Myosin II Motors and F-Actin Dynamics Drive the Coordinated Movement of the Centrosome and Soma during CNS Glial-Guided Neuronal Migration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Solecki, Dr. David; Trivedi, Dr. Niraj; Govek, Eve-Ellen

2009-01-01

Lamination of cortical regions of the vertebrate brain depends on glial-guided neuronal migration. The conserved polarity protein Par6{alpha} localizes to the centrosome and coordinates forward movement of the centrosome and soma in migrating neurons. The cytoskeletal components that produce this unique form of cell polarity and their relationship to polarity signaling cascades are unknown. We show that F-actin and Myosin II motors are enriched in the neuronal leading process and that Myosin II activity is necessary for leading process actin dynamics. Inhibition of Myosin II decreased the speed of centrosome and somal movement, whereas Myosin II activation increased coordinated movement.more » Ectopic expression or silencing of Par6{alpha} inhibited Myosin II motors by decreasing Myosin light-chain phosphorylation. These findings suggest leading-process Myosin II may function to 'pull' the centrosome and soma forward during glial-guided migration by a mechanism involving the conserved polarity protein Par6{alpha}.« less

Equipartition terms in transition path ensemble: Insights from molecular dynamics simulations of alanine dipeptide.

PubMed

Li, Wenjin

2018-02-28

Transition path ensemble consists of reactive trajectories and possesses all the information necessary for the understanding of the mechanism and dynamics of important condensed phase processes. However, quantitative description of the properties of the transition path ensemble is far from being established. Here, with numerical calculations on a model system, the equipartition terms defined in thermal equilibrium were for the first time estimated in the transition path ensemble. It was not surprising to observe that the energy was not equally distributed among all the coordinates. However, the energies distributed on a pair of conjugated coordinates remained equal. Higher energies were observed to be distributed on several coordinates, which are highly coupled to the reaction coordinate, while the rest were almost equally distributed. In addition, the ensemble-averaged energy on each coordinate as a function of time was also quantified. These quantitative analyses on energy distributions provided new insights into the transition path ensemble.

Current Approaches to Intervention in Children with Developmental Coordination Disorder

ERIC Educational Resources Information Center

Sugden, David

2007-01-01

This review analyzes approaches to intervention in children with developmental coordination disorder within the framework of how children develop and learn motor skills, drawing upon maturational, cognitive, and dynamic systems models. The approaches to intervention are divided into two categories: (1) process or deficit-oriented approaches; and…

Coordinated approaches to quantify long-term ecosystem dynamics in response to global change

Treesearch

Yiqi Luo; Jerry Melillo; Shuli Niu; Claus Beier; James S. Clark; Aime E.T. Classen; Eric Dividson; Jeffrey S. Dukes; R. Dave Evans; Christopher B. Field; Claudia I. Czimczik; Michael Keller; Bruce A. Kimball; Lara M. Kueppers; Richard J. Norby; Shannon L. Pelini; Elise Pendall; Edward Rastetter; Johan Six; Melinda Smith; Mark G. Tjoelker; Margaret S. Torn

2011-01-01

Many serious ecosystem consequences of climate change will take decades or even centuries to emerge. Long-term ecological responses to global change are strongly regulated by slow processes, such as changes in species composition, carbon dynamics in soil and by long-lived plants, and accumulation of nutrient capitals. Understanding and predicting these processes...

Cellular reprogramming dynamics follow a simple 1D reaction coordinate

NASA Astrophysics Data System (ADS)

Teja Pusuluri, Sai; Lang, Alex H.; Mehta, Pankaj; Castillo, Horacio E.

2018-01-01

Cellular reprogramming, the conversion of one cell type to another, induces global changes in gene expression involving thousands of genes, and understanding how cells globally alter their gene expression profile during reprogramming is an ongoing problem. Here we reanalyze time-course data on cellular reprogramming from differentiated cell types to induced pluripotent stem cells (iPSCs) and show that gene expression dynamics during reprogramming follow a simple 1D reaction coordinate. This reaction coordinate is independent of both the time it takes to reach the iPSC state as well as the details of the experimental protocol used. Using Monte-Carlo simulations, we show that such a reaction coordinate emerges from epigenetic landscape models where cellular reprogramming is viewed as a ‘barrier-crossing’ process between cell fates. Overall, our analysis and model suggest that gene expression dynamics during reprogramming follow a canonical trajectory consistent with the idea of an ‘optimal path’ in gene expression space for reprogramming.

Flexibility-Rigidity Coordination of the Dense Exopolysaccharide Matrix in Terrestrial Cyanobacteria Acclimated to Periodic Desiccation.

PubMed

Liu, Wen; Cui, Lijuan; Xu, Haiyan; Zhu, Zhaoxia; Gao, Xiang

2017-11-15

A dense exopolysaccharide (EPS) matrix is crucial for cyanobacterial survival in terrestrial xeric environments, in which cyanobacteria undergo frequent expansion and shrinkage processes during environmental desiccation-rehydration cycles. However, it is unclear how terrestrial cyanobacteria coordinate the structural dynamics of the EPS matrix upon expansion and shrinkage to avoid potential mechanical stress while benefiting from the matrix. In the present study, we sought to answer this question by investigating the gene expression, protein dynamics, enzymatic characteristics, and biological roles of WspA, an abundantly secreted protein, in the representative terrestrial cyanobacterium Nostoc flagelliforme The results demonstrated that WspA is a novel β-galactosidase that facilitates softening of the EPS matrix by breaking the polysaccharide backbone under substantial moisture or facilitates the thickening and relinkage of the broken matrix during the drying process, and thus these regulations are well correlated with moisture availability or desiccation-rehydration cycles. This coordination of flexibility and rigidity of the cyanobacterial extracellular matrix may contribute to a favorable balance of cell growth and stress resistance in xeric environments. IMPORTANCE How the exopolysaccharide matrix is dynamically coordinated by exoproteins to cope with frequent expansion and shrinkage processes in terrestrial colonial cyanobacteria remains unclear. Here we elucidated the biochemical identity and biological roles of a dominant exoprotein in these regulation processes. Our study thus gained insight into this regulative mechanism in cyanobacteria to combat periodic desiccation. In addition, the filamentous drought-adapted cyanobacterium Nostoc flagelliforme serves as an ideal model for us to explore this issue in this study. Copyright © 2017 American Society for Microbiology.

'We didn't know anything, it was a mess!' Emergent structures and the effectiveness of a rescue operation multi-team system.

PubMed

Fleştea, Alina Maria; Fodor, Oana Cătălina; Curşeu, Petru Lucian; Miclea, Mircea

2017-01-01

Multi-team systems (MTS) are used to tackle unpredictable events and to respond effectively to fast-changing environmental contingencies. Their effectiveness is influenced by within as well as between team processes (i.e. communication, coordination) and emergent phenomena (i.e. situational awareness). The present case study explores the way in which the emergent structures and the involvement of bystanders intertwine with the dynamics of processes and emergent states both within and between the component teams. Our findings show that inefficient transition process and the ambiguous leadership generated poor coordination and hindered the development of emergent phenomena within the whole system. Emergent structures and bystanders substituted leadership functions and provided a pool of critical resources for the MTS. Their involvement fostered the emergence of situational awareness and facilitated contingency planning processes. However, bystander involvement impaired the emergence of cross-understandings and interfered with coordination processes between the component teams. Practitioner Summary: Based on a real emergency situation, the present research provides important theoretical and practical insights about the role of bystander involvement in the dynamics of multi-team systems composed to tackle complex tasks and respond to fast changing and unpredictable environmental contingencies.

Evidence of Early Strategies in Learning to Walk

ERIC Educational Resources Information Center

Snapp-Childs, Winona; Corbetta, Daniela

2009-01-01

Learning to walk is a dynamic process requiring the fine coordination, assembly, and balancing of many body segments at once. For the young walker, coordinating all these behavioral levels may be quite daunting. In this study, we examine the whole-body strategies to which infants resort to produce their first independent steps and progress over…

Coordination of Cellular Dynamics Contributes to Tooth Epithelium Deformations

PubMed Central

Morita, Ritsuko; Kihira, Miho; Nakatsu, Yousuke; Nomoto, Yohei; Ogawa, Miho; Ohashi, Kazumasa; Mizuno, Kensaku; Tachikawa, Tetsuhiko; Ishimoto, Yukitaka; Morishita, Yoshihiro; Tsuji, Takashi

2016-01-01

The morphologies of ectodermal organs are shaped by appropriate combinations of several deformation modes, such as invagination and anisotropic tissue elongation. However, how multicellular dynamics are coordinated during deformation processes remains to be elucidated. Here, we developed a four-dimensional (4D) analysis system for tracking cell movement and division at a single-cell resolution in developing tooth epithelium. The expression patterns of a Fucci probe clarified the region- and stage-specific cell cycle patterns within the tooth germ, which were in good agreement with the pattern of the volume growth rate estimated from tissue-level deformation analysis. Cellular motility was higher in the regions with higher growth rates, while the mitotic orientation was significantly biased along the direction of tissue elongation in the epithelium. Further, these spatio-temporal patterns of cellular dynamics and tissue-level deformation were highly correlated with that of the activity of cofilin, which is an actin depolymerization factor, suggesting that the coordination of cellular dynamics via actin remodeling plays an important role in tooth epithelial morphogenesis. Our system enhances the understanding of how cellular behaviors are coordinated during ectodermal organogenesis, which cannot be observed from histological analyses. PMID:27588418

Transition Pathway and Its Free-Energy Profile: A Protocol for Protein Folding Simulations

PubMed Central

Lee, In-Ho; Kim, Seung-Yeon; Lee, Jooyoung

2013-01-01

We propose a protocol that provides a systematic definition of reaction coordinate and related free-energy profile as the function of temperature for the protein-folding simulation. First, using action-derived molecular dynamics (ADMD), we investigate the dynamic folding pathway model of a protein between a fixed extended conformation and a compact conformation. We choose the pathway model to be the reaction coordinate, and the folding and unfolding processes are characterized by the ADMD step index, in contrast to the common a priori reaction coordinate as used in conventional studies. Second, we calculate free-energy profile as the function of temperature, by employing the replica-exchange molecular dynamics (REMD) method. The current method provides efficient exploration of conformational space and proper characterization of protein folding/unfolding dynamics from/to an arbitrary extended conformation. We demonstrate that combination of the two simulation methods, ADMD and REMD, provides understanding on molecular conformational changes in proteins. The protocol is tested on a small protein, penta-peptide of met-enkephalin. For the neuropeptide met-enkephalin system, folded, extended, and intermediate sates are well-defined through the free-energy profile over the reaction coordinate. Results are consistent with those in the literature. PMID:23917881

Climate Simulations with an Isentropic Finite Volume Dynamical Core

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Chih-Chieh; Rasch, Philip J.

2012-04-15

This paper discusses the impact of changing the vertical coordinate from a hybrid pressure to a hybrid-isentropic coordinate within the finite volume dynamical core of the Community Atmosphere Model (CAM). Results from a 20-year climate simulation using the new model coordinate configuration are compared to control simulations produced by the Eulerian spectral and FV dynamical cores of CAM which both use a pressure-based ({sigma}-p) coordinate. The same physical parameterization package is employed in all three dynamical cores. The isentropic modeling framework significantly alters the simulated climatology and has several desirable features. The revised model produces a better representation of heatmore » transport processes in the atmosphere leading to much improved atmospheric temperatures. We show that the isentropic model is very effective in reducing the long standing cold temperature bias in the upper troposphere and lower stratosphere, a deficiency shared among most climate models. The warmer upper troposphere and stratosphere seen in the isentropic model reduces the global coverage of high clouds which is in better agreement with observations. The isentropic model also shows improvements in the simulated wintertime mean sea-level pressure field in the northern hemisphere.« less

Movement Forms: A Graph-Dynamic Perspective

PubMed Central

Saltzman, Elliot; Holt, Ken

2014-01-01

The focus of this paper is on characterizing the physical movement forms (e.g., walk, crawl, roll, etc.) that can be used to actualize abstract, functionally-specified behavioral goals (e.g., locomotion). Emphasis is placed on how such forms are distinguished from one another, in part, by the set of topological patterns of physical contact between agent and environment (i.e., the set of physical graphs associated with each form) and the transitions among these patterns displayed over the course of performance (i.e., the form’s physical graph dynamics). Crucial in this regard is the creation and dissolution of loops in these graphs, which can be related to the distinction between open and closed kinematic chains. Formal similarities are described within the theoretical framework of task-dynamics between physically-closed kinematic chains (physical loops) that are created during various movement forms and functionally-closed kinematic chains (functional loops) that are associated with task-space control of end-effectors; it is argued that both types of loop must be flexibly incorporated into the coordinative structures that govern skilled action. Final speculation is focused on the role of graphs and their dynamics, not only in processes of coordination and control for individual agents, but also in processes of inter-agent coordination and the coupling of agents with (non-sentient) environmental objects. PMID:24910507

Movement Forms: A Graph-Dynamic Perspective.

PubMed

Saltzman, Elliot; Holt, Ken

2014-01-01

The focus of this paper is on characterizing the physical movement forms (e.g., walk, crawl, roll, etc.) that can be used to actualize abstract, functionally-specified behavioral goals (e.g., locomotion). Emphasis is placed on how such forms are distinguished from one another, in part, by the set of topological patterns of physical contact between agent and environment (i.e., the set of physical graphs associated with each form) and the transitions among these patterns displayed over the course of performance (i.e., the form's physical graph dynamics ). Crucial in this regard is the creation and dissolution of loops in these graphs, which can be related to the distinction between open and closed kinematic chains. Formal similarities are described within the theoretical framework of task-dynamics between physically-closed kinematic chains (physical loops) that are created during various movement forms and functionally-closed kinematic chains (functional loops) that are associated with task-space control of end-effectors; it is argued that both types of loop must be flexibly incorporated into the coordinative structures that govern skilled action. Final speculation is focused on the role of graphs and their dynamics, not only in processes of coordination and control for individual agents, but also in processes of inter-agent coordination and the coupling of agents with (non-sentient) environmental objects.

Direct and Quantitative Characterization of Dynamic Ligand Exchange between Coordination-Driven Self-Assembled Supramolecular Polygons

PubMed Central

Zheng, Yao-Rong; Stang, Peter J.

2009-01-01

The direct observation of dynamic ligand exchange beween Pt-N coordination-driven self-assembled supramolecular polygons (triangles and rectangles) has been achieved using stable isotope labeling (1H/2D) of the pyridyl donors and electrospray ionization mass spectrometry (ESI-MS) together with NMR spectroscopy. Both the thermodynamic and kinetic aspects of such exchange processes have been established based on quantitative mass spectral results. Further investigation showed that the exchange is highly dependent on experimental conditions such as temperature, solvent, and the counter anions. PMID:19243144

Direct and quantitative characterization of dynamic ligand exchange between coordination-driven self-assembled supramolecular polygons.

PubMed

Zheng, Yao-Rong; Stang, Peter J

2009-03-18

The direct observation of dynamic ligand exchange between Pt-N coordination-driven self-assembled supramolecular polygons (triangles and rectangles) has been achieved using stable (1)H/(2)D isotope labeling of the pyridyl donors and electrospray ionization mass spectrometry combined with NMR spectroscopy. Both the thermodynamic and kinetic aspects of such exchange processes have been established on the basis of quantitative mass spectral results. Further investigation has shown that the exchange is highly dependent on experimental conditions such as temperature, solvent, and the counteranions.

On the enhanced sampling over energy barriers in molecular dynamics simulations.

PubMed

Gao, Yi Qin; Yang, Lijiang

2006-09-21

We present here calculations of free energies of multidimensional systems using an efficient sampling method. The method uses a transformed potential energy surface, which allows an efficient sampling of both low and high energy spaces and accelerates transitions over barriers. It allows efficient sampling of the configuration space over and only over the desired energy range(s). It does not require predetermined or selected reaction coordinate(s). We apply this method to study the dynamics of slow barrier crossing processes in a disaccharide and a dipeptide system.

Reaction mechanism and reaction coordinates from the viewpoint of energy flow

PubMed Central

2016-01-01

Reaction coordinates are of central importance for correct understanding of reaction dynamics in complex systems, but their counter-intuitive nature made it a daunting challenge to identify them. Starting from an energetic view of a reaction process as stochastic energy flows biased towards preferred channels, which we deemed the reaction coordinates, we developed a rigorous scheme for decomposing energy changes of a system, both potential and kinetic, into pairwise components. The pairwise energy flows between different coordinates provide a concrete statistical mechanical language for depicting reaction mechanisms. Application of this scheme to the C7eq → C7ax transition of the alanine dipeptide in vacuum revealed novel and intriguing mechanisms that eluded previous investigations of this well studied prototype system for biomolecular conformational dynamics. Using a cost function developed from the energy decomposition components by proper averaging over the transition path ensemble, we were able to identify signatures of the reaction coordinates of this system without requiring any input from human intuition. PMID:27004858

Reaction mechanism and reaction coordinates from the viewpoint of energy flow

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Wenjin; Ma, Ao, E-mail: aoma@uic.edu

Reaction coordinates are of central importance for correct understanding of reaction dynamics in complex systems, but their counter-intuitive nature made it a daunting challenge to identify them. Starting from an energetic view of a reaction process as stochastic energy flows biased towards preferred channels, which we deemed the reaction coordinates, we developed a rigorous scheme for decomposing energy changes of a system, both potential and kinetic, into pairwise components. The pairwise energy flows between different coordinates provide a concrete statistical mechanical language for depicting reaction mechanisms. Application of this scheme to the C{sub 7eq} → C{sub 7ax} transition of themore » alanine dipeptide in vacuum revealed novel and intriguing mechanisms that eluded previous investigations of this well studied prototype system for biomolecular conformational dynamics. Using a cost function developed from the energy decomposition components by proper averaging over the transition path ensemble, we were able to identify signatures of the reaction coordinates of this system without requiring any input from human intuition.« less

Voltage Imaging of Waking Mouse Cortex Reveals Emergence of Critical Neuronal Dynamics

PubMed Central

Scott, Gregory; Fagerholm, Erik D.; Mutoh, Hiroki; Leech, Robert; Sharp, David J.; Shew, Woodrow L.

2014-01-01

Complex cognitive processes require neuronal activity to be coordinated across multiple scales, ranging from local microcircuits to cortex-wide networks. However, multiscale cortical dynamics are not well understood because few experimental approaches have provided sufficient support for hypotheses involving multiscale interactions. To address these limitations, we used, in experiments involving mice, genetically encoded voltage indicator imaging, which measures cortex-wide electrical activity at high spatiotemporal resolution. Here we show that, as mice recovered from anesthesia, scale-invariant spatiotemporal patterns of neuronal activity gradually emerge. We show for the first time that this scale-invariant activity spans four orders of magnitude in awake mice. In contrast, we found that the cortical dynamics of anesthetized mice were not scale invariant. Our results bridge empirical evidence from disparate scales and support theoretical predictions that the awake cortex operates in a dynamical regime known as criticality. The criticality hypothesis predicts that small-scale cortical dynamics are governed by the same principles as those governing larger-scale dynamics. Importantly, these scale-invariant principles also optimize certain aspects of information processing. Our results suggest that during the emergence from anesthesia, criticality arises as information processing demands increase. We expect that, as measurement tools advance toward larger scales and greater resolution, the multiscale framework offered by criticality will continue to provide quantitative predictions and insight on how neurons, microcircuits, and large-scale networks are dynamically coordinated in the brain. PMID:25505314

Ab initio molecular dynamics determination of competitive O 2 vs. N 2 adsorption at open metal sites of M 2 (dobdc)

DOE PAGES

Parkes, Marie V.; Greathouse, Jeffery A.; Hart, David B.; ...

2016-04-04

The separation of oxygen from nitrogen using metal–organic frameworks (MOFs) is of great interest for potential pressure-swing adsorption processes for the generation of purified O 2 on industrial scales. This study uses ab initio molecular dynamics (AIMD) simulations to examine for the first time the pure-gas and competitive gas adsorption of O 2 and N 2 in the M 2(dobdc) (M = Cr, Mn, Fe) MOF series with coordinatively unsaturated metal centers. Effects of metal, temperature, and gas composition are explored. Lastly, this unique application of AIMD allows us to study in detail the adsorption/desorption processes and to visualize themore » process of multiple guests competitively binding to coordinatively unsaturated metal sites of a MOF.« less

Nonparametric variational optimization of reaction coordinates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Banushkina, Polina V.; Krivov, Sergei V., E-mail: s.krivov@leeds.ac.uk

State of the art realistic simulations of complex atomic processes commonly produce trajectories of large size, making the development of automated analysis tools very important. A popular approach aimed at extracting dynamical information consists of projecting these trajectories into optimally selected reaction coordinates or collective variables. For equilibrium dynamics between any two boundary states, the committor function also known as the folding probability in protein folding studies is often considered as the optimal coordinate. To determine it, one selects a functional form with many parameters and trains it on the trajectories using various criteria. A major problem with such anmore » approach is that a poor initial choice of the functional form may lead to sub-optimal results. Here, we describe an approach which allows one to optimize the reaction coordinate without selecting its functional form and thus avoiding this source of error.« less

Ligand diffusion in proteins via enhanced sampling in molecular dynamics.

PubMed

Rydzewski, J; Nowak, W

2017-12-01

Computational simulations in biophysics describe the dynamics and functions of biological macromolecules at the atomic level. Among motions particularly important for life are the transport processes in heterogeneous media. The process of ligand diffusion inside proteins is an example of a complex rare event that can be modeled using molecular dynamics simulations. The study of physical interactions between a ligand and its biological target is of paramount importance for the design of novel drugs and enzymes. Unfortunately, the process of ligand diffusion is difficult to study experimentally. The need for identifying the ligand egress pathways and understanding how ligands migrate through protein tunnels has spurred the development of several methodological approaches to this problem. The complex topology of protein channels and the transient nature of the ligand passage pose difficulties in the modeling of the ligand entry/escape pathways by canonical molecular dynamics simulations. In this review, we report a methodology involving a reconstruction of the ligand diffusion reaction coordinates and the free-energy profiles along these reaction coordinates using enhanced sampling of conformational space. We illustrate the above methods on several ligand-protein systems, including cytochromes and G-protein-coupled receptors. The methods are general and may be adopted to other transport processes in living matter. Copyright © 2017 Elsevier B.V. All rights reserved.

Novel developments and applications of the classical adiabatic dynamics technique

NASA Astrophysics Data System (ADS)

Rosso, Lula

The present work aims to apply and develop modern molecular dynamics techniques based on a novel analysis of the classical adiabatic dynamics approach. In the first part of this thesis, Car-Parrinello ab-initio molecular dynamics, a successful technique based on adiabatic dynamics, is used to study the charge transport mechanism in solid ammonium perchlorate (AP) crystal exposed to an ammonia-rich environment. AP is a solid-state proton conductor composed of NH+4 and ClO-4 units that can undergo a decomposition process at high temperature, leading to its use such as rocket fuel. After computing IR spectra and carefully analysing the dynamics at different temperatures, we found that the charge transport mechanism in the pure crystal is dominated by diffusion of the ammonium ions and that the translational diffusion is strongly coupled to rotational diffusion of the two types of ions present. When the pure ammonium-perchlorate crystal is doped with neutral ammonia, another mechanism comes into play, namely, the Grotthuss proton hopping mechanism via short-lived N2H+7 complexes. In the second part of this thesis, adiabatic dynamics will be used to develop an alternative approach to the calculation of free energy profiles along reaction paths. The new method (AFED) is based on the creation of an adiabatic separation between the reaction coordinate subspace and the remaining degrees of freedom within a molecular dynamics run. This is achieved by associating with the reaction coordinate(s) a high temperature and large mass. These conditions allow the activated process to occur while permitting the remaining degrees of freedom to respond adiabatically. In this limit, by applying a formal multiple time scale Liouville operator factorization, it can be rigorously shown that the free energy profile is obtained directly from the probability distribution of the reaction coordinate subspace and, therefore, no postprocessing of the output data is required. The new method is applied to a variety of model problems and extended to calculate conformational surfaces of small peptides and the chemical potential of a Lennard-Jones liquid. The comparison with established methods shows that the new approach calculates free energy profiles with greater ease and efficiency.

A Systems Biology Approach to the Coordination of Defensive and Offensive Molecular Mechanisms in the Innate and Adaptive Host–Pathogen Interaction Networks

PubMed Central

Wu, Chia-Chou; Chen, Bor-Sen

2016-01-01

Infected zebrafish coordinates defensive and offensive molecular mechanisms in response to Candida albicans infections, and invasive C. albicans coordinates corresponding molecular mechanisms to interact with the host. However, knowledge of the ensuing infection-activated signaling networks in both host and pathogen and their interspecific crosstalk during the innate and adaptive phases of the infection processes remains incomplete. In the present study, dynamic network modeling, protein interaction databases, and dual transcriptome data from zebrafish and C. albicans during infection were used to infer infection-activated host–pathogen dynamic interaction networks. The consideration of host–pathogen dynamic interaction systems as innate and adaptive loops and subsequent comparisons of inferred innate and adaptive networks indicated previously unrecognized crosstalk between known pathways and suggested roles of immunological memory in the coordination of host defensive and offensive molecular mechanisms to achieve specific and powerful defense against pathogens. Moreover, pathogens enhance intraspecific crosstalk and abrogate host apoptosis to accommodate enhanced host defense mechanisms during the adaptive phase. Accordingly, links between physiological phenomena and changes in the coordination of defensive and offensive molecular mechanisms highlight the importance of host–pathogen molecular interaction networks, and consequent inferences of the host–pathogen relationship could be translated into biomedical applications. PMID:26881892

A Systems Biology Approach to the Coordination of Defensive and Offensive Molecular Mechanisms in the Innate and Adaptive Host-Pathogen Interaction Networks.

PubMed

Wu, Chia-Chou; Chen, Bor-Sen

2016-01-01

Infected zebrafish coordinates defensive and offensive molecular mechanisms in response to Candida albicans infections, and invasive C. albicans coordinates corresponding molecular mechanisms to interact with the host. However, knowledge of the ensuing infection-activated signaling networks in both host and pathogen and their interspecific crosstalk during the innate and adaptive phases of the infection processes remains incomplete. In the present study, dynamic network modeling, protein interaction databases, and dual transcriptome data from zebrafish and C. albicans during infection were used to infer infection-activated host-pathogen dynamic interaction networks. The consideration of host-pathogen dynamic interaction systems as innate and adaptive loops and subsequent comparisons of inferred innate and adaptive networks indicated previously unrecognized crosstalk between known pathways and suggested roles of immunological memory in the coordination of host defensive and offensive molecular mechanisms to achieve specific and powerful defense against pathogens. Moreover, pathogens enhance intraspecific crosstalk and abrogate host apoptosis to accommodate enhanced host defense mechanisms during the adaptive phase. Accordingly, links between physiological phenomena and changes in the coordination of defensive and offensive molecular mechanisms highlight the importance of host-pathogen molecular interaction networks, and consequent inferences of the host-pathogen relationship could be translated into biomedical applications.

Characteristics and Concepts of Dynamic Hub Proteins in DNA Processing Machinery from Studies of RPA

PubMed Central

Sugitani, Norie; Chazin, Walter J.

2015-01-01

DNA replication, damage response and repair require the coordinated action of multi-domain proteins operating within dynamic multi-protein machines that act upon the DNA substrate. These modular proteins contain flexible linkers of various lengths, which enable changes in the spatial distribution of the globular domains (architecture) that harbor their essential biochemical functions. This mobile architecture is uniquely suited to follow the evolving substrate landscape present over the course of the specific process performed by the multi-protein machinery. A fundamental advance in understanding of protein machinery is the realization of the pervasive role of dynamics. Not only is the machine undergoing dynamic transformations, but the proteins themselves are flexible and constantly adapting to the progression through the steps of the overall process. Within this dynamic context the activity of the constituent proteins must be coordinated, a role typically played by hub proteins. A number of important characteristics of modular proteins and concepts about the operation of dynamic machinery have been discerned. These provide the underlying basis for the action of the machinery that reads DNA, and responds to and repairs DNA damage. Here, we introduce a number of key characteristics and concepts, including the modularity of the proteins, linkage of weak binding sites, direct competition between sites, and allostery, using the well recognized hub protein replication protein A (RPA). PMID:25542993

A Multiagent System for Dynamic Data Aggregation in Medical Research

PubMed Central

Urovi, Visara; Barba, Imanol; Aberer, Karl; Schumacher, Michael Ignaz

2016-01-01

The collection of medical data for research purposes is a challenging and long-lasting process. In an effort to accelerate and facilitate this process we propose a new framework for dynamic aggregation of medical data from distributed sources. We use agent-based coordination between medical and research institutions. Our system employs principles of peer-to-peer network organization and coordination models to search over already constructed distributed databases and to identify the potential contributors when a new database has to be built. Our framework takes into account both the requirements of a research study and current data availability. This leads to better definition of database characteristics such as schema, content, and privacy parameters. We show that this approach enables a more efficient way to collect data for medical research. PMID:27975063

Coordinated Approaches to Quantify Long-Term Ecosystem dynamics in Response to Global Change

USDA-ARS?s Scientific Manuscript database

Climate change and its impact on ecosystems are usually assessed at decadal and century time scales. Ecological responses to climate change at those scales are strongly regulated by long-term processes, such as changes in species composition, carbon dynamics in soil and by big trees, and nutrient r...

Frontal Oscillatory Dynamics Predict Feedback Learning and Action Adjustment

ERIC Educational Resources Information Center

van de Vijver, Irene; Ridderinkhof, K. Richard; Cohen, Michael X.

2011-01-01

Frontal oscillatory dynamics in the theta (4-8 Hz) and beta (20-30 Hz) frequency bands have been implicated in cognitive control processes. Here we investigated the changes in coordinated activity within and between frontal brain areas during feedback-based response learning. In a time estimation task, participants learned to press a button after…

Configurational and constitutional information storage: multiple dynamics in systems based on pyridyl and acyl hydrazones.

PubMed

Chaur, Manuel N; Collado, Daniel; Lehn, Jean-Marie

2011-01-03

The C=N group of hydrazones can undergo E/Z isomerization both photochemically and thermally, allowing the generation of a closed process that can be tuned by either of these two physical stimuli. On the other hand, hydrazine-exchange reactions enable a constitutional change in a given hydrazone. The two classes of processes: 1) configurational (physically stimulated) and 2) constitutional (chemically stimulated) give access to short-term and long-term information storage, respectively. Such transformations are reported herein for two hydrazones (bis-pyridyl hydrazone and 2-pyridinecarboxaldehyde phenylhydrazone) that undergo a closed, chemically or physically driven process, and, in addition, can be locked or unlocked at will by metal-ion coordination or removal. These features also extend to acyl hydrazones derived from 2-pyridinecarboxaldehyde. Similarly to the terpydine-like hydrazones, such acyl hydrazones can undergo both constitutional and configurational changes, as well as metal-ion coordination. All these types of hydrazones represent dynamic systems capable of acting as multiple state molecular devices, in which the presence of coordination sites furthermore allows the metal ion-controlled locking and unlocking of the interconversion of the different states. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

ROS as Regulators of Mitochondrial Dynamics in Neurons.

PubMed

Cid-Castro, Carolina; Hernández-Espinosa, Diego Rolando; Morán, Julio

2018-07-01

Mitochondrial dynamics is a complex process, which involves the fission and fusion of mitochondrial outer and inner membranes. These processes organize the mitochondrial size and morphology, as well as their localization throughout the cells. In the last two decades, it has become a spotlight due to their importance in the pathophysiological processes, particularly in neurological diseases. It is known that Drp1, mitofusin 1 and 2, and Opa1 constitute the core of proteins that coordinate this intricate and dynamic process. Likewise, changes in the levels of reactive oxygen species (ROS) lead to modifications in the expression and/or activity of the proteins implicated in the mitochondrial dynamics, suggesting an involvement of these molecules in the process. In this review, we discuss the role of ROS in the regulation of fusion/fission in the nervous system, as well as the involvement of mitochondrial dynamics proteins in neurodegenerative diseases.

A Soluble Dynamic Complex Strategy for the Solution-Processed Fabrication of Organic Thin-Film Transistors of a Boron-Containing Polycyclic Aromatic Hydrocarbon.

PubMed

Matsuo, Kyohei; Saito, Shohei; Yamaguchi, Shigehiro

2016-09-19

The solution-processed fabrication of thin films of organic semiconductors enables the production of cost-effective, large-area organic electronic devices under mild conditions. The formation/dissociation of a dynamic B-N coordination bond can be used for the solution-processed fabrication of semiconducting films of polycyclic aromatic hydrocarbon (PAH) materials. The poor solubility of a boron-containing PAH in chloroform, toluene, and chlorobenzene was significantly improved by addition of minor amounts (1 wt % of solvent) of pyridine derivatives, as their coordination to the boron atom suppresses the inherent propensity of the PAHs to form π-stacks. Spin-coating solutions of the thus formed Lewis acid-base complexes resulted in the formation of amorphous thin films, which could be converted into polycrystalline films of the boron-containing PAH upon thermal annealing. Organic thin-film transistors prepared by this solution process displayed typical p-type characteristics. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bidirectional Coupling between Astrocytes and Neurons Mediates Learning and Dynamic Coordination in the Brain: A Multiple Modeling Approach

PubMed Central

Wade, John J.; McDaid, Liam J.; Harkin, Jim; Crunelli, Vincenzo; Kelso, J. A. Scott

2011-01-01

In recent years research suggests that astrocyte networks, in addition to nutrient and waste processing functions, regulate both structural and synaptic plasticity. To understand the biological mechanisms that underpin such plasticity requires the development of cell level models that capture the mutual interaction between astrocytes and neurons. This paper presents a detailed model of bidirectional signaling between astrocytes and neurons (the astrocyte-neuron model or AN model) which yields new insights into the computational role of astrocyte-neuronal coupling. From a set of modeling studies we demonstrate two significant findings. Firstly, that spatial signaling via astrocytes can relay a “learning signal” to remote synaptic sites. Results show that slow inward currents cause synchronized postsynaptic activity in remote neurons and subsequently allow Spike-Timing-Dependent Plasticity based learning to occur at the associated synapses. Secondly, that bidirectional communication between neurons and astrocytes underpins dynamic coordination between neuron clusters. Although our composite AN model is presently applied to simplified neural structures and limited to coordination between localized neurons, the principle (which embodies structural, functional and dynamic complexity), and the modeling strategy may be extended to coordination among remote neuron clusters. PMID:22242121

The coordination dynamics of social neuromarkers.

PubMed

Tognoli, Emmanuelle; Kelso, J A Scott

2015-01-01

Social behavior is a complex integrative function that entails many aspects of the brain's sensory, cognitive, emotional and movement capacities. Its neural processes are seldom simultaneous but occur according to precise spatiotemporal choreographies, manifested by the coordination of their oscillations within and between brains. Methods with good temporal resolution can help to identify so-called "neuromarkers" of social function and aid in disentangling the dynamical architecture of social brains. In our ongoing research, we have used dual-electroencephalography (EEG) to study neuromarker dynamics during synchronic interactions in which pairs of subjects coordinate behavior spontaneously and intentionally (social coordination) and during diachronic transactions that require subjects to perceive or behave in turn (action observation, delayed imitation). In this paper, after outlining our dynamical approach to the neurophysiological basis of social behavior, we examine commonalities and differences in the neuromarkers that are recruited for both kinds of tasks. We find the neuromarker landscape to be task-specific: synchronic paradigms of social coordination reveal medial mu, alpha and the phi complex as contributing neuromarkers. Diachronic tasks recruit alpha as well, in addition to lateral mu rhythms and the newly discovered nu and kappa rhythms whose functional significance is still unclear. Social coordination, observation, and delayed imitation share commonality of context: in each of our experiments, subjects exchanged information through visual perception and moved in similar ways. Nonetheless, there was little overlap between their neuromarkers, a result that hints strongly of task-specific neural mechanisms for social behavior. The only neuromarker that transcended both synchronic and diachronic social behaviors was the ubiquitous alpha rhythm, which appears to be a key signature of visually-mediated social behaviors. The present paper is both an entry point and a challenge: much work remains to determine the nature and scope of recruitment of other neuromarkers, and to create theoretical models of their within- and between-brain dynamics during social interaction.

The coordination dynamics of social neuromarkers

PubMed Central

Tognoli, Emmanuelle; Kelso, J. A. Scott

2015-01-01

Social behavior is a complex integrative function that entails many aspects of the brain’s sensory, cognitive, emotional and movement capacities. Its neural processes are seldom simultaneous but occur according to precise spatiotemporal choreographies, manifested by the coordination of their oscillations within and between brains. Methods with good temporal resolution can help to identify so-called “neuromarkers” of social function and aid in disentangling the dynamical architecture of social brains. In our ongoing research, we have used dual-electroencephalography (EEG) to study neuromarker dynamics during synchronic interactions in which pairs of subjects coordinate behavior spontaneously and intentionally (social coordination) and during diachronic transactions that require subjects to perceive or behave in turn (action observation, delayed imitation). In this paper, after outlining our dynamical approach to the neurophysiological basis of social behavior, we examine commonalities and differences in the neuromarkers that are recruited for both kinds of tasks. We find the neuromarker landscape to be task-specific: synchronic paradigms of social coordination reveal medial mu, alpha and the phi complex as contributing neuromarkers. Diachronic tasks recruit alpha as well, in addition to lateral mu rhythms and the newly discovered nu and kappa rhythms whose functional significance is still unclear. Social coordination, observation, and delayed imitation share commonality of context: in each of our experiments, subjects exchanged information through visual perception and moved in similar ways. Nonetheless, there was little overlap between their neuromarkers, a result that hints strongly of task-specific neural mechanisms for social behavior. The only neuromarker that transcended both synchronic and diachronic social behaviors was the ubiquitous alpha rhythm, which appears to be a key signature of visually-mediated social behaviors. The present paper is both an entry point and a challenge: much work remains to determine the nature and scope of recruitment of other neuromarkers, and to create theoretical models of their within- and between-brain dynamics during social interaction. PMID:26557067

A Petri-net coordination model for an intelligent mobile robot

NASA Technical Reports Server (NTRS)

Wang, F.-Y.; Kyriakopoulos, K. J.; Tsolkas, A.; Saridis, G. N.

1990-01-01

The authors present a Petri net model of the coordination level of an intelligent mobile robot system (IMRS). The purpose of this model is to specify the integration of the individual efforts on path planning, supervisory motion control, and vision systems that are necessary for the autonomous operation of the mobile robot in a structured dynamic environment. This is achieved by analytically modeling the various units of the system as Petri net transducers and explicitly representing the task precedence and information dependence among them. The model can also be used to simulate the task processing and to evaluate the efficiency of operations and the responsibility of decisions in the coordination level of the IMRS. Some simulation results on the task processing and learning are presented.

Measuring, managing and maximizing refinery performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bascur, O.A.; Kennedy, J.P.

1996-01-01

Implementing continuous quality improvement is a confluence of total quality management, people empowerment, performance indicators and information engineering. Supporting information technologies allow a refiner to narrow the gap between management objectives and the process control level. Dynamic performance monitoring benefits come from production cost savings, improved communications and enhanced decision making. A refinery workgroup information flow model helps automate continuous improvement of processes, performance and the organization. The paper discusses the rethinking of refinery operations, dynamic performance monitoring, continuous process improvement, the knowledge coordinator and repository manager, an integrated plant operations workflow, and successful implementation.

Transition Manifolds of Complex Metastable Systems: Theory and Data-Driven Computation of Effective Dynamics.

PubMed

Bittracher, Andreas; Koltai, Péter; Klus, Stefan; Banisch, Ralf; Dellnitz, Michael; Schütte, Christof

2018-01-01

We consider complex dynamical systems showing metastable behavior, but no local separation of fast and slow time scales. The article raises the question of whether such systems exhibit a low-dimensional manifold supporting its effective dynamics. For answering this question, we aim at finding nonlinear coordinates, called reaction coordinates, such that the projection of the dynamics onto these coordinates preserves the dominant time scales of the dynamics. We show that, based on a specific reducibility property, the existence of good low-dimensional reaction coordinates preserving the dominant time scales is guaranteed. Based on this theoretical framework, we develop and test a novel numerical approach for computing good reaction coordinates. The proposed algorithmic approach is fully local and thus not prone to the curse of dimension with respect to the state space of the dynamics. Hence, it is a promising method for data-based model reduction of complex dynamical systems such as molecular dynamics.

Network structure shapes spontaneous functional connectivity dynamics.

PubMed

Shen, Kelly; Hutchison, R Matthew; Bezgin, Gleb; Everling, Stefan; McIntosh, Anthony R

2015-04-08

The structural organization of the brain constrains the range of interactions between different regions and shapes ongoing information processing. Therefore, it is expected that large-scale dynamic functional connectivity (FC) patterns, a surrogate measure of coordination between brain regions, will be closely tied to the fiber pathways that form the underlying structural network. Here, we empirically examined the influence of network structure on FC dynamics by comparing resting-state FC (rsFC) obtained using BOLD-fMRI in macaques (Macaca fascicularis) to structural connectivity derived from macaque axonal tract tracing studies. Consistent with predictions from simulation studies, the correspondence between rsFC and structural connectivity increased as the sample duration increased. Regions with reciprocal structural connections showed the most stable rsFC across time. The data suggest that the transient nature of FC is in part dependent on direct underlying structural connections, but also that dynamic coordination can occur via polysynaptic pathways. Temporal stability was found to be dependent on structural topology, with functional connections within the rich-club core exhibiting the greatest stability over time. We discuss these findings in light of highly variable functional hubs. The results further elucidate how large-scale dynamic functional coordination exists within a fixed structural architecture. Copyright © 2015 the authors 0270-6474/15/355579-10$15.00/0.

Coordination of the health policy dialogue process in Guinea: pre- and post-Ebola.

PubMed

Ade, Nadege; Réne, Adzodo; Khalifa, Mara; Babila, Kevin Ousman; Monono, Martin Ekeke; Tarcisse, Elongo; Nabyonga-Orem, Juliet

2016-07-18

Policy dialogue can be defined as an iterative process that involves a broad range of stakeholders discussing a particular issue with a concrete purpose in mind. Policy dialogue in health is increasingly being recognised by health stakeholders in developing countries, as an important process or mechanism for improving collaboration and harmonization in health and for developing comprehensive and evidence-based health sector strategies and plans. It is with this perspective in mind that Guinea, in 2013, started a policy dialogue process, engaging a plethora of actors to revise the country's national health policy and develop a new national health development plan (2015-2024). This study examines the coordination of the policy dialogue process in developing these key strategic governance documents of the Guinean health sector from the actors' perspective. A qualitative case study approach was undertaken, comprising of interviews with key stakeholders who participated in the policy dialogue process. A review of the literature informed the development of a conceptual framework and the data collection survey questionnaire. The results were analysed both inductively and deductively. A total of 22 out of 32 individuals were interviewed. The results suggest both areas of strengths and weaknesses in the coordination of the policy dialogue process in Guinea. The aspects of good coordination observed were the iterative nature of the dialogue and the availability of neutral and well-experienced facilitators. Weak coordination was perceived through the unavailability of supporting documentation, time and financial constraints experienced during the dialogue process. The onset of the Ebola epidemic in Guinea impacted on coordination dynamics by causing a slowdown of its activities and then its virtual halt. The findings herein highlight the need for policy dialogue coordination structures to have the necessary administrative and institutional support to facilitate their effective functioning. The findings also point to the need for further research on the practical and operational aspects of national dialogue coordination structures to determine how to best strengthen their capacities.

Large fluctuations in anti-coordination games on scale-free graphs

NASA Astrophysics Data System (ADS)

Sabsovich, Daniel; Mobilia, Mauro; Assaf, Michael

2017-05-01

We study the influence of the complex topology of scale-free graphs on the dynamics of anti-coordination games (e.g. snowdrift games). These reference models are characterized by the coexistence (evolutionary stable mixed strategy) of two competing species, say ‘cooperators’ and ‘defectors’, and, in finite systems, by metastability and large-fluctuation-driven fixation. In this work, we use extensive computer simulations and an effective diffusion approximation (in the weak selection limit) to determine under which circumstances, depending on the individual-based update rules, the topology drastically affects the long-time behavior of anti-coordination games. In particular, we compute the variance of the number of cooperators in the metastable state and the mean fixation time when the dynamics is implemented according to the voter model (death-first/birth-second process) and the link dynamics (birth/death or death/birth at random). For the voter update rule, we show that the scale-free topology effectively renormalizes the population size and as a result the statistics of observables depend on the network’s degree distribution. In contrast, such a renormalization does not occur with the link dynamics update rule and we recover the same behavior as on complete graphs.

Reorganization of the human central nervous system.

PubMed

Schalow, G; Zäch, G A

2000-10-01

The key strategies on which the discovery of the functional organization of the central nervous system (CNS) under physiologic and pathophysiologic conditions have been based included (1) our measurements of phase and frequency coordination between the firings of alpha- and gamma-motoneurons and secondary muscle spindle afferents in the human spinal cord, (2) knowledge on CNS reorganization derived upon the improvement of the functions of the lesioned CNS in our patients in the short-term memory and the long-term memory (reorganization), and (3) the dynamic pattern approach for re-learning rhythmic coordinated behavior. The theory of self-organization and pattern formation in nonequilibrium systems is explicitly related to our measurements of the natural firing patterns of sets of identified single neurons in the human spinal premotor network and re-learned coordinated movements following spinal cord and brain lesions. Therapy induced cell proliferation, and maybe, neurogenesis seem to contribute to the host of structural changes during the process of re-learning of the lesioned CNS. So far, coordinated functions like movements could substantially be improved in every of the more than 100 patients with a CNS lesion by applying coordination dynamic therapy. As suggested by the data of our patients on re-learning, the human CNS seems to have a second integrative strategy for learning, re-learning, storing and recalling, which makes an essential contribution of the functional plasticity following a CNS lesion. A method has been developed by us for the simultaneous recording with wire electrodes of extracellular action potentials from single human afferent and efferent nerve fibres of undamaged sacral nerve roots. A classification scheme of the nerve fibres in the human peripheral nervous system (PNS) could be set up in which the individual classes of nerve fibres are characterized by group conduction velocities and group nerve fibre diameters. Natural impulse patterns of several identified single afferent and efferent nerve fibres (motoneuron axons) were extracted from multi-unit impulse patterns, and human CNS functions could be analyzed under physiologic and pathophysiologic conditions. With our discovery of premotor spinal oscillators it became possible to judge upon CNS neuronal network organization based on the firing patterns of these spinal oscillators and their driving afferents. Since motoneurons fire occasionally for low activation and oscillatory for high activation, the coherent organization of subnetworks to generate macroscopic function is very complex and for the time being, may be best described by the theory of coordination dynamics. Since oscillatory firing has also been observed by us in single motor unit firing patterns measured electromyographically, it seems possible to follow up therapeutic intervention in patients with spinal cord and brain lesions not only based on the activity levels and phases of motor programs during locomotion but also based on the physiologic and pathophysiologic firing patterns and recruitment of spinal oscillators. The improvement of the coordination dynamics of the CNS can be partly measured directly by rhythmicity upon the patient performing rhythmic movements coordinated up to milliseconds. Since rhythmic dynamic, coordinated, stereotyped movements are mainly located in the spinal cord and only little supraspinal drive is necessary to initiate, maintain, and terminate them, rhythmic, dynamic, coordinated movements were used in therapy to enforce reorganization of the lesioned CNS by improving the self-organization and relative coordination of spinal oscillators (and their interactions with occasionally firing motoneurons) which became pathologic in their firing following CNS lesion. Paraparetic, tetraparetic spinal cord and brain-lesioned patients re-learned running and other movements by an oscillator formation and coordination dynamic therapy. Our development in neurorehabilitation is in accordance with those of theoretical and computational neurosciences which deal with the self-organization of neuronal networks. In particular, jumping on a springboard 'in-phase' and in 'anti-phase' to re-learn phase relations of oscillator coupling can be understood in the framework of the Haken-Kelso-Bunz coordination dynamic model. By introducing broken symmetry, intention, learning and spasticity in the landscape of the potential function of the integrated CNS activity, the change in self-organization becomes understandable. Movement patterns re-learned by oscillator formation and coordination dynamic therapy evolve from reorganization and regeneration of the lesioned CNS by cooperative and competitive interplay between intrinsic coordination dynamics, extrinsic therapy related inputs with physiologic re-afferent input, including intention, motivation, supervised learning, interpersonal coordination, and genetic constraints including neurogenesis. (ABSTRACT TRUNCATED)

Team dynamics, clinical work satisfaction, and patient care coordination between primary care providers: A mixed methods study.

PubMed

Song, Hummy; Ryan, Molly; Tendulkar, Shalini; Fisher, Josephine; Martin, Julia; Peters, Antoinette S; Frolkis, Joseph P; Rosenthal, Meredith B; Chien, Alyna T; Singer, Sara J

Team-based care is essential for delivering high-quality, comprehensive, and coordinated care. Despite considerable research about the effects of team-based care on patient outcomes, few studies have examined how team dynamics relate to provider outcomes. The aim of this study was to examine relationships among team dynamics, primary care provider (PCP) clinical work satisfaction, and patient care coordination between PCPs in 18 Harvard-affiliated primary care practices participating in Harvard's Academic Innovations Collaborative. First, we administered a cross-sectional survey to all 548 PCPs (267 attending clinicians, 281 resident physicians) working at participating practices; 65% responded. We assessed the relationship of team dynamics with PCPs' clinical work satisfaction and perception of patient care coordination between PCPs, respectively, and the potential mediating effect of patient care coordination on the relationship between team dynamics and work satisfaction. In addition, we embedded a qualitative evaluation within the quantitative evaluation to achieve a convergent mixed methods design to help us better understand our findings and illuminate relationships among key variables. Better team dynamics were positively associated with clinical work satisfaction and quality of patient care coordination between PCPs. Coordination partially mediated the relationship between team dynamics and satisfaction for attending clinicians, suggesting that higher satisfaction depends, in part, on better teamwork, yielding more coordinated patient care. We found no mediating effects for resident physicians. Qualitative results suggest that sources of satisfaction from positive team dynamics for PCPs may be most relevant to attending clinicians. Improving primary care team dynamics could improve clinical work satisfaction among PCPs and patient care coordination between PCPs. In addition to improving outcomes that directly concern health care providers, efforts to improve aspects of team dynamics may also help resolve critical challenges in workforce planning in primary care.

Decision-making ability of Physarum polycephalum enhanced by its coordinated spatiotemporal oscillatory dynamics.

PubMed

Iwayama, Koji; Zhu, Liping; Hirata, Yoshito; Aono, Masashi; Hara, Masahiko; Aihara, Kazuyuki

2016-04-12

An amoeboid unicellular organism, a plasmodium of the true slime mold Physarum polycephalum, exhibits complex spatiotemporal oscillatory dynamics and sophisticated information processing capabilities while deforming its amorphous body. We previously devised an 'amoeba-based computer (ABC),' that implemented optical feedback control to lead this amoeboid organism to search for a solution to the traveling salesman problem (TSP). In the ABC, the shortest TSP route (the optimal solution) is represented by the shape of the organism in which the body area (nutrient absorption) is maximized while the risk of being exposed to aversive light stimuli is minimized. The shortness of the TSP route found by ABC, therefore, serves as a quantitative measure of the optimality of the decision made by the organism. However, it remains unclear how the decision-making ability of the organism originates from the oscillatory dynamics of the organism. We investigated the number of coexisting traveling waves in the spatiotemporal patterns of the oscillatory dynamics of the organism. We show that a shorter TSP route can be found when the organism exhibits a lower number of traveling waves. The results imply that the oscillatory dynamics are highly coordinated throughout the global body. Based on the results, we discuss the fact that the decision-making ability of the organism can be enhanced not by uncorrelated random fluctuations, but by its highly coordinated oscillatory dynamics.

The Interplay Between Language, Gesture, and Affect During Communicative Transition: A Dynamic Systems Approach

PubMed Central

Parladé, Meaghan V.; Iverson, Jana M.

2012-01-01

From a dynamic systems perspective, transition points in development are times of increased instability, during which behavioral patterns are susceptible to temporary decoupling. This study investigated the impact of the vocabulary spurt on existing patterns of communicative coordination. Eighteen typically developing infants were videotaped at home 1 month before, at, and after the vocabulary spurt. Infants were identified as spurters if they underwent a discrete phase transition in vocabulary development (marked by an inflection point), and compared with a group of nonspurters whose word-learning rates followed a trajectory of continuous change. Relative to surrounding sessions, there were significant reductions in overall coordination of communicative behaviors and in words produced in coordination at the vocabulary spurt session for infants who experienced more dramatic vocabulary growth. In contrast, nonspurters demonstrated little change across sessions. Findings underscore the importance of transitions as opportunities for observing processes of developmental change. PMID:21219063

Transition Manifolds of Complex Metastable Systems

NASA Astrophysics Data System (ADS)

Bittracher, Andreas; Koltai, Péter; Klus, Stefan; Banisch, Ralf; Dellnitz, Michael; Schütte, Christof

2018-04-01

We consider complex dynamical systems showing metastable behavior, but no local separation of fast and slow time scales. The article raises the question of whether such systems exhibit a low-dimensional manifold supporting its effective dynamics. For answering this question, we aim at finding nonlinear coordinates, called reaction coordinates, such that the projection of the dynamics onto these coordinates preserves the dominant time scales of the dynamics. We show that, based on a specific reducibility property, the existence of good low-dimensional reaction coordinates preserving the dominant time scales is guaranteed. Based on this theoretical framework, we develop and test a novel numerical approach for computing good reaction coordinates. The proposed algorithmic approach is fully local and thus not prone to the curse of dimension with respect to the state space of the dynamics. Hence, it is a promising method for data-based model reduction of complex dynamical systems such as molecular dynamics.

Simulating coupled dynamics of a rigid-flexible multibody system and compressible fluid

NASA Astrophysics Data System (ADS)

Hu, Wei; Tian, Qiang; Hu, HaiYan

2018-04-01

As a subsequent work of previous studies of authors, a new parallel computation approach is proposed to simulate the coupled dynamics of a rigid-flexible multibody system and compressible fluid. In this approach, the smoothed particle hydrodynamics (SPH) method is used to model the compressible fluid, the natural coordinate formulation (NCF) and absolute nodal coordinate formulation (ANCF) are used to model the rigid and flexible bodies, respectively. In order to model the compressible fluid properly and efficiently via SPH method, three measures are taken as follows. The first is to use the Riemann solver to cope with the fluid compressibility, the second is to define virtual particles of SPH to model the dynamic interaction between the fluid and the multibody system, and the third is to impose the boundary conditions of periodical inflow and outflow to reduce the number of SPH particles involved in the computation process. Afterwards, a parallel computation strategy is proposed based on the graphics processing unit (GPU) to detect the neighboring SPH particles and to solve the dynamic equations of SPH particles in order to improve the computation efficiency. Meanwhile, the generalized-alpha algorithm is used to solve the dynamic equations of the multibody system. Finally, four case studies are given to validate the proposed parallel computation approach.

Nonlinear dynamics of team performance and adaptability in emergency response.

PubMed

Guastello, Stephen J

2010-04-01

The impact of team size and performance feedback on adaptation levels and performance of emergency response (ER) teams was examined to introduce a metric for quantifying adaptation levels based on nonlinear dynamical systems (NDS) theory. NDS principles appear in reports surrounding Hurricane Katrina, earthquakes, floods, a disease epidemic, and the Southeast Asian tsunami. They are also intrinsic to coordination within teams, adaptation levels, and performance in dynamic decision processes. Performance was measured in a dynamic decision task in which ER teams of different sizes worked against an attacker who was trying to destroy a city (total N = 225 undergraduates). The complexity of teams' and attackers' adaptation strategies and the role of the opponents' performance were assessed by nonlinear regression analysis. An optimal group size for team performance was identified. Teams were more readily influenced by the attackers' performance than vice versa. The adaptive capabilities of attackers and teams were impaired by their opponents in some conditions. ER teams should be large enough to contribute a critical mass of ideas but not so large that coordination would be compromised. ER teams used self-organized strategies that could have been more adaptive, whereas attackers used chaotic strategies. The model and results are applicable to ER processes or training maneuvers involving dynamic decisions but could be limited to nonhierarchical groups.

Shared knowledge or shared affordances? Insights from an ecological dynamics approach to team coordination in sports.

PubMed

Silva, Pedro; Garganta, Júlio; Araújo, Duarte; Davids, Keith; Aguiar, Paulo

2013-09-01

Previous research has proposed that team coordination is based on shared knowledge of the performance context, responsible for linking teammates' mental representations for collective, internalized action solutions. However, this representational approach raises many questions including: how do individual schemata of team members become reformulated together? How much time does it take for this collective cognitive process to occur? How do different cues perceived by different individuals sustain a general shared mental representation? This representational approach is challenged by an ecological dynamics perspective of shared knowledge in team coordination. We argue that the traditional shared knowledge assumption is predicated on 'knowledge about' the environment, which can be used to share knowledge and influence intentions of others prior to competition. Rather, during competitive performance, the control of action by perceiving surrounding informational constraints is expressed in 'knowledge of' the environment. This crucial distinction emphasizes perception of shared affordances (for others and of others) as the main communication channel between team members during team coordination tasks. From this perspective, the emergence of coordinated behaviours in sports teams is based on the formation of interpersonal synergies between players resulting from collective actions predicated on shared affordances.

Binding of anions in triply interlocked coordination catenanes and dynamic allostery for dehalogenation reactions.

PubMed

Yang, Linlin; Jing, Xu; An, Bowen; He, Cheng; Yang, Yang; Duan, Chunying

2018-01-28

By synergistic combination of multicomponent self-assembly and template-directed approaches, triply interlocked metal organic catenanes that consist of two isolated chirally identical tetrahedrons were constructed and stabilized as thermodynamic minima. In the presence of suitable template anions, the structural conversion from the isolated tetrahedral conformers into locked catenanes occurred via the cleavage of an intrinsically reversible coordination bond in each of the tetrahedrons, followed by the reengineering and interlocking of two fragments with the regeneration of the broken coordination bonds. The presence of several kinds of individual pocket that were attributed to the triply interlocked patterns enabled the possibility of encapsulating different anions, allowing the dynamic allostery between the unlocked/locked conformers to promote the dehalogenation reaction of 3-bromo-cyclohexene efficiently, as with the use of dehalogenase enzymes. The interlocked structures could be unlocked into two individual tetrahedrons through removal of the well-matched anion templates. The stability and reversibility of the locked/unlocked structures were further confirmed by the catching/releasing process that accompanied emission switching, providing opportunities for the system to be a dynamic molecular logic system.

m-AAA and i-AAA complexes coordinate to regulate OMA1, the stress-activated supervisor of mitochondrial dynamics.

PubMed

Consolato, Francesco; Maltecca, Francesca; Tulli, Susanna; Sambri, Irene; Casari, Giorgio

2018-04-09

The proteolytic processing of dynamin-like GTPase OPA1, mediated by the activity of both YME1L1 [intermembrane (i)-AAA protease complex] and OMA1, is a crucial step in the regulation of mitochondrial dynamics. OMA1 is a zinc metallopeptidase of the inner mitochondrial membrane that undergoes pre-activating proteolytic and auto-proteolytic cleavage after mitochondrial import. Here, we identify AFG3L2 [matrix (m) - AAA complex] as the major protease mediating this event, which acts by maturing the 60 kDa pre-pro-OMA1 to the 40 kDa pro-OMA1 form by severing the N-terminal portion without recognizing a specific consensus sequence. Therefore, m - AAA and i - AAA complexes coordinately regulate OMA1 processing and turnover, and consequently control which OPA1 isoforms are present, thus adding new information on the molecular mechanisms of mitochondrial dynamics and neurodegenerative diseases affected by these phenomena.This article has an associated First Person interview with the first author of the paper. © 2018. Published by The Company of Biologists Ltd.

Mode transition coordinated control for a compound power-split hybrid car

NASA Astrophysics Data System (ADS)

Wang, Chen; Zhao, Zhiguo; Zhang, Tong; Li, Mengna

2017-03-01

With a compound power-split transmission directly connected to the engine in hybrid cars, dramatic fluctuations in engine output torque result in noticeable jerks when the car is in mode transition from electric drive mode to hybrid drive mode. This study designed a mode transition coordinated control strategy, and verified that strategy's effectiveness with both simulations and experiments. Firstly, the mode transition process was analyzed, and ride comfort issues during the mode transition process were demonstrated. Secondly, engine ripple torque was modeled using the measured cylinder pumping pressure when the engine was not in operation. The complete dynamic plant model of the power-split hybrid car was deduced, and its effectiveness was validated by a comparison of experimental and simulation results. Thirdly, a coordinated control strategy was designed to determine the desired engine torque, motor torque, and the moment of fuel injection. Active damping control with two degrees of freedom, based on reference output shaft speed estimation, was designed to mitigate driveline speed oscillations. Carrier torque estimation based on transmission kinematics and dynamics was used to suppress torque disturbance during engine cranking. The simulation and experimental results indicate that the proposed strategy effectively suppressed vehicle jerks and improved ride comfort during mode transition.

A Molecular Titration System Coordinates Ribosomal Protein Gene Transcription with Ribosomal RNA Synthesis.

PubMed

Albert, Benjamin; Knight, Britta; Merwin, Jason; Martin, Victoria; Ottoz, Diana; Gloor, Yvonne; Bruzzone, Maria Jessica; Rudner, Adam; Shore, David

2016-11-17

Cell growth potential is determined by the rate of ribosome biogenesis, a complex process that requires massive and coordinated transcriptional output. In the yeast Saccharomyces cerevisiae, ribosome biogenesis is highly regulated at the transcriptional level. Although evidence for a system that coordinates ribosomal RNA (rRNA) and ribosomal protein gene (RPG) transcription has been described, the molecular mechanisms remain poorly understood. Here we show that an interaction between the RPG transcriptional activator Ifh1 and the rRNA processing factor Utp22 serves to coordinate RPG transcription with that of rRNA. We demonstrate that Ifh1 is rapidly released from RPG promoters by a Utp22-independent mechanism following growth inhibition, but that its long-term dissociation requires Utp22. We present evidence that RNA polymerase I activity inhibits the ability of Utp22 to titrate Ifh1 from RPG promoters and propose that a dynamic Ifh1-Utp22 interaction fine-tunes RPG expression to coordinate RPG and rRNA transcription. Copyright © 2016 Elsevier Inc. All rights reserved.

Chaotic coordinates for the Large Helical Device

NASA Astrophysics Data System (ADS)

Hudson, Stuart; Suzuki, Yasuhiro

2014-10-01

The study of dynamical systems is facilitated by a coordinate framework with coordinate surfaces that coincide with invariant structures of the dynamical flow. For axisymmetric systems, a continuous family of invariant surfaces is guaranteed and straight-fieldline coordinates may be constructed. For non-integrable systems, e.g. stellarators, perturbed tokamaks, this continuous family is broken. Nevertheless, coordinates can still be constructed that simplify the description of the dynamics. The Poincare-Birkhoff theorem, the Aubry-Mather theorem, and the KAM theorem show that there are important structures that are invariant under the perturbed dynamics; namely the periodic orbits, the cantori, and the irrational flux surfaces. Coordinates adapted to these invariant sets, which we call chaotic coordinates, provide substantial advantages. The regular motion becomes straight, and the irregular motion is bounded by, and dissected by, coordinate surfaces that coincide with surfaces of locally-minimal magnetic-fieldline flux. The chaotic edge of the magnetic field, as calculated by HINT2 code, in the Large Helical Device (LHD) is examined, and a coordinate system is constructed so that the flux surfaces are ``straight'' and the islands become ``square.''

Quantitative imaging of mammalian transcriptional dynamics: from single cells to whole embryos.

PubMed

Zhao, Ziqing W; White, Melanie D; Bissiere, Stephanie; Levi, Valeria; Plachta, Nicolas

2016-12-23

Probing dynamic processes occurring within the cell nucleus at the quantitative level has long been a challenge in mammalian biology. Advances in bio-imaging techniques over the past decade have enabled us to directly visualize nuclear processes in situ with unprecedented spatial and temporal resolution and single-molecule sensitivity. Here, using transcription as our primary focus, we survey recent imaging studies that specifically emphasize the quantitative understanding of nuclear dynamics in both time and space. These analyses not only inform on previously hidden physical parameters and mechanistic details, but also reveal a hierarchical organizational landscape for coordinating a wide range of transcriptional processes shared by mammalian systems of varying complexity, from single cells to whole embryos.

Dynamic evolution characteristics of a fractional order hydropower station system

NASA Astrophysics Data System (ADS)

Gao, Xiang; Chen, Diyi; Yan, Donglin; Xu, Beibei; Wang, Xiangyu

2018-01-01

This paper investigates the dynamic evolution characteristics of the hydropower station by introducing the fractional order damping forces. A careful analysis of the dynamic characteristics of the generator shaft system is carried out under different values of fractional order. It turns out the vibration state of the axis coordinates has a certain evolution law with the increase of the fractional order. Significantly, the obtained law exists in the horizontal evolution and vertical evolution of the dynamical behaviors. Meanwhile, some interesting dynamical phenomena were found in this process. The outcomes of this study enrich the nonlinear dynamic theory from the engineering practice of hydropower stations.

Simulating Picosecond X-ray Diffraction from shocked crystals by Post-processing Molecular Dynamics Calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kimminau, G; Nagler, B; Higginbotham, A

2008-06-19

Calculations of the x-ray diffraction patterns from shocked crystals derived from the results of Non-Equilibrium-Molecular-Dynamics (NEMD) simulations are presented. The atomic coordinates predicted by the NEMD simulations combined with atomic form factors are used to generate a discrete distribution of electron density. A Fast-Fourier-Transform (FFT) of this distribution provides an image of the crystal in reciprocal space, which can be further processed to produce quantitative simulated data for direct comparison with experiments that employ picosecond x-ray diffraction from laser-irradiated crystalline targets.

Dynamic Heights in the Great Lakes using OPUS Projects

NASA Astrophysics Data System (ADS)

Roman, D. R.; Li, X.

2015-12-01

The U.S. will be implementing new geometric and vertical reference frames in 2022 to replace the North American Datum of 1983 (NAD 83) and the North American Vertical Datum of 1988 (NAVD 88), respectively. Less emphasized is the fact that a new dynamic height datum will also be defined about the same time to replace the International Great Lakes Datum of 1985 (IGLD 85). IGLD 85 was defined concurrent with NAVD 88 and used the same geopotential values. This paper focuses on the use of an existing tool for determining geometric coordinates and a developing geopotential model as a means of determining dynamic heights. The Online Positioning User Service (OPUS) Projects (OP) is an online tool available from the National Geodetic Survey (NGS) for use in developing geometric coordinates from simultaneous observations at multiple sites during multiple occupations. With observations performed at the water level gauges throughout the Great Lakes, the geometric coordinates of the mean water level surface can be determined. NGS has also developed the xGEOID15B model from satellite, airborne and surface gravity data. Using the input geometric coordinates determined through OP, the geopotential values for the water surface at the water level stations around the Great Lakes were determined using the xGEOID15B model. Comparisons were made between water level sites for each Lake as well as to existing IGLD 85 heights. A principal advantage to this approach is the ability to generate new water level control stations using OP, while maintaining the consistency between orthometric and dynamic heights by using the same gravity field model. Such a process may provide a means for determining dynamic heights for a future Great Lakes Datum.

Dynamic changes in cortical tensions in multiple cell types during germband retraction

NASA Astrophysics Data System (ADS)

Hutson, M. Shane; Lacy, Monica E.; McCleery, W. Tyler

The process of germband retraction in Drosophila embryogenesis involves the coordinated mechanics of both germband and amnioserosa cells. These two tissues simultaneously and coordinately uncurl from their interlocking U-like shapes. As tissue-level retraction proceeds, individual cells change shape in stereotypical ways. Using time-lapse confocal images, analysis of dynamic cellular triple-junction angles, and whole-embryo finite-element models, we have quantified dynamic changes in cortical tensions - including their anisotropy - in both germband and amnioserosa cells. We find a strong transition midway through the two-hour course of retraction at which point tensions and anisotropies undergo a near step change. These changes take place among amnioserosa cells, in multiple segments of the germband, and at the interface between these two tissues. Research was supported by NIH Grant Numbers 1R01GM099107 and 1R21AR068933.

Neuromechanics: an integrative approach for understanding motor control.

PubMed

Nishikawa, Kiisa; Biewener, Andrew A; Aerts, Peter; Ahn, Anna N; Chiel, Hillel J; Daley, Monica A; Daniel, Thomas L; Full, Robert J; Hale, Melina E; Hedrick, Tyson L; Lappin, A Kristopher; Nichols, T Richard; Quinn, Roger D; Satterlie, Richard A; Szymik, Brett

2007-07-01

Neuromechanics seeks to understand how muscles, sense organs, motor pattern generators, and brain interact to produce coordinated movement, not only in complex terrain but also when confronted with unexpected perturbations. Applications of neuromechanics include ameliorating human health problems (including prosthesis design and restoration of movement following brain or spinal cord injury), as well as the design, actuation and control of mobile robots. In animals, coordinated movement emerges from the interplay among descending output from the central nervous system, sensory input from body and environment, muscle dynamics, and the emergent dynamics of the whole animal. The inevitable coupling between neural information processing and the emergent mechanical behavior of animals is a central theme of neuromechanics. Fundamentally, motor control involves a series of transformations of information, from brain and spinal cord to muscles to body, and back to brain. The control problem revolves around the specific transfer functions that describe each transformation. The transfer functions depend on the rules of organization and operation that determine the dynamic behavior of each subsystem (i.e., central processing, force generation, emergent dynamics, and sensory processing). In this review, we (1) consider the contributions of muscles, (2) sensory processing, and (3) central networks to motor control, (4) provide examples to illustrate the interplay among brain, muscles, sense organs and the environment in the control of movement, and (5) describe advances in both robotics and neuromechanics that have emerged from application of biological principles in robotic design. Taken together, these studies demonstrate that (1) intrinsic properties of muscle contribute to dynamic stability and control of movement, particularly immediately after perturbations; (2) proprioceptive feedback reinforces these intrinsic self-stabilizing properties of muscle; (3) control systems must contend with inevitable time delays that can simplify or complicate control; and (4) like most animals under a variety of circumstances, some robots use a trial and error process to tune central feedforward control to emergent body dynamics.

Theoretical study on mechanisms of structural rearrangement and ionic dissociation in the HCl(H 2O) 4 cluster with path-integral molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Sugawara, Shuichi; Yoshikawa, Takehiro; Takayanagi, Toshiyuki; Tachikawa, Masanori

2011-01-01

The structural rearrangement process for the HCl(H2O)4 cluster has been studied by path-integral molecular dynamics simulations, where 'on-the-fly' calculation of the potential energy surface is done with the PM3-MAIS semiempirical level. The mechanisms of the rearrangement were analyzed using appropriate collective coordinates as well as detailed potential energy diagrams derived from low-lying stationary points. It was found that the vibrational entropy mainly determines the stability of the cluster structure especially at high temperatures. We have also found that the acidity of HCl in the cluster correlates with the coordination number of chlorine with respect water molecules.

Motor Coordination Dynamics Underlying Graphic Motion in 7- to 11-Year-Old Children

ERIC Educational Resources Information Center

Danna, Jeremy; Enderli, Fabienne; Athenes, Sylvie; Zanone, Pier-Giorgio

2012-01-01

Using concepts and tools of a dynamical system approach in order to understand motor coordination underlying graphomotor skills, the aim of the current study was to establish whether the basic coordination dynamics found in adults is already established in children at elementary school, when handwriting is trained and eventually acquired. In the…

Dynamic coordinated control during mode transition process for a compound power-split hybrid electric vehicle

NASA Astrophysics Data System (ADS)

Su, Yanzhao; Hu, Minghui; Su, Ling; Qin, Datong; Zhang, Tong; Fu, Chunyun

2018-07-01

The fuel economy of the hybrid electric vehicles (HEVs) can be effectively improved by the mode transition (MT). However, for a power-split powertrain whose power-split transmission is directly connected to the engine, the engine ripple torque (ERT), inconsistent dynamic characteristics (IDC) of engine and motors, model estimation inaccuracies (MEI), system parameter uncertainties (SPU) can cause jerk and vibration of transmission system during the MT process, which will reduce the driving comfort and the life of the drive parts. To tackle these problems, a dynamic coordinated control strategy (DCCS), including a staged engine torque feedforward and feedback estimation (ETFBC) and an active damping feedback compensation (ADBC) based on drive shaft torque estimation (DSTE), is proposed. And the effectiveness of this strategy is verified using a plant model. Firstly, the powertrain plant model is established, and the MT process and problems are analyzed. Secondly, considering the characteristics of the engine torque estimation (ETE) model before and after engine ignition, a motor torque compensation control based on the staged ERT estimation is developed. Then, considering the MEI, SPU and the load change, an ADBC based on a real-time nonlinear reduced-order robust observer of the DSTE is designed. Finally, the simulation results show that the proposed DCCS can effectively improve the driving comfort.

Dynamics and Kinetics Study of "In-Water" Chemical Reactions by Enhanced Sampling of Reactive Trajectories.

PubMed

Zhang, Jun; Yang, Y Isaac; Yang, Lijiang; Gao, Yi Qin

2015-11-12

High potential energy barriers and engagement of solvent coordinates set challenges for in silico studies of chemical reactions, and one is quite commonly limited to study reactions along predefined reaction coordinate(s). A systematic protocol, QM/MM MD simulations using enhanced sampling of reactive trajectories (ESoRT), is established to quantitatively study chemical transitions in complex systems. A number of trajectories for Claisen rearrangement in water and toluene were collected and analyzed, respectively. Evidence was found that the bond making and breaking during this reaction are concerted processes in solutions, preferentially through a chairlike configuration. Water plays an important dynamic role that helps stabilize the transition sate, and the dipole-dipole interaction between water and the solute also lowers the transition barrier. The calculated rate coefficient is consistent with the experimental measurement. Compared with water, the reaction pathway in toluene is "narrower" and the reaction rate is slower by almost three orders of magnitude due to the absence of proper interactions to stabilize the transition state. This study suggests that the "in-water" nature of the Claisen rearrangement in aqueous solution influences its thermodynamics, kinetics, as well as dynamics.

Dynamic ubiquitin signaling in cell cycle regulation

PubMed Central

Gilberto, Samuel

2017-01-01

The cell division cycle is driven by a collection of enzymes that coordinate DNA duplication and separation, ensuring that genomic information is faithfully and perpetually maintained. The activity of the effector proteins that perform and coordinate these biological processes oscillates by regulated expression and/or posttranslational modifications. Ubiquitylation is a cardinal cellular modification and is long known for driving cell cycle transitions. In this review, we emphasize emerging concepts of how ubiquitylation brings the necessary dynamicity and plasticity that underlie the processes of DNA replication and mitosis. New studies, often focusing on the regulation of chromosomal proteins like DNA polymerases or kinetochore kinases, are demonstrating that ubiquitylation is a versatile modification that can be used to fine-tune these cell cycle events, frequently through processes that do not involve proteasomal degradation. Understanding how the increasing variety of identified ubiquitin signals are transduced will allow us to develop a deeper mechanistic perception of how the multiple factors come together to faithfully propagate genomic information. Here, we discuss these and additional conceptual challenges that are currently under study toward understanding how ubiquitin governs cell cycle regulation. PMID:28684425

Dynamic ubiquitin signaling in cell cycle regulation.

PubMed

Gilberto, Samuel; Peter, Matthias

2017-08-07

The cell division cycle is driven by a collection of enzymes that coordinate DNA duplication and separation, ensuring that genomic information is faithfully and perpetually maintained. The activity of the effector proteins that perform and coordinate these biological processes oscillates by regulated expression and/or posttranslational modifications. Ubiquitylation is a cardinal cellular modification and is long known for driving cell cycle transitions. In this review, we emphasize emerging concepts of how ubiquitylation brings the necessary dynamicity and plasticity that underlie the processes of DNA replication and mitosis. New studies, often focusing on the regulation of chromosomal proteins like DNA polymerases or kinetochore kinases, are demonstrating that ubiquitylation is a versatile modification that can be used to fine-tune these cell cycle events, frequently through processes that do not involve proteasomal degradation. Understanding how the increasing variety of identified ubiquitin signals are transduced will allow us to develop a deeper mechanistic perception of how the multiple factors come together to faithfully propagate genomic information. Here, we discuss these and additional conceptual challenges that are currently under study toward understanding how ubiquitin governs cell cycle regulation. © 2017 Gilberto and Peter.

Optoelectronic scanning system upgrade by energy center localization methods

NASA Astrophysics Data System (ADS)

Flores-Fuentes, W.; Sergiyenko, O.; Rodriguez-Quiñonez, J. C.; Rivas-López, M.; Hernández-Balbuena, D.; Básaca-Preciado, L. C.; Lindner, L.; González-Navarro, F. F.

2016-11-01

A problem of upgrading an optoelectronic scanning system with digital post-processing of the signal based on adequate methods of energy center localization is considered. An improved dynamic triangulation analysis technique is proposed by an example of industrial infrastructure damage detection. A modification of our previously published method aimed at searching for the energy center of an optoelectronic signal is described. Application of the artificial intelligence algorithm of compensation for the error of determining the angular coordinate in calculating the spatial coordinate through dynamic triangulation is demonstrated. Five energy center localization methods are developed and tested to select the best method. After implementation of these methods, digital compensation for the measurement error, and statistical data analysis, a non-parametric behavior of the data is identified. The Wilcoxon signed rank test is applied to improve the result further. For optical scanning systems, it is necessary to detect a light emitter mounted on the infrastructure being investigated to calculate its spatial coordinate by the energy center localization method.

Combined Optimal Control System for excavator electric drive

NASA Astrophysics Data System (ADS)

Kurochkin, N. S.; Kochetkov, V. P.; Platonova, E. V.; Glushkin, E. Y.; Dulesov, A. S.

2018-03-01

The article presents a synthesis of the combined optimal control algorithms of the AC drive rotation mechanism of the excavator. Synthesis of algorithms consists in the regulation of external coordinates - based on the theory of optimal systems and correction of the internal coordinates electric drive using the method "technical optimum". The research shows the advantage of optimal combined control systems for the electric rotary drive over classical systems of subordinate regulation. The paper presents a method for selecting the optimality criterion of coefficients to find the intersection of the range of permissible values of the coordinates of the control object. There is possibility of system settings by choosing the optimality criterion coefficients, which allows one to select the required characteristics of the drive: the dynamic moment (M) and the time of the transient process (tpp). Due to the use of combined optimal control systems, it was possible to significantly reduce the maximum value of the dynamic moment (M) and at the same time - reduce the transient time (tpp).

The coordination chemistry of group 15 element ligand complexes--a developing area.

PubMed

Scheer, Manfred

2008-09-07

A survey of the contemporary challenges of the field of unsubstituted group 15 element ligand complexes (excluding N) is given. The focus of the article is on the coordination chemistry behaviour of such E(n) ligand complexes. This field is subdivided into two areas of reactivity: E(n) ligand complexes with (i) noncoordinated Lewis-acidic cations and (ii) Lewis-acidic coordination compounds containing at least one permanently coordinating ligand. In the latter case, insoluble 1D and 2D polymers respectively are obtained; however, under special conditions soluble, spherical, fullerene-like giant molecules are formed. These nano-sized molecules are up to 2.4 nm in diameter and are able to encapsulate small molecules in their holes. In contrast, the first-mentioned field uses weakly coordinating anions to obtain readily soluble di- and polycationic products. These show depolymerisation tendencies in solution under the formation of oligomer-monomer equilibria and thus reveal dynamic supramolecular aggregation processes.

Thermal shock induced dynamics of a spacecraft with a flexible deploying boom

NASA Astrophysics Data System (ADS)

Shen, Zhenxing; Li, Huijian; Liu, Xiaoning; Hu, Gengkai

2017-12-01

The dynamics in the process of deployment of a flexible extendible boom as a deployable structure on the spacecraft is studied. For determining the thermally induced vibrations of the boom subjected to an incident solar heat flux, an axially moving thermal-dynamic beam element based on the absolute nodal coordinate formulation which is able to precisely describe the large displacement, rotation and deformation of flexible body is presented. For the elastic forces formulation of variable-length beam element, the enhanced continuum mechanics approach is adopted, which can eliminate the Poisson locking effect, and take into account the tension-bending-torsion coupling deformations. The main body of the spacecraft, modeled as a rigid body, is described using the natural coordinates method. In the derived nonlinear thermal-dynamic equations of rigid-flexible multibody system, the mass matrix is time-variant, and a pseudo damping matrix which is without actual energy dissipation, and a heat conduction matrix which is relative to the moving speed and the number of beam element are arisen. Numerical results give the dynamic and thermal responses of the nonrotating and spinning spacecraft, respectively, and show that thermal shock has a significant influence on the dynamics of spacecraft.

The Effect of Aging on Muscular Dynamics Underlying Movement Patterns Changes.

PubMed

Vernooij, Carlijn A; Rao, Guillaume; Berton, Eric; Retornaz, Frédérique; Temprado, Jean-Jacques

2016-01-01

Introduction: Aging leads to alterations not only within the complex subsystems of the neuro-musculo-skeletal system, but also in the coupling between them. Here, we studied how aging affects functional reorganizations that occur both within and between the behavioral and muscular levels, which must be coordinated to produce goal-directed movements. Using unimanual reciprocal Fitts' task, we examined the behavioral and muscular dynamics of older adults (74.4 ± 3.7 years) and compared them to those found for younger adults (23.2 ± 2.0 years). Methods: To achieve this objective, we manipulated the target size to trigger a phase transition in the behavioral regime and searched for concomitant signatures of a phase transition in the muscular coordination. Here, muscular coordination was derived by using the method of muscular synergy extraction. With this technique, we obtained functional muscular patterns through non-negative matrix factorization of the muscular signals followed by clustering the resulting synergies. Results: Older adults showed a phase transition in behavioral regime, although, in contrast to young participants, their kinematic profiles did not show a discontinuity. In parallel, muscular coordination displayed two typical signatures of a phase transition, that is, increased variability of coordination patterns and a reorganization of muscular synergies. Both signatures confirmed the existence of muscular reorganization in older adults, which is coupled with change in dynamical regime at behavioral level. However, relative to young adults, transition occurred at lower index of difficulty (ID) in older participants and the reorganization of muscular patterns lasted longer (over multiple IDs). Discussion: This implies that consistent changes occur in coordination processes across behavior and muscle. Furthermore, the repertoire of muscular patterns was reduced and somewhat modified for older adults, relative to young participants. This suggests that aging is not only related to changes in individual muscles (e.g., caused by dynapenia) but also in their coordination.

Relationship among team dynamics, care coordination and perception of safety culture in primary care.

PubMed

Blumenthal, Karen J; Chien, Alyna T; Singer, Sara J

2018-05-18

There remains a need to improve patient safety in primary care settings. Studies have demonstrated that creating high-performing teams can improve patient safety and encourage a safety culture within hospital settings, but little is known about this relationship in primary care. To examine how team dynamics relate to perceptions of safety culture in primary care and whether care coordination plays an intermediating role. This is a cross-sectional survey study with 63% response (n = 1082). The study participants were attending clinicians, resident physicians and other staff who interacted with patients from 19 primary care practices affiliated with Harvard Medical School. Three domains corresponding with our main measures: team dynamics, care coordination and safety culture. All items were measured on a 5-point Likert scale. We used linear regression clustered by practice site to assess the relationship between team dynamics and perceptions of safety culture. We also performed a mediation analysis to determine the extent to which care coordination explains the relationship between perceptions of team dynamics and of safety culture. For every 1-point increase in overall team dynamics, there was a 0.76-point increase in perception of safety culture [95% confidence interval (CI) 0.70-0.82, P < 0.001]. Care coordination mediated the relationship between team dynamics and the perception of safety culture. Our findings suggest there is a relationship between team dynamics, care coordination and perceptions of patient safety in a primary care setting. To make patients safer, we may need to pay more attention to how primary care providers work together to coordinate care.

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

PubMed Central

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

2015-01-01

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. PMID:26174482

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

NASA Astrophysics Data System (ADS)

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.

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

PubMed

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

2015-07-15

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.

Connected vehicle data capture and management (DCM) and dynamic mobility applications (DMA) : focused standards coordination plan.

DOT National Transportation Integrated Search

2012-11-01

The Connected Vehicle Mobility Standards Coordination Plan project links activities in three programs (Data Capture and Management, Dynamic Mobility Applications, and ITS Standards). The plan coordinates the timing, intent and relationship of activit...

Complex Problem Solving in Teams: The Impact of Collective Orientation on Team Process Demands.

PubMed

Hagemann, Vera; Kluge, Annette

2017-01-01

Complex problem solving is challenging and a high-level cognitive process for individuals. When analyzing complex problem solving in teams, an additional, new dimension has to be considered, as teamwork processes increase the requirements already put on individual team members. After introducing an idealized teamwork process model, that complex problem solving teams pass through, and integrating the relevant teamwork skills for interdependently working teams into the model and combining it with the four kinds of team processes (transition, action, interpersonal, and learning processes), the paper demonstrates the importance of fulfilling team process demands for successful complex problem solving within teams. Therefore, results from a controlled team study within complex situations are presented. The study focused on factors that influence action processes, like coordination, such as emergent states like collective orientation, cohesion, and trust and that dynamically enable effective teamwork in complex situations. Before conducting the experiments, participants were divided by median split into two-person teams with either high ( n = 58) or low ( n = 58) collective orientation values. The study was conducted with the microworld C3Fire, simulating dynamic decision making, and acting in complex situations within a teamwork context. The microworld includes interdependent tasks such as extinguishing forest fires or protecting houses. Two firefighting scenarios had been developed, which takes a maximum of 15 min each. All teams worked on these two scenarios. Coordination within the team and the resulting team performance were calculated based on a log-file analysis. The results show that no relationships between trust and action processes and team performance exist. Likewise, no relationships were found for cohesion. Only collective orientation of team members positively influences team performance in complex environments mediated by action processes such as coordination within the team. The results are discussed in relation to previous empirical findings and to learning processes within the team with a focus on feedback strategies.

Complex Problem Solving in Teams: The Impact of Collective Orientation on Team Process Demands

PubMed Central

Hagemann, Vera; Kluge, Annette

2017-01-01

Complex problem solving is challenging and a high-level cognitive process for individuals. When analyzing complex problem solving in teams, an additional, new dimension has to be considered, as teamwork processes increase the requirements already put on individual team members. After introducing an idealized teamwork process model, that complex problem solving teams pass through, and integrating the relevant teamwork skills for interdependently working teams into the model and combining it with the four kinds of team processes (transition, action, interpersonal, and learning processes), the paper demonstrates the importance of fulfilling team process demands for successful complex problem solving within teams. Therefore, results from a controlled team study within complex situations are presented. The study focused on factors that influence action processes, like coordination, such as emergent states like collective orientation, cohesion, and trust and that dynamically enable effective teamwork in complex situations. Before conducting the experiments, participants were divided by median split into two-person teams with either high (n = 58) or low (n = 58) collective orientation values. The study was conducted with the microworld C3Fire, simulating dynamic decision making, and acting in complex situations within a teamwork context. The microworld includes interdependent tasks such as extinguishing forest fires or protecting houses. Two firefighting scenarios had been developed, which takes a maximum of 15 min each. All teams worked on these two scenarios. Coordination within the team and the resulting team performance were calculated based on a log-file analysis. The results show that no relationships between trust and action processes and team performance exist. Likewise, no relationships were found for cohesion. Only collective orientation of team members positively influences team performance in complex environments mediated by action processes such as coordination within the team. The results are discussed in relation to previous empirical findings and to learning processes within the team with a focus on feedback strategies. PMID:29033886

Electron-nuclear corellations for photoinduced dynamics in molecular dimers

NASA Astrophysics Data System (ADS)

Kilin, Dmitri S.; Pereversev, Yuryi V.; Prezhdo, Oleg V.

2003-03-01

Ultrafast photoinduced dynamics of electronic excitation in molecular dimers is drastically affected by dynamic reorganization of of inter- and intra- molecular nuclear configuration modelled by quantized nuclear degree of freedom [1]. The dynamics of the electronic population and nuclear coherence is analyzed with help of both numerical solution of the chain of coupled differential equations for mean coordinate, population inversion, electronic-vibrational correlation etc.[2] and by propagating the Gaussian wavepackets in relevant adiabatic potentials. Intriguing results were obtained in the approximation of small energy difference and small change of nuclear equilibrium configuration for excited electronic states. In the limiting case of resonance between electronic states energy difference and frequency of the nuclear mode these results have been justified by comparison to exactly solvable Jaynes-Cummings model. It has been found that the photoinduced processes in dimer are arranged according to their time scales:(i) fast scale of nuclear motion,(ii) intermediate scale of dynamical redistribution of electronic population between excited states as well as growth and dynamics of electronic -nuclear correlation,(iii) slow scale of electronic population approaching to the quasiequilibrium distribution, decay of electronic-nuclear correlation, and diminishing the amplitude of mean coordinate oscillations, accompanied by essential growth of the nuclear coordinate dispersion associated with the overall nuclear wavepacket width. Demonstrated quantum-relaxational features of photoinduced vibronic dinamical processess in molecular dimers are obtained by simple method, applicable to large biological systems with many degrees of freedom. [1] J. A. Cina, D. S. Kilin, T. S. Humble, J. Chem. Phys. (2003) in press. [2] O. V. Prezhdo, J. Chem. Phys. 117, 2995 (2002).

Self-assembly of a constitutional dynamic library of Cu(II) coordination polygons and reversible sorting by crystallization.

PubMed

Rancan, Marzio; Tessarolo, Jacopo; Zanonato, Pier Luigi; Seraglia, Roberta; Quici, Silvio; Armelao, Lidia

2013-06-07

A small coordination constitutional dynamic library (CDL) is self-assembled from Cu(2+) ions and the ortho bis-(3-acetylacetone)benzene ligand. Two coordination polygons, a rhomboid and a triangle, establish a dynamic equilibrium. Quantitative sorting of the rhomboidal polygon is reversibly obtained by crystallization. Thermodynamic and kinetic aspects ruling the CDL system have been elucidated.

N-MODY: A Code for Collisionless N-body Simulations in Modified Newtonian Dynamics

NASA Astrophysics Data System (ADS)

Londrillo, Pasquale; Nipoti, Carlo

2011-02-01

N-MODY is a parallel particle-mesh code for collisionless N-body simulations in modified Newtonian dynamics (MOND). N-MODY is based on a numerical potential solver in spherical coordinates that solves the non-linear MOND field equation, and is ideally suited to simulate isolated stellar systems. N-MODY can be used also to compute the MOND potential of arbitrary static density distributions. A few applications of N-MODY indicate that some astrophysically relevant dynamical processes are profoundly different in MOND and in Newtonian gravity with dark matter.

Relation between coordinate systems describing the dynamics of a loaded Stewart platform

NASA Astrophysics Data System (ADS)

Petrova, V. I.

2018-05-01

The paper puts forward formulae for transformation of coordinates in three coordinate frames used for the study of motion of a loaded Stewart platform, which is the central mechanism of the dynamic bench. A new method for finding the law of variation of coordinates is proposed. This method depends on solving the problem-specific system of differential equations.

Flexibility of Catalytic Zinc Coordination in Thermolysin and HDAC8: A Born-Oppenheimer ab initio QM/MM Molecular Dynamics Study

PubMed Central

Wu, Ruibo; Hu, Po; Wang, Shenglong; Cao, Zexing; Zhang, Yingkai

2009-01-01

Abstracs The different coordination modes and fast ligand exchange of zinc coordination has been suggested to be one key catalytic feature of the zinc ion which makes it an invaluable metal in biological catalysis. However, partly due to the well known difficulties for zinc to be characterized by spectroscopy methods, evidence for dynamic nature of the catalytic zinc coordination has so far mainly been indirect. In this work, Born-Oppenheimer ab initio QM/MM molecular dynamics simulation has been employed, which allows for a first-principle description of the dynamics of the metal active site while properly including effects of the heterogeneous and fluctuating protein environment. Our simulations have provided direct evidence regarding inherent flexibility of the catalytic zinc coordination shell in Thermolysin (TLN) and Histone Deacetylase 8 (HDAC8). We have observed different coordination modes and fast ligand exchange during the picosecond's time-scale. For TLN, the coordination of the carboxylate group of Glu166 to Zinc is found to continuously change between monodentate and bidentate manner dynamically; while for HDAC8, the flexibility mainly comes from the coordination to a non-amino-acid ligand. Such distinct dynamics in the zinc coordination shell between two enzymes suggests that the catalytic role of Zinc in TLN and HDAC8 is likely to be different in spite of the fact that both catalyze the hydrolysis of amide bond. Meanwhile, considering that such Born-Oppenheimer ab initio QM/MM MD simulations are very much desired but are widely considered to be too computationally expensive to be feasible, our current study demonstrates the viability and powerfulness of this state-of-the-art approach in simulating metalloenzymes. PMID:20161624

Two-phase strategy of controlling motor coordination determined by task performance optimality.

PubMed

Shimansky, Yury P; Rand, Miya K

2013-02-01

A quantitative model of optimal coordination between hand transport and grip aperture has been derived in our previous studies of reach-to-grasp movements without utilizing explicit knowledge of the optimality criterion or motor plant dynamics. The model's utility for experimental data analysis has been demonstrated. Here we show how to generalize this model for a broad class of reaching-type, goal-directed movements. The model allows for measuring the variability of motor coordination and studying its dependence on movement phase. The experimentally found characteristics of that dependence imply that execution noise is low and does not affect motor coordination significantly. From those characteristics it is inferred that the cost of neural computations required for information acquisition and processing is included in the criterion of task performance optimality as a function of precision demand for state estimation and decision making. The precision demand is an additional optimized control variable that regulates the amount of neurocomputational resources activated dynamically. It is shown that an optimal control strategy in this case comprises two different phases. During the initial phase, the cost of neural computations is significantly reduced at the expense of reducing the demand for their precision, which results in speed-accuracy tradeoff violation and significant inter-trial variability of motor coordination. During the final phase, neural computations and thus motor coordination are considerably more precise to reduce the cost of errors in making a contact with the target object. The generality of the optimal coordination model and the two-phase control strategy is illustrated on several diverse examples.

A theoretical model for the collective motion of proteins by means of principal component analysis

NASA Astrophysics Data System (ADS)

Kamberaj, Hiqmet

2011-02-01

A coarse grained model in the frame work of principal component analysis is presented. We used a bath of harmonic oscillators approach, based on classical mechanics, to derive the generalized Langevin equations of motion for the collective coordinates. The dynamics of the protein collective coordinates derived from molecular dynamics simulations have been studied for the Bovine Pancreatic Trypsin Inhibitor. We analyzed the stability of the method by studying structural fluctuations of the C a atoms obtained from a 20 ns molecular dynamics simulation. Subsequently, the dynamics of the collective coordinates of protein were characterized by calculating the dynamical friction coefficient and diffusion coefficients along with time-dependent correlation functions of collective coordinates. A dual diffusion behavior was observed with a fast relaxation time of short diffusion regime 0.2-0.4 ps and slow relaxation time of long diffusion about 1-2 ps. In addition, we observed a power law decay of dynamical friction coefficient with exponent for the first five collective coordinates varying from -0.746 to -0.938 for the real part and from -0.528 to -0.665 for its magnitude. It was found that only the first ten collective coordinates are responsible for configuration transitions occurring on time scale longer than 50 ps.

A benchmark for reaction coordinates in the transition path ensemble

PubMed Central

2016-01-01

The molecular mechanism of a reaction is embedded in its transition path ensemble, the complete collection of reactive trajectories. Utilizing the information in the transition path ensemble alone, we developed a novel metric, which we termed the emergent potential energy, for distinguishing reaction coordinates from the bath modes. The emergent potential energy can be understood as the average energy cost for making a displacement of a coordinate in the transition path ensemble. Where displacing a bath mode invokes essentially no cost, it costs significantly to move the reaction coordinate. Based on some general assumptions of the behaviors of reaction and bath coordinates in the transition path ensemble, we proved theoretically with statistical mechanics that the emergent potential energy could serve as a benchmark of reaction coordinates and demonstrated its effectiveness by applying it to a prototypical system of biomolecular dynamics. Using the emergent potential energy as guidance, we developed a committor-free and intuition-independent method for identifying reaction coordinates in complex systems. We expect this method to be applicable to a wide range of reaction processes in complex biomolecular systems. PMID:27059559

Potential application of artificial concepts to aerodynamic simulation

NASA Technical Reports Server (NTRS)

Kutler, P.; Mehta, U. B.; Andrews, A.

1984-01-01

The concept of artificial intelligence as it applies to computational fluid dynamics simulation is investigated. How expert systems can be adapted to speed the numerical aerodynamic simulation process is also examined. A proposed expert grid generation system is briefly described which, given flow parameters, configuration geometry, and simulation constraints, uses knowledge about the discretization process to determine grid point coordinates, computational surface information, and zonal interface parameters.

An Overview of OCTAV-UTLS (Observed Composition Trends and Variability in the UTLS), a SPARC Emerging Activity

NASA Astrophysics Data System (ADS)

Petropavlovskikh, I. V.; Manney, G. L.; Hoor, P. M.; Bourassa, A. E.; Braathen, G.; Chang, K. L.; Hegglin, M. I.; Kramarova, N. A.; Kunkel, D.; Lawrence, Z. D.; Leblanc, T.; Livesey, N. J.; Millan Valle, L. F.; Stiller, G. P.; Tegtmeier, S.; Thouret, V.; Voigt, C.; Walker, K. A.

2017-12-01

The distribution of tracers in the upper troposphere and lower stratosphere (UTLS) shows large spatial and temporal variability because of interactions of transport, chemical, and mixing processes near the tropopause, as well as variations in the location of the tropopause itself. This strongly affects quantitative estimates of the impact of radiatively active substances, including ozone and water vapour, on surface temperatures, and complicates diagnosis of dynamical processes such as stratosphere troposphere exchange (STE). The Stratosphere-troposphere Processes And their Role in Climate (SPARC) emerging activity OCTAV-UTLS (Observed Composition Trends and Variability in the UTLS) aims to reduce the uncertainties in trend estimates by accounting for these dynamically induced sources of variability. Achieving these goals by using existing UTLS trace gas observations from aircraft, ground-based, balloon and satellite platforms requires a consistent analysis of these different data with respect to the tropopause or the jets. As a central task for OCTAV-UTLS, we are developing and applying common metrics, calculated using the same reanalysis datasets, to compare UTLS data using geophysically-based coordinate systems including tropopause and upper tropospheric jet relative coordinates. In addition to assessing present day measurement capabilities, OCTAV-UTLS will assess gaps in current geographical / temporal sampling of the UTLS that limit our ability to determine atmospheric composition variability and trends. This talk will provide an overview of the OCTAV-UTLS activity and some examples of initial calculations of geophysically-based coordinates and comparisons of remapped data.

Hydrogen and methanol exchange processes for (TMP)Rh-OCH3(CH3OH) in binary solutions of methanol and benzene.

PubMed

Sarkar, Sounak; Li, Shan; Wayland, Bradford B

2011-04-18

Tetramesityl porphinato rhodium(III) methoxide ((TMP)Rh-OCH(3)) binds with methanol in benzene to form a 1:1 methanol complex ((TMP)Rh-OCH(3)(CH(3)OH)) (1). Dynamic processes are observed to occur for the rhodium(III) methoxide methanol complex (1) that involve both hydrogen and methanol exchange. Hydrogen exchange between coordinated methanol and methoxide through methanol in solution results in an interchange of the environments for the non-equivalent porphyrin faces that contain methoxide and methanol ligands. Interchange of the environments of the coordinated methanol and methoxide sites in 1 produces interchange of the inequivalent mesityl o-CH(3) groups, but methanol ligand exchange occurs on one face of the porphyrin and the mesityl o-CH(3) groups remain inequivalent. Rate constants for dynamic processes are evaluated by full line shape analysis for the (1)H NMR of the mesityl o-CH(3) and high field methyl resonances of coordinated methanol and methoxide groups in 1. The rate constant for interchange of the inequivalent porphyrin faces is associated with hydrogen exchange between 1 and methanol in solution and is observed to increase regularly with the increase in the mole fraction of methanol. The rate constant for methanol ligand exchange between 1 and the solution varies with the solution composition and fluctuates in a manner that parallels the change in the activation energy for methanol diffusion which is a consequence of solution non-ideality from hydrogen bonded clusters.

Determination of the formation of dark state via depleted spontaneous emission in a complex solvated molecule.

PubMed

Guo, Xunmin; Wang, Sufan; Xia, Andong; Su, Hongmei

2007-07-05

We present a general two-color two-pulse femtosecond pump-dump approach to study the specific population transfer along the reaction coordinate through the higher vibrational energy levels of excited states of a complex solvated molecule via the depleted spontaneous emission. The time-dependent fluorescence depletion provides the correlated dynamical information between the monitored fluorescence state and the SEP "dumped" dark states, and therefore allow us to obtain the dynamics of the formation of the dark states corresponding to the ultrafast photoisomerization processes. The excited-state dynamics of LDS 751 have been investigated as a function of solvent viscosity and solvent polarity, where a cooperative two-step isomerization process is clearly identified within LDS 751 upon excitation.

Social Motor Synchronization: Insights for Understanding Social Behavior in Autism

ERIC Educational Resources Information Center

Fitzpatrick, Paula; Romero, Veronica; Amaral, Joseph L.; Duncan, Amie; Barnard, Holly; Richardson, Michael J.; Schmidt, R. C.

2017-01-01

Impairments in social interaction and communication are critical features of ASD but the underlying processes are poorly understood. An under-explored area is the social motor synchronization that happens when we coordinate our bodies with others. Here, we explored the relationships between dynamical measures of social motor synchronization and…

The Self-Organization of a Spoken Word

PubMed Central

Holden, John G.; Rajaraman, Srinivasan

2012-01-01

Pronunciation time probability density and hazard functions from large speeded word naming data sets were assessed for empirical patterns consistent with multiplicative and reciprocal feedback dynamics – interaction dominant dynamics. Lognormal and inverse power law distributions are associated with multiplicative and interdependent dynamics in many natural systems. Mixtures of lognormal and inverse power law distributions offered better descriptions of the participant’s distributions than the ex-Gaussian or ex-Wald – alternatives corresponding to additive, superposed, component processes. The evidence for interaction dominant dynamics suggests fundamental links between the observed coordinative synergies that support speech production and the shapes of pronunciation time distributions. PMID:22783213

A lateral signalling pathway coordinates shape volatility during cell migration

PubMed Central

Zhang, Liang; Luga, Valbona; Armitage, Sarah K.; Musiol, Martin; Won, Amy; Yip, Christopher M.; Plotnikov, Sergey V.; Wrana, Jeffrey L.

2016-01-01

Cell migration is fundamental for both physiological and pathological processes. Migrating cells usually display high dynamics in morphology, which is orchestrated by an integrative array of signalling pathways. Here we identify a novel pathway, we term lateral signalling, comprised of the planar cell polarity (PCP) protein Pk1 and the RhoGAPs, Arhgap21/23. We show that the Pk1–Arhgap21/23 complex inhibits RhoA, is localized on the non-protrusive lateral membrane cortex and its disruption leads to the disorganization of the actomyosin network and altered focal adhesion dynamics. Pk1-mediated lateral signalling confines protrusive activity and is regulated by Smurf2, an E3 ubiquitin ligase in the PCP pathway. Furthermore, we demonstrate that dynamic interplay between lateral and protrusive signalling generates cyclical fluctuations in cell shape that we quantify here as shape volatility, which strongly correlates with migration speed. These studies uncover a previously unrecognized lateral signalling pathway that coordinates shape volatility during productive cell migration. PMID:27226243

ACF7 regulates inflammatory colitis and intestinal wound response by orchestrating tight junction dynamics

PubMed Central

Ma, Yanlei; Yue, Jiping; Zhang, Yao; Shi, Chenzhang; Odenwald, Matt; Liang, Wenguang G.; Wei, Qing; Goel, Ajay; Gou, Xuewen; Zhang, Jamie; Chen, Shao-Yu; Tang, Wei-Jen; Turner, Jerrold R.; Yang, Feng; Liang, Hong; Qin, Huanlong; Wu, Xiaoyang

2017-01-01

In the intestinal epithelium, the aberrant regulation of cell/cell junctions leads to intestinal barrier defects, which may promote the onset and enhance the severity of inflammatory bowel disease (IBD). However, it remains unclear how the coordinated behaviour of cytoskeletal network may contribute to cell junctional dynamics. In this report, we identified ACF7, a crosslinker of microtubules and F-actin, as an essential player in this process. Loss of ACF7 leads to aberrant microtubule organization, tight junction stabilization and impaired wound closure in vitro. With the mouse genetics approach, we show that ablation of ACF7 inhibits intestinal wound healing and greatly increases susceptibility to experimental colitis in mice. ACF7 level is also correlated with development and progression of ulcerative colitis (UC) in human patients. Together, our results reveal an important molecular mechanism whereby coordinated cytoskeletal dynamics contributes to cell adhesion regulation during intestinal wound repair and the development of IBD. PMID:28541346

Mind-to-mind heteroclinic coordination: Model of sequential episodic memory initiation.

PubMed

Afraimovich, V S; Zaks, M A; Rabinovich, M I

2018-05-01

Retrieval of episodic memory is a dynamical process in the large scale brain networks. In social groups, the neural patterns, associated with specific events directly experienced by single members, are encoded, recalled, and shared by all participants. Here, we construct and study the dynamical model for the formation and maintaining of episodic memory in small ensembles of interacting minds. We prove that the unconventional dynamical attractor of this process-the nonsmooth heteroclinic torus-is structurally stable within the Lotka-Volterra-like sets of equations. Dynamics on this torus combines the absence of chaos with asymptotic instability of every separate trajectory; its adequate quantitative characteristics are length-related Lyapunov exponents. Variation of the coupling strength between the participants results in different types of sequential switching between metastable states; we interpret them as stages in formation and modification of the episodic memory.

Förster resonance energy transfer as a tool to study photoreceptor biology

PubMed Central

Hovan, Stephanie C.; Howell, Scott; Park, Paul S.-H.

2010-01-01

Vision is initiated in photoreceptor cells of the retina by a set of biochemical events called phototransduction. These events occur via coordinated dynamic processes that include changes in secondary messenger concentrations, conformational changes and post-translational modifications of signaling proteins, and protein-protein interactions between signaling partners. A complete description of the orchestration of these dynamic processes is still unavailable. Described in this work is the first step in the development of tools combining fluorescent protein technology, Förster resonance energy transfer (FRET), and transgenic animals that have the potential to reveal important molecular insights about the dynamic processes occurring in photoreceptor cells. We characterize the fluorescent proteins SCFP3A and SYFP2 for use as a donor-acceptor pair in FRET assays, which will facilitate the visualization of dynamic processes in living cells. We also demonstrate the targeted expression of these fluorescent proteins to the rod photoreceptor cells of Xenopus laevis, and describe a general method for detecting FRET in these cells. The general approaches described here can address numerous types of questions related to phototransduction and photoreceptor biology by providing a platform to visualize dynamic processes in molecular detail within a native context. PMID:21198205

Self-Organized Information Processing in Neuronal Networks: Replacing Layers in Deep Networks by Dynamics

NASA Astrophysics Data System (ADS)

Kirst, Christoph

It is astonishing how the sub-parts of a brain co-act to produce coherent behavior. What are mechanism that coordinate information processing and communication and how can those be changed flexibly in order to cope with variable contexts? Here we show that when information is encoded in the deviations around a collective dynamical reference state of a recurrent network the propagation of these fluctuations is strongly dependent on precisely this underlying reference. Information here 'surfs' on top of the collective dynamics and switching between states enables fast and flexible rerouting of information. This in turn affects local processing and consequently changes in the global reference dynamics that re-regulate the distribution of information. This provides a generic mechanism for self-organized information processing as we demonstrate with an oscillatory Hopfield network that performs contextual pattern recognition. Deep neural networks have proven to be very successful recently. Here we show that generating information channels via collective reference dynamics can effectively compress a deep multi-layer architecture into a single layer making this mechanism a promising candidate for the organization of information processing in biological neuronal networks.

Geometric and energetic considerations of surface fluctuations during ion transfer across the water-immiscible organic liquid interface

NASA Astrophysics Data System (ADS)

Karnes, John J.; Benjamin, Ilan

2016-07-01

Molecular dynamics simulations and umbrella sampling free energy calculations are used to examine the thermodynamics, energetics, and structural fluctuations that accompany the transfer of a small hydrophilic ion (Cl-) across the water/nitrobenzene interface. By examining several constrained interface structures, we isolate the energetic costs of interfacial deformation and co-transfer of hydration waters during the ion transfer. The process is monitored using both energy-based solvation coordinates and a geometric coordinate recently introduced by Morita and co-workers to describe surface fluctuations. Our simulations show that these coordinates provide a complimentary description of the water surface fluctuations during the transfer and are necessary for elucidating the mechanism of the ion transfer.

Numerical modeling of the atmosphere with an isentropic vertical coordinate

NASA Technical Reports Server (NTRS)

Hsu, Yueh-Jiuan G.; Arakawa, Akio

1990-01-01

A theta-coordinate model simulating the nonlinear evolution of a baroclinic wave is presented. In the model, vertical discretization maintains important integral constraints such as conservation of the angular momentum and total energy. A massless-layer approach is used in the treatment of the intersections of coordinate surfaces with the lower boundary. This formally eliminates the intersection problem, but raises other computational problems. Horizontal discretization of the continuity and momentum equations in the model are designed to overcome these problems. Selected results from a 10-day integration with the 25-layer, beta-plane version of the model are presented. It is concluded that the model can simulate the nonlinear evolution of a baroclinic wave and associated dynamical processes without major computational difficulties.

The heart tube forms and elongates through dynamic cell rearrangement coordinated with foregut extension.

PubMed

Kidokoro, Hinako; Yonei-Tamura, Sayuri; Tamura, Koji; Schoenwolf, Gary C; Saijoh, Yukio

2018-03-29

In the initiation of cardiogenesis, the heart primordia transform from bilateral flat sheets of mesoderm into an elongated midline tube. Here, we discover that this rapid architectural change is driven by actomyosin-based oriented cell rearrangement and resulting dynamic tissue reshaping (convergent extension, CE). By labeling clusters of cells spanning the entire heart primordia, we show that the heart primordia converge toward the midline to form a narrow tube, while extending perpendicularly to rapidly lengthen it. Our data for the first time visualize the process of early heart tube formation from both the medial (second) and lateral (first) heart fields, revealing that both fields form the early heart tube by essentially the same mechanism. Additionally, the adjacent endoderm coordinately forms the foregut through previously unrecognized movements that parallel those of the heart mesoderm and elongates by CE. In conclusion, our data illustrate how initially two-dimensional flat primordia rapidly change their shapes and construct the three-dimensional morphology of emerging organs in coordination with neighboring morphogenesis. © 2018. Published by The Company of Biologists Ltd.

Attitude coordination of multi-HUG formation based on multibody system theory

NASA Astrophysics Data System (ADS)

Xue, Dong-yang; Wu, Zhi-liang; Qi, Er-mai; Wang, Yan-hui; Wang, Shu-xin

2017-04-01

Application of multiple hybrid underwater gliders (HUGs) is a promising method for large scale, long-term ocean survey. Attitude coordination has become a requisite for task execution of multi-HUG formation. In this paper, a multibody model is presented for attitude coordination among agents in the HUG formation. The HUG formation is regarded as a multi-rigid body system. The interaction between agents in the formation is described by artificial potential field (APF) approach. Attitude control torque is composed of a conservative torque generated by orientation potential field and a dissipative term related with angular velocity. Dynamic modeling of the multibody system is presented to analyze the dynamic process of the HUG formation. Numerical calculation is carried out to simulate attitude synchronization with two kinds of formation topologies. Results show that attitude synchronization can be fulfilled based on the multibody method described in this paper. It is also indicated that different topologies affect attitude control quality with respect to energy consumption and adjusting time. Low level topology should be adopted during formation control scheme design to achieve a better control effect.

N-MODY: a code for collisionless N-body simulations in modified Newtonian dynamics.

NASA Astrophysics Data System (ADS)

Londrillo, P.; Nipoti, C.

We describe the numerical code N-MODY, a parallel particle-mesh code for collisionless N-body simulations in modified Newtonian dynamics (MOND). N-MODY is based on a numerical potential solver in spherical coordinates that solves the non-linear MOND field equation, and is ideally suited to simulate isolated stellar systems. N-MODY can be used also to compute the MOND potential of arbitrary static density distributions. A few applications of N-MODY indicate that some astrophysically relevant dynamical processes are profoundly different in MOND and in Newtonian gravity with dark matter.

Gravity-oriented satellite dynamics subject to gravitational and active damping torques

NASA Astrophysics Data System (ADS)

Sarychev, V. A.; Gutnik, S. A.

2018-01-01

The dynamics of the rotational motion of a satellite moving in the central Newtonian field of force over a circular orbit under the effect of gravitational and active damping torques, which depend on the satellite angular velocity projections, has been investigated. The paper proposes a method of determining all equilibrium positions (equilibrium orientations) of a satellite in the orbital coordinate system for specified values of damping coefficients and principal central moments of inertia. The conditions of their existence have been obtained. For a zero equilibrium position where the axes of the satellite-centered coordinate system coincide with the axes of the orbital coordinate system, the necessary and sufficient conditions for asymptotic stability are obtained using the Routh-Hurwitz criterion. A detailed analysis of the regions where the conditions of the asymptotic stability of a zero equilibrium position are fulfilled have been obtained depending on three dimensionless parameters of the problem, and the numerical study of the process of attenuation of satellite's spatial oscillations for various damping coefficients has been carried out. It has been shown that there is a wide range of damping parameters from which, by choosing the necessary values, one can provide the asymptotic stability of satellite's zero equilibrium position in the orbital coordinate system.

Rapid Structured Volume Grid Smoothing and Adaption Technique

NASA Technical Reports Server (NTRS)

Alter, Stephen J.

2006-01-01

A rapid, structured volume grid smoothing and adaption technique, based on signal processing methods, was developed and applied to the Shuttle Orbiter at hypervelocity flight conditions in support of the Columbia Accident Investigation. Because of the fast pace of the investigation, computational aerothermodynamicists, applying hypersonic viscous flow solving computational fluid dynamic (CFD) codes, refined and enhanced a grid for an undamaged baseline vehicle to assess a variety of damage scenarios. Of the many methods available to modify a structured grid, most are time-consuming and require significant user interaction. By casting the grid data into different coordinate systems, specifically two computational coordinates with arclength as the third coordinate, signal processing methods are used for filtering the data [Taubin, CG v/29 1995]. Using a reverse transformation, the processed data are used to smooth the Cartesian coordinates of the structured grids. By coupling the signal processing method with existing grid operations within the Volume Grid Manipulator tool, problems related to grid smoothing are solved efficiently and with minimal user interaction. Examples of these smoothing operations are illustrated for reductions in grid stretching and volume grid adaptation. In each of these examples, other techniques existed at the time of the Columbia accident, but the incorporation of signal processing techniques reduced the time to perform the corrections by nearly 60%. This reduction in time to perform the corrections therefore enabled the assessment of approximately twice the number of damage scenarios than previously possible during the allocated investigation time.

Rapid Structured Volume Grid Smoothing and Adaption Technique

NASA Technical Reports Server (NTRS)

Alter, Stephen J.

2004-01-01

A rapid, structured volume grid smoothing and adaption technique, based on signal processing methods, was developed and applied to the Shuttle Orbiter at hypervelocity flight conditions in support of the Columbia Accident Investigation. Because of the fast pace of the investigation, computational aerothermodynamicists, applying hypersonic viscous flow solving computational fluid dynamic (CFD) codes, refined and enhanced a grid for an undamaged baseline vehicle to assess a variety of damage scenarios. Of the many methods available to modify a structured grid, most are time-consuming and require significant user interaction. By casting the grid data into different coordinate systems, specifically two computational coordinates with arclength as the third coordinate, signal processing methods are used for filtering the data [Taubin, CG v/29 1995]. Using a reverse transformation, the processed data are used to smooth the Cartesian coordinates of the structured grids. By coupling the signal processing method with existing grid operations within the Volume Grid Manipulator tool, problems related to grid smoothing are solved efficiently and with minimal user interaction. Examples of these smoothing operations are illustrated for reduction in grid stretching and volume grid adaptation. In each of these examples, other techniques existed at the time of the Columbia accident, but the incorporation of signal processing techniques reduced the time to perform the corrections by nearly 60%. This reduction in time to perform the corrections therefore enabled the assessment of approximately twice the number of damage scenarios than previously possible during the allocated investigation time.

Spectraplakins: Master orchestrators of cytoskeletal dynamics

PubMed Central

Suozzi, Kathleen C.; Wu, Xiaoyang

2012-01-01

The dynamics of different cytoskeletal networks are coordinated to bring about many fundamental cellular processes, from neuronal pathfinding to cell division. Increasing evidence points to the importance of spectraplakins in integrating cytoskeletal networks. Spectraplakins are evolutionarily conserved giant cytoskeletal cross-linkers, which belong to the spectrin superfamily. Their genes consist of multiple promoters and many exons, yielding a vast array of differential splice forms with distinct functions. Spectraplakins are also unique in their ability to associate with all three elements of the cytoskeleton: F-actin, microtubules, and intermediate filaments. Recent studies have begun to unveil their role in a wide range of processes, from cell migration to tissue integrity. PMID:22584905

Constrained paths based on the Farey sequence in learning to juggle.

PubMed

Yamamoto, Kota; Tsutsui, Seijiro; Yamamoto, Yuji

2015-12-01

In this article we report the results of a study conducted to investigate the learning dynamics of three-ball juggling from the perspective of frequency locking. Based on the Farey sequence, we predicted that four stable coordination patterns, corresponding to dwell ratios of 0.83, 0.75, 0.67, and 0.50, would appear in the learning process. We examined the learning process in terms of task performance, taking into account individual differences in the amount of learning. We observed that the participants acquired individual-specific coordination patterns in a relatively early stage of learning, and that those coordination patterns were preserved in subsequent learning, even though performance in terms of number of successful consecutive throws increased substantially. This increase appeared to be related to a reduction in spatial variability of the juggling movements. Finally, the observed coordination patterns were in agreement with the predicted patterns, with the proviso that the pattern corresponding to a dwell ratio of 0.50 was not realized and only a hint of evidence was found for the dwell ratio of 0.67. This implies that the dwell ratios of 0.83 and 0.75 in particular exhibited a stable coordination structure due to strong frequency locking between the temporal variables of juggling. Copyright © 2015 Elsevier B.V. All rights reserved.

Dynamics of hemispheric specialization and integration in the context of motor control.

PubMed

Serrien, Deborah J; Ivry, Richard B; Swinnen, Stephan P

2006-02-01

Behavioural and neurophysiological evidence convincingly establish that the left hemisphere is dominant for motor skills that are carried out with either hand or those that require bimanual coordination. As well as this prioritization, we argue that specialized functions of the right hemisphere are also indispensable for the realization of goal-directed behaviour. As such, lateralization of motor function is a dynamic and multifaceted process that emerges across different timescales and is contingent on task- and performer-related determinants.

Dynamical modelling of coordinated multiple robot systems

NASA Technical Reports Server (NTRS)

Hayati, Samad

1987-01-01

The state of the art in the modeling of the dynamics of coordinated multiple robot manipulators is summarized and various problems related to this subject are discussed. It is recognized that dynamics modeling is a component used in the design of controllers for multiple cooperating robots. As such, the discussion addresses some problems related to the control of multiple robots. The techniques used to date in the modeling of closed kinematic chains are summarized. Various efforts made to date for the control of coordinated multiple manipulators is summarized.

Impairments of Social Motor Coordination in Schizophrenia

PubMed Central

Varlet, Manuel; Marin, Ludovic; Raffard, Stéphane; Schmidt, R. C.; Capdevielle, Delphine; Boulenger, Jean-Philippe; Del-Monte, Jonathan; Bardy, Benoît G.

2012-01-01

It has been demonstrated that motor coordination of interacting people plays a crucial role in the success of social exchanges. Abnormal movements have been reported during interpersonal interactions of patients suffering from schizophrenia and a motor coordination breakdown could explain this social interaction deficit, which is one of the main and earliest features of the illness. Using the dynamical systems framework, the goal of the current study was (i) to investigate whether social motor coordination is impaired in schizophrenia and (ii) to determine the underlying perceptual or cognitive processes that may be affected. We examined intentional and unintentional social motor coordination in participants oscillating hand-held pendulums from the wrist. The control group consisted of twenty healthy participant pairs while the experimental group consisted of twenty participant pairs that included one participant suffering from schizophrenia. The results showed that unintentional social motor coordination was preserved while intentional social motor coordination was impaired. In intentional coordination, the schizophrenia group displayed coordination patterns that had lower stability and in which the patient never led the coordination. A coupled oscillator model suggests that the schizophrenia group coordination pattern was due to a decrease in the amount of available information together with a delay in information transmission. Our study thus identified relational motor signatures of schizophrenia and opens new perspectives for detecting the illness and improving social interactions of patients. PMID:22272247

Qualitative Analysis of Microbial Dynamics during Anaerobic Digestion of Microalgal Biomass in a UASB Reactor

PubMed Central

Doloman, Anna; Soboh, Yousef; Walters, Andrew J.; Sims, Ronald C.

2017-01-01

Anaerobic digestion (AD) is a microbiologically coordinated process with dynamic relationships between bacterial players. Current understanding of dynamic changes in the bacterial composition during the AD process is incomplete. The objective of this research was to assess changes in bacterial community composition that coordinates with anaerobic codigestion of microalgal biomass cultivated on municipal wastewater. An upflow anaerobic sludge blanket reactor was used to achieve high rates of microalgae decomposition and biogas production. Samples of the sludge were collected throughout AD and extracted DNA was subjected to next-generation sequencing using methanogen mcrA gene specific and universal bacterial primers. Analysis of the data revealed that samples taken at different stages of AD had varying bacterial composition. A group consisting of Bacteroidales, Pseudomonadales, and Enterobacteriales was identified to be putatively responsible for the hydrolysis of microalgal biomass. The methanogenesis phase was dominated by Methanosarcina mazei. Results of observed changes in the composition of microbial communities during AD can be used as a road map to stimulate key bacterial species identified at each phase of AD to increase yield of biogas and rate of substrate decomposition. This research demonstrates a successful exploitation of methane production from microalgae without any biomass pretreatment. PMID:29259629

Chaotic dynamics of controlled electric power systems

NASA Astrophysics Data System (ADS)

Kozlov, V. N.; Trosko, I. U.

2016-12-01

The conditions for appearance of chaotic dynamics of electromagnetic and electromechanical processes in energy systems described by the Park-Gorev bilinear differential equations with account for lags of coordinates and restrictions on control have been formulated. On the basis of classical equations, the parameters of synchronous generators and power lines, at which the chaotic dynamics of energy systems appears, have been found. The qualitative and quantitative characteristics of chaotic processes in energy associations of two types, based on the Hopf theorem, and methods of nonstationary linearization and decompositions are given. The properties of spectral characteristics of chaotic processes have been investigated, and the qualitative similarity of bilinear equations of power systems and Lorentz equations have been found. These results can be used for modernization of the systems of control of energy objects. The qualitative and quantitative characteristics for power energy systems as objects of control and for some laws of control with the feedback have been established.

Coordinating Decentralized Learning and Conflict Resolution across Agent Boundaries

ERIC Educational Resources Information Center

Cheng, Shanjun

2012-01-01

It is crucial for embedded systems to adapt to the dynamics of open environments. This adaptation process becomes especially challenging in the context of multiagent systems because of scalability, partial information accessibility and complex interaction of agents. It is a challenge for agents to learn good policies, when they need to plan and…

Research and implementation of the algorithm for unwrapped and distortion correction basing on CORDIC for panoramic image

NASA Astrophysics Data System (ADS)

Zhang, Zhenhai; Li, Kejie; Wu, Xiaobing; Zhang, Shujiang

2008-03-01

The unwrapped and correcting algorithm based on Coordinate Rotation Digital Computer (CORDIC) and bilinear interpolation algorithm was presented in this paper, with the purpose of processing dynamic panoramic annular image. An original annular panoramic image captured by panoramic annular lens (PAL) can be unwrapped and corrected to conventional rectangular image without distortion, which is much more coincident with people's vision. The algorithm for panoramic image processing is modeled by VHDL and implemented in FPGA. The experimental results show that the proposed panoramic image algorithm for unwrapped and distortion correction has the lower computation complexity and the architecture for dynamic panoramic image processing has lower hardware cost and power consumption. And the proposed algorithm is valid.

Physical Models of Cognition

NASA Technical Reports Server (NTRS)

Zak, Michail

1994-01-01

This paper presents and discusses physical models for simulating some aspects of neural intelligence, and, in particular, the process of cognition. The main departure from the classical approach here is in utilization of a terminal version of classical dynamics introduced by the author earlier. Based upon violations of the Lipschitz condition at equilibrium points, terminal dynamics attains two new fundamental properties: it is spontaneous and nondeterministic. Special attention is focused on terminal neurodynamics as a particular architecture of terminal dynamics which is suitable for modeling of information flows. Terminal neurodynamics possesses a well-organized probabilistic structure which can be analytically predicted, prescribed, and controlled, and therefore which presents a powerful tool for modeling real-life uncertainties. Two basic phenomena associated with random behavior of neurodynamic solutions are exploited. The first one is a stochastic attractor ; a stable stationary stochastic process to which random solutions of a closed system converge. As a model of the cognition process, a stochastic attractor can be viewed as a universal tool for generalization and formation of classes of patterns. The concept of stochastic attractor is applied to model a collective brain paradigm explaining coordination between simple units of intelligence which perform a collective task without direct exchange of information. The second fundamental phenomenon discussed is terminal chaos which occurs in open systems. Applications of terminal chaos to information fusion as well as to explanation and modeling of coordination among neurons in biological systems are discussed. It should be emphasized that all the models of terminal neurodynamics are implementable in analog devices, which means that all the cognition processes discussed in the paper are reducible to the laws of Newtonian mechanics.

Collective dynamics of cell migration and cell rearrangements

NASA Astrophysics Data System (ADS)

Kabla, Alexandre

Understanding multicellular processes such as embryo development or cancer metastasis requires to decipher the contributions of local cell autonomous behaviours and long range interactions with the tissue environment. A key question in this context concerns the emergence of large scale coordination in cell behaviours, a requirement for collective cell migration or convergent extension. I will present a few examples where physical and mechanical aspects play a significant role in driving tissue scale dynamics.

A GPU Parallelization of the Absolute Nodal Coordinate Formulation for Applications in Flexible Multibody Dynamics

DTIC Science & Technology

2012-02-17

to be solved. Disclaimer: Reference herein to any specific commercial company , product, process, or service by trade name, trademark...data processing rather than data caching and control flow. To make use of this computational power, NVIDIA introduced a general purpose parallel...GPU implementations were run on an Intel Nehalem Xeon E5520 2.26GHz processor with an NVIDIA Tesla C2070 graphics card for varying numbers of

3D Analysis of Human Embryos and Fetuses Using Digitized Datasets From the Kyoto Collection.

PubMed

Takakuwa, Tetsuya

2018-06-01

Three-dimensional (3D) analysis of the human embryonic and early-fetal period has been performed using digitized datasets obtained from the Kyoto Collection, in which the digital datasets play a primary role in research. Datasets include magnetic resonance imaging (MRI) acquired with 1.5 T, 2.35 T, and 7 T magnet systems, phase-contrast X-ray computed tomography (CT), and digitized histological serial sections. Large, high-resolution datasets covering a broad range of developmental periods obtained with various methods of acquisition are key elements for the studies. The digital data have gross merits that enabled us to develop various analysis. Digital data analysis accelerated the speed of morphological observations using precise and improved methods by providing a suitable plane for a morphometric analysis from staged human embryos. Morphometric data are useful for quantitatively evaluating and demonstrating the features of development and for screening abnormal samples, which may be suggestive in the pathogenesis of congenital malformations. Morphometric data are also valuable for comparing sonographic data in a process known as "sonoembryology." The 3D coordinates of anatomical landmarks may be useful tools for analyzing the positional change of interesting landmarks and their relationships during development. Several dynamic events could be explained by differential growth using 3D coordinates. Moreover, 3D coordinates can be utilized in mathematical analysis as well as statistical analysis. The 3D analysis in our study may serve to provide accurate morphologic data, including the dynamics of embryonic structures related to developmental stages, which is required for insights into the dynamic and complex processes occurring during organogenesis. Anat Rec, 301:960-969, 2018. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Solution NMR Refinement of a Metal Ion Bound Protein Using Metal Ion Inclusive Restrained Molecular Dynamics Methods

PubMed Central

Chakravorty, Dhruva K.; Wang, Bing; Lee, Chul Won; Guerra, Alfredo J.; Giedroc, David P.; Merz, Kenneth M.

2013-01-01

Correctly calculating the structure of metal coordination sites in a protein during the process of nuclear magnetic resonance (NMR) structure determination and refinement continues to be a challenging task. In this study, we present an accurate and convenient means by which to include metal ions in the NMR structure determination process using molecular dynamics (MD) constrained by NMR-derived data to obtain a realistic and physically viable description of the metal binding site(s). This method provides the framework to accurately portray the metal ions and its binding residues in a pseudo-bond or dummy-cation like approach, and is validated by quantum mechanical/molecular mechanical (QM/MM) MD calculations constrained by NMR-derived data. To illustrate this approach, we refine the zinc coordination complex structure of the zinc sensing transcriptional repressor protein Staphylococcus aureus CzrA, generating over 130 ns of MD and QM/MM MD NMR-data compliant sampling. In addition to refining the first coordination shell structure of the Zn(II) ion, this protocol benefits from being performed in a periodically replicated solvation environment including long-range electrostatics. We determine that unrestrained (not based on NMR data) MD simulations correlated to the NMR data in a time-averaged ensemble. The accurate solution structure ensemble of the metal-bound protein accurately describes the role of conformational dynamics in allosteric regulation of DNA binding by zinc and serves to validate our previous unrestrained MD simulations of CzrA. This methodology has potentially broad applicability in the structure determination of metal ion bound proteins, protein folding and metal template protein-design studies. PMID:23609042

Evolutionary dynamics of the traveler's dilemma and minimum-effort coordination games on complex networks.

PubMed

Iyer, Swami; Killingback, Timothy

2014-10-01

The traveler's dilemma game and the minimum-effort coordination game are social dilemmas that have received significant attention resulting from the fact that the predictions of classical game theory are inconsistent with the results found when the games are studied experimentally. Moreover, both the traveler's dilemma and the minimum-effort coordination games have potentially important applications in evolutionary biology. Interestingly, standard deterministic evolutionary game theory, as represented by the replicator dynamics in a well-mixed population, is also inadequate to account for the behavior observed in these games. Here we study the evolutionary dynamics of both these games in populations with interaction patterns described by a variety of complex network topologies. We investigate the evolutionary dynamics of these games through agent-based simulations on both model and empirical networks. In particular, we study the effects of network clustering and assortativity on the evolutionary dynamics of both games. In general, we show that the evolutionary behavior of the traveler's dilemma and minimum-effort coordination games on complex networks is in good agreement with that observed experimentally. Thus, formulating the traveler's dilemma and the minimum-effort coordination games on complex networks neatly resolves the paradoxical aspects of these games.

Evolutionary dynamics of the traveler's dilemma and minimum-effort coordination games on complex networks

NASA Astrophysics Data System (ADS)

Iyer, Swami; Killingback, Timothy

2014-10-01

The traveler's dilemma game and the minimum-effort coordination game are social dilemmas that have received significant attention resulting from the fact that the predictions of classical game theory are inconsistent with the results found when the games are studied experimentally. Moreover, both the traveler's dilemma and the minimum-effort coordination games have potentially important applications in evolutionary biology. Interestingly, standard deterministic evolutionary game theory, as represented by the replicator dynamics in a well-mixed population, is also inadequate to account for the behavior observed in these games. Here we study the evolutionary dynamics of both these games in populations with interaction patterns described by a variety of complex network topologies. We investigate the evolutionary dynamics of these games through agent-based simulations on both model and empirical networks. In particular, we study the effects of network clustering and assortativity on the evolutionary dynamics of both games. In general, we show that the evolutionary behavior of the traveler's dilemma and minimum-effort coordination games on complex networks is in good agreement with that observed experimentally. Thus, formulating the traveler's dilemma and the minimum-effort coordination games on complex networks neatly resolves the paradoxical aspects of these games.

Calcium environment in silicate and aluminosilicate glasses probed by ⁴³Ca MQMAS NMR experiments and MD-GIPAW calculations.

PubMed

Gambuzzi, Elisa; Pedone, Alfonso; Menziani, Maria Cristina; Angeli, Frédéric; Florian, Pierre; Charpentier, Thibault

2015-01-01

⁴³Ca MQMAS NMR spectra of three silica-based glasses in which Ca²⁺ ions play different structural roles have been collected and processed in order to extract the underlying NMR parameter distributions. The NMR parameters have been interpreted with the help of molecular dynamics simulations and DFT-GIPAW calculations. This synergetic experimental-computational approach has allowed us to investigate the Ca environment, to estimate Ca coordination numbers from MD-derived models, and to push further the discussion about ⁴³Ca NMR sensitivity to the first and second coordination spheres: ⁴³Ca δiso and Ca-O distance can be successfully correlated as a function of Ca coordination number. Copyright © 2015 Elsevier Inc. All rights reserved.

Neural network modelling and dynamical system theory: are they relevant to study the governing dynamics of association football players?

PubMed

Dutt-Mazumder, Aviroop; Button, Chris; Robins, Anthony; Bartlett, Roger

2011-12-01

Recent studies have explored the organization of player movements in team sports using a range of statistical tools. However, the factors that best explain the performance of association football teams remain elusive. Arguably, this is due to the high-dimensional behavioural outputs that illustrate the complex, evolving configurations typical of team games. According to dynamical system analysts, movement patterns in team sports exhibit nonlinear self-organizing features. Nonlinear processing tools (i.e. Artificial Neural Networks; ANNs) are becoming increasingly popular to investigate the coordination of participants in sports competitions. ANNs are well suited to describing high-dimensional data sets with nonlinear attributes, however, limited information concerning the processes required to apply ANNs exists. This review investigates the relative value of various ANN learning approaches used in sports performance analysis of team sports focusing on potential applications for association football. Sixty-two research sources were summarized and reviewed from electronic literature search engines such as SPORTDiscus, Google Scholar, IEEE Xplore, Scirus, ScienceDirect and Elsevier. Typical ANN learning algorithms can be adapted to perform pattern recognition and pattern classification. Particularly, dimensionality reduction by a Kohonen feature map (KFM) can compress chaotic high-dimensional datasets into low-dimensional relevant information. Such information would be useful for developing effective training drills that should enhance self-organizing coordination among players. We conclude that ANN-based qualitative analysis is a promising approach to understand the dynamical attributes of association football players.

The dynamics of social innovation

PubMed Central

Young, H. Peyton

2011-01-01

Social norms and institutions are mechanisms that facilitate coordination between individuals. A social innovation is a novel mechanism that increases the welfare of the individuals who adopt it compared with the status quo. We model the dynamics of social innovation as a coordination game played on a network. Individuals experiment with a novel strategy that would increase their payoffs provided that it is also adopted by their neighbors. The rate at which a social innovation spreads depends on three factors: the topology of the network and in particular the extent to which agents interact in small local clusters, the payoff gain of the innovation relative to the status quo, and the amount of noise in the best response process. The analysis shows that local clustering greatly enhances the speed with which social innovations spread. It also suggests that the welfare gains from innovation are more likely to occur in large jumps than in a series of small incremental improvements. PMID:22198762

The Role of Molecular Dynamics Potential of Mean Force Calculations in the Investigation of Enzyme Catalysis.

PubMed

Yang, Y; Pan, L; Lightstone, F C; Merz, K M

2016-01-01

The potential of mean force simulations, widely applied in Monte Carlo or molecular dynamics simulations, are useful tools to examine the free energy variation as a function of one or more specific reaction coordinate(s) for a given system. Implementation of the potential of mean force in the simulations of biological processes, such as enzyme catalysis, can help overcome the difficulties of sampling specific regions on the energy landscape and provide useful insights to understand the catalytic mechanism. The potential of mean force simulations usually require many, possibly parallelizable, short simulations instead of a few extremely long simulations and, therefore, are fairly manageable for most research facilities. In this chapter, we provide detailed protocols for applying the potential of mean force simulations to investigate enzymatic mechanisms for several different enzyme systems. © 2016 Elsevier Inc. All rights reserved.

Simultaneous observation solutions for NASA-MOTS and SPEOPT station positions on the North American datum

NASA Technical Reports Server (NTRS)

Reece, J. S.; Marsh, J.

1973-01-01

Simultaneous observations of the GEOS-I and II flashing lamps by the NASA MOTS and SPEOPT cameras on the North American Datum (NAD) were analyzed using geometrical techniques to provide an adjustment of the station coordinates. Two separate adjustments were obtained. An optical data only solution was computed in which the solution scale was provided by the Rosman-Mojave distance obtained from a dynamic station solution. In a second adjustment, scaling was provided by processing simultaneous laser ranging data from Greenbelt and Wallops Island in a combined optical-laser solution. Comparisons of these results with previous GSFC dynamical solutions indicate an rms agreement on the order of 4 meters or better in each coordinate. Comparison with a detailed gravimetric geoid of North America yields agreement of 3 meters or better for mainland U.S. stations and 7 and 3 meters, respectively, for Bermuda and Puerto Rico.

The dynamics of social innovation.

PubMed

Young, H Peyton

2011-12-27

Social norms and institutions are mechanisms that facilitate coordination between individuals. A social innovation is a novel mechanism that increases the welfare of the individuals who adopt it compared with the status quo. We model the dynamics of social innovation as a coordination game played on a network. Individuals experiment with a novel strategy that would increase their payoffs provided that it is also adopted by their neighbors. The rate at which a social innovation spreads depends on three factors: the topology of the network and in particular the extent to which agents interact in small local clusters, the payoff gain of the innovation relative to the status quo, and the amount of noise in the best response process. The analysis shows that local clustering greatly enhances the speed with which social innovations spread. It also suggests that the welfare gains from innovation are more likely to occur in large jumps than in a series of small incremental improvements.

Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations.

PubMed

Wu, Jingheng; Shen, Lin; Yang, Weitao

2017-10-28

Ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation is a useful tool to calculate thermodynamic properties such as potential of mean force for chemical reactions but intensely time consuming. In this paper, we developed a new method using the internal force correction for low-level semiempirical QM/MM molecular dynamics samplings with a predefined reaction coordinate. As a correction term, the internal force was predicted with a machine learning scheme, which provides a sophisticated force field, and added to the atomic forces on the reaction coordinate related atoms at each integration step. We applied this method to two reactions in aqueous solution and reproduced potentials of mean force at the ab initio QM/MM level. The saving in computational cost is about 2 orders of magnitude. The present work reveals great potentials for machine learning in QM/MM simulations to study complex chemical processes.

VAMPnets for deep learning of molecular kinetics.

PubMed

Mardt, Andreas; Pasquali, Luca; Wu, Hao; Noé, Frank

2018-01-02

There is an increasing demand for computing the relevant structures, equilibria, and long-timescale kinetics of biomolecular processes, such as protein-drug binding, from high-throughput molecular dynamics simulations. Current methods employ transformation of simulated coordinates into structural features, dimension reduction, clustering the dimension-reduced data, and estimation of a Markov state model or related model of the interconversion rates between molecular structures. This handcrafted approach demands a substantial amount of modeling expertise, as poor decisions at any step will lead to large modeling errors. Here we employ the variational approach for Markov processes (VAMP) to develop a deep learning framework for molecular kinetics using neural networks, dubbed VAMPnets. A VAMPnet encodes the entire mapping from molecular coordinates to Markov states, thus combining the whole data processing pipeline in a single end-to-end framework. Our method performs equally or better than state-of-the-art Markov modeling methods and provides easily interpretable few-state kinetic models.

Regional forecasting system of marine state and variability of dynamical processes in the easternmost part of the Black Sea

NASA Astrophysics Data System (ADS)

Kordzadze, Avtandil; Demetrashvili, Demuri

2014-05-01

The regional forecasting system for the easternmost part of the Black Sea developed at M. Nodia Institute of Geophysics of I. Javakhishvili Tbilisi State University under the EU framework projects ARENA and ECOOP is a part of the Black Sea basin-scale Nowcasting/Forecasting System. A core of the regional forecasting system is a baroclinic regional model of Black Sea dynamics with 1 km spacing based on hydrostatic primitive equations of ocean hydrothermodynamics, which are written in z-coordinates for deviations of thermodynamic values from their standard vertical distributions. To solve the problem the two-cycle method of splitting the model equation system with respect to both physical processes and coordinate planes and lines is used. The regional model of M. Nodia Institute of Geophysics is nested in the basin-scale model of Black Sea dynamics of Marine Hydrophysical Institute (Sevastopol/Ukraine). The regional forecasting system provides 3 days' forecasts of current, temperature and salinity for the easternmost part of the Black Sea, which is limited to the Caucasian and Turkish coastal lines and the western liquid boundary coinciding with the meridian 39.080E. Data needed on liquid and upper boundaries, also the 3-D initial hydrophysical fields for the easternmost regional area are provided in near operative mode from Marine hydrophysical Institute via Internet. These data on the liquid boundary are values of velocity components, temperature and salinity predicted by the basin-scale model of Black Sea dynamics of Marine Hydrophysical Institute and on the sea surface 2-D meteorological boundary fields - wind stress, heat fluxes, evaporation and precipitation rates predicted by the regional atmospheric model ALADIN are used. The analysis of the results of modeling and forecast of dynamic processes developed for 2010-2014 showed that the easternmost water area of the Black Sea is a dynamically very active zone, where continuously there are processes of generation, deformation and disappearance of the cyclonic and anticyclonic vortex formations of different sizes. Acknowledgement. The significant part of the researches was supported by the Shota Rustaveli National Science Foundation, Grant No. AR/373/9-120/12.

Perspective: Maximum caliber is a general variational principle for dynamical systems

NASA Astrophysics Data System (ADS)

Dixit, Purushottam D.; Wagoner, Jason; Weistuch, Corey; Pressé, Steve; Ghosh, Kingshuk; Dill, Ken A.

2018-01-01

We review here Maximum Caliber (Max Cal), a general variational principle for inferring distributions of paths in dynamical processes and networks. Max Cal is to dynamical trajectories what the principle of maximum entropy is to equilibrium states or stationary populations. In Max Cal, you maximize a path entropy over all possible pathways, subject to dynamical constraints, in order to predict relative path weights. Many well-known relationships of non-equilibrium statistical physics—such as the Green-Kubo fluctuation-dissipation relations, Onsager's reciprocal relations, and Prigogine's minimum entropy production—are limited to near-equilibrium processes. Max Cal is more general. While it can readily derive these results under those limits, Max Cal is also applicable far from equilibrium. We give examples of Max Cal as a method of inference about trajectory distributions from limited data, finding reaction coordinates in bio-molecular simulations, and modeling the complex dynamics of non-thermal systems such as gene regulatory networks or the collective firing of neurons. We also survey its basis in principle and some limitations.

Perspective: Maximum caliber is a general variational principle for dynamical systems.

PubMed

Dixit, Purushottam D; Wagoner, Jason; Weistuch, Corey; Pressé, Steve; Ghosh, Kingshuk; Dill, Ken A

2018-01-07

We review here Maximum Caliber (Max Cal), a general variational principle for inferring distributions of paths in dynamical processes and networks. Max Cal is to dynamical trajectories what the principle of maximum entropy is to equilibrium states or stationary populations. In Max Cal, you maximize a path entropy over all possible pathways, subject to dynamical constraints, in order to predict relative path weights. Many well-known relationships of non-equilibrium statistical physics-such as the Green-Kubo fluctuation-dissipation relations, Onsager's reciprocal relations, and Prigogine's minimum entropy production-are limited to near-equilibrium processes. Max Cal is more general. While it can readily derive these results under those limits, Max Cal is also applicable far from equilibrium. We give examples of Max Cal as a method of inference about trajectory distributions from limited data, finding reaction coordinates in bio-molecular simulations, and modeling the complex dynamics of non-thermal systems such as gene regulatory networks or the collective firing of neurons. We also survey its basis in principle and some limitations.

Binding of anions in triply interlocked coordination catenanes and dynamic allostery for dehalogenation reactions† †Electronic supplementary information (ESI) available: Characterization data and additional tables and figures. CCDC 1515722 and 1515723. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc04070a

PubMed Central

Yang, Linlin; Jing, Xu; An, Bowen; Yang, Yang

2017-01-01

By synergistic combination of multicomponent self-assembly and template-directed approaches, triply interlocked metal organic catenanes that consist of two isolated chirally identical tetrahedrons were constructed and stabilized as thermodynamic minima. In the presence of suitable template anions, the structural conversion from the isolated tetrahedral conformers into locked catenanes occurred via the cleavage of an intrinsically reversible coordination bond in each of the tetrahedrons, followed by the reengineering and interlocking of two fragments with the regeneration of the broken coordination bonds. The presence of several kinds of individual pocket that were attributed to the triply interlocked patterns enabled the possibility of encapsulating different anions, allowing the dynamic allostery between the unlocked/locked conformers to promote the dehalogenation reaction of 3-bromo-cyclohexene efficiently, as with the use of dehalogenase enzymes. The interlocked structures could be unlocked into two individual tetrahedrons through removal of the well-matched anion templates. The stability and reversibility of the locked/unlocked structures were further confirmed by the catching/releasing process that accompanied emission switching, providing opportunities for the system to be a dynamic molecular logic system. PMID:29675152

Bodywork as systemic and inter-enactive competence: participatory process management in Feldenkrais® Method and Zen Shiatsu

PubMed Central

Kimmel, Michael; Irran, Christine; Luger, Martin A.

2014-01-01

Feldenkrais and Shiatsu enable somatic learning through continuous tactile coupling, a real-time interpersonal dynamic unfolding in a safe dyadic sphere. The first part of our micro-ethnographic study draws on process vignettes and subjective theories to demonstrate how bodywork is infused with systemic sensitivities and awareness for non-linear process management. Expressed in dynamic systems parlance, both disciplines foster metastability, adaptivity, and self-organization in the client's somato-personal system by progressively reconfiguring systemic dispositions, i.e., an attractor landscape. Doing so requires a keen embodied apperception of hierarchies of somato-systemic order. Bodyworkers learn to explore these in their eigenfunction (joints, muscles, fascia), discriminate coordinative organization in small ensembles, and monitor large-scale dynamic interplay. The practitioner's “extended body” reaching forth into the client's through a resonance loop eventually becomes part of this. Within a bodywork session, practitioners modulate this hierarchical functional architecture. Their ability for sensorially staying apace of systemic emergence allows them to respond to minute changes and customize reactions in a zone of proximal development (dynamic immediacy). They stimulate the client's system with a mix of perturbing and stabilizing interventions that oscillate between eigenfunctions and their coordinative integration. Practical knowledge for “soft-assembling” non-linear synergies is crucial for this (cumulative local effects, high-level functions “slaving” the system, etc.). The paper's second part inventorizes the bodyworker's operative tool-box—micro-skills providing the wherewithal for context-intelligent intervention. Practitioners deploy “educated senses” and a repertoire of hands-on techniques (grips, stretches, etc.) against a backdrop of somatic habits (proper posture, muscle activation, gaze patterns, etc.). At this level, our study addresses a host of micro-skills through the lens of enactive cognitive science. PMID:25628576

Measuring mitotic spindle dynamics in budding yeast

NASA Astrophysics Data System (ADS)

Plumb, Kemp

In order to carry out its life cycle and produce viable progeny through cell division, a cell must successfully coordinate and execute a number of complex processes with high fidelity, in an environment dominated by thermal noise. One important example of such a process is the assembly and positioning of the mitotic spindle prior to chromosome segregation. The mitotic spindle is a modular structure composed of two spindle pole bodies, separated in space and spanned by filamentous proteins called microtubules, along which the genetic material of the cell is held. The spindle is responsible for alignment and subsequent segregation of chromosomes into two equal parts; proper spindle positioning and timing ensure that genetic material is appropriately divided amongst mother and daughter cells. In this thesis, I describe fluorescence confocal microscopy and automated image analysis algorithms, which I have used to observe and analyze the real space dynamics of the mitotic spindle in budding yeast. The software can locate structures in three spatial dimensions and track their movement in time. By selecting fluorescent proteins which specifically label the spindle poles and cell periphery, mitotic spindle dynamics have been measured in a coordinate system relevant to the cell division. I describe how I have characterised the accuracy and precision of the algorithms by simulating fluorescence data for both spindle poles and the budding yeast cell surface. In this thesis I also describe the construction of a microfluidic apparatus that allows for the measurement of long time-scale dynamics of individual cells and the development of a cell population. The tools developed in this thesis work will facilitate in-depth quantitative analysis of the non-equilibrium processes in living cells.

Some fundamentals regarding kinematics and generalized forces for multibody dynamics

NASA Technical Reports Server (NTRS)

Hodges, Dewey H.

1990-01-01

In order to illustrate the various forms in which generalized forces can arise from diverse subsystem analyses in multibody dynamics, intrinsic dynamical equations for the rotational dynamics of a rigid body are derived from Hamilton's principle. Two types of generalized forces are derived: (1) those associated with the virtual rotation vector in some orthogonal basis, and (2) those associated with varying generalized coordinates. As one physical or kinematical result (such as a frequency or a specific direction cosine) cannot rely on this selection, a 'blind' coupling of two models in which generalized forces are calculated in different ways would be wrong. Both types should use the same rotational coordinates and should denote the virtual rotation on a similar basis according to method 1, or in terms of common rotational coordinates and their diversifications as in method 2. Alternatively, the generalized forces and coordinates of one model may be transformed to those of the other.

A transcriptional dynamic network during Arabidopsis thaliana pollen development.

PubMed

Wang, Jigang; Qiu, Xiaojie; Li, Yuhua; Deng, Youping; Shi, Tieliu

2011-01-01

To understand transcriptional regulatory networks (TRNs), especially the coordinated dynamic regulation between transcription factors (TFs) and their corresponding target genes during development, computational approaches would represent significant advances in the genome-wide expression analysis. The major challenges for the experiments include monitoring the time-specific TFs' activities and identifying the dynamic regulatory relationships between TFs and their target genes, both of which are currently not yet available at the large scale. However, various methods have been proposed to computationally estimate those activities and regulations. During the past decade, significant progresses have been made towards understanding pollen development at each development stage under the molecular level, yet the regulatory mechanisms that control the dynamic pollen development processes remain largely unknown. Here, we adopt Networks Component Analysis (NCA) to identify TF activities over time course, and infer their regulatory relationships based on the coexpression of TFs and their target genes during pollen development. We carried out meta-analysis by integrating several sets of gene expression data related to Arabidopsis thaliana pollen development (stages range from UNM, BCP, TCP, HP to 0.5 hr pollen tube and 4 hr pollen tube). We constructed a regulatory network, including 19 TFs, 101 target genes and 319 regulatory interactions. The computationally estimated TF activities were well correlated to their coordinated genes' expressions during the development process. We clustered the expression of their target genes in the context of regulatory influences, and inferred new regulatory relationships between those TFs and their target genes, such as transcription factor WRKY34, which was identified that specifically expressed in pollen, and regulated several new target genes. Our finding facilitates the interpretation of the expression patterns with more biological relevancy, since the clusters corresponding to the activity of specific TF or the combination of TFs suggest the coordinated regulation of TFs to their target genes. Through integrating different resources, we constructed a dynamic regulatory network of Arabidopsis thaliana during pollen development with gene coexpression and NCA. The network illustrated the relationships between the TFs' activities and their target genes' expression, as well as the interactions between TFs, which provide new insight into the molecular mechanisms that control the pollen development.

Effect of Alignment on L2 Written Production

ERIC Educational Resources Information Center

Wang, Chuming; Wang, Min

2015-01-01

This article aims to uncover how L2 writing is affected by alignment, a socio-cognitive process involving dynamic coordination and adaptation. For this, two studies were conducted. Study 1 required two groups of 24 learners of English as a foreign language (EFL) to continue in English two stories with their endings removed, both of which had a…

Redesigning Task Sequences to Support Instrumental Genesis in the Use of Movable Points and Slider Bars

ERIC Educational Resources Information Center

Fahlgren, Maria

2017-01-01

This paper examines the process of instrumental genesis through which students develop their proficiency in making use of movable points and slider bars--two tools that dynamic mathematics software provides for working with variable coordinates and parameters in the field of functions. The paper analyses students' responses to task sequences…

Enabling Healthcare IT Governance: Human Task Management Service for Administering Emergency Department's Resources for Efficient Patient Flow.

PubMed

Rodriguez, Salvador; Aziz, Ayesha; Chatwin, Chris

2014-01-01

The use of Health Information Technology (HIT) to improve healthcare service delivery is constantly increasing due to research advances in medical science and information systems. Having a fully automated process solution for a Healthcare Organization (HCO) requires a combination of organizational strategies along with a selection of technologies that facilitate the goal of improving clinical outcomes. HCOs, requires dynamic management of care capability to realize the full potential of HIT. Business Process Management (BPM) is being increasingly adopted to streamline the healthcare service delivery and management processes. Emergency Departments (EDs) provide a case in point, which require multidisciplinary resources and services to deliver effective clinical outcomes. Managed care involves the coordination of a range of services in an ED. Although fully automated processes in emergency care provide a cutting edge example of service delivery, there are many situations that require human interactions with the computerized systems; e.g. Medication Approvals, care transfer, acute patient care. This requires a coordination mechanism for all the resources, computer and human, to work side by side to provide the best care. To ensure evidence-based medical practice in ED, we have designed a Human Task Management service to model the process of coordination of ED resources based on the UK's NICE Clinical guideline for managing the care of acutely ill patients. This functionality is implemented using Java Business process Management (jBPM).

Brain synchronization during perception of facial emotional expressions with natural and unnatural dynamics

PubMed Central

Volhard, Jakob; Müller, Viktor; Kaulard, Kathrin; Brick, Timothy R.; Wallraven, Christian; Lindenberger, Ulman

2017-01-01

Research on the perception of facial emotional expressions (FEEs) often uses static images that do not capture the dynamic character of social coordination in natural settings. Recent behavioral and neuroimaging studies suggest that dynamic FEEs (videos or morphs) enhance emotion perception. To identify mechanisms associated with the perception of FEEs with natural dynamics, the present EEG (Electroencephalography)study compared (i) ecologically valid stimuli of angry and happy FEEs with natural dynamics to (ii) FEEs with unnatural dynamics, and to (iii) static FEEs. FEEs with unnatural dynamics showed faces moving in a biologically possible but unpredictable and atypical manner, generally resulting in ambivalent emotional content. Participants were asked to explicitly recognize FEEs. Using whole power (WP) and phase synchrony (Phase Locking Index, PLI), we found that brain responses discriminated between natural and unnatural FEEs (both static and dynamic). Differences were primarily observed in the timing and brain topographies of delta and theta PLI and WP, and in alpha and beta WP. Our results support the view that biologically plausible, albeit atypical, FEEs are processed by the brain by different mechanisms than natural FEEs. We conclude that natural movement dynamics are essential for the perception of FEEs and the associated brain processes. PMID:28723957

Brain synchronization during perception of facial emotional expressions with natural and unnatural dynamics.

PubMed

Perdikis, Dionysios; Volhard, Jakob; Müller, Viktor; Kaulard, Kathrin; Brick, Timothy R; Wallraven, Christian; Lindenberger, Ulman

2017-01-01

Research on the perception of facial emotional expressions (FEEs) often uses static images that do not capture the dynamic character of social coordination in natural settings. Recent behavioral and neuroimaging studies suggest that dynamic FEEs (videos or morphs) enhance emotion perception. To identify mechanisms associated with the perception of FEEs with natural dynamics, the present EEG (Electroencephalography)study compared (i) ecologically valid stimuli of angry and happy FEEs with natural dynamics to (ii) FEEs with unnatural dynamics, and to (iii) static FEEs. FEEs with unnatural dynamics showed faces moving in a biologically possible but unpredictable and atypical manner, generally resulting in ambivalent emotional content. Participants were asked to explicitly recognize FEEs. Using whole power (WP) and phase synchrony (Phase Locking Index, PLI), we found that brain responses discriminated between natural and unnatural FEEs (both static and dynamic). Differences were primarily observed in the timing and brain topographies of delta and theta PLI and WP, and in alpha and beta WP. Our results support the view that biologically plausible, albeit atypical, FEEs are processed by the brain by different mechanisms than natural FEEs. We conclude that natural movement dynamics are essential for the perception of FEEs and the associated brain processes.

A Computational Algorithm for Functional Clustering of Proteome Dynamics During Development

PubMed Central

Wang, Yaqun; Wang, Ningtao; Hao, Han; Guo, Yunqian; Zhen, Yan; Shi, Jisen; Wu, Rongling

2014-01-01

Phenotypic traits, such as seed development, are a consequence of complex biochemical interactions among genes, proteins and metabolites, but the underlying mechanisms that operate in a coordinated and sequential manner remain elusive. Here, we address this issue by developing a computational algorithm to monitor proteome changes during the course of trait development. The algorithm is built within the mixture-model framework in which each mixture component is modeled by a specific group of proteins that display a similar temporal pattern of expression in trait development. A nonparametric approach based on Legendre orthogonal polynomials was used to fit dynamic changes of protein expression, increasing the power and flexibility of protein clustering. By analyzing a dataset of proteomic dynamics during early embryogenesis of the Chinese fir, the algorithm has successfully identified several distinct types of proteins that coordinate with each other to determine seed development in this forest tree commercially and environmentally important to China. The algorithm will find its immediate applications for the characterization of mechanistic underpinnings for any other biological processes in which protein abundance plays a key role. PMID:24955031

Requirements for efficient cell-type proportioning: regulatory timescales, stochasticity and lateral inhibition

NASA Astrophysics Data System (ADS)

Pfeuty, B.; Kaneko, K.

2016-04-01

The proper functioning of multicellular organisms requires the robust establishment of precise proportions between distinct cell types. This developmental differentiation process typically involves intracellular regulatory and stochastic mechanisms to generate cell-fate diversity as well as intercellular signaling mechanisms to coordinate cell-fate decisions at tissue level. We thus surmise that key insights about the developmental regulation of cell-type proportion can be captured by the modeling study of clustering dynamics in population of inhibitory-coupled noisy bistable systems. This general class of dynamical system is shown to exhibit a very stable two-cluster state, but also metastability, collective oscillations or noise-induced state hopping, which can prevent from timely and reliably reaching a robust and well-proportioned clustered state. To circumvent these obstacles or to avoid fine-tuning, we highlight a general strategy based on dual-time positive feedback loops, such as mediated through transcriptional versus epigenetic mechanisms, which improves proportion regulation by coordinating early and flexible lineage priming with late and firm commitment. This result sheds new light on the respective and cooperative roles of multiple regulatory feedback, stochasticity and lateral inhibition in developmental dynamics.

Determination of crustal motions using satellite laser ranging

NASA Technical Reports Server (NTRS)

1991-01-01

Satellite laser ranging has matured over the last decade into one of the essential space geodesy techniques. It has demonstrated centimeter site positioning and millimeter per year velocity determinations in a frame tied dynamically to the mass center of the solid Earth hydrosphere atmosphere system. Such a coordinate system is a requirement for studying long term eustatic sea level rise and other global change phenomena. Earth orientation parameters determined with the coordinate system have been produced in near real time operationally since 1983, at a relatively modest cost. The SLR ranging to Lageos has also provided a rich spectrum of results based upon the analysis of Lageos orbital dynamics. These include significant improvements in the knowledge of the mean and variable components of the Earth's gravity field and the Earth's gravitational parameter. The ability to measure the time variations of the Earth's gravity field has opened as exciting area of study in relating global processes, including meteorologically derived mass transport through changes in the satellite dynamics. New confirmation of general relativity was obtained using the Lageos SLR data.

Outline of a general theory of behavior and brain coordination.

PubMed

Kelso, J A Scott; Dumas, Guillaume; Tognoli, Emmanuelle

2013-01-01

Much evidence suggests that dynamic laws of neurobehavioral coordination are sui generis: they deal with collective properties that are repeatable from one system to another and emerge from microscopic dynamics but may not (even in principle) be deducible from them. Nevertheless, it is useful to try to understand the relationship between different levels while all the time respecting the autonomy of each. We report a program of research that uses the theoretical concepts of coordination dynamics and quantitative measurements of simple, well-defined experimental model systems to explicitly relate neural and behavioral levels of description in human beings. Our approach is both top-down and bottom-up and aims at ending up in the same place: top-down to derive behavioral patterns from neural fields, and bottom-up to generate neural field patterns from bidirectional coupling between astrocytes and neurons. Much progress can be made by recognizing that the two approaches--reductionism and emergentism--are complementary. A key to understanding is to couch the coordination of very different things--from molecules to thoughts--in the common language of coordination dynamics. Copyright © 2012 Elsevier Ltd. All rights reserved.

Outline of a General Theory of Behavior and Brain Coordination

PubMed Central

Kelso, J. A. Scott; Dumas, Guillaume; Tognoli, Emmanuelle

2012-01-01

Much evidence suggests that dynamic laws of neurobehavioral coordination are sui generis: they deal with collective properties that are repeatable from one system to another and emerge from microscopic dynamics but may not (even in principle) be deducible from them. Nevertheless, it is useful to try to understand the relationship between different levels while all the time respecting the autonomy of each. We report a program of research that uses the theoretical concepts of coordination dynamics and quantitative measurements of simple, well-defined experimental model systems to explicitly relate neural and behavioral levels of description in human beings. Our approach is both top-down and bottom-up and aims at ending up in the same place: top-down to derive behavioral patterns from neural fields, and bottom-up to generate neural field patterns from bidirectional coupling between astrocytes and neurons. Much progress can be made by recognizing that the two approaches —reductionism and emergentism— are complementary. A key to understanding is to couch the coordination of very different things —from molecules to thoughts— in the common language of coordination dynamics. PMID:23084845

Constitutional Dynamics of Metal-Organic Motifs on a Au(111) Surface.

PubMed

Kong, Huihui; Zhang, Chi; Xie, Lei; Wang, Likun; Xu, Wei

2016-06-13

Constitutional dynamic chemistry (CDC), including both dynamic covalent chemistry and dynamic noncovalent chemistry, relies on reversible formation and breakage of bonds to achieve continuous changes in constitution by reorganization of components. In this regard, CDC is considered to be an efficient and appealing strategy for selective fabrication of surface nanostructures by virtue of dynamic diversity. Although constitutional dynamics of monolayered structures has been recently demonstrated at liquid/solid interfaces, most of molecular reorganization/reaction processes were thought to be irreversible under ultrahigh vacuum (UHV) conditions where CDC is therefore a challenge to be achieved. Here, we have successfully constructed a system that presents constitutional dynamics on a solid surface based on dynamic coordination chemistry, in which selective formation of metal-organic motifs is achieved under UHV conditions. The key to making this reversible switching successful is the molecule-substrate interaction as revealed by DFT calculations. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bio-Inspired Metal-Coordination Dynamics: A Unique Tool for Engineering Soft Matter Mechanics

NASA Astrophysics Data System (ADS)

Holten-Andersen, Niels

Growing evidence supports a critical role of metal-coordination in soft biological material properties such as self-healing, underwater adhesion and autonomous wound plugging. Using bio-inspired metal-binding polymers, initial efforts to mimic these properties with metal-coordination crosslinked polymer materials have shown promise. In addition, with polymer network mechanics strongly coupled to coordinate crosslink dynamics material properties can be easily tuned from visco-elastic fluids to solids. Given their exploitation in desirable material applications in Nature, bio-inspired metal-coordinate complex crosslinking provides an opportunity to further advance synthetic polymer materials design. Early lessons from this pursuit are presented.

Dynamic network communication as a unifying neural basis for cognition, development, aging, and disease.

PubMed

Voytek, Bradley; Knight, Robert T

2015-06-15

Perception, cognition, and social interaction depend upon coordinated neural activity. This coordination operates within noisy, overlapping, and distributed neural networks operating at multiple timescales. These networks are built upon a structural scaffolding with intrinsic neuroplasticity that changes with development, aging, disease, and personal experience. In this article, we begin from the perspective that successful interregional communication relies upon the transient synchronization between distinct low-frequency (<80 Hz) oscillations, allowing for brief windows of communication via phase-coordinated local neuronal spiking. From this, we construct a theoretical framework for dynamic network communication, arguing that these networks reflect a balance between oscillatory coupling and local population spiking activity and that these two levels of activity interact. We theorize that when oscillatory coupling is too strong, spike timing within the local neuronal population becomes too synchronous; when oscillatory coupling is too weak, spike timing is too disorganized. Each results in specific disruptions to neural communication. These alterations in communication dynamics may underlie cognitive changes associated with healthy development and aging, in addition to neurological and psychiatric disorders. A number of neurological and psychiatric disorders-including Parkinson's disease, autism, depression, schizophrenia, and anxiety-are associated with abnormalities in oscillatory activity. Although aging, psychiatric and neurological disease, and experience differ in the biological changes to structural gray or white matter, neurotransmission, and gene expression, our framework suggests that any resultant cognitive and behavioral changes in normal or disordered states or their treatment are a product of how these physical processes affect dynamic network communication. Copyright © 2015 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Model Classes, Approximation, and Metrics for Dynamic Processing of Urban Terrain Data

DTIC Science & Technology

2013-01-01

Sensing,” DARPA IPTO Retreat, Annapolis, 2008. R. Baraniuk, “Compressive Sensing, Wavelets, and Sparsity,” SPIE Defense + Security (acceptance speech ... Speech and Signal Processing (ICASSP). 2011/05/22 00:00:00, Prague, Czech Republic. : , 08/31/2011 33.00 Sang-Mook Lee, Jeong Joon Im, Bo-Hee Lee... KNN ) points to define a local intrinsic coordinate system using PCA and to construct the manifold and function locally using least squares. Local

Formalizing Knowledge in Multi-Scale Agent-Based Simulations

PubMed Central

Somogyi, Endre; Sluka, James P.; Glazier, James A.

2017-01-01

Multi-scale, agent-based simulations of cellular and tissue biology are increasingly common. These simulations combine and integrate a range of components from different domains. Simulations continuously create, destroy and reorganize constituent elements causing their interactions to dynamically change. For example, the multi-cellular tissue development process coordinates molecular, cellular and tissue scale objects with biochemical, biomechanical, spatial and behavioral processes to form a dynamic network. Different domain specific languages can describe these components in isolation, but cannot describe their interactions. No current programming language is designed to represent in human readable and reusable form the domain specific knowledge contained in these components and interactions. We present a new hybrid programming language paradigm that naturally expresses the complex multi-scale objects and dynamic interactions in a unified way and allows domain knowledge to be captured, searched, formalized, extracted and reused. PMID:29338063

Formalizing Knowledge in Multi-Scale Agent-Based Simulations.

PubMed

Somogyi, Endre; Sluka, James P; Glazier, James A

2016-10-01

Multi-scale, agent-based simulations of cellular and tissue biology are increasingly common. These simulations combine and integrate a range of components from different domains. Simulations continuously create, destroy and reorganize constituent elements causing their interactions to dynamically change. For example, the multi-cellular tissue development process coordinates molecular, cellular and tissue scale objects with biochemical, biomechanical, spatial and behavioral processes to form a dynamic network. Different domain specific languages can describe these components in isolation, but cannot describe their interactions. No current programming language is designed to represent in human readable and reusable form the domain specific knowledge contained in these components and interactions. We present a new hybrid programming language paradigm that naturally expresses the complex multi-scale objects and dynamic interactions in a unified way and allows domain knowledge to be captured, searched, formalized, extracted and reused.

Practice effects on intra-team synergies in football teams.

PubMed

Silva, Pedro; Chung, Dante; Carvalho, Thiago; Cardoso, Tiago; Davids, Keith; Araújo, Duarte; Garganta, Júlio

2016-04-01

Developing synchronised player movements for fluent competitive match play is a common goal for coaches of team games. An ecological dynamics approach advocates that intra-team synchronization is governed by locally created information, which specifies shared affordances responsible for synergy formation. To verify this claim we evaluated coordination tendencies in two newly-formed teams of recreational players during association football practice games, weekly, for fifteen weeks (thirteen matches). We investigated practice effects on two central features of synergies in sports teams - dimensional compression and reciprocal compensation here captured through near in-phase modes of coordination and time delays between coupled players during forward and backwards movements on field while attacking and defending. Results verified that synergies were formed and dissolved rapidly as a result of the dynamic creation of informational properties, perceived as shared affordances among performers. Practising once a week led to small improvements in the readjustment delays between co-positioning team members, enabling faster regulation of coordinated team actions. Mean values of the number of player and team synergies displayed only limited improvements, possibly due to the timescales of practice. No relationship between improvements in dimensional compression and reciprocal compensation were found for number of shots, amount of ball possession and number of ball recoveries made. Findings open up new perspectives for monitoring team coordination processes in sport. Copyright © 2015 Elsevier B.V. All rights reserved.

Automation Framework for Flight Dynamics Products Generation

NASA Technical Reports Server (NTRS)

Wiegand, Robert E.; Esposito, Timothy C.; Watson, John S.; Jun, Linda; Shoan, Wendy; Matusow, Carla

2010-01-01

XFDS provides an easily adaptable automation platform. To date it has been used to support flight dynamics operations. It coordinates the execution of other applications such as Satellite TookKit, FreeFlyer, MATLAB, and Perl code. It provides a mechanism for passing messages among a collection of XFDS processes, and allows sending and receiving of GMSEC messages. A unified and consistent graphical user interface (GUI) is used for the various tools. Its automation configuration is stored in text files, and can be edited either directly or using the GUI.

Understanding the relation between urbanization and the eco-environment in China's Yangtze River Delta using an improved EKC model and coupling analysis.

PubMed

Zhao, Yabo; Wang, Shaojian; Zhou, Chunshan

2016-11-15

Better understanding the relationship between urbanization (U) and the eco-environment (E) is necessary to coordinate the development of them. Using a comprehensive index system for U and E with statistic data, and an improved environmental Kuznets curve (EKC) model and dynamic coordination coupling degree (CCD) model, this study addressed the relationship between U and E in the Yangtze River Delta (YRD) in the period 1980-2013. The main conclusions were as follows: (1) Economic urbanization and eco-environment endowment were the highest weighted factors in the U and E system respectively, and thus constitute the key factors. (2) Differentiated inverted-U curves were shown to exist in the relation between U and E across the cities studied, thereby confirming the improved EKC hypothesis. We further found economically developed areas to have higher urbanization levels than less developed areas at the point at which the curve inflects, less developed areas have higher eco-environmental pressure at inflection. Before the appearance of the inflection point, a striking positive correlation was observed between eco-environmental pressure and the urbanization level, while a negative correlation was found to follow it. (3) A dynamic coordination coupling relation was found to exist between U and E, which conforms to an S-shaped curve. The coordination coupling process in the YRD has gradually moved from a "low-grade symbiosis" stage into a "break-in development" stage, but the pattern of coordination belonging to the eco-environment part of the relation was found to always show some lag. The dynamic CCD model showed a difference in the spatial distribution of CCD, presenting higher values in the periphery of the region, and lower values in the center during the study period. The improved EKC and coupling analysis detailed in this study may help Chinese decision makers to formulate sustainable measures to balance urbanization development and eco-environment protection. Copyright © 2016 Elsevier B.V. All rights reserved.

VISTILES: Coordinating and Combining Co-located Mobile Devices for Visual Data Exploration.

PubMed

Langner, Ricardo; Horak, Tom; Dachselt, Raimund

2017-08-29

We present VISTILES, a conceptual framework that uses a set of mobile devices to distribute and coordinate visualization views for the exploration of multivariate data. In contrast to desktop-based interfaces for information visualization, mobile devices offer the potential to provide a dynamic and user-defined interface supporting co-located collaborative data exploration with different individual workflows. As part of our framework, we contribute concepts that enable users to interact with coordinated & multiple views (CMV) that are distributed across several mobile devices. The major components of the framework are: (i) dynamic and flexible layouts for CMV focusing on the distribution of views and (ii) an interaction concept for smart adaptations and combinations of visualizations utilizing explicit side-by-side arrangements of devices. As a result, users can benefit from the possibility to combine devices and organize them in meaningful spatial layouts. Furthermore, we present a web-based prototype implementation as a specific instance of our concepts. This implementation provides a practical application case enabling users to explore a multivariate data collection. We also illustrate the design process including feedback from a preliminary user study, which informed the design of both the concepts and the final prototype.

X-ray microtomography study of the compaction process of rods under tapping.

PubMed

Fu, Yang; Xi, Yan; Cao, Yixin; Wang, Yujie

2012-05-01

We present an x-ray microtomography study of the compaction process of cylindrical rods under tapping. The process is monitored by measuring the evolution of the orientational order parameter, local, and overall packing densities as a function of the tapping number for different tapping intensities. The slow relaxation dynamics of the orientational order parameter can be well fitted with a stretched-exponential law with stretching exponents ranging from 0.9 to 1.6. The corresponding relaxation time versus tapping intensity follows an Arrhenius behavior which is reminiscent of the slow dynamics in thermal glassy systems. We also investigated the boundary effect on the ordering process and found that boundary rods order faster than interior ones. In searching for the underlying mechanism of the slow dynamics, we estimated the initial random velocities of the rods under tapping and found that the ordering process is compatible with a diffusion mechanism. The average coordination number as a function of the tapping number at different tapping intensities has also been measured, which spans a range from 6 to 8.

BRIEF COMMUNICATION: A note on the Coulomb collision operator in curvilinear coordinates

NASA Astrophysics Data System (ADS)

Goncharov, P. R.

2010-10-01

The dynamic friction force, diffusion tensor, flux density in velocity space and Coulomb collision term are expressed in curvilinear coordinates via Trubnikov potential functions corresponding to each species of a background plasma. For comparison, explicit formulae are given for the dynamic friction force, diffusion tensor and collisional flux density in velocity space in curvilinear coordinates via Rosenbluth potential functions summed over all species of the background plasma.

A self-learning algorithm for biased molecular dynamics

PubMed Central

Tribello, Gareth A.; Ceriotti, Michele; Parrinello, Michele

2010-01-01

A new self-learning algorithm for accelerated dynamics, reconnaissance metadynamics, is proposed that is able to work with a very large number of collective coordinates. Acceleration of the dynamics is achieved by constructing a bias potential in terms of a patchwork of one-dimensional, locally valid collective coordinates. These collective coordinates are obtained from trajectory analyses so that they adapt to any new features encountered during the simulation. We show how this methodology can be used to enhance sampling in real chemical systems citing examples both from the physics of clusters and from the biological sciences. PMID:20876135

Dynamical Coordination of Hand Intrinsic Muscles for Precision Grip in Diabetes Mellitus.

PubMed

Li, Ke; Wei, Na; Cheng, Mei; Hou, Xingguo; Song, Jun

2018-03-12

This study investigated the effects of diabetes mellitus (DM) on dynamical coordination of hand intrinsic muscles during precision grip. Precision grip was tested using a custom designed apparatus with stable and unstable loads, during which the surface electromyographic (sEMG) signals of the abductor pollicis brevis (APB) and first dorsal interosseous (FDI) were recorded simultaneously. Recurrence quantification analysis (RQA) was applied to quantify the dynamical structure of sEMG signals of the APB and FDI; and cross recurrence quantification analysis (CRQA) was used to assess the intermuscular coupling between the two intrinsic muscles. This study revealed that the DM altered the dynamical structure of muscle activation for the FDI and the dynamical intermuscular coordination between the APB and FDI during precision grip. A reinforced feedforward mechanism that compensates the loss of sensory feedbacks in DM may be responsible for the stronger intermuscular coupling between the APB and FDI muscles. Sensory deficits in DM remarkably decreased the capacity of online motor adjustment based on sensory feedback, rendering a lower adaptability to the uncertainty of environment. This study shed light on inherent dynamical properties underlying the intrinsic muscle activation and intermuscular coordination for precision grip and the effects of DM on hand sensorimotor function.

Hierarchical Time-Lagged Independent Component Analysis: Computing Slow Modes and Reaction Coordinates for Large Molecular Systems.

PubMed

Pérez-Hernández, Guillermo; Noé, Frank

2016-12-13

Analysis of molecular dynamics, for example using Markov models, often requires the identification of order parameters that are good indicators of the rare events, i.e. good reaction coordinates. Recently, it has been shown that the time-lagged independent component analysis (TICA) finds the linear combinations of input coordinates that optimally represent the slow kinetic modes and may serve in order to define reaction coordinates between the metastable states of the molecular system. A limitation of the method is that both computing time and memory requirements scale with the square of the number of input features. For large protein systems, this exacerbates the use of extensive feature sets such as the distances between all pairs of residues or even heavy atoms. Here we derive a hierarchical TICA (hTICA) method that approximates the full TICA solution by a hierarchical, divide-and-conquer calculation. By using hTICA on distances between heavy atoms we identify previously unknown relaxation processes in the bovine pancreatic trypsin inhibitor.

Beyond the blank slate: routes to learning new coordination patterns depend on the intrinsic dynamics of the learner—experimental evidence and theoretical model

PubMed Central

Kostrubiec, Viviane; Zanone, Pier-Giorgio; Fuchs, Armin; Kelso, J. A. Scott

2012-01-01

Using an approach that combines experimental studies of bimanual movements to visual stimuli and theoretical modeling, the present paper develops a dynamical account of sensorimotor learning, that is, how new skills are acquired and old ones modified. A significant aspect of our approach is the focus on the individual learner as the basic unit of analysis, in particular the quantification of predispositions and capabilities that the individual learner brings to the learning environment. Such predispositions constitute the learner's behavioral repertoire, captured here theoretically as a dynamical landscape (“intrinsic dynamics”). The learning process is demonstrated to not only lead to a relatively permanent improvement of performance in the required task—the usual outcome—but also to alter the individual's entire repertoire. Changes in the dynamical landscape due to learning are shown to result from two basic mechanisms or “routes”: bifurcation and shift. Which mechanism is selected depends the initial individual repertoire before new learning begins. Both bifurcation and shift mechanisms are accommodated by a dynamical model, a relatively straightforward development of the well-established HKB model of movement coordination. Model simulations show that although environmental or task demands may be met equally well using either mechanism, the bifurcation route results in greater stabilization of the to-be-learned behavior. Thus, stability not (or not only) error is demonstrated to be the basis of selection, both of a new pattern of behavior and the path (smooth shift versus abrupt qualitative change) that learning takes. In line with these results, recent neurophysiological evidence indicates that stability is a relevant feature around which brain activity is organized while an individual performs a coordination task. Finally, we explore the consequences of the dynamical approach to learning for theories of biological change. PMID:22876227

Inflatable antenna for earth observing systems

NASA Astrophysics Data System (ADS)

Wang, Hong-Jian; Guan, Fu-ling; Xu, Yan; Yi, Min

2010-09-01

This paper describe mechanical design, dynamic analysis, and deployment demonstration of the antenna , and the photogrammetry detecting RMS of inflatable antenna surface, the possible errors results form the measurement are also analysed. Ticra's Grasp software are used to predict the inflatable antenna pattern based on the coordinates of the 460 points on the parabolic surface, the final results verified the whole design process.

The Pathway of Oligomeric DNA Melting Investigated by Molecular Dynamics Simulations

PubMed Central

Wong, Ka-Yiu; Pettitt, B. Montgomery

2008-01-01

Details of the reaction coordinate for DNA melting are fundamental to much of biology and biotechnology. Recently, it has been shown experimentally that there are at least three states involved. To clarify the reaction mechanism of the melting transition of DNA, we perform 100-ns molecular dynamics simulations of a homo-oligomeric, 12-basepair DNA duplex, d(A12)·d(T12), with explicit salt water at 400 K. Analysis of the trajectory reveals the various biochemically important processes that occur on different timescales. Peeling (including fraying from the ends), searching for Watson-Crick complements, and dissociation are recognizable processes. However, we find that basepair searching for Watson-Crick complements along a strand is not mechanistically tied to or directly accessible from the dissociation steps of strand melting. A three-step melting mechanism is proposed where the untwisting of the duplex is determined to be the major component of the reaction coordinate at the barrier. Though the observations are limited to the characteristics of the system being studied, they provide important insight into the mechanism of melting of other more biologically relevant forms of DNA, which will certainly differ in details from those here. PMID:18952784

Distributed Coordination of Heterogeneous Agents Using a Semantic Overlay Network and a Goal-Directed Graphplan Planner

PubMed Central

Lopes, António Luís; Botelho, Luís Miguel

2013-01-01

In this paper, we describe a distributed coordination system that allows agents to seamlessly cooperate in problem solving by partially contributing to a problem solution and delegating the subproblems for which they do not have the required skills or knowledge to appropriate agents. The coordination mechanism relies on a dynamically built semantic overlay network that allows the agents to efficiently locate, even in very large unstructured networks, the necessary skills for a specific problem. Each agent performs partial contributions to the problem solution using a new distributed goal-directed version of the Graphplan algorithm. This new goal-directed version of the original Graphplan algorithm provides an efficient solution to the problem of "distraction", which most forward-chaining algorithms suffer from. We also discuss a set of heuristics to be used in the backward-search process of the planning algorithm in order to distribute this process amongst idle agents in an attempt to find a solution in less time. The evaluation results show that our approach is effective in building a scalable and efficient agent society capable of solving complex distributable problems. PMID:23704885

Physical activity and the elderly.

PubMed

Hollmann, Wildor; Strüder, Heiko K; Tagarakis, Christos V M; King, Gerard

2007-12-01

Functional ageing processes are characterized by a loss of performance capabilities regarding coordination, flexibility, strength, speed, and endurance. The effects of ageing processes on the cardiovascular system and skeletal muscle are the foci of attention. After age 30, the maximum aerobic dynamic performance capacity decreases by an average of 8% per decade. The causes are mainly a reduction in the maximum cardiac output and decreases in capillarization and in the skeletal muscle mass. An improvement in the maximum oxygen uptake by 18% and in the aerobic-anaerobic threshold by 22% was achieved in untrained men aged 55-70 years, in a 12-week-long bicycle ergometer-training programme. The strength of the skeletal muscle decreases particularly after 50-60 years of age. The main cause is the reduction in the number of motor units and muscle fibres. Further, modifications of the endothelial function and the development of sarcopenia are of particular importance in ageing processes. General aerobic dynamic training can improve the endothelial function in old age and thus help prevent cardiovascular diseases. Strength training is most appropriate for the prevention of sarcopenia. Imaging techniques over the last 20 years have provided new findings on the influence and the significance of physical activity on the brain. We call this new interdisciplinary area 'Exercise Neuroscience'. Demands on coordination and aerobic dynamic endurance are suitable in counteracting age-related neuronal cellular loss, synapsis hypotrophy, and in improving neurogenesis and capillarization. Adjusted physical activity is thus capable of counteracting age-related changes and performance loss not only in the cardiovascular system but also in the brain.

Roi-Orientated Sensor Correction Based on Virtual Steady Reimaging Model for Wide Swath High Resolution Optical Satellite Imagery

NASA Astrophysics Data System (ADS)

Zhu, Y.; Jin, S.; Tian, Y.; Wang, M.

2017-09-01

To meet the requirement of high accuracy and high speed processing for wide swath high resolution optical satellite imagery under emergency situation in both ground processing system and on-board processing system. This paper proposed a ROI-orientated sensor correction algorithm based on virtual steady reimaging model for wide swath high resolution optical satellite imagery. Firstly, the imaging time and spatial window of the ROI is determined by a dynamic search method. Then, the dynamic ROI sensor correction model based on virtual steady reimaging model is constructed. Finally, the corrected image corresponding to the ROI is generated based on the coordinates mapping relationship which is established by the dynamic sensor correction model for corrected image and rigours imaging model for original image. Two experimental results show that the image registration between panchromatic and multispectral images can be well achieved and the image distortion caused by satellite jitter can be also corrected efficiently.

An Approach for High-precision Stand-alone Positioning in a Dynamic Environment

NASA Astrophysics Data System (ADS)

Halis Saka, M.; Metin Alkan, Reha; Ozpercin, Alişir

2015-04-01

In this study, an algorithm is developed for precise positioning in dynamic environment utilizing a single geodetic GNSS receiver using carrier phase data. In this method, users should start the measurement on a known point near the project area for a couple of seconds making use of a single dual-frequency geodetic-grade receiver. The technique employs iono-free carrier phase observations with precise products. The equation of the algorithm is given below; Sm(t(i+1))=SC(ti)+[ΦIF (t(i+1) )-ΦIF (ti)] where, Sm(t(i+1)) is the phase-range between satellites and the receiver, SC(ti) is the initial range computed from the initial known point coordinates and the satellite coordinates and ΦIF is the ionosphere-free phase measurement (in meters). Tropospheric path delays are modelled using the standard tropospheric model. To accomplish the process, an in-house program was coded and some functions were adopted from Easy-Suite available at http://kom.aau.dk/~borre/easy. In order to assess the performance of the introduced algorithm in a dynamic environment, a dataset from a kinematic test measurement was used. The data were collected from a kinematic test measurement in Istanbul, Turkey. In the test measurement, a geodetic dual-frequency GNSS receiver, Ashtech Z-Xtreme, was set up on a known point on the shore and a couple of epochs were recorded for initialization. The receiver was then moved to a vessel and data were collected for approximately 2.5 hours and the measurement was finalized on a known point on the shore. While the kinematic measurement on the vessel were carried out, another GNSS receiver was set up on a geodetic point with known coordinates on the shore and data were collected in static mode to calculate the reference trajectory of the vessel using differential technique. The coordinates of the vessel were calculated for each measurement epoch with the introduced method. With the purpose of obtaining more robust results, all coordinates were calculated once again by inversely, i.e. from the last epoch to the first one. In this way, the estimated coordinates were also controlled. The average of both computed coordinates were used as vessel coordinates and then compared with the known-coordinates those of geodetic receiver epoch by epoch. The results indicate that the calculated coordinates from the introduced method are consistent with the reference trajectory with an accuracy of about 1 decimeter. In contrast, the findings imply lower accuracy for height components with an accuracy of about 2 decimeters. This accuracy level meets the requirement of many applications including some marine applications, precise hydrographic surveying, dredging, attitude control of ships, buoys and floating platforms, marine geodesy, navigation and oceanography.

Connection forces in deformable multibody dynamics

NASA Technical Reports Server (NTRS)

Shabana, A. A.; Chang, C. W.

1989-01-01

In the dynamic formulation of holonomic and nonholonomic systems based on D'Alembert-Lagrange equation, the forces of constraints are maintained in the dynamic equations by introducing auxiliary variables, called Lagrange multipliers. This approach introduces a set of generalized reaction forces associated with the system generalized coordinates. Different sets of variables can be used as generalized coordinates and accordingly, the generalized reactions associated with these generalized coordinates may not be the actual reaction forces at the joints. In rigid body dynamics, the generalized reaction forces and the actual reaction forces at the joints represent equipollent systems of forces since they produce the same total forces and moments at and about any point on the rigid body. This is not, however, the case in deformable body analyses wherein the generalized reaction forces depend on the system generalized reference and elastic coordinates. In this paper, a method for determining the actual reaction forces at the joints from the generalized reaction forces in deformable multibody systems is presented.

Gaussian process inference for estimating pharmacokinetic parameters of dynamic contrast-enhanced MR images.

PubMed

Wang, Shijun; Liu, Peter; Turkbey, Baris; Choyke, Peter; Pinto, Peter; Summers, Ronald M

2012-01-01

In this paper, we propose a new pharmacokinetic model for parameter estimation of dynamic contrast-enhanced (DCE) MRI by using Gaussian process inference. Our model is based on the Tofts dual-compartment model for the description of tracer kinetics and the observed time series from DCE-MRI is treated as a Gaussian stochastic process. The parameter estimation is done through a maximum likelihood approach and we propose a variant of the coordinate descent method to solve this likelihood maximization problem. The new model was shown to outperform a baseline method on simulated data. Parametric maps generated on prostate DCE data with the new model also provided better enhancement of tumors, lower intensity on false positives, and better boundary delineation when compared with the baseline method. New statistical parameter maps from the process model were also found to be informative, particularly when paired with the PK parameter maps.

Nanometrization of Lanthanide-Based Coordination Polymers.

PubMed

Neaime, Chrystelle; Daiguebonne, Carole; Calvez, Guillaume; Freslon, Stéphane; Bernot, Kevin; Grasset, Fabien; Cordier, Stéphane; Guillou, Olivier

2015-11-23

Heteronuclear lanthanide-based coordination polymers are microcrystalline powders, the luminescence properties of which can be precisely tuned by judicious choice of the rare-earth ions. In this study, we demonstrate that such materials can also be obtained as stable solutions of nanoparticles in non-toxic polyols. Bulk powders of the formula [Ln2-2x Ln'2x (bdc)3 ⋅4 H2 O]∞ (where H2 bdc denotes 1,4-benzene-dicarboxylic acid, 0≤x≤1, and Ln and Ln' denote lanthanide ions of the series La to Tm plus Y) afford nanoparticles that have been characterized by dynamic light-scattering (DLS) and transmission electron microscopy (TEM) measurements. Their luminescence properties are similar to those of the bulk materials. Stabilities versus time and versus dilution with another solvent have been studied. This study has revealed that it is possible to tune the size of the nanoparticles. This process offers a reliable means of synthesizing suspensions of nanoparticles with tunable luminescence properties and tunable size distributions in a green solvent (glycerol). The process is also extendable to other coordination polymers and other solvents (ethylene glycol, for example). It constitutes a new route for the facile solubilization of lanthanide-based coordination polymers. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dynamic Agent Classification and Tracking Using an Ad Hoc Mobile Acoustic Sensor Network

NASA Astrophysics Data System (ADS)

Friedlander, David; Griffin, Christopher; Jacobson, Noah; Phoha, Shashi; Brooks, Richard R.

2003-12-01

Autonomous networks of sensor platforms can be designed to interact in dynamic and noisy environments to determine the occurrence of specified transient events that define the dynamic process of interest. For example, a sensor network may be used for battlefield surveillance with the purpose of detecting, identifying, and tracking enemy activity. When the number of nodes is large, human oversight and control of low-level operations is not feasible. Coordination and self-organization of multiple autonomous nodes is necessary to maintain connectivity and sensor coverage and to combine information for better understanding the dynamics of the environment. Resource conservation requires adaptive clustering in the vicinity of the event. This paper presents methods for dynamic distributed signal processing using an ad hoc mobile network of microsensors to detect, identify, and track targets in noisy environments. They seamlessly integrate data from fixed and mobile platforms and dynamically organize platforms into clusters to process local data along the trajectory of the targets. Local analysis of sensor data is used to determine a set of target attribute values and classify the target. Sensor data from a field test in the Marine base at Twentynine Palms, Calif, was analyzed using the techniques described in this paper. The results were compared to "ground truth" data obtained from GPS receivers on the vehicles.

A Method for Molecular Dynamics on Curved Surfaces

PubMed Central

Paquay, Stefan; Kusters, Remy

2016-01-01

Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in the field of diffusive transport have focused on solving the diffusion equation on curved surfaces, for which it is not tractable to incorporate particle interactions even though these play a crucial role in crowded systems. We show here that it is possible to take such interactions into account by combining standard constraint algorithms with the classical velocity Verlet scheme to perform molecular dynamics simulations of particles constrained to an arbitrarily curved surface. Furthermore, unlike Brownian dynamics schemes in local coordinates, our method is based on Cartesian coordinates, allowing for the reuse of many other standard tools without modifications, including parallelization through domain decomposition. We show that by applying the schemes to the Langevin equation for various surfaces, we obtain confined Brownian motion, which has direct applications to many biological and physical problems. Finally we present two practical examples that highlight the applicability of the method: 1) the influence of crowding and shape on the lateral diffusion of proteins in curved membranes; and 2) the self-assembly of a coarse-grained virus capsid protein model. PMID:27028633

A Method for Molecular Dynamics on Curved Surfaces

NASA Astrophysics Data System (ADS)

Paquay, Stefan; Kusters, Remy

2016-03-01

Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in the field of diffusive transport have focussed on solving the diffusion equation on curved surfaces, for which it is not tractable to incorporate particle interactions even though these play a crucial role in crowded systems. We show here that it is possible to combine standard constraint algorithms with the classical velocity Verlet scheme to perform molecular dynamics simulations of particles constrained to an arbitrarily curved surface, in which such interactions can be taken into account. Furthermore, unlike Brownian dynamics schemes in local coordinates, our method is based on Cartesian coordinates allowing for the reuse of many other standard tools without modifications, including parallelisation through domain decomposition. We show that by applying the schemes to the Langevin equation for various surfaces, confined Brownian motion is obtained, which has direct applications to many biological and physical problems. Finally we present two practical examples that highlight the applicability of the method: (i) the influence of crowding and shape on the lateral diffusion of proteins in curved membranes and (ii) the self-assembly of a coarse-grained virus capsid protein model.

Theoretical investigation of the electron capture and loss processes in the collisions of He2+ + Ne.

PubMed

Hong, Xuhai; Wang, Feng; Jiao, Yalong; Su, Wenyong; Wang, Jianguo; Gou, Bingcong

2013-08-28

Based on the time-dependent density functional theory, a method is developed to study ion-atom collision dynamics, which self-consistently couples the quantum mechanical description of electron dynamics with the classical treatment of the ion motion. Employing real-time and real-space method, the coordinate space translation technique is introduced to allow one to focus on the region of target or projectile depending on the actual concerned process. The benchmark calculations are performed for the collisions of He(2+) + Ne, and the time evolution of electron density distribution is monitored, which provides interesting details of the interaction dynamics between the electrons and ion cores. The cross sections of single and many electron capture and loss have been calculated in the energy range of 1-1000 keV/amu, and the results show a good agreement with the available experiments over a wide range of impact energies.

The Center for Multiscale Plasma Dynamics, Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gombosi, Tamas I.

The University of Michigan participated in the joint UCLA/Maryland fusion science center focused on plasma physics problems for which the traditional separation of the dynamics into microscale and macroscale processes breaks down. These processes involve large scale flows and magnetic fields tightly coupled to the small scale, kinetic dynamics of turbulence, particle acceleration and energy cascade. The interaction between these vastly disparate scales controls the evolution of the system. The enormous range of temporal and spatial scales associated with these problems renders direct simulation intractable even in computations that use the largest existing parallel computers. Our efforts focused on twomore » main problems: the development of Hall MHD solvers on solution adaptive grids and the development of solution adaptive grids using generalized coordinates so that the proper geometry of inertial confinement can be taken into account and efficient refinement strategies can be obtained.« less

Dynamics and Control of Flexible Space Vehicles

NASA Technical Reports Server (NTRS)

Likins, P. W.

1970-01-01

The purpose of this report is twofold: (1) to survey the established analytic procedures for the simulation of controlled flexible space vehicles, and (2) to develop in detail methods that employ a combination of discrete and distributed ("modal") coordinates, i.e., the hybrid-coordinate methods. Analytic procedures are described in three categories: (1) discrete-coordinate methods, (2) hybrid-coordinate methods, and (3) vehicle normal-coordinate methods. Each of these approaches is described and analyzed for its advantages and disadvantages, and each is found to have an area of applicability. The hybrid-coordinate method combines the efficiency of the vehicle normal-coordinate method with the versatility of the discrete-coordinate method, and appears to have the widest range of practical application. The results in this report have practical utility in two areas: (1) complex digital computer simulation of flexible space vehicles of arbitrary configuration subject to realistic control laws, and (2) preliminary control system design based on transfer functions for linearized models of dynamics and control laws.

Connected vehicle Data Capture and Management (DCM) and dynamic mobility applications (DMA) : assessment of relevant standards and gaps for candidate applications.

DOT National Transportation Integrated Search

2012-10-01

The Connected Vehicle Mobility Standards Coordination Plan project links activities in three programs (Data Capture and Management, Dynamic Mobility Applications, and ITS Standards). The plan coordinates the timing, intent and relationship of activit...

Internal Coordinate Molecular Dynamics: A Foundation for Multiscale Dynamics

PubMed Central

2015-01-01

Internal coordinates such as bond lengths, bond angles, and torsion angles (BAT) are natural coordinates for describing a bonded molecular system. However, the molecular dynamics (MD) simulation methods that are widely used for proteins, DNA, and polymers are based on Cartesian coordinates owing to the mathematical simplicity of the equations of motion. However, constraints are often needed with Cartesian MD simulations to enhance the conformational sampling. This makes the equations of motion in the Cartesian coordinates differential-algebraic, which adversely impacts the complexity and the robustness of the simulations. On the other hand, constraints can be easily placed in BAT coordinates by removing the degrees of freedom that need to be constrained. Thus, the internal coordinate MD (ICMD) offers an attractive alternative to Cartesian coordinate MD for developing multiscale MD method. The torsional MD method is a special adaptation of the ICMD method, where all the bond lengths and bond angles are kept rigid. The advantages of ICMD simulation methods are the longer time step size afforded by freezing high frequency degrees of freedom and performing a conformational search in the more important low frequency torsional degrees of freedom. However, the advancements in the ICMD simulations have been slow and stifled by long-standing mathematical bottlenecks. In this review, we summarize the recent mathematical advancements we have made based on spatial operator algebra, in developing a robust long time scale ICMD simulation toolkit useful for various applications. We also present the applications of ICMD simulations to study conformational changes in proteins and protein structure refinement. We review the advantages of the ICMD simulations over the Cartesian simulations when used with enhanced sampling methods and project the future use of ICMD simulations in protein dynamics. PMID:25517406

The Sensorimotor System Can Sculpt Behaviorally Relevant Representations for Motor Learning

PubMed Central

2016-01-01

Abstract The coordinate system in which humans learn novel motor skills is controversial. The representation of sensorimotor skills has been extensively studied by examining generalization after learning perturbations specifically designed to be ambiguous as to their coordinate system. Recent studies have found that learning is not represented in any simple coordinate system and can potentially be accounted for by a mixed representation. Here, instead of probing generalization, which has led to conflicting results, we examine whether novel dynamics can be learned when explicitly and unambiguously presented in particular coordinate systems. Subjects performed center–out reaches to targets in the presence of a force field, while varying the orientation of their hand (i.e., the wrist angle) across trials. Different groups of subjects experienced force fields that were explicitly presented either in Cartesian coordinates (field independent of hand orientation), in object coordinates (field rotated with hand orientation), or in anti-object coordinates (field rotated counter to hand orientation). Subjects learned to represent the dynamics when presented in either Cartesian or object coordinates, learning these as well as an ambiguous force field. However, learning was slower for the object-based dynamics and substantially impaired for the anti-object presentation. Our results show that the motor system is able to tune its representation to at least two natural coordinate systems but is impaired when the representation of the task does not correspond to a behaviorally relevant coordinate system. Our results show that the motor system can sculpt its representation through experience to match those of natural tasks. PMID:27588304

Principal component analysis of molecular dynamics: On the use of Cartesian vs. internal coordinates

NASA Astrophysics Data System (ADS)

Sittel, Florian; Jain, Abhinav; Stock, Gerhard

2014-07-01

Principal component analysis of molecular dynamics simulations is a popular method to account for the essential dynamics of the system on a low-dimensional free energy landscape. Using Cartesian coordinates, first the translation and overall rotation need to be removed from the trajectory. Since the rotation depends via the moment of inertia on the molecule's structure, this separation is only straightforward for relatively rigid systems. Adopting millisecond molecular dynamics simulations of the folding of villin headpiece and the functional dynamics of BPTI provided by D. E. Shaw Research, it is demonstrated via a comparison of local and global rotational fitting that the structural dynamics of flexible molecules necessarily results in a mixing of overall and internal motion. Even for the small-amplitude functional motion of BPTI, the conformational distribution obtained from a Cartesian principal component analysis therefore reflects to some extend the dominant overall motion rather than the much smaller internal motion of the protein. Internal coordinates such as backbone dihedral angles, on the other hand, are found to yield correct and well-resolved energy landscapes for both examples. The virtues and shortcomings of the choice of various fitting schemes and coordinate sets as well as the generality of these results are discussed in some detail.

Principal component analysis of molecular dynamics: on the use of Cartesian vs. internal coordinates.

PubMed

Sittel, Florian; Jain, Abhinav; Stock, Gerhard

2014-07-07

Principal component analysis of molecular dynamics simulations is a popular method to account for the essential dynamics of the system on a low-dimensional free energy landscape. Using Cartesian coordinates, first the translation and overall rotation need to be removed from the trajectory. Since the rotation depends via the moment of inertia on the molecule's structure, this separation is only straightforward for relatively rigid systems. Adopting millisecond molecular dynamics simulations of the folding of villin headpiece and the functional dynamics of BPTI provided by D. E. Shaw Research, it is demonstrated via a comparison of local and global rotational fitting that the structural dynamics of flexible molecules necessarily results in a mixing of overall and internal motion. Even for the small-amplitude functional motion of BPTI, the conformational distribution obtained from a Cartesian principal component analysis therefore reflects to some extend the dominant overall motion rather than the much smaller internal motion of the protein. Internal coordinates such as backbone dihedral angles, on the other hand, are found to yield correct and well-resolved energy landscapes for both examples. The virtues and shortcomings of the choice of various fitting schemes and coordinate sets as well as the generality of these results are discussed in some detail.

Modeling Multi-Agent Self-Organization through the Lens of Higher Order Attractor Dynamics.

PubMed

Butner, Jonathan E; Wiltshire, Travis J; Munion, A K

2017-01-01

Social interaction occurs across many time scales and varying numbers of agents; from one-on-one to large-scale coordination in organizations, crowds, cities, and colonies. These contexts, are characterized by emergent self-organization that implies higher order coordinated patterns occurring over time that are not due to the actions of any particular agents, but rather due to the collective ordering that occurs from the interactions of the agents. Extant research to understand these social coordination dynamics (SCD) has primarily examined dyadic contexts performing rhythmic tasks. To advance this area of study, we elaborate on attractor dynamics, our ability to depict them visually, and quantitatively model them. Primarily, we combine difference/differential equation modeling with mixture modeling as a way to infer the underlying topological features of the data, which can be described in terms of attractor dynamic patterns. The advantage of this approach is that we are able to quantify the self-organized dynamics that agents exhibit, link these dynamics back to activity from individual agents, and relate it to other variables central to understanding the coordinative functionality of a system's behavior. We present four examples that differ in the number of variables used to depict the attractor dynamics (1, 2, and 6) and range from simulated to non-simulated data sources. We demonstrate that this is a flexible method that advances scientific study of SCD in a variety of multi-agent systems.

Multi-GNSS high-rate RTK, PPP and novel direct phase observation processing method: application to precise dynamic displacement detection

NASA Astrophysics Data System (ADS)

Paziewski, Jacek; Sieradzki, Rafal; Baryla, Radoslaw

2018-03-01

This paper provides the methodology and performance assessment of multi-GNSS signal processing for the detection of small-scale high-rate dynamic displacements. For this purpose, we used methods of relative (RTK) and absolute positioning (PPP), and a novel direct signal processing approach. The first two methods are recognized as providing accurate information on position in many navigation and surveying applications. The latter is an innovative method for dynamic displacement determination with the use of GNSS phase signal processing. This method is based on the developed functional model with parametrized epoch-wise topocentric relative coordinates derived from filtered GNSS observations. Current regular kinematic PPP positioning, as well as medium/long range RTK, may not offer coordinate estimates with subcentimeter precision. Thus, extended processing strategies of absolute and relative GNSS positioning have been developed and applied for displacement detection. The study also aimed to comparatively analyze the developed methods as well as to analyze the impact of combined GPS and BDS processing and the dependence of the results of the relative methods on the baseline length. All the methods were implemented with in-house developed software allowing for high-rate precise GNSS positioning and signal processing. The phase and pseudorange observations collected with a rate of 50 Hz during the field test served as the experiment’s data set. The displacements at the rover station were triggered in the horizontal plane using a device which was designed and constructed to ensure a periodic motion of GNSS antenna with an amplitude of ~3 cm and a frequency of ~4.5 Hz. Finally, a medium range RTK, PPP, and direct phase observation processing method demonstrated the capability of providing reliable and consistent results with the precision of the determined dynamic displacements at the millimeter level. Specifically, the research shows that the standard deviation of the displacement residuals obtained as the difference between a benchmark-ultra-short baseline RTK solution and selected scenarios ranged between 1.1 and 3.4 mm. At the same time, the differences in the mean amplitude of the oscillations derived from the established scenarios did not exceed 1.3 mm, whereas the frequency of the motion detected with the use of Fourier transformation was the same.

Mathematical Modeling of Thermofrictional Milling Process Using ANSYS WB Software

NASA Astrophysics Data System (ADS)

Sherov, K. T.; Sikhimbayev, M. R.; Sherov, A. K.; Donenbayev, B. S.; Rakishev, A. K.; Mazdubai, A. B.; Musayev, M. M.; Abeuova, A. M.

2017-06-01

This article presents ANSYS WB-based mathematical modelling of the thermofrictional milling process, which allowed studying the dynamics of thermal and physical processes occurring during the processing. The technique used also allows determination of the optimal cutting conditions of thermofrictional milling for processing various materials, in particular steel 40CN2MA, 30CGSA, 45, 3sp. In our study, from among a number of existing models of cutting fracture, we chose the criterion first proposed by prof. V. L. Kolmogorov. In order to increase the calculations performance, a mathematical model was proposed, that used only two objects: a parallelepiped-shaped workpiece and a cutting insert in the form of a pentagonal prism. In addition, the work takes into account the friction coefficient between a cutting insert and a workpiece taken equal to 0.4 mm. To determine the temperature in the subcontact layer of the workpiece, we introduced the coordinates of nine characteristic points with the same interval in the local coordinate system. As a result, the temperature values were obtained for different materials at the studied points during the cutter speed change. The research results showed the possibility of controlling thermal processes during processing by choosing the optimum cutting modes.

Effective removal of coordinated copper from wastewater using a new dithiocarbamate-type supramolecular heavy metal precipitant.

PubMed

Fu, Fenglian; Zeng, Haiyan; Cai, Qinhong; Qiu, Rongliang; Yu, Jimmy; Xiong, Ya

2007-11-01

A new dithiocarbamate-type heavy metal precipitant, sodium 1,3,5-hexahydrotriazinedithiocarbamate (HTDC), was prepared and used to remove coordinated copper from wastewater. In the reported dithiocarbamate-type precipitants, HTDC possesses the highest percentage of the effective functional groups. It could effectively precipitate copper to less than 0.5mgl(-1) from both synthetic and actual industrial wastewater containing CuEDTA in the range of pH 3-9. UV-vis spectral investigation and elemental analysis suggested that the precipitate was a kind of coordination supramolecular compound, [Cu(3)(HTDC)(2)](n). The toxicity characteristic leaching procedure (TCLP) and semi-dynamic leaching test (SDLT) indicated that the supramolecular precipitate was non-hazardous and stable in weak acid and alkaline conditions. Tests of an anion exchange resin D231 provided a clue to simultaneously remove excess HTDC and residual CuEDTA in practical process of wastewater treatment.

Beyond the Niche: Tissue-Level Coordination of Stem Cell Dynamics

PubMed Central

O’Brien, Lucy Erin; Bilder, David

2014-01-01

Adult animals rely on populations of stem cells to ensure organ function throughout their lifetime. Stem cells are governed by signals from stem cell niches, and much is known about how single niches promote stemness and direct stem cell behavior. However, most organs contain a multitude of stem cell–niche units, which are often distributed across the entire expanse of the tissue. Beyond the biology of individual stem cell–niche interactions, the next challenge is to uncover the tissue-level processes that orchestrate spatial control of stem-based renewal, repair, and remodeling throughout a whole organ. Here we examine what is known about higher order mechanisms for interniche coordination in epithelial organs, whose simple geometry offers a promising entry point for understanding the regulation of niche number, distribution, and activity. We also consider the potential existence of stem cell territories and how tissue architecture may influence niche coordination. PMID:23937350

Model predictive control system and method for integrated gasification combined cycle power generation

DOEpatents

Kumar, Aditya; Shi, Ruijie; Kumar, Rajeeva; Dokucu, Mustafa

2013-04-09

Control system and method for controlling an integrated gasification combined cycle (IGCC) plant are provided. The system may include a controller coupled to a dynamic model of the plant to process a prediction of plant performance and determine a control strategy for the IGCC plant over a time horizon subject to plant constraints. The control strategy may include control functionality to meet a tracking objective and control functionality to meet an optimization objective. The control strategy may be configured to prioritize the tracking objective over the optimization objective based on a coordinate transformation, such as an orthogonal or quasi-orthogonal projection. A plurality of plant control knobs may be set in accordance with the control strategy to generate a sequence of coordinated multivariable control inputs to meet the tracking objective and the optimization objective subject to the prioritization resulting from the coordinate transformation.

Elements of the cellular metabolic structure

PubMed Central

De la Fuente, Ildefonso M.

2015-01-01

A large number of studies have demonstrated the existence of metabolic covalent modifications in different molecular structures, which are able to store biochemical information that is not encoded by DNA. Some of these covalent mark patterns can be transmitted across generations (epigenetic changes). Recently, the emergence of Hopfield-like attractor dynamics has been observed in self-organized enzymatic networks, which have the capacity to store functional catalytic patterns that can be correctly recovered by specific input stimuli. Hopfield-like metabolic dynamics are stable and can be maintained as a long-term biochemical memory. In addition, specific molecular information can be transferred from the functional dynamics of the metabolic networks to the enzymatic activity involved in covalent post-translational modulation, so that determined functional memory can be embedded in multiple stable molecular marks. The metabolic dynamics governed by Hopfield-type attractors (functional processes), as well as the enzymatic covalent modifications of specific molecules (structural dynamic processes) seem to represent the two stages of the dynamical memory of cellular metabolism (metabolic memory). Epigenetic processes appear to be the structural manifestation of this cellular metabolic memory. Here, a new framework for molecular information storage in the cell is presented, which is characterized by two functionally and molecularly interrelated systems: a dynamic, flexible and adaptive system (metabolic memory) and an essentially conservative system (genetic memory). The molecular information of both systems seems to coordinate the physiological development of the whole cell. PMID:25988183

Biomechanics and muscle coordination of human walking. Part I: introduction to concepts, power transfer, dynamics and simulations.

PubMed

Zajac, Felix E; Neptune, Richard R; Kautz, Steven A

2002-12-01

Current understanding of how muscles coordinate walking in humans is derived from analyses of body motion, ground reaction force and EMG measurements. This is Part I of a two-part review that emphasizes how muscle-driven dynamics-based simulations assist in the understanding of individual muscle function in walking, especially the causal relationships between muscle force generation and walking kinematics and kinetics. Part I reviews the strengths and limitations of Newton-Euler inverse dynamics and dynamical simulations, including the ability of each to find the contributions of individual muscles to the acceleration/deceleration of the body segments. We caution against using the concept of biarticular muscles transferring power from one joint to another to infer muscle coordination principles because energy flow among segments, even the adjacent segments associated with the joints, cannot be inferred from computation of joint powers and segmental angular velocities alone. Rather, we encourage the use of dynamical simulations to perform muscle-induced segmental acceleration and power analyses. Such analyses have shown that the exchange of segmental energy caused by the forces or accelerations induced by a muscle can be fundamentally invariant to whether the muscle is shortening, lengthening, or neither. How simulation analyses lead to understanding the coordination of seated pedaling, rather than walking, is discussed in this first part because the dynamics of pedaling are much simpler, allowing important concepts to be revealed. We elucidate how energy produced by muscles is delivered to the crank through the synergistic action of other non-energy producing muscles; specifically, that a major function performed by a muscle arises from the instantaneous segmental accelerations and redistribution of segmental energy throughout the body caused by its force generation. Part II reviews how dynamical simulations provide insight into muscle coordination of walking.

Investigating the social behavioral dynamics and differentiation of skill in a martial arts technique.

PubMed

Caron, Robert R; Coey, Charles A; Dhaim, Ashley N; Schmidt, R C

2017-08-01

Coordinating interpersonal motor activity is crucial in martial arts, where managing spatiotemporal parameters is emphasized to produce effective techniques. Modeling arm movements in an Aikido technique as coupled oscillators, we investigated whether more-skilled participants would adapt to the perturbation of weighted arms in different and predictable ways compared to less-skilled participants. Thirty-four participants ranging from complete novice to veterans of more than twenty years were asked to perform an Aikido exercise with a repeated attack and response, resulting in a period of steady-state coordination, followed by a take down. We used mean relative phase and its variability to measure the steady-state dynamics of both the inter- and intrapersonal coordination. Our findings suggest that interpersonal coordination of less-skilled participants is disrupted in highly predictable ways based on oscillatory dynamics; however, more-skilled participants overcome these natural dynamics to maintain critical performance variables. Interestingly, the more-skilled participants exhibited more variability in their intrapersonal dynamics while meeting these interpersonal demands. This work lends insight to the development of skill in competitive social motor activities. Copyright © 2017 Elsevier B.V. All rights reserved.

Impairments of Social Motor Synchrony Evident in Autism Spectrum Disorder

PubMed Central

Fitzpatrick, Paula; Frazier, Jean A.; Cochran, David M.; Mitchell, Teresa; Coleman, Caitlin; Schmidt, R. C.

2016-01-01

Social interactions typically involve movements of the body that become synchronized over time and both intentional and spontaneous interactional synchrony have been found to be an essential part of successful human interaction. However, our understanding of the importance of temporal dimensions of social motor synchrony in social dysfunction is limited. Here, we used a pendulum coordination paradigm to assess dynamic, process-oriented measures of social motor synchrony in adolescents with and without autism spectrum disorder (ASD). Our data indicate that adolescents with ASD demonstrate less synchronization in both spontaneous and intentional interpersonal coordination. Coupled oscillator modeling suggests that ASD participants assembled a synchronization dynamic with a weaker coupling strength, which corresponds to a lower sensitivity and decreased attention to the movements of the other person, but do not demonstrate evidence of a delay in information transmission. The implication of these findings for isolating an ASD-specific social synchronization deficit that could serve as an objective, bio-behavioral marker is discussed. PMID:27630599

Analysis of the dynamic co-expression network of heart regeneration in the zebrafish

PubMed Central

Rodius, Sophie; Androsova, Ganna; Götz, Lou; Liechti, Robin; Crespo, Isaac; Merz, Susanne; Nazarov, Petr V.; de Klein, Niek; Jeanty, Céline; González-Rosa, Juan M.; Muller, Arnaud; Bernardin, Francois; Niclou, Simone P.; Vallar, Laurent; Mercader, Nadia; Ibberson, Mark; Xenarios, Ioannis; Azuaje, Francisco

2016-01-01

The zebrafish has the capacity to regenerate its heart after severe injury. While the function of a few genes during this process has been studied, we are far from fully understanding how genes interact to coordinate heart regeneration. To enable systematic insights into this phenomenon, we generated and integrated a dynamic co-expression network of heart regeneration in the zebrafish and linked systems-level properties to the underlying molecular events. Across multiple post-injury time points, the network displays topological attributes of biological relevance. We show that regeneration steps are mediated by modules of transcriptionally coordinated genes, and by genes acting as network hubs. We also established direct associations between hubs and validated drivers of heart regeneration with murine and human orthologs. The resulting models and interactive analysis tools are available at http://infused.vital-it.ch. Using a worked example, we demonstrate the usefulness of this unique open resource for hypothesis generation and in silico screening for genes involved in heart regeneration. PMID:27241320

Spatially coordinated dynamic gene transcription in living pituitary tissue

PubMed Central

Featherstone, Karen; Hey, Kirsty; Momiji, Hiroshi; McNamara, Anne V; Patist, Amanda L; Woodburn, Joanna; Spiller, David G; Christian, Helen C; McNeilly, Alan S; Mullins, John J; Finkenstädt, Bärbel F; Rand, David A; White, Michael RH; Davis, Julian RE

2016-01-01

Transcription at individual genes in single cells is often pulsatile and stochastic. A key question emerges regarding how this behaviour contributes to tissue phenotype, but it has been a challenge to quantitatively analyse this in living cells over time, as opposed to studying snap-shots of gene expression state. We have used imaging of reporter gene expression to track transcription in living pituitary tissue. We integrated live-cell imaging data with statistical modelling for quantitative real-time estimation of the timing of switching between transcriptional states across a whole tissue. Multiple levels of transcription rate were identified, indicating that gene expression is not a simple binary ‘on-off’ process. Immature tissue displayed shorter durations of high-expressing states than the adult. In adult pituitary tissue, direct cell contacts involving gap junctions allowed local spatial coordination of prolactin gene expression. Our findings identify how heterogeneous transcriptional dynamics of single cells may contribute to overall tissue behaviour. DOI: http://dx.doi.org/10.7554/eLife.08494.001 PMID:26828110

Autonomy and Non-autonomy of Angiogenic Cell Movements Revealed by Experiment-Driven Mathematical Modeling.

PubMed

Sugihara, Kei; Nishiyama, Koichi; Fukuhara, Shigetomo; Uemura, Akiyoshi; Arima, Satoshi; Kobayashi, Ryo; Köhn-Luque, Alvaro; Mochizuki, Naoki; Suda, Toshio; Ogawa, Hisao; Kurihara, Hiroki

2015-12-01

Angiogenesis is a multicellular phenomenon driven by morphogenetic cell movements. We recently reported morphogenetic vascular endothelial cell (EC) behaviors to be dynamic and complex. However, the principal mechanisms orchestrating individual EC movements in angiogenic morphogenesis remain largely unknown. Here we present an experiment-driven mathematical model that enables us to systematically dissect cellular mechanisms in branch elongation. We found that cell-autonomous and coordinated actions governed these multicellular behaviors, and a cell-autonomous process sufficiently illustrated essential features of the morphogenetic EC dynamics at both the single-cell and cell-population levels. Through refining our model and experimental verification, we further identified a coordinated mode of tip EC behaviors regulated via a spatial relationship between tip and follower ECs, which facilitates the forward motility of tip ECs. These findings provide insights that enhance our mechanistic understanding of not only angiogenic morphogenesis, but also other types of multicellular phenomenon. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Analysis of the dynamic co-expression network of heart regeneration in the zebrafish

NASA Astrophysics Data System (ADS)

Rodius, Sophie; Androsova, Ganna; Götz, Lou; Liechti, Robin; Crespo, Isaac; Merz, Susanne; Nazarov, Petr V.; de Klein, Niek; Jeanty, Céline; González-Rosa, Juan M.; Muller, Arnaud; Bernardin, Francois; Niclou, Simone P.; Vallar, Laurent; Mercader, Nadia; Ibberson, Mark; Xenarios, Ioannis; Azuaje, Francisco

2016-05-01

The zebrafish has the capacity to regenerate its heart after severe injury. While the function of a few genes during this process has been studied, we are far from fully understanding how genes interact to coordinate heart regeneration. To enable systematic insights into this phenomenon, we generated and integrated a dynamic co-expression network of heart regeneration in the zebrafish and linked systems-level properties to the underlying molecular events. Across multiple post-injury time points, the network displays topological attributes of biological relevance. We show that regeneration steps are mediated by modules of transcriptionally coordinated genes, and by genes acting as network hubs. We also established direct associations between hubs and validated drivers of heart regeneration with murine and human orthologs. The resulting models and interactive analysis tools are available at http://infused.vital-it.ch. Using a worked example, we demonstrate the usefulness of this unique open resource for hypothesis generation and in silico screening for genes involved in heart regeneration.

Incorporation of feedback during beat synchronization is an index of neural maturation and reading skills.

PubMed

Woodruff Carr, Kali; Fitzroy, Ahren B; Tierney, Adam; White-Schwoch, Travis; Kraus, Nina

2017-01-01

Speech communication involves integration and coordination of sensory perception and motor production, requiring precise temporal coupling. Beat synchronization, the coordination of movement with a pacing sound, can be used as an index of this sensorimotor timing. We assessed adolescents' synchronization and capacity to correct asynchronies when given online visual feedback. Variability of synchronization while receiving feedback predicted phonological memory and reading sub-skills, as well as maturation of cortical auditory processing; less variable synchronization during the presence of feedback tracked with maturation of cortical processing of sound onsets and resting gamma activity. We suggest the ability to incorporate feedback during synchronization is an index of intentional, multimodal timing-based integration in the maturing adolescent brain. Precision of temporal coding across modalities is important for speech processing and literacy skills that rely on dynamic interactions with sound. Synchronization employing feedback may prove useful as a remedial strategy for individuals who struggle with timing-based language learning impairments. Copyright © 2016 Elsevier Inc. All rights reserved.

Abiotic stress and the plant circadian clock

PubMed Central

Sanchez, Alfredo; Shin, Jieun

2011-01-01

In this review, we focus on the interaction between the circadian clock of higher plants to that of metabolic and physiological processes that coordinate growth and performance under a predictable, albeit changing environment. In this, the phytochrome and cryptochrome photoreceptors have shown to be important, but not essential for oscillator control under diurnal cycles of light and dark. From this foundation, we will examine how emerging findings have firmly linked the circadian clock, as a central mediator in the coordination of metabolism, to maintain homeostasis. This occurs by oscillator synchronization of global transcription, which leads to a dynamic control of a host of physiological processes. These include the determination of the levels of primary and secondary metabolites, and the anticipation of future environmental stresses, such as mid-day drought and midnight coldness. Interestingly, metabolic and stress cues themselves appear to feedback on oscillator function. In such a way, the circadian clock of plants and abiotic-stress tolerance appear to be firmly interconnected processes. PMID:21325898

Dissociative electron attachment and vibrational excitation of CF{sub 3}Cl: Effect of two vibrational modes revisited

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tarana, Michal; JILA, University of Colorado and NIST, Boulder, Colorado 80309-0440; Houfek, Karel

We present a study of dissociative electron attachment and vibrational excitation processes in electron collisions with the CF{sub 3}Cl molecule. The calculations are based on the two-dimensional nuclear dynamics including the C-Cl symmetric stretch coordinate and the CF{sub 3} symmetric deformation (umbrella) coordinate. The complex potential energy surfaces are calculated using the ab initio R-matrix method. The results for dissociative attachment and vibrational excitation of the umbrella mode agree quite well with experiment whereas the cross section for excitation of the C-Cl symmetric stretch vibrations is about a factor-of-three too low in comparison with experimental data.

A soft biomimetic tongue: model reconstruction and motion tracking

NASA Astrophysics Data System (ADS)

Lu, Xuanming; Xu, Weiliang; Li, Xiaoning

2016-04-01

A bioinspired robotic tongue which is actuated by a network of compressed air is proposed for the purpose of mimicking the movements of human tongue. It can be applied in the fields such as medical science and food engineering. The robotic tongue is made of two kinds of silicone rubber Ecoflex 0030 and PDMS with the shape simplified from real human tongue. In order to characterize the robotic tongue, a series of experiments were carried out. Laser scan was applied to reconstruct the static model of robotic tongue when it was under pressurization. After each scan, the robotic tongue was scattered into dense points in the same 3D coordinate system and the coordinates of each point were recorded. Motion tracking system (OptiTrack) was used to track and record the whole process of deformation dynamically during the loading and unloading phase. In the experiments, five types of deformation were achieved including roll-up, roll-down, elongation, groove and twist. Utilizing the discrete points generated by laser scan, the accurate parameterized outline of robotic tongue under different pressure was obtained, which could help demonstrate the static characteristic of robotic tongue. The precise deformation process under one pressure was acquired through the OptiTrack system which contains a series of digital cameras, markers on the robotic tongue and a set of hardware and software for data processing. By means of tracking and recording different process of deformation under different pressure, the dynamic characteristic of robotic tongue could be achieved.

Metal-coordination: Using one of nature’s tricks to control soft material mechanics

PubMed Central

Holten-Andersen, Niels; Jaishankar, Aditya; Harrington, Matthew; Fullenkamp, Dominic E.; DiMarco, Genevieve; He, Lihong; McKinley, Gareth H.; Messersmith, Phillip B.; Lee, Ka Yee C.

2015-01-01

Growing evidence supports a critical role of dynamic metal-coordination crosslinking in soft biological material properties such as self-healing and underwater adhesion1. Using bio-inspired metal-coordinating polymers, initial efforts to mimic these properties have shown promise2. Here we demonstrate how bio-inspired aqueous polymer network mechanics can be easily controlled via metal-coordination crosslink dynamics; metal ion-based crosslink stability control allows aqueous polymer network relaxation times to be finely tuned over several orders of magnitude. In addition to further biological material insights, our demonstration of this compositional scaling mechanism should provide inspiration for new polymer material property-control designs. PMID:26413297

Static Analysis of Large-Scale Multibody System Using Joint Coordinates and Spatial Algebra Operator

PubMed Central

Omar, Mohamed A.

2014-01-01

Initial transient oscillations inhibited in the dynamic simulations responses of multibody systems can lead to inaccurate results, unrealistic load prediction, or simulation failure. These transients could result from incompatible initial conditions, initial constraints violation, and inadequate kinematic assembly. Performing static equilibrium analysis before the dynamic simulation can eliminate these transients and lead to stable simulation. Most exiting multibody formulations determine the static equilibrium position by minimizing the system potential energy. This paper presents a new general purpose approach for solving the static equilibrium in large-scale articulated multibody. The proposed approach introduces an energy drainage mechanism based on Baumgarte constraint stabilization approach to determine the static equilibrium position. The spatial algebra operator is used to express the kinematic and dynamic equations of the closed-loop multibody system. The proposed multibody system formulation utilizes the joint coordinates and modal elastic coordinates as the system generalized coordinates. The recursive nonlinear equations of motion are formulated using the Cartesian coordinates and the joint coordinates to form an augmented set of differential algebraic equations. Then system connectivity matrix is derived from the system topological relations and used to project the Cartesian quantities into the joint subspace leading to minimum set of differential equations. PMID:25045732

Static analysis of large-scale multibody system using joint coordinates and spatial algebra operator.

PubMed

Omar, Mohamed A

2014-01-01

Initial transient oscillations inhibited in the dynamic simulations responses of multibody systems can lead to inaccurate results, unrealistic load prediction, or simulation failure. These transients could result from incompatible initial conditions, initial constraints violation, and inadequate kinematic assembly. Performing static equilibrium analysis before the dynamic simulation can eliminate these transients and lead to stable simulation. Most exiting multibody formulations determine the static equilibrium position by minimizing the system potential energy. This paper presents a new general purpose approach for solving the static equilibrium in large-scale articulated multibody. The proposed approach introduces an energy drainage mechanism based on Baumgarte constraint stabilization approach to determine the static equilibrium position. The spatial algebra operator is used to express the kinematic and dynamic equations of the closed-loop multibody system. The proposed multibody system formulation utilizes the joint coordinates and modal elastic coordinates as the system generalized coordinates. The recursive nonlinear equations of motion are formulated using the Cartesian coordinates and the joint coordinates to form an augmented set of differential algebraic equations. Then system connectivity matrix is derived from the system topological relations and used to project the Cartesian quantities into the joint subspace leading to minimum set of differential equations.

Impact Dynamics: Theory and Experiment

DTIC Science & Technology

1980-10-01

in the HEMP QHydrodynamic, Elastic, Magneto & Plastic ) code, employ a quadrilateral grid and may be solved in plane coordinates or with cylindrical...material constitution, strain rate. localized plastic flow, and failure are manifest at various stages of the impact process. Typically, loading and...STRENGTH; DENSITY /A DOMINANT’ PARAMETER 104 - 500-1000ms-1 VISCOUS-MATERIAL POWDER GUNS STRENGTH STILL SIGNIFICANT 10 2 50- 500 ms- PRIMARILY PLASTIC

The Role of Metaphors in Fostering Macrocognitive Processes in Distributed Teams

DTIC Science & Technology

2012-07-30

temporal dynamics, and storytelling towards the goal of improving team coordination and performance in distributed decision making teams. Specifically...better reflect the context of organizational and military teams and 3) to investigate how storytelling (complex form of metaphor) can be used as a...Information Sharing, Situation Awareness, Storytelling , Metaphors, Reflexivity.Team Simulation, NeoCITIES 16. SECURITY CLASSIFICATION OF: a. REPORT b

A mass assembly of associative mechanisms: a dynamical systems account of natural social interaction.

PubMed

Duran, Nicholas D; Dale, Rick; Richardson, Daniel C

2014-04-01

The target article offers a negative, eliminativist thesis, dissolving the specialness of mirroring processes into a solution of associative mechanisms. We support the authors' project enthusiastically. What they are currently missing, we argue, is a positive, generative thesis about associative learning mechanisms and how they might give way to the complex, multimodal coordination that naturally arises in social interaction.

Dynamic modeling and optimal joint torque coordination of advanced robotic systems

NASA Astrophysics Data System (ADS)

Kang, Hee-Jun

The development is documented of an efficient dynamic modeling algorithm and the subsequent optimal joint input load coordination of advanced robotic systems for industrial application. A closed-form dynamic modeling algorithm for the general closed-chain robotic linkage systems is presented. The algorithm is based on the transfer of system dependence from a set of open chain Lagrangian coordinates to any desired system generalized coordinate set of the closed-chain. Three different techniques for evaluation of the kinematic closed chain constraints allow the representation of the dynamic modeling parameters in terms of system generalized coordinates and have no restriction with regard to kinematic redundancy. The total computational requirement of the closed-chain system model is largely dependent on the computation required for the dynamic model of an open kinematic chain. In order to improve computational efficiency, modification of an existing open-chain KIC based dynamic formulation is made by the introduction of the generalized augmented body concept. This algorithm allows a 44 pct. computational saving over the current optimized one (O(N4), 5995 when N = 6). As means of resolving redundancies in advanced robotic systems, local joint torque optimization is applied for effectively using actuator power while avoiding joint torque limits. The stability problem in local joint torque optimization schemes is eliminated by using fictitious dissipating forces which act in the necessary null space. The performance index representing the global torque norm is shown to be satisfactory. In addition, the resulting joint motion trajectory becomes conservative, after a transient stage, for repetitive cyclic end-effector trajectories. The effectiveness of the null space damping method is shown. The modular robot, which is built of well defined structural modules from a finite-size inventory and is controlled by one general computer system, is another class of evolving, highly versatile, advanced robotic systems. Therefore, finally, a module based dynamic modeling algorithm is presented for the dynamic coordination of such reconfigurable modular robotic systems. A user interactive module based manipulator analysis program (MBMAP) has been coded in C language running on 4D/70 Silicon Graphics.

Characterization of the TolB-Pal trans-envelope complex from Xylella fastidiosa reveals a dynamic and coordinated protein expression profile during the biofilm development process.

PubMed

Santos, Clelton A; Janissen, Richard; Toledo, Marcelo A S; Beloti, Lilian L; Azzoni, Adriano R; Cotta, Monica A; Souza, Anete P

2015-10-01

The intriguing roles of the bacterial Tol-Pal trans-envelope protein complex range from maintenance of cell envelope integrity to potential participation in the process of cell division. In this study, we report the characterization of the XfTolB and XfPal proteins of the Tol-Pal complex of Xylella fastidiosa. X. fastidiosa is a major plant pathogen that forms biofilms inside xylem vessels, triggering the development of diseases in important cultivable plants around the word. Based on functional complementation experiments in Escherichia coli tolB and pal mutant strains, we confirmed the role of xftolB and xfpal in outer membrane integrity. In addition, we observed a dynamic and coordinated protein expression profile during the X. fastidiosa biofilm development process. Using small-angle X-ray scattering (SAXS), the low-resolution structure of the isolated XfTolB-XfPal complex in solution was solved for the first time. Finally, the localization of the XfTolB and XfPal polar ends was visualized via immunofluorescence labeling in vivo during bacterial cell growth. Our results highlight the major role of the components of the cell envelope, particularly the TolB-Pal complex, during the different phases of bacterial biofilm development. Copyright © 2015 Elsevier B.V. All rights reserved.

Bottom-up linking of carbon markets under far-sighted cap coordination and reversibility

NASA Astrophysics Data System (ADS)

Heitzig, Jobst; Kornek, Ulrike

2018-03-01

The Paris Agreement relies on nationally determined contributions to reach its targets and asks countries to increase ambitions over time, leaving open the details of this process. Although overcoming countries' myopic `free-riding' incentives requires cooperation, the global public good character of mitigation makes forming coalitions difficult. To cooperate, countries may link their carbon markets1, but is this option beneficial2? Some countries might not participate, not agree to lower caps, or not comply to agreements. While non-compliance might be deterred3, countries can hope that if they don't participate, others might still form a coalition. When considering only one coalition whose members can leave freely, the literature following the publication of refs 4,5 finds meagre prospects for effective collaboration6. Countries also face incentives to increase emissions when linking their markets without a cap agreement7,8. Here, we analyse the dynamics of market linkage using a game-theoretic model of far-sighted coalition formation. In contrast to non-dynamic models and dynamic models without far-sightedness9,10, in our model an efficient global coalition always forms eventually if players are sufficiently far-sighted or caps are coordinated immediately when markets are linked.

[Networks, disease management programs, GP coordinator: analysis of recent ambulatory reforms in Germany].

PubMed

Giovanella, Ligia

2011-01-01

Strengthening the role of the general practitioner in the conduction and coordination of specialized, inpatient and social care to ensure the continuity is a trend observed in recent health reforms in European countries. In Germany, from the second half of the 1990s, driven by economic pressures, a specific legislation and initiatives of the providers themselves have developed new organizational structures and care models for the purpose of the integration of the health care system and the coordination of health care in the form of: physicians networks, practitioner coordinator model, diseases management programs and integrated care. From a literature review, document analysis, visits to services and interviews with key informants, this paper analyzes the dynamics of these organizational changes in the German outpatient sector. The mechanisms of integration and coordination proposed are examined, and the potential impacts on the efficiency and quality of new organizational arrangements are discussed. Also it is analyzed the reasons and interests involved that point out the obstacles to the implementation. It was observed the process of an incremental reform with a tendency of diversification of the healthcare panorama in Germany with the presence of integrated models of care and strengthening the role of general practitioners in the coordination of patient care.

Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions

PubMed Central

Wang, Qing; Xue, Tuo; Song, Chunnian; Wang, Yan; Chen, Guangju

2016-01-01

Free energy calculations of the potential of mean force (PMF) based on the combination of targeted molecular dynamics (TMD) simulations and umbrella samplings as a function of physical coordinates have been applied to explore the detailed pathways and the corresponding free energy profiles for the conformational transition processes of the butane molecule and the 35-residue villin headpiece subdomain (HP35). The accurate PMF profiles for describing the dihedral rotation of butane under both coordinates of dihedral rotation and root mean square deviation (RMSD) variation were obtained based on the different umbrella samplings from the same TMD simulations. The initial structures for the umbrella samplings can be conveniently selected from the TMD trajectories. For the application of this computational method in the unfolding process of the HP35 protein, the PMF calculation along with the coordinate of the radius of gyration (Rg) presents the gradual increase of free energies by about 1 kcal/mol with the energy fluctuations. The feature of conformational transition for the unfolding process of the HP35 protein shows that the spherical structure extends and the middle α-helix unfolds firstly, followed by the unfolding of other α-helices. The computational method for the PMF calculations based on the combination of TMD simulations and umbrella samplings provided a valuable strategy in investigating detailed conformational transition pathways for other allosteric processes. PMID:27171075

Information processing in the primate visual system - An integrated systems perspective

NASA Technical Reports Server (NTRS)

Van Essen, David C.; Anderson, Charles H.; Felleman, Daniel J.

1992-01-01

The primate visual system contains dozens of distinct areas in the cerebral cortex and several major subcortical structures. These subdivisions are extensively interconnected in a distributed hierarchical network that contains several intertwined processing streams. A number of strategies are used for efficient information processing within this hierarchy. These include linear and nonlinear filtering, passage through information bottlenecks, and coordinated use of multiple types of information. In addition, dynamic regulation of information flow within and between visual areas may provide the computational flexibility needed for the visual system to perform a broad spectrum of tasks accurately and at high resolution.

Developmental Relations Among Motor and Cognitive Processes and Mathematics Skills.

PubMed

Kim, Helyn; Duran, Chelsea A K; Cameron, Claire E; Grissmer, David

2018-03-01

This study explored transactional associations among visuomotor integration, attention, fine motor coordination, and mathematics skills in a diverse sample of one hundred thirty-five 5-year-olds (kindergarteners) and one hundred nineteen 6-year-olds (first graders) in the United States who were followed over the course of 2 school years. Associations were dynamic, with more reciprocal transactions occurring in kindergarten than in the later grades. Specifically, visuomotor integration and mathematics exhibited ongoing reciprocity in kindergarten and first grade, attention contributed to mathematics in kindergarten and first grade, mathematics contributed to attention across the kindergarten year only, and fine motor coordination contributed to mathematics indirectly, through visuomotor integration, across kindergarten and first grade. Implications of examining the hierarchical interrelations among processes underlying the development of children's mathematics skills are discussed. © 2017 The Authors. Child Development © 2017 Society for Research in Child Development, Inc.

The neural component-process architecture of endogenously generated emotion

PubMed Central

Kanske, Philipp; Singer, Tania

2017-01-01

Abstract Despite the ubiquity of endogenous emotions and their role in both resilience and pathology, the processes supporting their generation are largely unknown. We propose a neural component process model of endogenous generation of emotion (EGE) and test it in two functional magnetic resonance imaging (fMRI) experiments (N = 32/293) where participants generated and regulated positive and negative emotions based on internal representations, usin self-chosen generation methods. EGE activated nodes of salience (SN), default mode (DMN) and frontoparietal control (FPCN) networks. Component processes implemented by these networks were established by investigating their functional associations, activation dynamics and integration. SN activation correlated with subjective affect, with midbrain nodes exclusively distinguishing between positive and negative affect intensity, showing dynamics consistent generation of core affect. Dorsomedial DMN, together with ventral anterior insula, formed a pathway supporting multiple generation methods, with activation dynamics suggesting it is involved in the generation of elaborated experiential representations. SN and DMN both coupled to left frontal FPCN which in turn was associated with both subjective affect and representation formation, consistent with FPCN supporting the executive coordination of the generation process. These results provide a foundation for research into endogenous emotion in normal, pathological and optimal function. PMID:27522089

Modeling 3D Dynamic Rupture on Arbitrarily-Shaped faults by Boundary-Conforming Finite Difference Method

NASA Astrophysics Data System (ADS)

Zhu, D.; Zhu, H.; Luo, Y.; Chen, X.

2008-12-01

We use a new finite difference method (FDM) and the slip-weakening law to model the rupture dynamics of a non-planar fault embedded in a 3-D elastic media with free surface. The new FDM, based on boundary- conforming grid, sets up the mapping equations between the curvilinear coordinate and the Cartesian coordinate and transforms irregular physical space to regular computational space; it also employs a higher- order non-staggered DRP/opt MacCormack scheme which is of low dispersion and low dissipation so that the high accuracy and stability of our rupture modeling are guaranteed. Compared with the previous methods, not only we can compute the spontaneous rupture of an arbitrarily shaped fault, but also can model the influence of the surface topography on the rupture process of earthquake. In order to verify the feasibility of this method, we compared our results and other previous results, and found out they matched perfectly. Thanks to the boundary-conforming FDM, problems such as dynamic rupture with arbitrary dip, strike and rake over an arbitrary curved plane can be handled; and supershear or subshear rupture can be simulated with different parameters such as the initial stresses and the critical slip displacement Dc. Besides, our rupture modeling is economical to be implemented owing to its high efficiency and does not suffer from displacement leakage. With the help of inversion data of rupture by field observations, this method is convenient to model rupture processes and seismograms of natural earthquakes.

Coupling Dynamics Interlip Coordination in Lower Lip Load Compensation

ERIC Educational Resources Information Center

van Lieshout, Pascal; Neufeld, Chris

2014-01-01

Purpose: To study the effects of lower lip loading on lower and upper lip movements and their coordination to test predictions on coupling dynamics derived from studies in limb control. Method: Movement data were acquired using electromagnetic midsagittal articulography under 4 conditions: (a) without restrictions, serving as a baseline; (b) with…

The Teaching of Polar Coordinates with Dynamic Mathematics Software

ERIC Educational Resources Information Center

Zengin, Yilmaz; Tatar, Enver

2015-01-01

The purpose of this study was to determine the effects of dynamic mathematics software on the achievement of pre-service mathematics teachers in the topic of polar coordinates and to solicit their opinions about computer-assisted instruction. The study was conducted for 11 weeks with 33 pre-service teachers in the Department of Mathematics…

Postural Coordination during Socio-motor Improvisation

PubMed Central

Gueugnon, Mathieu; Salesse, Robin N.; Coste, Alexandre; Zhao, Zhong; Bardy, Benoît G.; Marin, Ludovic

2016-01-01

Human interaction often relies on socio-motor improvisation. Creating unprepared movements during social interaction is not a random process but relies on rules of synchronization. These situations do not only involve people to be coordinated, but also require the adjustment of their posture in order to maintain balance and support movements. The present study investigated posture in such a context. More precisely, we first evaluated the impact of amplitude and complexity of arm movements on posture in solo situation. Then, we assessed the impact of interpersonal coordination on posture using the mirror game in which dyads performed improvised and synchronized movements (i.e., duo situation). Posture was measured through ankle-hip coordination in medio-lateral and antero-posterior directions (ML and AP respectively). Our results revealed the spontaneous emergence of in-phase pattern in ML direction and antiphase pattern in AP direction for solo and duo situations. These two patterns respectively refer to the simultaneous flexion/extension of the ankles and the hips in the same or opposite direction. It suggests different functional roles of postural coordination patterns in each direction, with in-phase supporting task performance in ML (dynamical stability) and antiphase supporting postural control in AP (mechanical stability). Although amplitude of movement did not influence posture, movement complexity disturbed postural stability in both directions. Conversely, interpersonal coordination promoted postural stability in ML but not in AP direction. These results are discussed in terms of the difference in coupling strength between ankle-hip coordination and interpersonal coordination. PMID:27547193

Postural Coordination during Socio-motor Improvisation.

PubMed

Gueugnon, Mathieu; Salesse, Robin N; Coste, Alexandre; Zhao, Zhong; Bardy, Benoît G; Marin, Ludovic

2016-01-01

Human interaction often relies on socio-motor improvisation. Creating unprepared movements during social interaction is not a random process but relies on rules of synchronization. These situations do not only involve people to be coordinated, but also require the adjustment of their posture in order to maintain balance and support movements. The present study investigated posture in such a context. More precisely, we first evaluated the impact of amplitude and complexity of arm movements on posture in solo situation. Then, we assessed the impact of interpersonal coordination on posture using the mirror game in which dyads performed improvised and synchronized movements (i.e., duo situation). Posture was measured through ankle-hip coordination in medio-lateral and antero-posterior directions (ML and AP respectively). Our results revealed the spontaneous emergence of in-phase pattern in ML direction and antiphase pattern in AP direction for solo and duo situations. These two patterns respectively refer to the simultaneous flexion/extension of the ankles and the hips in the same or opposite direction. It suggests different functional roles of postural coordination patterns in each direction, with in-phase supporting task performance in ML (dynamical stability) and antiphase supporting postural control in AP (mechanical stability). Although amplitude of movement did not influence posture, movement complexity disturbed postural stability in both directions. Conversely, interpersonal coordination promoted postural stability in ML but not in AP direction. These results are discussed in terms of the difference in coupling strength between ankle-hip coordination and interpersonal coordination.

Overreaching in coordination dynamics therapy in an athlete with a spinal cord injury.

PubMed

Schalow, G; Vaher, I; Jaigma, P

2008-03-01

A motocross athlete suffered a clinically complete spinal cord injury (SCI) during competition. Although MRIs (magnetic resonance imaging) showed a complete spinal cord injury at the Thoracic 11/12 levels, surface EMG recordings indicated the survival of few tract fibres across the injury site. Six weeks after the accident the subject began intensive Coordination Dynamics Therapy (CDT) at an up-to-date therapy centre. The subject trained at his physical limits to induce structural and functional repair. Exercising at variable loads between 20 and 200N (on a special CDT and recording device) generated periods of overreaching and super-compensation. By plotting coordination dynamics values (kinesiology), including high-load exertion (200N) and hysteresis curves, periods of overreaching and super-compensation were made graphically visible. It was found that symmetrical improvements of central nervous system (CNS) functioning occurred during overreaching. Improvements in spinal cord functioning were achieved throughout one year of CDT in this chronically injured subject with an almost anatomically complete SCI. It is discussed that the measuring of CNS functions by means of recording coordination dynamics is a powerful and non-invasive tool ideal for exact quantitative and qualitative measurements of improvement (or change) in CNS functioning. Such diagnostics may be of particular importance in sport during training and before competition. Also, coordination dynamics might be used to measure the effects of prolonged exposure to reduced gravitational conditions on CNS functions, such as faced by astronauts.

Molecular Facts on the Structure and Dynamics of Electrolyte Species in Cu-Cl Cycle for Hydrogen Generation: An Insight from Molecular Dynamic Simulations.

PubMed

Sahu, Pooja; Ali, Sk Musharaf; Shenoy, K T; Mohan, S

2018-04-12

The Cu complex, which is the key chemical species in well-known Cu-Cl hybrid thermochemical cycles and also in numerous metal hydrometallurgical and sedimentary deposit processes, displays a wide variety of structural and dynamical characteristics that are further complicated by the presence of multiple oxidation states of Cu ions with different coordination chemistries, therefore they are difficult to explore from experiments alone. In this article, an attempt has been made to understand the coordination behavior of the Cu complex using MD simulations. The study provides compelling evidence of the experimentally observed multiple stoichiometries of Cu ions, i.e., 1:6:0, 1:5:1, and 1:4:2 for Cu + :H 2 O:Cl - and 1:6:0 for Cu 2+ :H 2 O:Cl - . The presence of the anionic Cu complex, [Cu + Cl 2 ] - ·2H 2 O, [Cu + Cl 2 ] - ·3H 2 O, [Cu 2+ Cl 3 ] - ·H 2 O, and [Cu 2+ Cl 3 ] - ·2H 2 O, was captured in the presence of excess chloride ions. Furthermore, the probability distribution profiles have been estimated to determine the most possible complex in the considered systems. The results establish structural and dynamical reformation of the Cu complex with change in the salt concentration or variation in the solvent medium in which they are dissolved. Moreover, the structure and kinetics of the Cu ions in the Cu-Cl electrolyzer have been explored over a large range of the electric field by extending the simulated systems for varied strengths of the electric fields. It has been observed that with an increase in the strength of the electric field, the water molecules lose their coordination strength with central Cu ions, which, on the other hand, results in a significant change in the structure of the captured complex. The diffusion dynamics of the ions is altered while applying the electric field, which is furthermore modified while increasing the strength of electric field beyond a critical limit. In fact, the diffusion mechanism of the ions was seen to be transformed from Brownian-like to linear motion and then to hopping diffusion with the increasing strength of the electric field. To the best of our knowledge, this is the first time when the multiple oxidation states of the Cu ion are explored using MD simulations, and the coexisting pictures of the multiple coordinations and the solvent effects have been clearly revealed. Also to date, the present article is the first one to report the insights of the structure and the dynamics of the ions in the Cu-Cl electrolyzer over a wide range of the electric field. The present studies will be very helpful in understanding the mechanism involved in numerous metal hydrometallurgical and sedimentary deposit processes and to comprehend the analogies involved in the electrode reactions of the Cu-Cl cycle for hydrogen generation.

Free energy from molecular dynamics with multiple constraints

NASA Astrophysics Data System (ADS)

den Otter, W. K.; Briels, W. J.

In molecular dynamics simulations of reacting systems, the key step to determining the equilibrium constant and the reaction rate is the calculation of the free energy as a function of the reaction coordinate. Intuitively the derivative of the free energy is equal to the average force needed to constrain the reaction coordinate to a constant value, but the metric tensor effect of the constraint on the sampled phase space distribution complicates this relation. The appropriately corrected expression for the potential of mean constraint force method (PMCF) for systems in which only the reaction coordinate is constrained was published recently. Here we will consider the general case of a system with multiple constraints. This situation arises when both the reaction coordinate and the 'hard' coordinates are constrained, and also in systems with several reaction coordinates. The obvious advantage of this method over the established thermodynamic integration and free energy perturbation methods is that it avoids the cumbersome introduction of a full set of generalized coordinates complementing the constrained coordinates. Simulations of n -butane and n -pentane in vacuum illustrate the method.

The effect of implementing a care coordination program on team dynamics and the patient experience.

PubMed

Di Capua, Paul; Clarke, Robin; Tseng, Chi-Hong; Wilhalme, Holly; Sednew, Renee; McDonald, Kathryn M; Skootsky, Samuel A; Wenger, Neil

2017-08-01

Care coordination programs are frequently implemented in the redesign of primary care systems, focused on improving patient outcomes and reducing utilization. However, redesign can be disruptive, affect patient experiences, and undermine elements in the patient-centered medical home, such as team-based care. Case-controlled study with difference-in-differences (DID) and cross-sectional analyses. The phased implementation of a care coordination program permitted evaluation of a natural experiment to compare measures of patient experience and teamwork in practices with and without care coordinators. Patient experience scores were compared before and after the introduction of care coordinators, using DID analyses. Cross-sectional data were used to compare teamwork, based on the relational coordination survey, and physician-perceived barriers to coordinated care between clinics with and without care coordinators. We evaluated survey responses from 459 staff and physicians and 13,441 patients in 26 primary care practices. Practices with care coordinators did not have significantly different relational coordination scores compared with practices without care coordinators, and physicians in these practices did not report reduced barriers to coordinated care. After implementation of the program, patients in practices with care coordinators reported a more positive experience with staff over time (DID, 2.6 percentage points; P = .0009). A flexible program that incorporates care coordinators into the existing care team was minimally disruptive to existing team dynamics, and the embedded care coordinators were associated with a small increase in patient ratings that reflected a more positive experience with staff.

Multinuclear solid film state NMR studies of metal oxide catalysts and minerals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maxwell, R.S.; Stec, D.F.; Ellis, P.D.

1996-10-01

Several of our investigations of heterogeneous process by novel NMR experiments and analyses are reviewed and the utility and limitations of NMR spectroscopy for these areas discussed. Out studies have included the following: dynamics and arrangements of proton-containing adsorbates, primarily Bronsted acid sites and water, on the surface of zirconia and alumina catalysts; hydrogen dynamics and coordinates in synthetic aluminum oxyhydroxides; phase separation and crystallinity of synthetic minerals. In combination with the complementary results obtained in our laboratory via infrared spectroscopy, thermal analysis (primarily TGA and DSC), and catalytic activity measurements, these NMR data provide unique and valuable information onmore » atomic and molecular dynamics, identities, and structures without requiring pristine, single crystal specimens.« less

Long-range population dynamics of anatomically defined neocortical networks

PubMed Central

Chen, Jerry L; Voigt, Fabian F; Javadzadeh, Mitra; Krueppel, Roland; Helmchen, Fritjof

2016-01-01

The coordination of activity across neocortical areas is essential for mammalian brain function. Understanding this process requires simultaneous functional measurements across the cortex. In order to dissociate direct cortico-cortical interactions from other sources of neuronal correlations, it is furthermore desirable to target cross-areal recordings to neuronal subpopulations that anatomically project between areas. Here, we combined anatomical tracers with a novel multi-area two-photon microscope to perform simultaneous calcium imaging across mouse primary (S1) and secondary (S2) somatosensory whisker cortex during texture discrimination behavior, specifically identifying feedforward and feedback neurons. We find that coordination of S1-S2 activity increases during motor behaviors such as goal-directed whisking and licking. This effect was not specific to identified feedforward and feedback neurons. However, these mutually projecting neurons especially participated in inter-areal coordination when motor behavior was paired with whisker-texture touches, suggesting that direct S1-S2 interactions are sensory-dependent. Our results demonstrate specific functional coordination of anatomically-identified projection neurons across sensory cortices. DOI: http://dx.doi.org/10.7554/eLife.14679.001 PMID:27218452

A New Method of High-Precision Positioning for an Indoor Pseudolite without Using the Known Point Initialization.

PubMed

Zhao, Yinzhi; Zhang, Peng; Guo, Jiming; Li, Xin; Wang, Jinling; Yang, Fei; Wang, Xinzhe

2018-06-20

Due to the great influence of multipath effect, noise, clock and error on pseudorange, the carrier phase double difference equation is widely used in high-precision indoor pseudolite positioning. The initial position is determined mostly by the known point initialization (KPI) method, and then the ambiguities can be fixed with the LAMBDA method. In this paper, a new method without using the KPI to achieve high-precision indoor pseudolite positioning is proposed. The initial coordinates can be quickly obtained to meet the accuracy requirement of the indoor LAMBDA method. The detailed processes of the method follows: Aiming at the low-cost single-frequency pseudolite system, the static differential pseudolite system (DPL) method is used to obtain the low-accuracy positioning coordinates of the rover station quickly. Then, the ambiguity function method (AFM) is used to search for the coordinates in the corresponding epoch. The real coordinates obtained by AFM can meet the initial accuracy requirement of the LAMBDA method, so that the double difference carrier phase ambiguities can be correctly fixed. Following the above steps, high-precision indoor pseudolite positioning can be realized. Several experiments, including static and dynamic tests, are conducted to verify the feasibility of the new method. According to the results of the experiments, the initial coordinates with the accuracy of decimeter level through the DPL can be obtained. For the AFM part, both a one-meter search scope and two-centimeter or four-centimeter search steps are used to ensure the precision at the centimeter level and high search efficiency. After dealing with the problem of multiple peaks caused by the ambiguity cosine function, the coordinate information of the maximum ambiguity function value (AFV) is taken as the initial value of the LAMBDA, and the ambiguities can be fixed quickly. The new method provides accuracies at the centimeter level for dynamic experiments and at the millimeter level for static ones.

Emerging Imaging and Genomic Tools for Developmental Systems Biology.

PubMed

Liu, Zhe; Keller, Philipp J

2016-03-21

Animal development is a complex and dynamic process orchestrated by exquisitely timed cell lineage commitment, divisions, migration, and morphological changes at the single-cell level. In the past decade, extensive genetic, stem cell, and genomic studies provided crucial insights into molecular underpinnings and the functional importance of genetic pathways governing various cellular differentiation processes. However, it is still largely unknown how the precise coordination of these pathways is achieved at the whole-organism level and how the highly regulated spatiotemporal choreography of development is established in turn. Here, we discuss the latest technological advances in imaging and single-cell genomics that hold great promise for advancing our understanding of this intricate process. We propose an integrated approach that combines such methods to quantitatively decipher in vivo cellular dynamic behaviors and their underlying molecular mechanisms at the systems level with single-cell, single-molecule resolution. Copyright © 2016 Elsevier Inc. All rights reserved.

Spatial correlation of the dynamic propensity of a glass-forming liquid

NASA Astrophysics Data System (ADS)

Razul, M. Shajahan G.; Matharoo, Gurpreet S.; Poole, Peter H.

2011-06-01

We present computer simulation results on the dynamic propensity (as defined by Widmer-Cooper et al 2004 Phys. Rev. Lett. 93 135701) in a Kob-Andersen binary Lennard-Jones liquid system consisting of 8788 particles. We compute the spatial correlation function for the dynamic propensity as a function of both the reduced temperature T, and the time scale on which the particle displacements are measured. For T <= 0.6, we find that non-zero correlations occur at the largest length scale accessible in our system. We also show that a cluster-size analysis of particles with extremal values of the dynamic propensity, as well as 3D visualizations, reveal spatially correlated regions that approach the size of our system as T decreases, consistently with the behavior of the spatial correlation function. Next, we define and examine the 'coordination propensity', the isoconfigurational average of the coordination number of the minority B particles around the majority A particles. We show that a significant correlation exists between the spatial fluctuations of the dynamic and coordination propensities. In addition, we find non-zero correlations of the coordination propensity occurring at the largest length scale accessible in our system for all T in the range 0.466 < T < 1.0. We discuss the implications of these results for understanding the length scales of dynamical heterogeneity in glass-forming liquids.

What Can Be Learned from Nuclear Resonance Vibrational Spectroscopy: Vibrational Dynamics and Hemes

PubMed Central

2017-01-01

Nuclear resonance vibrational spectroscopy (NRVS; also known as nuclear inelastic scattering, NIS) is a synchrotron-based method that reveals the full spectrum of vibrational dynamics for Mössbauer nuclei. Another major advantage, in addition to its completeness (no arbitrary optical selection rules), is the unique selectivity of NRVS. The basics of this recently developed technique are first introduced with descriptions of the experimental requirements and data analysis including the details of mode assignments. We discuss the use of NRVS to probe 57Fe at the center of heme and heme protein derivatives yielding the vibrational density of states for the iron. The application to derivatives with diatomic ligands (O2, NO, CO, CN–) shows the strong capabilities of identifying mode character. The availability of the complete vibrational spectrum of iron allows the identification of modes not available by other techniques. This permits the correlation of frequency with other physical properties. A significant example is the correlation we find between the Fe–Im stretch in six-coordinate Fe(XO) hemes and the trans Fe–N(Im) bond distance, not possible previously. NRVS also provides uniquely quantitative insight into the dynamics of the iron. For example, it provides a model-independent means of characterizing the strength of iron coordination. Prediction of the temperature-dependent mean-squared displacement from NRVS measurements yields a vibrational “baseline” for Fe dynamics that can be compared with results from techniques that probe longer time scales to yield quantitative insights into additional dynamical processes. PMID:28921972

Mapping the Dynamics of Shear Stress—Induced Structural Changes in Endothelial Cells

PubMed Central

Mott, Rosalind E.; Helmke, Brian P.

2009-01-01

Hemodynamic shear stress regulates endothelial cell biochemical processes that govern cytoskeletal contractility, focal adhesion dynamics, and extracellular matrix assembly. Since shear stress causes rapid strain focusing at discrete locations in the cytoskeleton, we hypothesized that shear stress coordinately alters structural dynamics in the cytoskeleton, focal adhesion sites, and extracellular matrix on a time scale of minutes. Using multi-wavelength 4-D fluorescence microscopy, we measured the displacement of rhodamine-fibronectin and of GFP-labeled actin, vimentin, paxillin, and/or vinculin in aortic endothelial cells before and after onset of steady unidirectional shear stress. In the cytoskeleton, the onset of shear stress increased actin polymerization into lamellipodia, altered the angle of lateral displacement of actin stress fibers and vimentin filaments, and decreased centripetal remodeling of actin stress fibers in both subconfluent and confluent cell layers. Shear stress induced the formation of new focal complexes and reduced the centripetal remodeling of focal adhesions in regions of new actin polymerization. The structural dynamics of focal adhesions and the fibronectin matrix varied with cell density. In subconfluent cell layers, shear stress onset decreased the displacement of focal adhesions and fibronectin fibrils. In confluent monolayers, the direction of fibronectin and focal adhesion displacement shifted significantly towards the downstream direction within one minute after onset of shear stress. These spatially coordinated rapid changes in the structural dynamics of cytoskeleton, focal adhesions, and extracellular matrix are consistent with focusing of mechanical stress and/or strain near major sites of shear stress-mediated mechanotransduction. PMID:17855768

Spindle

DOE Office of Scientific and Technical Information (OSTI.GOV)

2013-04-04

Spindle is software infrastructure that solves file system scalabiltiy problems associated with starting dynamically linked applications in HPC environments. When an HPC applications starts up thousands of pricesses at once, and those processes simultaneously access a shared file system to look for shared libraries, it can cause significant performance problems for both the application and other users. Spindle scalably coordinates the distribution of shared libraries to an application to avoid hammering the shared file system.

Indicators of sailing performance in youth dinghy sailing.

PubMed

Callewaert, Margot; Boone, Jan; Celie, Bert; De Clercq, Dirk; Bourgois, Jan G

2015-01-01

This study aimed to determine indicators of sailing performance in 2 (age) groups of youth sailors by investigating the anthropometric, physical and motor coordination differences and factors discriminating between elite and non-elite male optimist sailors and young dynamic hikers. Anthropometric measurements from 23 optimist sailors (mean ± SD age = 12.3 ± 1.4 years) and 24 dynamic youth hikers (i.e. Laser 4.7, Laser radial and Europe sailors <18 years who have to sail the boat in a very dynamic manner, due to a high sailor to yacht weight ratio) (mean ± SD age = 16.5 ± 1.6 years) were conducted. They performed a physical fitness test battery (EUROFIT), motor coordination test battery (Körperkoordinationstest für Kinder) and the Bucket test. Both groups of sailors were divided into two subgroups (i.e. elites and non-elites) based on sailing expertise. The significant differences, taking biological maturation into account and factors discriminating between elite and non-elite optimist sailors and dynamic hikers were explored by means of multivariate analysis of covariance and discriminant analysis, respectively. The main results indicated that 100.0% of elite optimist sailors and 88.9% of elite dynamic hikers could be correctly classified by means of two motor coordination tests (i.e. side step and side jump) and Bucket test, respectively. As such, strength- and speed-oriented motor coordination and isometric knee-extension strength endurance can be identified as indicators of sailing performance in young optimist and dynamic youth sailors, respectively. Therefore, we emphasise the importance of motor coordination skill training in optimist sailors (<15 years) and maximum strength training later on (>15 years) in order to increase their isometric knee-extension strength endurance.

Intermanual transfer characteristics of dynamic learning: direction, coordinate frame, and consolidation of interlimb generalization

PubMed Central

Thürer, Benjamin; Focke, Anne; Stein, Thorsten

2015-01-01

Intermanual transfer, i.e., generalization of motor learning across hands, is a well-accepted phenomenon of motor learning. Yet, there are open questions regarding the characteristics of this transfer, particularly the intermanual transfer of dynamic learning. In this study, we investigated intermanual transfer in a force field adaptation task concerning the direction and the coordinate frame of transfer as well as the influence of a 24-h consolidation period on the transfer. We tested 48 healthy human subjects for transfer from dominant to nondominant hand, and vice versa. We considered two features of transfer. First, we examined transfer to the untrained hand using force channel trials that suppress error feedback and learning mechanisms to assess intermanual transfer in the form of a practice-dependent bias. Second, we considered transfer by exposing the subjects to the force field with the untrained hand to check for faster learning of the dynamics (interlimb savings). Half of the subjects were tested for transfer immediately after adaptation, whereas the other half were tested after a 24-h consolidation period. Our results showed intermanual transfer both from dominant to nondominant hand and vice versa in extrinsic coordinates. After the consolidation period, transfer effects were weakened. Moreover, the transfer effects were negligible compared with the subjects' ability to rapidly adapt to the force field condition. We conclude that intermanual transfer is a bidirectional phenomenon that vanishes with time. However, the ability to transfer motor learning seems to play a minor role compared with the rapid adaptation processes. PMID:26424581

Mind-to-mind heteroclinic coordination: Model of sequential episodic memory initiation

NASA Astrophysics Data System (ADS)

Afraimovich, V. S.; Zaks, M. A.; Rabinovich, M. I.

2018-05-01

Retrieval of episodic memory is a dynamical process in the large scale brain networks. In social groups, the neural patterns, associated with specific events directly experienced by single members, are encoded, recalled, and shared by all participants. Here, we construct and study the dynamical model for the formation and maintaining of episodic memory in small ensembles of interacting minds. We prove that the unconventional dynamical attractor of this process—the nonsmooth heteroclinic torus—is structurally stable within the Lotka-Volterra-like sets of equations. Dynamics on this torus combines the absence of chaos with asymptotic instability of every separate trajectory; its adequate quantitative characteristics are length-related Lyapunov exponents. Variation of the coupling strength between the participants results in different types of sequential switching between metastable states; we interpret them as stages in formation and modification of the episodic memory.

ISS method for coordination control of nonlinear dynamical agents under directed topology.

PubMed

Wang, Xiangke; Qin, Jiahu; Yu, Changbin

2014-10-01

The problems of coordination of multiagent systems with second-order locally Lipschitz continuous nonlinear dynamics under directed interaction topology are investigated in this paper. A completely nonlinear input-to-state stability (ISS)-based framework, drawing on ISS methods, with the aid of results from graph theory, matrix theory, and the ISS cyclic-small-gain theorem, is proposed for the coordination problem under directed topology, which can effectively tackle the technical challenges caused by locally Lipschitz continuous dynamics. Two coordination problems, i.e., flocking with a virtual leader and containment control, are considered. For both problems, it is assumed that only a portion of the agents can obtain the information from the leader(s). For the first problem, the proposed strategy is shown effective in driving a group of nonlinear dynamical agents reach the prespecified geometric pattern under the condition that at least one agent in each strongly connected component of the information-interconnection digraph with zero in-degree has access to the state information of the virtual leader; and the strategy proposed for the second problem can guarantee the nonlinear dynamical agents moving to the convex hull spanned by the positions of multiple leaders under the condition that for each agent there exists at least one leader that has a directed path to this agent.

Difficulty leading interpersonal coordination: towards an embodied signature of social anxiety disorder

PubMed Central

Varlet, Manuel; Marin, Ludovic; Capdevielle, Delphine; Del-Monte, Jonathan; Schmidt, R. C.; Salesse, Robin N.; Boulenger, Jean-Philippe; Bardy, Benoît G.; Raffard, Stéphane

2014-01-01

Defined by a persistent fear of embarrassment or negative evaluation while engaged in social interaction or public performance, social anxiety disorder (SAD) is one of the most common psychiatric syndromes. Previous research has made a considerable effort to better understand and assess this mental disorder. However, little attention has been paid to social motor behavior of patients with SAD despite its crucial importance in daily social interactions. Previous research has shown that the coordination of arm, head or postural movements of interacting people can reflect their mental states or feelings such as social connectedness and social motives, suggesting that interpersonal movement coordination may be impaired in patients suffering from SAD. The current study was specifically aimed at determining whether SAD affects the dynamics of social motor coordination. We compared the unintentional and intentional rhythmic coordination of a SAD group (19 patients paired with control participants) with the rhythmic coordination of a control group (19 control pairs) in an interpersonal pendulum coordination task. The results demonstrated that unintentional social motor coordination was preserved with SAD while intentional coordination was impaired. More specifically, intentional coordination became impaired when patients with SAD had to lead the coordination as indicated by poorer (i.e., more variable) coordination. These differences between intentional and unintentional coordination as well as between follower and leader roles reveal an impaired coordination dynamics that is specific to SAD, and thus, opens promising research directions to better understand, assess and treat this mental disorder. PMID:24567707

Symplectic integration of closed chain rigid body dynamics with internal coordinate equations of motion

NASA Astrophysics Data System (ADS)

Mazur, Alexey K.

1999-07-01

Internal coordinate molecular dynamics (ICMD) is a recent efficient method for modeling polymer molecules which treats them as chains of rigid bodies rather than ensembles of point particles as in Cartesian MD. Unfortunately, it is readily applicable only to linear or tree topologies without closed flexible loops. Important examples violating this condition are sugar rings of nucleic acids, proline residues in proteins, and also disulfide bridges. This paper presents the first complete numerical solution of the chain closure problem within the context of ICMD. The method combines natural implicit fixation of bond lengths and bond angles by the choice of internal coordinates with explicit constraints similar to Cartesian dynamics used to maintain the chain closure. It is affordable for large molecules and makes possible 3-5 times faster dynamics simulations of molecular systems with flexible rings, including important biological objects like nucleic acids and disulfide-bonded proteins.

A Control Scheme That Uses Dynamic Postural Synergies to Coordinate a Hybrid Walking Neuroprosthesis: Theory and Experiments.

PubMed

Alibeji, Naji A; Molazadeh, Vahidreza; Dicianno, Brad E; Sharma, Nitin

2018-01-01

A hybrid walking neuroprosthesis that combines functional electrical stimulation (FES) with a powered lower limb exoskeleton can be used to restore walking in persons with paraplegia. It provides therapeutic benefits of FES and torque reliability of the powered exoskeleton. Moreover, by harnessing metabolic power of muscles via FES, the hybrid combination has a potential to lower power consumption and reduce actuator size in the powered exoskeleton. Its control design, however, must overcome the challenges of actuator redundancy due to the combined use of FES and electric motor. Further, dynamic disturbances such as electromechanical delay (EMD) and muscle fatigue must be considered during the control design process. This ensures stability and control performance despite disparate dynamics of FES and electric motor. In this paper, a general framework to coordinate FES of multiple gait-governing muscles with electric motors is presented. A muscle synergy-inspired control framework is used to derive the controller and is motivated mainly to address the actuator redundancy issue. Dynamic postural synergies between FES of the muscles and the electric motors were artificially generated through optimizations and result in key dynamic postures when activated. These synergies were used in the feedforward path of the control system. A dynamic surface control technique, modified with a delay compensation term, is used as the feedback controller to address model uncertainty, the cascaded muscle activation dynamics, and EMD. To address muscle fatigue, the stimulation levels in the feedforward path were gradually increased based on a model-based fatigue estimate. A Lyapunov-based stability approach was used to derive the controller and guarantee its stability. The synergy-based controller was demonstrated experimentally on an able-bodied subject and person with an incomplete spinal cord injury.

The solar optical telescope

NASA Technical Reports Server (NTRS)

1990-01-01

Objectives of the Solar Optical Telescope are to study the physics of the Sun on the scale at which many of the important physical processes occur and to attain a resolution of 73km on the Sun or 0.1 arc seconds of angular resolution. Topics discussed in this overview of the Solar Optical Telescope include: why is the Solar Optical Telescope needed; current picture of the Sun's atmosphere and convection zone; scientific problems for the Solar Optical Telescope; a description of the telescope; the facility - science management, contamination control, and accessibility to the instruments; the scientific instruments - a coordinated instrument package for unlocking the Sun's secrets; parameters of the coordinated instrument package; science operations from the Space Shuttle; and the dynamic solar atmosphere.

Rhythmic coordination of hippocampal neurons during associative memory processing

PubMed Central

Rangel, Lara M; Rueckemann, Jon W; Riviere, Pamela D; Keefe, Katherine R; Porter, Blake S; Heimbuch, Ian S; Budlong, Carl H; Eichenbaum, Howard

2016-01-01

Hippocampal oscillations are dynamic, with unique oscillatory frequencies present during different behavioral states. To examine the extent to which these oscillations reflect neuron engagement in distinct local circuit processes that are important for memory, we recorded single cell and local field potential activity from the CA1 region of the hippocampus as rats performed a context-guided odor-reward association task. We found that theta (4–12 Hz), beta (15–35 Hz), low gamma (35–55 Hz), and high gamma (65–90 Hz) frequencies exhibited dynamic amplitude profiles as rats sampled odor cues. Interneurons and principal cells exhibited unique engagement in each of the four rhythmic circuits in a manner that related to successful performance of the task. Moreover, principal cells coherent to each rhythm differentially represented task dimensions. These results demonstrate that distinct processing states arise from the engagement of rhythmically identifiable circuits, which have unique roles in organizing task-relevant processing in the hippocampus. DOI: http://dx.doi.org/10.7554/eLife.09849.001 PMID:26751780

Differing Dynamics of Intrapersonal and Interpersonal Coordination: Two-finger and Four-Finger Tapping Experiments

PubMed Central

Kodama, Kentaro; Furuyama, Nobuhiro; Inamura, Tetsunari

2015-01-01

Finger-tapping experiments were conducted to examine whether the dynamics of intrapersonal and interpersonal coordination systems can be described equally by the Haken—Kelso—Bunz model, which describes inter-limb coordination dynamics. This article reports the results of finger-tapping experiments conducted in both systems. Two within-subject factors were investigated: the phase mode and the number of fingers. In the intrapersonal experiment (Experiment 1), the participants were asked to tap, paced by a gradually hastening auditory metronome, looking at their fingers moving, using the index finger in the two finger condition, or the index and middle finger in the four-finger condition. In the interpersonal experiment (Experiment 2), pairs of participants performed the task while each participant used the outside hand, tapping with the index finger in the two finger condition, or the index and middle finger in the four-finger condition. Some results did not agree with the HKB model predictions. First, from Experiment 1, no significant difference was observed in the movement stability between the in-phase and anti-phase modes in the two finger condition. Second, from Experiment 2, no significant difference was found in the movement stability between the in-phase and anti-phase mode in the four-finger condition. From these findings, different coordination dynamics were inferred between intrapersonal and interpersonal coordination systems against prediction from the previous studies. Results were discussed according to differences between intrapersonal and interpersonal coordination systems in the availability of perceptual information and the complexity in the interaction between limbs derived from a nested structure. PMID:26070119

Lipid-converter, a framework for lipid manipulations in molecular dynamics simulations

PubMed Central

Larsson, Per; Kasson, Peter M.

2014-01-01

Construction of lipid membrane and membrane protein systems for molecular dynamics simulations can be a challenging process. In addition, there are few available tools to extend existing studies by repeating simulations using other force fields and lipid compositions. To facilitate this, we introduce lipidconverter, a modular Python framework for exchanging force fields and lipid composition in coordinate files obtained from simulations. Force fields and lipids are specified by simple text files, making it easy to introduce support for additional force fields and lipids. The converter produces simulation input files that can be used for structural relaxation of the new membranes. PMID:25081234

A simple orbit-attitude coupled modelling method for large solar power satellites

NASA Astrophysics Data System (ADS)

Li, Qingjun; Wang, Bo; Deng, Zichen; Ouyang, Huajiang; Wei, Yi

2018-04-01

A simple modelling method is proposed to study the orbit-attitude coupled dynamics of large solar power satellites based on natural coordinate formulation. The generalized coordinates are composed of Cartesian coordinates of two points and Cartesian components of two unitary vectors instead of Euler angles and angular velocities, which is the reason for its simplicity. Firstly, in order to develop natural coordinate formulation to take gravitational force and gravity gradient torque of a rigid body into account, Taylor series expansion is adopted to approximate the gravitational potential energy. The equations of motion are constructed through constrained Hamilton's equations. Then, an energy- and constraint-conserving algorithm is presented to solve the differential-algebraic equations. Finally, the proposed method is applied to simulate the orbit-attitude coupled dynamics and control of a large solar power satellite considering gravity gradient torque and solar radiation pressure. This method is also applicable to dynamic modelling of other rigid multibody aerospace systems.

Designing an architectural style for dynamic medical Cross-Organizational Workflow management system: an approach based on agents and web services.

PubMed

Bouzguenda, Lotfi; Turki, Manel

2014-04-01

This paper shows how the combined use of agent and web services technologies can help to design an architectural style for dynamic medical Cross-Organizational Workflow (COW) management system. Medical COW aims at supporting the collaboration between several autonomous and possibly heterogeneous medical processes, distributed over different organizations (Hospitals, Clinic or laboratories). Dynamic medical COW refers to occasional cooperation between these health organizations, free of structural constraints, where the medical partners involved and their number are not pre-defined. More precisely, this paper proposes a new architecture style based on agents and web services technologies to deal with two key coordination issues of dynamic COW: medical partners finding and negotiation between them. It also proposes how the proposed architecture for dynamic medical COW management system can connect to a multi-agent system coupling the Clinical Decision Support System (CDSS) with Computerized Prescriber Order Entry (CPOE). The idea is to assist the health professionals such as doctors, nurses and pharmacists with decision making tasks, as determining diagnosis or patient data analysis without stopping their clinical processes in order to act in a coherent way and to give care to the patient.

A Comparative Study of [CaEDTA](2-) and [MgEDTA](2-): Structural and Dynamical Insights from Quantum Mechanical Charge Field Molecular Dynamics.

PubMed

Tirler, Andreas O; Hofer, Thomas S

2015-07-09

Structure and dynamics of [MgEDTA](2-) and [CaEDTA](2-) complexes in aqueous solution have been investigated via quantum mechanical/molecular mechanical (QM/MM) simulations. While for the first a 6-fold octahedral complex has been observed, the presence of an additional coordinating water ligand has been observed in the latter case. Because of rapidly exchanging water molecules, this 7-fold coordination complex was found to form pentagonal bipyramidal as well as capped trigonal prismatic configurations along the simulation interchanging on the picosecond time scale. Also in the case of [MgEDTA](2-) a trigonal prismatic configuration has been observed for a very short time period of approximately 1 ps. This work reports for the first time the presence of trigonal prismatic structures observed in the coordination sphere of [MgEDTA](2-) and [CaEDTA](2-) complexes in aqueous solution. In addition to the detailed characterization of structure and dynamics of the systems, the prediction of the associated infrared spectra indicates that the ion-water vibrational mode found at approximately 250 cm(-1) provides a distinctive measure to experimentally detect the presence of the coordinating water molecule via low-frequency IR setups.

Cell cycle-regulated PLEIADE/AtMAP65-3 links membrane and microtubule dynamics during plant cytokinesis.

PubMed

Steiner, Alexander; Rybak, Katarzyna; Altmann, Melina; McFarlane, Heather E; Klaeger, Susan; Nguyen, Ngoc; Facher, Eva; Ivakov, Alexander; Wanner, Gerhard; Kuster, Bernhard; Persson, Staffan; Braun, Pascal; Hauser, Marie-Theres; Assaad, Farhah F

2016-11-01

Cytokinesis, the partitioning of the cytoplasm following nuclear division, requires extensive coordination between cell cycle cues, membrane trafficking and microtubule dynamics. Plant cytokinesis occurs within a transient membrane compartment known as the cell plate, to which vesicles are delivered by a plant-specific microtubule array, the phragmoplast. While membrane proteins required for cytokinesis are known, how these are coordinated with microtubule dynamics and regulated by cell cycle cues remains unclear. Here, we document physical and genetic interactions between Transport Protein Particle II (TRAPPII) tethering factors and microtubule-associated proteins of the PLEIADE/AtMAP65 family. These interactions do not specifically affect the recruitment of either TRAPPII or MAP65 proteins to the cell plate or midzone. Rather, and based on single versus double mutant phenotypes, it appears that they are required to coordinate cytokinesis with the nuclear division cycle. As MAP65 family members are known to be targets of cell cycle-regulated kinases, our results provide a conceptual framework for how membrane and microtubule dynamics may be coordinated with each other and with the nuclear cycle during plant cytokinesis. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Coordination Polymer Gels with Modular Nanomorphologies, Tunable Emissions, and Stimuli-Responsive Behavior Based on an Amphiphilic Tripodal Gelator.

PubMed

Sutar, Papri; Maji, Tapas Kumar

2017-08-21

The recent upsurge in research on coordination polymer gels (CPGs) stems from their synthetic modularity, nanoscale processability, and versatile functionalities. Here we report self-assembly of an amphiphilic, tripodal low-molecular weight gelator (L) that consists of 4,4',4-[1,3,5-phenyl-tri(methoxy)]-tris-benzene core and 2,2':6',2″-terpyridyl termini, with different metal ions toward the formation of CPGs that show controllable nanomorphologies, tunable emission, and stimuli-responsive behaviors. L can also act as a selective chemosensor for Zn II with very low limit of detection (0.18 ppm) in aqueous medium. Coordination-driven self-assembly of L with Zn II in H 2 O/MeOH solvent mixture results in a coordination polymer hydrogel (ZnL) that exhibits sheet like morphology and charge-transfer emission. On the other hand, coordination of L with Tb III and Eu III in CHCl 3 /tetrahydrofuran solvent mixture results in green- and red-emissive CPGs, respectively, with nanotubular morphology. Moreover, precise stoichiometric control of L/Eu III /Tb III ratio leads to the formation of bimetallic CPGs that show emissions over a broad spectral range, including white-light-emission. We also explore the multistimuli responsive properties of the white-light-emitting CPG by exploiting the dynamics of Ln III -tpy coordination.

Turbulence Modeling: Progress and Future Outlook

NASA Technical Reports Server (NTRS)

Marvin, Joseph G.; Huang, George P.

1996-01-01

Progress in the development of the hierarchy of turbulence models for Reynolds-averaged Navier-Stokes codes used in aerodynamic applications is reviewed. Steady progress is demonstrated, but transfer of the modeling technology has not kept pace with the development and demands of the computational fluid dynamics (CFD) tools. An examination of the process of model development leads to recommendations for a mid-course correction involving close coordination between modelers, CFD developers, and application engineers. In instances where the old process is changed and cooperation enhanced, timely transfer is realized. A turbulence modeling information database is proposed to refine the process and open it to greater participation among modeling and CFD practitioners.

Radiation Belt Storm Probes: Resolving Fundamental Physics with Practical Consequences

NASA Technical Reports Server (NTRS)

Ukhorskiy, Aleksandr Y.; Mauk, Barry H.; Fox, Nicola J.; Sibeck, David G.; Grebowsky, Joseph M.

2011-01-01

The fundamental processes that energize, transport, and cause the loss of charged particles operate throughout the universe at locations as diverse as magnetized planets, the solar wind, our Sun, and other stars. The same processes operate within our immediate environment, the Earth's radiation belts. The Radiation Belt Storm Probes (RBSP) mission will provide coordinated two-spacecraft observations to obtain understanding of these fundamental processes controlling the dynamic variability of the near-Earth radiation environment. In this paper we discuss some of the profound mysteries of the radiation belt physics that will be addressed by RBSP and briefly describe the mission and its goals.

Coordinated dynamic encoding in the retina using opposing forms of plasticity

PubMed Central

Kastner, David B.; Baccus, Stephen A.

2011-01-01

The range of natural inputs encoded by a neuron often exceeds its dynamic range. To overcome this limitation, neural populations divide their inputs among different cell classes, as with rod and cone photoreceptors, and adapt by shifting their dynamic range. We report that the dynamic behavior of retinal ganglion cells in salamanders, mice, and rabbits is divided into two opposing forms of short-term plasticity in different cell classes. One population of cells exhibited sensitization—a persistent elevated sensitivity following a strong stimulus. This novel dynamic behavior compensates for the information loss caused by the known process of adaptation occurring in a separate cell population. The two populations divide the dynamic range of inputs, with sensitizing cells encoding weak signals, and adapting cells encoding strong signals. In the two populations, the linear, threshold and adaptive properties are linked to preserve responsiveness when stimulus statistics change, with one population maintaining the ability to respond when the other fails. PMID:21909086

A Vertically Lagrangian Finite-Volume Dynamical Core for Global Models

NASA Technical Reports Server (NTRS)

Lin, Shian-Jiann

2003-01-01

A finite-volume dynamical core with a terrain-following Lagrangian control-volume discretization is described. The vertically Lagrangian discretization reduces the dimensionality of the physical problem from three to two with the resulting dynamical system closely resembling that of the shallow water dynamical system. The 2D horizontal-to-Lagrangian-surface transport and dynamical processes are then discretized using the genuinely conservative flux-form semi-Lagrangian algorithm. Time marching is split- explicit, with large-time-step for scalar transport, and small fractional time step for the Lagrangian dynamics, which permits the accurate propagation of fast waves. A mass, momentum, and total energy conserving algorithm is developed for mapping the state variables periodically from the floating Lagrangian control-volume to an Eulerian terrain-following coordinate for dealing with physical parameterizations and to prevent severe distortion of the Lagrangian surfaces. Deterministic baroclinic wave growth tests and long-term integrations using the Held-Suarez forcing are presented. Impact of the monotonicity constraint is discussed.

Linking Individual and Collective Behavior in Adaptive Social Networks

NASA Astrophysics Data System (ADS)

Pinheiro, Flávio L.; Santos, Francisco C.; Pacheco, Jorge M.

2016-03-01

Adaptive social structures are known to promote the evolution of cooperation. However, up to now the characterization of the collective, population-wide dynamics resulting from the self-organization of individual strategies on a coevolving, adaptive network has remained unfeasible. Here we establish a (reversible) link between individual (micro)behavior and collective (macro)behavior for coevolutionary processes. We demonstrate that an adaptive network transforms a two-person social dilemma locally faced by individuals into a collective dynamics that resembles that associated with an N -person coordination game, whose characterization depends sensitively on the relative time scales between the entangled behavioral and network evolutions. In particular, we show that the faster the relative rate of adaptation of the network, the smaller the critical fraction of cooperators required for cooperation to prevail, thus establishing a direct link between network adaptation and the evolution of cooperation. The framework developed here is general and may be readily applied to other dynamical processes occurring on adaptive networks, notably, the spreading of contagious diseases or the diffusion of innovations.

Cell fate determination dynamics in bacteria

NASA Astrophysics Data System (ADS)

Kuchina, Anna; Espinar, Lorena; Cagatay, Tolga; Garcia-Ojalvo, Jordi; Suel, Gurol

2010-03-01

The fitness of an organism depends on many processes that serve the purpose to adapt to changing environment in a robust and coordinated fashion. One example of such process is cellular fate determination. In the presence of a variety of alternative responses each cell adopting a particular fate represents a ``choice'' that must be tightly regulated to ensure the best survival strategy for the population taking into account the broad range of possible environmental challenges. We investigated this problem in the model organism B.Subtilis which under stress conditions differentiates terminally into highly resistant spores or initiates an alternative transient state of competence. The dynamics underlying cell fate choice remains largely unknown. We utilize quantitative fluorescent microscopy to track the activities of genes involved in these responses on a single-cell level. We explored the importance of temporal interactions between competing cell fates by re- engineering the differentiation programs. I will discuss how the precise dynamics of cellular ``decision-making'' governed by the corresponding biological circuits may enable cells to adjust to diverse environments and determine survival.

Perceptual and Motor Performance of Combat-Sport Athletes Differs According to Specific Demands of the Discipline.

PubMed

Chen, Wei-Ying; Wu, Sheng K; Song, Tai-Fen; Chou, Kuei-Ming; Wang, Kuei-Yuan; Chang, Yao-Ching; Goodbourn, Patrick T

2016-12-07

The specific demands of a combat-sport discipline may be reflected in the perceptual-motor performance of its athletes. Taekwondo, which emphasizes kicking, might require faster perceptual processing to compensate for longer latencies to initiate lower-limb movements and to give rapid visual feedback for dynamic postural control, while Karate, which emphasizes both striking with the hands and kicking, might require exceptional eye-hand coordination and fast perceptual processing. In samples of 38 Taekwondo athletes (16 females, 22 males; mean age = 19.9 years, SD = 1.2), 24 Karate athletes (9 females, 15 males; mean age = 18.9 years, SD = 0.9), and 35 Nonathletes (20 females, 15 males; mean age = 20.6 years, SD = 1.5), we measured eye-hand coordination with the Finger-Nose-Finger task, and both perceptual-processing speed and attentional control with the Covert Orienting of Visual Attention (COVAT) task. Eye-hand coordination was significantly better for Karate athletes than for Taekwondo athletes and Nonathletes, but reaction times for the upper extremities in the COVAT task-indicative of perceptual-processing speed-were faster for Taekwondo athletes than for Karate athletes and Nonathletes. In addition, we found no significant difference among groups in attentional control, as indexed by the reaction-time cost of an invalid cue in the COVAT task. The results suggest that athletes in different combat sports exhibit distinct profiles of perceptual-motor performance. © The Author(s) 2016.

Perceptuo-motor compatibility governs multisensory integration in bimanual coordination dynamics.

PubMed

Zelic, Gregory; Mottet, Denis; Lagarde, Julien

2016-02-01

The brain has the remarkable ability to bind together inputs from different sensory origin into a coherent percept. Behavioral benefits can result from such ability, e.g., a person typically responds faster and more accurately to cross-modal stimuli than to unimodal stimuli. To date, it is, however, largely unknown whether such multisensory benefits, shown for discrete reactive behaviors, generalize to the continuous coordination of movements. The present study addressed multisensory integration from the perspective of bimanual coordination dynamics, where the perceptual activity no longer triggers a single response but continuously guides the motor action. The task consisted in coordinating anti-symmetrically the continuous flexion-extension of the index fingers, while synchronizing with an external pacer. Three different configurations of metronome were tested, for which we examined whether a cross-modal pacing (audio-tactile beats) improved the stability of the coordination in comparison with unimodal pacing condition (auditory or tactile beats). We found a more stable bimanual coordination for cross-modal pacing, but only when the metronome configuration directly matched the anti-symmetric coordination pattern. We conclude that multisensory integration can benefit the continuous coordination of movements; however, this is constrained by whether the perceptual and motor activities match in space and time.

Synchronization and coordination of sequences in two neural ensembles

NASA Astrophysics Data System (ADS)

Venaille, Antoine; Varona, Pablo; Rabinovich, Mikhail I.

2005-06-01

There are many types of neural networks involved in the sequential motor behavior of animals. For high species, the control and coordination of the network dynamics is a function of the higher levels of the central nervous system, in particular the cerebellum. However, in many cases, especially for invertebrates, such coordination is the result of direct synaptic connections between small circuits. We show here that even the chaotic sequential activity of small model networks can be coordinated by electrotonic synapses connecting one or several pairs of neurons that belong to two different networks. As an example, we analyzed the coordination and synchronization of the sequential activity of two statocyst model networks of the marine mollusk Clione. The statocysts are gravity sensory organs that play a key role in postural control of the animal and the generation of a complex hunting motor program. Each statocyst network was modeled by a small ensemble of neurons with Lotka-Volterra type dynamics and nonsymmetric inhibitory interactions. We studied how two such networks were synchronized by electrical coupling in the presence of an external signal which lead to winnerless competition among the neurons. We found that as a function of the number and the strength of connections between the two networks, it is possible to coordinate and synchronize the sequences that each network generates with its own chaotic dynamics. In spite of the chaoticity, the coordination of the signals is established through an activation sequence lock for those neurons that are active at a particular instant of time.

Gravisensing in single-celled systems - update on characean rhizoids and protonemata

NASA Astrophysics Data System (ADS)

Braun, M.; Limbach, C.

Single-celled and tip-growing rhizoids and protonemata of the characean algae have been intensively studied and there is considerable progress in the understanding of the molecular and cellular mechanisms underlying gravisensing and gravity-dependent growth. In higher plant statocytes, the role of actin in both processes is still a matter of intense debate, but there is clear evidence that actin coordinates both processes in characean rhizoids and protonemata. The multiple functions and dynamic nature of the actin cytoskeleton in these cells are based on the concerted action of a variety of actin-binding proteins. Profilin, actin-depolymerizing factor, a spectrin-like protein, villin and fimbrin have been detected which control apical actin polymerization and regulate the dynamic remodeling of the actin arrangement. An actomyosin-based system was shown to (i) mediate the transport of secretory vesicles to the growing tip, (ii) establish the incorporation of cell wall material and (iii) coordinate the tip-focussed distribution of calcium channels which establish the tip-high calcium gradient for local exocytosis. Experiments performed in microgravity have shown that the actomyosin system precisely coordinates the position of statoliths in rhizoids and protonemata and, upon a change in orientation, directs sedimenting statoliths to specific areas at the plasma membrane where physical contact with gravisensor molecules initiates growth reorientation. The upward growth response of protonemata was shown to be preceded by a statolith-induced and actin-dependent relocalization of the Ca2+-gradient to the upper flank that does not occur in positively gravitropic rhizoids, in which sedimented statoliths cause differential growth of the opposite subapical cell flank. Thus, constant actin polymerization in the growing tip and the spatiotemporal control of actin remodeling by numerous actin-binding proteins are essential for gravity sensing and polarized growth of characean rhizoids and protonemata.

Classification of octet AB-type binary compounds using dynamical charges: A materials informatics perspective

DOE PAGES

Pilania, G.; Gubernatis, J. E.; Lookman, T.

2015-12-03

The role of dynamical (or Born effective) charges in classification of octet AB-type binary compounds between four-fold (zincblende/wurtzite crystal structures) and six-fold (rocksalt crystal structure) coordinated systems is discussed. We show that the difference in the dynamical charges of the fourfold and sixfold coordinated structures, in combination with Harrison’s polarity, serves as an excellent feature to classify the coordination of 82 sp–bonded binary octet compounds. We use a support vector machine classifier to estimate the average classification accuracy and the associated variance in our model where a decision boundary is learned in a supervised manner. Lastly, we compare the out-of-samplemore » classification accuracy achieved by our feature pair with those reported previously.« less

Nonlinear normal vibration modes in the dynamics of nonlinear elastic systems

NASA Astrophysics Data System (ADS)

Mikhlin, Yu V.; Perepelkin, N. V.; Klimenko, A. A.; Harutyunyan, E.

2012-08-01

Nonlinear normal modes (NNMs) are a generalization of the linear normal vibrations. By the Kauderer-Rosenberg concept in the regime of the NNM all position coordinates are single-values functions of some selected position coordinate. By the Shaw-Pierre concept, the NNM is such a regime when all generalized coordinates and velocities are univalent functions of a couple of dominant (active) phase variables. The NNMs approach is used in some applied problems. In particular, the Kauderer-Rosenberg NNMs are analyzed in the dynamics of some pendulum systems. The NNMs of forced vibrations are investigated in a rotor system with an isotropic-elastic shaft. A combination of the Shaw-Pierre NNMs and the Rauscher method is used to construct the forced NNMs and the frequency responses in the rotor dynamics.

Large-deformation modal coordinates for nonrigid vehicle dynamics

NASA Technical Reports Server (NTRS)

Likins, P. W.; Fleischer, G. E.

1972-01-01

The derivation of minimum-dimension sets of discrete-coordinate and hybrid-coordinate equations of motion of a system consisting of an arbitrary number of hinge-connected rigid bodies assembled in tree topology is presented. These equations are useful for the simulation of dynamical systems that can be idealized as tree-like arrangements of substructures, with each substructure consisting of either a rigid body or a collection of elastically interconnected rigid bodies restricted to small relative rotations at each connection. Thus, some of the substructures represent elastic bodies subjected to small strains or local deformations, but possibly large gross deformations, in the hybrid formulation, distributed coordinates referred to herein as large-deformation modal coordinates, are used for the deformations of these substructures. The equations are in a form suitable for incorporation into one or more computer programs to be used as multipurpose tools in the simulation of spacecraft and other complex electromechanical systems.

Parsimonious description for predicting high-dimensional dynamics

PubMed Central

Hirata, Yoshito; Takeuchi, Tomoya; Horai, Shunsuke; Suzuki, Hideyuki; Aihara, Kazuyuki

2015-01-01

When we observe a system, we often cannot observe all its variables and may have some of its limited measurements. Under such a circumstance, delay coordinates, vectors made of successive measurements, are useful to reconstruct the states of the whole system. Although the method of delay coordinates is theoretically supported for high-dimensional dynamical systems, practically there is a limitation because the calculation for higher-dimensional delay coordinates becomes more expensive. Here, we propose a parsimonious description of virtually infinite-dimensional delay coordinates by evaluating their distances with exponentially decaying weights. This description enables us to predict the future values of the measurements faster because we can reuse the calculated distances, and more accurately because the description naturally reduces the bias of the classical delay coordinates toward the stable directions. We demonstrate the proposed method with toy models of the atmosphere and real datasets related to renewable energy. PMID:26510518

Real-time 3D measurement based on structured light illumination considering camera lens distortion

NASA Astrophysics Data System (ADS)

Feng, Shijie; Chen, Qian; Zuo, Chao; Sun, Jiasong; Yu, ShiLing

2014-12-01

Optical three-dimensional (3-D) profilometry is gaining increasing attention for its simplicity, flexibility, high accuracy, and non-contact nature. Recent advances in imaging sensors and digital projection technology further its progress in high-speed, real-time applications, enabling 3-D shapes reconstruction of moving objects and dynamic scenes. In traditional 3-D measurement system where the processing time is not a key factor, camera lens distortion correction is performed directly. However, for the time-critical high-speed applications, the time-consuming correction algorithm is inappropriate to be performed directly during the real-time process. To cope with this issue, here we present a novel high-speed real-time 3-D coordinates measuring technique based on fringe projection with the consideration of the camera lens distortion. A pixel mapping relation between a distorted image and a corrected one is pre-determined and stored in computer memory for real-time fringe correction. And a method of lookup table (LUT) is introduced as well for fast data processing. Our experimental results reveal that the measurement error of the in-plane coordinates has been reduced by one order of magnitude and the accuracy of the out-plane coordinate been tripled after the distortions being eliminated. Moreover, owing to the merit of the LUT, the 3-D reconstruction can be achieved at 92.34 frames per second.

Spatial interactions during bimanual coordination patterns: the effect of directional compatibility.

PubMed

Bogaerts, H; Swinnen, S P

2001-04-01

Whereas previous bimanual coordination research has predominantly focused on the constraining role of timing, the present study addressed the role of spatial (i.e., directional) constraints during the simultaneous production of equilateral triangles with both upper limbs. In addition to coordination modes in which mirror-image and isodirectional movements were performed (compatible patterns), new modes were tested in which the left limb lagged with respect to the right by one triangle side (non-compatible patterns). This resulted in the experimental manipulation of directional compatibility between the limbs. In addition, triangles with either horizontal or vertical orientations were to be drawn in order to assess the role of static images on movement production. Results supported the important role of directional constraints in bimanual coordination. Furthermore, triangles in vertical orientations (with a vertical symmetry axis, i.e., one apex pointing up) were drawn more successfully than those in horizontal orientations (with a horizontal symmetry axis, i.e., one apex pointing left or right), suggesting that the static aspects of a geometric form may affect movement dynamics. Finally, evidence suggested that cognitive processes related to integration of the submovements into a unified plan mediate the performance of new coordination patterns. The implications of the present finding for clinical populations are discussed

Heterobimetallic porphyrin complexes displaying triple dynamics: coupled metal motions controlled by constitutional evolution.

PubMed

Le Gac, Stéphane; Fusaro, Luca; Roisnel, Thierry; Boitrel, Bernard

2014-05-07

A bis-strap porphyrin ligand (1), with an overhanging carboxylic acid group on each side of the macrocycle, has been investigated toward the formation of dynamic libraries of bimetallic complexes with Hg(II), Cd(II), and Pb(II). Highly heteroselective metalation processes occurred in the presence of Pb(II), with Hg(II) or Cd(II) bound out-of-plane to the N-core and "PbOAc" bound to a carboxylate group of a strap on the opposite side. The resulting complexes, 1(Hg)·PbOAc and 1(Cd)·PbOAc, display three levels of dynamics. The first is strap-level (interactional dynamics), where the PbOAc moiety swings between the left and right side of the strap owing to a second sphere of coordination with lateral amide functions. The second is ligand-level (motional dynamics), where 1(Hg)·PbOAc and 1(Cd)·PbOAc exist as two degenerate states in equilibrium controlled by a chemical effector (AcO(-)). The process corresponds to a double translocation of the metal ions according to an intramolecular migration of Hg(II) or Cd(II) through the N-core, oscillating between the two equivalent overhanging carbonyl groups, coupled to an intermolecular pathway for PbOAc exchanging between the two equivalent overhanging carboxylate groups (N-core(up) ⇆ N-core(down) coupled to strap(down) ⇆ strap(up), i.e., coupled motion #1 in the abstract graphic). The third is library-level (constitutional dynamics), where a dynamic constitutional evolution of the system was achieved by the successive addition of two chemical effectors (DMAP and then AcO(-)). It allowed shifting equilibrium forward and backward between 1(Hg)·PbOAc and the corresponding homobimetallic complexes 1(Hg2)·DMAP and 1(Pb)·PbOAc. The latter displays a different ligand-level dynamics, in the form of an intraligand coupled migration of the Pb(II) ions (N-core(up) ⇆ strap(up) coupled to strap(down) ⇆ N-core(down), i.e., coupled motion #2 in the abstract graphic). In addition, the neutral "bridged" complexes 1HgPb and 1CdPb, with the metal ions on opposite sides both bound to the N-core and to a carboxylate of a strap, were structurally characterized. These results establish an unprecedented approach in supramolecular coordination chemistry, by considering the reversible interaction of a metal ion with the porphyrin N-core as a new source of self-organization processes. This work should provide new inspirations for the design of innovative adaptative materials and devices.

Conservation form of the equations of fluid dynamics in general nonsteady coordinates

NASA Astrophysics Data System (ADS)

Zhang, H.; Camarero, R.; Kahawita, R.

1985-11-01

Many of the differential equations arising in fluid dynamics may be stated in conservation-law form. A number of investigations have been conducted with the aim to derive the conservation-law form of the Navier-Stokes equations in general nonsteady coordinate systems. The present note has the objective to illustrate a mathematical methodology with which such forms of the equations may be derived in an easier and more general fashion. For numerical applications, the scalar form of the equations is eventually provided. Attention is given to the conservation form of equations in curvilinear coordinates and numerical considerations.

Constitutive models for static and dynamic response of geotechnical materials

NASA Astrophysics Data System (ADS)

Nemat-Nasser, S.

1983-11-01

The objective of this research program has been to develop realistic macroscopic constitutive relations which describe static and dynamic properties of geotechnical materials (soils and rocks). To this end a coordinated theoretical and experimental activity has been followed. The theoretical work includes a balanced combination of statistical microscopic (at the grain size level) modeling and a nonclassical elasto-plastic macroscopic formulation. The latter includes the effects of internal friction, plastic compressibility, and pressure sensitivity, as well as anisotropy which is commonly observed in geotechnical materials. The following specific goals have been sought: (1) to develop three-dimensional constitutive relations under ordinary or high pressures (such as those induced by blasting or tectonic forces which may cause a large amount of densification by relative motion and possible crushing of grains); and (2) to examine and characterize the behavior of saturated granular materials under dynamic loading. The latter item includes characterization of possible liquefaction and subsidence which may be induced in granular materials under confining pressure by ground vibration or passage of waves. The theoretical work has been carefully coordinated with key experiments in order to: (1) understand the basic physics of the process, both at macroscopic and microscopic levels; (2) to verify the corresponding theoretical predictions; and (3) to establish relevant material parameters.

Desolvation-Driven 100-Fold Slow-down of Tunneling Relaxation Rate in Co(II)-Dy(III) Single-Molecule Magnets through a Single-Crystal-to-Single-Crystal Process

NASA Astrophysics Data System (ADS)

Liu, Jun-Liang; Wu, Jie-Yi; Huang, Guo-Zhang; Chen, Yan-Cong; Jia, Jian-Hua; Ungur, Liviu; Chibotaru, Liviu F.; Chen, Xiao-Ming; Tong, Ming-Liang

2015-11-01

Single-molecule magnets (SMMs) are regarded as a class of promising materials for spintronic and ultrahigh-density storage devices. Tuning the magnetic dynamics of single-molecule magnets is a crucial challenge for chemists. Lanthanide ions are not only highly magnetically anisotropic but also highly sensitive to the changes in the coordination environments. We developed a feasible approach to understand parts of the magneto-structure correlations and propose to regulate the relaxation behaviors via rational design. A series of Co(II)-Dy(III)-Co(II) complexes were obtained using in situ synthesis; in this system of complexes, the relaxation dynamics can be greatly improved, accompanied with desolvation, via single-crystal to single-crystal transformation. The effective energy barrier can be increased from 293 cm-1 (422 K) to 416 cm-1 (600 K), and the tunneling relaxation time can be grown from 8.5 × 10-4 s to 7.4 × 10-2 s. These remarkable improvements are due to the change in the coordination environments of Dy(III) and Co(II). Ab initio calculations were performed to better understand the magnetic dynamics.

A coordination theory for intelligent machines

NASA Technical Reports Server (NTRS)

Wang, Fei-Yue; Saridis, George N.

1990-01-01

A formal model for the coordination level of intelligent machines is established. The framework of the coordination level investigated consists of one dispatcher and a number of coordinators. The model called coordination structure has been used to describe analytically the information structure and information flow for the coordination activities in the coordination level. Specifically, the coordination structure offers a formalism to (1) describe the task translation of the dispatcher and coordinators; (2) represent the individual process within the dispatcher and coordinators; (3) specify the cooperation and connection among the dispatcher and coordinators; (4) perform the process analysis and evaluation; and (5) provide a control and communication mechanism for the real-time monitor or simulation of the coordination process. A simple procedure for the task scheduling in the coordination structure is presented. The task translation is achieved by a stochastic learning algorithm. The learning process is measured with entropy and its convergence is guaranteed. Finally, a case study of the coordination structure with three coordinators and one dispatcher for a simple intelligent manipulator system illustrates the proposed model and the simulation of the task processes performed on the model verifies the soundness of the theory.

Quantum Computational Calculations of the Ionization Energies of Acidic and Basic Amino Acids: Aspartate, Glutamate, Arginine, Lysine, and Histidine

NASA Astrophysics Data System (ADS)

de Guzman, C. P.; Andrianarijaona, M.; Lee, Y. S.; Andrianarijaona, V.

An extensive knowledge of the ionization energies of amino acids can provide vital information on protein sequencing, structure, and function. Acidic and basic amino acids are unique because they have three ionizable groups: the C-terminus, the N-terminus, and the side chain. The effects of multiple ionizable groups can be seen in how Aspartate's ionizable side chain heavily influences its preferred conformation (J Phys Chem A. 2011 April 7; 115(13): 2900-2912). Theoretical and experimental data on the ionization energies of many of these molecules is sparse. Considering each atom of the amino acid as a potential departing site for the electron gives insight on how the three ionizable groups affect the ionization process of the molecule and the dynamic coupling between the vibrational modes. In the following study, we optimized the structure of each acidic and basic amino acid then exported the three dimensional coordinates of the amino acids. We used ORCA to calculate single point energies for a region near the optimized coordinates and systematically went through the x, y, and z coordinates of each atom in the neutral and ionized forms of the amino acid. With the calculations, we were able to graph energy potential curves to better understand the quantum dynamic properties of the amino acids. The authors thank Pacific Union College Student Association for providing funds.

Sumoylation Dynamics During Keratinocyte Differentiation

PubMed Central

Deyrieux, Adeline F.; Rosas-Acosta, Germán; Ozbun, Michelle A.; Wilson, Van G.

2012-01-01

Summary SUMO modification regulates the activity of numerous transcription factors that have a direct role in cell cycle progression, apoptosis, cellular proliferation, and development, but its role in differentiation processes is less clear. Keratinocyte differentiation requires the coordinated activation of a series of transcription factors, and as several critical keratinocyte transcription factors are known to be SUMO substrates, we investigated the role of sumoylation in keratinocyte differentiation. In a human keratinocyte cell line model (HaCaT cells), calcium-induced differentiation led to the transient and coordinated transcriptional activation of the genes encoding critical sumoylation system components, including SAE1, SAE2, Ubc9, SENP1, Miz-1 (PIASxβ), SUMO2, and SUMO3. The increased gene expression resulted in higher levels of the respective proteins and changes in the pattern of sumoylated substrate proteins during the differentiation process. Similar to the HaCaT results, stratified human foreskin keratinocytes showed an upregulation of Ubc9 in the suprabasal layers. Lastly, abrogation of sumoylation by Gam1 expression severely disrupted normal HaCaT differentiation, consistent with an important role for sumoylation in the proper progression of this biological process. PMID:17164289

Distinct dissociation kinetics between ion pairs: Solvent-coordinate free-energy landscape analysis.

PubMed

Yonetani, Yoshiteru

2015-07-28

Different ion pairs exhibit different dissociation kinetics; however, while the nature of this process is vital for understanding various molecular systems, the underlying mechanism remains unclear. In this study, to examine the origin of different kinetic rate constants for this process, molecular dynamics simulations were conducted for LiCl, NaCl, KCl, and CsCl in water. The results showed substantial differences in dissociation rate constant, following the trend kLiCl < kNaCl < kKCl < kCsCl. Analysis of the free-energy landscape with a solvent reaction coordinate and subsequent rate component analysis showed that the differences in these rate constants arose predominantly from the variation in solvent-state distribution between the ion pairs. The formation of a water-bridging configuration, in which the water molecule binds to an anion and a cation simultaneously, was identified as a key step in this process: water-bridge formation lowers the related dissociation free-energy barrier, thereby increasing the probability of ion-pair dissociation. Consequently, a higher probability of water-bridge formation leads to a higher ion-pair dissociation rate.

Dynamic model updating based on strain mode shape and natural frequency using hybrid pattern search technique

NASA Astrophysics Data System (ADS)

Guo, Ning; Yang, Zhichun; Wang, Le; Ouyang, Yan; Zhang, Xinping

2018-05-01

Aiming at providing a precise dynamic structural finite element (FE) model for dynamic strength evaluation in addition to dynamic analysis. A dynamic FE model updating method is presented to correct the uncertain parameters of the FE model of a structure using strain mode shapes and natural frequencies. The strain mode shape, which is sensitive to local changes in structure, is used instead of the displacement mode for enhancing model updating. The coordinate strain modal assurance criterion is developed to evaluate the correlation level at each coordinate over the experimental and the analytical strain mode shapes. Moreover, the natural frequencies which provide the global information of the structure are used to guarantee the accuracy of modal properties of the global model. Then, the weighted summation of the natural frequency residual and the coordinate strain modal assurance criterion residual is used as the objective function in the proposed dynamic FE model updating procedure. The hybrid genetic/pattern-search optimization algorithm is adopted to perform the dynamic FE model updating procedure. Numerical simulation and model updating experiment for a clamped-clamped beam are performed to validate the feasibility and effectiveness of the present method. The results show that the proposed method can be used to update the uncertain parameters with good robustness. And the updated dynamic FE model of the beam structure, which can correctly predict both the natural frequencies and the local dynamic strains, is reliable for the following dynamic analysis and dynamic strength evaluation.

Estrogen-Related Receptor α (ERRα) and ERRγ Are Essential Coordinators of Cardiac Metabolism and Function

PubMed Central

Wang, Ting; McDonald, Caitlin; Petrenko, Nataliya B.; Leblanc, Mathias; Wang, Tao; Giguere, Vincent; Evans, Ronald M.; Patel, Vickas V.

2015-01-01

Almost all cellular functions are powered by a continuous energy supply derived from cellular metabolism. However, it is little understood how cellular energy production is coordinated with diverse energy-consuming cellular functions. Here, using the cardiac muscle system, we demonstrate that nuclear receptors estrogen-related receptor α (ERRα) and ERRγ are essential transcriptional coordinators of cardiac energy production and consumption. On the one hand, ERRα and ERRγ together are vital for intact cardiomyocyte metabolism by directly controlling expression of genes important for mitochondrial functions and dynamics. On the other hand, ERRα and ERRγ influence major cardiomyocyte energy consumption functions through direct transcriptional regulation of key contraction, calcium homeostasis, and conduction genes. Mice lacking both ERRα and cardiac ERRγ develop severe bradycardia, lethal cardiomyopathy, and heart failure featuring metabolic, contractile, and conduction dysfunctions. These results illustrate that the ERR transcriptional pathway is essential to couple cellular energy metabolism with energy consumption processes in order to maintain normal cardiac function. PMID:25624346

Actin–microtubule coordination at growing microtubule ends

PubMed Central

López, Magdalena Preciado; Huber, Florian; Grigoriev, Ilya; Steinmetz, Michel O.; Akhmanova, Anna; Koenderink, Gijsje H.; Dogterom, Marileen

2014-01-01

To power dynamic processes in cells, the actin and microtubule cytoskeletons organize into complex structures. Although it is known that cytoskeletal coordination is vital for cell function, the mechanisms by which cross-linking proteins coordinate actin and microtubule activities remain poorly understood. In particular, it is unknown how the distinct mechanical properties of different actin architectures modulate the outcome of actin–microtubule interactions. To address this question, we engineered the protein TipAct, which links growing microtubule ends via end-binding proteins to actin filaments. We show that growing microtubules can be captured and guided by stiff actin bundles, leading to global actin–microtubule alignment. Conversely, growing microtubule ends can transport, stretch and bundle individual actin filaments, thereby globally defining actin filament organization. Our results provide a physical basis to understand actin–microtubule cross-talk, and reveal that a simple cross-linker can enable a mechanical feedback between actin and microtubule organization that is relevant to diverse biological contexts. PMID:25159196

Fanconi anemia FANCD2 and FANCI proteins regulate the nuclear dynamics of splicing factors.

PubMed

Moriel-Carretero, María; Ovejero, Sara; Gérus-Durand, Marie; Vryzas, Dimos; Constantinou, Angelos

2017-12-04

Proteins disabled in the cancer-prone disorder Fanconi anemia (FA) ensure the maintenance of chromosomal stability during DNA replication. FA proteins regulate replication dynamics, coordinate replication-coupled repair of interstrand DNA cross-links, and mitigate conflicts between replication and transcription. Here we show that FANCI and FANCD2 associate with splicing factor 3B1 (SF3B1), a key spliceosomal protein of the U2 small nuclear ribonucleoprotein (U2 snRNP). FANCI is in close proximity to SF3B1 in the nucleoplasm of interphase and mitotic cells. Furthermore, we find that DNA replication stress induces the release of SF3B1 from nuclear speckles in a manner that depends on FANCI and on the activity of the checkpoint kinase ATR. In chromatin, both FANCD2 and FANCI associate with SF3B1, prevent accumulation of postcatalytic intron lariats, and contribute to the timely eviction of splicing factors. We propose that FANCD2 and FANCI contribute to the organization of functional domains in chromatin, ensuring the coordination of DNA replication and cotranscriptional processes. © 2017 Moriel-Carretero et al.

Chromatin-associated degradation is defined by UBXN-3/FAF1 to safeguard DNA replication fork progression.

PubMed

Franz, André; Pirson, Paul A; Pilger, Domenic; Halder, Swagata; Achuthankutty, Divya; Kashkar, Hamid; Ramadan, Kristijan; Hoppe, Thorsten

2016-02-04

The coordinated activity of DNA replication factors is a highly dynamic process that involves ubiquitin-dependent regulation. In this context, the ubiquitin-directed ATPase CDC-48/p97 recently emerged as a key regulator of chromatin-associated degradation in several of the DNA metabolic pathways that assure genome integrity. However, the spatiotemporal control of distinct CDC-48/p97 substrates in the chromatin environment remained unclear. Here, we report that progression of the DNA replication fork is coordinated by UBXN-3/FAF1. UBXN-3/FAF1 binds to the licensing factor CDT-1 and additional ubiquitylated proteins, thus promoting CDC-48/p97-dependent turnover and disassembly of DNA replication factor complexes. Consequently, inactivation of UBXN-3/FAF1 stabilizes CDT-1 and CDC-45/GINS on chromatin, causing severe defects in replication fork dynamics accompanied by pronounced replication stress and eventually resulting in genome instability. Our work identifies a critical substrate selection module of CDC-48/p97 required for chromatin-associated protein degradation in both Caenorhabditis elegans and humans, which is relevant to oncogenesis and aging.

Symmetry Breaking in Space-Time Hierarchies Shapes Brain Dynamics and Behavior.

PubMed

Pillai, Ajay S; Jirsa, Viktor K

2017-06-07

In order to maintain brain function, neural activity needs to be tightly coordinated within the brain network. How this coordination is achieved and related to behavior is largely unknown. It has been previously argued that the study of the link between brain and behavior is impossible without a guiding vision. Here we propose behavioral-level concepts and mechanisms embodied as structured flows on manifold (SFM) that provide a formal description of behavior as a low-dimensional process emerging from a network's dynamics dependent on the symmetry and invariance properties of the network connectivity. Specifically, we demonstrate that the symmetry breaking of network connectivity constitutes a timescale hierarchy resulting in the emergence of an attractive functional subspace. We show that behavior emerges when appropriate conditions imposed upon the couplings are satisfied, justifying the conductance-based nature of synaptic couplings. Our concepts propose design principles for networks predicting how behavior and task rules are represented in real neural circuits and open new avenues for the analyses of neural data. Copyright © 2017 Elsevier Inc. All rights reserved.

Light exposure at night disrupts host/cancer circadian regulatory dynamics: impact on the Warburg effect, lipid signaling and tumor growth prevention.

PubMed

Blask, David E; Dauchy, Robert T; Dauchy, Erin M; Mao, Lulu; Hill, Steven M; Greene, Michael W; Belancio, Victoria P; Sauer, Leonard A; Davidson, Leslie

2014-01-01

The central circadian clock within the suprachiasmatic nucleus (SCN) plays an important role in temporally organizing and coordinating many of the processes governing cancer cell proliferation and tumor growth in synchrony with the daily light/dark cycle which may contribute to endogenous cancer prevention. Bioenergetic substrates and molecular intermediates required for building tumor biomass each day are derived from both aerobic glycolysis (Warburg effect) and lipid metabolism. Using tissue-isolated human breast cancer xenografts grown in nude rats, we determined that circulating systemic factors in the host and the Warburg effect, linoleic acid uptake/metabolism and growth signaling activities in the tumor are dynamically regulated, coordinated and integrated within circadian time structure over a 24-hour light/dark cycle by SCN-driven nocturnal pineal production of the anticancer hormone melatonin. Dim light at night (LAN)-induced melatonin suppression disrupts this circadian-regulated host/cancer balance among several important cancer preventative signaling mechanisms, leading to hyperglycemia and hyperinsulinemia in the host and runaway aerobic glycolysis, lipid signaling and proliferative activity in the tumor.

Chromatin-associated degradation is defined by UBXN-3/FAF1 to safeguard DNA replication fork progression

PubMed Central

Franz, André; Pirson, Paul A.; Pilger, Domenic; Halder, Swagata; Achuthankutty, Divya; Kashkar, Hamid; Ramadan, Kristijan; Hoppe, Thorsten

2016-01-01

The coordinated activity of DNA replication factors is a highly dynamic process that involves ubiquitin-dependent regulation. In this context, the ubiquitin-directed ATPase CDC-48/p97 recently emerged as a key regulator of chromatin-associated degradation in several of the DNA metabolic pathways that assure genome integrity. However, the spatiotemporal control of distinct CDC-48/p97 substrates in the chromatin environment remained unclear. Here, we report that progression of the DNA replication fork is coordinated by UBXN-3/FAF1. UBXN-3/FAF1 binds to the licensing factor CDT-1 and additional ubiquitylated proteins, thus promoting CDC-48/p97-dependent turnover and disassembly of DNA replication factor complexes. Consequently, inactivation of UBXN-3/FAF1 stabilizes CDT-1 and CDC-45/GINS on chromatin, causing severe defects in replication fork dynamics accompanied by pronounced replication stress and eventually resulting in genome instability. Our work identifies a critical substrate selection module of CDC-48/p97 required for chromatin-associated protein degradation in both Caenorhabditis elegans and humans, which is relevant to oncogenesis and aging. PMID:26842564

Structure and lifetimes in ionic liquids and their mixtures.

PubMed

Gehrke, Sascha; von Domaros, Michael; Clark, Ryan; Hollóczki, Oldamur; Brehm, Martin; Welton, Tom; Luzar, Alenka; Kirchner, Barbara

2018-01-01

With the aid of molecular dynamics simulations, we study the structure and dynamics of different ionic liquid systems, with focus on hydrogen bond, ion pair and ion cage formation. To do so, we report radial distribution functions, their number integrals, and various time-correlation functions, from which we extract well-defined lifetimes by means of the reactive flux formalism. We explore the influence of polarizable force fields vs. non-polarizable ones with downscaled charges (±0.8) for the example of 1-butyl-3-methylimidazolium bromide. Furthermore, we use 1-butyl-3-methylimidazolium trifluoromethanesulfonate to investigate the impact of temperature and mixing with water as well as with the chloride ionic liquid. Smaller coordination numbers, larger distances, and tremendously accelerated dynamics are observed when the polarizable force field is applied. The same trends are found with increasing temperature. Adding water decreases the ion-ion coordination numbers whereas the water-ion and water-water coordination is enhanced. A domain analysis reveals that the nonpolar parts of the ions are dispersed and when more water is added the water clusters increase in size. The dynamics accelerate in general upon addition of water. In the ionic liquid mixture, the coordination number around the cation changes between the two anions, but the number integrals of the cation around the anions remain constant and the dynamics slow down with increasing content of the chloride ionic liquid.

Video game-based coordinative training improves ataxia in children with degenerative ataxia.

PubMed

Ilg, Winfried; Schatton, Cornelia; Schicks, Julia; Giese, Martin A; Schöls, Ludger; Synofzik, Matthis

2012-11-13

Degenerative ataxias in children present a rare condition where effective treatments are lacking. Intensive coordinative training based on physiotherapeutic exercises improves degenerative ataxia in adults, but such exercises have drawbacks for children, often including a lack of motivation for high-frequent physiotherapy. Recently developed whole-body controlled video game technology might present a novel treatment strategy for highly interactive and motivational coordinative training for children with degenerative ataxias. We examined the effectiveness of an 8-week coordinative training for 10 children with progressive spinocerebellar ataxia. Training was based on 3 Microsoft Xbox Kinect video games particularly suitable to exercise whole-body coordination and dynamic balance. Training was started with a laboratory-based 2-week training phase and followed by 6 weeks training in children's home environment. Rater-blinded assessments were performed 2 weeks before laboratory-based training, immediately prior to and after the laboratory-based training period, as well as after home training. These assessments allowed for an intraindividual control design, where performance changes with and without training were compared. Ataxia symptoms were significantly reduced (decrease in Scale for the Assessment and Rating of Ataxia score, p = 0.0078) and balance capacities improved (dynamic gait index, p = 0.04) after intervention. Quantitative movement analysis revealed improvements in gait (lateral sway: p = 0.01; step length variability: p = 0.01) and in goal-directed leg placement (p = 0.03). Despite progressive cerebellar degeneration, children are able to improve motor performance by intensive coordination training. Directed training of whole-body controlled video games might present a highly motivational, cost-efficient, and home-based rehabilitation strategy to train dynamic balance and interaction with dynamic environments in a large variety of young-onset neurologic conditions. This study provides Class III evidence that directed training with Xbox Kinect video games can improve several signs of ataxia in adolescents with progressive ataxia as measured by SARA score, Dynamic Gait Index, and Activity-specific Balance Confidence Scale at 8 weeks of training.

Additional helmet and pack loading reduce situational awareness during the establishment of marksmanship posture.

PubMed

Lim, Jongil; Palmer, Christopher J; Busa, Michael A; Amado, Avelino; Rosado, Luis D; Ducharme, Scott W; Simon, Darnell; Van Emmerik, Richard E A

2017-06-01

The pickup of visual information is critical for controlling movement and maintaining situational awareness in dangerous situations. Altered coordination while wearing protective equipment may impact the likelihood of injury or death. This investigation examined the consequences of load magnitude and distribution on situational awareness, segmental coordination and head gaze in several protective equipment ensembles. Twelve soldiers stepped down onto force plates and were instructed to quickly and accurately identify visual information while establishing marksmanship posture in protective equipment. Time to discriminate visual information was extended when additional pack and helmet loads were added, with the small increase in helmet load having the largest effect. Greater head-leading and in-phase trunk-head coordination were found with lighter pack loads, while trunk-leading coordination increased and head gaze dynamics were more disrupted in heavier pack loads. Additional armour load in the vest had no consequences for Time to discriminate, coordination or head dynamics. This suggests that the addition of head borne load be carefully considered when integrating new technology and that up-armouring does not necessarily have negative consequences for marksmanship performance. Practitioner Summary: Understanding the trade-space between protection and reductions in task performance continue to challenge those developing personal protective equipment. These methods provide an approach that can help optimise equipment design and loading techniques by quantifying changes in task performance and the emergent coordination dynamics that underlie that performance.

Brain Responses to Dynamic Facial Expressions: A Normative Meta-Analysis.

PubMed

Zinchenko, Oksana; Yaple, Zachary A; Arsalidou, Marie

2018-01-01

Identifying facial expressions is crucial for social interactions. Functional neuroimaging studies show that a set of brain areas, such as the fusiform gyrus and amygdala, become active when viewing emotional facial expressions. The majority of functional magnetic resonance imaging (fMRI) studies investigating face perception typically employ static images of faces. However, studies that use dynamic facial expressions (e.g., videos) are accumulating and suggest that a dynamic presentation may be more sensitive and ecologically valid for investigating faces. By using quantitative fMRI meta-analysis the present study examined concordance of brain regions associated with viewing dynamic facial expressions. We analyzed data from 216 participants that participated in 14 studies, which reported coordinates for 28 experiments. Our analysis revealed bilateral fusiform and middle temporal gyri, left amygdala, left declive of the cerebellum and the right inferior frontal gyrus. These regions are discussed in terms of their relation to models of face processing.

The Equations of Oceanic Motions

NASA Astrophysics Data System (ADS)

Müller, Peter

2006-10-01

Modeling and prediction of oceanographic phenomena and climate is based on the integration of dynamic equations. The Equations of Oceanic Motions derives and systematically classifies the most common dynamic equations used in physical oceanography, from large scale thermohaline circulations to those governing small scale motions and turbulence. After establishing the basic dynamical equations that describe all oceanic motions, M|ller then derives approximate equations, emphasizing the assumptions made and physical processes eliminated. He distinguishes between geometric, thermodynamic and dynamic approximations and between the acoustic, gravity, vortical and temperature-salinity modes of motion. Basic concepts and formulae of equilibrium thermodynamics, vector and tensor calculus, curvilinear coordinate systems, and the kinematics of fluid motion and wave propagation are covered in appendices. Providing the basic theoretical background for graduate students and researchers of physical oceanography and climate science, this book will serve as both a comprehensive text and an essential reference.

Computational fluid dynamics for propulsion technology: Geometric grid visualization in CFD-based propulsion technology research

NASA Technical Reports Server (NTRS)

Ziebarth, John P.; Meyer, Doug

1992-01-01

The coordination is examined of necessary resources, facilities, and special personnel to provide technical integration activities in the area of computational fluid dynamics applied to propulsion technology. Involved is the coordination of CFD activities between government, industry, and universities. Current geometry modeling, grid generation, and graphical methods are established to use in the analysis of CFD design methodologies.

Can human activities alter the drowning fate of barrier islands?

NASA Astrophysics Data System (ADS)

Lorenzo-Trueba, J.; Ashton, A. D.; Jin, D.; Hoagland, P.; Kite-Powell, H.

2012-12-01

Low-lying coastal barriers face an uncertain future over the coming century and beyond as sea levels rise, with many projections suggesting end-of-century rates of sea-level rise as high or higher than 1 cm/yr. Geologically, such rates of sea-level rise have been experienced several thousand years ago and we can use our understanding of geological processes and sedimentary evidence to help unravel the dynamics of natural barriers experiencing sea-level rise. Along many modern coastal barriers, however, anthropic change, such as beach nourishment, dune construction, and emplacement of hard structures, plays a dominant role in coastline dynamics. A fundamental question to be addressed is whether human activities intended to preserve infrastructure and beach recreation may make wholesale collapse, or 'drowning,' of barrier systems more likely. Here we present a numerical modeling tool that couples natural processes and the human responses to these changes (and the subsequent of human responses on natural processes). Recent theoretical model development suggests that barriers are intrinsically morphodynamic features, responding to sea-level rise in complex ways through the interactions of marine processes and barrier overwash. Undeveloped coastal barriers would therefore respond to an accelerated sea-level rise in complex, less predictable manners than suggested by existing long-term models. We have developed a model that examines non-equilibrium cross-shore evolution of barrier systems at decadal to centennial temporal scales, focusing on the interactions between processes of shoreface evolution and overwash deposition. Model responses demonstrate two means of barrier collapse during sea-level rise: 'height drowning', which occurs when overwash fluxes are insufficient to maintain the landward migration rate required to keep in pace with sea-level rise, and 'width drowning', which occurs when the shoreface response is insufficient to maintain the barrier geometry during landward migration. The model also demonstrates the potential for discontinuous shoreline retreat, with alternating periods of barrier stability and rapid migration, even for constant rates of sea-level rise. Anthropic activities can strongly interact with these behaviors. In particular, considering only cross-shore processes, beach nourishment activities widen the beach and can affect shoreface fluxes, and dune building, which curtails the overwash process, can potentially enhance barrier drowning by reducing overwash fluxes. Furthermore, coastal protection activities of adjacent communities or even individual property holders can be uncoordinated or coordinated, with their effects coupled along the coast through coastal reorientation and gradients in alongshore sediment transport. In the coordinated framework, owners act in concert to alter the barrier based upon community benefits, whereas in the non-coordinated framework owners alter only their own property. Another important role in management is the perception of future sea-level-rise-associated losses—communities manage their coast differently depending on their adopted forecast for sea-level rise. We find that coordinated behavior coupled with natural processes can substantially affect the drowning scenarios from the individual decision-making process.

Bacterial Serine/Threonine Protein Kinases in Host-Pathogen Interactions*

PubMed Central

Canova, Marc J.; Molle, Virginie

2014-01-01

In bacterial pathogenesis, monitoring and adapting to the dynamically changing environment in the host and an ability to disrupt host immune responses are critical. The virulence determinants of pathogenic bacteria include the sensor/signaling proteins of the serine/threonine protein kinase (STPK) family that have a dual role of sensing the environment and subverting specific host defense processes. STPKs can sense a wide range of signals and coordinate multiple cellular processes to mount an appropriate response. Here, we review some of the well studied bacterial STPKs that are essential virulence factors and that modify global host responses during infection. PMID:24554701

Bacterial serine/threonine protein kinases in host-pathogen interactions.

PubMed

Canova, Marc J; Molle, Virginie

2014-04-04

In bacterial pathogenesis, monitoring and adapting to the dynamically changing environment in the host and an ability to disrupt host immune responses are critical. The virulence determinants of pathogenic bacteria include the sensor/signaling proteins of the serine/threonine protein kinase (STPK) family that have a dual role of sensing the environment and subverting specific host defense processes. STPKs can sense a wide range of signals and coordinate multiple cellular processes to mount an appropriate response. Here, we review some of the well studied bacterial STPKs that are essential virulence factors and that modify global host responses during infection.

The mechanism of water/ion exchange at a protein surface: a weakly bound chloride in Helicobacter pylori apoflavodoxin.

PubMed

Galano-Frutos, Juan J; Morón, M Carmen; Sancho, Javier

2015-11-21

Binding/unbinding of small ligands, such as ions, to/from proteins influences biochemical processes such as protein folding, enzyme catalysis or protein/ligand recognition. We have investigated the mechanism of chloride/water exchange at a protein surface (that of the apoflavodoxin from Helicobacter pylori) using classical all-atom molecular dynamics simulations. They reveal a variety of chloride exit routes and residence times; the latter is related to specific coordination modes of the anion. The role of solvent molecules in the mechanism of chloride unbinding has been studied in detail. We see no temporary increase in chloride coordination along the release process. Instead, the coordination of new water molecules takes place in most cases after the chloride/protein atom release event has begun. Moreover, the distribution function of water entrance events into the first chloride solvation shell peaks after chloride protein atom dissociation events. All these observations together seem to indicate that water molecules simply fill the vacancies left by the previously coordinating protein residues. We thus propose a step-by-step dissociation pathway in which protein/chloride interactions gradually break down before new water molecules progressively fill the vacant positions left by protein atoms. As observed for other systems, water molecules associated with bound chloride or with protein atoms have longer residence times than those bound to the free anion. The implications of the exchange mechanism proposed for the binding of the FMN (Flavin Mononucleotide) protein cofactor are discussed.

Early-Time Excited-State Relaxation Dynamics of Iridium Compounds: Distinct Roles of Electron and Hole Transfer.

PubMed

Liu, Xiang-Yang; Zhang, Ya-Hui; Fang, Wei-Hai; Cui, Ganglong

2018-06-28

Excited-state and photophysical properties of Ir-containing complexes have been extensively studied because of their potential applications as organic light-emitting diode emitting materials. However, their early time excited-state relaxation dynamics are less explored computationally. Herein we have employed our recently implemented TDDFT-based generalized surface-hopping dynamics method to simulate excited-state relaxation dynamics of three Ir(III) compounds having distinct ligands. According to our multistate dynamics simulations including five excited singlet states i.e., S n ( n = 1-5) and ten excited triplet states, i.e., T n ( n = 1-10), we have found that the intersystem crossing (ISC) processes from the S n to T n are very efficient and ultrafast in these three Ir(III) compounds. The corresponding ISC rates are estimated to be 65, 81, and 140 fs, which are reasonably close to the experimentally measured ca. 80, 80, and 110 fs. In addition, the internal conversion (IC) processes within respective singlet and triplet manifolds are also ultrafast. These ultrafast IC and ISC processes are caused by large nonadiabatic and spin-orbit couplings, respectively, as well as small energy gaps. Importantly, although these Ir(III) complexes share similar macroscopic phenomena, i.e., ultrafast IC and ISC, their microscopic excited-state relaxation mechanism and dynamics are qualitatively distinct. Specifically, the dynamical behaviors of electron and hole and their roles are variational in modulating the excited-state relaxation dynamics of these Ir(III) compounds. In other words, the electronic properties of the ligands that are coordinated with the central Ir(III) atom play important roles in regulating the microscopic excited-state relaxation dynamics. These gained insights could be useful for rationally designing Ir(III) compounds with excellent photoluminescence.

Separation dynamics of the COMET FreeFlyer and an upper stage STAR-48V motor

NASA Technical Reports Server (NTRS)

Fuller, Kevin M.; Myers, Carter H.

1993-01-01

In this report, the orbital separation between a STAR-48V upperstage motor and the COMET FreeFlyer is investigated. The time from nominal STAR-48 engine burnout is to be determined such that the STAR-48 will not collide with the FreeFlyer once the separation process has been initiated. To analyze this separation, the forces acting upon both the FreeFlyer and the STAR-48 are described in a body fixed coordinate system. These coordinates are then transformed into an Euler coordinate system and then further transformed into a relative inertial coordinate system. From this analysis and some basic assumptions about the Star-48/FreeFlyer vehicle, it can be concluded that the STAR-48 will not collide with the Free Flyer if the separation occurs at 120 seconds after nominal burnout of the STAR-48. In fact, the separation delay could be a shorter period of time, but it is recommended that this separation delay be as long as possible for risk mitigation. This delay is currently designed to be 120 seconds and the analysis presented in this report shows that this time is acceptable.

A developmental and clinical perspective of rhythmic interpersonal coordination: From mimicry toward the interconnection of minds.

PubMed

Xavier, Jean; Magnat, Julien; Sherman, Alain; Gauthier, Soizic; Cohen, David; Chaby, Laurence

2016-11-01

Imitation plays a critical role in the development of intersubjectivity and serves as a prerequisite for understanding the emotions and intentions of others. In our review, we consider spontaneous motor imitation between children and their peers as a developmental process involving repetition and perspective-taking as well as flexibility and reciprocity. During childhood, this playful dynamic challenges developing visuospatial abilities and requires temporal coordination between partners. As such, we address synchrony as form of communication and social signal per se, that leads, from an experience of similarity, to the interconnection of minds. In this way, we argue that, from a developmental perspective, rhythmic interpersonal coordination through childhood imitative interactions serves as a precursor to higher- level social and cognitive abilities, such as theory of mind (TOM) and empathy. Finally, to clinically illustrate our idea, we focus on developmental coordination disorder (DCD), a condition characterized not only by learning difficulties, but also childhood deficits in motor imitation. We address the challenges faced by these children on an emotional and socio-interactional level through the perspective of their impairments in intra- and interpersonal synchrony. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Cdc42 guanine nucleotide exchange factor FGD6 coordinates cell polarity and endosomal membrane recycling in osteoclasts.

PubMed

Steenblock, Charlotte; Heckel, Tobias; Czupalla, Cornelia; Espírito Santo, Ana Isabel; Niehage, Christian; Sztacho, Martin; Hoflack, Bernard

2014-06-27

The initial step of bone digestion is the adhesion of osteoclasts onto bone surfaces and the assembly of podosomal belts that segregate the bone-facing ruffled membrane from other membrane domains. During bone digestion, membrane components of the ruffled border also need to be recycled after macropinocytosis of digested bone materials. How osteoclast polarity and membrane recycling are coordinated remains unknown. Here, we show that the Cdc42-guanine nucleotide exchange factor FGD6 coordinates these events through its Src-dependent interaction with different actin-based protein networks. At the plasma membrane, FGD6 couples cell adhesion and actin dynamics by regulating podosome formation through the assembly of complexes comprising the Cdc42-interactor IQGAP1, the Rho GTPase-activating protein ARHGAP10, and the integrin interactors Talin-1/2 or Filamin A. On endosomes and transcytotic vesicles, FGD6 regulates retromer-dependent membrane recycling through its interaction with the actin nucleation-promoting factor WASH. These results provide a mechanism by which a single Cdc42-exchange factor controlling different actin-based processes coordinates cell adhesion, cell polarity, and membrane recycling during bone degradation. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

A Lagrangian cylindrical coordinate system for characterizing dynamic surface geometry of tubular anatomic structures.

PubMed

Lundh, Torbjörn; Suh, Ga-Young; DiGiacomo, Phillip; Cheng, Christopher

2018-03-03

Vascular morphology characterization is useful for disease diagnosis, risk stratification, treatment planning, and prediction of treatment durability. To quantify the dynamic surface geometry of tubular-shaped anatomic structures, we propose a simple, rigorous Lagrangian cylindrical coordinate system to monitor well-defined surface points. Specifically, the proposed system enables quantification of surface curvature and cross-sectional eccentricity. Using idealized software phantom examples, we validate the method's ability to accurately quantify longitudinal and circumferential surface curvature, as well as eccentricity and orientation of eccentricity. We then apply the method to several medical imaging data sets of human vascular structures to exemplify the utility of this coordinate system for analyzing morphology and dynamic geometric changes in blood vessels throughout the body. Graphical abstract Pointwise longitudinal curvature of a thoracic aortic endograft surface for systole and diastole, with their absolute difference.

Adaptive, fast walking in a biped robot under neuronal control and learning.

PubMed

Manoonpong, Poramate; Geng, Tao; Kulvicius, Tomas; Porr, Bernd; Wörgötter, Florentin

2007-07-01

Human walking is a dynamic, partly self-stabilizing process relying on the interaction of the biomechanical design with its neuronal control. The coordination of this process is a very difficult problem, and it has been suggested that it involves a hierarchy of levels, where the lower ones, e.g., interactions between muscles and the spinal cord, are largely autonomous, and where higher level control (e.g., cortical) arises only pointwise, as needed. This requires an architecture of several nested, sensori-motor loops where the walking process provides feedback signals to the walker's sensory systems, which can be used to coordinate its movements. To complicate the situation, at a maximal walking speed of more than four leg-lengths per second, the cycle period available to coordinate all these loops is rather short. In this study we present a planar biped robot, which uses the design principle of nested loops to combine the self-stabilizing properties of its biomechanical design with several levels of neuronal control. Specifically, we show how to adapt control by including online learning mechanisms based on simulated synaptic plasticity. This robot can walk with a high speed (>3.0 leg length/s), self-adapting to minor disturbances, and reacting in a robust way to abruptly induced gait changes. At the same time, it can learn walking on different terrains, requiring only few learning experiences. This study shows that the tight coupling of physical with neuronal control, guided by sensory feedback from the walking pattern itself, combined with synaptic learning may be a way forward to better understand and solve coordination problems in other complex motor tasks.

Wheels within Wheels: Hamiltonian Dynamics as a Hierarchy of Action Variables

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perkins, Rory J.; Bellan, Paul M.

2010-09-17

In systems where one coordinate undergoes periodic oscillation, the net displacement in any other coordinate over a single period is shown to be given by differentiation of the action integral associated with the oscillating coordinate. This result is then used to demonstrate that the action integral acts as a Hamiltonian for slow coordinates providing time is scaled to the 'tick time' of the oscillating coordinate. Numerous examples, including charged particle drifts and relativistic motion, are supplied to illustrate the varied application of these results.

The coupling effects of kinematics and flexibility on the Lagrangian dynamic formulation of open chain deformable links

NASA Technical Reports Server (NTRS)

Changizi, Koorosh

1989-01-01

A nonlinear Lagrangian formulation for the spatial kinematic and dynamic analysis of open chain deformable links consisting of cylindrical joints that connect pairs of flexible links is developed. The special cases of revolute or prismatic joint can also be obtained from the kinematic equations. The kinematic equations are described using a 4x4 matrix method. The configuration of each deformable link in the open loop kinematic chain is identified using a coupled set of relative joint variables, constant geometric parameters, and elastic coordinates. The elastic coordinates define the link deformation with respect to a selected joint coordinate system that is consistent with the kinematic constraints on the boundary of the deformable link. These coordinates can be introduced using approximation techniques such as Rayleigh-Ritz method, finite element technique or any other desired approach. The large relative motion between two neighboring links are defined by a set of joint coordinates which describes the large relative translational and rotational motion between two neighboring joint coordinate systems. The origin of these coordinate systems are rigidly attached to the neighboring links at the joint definition points along the axis of motion.

Signaling from the Podocyte Intercellular Junction to the Actin Cytoskeleton

PubMed Central

George, Britta; Holzman, Lawrence B.

2012-01-01

Observations of hereditary glomerular disease support the contention that podocyte intercellular junction proteins are essential for junction formation and maintenance. Genetic deletion of most of these podocyte intercellular junction proteins results in foot process effacement and proteinuria. This review focuses on the current understanding of molecular mechanisms by which podocyte intercellular junction proteins such as the Nephrin-Neph1-Podocin receptor complex coordinate cytoskeletal dynamics and thus intercellular junction formation, maintenance and injury-dependent remodeling. PMID:22958485

An Investigation of Embodied Language Comprehension from the Perspective of Coordination Dynamics

ERIC Educational Resources Information Center

Olmstead, Anne Jane

2009-01-01

In four experiments, participants performed sentence comprehension tasks simultaneously with bimanual coordination. Half of the sentences described events that could not be performed by a human (non-performable) and half described actions that could be performed by a human (performable). Effects of sentence type on coordination were indexed by…

The Developmental Effect of Concurrent Cognitive and Locomotor Skills: Time-Sharing from a Dynamical Perspective.

ERIC Educational Resources Information Center

Whitall, Jill

1991-01-01

Presents research on the effects of concurrent verbal cognition on locomotor skills. Results revealed no interference with coordination variables across age, but some interference with control variables, particularly in younger subjects. Coordination of gait required less attention than setting of control parameters. This coordination was in place…

Improvisation and the self-organization of multiple musical bodies.

PubMed

Walton, Ashley E; Richardson, Michael J; Langland-Hassan, Peter; Chemero, Anthony

2015-01-01

Understanding everyday behavior relies heavily upon understanding our ability to improvise, how we are able to continuously anticipate and adapt in order to coordinate with our environment and others. Here we consider the ability of musicians to improvise, where they must spontaneously coordinate their actions with co-performers in order to produce novel musical expressions. Investigations of this behavior have traditionally focused on describing the organization of cognitive structures. The focus, here, however, is on the ability of the time-evolving patterns of inter-musician movement coordination as revealed by the mathematical tools of complex dynamical systems to provide a new understanding of what potentiates the novelty of spontaneous musical action. We demonstrate this approach through the application of cross wavelet spectral analysis, which isolates the strength and patterning of the behavioral coordination that occurs between improvising musicians across a range of nested time-scales. Revealing the sophistication of the previously unexplored dynamics of movement coordination between improvising musicians is an important step toward understanding how creative musical expressions emerge from the spontaneous coordination of multiple musical bodies.

Implementation of system dynamic simulation method to optimize profit in supply chain network of vegetable product

NASA Astrophysics Data System (ADS)

Tama, I. P.; Akbar, Z.; Eunike, A.

2018-04-01

Vegetables are categorized as a perishable product, which is a product with short lifespan thus requires proper handling and planning to reduce losses caused by the short lifespan. In order to reduce the losses, coordination among the players in the supply chain is required. On the other hand, the decision in the supply chain of vegetables and other farming products in the traditional market of developing country is independent among the players. This research is conducted by using System Dynamic Simulation method to develop model and scenario by coordinating the supply quantity amongst players in the supply chain. The scenarios are developed based on newsboy inventory model. This study aims to compare scenarios combining tiers involved in coordination program. The result shows that coordination in supply chain increases total supply chain profit, although there will always be players who experienced decrements in profit. The scenario of coordination among the farmer, the distributor, and the wholesaler resulted in the highest increase in total supply chain profit compared to other coordination scenarios, with an increased value of 10.49%.

Improvisation and the self-organization of multiple musical bodies

PubMed Central

Walton, Ashley E.; Richardson, Michael J.; Langland-Hassan, Peter; Chemero, Anthony

2015-01-01

Understanding everyday behavior relies heavily upon understanding our ability to improvise, how we are able to continuously anticipate and adapt in order to coordinate with our environment and others. Here we consider the ability of musicians to improvise, where they must spontaneously coordinate their actions with co-performers in order to produce novel musical expressions. Investigations of this behavior have traditionally focused on describing the organization of cognitive structures. The focus, here, however, is on the ability of the time-evolving patterns of inter-musician movement coordination as revealed by the mathematical tools of complex dynamical systems to provide a new understanding of what potentiates the novelty of spontaneous musical action. We demonstrate this approach through the application of cross wavelet spectral analysis, which isolates the strength and patterning of the behavioral coordination that occurs between improvising musicians across a range of nested time-scales. Revealing the sophistication of the previously unexplored dynamics of movement coordination between improvising musicians is an important step toward understanding how creative musical expressions emerge from the spontaneous coordination of multiple musical bodies. PMID:25941499

Optimal wide-area monitoring and nonlinear adaptive coordinating neurocontrol of a power system with wind power integration and multiple FACTS devices.

PubMed

Qiao, Wei; Venayagamoorthy, Ganesh K; Harley, Ronald G

2008-01-01

Wide-area coordinating control is becoming an important issue and a challenging problem in the power industry. This paper proposes a novel optimal wide-area coordinating neurocontrol (WACNC), based on wide-area measurements, for a power system with power system stabilizers, a large wind farm and multiple flexible ac transmission system (FACTS) devices. An optimal wide-area monitor (OWAM), which is a radial basis function neural network (RBFNN), is designed to identify the input-output dynamics of the nonlinear power system. Its parameters are optimized through particle swarm optimization (PSO). Based on the OWAM, the WACNC is then designed by using the dual heuristic programming (DHP) method and RBFNNs, while considering the effect of signal transmission delays. The WACNC operates at a global level to coordinate the actions of local power system controllers. Each local controller communicates with the WACNC, receives remote control signals from the WACNC to enhance its dynamic performance and therefore helps improve system-wide dynamic and transient performance. The proposed control is verified by simulation studies on a multimachine power system.

Dynamic coupling between coordinates in a model for biomolecular isomerization

NASA Astrophysics Data System (ADS)

Ma, Ao; Nag, Ambarish; Dinner, Aaron R.

2006-04-01

To understand a complex reaction, it is necessary to project the dynamics of the system onto a low-dimensional subspace of physically meaningful coordinates. We recently introduced an automatic method for identifying coordinates that relate closely to stable-state commitment probabilities and successfully applied it to a model for biomolecular isomerization, the C7eq→αR transition of the alanine dipeptide [A. Ma and A. R. Dinner, J. Phys. Chem. B 109, 6769 (2005)]. Here, we explore approximate means for estimating diffusion tensors for systems subject to restraints in one and two dimensions and then use the results together with an extension of Kramers theory for unimolecular reaction rates [A. Berezhkovskii and A. Szabo, J. Chem. Phys. 122, 014503 (2005)] to show explicitly that both the potential of mean force and the diffusion tensor are essential for describing the dynamics of the alanine dipeptide quantitatively. In particular, the signficance of off-diagonal elements of the diffusion tensor suggests that the coordinates of interest are coupled by the hydrodynamic-like response of the bath of remaining degrees of freedom.

Torque coordinating robust control of shifting process for dry dual clutch transmission equipped in a hybrid car

NASA Astrophysics Data System (ADS)

Zhao, Z.-G.; Chen, H.-J.; Yang, Y.-Y.; He, L.

2015-09-01

For a hybrid car equipped with dual clutch transmission (DCT), the coordination control problems of clutches and power sources are investigated while taking full advantage of the integrated starter generator motor's fast response speed and high accuracy (speed and torque). First, a dynamic model of the shifting process is established, the vehicle acceleration is quantified according to the intentions of the driver, and the torque transmitted by clutches is calculated based on the designed disengaging principle during the torque phase. Next, a robust H∞ controller is designed to ensure speed synchronisation despite the existence of model uncertainties, measurement noise, and engine torque lag. The engine torque lag and measurement noise are used as external disturbances to initially modify the output torque of the power source. Additionally, during the torque switch phase, the torque of the power sources is smoothly transitioned to the driver's demanded torque. Finally, the torque of the power sources is further distributed based on the optimisation of system efficiency, and the throttle opening of the engine is constrained to avoid sharp torque variations. The simulation results verify that the proposed control strategies effectively address the problem of coordinating control of clutches and power sources, establishing a foundation for the application of DCT in hybrid cars.

Brain coordination dynamics: True and false faces of phase synchrony and metastability

PubMed Central

Tognoli, Emmanuelle; Kelso, J.A. Scott

2009-01-01

Understanding the coordination of multiple parts in a complex system such as the brain is a fundamental challenge. We present a theoretical model of cortical coordination dynamics that shows how brain areas may cooperate (integration) and at the same time retain their functional specificity (segregation). This model expresses a range of desirable properties that the brain is known to exhibit, including self-organization, multi-functionality, metastability and switching. Empirically, the model motivates a thorough investigation of collective phase relationships among brain oscillations in neurophysiological data. The most serious obstacle to interpreting coupled oscillations as genuine evidence of inter-areal coordination in the brain stems from volume conduction of electrical fields. Spurious coupling due to volume conduction gives rise to zero-lag (inphase) and antiphase synchronization whose magnitude and persistence obscure the subtle expression of real synchrony. Through forward modeling and the help of a novel colorimetric method, we show how true synchronization can be deciphered from continuous EEG patterns. Developing empirical efforts along the lines of continuous EEG analysis constitutes a major response to the challenge of understanding how different brain areas work together. Key predictions of cortical coordination dynamics can now be tested thereby revealing the essential modus operandi of the intact living brain. PMID:18938209

Phase transitions in the common brainstem and related systems investigated by nonstationary time series analysis.

PubMed

Lambertz, M; Vandenhouten, R; Grebe, R; Langhorst, P

2000-01-14

Neuronal activities of the reticular formation (RF) of the lower brainstem and the nucleus tractus solitarii (NTS, first relay station of baroreceptor afferents) were recorded together in the anesthized dog with related parameters of EEG, respiration and cardiovascular system. The RF neurons are part of the common brainstem system (CBS) which participates in regulation and coordination of cardiovascular, respiratory, somatomotor systems, and vigilance. Multiple time series of these physiological subsystems yield useful information about internal dynamic coordination of the organism. Essential problems are nonlinearity and instationarity of the signals, due to the dynamic complexity of the systems. Several time-resolving methods are presented to describe nonlinear dynamic couplings in the time course, particularly during phase transitions. The methods are applied to the recorded signals representing the complex couplings of the physiological subsystems. Phase transitions in these systems are detected by recurrence plots of the instationary signals. The pointwise transinformation and the pointwise conditional coupling divergence are measures of the mutual interaction of the subsystems in the state space. If the signals show marked rhythms, instantaneous frequencies and their shiftings are demonstrated by time frequency distributions, and instantaneous phase differences show couplings of oscillating subsystems. Transient signal components are reconstructed by wavelet packet time selective transient reconstruction. These methods are useful means for analyzing coupling characteristics of the complex physiological system, and detailed analyses of internal dynamic coordination of subsystems become possible. During phase transitions of the functional organization (a) the rhythms of the central neuronal activities and the peripheral systems are altered, (b) changes in the coupling between CBS neurons and cardiovascular signals, respiration and the EEG, and (c) between NTS neurons (influenced by baroreceptor afferents) and CBS neurons occur, and (d) the processing of baroreceptor input at the NTS neurons changes. The results of this complex analysis, which could not be done formerly in this manner, confirm and complete former investigations on the dynamic organization of the CBS with its changing relations to peripheral and other central nervous subsystems.

Numerical Manifold Method for the Forced Vibration of Thin Plates during Bending

PubMed Central

Jun, Ding; Song, Chen; Wei-Bin, Wen; Shao-Ming, Luo; Xia, Huang

2014-01-01

A novel numerical manifold method was derived from the cubic B-spline basis function. The new interpolation function is characterized by high-order coordination at the boundary of a manifold element. The linear elastic-dynamic equation used to solve the bending vibration of thin plates was derived according to the principle of minimum instantaneous potential energy. The method for the initialization of the dynamic equation and its solution process were provided. Moreover, the analysis showed that the calculated stiffness matrix exhibited favorable performance. Numerical results showed that the generalized degrees of freedom were significantly fewer and that the calculation accuracy was higher for the manifold method than for the conventional finite element method. PMID:24883403

How Messenger RNA and Nascent Chain Sequences Regulate Translation Elongation.

PubMed

Choi, Junhong; Grosely, Rosslyn; Prabhakar, Arjun; Lapointe, Christopher P; Wang, Jinfan; Puglisi, Joseph D

2018-06-20

Translation elongation is a highly coordinated, multistep, multifactor process that ensures accurate and efficient addition of amino acids to a growing nascent-peptide chain encoded in the sequence of translated messenger RNA (mRNA). Although translation elongation is heavily regulated by external factors, there is clear evidence that mRNA and nascent-peptide sequences control elongation dynamics, determining both the sequence and structure of synthesized proteins. Advances in methods have driven experiments that revealed the basic mechanisms of elongation as well as the mechanisms of regulation by mRNA and nascent-peptide sequences. In this review, we highlight how mRNA and nascent-peptide elements manipulate the translation machinery to alter the dynamics and pathway of elongation.

Impact of orbit modeling on DORIS station position and Earth rotation estimates

NASA Astrophysics Data System (ADS)

Štěpánek, Petr; Rodriguez-Solano, Carlos Javier; Hugentobler, Urs; Filler, Vratislav

2014-04-01

The high precision of estimated station coordinates and Earth rotation parameters (ERP) obtained from satellite geodetic techniques is based on the precise determination of the satellite orbit. This paper focuses on the analysis of the impact of different orbit parameterizations on the accuracy of station coordinates and the ERPs derived from DORIS observations. In a series of experiments the DORIS data from the complete year 2011 were processed with different orbit model settings. First, the impact of precise modeling of the non-conservative forces on geodetic parameters was compared with results obtained with an empirical-stochastic modeling approach. Second, the temporal spacing of drag scaling parameters was tested. Third, the impact of estimating once-per-revolution harmonic accelerations in cross-track direction was analyzed. And fourth, two different approaches for solar radiation pressure (SRP) handling were compared, namely adjusting SRP scaling parameter or fixing it on pre-defined values. Our analyses confirm that the empirical-stochastic orbit modeling approach, which does not require satellite attitude information and macro models, results for most of the monitored station parameters in comparable accuracy as the dynamical model that employs precise non-conservative force modeling. However, the dynamical orbit model leads to a reduction of the RMS values for the estimated rotation pole coordinates by 17% for x-pole and 12% for y-pole. The experiments show that adjusting atmospheric drag scaling parameters each 30 min is appropriate for DORIS solutions. Moreover, it was shown that the adjustment of cross-track once-per-revolution empirical parameter increases the RMS of the estimated Earth rotation pole coordinates. With recent data it was however not possible to confirm the previously known high annual variation in the estimated geocenter z-translation series as well as its mitigation by fixing the SRP parameters on pre-defined values.

Selective ultrafast probing of transient hot chemisorbed and precursor states of CO on Ru(0001).

PubMed

Beye, M; Anniyev, T; Coffee, R; Dell'Angela, M; Föhlisch, A; Gladh, J; Katayama, T; Kaya, S; Krupin, O; Møgelhøj, A; Nilsson, A; Nordlund, D; Nørskov, J K; Öberg, H; Ogasawara, H; Pettersson, L G M; Schlotter, W F; Sellberg, J A; Sorgenfrei, F; Turner, J J; Wolf, M; Wurth, W; Oström, H

2013-05-03

We have studied the femtosecond dynamics following optical laser excitation of CO adsorbed on a Ru surface by monitoring changes in the occupied and unoccupied electronic structure using ultrafast soft x-ray absorption and emission. We recently reported [M. Dell'Angela et al. Science 339, 1302 (2013)] a phonon-mediated transition into a weakly adsorbed precursor state occurring on a time scale of >2 ps prior to desorption. Here we focus on processes within the first picosecond after laser excitation and show that the metal-adsorbate coordination is initially increased due to hot-electron-driven vibrational excitations. This process is faster than, but occurs in parallel with, the transition into the precursor state. With resonant x-ray emission spectroscopy, we probe each of these states selectively and determine the respective transient populations depending on optical laser fluence. Ab initio molecular dynamics simulations of CO adsorbed on Ru(0001) were performed at 1500 and 3000 K providing insight into the desorption process.

Editor's Introduction and Review: Coordination and Context in Cognitive Science.

PubMed

Kello, Christopher T

2018-01-01

The role of coordination in cognitive science has been on the rise in recent years, in terms of coordination among neurons, coordination among sensory and motor systems, and coordination among individuals. Research has shown that coordination patterns corresponding to cognitive activities depend on the various contexts in which the underlying interactions are situated. The present issue of Topics in Cognitive Science centers on studies of coordination that address the role of context in shaping or interpreting dynamical patterns of human behavior. This introductory article reviews some of the prior literature leading up to current and future research on coordination and context in cognitive science. Copyright © 2017 Cognitive Science Society, Inc.

Ultrafast dynamics of liquid water: Energy relaxation and transfer processes of the OH stretch and the HOH bend

DOE Office of Scientific and Technical Information (OSTI.GOV)

Imoto, Sho; Xantheas, Sotiris S.; Saito, Shinji

2015-08-27

The vibrational energy relaxation and transfer processes of the OH stretching and the HOH bending vibrations in liquid water are investigated via the theoretical calculation of the pump-probe spectra obtained from non-equilibrium molecular dynamics simulations with the TTM3-F interaction potential. The excitation of the OH stretch induces an instantaneous response of the high frequency librational motions in the 600-1000 cm-1 range. In addition, the excess energy of the OH stretch of a water molecule quickly transfers to the OH stretches of molecules in its first hydration shell with a time constant of ~50 fs, followed by relaxation to the HOHmore » bends of the surrounding molecules with a time constant of 230 fs. The excitation of the HOH bend also results in the ultrafast excitation of the high frequency librational motions. The energy of the excited HOH bend of a water molecule decays, with a time constant of 200 fs, mainly to the relaxation of the HOH bends of its surrounding molecules. The energies of the HOH bends were found to transfer quickly to the intermolecular motions via the coupling with the high frequency librational motions. The excess energy of the OH stretch or the HOH bend relaxes to the high frequency intermolecular librational motions and eventually to the hot ground state with a time scale of ~1 ps via the coupling with the librational and translational motions. The energy relaxation and transfer processes were found to depend on the local hydrogen bonding network; the relaxations of the excess energy of the OH stretch and the HOH bend of four- and five-coordinated molecules are faster than those of a three-coordinated molecule due to the delocalization of the vibrational motions of the former (four- and five-coordinated molecules) compared to those of the later (three-coordinated molecules). The present results highlight the importance of the high frequency intermolecular librational modes in facilitating the ultrafast energy relaxation process in liquid water via their strong nonlinear couplings with the intramolecular OH stretching and HOH bending vibrations. S.S.X. acknowledges the support of the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. The calculation was carried out using the computing resources at the Research Center for Computational Science in Okazaki, Japan.« less

Unfolding Visual Lexical Decision in Time

PubMed Central

Barca, Laura; Pezzulo, Giovanni

2012-01-01

Visual lexical decision is a classical paradigm in psycholinguistics, and numerous studies have assessed the so-called “lexicality effect" (i.e., better performance with lexical than non-lexical stimuli). Far less is known about the dynamics of choice, because many studies measured overall reaction times, which are not informative about underlying processes. To unfold visual lexical decision in (over) time, we measured participants' hand movements toward one of two item alternatives by recording the streaming x,y coordinates of the computer mouse. Participants categorized four kinds of stimuli as “lexical" or “non-lexical:" high and low frequency words, pseudowords, and letter strings. Spatial attraction toward the opposite category was present for low frequency words and pseudowords. Increasing the ambiguity of the stimuli led to greater movement complexity and trajectory attraction to competitors, whereas no such effect was present for high frequency words and letter strings. Results fit well with dynamic models of perceptual decision-making, which describe the process as a competition between alternatives guided by the continuous accumulation of evidence. More broadly, our results point to a key role of statistical decision theory in studying linguistic processing in terms of dynamic and non-modular mechanisms. PMID:22563419

Dynamic Simulation of Random Packing of Polydispersive Fine Particles

NASA Astrophysics Data System (ADS)

Ferraz, Carlos Handrey Araujo; Marques, Samuel Apolinário

2018-02-01

In this paper, we perform molecular dynamic (MD) simulations to study the two-dimensional packing process of both monosized and random size particles with radii ranging from 1.0 to 7.0 μm. The initial positions as well as the radii of five thousand fine particles were defined inside a rectangular box by using a random number generator. Both the translational and rotational movements of each particle were considered in the simulations. In order to deal with interacting fine particles, we take into account both the contact forces and the long-range dispersive forces. We account for normal and static/sliding tangential friction forces between particles and between particle and wall by means of a linear model approach, while the long-range dispersive forces are computed by using a Lennard-Jones-like potential. The packing processes were studied assuming different long-range interaction strengths. We carry out statistical calculations of the different quantities studied such as packing density, mean coordination number, kinetic energy, and radial distribution function as the system evolves over time. We find that the long-range dispersive forces can strongly influence the packing process dynamics as they might form large particle clusters, depending on the intensity of the long-range interaction strength.

Milestoning with coarse memory

NASA Astrophysics Data System (ADS)

Hawk, Alexander T.

2013-04-01

Milestoning is a method used to calculate the kinetics of molecular processes occurring on timescales inaccessible to traditional molecular dynamics (MD) simulations. In the method, the phase space of the system is partitioned by milestones (hypersurfaces), trajectories are initialized on each milestone, and short MD simulations are performed to calculate transitions between neighboring milestones. Long trajectories of the system are then reconstructed with a semi-Markov process from the observed statistics of transition. The procedure is typically justified by the assumption that trajectories lose memory between crossing successive milestones. Here we present Milestoning with Coarse Memory (MCM), a generalization of Milestoning that relaxes the memory loss assumption of conventional Milestoning. In the method, milestones are defined and sample transitions are calculated in the standard Milestoning way. Then, after it is clear where trajectories sample milestones, the milestones are broken up into distinct neighborhoods (clusters), and each sample transition is associated with two clusters: the cluster containing the coordinates the trajectory was initialized in, and the cluster (on the terminal milestone) containing trajectory's final coordinates. Long trajectories of the system are then reconstructed with a semi-Markov process in an extended state space built from milestone and cluster indices. To test the method, we apply it to a process that is particularly ill suited for Milestoning: the dynamics of a polymer confined to a narrow cylinder. We show that Milestoning calculations of both the mean first passage time and the mean transit time of reversal—which occurs when the end-to-end vector reverses direction—are significantly improved when MCM is applied. Finally, we note the overhead of performing MCM on top of conventional Milestoning is negligible.

Visualizing Hyolaryngeal Mechanics in Swallowing Using Dynamic MRI

PubMed Central

Pearson, William G.; Zumwalt, Ann C.

2013-01-01

Introduction Coordinates of anatomical landmarks are captured using dynamic MRI to explore whether a proposed two-sling mechanism underlies hyolaryngeal elevation in pharyngeal swallowing. A principal components analysis (PCA) is applied to coordinates to determine the covariant function of the proposed mechanism. Methods Dynamic MRI (dMRI) data were acquired from eleven healthy subjects during a repeated swallows task. Coordinates mapping the proposed mechanism are collected from each dynamic (frame) of a dynamic MRI swallowing series of a randomly selected subject in order to demonstrate shape changes in a single subject. Coordinates representing minimum and maximum hyolaryngeal elevation of all 11 subjects were also mapped to demonstrate shape changes of the system among all subjects. MophoJ software was used to perform PCA and determine vectors of shape change (eigenvectors) for elements of the two-sling mechanism of hyolaryngeal elevation. Results For both single subject and group PCAs, hyolaryngeal elevation accounted for the first principal component of variation. For the single subject PCA, the first principal component accounted for 81.5% of the variance. For the between subjects PCA, the first principal component accounted for 58.5% of the variance. Eigenvectors and shape changes associated with this first principal component are reported. Discussion Eigenvectors indicate that two-muscle slings and associated skeletal elements function as components of a covariant mechanism to elevate the hyolaryngeal complex. Morphological analysis is useful to model shape changes in the two-sling mechanism of hyolaryngeal elevation. PMID:25090608

Enhanced emotional responses during social coordination with a virtual partner

PubMed Central

Dumas, Guillaume; Kelso, J.A. Scott; Tognoli, Emmanuelle

2016-01-01

Emotion and motion, though seldom studied in tandem, are complementary aspects of social experience. This study investigates variations in emotional responses during movement coordination between a human and a Virtual Partner (VP), an agent whose virtual finger movements are driven by the Haken-Kelso-Bunz (HKB) equations of Coordination Dynamics. Twenty-one subjects were instructed to coordinate finger movements with the VP in either inphase or antiphase patterns. By adjusting model parameters, we manipulated the ‘intention’ of VP as cooperative or competitive with the human's instructed goal. Skin potential responses (SPR) were recorded to quantify the intensity of emotional response. At the end of each trial, subjects rated the VP's intention and whether they thought their partner was another human being or a machine. We found greater emotional responses when subjects reported that their partner was human and when coordination was stable. That emotional responses are strongly influenced by dynamic features of the VP's behavior, has implications for mental health, brain disorders and the design of socially cooperative machines. PMID:27094374

Boundary conditions for the paleoenvironment: Chemical and Physical Processes in dense interstellar clouds

NASA Technical Reports Server (NTRS)

Irvine, W. M.; Schloerb, F. P.; Ziurys, L. M.

1986-01-01

The present research includes searches for important new interstellar constituents; observations relevant to differentiating between different models for the chemical processes that are important in the interstellar environment; and coordinated studies of the chemistry, physics, and dynamics of molecular clouds which are the sites or possible future sites of star formation. Recent research has included the detection and study of four new interstellar molecules; searches which have placed upper limits on the abundance of several other potential constituents of interstellar clouds; quantitative studies of comparative molecular abundances in different types of interstellar clouds; investigation of reaction pathways for astrochemistry from a comparison of theory and the observed abundance of related species such as isomers and isotopic variants; studies of possible tracers of energenic events related to star formation, including silicon and sulfur containing molecules; and mapping of physical, chemical, and dynamical properties over extended regions of nearby cold molecular clouds.

A central role for vesicle trafficking in epithelial neoplasia: Intracellular highways to carcinogenesis

PubMed Central

Goldenring, James R.

2014-01-01

Epithelial cell carcinogenesis involves the loss of polarity, alteration of polarized protein presentation, dynamic cell morphology changes, increased proliferation and increased cell motility and invasion. Elements of membrane vesicle trafficking underlie all of these processes. Specific membrane trafficking regulators, including Rab small GTPases, through the coordinated dynamics of intracellular trafficking along cytoskeletal pathways, determine cell surface presentation of proteins and overall function of both differentiated and neoplastic cells. While mutations in vesicle trafficking proteins may not be direct drivers of transformation, elements of the machinery of vesicle movement play critical roles in the phenotypes of neoplastic cells. Therefore, the regulators of membrane vesicle trafficking decisions are critical mediators of the full spectrum of cell physiologies driving cancer cell biology, including initial loss of polarity, invasion and metastasis. Targeting of these fundamental intracellular processes may provide important points for manipulation of cancer cell behaviour. PMID:24108097

Controlled Folding, Motional, and Constitutional Dynamic Processes of Polyheterocyclic Molecular Strands.

PubMed

Barboiu, Mihail; Stadler, Adrian-Mihail; Lehn, Jean-Marie

2016-03-18

General design principles have been developed for the control of the structural features of polyheterocyclic strands and their effector-modulated shape changes. Induced defined molecular motions permit designed enforcement of helical as well as linear molecular shapes. The ability of such molecular strands to bind metal cations allows the generation of coiling/uncoiling processes between helically folded and extended linear states. Large molecular motions are produced on coordination of metal ions, which may be made reversible by competition with an ancillary complexing agent and fueled by sequential acid/base neutralization energy. The introduction of hydrazone units into the strands confers upon them constitutional dynamics, whereby interconversion between different strand compositions is achieved through component exchange. These features have relevance for nanomechanical devices. We present a morphological and functional analysis of such systems developed in our laboratories. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A decentralised multi-agent approach to enhance the stability of smart microgrids with renewable energy

NASA Astrophysics Data System (ADS)

Rahman, M. S.; Pota, H. R.; Mahmud, M. A.; Hossain, M. J.

2016-05-01

This paper presents the impact of large penetration of wind power on the transient stability through a dynamic evaluation of the critical clearing times (CCTs) by using intelligent agent-based approach. A decentralised multi-agent-based framework is developed, where agents represent a number of physical device models to form a complex infrastructure for computation and communication. They enable the dynamic flow of information and energy for the interaction between the physical processes and their activities. These agents dynamically adapt online measurements and use the CCT information for relay coordination to improve the transient stability of power systems. Simulations are carried out on a smart microgrid system for faults at increasing wind power penetration levels and the improvement in transient stability using the proposed agent-based framework is demonstrated.

Head Stability and Head-Trunk Coordination in Horseback Riders: The Contribution of Visual Information According to Expertise

PubMed Central

Olivier, Agnès; Faugloire, Elise; Lejeune, Laure; Biau, Sophie; Isableu, Brice

2017-01-01

Maintaining equilibrium while riding a horse is a challenging task that involves complex sensorimotor processes. We evaluated the relative contribution of visual information (static or dynamic) to horseback riders' postural stability (measured from the variability of segment position in space) and the coordination modes they adopted to regulate balance according to their level of expertise. Riders' perceptual typologies and their possible relation to postural stability were also assessed. Our main assumption was that the contribution of visual information to postural control would be reduced among expert riders in favor of vestibular and somesthetic reliance. Twelve Professional riders and 13 Club riders rode an equestrian simulator at a gallop under four visual conditions: (1) with the projection of a simulated scene reproducing what a rider sees in the real context of a ride in an outdoor arena, (2) under stroboscopic illumination, preventing access to dynamic visual cues, (3) in normal lighting but without the projected scene (i.e., without the visual consequences of displacement) and (4) with no visual cues. The variability of the position of the head, upper trunk and lower trunk was measured along the anteroposterior (AP), mediolateral (ML), and vertical (V) axes. We computed discrete relative phase to assess the coordination between pairs of segments in the anteroposterior axis. Visual field dependence-independence was evaluated using the Rod and Frame Test (RFT). The results showed that the Professional riders exhibited greater overall postural stability than the Club riders, revealed mainly in the AP axis. In particular, head variability was lower in the Professional riders than in the Club riders in visually altered conditions, suggesting a greater ability to use vestibular and somesthetic information according to task constraints with expertise. In accordance with this result, RFT perceptual scores revealed that the Professional riders were less dependent on the visual field than were the Club riders. Finally, the Professional riders exhibited specific coordination modes that, unlike the Club riders, departed from pure in-phase and anti-phase patterns and depended on visual conditions. The present findings provide evidence of major differences in the sensorimotor processes contributing to postural control with expertise in horseback riding. PMID:28194100

[The formation of the self-maintenance skills in the pre-school children presenting with locomotor and coordination disorders].

PubMed

Poletaeva-Dubrovina, N A; Burkova, A M

2016-01-01

The Ministry of Health of the Russian Federation acknowledges the sharp rise in the prevalence of congenital malformation in this country during the past 30 years. In 2010-2011, this pathology was estimated to occur in 3% of the children. It includes a variety of locomotor and coordination disorders of which the most widespread are infantile cerebral paralysis, ataxia, consequences of perinatal lesions of the central nervous system, etc. This article contains a detailed description of these locomotor and coordination disorders. The objective of the present work was to elaborate and evaluate the program for the formation of the self-maintenance skills in the pre-school children presenting with locomotor and coordination disorders under conditions of family guidance and education. The study was carried out from September 2013 till May 2014 based at MUP DOD "Semeiny klub Nadezhda" ("The Hope Family Club", Municipal unitary facility for children's additional education) and supported by B.N. El'tsin Ural Federal University. It included 10 children suffering from locomotor and coordination disorders of different severity and members of their families. The following methods were used: the self-service skills scorecard , monitoring formation of the motor skills, and Wilcoxon's T-test. The use of the program based on the cooperation with the children's families allowed to achieve positive dynamics in the patients' conditions. Moreover, 30% of them acquired the full scope of the self-maintenance skills. The most pronounced changes in the motor abilities were apparent in the movements of the upper and lower extremitis, walking, and motion in space. The proposed program for the formation of the self-maintenance skills in the pre-school children presenting with locomotor and coordination disorders proved to be highly efficacious. The study has demonstrated the importance of the parents' involvement in the process of formation of the self-maintenance skills and motor abilities. It is concluded that the formation of the self-maintenance skills and locomotor abilities are two interdependent processes.

Application of singular value decomposition to structural dynamics systems with constraints

NASA Technical Reports Server (NTRS)

Juang, J.-N.; Pinson, L. D.

1985-01-01

Singular value decomposition is used to construct a coordinate transformation for a linear dynamic system subject to linear, homogeneous constraint equations. The method is compared with two commonly used methods, namely classical Gaussian elimination and Walton-Steeves approach. Although the classical method requires fewer numerical operations, the singular value decomposition method is more accurate and convenient in eliminating the dependent coordinates. Numerical examples are presented to demonstrate the application of the method.

Multidimensional joint coupling: a case study visualisation approach to movement coordination and variability.

PubMed

Irwin, Gareth; Kerwin, David G; Williams, Genevieve; Van Emmerik, Richard E A; Newell, Karl M; Hamill, Joseph

2018-06-18

A case study visualisation approach to examining the coordination and variability of multiple interacting segments is presented using a whole-body gymnastic skill as the task example. One elite male gymnast performed 10 trials of 10 longswings whilst three-dimensional locations of joint centres were tracked using a motion analysis system. Segment angles were used to define coupling between the arms and trunk, trunk and thighs and thighs and shanks. Rectified continuous relative phase profiles for each interacting couple for 80 longswings were produced. Graphical representations of coordination couplings are presented that include the traditional single coupling, followed by the relational dynamics of two couplings and finally three couplings simultaneously plotted. This method highlights the power of visualisation of movement dynamics and identifies properties of the global interacting segmental couplings that a more formal analysis may not reveal. Visualisation precedes and informs the appropriate qualitative and quantitative analysis of the dynamics.

Conditions for order and chaos in the dynamics of a trapped Bose-Einstein condensate in coordinate and energy space

NASA Astrophysics Data System (ADS)

Sakhel, Roger R.; Sakhel, Asaad R.; Ghassib, Humam B.; Balaz, Antun

2016-03-01

We investigate numerically conditions for order and chaos in the dynamics of an interacting Bose-Einstein condensate (BEC) confined by an external trap cut off by a hard-wall box potential. The BEC is stirred by a laser to induce excitations manifesting as irregular spatial and energy oscillations of the trapped cloud. Adding laser stirring to the external trap results in an effective time-varying trapping frequency in connection with the dynamically changing combined external+laser potential trap. The resulting dynamics are analyzed by plotting their trajectories in coordinate phase space and in energy space. The Lyapunov exponents are computed to confirm the existence of chaos in the latter space. Quantum effects and trap anharmonicity are demonstrated to generate chaos in energy space, thus confirming its presence and implicating either quantum effects or trap anharmonicity as its generator. The presence of chaos in energy space does not necessarily translate into chaos in coordinate space. In general, a dynamic trapping frequency is found to promote chaos in a trapped BEC. An apparent means to suppress chaos in a trapped BEC is achieved by increasing the characteristic scale of the external trap with respect to the condensate size.

Coordination processes and outcomes in the public service: the challenge of inter-organizational food safety coordination in Norway.

PubMed

Lie, Amund

2011-01-01

In 2004 Norway implemented a food safety reform programme aimed at enhancing inter-organizational coordination processes and outcomes. Has this programme affected inter-organizational coordination processes and outcomes, both vertically and horizontally – and if so how? This article employs the concept of inter-organizational coordination as an analytical tool, examining it in the light of two theoretical perspectives and coupling it with the empirical findings. The argument presented is that the chances of strong coordination outcomes may increase if inter-organizational processes feature a clear division of labour, arenas for coordination, active leadership, a lack of major conflicting goals, and shared obligations.

A theoretical study of the dynamic behavior of alkane hydroxylation by a compound I model of cytochrome P450.

PubMed

Yoshizawa, K; Kamachi, T; Shiota, Y

2001-10-10

Dynamic aspects of alkane hydroxylation mediated by Compound I of cytochrome P450 are discussed from classical trajectory calculations at the B3LYP level of density functional theory. The nuclei of the reacting system are propagated from a transition state to a reactant or product direction according to classical dynamics on a Born-Oppenheimer potential energy surface. Geometric and energetic changes in both low-spin doublet and high-spin quartet states are followed along the ethane to ethanol reaction pathway, which is partitioned into two chemical steps: the first is the H-atom abstraction from ethane by the iron-oxo species of Compound I and the second is the rebound step in which the resultant iron-hydroxo complex and the ethyl radical intermediate react to form the ethanol complex. Molecular vibrations of the C-H bond being dissociated and the O-H bond being formed are significantly activated before and after the transition state, respectively, in the H-atom abstraction. The principal reaction coordinate that can represent the first chemical step is the C-H distance or the O-H distance while other geometric parameters remain almost unchanged. The rebound process begins with the iron-hydroxo complex and the ethyl radical intermediate and ends with the formation of the ethanol complex, the essential process in this reaction being the formation of the C-O bond. The H-O-Fe-C dihedral angle corresponds to the principal reaction coordinate for the rebound step. When sufficient kinetic energy is supplied to this rotational mode, the rebound process should efficiently take place. Trajectory calculations suggest that about 200 fs is required for the rebound process under specific initial conditions, in which a small amount of kinetic energy (0.1 kcal/mol) is supplied to the transition state exactly along the reaction coordinate. An important issue about which normal mode of vibration is activated during the hydroxylation reaction is investigated in detail from trajectory calculations. A large part of the kinetic energy is distributed to the C-H and O-H stretching modes before and after the transition state for the H-atom abstraction, respectively, and a small part of the kinetic energy is distributed to the Fe-O and Fe-S stretching modes and some characteristic modes of the porphyrin ring. The porphyrin marker modes of nu(3) and nu(4) that explicitly involve Fe-N stretching motion are effectively enhanced in the hydroxylation reaction. These vibrational modes of the porphyrin ring can play an important role in the energy transfer during the enzymatic process.

Sensitivity study of a dynamic thermodynamic sea ice model

NASA Astrophysics Data System (ADS)

Holland, David M.; Mysak, Lawrence A.; Manak, Davinder K.; Oberhuber, Josef M.

1993-02-01

A numerical simulation of the seasonal sea ice cover in the Arctic Ocean and the Greenland, Iceland, and Norwegian seas is presented. The sea ice model is extracted from Oberhuber's (1990) coupled sea ice-mixed layer-isopycnal general circulation model and is written in spherical coordinates. The advantage of such a model over previous sea ice models is that it can be easily coupled to either global atmospheric or ocean general circulation models written in spherical coordinates. In this model, the thermodynamics are a modification of that of Parkinson and Washington (1979), while the dynamics use the full Hibler (1979) viscous-plastic rheology. Monthly thermodynamic and dynamic forcing fields for the atmosphere and ocean are specified. The simulations of the seasonal cycle of ice thickness, compactness, and velocity, for a control set of parameters, compare favorably with the known seasonal characteristics of these fields. A sensitivity study of the control simulation of the seasonal sea ice cover is presented. The sensitivity runs are carried out under three different themes, namely, numerical conditions, parameter values, and physical processes. This last theme refers to experiments in which physical processes are either newly added or completely removed from the model. Approximately 80 sensitivity runs have been performed in which a change from the control run environment has been implemented. Comparisons have been made between the control run and a particular sensitivity run based on time series of the seasonal cycle of the domain-averaged ice thickness, compactness, areal coverage, and kinetic energy. In addition, spatially varying fields of ice thickness, compactness, velocity, and surface temperature for each season are presented for selected experiments. A brief description and discussion of the more interesting experiments are presented. The simulation of the seasonal cycle of Arctic sea ice cover is shown to be robust.

Coordinated within-trial dynamics of low-frequency neural rhythms controls evidence accumulation.

PubMed

Werkle-Bergner, Markus; Grandy, Thomas H; Chicherio, Christian; Schmiedek, Florian; Lövdén, Martin; Lindenberger, Ulman

2014-06-18

Higher cognitive functions, such as human perceptual decision making, require information processing and transmission across wide-spread cortical networks. Temporally synchronized neural firing patterns are advantageous for efficiently representing and transmitting information within and between assemblies. Computational, empirical, and conceptual considerations all lead to the expectation that the informational redundancy of neural firing rates is positively related to their synchronization. Recent theorizing and initial evidence also suggest that the coding of stimulus characteristics and their integration with behavioral goal states require neural interactions across a hierarchy of timescales. However, most studies thus have focused on neural activity in a single frequency range or on a restricted set of brain regions. Here we provide evidence for cooperative spatiotemporal dynamics of slow and fast EEG signals during perceptual decision making at the single-trial level. Participants performed three masked two-choice decision tasks, one each with numerical, verbal, or figural content. Decrements in posterior α power (8-14 Hz) were paralleled by increments in high-frequency (>30 Hz) signal entropy in trials demanding active sensory processing. Simultaneously, frontocentral θ power (4-7 Hz) increased, indicating evidence integration. The coordinated α/θ dynamics were tightly linked to decision speed and remarkably similar across tasks, suggesting a domain-general mechanism. In sum, we demonstrate an inverse association between decision-related changes in widespread low-frequency power and local high-frequency entropy. The cooperation among mechanisms captured by these changes enhances the informational density of neural response patterns and qualifies as a neural coding system in the service of perceptual decision making. Copyright © 2014 the authors 0270-6474/14/348519-10$15.00/0.

Reference coordinate systems: An update. Supplement 11

NASA Technical Reports Server (NTRS)

Mueller, Ivan I.

1988-01-01

A common requirement for all geodetic investigations is a well-defined coordinate system attached to the earth in some prescribed way, as well as a well-defined inertial coordinate system in which the motions of the terrestrial frame can be monitored. The paper deals with the problems encountered when establishing such coordinate systems and the transformations between them. In addition, problems related to the modeling of the deformable earth are discussed. This paper is an updated version of the earlier work, Reference Coordinate Systems for Earth Dynamics: A Preview, by the author.

Dynamically Coupled Residues within the SH2 Domain of FYN Are Key to Unlocking Its Activity.

PubMed

Huculeci, Radu; Cilia, Elisa; Lyczek, Agatha; Buts, Lieven; Houben, Klaartje; Seeliger, Markus A; van Nuland, Nico; Lenaerts, Tom

2016-11-01

Src kinase activity is controlled by various mechanisms involving a coordinated movement of kinase and regulatory domains. Notwithstanding the extensive knowledge related to the backbone dynamics, little is known about the more subtle side-chain dynamics within the regulatory domains and their role in the activation process. Here, we show through experimental methyl dynamic results and predicted changes in side-chain conformational couplings that the SH2 structure of Fyn contains a dynamic network capable of propagating binding information. We reveal that binding the phosphorylated tail of Fyn perturbs a residue cluster near the linker connecting the SH2 and SH3 domains of Fyn, which is known to be relevant in the regulation of the activity of Fyn. Biochemical perturbation experiments validate that those residues are essential for inhibition of Fyn, leading to a gain of function upon mutation. These findings reveal how side-chain dynamics may facilitate the allosteric regulation of the different members of the Src kinase family. Copyright © 2016 Elsevier Ltd. All rights reserved.

SENR /NRPy + : Numerical relativity in singular curvilinear coordinate systems

NASA Astrophysics Data System (ADS)

Ruchlin, Ian; Etienne, Zachariah B.; Baumgarte, Thomas W.

2018-03-01

We report on a new open-source, user-friendly numerical relativity code package called SENR /NRPy + . Our code extends previous implementations of the BSSN reference-metric formulation to a much broader class of curvilinear coordinate systems, making it ideally suited to modeling physical configurations with approximate or exact symmetries. In the context of modeling black hole dynamics, it is orders of magnitude more efficient than other widely used open-source numerical relativity codes. NRPy + provides a Python-based interface in which equations are written in natural tensorial form and output at arbitrary finite difference order as highly efficient C code, putting complex tensorial equations at the scientist's fingertips without the need for an expensive software license. SENR provides the algorithmic framework that combines the C codes generated by NRPy + into a functioning numerical relativity code. We validate against two other established, state-of-the-art codes, and achieve excellent agreement. For the first time—in the context of moving puncture black hole evolutions—we demonstrate nearly exponential convergence of constraint violation and gravitational waveform errors to zero as the order of spatial finite difference derivatives is increased, while fixing the numerical grids at moderate resolution in a singular coordinate system. Such behavior outside the horizons is remarkable, as numerical errors do not converge to zero near punctures, and all points along the polar axis are coordinate singularities. The formulation addresses such coordinate singularities via cell-centered grids and a simple change of basis that analytically regularizes tensor components with respect to the coordinates. Future plans include extending this formulation to allow dynamical coordinate grids and bispherical-like distribution of points to efficiently capture orbiting compact binary dynamics.

The Role of Solvent Reorganization Dynamics in Electron-Transfer Processes. Theory-Experiment Comparisons for Electrochemical and Homogeneous Electron Exchange Involving Metallocene Redox Couples

DTIC Science & Technology

1985-08-01

Kodak) by crystallization from acetone; it was recrystallized twice from ethanol and dried in a vacuum oven. Tetraethylamonium perchlorate (TEAP) (G...the electrooxidation of in(Cp’) 2 , which yielded significantly smaller reverse (cathodic) currents in the most strongly coordinating solvents (DMX...DM50) at slower scan rates (< 0.5 V sec-1). Nevertheless, satisfactory a.c. polarograms were obtained for each of these system=. 5 4 Temperature

Investigation of rubidium(I) ion solvation in liquid ammonia using QMCF-MD simulation and NBO analysis of first solvation shell structure.

PubMed

Hidayat, Yuniawan; Armunanto, Ria; Pranowo, Harno Dwi

2018-04-27

Rb(I) ion solvation in liquid ammonia has been studied by an ab initio quantum mechanical charge field molecular dynamics simulation, and the first solvation shell structure has been analyzed using natural bond orbital. The simulation was performed for an ion and 593 ammonia molecules in a box with a length of 29.03 Å corresponding to a liquid ammonia density of 0.69 g/mL at 235.16 K. The quantum mechanical calculation was carried out for atomic interactions in the radius of 6.4 Å from the ion using LANL2DZ ECP and DZP (Dunning) basis sets for Rb(I) ion and ammonia respectively. The trajectories of the simulation were analyzed in terms of radial, angular, and coordination number distribution functions, vibration, and mean residence time (MRT). Two solvation shell regions are observed for the Rb(I)-N as well as the Rb(I)-H. The maximum distance of Rb(I)-N in the first solvation shell is in accordance with experimental data where a coordination number of 8 is favorable. A non-single coordination number of the first and second shell indicates dynamic solvation structure. It is confirmed by frequent exchange ligand processes observed within a simulation time of 15 ps. The low stabilization energy of donor acceptor ion-ligand interaction with a small Wiberg bond index affirms that the Rb(I)-NH 3 interaction is weak electrostatically.

A new structural framework for integrating replication protein A into DNA processing machinery

PubMed Central

Brosey, Chris A.; Yan, Chunli; Tsutakawa, Susan E.; Heller, William T.; Rambo, Robert P.; Tainer, John A.; Ivanov, Ivaylo; Chazin, Walter J.

2013-01-01

By coupling the protection and organization of single-stranded DNA (ssDNA) with recruitment and alignment of DNA processing factors, replication protein A (RPA) lies at the heart of dynamic multi-protein DNA processing machinery. Nevertheless, how RPA coordinates biochemical functions of its eight domains remains unknown. We examined the structural biochemistry of RPA’s DNA-binding activity, combining small-angle X-ray and neutron scattering with all-atom molecular dynamics simulations to investigate the architecture of RPA’s DNA-binding core. The scattering data reveal compaction promoted by DNA binding; DNA-free RPA exists in an ensemble of states with inter-domain mobility and becomes progressively more condensed and less dynamic on binding ssDNA. Our results contrast with previous models proposing RPA initially binds ssDNA in a condensed state and becomes more extended as it fully engages the substrate. Moreover, the consensus view that RPA engages ssDNA in initial, intermediate and final stages conflicts with our data revealing that RPA undergoes two (not three) transitions as it binds ssDNA with no evidence for a discrete intermediate state. These results form a framework for understanding how RPA integrates the ssDNA substrate into DNA processing machinery, provides substrate access to its binding partners and promotes the progression and selection of DNA processing pathways. PMID:23303776

Controlling Proton Delivery through Catalyst Structural Dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cardenas, Allan Jay P.; Ginovska, Bojana; Kumar, Neeraj

The fastest synthetic molecular catalysts for production and oxidation of H2 emulate components of the active site of natural hydrogenases. The role of controlled structural dynamics is recognized as a critical component in the catalytic performance of many enzymes, including hydrogenases, but is largely neglected in the design of synthetic molecular cata-lysts. In this work, the impact of controlling structural dynamics on the rate of production of H2 was studied for a series of [Ni(PPh2NC6H4-R2)2]2+ catalysts including R = n-hexyl, n-decyl, n-tetradecyl, n-octadecyl, phenyl, or cyclohexyl. A strong correlation was observed between the ligand structural dynamics and the rates ofmore » electrocatalytic hydrogen production in acetonitrile, acetonitrile-water, and protic ionic liquid-water mixtures. Specifically, the turnover frequencies correlate inversely with the rates of ring inversion of the amine-containing ligand, as this dynamic process dictates the positioning of the proton relay in the second coordination sphere and therefore governs protonation at either catalytically productive or non-productive sites. This study demonstrates that the dynamic processes involved in proton delivery can be controlled through modifications of the outer coordination sphere of the catalyst, similar to the role of the protein architecture in many enzymes. The present work provides new mechanistic insight into the large rate enhancements observed in aqueous protic ionic liquid media for the [Ni(PPh2NR2)]2+ family of catalysts. The incorporation of controlled structural dynamics as a design parameter to modulate proton delivery in molecular catalysts has enabled H2 production rates that are up to three orders of magnitude faster than the [Ni(PPh2NPh2)]2+complex. The observed turnover frequencies are up to 106 s-1 in acetonitrile-water, and over 107 s-1 in protic ionic liquid-water mixtures, with a minimal increase in overpotential. This material is based upon work supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, and was performed in part using the Molecular Science Computing Facility (MSCF) in the William R. Wiley Environmental Molecular Sciences Laboratory, a DOE national scientific user facility located at Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for DOE.« less

31 CFR 33.102 - Coordinated waiver process.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 31 Money and Finance: Treasury 1 2013-07-01 2013-07-01 false Coordinated waiver process. 33.102 Section 33.102 Money and Finance: Treasury Office of the Secretary of the Treasury WAIVERS FOR STATE INNOVATION § 33.102 Coordinated waiver process. (a) Coordination with applications for waivers under other...

31 CFR 33.102 - Coordinated waiver process.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 31 Money and Finance: Treasury 1 2012-07-01 2012-07-01 false Coordinated waiver process. 33.102 Section 33.102 Money and Finance: Treasury Office of the Secretary of the Treasury WAIVERS FOR STATE INNOVATION § 33.102 Coordinated waiver process. (a) Coordination with applications for waivers under other...

31 CFR 33.102 - Coordinated waiver process.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 31 Money and Finance: Treasury 1 2014-07-01 2014-07-01 false Coordinated waiver process. 33.102 Section 33.102 Money and Finance: Treasury Office of the Secretary of the Treasury WAIVERS FOR STATE INNOVATION § 33.102 Coordinated waiver process. (a) Coordination with applications for waivers under other...

Gala: A Python package for galactic dynamics

NASA Astrophysics Data System (ADS)

Price-Whelan, Adrian M.

2017-10-01

Gala is an Astropy-affiliated Python package for galactic dynamics. Python enables wrapping low-level languages (e.g., C) for speed without losing flexibility or ease-of-use in the user-interface. The API for Gala was designed to provide a class-based and user-friendly interface to fast (C or Cython-optimized) implementations of common operations such as gravitational potential and force evaluation, orbit integration, dynamical transformations, and chaos indicators for nonlinear dynamics. Gala also relies heavily on and interfaces well with the implementations of physical units and astronomical coordinate systems in the Astropy package (astropy.units and astropy.coordinates). Gala was designed to be used by both astronomical researchers and by students in courses on gravitational dynamics or astronomy. It has already been used in a number of scientific publications and has also been used in graduate courses on Galactic dynamics to, e.g., provide interactive visualizations of textbook material.

Rotation of endosomes demonstrates coordination of molecular motors during axonal transport.

PubMed

Kaplan, Luke; Ierokomos, Athena; Chowdary, Praveen; Bryant, Zev; Cui, Bianxiao

2018-03-01

Long-distance axonal transport is critical to the maintenance and function of neurons. Robust transport is ensured by the coordinated activities of multiple molecular motors acting in a team. Conventional live-cell imaging techniques used in axonal transport studies detect this activity by visualizing the translational dynamics of a cargo. However, translational measurements are insensitive to torques induced by motor activities. By using gold nanorods and multichannel polarization microscopy, we simultaneously measure the rotational and translational dynamics for thousands of axonally transported endosomes. We find that the rotational dynamics of an endosome provide complementary information regarding molecular motor activities to the conventionally tracked translational dynamics. Rotational dynamics correlate with translational dynamics, particularly in cases of increased rotation after switches between kinesin- and dynein-mediated transport. Furthermore, unambiguous measurement of nanorod angle shows that endosome-contained nanorods align with the orientation of microtubules, suggesting a direct mechanical linkage between the ligand-receptor complex and the microtubule motors.

Large-Eddy Simulation Analysis of Unsteady Separation Over a Pitching Airfoil at High Reynolds Number

DTIC Science & Technology

2013-12-24

channel flow using explicit filtering and dynamic mixed models, Physics of Fluids, (08 2012): 0. doi : 10.1063/1.4745007 Satbir Singh, Donghyun You...08 2013): 0. doi : 10.1016/j.ijheatfluidflow.2013.02.008 TOTAL: 2 Received Paper TOTAL: Number of Papers published in non peer-reviewed journals...coordinate xi Cartesian coordinates y Wall-normal coordinate z Cross-stream coordinate Greek Symbols α Angle of attack δ Dirac delta function; boundary

CELFE: Coupled Eulerian-Lagrangian Finite Element program for high velocity impact. Part 1: Theory and formulation. [hydroelasto-viscoplastic model

NASA Technical Reports Server (NTRS)

Lee, C. H.

1978-01-01

A 3-D finite element program capable of simulating the dynamic behavior in the vicinity of the impact point, together with predicting the dynamic response in the remaining part of the structural component subjected to high velocity impact is discussed. The finite algorithm is formulated in a general moving coordinate system. In the vicinity of the impact point contained by a moving failure front, the relative velocity of the coordinate system will approach the material particle velocity. The dynamic behavior inside the region is described by Eulerian formulation based on a hydroelasto-viscoplastic model. The failure front which can be regarded as the boundary of the impact zone is described by a transition layer. The layer changes the representation from the Eulerian mode to the Lagrangian mode outside the failure front by varying the relative velocity of the coordinate system to zero. The dynamic response in the remaining part of the structure described by the Lagrangian formulation is treated using advanced structural analysis. An interfacing algorithm for coupling CELFE with NASTRAN is constructed to provide computational capabilities for large structures.

Design of specially adapted reactive coordinates to economically compute potential and kinetic energy operators including geometry relaxation

NASA Astrophysics Data System (ADS)

Thallmair, Sebastian; Roos, Matthias K.; de Vivie-Riedle, Regina

2016-06-01

Quantum dynamics simulations require prior knowledge of the potential energy surface as well as the kinetic energy operator. Typically, they are evaluated in a low-dimensional subspace of the full configuration space of the molecule as its dimensionality increases proportional to the number of atoms. This entails the challenge to find the most suitable subspace. We present an approach to design specially adapted reactive coordinates spanning this subspace. In addition to the essential geometric changes, these coordinates take into account the relaxation of the non-reactive coordinates without the necessity of performing geometry optimizations at each grid point. The method is demonstrated for an ultrafast photoinduced bond cleavage in a commonly used organic precursor for the generation of electrophiles. The potential energy surfaces for the reaction as well as the Wilson G-matrix as part of the kinetic energy operator are shown for a complex chemical reaction, both including the relaxation of the non-reactive coordinates on equal footing. A microscopic interpretation of the shape of the G-matrix elements allows to analyze the impact of the non-reactive coordinates on the kinetic energy operator. Additionally, we compare quantum dynamics simulations with and without the relaxation of the non-reactive coordinates included in the kinetic energy operator to demonstrate its influence.

Design of specially adapted reactive coordinates to economically compute potential and kinetic energy operators including geometry relaxation.

PubMed

Thallmair, Sebastian; Roos, Matthias K; de Vivie-Riedle, Regina

2016-06-21

Quantum dynamics simulations require prior knowledge of the potential energy surface as well as the kinetic energy operator. Typically, they are evaluated in a low-dimensional subspace of the full configuration space of the molecule as its dimensionality increases proportional to the number of atoms. This entails the challenge to find the most suitable subspace. We present an approach to design specially adapted reactive coordinates spanning this subspace. In addition to the essential geometric changes, these coordinates take into account the relaxation of the non-reactive coordinates without the necessity of performing geometry optimizations at each grid point. The method is demonstrated for an ultrafast photoinduced bond cleavage in a commonly used organic precursor for the generation of electrophiles. The potential energy surfaces for the reaction as well as the Wilson G-matrix as part of the kinetic energy operator are shown for a complex chemical reaction, both including the relaxation of the non-reactive coordinates on equal footing. A microscopic interpretation of the shape of the G-matrix elements allows to analyze the impact of the non-reactive coordinates on the kinetic energy operator. Additionally, we compare quantum dynamics simulations with and without the relaxation of the non-reactive coordinates included in the kinetic energy operator to demonstrate its influence.

Global Langevin model of multidimensional biomolecular dynamics.

PubMed

Schaudinnus, Norbert; Lickert, Benjamin; Biswas, Mithun; Stock, Gerhard

2016-11-14

Molecular dynamics simulations of biomolecular processes are often discussed in terms of diffusive motion on a low-dimensional free energy landscape F(). To provide a theoretical basis for this interpretation, one may invoke the system-bath ansatz á la Zwanzig. That is, by assuming a time scale separation between the slow motion along the system coordinate x and the fast fluctuations of the bath, a memory-free Langevin equation can be derived that describes the system's motion on the free energy landscape F(), which is damped by a friction field and driven by a stochastic force that is related to the friction via the fluctuation-dissipation theorem. While the theoretical formulation of Zwanzig typically assumes a highly idealized form of the bath Hamiltonian and the system-bath coupling, one would like to extend the approach to realistic data-based biomolecular systems. Here a practical method is proposed to construct an analytically defined global model of structural dynamics. Given a molecular dynamics simulation and adequate collective coordinates, the approach employs an "empirical valence bond"-type model which is suitable to represent multidimensional free energy landscapes as well as an approximate description of the friction field. Adopting alanine dipeptide and a three-dimensional model of heptaalanine as simple examples, the resulting Langevin model is shown to reproduce the results of the underlying all-atom simulations. Because the Langevin equation can also be shown to satisfy the underlying assumptions of the theory (such as a delta-correlated Gaussian-distributed noise), the global model provides a correct, albeit empirical, realization of Zwanzig's formulation. As an application, the model can be used to investigate the dependence of the system on parameter changes and to predict the effect of site-selective mutations on the dynamics.

Symbolic generation of elastic rotor blade equations using a FORTRAN processor and numerical study on dynamic inflow effects on the stability of helicopter rotors

NASA Technical Reports Server (NTRS)

Reddy, T. S. R.

1986-01-01

The process of performing an automated stability analysis for an elastic-bladed helicopter rotor is discussed. A symbolic manipulation program, written in FORTRAN, is used to aid in the derivation of the governing equations of motion for the rotor. The blades undergo coupled bending and torsional deformations. Two-dimensional quasi-steady aerodynamics below stall are used. Although reversed flow effects are neglected, unsteady effects, modeled as dynamic inflow are included. Using a Lagrangian approach, the governing equations are derived in generalized coordinates using the symbolic program. The program generates the steady and perturbed equations and writes into subroutines to be called by numerical routines. The symbolic program can operate on both expressions and matrices. For the case of hovering flight, the blade and dynamic inflow equations are converted to equations in a multiblade coordinate system by rearranging the coefficients of the equations. For the case of forward flight, the multiblade equations are obtained through the symbolic program. The final multiblade equations are capable of accommodating any number of elastic blade modes. The computer implementation of this procedure consists of three stages: (1) the symbolic derivation of equations; (2) the coding of the equations into subroutines; and (3) the numerical study after identifying mass, damping, and stiffness coefficients. Damping results are presented in hover and in forward flight with and without dynamic inflow effects for various rotor blade models, including rigid blade lag-flap, elastic flap-lag, flap-lag-torsion, and quasi-static torsion. Results from dynamic inflow effects which are obtained from a lift deficiency function for a quasi-static inflow model in hover are also presented.

Global Langevin model of multidimensional biomolecular dynamics

NASA Astrophysics Data System (ADS)

Schaudinnus, Norbert; Lickert, Benjamin; Biswas, Mithun; Stock, Gerhard

2016-11-01

Molecular dynamics simulations of biomolecular processes are often discussed in terms of diffusive motion on a low-dimensional free energy landscape F ( 𝒙 ) . To provide a theoretical basis for this interpretation, one may invoke the system-bath ansatz á la Zwanzig. That is, by assuming a time scale separation between the slow motion along the system coordinate x and the fast fluctuations of the bath, a memory-free Langevin equation can be derived that describes the system's motion on the free energy landscape F ( 𝒙 ) , which is damped by a friction field and driven by a stochastic force that is related to the friction via the fluctuation-dissipation theorem. While the theoretical formulation of Zwanzig typically assumes a highly idealized form of the bath Hamiltonian and the system-bath coupling, one would like to extend the approach to realistic data-based biomolecular systems. Here a practical method is proposed to construct an analytically defined global model of structural dynamics. Given a molecular dynamics simulation and adequate collective coordinates, the approach employs an "empirical valence bond"-type model which is suitable to represent multidimensional free energy landscapes as well as an approximate description of the friction field. Adopting alanine dipeptide and a three-dimensional model of heptaalanine as simple examples, the resulting Langevin model is shown to reproduce the results of the underlying all-atom simulations. Because the Langevin equation can also be shown to satisfy the underlying assumptions of the theory (such as a delta-correlated Gaussian-distributed noise), the global model provides a correct, albeit empirical, realization of Zwanzig's formulation. As an application, the model can be used to investigate the dependence of the system on parameter changes and to predict the effect of site-selective mutations on the dynamics.

Rho-guanine nucleotide exchange factors during development

PubMed Central

Mulinari, Shai

2010-01-01

The development of multicellular organisms is associated with extensive rearrangements of tissues and cell sheets. The driving force for these rearrangements is generated mostly by the actin cytoskeleton. In order to permit the reproducible development of a specific body plan, dynamic reorganization of the actin cytoskeleton must be precisely coordinated in space and time. GTP-exchange factors that activate small GTPases of the Rho family play an important role in this process. Here we review the role of this class of cytoskeletal regulators during important developmental processes such as epithelial morphogenesis, cytokinesis, cell migration, cell polarity, neuronal growth cone extension and phagocytosis in different model systems. PMID:21686118

Collaboration in a Wireless Grid Innovation Testbed by Virtual Consortium

NASA Astrophysics Data System (ADS)

Treglia, Joseph; Ramnarine-Rieks, Angela; McKnight, Lee

This paper describes the formation of the Wireless Grid Innovation Testbed (WGiT) coordinated by a virtual consortium involving academic and non-academic entities. Syracuse University and Virginia Tech are primary university partners with several other academic, government, and corporate partners. Objectives include: 1) coordinating knowledge sharing, 2) defining key parameters for wireless grids network applications, 3) dynamically connecting wired and wireless devices, content and users, 4) linking to VT-CORNET, Virginia Tech Cognitive Radio Network Testbed, 5) forming ad hoc networks or grids of mobile and fixed devices without a dedicated server, 6) deepening understanding of wireless grid application, device, network, user and market behavior through academic, trade and popular publications including online media, 7) identifying policy that may enable evaluated innovations to enter US and international markets and 8) implementation and evaluation of the international virtual collaborative process.

Neural coordination during reach-to-grasp

PubMed Central

Vaidya, Mukta; Kording, Konrad; Saleh, Maryam; Takahashi, Kazutaka

2015-01-01

When reaching to grasp, we coordinate how we preshape the hand with how we move it. To ask how motor cortical neurons participate in this coordination, we examined the interactions between reach- and grasp-related neuronal ensembles while monkeys reached to grasp a variety of different objects in different locations. By describing the dynamics of these two ensembles as trajectories in a low-dimensional state space, we examined their coupling in time. We found evidence for temporal compensation across many different reach-to-grasp conditions such that if one neural trajectory led in time the other tended to catch up, reducing the asynchrony between the trajectories. Granger causality revealed bidirectional interactions between reach and grasp neural trajectories beyond that which could be attributed to the joint kinematics that were consistently stronger in the grasp-to-reach direction. Characterizing cortical coordination dynamics provides a new framework for understanding the functional interactions between neural populations. PMID:26224773

Analysis on the dynamic error for optoelectronic scanning coordinate measurement network

NASA Astrophysics Data System (ADS)

Shi, Shendong; Yang, Linghui; Lin, Jiarui; Guo, Siyang; Ren, Yongjie

2018-01-01

Large-scale dynamic three-dimension coordinate measurement technique is eagerly demanded in equipment manufacturing. Noted for advantages of high accuracy, scale expandability and multitask parallel measurement, optoelectronic scanning measurement network has got close attention. It is widely used in large components jointing, spacecraft rendezvous and docking simulation, digital shipbuilding and automated guided vehicle navigation. At present, most research about optoelectronic scanning measurement network is focused on static measurement capacity and research about dynamic accuracy is insufficient. Limited by the measurement principle, the dynamic error is non-negligible and restricts the application. The workshop measurement and positioning system is a representative which can realize dynamic measurement function in theory. In this paper we conduct deep research on dynamic error resources and divide them two parts: phase error and synchronization error. Dynamic error model is constructed. Based on the theory above, simulation about dynamic error is carried out. Dynamic error is quantized and the rule of volatility and periodicity has been found. Dynamic error characteristics are shown in detail. The research result lays foundation for further accuracy improvement.

Switching among graphic patterns is governed by oscillatory coordination dynamics: implications for understanding handwriting

PubMed Central

Zanone, Pier-Giorgio; Athènes, Sylvie

2013-01-01

Revisiting an original idea by Hollerbach (1981), previous work has established that the production of graphic shapes, assumed to be the blueprint for handwriting, is governed by the dynamics of orthogonal non-linear coupled oscillators. Such dynamics determines few stable coordination patterns, giving rise to a limited set of preferred graphic shapes, namely, four lines and four ellipsoids independent of orientation. The present study investigates the rules of switching among such graphic coordination patterns. Seven participants were required to voluntarily switch within twelve pairs of shapes presented on a graphic tablet. In line with previous theoretical and experimental work on bimanual coordination, results corroborated our hypothesis that the relative stability of the produced coordination patterns determines the time needed for switching: the transition to a more stable pattern was shorter, and inversely. Moreover, switching between patterns with the same orientation but different eccentricities was faster than with a change in orientation. Nonetheless, the switching time covaried strictly with the change in relative phase effected by the transition between two shapes, whether this implied a change in eccentricity or in orientation. These findings suggest a new operational definition of what the (motor) units or strokes of handwriting are and shed a novel light on how coarticulation and recruitment of degrees of freedom may occur in graphic skills. They also yield some leads for understanding the acquisition and the neural underpinnings of handwriting. PMID:24069014

Coordinated Speed Oscillations in Schooling Killifish Enrich Social Communication

NASA Astrophysics Data System (ADS)

Swain, Daniel T.; Couzin, Iain D.; Leonard, Naomi Ehrich

2015-10-01

We examine the spatial dynamics of individuals in small schools of banded killifish ( Fundulus diaphanus) that exhibit rhythmic, oscillating speed, typically with sustained, coordinated, out-of-phase speed oscillations as they move around a shallow water tank. We show that the relative motion among the fish yields a periodically time-varying network of social interactions that enriches visually driven social communication. The oscillations lead to the regular making and breaking of occlusions, which we term "switching." We show that the rate of convergence to consensus (biologically, the capacity for individuals in groups to achieve effective coordinated motion) governed by the switching outperforms static alternatives, and performs as well as the less practical case of every fish sensing every other fish. We show further that the oscillations in speed yield oscillations in relative bearing between fish over a range that includes the angles previously predicted to be optimal for a fish to detect changes in heading and speed of its neighbors. To investigate systematically, we derive and analyze a dynamic model of interacting agents that move with oscillatory speed. We show that coordinated circular motion of the school leads to systematic cycling of spatial ordering of agents and possibilities for enriched spatial density of measurements of the external environment. Our results highlight the potential benefits of dynamic communication topologies in collective animal behavior, and suggest new, useful control laws for the distributed coordination of mobile robotic networks.

Potential coordination role between O-GlcNAcylation and epigenetics.

PubMed

Wu, Donglu; Cai, Yong; Jin, Jingji

2017-10-01

Dynamic changes of the post-translational O-GlcNAc modification (O-GlcNAcylation) are controlled by O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) and the glycoside hydrolase O-GlcNAcase (OGA) in cells. O-GlcNAcylation often occurs on serine (Ser) and threonine (Thr) residues of the specific substrate proteins via the addition of O-GlcNAc group by OGT. It has been known that O-GlcNAcylation is not only involved in many fundamental cellular processes, but also plays an important role in cancer development through various mechanisms. Recently, accumulating data reveal that O-GlcNAcylation at histones or non-histone proteins can lead to the start of the subsequent biological processes, suggesting that O-GlcNAcylation as 'protein code' or 'histone code' may provide recognition platforms or executive instructions for subsequent recruitment of proteins to carry out the specific functions. In this review, we summarize the interaction of O-GlcNAcylation and epigenetic changes, introduce recent research findings that link crosstalk between O-GlcNAcylation and epigenetic changes, and speculate on the potential coordination role of O-GlcNAcylation with epigenetic changes in intracellular biological processes.

Structural and dynamic properties of propane coordinated to TpRh(CNR) from a confrontation between theory and experiment

PubMed Central

Clot, Eric; Eisenstein, Odile; Jones, William D.

2007-01-01

Density functional calculations with the B3PW91 functional have been carried out on the TpRh(CNMe) species [Tp = HB(pyrazolyl)3] as a model for Tp′Rh(CNCH2CMe3) [Tp′ = HB(3,5-dimethylpyrazolyl)3] in interaction with propane. Two σ complexes have been found as minima coordinated through either a methyl or a methylene CH bond, the former being more stable. The approach of the alkane to TpRh(CNMe) has been studied. Although no transition state could be located, study of this path reveals the key importance of the partial decoordination of one pyrazole ring. The full coordination of the alkane can only be achieved when the metal is essentially in a square pyramid coordination with one of the three pyrazole groups only weakly interacting with Rh. The main reaction of the methyl σ complex is oxidative addition, leading to the n-propyl hydride complex. In contrast, two reactions are found for the methylene σ complex: (i) oxidative addition to give the isopropyl complex and (ii) exchange between the secondary and primary CH bonds to convert the methylene complex of propane into a methyl complex of propane. This latter reaction has a much lower barrier than the oxidative addition at the methylene CH bond. The results account well for most of the experimental results obtained from kinetic studies. Steric factors are found to control the energy barriers between these various processes, disfavoring any process that brings the central carbon into close proximity to Rh. PMID:17412834

Characterization of bacterial community dynamics in a full-scale drinking water treatment plant.

PubMed

Li, Cuiping; Ling, Fangqiong; Zhang, Minglu; Liu, Wen-Tso; Li, Yuxian; Liu, Wenjun

2017-01-01

Understanding the spatial and temporal dynamics of microbial communities in drinking water systems is vital to securing the microbial safety of drinking water. The objective of this study was to comprehensively characterize the dynamics of microbial biomass and bacterial communities at each step of a full-scale drinking water treatment plant in Beijing, China. Both bulk water and biofilm samples on granular activated carbon (GAC) were collected over 9months. The proportion of cultivable cells decreased during the treatment processes, and this proportion was higher in warm season than cool season, suggesting that treatment processes and water temperature probably had considerable impact on the R2A cultivability of total bacteria. 16s rRNA gene based 454 pyrosequencing analysis of the bacterial community revealed that Proteobacteria predominated in all samples. The GAC biofilm harbored a distinct population with a much higher relative abundance of Acidobacteria than water samples. Principle coordinate analysis and one-way analysis of similarity indicated that the dynamics of the microbial communities in bulk water and biofilm samples were better explained by the treatment processes rather than by sampling time, and distinctive changes of the microbial communities in water occurred after GAC filtration. Furthermore, 20 distinct OTUs contributing most to the dissimilarity among samples of different sampling locations and 6 persistent OTUs present in the entire treatment process flow were identified. Overall, our findings demonstrate the significant effects that treatment processes have on the microbial biomass and community fluctuation and provide implications for further targeted investigation on particular bacteria populations. Copyright © 2016. Published by Elsevier B.V.

Coupling dynamics in speech gestures: amplitude and rate influences.

PubMed

van Lieshout, Pascal H H M

2017-08-01

Speech is a complex oral motor function that involves multiple articulators that need to be coordinated in space and time at relatively high movement speeds. How this is accomplished remains an important and largely unresolved empirical question. From a coordination dynamics perspective, coordination involves the assembly of coordinative units that are characterized by inherently stable coupling patterns that act as attractor states for task-specific actions. In the motor control literature, one particular model formulated by Haken et al. (Biol Cybern 51(5):347-356, 1985) or HKB has received considerable attention in the way it can account for changes in the nature and stability of specific coordination patterns between limbs or between limbs and external stimuli. In this model (and related versions), movement amplitude is considered a critical factor in the formation of these patterns. Several studies have demonstrated its role for bimanual coordination and similar types of tasks, but for speech motor control such studies are lacking. The current study describes a systematic approach to evaluate the impact of movement amplitude and movement duration on coordination stability in the production of bilabial and tongue body gestures for specific vowel-consonant-vowel strings. The vowel combinations that were used induced a natural contrast in movement amplitude at three speaking rate conditions (slow, habitual, fast). Data were collected on ten young adults using electromagnetic articulography, recording movement data from lips and tongue with high temporal and spatial precision. The results showed that with small movement amplitudes there is a decrease in coordination stability, independent from movement duration. These findings were found to be robust across all individuals and are interpreted as further evidence that principles of coupling dynamics operate in the oral motor control system similar to other motor systems and can be explained in terms of coupling mechanisms between neural oscillators (organized in networks) and effector systems. The relevance of these findings for understanding motor control issues in people with speech disorders is discussed as well.

Cerebral hierarchies: predictive processing, precision and the pulvinar

PubMed Central

Kanai, Ryota; Komura, Yutaka; Shipp, Stewart; Friston, Karl

2015-01-01

This paper considers neuronal architectures from a computational perspective and asks what aspects of neuroanatomy and neurophysiology can be disclosed by the nature of neuronal computations? In particular, we extend current formulations of the brain as an organ of inference—based upon hierarchical predictive coding—and consider how these inferences are orchestrated. In other words, what would the brain require to dynamically coordinate and contextualize its message passing to optimize its computational goals? The answer that emerges rests on the delicate (modulatory) gain control of neuronal populations that select and coordinate (prediction error) signals that ascend cortical hierarchies. This is important because it speaks to a hierarchical anatomy of extrinsic (between region) connections that form two distinct classes, namely a class of driving (first-order) connections that are concerned with encoding the content of neuronal representations and a class of modulatory (second-order) connections that establish context—in the form of the salience or precision ascribed to content. We explore the implications of this distinction from a formal perspective (using simulations of feature–ground segregation) and consider the neurobiological substrates of the ensuing precision-engineered dynamics, with a special focus on the pulvinar and attention. PMID:25823866

Furfural reduction mechanism of a zinc-dependent alcohol dehydrogenase from Cupriavidus necator JMP134

PubMed Central

Kang, ChulHee; Hayes, Robert; Sanchez, Emiliano J.; Webb, Brian N.; Li, Qunrui; Hooper, Travis; Nissen, Mark S.; Xun, Luying

2012-01-01

Summary FurX is a tetrameric Zn-dependent alcohol dehydrogenase (ADH) from Cupriavidus necator JMP134. The enzyme rapidly reduces furfural with NADH as the reducing power. For the first time among characterized ADHs, the high-resolution structures of all reaction steps were obtained in a time-resolved manner, thereby illustrating the complete catalytic events of NADH-dependent reduction of furfural and the dynamic Zn2+ coordination among Glu66, water, substrate and product. In the fully closed conformation of the NADH complex, the catalytic turnover proved faster than observed for the partially closed conformation due to an effective proton transfer network. The domain motion triggered by NAD(H) association/dissociation appeared to facilitate dynamic interchanges in Zn2+ coordination with substrate and product molecules, ultimately increasing the enzymatic turnover rate. NAD+ dissociation appeared to be a slow process, involving multiple steps in concert with a domain opening and reconfiguration of Glu66. This agrees with the report that the cofactor is not dissociated from FurX during ethanol-dependent reduction of furfural, in which ethanol reduces NAD+ to NADH that is subsequently used for furfural reduction. PMID:22081946

High-Resolution Free-Energy Landscape Analysis of α-Helical Protein Folding: HP35 and Its Double Mutant

PubMed Central

2013-01-01

The free-energy landscape can provide a quantitative description of folding dynamics, if determined as a function of an optimally chosen reaction coordinate. Here, we construct the optimal coordinate and the associated free-energy profile for all-helical proteins HP35 and its norleucine (Nle/Nle) double mutant, based on realistic equilibrium folding simulations [Piana et al. Proc. Natl. Acad. Sci. U.S.A.2012, 109, 17845]. From the obtained profiles, we directly determine such basic properties of folding dynamics as the configurations of the minima and transition states (TS), the formation of secondary structure and hydrophobic core during the folding process, the value of the pre-exponential factor and its relation to the transition path times, the relation between the autocorrelation times in TS and minima. We also present an investigation of the accuracy of the pre-exponential factor estimation based on the transition-path times. Four different estimations of the pre-exponential factor for both proteins give k0–1 values of approximately a few tens of nanoseconds. Our analysis gives detailed information about folding of the proteins and can serve as a rigorous common language for extensive comparison between experiment and simulation. PMID:24348206

High-Resolution Free-Energy Landscape Analysis of α-Helical Protein Folding: HP35 and Its Double Mutant.

PubMed

Banushkina, Polina V; Krivov, Sergei V

2013-12-10

The free-energy landscape can provide a quantitative description of folding dynamics, if determined as a function of an optimally chosen reaction coordinate. Here, we construct the optimal coordinate and the associated free-energy profile for all-helical proteins HP35 and its norleucine (Nle/Nle) double mutant, based on realistic equilibrium folding simulations [Piana et al. Proc. Natl. Acad. Sci. U.S.A. 2012 , 109 , 17845]. From the obtained profiles, we directly determine such basic properties of folding dynamics as the configurations of the minima and transition states (TS), the formation of secondary structure and hydrophobic core during the folding process, the value of the pre-exponential factor and its relation to the transition path times, the relation between the autocorrelation times in TS and minima. We also present an investigation of the accuracy of the pre-exponential factor estimation based on the transition-path times. Four different estimations of the pre-exponential factor for both proteins give k 0 -1 values of approximately a few tens of nanoseconds. Our analysis gives detailed information about folding of the proteins and can serve as a rigorous common language for extensive comparison between experiment and simulation.

Collective Cellular Decision-Making Gives Developmental Plasticity: A Model of Signaling in Branching Roots

NASA Astrophysics Data System (ADS)

McCleery, W. Tyler; Mohd-Radzman, Nadiatul A.; Grieneisen, Veronica A.

Cells within tissues can be regarded as autonomous entities that respond to their local environment and signaling from neighbors. Cell coordination is particularly important in plants, where root architecture must strategically invest resources for growth to optimize nutrient acquisition. Thus, root cells are constantly adapting to environmental cues and neighbor communication in a non-linear manner. To explain such plasticity, we view the root as a swarm of coupled multi-cellular structures, ''metamers'', rather than as a continuum of identical cells. These metamers are individually programmed to achieve a local objective - developing a lateral root primordia, which aids in local foraging of nutrients. Collectively, such individual attempts may be halted, structuring root architecture as an emergent behavior. Each metamer's decision to branch is coordinated locally and globally through hormone signaling, including processes of controlled diffusion, active polar transport, and dynamic feedback. We present a physical model of the signaling mechanism that coordinates branching decisions in response to the environment. This work was funded by the European Commission 7th Framework Program, Project No. 601062, SWARM-ORGAN.

Coordinating IMC-PID and adaptive SMC controllers for a PEMFC.

PubMed

Wang, Guo-Liang; Wang, Yong; Shi, Jun-Hai; Shao, Hui-He

2010-01-01

For a Proton Exchange Membrane Fuel Cell (PEMFC) power plant with a methanol reformer, the process parameters and power output are considered simultaneously to avoid violation of the constraints and to keep the fuel cell power plant safe and effective. In this paper, a novel coordinating scheme is proposed by combining an Internal Model Control (IMC) based PID Control and adaptive Sliding Mode Control (SMC). The IMC-PID controller is designed for the reformer of the fuel flow rate according to the expected first-order dynamic properties. The adaptive SMC controller of the fuel cell current has been designed using the constant plus proportional rate reaching law. The parameters of the SMC controller are adaptively tuned according to the response of the fuel flow rate control system. When the power output controller feeds back the current references to these two controllers, the coordinating controllers system works in a system-wide way. The simulation results of the PEMFC power plant demonstrate the effectiveness of the proposed method. 2009 ISA. Published by Elsevier Ltd. All rights reserved.

Beyond a series of security nets: Applying STAMP & STPA to port security

DOE PAGES

Williams, Adam D.

2015-11-17

Port security is an increasing concern considering the significant role of ports in global commerce and today’s increasingly complex threat environment. Current approaches to port security mirror traditional models of accident causality -- ‘a series of security nets’ based on component reliability and probabilistic assumptions. Traditional port security frameworks result in isolated and inconsistent improvement strategies. Recent work in engineered safety combines the ideas of hierarchy, emergence, control and communication into a new paradigm for understanding port security as an emergent complex system property. The ‘System-Theoretic Accident Model and Process (STAMP)’ is a new model of causality based on systemsmore » and control theory. The associated analysis process -- System Theoretic Process Analysis (STPA) -- identifies specific technical or procedural security requirements designed to work in coordination with (and be traceable to) overall port objectives. This process yields port security design specifications that can mitigate (if not eliminate) port security vulnerabilities related to an emphasis on component reliability, lack of coordination between port security stakeholders or economic pressures endemic in the maritime industry. As a result, this article aims to demonstrate how STAMP’s broader view of causality and complexity can better address the dynamic and interactive behaviors of social, organizational and technical components of port security.« less

Beyond a series of security nets: Applying STAMP & STPA to port security

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, Adam D.

Port security is an increasing concern considering the significant role of ports in global commerce and today’s increasingly complex threat environment. Current approaches to port security mirror traditional models of accident causality -- ‘a series of security nets’ based on component reliability and probabilistic assumptions. Traditional port security frameworks result in isolated and inconsistent improvement strategies. Recent work in engineered safety combines the ideas of hierarchy, emergence, control and communication into a new paradigm for understanding port security as an emergent complex system property. The ‘System-Theoretic Accident Model and Process (STAMP)’ is a new model of causality based on systemsmore » and control theory. The associated analysis process -- System Theoretic Process Analysis (STPA) -- identifies specific technical or procedural security requirements designed to work in coordination with (and be traceable to) overall port objectives. This process yields port security design specifications that can mitigate (if not eliminate) port security vulnerabilities related to an emphasis on component reliability, lack of coordination between port security stakeholders or economic pressures endemic in the maritime industry. As a result, this article aims to demonstrate how STAMP’s broader view of causality and complexity can better address the dynamic and interactive behaviors of social, organizational and technical components of port security.« less

The Population Care Coordination Process.

PubMed

Rushton, Sharron

2015-01-01

The purpose of the article was to outline a population-based approach to providing care coordination. The Population Care Coordination Process provides a framework for each provider and/or organization to provide multilevel care based on population- and patient-centered principles. The Population Care Coordination Process is scalable. It can be utilized in a smaller scale such as single provider office or in a larger scale such as an accountable care organization. There are many issues within our current health care structure that must be addressed. Care coordination has been identified as a potential solution to address the needs of complex patients within the system. The expansion to consider populations allows for a more targeted and efficient approach. The population care process entails a data-driven approach to care coordination. The inclusion of populations in the care coordination process provides an opportunity to maximize efforts and improve outcomes.

Scientific basis for learning transfer from movements to urinary bladder functions for bladder repair in human patients with CNS injury.

PubMed

Schalow, G

2010-01-01

Coordination Dynamics Therapy (CDT) has been shown to be able to partly repair CNS injury. The repair is based on a movement-based re-learning theory which requires at least three levels of description: the movement or pattern (and anamnesis) level, the collective variable level, and the neuron level. Upon CDT not only the actually performed movement pattern itself is repaired, but the entire dynamics of CNS organization is improved, which is the theoretical basis for (re-) learning transfer. The transfer of learning for repair from jumping on springboard and exercising on a special CDT and recording device to urinary bladder functions is investigated at the neuron level. At the movement or pattern level, the improvement of central nervous system (CNS) functioning in human patients can be seen (or partly measured) by the improvement of the performance of the pattern. At the collective variable level, coordination tendencies can be measured by the so-called 'coordination dynamics' before, during and after treatment. At the neuron level, re-learning can additionally be assessed by surface electromyography (sEMG) as alterations of single motor unit firings and motor programs. But to express the ongoing interaction between the numerous neural, muscular, and metabolic elements involved in perception and action, it is relevant to inquire how the individual afferent and efferent neurons adjust their phase and frequency coordination to other neurons to satisfy learning task requirements. With the single-nerve fibre action potential recording method it was possible to measure that distributed single neurons communicate by phase and frequency coordination. It is shown that this timed firing of neurons is getting impaired upon injury and has to be improved by learning The stability of phase and frequency coordination among afferent and efferent neuron firings can be related to pattern stability. The stability of phase and frequency coordination at the neuron level can therefore be assessed integratively at the (non-invasive) collective variable level by the arrhythmicity of turning (coordination dynamics) when a patient is exercising on a special CDT device. Upon jumping on springboard and exercising on the special CDT device, the intertwined neuronal networks, subserving movements (somatic) and urinary bladder functions (autonomic and somatic) in the sacral spinal cord, are synchronously activated and entrained to give rise to learning transfer from movements to bladder functions. Jumping on springboard and other movements primarily repair the pattern dynamics, whereas the exactly coordinated performed movements, performed on the special CDT device for turning, primarily improve the preciseness of the timed firing of neurons. The synchronous learning of perceptuomotor and perceptuobladder functioning from a dynamical perspective (giving rise to learning transfer) can be understood at the neuron level. Especially the activated phase and frequency coordination upon natural stimulation under physiologic and pathophysiologic conditions among a and gamma-motoneurons, muscle spindle afferents, touch and pain afferents, and urinary bladder stretch and tension receptor afferents in the human sacral spinal cord make understandable that somatic and parasympathetic functions are integrated in their functioning and give rise to learning transfer from movements to bladder functions. The power of this human treatment research project lies in the unit of theory, diagnostic/measurement, and praxis, namely that CNS injury can partly be repaired, including urinary bladder functions, and the repair can partly be understood even at the neuron level of description in human.

Dynamics of Geometrically Nonlinear Elastic Nonthin Anisotropic Shells of Variable Thickness

NASA Astrophysics Data System (ADS)

Marchuk, M. V.; Tuchapskii, R. I.

2017-11-01

A theory of dynamic elastic geometrically nonlinear deformation of nonthin anisotropic shells with variable thickness is constructed. Shells are assumed asymmetric about the reference surface. Functions are expanded into Legendre series. The basic equations are written in a coordinate system aligned with the lines of curvature of the reference surface. The equations of motion and appropriate boundary conditions are obtained using the Hamilton-Ostrogradsky variational principle. The change in metric across the thickness is taken into account. The theory assumes that the refinement process is regular and allows deriving equations including products of terms of Legendre series of unknown functions of arbitrary order. The behavior of a square metallic plate acted upon by a pressure pulse distributed over its face is studied.

Imaging of dynamic ion signaling during root gravitropism.

PubMed

Monshausen, Gabriele B

2015-01-01

Gravitropic signaling is a complex process that requires the coordinated action of multiple cell types and tissues. Ca(2+) and pH signaling are key components of gravitropic signaling cascades and can serve as useful markers to dissect the molecular machinery mediating plant gravitropism. To monitor dynamic ion signaling, imaging approaches combining fluorescent ion sensors and confocal fluorescence microscopy are employed, which allow the visualization of pH and Ca(2+) changes at the level of entire tissues, while also providing high spatiotemporal resolution. Here, I describe procedures to prepare Arabidopsis seedlings for live cell imaging and to convert a microscope for vertical stage fluorescence microscopy. With this imaging system, ion signaling can be monitored during all phases of the root gravitropic response.

Scaling Limit of Symmetric Random Walk in High-Contrast Periodic Environment

NASA Astrophysics Data System (ADS)

Piatnitski, A.; Zhizhina, E.

2017-11-01

The paper deals with the asymptotic properties of a symmetric random walk in a high contrast periodic medium in Z^d, d≥1. From the existing homogenization results it follows that under diffusive scaling the limit behaviour of this random walk need not be Markovian. The goal of this work is to show that if in addition to the coordinate of the random walk in Z^d we introduce an extra variable that characterizes the position of the random walk inside the period then the limit dynamics of this two-component process is Markov. We describe the limit process and observe that the components of the limit process are coupled. We also prove the convergence in the path space for the said random walk.

Event-by-Event Study of Space-Time Dynamics in Flux-Tube Fragmentation

DOE PAGES

Wong, Cheuk-Yin

2017-05-25

In the semi-classical description of the flux-tube fragmentation process for hadron production and hadronization in high-energymore » $e^+e^-$ annihilations and $pp$ collisions, the rapidity-space-time ordering and the local conservation laws of charge, flavor, and momentum provide a set of powerful tools that may allow the reconstruction of the space-time dynamics of quarks and mesons in exclusive measurements of produced hadrons, on an event-by-event basis. We propose procedures to reconstruct the space-time dynamics from event-by-event exclusive hadron data to exhibit explicitly the ordered chain of hadrons produced in a flux tube fragmentation. As a supplementary tool, we infer the average space-time coordinates of the $q$-$$\\bar q$$ pair production vertices from the $$\\pi^-$$ rapidity distribution data obtained by the NA61/SHINE Collaboration in $pp$ collisions at $$\\sqrt{s}$$ = 6.3 to 17.3 GeV.« less

Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes.

PubMed

Lin, Milo M; Meinhold, Lars; Shorokhov, Dmitry; Zewail, Ahmed H

2008-08-07

A 2D free-energy landscape model is presented to describe the (un)folding transition of DNA/RNA hairpins, together with molecular dynamics simulations and experimental findings. The dependence of the (un)folding transition on the stem sequence and the loop length is shown in the enthalpic and entropic contributions to the free energy. Intermediate structures are well defined by the two coordinates of the landscape during (un)zipping. Both the free-energy landscape model and the extensive molecular dynamics simulations totaling over 10 mus predict the existence of temperature-dependent kinetic intermediate states during hairpin (un)zipping and provide the theoretical description of recent ultrafast temperature-jump studies which indicate that hairpin (un)zipping is, in general, not a two-state process. The model allows for lucid prediction of the collapsed state(s) in simple 2D space and we term it the kinetic intermediate structure (KIS) model.

Satellite-tracking and Earth dynamics research programs

NASA Technical Reports Server (NTRS)

1982-01-01

The activities carried out by the Smithsonian Astrophysical Observatory (SAO) are described. The SAO network continued to track LAGEOS at highest priority for polar motion and Earth rotation studies, and for other geophysical investigations, including crustal dynamics, Earth and ocean tides, and the general development of precision orbit determination. The network performed regular tracking of several other retroreflector satellites including GEOS-1, GEOS-3, BE-C, and Starlette for refined determinations of station coordinates and the Earth's gravity field and for studies of solid Earth dynamics. A major program in laser upgrading continued to improve ranging accuracy and data yield. This program includes an increase in pulse repetition rate from 8 ppm to 30 ppm, a reduction in laser pulse width from 6 nsec to 2 to 3 nsec, improvements in the photoreceiver and the electronics to improve daylight ranging, and an analog pulse detection system to improve range noise and accuracy. Data processing hardware and software are discussed.

Event-by-Event Study of Space-Time Dynamics in Flux-Tube Fragmentation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wong, Cheuk-Yin

In the semi-classical description of the flux-tube fragmentation process for hadron production and hadronization in high-energymore » $e^+e^-$ annihilations and $pp$ collisions, the rapidity-space-time ordering and the local conservation laws of charge, flavor, and momentum provide a set of powerful tools that may allow the reconstruction of the space-time dynamics of quarks and mesons in exclusive measurements of produced hadrons, on an event-by-event basis. We propose procedures to reconstruct the space-time dynamics from event-by-event exclusive hadron data to exhibit explicitly the ordered chain of hadrons produced in a flux tube fragmentation. As a supplementary tool, we infer the average space-time coordinates of the $q$-$$\\bar q$$ pair production vertices from the $$\\pi^-$$ rapidity distribution data obtained by the NA61/SHINE Collaboration in $pp$ collisions at $$\\sqrt{s}$$ = 6.3 to 17.3 GeV.« less

Improving care coordination in the specialty referral process between primary and specialty care.

PubMed

Lin, Caroline Y

2012-01-01

There is growing evidence of sub-optimal care coordination in the US. Care coordination includes the specialty referral process, which involves referral decision-making and information transfer between primary and specialty care. This article summarizes the evidence of sub-optimal care coordination in this process, as well as potential strategies to improve it.

Marcus Theory of Ion-Pairing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roy, Santanu; Baer, Marcel D.; Mundy, Christopher J.

We present a theory for ion pair dissociation and association, motivated by the concepts of the Marcus theory of electron transfer. Despite the extensive research on ion-pairing in many chemical and biological processes, much can be learned from the exploration of collective reaction coordinates. To this end, we explore two reaction coordinates, ion pair distance and coordination number. The study of the correlation between these reaction coordinates provides a new insight into the mechanism and kinetics of ion pair dissociation and association in water. The potential of mean force on these 2D-surfaces computed from molecular dynamics simulations of different monovalentmore » ion pairs reveal a Marcus-like mechanism for ion-pairing: Water molecules rearrange forming an activated coordination state prior to ion pair dissociation or association, followed by relaxation of the coordination state due to further water rearrangement. Like Marcus theory, we find the existence of an inverted region where the transition rates are slower with increasing exergonicity. This study provides a new perspective for the future investigations of ion-pairing and transport. SR, CJM, and GKS were supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative, a Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory (PNNL). The research was performed using PNNL Institutional Computing. PNNL is a multi-program national laboratory operated by Battelle for the U.S. Department of Energy.« less

Movement dynamics reflect a functional role for weak coupling and role structure in dyadic problem solving.

PubMed

Abney, Drew H; Paxton, Alexandra; Dale, Rick; Kello, Christopher T

2015-11-01

Successful interaction requires complex coordination of body movements. Previous research has suggested a functional role for coordination and especially synchronization (i.e., time-locked movement across individuals) in different types of human interaction contexts. Although such coordination has been shown to be nearly ubiquitous in human interaction, less is known about its function. One proposal is that synchrony supports and facilitates communication (Topics Cogn Sci 1:305-319, 2009). However, questions still remain about what the properties of coordination for optimizing communication might look like. In the present study, dyads worked together to construct towers from uncooked spaghetti and marshmallows. Using cross-recurrence quantification analysis, we found that dyads with loosely coupled gross body movements performed better, supporting recent work suggesting that simple synchrony may not be the key to effective performance (Riley et al. 2011). We also found evidence that leader-follower dynamics-when sensitive to the specific role structure of the interaction-impact task performance. We discuss our results with respect to the functional role of coordination in human interaction.

Variationally optimal selection of slow coordinates and reaction coordinates in macromolecular systems

NASA Astrophysics Data System (ADS)

Noe, Frank

To efficiently simulate and generate understanding from simulations of complex macromolecular systems, the concept of slow collective coordinates or reaction coordinates is of fundamental importance. Here we will introduce variational approaches to approximate the slow coordinates and the reaction coordinates between selected end-states given MD simulations of the macromolecular system and a (possibly large) basis set of candidate coordinates. We will then discuss how to select physically intuitive order paremeters that are good surrogates of this variationally optimal result. These result can be used in order to construct Markov state models or other models of the stationary and kinetics properties, in order to parametrize low-dimensional / coarse-grained model of the dynamics. Deutsche Forschungsgemeinschaft, European Research Council.

Communication: Coordinate-dependent diffusivity from single molecule trajectories

NASA Astrophysics Data System (ADS)

Berezhkovskii, Alexander M.; Makarov, Dmitrii E.

2017-11-01

Single-molecule observations of biomolecular folding are commonly interpreted using the model of one-dimensional diffusion along a reaction coordinate, with a coordinate-independent diffusion coefficient. Recent analysis, however, suggests that more general models are required to account for single-molecule measurements performed with high temporal resolution. Here, we consider one such generalization: a model where the diffusion coefficient can be an arbitrary function of the reaction coordinate. Assuming Brownian dynamics along this coordinate, we derive an exact expression for the coordinate-dependent diffusivity in terms of the splitting probability within an arbitrarily chosen interval and the mean transition path time between the interval boundaries. This formula can be used to estimate the effective diffusion coefficient along a reaction coordinate directly from single-molecule trajectories.

Analysis For Monitoring the Earth Science Afternoon Constellation

NASA Technical Reports Server (NTRS)

Demarest, Peter; Richon, Karen V.; Wright, Frank

2005-01-01

The Earth Science Afternoon Constellation consists of Aqua, Aura, PARASOL, CALIPSO, Cloudsat, and the Orbiting Carbon Observatory (OCO). The coordination of flight dynamics activities between these missions is critical to the safety and success of the Afternoon Constellation. This coordination is based on two main concepts, the control box and the zone-of-exclusion. This paper describes how these two concepts are implemented in the Constellation Coordination System (CCS). The CCS is a collection of tools that enables the collection and distribution of flight dynamics products among the missions, allows cross-mission analyses to be performed through a web-based interface, performs automated analyses to monitor the overall constellation, and notifies the missions of changes in the status of the other missions.

Theory of Gearing

DTIC Science & Technology

1989-12-01

motion of rigid bodies and their kinematical and dynamic characteristics, which are associated with different coordinate systems. In the theory of...rigidly connected surfaces EF and Ep with respect to gears I and 2 may be represented as the motion of a rigid body . However, we assume that in the... rigid body . Coordinate tran:;formation will be considered for systems with (1) common origin and noncoincident coordinate axes and (2) noncoincident

The performance analysis of three-dimensional track-before-detect algorithm based on Fisher-Tippett-Gnedenko theorem

NASA Astrophysics Data System (ADS)

Cho, Hoonkyung; Chun, Joohwan; Song, Sungchan

2016-09-01

The dim moving target tracking from the infrared image sequence in the presence of high clutter and noise has been recently under intensive investigation. The track-before-detect (TBD) algorithm processing the image sequence over a number of frames before decisions on the target track and existence is known to be especially attractive in very low SNR environments (⩽ 3 dB). In this paper, we shortly present a three-dimensional (3-D) TBD with dynamic programming (TBD-DP) algorithm using multiple IR image sensors. Since traditional two-dimensional TBD algorithm cannot track and detect the along the viewing direction, we use 3-D TBD with multiple sensors and also strictly analyze the detection performance (false alarm and detection probabilities) based on Fisher-Tippett-Gnedenko theorem. The 3-D TBD-DP algorithm which does not require a separate image registration step uses the pixel intensity values jointly read off from multiple image frames to compute the merit function required in the DP process. Therefore, we also establish the relationship between the pixel coordinates of image frame and the reference coordinates.

Local atomic structure inheritance in Ag{sub 50}Sn{sub 50} melt

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bai, Yanwen; Bian, Xiufang, E-mail: xfbian@sdu.edu.cn; Qin, Jingyu

2014-01-28

Local structure inheritance signatures were observed during the alloying process of the Ag{sub 50}Sn{sub 50} melt, using high-temperature X-ray diffraction and ab initio molecular dynamics simulations. The coordination number N{sub m} around Ag atom is similar in the alloy and in pure Ag melts (N{sub m} ∼ 10), while, during the alloying process, the local structure around Sn atoms rearranges. Sn-Sn covalent bonds were substituted by Ag-Sn chemical bonds, and the total coordination number around Sn increases by about 70% as compared with those in the pure Sn melt. Changes in the electronic structure of the alloy have been studied by Agmore » and Sn K-edge X-ray absorption spectroscopy, as well as by calculations of the partial density of states. We propose that a leading mechanism for local structure inheritance in Ag{sub 50}Sn{sub 50} is due to s-p dehybridization of Sn and to the interplay between Sn-s and Ag-d electrons.« less

Developing and Validating a Synthetic Teammate

DTIC Science & Technology

2010-01-31

reveals the stability of team coordination dynamics, the Hurst exponent , was also analyzed to determine if there was a coordination stability...difference between communication groups. An independent samples Mest on the average Hurst exponents across teams revealed that text-comm teams were, on

An Overview of the NASA Energy and Water cycle Study (NEWS) and the North American Water Program (NAWP)

NASA Astrophysics Data System (ADS)

Houser, P. R.

2014-12-01

NEWS: 10 years ago, NASA established the NASA Energy and Water-cycle Study (NEWS), whose long-term grand challenge is to document and enable improved, observationally based, predictions of water and energy cycle consequences of Earth system variability and change. The NEWS program builds upon existing NASA-supported basic research in atmospheric physics and dynamics, radiation, climate modeling, and terrestrial hydrology. While these NASA programs fund research activities that address individual aspects of the global energy and water cycles, they are not specifically designed to generate a coordinated result. NEWS developed the first coordinated attempt to describe the complete global energy and water cycle using existing and forthcoming satellite and ground based observations, and laying the foundation for essential NEWS developments in model representations of atmospheric energy and water exchange processes. This comprehensive energy and water data analysis program exploited crucial datasets, some requiring complete re-processing, and new satellite measurements. NAWP: Dramatically changing climates has had an indelible impact on North America's water crisis. To decisively address these challenges, we recommend that NAWP coalesce an interdisciplinary, international and interagency effort to make significant contributions to continental- to decision-scale hydroclimate science and solutions. By entraining, integrating and coordinating the vast array of interdisciplinary observational and prediction resources available, NAWP will significantly advance skill in predicting, assessing and managing variability and changes in North American water resources. We adopt three challenges to organize NAWP efforts. The first deals with developing a scientific basis and tools for mitigating and adapting to changes in the water supply-demand balance. The second challenge is benchmarking; to use incomplete and uncertain observations to assess water storage and quality dynamics, and to characterize the information content of water cycle predictions in a way that allows for model improvement. The final challenge is to establish clear pathways to inform water managers, practitioners and decision makers about newly developed tools, observations and research results.

Adaptive Observatories for Observing Moving Marine Organisms (Invited)

NASA Astrophysics Data System (ADS)

Bellingham, J. G.; Scholin, C.; Zhang, Y.; Godin, M. A.; Hobson, B.; Frolov, S.

2010-12-01

The ability to characterize the response of small marine organisms to each other, and to their environment, is a demanding observational challenge. Small organisms live in a water reference frame, while existing cable or mooring-based observatories operate in an Earth reference frame. Thus repeated observations from a fixed system observe different populations as currents sweep organisms by the sensors. In contrast, mobile systems are typically optimized for spatial coverage rather than repeated observations of the same water volume. Lagrangian drifters track water mass, but are unable to find or reposition themselves relative to ocean features. We are developing a system capable of finding, following and observing discrete populations of marine organisms over time, leveraging a decade and a half investment in the Autonomous Ocean Sampling Network (AOSN) program. AOSN undertook the development of platforms to enable multi-platform coordinated measurement of ocean properties in the late 1990s, leading to the development of a variety of autonomous underwater vehicles (AUVs) and associated technologies, notably several glider systems, now in common use. Efforts by a number of research groups have focused on methods to employ these networked systems to observe and predict dynamic physical ocean phenomena. For example, periodic large scale field programs in Monterey Bay have progressively integrated these systems with data systems, predictive models, and web-based collaborative portals. We are adapting these approaches to follow and observe the dynamics of marine organisms. Compared to physical processes, the temporal and spatial variability of small marine organisms, particularly micro-organisms, is typical greater. Consequently, while multi-platform observations of physical processes can be coordinated via intermittent communications links from shore, biological observations require a higher degree of adaptability of the observation system in situ. This talk will describe the platform capabilities developed for such observations, the onboard intelligence for finding and observing discrete populations, and the cyberinfrastructure employed to understand and coordinate observations from shore.

Collective relaxation dynamics of small-world networks

NASA Astrophysics Data System (ADS)

Grabow, Carsten; Grosskinsky, Stefan; Kurths, Jürgen; Timme, Marc

2015-05-01

Complex networks exhibit a wide range of collective dynamic phenomena, including synchronization, diffusion, relaxation, and coordination processes. Their asymptotic dynamics is generically characterized by the local Jacobian, graph Laplacian, or a similar linear operator. The structure of networks with regular, small-world, and random connectivities are reasonably well understood, but their collective dynamical properties remain largely unknown. Here we present a two-stage mean-field theory to derive analytic expressions for network spectra. A single formula covers the spectrum from regular via small-world to strongly randomized topologies in Watts-Strogatz networks, explaining the simultaneous dependencies on network size N , average degree k , and topological randomness q . We present simplified analytic predictions for the second-largest and smallest eigenvalue, and numerical checks confirm our theoretical predictions for zero, small, and moderate topological randomness q , including the entire small-world regime. For large q of the order of one, we apply standard random matrix theory, thereby overarching the full range from regular to randomized network topologies. These results may contribute to our analytic and mechanistic understanding of collective relaxation phenomena of network dynamical systems.

Collective relaxation dynamics of small-world networks.

PubMed

Grabow, Carsten; Grosskinsky, Stefan; Kurths, Jürgen; Timme, Marc

2015-05-01

Complex networks exhibit a wide range of collective dynamic phenomena, including synchronization, diffusion, relaxation, and coordination processes. Their asymptotic dynamics is generically characterized by the local Jacobian, graph Laplacian, or a similar linear operator. The structure of networks with regular, small-world, and random connectivities are reasonably well understood, but their collective dynamical properties remain largely unknown. Here we present a two-stage mean-field theory to derive analytic expressions for network spectra. A single formula covers the spectrum from regular via small-world to strongly randomized topologies in Watts-Strogatz networks, explaining the simultaneous dependencies on network size N, average degree k, and topological randomness q. We present simplified analytic predictions for the second-largest and smallest eigenvalue, and numerical checks confirm our theoretical predictions for zero, small, and moderate topological randomness q, including the entire small-world regime. For large q of the order of one, we apply standard random matrix theory, thereby overarching the full range from regular to randomized network topologies. These results may contribute to our analytic and mechanistic understanding of collective relaxation phenomena of network dynamical systems.

Enhancing response coordination through the assessment of response network structural dynamics

PubMed Central

Jalili, Mahdi; Choi, Soo-Mi

2018-01-01

Preparing for intensifying threats of emergencies in unexpected, dangerous, and serious natural or man-made events, and consequent management of the situation, is highly demanding in terms of coordinating the personnel and resources to support human lives and the environment. This necessitates prompt action to manage the uncertainties and risks imposed by such extreme events, which requires collaborative operation among different stakeholders (i.e., the personnel from both the state and local communities). This research aims to find a way to enhance the coordination of multi-organizational response operations. To do so, this manuscript investigates the role of participants in the formed coordination response network and also the emergence and temporal dynamics of the network. By analyzing an inter-personal response coordination operation to an extreme bushfire event, the networks’ and participants’ structural change is evaluated during the evolution of the operation network over four time durations. The results reveal that the coordination response network becomes more decentralized over time due to the high volume of communication required to exchange information. New emerging communication structures often do not fit the developed plans, which stress the need for coordination by feedback in addition to by plan. In addition, we find that the participant’s brokering role in the response operation network identifies a formal and informal coordination role. This is useful for comparison of network structures to examine whether what really happens during response operations complies with the initial policy. PMID:29447192

Enhancing response coordination through the assessment of response network structural dynamics.

PubMed

Abbasi, Alireza; Sadeghi-Niaraki, Abolghasem; Jalili, Mahdi; Choi, Soo-Mi

2018-01-01

Preparing for intensifying threats of emergencies in unexpected, dangerous, and serious natural or man-made events, and consequent management of the situation, is highly demanding in terms of coordinating the personnel and resources to support human lives and the environment. This necessitates prompt action to manage the uncertainties and risks imposed by such extreme events, which requires collaborative operation among different stakeholders (i.e., the personnel from both the state and local communities). This research aims to find a way to enhance the coordination of multi-organizational response operations. To do so, this manuscript investigates the role of participants in the formed coordination response network and also the emergence and temporal dynamics of the network. By analyzing an inter-personal response coordination operation to an extreme bushfire event, the networks' and participants' structural change is evaluated during the evolution of the operation network over four time durations. The results reveal that the coordination response network becomes more decentralized over time due to the high volume of communication required to exchange information. New emerging communication structures often do not fit the developed plans, which stress the need for coordination by feedback in addition to by plan. In addition, we find that the participant's brokering role in the response operation network identifies a formal and informal coordination role. This is useful for comparison of network structures to examine whether what really happens during response operations complies with the initial policy.

A study of overflow simulations using MPAS-Ocean: Vertical grids, resolution, and viscosity

NASA Astrophysics Data System (ADS)

Reckinger, Shanon M.; Petersen, Mark R.; Reckinger, Scott J.

2015-12-01

MPAS-Ocean is used to simulate an idealized, density-driven overflow using the dynamics of overflow mixing and entrainment (DOME) setup. Numerical simulations are carried out using three of the vertical coordinate types available in MPAS-Ocean, including z-star with partial bottom cells, z-star with full cells, and sigma coordinates. The results are first benchmarked against other models, including the MITgcm's z-coordinate model and HIM's isopycnal coordinate model, which are used to set the base case used for this work. A full parameter study is presented that looks at how sensitive overflow simulations are to vertical grid type, resolution, and viscosity. Horizontal resolutions with 50 km grid cells are under-resolved and produce poor results, regardless of other parameter settings. Vertical grids ranging in thickness from 15 m to 120 m were tested. A horizontal resolution of 10 km and a vertical resolution of 60 m are sufficient to resolve the mesoscale dynamics of the DOME configuration, which mimics real-world overflow parameters. Mixing and final buoyancy are least sensitive to horizontal viscosity, but strongly sensitive to vertical viscosity. This suggests that vertical viscosity could be adjusted in overflow water formation regions to influence mixing and product water characteristics. Lastly, the study shows that sigma coordinates produce much less mixing than z-type coordinates, resulting in heavier plumes that go further down slope. Sigma coordinates are less sensitive to changes in resolution but as sensitive to vertical viscosity compared to z-coordinates.

Modeling Zone-3 Protection with Generic Relay Models for Dynamic Contingency Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Qiuhua; Vyakaranam, Bharat GNVSR; Diao, Ruisheng

This paper presents a cohesive approach for calculating and coordinating the settings of multiple zone-3 protections for dynamic contingency analysis. The zone-3 protections are represented by generic distance relay models. A two-step approach for determining zone-3 relay settings is proposed. The first step is to calculate settings, particularly, the reach, of each zone-3 relay individually by iteratively running line open-end fault short circuit analysis; the blinder is also employed and properly set to meet the industry standard under extreme loading conditions. The second step is to systematically coordinate the protection settings of the zone-3 relays. The main objective of thismore » coordination step is to address the over-reaching issues. We have developed a tool to automate the proposed approach and generate the settings of all distance relays in a PSS/E dyr format file. The calculated zone-3 settings have been tested on a modified IEEE 300 system using a dynamic contingency analysis tool (DCAT).« less

Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates

NASA Astrophysics Data System (ADS)

García-Meseguer, Rafael; Martí, Sergio; Ruiz-Pernía, J. Javier; Moliner, Vicent; Tuñón, Iñaki

2013-07-01

Conformational changes are known to be able to drive an enzyme through its catalytic cycle, allowing, for example, substrate binding or product release. However, the influence of protein motions on the chemical step is a controversial issue. One proposal is that the simple equilibrium fluctuations incorporated into transition-state theory are insufficient to account for the catalytic effect of enzymes and that protein motions should be treated dynamically. Here, we propose the use of free-energy surfaces, obtained as a function of both a chemical coordinate and an environmental coordinate, as an efficient way to elucidate the role of protein structure and motions during the reaction. We show that the structure of the protein provides an adequate environment for the progress of the reaction, although a certain degree of flexibility is needed to attain the full catalytic effect. However, these motions do not introduce significant dynamical corrections to the rate constant and can be described as equilibrium fluctuations.

Spatio-temporal hierarchy in the dynamics of a minimalist protein model

NASA Astrophysics Data System (ADS)

Matsunaga, Yasuhiro; Baba, Akinori; Li, Chun-Biu; Straub, John E.; Toda, Mikito; Komatsuzaki, Tamiki; Berry, R. Stephen

2013-12-01

A method for time series analysis of molecular dynamics simulation of a protein is presented. In this approach, wavelet analysis and principal component analysis are combined to decompose the spatio-temporal protein dynamics into contributions from a hierarchy of different time and space scales. Unlike the conventional Fourier-based approaches, the time-localized wavelet basis captures the vibrational energy transfers among the collective motions of proteins. As an illustrative vehicle, we have applied our method to a coarse-grained minimalist protein model. During the folding and unfolding transitions of the protein, vibrational energy transfers between the fast and slow time scales were observed among the large-amplitude collective coordinates while the other small-amplitude motions are regarded as thermal noise. Analysis employing a Gaussian-based measure revealed that the time scales of the energy redistribution in the subspace spanned by such large-amplitude collective coordinates are slow compared to the other small-amplitude coordinates. Future prospects of the method are discussed in detail.

Siberia Integrated Regional Study megaproject: approaches, first results and challenges

NASA Astrophysics Data System (ADS)

Gordov, E. P.; Vaganov, E. A.

2010-12-01

Siberia Integrated Regional Study (SIRS, http://sirs.scert.ru/en/) is a NEESPI megaproject coordinating national and international activity in the region in line with Earth System Science Program approach whose overall objectives are to understand impact of Global change on on-going regional climate and ecosystems dynamics; to study future potential changes in both, and to estimate possible influence of those processes on the whole Earth System dynamics. Needs for SIRS are caused by accelerated warming occurring in Siberia, complexity of on-going and potential land-surface processes sharpened by inherent hydrology pattern and permafrost presence, and lack of reliable high-resolution meteorological and climatic modeling data. The SIRS approaches include coordination of different scale national and international projects, capacity building targeted to early career researchers thematic education and training, and development of distributed information-computational infrastructure required in support of multidisciplinary teams of specialists performing cooperative work with tools for sharing of data, models and knowledge. Coordination within SIRS projects is devoted to major regional and global risks rising with regional environment changes and currently is concentrated on three interrelated problems, whose solution has strong regional environmental and socio-economical impacts and is very important for understanding potential change of the whole Earth System dynamics: Permafrost border shift, which seriously threatens the oil and gas transporting infrastructure and leads to additional carbon release; Desert - steppe- forest-tundra ecosystems changes, which might vary region input into global carbon cycle as well as provoke serious socio-economical consequences for local population; and Temperature/precipitation/hydrology regime changes, which might increase risks of forest and peat fires, thus causing significant carbon release from the region under study. Some findings of those projects will be presented in the report. The information-computational infrastructure is aimed to manage multidisciplinary environmental data and to generate high resolution data sets on demand. One of its key elements, optimizing the usage of information-computational resources, services and applications is the climatic web portal under development. The prototype (http://climate.risks.scert.ru/) is now providing an access to an interactive web- GIS system for climate change assessment on the base of available meteorological data archives in the selected region. SIRS education and training program is run via annual organization in the region either international multidisciplinary conference with elements of young scientists school ENVIROMIS or young scientists school and collocated international conference CITES (http://www.scert.ru/en/conferences/). All the listed above activities have an international dimension whose enlargement might significantly assist in profound understanding of regional and global consequences in on-going Siberia processes.

Self-optimizing charge-transfer energy phenomena in metallosupramolecular complexes by dynamic constitutional self-sorting.

PubMed

Legrand, Yves-Marie; van der Lee, Arie; Barboiu, Mihail

2007-11-12

In this paper we report an extended series of 2,6-(iminoarene)pyridine-type ZnII complexes [(Lii)2Zn]II, which were surveyed for their ability to self-exchange both their ligands and their aromatic arms and to form different homoduplex and heteroduplex complexes in solution. The self-sorting of heteroduplex complexes is likely to be the result of geometric constraints. Whereas the imine-exchange process occurs quantitatively in 1:1 mixtures of [(Lii)2Zn]II complexes, the octahedral coordination process around the metal ion defines spatial-frustrated exchanges that involve the selective formation of heterocomplexes of two, by two different substituents; the bulkiest ones (pyrene in principle) specifically interact with the pseudoterpyridine core, sterically hindering the least bulky ones, which are intermolecularly stacked with similar ligands of neighboring molecules. Such a self-sorting process defined by the specific self-constitution of the ligands exchanging their aromatic substituents is self-optimized by a specific control over their spatial orientation around a metal center within the complex. They ultimately show an improved charge-transfer energy function by virtue of the dynamic amplification of self-optimized heteroduplex architectures. These systems therefore illustrate the convergence of the combinatorial self-sorting of the dynamic combinatorial libraries (DCLs) strategy and the constitutional self-optimized function.

Two-step crystal growth mechanism during crystallization of an undercooled Ni50Al50 alloy

NASA Astrophysics Data System (ADS)

An, Simin; Li, Jiahao; Li, Yang; Li, Shunning; Wang, Qi; Liu, Baixin

2016-08-01

Crystallization processes are always accompanied by the emergence of multiple intermediate states, of which the structures and transition dynamics are far from clarity, since it is difficult to experimentally observe the microscopic pathway. To insight the structural evolution and the crystallization dynamics, we perform large-scale molecular dynamics simulations to investigate the time-dependent crystallization behavior of the NiAl intermetallic upon rapid solidification. The simulation results reveal that the crystallization process occurs via a two-step growth mechanism, involving the formation of initial non-equilibrium long range order (NLRO) regions and of the subsequent equilibrium long range order (ELRO) regions. The formation of the NLRO regions makes the grains rather inhomogeneous, while the rearrangement of the NLRO regions into the ELRO regions makes the grains more ordered and compact. This two-step growth mechanism is actually controlled by the evolution of the coordination polyhedra, which are characterized predominantly by the transformation from five-fold symmetry to four-fold and six-fold symmetry. From liquids to NLRO and further to ELRO, the five-fold symmetry of these polyhedra gradually fades, and finally vanishes when B2 structure is distributed throughout the grain bulk. The energy decrease along the pathway further implies the reliability of the proposed crystallization processes.

Coordination dynamics in a socially situated nervous system

PubMed Central

Coey, Charles A.; Varlet, Manuel; Richardson, Michael J.

2012-01-01

Traditional theories of cognitive science have typically accounted for the organization of human behavior by detailing requisite computational/representational functions and identifying neurological mechanisms that might perform these functions. Put simply, such approaches hold that neural activity causes behavior. This same general framework has been extended to accounts of human social behavior via concepts such as “common-coding” and “co-representation” and much recent neurological research has been devoted to brain structures that might execute these social-cognitive functions. Although these neural processes are unquestionably involved in the organization and control of human social interactions, there is good reason to question whether they should be accorded explanatory primacy. Alternatively, we propose that a full appreciation of the role of neural processes in social interactions requires appropriately situating them in their context of embodied-embedded constraints. To this end, we introduce concepts from dynamical systems theory and review research demonstrating that the organization of human behavior, including social behavior, can be accounted for in terms of self-organizing processes and lawful dynamics of animal-environment systems. Ultimately, we hope that these alternative concepts can complement the recent advances in cognitive neuroscience and thereby provide opportunities to develop a complete and coherent account of human social interaction. PMID:22701413

Design of specially adapted reactive coordinates to economically compute potential and kinetic energy operators including geometry relaxation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thallmair, Sebastian; Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians-Universität München, D-80538 München; Roos, Matthias K.

Quantum dynamics simulations require prior knowledge of the potential energy surface as well as the kinetic energy operator. Typically, they are evaluated in a low-dimensional subspace of the full configuration space of the molecule as its dimensionality increases proportional to the number of atoms. This entails the challenge to find the most suitable subspace. We present an approach to design specially adapted reactive coordinates spanning this subspace. In addition to the essential geometric changes, these coordinates take into account the relaxation of the non-reactive coordinates without the necessity of performing geometry optimizations at each grid point. The method is demonstratedmore » for an ultrafast photoinduced bond cleavage in a commonly used organic precursor for the generation of electrophiles. The potential energy surfaces for the reaction as well as the Wilson G-matrix as part of the kinetic energy operator are shown for a complex chemical reaction, both including the relaxation of the non-reactive coordinates on equal footing. A microscopic interpretation of the shape of the G-matrix elements allows to analyze the impact of the non-reactive coordinates on the kinetic energy operator. Additionally, we compare quantum dynamics simulations with and without the relaxation of the non-reactive coordinates included in the kinetic energy operator to demonstrate its influence.« less

High-speed real-time 3-D coordinates measurement based on fringe projection profilometry considering camera lens distortion

NASA Astrophysics Data System (ADS)

Feng, Shijie; Chen, Qian; Zuo, Chao; Sun, Jiasong; Yu, Shi Ling

2014-10-01

Optical three-dimensional (3-D) profilometry is gaining increasing attention for its simplicity, flexibility, high accuracy, and non-contact nature. Recent advances in imaging sensors and digital projection technology further its progress in high-speed, real-time applications, enabling 3-D shapes reconstruction of moving objects and dynamic scenes. However, the camera lens is never perfect and the lens distortion does influence the accuracy of the measurement result, which is often overlooked in the existing real-time 3-D shape measurement systems. To this end, here we present a novel high-speed real-time 3-D coordinates measuring technique based on fringe projection with the consideration of the camera lens distortion. A pixel mapping relation between a distorted image and a corrected one is pre-determined and stored in computer memory for real-time fringe correction. The out-of-plane height is obtained firstly and the acquisition for the two corresponding in-plane coordinates follows on the basis of the solved height. Besides, a method of lookup table (LUT) is introduced as well for fast data processing. Our experimental results reveal that the measurement error of the in-plane coordinates has been reduced by one order of magnitude and the accuracy of the out-plane coordinate been tripled after the distortions being eliminated. Moreover, owing to the generated LUTs, a 3-D reconstruction speed of 92.34 frames per second can be achieved.

On the dynamical and geometrical symmetries of Keplerian motion

NASA Astrophysics Data System (ADS)

Wulfman, Carl E.

2009-05-01

The dynamical symmetries of classical, relativistic and quantum-mechanical Kepler systems are considered to arise from geometric symmetries in PQET phase space. To establish their interconnection, the symmetries are related with the aid of a Lie-algebraic extension of Dirac's correspondence principle, a canonical transformation containing a Cunningham-Bateman inversion, and a classical limit involving a preliminary canonical transformation in ET space. The Lie-algebraic extension establishes the conditions under which the uncertainty principle allows the local dynamical symmetry of a quantum-mechanical system to be the same as the geometrical phase-space symmetry of its classical counterpart. The canonical transformation converts Poincaré-invariant free-particle systems into ISO(3,1) invariant relativistic systems whose classical limit produces Keplerian systems. Locally Cartesian relativistic PQET coordinates are converted into a set of eight conjugate position and momentum coordinates whose classical limit contains Fock projective momentum coordinates and the components of Runge-Lenz vectors. The coordinate systems developed via the transformations are those in which the evolution and degeneracy groups of the classical system are generated by Poisson-bracket operators that produce ordinary rotation, translation and hyperbolic motions in phase space. The way in which these define classical Keplerian symmetries and symmetry coordinates is detailed. It is shown that for each value of the energy of a Keplerian system, the Poisson-bracket operators determine two invariant functions of positions and momenta, which together with its regularized Hamiltonian, define the manifold in six-dimensional phase space upon which motions evolve.

Fe behavior in iron-bearing phonolitic and pantelleritic melts and its significance for magma dynamics in the volcanic conduits

NASA Astrophysics Data System (ADS)

Borovkov, Nikita; Hess, Kai-Uwe; Fehr, Karl-Thomas; Cimarelli, Corrado; Dingwell, Donald Bruce

2014-05-01

The style of volcanic eruptions is determined entirely by dynamics of magma ascent in conduits. Physical properties of a silicate melt, particulary viscosity, are responsible for fragmentation processes, bubble growth and their ascent, which are in their turn related to explosivity of eruptions. Therefore, comprehension of the macroscopic properties of silicate melts is required for adequate conduit modelling. Considering eruptions of Mt. Vesuvius, Italy, we observe that eruption style varies from strombolian to plinean and sub-plinean which is related to the changes of melts viscosity in conduits. At Vesuvius the composition of volcanic deposits (III phase) is mainly phonolitic with 5 - 8 wt. % FeO. Fe changes the valence and coordination depending on oxidation state. The changing of iron coordination causes increasing or decreasing viscosity because of the presence of higher or lower amounts of Fe species coordinated with stronger covalence bonds. Mossbauer spectra of iron-bearing natural pantelleritic and phonolitic glasses were studied to get data on speciation and coordination state of iron. Mössbauer spectroscopy measures hyperfine interactions (isomer shift (IS)) and quadrupole splitting (QS)) at Fe atoms embedded in glass structure, which provide the amount of ferric and ferrous iron and their coordination state depending on Redox conditions. Based on these data, we have considered redox-viscosity relationships and also iron coordination effects on viscosity of both mentioned natural melt compositions. For glasses, due to short range order, the Mössbauer spectra were fitted using mathematical procedures based on functional analysis (extended Voight lineshape included in "Recoil" and "Mosslab" software). Mössbauer spectra are deconvoluted in two sites: ferrous iron (IS=0,79-1,00 mm/s; QS= 1,78-2,25 mm/s) and ferric iron (IS=0,26-0,50 mm/s; QS= 0,75-0,95 mm/s). For both sites we observe that IS and QS gradually decrease towards more oxidized conditions. From functional analysis of Mössbauer spectra this increasing is due to transformation of iron coordination: Fe2+ [5]-Fe2+ [4] and Fe3+ [5]-Fe3+ [4], depending on Redox conditions. XANES data helps us to prove coordination transformation of Fe clearly. This methods (Giuli et al., 2011) reveal that Fe3+ is always in tetrahedral coordination and Fe2+ is in the form of both [4] and [5] species. The presence of minor [5] or even [6] cannot be excluded. Combining Mössbauer and XANES methods, we can suggest that more reduced samples include more high coordinated Fe species. Under oxidized conditions Fe3+ tends to be [4] - coordinated completely and amount of Fe2+ [5] decreases. Viscosity for phonolitic and pantelleritic melts increases as well with more oxidized conditions, suggesting more polymerized structure. Under reduced conditions, low viscosity means that some higher coordinated Fe2+ and Fe3+ sites occur in structure and function as a depolymerizing factor. Therefore, in the presence of iron-bearing peralkaline melts, the prediction of an eruptive style requires knowledge of the dependence of viscosity on thermodynamic parameters as well as dependence on RedOx conditions, which are responsible for ferric and ferrous iron structural transformations.

Monitoring Replication Protein A (RPA) dynamics in homologous recombination through site-specific incorporation of non-canonical amino acids

PubMed Central

Pokhrel, Nilisha; Origanti, Sofia; Davenport, Eric Parker; Gandhi, Disha; Kaniecki, Kyle; Mehl, Ryan A.; Greene, Eric C.; Dockendorff, Chris

2017-01-01

Abstract An essential coordinator of all DNA metabolic processes is Replication Protein A (RPA). RPA orchestrates these processes by binding to single-stranded DNA (ssDNA) and interacting with several other DNA binding proteins. Determining the real-time kinetics of single players such as RPA in the presence of multiple DNA processors to better understand the associated mechanistic events is technically challenging. To overcome this hurdle, we utilized non-canonical amino acids and bio-orthogonal chemistry to site-specifically incorporate a chemical fluorophore onto a single subunit of heterotrimeric RPA. Upon binding to ssDNA, this fluorescent RPA (RPAf) generates a quantifiable change in fluorescence, thus serving as a reporter of its dynamics on DNA in the presence of multiple other DNA binding proteins. Using RPAf, we describe the kinetics of facilitated self-exchange and exchange by Rad51 and mediator proteins during various stages in homologous recombination. RPAf is widely applicable to investigate its mechanism of action in processes such as DNA replication, repair and telomere maintenance. PMID:28934470

Application of 3D Laser Scanning Technology in Inspection and Dynamic Reserves Detection of Open-Pit Mine

NASA Astrophysics Data System (ADS)

Hu, Zhumin; Wei, Shiyu; Jiang, Jun

2017-10-01

The traditional open-pit mine mining rights verification and dynamic reserve detection means rely on the total station and RTK to collect the results of the turning point coordinates of mining surface contours. It resulted in obtaining the results of low precision and large error in the means that is limited by the traditional measurement equipment accuracy and measurement methods. The three-dimensional scanning technology can obtain the three-dimensional coordinate data of the surface of the measured object in a large area at high resolution. This paper expounds the commonly used application of 3D scanning technology in the inspection and dynamic reserve detection of open mine mining rights.

Reproducing kernel potential energy surfaces in biomolecular simulations: Nitric oxide binding to myoglobin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soloviov, Maksym; Meuwly, Markus, E-mail: m.meuwly@unibas.ch

2015-09-14

Multidimensional potential energy surfaces based on reproducing kernel-interpolation are employed to explore the energetics and dynamics of free and bound nitric oxide in myoglobin (Mb). Combining a force field description for the majority of degrees of freedom and the higher-accuracy representation for the NO ligand and the Fe out-of-plane motion allows for a simulation approach akin to a mixed quantum mechanics/molecular mechanics treatment. However, the kernel-representation can be evaluated at conventional force-field speed. With the explicit inclusion of the Fe-out-of-plane (Fe-oop) coordinate, the dynamics and structural equilibrium after photodissociation of the ligand are correctly described compared to experiment. Experimentally, themore » Fe-oop coordinate plays an important role for the ligand dynamics. This is also found here where the isomerization dynamics between the Fe–ON and Fe–NO state is significantly affected whether or not this co-ordinate is explicitly included. Although the Fe–ON conformation is metastable when considering only the bound {sup 2}A state, it may disappear once the {sup 4}A state is included. This explains the absence of the Fe–ON state in previous experimental investigations of MbNO.« less

Coordinate space translation technique for simulation of electronic process in the ion-atom collision.

PubMed

Wang, Feng; Hong, Xuhai; Wang, Jian; Kim, Kwang S

2011-04-21

Recently we developed a theoretical model of ion-atom collisions, which was made on the basis of a time-dependent density functional theory description of the electron dynamics and a classical treatment of the heavy particle motion. Taking advantage of the real-space grid method, we introduce a "coordinate space translation" technique to allow one to focus on a certain space of interest such as the region around the projectile or the target. Benchmark calculations are given for collisions between proton and oxygen over a wide range of impact energy. To extract the probability of charge transfer, the formulation of Lüdde and Dreizler [J. Phys. B 16, 3973 (1983)] has been generalized to ensemble-averaging application in the particular case of O((3)P). Charge transfer total cross sections are calculated, showing fairly good agreements between experimental data and present theoretical results.

Hypoxia-driven angiogenesis: role of tip cells and extracellular matrix scaffolding.

PubMed

Germain, Stéphane; Monnot, Catherine; Muller, Laurent; Eichmann, Anne

2010-05-01

Angiogenesis is a highly coordinated tissue remodeling process leading to blood vessel formation. Hypoxia triggers angiogenesis via induction of expression of growth factors such as vascular endothelial growth factor (VEGF). VEGF instructs endothelial cells to form tip cells, which lead outgrowing capillary sprouts, whereas Notch signaling inhibits sprout formation. Basement membrane deposition and mechanical cues from the extracellular matrix (ECM) induced by hypoxia may participate to coordinated vessel sprouting in conjunction with the VEGF and Notch signaling pathways. Hypoxia regulates ECM composition, deposition, posttranslational modifications and rearrangement. In particular, hypoxia-driven vascular remodeling is dynamically regulated through modulation of ECM-modifying enzyme activities that eventually affect both matricellular proteins and growth factor availability. Better understanding of the complex interplay between endothelial cells and soluble growth factors and mechanical factors from the ECM will certainly have significant implications for understanding the regulation of developmental and pathological angiogenesis driven by hypoxia.

Capturing Revolute Motion and Revolute Joint Parameters with Optical Tracking

NASA Astrophysics Data System (ADS)

Antonya, C.

2017-12-01

Optical tracking of users and various technical systems are becoming more and more popular. It consists of analysing sequence of recorded images using video capturing devices and image processing algorithms. The returned data contains mainly point-clouds, coordinates of markers or coordinates of point of interest. These data can be used for retrieving information related to the geometry of the objects, but also to extract parameters for the analytical model of the system useful in a variety of computer aided engineering simulations. The parameter identification of joints deals with extraction of physical parameters (mainly geometric parameters) for the purpose of constructing accurate kinematic and dynamic models. The input data are the time-series of the marker’s position. The least square method was used for fitting the data into different geometrical shapes (ellipse, circle, plane) and for obtaining the position and orientation of revolute joins.

An integrated control scheme for space robot after capturing non-cooperative target

NASA Astrophysics Data System (ADS)

Wang, Mingming; Luo, Jianjun; Yuan, Jianping; Walter, Ulrich

2018-06-01

How to identify the mass properties and eliminate the unknown angular momentum of space robotic system after capturing a non-cooperative target is of great challenge. This paper focuses on designing an integrated control framework which includes detumbling strategy, coordination control and parameter identification. Firstly, inverted and forward chain approaches are synthesized for space robot to obtain dynamic equation in operational space. Secondly, a detumbling strategy is introduced using elementary functions with normalized time, while the imposed end-effector constraints are considered. Next, a coordination control scheme for stabilizing both base and end-effector based on impedance control is implemented with the target's parameter uncertainty. With the measurements of the forces and torques exerted on the target, its mass properties are estimated during the detumbling process accordingly. Simulation results are presented using a 7 degree-of-freedom kinematically redundant space manipulator, which verifies the performance and effectiveness of the proposed method.

Proactive transfer of learning depends on the evolution of prior learned task in memory.

PubMed

Tallet, Jessica; Kostrubiec, Viviane; Zanone, Pier-Giorgio

2010-06-01

The aim of the present study was to investigate the processes underlying the proactive interference effect using bimanual coordination. Our rationale was that interference would only occur when the prior learned A coordination pattern enters in competition with the required subsequent B pattern. We hypothesized that competition would arise only if the A pattern persists in memory before introducing the B pattern. In the experimental group, both A and B patterns were practiced and recalled, whereas in the control group only the B pattern was practiced and recalled. In Experiment 1, which involved initially bistable participants, the persistence of the A pattern led to interference, while, surprisingly, the A pattern forgetting entailed facilitation. In Experiment 2, which involved initially tristable participants, no such transfer effect was found. The apparently contradictory results can be interpreted coherently in the light of dynamical principles of learning. (c) 2010 Elsevier B.V. All rights reserved.

Rotation of endosomes demonstrates coordination of molecular motors during axonal transport

PubMed Central

Kaplan, Luke; Ierokomos, Athena; Chowdary, Praveen; Bryant, Zev; Cui, Bianxiao

2018-01-01

Long-distance axonal transport is critical to the maintenance and function of neurons. Robust transport is ensured by the coordinated activities of multiple molecular motors acting in a team. Conventional live-cell imaging techniques used in axonal transport studies detect this activity by visualizing the translational dynamics of a cargo. However, translational measurements are insensitive to torques induced by motor activities. By using gold nanorods and multichannel polarization microscopy, we simultaneously measure the rotational and translational dynamics for thousands of axonally transported endosomes. We find that the rotational dynamics of an endosome provide complementary information regarding molecular motor activities to the conventionally tracked translational dynamics. Rotational dynamics correlate with translational dynamics, particularly in cases of increased rotation after switches between kinesin- and dynein-mediated transport. Furthermore, unambiguous measurement of nanorod angle shows that endosome-contained nanorods align with the orientation of microtubules, suggesting a direct mechanical linkage between the ligand-receptor complex and the microtubule motors. PMID:29536037

Analytical Solution for Low-Thrust Minimum Time Control of a Satellite Formation

DTIC Science & Technology

2004-09-01

The Classical Clohessy - Wiltshire Equations . . . . . . . . . A-1 A.1 Hill’s Rotating Coordinate Frame . . . . . . . . . . . . . . . A-1 A.2 Kinematics...9 A.1. The Clohessy and Wiltshire coordinate frame with x in the radial direction and y in the velocity direction. . . . . . . . . . . . . . . . A-1 B...coordinate system and approx- imations made by Clohessy and Wiltshire , combined with body-fixed thruster control, result in a linearized dynamic system. The

Numeric kinetic energy operators for molecules in polyspherical coordinates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sadri, Keyvan; Meyer, Hans-Dieter; Lauvergnat, David

Generalized curvilinear coordinates, as, e.g., polyspherical coordinates, are in general better adapted to the resolution of the nuclear Schroedinger equation than rectilinear ones like the normal mode coordinates. However, analytical expressions of the kinetic energy operators (KEOs) for molecular systems in polyspherical coordinates may be prohibitively complicated for large systems. In this paper we propose a method to generate a KEO numerically and bring it to a form practicable for dynamical calculations. To examine the new method we calculated vibrational spectra and eigenenergies for nitrous acid (HONO) and compare it with results obtained with an exact analytical KEO derived previouslymore » [F. Richter, P. Rosmus, F. Gatti, and H.-D. Meyer, J. Chem. Phys. 120, 6072 (2004)]. In a second example we calculated {pi}{yields}{pi}* photoabsorption spectrum and eigenenergies of ethene (C{sub 2}H{sub 4}) and compared it with previous work [M. R. Brill, F. Gatti, D. Lauvergnat, and H.-D. Meyer, Chem. Phys. 338, 186 (2007)]. In this ethene study the dimensionality was reduced from 12 to 6 by freezing six internal coordinates. Results for both molecules show that the proposed method for obtaining an approximate KEO is reliable for dynamical calculations. The error in eigenenergies was found to be below 1 cm{sup -1} for most states calculated.« less

Overflow Simulations using MPAS-Ocean in Idealized and Realistic Domains

NASA Astrophysics Data System (ADS)

Reckinger, S.; Petersen, M. R.; Reckinger, S. J.

2016-02-01

MPAS-Ocean is used to simulate an idealized, density-driven overflow using the dynamics of overflow mixing and entrainment (DOME) setup. Numerical simulations are benchmarked against other models, including the MITgcm's z-coordinate model and HIM's isopycnal coordinate model. A full parameter study is presented that looks at how sensitive overflow simulations are to vertical grid type, resolution, and viscosity. Horizontal resolutions with 50 km grid cells are under-resolved and produce poor results, regardless of other parameter settings. Vertical grids ranging in thickness from 15 m to 120 m were tested. A horizontal resolution of 10 km and a vertical resolution of 60 m are sufficient to resolve the mesoscale dynamics of the DOME configuration, which mimics real-world overflow parameters. Mixing and final buoyancy are least sensitive to horizontal viscosity, but strongly sensitive to vertical viscosity. This suggests that vertical viscosity could be adjusted in overflow water formation regions to influence mixing and product water characteristics. Also, the study shows that sigma coordinates produce much less mixing than z-type coordinates, resulting in heavier plumes that go further down slope. Sigma coordinates are less sensitive to changes in resolution but as sensitive to vertical viscosity compared to z-coordinates. Additionally, preliminary measurements of overflow diagnostics on global simulations using a realistic oceanic domain are presented.

On some control problems of dynamic of reactor

NASA Astrophysics Data System (ADS)

Baskakov, A. V.; Volkov, N. P.

2017-12-01

The paper analyzes controllability of the transient processes in some problems of nuclear reactor dynamics. In this case, the mathematical model of nuclear reactor dynamics is described by a system of integro-differential equations consisting of the non-stationary anisotropic multi-velocity kinetic equation of neutron transport and the balance equation of delayed neutrons. The paper defines the formulation of the linear problem on control of transient processes in nuclear reactors with application of spatially distributed actions on internal neutron sources, and the formulation of the nonlinear problems on control of transient processes with application of spatially distributed actions on the neutron absorption coefficient and the neutron scattering indicatrix. The required control actions depend on the spatial and velocity coordinates. The theorems on existence and uniqueness of these control actions are proved in the paper. To do this, the control problems mentioned above are reduced to equivalent systems of integral equations. Existence and uniqueness of the solution for this system of integral equations is proved by the method of successive approximations, which makes it possible to construct an iterative scheme for numerical analyses of transient processes in a given nuclear reactor with application of the developed mathematical model. Sufficient conditions for controllability of transient processes are also obtained. In conclusion, a connection is made between the control problems and the observation problems, which, by to the given information, allow us to reconstruct either the function of internal neutron sources, or the neutron absorption coefficient, or the neutron scattering indicatrix....

The influence of cations on lithium ion coordination and transport in ionic liquid electrolytes: a MD simulation study.

PubMed

Lesch, Volker; Li, Zhe; Bedrov, Dmitry; Borodin, Oleg; Heuer, Andreas

2016-01-07

The dynamical and structural properties in two ionic liquid electrolytes (ILEs) based on 1-ethyl-3-methylimidazolium bis-(trifluoromethanesulfonyl)-imide ([emim][TFSI]) and N-methyl-N-propylpyrrolidinium bis-(trifluoromethanesulfonyl)imide([pyr13][TFSI]) were compared as a function of lithium bis-(trifluoromethanesulfonyl)-imide (LiTFSI) salt concentrations using atomistic molecular dynamics (MD) simulations. The many-body polarizable APPLE&P force field has been utilized. The influence of anion polarization on the structure of the first coordination shell of Li(+) was examined. In particular, the reduction of the oxygen of the TFSI anion (OTFSI) polarizability from 1.36 Å(3) to 1.00 Å(3) resulted in an increased fraction of the TFSI anion bidentate coordination to the Li(+). While the overall dynamics in [pyr13][TFSI]-based ILEs was slower than in [emim][TFSI]-based ILEs, the exchange of TFSI anions in and out of the first coordination shell of Li(+) was found to be faster in pyr13-based systems. The Li(+) ion transference number is higher for these systems as well. These trends can be related to the difference in interaction of TFSI with the IL cation which is stronger for pyr13 than for emim.

Numerical modelling of physical processes in a ballistic laboratory setup with a tapered adapter and plastic piston used for obtaining high muzzle velocities

NASA Astrophysics Data System (ADS)

Bykov, N. V.

2014-12-01

Numerical modelling of a ballistic setup with a tapered adapter and plastic piston is considered. The processes in the firing chamber are described within the framework of quasi- one-dimensional gas dynamics and a geometrical law of propellant burn by means of Lagrangian mass coordinates. The deformable piston is considered to be an ideal liquid with specific equations of state. The numerical solution is obtained by means of a modified explicit von Neumann scheme. The calculation results given show that the ballistic setup with a tapered adapter and plastic piston produces increased shell muzzle velocities by a factor of more than 1.5-2.

Model-Based Analysis of Cell Cycle Responses to Dynamically Changing Environments

PubMed Central

Seaton, Daniel D; Krishnan, J

2016-01-01

Cell cycle progression is carefully coordinated with a cell’s intra- and extracellular environment. While some pathways have been identified that communicate information from the environment to the cell cycle, a systematic understanding of how this information is dynamically processed is lacking. We address this by performing dynamic sensitivity analysis of three mathematical models of the cell cycle in Saccharomyces cerevisiae. We demonstrate that these models make broadly consistent qualitative predictions about cell cycle progression under dynamically changing conditions. For example, it is shown that the models predict anticorrelated changes in cell size and cell cycle duration under different environments independently of the growth rate. This prediction is validated by comparison to available literature data. Other consistent patterns emerge, such as widespread nonmonotonic changes in cell size down generations in response to parameter changes. We extend our analysis by investigating glucose signalling to the cell cycle, showing that known regulation of Cln3 translation and Cln1,2 transcription by glucose is sufficient to explain the experimentally observed changes in cell cycle dynamics at different glucose concentrations. Together, these results provide a framework for understanding the complex responses the cell cycle is capable of producing in response to dynamic environments. PMID:26741131

Collective coordinates theory for discrete soliton ratchets in the sine-Gordon model

NASA Astrophysics Data System (ADS)

Sánchez-Rey, Bernardo; Quintero, Niurka R.; Cuevas-Maraver, Jesús; Alejo, Miguel A.

2014-10-01

A collective coordinate theory is developed for soliton ratchets in the damped discrete sine-Gordon model driven by a biharmonic force. An ansatz with two collective coordinates, namely the center and the width of the soliton, is assumed as an approximated solution of the discrete nonlinear equation. The dynamical equations of these two collective coordinates, obtained by means of the generalized travelling wave method, explain the mechanism underlying the soliton ratchet and capture qualitatively all the main features of this phenomenon. The numerical simulation of these equations accounts for the existence of a nonzero depinning threshold, the nonsinusoidal behavior of the average velocity as a function of the relative phase between the harmonics of the driver, the nonmonotonic dependence of the average velocity on the damping, and the existence of nontransporting regimes beyond the depinning threshold. In particular, it provides a good description of the intriguing and complex pattern of subspaces corresponding to different dynamical regimes in parameter space.

Collective coordinates theory for discrete soliton ratchets in the sine-Gordon model.

PubMed

Sánchez-Rey, Bernardo; Quintero, Niurka R; Cuevas-Maraver, Jesús; Alejo, Miguel A

2014-10-01

A collective coordinate theory is developed for soliton ratchets in the damped discrete sine-Gordon model driven by a biharmonic force. An ansatz with two collective coordinates, namely the center and the width of the soliton, is assumed as an approximated solution of the discrete nonlinear equation. The dynamical equations of these two collective coordinates, obtained by means of the generalized travelling wave method, explain the mechanism underlying the soliton ratchet and capture qualitatively all the main features of this phenomenon. The numerical simulation of these equations accounts for the existence of a nonzero depinning threshold, the nonsinusoidal behavior of the average velocity as a function of the relative phase between the harmonics of the driver, the nonmonotonic dependence of the average velocity on the damping, and the existence of nontransporting regimes beyond the depinning threshold. In particular, it provides a good description of the intriguing and complex pattern of subspaces corresponding to different dynamical regimes in parameter space.

On the decentralized control of large-scale systems. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Chong, C.

1973-01-01

The decentralized control of stochastic large scale systems was considered. Particular emphasis was given to control strategies which utilize decentralized information and can be computed in a decentralized manner. The deterministic constrained optimization problem is generalized to the stochastic case when each decision variable depends on different information and the constraint is only required to be satisfied on the average. For problems with a particular structure, a hierarchical decomposition is obtained. For the stochastic control of dynamic systems with different information sets, a new kind of optimality is proposed which exploits the coupled nature of the dynamic system. The subsystems are assumed to be uncoupled and then certain constraints are required to be satisfied, either in a off-line or on-line fashion. For off-line coordination, a hierarchical approach of solving the problem is obtained. The lower level problems are all uncoupled. For on-line coordination, distinction is made between open loop feedback optimal coordination and closed loop optimal coordination.

Molecular dynamics study on the microscopic details of the evaporation of water.

PubMed

Mason, Phillip E

2011-06-16

Molecular dynamics simulations were conducted on a drop of water (containing 4890 TIP3P waters) at 350 K. About 70 evaporation events were found and characterized in enough detail to determine significant patterns relating to the mechanism of evaporation. It was found that in almost all evaporation events that a single, high-energy state immediately preceded the evaporation event. In ∼50% of the cases, this high-energy state involved a short oxygen-oxygen distance, suggesting a van der Waals collision, whereas in the remaining cases, a short hydrogen-hydrogen distance was found, suggesting an electrostatic "collision". Of the high-energy states that led to evaporation, about half occurred when the coordination number of water was 1, and about half, when the coordination number was 2. It was found that the 1-coordinated waters (∼1% of the surface waters) and 2-coordinated waters (6% of the surface waters) were responsible for almost all the evaporation events. © 2011 American Chemical Society

The Effects of Shoe Traction and Obstacle Height on Lower Extremity Coordination Dynamics during Walking

PubMed Central

Decker, Leslie; Houser, Jeremy J.; Noble, John M.; Karst, Gregory M.; Stergiou, Nicholas

2009-01-01

This study aims to investigate the effects of shoe traction and obstacle height on lower extremity relative phase dynamics (analysis of intralimb coordination) during walking to better understand the mechanisms employed to avoid slippage following obstacle clearance. Ten participants walked at a self-selected pace during eight conditions: four obstacle heights (0%, 10%, 20%, and 40% of limb length) while wearing two pairs of shoes (low and high traction). A coordination analysis was used and phasing relationships between lower extremity segments were examined. The results demonstrated that significant behavioral changes were elicited under varied obstacle heights and frictional conditions. Both decreasing shoe traction and increasing obstacle height resulted in a more in-phase relationship between the interacting lower limb segments. The higher the obstacle and the lower the shoe traction, the more unstable the system became. These changes in phasing relationship and variability are indicators of alterations in coordinative behavior, which if pushed further may have lead to falling. PMID:19187929

Pattern formation and collective effects in populations of magnetic microswimmers

NASA Astrophysics Data System (ADS)

Vach, Peter J.; Walker, Debora; Fischer, Peer; Fratzl, Peter; Faivre, Damien

2017-03-01

Self-propelled particles are one prototype of synthetic active matter used to understand complex biological processes, such as the coordination of movement in bacterial colonies or schools of fishes. Collective patterns such as clusters were observed for such systems, reproducing features of biological organization. However, one limitation of this model is that the synthetic assemblies are made of identical individuals. Here we introduce an active system based on magnetic particles at colloidal scales. We use identical but also randomly-shaped magnetic micropropellers and show that they exhibit dynamic and reversible pattern formation.

Metal-driven and covalent synthesis of supramolecular grids from racks: a convergent approach to heterometallic and heteroleptic nanostructures.

PubMed

Schmittel, Michael; Kalsani, Venkateshwarlu; Bats, Jan W

2005-06-13

Supramolecular nanogrids were prepared from dynamic supramolecular racks through the coupling of terminal alkynes using either a covalent (with CuCl/O(2)) or a coordinative (with [trans-(PEt(3))(2)PtCl(2)]) approach. Because of the rapid equilibration of the racks (as tested by exchange reactions), oligomeric adducts potentially formed in the coupling process will selectively furnish the nanogrids through an entropically driven self-repair mechanism. To ascertain the structural assignment, the nanogrids were also synthesized by an independent strategy.

String method for calculation of minimum free-energy paths in Cartesian space in freely-tumbling systems.

PubMed

Branduardi, Davide; Faraldo-Gómez, José D

2013-09-10

The string method is a molecular-simulation technique that aims to calculate the minimum free-energy path of a chemical reaction or conformational transition, in the space of a pre-defined set of reaction coordinates that is typically highly dimensional. Any descriptor may be used as a reaction coordinate, but arguably the Cartesian coordinates of the atoms involved are the most unprejudiced and intuitive choice. Cartesian coordinates, however, present a non-trivial problem, in that they are not invariant to rigid-body molecular rotations and translations, which ideally ought to be unrestricted in the simulations. To overcome this difficulty, we reformulate the framework of the string method to integrate an on-the-fly structural-alignment algorithm. This approach, referred to as SOMA (String method with Optimal Molecular Alignment), enables the use of Cartesian reaction coordinates in freely tumbling molecular systems. In addition, this scheme permits the dissection of the free-energy change along the most probable path into individual atomic contributions, thus revealing the dominant mechanism of the simulated process. This detailed analysis also provides a physically-meaningful criterion to coarse-grain the representation of the path. To demonstrate the accuracy of the method we analyze the isomerization of the alanine dipeptide in vacuum and the chair-to-inverted-chair transition of β -D mannose in explicit water. Notwithstanding the simplicity of these systems, the SOMA approach reveals novel insights into the atomic mechanism of these isomerizations. In both cases, we find that the dynamics and the energetics of these processes are controlled by interactions involving only a handful of atoms in each molecule. Consistent with this result, we show that a coarse-grained SOMA calculation defined in terms of these subsets of atoms yields nearidentical minimum free-energy paths and committor distributions to those obtained via a highly-dimensional string.

String method for calculation of minimum free-energy paths in Cartesian space in freely-tumbling systems

PubMed Central

Branduardi, Davide; Faraldo-Gómez, José D.

2014-01-01

The string method is a molecular-simulation technique that aims to calculate the minimum free-energy path of a chemical reaction or conformational transition, in the space of a pre-defined set of reaction coordinates that is typically highly dimensional. Any descriptor may be used as a reaction coordinate, but arguably the Cartesian coordinates of the atoms involved are the most unprejudiced and intuitive choice. Cartesian coordinates, however, present a non-trivial problem, in that they are not invariant to rigid-body molecular rotations and translations, which ideally ought to be unrestricted in the simulations. To overcome this difficulty, we reformulate the framework of the string method to integrate an on-the-fly structural-alignment algorithm. This approach, referred to as SOMA (String method with Optimal Molecular Alignment), enables the use of Cartesian reaction coordinates in freely tumbling molecular systems. In addition, this scheme permits the dissection of the free-energy change along the most probable path into individual atomic contributions, thus revealing the dominant mechanism of the simulated process. This detailed analysis also provides a physically-meaningful criterion to coarse-grain the representation of the path. To demonstrate the accuracy of the method we analyze the isomerization of the alanine dipeptide in vacuum and the chair-to-inverted-chair transition of β-D mannose in explicit water. Notwithstanding the simplicity of these systems, the SOMA approach reveals novel insights into the atomic mechanism of these isomerizations. In both cases, we find that the dynamics and the energetics of these processes are controlled by interactions involving only a handful of atoms in each molecule. Consistent with this result, we show that a coarse-grained SOMA calculation defined in terms of these subsets of atoms yields nearidentical minimum free-energy paths and committor distributions to those obtained via a highly-dimensional string. PMID:24729762

A new structural framework for integrating replication protein A into DNA processing machinery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brosey, Chris A; Yan, Chunli; Tsutakawa, Susan E

2013-01-01

By coupling the protection and organization of ssDNA with the recruitment and alignment of DNA processing factors, Replication Protein A (RPA) lies at the heart of dynamic multi-protein DNA processing machinery. Nevertheless, how RPA manages to coordinate the biochemical functions of its eight domains remains unknown. We examined the structural biochemistry of RPA s DNA binding activity, combining small-angle x-ray and neutron scattering with all-atom molecular dynamics simulations to investigate the architecture of RPA s DNA-binding core. It has been long held that RPA engages ssDNA in three stages, but our data reveal that RPA undergoes two rather than threemore » transitions as it binds ssDNA. In contrast to previous models, RPA is more compact when fully engaged on 20-30 nucleotides of ssDNA than when DNA-free, and there is no evidence for significant population of a highly compacted structure in the initial 8-10 nucleotide binding mode. These results provide a new framework for understanding the integration of ssDNA into DNA processing machinery and how binding partners may manipulate RPA architecture to gain access to the substrate.« less

Development and Experimental Validation of Large Eddy Simulation Techniques for the Prediction of Combustion-Dynamic Process in Syngas Combustion: Characterization of Autoignition, Flashback, and Flame-Liftoff at Gas-Turbine Relevant Operating Conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ihme, Matthias; Driscoll, James

2015-08-31

The objective of this closely coordinated experimental and computational research effort is the development of simulation techniques for the prediction of combustion processes, relevant to the oxidation of syngas and high hydrogen content (HHC) fuels at gas-turbine relevant operating conditions. Specifically, the research goals are (i) the characterization of the sensitivity of syngas ignition processes to hydrodynamic processes and perturbations in temperature and mixture composition in rapid compression machines and ow-reactors and (ii) to conduct comprehensive experimental investigations in a swirl-stabilized gas turbine (GT) combustor under realistic high-pressure operating conditions in order (iii) to obtain fundamental understanding about mechanisms controllingmore » unstable flame regimes in HHC-combustion.« less

Nonlinear intrinsic variables and state reconstruction in multiscale simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dsilva, Carmeline J., E-mail: cdsilva@princeton.edu; Talmon, Ronen, E-mail: ronen.talmon@yale.edu; Coifman, Ronald R., E-mail: coifman@math.yale.edu

2013-11-14

Finding informative low-dimensional descriptions of high-dimensional simulation data (like the ones arising in molecular dynamics or kinetic Monte Carlo simulations of physical and chemical processes) is crucial to understanding physical phenomena, and can also dramatically assist in accelerating the simulations themselves. In this paper, we discuss and illustrate the use of nonlinear intrinsic variables (NIV) in the mining of high-dimensional multiscale simulation data. In particular, we focus on the way NIV allows us to functionally merge different simulation ensembles, and different partial observations of these ensembles, as well as to infer variables not explicitly measured. The approach relies on certainmore » simple features of the underlying process variability to filter out measurement noise and systematically recover a unique reference coordinate frame. We illustrate the approach through two distinct sets of atomistic simulations: a stochastic simulation of an enzyme reaction network exhibiting both fast and slow time scales, and a molecular dynamics simulation of alanine dipeptide in explicit water.« less

Nonlinear intrinsic variables and state reconstruction in multiscale simulations

NASA Astrophysics Data System (ADS)

Dsilva, Carmeline J.; Talmon, Ronen; Rabin, Neta; Coifman, Ronald R.; Kevrekidis, Ioannis G.

2013-11-01

Finding informative low-dimensional descriptions of high-dimensional simulation data (like the ones arising in molecular dynamics or kinetic Monte Carlo simulations of physical and chemical processes) is crucial to understanding physical phenomena, and can also dramatically assist in accelerating the simulations themselves. In this paper, we discuss and illustrate the use of nonlinear intrinsic variables (NIV) in the mining of high-dimensional multiscale simulation data. In particular, we focus on the way NIV allows us to functionally merge different simulation ensembles, and different partial observations of these ensembles, as well as to infer variables not explicitly measured. The approach relies on certain simple features of the underlying process variability to filter out measurement noise and systematically recover a unique reference coordinate frame. We illustrate the approach through two distinct sets of atomistic simulations: a stochastic simulation of an enzyme reaction network exhibiting both fast and slow time scales, and a molecular dynamics simulation of alanine dipeptide in explicit water.

Externally induced frontoparietal synchronization modulates network dynamics and enhances working memory performance.

PubMed

Violante, Ines R; Li, Lucia M; Carmichael, David W; Lorenz, Romy; Leech, Robert; Hampshire, Adam; Rothwell, John C; Sharp, David J

2017-03-14

Cognitive functions such as working memory (WM) are emergent properties of large-scale network interactions. Synchronisation of oscillatory activity might contribute to WM by enabling the coordination of long-range processes. However, causal evidence for the way oscillatory activity shapes network dynamics and behavior in humans is limited. Here we applied transcranial alternating current stimulation (tACS) to exogenously modulate oscillatory activity in a right frontoparietal network that supports WM. Externally induced synchronization improved performance when cognitive demands were high. Simultaneously collected fMRI data reveals tACS effects dependent on the relative phase of the stimulation and the internal cognitive processing state. Specifically, synchronous tACS during the verbal WM task increased parietal activity, which correlated with behavioral performance. Furthermore, functional connectivity results indicate that the relative phase of frontoparietal stimulation influences information flow within the WM network. Overall, our findings demonstrate a link between behavioral performance in a demanding WM task and large-scale brain synchronization.

The Yeast Cyclin-Dependent Kinase Routes Carbon Fluxes to Fuel Cell Cycle Progression.

PubMed

Ewald, Jennifer C; Kuehne, Andreas; Zamboni, Nicola; Skotheim, Jan M

2016-05-19

Cell division entails a sequence of processes whose specific demands for biosynthetic precursors and energy place dynamic requirements on metabolism. However, little is known about how metabolic fluxes are coordinated with the cell division cycle. Here, we examine budding yeast to show that more than half of all measured metabolites change significantly through the cell division cycle. Cell cycle-dependent changes in central carbon metabolism are controlled by the cyclin-dependent kinase (Cdk1), a major cell cycle regulator, and the metabolic regulator protein kinase A. At the G1/S transition, Cdk1 phosphorylates and activates the enzyme Nth1, which funnels the storage carbohydrate trehalose into central carbon metabolism. Trehalose utilization fuels anabolic processes required to reliably complete cell division. Thus, the cell cycle entrains carbon metabolism to fuel biosynthesis. Because the oscillation of Cdk activity is a conserved feature of the eukaryotic cell cycle, we anticipate its frequent use in dynamically regulating metabolism for efficient proliferation. Copyright © 2016 Elsevier Inc. All rights reserved.

Transferring the entatic-state principle to copper photochemistry

NASA Astrophysics Data System (ADS)

Dicke, B.; Hoffmann, A.; Stanek, J.; Rampp, M. S.; Grimm-Lebsanft, B.; Biebl, F.; Rukser, D.; Maerz, B.; Göries, D.; Naumova, M.; Biednov, M.; Neuber, G.; Wetzel, A.; Hofmann, S. M.; Roedig, P.; Meents, A.; Bielecki, J.; Andreasson, J.; Beyerlein, K. R.; Chapman, H. N.; Bressler, C.; Zinth, W.; Rübhausen, M.; Herres-Pawlis, S.

2018-03-01

The entatic state denotes a distorted coordination geometry of a complex from its typical arrangement that generates an improvement to its function. The entatic-state principle has been observed to apply to copper electron-transfer proteins and it results in a lowering of the reorganization energy of the electron-transfer process. It is thus crucial for a multitude of biochemical processes, but its importance to photoactive complexes is unexplored. Here we study a copper complex—with a specifically designed constraining ligand geometry—that exhibits metal-to-ligand charge-transfer state lifetimes that are very short. The guanidine-quinoline ligand used here acts on the bis(chelated) copper(I) centre, allowing only small structural changes after photoexcitation that result in very fast structural dynamics. The data were collected using a multimethod approach that featured time-resolved ultraviolet-visible, infrared and X-ray absorption and optical emission spectroscopy. Through supporting density functional calculations, we deliver a detailed picture of the structural dynamics in the picosecond-to-nanosecond time range.

Externally induced frontoparietal synchronization modulates network dynamics and enhances working memory performance

PubMed Central

Violante, Ines R; Li, Lucia M; Carmichael, David W; Lorenz, Romy; Leech, Robert; Hampshire, Adam; Rothwell, John C; Sharp, David J

2017-01-01

Cognitive functions such as working memory (WM) are emergent properties of large-scale network interactions. Synchronisation of oscillatory activity might contribute to WM by enabling the coordination of long-range processes. However, causal evidence for the way oscillatory activity shapes network dynamics and behavior in humans is limited. Here we applied transcranial alternating current stimulation (tACS) to exogenously modulate oscillatory activity in a right frontoparietal network that supports WM. Externally induced synchronization improved performance when cognitive demands were high. Simultaneously collected fMRI data reveals tACS effects dependent on the relative phase of the stimulation and the internal cognitive processing state. Specifically, synchronous tACS during the verbal WM task increased parietal activity, which correlated with behavioral performance. Furthermore, functional connectivity results indicate that the relative phase of frontoparietal stimulation influences information flow within the WM network. Overall, our findings demonstrate a link between behavioral performance in a demanding WM task and large-scale brain synchronization. DOI: http://dx.doi.org/10.7554/eLife.22001.001 PMID:28288700

Flight Dynamics Operations: Methods and Lessons Learned from Space Shuttle Orbit Operations

NASA Technical Reports Server (NTRS)

Cutri-Kohart, Rebecca M.

2011-01-01

The Flight Dynamics Officer is responsible for trajectory maintenance of the Space Shuttle. This paper will cover high level operational considerations, methodology, procedures, and lessons learned involved in performing the functions of orbit and rendezvous Flight Dynamics Officer and leading the team of flight dynamics specialists during different phases of flight. The primary functions that will be address are: onboard state vector maintenance, ground ephemeris maintenance, calculation of ground and spacecraft acquisitions, collision avoidance, burn targeting for the primary mission, rendezvous, deorbit and contingencies, separation sequences, emergency deorbit preparation, mass properties coordination, payload deployment planning, coordination with the International Space Station, and coordination with worldwide trajectory customers. Each of these tasks require the Flight Dynamics Officer to have cognizance of the current trajectory state as well as the impact of future events on the trajectory plan in order to properly analyze and react to real-time changes. Additionally, considerations are made to prepare flexible alternative trajectory plans in the case timeline changes or a systems failure impact the primary plan. The evolution of the methodology, procedures, and techniques used by the Flight Dynamics Officer to perform these tasks will be discussed. Particular attention will be given to how specific Space Shuttle mission and training simulation experiences, particularly off-nominal or unexpected events such as shortened mission durations, tank failures, contingency deorbit, navigation errors, conjunctions, and unexpected payload deployments, have influenced the operational procedures and training for performing Space Shuttle flight dynamics operations over the history of the program. These lessons learned can then be extended to future vehicle trajectory operations.

Dynamically assisted Schwinger effect beyond the spatially-uniform-field approximation

NASA Astrophysics Data System (ADS)

Aleksandrov, I. A.; Plunien, G.; Shabaev, V. M.

2018-06-01

We investigate the phenomenon of electron-positron pair production from vacuum in the presence of a strong electric field superimposed by a weak but fast varying pulse which substantially increases the total particle yield. We employ a nonperturbative numerical technique and perform the calculations beyond the spatially-uniform-field approximation, i.e., dipole approximation, taking into account the coordinate dependence of the fast component. The analysis of the main characteristics of the pair-production process (momentum spectra of particles and total amount of pairs) reveals a number of important features which are absent within the previously used approximation. In particular, the structure of the momentum distribution is modified both qualitatively and quantitatively, and the total number of pairs created as well as the enhancement factor due to dynamical assistance become significantly smaller.

Symbolic-Numerical Modeling of the Influence of Damping Moments on Satellite Dynamics

NASA Astrophysics Data System (ADS)

Gutnik, Sergey A.; Sarychev, Vasily A.

2018-02-01

The dynamics of a satellite on a circular orbit under the influence of gravitational and active damping torques, which are proportional to the projections of the angular velocity of the satellite, is investigated. Computer algebra Gröbner basis methods for the determination of all equilibrium orientations of the satellite in the orbital coordinate system with given damping torque and given principal central moments of inertia were used. The conditions of the equilibria existence depending on three damping parameters were obtained from the analysis of the real roots of the algebraic equations spanned by the constructed Gröbner basis. Conditions of asymptotic stability of the satellite equilibria and the transition decay processes of the spatial oscillations of the satellite at different damping parameters have also been obtained.

Developmental coordination disorders and sensory processing and integration: Incidence, associations and co-morbidities.

PubMed

Allen, Susan; Casey, Jackie

2017-09-01

Children with developmental coordination disorder or sensory processing and integration difficulties face challenges to participation in daily living. To date there has been no exploration of the co-occurrence of developmental coordination disorders and sensory processing and integration difficulties. Records of children meeting Diagnostic and Statistical Manual - V criteria for developmental coordination disorder ( n  = 93) age 5 to 12 years were examined. Data on motor skills (Movement Assessment Battery for Children - 2) and sensory processing and integration (Sensory Processing Measure) were interrogated. Of the total sample, 88% exhibited some or definite differences in sensory processing and integration. No apparent relationship was observed between motor coordination and sensory processing and integration. The full sample showed high rates of some difficulties in social participation, hearing, body awareness, balance and motion, and planning and ideation. Further, children with co-morbid autistic spectrum disorder showed high rates of difficulties with touch and vision. Most, but not all, children with developmental coordination disorder presented with some difficulties in sensory processing and integration that impacted on their participation in everyday activities. Sensory processing and integration difficulties differed significantly between those with and without co-morbid autistic spectrum disorder.

Emergence of HGF/SF-Induced Coordinated Cellular Motility

PubMed Central

Zaritsky, Assaf; Natan, Sari; Ben-Jacob, Eshel; Tsarfaty, Ilan

2012-01-01

Collective cell migration plays a major role in embryonic morphogenesis, tissue remodeling, wound repair and cancer invasion. Despite many decades of extensive investigations, only few analytical tools have been developed to enhance the biological understanding of this important phenomenon. Here we present a novel quantitative approach to analyze long term kinetics of bright field time-lapse wound healing. Fully-automated spatiotemporal measures and visualization of cells' motility and implicit morphology were proven to be sound, repetitive and highly informative compared to single-cell tracking analysis. We study cellular collective migration induced by tyrosine kinase-growth factor signaling (Met-Hepatocyte Growth Factor/Scatter Factor (HGF/SF)). Our quantitative approach is applied to demonstrate that collective migration of the adenocarcinoma cell lines is characterized by simple morpho-kinetics. HGF/SF induces complex morpho-kinetic coordinated collective migration: cells at the front move faster and are more spread than those further away from the wound edge. As the wound heals, distant cells gradually accelerate and enhance spread and elongation –resembling the epithelial to mesenchymal transition (EMT), and then the cells become more spread and maintain higher velocity than cells located closer to the wound. Finally, upon wound closure, front cells halt, shrink and round up (resembling mesenchymal to epithelial transition (MET) phenotype) while distant cells undergo the same process gradually. Met inhibition experiments further validate that Met signaling dramatically alters the morpho-kinetic dynamics of the healing wound. Machine-learning classification was applied to demonstrate the generalization of our findings, revealing even subtle changes in motility patterns induced by Met-inhibition. It is concluded that activation of Met-signaling induces an elaborated model in which cells lead a coordinated increased motility along with gradual differentiation-based collective cell motility dynamics. Our quantitative phenotypes may guide future investigation on the molecular and cellular mechanisms of tyrosine kinase-induced coordinate cell motility and morphogenesis in metastasis. PMID:22970283

Rowing Crew Coordination Dynamics at Increasing Stroke Rates

PubMed Central

2015-01-01

In rowing, perfect synchronisation is important for optimal performance of a crew. Remarkably, a recent study on ergometers demonstrated that antiphase crew coordination might be mechanically more efficient by reducing the power lost to within-cycle velocity fluctuations of the boat. However, coupled oscillator dynamics predict the stability of the coordination to decrease with increasing stroke rate, which in case of antiphase may eventually yield breakdowns to in-phase. Therefore, this study examined the effects of increasing stroke rate on in- and antiphase crew coordination in rowing dyads. Eleven experienced dyads rowed on two mechanically coupled ergometers on slides, which allowed the ergometer system to move back and forth as one ‘boat’. The dyads performed a ramp trial in both in- and antiphase pattern, in which stroke rates gradually increased from 30 strokes per minute (spm) to as fast as possible in steps of 2 spm. Kinematics of rowers, handles and ergometers were captured. Two dyads showed a breakdown of antiphase into in-phase coordination at the first stroke rate of the ramp trial. The other nine dyads reached between 34–42 spm in antiphase but achieved higher rates in in-phase. As expected, the coordinative accuracy in antiphase was worse than in in-phase crew coordination, while, somewhat surprisingly, the coordinative variability did not differ between the patterns. Whereas crew coordination did not substantially deteriorate with increasing stroke rate, stroke rate did affect the velocity fluctuations of the ergometers: fluctuations were clearly larger in the in-phase pattern than in the antiphase pattern, and this difference significantly increased with stroke rate. Together, these results suggest that although antiphase rowing is less stable (i.e., less resistant to perturbation), potential on-water benefits of antiphase over in-phase rowing may actually increase with stroke rate. PMID:26185987

Transfer of learning between unimanual and bimanual rhythmic movement coordination: transfer is a function of the task dynamic.

PubMed

Snapp-Childs, Winona; Wilson, Andrew D; Bingham, Geoffrey P

2015-07-01

Under certain conditions, learning can transfer from a trained task to an untrained version of that same task. However, it is as yet unclear what those certain conditions are or why learning transfers when it does. Coordinated rhythmic movement is a valuable model system for investigating transfer because we have a model of the underlying task dynamic that includes perceptual coupling between the limbs being coordinated. The model predicts that (1) coordinated rhythmic movements, both bimanual and unimanual, are organised with respect to relative motion information for relative phase in the coupling function, (2) unimanual is less stable than bimanual coordination because the coupling is unidirectional rather than bidirectional, and (3) learning a new coordination is primarily about learning to perceive and use the relevant information which, with equal perceptual improvement due to training, yields equal transfer of learning from bimanual to unimanual coordination and vice versa [but, given prediction (2), the resulting performance is also conditioned by the intrinsic stability of each task]. In the present study, two groups were trained to produce 90° either unimanually or bimanually, respectively, and tested in respect to learning (namely improved performance in the trained 90° coordination task and improved visual discrimination of 90°) and transfer of learning (to the other, untrained 90° coordination task). Both groups improved in the task condition in which they were trained and in their ability to visually discriminate 90°, and this learning transferred to the untrained condition. When scaled by the relative intrinsic stability of each task, transfer levels were found to be equal. The results are discussed in the context of the perception-action approach to learning and performance.

A study on predicting network corrections in PPP-RTK processing

NASA Astrophysics Data System (ADS)

Wang, Kan; Khodabandeh, Amir; Teunissen, Peter

2017-10-01

In PPP-RTK processing, the network corrections including the satellite clocks, the satellite phase biases and the ionospheric delays are provided to the users to enable fast single-receiver integer ambiguity resolution. To solve the rank deficiencies in the undifferenced observation equations, the estimable parameters are formed to generate full-rank design matrix. In this contribution, we firstly discuss the interpretation of the estimable parameters without and with a dynamic satellite clock model incorporated in a Kalman filter during the network processing. The functionality of the dynamic satellite clock model is tested in the PPP-RTK processing. Due to the latency generated by the network processing and data transfer, the network corrections are delayed for the real-time user processing. To bridge the latencies, we discuss and compare two prediction approaches making use of the network corrections without and with the dynamic satellite clock model, respectively. The first prediction approach is based on the polynomial fitting of the estimated network parameters, while the second approach directly follows the dynamic model in the Kalman filter of the network processing and utilises the satellite clock drifts estimated in the network processing. Using 1 Hz data from two networks in Australia, the influences of the two prediction approaches on the user positioning results are analysed and compared for latencies ranging from 3 to 10 s. The accuracy of the positioning results decreases with the increasing latency of the network products. For a latency of 3 s, the RMS of the horizontal and the vertical coordinates (with respect to the ground truth) do not show large differences applying both prediction approaches. For a latency of 10 s, the prediction approach making use of the satellite clock model has generated slightly better positioning results with the differences of the RMS at mm-level. Further advantages and disadvantages of both prediction approaches are also discussed in this contribution.

A scalable approach to solving dense linear algebra problems on hybrid CPU-GPU systems

DOE PAGES

Song, Fengguang; Dongarra, Jack

2014-10-01

Aiming to fully exploit the computing power of all CPUs and all graphics processing units (GPUs) on hybrid CPU-GPU systems to solve dense linear algebra problems, in this paper we design a class of heterogeneous tile algorithms to maximize the degree of parallelism, to minimize the communication volume, and to accommodate the heterogeneity between CPUs and GPUs. The new heterogeneous tile algorithms are executed upon our decentralized dynamic scheduling runtime system, which schedules a task graph dynamically and transfers data between compute nodes automatically. The runtime system uses a new distributed task assignment protocol to solve data dependencies between tasksmore » without any coordination between processing units. By overlapping computation and communication through dynamic scheduling, we are able to attain scalable performance for the double-precision Cholesky factorization and QR factorization. Finally, our approach demonstrates a performance comparable to Intel MKL on shared-memory multicore systems and better performance than both vendor (e.g., Intel MKL) and open source libraries (e.g., StarPU) in the following three environments: heterogeneous clusters with GPUs, conventional clusters without GPUs, and shared-memory systems with multiple GPUs.« less

Experiential knowledge of expert coaches can help identify informational constraints on performance of dynamic interceptive actions.

PubMed

Greenwood, Daniel; Davids, Keith; Renshaw, Ian

2014-01-01

Coordination of dynamic interceptive movements is predicated on cyclical relations between an individual's actions and information sources from the performance environment. To identify dynamic informational constraints, which are interwoven with individual and task constraints, coaches' experiential knowledge provides a complementary source to support empirical understanding of performance in sport. In this study, 15 expert coaches from 3 sports (track and field, gymnastics and cricket) participated in a semi-structured interview process to identify potential informational constraints which they perceived to regulate action during run-up performance. Expert coaches' experiential knowledge revealed multiple information sources which may constrain performance adaptations in such locomotor pointing tasks. In addition to the locomotor pointing target, coaches' knowledge highlighted two other key informational constraints: vertical reference points located near the locomotor pointing target and a check mark located prior to the locomotor pointing target. This study highlights opportunities for broadening the understanding of perception and action coupling processes, and the identified information sources warrant further empirical investigation as potential constraints on athletic performance. Integration of experiential knowledge of expert coaches with theoretically driven empirical knowledge represents a promising avenue to drive future applied science research and pedagogical practice.

A scalable approach to solving dense linear algebra problems on hybrid CPU-GPU systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Fengguang; Dongarra, Jack

Aiming to fully exploit the computing power of all CPUs and all graphics processing units (GPUs) on hybrid CPU-GPU systems to solve dense linear algebra problems, in this paper we design a class of heterogeneous tile algorithms to maximize the degree of parallelism, to minimize the communication volume, and to accommodate the heterogeneity between CPUs and GPUs. The new heterogeneous tile algorithms are executed upon our decentralized dynamic scheduling runtime system, which schedules a task graph dynamically and transfers data between compute nodes automatically. The runtime system uses a new distributed task assignment protocol to solve data dependencies between tasksmore » without any coordination between processing units. By overlapping computation and communication through dynamic scheduling, we are able to attain scalable performance for the double-precision Cholesky factorization and QR factorization. Finally, our approach demonstrates a performance comparable to Intel MKL on shared-memory multicore systems and better performance than both vendor (e.g., Intel MKL) and open source libraries (e.g., StarPU) in the following three environments: heterogeneous clusters with GPUs, conventional clusters without GPUs, and shared-memory systems with multiple GPUs.« less

The role of general dynamic coordination in the handwriting skills of children

PubMed Central

Scordella, Andrea; Di Sano, Sergio; Aureli, Tiziana; Cerratti, Paola; Verratti, Vittore; Fanò-Illic, Giorgio; Pietrangelo, Tiziana

2015-01-01

Difficulties in handwriting are often reported in children with developmental coordination disorder, and they represent an important element in the diagnosis. The present study was aimed at investigating the relation between motor coordination and handwriting skills, and to identify differences in handwriting between children without and with coordination difficulties. In particular, we asked whether visual–spatial skills have a role as mediating variables between motor coordination and handwriting. We assessed motor coordination as well as graphic abilities in children aged 7–10 years. Moreover, we evaluated their visual–motor integration, visual–spatial skills, and other cognitive abilities (memory and planning). We found no relation between motor coordination and handwriting skills, while visual–spatial skills (measured by a visual-constructive task) were related with both. Our conclusion is that visual–spatial skills are involved both in general motor coordination and in handwriting, but the relationship involves different aspects in the two cases. PMID:25999893

Time References in US and UK Astronomical and Navigational Almanacs

DTIC Science & Technology

2011-01-01

are also compatible with Teph and TDB. 2.4. Terrestrial and Barycentric Dynamic Times An apparent place, or equivalently the geocentric intermediate...right ascension and declination with respect to the CIO and equator of date, is defined in the Geocentric Celestial Reference System where the... Geocentric Coordinate Time (TCG) nor Barycentric Coordinate Time (TCB) is used in the US and UK almanacs for different reasons. TCG is a coordinate time

Functionally relevant protein motions: Extracting basin-specific collective coordinates from molecular dynamics trajectories

NASA Astrophysics Data System (ADS)

Pan, Patricia Wang; Dickson, Russell J.; Gordon, Heather L.; Rothstein, Stuart M.; Tanaka, Shigenori

2005-01-01

Functionally relevant motion of proteins has been associated with a number of atoms moving in a concerted fashion along so-called "collective coordinates." We present an approach to extract collective coordinates from conformations obtained from molecular dynamics simulations. The power of this technique for differentiating local structural fuctuations between classes of conformers obtained by clustering is illustrated by analyzing nanosecond-long trajectories for the response regulator protein Spo0F of Bacillus subtilis, generated both in vacuo and using an implicit-solvent representation. Conformational clustering is performed using automated histogram filtering of the inter-Cα distances. Orthogonal (varimax) rotation of the vectors obtained by principal component analysis of these interresidue distances for the members of individual clusters is key to the interpretation of collective coordinates dominating each conformational class. The rotated loadings plots isolate significant variation in interresidue distances, and these are associated with entire mobile secondary structure elements. From this we infer concerted motions of these structural elements. For the Spo0F simulations employing an implicit-solvent representation, collective coordinates obtained in this fashion are consistent with the location of the protein's known active sites and experimentally determined mobile regions.

Asymmetric Preorganization of Inverted Pair Residues in the Sodium-Calcium Exchanger

PubMed Central

Giladi, Moshe; Almagor, Lior; van Dijk, Liat; Hiller, Reuben; Man, Petr; Forest, Eric; Khananshvili, Daniel

2016-01-01

In analogy with many other proteins, Na+/Ca2+ exchangers (NCX) adapt an inverted twofold symmetry of repeated structural elements, while exhibiting a functional asymmetry by stabilizing an outward-facing conformation. Here, structure-based mutant analyses of the Methanococcus jannaschii Na+/Ca2+ exchanger (NCX_Mj) were performed in conjunction with HDX-MS (hydrogen/deuterium exchange mass spectrometry) to identify the structure-dynamic determinants of functional asymmetry. HDX-MS identified hallmark differences in backbone dynamics at ion-coordinating residues of apo-NCX_Mj, whereas Na+or Ca2+ binding to the respective sites induced relatively small, but specific, changes in backbone dynamics. Mutant analysis identified ion-coordinating residues affecting the catalytic capacity (kcat/Km), but not the stability of the outward-facing conformation. In contrast, distinct “noncatalytic” residues (adjacent to the ion-coordinating residues) control the stability of the outward-facing conformation, but not the catalytic capacity. The helix-breaking signature sequences (GTSLPE) on the α1 and α2 repeats (at the ion-binding core) differ in their folding/unfolding dynamics, while providing asymmetric contributions to transport activities. The present data strongly support the idea that asymmetric preorganization of the ligand-free ion-pocket predefines catalytic reorganization of ion-bound residues, where secondary interactions with adjacent residues couple the alternating access. These findings provide a structure-dynamic basis for ion-coupled alternating access in NCX and similar proteins. PMID:26876271

HIV-1 requires Arf6-mediated membrane dynamics to efficiently enter and infect T lymphocytes

PubMed Central

García-Expósito, Laura; Barroso-González, Jonathan; Puigdomènech, Isabel; Machado, José-David; Blanco, Julià; Valenzuela-Fernández, Agustín

2011-01-01

As the initial barrier to viral entry, the plasma membrane along with the membrane trafficking machinery and cytoskeleton are of fundamental importance in the viral cycle. However, little is known about the contribution of plasma membrane dynamics during early human immunodeficiency virus type 1 (HIV-1) infection. Considering that ADP ribosylation factor 6 (Arf6) regulates cellular invasion via several microorganisms by coordinating membrane trafficking, our aim was to study the function of Arf6-mediated membrane dynamics on HIV-1 entry and infection of T lymphocytes. We observed that an alteration of the Arf6–guanosine 5′-diphosphate/guanosine 5′-triphosphate (GTP/GDP) cycle, by GDP-bound or GTP-bound inactive mutants or by specific Arf6 silencing, inhibited HIV-1 envelope–induced membrane fusion, entry, and infection of T lymphocytes and permissive cells, regardless of viral tropism. Furthermore, cell-to-cell HIV-1 transmission of primary human CD4+ T lymphocytes was inhibited by Arf6 knockdown. Total internal reflection fluorescence microscopy showed that Arf6 mutants provoked the accumulation of phosphatidylinositol-(4,5)-biphosphate–associated structures on the plasma membrane of permissive cells, without affecting CD4-viral attachment but impeding CD4-dependent HIV-1 entry. Arf6 silencing or its mutants did not affect fusion, entry, and infection of vesicular stomatitis virus G–pseudotyped viruses or ligand-induced CXCR4 or CCR5 endocytosis, both clathrin-dependent processes. Therefore we propose that efficient early HIV-1 infection of CD4+ T lymphocytes requires Arf6-coordinated plasma membrane dynamics that promote viral fusion and entry. PMID:21346189

Autonomous Multi-Sensor Coordination: The Science Goal Monitor

NASA Technical Reports Server (NTRS)

Koratkar, Anuradha; Grosvenor, Sandy; Jung, John; Hess, Melissa; Jones, Jeremy

2004-01-01

Many dramatic earth phenomena are dynamic and coupled. In order to fully understand them, we need to obtain timely coordinated multi-sensor observations from widely dispersed instruments. Such a dynamic observing system must include the ability to Schedule flexibly and react autonomously to sciencehser driven events; Understand higher-level goals of a sciencehser defined campaign; Coordinate various space-based and ground-based resources/sensors effectively and efficiently to achieve goals. In order to capture transient events, such a 'sensor web' system must have an automated reactive capability built into its scientific operations. To do this, we must overcome a number of challenges inherent in infusing autonomy. The Science Goal Monitor (SGM) is a prototype software tool being developed to explore the nature of automation necessary to enable dynamic observing. The tools being developed in SGM improve our ability to autonomously monitor multiple independent sensors and coordinate reactions to better observe dynamic phenomena. The SGM system enables users to specify what to look for and how to react in descriptive rather than technical terms. The system monitors streams of data to identify occurrences of the key events previously specified by the scientisther. When an event occurs, the system autonomously coordinates the execution of the users' desired reactions between different sensors. The information can be used to rapidly respond to a variety of fast temporal events. Investigators will no longer have to rely on after-the-fact data analysis to determine what happened. Our paper describes a series of prototype demonstrations that we have developed using SGM and NASA's Earth Observing-1 (EO-1) satellite and Earth Observing Systems' Aqua/Terra spacecrafts' MODIS instrument. Our demonstrations show the promise of coordinating data from different sources, analyzing the data for a relevant event, autonomously updating and rapidly obtaining a follow-on relevant image. SGM was used to investigate forest fires, floods and volcanic eruptions. We are now identifying new Earth science scenarios that will have more complex SGM reasoning. By developing and testing a prototype in an operational environment, we are also establishing and gathering metrics to gauge the success of automating science campaigns.

Natural transformation occurs independently of the essential actin-like MreB cytoskeleton in Legionella pneumophila

PubMed Central

Juan, Pierre-Alexandre; Attaiech, Laetitia; Charpentier, Xavier

2015-01-01

Natural transformation is the process by which bacteria can actively take up and integrate exogenous DNA thereby providing a source of genetic diversity. Under specific growth conditions the coordinated expression of several genes – a situation referred to as “competence” – allows bacteria to assemble a highly processive and dedicated system that can import high molecular weight DNA. Within the cell these large imported DNA molecules are protected from degradation and brought to the chromosome for recombination. Here, we report elevated expression of mreB during competence in the Gram-negative pathogen Legionella pneumophila. Interestingly a similar observation had previously been reported in the distantly-related Gram-positive organism Bacillus subtilis. MreB is often viewed as the bacterial actin homolog contributing to bacterial morphogenesis by coordinating peptidoglycan-synthesising complexes. In addition MreB is increasingly found to be involved in a growing number of processes including chromosome segregation and motor-driven motility. Using genetic and pharmacological approaches, we examined the possible role of MreB during natural transformation in L. pneumophila. Our data show that natural transformation does not require MreB dynamics and exclude a direct role of MreB filaments in the transport of foreign DNA and its recombination in the chromosome. PMID:26526572

Natural transformation occurs independently of the essential actin-like MreB cytoskeleton in Legionella pneumophila.

PubMed

Juan, Pierre-Alexandre; Attaiech, Laetitia; Charpentier, Xavier

2015-11-03

Natural transformation is the process by which bacteria can actively take up and integrate exogenous DNA thereby providing a source of genetic diversity. Under specific growth conditions the coordinated expression of several genes--a situation referred to as "competence"--allows bacteria to assemble a highly processive and dedicated system that can import high molecular weight DNA. Within the cell these large imported DNA molecules are protected from degradation and brought to the chromosome for recombination. Here, we report elevated expression of mreB during competence in the Gram-negative pathogen Legionella pneumophila. Interestingly a similar observation had previously been reported in the distantly-related Gram-positive organism Bacillus subtilis. MreB is often viewed as the bacterial actin homolog contributing to bacterial morphogenesis by coordinating peptidoglycan-synthesising complexes. In addition MreB is increasingly found to be involved in a growing number of processes including chromosome segregation and motor-driven motility. Using genetic and pharmacological approaches, we examined the possible role of MreB during natural transformation in L. pneumophila. Our data show that natural transformation does not require MreB dynamics and exclude a direct role of MreB filaments in the transport of foreign DNA and its recombination in the chromosome.

Goddard trajectory determination subsystem: Mathematical specifications

NASA Technical Reports Server (NTRS)

Wagner, W. E. (Editor); Velez, C. E. (Editor)

1972-01-01

The mathematical specifications of the Goddard trajectory determination subsystem of the flight dynamics system are presented. These specifications include the mathematical description of the coordinate systems, dynamic and measurement model, numerical integration techniques, and statistical estimation concepts.

Self-sorting of dynamic metallosupramolecular libraries (DMLs) via metal-driven selection.

PubMed

Kocsis, Istvan; Dumitrescu, Dan; Legrand, Yves-Marie; van der Lee, Arie; Grosu, Ion; Barboiu, Mihail

2014-03-11

"Metal-driven" selection between finite mononuclear and polymeric metallosupramolecular species can be quantitatively achieved in solution and in a crystalline state via coupled coordination/stacking interactional algorithms within dynamic metallosupramolecular libraries - DMLs.

A molecular dynamics study of the atomic structure of (CaO)x(Al2O3)1-x glass with x = 0.625 close to the eutectic

NASA Astrophysics Data System (ADS)

Thomas, B. W. M.; Mead, R. N.; Mountjoy, G.

2006-05-01

Aluminate glasses are difficult to prepare as they do not contain traditional network formers, but they are promising materials for optical applications. The atomic structure of calcium aluminate glasses has been studied using several experimental techniques. The current study uses molecular dynamics to obtain a model of a (CaO)0.625(Al2O3)0.375 glass close to the eutectic. The glass consists of a tetrahedral alumina network with average network polymerization \\langle Q^{n}\\rangle of n = 3.3. Ca acts as a network modifier with average coordination of 6.2. Ca is typically coordinated to three bridging oxygens (Ob) and three non-bridging oxygens (Onb), with Ca-Onb bonds noticeably shorter than the Ca-Ob bonds. A new method of analysing modifier cation coordination is presented, which specifically shows the distribution of Ca coordination NCaO in terms of combinations of NCaOb and NCaOnb. Ob is most often coordinated to two Al plus two Ca, and Onb is most often coordinated to one Al plus three Ca. The typical coordinations of Ca, Ob, and Onb all have a noticeable similarity to those for the 5CaO·3Al2O3 crystal. The Ca-Ca distribution shows a clear similarity to that for (CaO)0.5(SiO2)0.5 glass, and this is attributed to the equal atomic number densities of Ca in these glasses.

Boundary-fitted coordinate systems for numerical solution of partial differential equations - A review

NASA Technical Reports Server (NTRS)

Thompson, J. F.; Warsi, Z. U. A.; Mastin, C. W.

1982-01-01

A comprehensive review of methods of numerically generating curvilinear coordinate systems with coordinate lines coincident with all boundary segments is given. Some general mathematical framework and error analysis common to such coordinate systems is also included. The general categories of generating systems are those based on conformal mapping, orthogonal systems, nearly orthogonal systems, systems produced as the solution of elliptic and hyperbolic partial differential equations, and systems generated algebraically by interpolation among the boundaries. Also covered are the control of coordinate line spacing by functions embedded in the partial differential operators of the generating system and by subsequent stretching transformation. Dynamically adaptive coordinate systems, coupled with the physical solution, and time-dependent systems that follow moving boundaries are treated. References reporting experience using such coordinate systems are reviewed as well as those covering the system development.

Adaptive Variability in Skilled Human Movements

NASA Astrophysics Data System (ADS)

Kudo, Kazutoshi; Ohtsuki, Tatsuyuki

Human movements are produced in variable external/internal environments. Because of this variability, the same motor command can result in quite different movement patterns. Therefore, to produce skilled movements humans must coordinate the variability, not try to exclude it. In addition, because human movements are produced in redundant and complex systems, a combination of variability should be observed in different anatomical/physiological levels. In this paper, we introduce our research about human movement variability that shows remarkable coordination among components, and between organism and environment. We also introduce nonlinear dynamical models that can describe a variety of movements as a self-organization of a dynamical system, because the dynamical systems approach is a major candidate to understand the principle underlying organization of varying systems with huge degrees-of-freedom.

Dynamic HypA zinc site is essential for acid viability and proper urease maturation in Helicobacter pylori.

PubMed

Johnson, Ryan C; Hu, Heidi Q; Merrell, D Scott; Maroney, Michael J

2015-04-01

Helicobacter pylori requires urease activity in order to survive in the acid environment of the human stomach. Urease is regulated in part by nickelation, a process that requires the HypA protein, which is a putative nickel metallochaperone that is generally associated with hydrogenase maturation. However, in H. pylori, HypA plays a dual role. In addition to an N-terminal nickel binding site, HypA proteins also contain a structural zinc site that is coordinated by two rigorously conserved CXXC sequences, which in H. pylori are flanked by His residues. These structural Zn sites are known to be dynamic, converting from Zn(Cys)4 centers at pH 7.2 to Zn(Cys)2(His)2 centers at pH 6.3 in the presence of Ni(ii) ions. In this study, mutant strains of H. pylori that express zinc site variants of the HypA protein are used to show that the structural changes in the zinc site are important for the acid viability of the bacterium, and that a reduction in acid viability in these variants can be traced in large measure to deficient urease activity. This in turn leads to a model that connects the Zn(Cys)4 coordination to urease maturation.

Description of dynamic shared knowledge: an exploratory study during a competitive team sports interaction.

PubMed

Bourbousson, J; Poizat, G; Saury, J; Seve, C

2011-02-01

This exploratory case study describes the sharedness of knowledge within a basketball team (nine players) and how it changes during an official match. To determine how knowledge is mobilised in an actual game situation, the data were collected and processed following course-of-action theory (Theureau 2003). The results were used to characterise the contents of the shared knowledge (i.e. regarding teammate characteristics, team functioning, opponent characteristics, opposing team functioning and game conditions) and to identify the characteristic types of change: (a) the reinforcement of a previous element of shared knowledge; (b) the invalidation of an element of shared knowledge; (c) fragmentation of an element of shared knowledge; (d) the creation of a new element of shared knowledge. The discussion deals with the diverse types of change in shared knowledge and the heterogeneous and dynamic nature of common ground within the team. STATEMENT OF RELEVANCE: The present case study focused on how the cognitions of individual members of a team coordinate to produce a team performance (e.g. surgical teams in hospitals, military teams) and how the shared knowledge changes during team activity. Traditional methods to increase knowledge sharedness can be enhanced by making use of 'opportunities for coordination' to optimise team adaptiveness.

A biologically inspired approach to modeling unmanned vehicle teams

NASA Astrophysics Data System (ADS)

Cortesi, Roger S.; Galloway, Kevin S.; Justh, Eric W.

2008-04-01

Cooperative motion control of teams of agile unmanned vehicles presents modeling challenges at several levels. The "microscopic equations" describing individual vehicle dynamics and their interaction with the environment may be known fairly precisely, but are generally too complicated to yield qualitative insights at the level of multi-vehicle trajectory coordination. Interacting particle models are suitable for coordinating trajectories, but require care to ensure that individual vehicles are not driven in a "costly" manner. From the point of view of the cooperative motion controller, the individual vehicle autopilots serve to "shape" the microscopic equations, and we have been exploring the interplay between autopilots and cooperative motion controllers using a multivehicle hardware-in-the-loop simulator. Specifically, we seek refinements to interacting particle models in order to better describe observed behavior, without sacrificing qualitative understanding. A recent analogous example from biology involves introducing a fixed delay into a curvature-control-based feedback law for prey capture by an echolocating bat. This delay captures both neural processing time and the flight-dynamic response of the bat as it uses sensor-driven feedback. We propose a comparable approach for unmanned vehicle modeling; however, in contrast to the bat, with unmanned vehicles we have an additional freedom to modify the autopilot. Simulation results demonstrate the effectiveness of this biologically guided modeling approach.

An insight to conserved water molecular dynamics of catalytic and structural Zn(+2) ions in matrix metalloproteinase 13 of human.

PubMed

Chakrabarti, Bornali; Bairagya, Hridoy R; Mallik, Payel; Mukhopadhyay, Bishnu P; Bera, Asim K

2011-02-01

Matrix Metalloproteinase (MMP)--13 or Collagenase--3 plays a significant role in the formation and remodeling of bone, tumor invasion and causes osteoarthritis. Water molecular dynamic studies of the five (1XUC, 1XUD, 1XUR, 456C, 830C) PDB and solvated structures of MMP-13 in human have been carried out upto 5 ns on assigning the differential charges (+2, +1, +0.5 e) to both the Zinc ions. The MM and MD-studies have revealed the coordination of three water molecules (W(H), W(I) and W(S)) to Zn(c) and one water to Zn(s). The transition of geometry around the Znc from tetrahedral to octahedral via trigonal bipyramidal, and for Zn(s) from tetrahedral to trigonal bipyramidal are seem interesting. Recognition of two zinc ions through water molecular bridging (Zn(c) - W(H) (W(1))...W(2)....W(3)....H(187) Zn(s)) and the stabilization of variable coordination geometries around metal ions may indicate the possible involvement of Zn(c) ...Zn(s) coupled mechanism in the catalytic process. So the hydrophilic topology and stereochemistry of water mediated coupling between Zn-ions may provide some plausible hope towards the design of some bidentate/polydentate bridging ligands or inhibitors for MMP-13.

A design of optical modulation system with pixel-level modulation accuracy

NASA Astrophysics Data System (ADS)

Zheng, Shiwei; Qu, Xinghua; Feng, Wei; Liang, Baoqiu

2018-01-01

Vision measurement has been widely used in the field of dimensional measurement and surface metrology. However, traditional methods of vision measurement have many limits such as low dynamic range and poor reconfigurability. The optical modulation system before image formation has the advantage of high dynamic range, high accuracy and more flexibility, and the modulation accuracy is the key parameter which determines the accuracy and effectiveness of optical modulation system. In this paper, an optical modulation system with pixel level accuracy is designed and built based on multi-points reflective imaging theory and digital micromirror device (DMD). The system consisted of digital micromirror device, CCD camera and lens. Firstly we achieved accurate pixel-to-pixel correspondence between the DMD mirrors and the CCD pixels by moire fringe and an image processing of sampling and interpolation. Then we built three coordinate systems and calculated the mathematic relationship between the coordinate of digital micro-mirror and CCD pixels using a checkerboard pattern. A verification experiment proves that the correspondence error is less than 0.5 pixel. The results show that the modulation accuracy of system meets the requirements of modulation. Furthermore, the high reflecting edge of a metal circular piece can be detected using the system, which proves the effectiveness of the optical modulation system.

Intrinsic, Functional, and Structural Properties of β-Thymosins and β-Thymosin/WH2 Domains in the Regulation and Coordination of Actin Self-Assembly Dynamics and Cytoskeleton Remodeling.

PubMed

Renault, L

2016-01-01

β-Thymosins are a family of heat-stable multifunctional polypeptides that are expressed as small proteins of about 5kDa (~45 amino acids) almost exclusively in multicellular animals. They were first isolated from the thymus. As full-length or truncated polypeptides, they appear to stimulate a broad range of extracellular activities in various signaling pathways, including tissue repair and regeneration, inflammation, cell migration, and immune defense. However, their cell surface receptors and structural mechanisms of regulations in these multiple pathways remain still poorly understood. Besides their extracellular activities, they belong to a larger family of small, intrinsically disordered actin-binding domains called WH2/β-thymosin domains that have been identified in more than 1800 multidomain proteins found in different taxonomic domains of life and involved in various actin-based motile processes including cell morphogenesis, motility, adhesions, tissue development, intracellular trafficking, or pathogen infections. This review briefly surveys the main recent findings to understand how these small, intrinsically disordered but functional domains can interact with many unrelated partners and can thus integrate and coordinate various intracellular activities in actin self-assembly dynamics and cell signaling pathways linked to their cytoskeleton remodeling. © 2016 Elsevier Inc. All rights reserved.

Effect on physical fitness of a 10-year physical activity intervention in primary health care settings.

PubMed

Nakamura, Priscila M; Papini, Camila B; Teixeira, Inaian P; Chiyoda, Alberto; Luciano, Eliete; Cordeira, Kelly Lynn; Kokubun, Eduardo

2015-01-01

Interventions in primary health care settings have been effective in increasing physical fitness. In 2001, the Programa de Exercício Físico em Unidades de Saúde (Physical Exercise in Health Primary Care Program-PEHPCP) was launched in Rio Claro City, Brazil. The intervention consisted of biweekly, 60-minute group sessions in all primary health care settings in the city. This study evaluated the effect of PEHPCP on physical fitness and on the aging process after a decade of ongoing implementation. There were 409 women (50 ± 26 y old) and 31 men (64 ± 10 y old) who were eligible for this study. Every 4 months, participants completed the American Alliance for Health, Physical Education, Recreation and Dance standardized tests. Program participation was associated with a reduced effect, compared with baseline, of the natural decline of physical fitness caused by aging, as represented by changes in the following measures: coordination test time, -0.44 seconds; agility and dynamic balance test time; -1.81 seconds; aerobic capacity test time, 3.57 seconds; and muscle strength exercises, +0.60 repetitions. No significant effect on flexibility was found. The PEHPCP showed potential in improving muscle strength, coordination, aerobic capacity, and agility and dynamic balance in participants and in maintaining flexibility in participants.

Modelling human behaviour in a bumper car ride using molecular dynamics tools: a student project

NASA Astrophysics Data System (ADS)

Buendía, Jorge J.; Lopez, Hector; Sanchis, Guillem; Pardo, Luis Carlos

2017-05-01

Amusement parks are excellent laboratories of physics, not only to check physical laws, but also to investigate if those physical laws might also be applied to human behaviour. A group of Physics Engineering students from Universitat Politècnica de Catalunya has investigated if human behaviour, when driving bumper cars, can be modelled using tools borrowed from the analysis of molecular dynamics simulations, such as the radial and angular distribution functions. After acquiring several clips and obtaining the coordinates of the cars, those magnitudes are computed and analysed. Additionally, an analogous hard disks system is simulated to compare its distribution functions to those obtained from the cars’ coordinates. Despite the clear difference between bumper cars and a hard disk-like particle system, the obtained distribution functions are very similar. This suggests that there is no important effect of the individuals in the collective behaviour of the system in terms of structure. The research, performed by the students, has been undertaken in the frame of a motivational project designed to approach the scientific method for university students named FISIDABO. This project offers both the logistical and technical support to undertake the experiments designed by students at the amusement park of Barcelona TIBIDABO and accompanies them all along the scientific process.

MROrchestrator: A Fine-Grained Resource Orchestration Framework for MapReduce Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharma, Bikash; Prabhakar, Ramya; Kandemir, Mahmut

2012-01-01

Efficient resource management in data centers and clouds running large distributed data processing frameworks like MapReduce is crucial for enhancing the performance of hosted applications and boosting resource utilization. However, existing resource scheduling schemes in Hadoop MapReduce allocate resources at the granularity of fixed-size, static portions of nodes, called slots. In this work, we show that MapReduce jobs have widely varying demands for multiple resources, making the static and fixed-size slot-level resource allocation a poor choice both from the performance and resource utilization standpoints. Furthermore, lack of co-ordination in the management of mul- tiple resources across nodes prevents dynamic slotmore » reconfigura- tion, and leads to resource contention. Motivated by this, we propose MROrchestrator, a MapReduce resource Orchestrator framework, which can dynamically identify resource bottlenecks, and resolve them through fine-grained, co-ordinated, and on- demand resource allocations. We have implemented MROrches- trator on two 24-node native and virtualized Hadoop clusters. Experimental results with a suite of representative MapReduce benchmarks demonstrate up to 38% reduction in job completion times, and up to 25% increase in resource utilization. We further show how popular resource managers like NGM and Mesos when augmented with MROrchestrator can hike up their performance.« less

Metal Cations in G-Quadruplex Folding and Stability

NASA Astrophysics Data System (ADS)

Bhattacharyya, Debmalya; Mirihana Arachchilage, Gayan; Basu, Soumitra

2016-09-01

This review is focused on the structural and physico-chemical aspects of metal cation coordination to G-Quadruplexes (GQ) and their effects on GQ stability and conformation. G-Quadruplex structures are non-canonical secondary structures formed by both DNA and RNA. G-quadruplexes regulate a wide range of important biochemical processes. Besides the sequence requirements, the coordination of monovalent cations in the GQ is essential for its formation and determines the stability and polymorphism of GQ structures. The nature, location and dynamics of the cation coordination and their impact on the overall GQ stability are dependent on several factors such as the ionic radii, hydration energy and the bonding strength to the O6 of guanines. The intracellular monovalent cation concentration and the localized ion concentrations determine the formation of GQs and can potentially dictate their regulatory roles. A wide range of biochemical and biophysical studies on an array of GQ enabling sequences have generated at a minimum the knowledge base that allows us to often predict the stability of GQs in presence of the physiologically relevant metal ions, however, prediction of conformation of such GQs is still out of the realm.

Photophysics of self-assembled zinc porphyrin-bidentate diamine ligand complexes.

PubMed

Danger, Brook R; Bedient, Krysta; Maiti, Manisankar; Burgess, Ian J; Steer, Ronald P

2010-10-21

The effects of complexation--by bidentate nitrogen-containing ligands such as pyrazine and 4,4'-bipyridine commonly used for porphyrin self-assembly--on the photophysics of the model metalloporphyrin, ZnTPP, are reported. Ligation to form the 5-coordinate species introduces an intramolecular charge transfer (ITC) state that, depending on the oxidation and reduction potentials of the electron donor and acceptor, can become involved in the excited state relaxation processes. For ZnTPP, ligation with pyridine has little effect on excited state relaxation following either Q-band or Soret band excitation. However, coordination of ZnTPP with pyrazine and bipyridine causes the S(2) (Soret) state of the ligated species to decay almost exclusively via an S(2)-ICT-S(1) pathway, while affecting the S(1) decay route only slightly. In these 5-coordinate species the S(2)-ICT-S(1) decay route is ultrafast and nearly quantitative. Literature redox data for other bidentate ligands such as DABCO and multidentate ligands commonly used for pophyrin assembly suggest that the ITC states introduced by them could also modify the excited state relaxation dynamics of a wide variety of multiporphyrin arrays.

Coordinated Mapping of Sea Ice Deformation Features with Autonomous Vehicles

NASA Astrophysics Data System (ADS)

Maksym, T.; Williams, G. D.; Singh, H.; Weissling, B.; Anderson, J.; Maki, T.; Ackley, S. F.

2016-12-01

Decreases in summer sea ice extent in the Beaufort and Chukchi Seas has lead to a transition from a largely perennial ice cover, to a seasonal ice cover. This drives shifts in sea ice production, dynamics, ice types, and thickness distribution. To examine how the processes driving ice advance might also impact the morphology of the ice cover, a coordinated ice mapping effort was undertaken during a field campaign in the Beaufort Sea in October, 2015. Here, we present observations of sea ice draft topography from six missions of an Autonomous Underwater Vehicle run under different ice types and deformation features observed during autumn freeze-up. Ice surface features were also mapped during coordinated drone photogrammetric missions over each site. We present preliminary results of a comparison between sea ice surface topography and ice underside morphology for a range of sample ice types, including hummocked multiyear ice, rubble fields, young ice ridges and rafts, and consolidated pancake ice. These data are compared to prior observations of ice morphological features from deformed Antarctic sea ice. Such data will be useful for improving parameterizations of sea ice redistribution during deformation, and for better constraining estimates of airborne or satellite sea ice thickness.

Genomic Pangea: coordinate gene regulation and cell-specific chromosomal topologies.

PubMed

Laster, Kyle; Kosak, Steven T

2010-06-01

The eukaryotic nucleus is functionally organized. Gene loci, for example, often reveal altered localization patterns according to their developmental regulation. Whole chromosomes also demonstrate non-random nuclear positions, correlated with inherent characteristics such as gene density or size. Given that hundreds to thousands of genes are coordinately regulated in any given cell type, interest has grown in whether chromosomes may be specifically localized according to gene regulation. A synthesis of the evidence for preferential chromosomal organization suggests that, beyond basic characteristics, chromosomes can assume positions functionally related to gene expression. Moreover, analysis of total chromosome organization during cellular differentiation indicates that unique chromosome topologies, albeit probabilistic, in effect define a cell lineage. Future work with new techniques, including the advanced forms of the chromosome conformation capture (3C), and the development of next-generation whole-genome imaging approaches, will help to refine our view of chromosomal organization. We suggest that genomic organization during cellular differentiation should be viewed as a dynamic process, with gene expression patterns leading to chromosome associations that feed back on themselves, leading to the self-organization of the genome according to coordinate gene regulation. Copyright 2010 Elsevier Ltd. All rights reserved.

Further insights into the metal ion binding abilities and the metalation pathway of a plant metallothionein from Musa acuminata

PubMed Central

Cabral, Augusto C. S.; Jakovleska, Jovana; Deb, Aniruddha; Penner-Hahn, James E.; Pecoraro, Vincent L.

2017-01-01

The superfamily of metallothioneins (MTs) combines a diverse group of metalloproteins, sharing the characteristics of rather low molecular weight and high cysteine content. The latter provides MTs with the capability to coordinate thiophilic metal ions, in particular those with a d10 electron configuration. The sub-family of plant MT3 proteins is only poorly characterized and there is a complete lack of three-dimensional structure information. Building upon our previous results on the Musa acuminata MT3 (musMT3) protein, the focus of the present work is to understand the metal cluster formation process, the role of the single histidine residue present in musMT3, and the metal ion binding affinity. We concentrate our efforts on the coordination of ZnII and CdII ions, using CoII as a spectroscopic probe for ZnII binding. The overall protein-fold is analysed with a combination of limited proteolytic digestion, mass spectrometry, and dynamic light scattering. Histidine coordination of metal ions is probed with extended X-ray absorption fine structure spectroscopy and CoII titration experiments. Initial experiments with isothermal titration calorimetry provide insights into the thermodynamics of metal ion binding. PMID:29218632

Analyzing Group Coordination when Solving Geometry Problems with Dynamic Geometry Software

ERIC Educational Resources Information Center

Oner, Diler

2013-01-01

In CSCL research, collaborative activity is conceptualized along various yet intertwined dimensions. When functioning within these multiple dimensions, participants make use of several resources, which can be social or content-related (and sometimes temporal) in nature. It is the effective coordination of these resources that appears to…

(De)stabilization of Required and Spontaneous Postural Dynamics with Learning

ERIC Educational Resources Information Center

Faugloire, Elise; Bardy, Benoit G.; Stoffregen, Thomas A.

2009-01-01

The present research examined how learning a new ankle-hip coordination influenced the preexisting postural repertoire. Standing participants learned a new ankle-hip coordination mode (relative phase of 90[degrees]). Before and after practice, postural patterns were evaluated in two different tasks. In the required task, specific ankle-hip…