operator valued measure (POVM). The POVM approach unifies the theory of measurements with a general description of dynamics, the theory of open quantum systems. Engineering a particular measurement and engineering a particular dynamics for the system are thus two complementary aspects of the same conceptual framework. This correspondence is directly applied in quantum simulations and quantum control theory . With this motivation, we study what types of dynamics can emerge from a model of repeated short interactions of a system with a set of ancillae. We show that contingent on the model parameters the resulting dynamics ranges from exact unitarity to arbitrary fast decoherence. For a series of measurements the effective dynamics includes feedback-control, which for a composite system yields effective interactions between the subsystems. We quantify the amount of decoherence accompanying such induced interactions. The simple framework used in the present study can find applications in devising novel quantum control protocols, or quantum simulations.

Simplified Model for the Population Dynamics Involved in a Malaria Crisis

International Nuclear Information System (INIS)

Kenfack-Jiotsa, A.; Fotsa-Ngaffo, F.

2009-12-01

We adapt a simple model of predator-prey to the population involved in a crisis of malaria. The study is made only in the stream blood inside the human body except for the liver. Particularly we look at the dynamics of the malaria parasites 'merozoites' and their interaction with the blood components, more specifically the red blood cells (RBC) and the immune response grouped under the white blood cells (WBC). The stability analysis of the system reveals an important practical direction to investigate as regards the ratio WBC over RBC since it is a fundamental parameter that characterizes stable regions. The model numerically presents a wide range of possible features of the disease. Even with its simplified form, the model not only recovers well-known results but in addition predicts possible hidden phenomenon and an interesting clinical feature a malaria crisis. (author)

Drug-drug interactions involving lysosomes: mechanisms and potential clinical implications.

Science.gov (United States)

Logan, Randall; Funk, Ryan S; Axcell, Erick; Krise, Jeffrey P

2012-08-01

Many commercially available, weakly basic drugs have been shown to be lysosomotropic, meaning they are subject to extensive sequestration in lysosomes through an ion trapping-type mechanism. The extent of lysosomal trapping of a drug is an important therapeutic consideration because it can influence both activity and pharmacokinetic disposition. The administration of certain drugs can alter lysosomes such that their accumulation capacity for co-administered and/or secondarily administered drugs is altered. In this review the authors explore what is known regarding the mechanistic basis for drug-drug interactions involving lysosomes. Specifically, the authors address the influence of drugs on lysosomal pH, volume and lipid processing. Many drugs are known to extensively accumulate in lysosomes and significantly alter their structure and function; however, the therapeutic and toxicological implications of this remain controversial. The authors propose that drug-drug interactions involving lysosomes represent an important potential source of variability in drug activity and pharmacokinetics. Most evaluations of drug-drug interactions involving lysosomes have been performed in cultured cells and isolated tissues. More comprehensive in vivo evaluations are needed to fully explore the impact of this drug-drug interaction pathway on therapeutic outcomes.

Playing Goffman's Information Game: A Classroom Activity Involving Student Interactions

Science.gov (United States)

McCoy, Charles Allan

2017-01-01

Goffman's dramaturgical approach is frequently used to introduce undergraduate students to the sociological understanding of human interaction. While a number of scholars have designed engaging student activities that highlight Goffman's approach, most of these activities tend to involve atypical embarrassing interactions or norm-breaking…

Non-Linear Dynamics and Fundamental Interactions

CERN Document Server

Khanna, Faqir

2006-01-01

The book is directed to researchers and graduate students pursuing an advanced degree. It provides details of techniques directed towards solving problems in non-linear dynamics and chos that are, in general, not amenable to a perturbative treatment. The consideration of fundamental interactions is a prime example where non-perturbative techniques are needed. Extension of these techniques to finite temperature problems is considered. At present these ideas are primarily used in a perturbative context. However, non-perturbative techniques have been considered in some specific cases. Experts in the field on non-linear dynamics and chaos and fundamental interactions elaborate the techniques and provide a critical look at the present status and explore future directions that may be fruitful. The text of the main talks will be very useful to young graduate students who are starting their studies in these areas.

Interactive macroeconomics stochastic aggregate dynamics with heterogeneous and interacting agents

CERN Document Server

Di Guilmi, Corrado

2017-01-01

One of the major problems of macroeconomic theory is the way in which the people exchange goods in decentralized market economies. There are major disagreements among macroeconomists regarding tools to influence required outcomes. Since the mainstream efficient market theory fails to provide an internal coherent framework, there is a need for an alternative theory. The book provides an innovative approach for the analysis of agent based models, populated by the heterogeneous and interacting agents in the field of financial fragility. The text is divided in two parts; the first presents analytical developments of stochastic aggregation and macro-dynamics inference methods. The second part introduces macroeconomic models of financial fragility for complex systems populated by heterogeneous and interacting agents. The concepts of financial fragility and macroeconomic dynamics are explained in detail in separate chapters. The statistical physics approach is applied to explain theories of macroeconomic modelling a...

Modelling dynamic human-device interaction in healthcare

OpenAIRE

Niezen, Gerrit

2013-01-01

Errors are typically blamed on human factors, forgetting that the system should have been designed to take them into account and minimise these problems. In our research we are developing tools to design interactive medical devices using human-in-the-loop modelling. Manual control theory is used to describe and analyse the dynamic aspects of human-device interaction.

Study on Human-structure Dynamic Interaction in Civil Engineering

Science.gov (United States)

Gao, Feng; Cao, Li Lin; Li, Xing Hua

2018-06-01

The research of human-structure dynamic interaction are reviewed. Firstly, the influence of the crowd load on structural dynamic characteristics is introduced and the advantages and disadvantages of different crowd load models are analyzed. Then, discussing the influence of structural vibration on the human-induced load, especially the influence of different stiffness structures on the crowd load. Finally, questions about human-structure interaction that require further study are presented.

Interaction Involvement: A Cognitive Dimension of Communicative Competence.

Science.gov (United States)

Cegala, Donald J.

1981-01-01

Presents a conceptual and operational definition of one cognitive dimension of communicative competence--interaction involvement--based on Goffman's model of face-to-face society. Reports two studies to support the validity of the definition. Outlines the implications for future research on communicative competence as well as instructional…

Integration of Structural Dynamics and Molecular Evolution via Protein Interaction Networks: A New Era in Genomic Medicine

Science.gov (United States)

Kumar, Avishek; Butler, Brandon M.; Kumar, Sudhir; Ozkan, S. Banu

2016-01-01

Summary Sequencing technologies are revealing many new non-synonymous single nucleotide variants (nsSNVs) in each personal exome. To assess their functional impacts, comparative genomics is frequently employed to predict if they are benign or not. However, evolutionary analysis alone is insufficient, because it misdiagnoses many disease-associated nsSNVs, such as those at positions involved in protein interfaces, and because evolutionary predictions do not provide mechanistic insights into functional change or loss. Structural analyses can aid in overcoming both of these problems by incorporating conformational dynamics and allostery in nSNV diagnosis. Finally, protein-protein interaction networks using systems-level methodologies shed light onto disease etiology and pathogenesis. Bridging these network approaches with structurally resolved protein interactions and dynamics will advance genomic medicine. PMID:26684487

Identification of Inhibitors of Biological Interactions Involving Intrinsically Disordered Proteins

Directory of Open Access Journals (Sweden)

Daniela Marasco

2015-04-01

Full Text Available Protein–protein interactions involving disordered partners have unique features and represent prominent targets in drug discovery processes. Intrinsically Disordered Proteins (IDPs are involved in cellular regulation, signaling and control: they bind to multiple partners and these high-specificity/low-affinity interactions play crucial roles in many human diseases. Disordered regions, terminal tails and flexible linkers are particularly abundant in DNA-binding proteins and play crucial roles in the affinity and specificity of DNA recognizing processes. Protein complexes involving IDPs are short-lived and typically involve short amino acid stretches bearing few “hot spots”, thus the identification of molecules able to modulate them can produce important lead compounds: in this scenario peptides and/or peptidomimetics, deriving from structure-based, combinatorial or protein dissection approaches, can play a key role as hit compounds. Here, we propose a panoramic review of the structural features of IDPs and how they regulate molecular recognition mechanisms focusing attention on recently reported drug-design strategies in the field of IDPs.

Potyvirus helper component-proteinase self-interaction in the yeast two-hybrid system and delineation of the interaction domain involved.

Science.gov (United States)

Urcuqui-Inchima, S; Walter, J; Drugeon, G; German-Retana, S; Haenni, A L; Candresse, T; Bernardi, F; Le Gall, O

1999-05-25

Using the yeast two-hybrid system, a screen was performed for possible interactions between the proteins encoded by the 5' region of potyviral genomes [P1, helper component-proteinase (HC-Pro), and P3]. A positive self-interaction involving HC-Pro was detected with lettuce mosaic virus (LMV) and potato virus Y (PVY). The possibility of heterologous interaction between the HC-Pro of LMV and of PVY was also demonstrated. No interaction involving either the P1 or the P3 proteins was detected. A series of ordered deletions from either the N- or C-terminal end of the LMV HC-Pro was used to map the domain involved in interaction to the 72 N-terminal amino acids of the protein, a region known to be dispensable for virus viability but necessary for aphid transmission. A similar but less detailed analysis mapped the interacting domain to the N-terminal half of the PVY HC-Pro. Copyright 1999 Academic Press.

Dynamics of Strong Interactions and the S-Matrix

Energy Technology Data Exchange (ETDEWEB)

Omnes, R. [Laboratoire de Physique Theorique et Hautes Energies, Universite de Paris, Orsay (France)

1969-08-15

The physical principles underlying the S-matrix theory of strong interactions are reviewed. In particular, the problem of whether these principles are sufficient to completely determine the S-matrix, i.e. to yield a dynamical theory of strong interactions, is discussed. (author)

Coulomb interactions via local dynamics: a molecular-dynamics algorithm

International Nuclear Information System (INIS)

Pasichnyk, Igor; Duenweg, Burkhard

2004-01-01

We derive and describe in detail a recently proposed method for obtaining Coulomb interactions as the potential of mean force between charges which are dynamically coupled to a local electromagnetic field. We focus on the molecular dynamics version of the method and show that it is intimately related to the Car-Parrinello approach, while being equivalent to solving Maxwell's equations with a freely adjustable speed of light. Unphysical self-energies arise as a result of the lattice interpolation of charges, and are corrected by a subtraction scheme based on the exact lattice Green function. The method can be straightforwardly parallelized using standard domain decomposition. Some preliminary benchmark results are presented

DyNet: visualization and analysis of dynamic molecular interaction networks.

Science.gov (United States)

Goenawan, Ivan H; Bryan, Kenneth; Lynn, David J

2016-09-01

: The ability to experimentally determine molecular interactions on an almost proteome-wide scale under different conditions is enabling researchers to move from static to dynamic network analysis, uncovering new insights into how interaction networks are physically rewired in response to different stimuli and in disease. Dynamic interaction data presents a special challenge in network biology. Here, we present DyNet, a Cytoscape application that provides a range of functionalities for the visualization, real-time synchronization and analysis of large multi-state dynamic molecular interaction networks enabling users to quickly identify and analyze the most 'rewired' nodes across many network states. DyNet is available at the Cytoscape (3.2+) App Store (http://apps.cytoscape.org/apps/dynet). david.lynn@sahmri.com Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Dynamics of interaction of ultrashort laser pulses with solid targets

International Nuclear Information System (INIS)

Cang Yu; Wang Wei; Zhang Jie

2001-01-01

Using Saha equation, a simple model is proposed for the dynamics of interaction between ultrashort laser pulses and solid targets. An adiabatic expansion model is adopted to study the expansion phase after the heating phase. Temporal evolvement of the dynamics of the interaction is obtained, from which the electron temperature, density, ionization balances can be determined

Parental and Infant Gender Factors in Parent-Infant Interaction: State-Space Dynamic Analysis.

Science.gov (United States)

Cerezo, M Angeles; Sierra-García, Purificación; Pons-Salvador, Gemma; Trenado, Rosa M

2017-01-01

This study aimed to investigate the influence of parental gender on their interaction with their infants, considering, as well, the role of the infant's gender. The State Space Grid (SSG) method, a graphical tool based on the non-linear dynamic system (NDS) approach was used to analyze the interaction, in Free-Play setting, of 52 infants, aged 6 to 10 months, divided into two groups: half of the infants interacted with their fathers and half with their mothers. There were 50% boys in each group. MANOVA results showed no differential parenting of boys and girls. Additionally, mothers and fathers showed no differences in the Diversity of behavioral dyadic states nor in Predictability. However, differences associated with parent's gender were found in that the paternal dyads were more "active" than the maternal dyads: they were faster in the rates per second of behavioral events and transitions or change of state. In contrast, maternal dyads were more repetitive because, once they visited a certain dyadic state, they tend to be involved in more events. Results showed a significant discriminant function on the parental groups, fathers and mothers. Specifically, the content analyses carried out for the three NDS variables, that previously showed differences between groups, showed particular dyadic behavioral states associated with the rate of Transitions and the Events per Visit ratio. Thus, the transitions involving 'in-out' of 'Child Social Approach neutral - Sensitive Approach neutral' state and the repetitions of events in the dyadic state 'Child Play-Sensitive Approach neutral' distinguished fathers from mothers. The classification of dyads (with fathers and mothers) based on this discriminant function identified 73.10% (19/26) of the father-infant dyads and 88.5% (23/26) of the mother-infant dyads. The study of father-infant interaction using the SSG approach offers interesting possibilities because it characterizes and quantifies the actual moment-to-moment flow

Parental and Infant Gender Factors in Parent–Infant Interaction: State-Space Dynamic Analysis

Directory of Open Access Journals (Sweden)

M. Angeles Cerezo

2017-10-01

Full Text Available This study aimed to investigate the influence of parental gender on their interaction with their infants, considering, as well, the role of the infant’s gender. The State Space Grid (SSG method, a graphical tool based on the non-linear dynamic system (NDS approach was used to analyze the interaction, in Free-Play setting, of 52 infants, aged 6 to 10 months, divided into two groups: half of the infants interacted with their fathers and half with their mothers. There were 50% boys in each group. MANOVA results showed no differential parenting of boys and girls. Additionally, mothers and fathers showed no differences in the Diversity of behavioral dyadic states nor in Predictability. However, differences associated with parent’s gender were found in that the paternal dyads were more “active” than the maternal dyads: they were faster in the rates per second of behavioral events and transitions or change of state. In contrast, maternal dyads were more repetitive because, once they visited a certain dyadic state, they tend to be involved in more events. Results showed a significant discriminant function on the parental groups, fathers and mothers. Specifically, the content analyses carried out for the three NDS variables, that previously showed differences between groups, showed particular dyadic behavioral states associated with the rate of Transitions and the Events per Visit ratio. Thus, the transitions involving ‘in–out’ of ‘Child Social Approach neutral – Sensitive Approach neutral’ state and the repetitions of events in the dyadic state ‘Child Play-Sensitive Approach neutral’ distinguished fathers from mothers. The classification of dyads (with fathers and mothers based on this discriminant function identified 73.10% (19/26 of the father–infant dyads and 88.5% (23/26 of the mother–infant dyads. The study of father-infant interaction using the SSG approach offers interesting possibilities because it characterizes and

Entanglement Growth in Quench Dynamics with Variable Range Interactions

Directory of Open Access Journals (Sweden)

J. Schachenmayer

2013-09-01

Full Text Available Studying entanglement growth in quantum dynamics provides both insight into the underlying microscopic processes and information about the complexity of the quantum states, which is related to the efficiency of simulations on classical computers. Recently, experiments with trapped ions, polar molecules, and Rydberg excitations have provided new opportunities to observe dynamics with long-range interactions. We explore nonequilibrium coherent dynamics after a quantum quench in such systems, identifying qualitatively different behavior as the exponent of algebraically decaying spin-spin interactions in a transverse Ising chain is varied. Computing the buildup of bipartite entanglement as well as mutual information between distant spins, we identify linear growth of entanglement entropy corresponding to propagation of quasiparticles for shorter-range interactions, with the maximum rate of growth occurring when the Hamiltonian parameters match those for the quantum phase transition. Counterintuitively, the growth of bipartite entanglement for long-range interactions is only logarithmic for most regimes, i.e., substantially slower than for shorter-range interactions. Experiments with trapped ions allow for the realization of this system with a tunable interaction range, and we show that the different phenomena are robust for finite system sizes and in the presence of noise. These results can act as a direct guide for the generation of large-scale entanglement in such experiments, towards a regime where the entanglement growth can render existing classical simulations inefficient.

Lexical Cues of Interaction Involvement in Dyadic Instant Messaging Conversations

Science.gov (United States)

Nguyen, Duyen T.; Fussell, Susan R.

2014-01-01

We explore how people express and interpret lexical cues of interaction involvement in dyadic conversations via instant messaging (IM) in two studies. In Study 1, an experiment with 60 participants, we manipulated level of involvement in a conversation with a distraction task. We examined how participants' uses of verbal cues such as pronouns…

Communicative interactions involving plants: information, evolution, and ecology.

Science.gov (United States)

Mescher, Mark C; Pearse, Ian S

2016-08-01

The role of information obtained via sensory cues and signals in mediating the interactions of organisms with their biotic and abiotic environments has been a major focus of work on sensory and behavioral ecology. Information-mediated interactions also have important implications for broader ecological patterns emerging at the community and ecosystem levels that are only now beginning to be explored. Given the extent to which plants dominate the sensory landscapes of terrestrial ecosystems, information-mediated interactions involving plants should be a major focus of efforts to elucidate these broader patterns. Here we explore how such efforts might be enhanced by a clear understanding of information itself-a central and potentially unifying concept in biology that has nevertheless been the subject of considerable confusion-and of its relationship to adaptive evolution and ecology. We suggest that information-mediated interactions should be a key focus of efforts to more fully integrate evolutionary biology and ecology. Copyright © 2016 Elsevier Ltd. All rights reserved.

Integration of structural dynamics and molecular evolution via protein interaction networks: a new era in genomic medicine.

Science.gov (United States)

Kumar, Avishek; Butler, Brandon M; Kumar, Sudhir; Ozkan, S Banu

2015-12-01

Sequencing technologies are revealing many new non-synonymous single nucleotide variants (nsSNVs) in each personal exome. To assess their functional impacts, comparative genomics is frequently employed to predict if they are benign or not. However, evolutionary analysis alone is insufficient, because it misdiagnoses many disease-associated nsSNVs, such as those at positions involved in protein interfaces, and because evolutionary predictions do not provide mechanistic insights into functional change or loss. Structural analyses can aid in overcoming both of these problems by incorporating conformational dynamics and allostery in nSNV diagnosis. Finally, protein-protein interaction networks using systems-level methodologies shed light onto disease etiology and pathogenesis. Bridging these network approaches with structurally resolved protein interactions and dynamics will advance genomic medicine. Copyright © 2015 Elsevier Ltd. All rights reserved.

Dynamics of the diffusive DM-DE interaction – Dynamical system approach

Energy Technology Data Exchange (ETDEWEB)

Haba, Zbigniew [Institute of Theoretical Physics, University of Wroclaw, Plac Maxa Borna 9, 50-204 Wrocław (Poland); Stachowski, Aleksander; Szydłowski, Marek, E-mail: zhab@ift.uni.wroc.pl, E-mail: aleksander.stachowski@uj.edu.pl, E-mail: marek.szydlowski@uj.edu.pl [Astronomical Observatory, Jagiellonian University, Orla 171, 30-244 Krakow (Poland)

2016-07-01

We discuss dynamics of a model of an energy transfer between dark energy (DE) and dark matter (DM) . The energy transfer is determined by a non-conservation law resulting from a diffusion of dark matter in an environment of dark energy. The relativistic invariance defines the diffusion in a unique way. The system can contain baryonic matter and radiation which do not interact with the dark sector. We treat the Friedman equation and the conservation laws as a closed dynamical system. The dynamics of the model is examined using the dynamical systems methods for demonstration how solutions depend on initial conditions. We also fit the model parameters using astronomical observation: SNIa, H ( z ), BAO and Alcock-Paczynski test. We show that the model with diffuse DM-DE is consistent with the data.

Boundary element method in dynamic interaction of structures with multilayers media

International Nuclear Information System (INIS)

Mihalache, N.; Poterasu, V.F.

1993-01-01

The paper presents the problems of dynamic interaction between the multilayers media and structure by means of B.E.M., using Green's functions. The structure considered by the authors as a particular problem concerns a reinforced concrete shear wall and soil foundation of three layers having different thickness and mechanical characteristics. The authors will present comparatively the stresses and the displacements in static and dynamic regime interaction response of the structure. Theoretical part of the paper presents: Green's functions for the multilayers media in dynamic regime, stiffness matrices, stresses and displacements in the multilayers media exprimed by means of the Green's functions induced by the shear and horizontal forces, computer program, consideration for dynamic, structure-foundation-multilayers soil foundation interaction. (author)

Control dynamics of interaction quenched ultracold bosons in periodically driven lattices

Science.gov (United States)

Mistakidis, Simeon; Schmelcher, Peter; Group of Fundamental Processes in Quantum Physics Team

2016-05-01

The out-of-equilibrium dynamics of ultracold bosons following an interaction quench upon a periodically driven optical lattice is investigated. It is shown that an interaction quench triggers the inter-well tunneling dynamics, while for the intra-well dynamics breathing and cradle-like processes can be generated. In particular, the occurrence of a resonance between the cradle and tunneling modes is revealed. On the other hand, the employed periodic driving enforces the bosons in the mirror wells to oscillate out-of-phase and to exhibit a dipole mode, while in the central well the cloud experiences a breathing mode. The dynamical behaviour of the system is investigated with respect to the driving frequency revealing a resonant behaviour of the intra-well dynamics. To drive the system in a highly non-equilibrium state an interaction quench upon the driving is performed giving rise to admixtures of excitations in the outer wells, an enhanced breathing in the center and an amplification of the tunneling dynamics. As a result of the quench the system experiences multiple resonances between the inter- and intra-well dynamics at different quench amplitudes. Deutsche Forschungsgemeinschaft, SFB 925 ``Light induced dynamics and control of correlated quantum systems''.

DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions.

Science.gov (United States)

Lambrughi, Matteo; De Gioia, Luca; Gervasio, Francesco Luigi; Lindorff-Larsen, Kresten; Nussinov, Ruth; Urani, Chiara; Bruschi, Maurizio; Papaleo, Elena

2016-11-02

Binding-induced conformational changes of a protein at regions distant from the binding site may play crucial roles in protein function and regulation. The p53 tumour suppressor is an example of such an allosterically regulated protein. Little is known, however, about how DNA binding can affect distal sites for transcription factors. Furthermore, the molecular details of how a local perturbation is transmitted through a protein structure are generally elusive and occur on timescales hard to explore by simulations. Thus, we employed state-of-the-art enhanced sampling atomistic simulations to unveil DNA-induced effects on p53 structure and dynamics that modulate the recruitment of cofactors and the impact of phosphorylation at Ser215. We show that DNA interaction promotes a conformational change in a region 3 nm away from the DNA binding site. Specifically, binding to DNA increases the population of an occluded minor state at this distal site by more than 4-fold, whereas phosphorylation traps the protein in its major state. In the minor conformation, the interface of p53 that binds biological partners related to p53 transcription-independent functions is not accessible. Significantly, our study reveals a mechanism of DNA-mediated protection of p53 from interactions with partners involved in the p53 transcription-independent signalling. This also suggests that conformational dynamics is tightly related to p53 signalling. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Correlations and symmetry of interactions influence collective dynamics of molecular motors

International Nuclear Information System (INIS)

Celis-Garza, Daniel; Teimouri, Hamid; Kolomeisky, Anatoly B

2015-01-01

Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and they frequently work together in large groups. To understand the mechanisms of collective behavior of motor proteins we study the effect of interactions in the transport of molecular motors along linear filaments. It is done by analyzing a recently introduced class of totally asymmetric exclusion processes that takes into account the intermolecular interactions via thermodynamically consistent approach. We develop a new theoretical method that allows us to compute analytically all dynamic properties of the system. Our analysis shows that correlations play important role in dynamics of interacting molecular motors. Surprisingly, we find that the correlations for repulsive interactions are weaker and more short-range than the correlations for the attractive interactions. In addition, it is shown that symmetry of interactions affect dynamic properties of molecular motors. The implications of these findings for motor proteins transport are discussed. Our theoretical predictions are tested by extensive Monte Carlo computer simulations. (paper)

Anandamide-ceramide interactions in a membrane environment: Molecular dynamic simulations data.

Science.gov (United States)

Di Scala, Coralie; Mazzarino, Morgane; Yahi, Nouara; Varini, Karine; Garmy, Nicolas; Fantini, Jacques; Chahinian, Henri

2017-10-01

Anandamide is a lipid neurotransmitter that interacts with various plasma membrane lipids. The data here consists of molecular dynamics simulations of anandamide, C18-ceramide and cholesterol performed in vacuo and within a hydrated palmitoyl-oleoyl-phosphatidylcholine (POPC)/cholesterol membrane. Several models of anandamide/cholesterol and anandamide/ceramide complexes are presented. The energy of interaction and the nature of the intermolecular forces involved in each of these complexes are detailed. The impact of water molecules hydrating the POPC/cholesterol membrane for the stability of the anandamide/cholesterol and anandamide/ceramide complexes is also analyzed. From a total number of 1920 water molecules stochatiscally merged with the lipid matrix, 48 were eventually redistributed around the polar head groups of the anandamide/ceramide complex, whereas only 15 reached with the anandamide/cholesterol complex. The interpretation of this dataset is presented in the accompanying article "Ceramide binding to anandamide increases its half-life and potentiates its cytotoxicity in human neuroblastoma cells" [1].

Affective Dynamics in Triadic Peer Interactions in Early Childhood

NARCIS (Netherlands)

Lavictoire, L.A.; Snyder, J.; Stoolmiller, M.; Hollenstein, T.P.

2012-01-01

In interpersonal interaction research, moving beyond dyadic to triadic dynamics can be analytically daunting. We explored the affective states expressed during triadic peer interactions to understand how patterns were associated with childhood psychopathology and sociometric status. High-risk

Drum-mate: interaction dynamics and gestures in human-humanoid drumming experiments

Science.gov (United States)

Kose-Bagci, Hatice; Dautenhahn, Kerstin; Syrdal, Dag S.; Nehaniv, Chrystopher L.

2010-06-01

This article investigates the role of interaction kinesics in human-robot interaction (HRI). We adopted a bottom-up, synthetic approach towards interactive competencies in robots using simple, minimal computational models underlying the robot's interaction dynamics. We present two empirical, exploratory studies investigating a drumming experience with a humanoid robot (KASPAR) and a human. In the first experiment, the turn-taking behaviour of the humanoid is deterministic and the non-verbal gestures of the robot accompany its drumming to assess the impact of non-verbal gestures on the interaction. The second experiment studies a computational framework that facilitates emergent turn-taking dynamics, whereby the particular dynamics of turn-taking emerge from the social interaction between the human and the humanoid. The results from the HRI experiments are presented and analysed qualitatively (in terms of the participants' subjective experiences) and quantitatively (concerning the drumming performance of the human-robot pair). The results point out a trade-off between the subjective evaluation of the drumming experience from the perspective of the participants and the objective evaluation of the drumming performance. A certain number of gestures was preferred as a motivational factor in the interaction. The participants preferred the models underlying the robot's turn-taking which enable the robot and human to interact more and provide turn-taking closer to 'natural' human-human conversations, despite differences in objective measures of drumming behaviour. The results are consistent with the temporal behaviour matching hypothesis previously proposed in the literature which concerns the effect that the participants adapt their own interaction dynamics to the robot's.

Interaction dynamics of multiple mobile robots with simple navigation strategies

Science.gov (United States)

Wang, P. K. C.

1989-01-01

The global dynamic behavior of multiple interacting autonomous mobile robots with simple navigation strategies is studied. Here, the effective spatial domain of each robot is taken to be a closed ball about its mass center. It is assumed that each robot has a specified cone of visibility such that interaction with other robots takes place only when they enter its visibility cone. Based on a particle model for the robots, various simple homing and collision-avoidance navigation strategies are derived. Then, an analysis of the dynamical behavior of the interacting robots in unbounded spatial domains is made. The article concludes with the results of computer simulations studies of two or more interacting robots.

Monitoring peptide-surface interaction by means of molecular dynamics simulation

Energy Technology Data Exchange (ETDEWEB)

Nonella, Marco, E-mail: mnonella@pci.uzh.ch [Physikalisch-Chemisches Institut, Universitaet Zuerich, Winterthurerstrasse 190, CH-8057 Zuerich (Switzerland); Seeger, Stefan, E-mail: sseeger@pci.uzh.ch [Physikalisch-Chemisches Institut, Universitaet Zuerich, Winterthurerstrasse 190, CH-8057 Zuerich (Switzerland)

2010-12-09

Graphical abstract: Protein-surface interactions play a crucial role in a wide field of research areas like biology, biotechnology, or pharmacology. Only recently, it has been shown that not only peptide adsorption represents an important process but also spreading and clustering of adsorbed proteins. By means of classical molecular dynamics, peptide adsorption as well as the dynamics of adsorbed peptides have been investigated in order to gain deeper insight into such processes. The picture shows a snapshot of an adsorbed peptide on a silica surface showing strong direct hydrogen bonding. Research highlights: {yields} Simulation of peptide surface interaction. {yields} Dynamics of hydrogen bond formation and destruction. {yields} Internal flexibility of adsorbed peptides. - Abstract: Protein adsorption and protein surface interactions have become an important research topic in recent years. Very recently, for example, it has been shown that protein clusters can undergo a surface-induced spreading after adsorption. Such phenomena emphasize the need of a more detailed insight into protein-silica interaction at an atomic level. Therefore, we have studied a model system consisting of a short peptide, a silica slab, and water molecules by means of classical molecular dynamics simulations. The study reveals that, besides of electrostatic interactions caused by the chosen charge distribution, the peptide interacts with the silica surface through formation of direct peptide-surface hydrogen bonds as well as indirect peptide-water-surface hydrogen bonds. The number of created hydrogen bonds varies considerably among the simulated structures. The strength of hydrogen bonding determines the mobility of the peptide on the surface and the internal flexibility of the adsorbed peptide.

Spin and orbital exchange interactions from Dynamical Mean Field Theory

Energy Technology Data Exchange (ETDEWEB)

Secchi, A., E-mail: a.secchi@science.ru.nl [Radboud University, Institute for Molecules and Materials, 6525 AJ Nijmegen (Netherlands); Lichtenstein, A.I., E-mail: alichten@physnet.uni-hamburg.de [Universitat Hamburg, Institut für Theoretische Physik, Jungiusstraße 9, D-20355 Hamburg (Germany); Katsnelson, M.I., E-mail: m.katsnelson@science.ru.nl [Radboud University, Institute for Molecules and Materials, 6525 AJ Nijmegen (Netherlands)

2016-02-15

We derive a set of equations expressing the parameters of the magnetic interactions characterizing a strongly correlated electronic system in terms of single-electron Green's functions and self-energies. This allows to establish a mapping between the initial electronic system and a spin model including up to quadratic interactions between the effective spins, with a general interaction (exchange) tensor that accounts for anisotropic exchange, Dzyaloshinskii–Moriya interaction and other symmetric terms such as dipole–dipole interaction. We present the formulas in a format that can be used for computations via Dynamical Mean Field Theory algorithms. - Highlights: • We give formulas for the exchange interaction tensor in strongly correlated systems. • Interactions are written in terms of electronic Green's functions and self-energies. • The method is suitable for a Dynamical Mean Field Theory implementation. • No quenching of the orbital magnetic moments is assumed. • Spin and orbital contributions to magnetism can be computed separately.

Shape Displays: Spatial Interaction with Dynamic Physical Form.

Science.gov (United States)

Leithinger, Daniel; Follmer, Sean; Olwal, Alex; Ishii, Hiroshi

2015-01-01

Shape displays are an emerging class of devices that emphasize actuation to enable rich physical interaction, complementing concepts in virtual and augmented reality. The ability to render form introduces new opportunities to touch, grasp, and manipulate dynamic physical content and tangible objects, in both nearby and remote environments. This article presents novel hardware, interaction techniques, and applications, which point to the potential for extending the ways that we traditionally interact with the physical world, empowered by digital computation.

Magnetic dynamics of weakly and strongly interacting hematite nanoparticles

DEFF Research Database (Denmark)

Hansen, Mikkel Fougt; Bender Koch, Christian; Mørup, Steen

2000-01-01

The magnetic dynamics of two differently treated samples of hematite nanoparticles from the same batch with a particle size of about 20 nm have been studied by Mossbauer spectroscopy. The dynamics of the first sample, in which the particles are coated and dispersed in water, is in accordance with...... down by interparticle interactions and a magnetically split spectrum is retained at room temperature. The temperature variation or the magnetic hyperfine field, corresponding to different quantiles in the hyperfine field distribution, can be consistently described by a mean field model...... for "superferromagnetism" in which the magnetic anisotropy is included. The coupling between the particles is due to exchange interactions and the interaction strength can be accounted for by just a few exchange bridges between surface atoms in neighboring crystallites....

Interactive methods to involve users into workspace design process

DEFF Research Database (Denmark)

Souza da Conceição, Carolina; Broberg, Ole; Banke, Palle

2013-01-01

This paper addresses the question of whether the use of a combination of interactive methods involving workers can lead to a useful input to the (re)design of their workspace. The workbook and the layout design game methods were tested, and a comparison between their use and the ergonomic analysi...

In-Culture Cross-Linking of Bacterial Cells Reveals Large-Scale Dynamic Protein-Protein Interactions at the Peptide Level.

Science.gov (United States)

de Jong, Luitzen; de Koning, Edward A; Roseboom, Winfried; Buncherd, Hansuk; Wanner, Martin J; Dapic, Irena; Jansen, Petra J; van Maarseveen, Jan H; Corthals, Garry L; Lewis, Peter J; Hamoen, Leendert W; de Koster, Chris G

2017-07-07

Identification of dynamic protein-protein interactions at the peptide level on a proteomic scale is a challenging approach that is still in its infancy. We have developed a system to cross-link cells directly in culture with the special lysine cross-linker bis(succinimidyl)-3-azidomethyl-glutarate (BAMG). We used the Gram-positive model bacterium Bacillus subtilis as an exemplar system. Within 5 min extensive intracellular cross-linking was detected, while intracellular cross-linking in a Gram-negative species, Escherichia coli, was still undetectable after 30 min, in agreement with the low permeability in this organism for lipophilic compounds like BAMG. We were able to identify 82 unique interprotein cross-linked peptides with cross-links occur in assemblies involved in transcription and translation. Several of these interactions are new, and we identified a binding site between the δ and β' subunit of RNA polymerase close to the downstream DNA channel, providing a clue into how δ might regulate promoter selectivity and promote RNA polymerase recycling. Our methodology opens new avenues to investigate the functional dynamic organization of complex protein assemblies involved in bacterial growth. Data are available via ProteomeXchange with identifier PXD006287.

Dynamic Soil-Pile Interaction for large diameter monopile foundations

DEFF Research Database (Denmark)

Zania, Varvara

2013-01-01

of the study is to analyse the dynamic interaction of the soil and a single pile embedded in it by accounting for the geometric and stiffness properties of the pile. In doing so, a semi – analytical approach is adopted based on the fundamental solution of horizontal pile vibration by Novak and Nogami (1977...... eigenfrequencies of the soil layer do not affect the soil – pile interaction. The decrease of the eigefrequency of the OWT depends on the aforementioned variation of the dynamic stiffness and the slenderness ratio of the monopile.......Monopile foundations have been used in a large extent to support offshore wind turbines (OWT), being considered as a reliable and cost effective design solution. The accurate estimation of their dynamic response characteristics is essential, since the design of support structures for OWTs has been...

Crowding of Interacting Fluid Particles in Porous Media through Molecular Dynamics: Breakdown of Universality for Soft Interactions

Science.gov (United States)

Schnyder, Simon K.; Horbach, Jürgen

2018-02-01

Molecular dynamics simulations of interacting soft disks confined in a heterogeneous quenched matrix of soft obstacles show dynamics which is fundamentally different from that of hard disks. The interactions between the disks can enhance transport when their density is increased, as disks cooperatively help each other over the finite energy barriers in the matrix. The system exhibits a transition from a diffusive to a localized state, but the transition is strongly rounded. Effective exponents in the mean-squared displacement can be observed over three decades in time but depend on the density of the disks and do not correspond to asymptotic behavior in the vicinity of a critical point, thus, showing that it is incorrect to relate them to the critical exponents in the Lorentz model scenario. The soft interactions are, therefore, responsible for a breakdown of the universality of the dynamics.

Aerosol interactions with African/Atlantic climate dynamics

International Nuclear Information System (INIS)

Hosseinpour, F; Wilcox, E M

2014-01-01

Mechanistic relationships exist between variability of dust in the oceanic Saharan air layer (OSAL) and transient changes in the dynamics of Western Africa and the tropical Atlantic Ocean. This study provides evidence of possible interactions between dust in the OSAL region and African easterly jet–African easterly wave (AEJ–AEW) system in the climatology of boreal summer, when easterly wave activity peaks. Synoptic-scale changes in instability and precipitation in the African/Atlantic intertropical convergence zone are correlated with enhanced aerosol optical depth (AOD) in the OSAL region in response to anomalous 3D overturning circulations and upstream/downstream thermal anomalies at above and below the mean-AEJ level. Upstream and downstream anomalies are referred to the daily thermal/dynamical changes over the West African monsoon region and the Eastern Atlantic Ocean, respectively. Our hypothesis is that AOD in the OSAL is positively correlated with the downstream AEWs and negatively correlated with the upstream waves from climatological perspective. The similarity between the 3D pattern of thermal/dynamical anomalies correlated with dust outbreaks and those of AEWs provides a mechanism for dust radiative heating in the atmosphere to reinforce AEW activity. We proposed that the interactions of OSAL dust with regional climate mainly occur through coupling of dust with the AEWs. (paper)

Dynamic Analysis of Partially Embedded Structures Considering Soil-Structure Interaction in Time Domain

OpenAIRE

Mahmoudpour, Sanaz; Attarnejad, Reza; Behnia, Cambyse

2011-01-01

Analysis and design of structures subjected to arbitrary dynamic loadings especially earthquakes have been studied during past decades. In practice, the effects of soil-structure interaction on the dynamic response of structures are usually neglected. In this study, the effect of soil-structure interaction on the dynamic response of structures has been examined. The substructure method using dynamic stiffness of soil is used to analyze soil-structure system. A coupled model based on finite el...

An iterative method for hydrodynamic interactions in Brownian dynamics simulations of polymer dynamics

Science.gov (United States)

Miao, Linling; Young, Charles D.; Sing, Charles E.

2017-07-01

Brownian Dynamics (BD) simulations are a standard tool for understanding the dynamics of polymers in and out of equilibrium. Quantitative comparison can be made to rheological measurements of dilute polymer solutions, as well as direct visual observations of fluorescently labeled DNA. The primary computational challenge with BD is the expensive calculation of hydrodynamic interactions (HI), which are necessary to capture physically realistic dynamics. The full HI calculation, performed via a Cholesky decomposition every time step, scales with the length of the polymer as O(N3). This limits the calculation to a few hundred simulated particles. A number of approximations in the literature can lower this scaling to O(N2 - N2.25), and explicit solvent methods scale as O(N); however both incur a significant constant per-time step computational cost. Despite this progress, there remains a need for new or alternative methods of calculating hydrodynamic interactions; large polymer chains or semidilute polymer solutions remain computationally expensive. In this paper, we introduce an alternative method for calculating approximate hydrodynamic interactions. Our method relies on an iterative scheme to establish self-consistency between a hydrodynamic matrix that is averaged over simulation and the hydrodynamic matrix used to run the simulation. Comparison to standard BD simulation and polymer theory results demonstrates that this method quantitatively captures both equilibrium and steady-state dynamics after only a few iterations. The use of an averaged hydrodynamic matrix allows the computationally expensive Brownian noise calculation to be performed infrequently, so that it is no longer the bottleneck of the simulation calculations. We also investigate limitations of this conformational averaging approach in ring polymers.

Dynamical screening of the van der Waals interaction between graphene layers

International Nuclear Information System (INIS)

Dappe, Y J; Bolcatto, P G; Ortega, J; Flores, F

2012-01-01

The interaction between graphene layers is analyzed combining local orbital DFT and second order perturbation theory. For this purpose we use the linear combination of atomic orbitals-orbital occupancy (LCAO-OO) formalism, that allows us to separate the interaction energy as the sum of a weak chemical interaction between graphene layers plus the van der Waals interaction (Dappe et al 2006 Phys. Rev. B 74 205434). In this work, the weak chemical interaction is calculated by means of corrected-LDA calculations using an atomic-like sp 3 d 5 basis set. The van der Waals interaction is calculated by means of second order perturbation theory using an atom-atom interaction approximation and the atomic-like-orbital occupancies. We also analyze the effect of dynamical screening in the van der Waals interaction using a simple model. We find that this dynamical screening reduces by 40% the van der Waals interaction. Taking this effect into account, we obtain a graphene-graphene interaction energy of 70 ± 5 meV/atom in reasonable agreement with the experimental evidence.

Dynamical screening of the van der Waals interaction between graphene layers.

Science.gov (United States)

Dappe, Y J; Bolcatto, P G; Ortega, J; Flores, F

2012-10-24

The interaction between graphene layers is analyzed combining local orbital DFT and second order perturbation theory. For this purpose we use the linear combination of atomic orbitals-orbital occupancy (LCAO-OO) formalism, that allows us to separate the interaction energy as the sum of a weak chemical interaction between graphene layers plus the van der Waals interaction (Dappe et al 2006 Phys. Rev. B 74 205434). In this work, the weak chemical interaction is calculated by means of corrected-LDA calculations using an atomic-like sp(3)d(5) basis set. The van der Waals interaction is calculated by means of second order perturbation theory using an atom-atom interaction approximation and the atomic-like-orbital occupancies. We also analyze the effect of dynamical screening in the van der Waals interaction using a simple model. We find that this dynamical screening reduces by 40% the van der Waals interaction. Taking this effect into account, we obtain a graphene-graphene interaction energy of 70 ± 5 meV/atom in reasonable agreement with the experimental evidence.

Dynamic Speaking Assessments

Science.gov (United States)

Hill, Kent; Sabet, Mehran

2009-01-01

This article describes an attempt to adopt dynamic assessment (DA) methods in classroom speaking assessments. The study reported in this article focused on four particular applications of dynamic speaking assessment (DSA). The first, "mediated assistance" (MA), involves interaction between an assistor and a learner to reveal problems in…

Analysis of the dynamic interaction between SVOCs and airborne particles

DEFF Research Database (Denmark)

Liu, Cong; Shi, Shanshan; Weschler, Charles J.

2013-01-01

A proper quantitative understanding of the dynamic interaction between gas-phase semivolatile organic compounds (SVOCs) and airborne particles is important for human exposure assessment and risk evaluation. Questions regarding how to properly address gas/particle interactions have introduced...

Dynamic soil-structure interactions on embedded buildings

International Nuclear Information System (INIS)

Kobarg, J.; Werkle, H.; Henseleit, O.

1983-01-01

The dynamic soil-structure interaction on the horizontal seismic excitation is investigated on two typical embedded auxiliary buildings of a nuclear power plant. The structure and the soil are modelled by various analytical and numerical methods. Under the condition of the linear viscoelastic theory, i.e. soil characteristic constant in time and independent of strain, the interaction influences between a homogenous soil layer and a structure are analysied for the following parameters: 4) mathematical soil modells; 4) mathematical structure modells; 4) shear wave velocities; 3) embedment conditions; 4) earthquake time histories. (orig.) [de

The dynamics of the nuclei-nuclei interactions at very high energies

International Nuclear Information System (INIS)

Blaizot, J.P.

1988-01-01

The lectures on the dynamics of nuclei-nuclei interactions at very high energies, presented in the Summer School on Nuclear Physics and Particle Physics (1988), are shown. The equation of state of the hadronic matter is analyzed, by means of simple models, and some orders of magnitude can be asserted. The main characteristics of the high energy hadronic interactions are recalled. The basis of the dynamics of the relativistic fluids are given. Applications of this dynamics in the description of the space-time evolution of a plasma, generated by heavy ions collision, are carried out [fr

Interaction dynamics of electrostatic solitary waves

Directory of Open Access Journals (Sweden)

V. L. Krasovsky

1999-01-01

Full Text Available Interaction of nonlinear electrostatic pulses associated with electron phase density holes moving in a collisionless plasma is studied. An elementary event of the interaction is analyzed on the basis of the energy balance in the system consisting of two electrostatic solitary waves. It is established that an intrinsic property of the system is a specific irreversibility caused by a nonadiabatic modification of the internal structure of the holes and their effective heating in the process of the interaction. This dynamical irreversibility is closely connected with phase mixing of the trapped electrons comprising the holes and oscillating in the varying self-consistent potential wells. As a consequence of the irreversibility, the "collisions" of the solitary waves should be treated as "inelastic" ones. This explains the general tendency to the merging of the phase density holes frequently observed in numerical simulation and to corresponding coupling of the solitary waves.

Investigating chaotic wake dynamics past a flapping airfoil and the role of vortex interactions behind the chaotic transition

Science.gov (United States)

Bose, Chandan; Sarkar, Sunetra

2018-04-01

The present study investigates the complex vortex interactions in two-dimensional flow-field behind a symmetric NACA0012 airfoil undergoing a prescribed periodic pitching-plunging motion in low Reynolds number regime. The flow-field transitions from periodic to chaotic through a quasi-periodic route as the plunge amplitude is gradually increased. This study unravels the role of the complex interactions that take place among the main vortex structures in making the unsteady flow-field transition from periodicity to chaos. The leading-edge separation plays a key role in providing the very first trigger for aperiodicity. Subsequent mechanisms like shredding, merging, splitting, and collision of vortices in the near-field that propagate and sustain the disturbance have also been followed and presented. These fundamental mechanisms are seen to give rise to spontaneous and irregular formation of new vortex couples at arbitrary locations, which are the primary agencies for sustaining chaos in the flow-field. The interactions have been studied for each dynamical state to understand the course of transition in the flow-field. The qualitative changes observed in the flow-field are manifestation of changes in the underlying dynamical system. The overall dynamics are established in the present study by means of robust quantitative measures derived from classical and non-classical tools from the dynamical system theory. As the present analysis involves a high fidelity multi-unknown system, non-classical dynamical tools such as recurrence-based time series methods are seen to be very efficient. Moreover, their application is novel in the context of pitch-plunge flapping flight.

Dynamics of relaxation to a stationary state for interacting molecular motors

Science.gov (United States)

Gomes, Luiza V. F.; Kolomeisky, Anatoly B.

2018-01-01

Motor proteins are active enzymatic molecules that drive a variety of biological processes, including transfer of genetic information, cellular transport, cell motility and muscle contraction. It is known that these biological molecular motors usually perform their cellular tasks by acting collectively, and there are interactions between individual motors that specify the overall collective behavior. One of the fundamental issues related to the collective dynamics of motor proteins is the question if they function at stationary-state conditions. To investigate this problem, we analyze a relaxation to the stationary state for the system of interacting molecular motors. Our approach utilizes a recently developed theoretical framework, which views the collective dynamics of motor proteins as a totally asymmetric simple exclusion process of interacting particles, where interactions are taken into account via a thermodynamically consistent approach. The dynamics of relaxation to the stationary state is analyzed using a domain-wall method that relies on a mean-field description, which takes into account some correlations. It is found that the system quickly relaxes for repulsive interactions, while attractive interactions always slow down reaching the stationary state. It is also predicted that for some range of parameters the fastest relaxation might be achieved for a weak repulsive interaction. Our theoretical predictions are tested with Monte Carlo computer simulations. The implications of our findings for biological systems are briefly discussed.

Human-Structure Dynamic Interaction during Short-Distance Free Falls

Directory of Open Access Journals (Sweden)

E. Shahabpoor

2016-01-01

Full Text Available The dynamic interactions of falling human bodies with civil structures, regardless of their potentially critical effects, have sparsely been researched in contact biomechanics. The physical contact models suggested in the existing literature, particularly for short-distant falls in home settings, assume the human body falls on a “rigid” (not vibrating ground. A similar assumption is usually made during laboratory-based fall tests, including force platforms. Based on observations from a set of pediatric head-first free fall tests, the present paper shows that the dynamics of the grounded force plate are not always negligible when doing fall test in a laboratory setting. By using a similar analogy for lightweight floor structures, it is shown that ignoring the dynamics of floors in the contact model can result in an up to 35% overestimation of the peak force experienced by a falling human. A nonlinear contact model is suggested, featuring an agent-based modelling approach, where the dynamics of the falling human and the impact object (force plate or a floor structure here are each modelled using a single-degree-of-freedom model to simulate their dynamic interactions. The findings of this research can have wide applications in areas such as impact biomechanics and sports science.

Nonlinear dynamics of interacting populations

CERN Document Server

Bazykin, Alexander D

1998-01-01

This book contains a systematic study of ecological communities of two or three interacting populations. Starting from the Lotka-Volterra system, various regulating factors are considered, such as rates of birth and death, predation and competition. The different factors can have a stabilizing or a destabilizing effect on the community, and their interplay leads to increasingly complicated behavior. Studying and understanding this path to greater dynamical complexity of ecological systems constitutes the backbone of this book. On the mathematical side, the tool of choice is the qualitative the

Dynamics of Moment Neuronal Networks with Intra- and Inter-Interactions

Directory of Open Access Journals (Sweden)

Xuyan Xiang

2015-01-01

Full Text Available A framework of moment neuronal networks with intra- and inter-interactions is presented. It is to show how the spontaneous activity is propagated across the homogeneous and heterogeneous network. The input-output firing relationship and the stability are first explored for a homogeneous network. For heterogeneous network without the constraint of the correlation coefficients between neurons, a more sophisticated dynamics is then explored. With random interactions, the network gets easily synchronized. However, desynchronization is produced by a lateral interaction such as Mexico hat function. It is the external intralayer input unit that offers a more sophisticated and unexpected dynamics over the predecessors. Hence, the work further opens up the possibility of carrying out a stochastic computation in neuronal networks.

Interactive Dynamic Volume Illumination with Refraction and Caustics.

Science.gov (United States)

Magnus, Jens G; Bruckner, Stefan

2018-01-01

In recent years, significant progress has been made in developing high-quality interactive methods for realistic volume illumination. However, refraction - despite being an important aspect of light propagation in participating media - has so far only received little attention. In this paper, we present a novel approach for refractive volume illumination including caustics capable of interactive frame rates. By interleaving light and viewing ray propagation, our technique avoids memory-intensive storage of illumination information and does not require any precomputation. It is fully dynamic and all parameters such as light position and transfer function can be modified interactively without a performance penalty.

Novel co-culture plate enables growth dynamic-based assessment of contact-independent microbial interactions.

Directory of Open Access Journals (Sweden)

Thomas J Moutinho

Full Text Available Interactions between microbes are central to the dynamics of microbial communities. Understanding these interactions is essential for the characterization of communities, yet challenging to accomplish in practice. There are limited available tools for characterizing diffusion-mediated, contact-independent microbial interactions. A practical and widely implemented technique in such characterization involves the simultaneous co-culture of distinct bacterial species and subsequent analysis of relative abundance in the total population. However, distinguishing between species can be logistically challenging. In this paper, we present a low-cost, vertical membrane, co-culture plate to quantify contact-independent interactions between distinct bacterial populations in co-culture via real-time optical density measurements. These measurements can be used to facilitate the analysis of the interaction between microbes that are physically separated by a semipermeable membrane yet able to exchange diffusible molecules. We show that diffusion across the membrane occurs at a sufficient rate to enable effective interaction between physically separate cultures. Two bacterial species commonly found in the cystic fibrotic lung, Pseudomonas aeruginosa and Burkholderia cenocepacia, were co-cultured to demonstrate how this plate may be implemented to study microbial interactions. We have demonstrated that this novel co-culture device is able to reliably generate real-time measurements of optical density data that can be used to characterize interactions between microbial species.

The human dynamic clamp as a paradigm for social interaction.

Science.gov (United States)

Dumas, Guillaume; de Guzman, Gonzalo C; Tognoli, Emmanuelle; Kelso, J A Scott

2014-09-02

Social neuroscience has called for new experimental paradigms aimed toward real-time interactions. A distinctive feature of interactions is mutual information exchange: One member of a pair changes in response to the other while simultaneously producing actions that alter the other. Combining mathematical and neurophysiological methods, we introduce a paradigm called the human dynamic clamp (HDC), to directly manipulate the interaction or coupling between a human and a surrogate constructed to behave like a human. Inspired by the dynamic clamp used so productively in cellular neuroscience, the HDC allows a person to interact in real time with a virtual partner itself driven by well-established models of coordination dynamics. People coordinate hand movements with the visually observed movements of a virtual hand, the parameters of which depend on input from the subject's own movements. We demonstrate that HDC can be extended to cover a broad repertoire of human behavior, including rhythmic and discrete movements, adaptation to changes of pacing, and behavioral skill learning as specified by a virtual "teacher." We propose HDC as a general paradigm, best implemented when empirically verified theoretical or mathematical models have been developed in a particular scientific field. The HDC paradigm is powerful because it provides an opportunity to explore parameter ranges and perturbations that are not easily accessible in ordinary human interactions. The HDC not only enables to test the veracity of theoretical models, it also illuminates features that are not always apparent in real-time human social interactions and the brain correlates thereof.

Three-dimensional interactive Molecular Dynamics program for the study of defect dynamics in crystals

Science.gov (United States)

Patriarca, M.; Kuronen, A.; Robles, M.; Kaski, K.

2007-01-01

The study of crystal defects and the complex processes underlying their formation and time evolution has motivated the development of the program ALINE for interactive molecular dynamics experiments. This program couples a molecular dynamics code to a Graphical User Interface and runs on a UNIX-X11 Window System platform with the MOTIF library, which is contained in many standard Linux releases. ALINE is written in C, thus giving the user the possibility to modify the source code, and, at the same time, provides an effective and user-friendly framework for numerical experiments, in which the main parameters can be interactively varied and the system visualized in various ways. We illustrate the main features of the program through some examples of detection and dynamical tracking of point-defects, linear defects, and planar defects, such as stacking faults in lattice-mismatched heterostructures. Program summaryTitle of program:ALINE Catalogue identifier:ADYJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYJ_v1_0 Program obtainable from: CPC Program Library, Queen University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: Computers:DEC ALPHA 300, Intel i386 compatible computers, G4 Apple Computers Installations:Laboratory of Computational Engineering, Helsinki University of Technology, Helsinki, Finland Operating systems under which the program has been tested:True64 UNIX, Linux-i386, Mac OS X 10.3 and 10.4 Programming language used:Standard C and MOTIF libraries Memory required to execute with typical data:6 Mbytes but may be larger depending on the system size No. of lines in distributed program, including test data, etc.:16 901 No. of bytes in distributed program, including test data, etc.:449 559 Distribution format:tar.gz Nature of physical problem:Some phenomena involving defects take place inside three-dimensional crystals at times which can be hardly predicted. For this reason they are

Critical dynamics of an interacting magnetic nanoparticle system

DEFF Research Database (Denmark)

Hansen, Mikkel Fougt; Jonsson, P.E.; Nordblad, P.

2002-01-01

Effects of dipole-dipole interactions on the magnetic relaxation have been investigated for three Fe-C nanoparticle samples with volume concentrations of 0.06, 5 and 17 vol%. While both the 5 and 17 vol% samples exhibit collective behaviour due to dipolar interactions, only the 17 vol% sample dis...... displays critical behaviour close to its transition temperature. The behaviour of the 5 vol% sample can be attributed to a mixture of collective and single-particle dynamics....

On the Convergence of Piecewise Linear Strategic Interaction Dynamics on Networks

KAUST Repository

Gharesifard, Bahman; Touri, Behrouz; Basar, Tamer; Shamma, Jeff S.

2015-01-01

We prove that the piecewise linear best-response dynamical systems of strategic interactions are asymptotically convergent to their set of equilibria on any weighted undirected graph. We study various features of these dynamical systems, including

Depletion interactions in two-dimensional colloid-polymer mixtures: molecular dynamics simulations

International Nuclear Information System (INIS)

Kim, Soon-Chul; Seong, Baek-Seok; Suh, Soong-Hyuck

2009-01-01

The depletion interactions acting between two hard colloids immersed in a bath of polymers, in which the interaction potentials include the soft repulsion/attraction, are extensively studied by using the molecular dynamics simulations. The collision frequencies and collision angle distributions for both incidental and reflection conditions are computed to study the dynamic properties of the colloidal mixtures. The depletion effect induced by the polymer-polymer and colloid-polymer interactions are investigated as well as the size ratio of the colloid and polymer. The simulated results show that the strong depletion interaction between two hard colloids appears for the highly asymmetric hard-disc mixtures. The attractive depletion force at contact becomes deeper and the repulsive barrier becomes wider as the asymmetry in size ratio increases. The strong polymer-polymer attraction leads to the purely attractive depletion interaction between two hard colloids, whereas the purely repulsive depletion interaction is induced by the strong colloid-polymer attraction.

SDI: Statistical dynamic interactions

International Nuclear Information System (INIS)

Blann, M.; Mustafa, M.G.; Peilert, G.; Stoecker, H.; Greiner, W.

1991-01-01

We focus on the combined statistical and dynamical aspects of heavy ion induced reactions. The overall picture is illustrated by considering the reaction 36 Ar + 238 U at a projectile energy of 35 MeV/nucleon. We illustrate the time dependent bound excitation energy due to the fusion/relaxation dynamics as calculated with the Boltzmann master equation. An estimate of the mass, charge and excitation of an equilibrated nucleus surviving the fast (dynamic) fusion-relaxation process is used as input into an evaporation calculation which includes 20 heavy fragment exit channels. The distribution of excitations between residue and clusters is explicitly calculated, as is the further deexcitation of clusters to bound nuclei. These results are compared with the exclusive cluster multiplicity measurements of Kim et al., and are found to give excellent agreement. We consider also an equilibrated residue system at 25% lower initial excitation, which gives an unsatisfactory exclusive multiplicity distribution. This illustrates that exclusive fragment multiplicity may provide a thermometer for system excitation. This analysis of data involves successive binary decay with no compressional effects nor phase transitions. Several examples of primary versus final (stable) cluster decay probabilities for an A = 100 nucleus at excitations of 100 to 800 MeV are presented. From these results a large change in multifragmentation patterns may be understood as a simple phase space consequence, invoking neither phase transitions, nor equation of state information. These results are used to illustrate physical quantities which are ambiguous to deduce from experimental fragment measurements. 14 refs., 4 figs

Nuclear structure calculations in the dynamic-interaction propagator approach

International Nuclear Information System (INIS)

Engelbrecht, C.A.; Hahne, F.J.W.; Heiss, W.D.

1978-01-01

The dynamic-interaction propagator approach provides a natural method for the handling of energy-dependent effective two-body interactions induced by collective excitations of a many-body system. In this work this technique is applied to the calculation of energy spectra and two-particle strengths in mass-18 nuclei. The energy dependence is induced by the dynamic exchange of the lowest 3 - octupole phonon in O 16 , which is described within a normal static particle-hole RPA. This leads to poles in the two-body self-energy, which can be calculated if other fermion lines are restricted to particle states. The two-body interaction parameters are chosen to provide the correct phonon energy and reasonable negative-parity mass-17 and positive-parity mass-18 spectra. The fermion lines must be dressed consistently with the same exchange phonon to avoid redundant solutions or ghosts. The negative-parity states are then calculated in a parameter-free way which gives good agreement with the observed spectra [af

Dynamical interactions between solute and solvent studied by nonlinear infrared spectroscopy

International Nuclear Information System (INIS)

Ohta, K.; Tominaga, K.

2006-01-01

Interactions between solute and solvent play an important role in chemical reaction dynamics and in many relaxation processes in condensed phases. Recently third-order nonlinear infrared (IR) spectroscopy has shown to be useful to investigate solute-solvent interaction and dynamics of the vibrational transition. These studies provide detailed information on the energy relaxation of the vibrationally excited state, and the time scale and the magnitude of the time correlation functions of the vibrational frequency fluctuations. In this work we have studied vibrational energy relaxation (VER) of solutions and molecular complexes by nonlinear IR spectroscopy, especially IR pump-probe method, to understand the microscopic interactions in liquids. (authors)

The dynamics of general developmental mechanisms : From Piaget and Vygotsky to dynamic systems models

NARCIS (Netherlands)

van Geert, P

Dynamic systems theory conceives of development as a self-organizational process. Both complexity and order emerge as a product of elementary principles of interaction between components involved in the developmental process. This article presents a dynamic systems model based on a general dual

Local and dynamic properties of light interacting with subwavelength holes

NARCIS (Netherlands)

Prangsma, Jord

2009-01-01

The discovery of the extraordinary transmission phenomena has initiated an intense study of the interaction of light with subwavelength holes. In this thesis the dynamic and local properties of light interacting with subwavelength holes are investigated. First of all the role of hole shape on the

Major component analysis of dynamic networks of physiologic organ interactions

International Nuclear Information System (INIS)

Liu, Kang K L; Ma, Qianli D Y; Ivanov, Plamen Ch; Bartsch, Ronny P

2015-01-01

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. (paper)

Rethinking the logistic approach for population dynamics of mutualistic interactions.

Science.gov (United States)

García-Algarra, Javier; Galeano, Javier; Pastor, Juan Manuel; Iriondo, José María; Ramasco, José J

2014-12-21

Mutualistic communities have an internal structure that makes them resilient to external perturbations. Late research has focused on their stability and the topology of the relations between the different organisms to explain the reasons of the system robustness. Much less attention has been invested in analyzing the systems dynamics. The main population models in use are modifications of the r-K formulation of logistic equation with additional terms to account for the benefits produced by the interspecific interactions. These models have shortcomings as the so-called r-K formulation diverges under some conditions. In this work, we introduce a model for population dynamics under mutualism that preserves the original logistic formulation. It is mathematically simpler than the widely used type II models, although it shows similar complexity in terms of fixed points and stability of the dynamics. We perform an analytical stability analysis and numerical simulations to study the model behavior in general interaction scenarios including tests of the resilience of its dynamics under external perturbations. Despite its simplicity, our results indicate that the model dynamics shows an important richness that can be used to gain further insights in the dynamics of mutualistic communities. Copyright © 2014 Elsevier Ltd. All rights reserved.

Langevin dynamics of conformational transformations induced by the charge-curvature interaction

DEFF Research Database (Denmark)

Gaididei, Yuri Borisovich; Gorria, C.; Christiansen, Peter Leth

2009-01-01

The role of thermal fluctuations in the conformational dynamics of a single closed filament is studied. It is shown that, due to the interaction between charges and bending degrees of freedom, initially circular chains may undergo transformation to polygonal shape.......The role of thermal fluctuations in the conformational dynamics of a single closed filament is studied. It is shown that, due to the interaction between charges and bending degrees of freedom, initially circular chains may undergo transformation to polygonal shape....

Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy

Directory of Open Access Journals (Sweden)

Oyang Yen-Jen

2010-10-01

Full Text Available Abstract Background Molecular networks represent the backbone of molecular activity within cells and provide opportunities for understanding the mechanism of diseases. While protein-protein interaction data constitute static network maps, integration of condition-specific co-expression information provides clues to the dynamic features of these networks. Dilated cardiomyopathy is a leading cause of heart failure. Although previous studies have identified putative biomarkers or therapeutic targets for heart failure, the underlying molecular mechanism of dilated cardiomyopathy remains unclear. Results We developed a network-based comparative analysis approach that integrates protein-protein interactions with gene expression profiles and biological function annotations to reveal dynamic functional modules under different biological states. We found that hub proteins in condition-specific co-expressed protein interaction networks tended to be differentially expressed between biological states. Applying this method to a cohort of heart failure patients, we identified two functional modules that significantly emerged from the interaction networks. The dynamics of these modules between normal and disease states further suggest a potential molecular model of dilated cardiomyopathy. Conclusions We propose a novel framework to analyze the interaction networks in different biological states. It successfully reveals network modules closely related to heart failure; more importantly, these network dynamics provide new insights into the cause of dilated cardiomyopathy. The revealed molecular modules might be used as potential drug targets and provide new directions for heart failure therapy.

Dynamics of Disagreement: Large-Scale Temporal Network Analysis Reveals Negative Interactions in Online Collaboration

Science.gov (United States)

Tsvetkova, Milena; García-Gavilanes, Ruth; Yasseri, Taha

2016-11-01

Disagreement and conflict are a fact of social life. However, negative interactions are rarely explicitly declared and recorded and this makes them hard for scientists to study. In an attempt to understand the structural and temporal features of negative interactions in the community, we use complex network methods to analyze patterns in the timing and configuration of reverts of article edits to Wikipedia. We investigate how often and how fast pairs of reverts occur compared to a null model in order to control for patterns that are natural to the content production or are due to the internal rules of Wikipedia. Our results suggest that Wikipedia editors systematically revert the same person, revert back their reverter, and come to defend a reverted editor. We further relate these interactions to the status of the involved editors. Even though the individual reverts might not necessarily be negative social interactions, our analysis points to the existence of certain patterns of negative social dynamics within the community of editors. Some of these patterns have not been previously explored and carry implications for the knowledge collection practice conducted on Wikipedia. Our method can be applied to other large-scale temporal collaboration networks to identify the existence of negative social interactions and other social processes.

An Exploratory Study to Measure Excessive Involvement in Multitasking Interaction with Smart Devices.

Science.gov (United States)

Zhang, Yubo; Rau, Pei-Luen Patrick

2016-06-01

This study developed a scale measuring excessive involvement in multitasking interaction with smart devices. An online questionnaire was designed and surveyed in a sample of 380 respondents. The sample was split into two groups for exploratory and confirmatory factor analysis, respectively. A four-factor structure was identified with an acceptable goodness of fit. The first two factors, "Obsession and neglect" and "Problematic control," described the obsessive feelings, neglect behaviors, and behavior control problems accompanied by excessive multitasking interaction with smart devices. The latter two factors, "Multitasking preference" and "Polychronic orientation," referred to multitaskers' preference of engaging in multiple media use or interaction tasks rather than a single task from the time orientation perspective. The four-factor structure indicates that excessive involvement in multitasking interaction with smart devices shares some similarities with other behavioral addiction types, but demonstrates uniqueness compared with excessive engagement in single media use.

Stress, strain, and structural dynamics an interactive handbook of formulas, solutions, and Matlab toolboxes

CERN Document Server

Yang, Bingen

2005-01-01

Stress, Strain, and Structural Dynamics is a comprehensive and definitive reference to statics and dynamics of solids and structures, including mechanics of materials, structural mechanics, elasticity, rigid-body dynamics, vibrations, structural dynamics, and structural controls. This text integrates the development of fundamental theories, formulas and mathematical models with user-friendly interactive computer programs, written in the powerful and popular MATLAB. This unique merger of technical referencing and interactive computing allows instant solution of a variety of engineering problems

Quantification of cardiorespiratory interactions based on joint symbolic dynamics.

Science.gov (United States)

Kabir, Muammar M; Saint, David A; Nalivaiko, Eugene; Abbott, Derek; Voss, Andreas; Baumert, Mathias

2011-10-01

Cardiac and respiratory rhythms are highly nonlinear and nonstationary. As a result traditional time-domain techniques are often inadequate to characterize their complex dynamics. In this article, we introduce a novel technique to investigate the interactions between R-R intervals and respiratory phases based on their joint symbolic dynamics. To evaluate the technique, electrocardiograms (ECG) and respiratory signals were recorded in 13 healthy subjects in different body postures during spontaneous and controlled breathing. Herein, the R-R time series were extracted from ECG and respiratory phases were obtained from abdomen impedance belts using the Hilbert transform. Both time series were transformed into ternary symbol vectors based on the changes between two successive R-R intervals or respiratory phases. Subsequently, words of different symbol lengths were formed and the correspondence between the two series of words was determined to quantify the interaction between cardiac and respiratory cycles. To validate our results, respiratory sinus arrhythmia (RSA) was further studied using the phase-averaged characterization of the RSA pattern. The percentage of similarity of the sequence of symbols, between the respective words of the two series determined by joint symbolic dynamics, was significantly reduced in the upright position compared to the supine position (26.4 ± 4.7 vs. 20.5 ± 5.4%, p cardiorespiratory interaction that is highly sensitive to the effects of orthostatic challenge.

Multiphase Flow Dynamics 2 Mechanical Interactions

CERN Document Server

Kolev, Nikolay Ivanov

2012-01-01

Multi-phase flows are part of our natural environment such as tornadoes, typhoons, air and water pollution and volcanic activities as well as part of industrial technology such as power plants, combustion engines, propulsion systems, or chemical and biological industry. The industrial use of multi-phase systems requires analytical and numerical strategies for predicting their behavior. .In its fourth extended edition the successful monograph package “Multiphase Flow Daynmics” contains theory, methods and practical experience for describing complex transient multi-phase processes in arbitrary geometrical configurations, providing a systematic presentation of the theory and practice of numerical multi-phase fluid dynamics. In the present second volume the methods for describing the mechanical interactions in multiphase dynamics are provided. This fourth edition includes various updates, extensions, improvements and corrections.   "The literature in the field of multiphase flows is numerous. Therefore, it i...

Interaction as 'involvement' in writing for students: a corpus linguistic ...

African Journals Online (AJOL)

Interaction as 'involvement' in writing for students: a corpus linguistic analysis of a key readability feature. E Hilton Hubbard. Abstract. The rapid change in the demographics of South Africa's tertiary level student population over the last decade — and most specifically the huge increase in those who have to study at a ...

Advances on Modelling Riparian Vegetation-Hydromorphology Interactions

NARCIS (Netherlands)

Solari, L.; Van Oorschot, M.; Belletti, B.; Hendriks, D.; Rinaldi, M.; Vargas-Luna, A.

2016-01-01

Riparian vegetation actively interacts with fluvial systems affecting river hydrodynamics, morphodynamics and groundwater. These interactions can be coupled because both vegetation and hydromorphology (i.e. the combined scientific study of hydrology and fluvial geomorphology) involve dynamic

Interactive affective sharing versus non-interactive affective sharing in work groups : Comparative effects of group affect on work group performance and dynamics

NARCIS (Netherlands)

Klep, Annefloor; Wisse, Barbara; Van Der Flier, Henk

This study explores whether the dynamic path to group affect, which is characterized by interactive affective sharing processes, yields different effects on task performance and group dynamics than the static path to group affect, which arises from non-interactive affective sharing. The results of

Interactive affective sharing versus non-interactive affective sharing in work groups: Comparative effects of group affect on work group performance and dynamics

NARCIS (Netherlands)

Klep, A.H.M.; Wisse, B.M.; van der Flier, H.

2011-01-01

This study explores whether the dynamic path to group affect, which is characterized by interactive affective sharing processes, yields different effects on task performance and group dynamics than the static path to group affect, which arises from non-interactive affective sharing. The results of

Multiphase Flow Dynamics 3 Thermal Interactions

CERN Document Server

Kolev, Nikolay Ivanov

2012-01-01

Multi-phase flows are part of our natural environment such as tornadoes, typhoons, air and water pollution and volcanic activities as well as part of industrial technology such as power plants, combustion engines, propulsion systems, or chemical and biological industry. The industrial use of multi-phase systems requires analytical and numerical strategies for predicting their behavior. .In its fourth extended edition the successful monograph package “Multiphase Flow Daynmics” contains theory, methods and practical experience for describing complex transient multi-phase processes in arbitrary geometrical configurations, providing a systematic presentation of the theory and practice of numerical multi-phase fluid dynamics. In the present third volume methods for describing of the thermal interactions in multiphase dynamics are provided. In addition a large number of valuable experiments is collected and predicted using the methods introduced in this monograph. In this way the accuracy of the methods is reve...

Deciphering the Dynamic Interaction Profile of an Intrinsically Disordered Protein by NMR Exchange Spectroscopy.

Science.gov (United States)

Delaforge, Elise; Kragelj, Jaka; Tengo, Laura; Palencia, Andrés; Milles, Sigrid; Bouvignies, Guillaume; Salvi, Nicola; Blackledge, Martin; Jensen, Malene Ringkjøbing

2018-01-24

Intrinsically disordered proteins (IDPs) display a large number of interaction modes including folding-upon-binding, binding without major structural transitions, or binding through highly dynamic, so-called fuzzy, complexes. The vast majority of experimental information about IDP binding modes have been inferred from crystal structures of proteins in complex with short peptides of IDPs. However, crystal structures provide a mainly static view of the complexes and do not give information about the conformational dynamics experienced by the IDP in the bound state. Knowledge of the dynamics of IDP complexes is of fundamental importance to understand how IDPs engage in highly specific interactions without concomitantly high binding affinity. Here, we combine rotating-frame R 1ρ , Carr-Purcell-Meiboom Gill relaxation dispersion as well as chemical exchange saturation transfer to decipher the dynamic interaction profile of an IDP in complex with its partner. We apply the approach to the dynamic signaling complex formed between the mitogen-activated protein kinase (MAPK) p38α and the intrinsically disordered regulatory domain of the MAPK kinase MKK4. Our study demonstrates that MKK4 employs a subtle combination of interaction modes in order to bind to p38α, leading to a complex displaying significantly different dynamics across the bound regions.

Simulating market dynamics: interactions between consumer psychology and social networks.

Science.gov (United States)

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).

Artificial ferroic systems: novel functionality from structure, interactions and dynamics

International Nuclear Information System (INIS)

Heyderman, L J; Stamps, R L

2013-01-01

Lithographic processing and film growth technologies are continuing to advance, so that it is now possible to create patterned ferroic materials consisting of arrays of sub-1 μm elements with high definition. Some of the most fascinating behaviour of these arrays can be realised by exploiting interactions between the individual elements to create new functionality. The properties of these artificial ferroic systems differ strikingly from those of their constituent components, with novel emergent behaviour arising from the collective dynamics of the interacting elements, which are arranged in specific designs and can be activated by applying magnetic or electric fields. We first focus on artificial spin systems consisting of arrays of dipolar-coupled nanomagnets and, in particular, review the field of artificial spin ice, which demonstrates a wide range of fascinating phenomena arising from the frustration inherent in particular arrangements of nanomagnets, including emergent magnetic monopoles, domains of ordered macrospins, and novel avalanche behaviour. We outline how demagnetisation protocols have been employed as an effective thermal anneal in an attempt to reach the ground state, comment on phenomena that arise in thermally activated systems and discuss strategies for selectively generating specific configurations using applied magnetic fields. We then move on from slow field and temperature driven dynamics to high frequency phenomena, discussing spinwave excitations in the context of magnonic crystals constructed from arrays of patterned magnetic elements. At high frequencies, these arrays are studied in terms of potential applications including magnetic logic, linear and non-linear microwave optics, and fast, efficient switching, and we consider the possibility to create tunable magnonic crystals with artificial spin ice. Finally, we discuss how functional ferroic composites can be incorporated to realise magnetoelectric effects. Specifically, we discuss

Artificial ferroic systems: novel functionality from structure, interactions and dynamics.

Science.gov (United States)

Heyderman, L J; Stamps, R L

2013-09-11

Lithographic processing and film growth technologies are continuing to advance, so that it is now possible to create patterned ferroic materials consisting of arrays of sub-1 μm elements with high definition. Some of the most fascinating behaviour of these arrays can be realised by exploiting interactions between the individual elements to create new functionality. The properties of these artificial ferroic systems differ strikingly from those of their constituent components, with novel emergent behaviour arising from the collective dynamics of the interacting elements, which are arranged in specific designs and can be activated by applying magnetic or electric fields. We first focus on artificial spin systems consisting of arrays of dipolar-coupled nanomagnets and, in particular, review the field of artificial spin ice, which demonstrates a wide range of fascinating phenomena arising from the frustration inherent in particular arrangements of nanomagnets, including emergent magnetic monopoles, domains of ordered macrospins, and novel avalanche behaviour. We outline how demagnetisation protocols have been employed as an effective thermal anneal in an attempt to reach the ground state, comment on phenomena that arise in thermally activated systems and discuss strategies for selectively generating specific configurations using applied magnetic fields. We then move on from slow field and temperature driven dynamics to high frequency phenomena, discussing spinwave excitations in the context of magnonic crystals constructed from arrays of patterned magnetic elements. At high frequencies, these arrays are studied in terms of potential applications including magnetic logic, linear and non-linear microwave optics, and fast, efficient switching, and we consider the possibility to create tunable magnonic crystals with artificial spin ice. Finally, we discuss how functional ferroic composites can be incorporated to realise magnetoelectric effects. Specifically, we discuss

Dosimetric comparison of interactive planned and dynamic dose calculated prostate seed brachytherapy

International Nuclear Information System (INIS)

Meijer, Gert J.; Berg, Hetty A. van den; Hurkmans, Coen W.; Stijns, Pascal E.; Weterings, Jan H.

2006-01-01

Purpose: To compare the dosimetrical results of an interactive planning procedure and a procedure based on dynamic dose calculation for permanent prostate brachytherapy. Materials and methods: Between 6/2000 and 11/2005, 510 patients underwent 125 I implants for T1-T2 prostate cancer. Before 4/2003, 187 patients were treated using an interactive technique that included needle updating. After that period, 323 patients were treated with a more refined dynamic technique that included constant updating of the deposited seed position. The comparison is based on postimplant dose-volume parameters such as the V 100 and d 90 for the target, V 100 r for the rectum and d 10 u for the urethra. Furthermore, the target volume ratios (TVR=V 100 body /V 100 ), and the homogeneity indices (HI=[V 100 -V 150 ]/V 100 ) were calculated as additional quality parameters. Results: The dose outside the target volume was significantly reduced, the V 100 r decreased from 1.4cm 3 for the interactive technique to 0.6cm 3 for the dynamic technique. Similarly the mean TVR reduced from 1.66 to 1.44. In addition, the mean V 100 increased from 92% for the interactive procedure to 95% for the dynamic procedure. More importantly, the percentage of patients with a V 100 10 u (136% vs. 140%) and the HI (0.58 vs. 0.51). Conclusion: The dynamic implant procedure resulted in improved implants. Almost ideal dose coverage was achieved, while minimizing the dose outside the prostate

Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor.

Science.gov (United States)

Migliori, Amy D; Smith, Douglas E; Arya, Gaurav

2014-12-12

Many viruses utilize molecular motors to package their genomes into preformed capsids. A striking feature of these motors is their ability to generate large forces to drive DNA translocation against entropic, electrostatic, and bending forces resisting DNA confinement. A model based on recently resolved structures of the bacteriophage T4 motor protein gp17 suggests that this motor generates large forces by undergoing a conformational change from an extended to a compact state. This transition is proposed to be driven by electrostatic interactions between complementarily charged residues across the interface between the N- and C-terminal domains of gp17. Here we use atomistic molecular dynamics simulations to investigate in detail the molecular interactions and residues involved in such a compaction transition of gp17. We find that although electrostatic interactions between charged residues contribute significantly to the overall free energy change of compaction, interactions mediated by the uncharged residues are equally if not more important. We identify five charged residues and six uncharged residues at the interface that play a dominant role in the compaction transition and also reveal salt bridging, van der Waals, and solvent hydrogen-bonding interactions mediated by these residues in stabilizing the compact form of gp17. The formation of a salt bridge between Glu309 and Arg494 is found to be particularly crucial, consistent with experiments showing complete abrogation in packaging upon Glu309Lys mutation. The computed contributions of several other residues are also found to correlate well with single-molecule measurements of impairments in DNA translocation activity caused by site-directed mutations. Copyright © 2014 Elsevier Ltd. All rights reserved.

Nonequilibrium dynamics in an interacting Fe-C nanoparticle system

DEFF Research Database (Denmark)

Jönsson, P.; Hansen, Mikkel Fougt; Nordblad, P.

2000-01-01

Nonequilibrium dynamics in an interacting Fe-C nanoparticle sample, exhibiting a low-temperature spin-glass-like phase, has been studied by low-frequency ac susceptibility and magnetic relaxation experiments. The nonequilibrium behavior shows characteristic spin-glass features, but some qualitative...

Molecular dynamics simulations revealed structural differences among WRKY domain-DNA interaction in barley (Hordeum vulgare).

Science.gov (United States)

Pandey, Bharati; Grover, Abhinav; Sharma, Pradeep

2018-02-12

The WRKY transcription factors are a class of DNA-binding proteins involved in diverse plant processes play critical roles in response to abiotic and biotic stresses. Genome-wide divergence analysis of WRKY gene family in Hordeum vulgare provided a framework for molecular evolution and functional roles. So far, the crystal structure of WRKY from barley has not been resolved; moreover, knowledge of the three-dimensional structure of WRKY domain is pre-requisites for exploring the protein-DNA recognition mechanisms. Homology modelling based approach was used to generate structures for WRKY DNA binding domain (DBD) and its variants using AtWRKY1 as a template. Finally, the stability and conformational changes of the generated model in unbound and bound form was examined through atomistic molecular dynamics (MD) simulations for 100 ns time period. In this study, we investigated the comparative binding pattern of WRKY domain and its variants with W-box cis-regulatory element using molecular docking and dynamics (MD) simulations assays. The atomic insight into WRKY domain exhibited significant variation in the intermolecular hydrogen bonding pattern, leading to the structural anomalies in the variant type and differences in the DNA-binding specificities. Based on the MD analysis, residual contribution and interaction contour, wild-type WRKY (HvWRKY46) were found to interact with DNA through highly conserved heptapeptide in the pre- and post-MD simulated complexes, whereas heptapeptide interaction with DNA was missing in variants (I and II) in post-MD complexes. Consequently, through principal component analysis, wild-type WRKY was also found to be more stable by obscuring a reduced conformational space than the variant I (HvWRKY34). Lastly, high binding free energy for wild-type and variant II allowed us to conclude that wild-type WRKY-DNA complex was more stable relative to variants I. The results of our study revealed complete dynamic and structural information

Collective Phenomena Emerging from the Interactions between Dynamical Processes in Multiplex Networks.

Science.gov (United States)

Nicosia, Vincenzo; Skardal, Per Sebastian; Arenas, Alex; Latora, Vito

2017-03-31

We introduce a framework to intertwine dynamical processes of different nature, each with its own distinct network topology, using a multilayer network approach. As an example of collective phenomena emerging from the interactions of multiple dynamical processes, we study a model where neural dynamics and nutrient transport are bidirectionally coupled in such a way that the allocation of the transport process at one layer depends on the degree of synchronization at the other layer, and vice versa. We show numerically, and we prove analytically, that the multilayer coupling induces a spontaneous explosive synchronization and a heterogeneous distribution of allocations, otherwise not present in the two systems considered separately. Our framework can find application to other cases where two or more dynamical processes such as synchronization, opinion formation, information diffusion, or disease spreading, are interacting with each other.

Collective Phenomena Emerging from the Interactions between Dynamical Processes in Multiplex Networks

Science.gov (United States)

Nicosia, Vincenzo; Skardal, Per Sebastian; Arenas, Alex; Latora, Vito

2017-03-01

We introduce a framework to intertwine dynamical processes of different nature, each with its own distinct network topology, using a multilayer network approach. As an example of collective phenomena emerging from the interactions of multiple dynamical processes, we study a model where neural dynamics and nutrient transport are bidirectionally coupled in such a way that the allocation of the transport process at one layer depends on the degree of synchronization at the other layer, and vice versa. We show numerically, and we prove analytically, that the multilayer coupling induces a spontaneous explosive synchronization and a heterogeneous distribution of allocations, otherwise not present in the two systems considered separately. Our framework can find application to other cases where two or more dynamical processes such as synchronization, opinion formation, information diffusion, or disease spreading, are interacting with each other.

Higher-Order Synaptic Interactions Coordinate Dynamics in Recurrent Networks.

Directory of Open Access Journals (Sweden)

Brendan Chambers

2016-08-01

Full Text Available 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.

A MOLECULAR DYNAMICS STUDY ON SLOW ION INTERACTIONS WITH THE POLYCYCLIC AROMATIC HYDROCARBON MOLECULE ANTHRACENE

NARCIS (Netherlands)

Postma, J.; Hoekstra, Ronnie; Tielens, A. G. G. M.; Schlathölter, Thomas

2014-01-01

Atomic collisions with polycyclic aromatic hydrocarbon (PAH) molecules are astrophysically particularly relevant for collision energies of less than 1 keV. In this regime, the interaction dynamics are dominated by elastic interactions. We have employed a molecular dynamics simulation based on

Analysis of interactive fixed effects dynamic linear panel regression with measurement error

OpenAIRE

Nayoung Lee; Hyungsik Roger Moon; Martin Weidner

2011-01-01

This paper studies a simple dynamic panel linear regression model with interactive fixed effects in which the variable of interest is measured with error. To estimate the dynamic coefficient, we consider the least-squares minimum distance (LS-MD) estimation method.

LETTER TO THE EDITOR: Dynamics of interacting neural networks

Science.gov (United States)

Kinzel, W.; Metzler, R.; Kanter, I.

2000-04-01

The dynamics of interacting perceptrons is solved analytically. For a directed flow of information the system runs into a state which has a higher symmetry than the topology of the model. A symmetry-breaking phase transition is found with increasing learning rate. In addition, it is shown that a system of interacting perceptrons which is trained on the history of its minority decisions develops a good strategy for the problem of adaptive competition known as the bar problem or minority game.

Current-Current Interactions, Dynamical Symmetry - and Quantum Chromodynamics.

Science.gov (United States)

Neuenschwander, Dwight Edward, Jr.

Quantum Chromodynamics with massive gluons (gluon mass (TBOND) xm(,p)) in a contact-interaction limit called CQCD (strong coupling g (--->) (INFIN); x (--->) (INFIN)), despite its non-renormalizability and lack of hope of confinement, is nevertheless interesting for at least two reasons. (1) Some authors have suggested a relation between 4-Fermi and Yang-Mills theories. If g/x('2) slavery, perturbative evaluation of QCD in the infrared is a dubious practice. However, if g('2)/x('2) << 1 in CQCD, then the simplest 4-Fermi interaction is dominant, and CQCD admits perturbative treatment, but only in the infrared. With the dominant interaction, a dynamical Nambu-Goldstone realization of chiral symmetry -breaking (XSB) is found. Although in QCD the relation between confinement and XSB is controversial, XSB occurs in CQCD provided confinement is sacrificed.

Effects of three-body interactions on the dynamics of entanglement in spin chains

International Nuclear Information System (INIS)

Shi Cuihua; Wu Yinzhong; Li Zhenya

2009-01-01

With the consideration of three-body interaction, dynamics of pairwise entanglement in spin chains is studied. The dependence of pairwise entanglement dynamics on the type of coupling, and distance between the spins is analyzed in a finite chain for different initial states. It is found that, for an Ising chain, three-body interactions are not in favor of preparing entanglement between the nearest neighbor spins, while three-body interactions are favorable for creating entanglement between remote spins from a separable initial state. For an isotropic Heisenberg chain, the pairwise concurrence will decrease when three-body interactions are considered both for a separable initial state and for a maximally entangled initial state, however, three-body interactions will retard the decay of the concurrence in an Ising chain when the initial state takes the maximally entangled state.

Dosimetric comparison of interactive planned and dynamic dose calculated prostate seed brachytherapy.

Science.gov (United States)

Meijer, Gert J; van den Berg, Hetty A; Hurkmans, Coen W; Stijns, Pascal E; Weterings, Jan H

2006-09-01

To compare the dosimetrical results of an interactive planning procedure and a procedure based on dynamic dose calculation for permanent prostate brachytherapy. Between 6/2000 and 11/2005, 510 patients underwent (125)I implants for T1-T2 prostate cancer. Before 4/2003, 187 patients were treated using an interactive technique that included needle updating. After that period, 323 patients were treated with a more refined dynamic technique that included constant updating of the deposited seed position. The comparison is based on postimplant dose - volume parameters such as the V(100) and d(90) for the target, V(100)(r) for the rectum and d(10)(u) for the urethra. Furthermore, the target volume ratios (TVR identical with V(100)(body)/V(100)), and the homogeneity indices (HI identical with [V(100)-V(150)]/V(100)) were calculated as additional quality parameters. The dose outside the target volume was significantly reduced, the V(100)(r) decreased from 1.4 cm(3) for the interactive technique to 0.6 cm(3) for the dynamic technique. Similarly the mean TVR reduced from 1.66 to 1.44. In addition, the mean V(100) increased from 92% for the interactive procedure to 95% for the dynamic procedure. More importantly, the percentage of patients with a V(100) < 80% reduced from 5% to 1%. A slight decline was observed with regard to the d(10)(u) (136% vs. 140%) and the HI (0.58 vs. 0.51). The dynamic implant procedure resulted in improved implants. Almost ideal dose coverage was achieved, while minimizing the dose outside the prostate.

Coupled quintessence and the impossibility of an interaction: a dynamical analysis study

Energy Technology Data Exchange (ETDEWEB)

Bernardi, Fabrizio F.; Landim, Ricardo G. [Universidade de Sao Paulo, Instituto de Fisica, Caixa Postal 66318, Sao Paulo, SP (Brazil)

2017-05-15

We analyze the coupled quintessence in the light of the linear dynamical systems theory, with two different interactions: (1) proportional to the energy density of the dark energy and (2) proportional to the sum of the energy densities of the dark matter and dark energy. The results presented here enlarge the previous analyses in the literature, wherein the interaction has been only proportional to the energy density of the dark matter. In the first case it is possible to get the well-known sequence of cosmological eras. For the second interaction only the radiation and the dark-energy era can be described by the fixed points. Therefore, from the point of view of dynamical system theory, the interaction proportional to the sum of the energy densities of the dark matter and dark energy does not describe the universe we live in. (orig.)

Coupled quintessence and the impossibility of an interaction: a dynamical analysis study

International Nuclear Information System (INIS)

Bernardi, Fabrizio F.; Landim, Ricardo G.

2017-01-01

We analyze the coupled quintessence in the light of the linear dynamical systems theory, with two different interactions: (1) proportional to the energy density of the dark energy and (2) proportional to the sum of the energy densities of the dark matter and dark energy. The results presented here enlarge the previous analyses in the literature, wherein the interaction has been only proportional to the energy density of the dark matter. In the first case it is possible to get the well-known sequence of cosmological eras. For the second interaction only the radiation and the dark-energy era can be described by the fixed points. Therefore, from the point of view of dynamical system theory, the interaction proportional to the sum of the energy densities of the dark matter and dark energy does not describe the universe we live in. (orig.)

Molecular dynamics study of the silica-water-SDA interactions

NARCIS (Netherlands)

Szyja, B.M.; Jansen, A.P.J.; Verstraelen, T.; Santen, van R.A.

2009-01-01

In this paper we have applied the molecular dynamics simulations in order to analyse the role of the structure directing tetrapropylammonium ions in the aggregation process that leads to silicalite formation. We address the specific question of how the interactions between silica precursor species

Brain-to-Brain Synchrony Tracks Real-World Dynamic Group Interactions in the Classroom.

Science.gov (United States)

Dikker, Suzanne; Wan, Lu; Davidesco, Ido; Kaggen, Lisa; Oostrik, Matthias; McClintock, James; Rowland, Jess; Michalareas, Georgios; Van Bavel, Jay J; Ding, Mingzhou; Poeppel, David

2017-05-08

The human brain has evolved for group living [1]. Yet we know so little about how it supports dynamic group interactions that the study of real-world social exchanges has been dubbed the "dark matter of social neuroscience" [2]. Recently, various studies have begun to approach this question by comparing brain responses of multiple individuals during a variety of (semi-naturalistic) tasks [3-15]. These experiments reveal how stimulus properties [13], individual differences [14], and contextual factors [15] may underpin similarities and differences in neural activity across people. However, most studies to date suffer from various limitations: they often lack direct face-to-face interaction between participants, are typically limited to dyads, do not investigate social dynamics across time, and, crucially, they rarely study social behavior under naturalistic circumstances. Here we extend such experimentation drastically, beyond dyads and beyond laboratory walls, to identify neural markers of group engagement during dynamic real-world group interactions. We used portable electroencephalogram (EEG) to simultaneously record brain activity from a class of 12 high school students over the course of a semester (11 classes) during regular classroom activities (Figures 1A-1C; Supplemental Experimental Procedures, section S1). A novel analysis technique to assess group-based neural coherence demonstrates that the extent to which brain activity is synchronized across students predicts both student class engagement and social dynamics. This suggests that brain-to-brain synchrony is a possible neural marker for dynamic social interactions, likely driven by shared attention mechanisms. This study validates a promising new method to investigate the neuroscience of group interactions in ecologically natural settings. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Neural mirroring and social interaction: Motor system involvement during action observation relates to early peer cooperation.

Science.gov (United States)

Endedijk, H M; Meyer, M; Bekkering, H; Cillessen, A H N; Hunnius, S

2017-04-01

Whether we hand over objects to someone, play a team sport, or make music together, social interaction often involves interpersonal action coordination, both during instances of cooperation and entrainment. Neural mirroring is thought to play a crucial role in processing other's actions and is therefore considered important for social interaction. Still, to date, it is unknown whether interindividual differences in neural mirroring play a role in interpersonal coordination during different instances of social interaction. A relation between neural mirroring and interpersonal coordination has particularly relevant implications for early childhood, since successful early interaction with peers is predictive of a more favorable social development. We examined the relation between neural mirroring and children's interpersonal coordination during peer interaction using EEG and longitudinal behavioral data. Results showed that 4-year-old children with higher levels of motor system involvement during action observation (as indicated by lower beta-power) were more successful in early peer cooperation. This is the first evidence for a relation between motor system involvement during action observation and interpersonal coordination during other instances of social interaction. The findings suggest that interindividual differences in neural mirroring are related to interpersonal coordination and thus successful social interaction. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Conformational dynamism for DNA interaction in the Salmonella RcsB response regulator.

Science.gov (United States)

Casino, Patricia; Miguel-Romero, Laura; Huesa, Juanjo; García, Pablo; García-Del Portillo, Francisco; Marina, Alberto

2018-01-09

The RcsCDB phosphorelay system controls an extremely large regulon in Enterobacteriaceae that involves processes such as biofilm formation, flagella production, synthesis of extracellular capsules and cell division. Therefore, fine-tuning of this system is essential for virulence in pathogenic microorganisms of this group. The final master effector of the RcsCDB system is the response regulator (RR) RcsB, which activates or represses multiple genes by binding to different promoter regions. This regulatory activity of RcsB can be done alone or in combination with additional transcriptional factors in phosphorylated or dephosphorylated states. The capacity of RcsB to interact with multiple promoters and partners, either dephosphorylated or phosphorylated, suggests an extremely conformational dynamism for this RR. To shed light on the activation mechanism of RcsB and its implication on promoter recognition, we solved the crystal structure of full-length RcsB from Salmonella enterica serovar Typhimurium in the presence and absence of a phosphomimetic molecule BeF3-. These two novel structures have guided an extensive site-directed mutagenesis study at the structural and functional level that confirms RcsB conformational plasticity and dynamism. Our data allowed us to propose a β5-T switch mechanism where phosphorylation is coupled to alternative DNA binding ways and which highlights the conformational dynamism of RcsB to be so pleiotropic. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Entanglement dynamics of a Heisenberg chain with Dzyaloshinskii–Moriya interaction

International Nuclear Information System (INIS)

Qiang, Zheng; Xiao-Ping, Zhang; Zhong-Zhou, Ren; Qi-Jun, Zhi

2009-01-01

This paper investigates the entanglement dynamics of the system, composed of two qubits A and B with Heisenberg XX spin interactation. There is a third controller qubit C, which only has Dzyaloshinskii–Moriya (DM) spin-orbit interaction with the qubit B. It is found that depending on the initial state of the controller qubit C and DM interaction, the entanglement of the system displays amplification and sudden birth effects. These effects indicate that one can control the entanglement of the system, which may be helpful for quantum information processing. (general)

Influence of the Location of Attractive Polymer-Pore Interactions on Translocation Dynamics.

Science.gov (United States)

Ghosh, Bappa; Chaudhury, Srabanti

2018-01-11

We probe the influence of polymer-pore interactions on the translocation dynamics using Langevin dynamics simulations. We investigate the effect of the strength and location of the polymer-pore interaction using nanopores that are partially charged either at the entry or the exit or on both sides of the pore. We study the change in the translocation time as a function of the strength of the polymer-pore interaction for a given chain length and under the effect of an externally applied field. Under a moderate driving force and a chain length longer than the length of the pore, the translocation time shows a nonmonotonic increase with an increase in the attractive interaction. Also, an interaction on the cis side of the pore can increase the translocation probability. In the presence of an external field and a strong attractive force, the translocation time for shorter chains is independent of the polymer-pore interaction at the entry side of the pore, whereas an interaction on the trans side dominates the translocation process. Our simulation results are rationalized by a qualitative analysis of the free energy landscape for polymer translocation.

The Role of Father Involvement and Marital Satisfaction in the Development of Family Interactive Abilities: A Multilevel Approach.

Science.gov (United States)

Simonelli, Alessandra; Parolin, Micol; Sacchi, Chiara; De Palo, Francesca; Vieno, Alessio

2016-01-01

The study aims to investigate the development of family interactions from pregnancy to preschool age in a longitudinal perspective, using multilevel analysis. Also, it explored the impact of couple relationship and father involvement in childcare on the developmental trend of the quality of mother-father-child interactions. One hundred and three primiparous families were assessed at 7th month of pregnancy, 4th, 9th, and 18th months of child's life and during preschool age (36-48th), using the observational procedure named, Lausanne Trilogue Play. Parents' perception of marital satisfaction was assessed with the Dyadic Adjustment Scale at each point of measure; moreover, in the postnatal assessment, parents completed the Father Involvement Questionnaire. Results showed that family interactions increase over time. Secondly, a decrease of marital adjustment is associated with an improvement of the quality of family interactions. Moreover, father involvement predicts the quality of family interactions from the earliest stages of child's life. In a longitudinal perspective, family interactions and marital quality show opposite developmental trends and father's involvement represents a particularly important feature of the family.

A Numerical Study on Hydrodynamic Interactions between Dynamic Positioning Thrusters

Energy Technology Data Exchange (ETDEWEB)

Jin, Doo Hwa; Lee, Sang Wook [University of Ulsan, Ulsan (Korea, Republic of)

2017-06-15

In this study, we conducted computational fluid dynamics (CFD) simulations for the unsteady hydrodynamic interaction of multiple thrusters by solving Reynolds averaged Navier-Stokes equations. A commercial CFD software, STAR-CCM+ was used for all simulations by employing a ducted thruster model with combination of a propeller and No. 19a duct. A sliding mesh technique was used to treat dynamic motion of propeller rotation and non-conformal hexahedral grid system was considered. Four different combinations in tilting and azimuth angles of the thrusters were considered to investigate the effects on the propulsion performance. We could find that thruster-hull and thruster-thruster interactions has significant effect on propulsion performance and further study will be required for the optimal configurations with the best tilting and relative azimuth angle between thrusters.

Pyoverdine and PQS Mediated Subpopulation Interactions Involved in Pseudomonas aeruginosa Biofilm Formation

DEFF Research Database (Denmark)

Yang, Liang; Nilsson, Martin; Gjermansen, Morten

2009-01-01

Using flow chamber-grown Pseudomonas aeruginosa biofilms as model system, we show in the present study that formation of heterogeneous biofilms may occur through mechanisms that involve complex subpopulation interactions. One example of this phenomenon is expression of the iron...

Plasma Interaction and Energetic Particle Dynamics near Callisto

Science.gov (United States)

Liuzzo, L.; Simon, S.; Feyerabend, M.; Motschmann, U. M.

2017-12-01

Callisto's magnetic environment is characterized by a complex admixture of induction signals from its conducting subsurface ocean, the interaction of corotating Jovian magnetospheric plasma with the moon's ionosphere and induced dipole, and the non-linear coupling between the effects. In contrast to other Galilean moons, ion gyroradii near Callisto are comparable to its size, requiring a kinetic treatment of the interaction region near the moon. Thus, we apply the hybrid simulation code AIKEF to constrain the competing effects of plasma interaction and induction. We determine their influence on the magnetic field signatures measured by Galileo during various Callisto flybys. We use the magnetic field calculated by the model to investigate energetic particle dynamics and their effect on Callisto's environment. From this, we provide a map of global energetic particle precipitation onto Callisto's surface, which may contribute to the generation of its atmosphere.

Nonlinear dynamics of resonant electrons interacting with coherent Langmuir waves

Science.gov (United States)

Tobita, Miwa; Omura, Yoshiharu

2018-03-01

We study the nonlinear dynamics of resonant particles interacting with coherent waves in space plasmas. Magnetospheric plasma waves such as whistler-mode chorus, electromagnetic ion cyclotron waves, and hiss emissions contain coherent wave structures with various discrete frequencies. Although these waves are electromagnetic, their interaction with resonant particles can be approximated by equations of motion for a charged particle in a one-dimensional electrostatic wave. The equations are expressed in the form of nonlinear pendulum equations. We perform test particle simulations of electrons in an electrostatic model with Langmuir waves and a non-oscillatory electric field. We solve equations of motion and study the dynamics of particles with different values of inhomogeneity factor S defined as a ratio of the non-oscillatory electric field intensity to the wave amplitude. The simulation results demonstrate deceleration/acceleration, thermalization, and trapping of particles through resonance with a single wave, two waves, and multiple waves. For two-wave and multiple-wave cases, we describe the wave-particle interaction as either coherent or incoherent based on the probability of nonlinear trapping.

Identification of interfaces involved in weak interactions with application to F-actin-aldolase rafts.

Science.gov (United States)

Hu, Guiqing; Taylor, Dianne W; Liu, Jun; Taylor, Kenneth A

2018-03-01

Macromolecular interactions occur with widely varying affinities. Strong interactions form well defined interfaces but weak interactions are more dynamic and variable. Weak interactions can collectively lead to large structures such as microvilli via cooperativity and are often the precursors of much stronger interactions, e.g. the initial actin-myosin interaction during muscle contraction. Electron tomography combined with subvolume alignment and classification is an ideal method for the study of weak interactions because a 3-D image is obtained for the individual interactions, which subsequently are characterized collectively. Here we describe a method to characterize heterogeneous F-actin-aldolase interactions in 2-D rafts using electron tomography. By forming separate averages of the two constituents and fitting an atomic structure to each average, together with the alignment information which relates the raw motif to the average, an atomic model of each crosslink is determined and a frequency map of contact residues is computed. The approach should be applicable to any large structure composed of constituents that interact weakly and heterogeneously. Copyright © 2017 Elsevier Inc. All rights reserved.

A multiplexed microfluidic system for evaluation of dynamics of immune-tumor interactions.

Science.gov (United States)

Moore, N; Doty, D; Zielstorff, M; Kariv, I; Moy, L Y; Gimbel, A; Chevillet, J R; Lowry, N; Santos, J; Mott, V; Kratchman, L; Lau, T; Addona, G; Chen, H; Borenstein, J T

2018-05-25

Recapitulation of the tumor microenvironment is critical for probing mechanisms involved in cancer, and for evaluating the tumor-killing potential of chemotherapeutic agents, targeted therapies and immunotherapies. Microfluidic devices have emerged as valuable tools for both mechanistic studies and for preclinical evaluation of therapeutic agents, due to their ability to precisely control drug concentrations and gradients of oxygen and other species in a scalable and potentially high throughput manner. Most existing in vitro microfluidic cancer models are comprised of cultured cancer cells embedded in a physiologically relevant matrix, collocated with vascular-like structures. However, the recent emergence of immune checkpoint inhibitors (ICI) as a powerful therapeutic modality against many cancers has created a need for preclinical in vitro models that accommodate interactions between tumors and immune cells, particularly for assessment of unprocessed tumor fragments harvested directly from patient biopsies. Here we report on a microfluidic model, termed EVIDENT (ex vivo immuno-oncology dynamic environment for tumor biopsies), that accommodates up to 12 separate tumor biopsy fragments interacting with flowing tumor-infiltrating lymphocytes (TILs) in a dynamic microenvironment. Flow control is achieved with a single pump in a simple and scalable configuration, and the entire system is constructed using low-sorption materials, addressing two principal concerns with existing microfluidic cancer models. The system sustains tumor fragments for multiple days, and permits real-time, high-resolution imaging of the interaction between autologous TILs and tumor fragments, enabling mapping of TIL-mediated tumor killing and testing of various ICI treatments versus tumor response. Custom image analytic algorithms based on machine learning reported here provide automated and quantitative assessment of experimental results. Initial studies indicate that the system is capable of

Dynamic functional brain networks involved in simple visual discrimination learning.

Science.gov (United States)

Fidalgo, Camino; Conejo, Nélida María; González-Pardo, Héctor; Arias, Jorge Luis

2014-10-01

Visual discrimination tasks have been widely used to evaluate many types of learning and memory processes. However, little is known about the brain regions involved at different stages of visual discrimination learning. We used cytochrome c oxidase histochemistry to evaluate changes in regional brain oxidative metabolism during visual discrimination learning in a water-T maze at different time points during training. As compared with control groups, the results of the present study reveal the gradual activation of cortical (prefrontal and temporal cortices) and subcortical brain regions (including the striatum and the hippocampus) associated to the mastery of a simple visual discrimination task. On the other hand, the brain regions involved and their functional interactions changed progressively over days of training. Regions associated with novelty, emotion, visuo-spatial orientation and motor aspects of the behavioral task seem to be relevant during the earlier phase of training, whereas a brain network comprising the prefrontal cortex was found along the whole learning process. This study highlights the relevance of functional interactions among brain regions to investigate learning and memory processes. Copyright © 2014 Elsevier Inc. All rights reserved.

Dynamic adjustments in prefrontal, hippocampal, and inferior temporal interactions with increasing visual working memory load.

Science.gov (United States)

Rissman, Jesse; Gazzaley, Adam; D'Esposito, Mark

2008-07-01

The maintenance of visual stimuli across a delay interval in working memory tasks is thought to involve reverberant neural communication between the prefrontal cortex and posterior visual association areas. Recent studies suggest that the hippocampus might also contribute to this retention process, presumably via reciprocal interactions with visual regions. To characterize the nature of these interactions, we performed functional connectivity analysis on an event-related functional magnetic resonance imaging data set in which participants performed a delayed face recognition task. As the number of faces that participants were required to remember was parametrically increased, the right inferior frontal gyrus (IFG) showed a linearly decreasing degree of functional connectivity with the fusiform face area (FFA) during the delay period. In contrast, the hippocampus linearly increased its delay period connectivity with both the FFA and the IFG as the mnemonic load increased. Moreover, the degree to which participants' FFA showed a load-dependent increase in its connectivity with the hippocampus predicted the degree to which its connectivity with the IFG decreased with load. Thus, these neural circuits may dynamically trade off to accommodate the particular mnemonic demands of the task, with IFG-FFA interactions mediating maintenance at lower loads and hippocampal interactions supporting retention at higher loads.

Dynamics of a collisionless plasma interacting with an ultra-intense laser pulse

International Nuclear Information System (INIS)

Capdessus, Remi

2013-01-01

The interaction of a plasma with an ultra-intense laser pulse becomes more and more interesting as a result of the advances made in terms of numerical tools laser technology. The radiation reaction impacts the electrons dynamics, those of the synchrotron radiation as well as those of the ions by means of charge separation field, for laser intensities above 10 22 W/cm 2 . The kinetic equations governing the particles transport at ultra-high intensity have been obtained. The radiation reaction involves the shrinkage of the space volume of the electrons phases. It has been shown with numerical simulations the strong retro-action that the collective effects induce on the synchrotron radiation generated by the accelerated electrons. The importance of the collective effects depends strongly on the ions mass and of the thickness of the considered plasma. These effects could be verified experimentally with hydrogen cryogenic targets. (author) [fr

Current-current interactions, dynamical symmetry-breaking, and quantum chromodynamics

International Nuclear Information System (INIS)

Neuenschwander, D.E. Jr.

1983-01-01

Quantum Chromodynamics with massive gluons (gluon mass triple bond xm/sub p/) in a contact-interaction limit called CQCD (strong coupling g→infinity; x→infinity), despite its non-renormalizability and lack of hope of confinement, is nevertheless interesting for at least two reasons. Some authors have suggested a relation between 4-Fermi and Yang-Mills theories. If g/x 2 much less than 1, then CQCD is not merely a 4-Fermi interaction, but includes 4,6,8 etc-Fermi non-Abelian contact interactions. With possibility of infrared slavery, perturbative evaluation of QCD in the infrared is a dubious practice. However, if g 2 /x 2 much less than 1 in CQCD, then the simplest 4-Fermi interaction is dominant, and CQCD admits perturbative treatment, but only in the infrared. With the dominant interaction, a dynamical Nambu-Goldstone realization of chiral symmetry-breaking (XSB) is found. Although in QCD the relation between confinement and XSB is controversial, XSB occurs in CQCD provided confinement is sacrificed

Nonlinear evolution dynamics of holographic superconductor model with scalar self-interaction

Science.gov (United States)

Li, Ran; Zi, Tieguang; Zhang, Hongbao

2018-04-01

We investigate the holographic superconductor model that is described by the Einstein-Maxwell theory with the self-interaction term λ |Ψ |4 of complex scalar field in asymptotic anti-de Sitter (AdS) spacetime. Below critical temperature Tc, the planar Reissner-Nordström-AdS black hole is unstable due to the near-horizon scalar condensation instability. We study the full nonlinear development of this instability by numerically solving the gravitational dynamics in the asymptotic AdS spacetime, and observe a dynamical process from the perturbed Reissner-Nordström-AdS black hole to a hairy black hole when the initial black hole temperature T process is then holographically dual to the dynamical superconducting phase transition process in the boundary theory. Furthermore, we also study the effect of the scalar self-interaction on time evolution of superconducting condensate operator, event and apparent horizon areas of the final hairy black hole.

Bifurcation and complex dynamics of a discrete-time predator-prey system involving group defense

Directory of Open Access Journals (Sweden)

S. M. Sohel Rana

2015-09-01

Full Text Available In this paper, we investigate the dynamics of a discrete-time predator-prey system involving group defense. The existence and local stability of positive fixed point of the discrete dynamical system is analyzed algebraically. It is shown that the system undergoes a flip bifurcation and a Neimark-Sacker bifurcation in the interior of R+2 by using bifurcation theory. Numerical simulation results not only show the consistence with the theoretical analysis but also display the new and interesting dynamical behaviors, including phase portraits, period-7, 20-orbits, attracting invariant circle, cascade of period-doubling bifurcation from period-20 leading to chaos, quasi-periodic orbits, and sudden disappearance of the chaotic dynamics and attracting chaotic set. The Lyapunov exponents are numerically computed to characterize the complexity of the dynamical behaviors.

Dynamic Socio-technical System Design based on Stakeholder Interaction

Directory of Open Access Journals (Sweden)

Albert Fleischmann

2015-07-01

Full Text Available In order to directly involve stakeholders in socio-technical system design, we argue for streamlining executable process specifications with business process modeling. Due to current agility requirements of organizations, socio-technical system development is considered one of the key activities of members of the organizations. Dynamic process adaptation enable handling the volatility of business operation and IT infrastructure. Subject-oriented process representations are key enablers to dynamic adaptation due to their capability for stakeholders to create directly executable models. In this way stakeholder can be involved in change management pro-actively. Subject-oriented models (i represent all relevant features required for system control and decision making, and (ii are executable on demand. This effectiveness enables organizational change in a creative and efficient way, while establishing innovative design and change management tools. Subject-oriented Business Process Management capabilities are reflected in this realm revealing benefits and potential for further research.

Dynamic interaction of monowheel inclined vehicle-vibration platform coupled system with quadratic and cubic nonlinearities

Science.gov (United States)

Zhou, Shihua; Song, Guiqiu; Sun, Maojun; Ren, Zhaohui; Wen, Bangchun

2018-01-01

In order to analyze the nonlinear dynamics and stability of a novel design for the monowheel inclined vehicle-vibration platform coupled system (MIV-VPCS) with intermediate nonlinearity support subjected to a harmonic excitation, a multi-degree of freedom lumped parameter dynamic model taking into account the dynamic interaction of the MIV-VPCS with quadratic and cubic nonlinearities is presented. The dynamical equations of the coupled system are derived by applying the displacement relationship, interaction force relationship at the contact position and Lagrange's equation, which are further discretized into a set of nonlinear ordinary differential equations with coupled terms by Galerkin's truncation. Based on the mathematical model, the coupled multi-body nonlinear dynamics of the vibration system is investigated by numerical method, and the parameters influences of excitation amplitude, mass ratio and inclined angle on the dynamic characteristics are precisely analyzed and discussed by bifurcation diagram, Largest Lyapunov exponent and 3-D frequency spectrum. Depending on different ranges of system parameters, the results show that the different motions and jump discontinuity appear, and the coupled system enters into chaotic behavior through different routes (period-doubling bifurcation, inverse period-doubling bifurcation, saddle-node bifurcation and Hopf bifurcation), which are strongly attributed to the dynamic interaction of the MIV-VPCS. The decreasing excitation amplitude and inclined angle could reduce the higher order bifurcations, and effectively control the complicated nonlinear dynamic behaviors under the perturbation of low rotational speed. The first bifurcation and chaotic motion occur at lower value of inclined angle, and the chaotic behavior lasts for larger intervals with higher rotational speed. The investigation results could provide a better understanding of the nonlinear dynamic behaviors for the dynamic interaction of the MIV-VPCS.

Three-dimensional fluid-structure interaction dynamics of a pool-reactor in-tank component

International Nuclear Information System (INIS)

Kulak, R.F.

1979-01-01

The safety evaluation of reactor-components often involves the analysis of various types of fluid/structural components interacting in three-dimensional space. For example, in the design of a pool-type reactor several vital in-tank components such as the primary pumps and the intermediate heat exchangers are contained within the primary tank. Typically, these components are suspended from the deck structure and largely submersed in the sodium pool. Because of this positioning these components are vulnerable to structural damage due to pressure wave propagation in the tank during a CDA. In order to assess the structural integrity of these components it is necessary to perform a dynamic analysis in three-dimensional space which accounts for the fluid-structure coupling. A model is developed which has many of the salient features of this fluid-structural component system

Nanopore wall-liquid interaction under scope of molecular dynamics study: Review

Science.gov (United States)

Tsukanov, A. A.; Psakhie, S. G.

2017-12-01

The present review is devoted to the analysis of recent molecular dynamics based on the numerical studies of molecular aspects of solid-fluid interaction in nanoscale channels. Nanopore wall-liquid interaction plays the crucial role in such processes as gas separation, water desalination, liquids decontamination, hydrocarbons and water transport in nano-fractured geological formations. Molecular dynamics simulation is one of the most suitable tools to study molecular level effects occurred in such multicomponent systems. The nanopores are classified by their geometry to four groups: nanopore in nanosheet, nanotube-like pore, slit-shaped nanopore and soft-matter nanopore. The review is focused on the functionalized nanopores in boron nitride nanosheets as novel selective membranes and on the slit-shaped nanopores formed by minerals.

Molecular dynamics simulations of lipid bilayers : major artifacts due to truncating electrostatic interactions

NARCIS (Netherlands)

Patra, M.; Karttunen, M.E.J.; Hyvönen, M.T.; Falck, E.; Lindqvist, P.; Vattulainen, I.

2003-01-01

We study the influence of truncating the electrostatic interactions in a fully hydrated pure dipalmitoylphosphatidylcholine (DPPC) bilayer through 20 ns molecular dynamics simulations. The computations in which the electrostatic interactions were truncated are compared to similar simulations using

General two-species interacting Lotka-Volterra system: Population dynamics and wave propagation

Science.gov (United States)

Zhu, Haoqi; Wang, Mao-Xiang; Lai, Pik-Yin

2018-05-01

The population dynamics of two interacting species modeled by the Lotka-Volterra (LV) model with general parameters that can promote or suppress the other species is studied. It is found that the properties of the two species' isoclines determine the interaction of species, leading to six regimes in the phase diagram of interspecies interaction; i.e., there are six different interspecific relationships described by the LV model. Four regimes allow for nontrivial species coexistence, among which it is found that three of them are stable, namely, weak competition, mutualism, and predator-prey scenarios can lead to win-win coexistence situations. The Lyapunov function for general nontrivial two-species coexistence is also constructed. Furthermore, in the presence of spatial diffusion of the species, the dynamics can lead to steady wavefront propagation and can alter the population map. Propagating wavefront solutions in one dimension are investigated analytically and by numerical solutions. The steady wavefront speeds are obtained analytically via nonlinear dynamics analysis and verified by numerical solutions. In addition to the inter- and intraspecific interaction parameters, the intrinsic speed parameters of each species play a decisive role in species populations and wave properties. In some regimes, both species can copropagate with the same wave speeds in a finite range of parameters. Our results are further discussed in the light of possible biological relevance and ecological implications.

2010 Atomic & Molecular Interactions Gordon Research Conference

Energy Technology Data Exchange (ETDEWEB)

Todd Martinez

2010-07-23

The Atomic and Molecular Interactions Gordon Conferences is justifiably recognized for its broad scope, touching on areas ranging from fundamental gas phase and gas-condensed matter collision dynamics, to laser-molecule interactions, photophysics, and unimolecular decay processes. The meeting has traditionally involved scientists engaged in fundamental research in gas and condensed phases and those who apply these concepts to systems of practical chemical and physical interest. A key tradition in this meeting is the strong mixing of theory and experiment throughout. The program for 2010 conference continues these traditions. At the 2010 AMI GRC, there will be talks in 5 broadly defined and partially overlapping areas of intermolecular interactions and chemical dynamics: (1) Photoionization and Photoelectron Dynamics; (2) Quantum Control and Molecules in Strong Fields; (3) Photochemical Dynamics; (4) Complex Molecules and Condensed Phases; and (5) Clusters and Reaction Dynamics. These areas encompass many of the most productive and exciting areas of chemical physics, including both reactive and nonreactive processes, intermolecular and intramolecular energy transfer, and photodissociation and unimolecular processes. Gas phase dynamics, van der Waals and cluster studies, laser-matter interactions and multiple potential energy surface phenomena will all be discussed.

The Glauber dynamics for a spin-1 metamagnetic Ising system with bilinear and biquadratic interactions

Energy Technology Data Exchange (ETDEWEB)

Keskin, Mustafa [Department of Physics, Erciyes University, 38039 Kayseri (Turkey)], E-mail: keskin@erciyes.edu.tr; Canko, Osman [Department of Physics, Erciyes University, 38039 Kayseri (Turkey); Kantar, Ersin [Institute of Science, Erciyes University, 38039 Kayseri (Turkey)

2009-06-15

We present a study, within a mean-field approximation, of the dynamics of a spin-1 metamagnetic Ising system with bilinear and biquadratic interactions in the presence of a time-dependent oscillating external magnetic field. First, we employ the Glauber transition rates to construct the set of mean-field dynamic equations. Then, we study the time variation of the average order parameters to find the phases in the system. We also investigate the thermal behavior of dynamic order parameters to characterize the nature (first- or second-order) of the dynamic transitions. The dynamic phase transitions are obtained and the phase diagrams are constructed in two different the planes. The phase diagrams contain a disordered and ordered phases, and four different mixed phases that strongly depend on interaction parameters. Phase diagrams also display one or two dynamic tricritical points, a dynamic double critical end and dynamic quadruple points. A comparison is made with the results of the other metamagnetic Ising systems.

The Glauber dynamics for a spin-1 metamagnetic Ising system with bilinear and biquadratic interactions

International Nuclear Information System (INIS)

Keskin, Mustafa; Canko, Osman; Kantar, Ersin

2009-01-01

We present a study, within a mean-field approximation, of the dynamics of a spin-1 metamagnetic Ising system with bilinear and biquadratic interactions in the presence of a time-dependent oscillating external magnetic field. First, we employ the Glauber transition rates to construct the set of mean-field dynamic equations. Then, we study the time variation of the average order parameters to find the phases in the system. We also investigate the thermal behavior of dynamic order parameters to characterize the nature (first- or second-order) of the dynamic transitions. The dynamic phase transitions are obtained and the phase diagrams are constructed in two different the planes. The phase diagrams contain a disordered and ordered phases, and four different mixed phases that strongly depend on interaction parameters. Phase diagrams also display one or two dynamic tricritical points, a dynamic double critical end and dynamic quadruple points. A comparison is made with the results of the other metamagnetic Ising systems.

Interaction of 〈1 0 0〉 dislocation loops with dislocations studied by dislocation dynamics in α-iron

Energy Technology Data Exchange (ETDEWEB)

Shi, X.J.; Dupuy, L. [CEA, DEN, SRMA, F-91191 Gif-sur-Yvette (France); Devincre, B. [Laboratoire d’Etude des Microstructures, CNRS-ONERA, 29 av. de la Division Leclerc, 92322 Châtillon Cedex (France); Terentyev, D. [SCK–CEN, Nuclear Materials Science Institute, Boeretang 200, B-2400 Mol (Belgium); Vincent, L. [CEA, DEN, SRMA, F-91191 Gif-sur-Yvette (France)

2015-05-15

Highlights: • Interactions between edge dislocations and radiation-induced loops were studied by dislocation dynamics. • Dislocation dynamics results are directly compared to molecular dynamics results. • The complex elementary reactions are successfully reproduced. • The critical shear stress to overcome individual loops if reproduced quantitatively. - Abstract: Interstitial dislocation loops with Burgers vector of 〈1 0 0〉 type are formed in α-iron under neutron or heavy ion irradiation. As the density and size of these loops increase with radiation dose and temperature, these defects are thought to play a key role in hardening and subsequent embrittlement of iron-based steels. The aim of the present work is to study the pinning strength of the loops on mobile dislocations. Prior to run massive Dislocation Dynamics (DD) simulations involving experimentally representative array of radiation defects and dislocations, the DD code and its parameterization are validated by comparing the individual loop–dislocation reactions with those obtained from direct atomistic Molecular Dynamics (MD) simulations. Several loop–dislocation reaction mechanisms are successfully reproduced as well as the values of the unpinning stress to detach mobile dislocations from the defects.

Getting the ion-protein interactions right in molecular dynamics simulations

Czech Academy of Sciences Publication Activity Database

Duboué-Dijon, Elise; Mason, Philip E.; Jungwirth, Pavel

2017-01-01

Roč. 46, Suppl 1 (2017), S66 ISSN 0175-7571. [IUPAB congress /19./ and EBSA congress /11./. 16.07.2017-20.07.2017, Edinburgh] Institutional support: RVO:61388963 Keywords : ion-protein interaction * molecular dynamics simulations * neutron scattering * insulin Subject RIV: BO - Biophysics

On the decomposition of a dynamical system into non-interacting subsystems.

Science.gov (United States)

Rosen, R.

1972-01-01

It is shown that, under rather general conditions, it is possible to formally decompose the dynamics of an n-dimensional dynamical system into a number of non-interacting subsystems. It is shown that these decompositions are in general not simply related to the kinds of observational procedures in terms of which the original state variables of the system are defined. Some consequences of this construction for reductionism in biology are discussed.

Dynamic Analysis of Wind Turbines Including Soil-Structure Interaction

DEFF Research Database (Denmark)

Harte, M.; Basu, B.; Nielsen, Søren R.K.

2012-01-01

This paper investigates the along-wind forced vibration response of an onshore wind turbine. The study includes the dynamic interaction effects between the foundation and the underlying soil, as softer soils can influence the dynamic response of wind turbines. A Multi-Degree-of-Freedom (MDOF......) horizontal axes onshore wind turbine model is developed for dynamic analysis using an Euler–Lagrangian approach. The model is comprised of a rotor blade system, a nacelle and a flexible tower connected to a foundation system using a substructuring approach. The rotor blade system consists of three rotating...... for displacement of the turbine system are obtained and the modal frequencies of the combined turbine-foundation system are estimated. Simulations are presented for the MDOF turbine structure subjected to wind loading for different soil stiffness conditions. Steady state and turbulent wind loading, developed using...

Interactions of heavy ions with biomolecules: a dynamical microscopic approach

International Nuclear Information System (INIS)

Zhang Fengshou; Beijing Radiation Center, Beijing; National Laboratory of Heavy Ion Accelerator of Lanzhou, Lanzhou

2006-01-01

The status of studying biology system therapy with X-rays, γ-rays, neutron, proton, and heavy ions is reviewed. The depth dose profile, called Bragg profile, makes heavy ion an ideal tool for radiotherapy. The physical process of therapy with heavy ions is analyzed and a 3-step interaction processes of heavy ions with biomolecules is proposed, that is, nuclear fragmentation in nuclear interaction, electron excitation in Coulomb interaction, and the biomolecules relaxation in surroundings, finally leads to a new structure of biomolecule. Since this physical process is the base of the following chemical process and biological process, a dynamical microscopic approach is strongly demanded to be built. (authors)

Dynamic interactions of Leidenfrost droplets on liquid metal surface

Science.gov (United States)

Ding, Yujie; Liu, Jing

2016-09-01

Leidenfrost dynamic interaction effects of the isopentane droplets on the surface of heated liquid metal were disclosed. Unlike conventional rigid metal, such conductive and deformable liquid metal surface enables the levitating droplets to demonstrate rather abundant and complex dynamics. The Leidenfrost droplets at different diameters present diverse morphologies and behaviors like rotation and oscillation. Depending on the distance between the evaporating droplets, they attract and repulse each other through the curved surfaces beneath them and their vapor flows. With high boiling point up to 2000 °C, liquid metal offers a unique platform for testing the evaporating properties of a wide variety of liquid even solid.

Bioluminescence resonance energy transfer system for measuring dynamic protein-protein interactions in bacteria.

Science.gov (United States)

Cui, Boyu; Wang, Yao; Song, Yunhong; Wang, Tietao; Li, Changfu; Wei, Yahong; Luo, Zhao-Qing; Shen, Xihui

2014-05-20

Protein-protein interactions are important for virtually every biological process, and a number of elegant approaches have been designed to detect and evaluate such interactions. However, few of these methods allow the detection of dynamic and real-time protein-protein interactions in bacteria. Here we describe a bioluminescence resonance energy transfer (BRET) system based on the bacterial luciferase LuxAB. We found that enhanced yellow fluorescent protein (eYFP) accepts the emission from LuxAB and emits yellow fluorescence. Importantly, BRET occurred when LuxAB and eYFP were fused, respectively, to the interacting protein pair FlgM and FliA. Furthermore, we observed sirolimus (i.e., rapamycin)-inducible interactions between FRB and FKBP12 and a dose-dependent abolishment of such interactions by FK506, the ligand of FKBP12. Using this system, we showed that osmotic stress or low pH efficiently induced multimerization of the regulatory protein OmpR and that the multimerization induced by low pH can be reversed by a neutralizing agent, further indicating the usefulness of this system in the measurement of dynamic interactions. This method can be adapted to analyze dynamic protein-protein interactions and the importance of such interactions in bacterial processes such as development and pathogenicity. Real-time measurement of protein-protein interactions in prokaryotes is highly desirable for determining the roles of protein complex in the development or virulence of bacteria, but methods that allow such measurement are not available. Here we describe the development of a bioluminescence resonance energy transfer (BRET) technology that meets this need. The use of endogenous excitation light in this strategy circumvents the requirement for the sophisticated instrument demanded by standard fluorescence resonance energy transfer (FRET). Furthermore, because the LuxAB substrate decanal is membrane permeable, the assay can be performed without lysing the bacterial cells

Hard Break-Up of Two-Nucleons and QCD Dynamics of NN Interaction

International Nuclear Information System (INIS)

Sargsian, Misak

2008-01-01

We discus recent developments in theory of high energy two-body break-up of few-nucleon systems. The characteristics of these reactions are such that the hard two-body quasielastic subprocess can be clearly separated from the accompanying soft subprocesses. We discuss in details the hard rescattering model (HRM) in which hard photodisintegration develops in two stages. At first, photon knocks-out an energetic quark which rescatters subsequently with a quark of the other nucleon. The latter provides a mechanism of sharing the initial high momentum of the photon between two outgoing nucleons. This final state hard rescattering can be expressed through the hard NN scattering amplitude. Within HRM we discuss hard break-up reactions involving D and 3 He targets and demonstrate how these reactions are sensitive to the dynamics of hard pn and pp interaction. Another development of HRM is the prediction of new helicity selection mechanism for hard two-body reactions, which was apparently confirmed in the recent JLab experiment.

Dynamic Involvement of Real World Objects in the IoT: A Consensus-Based Cooperation Approach.

Science.gov (United States)

Pilloni, Virginia; Atzori, Luigi; Mallus, Matteo

2017-03-01

A significant role in the Internet of Things (IoT) will be taken by mobile and low-cost unstable devices, which autonomously self-organize and introduce highly dynamic and heterogeneous scenarios for the deployment of distributed applications. This entails the devices to cooperate to dynamically find the suitable combination of their involvement so as to improve the system reliability while following the changes in their status. Focusing on the above scenario, we propose a distributed algorithm for resources allocation that is run by devices that can perform the same task required by the applications, allowing for a flexible and dynamic binding of the requested services with the physical IoT devices. It is based on a consensus approach, which maximizes the lifetime of groups of nodes involved and ensures the fulfillment of the requested Quality of Information (QoI) requirements. Experiments have been conducted with real devices, showing an improvement of device lifetime of more than 20 % , with respect to a uniform distribution of tasks.

Domain Specific Languages for Interactive Web Services

DEFF Research Database (Denmark)

Brabrand, Claus

This dissertation shows how domain specific languages may be applied to the domain of interactive Web services to obtain flexible, safe, and efficient solutions. We show how each of four key aspects of interactive Web services involving sessions, dynamic creation of HTML/XML documents, form field......, , that supports virtually all aspects of the development of interactive Web services and provides flexible, safe, and efficient solutions....

Dynamics of vortex interactions in two-dimensional flows

DEFF Research Database (Denmark)

Juul Rasmussen, J.; Nielsen, A.H.; Naulin, V.

2002-01-01

The dynamics and interaction of like-signed vortex structures in two dimensional flows are investigated by means of direct numerical solutions of the two-dimensional Navier-Stokes equations. Two vortices with distributed vorticity merge when their distance relative to their radius, d/R-0l. is below...... a critical value, a(c). Using the Weiss-field, a(c) is estimated for vortex patches. Introducing an effective radius for vortices with distributed vorticity, we find that 3.3 ... is effectively producing small scale structures and the relation to the enstrophy "cascade" in developed 2D turbulence is discussed. The influence of finite viscosity on the merging is also investigated. Additionally, we examine vortex interactions on a finite domain, and discuss the results in connection...

Current-current interactions, dynamical symmetry-breaking, and quantum chromodynamics

Energy Technology Data Exchange (ETDEWEB)

Neuenschwander, D.E. Jr.

1983-01-01

Quantum Chromodynamics with massive gluons (gluon mass triple bond xm/sub p/) in a contact-interaction limit called CQCD (strong coupling g..-->..infinity; x..-->..infinity), despite its non-renormalizability and lack of hope of confinement, is nevertheless interesting for at least two reasons. Some authors have suggested a relation between 4-Fermi and Yang-Mills theories. If g/x/sup 2/ much less than 1, then CQCD is not merely a 4-Fermi interaction, but includes 4,6,8 etc-Fermi non-Abelian contact interactions. With possibility of infrared slavery, perturbative evaluation of QCD in the infrared is a dubious practice. However, if g/sup 2//x/sup 2/ much less than 1 in CQCD, then the simplest 4-Fermi interaction is dominant, and CQCD admits perturbative treatment, but only in the infrared. With the dominant interaction, a dynamical Nambu-Goldstone realization of chiral symmetry-breaking (XSB) is found. Although in QCD the relation between confinement and XSB is controversial, XSB occurs in CQCD provided confinement is sacrificed.

Global Dynamical Systems Involving Generalized -Projection Operators and Set-Valued Perturbation in Banach Spaces

Directory of Open Access Journals (Sweden)

Yun-zhi Zou

2012-01-01

Full Text Available A new class of generalized dynamical systems involving generalized f-projection operators is introduced and studied in Banach spaces. By using the fixed-point theorem due to Nadler, the equilibrium points set of this class of generalized global dynamical systems is proved to be nonempty and closed under some suitable conditions. Moreover, the solutions set of the systems with set-valued perturbation is showed to be continuous with respect to the initial value.

Conditional co-movement and dynamic interactions: US and BRIC equity markets

Directory of Open Access Journals (Sweden)

Singh Amanjot

2017-01-01

Full Text Available The present study attempts to capture conditional or time-varying co-movement and dynamic interactions between the US and BRIC (Brazil, Russia, India, and China equity markets across the sample period 2004 to 2014 by employing diverse econometric models. The sample period is further divided into three different sub-periods concerning the US financial crisis period, viz. pre-crisis, crisis, and post-crisis periods. The vector autoregression- dynamic conditional correlation-multivariate asymmetric generalized autoregressive conditional heteroskedastic [VAR-DCC-MVAGARCH (1.1] model and Toda-Yamamoto’s (1995 Granger causality tests are employed for the purpose of overall analysis in a multivariate framework. The results report the existence of time-varying co-movement between the US and BRIC equity markets, whereby co-movement between the US and Brazilian markets is found to be the highest, followed by the Russian, Indian, and Chinese equity markets. Dynamic interactions are also registered between the respective US/BRIC comovements during different sub-periods. The results have important implications for market participants and policymakers.

Nonlinear dynamic analysis of framed structures including soil-structure interaction effects

International Nuclear Information System (INIS)

Mahmood, M.N.; Ahmed, S.Y.

2008-01-01

The role of oil-structure interaction on seismic behavior of reinforced concrete structures is investigated in this paper. A finite element approach has been adopted to model the interaction system that consists of the reinforced concrete plane frame, soil deposit and interface which represents the frictional between foundation of the structure and subsoil. The analysis is based on the elasto-plastic behavior of the frame members (beams and columns) that is defined by the ultimate axial force-bending moment interaction curve, while the cap model is adopted to govern the elasto-plastic behavior of the soil material. Mohr-Coulomb failure law is used to determine the initiation of slippage at the interface, while the separation is assumed to determine the initiation of slippage at the interface, while the separation is assumed to occur when the stresses at the interface becomes tension stresses. New-Mark's Predictor-Corrector algorithm is adopted for nonlinear dynamic analysis. The main aim of present work is to evaluate the sensitivity of structures to different behavior of the soil and interface layer when subjected to an earthquake excitation. Predicted results of the dynamic analysis of the interaction system indicate that the soil-structure interaction problem can have beneficial effects on the structural behavior when different soil models (elastic and elasto-plastic) and interface conditions (perfect bond and permitted slip)are considered. (author)

DYNAMIC SURFACE BOUNDARY-CONDITIONS - A SIMPLE BOUNDARY MODEL FOR MOLECULAR-DYNAMICS SIMULATIONS

NARCIS (Netherlands)

JUFFER, AH; BERENDSEN, HJC

1993-01-01

A simple model for the treatment of boundaries in molecular dynamics simulations is presented. The method involves the positioning of boundary atoms on a surface that surrounds a system of interest. The boundary atoms interact with the inner region and represent the effect of atoms outside the

The Prediction of Key Cytoskeleton Components Involved in Glomerular Diseases Based on a Protein-Protein Interaction Network.

Science.gov (United States)

Ding, Fangrui; Tan, Aidi; Ju, Wenjun; Li, Xuejuan; Li, Shao; Ding, Jie

2016-01-01

Maintenance of the physiological morphologies of different types of cells and tissues is essential for the normal functioning of each system in the human body. Dynamic variations in cell and tissue morphologies depend on accurate adjustments of the cytoskeletal system. The cytoskeletal system in the glomerulus plays a key role in the normal process of kidney filtration. To enhance the understanding of the possible roles of the cytoskeleton in glomerular diseases, we constructed the Glomerular Cytoskeleton Network (GCNet), which shows the protein-protein interaction network in the glomerulus, and identified several possible key cytoskeletal components involved in glomerular diseases. In this study, genes/proteins annotated to the cytoskeleton were detected by Gene Ontology analysis, and glomerulus-enriched genes were selected from nine available glomerular expression datasets. Then, the GCNet was generated by combining these two sets of information. To predict the possible key cytoskeleton components in glomerular diseases, we then examined the common regulation of the genes in GCNet in the context of five glomerular diseases based on their transcriptomic data. As a result, twenty-one cytoskeleton components as potential candidate were highlighted for consistently down- or up-regulating in all five glomerular diseases. And then, these candidates were examined in relation to existing known glomerular diseases and genes to determine their possible functions and interactions. In addition, the mRNA levels of these candidates were also validated in a puromycin aminonucleoside(PAN) induced rat nephropathy model and were also matched with existing Diabetic Nephropathy (DN) transcriptomic data. As a result, there are 15 of 21 candidates in PAN induced nephropathy model were consistent with our predication and also 12 of 21 candidates were matched with differentially expressed genes in the DN transcriptomic data. By providing a novel interaction network and prediction, GCNet

Static/dynamic fluid-structure interaction analysis for 3-D rotary blade model

International Nuclear Information System (INIS)

Kim, Dong Hyun; Kim, Yu Sung; Kim, Dong Man; Park, Kang Kyun

2009-01-01

In this study, static/dynamic fluid-structure interaction analyses have been conducted for a 3D rotary blade model like a turbo-machinery or wind turbine blade. Advanced computational analysis system based on Computational Fluid Dynamics (CFD) and Computational Structural Dynamics (CSD) has been developed in order to investigate detailed dynamic responses of rotary type models. Fluid domains are modeled using the computational grid system with local grid deforming techniques. Reynolds-averaged Navier-Stokes equations with various turbulence model are solved for unsteady flow problems of the rotating blade model. Detailed static/dynamic responses and instantaneous pressure contours on the blade surfaces considering flow-separation effects are presented to show the multi-physical phenomenon of the rotating blades.

Dynamics simulations for engineering macromolecular interactions

Science.gov (United States)

Robinson-Mosher, Avi; Shinar, Tamar; Silver, Pamela A.; Way, Jeffrey

2013-01-01

The predictable engineering of well-behaved transcriptional circuits is a central goal of synthetic biology. The artificial attachment of promoters to transcription factor genes usually results in noisy or chaotic behaviors, and such systems are unlikely to be useful in practical applications. Natural transcriptional regulation relies extensively on protein-protein interactions to insure tightly controlled behavior, but such tight control has been elusive in engineered systems. To help engineer protein-protein interactions, we have developed a molecular dynamics simulation framework that simplifies features of proteins moving by constrained Brownian motion, with the goal of performing long simulations. The behavior of a simulated protein system is determined by summation of forces that include a Brownian force, a drag force, excluded volume constraints, relative position constraints, and binding constraints that relate to experimentally determined on-rates and off-rates for chosen protein elements in a system. Proteins are abstracted as spheres. Binding surfaces are defined radially within a protein. Peptide linkers are abstracted as small protein-like spheres with rigid connections. To address whether our framework could generate useful predictions, we simulated the behavior of an engineered fusion protein consisting of two 20 000 Da proteins attached by flexible glycine/serine-type linkers. The two protein elements remained closely associated, as if constrained by a random walk in three dimensions of the peptide linker, as opposed to showing a distribution of distances expected if movement were dominated by Brownian motion of the protein domains only. We also simulated the behavior of fluorescent proteins tethered by a linker of varying length, compared the predicted Förster resonance energy transfer with previous experimental observations, and obtained a good correspondence. Finally, we simulated the binding behavior of a fusion of two ligands that could

Dynamics of Entanglement in Qubit-Qutrit with x-Component of DM Interaction

International Nuclear Information System (INIS)

Sharma, Kapil K.; Pandey, S.N.

2016-01-01

In this present paper, we study the entanglement dynamics in qubit A-qutrit B pair under x component of Dzyaloshinshkii–Moriya interaction (D x ) by taking an auxiliary qubit C. Here, we consider an entangled qubit-qutrit pair initially prepared in two parameter qubit-qutrit states and one auxiliary qubit prepared in pure state interacts with the qutrit of the pair through DM interaction. We trace away the auxiliary qubit and calculate the reduced dynamics in qubit A-qutrit B pair to study the influence of the state of auxiliary qubit C and D x on entanglement. We find that the state (probability amplitude) of auxiliary qubit does not influence the entanglement, only D x influences the same. The phenomenon of entanglement sudden death (ESD) induced by D x has also been observed. We also present the affected and unaffected two parameter qubit-qutrit states by D x . (paper)

Dislocation-cavity interaction in Fe: a comparison between molecular dynamics and dislocation dynamics

International Nuclear Information System (INIS)

Hafez Haghighat, S.M.; Schaeublin, R.; Fivel, M.C.

2007-01-01

Full text of publication follows: multi-scale modeling, including molecular dynamics (MD) and discrete dislocation dynamics (DDD) methods, appears as a significant tool for the description of plasticity and mechanical properties of materials. This research is on the investigation of the subsequence effects of irradiation on the plasticity of pure Fe and focuses on the interaction of a single dislocation and a spherical cavity, as void or He bubble. Extensive MD simulations of the interaction under imposed strain rate [1, 2] have shown that various temperatures and cavity sizes result in different release stresses depending on dislocation bow out. It appears that a temperature increase and cavity size decrease reduce the cavity strength. MD simulation shows that the elastic field around the cavity is largely anisotropic. This anisotropy may influence the way the dislocation unpins from the cavity. Following the MD simulations, the interaction of a single dislocation and a spherical cavity is now simulated using a DDD discrete dislocation dynamics model. The simulation accounts for the non-Schmidt effect induced by the bcc structure of Fe through local rules derived from MD simulations [3]. The cavity is introduced in the simulation by computing the image forces using a finite element technique. The effective stress applied on the dislocation is then obtained as the superimposition of the applied stress field, the image stress field and the internal stresses. Note that such a model only uses elasticity theory and no core effect of dislocations is taken into account. One of the objectives of this work is to check whether elasticity is responsible of the behaviour observed by MD. Several cases are tested. First an edge dislocation in a (110) plane is pushed against the cavity under a pure shear loading. The local reaction of the dislocations and the cavity are compared to the MD simulations. Then, the case of a screw dislocation is studied. Finally, other loading

Combining user logging with eye tracking for interactive and dynamic applications.

Science.gov (United States)

Ooms, Kristien; Coltekin, Arzu; De Maeyer, Philippe; Dupont, Lien; Fabrikant, Sara; Incoul, Annelies; Kuhn, Matthias; Slabbinck, Hendrik; Vansteenkiste, Pieter; Van der Haegen, Lise

2015-12-01

User evaluations of interactive and dynamic applications face various challenges related to the active nature of these displays. For example, users can often zoom and pan on digital products, and these interactions cause changes in the extent and/or level of detail of the stimulus. Therefore, in eye tracking studies, when a user's gaze is at a particular screen position (gaze position) over a period of time, the information contained in this particular position may have changed. Such digital activities are commonplace in modern life, yet it has been difficult to automatically compare the changing information at the viewed position, especially across many participants. Existing solutions typically involve tedious and time-consuming manual work. In this article, we propose a methodology that can overcome this problem. By combining eye tracking with user logging (mouse and keyboard actions) with cartographic products, we are able to accurately reference screen coordinates to geographic coordinates. This referencing approach allows researchers to know which geographic object (location or attribute) corresponds to the gaze coordinates at all times. We tested the proposed approach through two case studies, and discuss the advantages and disadvantages of the applied methodology. Furthermore, the applicability of the proposed approach is discussed with respect to other fields of research that use eye tracking-namely, marketing, sports and movement sciences, and experimental psychology. From these case studies and discussions, we conclude that combining eye tracking and user-logging data is an essential step forward in efficiently studying user behavior with interactive and static stimuli in multiple research fields.

Characterization of Hydrophobic Interactions of Polymers with Water and Phospholipid Membranes Using Molecular Dynamics Simulations

Science.gov (United States)

Drenscko, Mihaela

Polymers and lipid membranes are both essential soft materials. The structure and hydrophobicity/hydrophilicity of polymers, as well as the solvent they are embedded in, ultimately determines their size and shape. Understating the variation of shape of the polymer as well as its interactions with model biological membranes can assist in understanding the biocompatibility of the polymer itself. Computer simulations, in particular molecular dynamics, can aid in characterization of the interaction of polymers with solvent, as well as polymers with model membranes. In this thesis, molecular dynamics serve to describe polymer interactions with a solvent (water) and with a lipid membrane. To begin with, we characterize the hydrophobic collapse of single polystyrene chains in water using molecular dynamics simulations. Specifically, we calculate the potential of mean force for the collapse of a single polystyrene chain in water using metadynamics, comparing the results between all atomistic with coarse-grained molecular simulation. We next explore the scaling behavior of the collapsed globular shape at the minimum energy configuration, characterized by the radius of gyration, as a function of chain length. The exponent is close to one third, consistent with that predicted for a polymer chain in bad solvent. We also explore the scaling behavior of the Solvent Accessible Surface Area (SASA) as a function of chain length, finding a similar exponent for both all-atomistic and coarse-grained simulations. Furthermore, calculation of the local water density as a function of chain length near the minimum energy configuration suggests that intermediate chain lengths are more likely to form dewetted states, as compared to shorter or longer chain lengths. Next, in order to investigate the molecular interactions between single hydrophobic polymer chains and lipids in biological membranes and at lipid membrane/solvent interface, we perform a series of molecular dynamics simulations of

Predicted Bacterial Interactions Affect in Vivo Microbial Colonization Dynamics in Nematostella

Science.gov (United States)

Domin, Hanna; Zurita-Gutiérrez, Yazmín H.; Scotti, Marco; Buttlar, Jann; Hentschel Humeida, Ute; Fraune, Sebastian

2018-01-01

The maintenance and resilience of host-associated microbiota during development is a fundamental process influencing the fitness of many organisms. Several host properties were identified as influencing factors on bacterial colonization, including the innate immune system, mucus composition, and diet. In contrast, the importance of bacteria–bacteria interactions on host colonization is less understood. Here, we use bacterial abundance data of the marine model organism Nematostella vectensis to reconstruct potential bacteria–bacteria interactions through co-occurrence networks. The analysis indicates that bacteria–bacteria interactions are dynamic during host colonization and change according to the host’s developmental stage. To assess the predictive power of inferred interactions, we tested bacterial isolates with predicted cooperative or competitive behavior for their ability to influence bacterial recolonization dynamics. Within 3 days of recolonization, all tested bacterial isolates affected bacterial community structure, while only competitive bacteria increased bacterial diversity. Only 1 week after recolonization, almost no differences in bacterial community structure could be observed between control and treatments. These results show that predicted competitive bacteria can influence community structure for a short period of time, verifying the in silico predictions. However, within 1 week, the effects of the bacterial isolates are neutralized, indicating a high degree of resilience of the bacterial community. PMID:29740401

Predicted Bacterial Interactions Affect in Vivo Microbial Colonization Dynamics in Nematostella

Directory of Open Access Journals (Sweden)

Hanna Domin

2018-04-01

Full Text Available The maintenance and resilience of host-associated microbiota during development is a fundamental process influencing the fitness of many organisms. Several host properties were identified as influencing factors on bacterial colonization, including the innate immune system, mucus composition, and diet. In contrast, the importance of bacteria–bacteria interactions on host colonization is less understood. Here, we use bacterial abundance data of the marine model organism Nematostella vectensis to reconstruct potential bacteria–bacteria interactions through co-occurrence networks. The analysis indicates that bacteria–bacteria interactions are dynamic during host colonization and change according to the host’s developmental stage. To assess the predictive power of inferred interactions, we tested bacterial isolates with predicted cooperative or competitive behavior for their ability to influence bacterial recolonization dynamics. Within 3 days of recolonization, all tested bacterial isolates affected bacterial community structure, while only competitive bacteria increased bacterial diversity. Only 1 week after recolonization, almost no differences in bacterial community structure could be observed between control and treatments. These results show that predicted competitive bacteria can influence community structure for a short period of time, verifying the in silico predictions. However, within 1 week, the effects of the bacterial isolates are neutralized, indicating a high degree of resilience of the bacterial community.

A rheonomic model for the dynamical analysis of the structure-soil interaction

International Nuclear Information System (INIS)

Chiroiu, V.; Nicolae, V.

1993-01-01

The dynamical analysis of the structure-soil interaction requires an adequate modeling of the geometrical radiation phenomenon (g.r.) i.e. the propagation of the vibrating energy of the structure in the infinite medium. Newton's law of motion is not including the g.r., considered in this paper like an irreversible phenomenon. To incorporate this, a new wave motion equation is proposed, according to a complete analysis of the structure-soil interactions with an adequate formulation of the g.r. By using a system of fundamental dynamical solutions, the rheonom constraint applied to the half-space is represented as a restriction to the displacement solutions. A dimensionless formulation of the problem and the variation of dynamical and energetical quantities in respect to the frequency, as according to the diagram of the characteristic curve of g.r. are presented numerically. Sample results showing the importance of radiation energy for several motions are also shown

Dynamic nonlinear interaction of elastic plates on discrete supports

International Nuclear Information System (INIS)

Coutinho, A.L.G.A.; Landau, L.; Lima, E.C.P. de; Ebecken, N.F.F.

1984-01-01

A study on the dynamic nonlinear interaction of elastic plates using the finite element method is presented. The elastic plate is discretized by 4-node isoparametric Mindlin elements. The constitutive relation of the discrete supports can be any nonlinear curve given by pairs of force-displacement points. The nonlinear behaviour is represented by the overlay approach. This model also allows the simulation of a progressive decrease on the supports stiffnesses during load cycles. The dynamic nonlinear incremental movement equations are integrated by the Newmark implicit operator. Two alternatives for the incremental-iterative formulation are compared. The paper ends with a discussion of the advantages and limitations of the presented numerical models. (Author) [pt

Joint symbolic dynamic analysis of cardiorespiratory interactions in patients on weaning trials.

Science.gov (United States)

Caminal, P; Giraldo, B; Zabaleta, H; Vallverdu, M; Benito, S; Ballesteros, D; Lopez-Rodriguez, L; Esteban, A; Baumert, M; Voss, A

2005-01-01

Assessing autonomic control provides information about patho-physiological imbalances. Measures of variability of the cardiac interbeat duration RR(n) and the variability of the breath duration TTot(n) are sensitive to those changes. The interactions between RR(n) and TTot(n) are complex and strongly non-linear. A study of joint symbolic dynamics is presented as a new short-term non-linear analysis method to investigate these interactions in patients on weaning trials. 78 patients from mechanical ventilation are studied: Group A (patients that failed to maintain spontaneous breathing and were reconnected) and Group B (patients with successful trials). Using the concept of joint symbolic dynamics, cardiac and respiratory changes were transformed into a word series, and the probability of occurrence of each word type was calculated and compared between both groups. Significant differences were found in 13 words, and the most significant pn(Wc010, r010): 0.0041 ± 0.0036 (group A) against 0.0012 ± 0.0024 (group B), p-value = 0.00001. The number of seldom occurring word types (forbidden words) also presents significant differences fwcr: 6.9 ± 6.6 against 13.5 ± 5.3, p-value = 0.00004. Joint symbolic dynamics provides an efficient non-linear representation of cardiorespiratory interactions that offers simple physiological interpretations.

Elastic interaction between defects during dynamic aging of stainless steels

International Nuclear Information System (INIS)

Journaux, J.; Monteiro, S.N.

1977-01-01

The study of the mechanical properties through traction tests, at temperatures above room temperature in 316 type stainless steel emphasizes the existence of the dynamic aging phenomenon (Portevin-Lechantelier effect). The present paper explains in a general way the fundamental causes of this effect by examining the elastic interactions that occur between the solute atoms in solid solution and the crystal dislocations. These interactions, which are present only at a certain temperature range, are responsible for the improvement of the mechanical properties always noticed in the alloys showing this phenomenon. (F.R.) [pt

Father-child and mother-child interaction in families with a child feeding disorder: The role of paternal involvement.

Science.gov (United States)

Atzaba-Poria, Naama; Meiri, Gal; Millikovsky, Maaian; Barkai, Anat; Dunaevsky-Idan, Maayan; Yerushalmi, Baruch

2010-11-01

To date, research about feeding disorder (FD) has focused almost exclusively on the mother-child dyad, ignoring fathers' roles. The current study investigated father-child interactions with children having FD. The sample consisted of 67 children (1-3 years old) and their mothers and fathers. Thirty-four children, diagnosed with a nonorganic-based FD (FD group) and 33 children without an FD (control group) were matched for age, gender, birth order, and maternal education. Data were collected during home visits. Mothers were interviewed about their and the father's involvement in childcare. In addition, mother-child and father-child interactions were videotaped during play and feeding. Both mothers and fathers from the FD group experienced less positive parent-child interactions than did parents in the control group. Furthermore, mothers in the FD group reported greater maternal versus paternal childcare involvement than did control group mothers. Finally, FD group mothers exhibited more parental sensitivity than did fathers during feeing interactions; however, this difference was observed only when coupled with low paternal involvement. In families where fathers were highly involved, no difference was evident in paternal and maternal sensitivity. These findings highlight the importance of fathers' involvement, especially in families with children exhibiting an FD. Copyright © 2010 Michigan Association for Infant Mental Health.

Component Based System Framework for Dynamic B2B Interaction

NARCIS (Netherlands)

Hu jinmin, Jinmin; Grefen, P.W.P.J.

Business-to-Business (B2B) collaboration is becoming a pivotal way to bring today's enterprises to success in the dynamically changing e-business environment. Though many business-to-business protocols are developed to support B2B interaction, none are generally accepted. A B2B system should support

Emergence of junction dynamics in a strongly interacting Bose mixture

DEFF Research Database (Denmark)

Barfknecht, Rafael Emilio; Foerster, Angela; Zinner, Nikolaj Thomas

We study the dynamics of a one-dimensional system composed of a bosonic background and one impurity in single- and double-well trapping geometries. In the limit of strong interactions, this system can be modeled by a spin chain where the exchange coefficients are determined by the geometry of the...

Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics

Science.gov (United States)

Brela, Mateusz Z.; Boczar, Marek; Malec, Leszek M.; Wójcik, Marek J.; Nakajima, Takahito

2018-05-01

Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers.

Water–Soil–Vegetation Dynamic Interactions in Changing Climate

Directory of Open Access Journals (Sweden)

Xixi Wang

2017-09-01

Full Text Available Previous studies of land degradation, topsoil erosion, and hydrologic alteration typically focus on these subjects individually, missing important interrelationships among these important aspects of the Earth’s system. However, an understanding of water–soil–vegetation dynamic interactions is needed to develop practical and effective solutions to sustain the globe’s eco-environment and grassland agriculture, which depends on grasses, legumes, and other fodder or soil-building crops. This special issue is intended to be a platform for a discussion of the relevant scientific findings based on experimental and/or modeling studies. Its 12 peer-reviewed articles present data, novel analysis/modeling approaches, and convincing results of water–soil–vegetation interactions under historical and future climates. Two of the articles examine how lake/pond water quality is related to human activity and climate. Overall, these articles can serve as important references for future studies to further advance our understanding of how water, soil, and vegetation interactively affect the health and productivity of the Earth’s ecosystem.

On the dynamic London-van der Waals interaction

International Nuclear Information System (INIS)

Guzman, A.

2003-08-01

We present a theory of atomic reflection by evanescent waves in the quantized electromagnetic field vacuum that yields an analytical expression for the radiation pressure resulting from the combined effect of the evanescent field and spontaneous emission. The dynamic London-van der Waals potential between atoms and a dielectric wall is introduced as the effective interaction between the induced oscillating atomic dipole and its dipole image. Dissipative effects due to the imaginary part of the London-van der Waals potential are predicted. (author)

Dynamic magnetic behavior of the mixed spin (2, 5/2) Ising system with antiferromagnetic/antiferromagnetic interactions on a bilayer square lattice

International Nuclear Information System (INIS)

Ertaş Mehmet; Keskin Mustafa

2013-01-01

Using the mean-field theory and Glauber-type stochastic dynamics, we study the dynamic magnetic properties of the mixed spin (2, 5/2) Ising system for the antiferromagnetic/antiferromagnetic (AFM/AFM) interactions on the bilayer square lattice under a time varying (sinusoidal) magnetic field. The time dependence of average magnetizations and the thermal variation of the dynamic magnetizations are examined to calculate the dynamic phase diagrams. The dynamic phase diagrams are presented in the reduced temperature and magnetic field amplitude plane and the effects of interlayer coupling interaction on the critical behavior of the system are investigated. We also investigate the influence of the frequency and find that the system displays richer dynamic critical behavior for higher values of frequency than that of the lower values of it. We perform a comparison with the ferromagnetic/ferromagnetic (FM/FM) and AFM/FM interactions in order to see the effects of AFM/AFM interaction and observe that the system displays richer and more interesting dynamic critical behaviors for the AFM/AFM interaction than those for the FM/FM and AFM/FM interactions. (general)

Dynamic analysis of liquid storage tank including hydrodynamic interaction by boundary element method

International Nuclear Information System (INIS)

Hwang, I.T.; Ting, K.

1987-01-01

Dynamic response of liquid storage tanks considering the hydrodynamic interactions due to earthquake ground motion has been extensively studied. Several finite element procedures, such as Balendra et. al. (1982) and Haroun (1983), have been devoted to investigate the dynamic interaction between the deformable wall of the tank and the liquid. Further, if the geometry of the storage tank can not be described by axi-symmetric case, the tank wall and the fluid domain must be discretized by three dimensional finite elements to investigate the fluid-structure-interactions. Thus, the need of large computer memory and expense of vast computer time usually make this analysis impractical. To demonstrate the accuracy and reliability of the solution technique developed herein, the dynamic behavior of ground-supported, deformed, cylindrical tank with incompressible fluid conducted by Haroun (1983) are analyzed. Good correlations of hydrodynamic pressure distribution between the computed results with the referenced solutions are noted. The fluid compressibility significantly affects the hydrodynamic pressures of the liquid-tank-interactions and the work which is done on this discussion is still little attention. Thus, the influences of the compressibility of the liquid on the reponse of the liquid storage due to ground motion are then drawn. By the way, the complex-valued frequency response functions for hydrodynamic forces of Haroun's problem are also displayed. (orig./GL)

New Frontiers in Analyzing Dynamic Group Interactions: Bridging Social and Computer Science.

Science.gov (United States)

Lehmann-Willenbrock, Nale; Hung, Hayley; Keyton, Joann

2017-10-01

This special issue on advancing interdisciplinary collaboration between computer scientists and social scientists documents the joint results of the international Lorentz workshop, "Interdisciplinary Insights into Group and Team Dynamics," which took place in Leiden, The Netherlands, July 2016. An equal number of scholars from social and computer science participated in the workshop and contributed to the papers included in this special issue. In this introduction, we first identify interaction dynamics as the core of group and team models and review how scholars in social and computer science have typically approached behavioral interactions in groups and teams. Next, we identify key challenges for interdisciplinary collaboration between social and computer scientists, and we provide an overview of the different articles in this special issue aimed at addressing these challenges.

Effect of Dynamical Phase on the Resonant Interaction Among Tsunami Edge Wave Modes

Science.gov (United States)

Geist, Eric L.

2018-04-01

Different modes of tsunami edge waves can interact through nonlinear resonance. During this process, edge waves that have very small initial amplitude can grow to be as large or larger than the initially dominant edge wave modes. In this study, the effects of dynamical phase are established for a single triad of edge waves that participate in resonant interactions. In previous studies, Jacobi elliptic functions were used to describe the slow variation in amplitude associated with the interaction. This analytical approach assumes that one of the edge waves in the triad has zero initial amplitude and that the combined phase of the three waves φ = θ 1 + θ 2 - θ 3 is constant at the value for maximum energy exchange ( φ = 0). To obtain a more general solution, dynamical phase effects and non-zero initial amplitudes for all three waves are incorporated using numerical methods for the governing differential equations. Results were obtained using initial conditions calculated from a subduction zone, inter-plate thrust fault geometry and a stochastic earthquake slip model. The effect of dynamical phase is most apparent when the initial amplitudes and frequencies of the three waves are within an order of magnitude. In this case, non-zero initial phase results in a marked decrease in energy exchange and a slight decrease in the period of the interaction. When there are large differences in frequency and/or initial amplitude, dynamical phase has less of an effect and typically one wave of the triad has very little energy exchange with the other two waves. Results from this study help elucidate under what conditions edge waves might be implicated in late, large-amplitude arrivals.

Effect of Dynamical Phase on the Resonant Interaction Among Tsunami Edge Wave Modes

Science.gov (United States)

Geist, Eric L.

2018-02-01

Different modes of tsunami edge waves can interact through nonlinear resonance. During this process, edge waves that have very small initial amplitude can grow to be as large or larger than the initially dominant edge wave modes. In this study, the effects of dynamical phase are established for a single triad of edge waves that participate in resonant interactions. In previous studies, Jacobi elliptic functions were used to describe the slow variation in amplitude associated with the interaction. This analytical approach assumes that one of the edge waves in the triad has zero initial amplitude and that the combined phase of the three waves φ = θ 1 + θ 2 - θ 3 is constant at the value for maximum energy exchange (φ = 0). To obtain a more general solution, dynamical phase effects and non-zero initial amplitudes for all three waves are incorporated using numerical methods for the governing differential equations. Results were obtained using initial conditions calculated from a subduction zone, inter-plate thrust fault geometry and a stochastic earthquake slip model. The effect of dynamical phase is most apparent when the initial amplitudes and frequencies of the three waves are within an order of magnitude. In this case, non-zero initial phase results in a marked decrease in energy exchange and a slight decrease in the period of the interaction. When there are large differences in frequency and/or initial amplitude, dynamical phase has less of an effect and typically one wave of the triad has very little energy exchange with the other two waves. Results from this study help elucidate under what conditions edge waves might be implicated in late, large-amplitude arrivals.

Interacting opinion and disease dynamics in multiplex networks: Discontinuous phase transition and nonmonotonic consensus times

Science.gov (United States)

Velásquez-Rojas, Fátima; Vazquez, Federico

2017-05-01

Opinion formation and disease spreading are among the most studied dynamical processes on complex networks. In real societies, it is expected that these two processes depend on and affect each other. However, little is known about the effects of opinion dynamics over disease dynamics and vice versa, since most studies treat them separately. In this work we study the dynamics of the voter model for opinion formation intertwined with that of the contact process for disease spreading, in a population of agents that interact via two types of connections, social and contact. These two interacting dynamics take place on two layers of networks, coupled through a fraction q of links present in both networks. The probability that an agent updates its state depends on both the opinion and disease states of the interacting partner. We find that the opinion dynamics has striking consequences on the statistical properties of disease spreading. The most important is that the smooth (continuous) transition from a healthy to an endemic phase observed in the contact process, as the infection probability increases beyond a threshold, becomes abrupt (discontinuous) in the two-layer system. Therefore, disregarding the effects of social dynamics on epidemics propagation may lead to a misestimation of the real magnitude of the spreading. Also, an endemic-healthy discontinuous transition is found when the coupling q overcomes a threshold value. Furthermore, we show that the disease dynamics delays the opinion consensus, leading to a consensus time that varies nonmonotonically with q in a large range of the model's parameters. A mean-field approach reveals that the coupled dynamics of opinions and disease can be approximately described by the dynamics of the voter model decoupled from that of the contact process, with effective probabilities of opinion and disease transmission.

The Dynamic Reactance Interaction - How Vested Interests Affect People's Experience, Behavior, and Cognition in Social Interactions.

Science.gov (United States)

Steindl, Christina; Jonas, Eva

2015-01-01

In social interactions, individuals may sometimes pursue their own interests at the expense of their interaction partner. Such self-interested behaviors impose a threat to the interaction partner's freedom to act. The current article investigates this threat in the context of interdependence and reactance theory. We explore how vested interests influence reactance process stages of an advisor-client interaction. We aim to explore the interactional process that evolves. In two studies, participants took the perspective of a doctor (advisor) or a patient (client). In both studies we incorporated a vested interest. In Study 1 (N = 82) we found that in response to a vested interest of their interaction partner, patients indicated a stronger experience of reactance, more aggressive behavioral intentions, and more biased cognitions than doctors. A serial multiple mediation revealed that a vested interest engendered mistrust toward the interaction partner and this mistrust led to an emerging reactance process. Study 2 (N = 207) further demonstrated that doctors expressed their reactance in a subtle way: they revealed a classic confirmation bias when searching for additional information on their preliminary decision preference, indicating stronger defense motivation. We discuss how these findings can help us to understand how social interactions develop dynamically.

Dynamic Analysis of Partially Embedded Structures Considering Soil-Structure Interaction in Time Domain

Directory of Open Access Journals (Sweden)

Sanaz Mahmoudpour

2011-01-01

Full Text Available Analysis and design of structures subjected to arbitrary dynamic loadings especially earthquakes have been studied during past decades. In practice, the effects of soil-structure interaction on the dynamic response of structures are usually neglected. In this study, the effect of soil-structure interaction on the dynamic response of structures has been examined. The substructure method using dynamic stiffness of soil is used to analyze soil-structure system. A coupled model based on finite element method and scaled boundary finite element method is applied. Finite element method is used to analyze the structure, and scaled boundary finite element method is applied in the analysis of unbounded soil region. Due to analytical solution in the radial direction, the radiation condition is satisfied exactly. The material behavior of soil and structure is assumed to be linear. The soil region is considered as a homogeneous half-space. The analysis is performed in time domain. A computer program is prepared to analyze the soil-structure system. Comparing the results with those in literature shows the exactness and competency of the proposed method.

Electron beam interaction with space plasmas.

Science.gov (United States)

Krafft, C.; Bolokitin, A. S.

1999-12-01

Active space experiments involving the controlled injection of electron beams and the formation of artificially generated currents can provide in many cases a calibration of natural phenomena connected with the dynamic interaction of charged particles with fields. They have a long history beginning from the launches of small rockets with electron guns in order to map magnetic fields lines in the Earth's magnetosphere or to excite artificial auroras. Moreover, natural beams of charged particles exist in many space and astrophysical plasmas and were identified in situ by several satellites; a few examples are beams connected with solar bursts, planetary foreshocks or suprathermal fluxes traveling in planetary magnetospheres. Many experimental and theoretical works have been performed in order to interpret or plan space experiments involving beam injection as well as to understand the physics of wave-particle interaction, as wave radiation, beam dynamics and background plasma modification.

Seasonal phenology of interactions involving short-lived annual plants, a multivoltine herbivore and its endoparasitoid wasp

NARCIS (Netherlands)

Fei, Minghui; Gols, R.; Harvey, J.A.

2014-01-01

Spatial-temporal realism is often missing in many studies of multitrophic interactions, which are conducted at a single time frame and/or involving interactions between insects with a single species of plant. In this scenario, an underlying assumption is that the host-plant species is ubiquitous

Brownian dynamics simulations of a flexible polymer chain which includes continuous resistance and multibody hydrodynamic interactions

Science.gov (United States)

Butler, Jason E.; Shaqfeh, Eric S. G.

2005-01-01

Using methods adapted from the simulation of suspension dynamics, we have developed a Brownian dynamics algorithm with multibody hydrodynamic interactions for simulating the dynamics of polymer molecules. The polymer molecule is modeled as a chain composed of a series of inextensible, rigid rods with constraints at each joint to ensure continuity of the chain. The linear and rotational velocities of each segment of the polymer chain are described by the slender-body theory of Batchelor [J. Fluid Mech. 44, 419 (1970)]. To include hydrodynamic interactions between the segments of the chain, the line distribution of forces on each segment is approximated by making a Legendre polynomial expansion of the disturbance velocity on the segment, where the first two terms of the expansion are retained in the calculation. Thus, the resulting linear force distribution is specified by a center of mass force, couple, and stresslet on each segment. This method for calculating the hydrodynamic interactions has been successfully used to simulate the dynamics of noncolloidal suspensions of rigid fibers [O. G. Harlen, R. R. Sundararajakumar, and D. L. Koch, J. Fluid Mech. 388, 355 (1999); J. E. Butler and E. S. G. Shaqfeh, J. Fluid Mech. 468, 204 (2002)]. The longest relaxation time and center of mass diffusivity are among the quantities calculated with the simulation technique. Comparisons are made for different levels of approximation of the hydrodynamic interactions, including multibody interactions, two-body interactions, and the "freely draining" case with no interactions. For the short polymer chains studied in this paper, the results indicate a difference in the apparent scaling of diffusivity with polymer length for the multibody versus two-body level of approximation for the hydrodynamic interactions.

Phonon-magnon interaction in low dimensional quantum magnets observed by dynamic heat transport measurements.

Science.gov (United States)

Montagnese, Matteo; Otter, Marian; Zotos, Xenophon; Fishman, Dmitry A; Hlubek, Nikolai; Mityashkin, Oleg; Hess, Christian; Saint-Martin, Romuald; Singh, Surjeet; Revcolevschi, Alexandre; van Loosdrecht, Paul H M

2013-04-05

Thirty-five years ago, Sanders and Walton [Phys. Rev. B 15, 1489 (1977)] proposed a method to measure the phonon-magnon interaction in antiferromagnets through thermal transport which so far has not been verified experimentally. We show that a dynamical variant of this approach allows direct extraction of the phonon-magnon equilibration time, yielding 400 μs for the cuprate spin-ladder system Ca(9)La(5)Cu(24)O(41). The present work provides a general method to directly address the spin-phonon interaction by means of dynamical transport experiments.

Phase transitions, nonequilibrium dynamics, and critical behavior of strongly interacting systems

International Nuclear Information System (INIS)

Mottola, E.; Bhattacharya, T.; Cooper, F.

1998-01-01

This is the final report of a three-year, Laboratory Directed Research and Development project at Los Alamos National Laboratory. In this effort, large-scale simulations of strongly interacting systems were performed and a variety of approaches to the nonequilibrium dynamics of phase transitions and critical behavior were investigated. Focus areas included (1) the finite-temperature quantum chromodynamics phase transition and nonequilibrium dynamics of a new phase of matter (the quark-gluon plasma) above the critical temperature, (2) nonequilibrium dynamics of a quantum fields using mean field theory, and (3) stochastic classical field theoretic models with applications to spinodal decomposition and structural phase transitions in a variety of systems, such as spin chains and shape memory alloys

Phase transitions, nonequilibrium dynamics, and critical behavior of strongly interacting systems

Energy Technology Data Exchange (ETDEWEB)

Mottola, E.; Bhattacharya, T.; Cooper, F. [and others

1998-12-31

This is the final report of a three-year, Laboratory Directed Research and Development project at Los Alamos National Laboratory. In this effort, large-scale simulations of strongly interacting systems were performed and a variety of approaches to the nonequilibrium dynamics of phase transitions and critical behavior were investigated. Focus areas included (1) the finite-temperature quantum chromodynamics phase transition and nonequilibrium dynamics of a new phase of matter (the quark-gluon plasma) above the critical temperature, (2) nonequilibrium dynamics of a quantum fields using mean field theory, and (3) stochastic classical field theoretic models with applications to spinodal decomposition and structural phase transitions in a variety of systems, such as spin chains and shape memory alloys.

Non-linear soil-structure interaction

International Nuclear Information System (INIS)

Wolf, J.P.

1984-01-01

The basic equation of motion to analyse the interaction of a non-linear structure and an irregular soil with the linear unbounded soil is formulated in the time domain. The contribution of the unbounded soil involves convolution integrals of the dynamic-stiffness coefficients in the time domain and the corresponding motions. As another possibility, a flexibility formulation fot the contribution of the unbounded soil using the dynamic-flexibility coefficients in the time domain, together with the direct-stiffness method for the structure and the irregular soil can be applied. As an example of a non-linear soil-structure-interaction analysis, the partial uplift of the basemat of a structure is examined. (Author) [pt

Laplace-SGBEM analysis of the dynamic stress intensity factors and the dynamic T-stress for the interaction between a crack and auxetic inclusions

Science.gov (United States)

Kwon, Kibum

A dynamic analysis of the interaction between a crack and an auxetic (negative Poisson ratio)/non-auxetic inclusion is presented. The two most important fracture parameters, namely the stress intensity factors and the T-stress are analyzed by using the symmetric Galerkin boundary element method in the Laplace domain for three different models of crack-inclusion interaction. To investigate the effects of auxetic inclusions on the fracture behavior of composites reinforced by this new type of material, comparisons of the dynamic stress intensity factors and the dynamic T-stress are made between the use of auxetic inclusions as opposed to the use of traditional inclusions. Furthermore, the technique presented in this research can be employed to analyze for the interaction between a crack and a cluster of auxetic/non-auxetic inclusions. Results from the latter models can be employed in crack growth analysis in auxetic-fiber-reinforced composites.

Computational strong-field quantum dynamics. Intense light-matter interactions

International Nuclear Information System (INIS)

Bauer, Dieter

2017-01-01

This graduate textbook introduces the computational techniques to study ultra-fast quantum dynamics of matter exposed to strong laser fields. Coverage includes methods to propagate wavefunctions according to the time dependent Schroedinger, Klein-Gordon or Dirac equation, the calculation of typical observables, time-dependent density functional theory, multi configurational time-dependent Hartree-Fock, time-dependent configuration interaction singles, the strong-field approximation, and the microscopic particle-in-cell approach.

Computational strong-field quantum dynamics. Intense light-matter interactions

Energy Technology Data Exchange (ETDEWEB)

Bauer, Dieter (ed.) [Rostock Univ. (Germany). Inst. fuer Physik

2017-09-01

This graduate textbook introduces the computational techniques to study ultra-fast quantum dynamics of matter exposed to strong laser fields. Coverage includes methods to propagate wavefunctions according to the time dependent Schroedinger, Klein-Gordon or Dirac equation, the calculation of typical observables, time-dependent density functional theory, multi configurational time-dependent Hartree-Fock, time-dependent configuration interaction singles, the strong-field approximation, and the microscopic particle-in-cell approach.

Computational strong-field quantum dynamics intense light-matter interactions

CERN Document Server

2017-01-01

This graduate textbook introduces the computational techniques to study ultra-fast quantum dynamics of matter exposed to strong laser fields. Coverage includes methods to propagate wavefunctions according to the time-dependent Schrödinger, Klein-Gordon or Dirac equation, the calculation of typical observables, time-dependent density functional theory, multi-configurational time-dependent Hartree-Fock, time-dependent configuration interaction singles, the strong-field approximation, and the microscopic particle-in-cell approach.

Involvement of apoptosis in host-parasite interactions in the zebra mussel.

Directory of Open Access Journals (Sweden)

Laëtitia Minguez

Full Text Available The question of whether cell death by apoptosis plays a biological function during infection is key to understanding host-parasite interactions. We investigated the involvement of apoptosis in several host-parasite systems, using zebra mussels Dreissena polymorpha as test organisms and their micro- and macroparasites. As a stress response associated with parasitism, heat shock proteins (Hsp can be induced. In this protein family, Hsp70 are known to be apoptosis inhibitors. Mussels were diagnosed for their respective infections by standard histological methods; apoptosis was detected using the TUNEL methods on paraffin sections and Hsp70 by immunohistochemistry on cryosections. Circulating hemocytes were the main cells observed in apoptosis whereas infected tissues displayed no or few apoptotic cells. Parasitism by intracellular bacteria Rickettsiales-like and the trematode Bucephalus polymorphus were associated with the inhibition of apoptosis whereas ciliates Ophryoglena spp. or the trematode Phyllodistomum folium did not involve significant differences in apoptosis. Even if some parasites were able to modulate apoptosis in zebra mussels, we did not see evidence of any involvement of Hsp70 on this mechanism.

Involvement of Apoptosis in Host-Parasite Interactions in the Zebra Mussel

Science.gov (United States)

Minguez, Laëtitia; Brulé, Nelly; Sohm, Bénédicte; Devin, Simon; Giambérini, Laure

2013-01-01

The question of whether cell death by apoptosis plays a biological function during infection is key to understanding host-parasite interactions. We investigated the involvement of apoptosis in several host-parasite systems, using zebra mussels Dreissena polymorpha as test organisms and their micro- and macroparasites. As a stress response associated with parasitism, heat shock proteins (Hsp) can be induced. In this protein family, Hsp70 are known to be apoptosis inhibitors. Mussels were diagnosed for their respective infections by standard histological methods; apoptosis was detected using the TUNEL methods on paraffin sections and Hsp70 by immunohistochemistry on cryosections. Circulating hemocytes were the main cells observed in apoptosis whereas infected tissues displayed no or few apoptotic cells. Parasitism by intracellular bacteria Rickettsiales-like and the trematode Bucephalus polymorphus were associated with the inhibition of apoptosis whereas ciliates Ophryoglena spp. or the trematode Phyllodistomum folium did not involve significant differences in apoptosis. Even if some parasites were able to modulate apoptosis in zebra mussels, we did not see evidence of any involvement of Hsp70 on this mechanism. PMID:23785455

Neotropical fish-fruit interactions: eco-evolutionary dynamics and conservation.

Science.gov (United States)

Correa, Sandra Bibiana; Costa-Pereira, Raul; Fleming, Theodore; Goulding, Michael; Anderson, Jill T

2015-11-01

Frugivorous fish play a prominent role in seed dispersal and reproductive dynamics of plant communities in riparian and floodplain habitats of tropical regions worldwide. In Neotropical wetlands, many plant species have fleshy fruits and synchronize their fruiting with the flood season, when fruit-eating fish forage in forest and savannahs for periods of up to 7 months. We conducted a comprehensive analysis to examine the evolutionary origin of fish-fruit interactions, describe fruit traits associated with seed dispersal and seed predation, and assess the influence of fish size on the effectiveness of seed dispersal by fish (ichthyochory). To date, 62 studies have documented 566 species of fruits and seeds from 82 plant families in the diets of 69 Neotropical fish species. Fish interactions with flowering plants are likely to be as old as 70 million years in the Neotropics, pre-dating most modern bird-fruit and mammal-fruit interactions, and contributing to long-distance seed dispersal and possibly the radiation of early angiosperms. Ichthyochory occurs across the angiosperm phylogeny, and is more frequent among advanced eudicots. Numerous fish species are capable of dispersing small seeds, but only a limited number of species can disperse large seeds. The size of dispersed seeds and the probability of seed dispersal both increase with fish size. Large-bodied species are the most effective seed dispersal agents and remain the primary target of fishing activities in the Neotropics. Thus, conservation efforts should focus on these species to ensure continuity of plant recruitment dynamics and maintenance of plant diversity in riparian and floodplain ecosystems. © 2015 Cambridge Philosophical Society.

Modeling the Effect of Fluid-Structure Interaction on the Impact Dynamics of Pressurized Tank Cars

Science.gov (United States)

2009-11-13

This paper presents a computational framework that : analyzes the effect of fluid-structure interaction (FSI) on the : impact dynamics of pressurized commodity tank cars using the : nonlinear dynamic finite element code ABAQUS/Explicit. : There exist...

Dynamic hubs show competitive and static hubs non-competitive regulation of their interaction partners.

Directory of Open Access Journals (Sweden)

Apurv Goel

Full Text Available Date hub proteins have 1 or 2 interaction interfaces but many interaction partners. This raises the question of whether all partner proteins compete for the interaction interface of the hub or if the cell carefully regulates aspects of this process? Here, we have used real-time rendering of protein interaction networks to analyse the interactions of all the 1 or 2 interface hubs of Saccharomyces cerevisiae during the cell cycle. By integrating previously determined structural and gene expression data, and visually hiding the nodes (proteins and their edges (interactions during their troughs of expression, we predict when interactions of hubs and their partners are likely to exist. This revealed that 20 out of all 36 one- or two- interface hubs in the yeast interactome fell within two main groups. The first was dynamic hubs with static partners, which can be considered as 'competitive hubs'. Their interaction partners will compete for the interaction interface of the hub and the success of any interaction will be dictated by the kinetics of interaction (abundance and affinity and subcellular localisation. The second was static hubs with dynamic partners, which we term 'non-competitive hubs'. Regulatory mechanisms are finely tuned to lessen the presence and/or effects of competition between the interaction partners of the hub. It is possible that these regulatory processes may also be used by the cell for the regulation of other, non-cell cycle processes.

Predictive Mechanisms Are Not Involved the Same Way during Human-Human vs. Human-Machine Interactions: A Review

Directory of Open Access Journals (Sweden)

Aïsha Sahaï

2017-10-01

Full Text Available Nowadays, interactions with others do not only involve human peers but also automated systems. Many studies suggest that the motor predictive systems that are engaged during action execution are also involved during joint actions with peers and during other human generated action observation. Indeed, the comparator model hypothesis suggests that the comparison between a predicted state and an estimated real state enables motor control, and by a similar functioning, understanding and anticipating observed actions. Such a mechanism allows making predictions about an ongoing action, and is essential to action regulation, especially during joint actions with peers. Interestingly, the same comparison process has been shown to be involved in the construction of an individual's sense of agency, both for self-generated and observed other human generated actions. However, the implication of such predictive mechanisms during interactions with machines is not consensual, probably due to the high heterogeneousness of the automata used in the experimentations, from very simplistic devices to full humanoid robots. The discrepancies that are observed during human/machine interactions could arise from the absence of action/observation matching abilities when interacting with traditional low-level automata. Consistently, the difficulties to build a joint agency with this kind of machines could stem from the same problem. In this context, we aim to review the studies investigating predictive mechanisms during social interactions with humans and with automated artificial systems. We will start by presenting human data that show the involvement of predictions in action control and in the sense of agency during social interactions. Thereafter, we will confront this literature with data from the robotic field. Finally, we will address the upcoming issues in the field of robotics related to automated systems aimed at acting as collaborative agents.

Flocking dynamics with voter-like interactions

Science.gov (United States)

Baglietto, Gabriel; Vazquez, Federico

2018-03-01

We study the collective motion of a large set of self-propelled particles subject to voter-like interactions. Each particle moves on a 2D space at a constant speed in a direction that is randomly assigned initially. Then, at every step of the dynamics, each particle adopts the direction of motion of a randomly chosen neighboring particle. We investigate the time evolution of the global alignment of particles measured by the order parameter φ, until complete order \\varphi=1.0 is reached (polar consensus). We find that φ increases as t 1/2 for short times and approaches 1.0 exponentially fast for longer times. Also, the mean time to consensus τ varies non-monotonically with the density of particles ρ, reaching a minimum at some intermediate density ρmin . At ρmin , the mean consensus time scales with the system size N as τmin ∼ N0.765 , and thus the consensus is faster than in the case of all-to-all interactions (large ρ) where τ=2N . We show that the fast consensus, also observed at intermediate and high densities, is a consequence of the segregation of the system into clusters of equally-oriented particles which breaks the balance of transitions between directional states in well mixed systems.

Fort Collins Science Center Ecosystem Dynamics Branch

Science.gov (United States)

Wilson, Jim; Melcher, C.; Bowen, Z.

2009-01-01

Complex natural resource issues require understanding a web of interactions among ecosystem components that are (1) interdisciplinary, encompassing physical, chemical, and biological processes; (2) spatially complex, involving movements of animals, water, and airborne materials across a range of landscapes and jurisdictions; and (3) temporally complex, occurring over days, weeks, or years, sometimes involving response lags to alteration or exhibiting large natural variation. Scientists in the Ecosystem Dynamics Branch of the U.S. Geological Survey, Fort Collins Science Center, investigate a diversity of these complex natural resource questions at the landscape and systems levels. This Fact Sheet describes the work of the Ecosystems Dynamics Branch, which is focused on energy and land use, climate change and long-term integrated assessments, herbivore-ecosystem interactions, fire and post-fire restoration, and environmental flows and river restoration.

Comparison of molecular dynamics and kinetic modeling of gas-surface interactions

NARCIS (Netherlands)

Frezzotti, A.; Gaastra - Nedea, S.V.; Markvoort, A.J.; Spijker, P.; Gibelli, L.

2008-01-01

The interaction of a dilute monatomic gas with a solid surface is studied byMolecular Dynamics (MD) simulations and by numerical solutions of a recently proposed kinetic model. Following previous investigations, the heat transport between parallel walls and Couette flow have been adopted as test

Dynamic covalent gels assembled from small molecules:from discrete gelators to dynamic covalent polymers

Institute of Scientific and Technical Information of China (English)

Jian-Yong Zhang; Li-Hua Zeng; Juan Feng

2017-01-01

Dynamic covalent chemistry has emerged recently to be a powerful tool to construct functional materials.This article reviews the progress in the research and development of dynamic covalent chemistry in gels assembled from small molecules.First dynamic covalent reactions used in gels are reviewed to understand the dynamic covalent bonding.Afterwards the catalogues of dynamic covalent gels are reviewed according to the nature of gelators and the interactions between gelators.Dynamic covalent bonding can be involved to form low molecular weight gelators.Low molecular weight molecules with multiple functional groups react to form dynamic covalent cross-linked polymers and act as gelators.Two catalogues of gels show different properties arising from their different structures.This review aims to illustrate the structure-property relationships of these dynamic covalent gels.

Exploration of the dynamic properties of protein complexes predicted from spatially constrained protein-protein interaction networks.

Directory of Open Access Journals (Sweden)

Eric A Yen

2014-05-01

Full Text Available Protein complexes are not static, but rather highly dynamic with subunits that undergo 1-dimensional diffusion with respect to each other. Interactions within protein complexes are modulated through regulatory inputs that alter interactions and introduce new components and deplete existing components through exchange. While it is clear that the structure and function of any given protein complex is coupled to its dynamical properties, it remains a challenge to predict the possible conformations that complexes can adopt. Protein-fragment Complementation Assays detect physical interactions between protein pairs constrained to ≤8 nm from each other in living cells. This method has been used to build networks composed of 1000s of pair-wise interactions. Significantly, these networks contain a wealth of dynamic information, as the assay is fully reversible and the proteins are expressed in their natural context. In this study, we describe a method that extracts this valuable information in the form of predicted conformations, allowing the user to explore the conformational landscape, to search for structures that correlate with an activity state, and estimate the abundance of conformations in the living cell. The generator is based on a Markov Chain Monte Carlo simulation that uses the interaction dataset as input and is constrained by the physical resolution of the assay. We applied this method to an 18-member protein complex composed of the seven core proteins of the budding yeast Arp2/3 complex and 11 associated regulators and effector proteins. We generated 20,480 output structures and identified conformational states using principle component analysis. We interrogated the conformation landscape and found evidence of symmetry breaking, a mixture of likely active and inactive conformational states and dynamic exchange of the core protein Arc15 between core and regulatory components. Our method provides a novel tool for prediction and

Unveiling protein functions through the dynamics of the interaction network.

Directory of Open Access Journals (Sweden)

Irene Sendiña-Nadal

Full Text Available Protein interaction networks have become a tool to study biological processes, either for predicting molecular functions or for designing proper new drugs to regulate the main biological interactions. Furthermore, such networks are known to be organized in sub-networks of proteins contributing to the same cellular function. However, the protein function prediction is not accurate and each protein has traditionally been assigned to only one function by the network formalism. By considering the network of the physical interactions between proteins of the yeast together with a manual and single functional classification scheme, we introduce a method able to reveal important information on protein function, at both micro- and macro-scale. In particular, the inspection of the properties of oscillatory dynamics on top of the protein interaction network leads to the identification of misclassification problems in protein function assignments, as well as to unveil correct identification of protein functions. We also demonstrate that our approach can give a network representation of the meta-organization of biological processes by unraveling the interactions between different functional classes.

Resonant Interaction, Approximate Symmetry, and Electromagnetic Interaction (EMI) in Low Energy Nuclear Reactions (LENR)

Science.gov (United States)

Chubb, Scott

2007-03-01

Only recently (talk by P.A. Mosier-Boss et al, in this session) has it become possible to trigger high energy particle emission and Excess Heat, on demand, in LENR involving PdD. Also, most nuclear physicists are bothered by the fact that the dominant reaction appears to be related to the least common deuteron(d) fusion reaction,d+d ->α+γ. A clear consensus about the underlying effect has also been illusive. One reason for this involves confusion about the approximate (SU2) symmetry: The fact that all d-d fusion reactions conserve isospin has been widely assumed to mean the dynamics is driven by the strong force interaction (SFI), NOT EMI. Thus, most nuclear physicists assume: 1. EMI is static; 2. Dominant reactions have smallest changes in incident kinetic energy (T); and (because of 2), d+d ->α+γ is suppressed. But this assumes a stronger form of SU2 symmetry than is present; d+d ->α+γ reactions are suppressed not because of large changes in T but because the interaction potential involves EMI, is dynamic (not static), the SFI is static, and because the two incident deuterons must have approximate Bose Exchange symmetry and vanishing spin. A generalization of this idea involves a resonant form of reaction, similar to the de-excitation of an atom. These and related (broken gauge) symmetry EMI effects on LENR are discussed.

Retarded Local Dynamics of Single Fluorescent Probes in Polymeric Glass due to Interaction Strengthening

Science.gov (United States)

Zhang, Hao; Yang, Jingfa; Zhao, Jiang

The effect of strengthening of interaction between single fluorescent probes and polymer matrix to the probes dynamics is investigated using single molecule fluorescence defocus microscopy. By introducing multiple hydroxyl groups to the fluorescent probes, which builds up hydrogen bonds between the probe and polymer matrix, the dynamics is discovered to be retarded. This is evidenced by the lowering of the frequency of the vibrational modes in the power spectra of the rotation trajectories of individual fluorescent probes, and also by the lowering of population of rotating probes. The results show that by strengthening the probe-matrix interaction, the local dynamics detected by the probes is equivalent to that detected by a bigger probe, due to the enhanced friction between the probe and the polymer matrix. the National Basic Research Program of China (2012CB821500).

On the Convergence of Piecewise Linear Strategic Interaction Dynamics on Networks

KAUST Repository

Gharesifard, Bahman

2015-09-11

We prove that the piecewise linear best-response dynamical systems of strategic interactions are asymptotically convergent to their set of equilibria on any weighted undirected graph. We study various features of these dynamical systems, including the uniqueness and abundance properties of the set of equilibria and the emergence of unstable equilibria. We also introduce the novel notions of social equivalence and social dominance on directed graphs, and demonstrate some of their interesting implications, including their correspondence to consensus and chromatic number of partite graphs. Examples illustrate our results.

Effect of dynamical phase on the resonant interaction among tsunami edge wave modes

Science.gov (United States)

Geist, Eric L.

2018-01-01

Different modes of tsunami edge waves can interact through nonlinear resonance. During this process, edge waves that have very small initial amplitude can grow to be as large or larger than the initially dominant edge wave modes. In this study, the effects of dynamical phase are established for a single triad of edge waves that participate in resonant interactions. In previous studies, Jacobi elliptic functions were used to describe the slow variation in amplitude associated with the interaction. This analytical approach assumes that one of the edge waves in the triad has zero initial amplitude and that the combined phase of the three waves φ = θ1 + θ2 − θ3 is constant at the value for maximum energy exchange (φ = 0). To obtain a more general solution, dynamical phase effects and non-zero initial amplitudes for all three waves are incorporated using numerical methods for the governing differential equations. Results were obtained using initial conditions calculated from a subduction zone, inter-plate thrust fault geometry and a stochastic earthquake slip model. The effect of dynamical phase is most apparent when the initial amplitudes and frequencies of the three waves are within an order of magnitude. In this case, non-zero initial phase results in a marked decrease in energy exchange and a slight decrease in the period of the interaction. When there are large differences in frequency and/or initial amplitude, dynamical phase has less of an effect and typically one wave of the triad has very little energy exchange with the other two waves. Results from this study help elucidate under what conditions edge waves might be implicated in late, large-amplitude arrivals.

System Dynamics Modeling of interactive cost factors for small modular reactors

International Nuclear Information System (INIS)

Ahn, Nam Sung; Lee, Keun Dae; Yoon, Suk Ho

2011-01-01

As a part of the Study on Economic Efficiency and Marketability of small modular reactors project, we at Nemo partners NEC consulting corporation were studying the various cost factors on small modular reactors (SMRs). To have a better knowledge of the interaction between the cost factors, System Dynamics Modeling has been developed. This model will contribute to our understanding of the interaction on the major factors effecting on the unit cost of SMRs to the SMRs' market share in the market economics as competition

Dynamic interaction between markets for leasing and selling automobiles

OpenAIRE

Andrikopoulos, Athanasios; Markellos, Raphael N.

2015-01-01

We develop a model of dynamic interactions between price variations in leasing and selling markets for automobiles. Our framework assumes a differential game between multiple Bertrand-type competing firms which offer differentiated products to forward-looking agents. Empirical analysis of our model using monthly US data from 2002 to 2011 shows that variations in selling (cash) market prices lead rapidly dissipating changes of leasing market prices in the opposite direction. We discuss the pra...

Interactions Controlling the Slow Dynamic Conformational Motions of Ubiquitin

Directory of Open Access Journals (Sweden)

Soichiro Kitazawa

2017-08-01

Full Text Available Rational mutation of proteins based on their structural and dynamic characteristics is a useful strategy for amplifying specific fluctuations in proteins. Here, we show the effects of mutation on the conformational fluctuations and thermodynamic stability of ubiquitin. In particular, we focus on the salt bridge between K11 and E34 and the hydrogen bond between I36 and Q41, which are predicted to control the fluctuation between the basic folded state, N1, and the alternatively folded state, N2, of the protein, using high-pressure NMR spectroscopy. The E34A mutation, which disrupts the salt bridge, did not alter picosecond–to–nanosecond, microsecond–to–millisecond dynamic motions, and stability of the protein, while the Q41N mutation, which destabilizes the hydrogen bond, specifically amplified the N1–N2 conformational fluctuation and decreased stability. Based on the observed thermodynamic stabilities of the various conformational states, we showed that in the Q41N mutant, the N1 state is more significantly destabilized than the N2 state, resulting in an increase in the relative population of N2. Identifying the interactions controlling specific motions of a protein will facilitate molecular design to achieve functional dynamics beyond native state dynamics.

Investigation of the heparin-thrombin interaction by dynamic force spectroscopy.

Science.gov (United States)

Wang, Congzhou; Jin, Yingzi; Desai, Umesh R; Yadavalli, Vamsi K

2015-06-01

The interaction between heparin and thrombin is a vital step in the blood (anti)coagulation process. Unraveling the molecular basis of the interactions is therefore extremely important in understanding the mechanisms of this complex biological process. In this study, we use a combination of an efficient thiolation chemistry of heparin, a self-assembled monolayer-based single molecule platform, and a dynamic force spectroscopy to provide new insights into the heparin-thrombin interaction from an energy viewpoint at the molecular scale. Well-separated single molecules of heparin covalently attached to mixed self-assembled monolayers are demonstrated, whereby interaction forces with thrombin can be measured via atomic force microscopy-based spectroscopy. Further these interactions are studied at different loading rates and salt concentrations to directly obtain kinetic parameters. An increase in the loading rate shows a higher interaction force between the heparin and thrombin, which can be directly linked to the kinetic dissociation rate constant (koff). The stability of the heparin/thrombin complex decreased with increasing NaCl concentration such that the off-rate was found to be driven primarily by non-ionic forces. These results contribute to understanding the role of specific and nonspecific forces that drive heparin-thrombin interactions under applied force or flow conditions. Copyright © 2015 Elsevier B.V. All rights reserved.

Spinal circuits can accommodate interaction torques during multijoint limb movements.

Science.gov (United States)

Buhrmann, Thomas; Di Paolo, Ezequiel A

2014-01-01

The dynamic interaction of limb segments during movements that involve multiple joints creates torques in one joint due to motion about another. Evidence shows that such interaction torques are taken into account during the planning or control of movement in humans. Two alternative hypotheses could explain the compensation of these dynamic torques. One involves the use of internal models to centrally compute predicted interaction torques and their explicit compensation through anticipatory adjustment of descending motor commands. The alternative, based on the equilibrium-point hypothesis, claims that descending signals can be simple and related to the desired movement kinematics only, while spinal feedback mechanisms are responsible for the appropriate creation and coordination of dynamic muscle forces. Partial supporting evidence exists in each case. However, until now no model has explicitly shown, in the case of the second hypothesis, whether peripheral feedback is really sufficient on its own for coordinating the motion of several joints while at the same time accommodating intersegmental interaction torques. Here we propose a minimal computational model to examine this question. Using a biomechanics simulation of a two-joint arm controlled by spinal neural circuitry, we show for the first time that it is indeed possible for the neuromusculoskeletal system to transform simple descending control signals into muscle activation patterns that accommodate interaction forces depending on their direction and magnitude. This is achieved without the aid of any central predictive signal. Even though the model makes various simplifications and abstractions compared to the complexities involved in the control of human arm movements, the finding lends plausibility to the hypothesis that some multijoint movements can in principle be controlled even in the absence of internal models of intersegmental dynamics or learned compensatory motor signals.

Spinal circuits can accommodate interaction torques during multijoint limb movements

Directory of Open Access Journals (Sweden)

Thomas eBuhrmann

2014-11-01

Full Text Available The dynamic interaction of limb segments during movements that involve multiple joints creates torques in one joint due to motion about another. Evidence shows that such interaction torques are taken into account during the planning or control of movement in humans. Two alternative hypotheses could explain the compensation of these dynamic torques. One involves the use of internal models to centrally compute predicted interaction torques and their explicit compensation through anticipatory adjustment of descending motor commands. The alternative, based on the equilibrium-point hypothesis, claims that descending signals can be simple and related to the desired movement kinematics only, while spinal feedback mechanisms are responsible for the appropriate creation and coordination of dynamic muscle forces. Partial supporting evidence exists in each case. However, until now no model has explicitly shown, in the case of the second hypothesis, whether peripheral feedback is really sufficient on its own for coordinating the motion of several joints while at the same time accommodating intersegmental interaction torques. Here we propose a minimal computational model to examine this question. Using a biomechanics simulation of a two-joint arm controlled by spinal neural circuitry, we show for the first time that it is indeed possible for the neuromusculoskeletal system to transform simple descending control signals into muscle activation patterns that accommodate interaction forces depending on their direction and magnitude. This is achieved without the aid of any central predictive signal. Even though the model makes various simplifications and abstractions compared to the complexities involved in the control of human arm movements, the finding lends plausibility to the hypothesis that some multijoint movements can in principle be controlled even in the absence of internal models of intersegmental dynamics or learned compensatory motor signals.

A Multiagent Cooperation Model Based on Trust Rating in Dynamic Infinite Interaction Environment

Directory of Open Access Journals (Sweden)

Sixia Fan

2018-01-01

Full Text Available To improve the liveness of agents and enhance trust and collaboration in multiagent system, a new cooperation model based on trust rating in dynamic infinite interaction environment (TR-DII is proposed. TR-DII model is used to control agent’s autonomy and selfishness and to make agent do the rational decision. TR-DII model is based on two important components. One is dynamic repeated interaction structure, and the other is trust rating. The dynamic repeated interaction structure is formed with multistage inviting and evaluating actions. It transforms agents’ interactions into an infinity task allocation environment, where controlled and renewable cycle is a component most agent models ignored. Additionally, it influences the expectations and behaviors of agents which may not appear in one-shot time but may appear in long-time cooperation. Moreover, with rewards and punishments mechanism (RPM, the trust rating (TR is proposed to control agent blindness in selection phase. However, RPM is the factor that directly influences decisions, not the reputation as other models have suggested. Meanwhile, TR could monitor agent’s statuses in which they could be trustworthy or untrustworthy. Also, it refines agent’s disrepute in a new way which is ignored by the others. Finally, grids puzzle experiment has been used to test TR-DII model and other five models are used as comparisons. The results show that TR-DII model can effectively adjust the trust level between agents and makes the solvers be more trustworthy and do choices that are more rational. Moreover, through interaction result feedback, TR-DII model could adjust the income function, to control cooperation reputation, and could achieve a closed-loop control.

Interaction Dynamics Determine Signaling and Output Pathway Responses

Directory of Open Access Journals (Sweden)

Klement Stojanovski

2017-04-01

Full Text Available The understanding of interaction dynamics in signaling pathways can shed light on pathway architecture and provide insights into targets for intervention. Here, we explored the relevance of kinetic rate constants of a key upstream osmosensor in the yeast high-osmolarity glycerol-mitogen-activated protein kinase (HOG-MAPK pathway to signaling output responses. We created mutant pairs of the Sln1-Ypd1 complex interface that caused major compensating changes in the association (kon and dissociation (koff rate constants (kinetic perturbations but only moderate changes in the overall complex affinity (Kd. Yeast cells carrying a Sln1-Ypd1 mutant pair with moderate increases in kon and koff displayed a lower threshold of HOG pathway activation than wild-type cells. Mutants with higher kon and koff rates gave rise to higher basal signaling and gene expression but impaired osmoadaptation. Thus, the kon and koff rates of the components in the Sln1 osmosensor determine proper signaling dynamics and osmoadaptation.

Environmental variability uncovers disruptive effects of species' interactions on population dynamics.

Science.gov (United States)

Gudmundson, Sara; Eklöf, Anna; Wennergren, Uno

2015-08-07

How species respond to changes in environmental variability has been shown for single species, but the question remains whether these results are transferable to species when incorporated in ecological communities. Here, we address this issue by analysing the same species exposed to a range of environmental variabilities when (i) isolated or (ii) embedded in a food web. We find that all species in food webs exposed to temporally uncorrelated environments (white noise) show the same type of dynamics as isolated species, whereas species in food webs exposed to positively autocorrelated environments (red noise) can respond completely differently compared with isolated species. This is owing to species following their equilibrium densities in a positively autocorrelated environment that in turn enables species-species interactions to come into play. Our results give new insights into species' response to environmental variation. They especially highlight the importance of considering both species' interactions and environmental autocorrelation when studying population dynamics in a fluctuating environment. © 2015 The Author(s).

Dynamic interactions of the asialoglycoprotein receptor subunits with coated pits. Enhanced interactions of H2 following association with H1.

Science.gov (United States)

Katzir, Z; Nardi, N; Geffen, I; Fuhrer, C; Henis, Y I

1994-08-26

Lateral mobility studies comparing native and mutated membrane proteins, combined with treatments that alter clathrin lattice structure, can measure membrane protein-coated pit interactions in intact cells (Fire, E., Zwart, D., Roth, M. G., and Henis, Y. I. (1991) J. Cell Biol. 115, 1585-1594). We applied this approach to study the interactions of the H1 and H2 human asialoglycoprotein receptor subunits with coated pits. The lateral mobilities of singly expressed and coexpressed H1 and H2B (the H2 species that reaches the cell surface) were measured by fluorescence photobleaching recovery. They were compared with mutant proteins, H1(5A) (Tyr-5 replaced by Ala) and H2(5A) (Phe-5 replaced by Ala). While the mobile fractions of H1, H2B, and their mutants were similar, the lateral diffusion rate (measured by D, the lateral diffusion coefficient) was significantly slower for H1, whether expressed alone or with H2B. Coexpression with H1 reduced D of H2B to that of H1. Disruption of the clathrin lattices by hypertonic medium elevated D of H1, H1(5A), H2B, and H2(5A) to the same final level, without affecting their mobile fractions. Cytosol acidification, which retains altered clathrin lattices attached to the membrane and prevents coated vesicle formation, immobilized part of the H1 molecules, reflecting stable entrapment in "frozen" coated pits. H1(5A), H2B, and H2(5A) were not affected; however, coexpression of H2B with H1 conferred the sensitivity to cytosol acidification on H2B. Our results suggest that H1 lateral mobility is inhibited by dynamic interactions with coated pits in which Tyr-5 is involved. H2B resembles H1(5A) rather than H1, and its interactions with coated pits are weaker; efficient interaction of H2B with coated pits depends on complex formation with H1.

Perceptions of the Effectiveness of System Dynamics-Based Interactive Learning Environments: An Empirical Study

Science.gov (United States)

Qudrat-Ullah, Hassan

2010-01-01

The use of simulations in general and of system dynamics simulation based interactive learning environments (SDILEs) in particular is well recognized as an effective way of improving users' decision making and learning in complex, dynamic tasks. However, the effectiveness of SDILEs in classrooms has rarely been evaluated. This article describes…

Investigating the Role of Large-Scale Domain Dynamics in Protein-Protein Interactions.

Science.gov (United States)

Delaforge, Elise; Milles, Sigrid; Huang, Jie-Rong; Bouvier, Denis; Jensen, Malene Ringkjøbing; Sattler, Michael; Hart, Darren J; Blackledge, Martin

2016-01-01

Intrinsically disordered linkers provide multi-domain proteins with degrees of conformational freedom that are often essential for function. These highly dynamic assemblies represent a significant fraction of all proteomes, and deciphering the physical basis of their interactions represents a considerable challenge. Here we describe the difficulties associated with mapping the large-scale domain dynamics and describe two recent examples where solution state methods, in particular NMR spectroscopy, are used to investigate conformational exchange on very different timescales.

Direct Observation of Dynamical Quantum Phase Transitions in an Interacting Many-Body System.

Science.gov (United States)

Jurcevic, P; Shen, H; Hauke, P; Maier, C; Brydges, T; Hempel, C; Lanyon, B P; Heyl, M; Blatt, R; Roos, C F

2017-08-25

The theory of phase transitions represents a central concept for the characterization of equilibrium matter. In this work we study experimentally an extension of this theory to the nonequilibrium dynamical regime termed dynamical quantum phase transitions (DQPTs). We investigate and measure DQPTs in a string of ions simulating interacting transverse-field Ising models. During the nonequilibrium dynamics induced by a quantum quench we show for strings of up to 10 ions the direct detection of DQPTs by revealing nonanalytic behavior in time. Moreover, we provide a link between DQPTs and the dynamics of other quantities such as the magnetization, and we establish a connection between DQPTs and entanglement production.

Direct Observation of Dynamical Quantum Phase Transitions in an Interacting Many-Body System

Science.gov (United States)

Jurcevic, P.; Shen, H.; Hauke, P.; Maier, C.; Brydges, T.; Hempel, C.; Lanyon, B. P.; Heyl, M.; Blatt, R.; Roos, C. F.

2017-08-01

The theory of phase transitions represents a central concept for the characterization of equilibrium matter. In this work we study experimentally an extension of this theory to the nonequilibrium dynamical regime termed dynamical quantum phase transitions (DQPTs). We investigate and measure DQPTs in a string of ions simulating interacting transverse-field Ising models. During the nonequilibrium dynamics induced by a quantum quench we show for strings of up to 10 ions the direct detection of DQPTs by revealing nonanalytic behavior in time. Moreover, we provide a link between DQPTs and the dynamics of other quantities such as the magnetization, and we establish a connection between DQPTs and entanglement production.

Molecular dynamics simulations of interfacial interactions between small nanoparticles during diffusion-limited aggregation

International Nuclear Information System (INIS)

Lu, Jing; Liu, Dongmei; Yang, Xiaonan; Zhao, Ying; Liu, Haixing; Tang, Huan; Cui, Fuyi

2015-01-01

Graphical abstract: - Highlights: • Diffusion-limited aggregation is analyzed using molecular dynamic simulations. • The aggregation processand aggregate structure vary with particle size. • Particle-particle interaction and surface diffusion result in direct bonding. • Water-mediated interaction is responsible for the separation betweennanoparticles. - Abstract: Due to the limitations of experimental methods at the atomic level, research on the aggregation of small nanoparticles (D < 5 nm) in aqueous solutions is quite rare. The aggregation of small nanoparticles in aqueous solutions is very different than that of normal sized nanoparticles. The interfacial interactions play a dominant role in the aggregation of small nanoparticles. In this paper, molecular dynamics simulations, which can explore the microscopic behavior of nanoparticles during the diffusion-limited aggregation at an atomic level, were employed to reveal the aggregation mechanism of small nanoparticles in aqueous solutions. First, the aggregation processes and aggregate structure were depicted. Second, the particle–particle interaction and surface diffusion of nanoparticles during aggregation were investigated. Third, the water-mediated interactions during aggregation were ascertained. The results indicate that the aggregation of nanoparticle in aqueous solutions is affected by particle size. The strong particle–particle interaction and high surface diffusion result in the formation of particle–particle bonds of 2 nm TiO 2 nanoparticles, and the water-mediated interaction plays an important role in the aggregation process of 3 and 4 nm TiO 2 nanoparticles.

Chitosan nanoparticles-trypsin interactions: Bio-physicochemical and molecular dynamics simulation studies.

Science.gov (United States)

Salar, Safoura; Mehrnejad, Faramarz; Sajedi, Reza H; Arough, Javad Mohammadnejad

2017-10-01

Herein, we investigated the effect of the chitosan nanoparticles (CsNP) on the structure, dynamics, and activity of trypsin. The enzyme activity in complex with the nanoparticles slightly increased, which represents the interactions between the nanoparticles and the enzyme. The kinetic parameters of the enzyme, K m and k cat , increased after adding the nanoparticles, resulting in a slight increase in the catalytic efficiency (k cat /K m ). However, the effect of the nanoparticles on the kinetic stability of trypsin has not exhibited significant variations. Fluorescence spectroscopy did not show remarkable changes in the trypsin conformation in the presence of the nanoparticles. The circular dichroism (CD) spectroscopy results also revealed the secondary structure of trypsin attached to the nanoparticles slightly changed. Furthermore, we used molecular dynamics (MD) simulation to find more information about the interaction mechanisms between the nanoparticles and trypsin. The root mean square deviation (RMSD) of Cα atoms results have shown that in the presence of the nanoparticles, trypsin was stable. The simulation and the calculation of the binding free energy demonstrate that the nonpolar interactions are the most important forces for the formation of stable nanoparticle-trypsin complex. This study has explicitly elucidated that the nanoparticles have not considerable effect on the trypsin. Copyright © 2017. Published by Elsevier B.V.

Dynamic and interacting complex networks

Science.gov (United States)

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

Involvement of lipid-protein complexes in plant-microorganism interactions

Directory of Open Access Journals (Sweden)

Blein Jean-Pierre

2002-01-01

Full Text Available Increasing concerns about the environmental impact of modern agricultural have prompted research for alternate practices to pesticide treatments, notably using plant defense mechanisms. Thus, isolation and characterization of plant defense elicitors have been the main step of studies in many groups. Moreover, in the global concept of interactions between organisms and their environment, a major concern is to discriminate recognition between exogenous and endogenous signals, notably during pathogenic or allergenic interactions involving small proteins, such as elicitins or lipid transfer proteins (LTPs. Elicitins and lipid transfer proteins (LTP are both able to load and transfer lipidic molecules and share some structural and functional properties. While elicitins are known as elicitors of plant defense mechanisms, the biological function of LTPs is still an enigma. They are ubiquitous plant proteins able to load and transfer hydrophobic molecules such as fatty acids or phospholipids. Among them, LTPs1 (type 1 lipid transfer proteins constitute a multigenic family of secreted plant lipid binding proteins that are constitutively expressed in specific tissues and/or induced in response to biotic and abiotic stress (for reviews [1-4]. Their biological function is still unknown, even if some data provide arguments for a role of these proteins in the assembly of extracellular hydrophobic polymers (i.e., cutin and suberin [2, 4] and/or in plant defense against fungal pathogens [1, 3]. Beside their involvement in plant defense, LTPs1 are also known to be pan-allergens of plant-derived foods [5]. Finally, the discovery of the sterol carrier-properties of elicitins has opened new perspectives dealing with the relationship between this function and the elicitor activity of these small cystein-rich proteins. Nevertheless, this elicitor activity is restrained to few plant species, and thus does not appear in accordance with a universal lipid transfer

Interaction between Dynamic Financing and Investments

DEFF Research Database (Denmark)

Dockner, Engelbert J.; Mæland, Jøril; Miltersen, Kristian R.

Debt priority rules, i.e., the rules determining how different classes of debt split the firm's assets after bankruptcy, influence the firm's investment decisions. Existing debt benefits from an investment either because the investment is equity financed or because new debt issued to (partly......) finance the investment has lower priority in the event of bankruptcy as is the case for the commonly used absolute priority rule (APR). This incentivizes equity holders to under invest. If debt priority rules are specified in such a way that existing debt can be exploited by issuing new debt, do equity...... holders have the incentive to over invest. We formulate a dynamic structural model to study the interaction of initial capital structure choice, investment policy, subsequent debt issues, and debt priority rules. We find that priority rules have a substantial impact on investment timing as well...

A Unification between Dynamical System Theory and Thermodynamics Involving an Energy, Mass, and Entropy State Space Formalism

Directory of Open Access Journals (Sweden)

Wassim M. Haddad

2013-05-01

Full Text Available In this paper, we combine the two universalisms of thermodynamics and dynamical systems theory to develop a dynamical system formalism for classical thermodynamics. Specifically, using a compartmental dynamical system energy flow model involving heat flow, work energy, and chemical reactions, we develop a state-space dynamical system model that captures the key aspects of thermodynamics, including its fundamental laws. In addition, we show that our thermodynamically consistent dynamical system model is globally semistable with system states converging to a state of temperature equipartition. Furthermore, in the presence of chemical reactions, we use the law of mass-action and the notion of chemical potential to show that the dynamic system states converge to a state of temperature equipartition and zero affinity corresponding to a state of chemical equilibrium.

A novel mechanism of hippocampal LTD involving muscarinic receptor-triggered interactions between AMPARs, GRIP and liprin-α

Directory of Open Access Journals (Sweden)

Dickinson Bryony A

2009-06-01

Full Text Available Abstract Background Long-term depression (LTD in the hippocampus can be induced by activation of different types of G-protein coupled receptors, in particular metabotropic glutamate receptors (mGluRs and muscarinic acethycholine receptors (mAChRs. Since mGluRs and mAChRs activate the same G-proteins and isoforms of phospholipase C (PLC, it would be expected that these two forms of LTD utilise the same molecular mechanisms. However, we find a distinct mechanism of LTD involving GRIP and liprin-α. Results Whilst both forms of LTD require activation of tyrosine phosphatases and involve internalisation of AMPARs, they use different molecular interactions. Specifically, mAChR-LTD, but not mGluR-LTD, is blocked by peptides that inhibit the binding of GRIP to the AMPA receptor subunit GluA2 and the binding of GRIP to liprin-α. Thus, different receptors that utilise the same G-proteins can regulate AMPAR trafficking and synaptic efficacy via distinct molecular mechanisms. Conclusion Our results suggest that mAChR-LTD selectively involves interactions between GRIP and liprin-α. These data indicate a novel mechanism of synaptic plasticity in which activation of M1 receptors results in AMPAR endocytosis, via a mechanism involving interactions between GluA2, GRIP and liprin-α.

Opinion dynamics on interacting networks: media competition and social influence.

Science.gov (United States)

Quattrociocchi, Walter; Caldarelli, Guido; Scala, Antonio

2014-05-27

The inner dynamics of the multiple actors of the informations systems - i.e, T.V., newspapers, blogs, social network platforms, - play a fundamental role on the evolution of the public opinion. Coherently with the recent history of the information system (from few main stream media to the massive diffusion of socio-technical system), in this work we investigate how main stream media signed interaction might shape the opinion space. In particular we focus on how different size (in the number of media) and interaction patterns of the information system may affect collective debates and thus the opinions' distribution. We introduce a sophisticated computational model of opinion dynamics which accounts for the coexistence of media and gossip as separated mechanisms and for their feedback loops. The model accounts also for the effect of the media communication patterns by considering both the simple case where each medium mimics the behavior of the most successful one (to maximize the audience) and the case where there is polarization and thus competition among media memes. We show that plurality and competition within information sources lead to stable configurations where several and distant cultures coexist.

Opinion dynamics on interacting networks: media competition and social influence

Science.gov (United States)

Quattrociocchi, Walter; Caldarelli, Guido; Scala, Antonio

2014-05-01

The inner dynamics of the multiple actors of the informations systems - i.e, T.V., newspapers, blogs, social network platforms, - play a fundamental role on the evolution of the public opinion. Coherently with the recent history of the information system (from few main stream media to the massive diffusion of socio-technical system), in this work we investigate how main stream media signed interaction might shape the opinion space. In particular we focus on how different size (in the number of media) and interaction patterns of the information system may affect collective debates and thus the opinions' distribution. We introduce a sophisticated computational model of opinion dynamics which accounts for the coexistence of media and gossip as separated mechanisms and for their feedback loops. The model accounts also for the effect of the media communication patterns by considering both the simple case where each medium mimics the behavior of the most successful one (to maximize the audience) and the case where there is polarization and thus competition among media memes. We show that plurality and competition within information sources lead to stable configurations where several and distant cultures coexist.

Distributed interactive graphics applications in computational fluid dynamics

International Nuclear Information System (INIS)

Rogers, S.E.; Buning, P.G.; Merritt, F.J.

1987-01-01

Implementation of two distributed graphics programs used in computational fluid dynamics is discussed. Both programs are interactive in nature. They run on a CRAY-2 supercomputer and use a Silicon Graphics Iris workstation as the front-end machine. The hardware and supporting software are from the Numerical Aerodynamic Simulation project. The supercomputer does all numerically intensive work and the workstation, as the front-end machine, allows the user to perform real-time interactive transformations on the displayed data. The first program was written as a distributed program that computes particle traces for fluid flow solutions existing on the supercomputer. The second is an older post-processing and plotting program modified to run in a distributed mode. Both programs have realized a large increase in speed over that obtained using a single machine. By using these programs, one can learn quickly about complex features of a three-dimensional flow field. Some color results are presented

Optodynamics: dynamic aspects of laser beam-surface interaction

International Nuclear Information System (INIS)

Možina, J; Diaci, J

2012-01-01

This paper presents a synthesis of the results of our original research in the area of laser-material interaction and pulsed laser material processing with a special emphasis on the dynamic aspects of laser beam-surface interaction, which include the links between the laser material removal and the resulting material motion. In view of laser material processing, a laser beam is not only considered as a tool but also as a generator of information about the material transformation. The information is retained and conveyed by different kinds of optically induced mechanical waves. Several generation/detection schemes have been developed to extract this information, especially in the field of non-destructive material evaluation. Blast and acoustic waves, which propagate in the air surrounding the work-piece, have been studied using microphone detection as well as various setups of the laser beam deflection probe. Stress waves propagating through the work-piece have been studied using piezoelectric transducers and laser interferometers.

Investigating the Role of Large-Scale Domain Dynamics in Protein-Protein Interactions

Directory of Open Access Journals (Sweden)

Elise Delaforge

2016-09-01

Full Text Available Intrinsically disordered linkers provide multi-domain proteins with degrees of conformational freedom that are often essential for function. These highly dynamic assemblies represent a significant fraction of all proteomes, and deciphering the physical basis of their interactions represents a considerable challenge. Here we describe the difficulties associated with mapping the large-scale domain dynamics and describe two recent examples where solution state methods, in particular NMR spectroscopy, are used to investigate conformational exchange on very different timescales.

Simulation of the dynamics of laser-cluster interaction

International Nuclear Information System (INIS)

Deiss, C.

2009-01-01

Ranging in size from a few atoms to several million atoms, clusters form a link between gases and solids. When irradiating clusters with intense femtosecond laser pulses, the production of energetic and highly charged ions, hot electrons, and extreme UV and X-ray photons, gives evidence of a very efficient energy conversion. The size of the system and the multitude of mechanisms at play provide a considerable challenge for the theoretical treatment of the interaction. In this thesis, we have developed a Classical Trajectory Monte Carlo simulation that gives insight into the particle dynamics during the interaction of laser pulses with large argon clusters (with more than 10000 atoms per cluster). Elastic electron-ion scattering, electron-electron scattering, electron-impact ionization and excitation, as well as three-body recombination and Auger decay are included via stochastic events. In a strongly simplified picture, the dynamics of the laser-cluster interaction can be summarized as follows: the intense laser field ionizes the cluster atoms and drives the population of quasi-free electrons. In collision events, further free electrons and high ionic charge states are created. As some electrons leave the cluster, the ions feel a net positive charge, and the cluster ultimately disintegrates in a Coulomb explosion. Even at moderate laser intensities (approx. 10 15 W/cm 2 ), impact ionization produces inner-shell vacancies in the cluster ions that decay by emitting characteristic X-ray radiation. The small population of fast electrons responsible for these ionization events is produced near the cluster poles, where the combination of polarization and charging of the cluster leads to strongly enhanced field strengths. We achieve a good agreement over large parameter ranges between the simulation and X-ray spectroscopy experiments. We also investigate the dependence of X-ray emission on laser intensity, pulse duration and cluster size. We find that in order to

Dynamic analysis of structures with solid-fluid interaction

International Nuclear Information System (INIS)

Nahavandi, A.N.; Pedrido, R.R.; Cloud, R.L.

1977-01-01

This study develops a finite element model for interaction between an elastic solid and fluid medium (flow-induced vibrations in nuclear reactor components). Plane triangular finite elements have been used separately for fluid, solid, and solid-fluid continuua and the equivalent mass, damping, and stiffness matrices and interaction load arrays for all elements are derived and assembled into global matrices. The global matrix differential equation of motion developed is solved in time to obtain the pressure and velocity distributions in the fluid, as well as the displacements in the solid. Two independent computer programs are used to obtain the dynamic solution. The first program is a finite element program developed for solid-fluid interaction studies. This program uses the modal superposition technique in which the eigenvalues and eigenvectors for the system are found and used to uncouple the equations. This approach allows an analytic solution in each integration time step. The second program is WECAN finite element program in which a new element library subroutine for solid-fluid interaction was incorporated. This program can employ a NASTRAN direct integration scheme based on a central difference formula for the acceleration and velocity terms and an implicit representation of the displacement term. This reduces the problem to a matrix equation whose right hand side is updated in every time step and is solved by a variation of the Gaussian elimination method known as the wave front technique. Results have been obtained for the case of water, between two flat elastic parallel plates, initially at rest and accelerated suddenly by applying a step pressure. The results obtained from the above-mentioned two independent finite element programs are in full agreement. This verification provides the confidence needed to initiate parametric studies. Both rigid wall (no solid-fluid interaction) and flexible wall (including solid-fluid interaction) cases were examined

Dynamical soil-structure interactions: influence of soil behaviour nonlinearities

International Nuclear Information System (INIS)

Gandomzadeh, Ali

2011-01-01

The interaction of the soil with the structure has been largely explored the assumption of material and geometrical linearity of the soil. Nevertheless, for moderate or strong seismic events, the maximum shear strain can easily reach the elastic limit of the soil behavior. Considering soil-structure interaction, the nonlinear effects may change the soil stiffness at the base of the structure and therefore energy dissipation into the soil. Consequently, ignoring the nonlinear characteristics of the dynamic soil-structure interaction (DSSI) this phenomenon could lead to erroneous predictions of structural response. The goal of this work is to implement a fully nonlinear constitutive model for soils into a numerical code in order to investigate the effect of soil nonlinearity on dynamic soil structure interaction. Moreover, different issues are taken into account such as the effect of confining stress on the shear modulus of the soil, initial static condition, contact elements in the soil-structure interface, etc. During this work, a simple absorbing layer method based on a Rayleigh/Caughey damping formulation, which is often already available in existing Finite Element softwares, is also presented. The stability conditions of the wave propagation problems are studied and it is shown that the linear and nonlinear behavior are very different when dealing with numerical dispersion. It is shown that the 10 points per wavelength rule, recommended in the literature for the elastic media is not sufficient for the nonlinear case. The implemented model is first numerically verified by comparing the results with other known numerical codes. Afterward, a parametric study is carried out for different types of structures and various soil profiles to characterize nonlinear effects. Different features of the DSSI are compared to the linear case: modification of the amplitude and frequency content of the waves propagated into the soil, fundamental frequency, energy dissipation in

Neighborhood structure effects on the Dynamic response of soil-structure interaction by harmonic analysis

Directory of Open Access Journals (Sweden)

Pan Dan-guang

2015-01-01

Full Text Available For realizing the variation of structural dynamic characteristics due to neighbor structure in buildings group, the surface structure is idealized as an equivalent single degree of freedom system with rigid base whose site consists of a single homogeneous layer. Based on the model, a equivalent method on the equivalent seismic excitation is proposed. Then, the differences of seismic response and equivalent seismic input between soil - structure interaction (SSI system and structure -soil-structure interaction (SSSI system are investigated by harmonic analysis. The numerical results show that dynamic responses would be underestimated in SSSI system when the forcing frequencies are close to the Natural frequency if the effects of neighborhood structure were ignored. Neighborhood structure would make the translational displacement increase and rocking vibration decrease. When establishing an effective seismic input, it is necessary to consider the impact of inertia interaction.

Discourse-voice regulatory strategies in the psychotherapeutic interaction: a state-space dynamics analysis.

Science.gov (United States)

Tomicic, Alemka; Martínez, Claudio; Pérez, J Carola; Hollenstein, Tom; Angulo, Salvador; Gerstmann, Adam; Barroux, Isabelle; Krause, Mariane

2015-01-01

This study seeks to provide evidence of the dynamics associated with the configurations of discourse-voice regulatory strategies in patient-therapist interactions in relevant episodes within psychotherapeutic sessions. Its central assumption is that discourses manifest themselves differently in terms of their prosodic characteristics according to their regulatory functions in a system of interactions. The association between discourse and vocal quality in patients and therapists was analyzed in a sample of 153 relevant episodes taken from 164 sessions of five psychotherapies using the state space grid (SSG) method, a graphical tool based on the dynamic systems theory (DST). The results showed eight recurrent and stable discourse-voice regulatory strategies of the patients and three of the therapists. Also, four specific groups of these discourse-voice strategies were identified. The latter were interpreted as regulatory configurations, that is to say, as emergent self-organized groups of discourse-voice regulatory strategies constituting specific interactional systems. Both regulatory strategies and their configurations differed between two types of relevant episodes: Change Episodes and Rupture Episodes. As a whole, these results support the assumption that speaking and listening, as dimensions of the interaction that takes place during therapeutic conversation, occur at different levels. The study not only shows that these dimensions are dependent on each other, but also that they function as a complex and dynamic whole in therapeutic dialog, generating relational offers which allow the patient and the therapist to regulate each other and shape the psychotherapeutic process that characterizes each type of relevant episode.

Discourse-Voice Regulatory Strategies in the Psychotherapeutic Interaction: A State-Space Dynamics Analysis

Directory of Open Access Journals (Sweden)

Alemka eTomicic

2015-04-01

Full Text Available This study seeks to provide evidence of the dynamics associated with the configurations of discourse-voice regulatory strategies in patient-therapist interactions in relevant episodes within psychotherapeutic sessions. Its central assumption is that discourses manifest themselves differently in terms of their prosodic characteristics according to their regulatory functions in a system of interactions. The association between discourse and vocal quality in patients and therapists was analyzed in a sample of 153 relevant episodes taken from 164 sessions of five psychotherapies using the State Space Grid (SSG method, a graphical tool based on the Dynamic Systems Theory (DST. The results showed eight recurrent and stable discourse-voice regulatory strategies of the patients and three of the therapists. Also, four specific groups of these discourse-voice strategies were identified. The latter were interpreted as regulatory configurations, that is to say, as emergent self-organized groups of discourse-voice regulatory strategies constituting specific interactional systems. Both regulatory strategies and their configurations differed between two types of relevant episodes: Change Episodes and Rupture Episodes. As a whole, these results support the assumption that speaking and listening, as dimensions of the interaction that takes place during therapeutic conversation, occur at different levels. The study not only shows that these dimensions are dependent on each other, but also that they function as a complex and dynamic whole in therapeutic dialogue, generating relational offers which allow the patient and the therapist to regulate each other and shape the psychotherapeutic process that characterizes each type of relevant episode.

Software Tools For Large Scale Interactive Hydrodynamic Modeling

NARCIS (Netherlands)

Donchyts, G.; Baart, F.; van Dam, A; Jagers, B; van der Pijl, S.; Piasecki, M.

2014-01-01

Developing easy-to-use software that combines components for simultaneous visualization, simulation and interaction is a great challenge. Mainly, because it involves a number of disciplines, like computational fluid dynamics, computer graphics, high-performance computing. One of the main

Dynamical aspects on FEL interaction in single passage and storage ring devices

Energy Technology Data Exchange (ETDEWEB)

Dattoli, G.; Renieri, A. [ENEA, Frascati (Italy)

1995-12-31

The dynamical behaviour of the free-electron lasers is investigated using appropriate scaling relations valid for devices operating in the low and high gain regimes, including saturation. The analysis is applied to both single passage and storage ring configurations. In the latter case the interplay between the interaction of the electron bean with the laser field and with the accelerator environment is investigated. In particular we discuss the effect of FEL interaction on the microwave instability.

Radio Frequency Station - Beam Dynamics Interaction in Circular Accelerators

Energy Technology Data Exchange (ETDEWEB)

Mastoridis, Themistoklis [Stanford Univ., CA (United States)

2010-08-01

The longitudinal beam dynamics in circular accelerators is mainly defined by the interaction of the beam current with the accelerating Radio Frequency (RF) stations. For stable operation, Low Level RF (LLRF) feedback systems are employed to reduce coherent instabilities and regulate the accelerating voltage. The LLRF system design has implications for the dynamics and stability of the closed-loop RF systems as well as for the particle beam, and is very sensitive to the operating range of accelerator currents and energies. Stability of the RF loop and the beam are necessary conditions for reliable machine operation. This dissertation describes theoretical formalisms and models that determine the longitudinal beam dynamics based on the LLRF implementation, time domain simulations that capture the dynamic behavior of the RF station-beam interaction, and measurements from the Positron-Electron Project (PEP-II) and the Large Hadron Collider (LHC) that validate the models and simulations. These models and simulations are structured to capture the technical characteristics of the system (noise contributions, non-linear elements, and more). As such, they provide useful results and insight for the development and design of future LLRF feedback systems. They also provide the opportunity to study diverse longitudinal beam dynamics effects such as coupled-bunch impedance driven instabilities and single bunch longitudinal emittance growth. Coupled-bunch instabilities and RF station power were the performance limiting effects for PEP-II. The sensitivity of the instabilities to individual LLRF parameters, the effectiveness of alternative operational algorithms, and the possible tradeoffs between RF loop and beam stability were studied. New algorithms were implemented, with significant performance improvement leading to a world record current during the last PEP-II run of 3212 mA for the Low Energy Ring. Longitudinal beam emittance growth due to RF noise is a major concern for LHC

Lateral dynamic interaction analysis of a train girder pier system

Science.gov (United States)

Xia, H.; Guo, W. W.; Wu, X.; Pi, Y. L.; Bradford, M. A.

2008-12-01

A dynamic model of a coupled train-girder-pier system is developed in this paper. Each vehicle in a train is modeled with 27 degrees-of-freedom for a 4-axle passenger coach or freight car, and 31 for a 6-axle locomotive. The bridge model is applicable to straight and curved bridges. The centrifugal forces of moving vehicles on curved bridges are considered in both the vehicle model and the bridge model. The dynamic interaction between the bridge and train is realized through an assumed wheel-hunting movement. A case study is performed for a test train traversing two straight and two curved multi-span bridges with high piers. The histories of the train traversing the bridges are simulated and the dynamic responses of the piers and the train vehicles are calculated. A field experiment is carried out to verify the results of the analysis, by which the lateral resonant train speed inducing the peak pier-top amplitudes and some other observations are validated.

Parental and Infant Gender Factors in Parent–Infant Interaction: State-Space Dynamic Analysis

OpenAIRE

M. Angeles Cerezo; Purificación Sierra-García; Gemma Pons-Salvador; Rosa M. Trenado

2017-01-01

This study aimed to investigate the influence of parental gender on their interaction with their infants, considering, as well, the role of the infant’s gender. The State Space Grid (SSG) method, a graphical tool based on the non-linear dynamic system (NDS) approach was used to analyze the interaction, in Free-Play setting, of 52 infants, aged 6 to 10 months, divided into two groups: half of the infants interacted with their fathers and half with their mothers. There were 50% boys in each gro...

Dynamical theory of hadron interactions based upon extended particle picture, 2

International Nuclear Information System (INIS)

Hara, Osamu

1977-01-01

The interaction of hadron is discussed on the basis of an extended particle model. We assume that the interaction between hadrons is due to the coupling between currents carried by excitons excited in the particles, which is mediated by some intermediate field. This picture enables us to write down all hadron interactions once this original interaction between excitons is given -- thus leading to a more unified and a dynamical understanding of the hadron interactions. As examples π-π, anti K-N and π-N interactions are discussed. As far as the comparison is possible, the resulting meson-meson interactions and the meson-baryon interactions are in agreement with those obtained by SU 6 or its relativistic generalization. But a great advantage of our model is that it gives furthermore new relations between these meson-meson interactions and meson-baryon interactions because of its unified structure. For example, we find that in our model the coupling constant for the rho ππ interaction g sub(rhoππ) is related to the (pseudo-scalar) π-N coupling constant g by g sub(rhoππ)sup(2)/4π = (6/5) 2 (m sub(rho) m sub(π)/M 2 )(G 2 /4π), where m sub(rho), m sub(π) and M denote respectively the mass for rho, π and the nucleon. This relation is satisfied very well experimentally. (auth.)

On the reduced dynamics of a subset of interacting bosonic particles

Science.gov (United States)

Gessner, Manuel; Buchleitner, Andreas

2018-03-01

The quantum dynamics of a subset of interacting bosons in a subspace of fixed particle number is described in terms of symmetrized many-particle states. A suitable partial trace operation over the von Neumann equation of an N-particle system produces a hierarchical expansion for the subdynamics of M ≤ N particles. Truncating this hierarchy with a pure product state ansatz yields the general, nonlinear coherent mean-field equation of motion. In the special case of a contact interaction potential, this reproduces the Gross-Pitaevskii equation. To account for incoherent effects on top of the mean-field evolution, we discuss possible extensions towards a second-order perturbation theory that accounts for interaction-induced decoherence in form of a nonlinear Lindblad-type master equation.

The electron beam dynamics simulation in the laser-electron storage ring involving compton and intrabeam scattering

International Nuclear Information System (INIS)

Gladkikh, P.I.; Telegin, Yu.N.; Karnaukhov, I.M.

2002-01-01

The feasibility of the development of intense X-ray sources based on Compton scattering in laser-electron storage rings is discussed. The results of the electron beam dynamics simulation involving Compton and intrabeam scattering are presented

The electron beam dynamics simulation in the laser-electron storage ring involving compton and intrabeam scattering

CERN Document Server

Gladkikh, P I; Karnaukhov, I M

2002-01-01

The feasibility of the development of intense X-ray sources based on Compton scattering in laser-electron storage rings is discussed. The results of the electron beam dynamics simulation involving Compton and intrabeam scattering are presented.

Interacting gaps model, dynamics of order book, and stock-market fluctuations

Czech Academy of Sciences Publication Activity Database

Svorenčík, A.; Slanina, František

2007-01-01

Roč. 57, - (2007), s. 453-462 ISSN 1434-6028 R&D Projects: GA MŠk 1P04OCP10.001 Institutional research plan: CEZ:AV0Z10100520 Keywords : interacting gaps model * dynamics of order book * stock - market fluctuations Subject RIV: BE - Theoretical Physics Impact factor: 1.356, year: 2007

Dynamic evolution of double Λ five-level atom interacting with one ...

Indian Academy of Sciences (India)

Home; Journals; Pramana – Journal of Physics; Volume 89; Issue 6. Dynamic evolution ... Five-level atom; squeezing; collapse revivals. Abstract. In this paper, the model describing a double Λ five-level atom interacting with a single mode electromagnetic cavity field in the (off) non-resonate case is studied. We obtained the ...

Dynamic Dipole-Dipole Interactions between Excitons in Quantum Dots of Different Sizes

DEFF Research Database (Denmark)

Matsueda, Hideaki; Leosson, Kristjan; Xu, Zhangcheng

2005-01-01

Micro-photoluminescence spectra of GaAs/AlGaAs coupled quantum dots (QDs) are given, and proposed to be analyzed by our resonance dynamic dipole-dipole interaction (RDDDI) model, based on parity inheritance and exchange of virtual photons among QDs of different sizes....

Quantitative Proteomics Reveals Dynamic Interactions of the Minichromosome Maintenance Complex (MCM) in the Cellular Response to Etoposide Induced DNA Damage.

Science.gov (United States)

Drissi, Romain; Dubois, Marie-Line; Douziech, Mélanie; Boisvert, François-Michel

2015-07-01

The minichromosome maintenance complex (MCM) proteins are required for processive DNA replication and are a target of S-phase checkpoints. The eukaryotic MCM complex consists of six proteins (MCM2-7) that form a heterohexameric ring with DNA helicase activity, which is loaded on chromatin to form the pre-replication complex. Upon entry in S phase, the helicase is activated and opens the DNA duplex to recruit DNA polymerases at the replication fork. The MCM complex thus plays a crucial role during DNA replication, but recent work suggests that MCM proteins could also be involved in DNA repair. Here, we employed a combination of stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative proteomics with immunoprecipitation of green fluorescent protein-tagged fusion proteins to identify proteins interacting with the MCM complex, and quantify changes in interactions in response to DNA damage. Interestingly, the MCM complex showed very dynamic changes in interaction with proteins such as Importin7, the histone chaperone ASF1, and the Chromodomain helicase DNA binding protein 3 (CHD3) following DNA damage. These changes in interactions were accompanied by an increase in phosphorylation and ubiquitination on specific sites on the MCM proteins and an increase in the co-localization of the MCM complex with γ-H2AX, confirming the recruitment of these proteins to sites of DNA damage. In summary, our data indicate that the MCM proteins is involved in chromatin remodeling in response to DNA damage. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Role of Dispersive Fluorous Interaction in the Solvation Dynamics of the Perfluoro Group Containing Molecules.

Science.gov (United States)

Mondal, Saptarsi; Chaterjee, Soumit; Halder, Ritaban; Jana, Biman; Singh, Prashant Chandra

2017-08-17

Perfluoro group containing molecules possess an important self-aggregation property through the fluorous (F···F) interaction which makes them useful for diverse applications such as medicinal chemistry, separation techniques, polymer technology, and biology. In this article, we have investigated the solvation dynamics of coumarin-153 (C153) and coumarin-6H (C6H) in ethanol (ETH), 2-fluoroethanol (MFE), and 2,2,2-trifluoroethanol (TFE) using the femtosecond upconversion technique and molecular dynamics (MD) simulation to understand the role of fluorous interaction between the solute and solvent molecules in the solvation dynamics of perfluoro group containing molecules. The femtosecond upconversion data show that the time scales of solvation dynamics of C6H in ETH, MFE, and TFE are approximately the same whereas the solvation dynamics of C153 in TFE is slow as compared to that of ETH and MFE. It has also been observed that the time scale of solvation dynamics of C6H in ETH and MFE is higher than that of C153 in the same solvents. MD simulation results show a qualitative agreement with the experimental data in terms of the time scale of the slow components of the solvation for all the systems. The experimental and simulation studies combined lead to the conclusion that the solvation dynamics of C6H in all solvents as well as C153 in ETH and MFE is mostly governed by the charge distribution of ester moieties (C═O and O) of dye molecules whereas the solvation of C153 in TFE is predominantly due to the dispersive fluorous interaction (F···F) between the perfluoro groups of the C153 and solvent molecules.

GOE-TYPE ENERGY-LEVEL STATISTICS AND REGULAR CLASSICAL DYNAMICS FOR ROTATIONAL NUCLEI IN THE INTERACTING BOSON MODEL

NARCIS (Netherlands)

PAAR, [No Value; VORKAPIC, D; DIERPERINK, AEL

1992-01-01

We study the fluctuation properties of 0+ levels in rotational nuclei using the framework of SU(3) dynamical symmetry of the interacting boson model. Computations of Poincare sections for SU(3) dynamical symmetry and its breaking confirm the expected relation between dynamical symmetry and classical

The role of fluctuations and interactions in pedestrian dynamics

Science.gov (United States)

Corbetta, Alessandro; Meeusen, Jasper; Benzi, Roberto; Lee, Chung-Min; Toschi, Federico

Understanding quantitatively the statistical behaviour of pedestrians walking in crowds is a major scientific challenge of paramount societal relevance. Walking humans exhibit a rich (stochastic) dynamics whose small and large deviations are driven, among others, by own will as well as by environmental conditions. Via 24/7 automatic pedestrian tracking from multiple overhead Microsoft Kinect depth sensors, we collected large ensembles of pedestrian trajectories (in the order of tens of millions) in different real-life scenarios. These scenarios include both narrow corridors and large urban hallways, enabling us to cover and compare a wide spectrum of typical pedestrian dynamics. We investigate the pedestrian motion measuring the PDFs, e.g. those of position, velocity and acceleration, and at unprecedentedly high statistical resolution. We consider the dependence of PDFs on flow conditions, focusing on diluted dynamics and pair-wise interactions (''collisions'') for mutual avoidance. By means of Langevin-like models we provide models for the measured data, inclusive typical fluctuations and rare events. This work is part of the JSTP research programme ``Vision driven visitor behaviour analysis and crowd management'' with Project Number 341-10-001, which is financed by the Netherlands Organisation for Scientific Research (NWO).

Dynamics of a durable commodity market involving trade at disequilibrium

Science.gov (United States)

Panchuk, A.; Puu, T.

2018-05-01

The present work considers a simple model of a durable commodity market involving two agents who trade stocks of two different types. Stock commodities, in contrast to flow commodities, remain on the market from period to period and, consequently, there is neither unique demand function nor unique supply function exists. We also set up exact conditions for trade at disequilibrium, the issue being usually neglected, though a fact of reality. The induced iterative system has infinite number of fixed points and path dependent dynamics. We show that a typical orbit is either attracted to one of the fixed points or eventually sticks at a no-trade point. For the latter the stock distribution always remains the same while the price displays periodic or chaotic oscillations.

ARE THE FIVE ASEAN STOCK PRICE INDICES DYNAMICALLY INTERACTED?

Directory of Open Access Journals (Sweden)

Adwin Surja Atmadja

2005-01-01

Full Text Available This study seeks to examine the dynamic interactions of stock price indices in five ASEAN countries, Indonesia; Malaysia; the Philippines; Singapore; and Thailand with particular attention to the 1997 Asian financial crisis and period onwards. Using monthly time series data of the stock price indices countries, a vector error correction model (VECM is employed to empirically examine the interaction among the variables. The finding is that the five ASEAN stock market prices were found to be integrated with two cointegrating vectors during the sample period, and that accounting innovation analyses show the short run dynamic interactions among those stock markets. The important implication might be drawn from the finding is that portfolio diversification across the five ASEAN stock markets is unlikely to reduce investment risk due to high degree of financial integration of these markets. Abstract in Bahasa Indonesia : Studi ini bertujuan meneliti interaksi dinamis antara indeks harga saham yang terdapat di lima negara ASEAN, yaitu Indonesia, Malaysia, Filipina, Singapura, dan Thailan yang terjadi selama masa krisis finansial Asia tahun 1997 dan periode sesudahnya. Dengan menggunakan data time series bulanan indeks harga saham dari kelima negara tersebut selama periode penelitian, suatu vector error correction model (VECM diaplikasikan untuk meneliti secara empiris interaksi dinamis yang terjadi diantara berbagai variabel yang dipergunakan dalam penelitian ini. Dari hasil penelitian ditemukan dua vektor kointegrasi (cointegration vector selama masa penelitian, dan analisa inovasi akuntansi (accounting innovation analyses menunjukan adanya interaksi dinamis jangka pendek diantara pasar saham tersebut. Implikasi penting yang mungkin perlu diperhatikan dari penemuan ini adalah bahwa diversifikasi portofolio saham pada lima pasar saham tersebut agaknya tidak akan secara signifikan mengurangi tingkat resiko investasi. Hal ini dikarenakan oleh tingginya

T-cell acute leukaemia exhibits dynamic interactions with bone marrow microenvironments.

Science.gov (United States)

Hawkins, Edwin D; Duarte, Delfim; Akinduro, Olufolake; Khorshed, Reema A; Passaro, Diana; Nowicka, Malgorzata; Straszkowski, Lenny; Scott, Mark K; Rothery, Steve; Ruivo, Nicola; Foster, Katie; Waibel, Michaela; Johnstone, Ricky W; Harrison, Simon J; Westerman, David A; Quach, Hang; Gribben, John; Robinson, Mark D; Purton, Louise E; Bonnet, Dominique; Lo Celso, Cristina

2016-10-27

It is widely accepted that complex interactions between cancer cells and their surrounding microenvironment contribute to disease development, chemo-resistance and disease relapse. In light of this observed interdependency, novel therapeutic interventions that target specific cancer stroma cell lineages and their interactions are being sought. Here we studied a mouse model of human T-cell acute lymphoblastic leukaemia (T-ALL) and used intravital microscopy to monitor the progression of disease within the bone marrow at both the tissue-wide and single-cell level over time, from bone marrow seeding to development/selection of chemo-resistance. We observed highly dynamic cellular interactions and promiscuous distribution of leukaemia cells that migrated across the bone marrow, without showing any preferential association with bone marrow sub-compartments. Unexpectedly, this behaviour was maintained throughout disease development, from the earliest bone marrow seeding to response and resistance to chemotherapy. Our results reveal that T-ALL cells do not depend on specific bone marrow microenvironments for propagation of disease, nor for the selection of chemo-resistant clones, suggesting that a stochastic mechanism underlies these processes. Yet, although T-ALL infiltration and progression are independent of the stroma, accumulated disease burden leads to rapid, selective remodelling of the endosteal space, resulting in a complete loss of mature osteoblastic cells while perivascular cells are maintained. This outcome leads to a shift in the balance of endogenous bone marrow stroma, towards a composition associated with less efficient haematopoietic stem cell function. This novel, dynamic analysis of T-ALL interactions with the bone marrow microenvironment in vivo, supported by evidence from human T-ALL samples, highlights that future therapeutic interventions should target the migration and promiscuous interactions of cancer cells with the surrounding microenvironment

Dynamic strength of the interaction between lung surfactant protein D (SP-D) and saccharide ligands

DEFF Research Database (Denmark)

Thormann, Esben; Dreyer, Jakob K; Simonsen, Adam C

2007-01-01

In order to investigate the dynamic strength of the interaction between lung surfactant protein D (SP-D) and different sugars, maltose, mannose, glucose, and galactose, we have used an atomic force microscope to monitor the interaction on a single molecule scale. The experiment is performed...

Coupled Fluid-Solid Interaction Under Shock Wave Loading: Part II - Dynamic Interfaces

Energy Technology Data Exchange (ETDEWEB)

Tipton, David Gregory [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Christon, Mark Allen [CTO Offce, Dassault Systµemes SIMULIA, Providence, RI (United States); Ingber, Marc Stuart [Univ. of New Mexico, Albuquerque, NM (United States). Department of Mechanical Engineering

2009-07-01

This article is the second of two that consider the treatment of fluid-solid interaction problems where the solid experiences wave loading and large bulk Lagrangian displacements. In part-I, we presented the formulation for the edge-based unstructured-grid Euler solver in the context of a discontinuous- Galerkin framework with the extensions used to treat internal fluid-solid interfaces. A super-sampled L² projection was used to construct level-set data from the Lagrangian interface, and a narrow-band approach was used to identify and construct appropriate ghost data and boundary conditions at the fluid-solid interface. A series of benchmark problems were used to verify the treatment of the fluid-solid interface conditions with a static interface position. In this paper, we consider the treatment of dynamic interfaces and the associated large bulk Lagrangian displacements of the solid.We present the coupled dynamic fluid-solid system, and develop an explicit, monolithic treatment of the fully-coupled system. The conditions associated with moving interfaces and their implementation are discussed. A comparison of moving vs. fixed reference frames is used to verify the dynamic interface treatment. Lastly, a series of two and and three-dimensional projectile and shock-body interaction calculations are presented. Ultimately, the use of the Lagrangian interface position and a super-sampled projection for fast level-set construction, the narrow-band extraction of ghost data, and monolithic explicit solution algorithm has proved to be a computationally efficient means for treating shock induced fluid-solid interaction problems.

Step dynamics and terrace-width distribution on flame-annealed gold films: The effect of step-step interaction

International Nuclear Information System (INIS)

Shimoni, Nira; Ayal, Shai; Millo, Oded

2000-01-01

Dynamics of atomic steps and the terrace-width distribution within step bunches on flame-annealed gold films are studied using scanning tunneling microscopy. The distribution is narrower than commonly observed for vicinal planes and has a Gaussian shape, indicating a short-range repulsive interaction between the steps, with an apparently large interaction constant. The dynamics of the atomic steps, on the other hand, appear to be influenced, in addition to these short-range interactions, also by a longer-range attraction of steps towards step bunches. Both types of interactions promote self-ordering of terrace structures on the surface. When current is driven through the films a step-fingering instability sets in, reminiscent of the Bales-Zangwill instability

Interaction of synchronized dynamics in cortex and basal ganglia in Parkinson's disease.

Science.gov (United States)

Ahn, Sungwoo; Zauber, S Elizabeth; Worth, Robert M; Witt, Thomas; Rubchinsky, Leonid L

2015-09-01

Parkinson's disease pathophysiology is marked by increased oscillatory and synchronous activity in the beta frequency band in cortical and basal ganglia circuits. This study explores the functional connections between synchronized dynamics of cortical areas and synchronized dynamics of subcortical areas in Parkinson's disease. We simultaneously recorded neuronal units (spikes) and local field potentials (LFP) from subthalamic nucleus (STN) and electroencephalograms (EEGs) from the scalp in parkinsonian patients, and analysed the correlation between the time courses of the spike-LFP synchronization and inter-electrode EEG synchronization. We found the (non-invasively obtained) time course of the synchrony strength between EEG electrodes and the (invasively obtained) time course of the synchrony between spiking units and LFP in STN to be weakly, but significantly, correlated with each other. This correlation is largest for the bilateral motor EEG synchronization, followed by bilateral frontal EEG synchronization. Our observations suggest that there may be multiple functional modes by which the cortical and basal ganglia circuits interact with each other in Parkinson's disease: not only may synchronization be observed between some areas in cortex and the basal ganglia, but also synchronization within cortex and within basal ganglia may be related, suggesting potentially a more global functional interaction. More coherent dynamics in one brain region may modulate or activate the dynamics of another brain region in a more powerful way, causing correlations between changes in synchrony strength in the two regions. © 2015 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

Molecular dynamics simulations of the DNA interaction with metallic nanoparticles and TiO2 surfaces

International Nuclear Information System (INIS)

Kholmurodov, Kh.T.; Krasavin, E.A.; Dushanov, E.B.; Hassan, H.K.; Galal, A.; ElHabashy, H.A.; Sweilam, N.H.; Yasuoka, K.

2013-01-01

The understanding of the mechanism of DNA interactions and binding with metallic nanoparticles (NPs) and surfaces represents a great interest in today's medicine applications due to diagnostic and treatment of oncology diseases. Recent experimental and simulation studies involve the DNA interaction with highly localized proton beams or metallic NPs (such as Ag, Au, etc.), aimed at targeted cancer therapy through the injection of metal micro- or nanoparticles into the tumor tissue with consequent local microwave or laser heating. The effects of mutational structure changes in DNA and protein structures could result in destroying of native chemical (hydrogen) bonds or, on the contrary, creating of new bonds that do not normally exist there. The cause of such changes might be the alteration of one or several nucleotides (in DNA) or the substitution of specific amino acid residues (in proteins) that can lead to the essential structural destabilization or unfolding. At the atomic or molecular level, the replacement of one nucleotide by another (in DNA double helices) or replacement of one amino acid residue by another (in proteins) cause essential modifications of the molecular force fields of the environment that break locally important hydrogen bonds underlying the structural stability of the biological molecules. In this work, the molecular dynamics(MD) simulations were performed for four DNA models and the flexibilities of the purine and pyrimidine nucleotides during the interaction process with the metallic NPs and TiO 2 surface were clarified

Fluid-structure interaction dynamic simulation of spring-loaded pressure relief valves under seismic wave

Science.gov (United States)

Lv, Dongwei; Zhang, Jian; Yu, Xinhai

2018-05-01

In this paper, a fluid-structure interaction dynamic simulation method of spring-loaded pressure relief valve was established. The dynamic performances of the fluid regions and the stress and strain of the structure regions were calculated at the same time by accurately setting up the contact pairs between the solid parts and the coupling surfaces between the fluid regions and the structure regions. A two way fluid-structure interaction dynamic simulation of a simplified pressure relief valve model was carried out. The influence of vertical sinusoidal seismic waves on the performance of the pressure relief valve was preliminarily investigated by loading sine waves. Under vertical seismic waves, the pressure relief valve will flutter, and the reseating pressure was affected by the amplitude and frequency of the seismic waves. This simulation method of the pressure relief valve under vertical seismic waves can provide effective means for investigating the seismic performances of the valves, and make up for the shortcomings of the experiment.

The dynamic reactance interaction – How vested interests affect people’s experience, behavior, and cognition in social interactions

Directory of Open Access Journals (Sweden)

Christina eSteindl

2015-11-01

Full Text Available In social interactions, individuals may sometimes pursue their own interests at the expense of their interaction partner. Such self-interested behaviors impose a threat to the interaction partner’s freedom to act. The current article investigates this threat in the context of interdependence and reactance theory. We explore how vested interests influence reactance process stages of an advisor-client interaction. We aim to explore the interactional process that evolves. In two studies, participants took the perspective of a doctor (advisor or a patient (client. In both studies we incorporated a vested interest. In Study 1 (N=82 we found that in response to a vested interest of their interaction partner, patients indicated a stronger experience of reactance, more aggressive behavioral intentions, and more biased cognitions than doctors. A serial multiple mediation revealed that a vested interest engendered mistrust toward the interaction partner and this mistrust led to an emerging reactance process. Study 2 (N=207 further demonstrated that doctors expressed their reactance in a subtle way: They revealed a classic confirmation bias when searching for additional information on their preliminary decision preference, indicating stronger defense motivation. We discuss how these findings can help us to understand how social interactions develop dynamically.

The Dynamic Reactance Interaction – How Vested Interests Affect People’s Experience, Behavior, and Cognition in Social Interactions

Science.gov (United States)

Steindl, Christina; Jonas, Eva

2015-01-01

In social interactions, individuals may sometimes pursue their own interests at the expense of their interaction partner. Such self-interested behaviors impose a threat to the interaction partner’s freedom to act. The current article investigates this threat in the context of interdependence and reactance theory. We explore how vested interests influence reactance process stages of an advisor–client interaction. We aim to explore the interactional process that evolves. In two studies, participants took the perspective of a doctor (advisor) or a patient (client). In both studies we incorporated a vested interest. In Study 1 (N = 82) we found that in response to a vested interest of their interaction partner, patients indicated a stronger experience of reactance, more aggressive behavioral intentions, and more biased cognitions than doctors. A serial multiple mediation revealed that a vested interest engendered mistrust toward the interaction partner and this mistrust led to an emerging reactance process. Study 2 (N = 207) further demonstrated that doctors expressed their reactance in a subtle way: they revealed a classic confirmation bias when searching for additional information on their preliminary decision preference, indicating stronger defense motivation. We discuss how these findings can help us to understand how social interactions develop dynamically. PMID:26640444

Molecular signaling involving intrinsically disordered proteins in prostate cancer

Directory of Open Access Journals (Sweden)

Anna Russo

2016-01-01

Full Text Available Investigations on cellular protein interaction networks (PINs reveal that proteins that constitute hubs in a PIN are notably enriched in Intrinsically Disordered Proteins (IDPs compared to proteins that constitute edges, highlighting the role of IDPs in signaling pathways. Most IDPs rapidly undergo disorder-to-order transitions upon binding to their biological targets to perform their function. Conformational dynamics enables IDPs to be versatile and to interact with a broad range of interactors under normal physiological conditions where their expression is tightly modulated. IDPs are involved in many cellular processes such as cellular signaling, transcriptional regulation, and splicing; thus, their high-specificity/low-affinity interactions play crucial roles in many human diseases including cancer. Prostate cancer (PCa is one of the leading causes of cancer-related mortality in men worldwide. Therefore, identifying molecular mechanisms of the oncogenic signaling pathways that are involved in prostate carcinogenesis is crucial. In this review, we focus on the aspects of cellular pathways leading to PCa in which IDPs exert a primary role.

Dynamic Interaction of Stress Granules, DDX3X, and IKK-α Mediates Multiple Functions in Hepatitis C Virus Infection.

Science.gov (United States)

Pène, Véronique; Li, Qisheng; Sodroski, Catherine; Hsu, Ching-Sheng; Liang, T Jake

2015-05-01

The ubiquitous ATP-dependent RNA helicase DDX3X is involved in many cellular functions, including innate immunity, and is a pivotal host factor for hepatitis C virus (HCV) infection. Recently, we showed that DDX3X specifically recognizes the HCV 3' untranslated region (UTR), leading to the activation of IKK-α and a cascade of lipogenic signaling to facilitate lipid droplet biogenesis and viral assembly (Q. Li, V. Pene, S. Krishnamurthy, H. Cha, and T. J. Liang, Nat Med 19:722-729, 2013, http://dx.doi.org/10.1038/nm.3190). The interaction of DDX3X with HCV core protein seems to be dispensable for its proviral role. In this study, through systematic imaging and biochemical and virologic approaches, we identified a dynamic association between DDX3X and various cellular compartments and viral elements mediating multiple functions of DDX3X in productive HCV infection. Upon HCV infection, the HCV 3'UTR interacts with DDX3X and IKK-α, which redistribute to speckle-like cytoplasmic structures shown to be stress granules (SGs). As viral proteins accumulate in infected cells, DDX3X granules together with SG-associated proteins redistribute and colocalize with HCV core protein around lipid droplets (LDs). IKK-α, however, does not relocate to the LD but translocates to the nucleus. In HCV-infected cells, various HCV nonstructural proteins also interact or colocalize with DDX3X in close proximity to SGs and LDs, consistent with the tight juxtaposition of the replication complex and the assembly site at the surface of LDs. Short interfering RNA (siRNA)-mediated silencing of DDX3X and multiple SG components markedly inhibits HCV infection. Our data suggest that DDX3X initiates a multifaceted cellular program involving dynamic associations with HCV RNA and proteins, IKK-α, SG, and LD surfaces for its crucial role in the HCV life cycle. IMPORTANCE DDX3X is a proviral host factor for HCV infection. Recently, we showed that DDX3X binds to the HCV 3'UTR, activating IKK-α and

Pion-pion interactions in particle physics

Energy Technology Data Exchange (ETDEWEB)

Martin, B R; Morgan, D; Shaw, G

1976-01-01

The aim of the book is to review the experimental and theoretical work on the processes involving pion-pion interactions. Sources of information on pion-pion scattering are examined, including pion production, dipion exchange, and weak and electromagnetic interactions. The theory and models of pion-pion scattering are discussed with reference to fixed momentum transfer, partial wave amplitudes, models and phenomenology, dynamical and field theoretic models, finite-energy sum rules, duality and the Veneziano model, resonance spectra and lastly, predictions from current algebra.

Genes related to antioxidant metabolism are involved in Methylobacterium mesophilicum-soybean interaction.

Science.gov (United States)

Araújo, Welington Luiz; Santos, Daiene Souza; Dini-Andreote, Francisco; Salgueiro-Londoño, Jennifer Katherine; Camargo-Neves, Aline Aparecida; Andreote, Fernando Dini; Dourado, Manuella Nóbrega

2015-10-01

The genus Methylobacterium is composed of pink-pigmented methylotrophic bacterial species that are widespread in natural environments, such as soils, stream water and plants. When in association with plants, this genus colonizes the host plant epiphytically and/or endophytically. This association is known to promote plant growth, induce plant systemic resistance and inhibit plant infection by phytopathogens. In the present study, we focused on evaluating the colonization of soybean seedling-roots by Methylobacterium mesophilicum strain SR1.6/6. We focused on the identification of the key genes involved in the initial step of soybean colonization by methylotrophic bacteria, which includes the plant exudate recognition and adaptation by planktonic bacteria. Visualization by scanning electron microscopy revealed that M. mesophilicum SR1.6/6 colonizes soybean roots surface effectively at 48 h after inoculation, suggesting a mechanism for root recognition and adaptation before this period. The colonization proceeds by the development of a mature biofilm on roots at 96 h after inoculation. Transcriptomic analysis of the planktonic bacteria (with plant) revealed the expression of several genes involved in membrane transport, thus confirming an initial metabolic activation of bacterial responses when in the presence of plant root exudates. Moreover, antioxidant genes were mostly expressed during the interaction with the plant exudates. Further evaluation of stress- and methylotrophic-related genes expression by qPCR showed that glutathione peroxidase and glutathione synthetase genes were up-regulated during the Methylobacterium-soybean interaction. These findings support that glutathione (GSH) is potentially a key molecule involved in cellular detoxification during plant root colonization. In addition to methylotrophic metabolism, antioxidant genes, mainly glutathione-related genes, play a key role during soybean exudate recognition and adaptation, the first step in

Conserved regions of ribonucleoprotein ribonuclease MRP are involved in interactions with its substrate.

Science.gov (United States)

Esakova, Olga; Perederina, Anna; Berezin, Igor; Krasilnikov, Andrey S

2013-08-01

Ribonuclease (RNase) MRP is a ubiquitous and essential site-specific eukaryotic endoribonuclease involved in the metabolism of a wide range of RNA molecules. RNase MRP is a ribonucleoprotein with a large catalytic RNA moiety that is closely related to the RNA component of RNase P, and multiple proteins, most of which are shared with RNase P. Here, we report the results of an ultraviolet-cross-linking analysis of interactions between a photoreactive RNase MRP substrate and the Saccharomyces cerevisiae RNase MRP holoenzyme. The results show that the substrate interacts with phylogenetically conserved RNA elements universally found in all enzymes of the RNase P/MRP family, as well as with a phylogenetically conserved RNA region that is unique to RNase MRP, and demonstrate that four RNase MRP protein components, all shared with RNase P, interact with the substrate. Implications for the structural organization of RNase MRP and the roles of its components are discussed.

Comparison of various clustered interaction regions with regard to chromatic and dynamic behavior

International Nuclear Information System (INIS)

Leemann, B.; Wrulich, A.

1986-05-01

Clustered interaction regions for the SSC may be preferable from the viewpoint of costs and operation. In going from distributed to clustered IR's the superperiodicity of the machine is reduced and therefore the number of resonances induced by chromaticity correcting sextupoles is increased. This break in symmetry may cause a reduction in dynamic stability. The chromatic and dynamic behavior of the bare lattice is investigated for various cluster configurations. That means only chromaticity correcting sextupoles have been included and no magnetic imperfection errors have been considered. Then, the dynamic apertures of lattices with various IR clustering schemes are compared when random magnetic imperfections are included

Dynamic Characterization and Interaction Control of the CBM-Motus Robot for Upper-Limb Rehabilitation

Directory of Open Access Journals (Sweden)

Loredana Zollo

2013-10-01

Full Text Available This paper presents dynamic characterization and control of an upper-limb rehabilitation machine aimed at improving robot performance in the interaction with the patient. An integrated approach between mechanics and control is the key issue of the paper for the development of a robotic machine with desirable dynamic properties. Robot inertial and acceleration properties are studied in the workspace via a graphical representation based on ellipses. Robot friction is experimentally retrieved by means of a parametric identification procedure. A current-based impedance control is developed in order to compensate for friction and enhance control performance in the interaction with the patient by means of force feedback, without increasing system inertia. To this end, servo-amplifier motor currents are monitored to provide force feedback in the interaction, thus avoiding the need for force sensors mounted at the robot end-effector. Current-based impedance control is implemented on the robot; experimental results in free space as well as in constrained space are provided.

Constraint Embedding for Vehicle Suspension Dynamics

Directory of Open Access Journals (Sweden)

Jain Abhinandan

2016-06-01

Full Text Available The goal of this research is to achieve close to real-time dynamics performance for allowing auto-pilot in-the-loop testing of unmanned ground vehicles (UGV for urban as well as off-road scenarios. The overall vehicle dynamics performance is governed by the multibody dynamics model for the vehicle, the wheel/terrain interaction dynamics and the onboard control system. The topic of this paper is the development of computationally efficient and accurate dynamics model for ground vehicles with complex suspension dynamics. A challenge is that typical vehicle suspensions involve closed-chain loops which require expensive DAE integration techniques. In this paper, we illustrate the use the alternative constraint embedding technique to reduce the cost and improve the accuracy of the dynamics model for the vehicle.

Dynamic dipole-dipole interactions between excitons in quantum dots of different sizes

DEFF Research Database (Denmark)

Matsueda, Hideaki; Leosson, Kristjan; Xu, Zhangcheng

2004-01-01

A model of the resonance dynamic dipole-dipole interaction between excitons confined in quantum dots (QDs) of different sizes at close enough distance is given in terms of parity inheritance and exchange of virtual photons. Microphotoluminescence spectra of GaAs-AlGaAs coupled QDs are proposed to...

Dynamic soil-structure interaction of monopod and polypod foundations

DEFF Research Database (Denmark)

Andersen, Lars Vabbersgaard

2016-01-01

within the time domain, frequency-independent lumped-parameter models are developed. The paper proposes a decision criterion for determination of which components must be included within a lumped-parameter model in order to account for the structure–soil–structure interaction in an adequate and efficient......The paper concerns the importance of through–soil coupling for structures having foundations with more footings. First, a model for dynamic analysis of polypod footings is established in the frequency domain, employing Green’s function for wave propagation in a layered half-space. To allow analysis...

A semiautomated computer-interactive dynamic impact testing system

International Nuclear Information System (INIS)

Alexander, D.J.; Nanstad, R.K.; Corwin, W.R.; Hutton, J.T.

1989-01-01

A computer-assisted semiautomated system has been developed for testing a variety of specimen types under dynamic impact conditions. The primary use of this system is for the testing of Charpy specimens. Full-, half-, and third-size specimens have been tested, both in the lab and remotely in a hot cell for irradiated specimens. Specimens are loaded into a transfer device which moves the specimen into a chamber, where a hot air gun is used to heat the specimen, or cold nitrogen gas is used for cooling, as required. The specimen is then quickly transferred from the furnace to the anvils and then broken. This system incorporates an instrumented tup to determine the change in voltage during the fracture process. These data are analyzed by the computer system after the test is complete. The voltage-time trace is recorded with a digital oscilloscope, transferred to the computer, and analyzed. The analysis program incorporates several unique features. It interacts with the operator and identifies the maximum voltage during the test, the amount of rapid fracture during the test (if any), and the end of the fracture process. The program then calculates the area to maximum voltage and the total area under the voltage-time curve. The data acquisition and analysis part of the system can also be used to conduct other dynamic testing. Dynamic tear and precracked specimens can be tested with an instrumented tup and analyzed in a similar manner. 3 refs., 7 figs

The selective interaction between silica nanoparticles and enzymes from molecular dynamics simulations.

Directory of Open Access Journals (Sweden)

Xiaotian Sun

Full Text Available Nanoscale particles have become promising materials in many fields, such as cancer therapeutics, diagnosis, imaging, drug delivery, catalysis, as well as biosensors. In order to stimulate and facilitate these applications, there is an urgent need for the understanding of the interaction mode between the nano-particles and proteins. In this study, we investigate the orientation and adsorption between several enzymes (cytochrome c, RNase A, lysozyme and 4 nm/11 nm silica nanoparticles (SNPs by using molecular dynamics (MD simulation. Our results show that three enzymes are adsorbed onto the surfaces of both 4 nm and 11 nm SNPs during our MD simulations and the small SNPs induce greater structural stabilization. The active site of cytochrome c is far away from the surface of 4 nm SNPs, while it is adsorbed onto the surface of 11 nm SNPs. We also explore the influences of different groups (-OH, -COOH, -NH2 and CH3 coated onto silica nanoparticles, which show significantly different impacts. Our molecular dynamics results indicate the selective interaction between silicon nanoparticles and enzymes, which is consistent with experimental results. Our study provides useful guides for designing/modifying nanomaterials to interact with proteins for their bio-applications.

Multiscale Molecular Dynamics Simulations of Beta-Amyloid Interactions with Neurons

Science.gov (United States)

Qiu, Liming; Vaughn, Mark; Cheng, Kelvin

2012-10-01

Early events of human beta-amyloid protein interactions with cholesterol-containing membranes are critical to understanding the pathogenesis of Alzheimer's disease (AD) and to exploring new therapeutic interventions of AD. Atomistic molecular dynamics (AMD) simulations have been extensively used to study the protein-lipid interaction at high atomic resolutions. However, traditional MD simulations are not efficient in sampling the phase space of complex lipid/protein systems with rugged free energy landscapes. Meanwhile, coarse-grained MD (CGD) simulations are efficient in the phase space sampling but suffered from low spatial resolutions and from the fact that the energy landscapes are not identical to those of the AMD. Here, a multiscale approach was employed to simulate the protein-lipid interactions of beta-amyloid upon its release from proteolysis residing in the neuronal membranes. We utilized a forward (AMD to CGD) and reverse (CGD-AMD) strategy to explore new transmembrane and surface protein configuration and evaluate the stabilization mechanisms by measuring the residue-specific protein-lipid or protein conformations. The detailed molecular interactions revealed in this multiscale MD approach will provide new insights into understanding the early molecular events leading to the pathogenesis of AD.

Changes in actin dynamics are involved in salicylic acid signaling pathway.

Science.gov (United States)

Matoušková, Jindřiška; Janda, Martin; Fišer, Radovan; Sašek, Vladimír; Kocourková, Daniela; Burketová, Lenka; Dušková, Jiřina; Martinec, Jan; Valentová, Olga

2014-06-01

Changes in actin cytoskeleton dynamics are one of the crucial players in many physiological as well as non-physiological processes in plant cells. Positioning of actin filament arrays is necessary for successful establishment of primary lines of defense toward pathogen attack, depolymerization leads very often to the enhanced susceptibility to the invading pathogen. On the other hand it was also shown that the disruption of actin cytoskeleton leads to the induction of defense response leading to the expression of PATHOGENESIS RELATED proteins (PR). In this study we show that pharmacological actin depolymerization leads to the specific induction of genes in salicylic acid pathway but not that involved in jasmonic acid signaling. Life imaging of leafs of Arabidopsis thaliana with GFP-tagged fimbrin (GFP-fABD2) treated with 1 mM salicylic acid revealed rapid disruption of actin filaments resembling the pattern viewed after treatment with 200 nM latrunculin B. The effect of salicylic acid on actin filament fragmentation was prevented by exogenous addition of phosphatidic acid, which binds to the capping protein and thus promotes actin polymerization. The quantitative evaluation of actin filament dynamics is also presented. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Interactions involving ozone, Botrytis cinerea, and B. squamosa on onion leaves

Energy Technology Data Exchange (ETDEWEB)

Rist, D.L.

1983-01-01

Interactions involving Botrytis cinerea Pers., B. squamosa Walker, and ozone on onion (alium cepae L.) were investigated. Initially, threshold dosages of ozone required to predispose onion leaves to greater infection by B. cinerea and B. squamosa were determined under controlled conditions in an ozone-exposure chamber. Subsequent experiments supported the hypothesis that nutrients leaking out of ozone-injured cells stimulated lesion production by B. cinerea. The electrical conductivity of, and carbohydrate concentration in, dew collected from leaves of onion plants which had been exposed to ozone were greater than the electrical conductivity of, and carbohydrate concentration in, dew collected from leaves of other, non-exposed onion plants. When conidia of B. cinerea were suspended in dew collected from leaves of plants which had been exposed to ozone and the resulting suspension atomized onto leaves of non-exposed plants, more lesions were induced than on leaves of other non-exposed plants inoculated with conidia suspended in dew collected from plants which had not been exposed to ozone. EDU protected onion leaves from ozone-induced predisposition to these fungi under controlled conditions. Experiments designed to detect interaction between B. cinerea and B. squamosa in onion leaf blighting indicated that such interaction did not occur. Leaves were blighted rapidly when inoculated with B. squamosa whether B. cinerea was present or absent.

Quantum trajectory analysis of multimode subsystem-bath dynamics.

Science.gov (United States)

Wyatt, Robert E; Na, Kyungsun

2002-01-01

The dynamics of a swarm of quantum trajectories is investigated for systems involving the interaction of an active mode (the subsystem) with an M-mode harmonic reservoir (the bath). Equations of motion for the position, velocity, and action function for elements of the probability fluid are integrated in the Lagrangian (moving with the fluid) picture of quantum hydrodynamics. These fluid elements are coupled through the Bohm quantum potential and as a result evolve as a correlated ensemble. Wave function synthesis along the trajectories permits an exact description of the quantum dynamics for the evolving probability fluid. The approach is fully quantum mechanical and does not involve classical or semiclassical approximations. Computational results are presented for three systems involving the interaction on an active mode with M=1, 10, and 15 bath modes. These results include configuration space trajectory evolution, flux analysis of the evolving ensemble, wave function synthesis along trajectories, and energy partitioning along specific trajectories. These results demonstrate the feasibility of using a small number of quantum trajectories to obtain accurate quantum results on some types of open quantum systems that are not amenable to standard quantum approaches involving basis set expansions or Eulerian space-fixed grids.

Exploring dynamic lighting, colour and form with smart textiles

Science.gov (United States)

Cabral, I.; Silva, C.; Worbin, L.; Souto, A. P.

2017-10-01

This paper addresses an ongoing research, aiming at the development of smart textiles that transform the incident light that passes through them - light transmittance - to design dynamic light without acting upon the light source. A colour and shape change prototype was developed with the objective of studying textile changes in time; to explore temperature as a dynamic variable through electrical activation of the smart materials and conductive threads integrated in the textile substrate; and to analyse the relation between textile chromic and morphologic behaviour in interaction with light. Based on the experiments conducted, results have highlighted some considerations of the dynamic parameters involved in the behaviour of thermo-responsive textiles and demonstrated design possibilities to create interactive lighting scenarios.

Dynamic stress of impeller blade of shaft extension tubular pump device based on bidirectional fluid-structure interaction

Energy Technology Data Exchange (ETDEWEB)

Kan, Kan; Liu, Huiwen; Yang, Chunxia [Hohai University, Nanjing (China); Zheng, Yuan [National Engineering Research Center of Water Resources Efficient Utilization and Engineering Safety, Nanjing (China); Fu, Shifeng; Zhang, Xin [Power China Huadong Engineering Corporation, Hangzhou (China)

2017-04-15

Current research on the stability of tubular pumps is mainly concerned with the transient hydrodynamic characteristics. However, the structural response under the influence of fluid-structure interaction hasn't been taken fully into consideration. The instability of the structure can cause vibration and cracks, which may threaten the safety of the unit. We used bidirectional fluid-structure interaction to comprehensively analyze the dynamic stress characteristics of the impeller blades of the shaft extension tubular pump device. Furthermore, dynamic stress of impeller blade of shaft extension tubular pump device was solved under different lift conditions of 0° blade angle. Based on Reynolds-average N-S equation and SST k-ω turbulence model, numerical simulation was carried out for three-dimensional unsteady incompressible turbulent flow field of the pump device whole flow passage. Meanwhile, the finite element method was used to calculate dynamic characteristics of the blade structure. The blade dynamic stress distribution was obtained on the basis of fourth strength theory. The research results indicate that the maximum blade dynamic stress appears at the joint between root of inlet side of the blade suction surface and the axis. Considering the influence of gravity, the fluctuation of the blade dynamic stress increases initially and decreases afterwards within a rotation period. In the meantime, the dynamic stress in the middle part of inlet edge presents larger relative fluctuation amplitude. Finally, a prediction method for dynamic stress distribution of tubular pump considering fluid-structure interaction and gravity effect was proposed. This method can be used in the design stage of tubular pump to predict dynamic stress distribution of the structure under different operating conditions, improve the reliability of pump impeller and analyze the impeller fatigue life.

Playing in or out of character: User role differences in the experience of Interactive Storytelling

NARCIS (Netherlands)

Roth, C.; Vermeulen, I.E.; Vorderer, P.A.; Klimmt, C.; Pizzi, D.; Lugrin, J-L.; Cavazza, M.

2012-01-01

Interactive storytelling (IS) is a promising new entertainment technology synthesizing preauthored narrative with dynamic user interaction. Existing IS prototypes employ different modes to involve users in a story, ranging from individual avatar control to comprehensive control over the virtual

Public Involvement in Repository Site Selection for Nuclear Waste: Towards a more Dynamic View in Decision-Making Processes

Energy Technology Data Exchange (ETDEWEB)

Kruetli, Pius; Stauffacher, Michael; Flueeler, Thomas; Scholz, Roland W. [ETH Zuerich (Switzerland). lnst. for Human-Environment Systems (HES)

2006-09-15

This paper discusses possibilities of public involvement in radioactive waste management. A general overview of the radioactive waste issue is presented referring to a proposed model of the respective decision-making process. Based on the well known participation ladder by Arnstein, we differentiate various intensities of public involvement. A matrix with public involvement and the decision-making process is introduced and three prototypical patterns are discussed. We conclude that time frame, the level of public involvement and the mission have to be considered as well as techniques and the overarching context - all in all, a systematic and dynamic approach for public involvement is needed.

Public Involvement in Repository Site Selection for Nuclear Waste: Towards a more Dynamic View in Decision-Making Processes

International Nuclear Information System (INIS)

Kruetli, Pius; Stauffacher, Michael; Flueeler, Thomas; Scholz, Roland W.

2006-01-01

This paper discusses possibilities of public involvement in radioactive waste management. A general overview of the radioactive waste issue is presented referring to a proposed model of the respective decision-making process. Based on the well known participation ladder by Arnstein, we differentiate various intensities of public involvement. A matrix with public involvement and the decision-making process is introduced and three prototypical patterns are discussed. We conclude that time frame, the level of public involvement and the mission have to be considered as well as techniques and the overarching context - all in all, a systematic and dynamic approach for public involvement is needed

Simulation of Quantum Many-Body Dynamics for Generic Strongly-Interacting Systems

Science.gov (United States)

Meyer, Gregory; Machado, Francisco; Yao, Norman

2017-04-01

Recent experimental advances have enabled the bottom-up assembly of complex, strongly interacting quantum many-body systems from individual atoms, ions, molecules and photons. These advances open the door to studying dynamics in isolated quantum systems as well as the possibility of realizing novel out-of-equilibrium phases of matter. Numerical studies provide insight into these systems; however, computational time and memory usage limit common numerical methods such as exact diagonalization to relatively small Hilbert spaces of dimension 215 . Here we present progress toward a new software package for dynamical time evolution of large generic quantum systems on massively parallel computing architectures. By projecting large sparse Hamiltonians into a much smaller Krylov subspace, we are able to compute the evolution of strongly interacting systems with Hilbert space dimension nearing 230. We discuss and benchmark different design implementations, such as matrix-free methods and GPU based calculations, using both pre-thermal time crystals and the Sachdev-Ye-Kitaev model as examples. We also include a simple symbolic language to describe generic Hamiltonians, allowing simulation of diverse quantum systems without any modification of the underlying C and Fortran code.

Interaction Involvement in Cross-Culture Computer-Mediated Communication: Examination of a Communication Process in Dyadic Instant Messaging Conversations

Science.gov (United States)

Nguyen, Thi Thao Duyen

2013-01-01

This dissertation explores how participants express and interpret verbal cues of interaction involvement in dyadic conversations via text-based Instant Messaging (IM). Moreover, it seeks to discover differences in the way American participants and Chinese participants use verbal cues when they are highly, or lowly involved. Based on previous…

Surface dynamics in allosteric regulation of protein-protein interactions: modulation of calmodulin functions by Ca2+.

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Yosef Y Kuttner

2013-04-01

Full Text Available Knowledge of the structural basis of protein-protein interactions (PPI is of fundamental importance for understanding the organization and functioning of biological networks and advancing the design of therapeutics which target PPI. Allosteric modulators play an important role in regulating such interactions by binding at site(s orthogonal to the complex interface and altering the protein's propensity for complex formation. In this work, we apply an approach recently developed by us for analyzing protein surfaces based on steered molecular dynamics simulation (SMD to the study of the dynamic properties of functionally distinct conformations of a model protein, calmodulin (CaM, whose ability to interact with target proteins is regulated by the presence of the allosteric modulator Ca(2+. Calmodulin is a regulatory protein that acts as an intracellular Ca(2+ sensor to control a wide variety of cellular processes. We demonstrate that SMD analysis is capable of pinpointing CaM surfaces implicated in the recognition of both the allosteric modulator Ca(2+ and target proteins. Our analysis of changes in the dynamic properties of the CaM backbone elicited by Ca(2+ binding yielded new insights into the molecular mechanism of allosteric regulation of CaM-target interactions.

Dynamic interactions between dermal macrophages and Staphylococcus aureus.

Science.gov (United States)

Feuerstein, Reinhild; Kolter, Julia; Henneke, Philipp

2017-01-01

The dermis, a major reservoir of immune cells in immediate vicinity to the colonizing skin microflora, serves as an important site of host-pathogen interactions. Macrophages (Mϕ) are the most frequent resident immune cell type in the dermis. They protect the host from invasive infections by highly adapted bacteria, such as staphylococci via pattern recognition of bacterial effectors, phagocytosis, and recruitment of other myeloid cells from the blood. Already under homeostatic conditions, the dermal Mϕ population receives a dynamic input of monocytes invading from the bloodstream. This quantitative renewal is promoted further at the beginning of life, when prenatally seeded cells are rapidly replaced and in healing phases after injuries or infections. Here, we discuss the potential implications of the dynamic dermal Mϕ biology on the establishment and maintenance of immunity against Staphylococcus aureus, which can either be a harmless colonizer or an invasive pathogen. The understanding of the heterogeneity of the "mature" dermal Mϕ compartment driven both by the influx of differentiating monocytes and by a bone marrow-independent Mϕ persistence and expansion may help to explain failing immunity and immunopathology originating from the skin, the important interface between host and environment. © Society for Leukocyte Biology.

Structure, dynamics, and interaction of Mycobacterium tuberculosis (Mtb DprE1 and DprE2 examined by molecular modeling, simulation, and electrostatic studies.

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Isha Bhutani

Full Text Available The enzymes decaprenylphosphoryl-β-D-ribose oxidase (DprE1 and decaprenylphosphoryl-β-D-ribose-2-epimerase (DprE2 catalyze epimerization of decaprenylphosporyl ribose (DPR todecaprenylphosporyl arabinose (DPA and are critical for the survival of Mtb. Crystal structures of DprE1 so far reported display significant disordered regions and no structural information is known for DprE2. We used homology modeling, protein threading, molecular docking and dynamics studies to investigate the structural and dynamic features of Mtb DprE1 and DprE2 and DprE1-DprE2 complex. A three-dimensional model for DprE2 was generated using the threading approach coupled with ab initio modeling. A 50 ns simulation of DprE1 and DprE2 revealed the overall stability of the structures. Principal Component Analysis (PCA demonstrated the convergence of sampling in both DprE1 and DprE2. In DprE1, residues in the 269-330 area showed considerable fluctuation in agreement with the regions of disorder observed in the reported crystal structures. In DprE2, large fluctuations were detected in residues 95-113, 146-157, and 197-226. The study combined docking and MD simulation studies to map and characterize the key residues involved in DprE1-DprE2 interaction. A 60 ns MD simulation for DprE1-DprE2 complex was also performed. Analysis of data revealed that the docked complex is stabilized by H-bonding, hydrophobic and ionic interactions. The key residues of DprE1 involved in DprE1-DprE2 interactions belong to the disordered region. We also examined the docked complex of DprE1-BTZ043 to investigate the binding pocket of DprE1 and its interactions with the inhibitor BTZ043. In summary, we hypothesize that DprE1-DprE2 interaction is crucial for the synthesis of DPA and DprE1-DprE2 complex may be a new therapeutic target amenable to pharmacological validation. The findings have important implications in tuberculosis (TB drug discovery and will facilitate drug development efforts against

Mass spectrometry in structural biology and biophysics architecture, dynamics, and interaction of biomolecules

CERN Document Server

Kaltashov, Igor A; Desiderio, Dominic M; Nibbering, Nico M

2012-01-01

The definitive guide to mass spectrometry techniques in biology and biophysics The use of mass spectrometry (MS) to study the architecture and dynamics of proteins is increasingly common within the biophysical community, and Mass Spectrometry in Structural Biology and Biophysics: Architecture, Dynamics, and Interaction of Biomolecules, Second Edition provides readers with detailed, systematic coverage of the current state of the art. Offering an unrivalled overview of modern MS-based armamentarium that can be used to solve the most challenging problems in biophysics, structural biol

Constrained dynamics of two interacting relativistic particles in the Faddeev-Jackiw symplectic framework

Science.gov (United States)

Rodríguez-Tzompantzi, Omar

2018-05-01

The Faddeev-Jackiw symplectic formalism for constrained systems is applied to analyze the dynamical content of a model describing two massive relativistic particles with interaction, which can also be interpreted as a bigravity model in one dimension. We systematically investigate the nature of the physical constraints, for which we also determine the zero-modes structure of the corresponding symplectic matrix. After identifying the whole set of constraints, we find out the transformation laws for all the set of dynamical variables corresponding to gauge symmetries, encoded in the remaining zero modes. In addition, we use an appropriate gauge-fixing procedure, the conformal gauge, to compute the quantization brackets (Faddeev-Jackiw brackets) and also obtain the number of physical degree of freedom. Finally, we argue that this symplectic approach can be helpful for assessing physical constraints and understanding the gauge structure of theories of interacting spin-2 fields.

Quasispecies dynamics on a network of interacting genotypes and idiotypes: formulation of the model

Science.gov (United States)

Barbosa, Valmir C.; Donangelo, Raul; Souza, Sergio R.

2015-01-01

A quasispecies is the stationary state of a set of interrelated genotypes that evolve according to the usual principles of selection and mutation. Quasispecies studies have for the most part concentrated on the possibility of errors during genotype replication and their role in promoting either the survival or the demise of the quasispecies. In a previous work, we introduced a network model of quasispecies dynamics, based on a single probability parameter (p) and capable of addressing several plausibility issues of previous models. Here we extend that model by pairing its network with another one aimed at modeling the dynamics of the immune system when confronted with the quasispecies. The new network is based on the idiotypic-network model of immunity and, together with the previous one, constitutes a network model of interacting genotypes and idiotypes. The resulting model requires further parameters and as a consequence leads to a vast phase space. We have focused on a particular niche in which it is possible to observe the trade-offs involved in the quasispecies' survival or destruction. Within this niche, we give simulation results that highlight some key preconditions for quasispecies survival. These include a minimum initial abundance of genotypes relative to that of the idiotypes and a minimum value of p. The latter, in particular, is to be contrasted with the stand-alone quasispecies network of our previous work, in which arbitrarily low values of p constitute a guarantee of quasispecies survival.

A molecular dynamics study on the interaction between epoxy and functionalized graphene sheets

DEFF Research Database (Denmark)

Melro, Liliana Sofia S. F. P.; Pyrz, Ryszard; Jensen, Lars Rosgaard

2016-01-01

The interaction between graphene and epoxy resin was studied using molecular dynamics simulations. The interfacial shear strength and pull out force were calculated for functionalised graphene layers (carboxyl, carbonyl, and hydroxyl) and epoxy composites interfaces. The influence of functional...... groups, as well as their distribution and coverage density on the graphene sheets were also analysed through the determination of the Young's modulus. Functionalisation proved to be detrimental to the mechanical properties, nonetheless according to interfacial studies the interaction between graphene...

Dynamical Integration of Language and Behavior in a Recurrent Neural Network for Human--Robot Interaction

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Tatsuro Yamada

2016-07-01

Full Text Available To work cooperatively with humans by using language, robots must not only acquire a mapping between language and their behavior but also autonomously utilize the mapping in appropriate contexts of interactive tasks online. To this end, we propose a novel learning method linking language to robot behavior by means of a recurrent neural network. In this method, the network learns from correct examples of the imposed task that are given not as explicitly separated sets of language and behavior but as sequential data constructed from the actual temporal flow of the task. By doing this, the internal dynamics of the network models both language--behavior relationships and the temporal patterns of interaction. Here, ``internal dynamics'' refers to the time development of the system defined on the fixed-dimensional space of the internal states of the context layer. Thus, in the execution phase, by constantly representing where in the interaction context it is as its current state, the network autonomously switches between recognition and generation phases without any explicit signs and utilizes the acquired mapping in appropriate contexts. To evaluate our method, we conducted an experiment in which a robot generates appropriate behavior responding to a human's linguistic instruction. After learning, the network actually formed the attractor structure representing both language--behavior relationships and the task's temporal pattern in its internal dynamics. In the dynamics, language--behavior mapping was achieved by the branching structure. Repetition of human's instruction and robot's behavioral response was represented as the cyclic structure, and besides, waiting to a subsequent instruction was represented as the fixed-point attractor. Thanks to this structure, the robot was able to interact online with a human concerning the given task by autonomously switching phases.

Dynamical Integration of Language and Behavior in a Recurrent Neural Network for Human-Robot Interaction.

Science.gov (United States)

Yamada, Tatsuro; Murata, Shingo; Arie, Hiroaki; Ogata, Tetsuya

2016-01-01

To work cooperatively with humans by using language, robots must not only acquire a mapping between language and their behavior but also autonomously utilize the mapping in appropriate contexts of interactive tasks online. To this end, we propose a novel learning method linking language to robot behavior by means of a recurrent neural network. In this method, the network learns from correct examples of the imposed task that are given not as explicitly separated sets of language and behavior but as sequential data constructed from the actual temporal flow of the task. By doing this, the internal dynamics of the network models both language-behavior relationships and the temporal patterns of interaction. Here, "internal dynamics" refers to the time development of the system defined on the fixed-dimensional space of the internal states of the context layer. Thus, in the execution phase, by constantly representing where in the interaction context it is as its current state, the network autonomously switches between recognition and generation phases without any explicit signs and utilizes the acquired mapping in appropriate contexts. To evaluate our method, we conducted an experiment in which a robot generates appropriate behavior responding to a human's linguistic instruction. After learning, the network actually formed the attractor structure representing both language-behavior relationships and the task's temporal pattern in its internal dynamics. In the dynamics, language-behavior mapping was achieved by the branching structure. Repetition of human's instruction and robot's behavioral response was represented as the cyclic structure, and besides, waiting to a subsequent instruction was represented as the fixed-point attractor. Thanks to this structure, the robot was able to interact online with a human concerning the given task by autonomously switching phases.

On the molecular dynamics in the hurricane interactions with its environment

Science.gov (United States)

Meyer, Gabriel; Vitiello, Giuseppe

2018-06-01

By resorting to the Burgers model for hurricanes, we study the molecular motion involved in the hurricane dynamics. We show that the Lagrangian canonical formalism requires the inclusion of the environment degrees of freedom. This also allows the description of the motion of charged particles. In view of the role played by moist convection, cumulus and cloud water droplets in the hurricane dynamics, we discuss on the basis of symmetry considerations the role played by the molecular electrical dipoles and the formation of topologically non-trivial structures. The mechanism of energy storage and dissipation, the non-stationary time dependent Ginzburg-Landau equation and the vortex equation are studied. Finally, we discuss the fractal self-similarity properties of hurricanes.

Spatial Attention and Audiovisual Interactions in Apparent Motion

Science.gov (United States)

Sanabria, Daniel; Soto-Faraco, Salvador; Spence, Charles

2007-01-01

In this study, the authors combined the cross-modal dynamic capture task (involving the horizontal apparent movement of visual and auditory stimuli) with spatial cuing in the vertical dimension to investigate the role of spatial attention in cross-modal interactions during motion perception. Spatial attention was manipulated endogenously, either…

Effects of profile wear on wheel–rail contact conditions and dynamic interaction of vehicle and turnout

Directory of Open Access Journals (Sweden)

Jingmang Xu

2016-01-01

Full Text Available Severe wear is a common damage mechanism in railway turnouts, which strongly affects the dynamic performance of railway vehicles and maintenance costs of tracks. This article explores the effects of profile wear on contact behaviors in the wheel–rail/switch contact and dynamic interaction, and nominal and measured worn turnout rail profiles are used as boundary conditions of wheel–rail contact. The calculation of the dynamic loads and the resultant contact stresses and internal stresses makes it possible to rationally design railway turnouts and correctly select the material to be applied for their components. For these reasons, the multi-body system SIMPACK and finite element software ANSYS are used to calculate the features of load and subsequently distributions of contact stresses and internal stresses in the regions of wheel–turnout components. The results show that profile wear disturbs the distribution of wheel–rail contact point pairs, changes the positions of wheel–rail contact points along the longitudinal direction, and affects the dynamic interaction of vehicle and turnout. For the measured profile in this article, profile wear aggravates vertical dynamic responses significantly but improves lateral dynamic responses. Profile wear disturbs the normal contact situations between the wheel and switch rail and worsens the stress state of the switch rail.

Electron beam interaction with space plasmas

International Nuclear Information System (INIS)

Krafft, C.; Volokitin, A.S.

1999-01-01

Active space experiments involving the controlled injection of electron beams and the formation of artificially generated currents can provide in many cases a calibration of natural phenomena connected with the dynamic interaction of charged particles with fields. They have a long history beginning from the launches of small rockets with electron guns in order to map magnetic fields lines in the Earth's magnetosphere or to excite artificial auroras. Moreover, natural beams of charged particles exist in many space and astrophysical plasmas and were identified in situ by several satellites; a few examples are beams connected with solar bursts, planetary foreshocks or suprathermal fluxes traveling in planetary magnetospheres. Many experimental and theoretical works have been performed in order to interpret or plan space experiments involving beam injection as well as to understand the physics of wave-particle interaction, as wave radiation, beam dynamics and background plasma modification. Recently, theoretical studies of the nonlinear evolution of a thin monoenergetic electron beam injected in a magnetized plasma and interacting with a whistler wave packet have led to new results. The influence of an effective dissipation process connected with whistler wave field leakage out of the beam volume to infinity (that is, effective radiation outside the beam) on the nonlinear evolution of beam electrons distribution in phase space has been studied under conditions relevant to active space experiments and related laboratory modelling. The beam-waves system's evolution reveals the formation of stable nonlinear structures continuously decelerated due to the effective friction imposed by the strongly dissipated waves. The nonlinear interaction between the electron bunches and the wave packet are discussed in terms of dynamic energy exchange, particle trapping, slowing down of the beam, wave dissipation and quasi-linear diffusion. (author)

Dynamically analyzing cell interactions in biological environments using multiagent social learning framework.

Science.gov (United States)

Zhang, Chengwei; Li, Xiaohong; Li, Shuxin; Feng, Zhiyong

2017-09-20

Biological environment is uncertain and its dynamic is similar to the multiagent environment, thus the research results of the multiagent system area can provide valuable insights to the understanding of biology and are of great significance for the study of biology. Learning in a multiagent environment is highly dynamic since the environment is not stationary anymore and each agent's behavior changes adaptively in response to other coexisting learners, and vice versa. The dynamics becomes more unpredictable when we move from fixed-agent interaction environments to multiagent social learning framework. Analytical understanding of the underlying dynamics is important and challenging. In this work, we present a social learning framework with homogeneous learners (e.g., Policy Hill Climbing (PHC) learners), and model the behavior of players in the social learning framework as a hybrid dynamical system. By analyzing the dynamical system, we obtain some conditions about convergence or non-convergence. We experimentally verify the predictive power of our model using a number of representative games. Experimental results confirm the theoretical analysis. Under multiagent social learning framework, we modeled the behavior of agent in biologic environment, and theoretically analyzed the dynamics of the model. We present some sufficient conditions about convergence or non-convergence and prove them theoretically. It can be used to predict the convergence of the system.

Hamiltonian aspects of three-wave resonant interactions in gas dynamics

Science.gov (United States)

Webb, G. M.; Zakharian, A.; Brio, M.; Zank, G. P.

1997-06-01

Equations describing three-wave resonant interactions in adiabatic gas dynamics in one Cartesian space dimension derived by Majda and Rosales are expressed in terms of Lagrangian and Hamiltonian variational principles. The equations consist of two coupled integro-differential Burgers equations for the backward and forward sound waves that are coupled by integral terms that describe the resonant reflection of a sound wave off an entropy wave disturbance to produce a reverse sound wave. Similarity solutions and conservation laws for the equations are derived using symmetry group methods for the special case where the entropy disturbance consists of a periodic saw-tooth profile. The solutions are used to illustrate the interplay between the nonlinearity represented by the Burgers self-wave interaction terms and wave dispersion represented by the three-wave resonant interaction terms. Hamiltonian equations in Fourier (p,t) space are also obtained where p is the Fourier space variable corresponding to the fast phase variable 0305-4470/30/12/013/img6 of the waves. The latter equations are transformed to normal form in order to isolate the normal modes of the system.

Models test on dynamic structure-structure interaction of nuclear power plant buildings

International Nuclear Information System (INIS)

Kitada, Y.; Hirotani, T.

1999-01-01

A reactor building of an NPP (nuclear power plant) is generally constructed closely adjacent to a turbine building and other buildings such as the auxiliary building, and in increasing numbers of NPPs, multiple plants are being planned and constructed closely on a single site. In these situations, adjacent buildings are considered to influence each other through the soil during earthquakes and to exhibit dynamic behaviour different from that of separate buildings, because those buildings in NPP are generally heavy and massive. The dynamic interaction between buildings during earthquake through the soil is termed here as 'dynamic cross interaction (DCI)'. In order to comprehend DCI appropriately, forced vibration tests and earthquake observation are needed using closely constructed building models. Standing on this background, Nuclear Power Engineering Corporation (NUPEC) had planned the project to investigate the DCI effect in 1993 after the preceding SSI (soil-structure interaction) investigation project, 'model tests on embedment effect of reactor building'. The project consists of field and laboratory tests. The field test is being carried out using three different building construction conditions, e.g. a single reactor building to be used for the comparison purposes as for a reference, two same reactor buildings used to evaluate pure DCI effects, and two different buildings, reactor and turbine building models to evaluate DCI effects under the actual plant conditions. Forced vibration tests and earthquake observations are planned in the field test. The laboratory test is planned to evaluate basic characteristics of the DCI effects using simple soil model made of silicon rubber and structure models made of aluminum. In this test, forced vibration tests and shaking table tests are planned. The project was started in April 1994 and will be completed in March 2002. This paper describes an outline and the summary of the current status of this project. (orig.)

Dynamic characteristics of Semi-active Hydraulic Engine Mount Based on Fluid-Structure Interaction FEA

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Tian Jiande

2015-01-01

Full Text Available A kind of semi-active hydraulic engine mount is studied in this paper. After careful analysis of its structure and working principle, the FEA simulation of it was divided into two cases. One is the solenoid valve is open, so the air chamber connects to the atmosphere, and Fluid-Structure Interaction was used. Another is the solenoid valve is closed, and the air chamber has pressure, so Fluid-Structure-Gas Interaction was used. The test of this semi-active hydraulic engine mount was carried out to compare with the simulation results, and verify the accuracy of the model. Then the dynamic characteristics-dynamic stiffness and damping angle were analysed by simulation and test. This paper provides theoretical support for the development and optimization of the semi-active hydraulic engine mount.

The effect of tube-support interaction on the dynamic response of heat exchanger tubes

International Nuclear Information System (INIS)

Shin, Y.S.; Jendrzejczyk, J.A.; Wambsganss, M.W.

1977-01-01

To avoid detrimental tube vibration in heat exchangers, resonant conditions and instabilitites must be avoided, and/or peak dynamic amplitudes must not exceed allowable limits. In attempting a theoretical analysis, questions arise as to the effects of tube/support interaction on tube vibrational characteristics (i.e. resonant frequencies, modes, damping) and response amplitude. As a part of ANL's Flow-Induced Vibration Program in support of the Clinch River Breeder Reactor Plant (CRBRP) steam generator design activity, tube/support interaction experiments are being performed not only to gain the insight into the dynamic behavior of CRBRP steam generator tubes, but also to provide the basis for developing design guidance. Test results were compared with anaytical results based on multispan tube with 'knife-edge' supports at the support locations. (Auth.)

Fault Diagnosis in Dynamic Systems Using Fuzzy Interacting Observers

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N. V. Kolesov

2013-01-01

Full Text Available A method of fault diagnosis in dynamic systems based on a fuzzy approach is proposed. The new method possesses two basic specific features which distinguish it from the other known fuzzy methods based on the application of fuzzy logic and a bank of state observers. First, this method uses a bank of interacting observers instead of traditional independent observers. The second specific feature of the proposed method is the assumption that there is no strict boundary between the serviceable and disabled technical states of the system, which makes it possible to specify a decision making rule for fault diagnosis.

ALS mutant SOD1 interacts with G3BP1 and affects stress granule dynamics.

Science.gov (United States)

Gal, Jozsef; Kuang, Lisha; Barnett, Kelly R; Zhu, Brian Z; Shissler, Susannah C; Korotkov, Konstantin V; Hayward, Lawrence J; Kasarskis, Edward J; Zhu, Haining

2016-10-01

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease. Mutations in Cu/Zn superoxide dismutase (SOD1) are responsible for approximately 20 % of the familial ALS cases. ALS-causing SOD1 mutants display a gain-of-toxicity phenotype, but the nature of this toxicity is still not fully understood. The Ras GTPase-activating protein-binding protein G3BP1 plays a critical role in stress granule dynamics. Alterations in the dynamics of stress granules have been reported in several other forms of ALS unrelated to SOD1. To our surprise, the mutant G93A SOD1 transgenic mice exhibited pathological cytoplasmic inclusions that co-localized with G3BP1-positive granules in spinal cord motor neurons. The co-localization was also observed in fibroblast cells derived from familial ALS patient carrying SOD1 mutation L144F. Mutant SOD1, unlike wild-type SOD1, interacted with G3BP1 in an RNA-independent manner. Moreover, the interaction is specific for G3BP1 since mutant SOD1 showed little interaction with four other RNA-binding proteins implicated in ALS. The RNA-binding RRM domain of G3BP1 and two particular phenylalanine residues (F380 and F382) are critical for this interaction. Mutant SOD1 delayed the formation of G3BP1- and TIA1-positive stress granules in response to hyperosmolar shock and arsenite treatment in N2A cells. In summary, the aberrant mutant SOD1-G3BP1 interaction affects stress granule dynamics, suggesting a potential link between pathogenic SOD1 mutations and RNA metabolism alterations in ALS.

Dynamically induced spin-dependent interaction in the elastic scattering of heavy-ions

International Nuclear Information System (INIS)

Imanishi, B.; Oertzen, W. von.

1982-02-01

Dynamical polarization effect in heavy-ion elastic scattering is investigated in the framework of the coupled-reaction-channel theory. By using the adiabatic approximation at low incident energies, this effect is expressed as a spin-orbit (L vector.S vector) interaction with a L vector and S vector independent radial function. The strength of the (L vector.S vector) interaction calculated for the 12 C + 13 C system is in the same order of magnitude as deduced from experiments and is about two orders of magnitude larger than that obtained from the folding model calculation. (author)

Modelling and simulation of dynamic wheel-rail interaction using a roller rig

International Nuclear Information System (INIS)

Anyakwo, A; Pislaru, C; Ball, A; Gu, F

2012-01-01

The interaction between the wheel and rail greatly influences the dynamic response of railway vehicles on the track. A roller rig facility can be used to study and monitor real time parameters that influence wheel-rail interaction such as wear, adhesion, friction and corrugation without actual field tests being carried out. This paper presents the development of the mathematical models for full scale roller rig and 1/5 scale roller rig and the wear prediction model based on KTH wear function. The simulated critical speed for the 1/5 scale roller rig is about one-fifth of the critical speed for the full scale model so the simulated results compare well with the theory related to wheel-rail contact and dynamics. Also the differences between the simulated rolling radii for the full scale model with and without wear function are analysed. This paper presents the initial stage of a large scale research project where the influence of wear on the wheel-rail performance will be studied in more depth.

Approximating Model Equivalence in Interactive Dynamic Influence Diagrams Using Top K Policy Paths

DEFF Research Database (Denmark)

Zeng, Y.; Chen, Y.; Doshi, Prashant

2011-01-01

Interactive dynamic influence diagrams (I-DIDs) are graphical models for sequential decision making in uncertain settings shared by other agents. Algorithms for solving I-DIDs face the challenge of an exponentially growing space of behavioral models ascribed to other agents over time. Previous ap...

Interaction involving the thymus and the hypothalamus-pituitary axis, immunomodulation by hormones

Directory of Open Access Journals (Sweden)

Marković Ljiljana 2

2004-01-01

Full Text Available Perfectly projected and impeccably created, the endocrine system precisely regulates the most delicate immune processes. The immune and neuroendocrine systems are two essential physiological components of mammalian organisms important for protection from the infection and disease on one hand, and on the other, for regulation of metabolism and other physiological activities; namely, the evidence has been found indicating that there is active and dynamic collaboration of these systems in the execution of their designated functions [1, 2,4]. These interactions occur at many stages of embryonic and neonatal development, and they are a continual part of normal homeostatic balance necessary to preserve health. There is communication between neuroendocrine and immune system via cytokines, neurotransmitters and peptide hormones which act, in both systems, through the same receptor molecules (Scheme 1. Many investigators have reported the increased thymic weight in experimental animals due to both castration and adrenalectomy [4]. The discovery from 1898 revealing that thymus was enlarged in castrated rabbits has been considered the embryo of hybrid medical discipline, i.e. the immunoendocrinology [1]. In the actual literature, at least in that available to us, it has not been noted that the appearance of the eunuchs, i.e. the castrates, stimulated the analytical approach to this phenomenon. Endocrine influences appear to be a part of bidirectional circuitry, namely, thymic hormones also regulate the release of hormones from the pituitary gland. Physiologically, thymus is under neuroendocrine control. It is apparent that the circulating levels of distinct peptide hormones are necessary to maintain a series of biological functions related both to micro environmental and lymphoid cells of the organ. The neuroendocrine control of the thymus appears to be extremely complex, with apparent presence of complete intrathymic biological circuitry involving the

Secretomics identifies Fusarium graminearum proteins involved in the interaction with barley and wheat

DEFF Research Database (Denmark)

Yang, Fen; Jensen, Jens D.; Svensson, Birte

2012-01-01

Fusarium graminearum is a phytopathogenic fungus primarily infecting small grain cereals, including barley and wheat. Secreted enzymes play important roles in the pathogenicity of many fungi. In order to access the secretome of F. graminearum, the fungus was grown in liquid culture with barley...... or wheat flour as the sole nutrient source to mimic the host–pathogen interaction. A gel‐based proteomics approach was employed to identify the proteins secreted into the culture medium. Sixty‐nine unique fungal proteins were identified in 154 protein spots, including enzymes involved in the degradation...... between wheat and barley flour medium were mainly involved in fungal cell wall remodelling and the degradation of plant cell walls, starch and proteins. The in planta expression of corresponding F. graminearum genes was confirmed by quantitative reverse transcriptase‐polymerase chain reaction in barley...

Asp30 of Aspergillus oryzae cutinase CutL1 is involved in the ionic interaction with fungal hydrophobin RolA.

Science.gov (United States)

Terauchi, Yuki; Kim, Yoon-Kyung; Tanaka, Takumi; Nanatani, Kei; Takahashi, Toru; Abe, Keietsu

2017-07-01

Aspergillus oryzae hydrophobin RolA adheres to the biodegradable polyester polybutylene succinate-co-adipate (PBSA) and promotes PBSA degradation by interacting with A. oryzae polyesterase CutL1 and recruiting it to the PBSA surface. In our previous studies, we found that positively charged amino acid residues (H32, K34) of RolA and negatively charged residues (E31, D142, D171) of CutL1 are important for the cooperative ionic interaction between RolA and CutL1, but some other charged residues in the triple mutant CutL1-E31S/D142S/D171S are also involved. In the present study, on the basis of the 3D-structure of CutL1, we hypothesized that D30 is also involved in the CutL1-RolA interaction. We substituted D30 with serine and performed kinetic analysis of the interaction between wild-type RolA and the single mutant CutL1-D30S or quadruple mutant CutL1-D30S/E31S/D142S/D171S by using quartz crystal microbalance. Our results indicate that D30 is a novel residue involved in the ionic interaction between RolA and CutL1.

Nonlinear dynamics of semiconductors in strong THz electric fields

DEFF Research Database (Denmark)

Tarekegne, Abebe Tilahun

In this thesis, we investigate nonlinear interactions of an intense terahertz (THz) field with semiconductors, in particular the technologically relevant materials silicon and silicon carbide. We reveal the time-resolved dynamics of the nonlinear processes by pump-probe experiments that involve...

Discrete dynamic modeling of cellular signaling networks.

Science.gov (United States)

Albert, Réka; Wang, Rui-Sheng

2009-01-01

Understanding signal transduction in cellular systems is a central issue in systems biology. Numerous experiments from different laboratories generate an abundance of individual components and causal interactions mediating environmental and developmental signals. However, for many signal transduction systems there is insufficient information on the overall structure and the molecular mechanisms involved in the signaling network. Moreover, lack of kinetic and temporal information makes it difficult to construct quantitative models of signal transduction pathways. Discrete dynamic modeling, combined with network analysis, provides an effective way to integrate fragmentary knowledge of regulatory interactions into a predictive mathematical model which is able to describe the time evolution of the system without the requirement for kinetic parameters. This chapter introduces the fundamental concepts of discrete dynamic modeling, particularly focusing on Boolean dynamic models. We describe this method step-by-step in the context of cellular signaling networks. Several variants of Boolean dynamic models including threshold Boolean networks and piecewise linear systems are also covered, followed by two examples of successful application of discrete dynamic modeling in cell biology.

Molecular dynamics simulations of matrix assisted laser desorption ionization: Matrix-analyte interactions

International Nuclear Information System (INIS)

Nangia, Shivangi; Garrison, Barbara J.

2011-01-01

There is synergy between matrix assisted laser desorption ionization (MALDI) experiments and molecular dynamics (MD) simulations. To understand analyte ejection from the matrix, MD simulations have been employed. Prior calculations show that the ejected analyte molecules remain solvated by the matrix molecules in the ablated plume. In contrast, the experimental data show free analyte ions. The main idea of this work is that analyte molecule ejection may depend on the microscopic details of analyte interaction with the matrix. Intermolecular matrix-analyte interactions have been studied by focusing on 2,5-dihydroxybenzoic acid (DHB; matrix) and amino acids (AA; analyte) using Chemistry at HARvard Molecular Mechanics (CHARMM) force field. A series of AA molecules have been studied to analyze the DHB-AA interaction. A relative scale of AA molecule affinity towards DHB has been developed.

Arid landscape dynamics along a precipitation gradient: addressing vegetation - landscape structure - resource interactions at different time scales

NARCIS (Netherlands)

Buis, E.

2008-01-01

This research is entitled ‘Arid landscape dynamics along a precipitation gradient: addressing
vegetation – landscape structure – resource interactions at different time scales’ with as subtitle
‘A case study for the Northern Negev Desert of Israel’. Landscape dynamics describes the

A scalable double-barcode sequencing platform for characterization of dynamic protein-protein interactions.

Science.gov (United States)

Schlecht, Ulrich; Liu, Zhimin; Blundell, Jamie R; St Onge, Robert P; Levy, Sasha F

2017-05-25

Several large-scale efforts have systematically catalogued protein-protein interactions (PPIs) of a cell in a single environment. However, little is known about how the protein interactome changes across environmental perturbations. Current technologies, which assay one PPI at a time, are too low throughput to make it practical to study protein interactome dynamics. Here, we develop a highly parallel protein-protein interaction sequencing (PPiSeq) platform that uses a novel double barcoding system in conjunction with the dihydrofolate reductase protein-fragment complementation assay in Saccharomyces cerevisiae. PPiSeq detects PPIs at a rate that is on par with current assays and, in contrast with current methods, quantitatively scores PPIs with enough accuracy and sensitivity to detect changes across environments. Both PPI scoring and the bulk of strain construction can be performed with cell pools, making the assay scalable and easily reproduced across environments. PPiSeq is therefore a powerful new tool for large-scale investigations of dynamic PPIs.

Evolution of the interaction between Runx2 and VDR, two transcription factors involved in osteoblastogenesis

Directory of Open Access Journals (Sweden)

Barriga Elias H

2010-03-01

Full Text Available Abstract Background The mineralized skeleton is a major evolutionary novelty that has contributed to the impressive morphological diversifications of the vertebrates. Essential to bone biology is the solidified extracellular matrix secreted by highly specialized cells, the osteoblasts. We now have a rather complete view of the events underlying osteogenesis, from a cellular, molecular, genetic, and epigenetic perspective. Because this knowledge is still largely restricted to mammals, it is difficult, if not impossible, to deduce the evolutionary history of the regulatory network involved in osteoblasts specification and differentiation. In this study, we focused on the transcriptional regulators Runx2 and VDR (the Vitamin D Receptor that, in mammals, directly interact together and stabilize complexes of co-activators and chromatin remodellers, thereby allowing the transcriptional activation of target genes involved in extracellular matrix mineralization. Using a combination of functional, biochemical, and histological approaches, we have asked if the interaction observed between Runx2 and VDR represents a recent mammalian innovation, or if it results from more ancient changes that have occurred deep in the vertebrate lineage. Results Using immunohistochemistry and in situ hybridization in developing embryos of chick, frog and teleost fishes, we have revealed that the co-expression of Runx2 and VDR in skeletal elements has been particularly strengthened in the lineage leading to amniotes. We show that the teleost Runx2 orthologue as well as the three mammalian Runx1, Runx2 and Runx3 paralogues are able to co-immunoprecipitate with the VDR protein present in nuclear extracts of rat osteoblasts stimulated with 1α,25-dihydroxyvitamin D3. In addition, the teleost Runx2 can activate the transcription of the mammalian osteocalcin promoter in transfection experiments, and this response can be further enhanced by 1α,25-dihydroxyvitamin D3. Finally

User involvement in the design of human-computer interactions: some similarities and differences between design approaches

NARCIS (Netherlands)

Bekker, M.M.; Long, J.B.

1998-01-01

This paper presents a general review of user involvement in the design of human-computer interactions, as advocated by a selection of different approaches to design. The selection comprises User-Centred Design, Participatory Design, Socio-Technical Design, Soft Systems Methodology, and Joint

Single camera analyses in studying pattern forming dynamics of player interactions in team sports.

OpenAIRE

Duarte, Ricardo; Fernandes, Orlando; Folgado, Hugo; Araújo, Duarte

2013-01-01

A network of patterned interactions between players characterises team ball sports. Thus, interpersonal coordination patterns are an important topic in the study of performance in such sports. A very useful method has been the study of inter-individual interactions captured by a single camera filming an extended performance area. The appropriate collection of positional data allows investigating the pattern forming dynamics emerging in different performance sub-phases of team ball sports. Thi...

University Physics Students' Use of Models in Explanations of Phenomena Involving Interaction between Metals and Electromagnetic Radiation.

Science.gov (United States)

Redfors, Andreas; Ryder, Jim

2001-01-01

Examines third year university physics students' use of models when explaining familiar phenomena involving interaction between metals and electromagnetic radiation. Concludes that few students use a single model consistently. (Contains 27 references.) (DDR)

Dynamic changes in the interchromosomal interaction of early histone gene loci during development of sea urchin.

Science.gov (United States)

Matsushita, Masaya; Ochiai, Hiroshi; Suzuki, Ken-Ichi T; Hayashi, Sayaka; Yamamoto, Takashi; Awazu, Akinori; Sakamoto, Naoaki

2017-12-15

The nuclear positioning and chromatin dynamics of eukaryotic genes are closely related to the regulation of gene expression, but they have not been well examined during early development, which is accompanied by rapid cell cycle progression and dynamic changes in nuclear organization, such as nuclear size and chromatin constitution. In this study, we focused on the early development of the sea urchin Hemicentrotus pulcherrimus and performed three-dimensional fluorescence in situ hybridization of gene loci encoding early histones (one of the types of histone in sea urchin). There are two non-allelic early histone gene loci per sea urchin genome. We found that during the morula stage, when the early histone gene expression levels are at their maximum, interchromosomal interactions were often formed between the early histone gene loci on separate chromosomes and that the gene loci were directed to locate to more interior positions. Furthermore, these interactions were associated with the active transcription of the early histone genes. Thus, such dynamic interchromosomal interactions may contribute to the efficient synthesis of early histone mRNA during the morula stage of sea urchin development. © 2017. Published by The Company of Biologists Ltd.

Mutations in actin used for structural studies partially disrupt β-thymosin/WH2 domains interaction.

Science.gov (United States)

Deville, Célia; Girard-Blanc, Christine; Assrir, Nadine; Nhiri, Naïma; Jacquet, Eric; Bontems, François; Renault, Louis; Petres, Stéphane; van Heijenoort, Carine

2016-10-01

Understanding the structural basis of actin cytoskeleton remodeling requires stabilization of actin monomers, oligomers, and filaments in complex with partner proteins, using various biochemical strategies. Here, we report a dramatic destabilization of the dynamic interaction with a model β-thymosin/WH2 domain induced by mutations in actin. This result underlines that mutant actins should be used with prudence to characterize interactions with intrinsically disordered partners as destabilization of dynamic interactions, although identifiable by NMR, may be invisible to other structural techniques. It also highlights how both β-thymosin/WH2 domains and actin tune local structure and dynamics in regulatory processes involving intrinsically disordered domains. © 2016 Federation of European Biochemical Societies.

Geometrical Similarity Transformations in Dynamic Geometry Environment Geogebra

Science.gov (United States)

Andraphanova, Natalia V.

2015-01-01

The subject of the article is usage of modern computer technologies through the example of interactive geometry environment Geogebra as an innovative technology of representing and studying of geometrical material which involves such didactical opportunities as vizualisation, simulation and dynamics. There is shown a classification of geometric…

How interactions between animal movement and landscape processes modify range dynamics and extinction risk

Science.gov (United States)

Range dynamics models now incorporate many of the mechanisms and interactions that drive species distributions. However, connectivity continues to be studied using overly simple distance-based dispersal models with little consideration of how the individual behavior of dispersin...

Microscopic dynamics of plasmas and chaos: the wave-particle interaction paradigm

International Nuclear Information System (INIS)

Escande, D F; Elskens, Y

2003-01-01

The wave-particle interaction is central to microscopic plasma dynamics. A paradigm of such an interaction is one occurring during the weak warm beam-plasma instability: a Langmuir turbulence sets in and saturates by the formation of a plateau in the particle distribution function. A new approach permits us to deal with the regular and chaotic aspects of this problem using the classical mechanics of the corresponding N-body problem only. The classical Landau-van Kampen theory is recovered by using mathematical tools not more intricate than a finite Fourier sum. A single calculation yields spontaneous emission and the particle dynamics as well; classical explicative models of Landau damping are found to be misleading. Recent tools of Hamiltonian chaos enable us to derive the quasilinear equations in the regime of saturation of the instability. The calculations are readable by graduate students and provide a simple solution to a 20 year old controversy in the Vlasovian frame. As a result, the macroscopic irreversible evolution of a plasma is described by fully accounting for its microscopic reversible mechanics; for the first time, an old dream of the 19th century comes true: the irreversible evolution of an N-body problem is described by taking into account the true character of its chaotic motion

Adverse risk: a 'dynamic interaction model of patient moving and handling'.

Science.gov (United States)

Griffiths, Howard

2012-09-01

The aim of the present study was to examine patient adverse events associated with sub-optimal patient moving and handling. Few studies have examined the patient's perspective on adverse risk during manual handling episodes. A narrative review was undertaken to develop the 'Dynamic Interaction Model of Patient Moving and Handling' in an orthopaedic rehabilitation setting, using peer-reviewed publications published in English between 1992 and 2010. Five predominant themes emerged from the narrative review: 'patient's need to know about analgesics prior to movement/ambulation'; 'comfort care'; 'mastery of and acceptance of mobility aids/equipment'; 'psychological adjustment to fear of falling'; and 'the need for movement to prevent tissue pressure damage'. Prevalence of discomfort, pain, falls, pressure sores together with a specific Direct Instrument Nursing Observation (DINO) tool enable back care advisers to measure quality of patient manual handling. Evaluation of patients' use of mobility aids together with fear of falling may be important in determining patients' recovery trajectory. Clinical governance places a responsibility on nurse managers to consider quality of care for their service users. 'Dynamic Interaction Model of Nurse-Patient Moving and Handling' provides back care advisers, clinical risk managers and occupational health managers with an alternative perspective to clinical risk and occupational risk. © 2011 Blackwell Publishing Ltd.

Implicit flux-split Euler schemes for unsteady aerodynamic analysis involving unstructured dynamic meshes

Science.gov (United States)

Batina, John T.

1990-01-01

Improved algorithm for the solution of the time-dependent Euler equations are presented for unsteady aerodynamic analysis involving unstructured dynamic meshes. The improvements were developed recently to the spatial and temporal discretizations used by unstructured grid flow solvers. The spatial discretization involves a flux-split approach which is naturally dissipative and captures shock waves sharply with at most one grid point within the shock structure. The temporal discretization involves an implicit time-integration scheme using a Gauss-Seidel relaxation procedure which is computationally efficient for either steady or unsteady flow problems. For example, very large time steps may be used for rapid convergence to steady state, and the step size for unsteady cases may be selected for temporal accuracy rather than for numerical stability. Steady and unsteady flow results are presented for the NACA 0012 airfoil to demonstrate applications of the new Euler solvers. The unsteady results were obtained for the airfoil pitching harmonically about the quarter chord. The resulting instantaneous pressure distributions and lift and moment coefficients during a cycle of motion compare well with experimental data. A description of the Euler solvers is presented along with results and comparisons which assess the capability.

a System Dynamics Approach for Looking at the Human and Environmental Interactions of Community-Based Irrigation Systems in New Mexico

Science.gov (United States)

Ochoa, C. G.; Tidwell, V. C.

2012-12-01

In the arid southwestern United States community water management systems have adapted to cope with climate variability and with socio-cultural and economic changes that have occurred since the establishment of these systems more than 300 years ago. In New Mexico, the community-based irrigation systems were established by Spanish settlers and have endured climate variability in the form of low levels of precipitation and have prevailed over important socio-political changes including the transfer of territory between Spain and Mexico, and between Mexico and the United States. Because of their inherent nature of integrating land and water use with society involvement these community-based systems have multiple and complex economic, ecological, and cultural interactions. Current urban population growth and more variable climate conditions are adding pressure to the survival of these systems. We are conducting a multi-disciplinary research project that focuses on characterizing these intrinsically complex human and natural interactions in three community-based irrigation systems in northern New Mexico. We are using a system dynamics approach to integrate different hydrological, ecological, socio-cultural and economic aspects of these three irrigation systems. Coupled with intensive field data collection, we are building a system dynamics model that will enable us to simulate important linkages and interactions between environmental and human elements occurring in each of these water management systems. We will test different climate variability and population growth scenarios and the expectation is that we will be able to identify critical tipping points of these systems. Results from this model can be used to inform policy recommendations relevant to the environment and to urban and agricultural land use planning in the arid southwestern United States.

Individual-Environment Interactions in Swimming: The Smallest Unit for Analysing the Emergence of Coordination Dynamics in Performance?

Science.gov (United States)

Guignard, Brice; Rouard, Annie; Chollet, Didier; Hart, John; Davids, Keith; Seifert, Ludovic

2017-08-01

Displacement in competitive swimming is highly dependent on fluid characteristics, since athletes use these properties to propel themselves. It is essential for sport scientists and practitioners to clearly identify the interactions that emerge between each individual swimmer and properties of an aquatic environment. Traditionally, the two protagonists in these interactions have been studied separately. Determining the impact of each swimmer's movements on fluid flow, and vice versa, is a major challenge. Classic biomechanical research approaches have focused on swimmers' actions, decomposing stroke characteristics for analysis, without exploring perturbations to fluid flows. Conversely, fluid mechanics research has sought to record fluid behaviours, isolated from the constraints of competitive swimming environments (e.g. analyses in two-dimensions, fluid flows passively studied on mannequins or robot effectors). With improvements in technology, however, recent investigations have focused on the emergent circular couplings between swimmers' movements and fluid dynamics. Here, we provide insights into concepts and tools that can explain these on-going dynamic interactions in competitive swimming within the theoretical framework of ecological dynamics.

Chaotic dynamics of Heisenberg ferromagnetic spin chain with bilinear and biquadratic interactions

Science.gov (United States)

Blessy, B. S. Gnana; Latha, M. M.

2017-10-01

We investigate the chaotic dynamics of one dimensional Heisenberg ferromagnetic spin chain by constructing the Hamiltonian equations of motion. We present the trajectory and phase plots of the system with bilinear and also biquadratic interactions. The stability of the system is analysed in both cases by constructing the Jacobian matrix and by measuring the Lyapunov exponents. The results are illustrated graphically.

Evidence from lateral mobility studies for dynamic interactions of a mutant influenza hemagglutinin with coated pits.

Science.gov (United States)

Fire, E; Zwart, D E; Roth, M G; Henis, Y I

1991-12-01

with coated pits are dynamic, involving multiple entries of Tyr 543 molecules into and out of coated pits. (c) Alterations in the clathrin lattice structure can modulate the above interactions.

Fluid dynamic interaction between water hammer and centrifugal pumps

International Nuclear Information System (INIS)

Ismaier, A.; Schluecker, E.

2009-01-01

Centrifugal pumps generate in piping systems noticeable pressure pulsations. In this paper the dynamic interaction between water hammer and pressure pulsations is presented. The experimental investigations were performed at a piping system with nominal diameter DN 100 (respectively NPS 4) and 75 m total length, built at the Institute for Process Technology and Machinery. Different measurements at this testing facility show that pulsating centrifugal pumps can damp pressure surges generated by fast valve closing. It is also shown that 1-dimensional fluid codes can be used to calculate this phenomenon. Furthermore it is presented that pressure surges pass centrifugal pumps almost unhindered, because they are hydraulic open.

CMEIAS-Aided Microscopy of the Spatial Ecology of Individual Bacterial Interactions Involving Cell-to-Cell Communication within Biofilms

Directory of Open Access Journals (Sweden)

Frank B. Dazzo

2012-05-01

Full Text Available This paper describes how the quantitative analytical tools of CMEIAS image analysis software can be used to investigate in situ microbial interactions involving cell-to-cell communication within biofilms. Various spatial pattern analyses applied to the data extracted from the 2-dimensional coordinate positioning of individual bacterial cells at single-cell resolution indicate that microbial colonization within natural biofilms is not a spatially random process, but rather involves strong positive interactions between communicating cells that influence their neighbors’ aggregated colonization behavior. Geostatistical analysis of the data provide statistically defendable estimates of the micrometer scale and interpolation maps of the spatial heterogeneity and local intensity at which these microbial interactions autocorrelate with their spatial patterns of distribution. Including in situ image analysis in cell communication studies fills an important gap in understanding the spatially dependent microbial ecophysiology that governs the intensity of biofilm colonization and its unique architecture.

Photoinduced charge-order melting dynamics in a one-dimensional interacting Holstein model

Science.gov (United States)

Hashimoto, Hiroshi; Ishihara, Sumio

2017-07-01

Transient quantum dynamics in an interacting fermion-phonon system are investigated with a focus on a charge order (CO) melting after a short optical-pulse irradiation and the roles of the quantum phonons in the transient dynamics. A spinless-fermion model in a one-dimensional chain coupled with local phonons is analyzed numerically. The infinite time-evolving block decimation algorithm is adopted as a reliable numerical method for one-dimensional quantum many-body systems. Numerical results for the photoinduced CO melting dynamics without phonons are well interpreted by the soliton picture for the CO domains. This interpretation is confirmed by numerical simulation of an artificial local excitation and the classical soliton model. In the case of large phonon frequencies corresponding to the antiadiabatic condition, CO melting is induced by propagations of the polaronic solitons with the renormalized soliton velocity. On the other hand, in the case of small phonon frequencies corresponding to the adiabatic condition, the first stage of the CO melting dynamics occurs due to the energy transfer from the fermionic to phononic systems, and the second stage is brought about by the soliton motions around the bottom of the soliton band. The analyses provide a standard reference for photoinduced CO melting dynamics in one-dimensional many-body quantum systems.

Prediction of drug-packaging interactions via molecular dynamics (MD) simulations.

Science.gov (United States)

Feenstra, Peter; Brunsteiner, Michael; Khinast, Johannes

2012-07-15

The interaction between packaging materials and drug products is an important issue for the pharmaceutical industry, since during manufacturing, processing and storage a drug product is continuously exposed to various packaging materials. The experimental investigation of a great variety of different packaging material-drug product combinations in terms of efficacy and safety can be a costly and time-consuming task. In our work we used molecular dynamics (MD) simulations in order to evaluate the applicability of such methods to pre-screening of the packaging material-solute compatibility. The solvation free energy and the free energy of adsorption of diverse solute/solvent/solid systems were estimated. The results of our simulations agree with experimental values previously published in the literature, which indicates that the methods in question can be used to semi-quantitatively reproduce the solid-liquid interactions of the investigated systems. Copyright © 2012 Elsevier B.V. All rights reserved.

Accessing Wireless Sensor Networks Via Dynamically Reconfigurable Interaction Models

Directory of Open Access Journals (Sweden)

Maria Cecília Gomes

2012-12-01

Full Text Available The Wireless Sensor Networks (WSNs technology is already perceived as fundamental for science across many domains, since it provides a low cost solution for environment monitoring. WSNs representation via the service concept and its inclusion in Web environments, e.g. through Web services, supports particularly their open/standard access and integration. Although such Web enabled WSNs simplify data access, network parameterization and aggregation, the existing interaction models and run-time adaptation mechanisms available to clients are still scarce. Nevertheless, applications increasingly demand richer and more flexible accesses besides the traditional client/server. For instance, applications may require a streaming model in order to avoid sequential data requests, or the asynchronous notification of subscribed data through the publish/subscriber. Moreover, the possibility to automatically switch between such models at runtime allows applications to define flexible context-based data acquisition. To this extent, this paper discusses the relevance of the session and pattern abstractions on the design of a middleware prototype providing richer and dynamically reconfigurable interaction models to Web enabled WSNs.

An Atomic Force Microscopy Study of the Interactions Involving Polymers and Silane Networks

Directory of Open Access Journals (Sweden)

Rodrigo L. Oréfice

1998-12-01

Full Text Available ABSTRACT: Silane coupling agents have been frequently used as interfacial agents in polymer composites to improve interfacial strength and resistance to fluid migration. Although the capability of these agents in improving properties and performance of composites has been reported, there are still many uncertainties regarding the processing-structure-property relationships and the mechanisms of coupling developed by silane agents. In this work, an Atomic Force Microscope (AFM was used to measure interactions between polymers and silica substrates, where silane networks with a series of different structures were processed. The influence of the structure of silane networks on the interactions with polymers was studied and used to determine the mechanisms involved in the coupling phenomenon. The AFM results showed that phenomena such as chain penetration, entanglements, intersegment bonding, chain conformation in the vicinities of rigid surfaces were identified as being relevant for the overall processes of adhesion and adsorption of polymeric chains within a silane network. AFM adhesion curves showed that penetration of polymeric chains through a more open silane network can lead to higher levels of interactions between polymer and silane agents.

Dynamic analysis of a nuclear reactor with fluid-structure interaction

International Nuclear Information System (INIS)

Sigrist, Jean-Francois; Broc, Daniel; Laine, Christian

2007-01-01

The present paper is related to the dynamic (shock) analysis of a naval propulsion (on-board) reactor with fluid-structure interaction modelling. In a previous study, low frequency analysis has been performed; the present study deals with high frequency analysis, i.e. taking into account compressibility effects in the fluid medium. Elasto-acoustic coupling effects are studied and described in the industrial case. The coupled problem is formulated using the so-called (u, p, φ) formulation which yields symmetric matrices. A modal analysis is first performed on the fluid problem alone, then for the coupled fluid-structure problem in the following cases: (i) with incompressible fluid; (ii) with compressible fluid at standard pressure and temperature conditions; (iii) with compressible fluid at the operating pressure and temperature conditions. Elasto-coupling effects are then highlighted, in particular through the calculation of an elastic energy ratio. As a general conclusion, compressibility effects are proved significant in the dynamic response of the reactor in the high frequency range

Ab initio/interpolated quantum dynamics on coupled electronic states with full configuration interaction wave functions

International Nuclear Information System (INIS)

Thompson, K.; Martinez, T.J.

1999-01-01

We present a new approach to first-principles molecular dynamics that combines a general and flexible interpolation method with ab initio evaluation of the potential energy surface. This hybrid approach extends significantly the domain of applicability of ab initio molecular dynamics. Use of interpolation significantly reduces the computational effort associated with the dynamics over most of the time scale of interest, while regions where potential energy surfaces are difficult to interpolate, for example near conical intersections, are treated by direct solution of the electronic Schroedinger equation during the dynamics. We demonstrate the concept through application to the nonadiabatic dynamics of collisional electronic quenching of Li(2p). Full configuration interaction is used to describe the wave functions of the ground and excited electronic states. The hybrid approach agrees well with full ab initio multiple spawning dynamics, while being more than an order of magnitude faster. copyright 1999 American Institute of Physics

Influence of pile–soil interaction on the dynamic properties of offshore wind turbines supported by jacket foundations

DEFF Research Database (Denmark)

Yi, Jin-Hak; Kim, Sun-Bin; Yoon, Gil-Lim

2015-01-01

Monopiles are the most widely utilized foundation for offshore wind turbines (OWTs) in shallow waters. However, jacket-type foundations are being considered as one of the good alternatives to monopole foundations for relatively deep water in the range of 25–50 m of water depth. Jacket structures...... are conventionally used in the oil and gas industry. However, there are still several issues unsolved for utilization of jacket structures for OWTs including pile–soil-interaction (PSI) effects, dynamically stable design, installation, and so on. In this study,the effects of pile–soil interaction on the dynamic...

Dynamic-chemistry-aerosol modelling interaction: the ESCOMPTE 2001 experiment

International Nuclear Information System (INIS)

Cousin, F.

2004-09-01

After most pollution studies independently devoted to gases and aerosols, there now appears an urgent need to consider their interactions. In this view, an aerosol module has been implemented in the Meso-NH-C model to simulate two IOPs documented during the ESCOMPTE campaign which took place in the Marseille/Fos-Berre region in June-July 2001. First, modelled dynamic parameters (winds, temperatures, boundary layer thickness) and gaseous chemistry have been validated with measurements issued from the exhaustive ESCOMPTE database. Sensitivity analysis have also been performed using different gaseous emission inventories at various resolution. These simulations have illustrated the deep impact of both synoptic and local dynamics on observed ozone concentrations on June 24 (IOP2b) in the ESCOMPTE domain. Afterwards, the ORISAM aerosol module has been introduced into the Meso-NH-C model. Dynamics, gaseous chemistry and aerosol processes have thus been coupled on-line. The particulate pollution episode on June 24 (IOP2b) has been characterised through a satisfactory comparison, specially from sub-micron particles, between modelling and measurements at different representative stations in the domain. This study, with validation of the particulate emission inventory has also highlighted the need for future improvements, such as further characterisation of organic and inorganic aerosol species and consideration of coarse particles. Aerosol impact on gaseous chemistry has been preliminary approached in view of future development and modification to be given to the Meso-NH-C model. (author)

Dynamic and interactive web-based radiology teaching file using layer and javascript

International Nuclear Information System (INIS)

Park, Seong Ho; Han, Joon Koo; Lee, Kyoung Ho

1999-01-01

To improve the Web-based radiology teaching file by means of a dynamic and interactive interface using Layer and JavaScript. The radiology teaching file for medical students at the author's medical school was used. By mean of a digital camera, films were digitized and compressed to Joint Photographic Expert Group (JPEG) format. Layers which had arrows or lines pointing out lesions and anatomical structures were converted to transparent CompuServe Graphics Interchange Format (GIF). Basically, HyperText Mark-up Language (HTML) was used for each Web page. Using JavaScript, Layers were made to be overlapped with radiologic images at the user's request. Each case page consisted of radiologic images and texts for additional information and explanation. By moving the cursor or clicking onto key words, indicators pointing out corresponding lesions and anatomical structures were automatically shown on radiologic images. Although not compatible with some Web-browsers, a dynamic and interactive interface using Layer and JavaScript has little effect on the time needed for data transfer through a network, and is therefore an effective method of accessing radiologic images using the World-Wide Web and using these for teaching and learning

Parton fragmentation and string dynamics

International Nuclear Information System (INIS)

Andersson, B.; Gustafson, G.; Ingelman, G.; Sjoestrand, T.

1983-01-01

While much has been learned recently about quark and gluon interactions in the framework of perturbative Quantum Chromodynamics, the relation between calculated parton properties and observed hadron densities involves models where dynamics and jet empirical rules have to be combined. The purpose of this article is to describe a presently successful approach which is based on a cascade jet model using String dynamics. It can readily lead to Monte Carlo jet programmes of great use when analyzing data. Production processes in an iterative cascade approach, with tunneling in a constant force field, are reviewed. Expected differences between quark and gluon jets are discussed. Low transverse momentum phenomena are also reviewed with emphasis on hyperon polarization. In so far as this approach uses a fragmentation scheme based on String dynamics, it was deemed appropriate to also include under the same cover a special report on the Classical theory of relativistic Strings, seen as the classical limit of the Dual Resonance model. The Equations of motion and interaction among strings are presented. (orig.)

Involvement of two classes of binding sites in the interactions of cyclophilin B with peripheral blood T-lymphocytes.

Science.gov (United States)

Denys, A; Allain, F; Carpentier, M; Spik, G

1998-12-15

Cyclophilin B (CyPB) is a cyclosporin A (CsA)-binding protein, mainly associated with the secretory pathway, and is released in biological fluids. We recently reported that CyPB specifically binds to T-lymphocytes and promotes enhanced incorporation of CsA. The interactions with cellular binding sites involved, at least in part, the specific N-terminal extension of the protein. In this study, we intended to specify further the nature of the CyPB-binding sites on peripheral blood T-lymphocytes. We first provide evidence that the CyPB binding to heparin-Sepharose is prevented by soluble sulphated glycosaminoglycans (GAG), raising the interesting possibility that such interactions may occur on the T-cell surface. We then characterized CyPB binding to T-cell surface GAG and found that these interactions involved the N-terminal extension of CyPB, but not its conserved CsA-binding domain. In addition, we determined the presence of a second CyPB binding site, which we termed a type I site, in contrast with type II for GAG interactions. The two binding sites exhibit a similar affinity but the expression of the type I site was 3-fold lower. The conclusion that CyPB binding to the type I site is distinct from the interactions with GAG was based on the findings that it was (1) resistant to NaCl wash and GAG-degrading enzyme treatments, (2) reduced in the presence of CsA or cyclophilin C, and (3) unmodified in the presence of either the N-terminal peptide of CyPB or protamine. Finally, we showed that the type I binding sites were involved in an endocytosis process, supporting the hypothesis that they may correspond to a functional receptor for CyPB.

Kolmogorov's constant and local interactions

International Nuclear Information System (INIS)

Kraichnan, R.H.

1987-01-01

Suppose that all the wave-vector triad interactions that involve no wavenumber ratio that exceeds β are removed from the Navier--Stokes equation. Within a class of closures, the paradoxical effect is to enhance energy cascade through the Kolmogorov inertial range for 1<β<β/sub c/, where β/sub c/ may be as large as 8. This may have implications with regard to force-free structures in the true Navier--Stokes dynamics

Capacitance, charge dynamics, and electrolyte-surface interactions in functionalized carbide-derived carbon electrodes

Directory of Open Access Journals (Sweden)

Boris Dyatkin

2015-12-01

Full Text Available This study analyzed the dynamics of ionic liquid electrolyte inside of defunctionalized, hydrogenated, and aminated pores of carbide-derived carbon supercapacitor electrodes. The approach tailors surface functionalities and tunes nanoporous structures to decouple the influence of pore wall composition on capacitance, ionic resistance, and long-term cyclability. Quasi-elastic neutron scattering probes the self-diffusion properties and electrode-ion interactions of electrolyte molecules confined in functionalized pores. Room-temperature ionic liquid interactions in confined pores are strongest when the hydrogen-containing groups are present on the surface. This property translates into higher capacitance and greater ion transport through pores during electrochemical cycling. Unlike hydrogenated pores, aminated pores do not favorably interact with ionic liquid ions and, subsequently, are outperformed by defunctionalized surfaces.

Capacitance, charge dynamics, and electrolyte-surface interactions in functionalized carbide-derived carbon electrodes

Energy Technology Data Exchange (ETDEWEB)

Dyatkin, Boris; Mamontov, Eugene; Cook, Kevin M.; Gogotsi, Yury

2015-12-01

This study analyzed the dynamics of ionic liquid electrolyte inside of defunctionalized, hydrogenated, and aminated pores of carbide-derived carbon supercapacitor electrodes. The approach tailors surface functionalities and tunes nanoporous structures to decouple the influence of pore wall composition on capacitance, ionic resistance, and long-term cyclability. Quasi-elastic neutron scattering probes the self-diffusion properties and electrode-ion interactions of electrolyte molecules confined in functionalized pores. Room-temperature ionic liquid interactions in confined pores are strongest when the hydrogen-containing groups are present on the surface. This property translates into higher capacitance and greater ion transport through pores during electrochemical cycling. Unlike hydrogenated pores, aminated pores do not favorably interact with ionic liquid ions and, subsequently, are outperformed by defunctionalized surfaces.

Dynamics of person-to-person interactions from distributed RFID sensor networks.

Directory of Open Access Journals (Sweden)

Ciro Cattuto

Full Text Available BACKGROUND: Digital networks, mobile devices, and the possibility of mining the ever-increasing amount of digital traces that we leave behind in our daily activities are changing the way we can approach the study of human and social interactions. Large-scale datasets, however, are mostly available for collective and statistical behaviors, at coarse granularities, while high-resolution data on person-to-person interactions are generally limited to relatively small groups of individuals. Here we present a scalable experimental framework for gathering real-time data resolving face-to-face social interactions with tunable spatial and temporal granularities. METHODS AND FINDINGS: We use active Radio Frequency Identification (RFID devices that assess mutual proximity in a distributed fashion by exchanging low-power radio packets. We analyze the dynamics of person-to-person interaction networks obtained in three high-resolution experiments carried out at different orders of magnitude in community size. The data sets exhibit common statistical properties and lack of a characteristic time scale from 20 seconds to several hours. The association between the number of connections and their duration shows an interesting super-linear behavior, which indicates the possibility of defining super-connectors both in the number and intensity of connections. CONCLUSIONS: Taking advantage of scalability and resolution, this experimental framework allows the monitoring of social interactions, uncovering similarities in the way individuals interact in different contexts, and identifying patterns of super-connector behavior in the community. These results could impact our understanding of all phenomena driven by face-to-face interactions, such as the spreading of transmissible infectious diseases and information.

Theory of ultra dense matter and the dynamics of high energy interactions involving nuclei. Progress report, December 15, 1993--December 14, 1994

Energy Technology Data Exchange (ETDEWEB)

Gyulassy, M.

1994-09-12

This report summarizes the progress made during the second year of the three year DOE agreement DE-FG02-93ER40764 on theoretical nuclear physics research performed at the Columbia University and presents a detailed budget adjustment for the third year period December 15, 1994 to December 14, 1995. Sections 1.1 to 1.8 highlight the technical progress made on the following general areas: Multiple scattering and radiative processes in QCD; the quark-gluon plasma transition in nuclear matter; QCD transport theory and dissipative mechanism in dense matter; phenomenological models of high energy interactions involving nuclei; signatures of quark-gluon plasma formation in A+A; neurocomputation theory. Section 2 contains a bibliography of published papers and invited conference papers. Section 3 lists the Columbia nuclear theory members for the December 15, 1994 to December 14, 1995 period. Finally, the budget adjustment requesting $319,830 for the third year relative to the original $320,000 is presented in section 6. Copies of the research papers accompany this report.

Theory of ultra dense matter and the dynamics of high energy interactions involving nuclei. Progress report, December 15, 1993--December 14, 1994

International Nuclear Information System (INIS)

Gyulassy, M.

1994-01-01

This report summarizes the progress made during the second year of the three year DOE agreement DE-FG02-93ER40764 on theoretical nuclear physics research performed at the Columbia University and presents a detailed budget adjustment for the third year period December 15, 1994 to December 14, 1995. Sections 1.1 to 1.8 highlight the technical progress made on the following general areas: Multiple scattering and radiative processes in QCD; the quark-gluon plasma transition in nuclear matter; QCD transport theory and dissipative mechanism in dense matter; phenomenological models of high energy interactions involving nuclei; signatures of quark-gluon plasma formation in A+A; neurocomputation theory. Section 2 contains a bibliography of published papers and invited conference papers. Section 3 lists the Columbia nuclear theory members for the December 15, 1994 to December 14, 1995 period. Finally, the budget adjustment requesting $319,830 for the third year relative to the original $320,000 is presented in section 6. Copies of the research papers accompany this report

Effect of plant-animal interactions on individual performance and population dynamics of Scorzonera hispanica

OpenAIRE

Červenková, Zita

2016-01-01

The population dynamics of plants with regard to plant-animal interactions is a remarkably complex topic. To look into how individual life stages are influenced in different directions by various animals is beyond the scope of a single paper. For each of the studies described below, I and my co-authors attempted to collect data that would cover as much of the plant life cycle as possible, focusing on interactions between plants and different animals during the flowering period and their conse...

Dynamic Behavior Analysis of Non-Contacting Hydrodynamic Finger Seal Based on Fluid-Solid-Interaction Method

Directory of Open Access Journals (Sweden)

Su Hua

2018-01-01

Full Text Available Finger seal is an advanced compliant seal and can be utilized to separate high (HP and low pressure (LP zones in high speed rotating shaft environment. The work to be presented concerns the dynamic behavior of a repetitive section of a two-layer finger seal with high-and padded low-pressure laminates. The dynamic performance of the finger seal are analyzed by the coupled fluid-solid-interaction (FSI simulations. By using the commercial software ANSYS-CFX, the numerical simulation results of interactions between the gas flow and fingers structural deformation are described when the radial periodic excitation from the shaft applies to the finger seal. And the gas film loading capacity, gas film stiffness and leakage varied with time are put forward in different working conditions. Compared with the dynamic performance analysis results based on equivalent dynamic method, the FSI dynamic analysis shows some different characteristics which are more accordance with actual circumstance. Moreover, it is shown that under low pressure differential and high rotation speed the non-contacting finger seal with advance features both in sealing effectiveness and potential unlimited life span can be obtained by rational structure design. But for the non-contacting finger seal with circumferential convergent pad working in high pressure and low rotating speed conditions, it is difficult to improve the sealing performance by the way of changing the structure parameters of finger seal. It is because the high pressure plays a major role on this sealing situation.

Multi-scale interactions of geological processes during mineralization: cascade dynamics model and multifractal simulation

Directory of Open Access Journals (Sweden)

L. Yao

2011-03-01

Full Text Available Relations between mineralization and certain geological processes are established mostly by geologist's knowledge of field observations. However, these relations are descriptive and a quantitative model of how certain geological processes strengthen or hinder mineralization is not clear, that is to say, the mechanism of the interactions between mineralization and the geological framework has not been thoroughly studied. The dynamics behind these interactions are key in the understanding of fractal or multifractal formations caused by mineralization, among which singularities arise due to anomalous concentration of metals in narrow space. From a statistical point of view, we think that cascade dynamics play an important role in mineralization and studying them can reveal the nature of the various interactions throughout the process. We have constructed a multiplicative cascade model to simulate these dynamics. The probabilities of mineral deposit occurrences are used to represent direct results of mineralization. Multifractal simulation of probabilities of mineral potential based on our model is exemplified by a case study dealing with hydrothermal gold deposits in southern Nova Scotia, Canada. The extent of the impacts of certain geological processes on gold mineralization is related to the scale of the cascade process, especially to the maximum cascade division number n_max. Our research helps to understand how the singularity occurs during mineralization, which remains unanswered up to now, and the simulation may provide a more accurate distribution of mineral deposit occurrences that can be used to improve the results of the weights of evidence model in mapping mineral potential.

Real and financial market interactions in a multiplier-accelerator model: Nonlinear dynamics, multistability and stylized facts

Science.gov (United States)

Cavalli, F.; Naimzada, A.; Pecora, N.

2017-10-01

In the present paper, we investigate the dynamics of a model in which the real part of the economy, described within a multiplier-accelerator framework, interacts with a financial market with heterogeneous speculators, in order to study the channels through which the two sectors influence each other. Employing analytical and numerical tools, we investigate stability conditions as well as bifurcations and possible periodic, quasi-periodic, and chaotic dynamics, enlightening how the degree of market interaction, together with the accelerator parameter and the intervention of the fiscal authority, may affect the business cycle and the course of the financial market. In particular, we show that even if the steady state is locally stable, multistability phenomena can occur, with several and complex dynamic structures coexisting with the steady state. Finally, simulations reveal that the proposed model is able to explain several statistical properties and stylized facts observed in real financial markets, including persistent high volatility, fat-tailed return distributions, volatility clustering, and positive autocorrelation of absolute returns.

The effect of training in an interactive dynamic stander on ankle dorsiflexion and gross motor function in children with cerebral palsy

DEFF Research Database (Denmark)

Curtis, Derek John; Bencke, Jesper; Mygind, Bente

2014-01-01

OBJECTIVE: To study the effect of active stretching of ankle plantarflexors using an interactive dynamic stander in children with cerebral palsy (CP). METHODS: Six children in Gross Motor Function Classification System classes I-III, aged 4-10 years, trained intensive active dorsiflexion...... in an interactive dynamic stander using ankle movement to play custom computer games following a 10-week control period. Gross Motor Function Measure Item Set, gait performance and passive and active dorsiflexion with extended and flexed knee were chosen as outcome parameters. RESULTS: Median active and passive......, these results may indicate that intensive active stretching in an interactive dynamic stander could be an effective new conservative clinical treatment of ankle plantarflexor contracture in children with CP....

Contact point generation for convex polytopes in interactive rigid body dynamics

DEFF Research Database (Denmark)

Silcowitz-Hansen, Morten; Abel, Sarah Maria Niebe; Erleben, Kenny

When computing contact forces in rigid body dynamics systems, most state-of-the-art solutions use iterative methods such as the projected Gauss–Seidel (PGS) method. Methods such as the PGS method are preferred for their robustness. However, the time-critical nature of interactive applications...... combined with the linear convergence rates of such methods, will often result in visual artifacts in the final simulation. With this paper, we address an issue which is of major impact on the animation quality, when using methods such as the PGS method. The issue is robust generation of contact points...... for convex polytopes. A novel contact point generation method is presented, which is based on growth distances and Gauss maps. We demonstrate improvements when using our method in the context of interactive rigid body simulation...

A Hybrid Artificial Reputation Model Involving Interaction Trust, Witness Information and the Trust Model to Calculate the Trust Value of Service Providers

Directory of Open Access Journals (Sweden)

Gurdeep Singh Ransi

2014-02-01

Full Text Available Agent interaction in a community, such as the online buyer-seller scenario, is often uncertain, as when an agent comes in contact with other agents they initially know nothing about each other. Currently, many reputation models are developed that help service consumers select better service providers. Reputation models also help agents to make a decision on who they should trust and transact with in the future. These reputation models are either built on interaction trust that involves direct experience as a source of information or they are built upon witness information also known as word-of-mouth that involves the reports provided by others. Neither the interaction trust nor the witness information models alone succeed in such uncertain interactions. In this paper we propose a hybrid reputation model involving both interaction trust and witness information to address the shortcomings of existing reputation models when taken separately. A sample simulation is built to setup buyer-seller services and uncertain interactions. Experiments reveal that the hybrid approach leads to better selection of trustworthy agents where consumers select more reputable service providers, eventually helping consumers obtain more gains. Furthermore, the trust model developed is used in calculating trust values of service providers.

The surface chemistry determines the spatio-temporal interaction dynamics of quantum dots in atherosclerotic lesions.

Science.gov (United States)

Uhl, Bernd; Hirn, Stephanie; Mildner, Karina; Coletti, Raffaele; Massberg, Steffen; Reichel, Christoph A; Rehberg, Markus; Zeuschner, Dagmar; Krombach, Fritz

2018-03-01

To optimize the design of nanoparticles for diagnosis or therapy of vascular diseases, it is mandatory to characterize the determinants of nano-bio interactions in vascular lesions. Using ex vivo and in vivo microscopy, we analyzed the interactive behavior of quantum dots with different surface functionalizations in atherosclerotic lesions of ApoE-deficient mice. We demonstrate that quantum dots with different surface functionalizations exhibit specific interactive behaviors with distinct molecular and cellular components of the injured vessel wall. Moreover, we show a role for fibrinogen in the regulation of the spatio-temporal interaction dynamics in atherosclerotic lesions. Our findings emphasize the relevance of surface chemistry-driven nano-bio interactions on the differential in vivo behavior of nanoparticles in diseased tissue.

Discordant tasks and motor adjustments affect interactions between adaptations to altered kinematics and dynamics

Directory of Open Access Journals (Sweden)

Fritzie Arce

2010-01-01

Full Text Available Motor control and adaptation are multi-determinate processes with complex interactions. This is reflected for example in the ambiguous nature of interactions during sequential adaptation of reaching under kinematics and dynamics perturbations. It has been suggested that perturbations based on the same kinematic parameter interfere. Others posited that opposing motor adjustments underlie interference. Here, we examined the influence of discordances in task and in motor adjustments on sequential adaptations to visuomotor rotation and viscous force field perturbations. These two factors – perturbation direction and task discordance – have been examined separately by previous studies, thus the inherent difficulty to identify the roots of interference. Forty-eight human subjects adapted sequentially to one or two types of perturbations, of matched or conflicting directions. We found a gradient of interaction effects based on perturbation direction and task discordance. Perturbations of matched directions showed facilitation while perturbations of opposite directions, which required opposing motor adjustments, interfered with each other. Further, interaction effects increased with greater task discordance. We also found that force field and visuomotor rotation had mutual anterograde and retrograde effects. However, we found independence between anterograde and retrograde interferences between similar tasks. The results suggest that the newly acquired internal models of kinematic and dynamic perturbations are not independent but they share common neuronal resources and interact between them. Such overlap does not necessarily imply competition of resources. Rather, our results point to an additional principle of sensorimotor adaptation allowing the system to tap or harness common features across diverse sensory inputs and task contexts whenever available.

A Dynamic Bayesian Model for Characterizing Cross-Neuronal Interactions During Decision-Making.

Science.gov (United States)

Zhou, Bo; Moorman, David E; Behseta, Sam; Ombao, Hernando; Shahbaba, Babak

2016-01-01

The goal of this paper is to develop a novel statistical model for studying cross-neuronal spike train interactions during decision making. For an individual to successfully complete the task of decision-making, a number of temporally-organized events must occur: stimuli must be detected, potential outcomes must be evaluated, behaviors must be executed or inhibited, and outcomes (such as reward or no-reward) must be experienced. Due to the complexity of this process, it is likely the case that decision-making is encoded by the temporally-precise interactions between large populations of neurons. Most existing statistical models, however, are inadequate for analyzing such a phenomenon because they provide only an aggregated measure of interactions over time. To address this considerable limitation, we propose a dynamic Bayesian model which captures the time-varying nature of neuronal activity (such as the time-varying strength of the interactions between neurons). The proposed method yielded results that reveal new insight into the dynamic nature of population coding in the prefrontal cortex during decision making. In our analysis, we note that while some neurons in the prefrontal cortex do not synchronize their firing activity until the presence of a reward, a different set of neurons synchronize their activity shortly after stimulus onset. These differentially synchronizing sub-populations of neurons suggests a continuum of population representation of the reward-seeking task. Secondly, our analyses also suggest that the degree of synchronization differs between the rewarded and non-rewarded conditions. Moreover, the proposed model is scalable to handle data on many simultaneously-recorded neurons and is applicable to analyzing other types of multivariate time series data with latent structure. Supplementary materials (including computer codes) for our paper are available online.

Water dynamics as affected by interaction with biomolecules and change of thermodynamic state: a neutron scattering study

International Nuclear Information System (INIS)

Orecchini, A; Paciaroni, A; Petrillo, C; Sebastiani, F; Sacchetti, F; De Francesco, A

2012-01-01

The dynamics of water as subtly perturbed by both the interaction with biomolecules and the variation of temperature and pressure has been investigated via neutron scattering spectroscopy. A measurement of inelastic neutron scattering devoted to the study of the coherent THz dynamics of water in a water-rich mixture with DNA (hydration level of 1 g DNA/15 g D 2 O) at room temperature is reported. The DNA hydration water coherent dynamics is characterised by the presence of collective modes, whose dispersion relations are similar to those observed in bulk water. These dispersion relations are well described by the interaction model developed in the case of bulk water, and the existence of a fast sound is experimentally demonstrated. The behaviour of the collective water dynamics was complemented by studying the single-particle dynamics of bulk water along the isotherm T = 298 K in the pressure range 0.1-350 MPa by means of incoherent scattering. This experiment is an attempt to simulate the change of the water molecular arrangement due to the interaction with DNA, by increasing the pressure as the presence of the biomolecule produces an increase in the density. An anomaly is found in the behaviour of the relaxation time derived from the quasi-elastic scattering signal, which can be related to the hypothetical second critical point in water. This anomaly and the transition from slow to fast sound take place in the same Q range, thus suggesting that the two phenomena could be related at some microscopic level.

Dynamical Bayesian inference of time-evolving interactions: From a pair of coupled oscillators to networks of oscillators

Science.gov (United States)

Duggento, Andrea; Stankovski, Tomislav; McClintock, Peter V. E.; Stefanovska, Aneta

2012-12-01

Living systems have time-evolving interactions that, until recently, could not be identified accurately from recorded time series in the presence of noise. Stankovski [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.109.024101 109, 024101 (2012)] introduced a method based on dynamical Bayesian inference that facilitates the simultaneous detection of time-varying synchronization, directionality of influence, and coupling functions. It can distinguish unsynchronized dynamics from noise-induced phase slips. The method is based on phase dynamics, with Bayesian inference of the time-evolving parameters being achieved by shaping the prior densities to incorporate knowledge of previous samples. We now present the method in detail using numerically generated data, data from an analog electronic circuit, and cardiorespiratory data. We also generalize the method to encompass networks of interacting oscillators and thus demonstrate its applicability to small-scale networks.

Network Dynamics with BrainX3: A Large-Scale Simulation of the Human Brain Network with Real-Time Interaction

OpenAIRE

Xerxes D. Arsiwalla; Riccardo eZucca; Alberto eBetella; Enrique eMartinez; David eDalmazzo; Pedro eOmedas; Gustavo eDeco; Gustavo eDeco; Paul F.M.J. Verschure; Paul F.M.J. Verschure

2015-01-01

BrainX3 is a large-scale simulation of human brain activity with real-time interaction, rendered in 3D in a virtual reality environment, which combines computational power with human intuition for the exploration and analysis of complex dynamical networks. We ground this simulation on structural connectivity obtained from diffusion spectrum imaging data and model it on neuronal population dynamics. Users can interact with BrainX3 in real-time by perturbing brain regions with transient stimula...

Network dynamics with BrainX3: a large-scale simulation of the human brain network with real-time interaction

OpenAIRE

Arsiwalla, Xerxes D.; Zucca, Riccardo; Betella, Alberto; Martínez, Enrique, 1961-; Dalmazzo, David; Omedas, Pedro; Deco, Gustavo; Verschure, Paul F. M. J.

2015-01-01

BrainX3 is a large-scale simulation of human brain activity with real-time interaction, rendered in 3D in a virtual reality environment, which combines computational power with human intuition for the exploration and analysis of complex dynamical networks. We ground this simulation on structural connectivity obtained from diffusion spectrum imaging data and model it on neuronal population dynamics. Users can interact with BrainX3 in real-time by perturbing brain regions with transient stimula...

The importance of herbivore interactions for the dynamics of African savanna woodlands : an hypothesis

NARCIS (Netherlands)

Van de Koppel, J; Prins, HHT

Current hypotheses to explain dynamic transitions between savanna grasslands and woodlands in Africa focus on grazing by elephant or the influence of fire. Using a simple mathematical model, this paper argues that interactions between small herbivores such as impala or buffalo and large herbivores

Controlled initiation and quantitative visualization of cell interaction dynamics - a novel hybrid microscopy method -

NARCIS (Netherlands)

Snijder-van As, M.I.

2010-01-01

This thesis describes the development, validation, and application of a hybrid microscopy technique to study cell-substrate and cell-cell interactions in a controlled and quantitative manner. We studied the spatial and temporal dynamics of the selected membrane molecules CD6 and the activated

Interactive and dynamic visualizations in teaching and learning of anatomy: A cognitive load perspective.

NARCIS (Netherlands)

Khalil, M.K.; Paas, Fred; Johnson, T.E.; Payer, A.F.

2007-01-01

With the increasing use of computers in the classroom and the advancement of information technology, a requirement to investigate and evaluate different strategies for the presentation of verbal information in interactive and dynamic visualizations has risen to a high level of importance. There is a

A spherical model with directional interactions: II. Dynamics and landscape properties

International Nuclear Information System (INIS)

Mayer, Christian; Sciortino, Francesco; Tartaglia, Piero; Zaccarelli, Emanuela

2010-01-01

We study a binary non-additive hard-sphere mixture with square well interactions only between dissimilar particles. An appropriate choice of the inter-particle potential parameters favors the formation of equilibrium structures with tetrahedral ordering (Zaccarelli et al 2007 J. Chem. Phys. 127 174501). By performing extensive event-driven molecular dynamics simulations, we monitor the dynamics of the system, locating the iso-diffusivity lines in the phase diagram, and discuss their location with respect to the gas-liquid phase separation. We observe the formation of an ideal gel which continuously crosses towards an attractive glass upon increasing the density. Moreover, we evaluate the statistical properties of the potential energy landscape for this model. We find that the configurational entropy, for densities within the optimal network-forming region, is finite even in the ground state and obeys a logarithmic dependence on the energy.

Antagonistic bacterial interactions help shape host-symbiont dynamics within the fungus-growing ant-microbe mutualism

DEFF Research Database (Denmark)

Poulsen, Michael; Erhardt, Daniel P; Molinaro, Daniel J

2007-01-01

Conflict within mutually beneficial associations is predicted to destabilize relationships, and theoretical and empirical work exploring this has provided significant insight into the dynamics of cooperative interactions. Within mutualistic associations, the expression and regulation of conflict ...

On the Relationality of Centers, Peripheries and Interactional Regimes: Translanguaging in a Community Interpreting Event

Science.gov (United States)

Baynham, Mike; Hanušová, Jolana

2017-01-01

In this paper we discuss a multilingual interactional event that involves both interpreting and literacy work, part of a large scale study on translanguaging in superdiverse urban settings. In the first part of the interaction, the center/periphery dynamic is played out in what might be called "contested translanguaging" between Standard…

The interactive alphabet with augmented reality as a form of involving children in educational process

Directory of Open Access Journals (Sweden)

Vladimir D. Sekerin

2017-01-01

Full Text Available Research objective: to prove the expediency of using technologies with augmented reality in educational process of children in order to increase the level of their involvement and to improve the efficiency of educational process. Materials and methods. The information base of the research was made by scientific publications, information and analytical reviews, periodicals, monographs, information placed in the Internet network, concerning practical application of technologies with augmented reality in educational process, descriptive and comparative methods of analysis form the methodical basis of this research. Results. It is shown that in educational process of children it is expedient to use the modern technological achievements allowing organizing productive interactions and relationship of the students among themselves and with teachers, lecturers. Educational, business, role-playing games, discussions promoting acceleration of acquiring  a new experience and receiving new knowledge are the perspective formats of realizing the educational process. The world of augmented reality has the following properties: combines the real and virtual, interacts in real time mode, and functions in three-dimensional space. The advantages of the Interactive alphabet on the basis of the augmented reality technology are as follows: 1 security of strong emotional responses; 2 the involvement and interactivity promoting steady memorizing; 3 possibilities of interaction with the artificial world by means of gadgets; 4 Digital and offline communication; 5 possibility of carrying out virtual lessons. One of the main features of virtual reality is the feeling of participation and the opportunity to observe everything from the first person. It makes expedient to carry out lessons entirely in the virtual reality. Achievement of full involvement in educational process promotes increase of motivation and progress in knowledge acquisition.  The use of the augmented

Conversational Dynamics in a Longitudinal Corpus of Caregiver-Child Interactions

DEFF Research Database (Denmark)

Weed, Ethan; Fusaroli, Riccardo; Tranbjerg, Jonas

Background:  Conversational turn-taking provides a scaffold that helps children learn the elements and rules of language (Dale & Spivey 2006, Yurofsky et al 2016). This relies heavily on social feedback and engagement (Fusaroli et al 2014), and thus conversations involving children with ASD are e...... their conversational turns to the child they are speaking with. This highlights the importance of investigating language acquisition in children with ASD within the context of dyadic interaction...

Effective interactions for description of multistep processes

International Nuclear Information System (INIS)

Avrigeanu, M.; Stetcu, I.; Avrigeanu, V.; Antonov, A.N.; Lenske, H.

2000-01-01

The reliability of realistic M3Y effective NN interactions to describe multistep direct (MSD) processes is proved by analysing the corresponding real optical potentials. This trial is done in order to overcome the uncertainties of the effective NN-interaction strength V 0 obtained by direct fit to the experimental data. The microscopic potential for the nucleon-nucleus scattering at energies lower than 100 MeV has been calculated by using nucleonic and mesonic form factors. It has been analysed through (i) a comparison with phenomenological optical potentials, and (ii) its use for description of nucleon elastic scattering angular distributions. It results that the strongly simplified model interactions usually involved within MSD reaction theory, e.g. 1 fm range Yukawa (1Y) term, neglect important dynamical details of such processes. An 1Y-equivalent V 0 strength of a realistic effective NN interaction is determined by corresponding optical-potential volume integrals, and involved within Feshbach-Kerman-Koonin theory calculations with the final goal of MSD studies without any V 0 free parameter. (authors)

A 3-D model of tumor progression based on complex automata driven by particle dynamics.

Science.gov (United States)

Wcisło, Rafał; Dzwinel, Witold; Yuen, David A; Dudek, Arkadiusz Z

2009-12-01

The dynamics of a growing tumor involving mechanical remodeling of healthy tissue and vasculature is neglected in most of the existing tumor models. This is due to the lack of efficient computational framework allowing for simulation of mechanical interactions. Meanwhile, just these interactions trigger critical changes in tumor growth dynamics and are responsible for its volumetric and directional progression. We describe here a novel 3-D model of tumor growth, which combines particle dynamics with cellular automata concept. The particles represent both tissue cells and fragments of the vascular network. They interact with their closest neighbors via semi-harmonic central forces simulating mechanical resistance of the cell walls. The particle dynamics is governed by both the Newtonian laws of motion and the cellular automata rules. These rules can represent cell life-cycle and other biological interactions involving smaller spatio-temporal scales. We show that our complex automata, particle based model can reproduce realistic 3-D dynamics of the entire system consisting of the tumor, normal tissue cells, blood vessels and blood flow. It can explain phenomena such as the inward cell motion in avascular tumor, stabilization of tumor growth by the external pressure, tumor vascularization due to the process of angiogenesis, trapping of healthy cells by invading tumor, and influence of external (boundary) conditions on the direction of tumor progression. We conclude that the particle model can serve as a general framework for designing advanced multiscale models of tumor dynamics and it is very competitive to the modeling approaches presented before.

Efficient computation of co-transcriptional RNA-ligand interaction dynamics.

Science.gov (United States)

Wolfinger, Michael T; Flamm, Christoph; Hofacker, Ivo L

2018-05-04

Riboswitches form an abundant class of cis-regulatory RNA elements that mediate gene expression by binding a small metabolite. For synthetic biology applications, they are becoming cheap and accessible systems for selectively triggering transcription or translation of downstream genes. Many riboswitches are kinetically controlled, hence knowledge of their co-transcriptional mechanisms is essential. We present here an efficient implementation for analyzing co-transcriptional RNA-ligand interaction dynamics. This approach allows for the first time to model concentration-dependent metabolite binding/unbinding kinetics. We exemplify this novel approach by means of the recently studied I-A 2 ' -deoxyguanosine (2 ' dG)-sensing riboswitch from Mesoplasma florum. Copyright © 2018 Elsevier Inc. All rights reserved.

A novel approach in Eliashberg theory of superconductivity with ab-initio static and dynamic Coulomb interaction applicable for real materials

Energy Technology Data Exchange (ETDEWEB)

Davydov, Arkadiy; Sanna, Antonio; Sharma, Sangeeta; Dewhurst, John Kay; Gross, E.K.U. [Max Planck Institute of Microstructure Physics, Halle (Saale) (Germany)

2016-07-01

In standard Eliashberg methods the Coulomb interaction is usually restricted to the use of a single phenomenological parameter μ{sup *} adjusted to give the right superconducting critical temperature (T{sub c}). In this work we present a parameter-free Eliashberg approach, in which we treat the screened Coulomb interaction within the random phase approximation (RPA) in its static and full dynamic limit. The full energy range of the Coulomb interaction is taken into account, which becomes computationally affordable with the introduction of a suitable isotropic approximation. We have tested the method on a set of conventional superconductors. We will discuss the reliability of the predicted T{sub c} both by using a static and a dynamic Coulomb interaction.

Lipid bilayers driven to a wrong lane in molecular dynamics simulations by subtle changes in long-range electrostatic interactions

NARCIS (Netherlands)

Patra, M.; Karttunen, M.E.J.; Hyvönen, M.T.; Falck, E.; Vattulainen, I.

2004-01-01

We provide compelling evidence that different treatments of electrostatic interactions in molecular dynamics simulations may dramatically affect dynamic properties of lipid bilayers. To this end, we consider a fully hydrated pure dipalmitoylphosphatidylcholine bilayer through 50-ns molecular

Dynamics of fermionic Hubbard models after interaction quenches in one and two dimensions

International Nuclear Information System (INIS)

Hamerla, Simone Anke

2013-10-01

calculation up to second order in the interaction. Then the dynamics of the one-dimensional model is discussed with a focus on the relation of the results derived by the iterated equations of motion approach to results obtained by bosonization theory, the behavior for strong interactions and the dynamical transition from the weak to the strong quench regime. Furthermore, the Hubbard model is studied on a two-dimensional square lattice. This model is fundamentally different from the one-dimensional model: In contrast to the one-dimensional model the two-dimensional model is not integrable allowing a true relaxation of the system. For this system a calculation up to second order in the interaction is performed and compared to the results of the iterated equation of motion approach. Besides, the time evolution of the momentum distribution and the influence of doping on the dynamics is studied. Moreover, a first estimate for relaxation times is provided without relying on the assumption of a mixed state.

Dynamics of fermionic Hubbard models after interaction quenches in one and two dimensions

Energy Technology Data Exchange (ETDEWEB)

Hamerla, Simone Anke

2013-10-15

calculation up to second order in the interaction. Then the dynamics of the one-dimensional model is discussed with a focus on the relation of the results derived by the iterated equations of motion approach to results obtained by bosonization theory, the behavior for strong interactions and the dynamical transition from the weak to the strong quench regime. Furthermore, the Hubbard model is studied on a two-dimensional square lattice. This model is fundamentally different from the one-dimensional model: In contrast to the one-dimensional model the two-dimensional model is not integrable allowing a true relaxation of the system. For this system a calculation up to second order in the interaction is performed and compared to the results of the iterated equation of motion approach. Besides, the time evolution of the momentum distribution and the influence of doping on the dynamics is studied. Moreover, a first estimate for relaxation times is provided without relying on the assumption of a mixed state.

A class of stochastic games with infinitely many interacting agents related to Glauber dynamics on random graphs

International Nuclear Information System (INIS)

De Santis, Emilio; Marinelli, Carlo

2007-01-01

We introduce and study a class of infinite-horizon non-zero-sum non-cooperative stochastic games with infinitely many interacting agents using ideas of statistical mechanics. First we show, in the general case of asymmetric interactions, the existence of a strategy that allows any player to eliminate losses after a finite random time. In the special case of symmetric interactions, we also prove that, as time goes to infinity, the game converges to a Nash equilibrium. Moreover, assuming that all agents adopt the same strategy, using arguments related to those leading to perfect simulation algorithms, spatial mixing and ergodicity are proved. In turn, ergodicity allows us to prove 'fixation', i.e. players will adopt a constant strategy after a finite time. The resulting dynamics is related to zero-temperature Glauber dynamics on random graphs of possibly infinite volume

Role of the noise on the transient dynamics of an ecosystem of interacting species

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Spagnolo, B.; La Barbera, A.

2002-11-01

We analyze the transient dynamics of an ecosystem described by generalized Lotka-Volterra equations in the presence of a multiplicative noise and a random interaction parameter between the species. We consider specifically three cases: (i) two competing species, (ii) three interacting species (one predator-two preys), (iii) n-interacting species. The interaction parameter in case (i) is a stochastic process which obeys a stochastic differential equation. We find noise delayed extinction of one of two species, which is akin to the noise-enhanced stability phenomenon. Other two noise-induced effects found are temporal oscillations and spatial patterns of the two competing species. In case (ii) the noise induces correlated spatial patterns of the predator and of the two preys concentrations. Finally, in case (iii) we find the asymptotic behavior of the time average of the ith population when the ecosystem is composed of a great number of interacting species.

GIS - Based data presentation and interactive communication system for public involvement in EIA

International Nuclear Information System (INIS)

Oprea, I.; Oprea, M.; Guta, V.; Pirvu, V.

2001-01-01

The data presentation and interactive communication system has as main task to integrate technical and administrative information, as well as to ensure an efficient public participation. The system can achieve desired inter-operability between specialists, government and public in decision-making and environmental impact assessment (EIA). It incorporates different modules relative to specific types of parameters and authorities involved. The GIS-based system provides mapping, database, automatic information collection and advanced presentation techniques. It includes a graphically oriented executive support, which has the ability to present information by geographical representation of the zones on the map. The public opinion is taking into account by consideration of alternatives and providing access to the monitoring of environmental effects. The system offers an effective way to avoid negative reactions by interactive communication based on real-time information exchange. The system can be integrated into national or international management systems, being a useful tool for an efficient communication, handling and exchanging a vast amount of information. (authors)

Interacting Learning Processes during Skill Acquisition: Learning to control with gradually changing system dynamics.

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Ludolph, Nicolas; Giese, Martin A; Ilg, Winfried

2017-10-16

There is increasing evidence that sensorimotor learning under real-life conditions relies on a composition of several learning processes. Nevertheless, most studies examine learning behaviour in relation to one specific learning mechanism. In this study, we examined the interaction between reward-based skill acquisition and motor adaptation to changes of object dynamics. Thirty healthy subjects, split into two groups, acquired the skill of balancing a pole on a cart in virtual reality. In one group, we gradually increased the gravity, making the task easier in the beginning and more difficult towards the end. In the second group, subjects had to acquire the skill on the maximum, most difficult gravity level. We hypothesized that the gradual increase in gravity during skill acquisition supports learning despite the necessary adjustments to changes in cart-pole dynamics. We found that the gradual group benefits from the slow increment, although overall improvement was interrupted by the changes in gravity and resulting system dynamics, which caused short-term degradations in performance and timing of actions. In conclusion, our results deliver evidence for an interaction of reward-based skill acquisition and motor adaptation processes, which indicates the importance of both processes for the development of optimized skill acquisition schedules.

The cultural implications of growth: Modeling nonlinear interaction of trait selection and population dynamics.

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Antoci, Angelo; Galeotti, Marcello; Russu, Paolo; Luigi Sacco, Pier

2018-05-01

In this paper, we study a nonlinear model of the interaction between trait selection and population dynamics, building on previous work of Ghirlanda et al. [Theor. Popul. Biol. 77, 181-188 (2010)] and Antoci et al. [Commun. Nonlinear Sci. Numer. Simul. 58, 92-106 (2018)]. We establish some basic properties of the model dynamics and present some simulations of the fine-grained structure of alternative dynamic regimes for chosen combinations of parameters. The role of the parameters that govern the reinforcement/corruption of maladaptive vs. adaptive traits is of special importance in determining the model's dynamic evolution. The main implication of this result is the need to pay special attention to the structural forces that may favor the emergence and consolidation of maladaptive traits in contemporary socio-economies, as it is the case, for example, for the stimulation of dysfunctional consumption habits and lifestyles in the pursuit of short-term profits.

The cultural implications of growth: Modeling nonlinear interaction of trait selection and population dynamics

Science.gov (United States)

Antoci, Angelo; Galeotti, Marcello; Russu, Paolo; Luigi Sacco, Pier

2018-05-01

In this paper, we study a nonlinear model of the interaction between trait selection and population dynamics, building on previous work of Ghirlanda et al. [Theor. Popul. Biol. 77, 181-188 (2010)] and Antoci et al. [Commun. Nonlinear Sci. Numer. Simul. 58, 92-106 (2018)]. We establish some basic properties of the model dynamics and present some simulations of the fine-grained structure of alternative dynamic regimes for chosen combinations of parameters. The role of the parameters that govern the reinforcement/corruption of maladaptive vs. adaptive traits is of special importance in determining the model's dynamic evolution. The main implication of this result is the need to pay special attention to the structural forces that may favor the emergence and consolidation of maladaptive traits in contemporary socio-economies, as it is the case, for example, for the stimulation of dysfunctional consumption habits and lifestyles in the pursuit of short-term profits.

Metastability and avalanche dynamics in strongly correlated gases with long-range interactions

Science.gov (United States)

Hruby, Lorenz; Dogra, Nishant; Landini, Manuele; Donner, Tobias; Esslinger, Tilman

2018-03-01

We experimentally study the stability of a bosonic Mott insulator against the formation of a density wave induced by long-range interactions and characterize the intrinsic dynamics between these two states. The Mott insulator is created in a quantum degenerate gas of 87-Rubidium atoms, trapped in a 3D optical lattice. The gas is located inside and globally coupled to an optical cavity. This causes interactions of global range, mediated by photons dispersively scattered between a transverse lattice and the cavity. The scattering comes with an atomic density modulation, which is measured by the photon flux leaking from the cavity. We initialize the system in a Mott-insulating state and then rapidly increase the global coupling strength. We observe that the system falls into either of two distinct final states. One is characterized by a low photon flux, signaling a Mott insulator, and the other is characterized by a high photon flux, which we associate with a density wave. Ramping the global coupling slowly, we observe a hysteresis loop between the two states—a further signature of metastability. A comparison with a theoretical model confirms that the metastability originates in the competition between short- and global-range interactions. From the increasing photon flux monitored during the switching process, we find that several thousand atoms tunnel to a neighboring site on the timescale of the single-particle dynamics. We argue that a density modulation, initially forming in the compressible surface of the trapped gas, triggers an avalanche tunneling process in the Mott-insulating region.

Novel recurrent neural network for modelling biological networks: oscillatory p53 interaction dynamics.

Science.gov (United States)

Ling, Hong; Samarasinghe, Sandhya; Kulasiri, Don

2013-12-01

Understanding the control of cellular networks consisting of gene and protein interactions and their emergent properties is a central activity of Systems Biology research. For this, continuous, discrete, hybrid, and stochastic methods have been proposed. Currently, the most common approach to modelling accurate temporal dynamics of networks is ordinary differential equations (ODE). However, critical limitations of ODE models are difficulty in kinetic parameter estimation and numerical solution of a large number of equations, making them more suited to smaller systems. In this article, we introduce a novel recurrent artificial neural network (RNN) that addresses above limitations and produces a continuous model that easily estimates parameters from data, can handle a large number of molecular interactions and quantifies temporal dynamics and emergent systems properties. This RNN is based on a system of ODEs representing molecular interactions in a signalling network. Each neuron represents concentration change of one molecule represented by an ODE. Weights of the RNN correspond to kinetic parameters in the system and can be adjusted incrementally during network training. The method is applied to the p53-Mdm2 oscillation system - a crucial component of the DNA damage response pathways activated by a damage signal. Simulation results indicate that the proposed RNN can successfully represent the behaviour of the p53-Mdm2 oscillation system and solve the parameter estimation problem with high accuracy. Furthermore, we presented a modified form of the RNN that estimates parameters and captures systems dynamics from sparse data collected over relatively large time steps. We also investigate the robustness of the p53-Mdm2 system using the trained RNN under various levels of parameter perturbation to gain a greater understanding of the control of the p53-Mdm2 system. Its outcomes on robustness are consistent with the current biological knowledge of this system. As more

Facilitating Students' Interaction with Real Gas Properties Using a Discovery-Based Approach and Molecular Dynamics Simulations

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Sweet, Chelsea; Akinfenwa, Oyewumi; Foley, Jonathan J., IV

2018-01-01

We present an interactive discovery-based approach to studying the properties of real gases using simple, yet realistic, molecular dynamics software. Use of this approach opens up a variety of opportunities for students to interact with the behaviors and underlying theories of real gases. Students can visualize gas behavior under a variety of…

The classical and quantum dynamics of molecular spins on graphene

Science.gov (United States)

Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo

2016-02-01

Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain’s threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices.