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

DEFF Research Database (Denmark)

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

2016-01-01

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

Variable Lysozyme Transport Dynamics on Oxidatively Functionalized Polystyrene Films.

Science.gov (United States)

Moringo, Nicholas A; Shen, Hao; Tauzin, Lawrence J; Wang, Wenxiao; Bishop, Logan D C; Landes, Christy F

2017-10-17

Tuning protein adsorption dynamics at polymeric interfaces is of great interest to many biomedical and material applications. Functionalization of polymer surfaces is a common method to introduce application-specific surface chemistries to a polymer interface. In this work, single-molecule fluorescence microscopy is utilized to determine the adsorption dynamics of lysozyme, a well-studied antibacterial protein, at the interface of polystyrene oxidized via UV exposure and oxygen plasma and functionalized by ligand grafting to produce varying degrees of surface hydrophilicity, surface roughness, and induced oxygen content. Single-molecule tracking indicates lysozyme loading capacities, and surface mobility at the polymer interface is hindered as a result of all functionalization techniques. Adsorption dynamics of lysozyme depend on the extent and the specificity of the oxygen functionalities introduced to the polystyrene surface. Hindered adsorption and mobility are dominated by hydrophobic effects attributed to water hydration layer formation at the functionalized polystyrene surfaces.

Functional System Dynamics

NARCIS (Netherlands)

Ligterink, N.E.

2007-01-01

Functional system dynamics is the analysis, modelling, and simulation of continuous systems usually described by partial differential equations. From the infinite degrees of freedom of such systems only a finite number of relevant variables have to be chosen for a practical model description. The

Dynamic radial distribution function from inelastic neutron scattering

International Nuclear Information System (INIS)

McQueeney, R.J.

1998-01-01

A real-space, local dynamic structure function g(r,ω) is defined from the dynamic structure function S(Q,ω), which can be measured using inelastic neutron scattering. At any particular frequency ω, S(Q,ω) contains Q-dependent intensity oscillations which reflect the spatial distribution and relative displacement directions for the atoms vibrating at that frequency. Information about local and dynamic atomic correlations is obtained from the Fourier transform of these oscillations g(r,ω) at the particular frequency. g(r,ω) can be formulated such that the elastic and frequency-summed limits correspond to the average and instantaneous radial distribution function, respectively, and is thus called the dynamic radial distribution function. As an example, the dynamic radial distribution function is calculated for fcc nickel in a model which considers only the harmonic atomic displacements due to phonons. The results of these calculations demonstrate that the magnitude of the atomic correlations can be quantified and g(r,ω) is a well-defined correlation function. This leads to a simple prescription for investigating local lattice dynamics. copyright 1998 The American Physical Society

Dynamic Stiffness Transfer Function of an Electromechanical Actuator Using System Identification

Science.gov (United States)

Kim, Sang Hwa; Tahk, Min-Jea

2018-04-01

In the aeroelastic analysis of flight vehicles with electromechanical actuators (EMAs), an accurate prediction of flutter requires dynamic stiffness characteristics of the EMA. The dynamic stiffness transfer function of the EMA with brushless direct current (BLDC) motor can be obtained by conducting complicated mathematical calculations of control algorithms and mechanical/electrical nonlinearities using linearization techniques. Thus, system identification approaches using experimental data, as an alternative, have considerable advantages. However, the test setup for system identification is expensive and complex, and experimental procedures for data collection are time-consuming tasks. To obtain the dynamic stiffness transfer function, this paper proposes a linear system identification method that uses information obtained from a reliable dynamic stiffness model with a control algorithm and nonlinearities. The results of this study show that the system identification procedure is compact, and the transfer function is able to describe the dynamic stiffness characteristics of the EMA. In addition, to verify the validity of the system identification method, the simulation results of the dynamic stiffness transfer function and the dynamic stiffness model were compared with the experimental data for various external loads.

Extracting neuronal functional network dynamics via adaptive Granger causality analysis.

Science.gov (United States)

Sheikhattar, Alireza; Miran, Sina; Liu, Ji; Fritz, Jonathan B; Shamma, Shihab A; Kanold, Patrick O; Babadi, Behtash

2018-04-24

Quantifying the functional relations between the nodes in a network based on local observations is a key challenge in studying complex systems. Most existing time series analysis techniques for this purpose provide static estimates of the network properties, pertain to stationary Gaussian data, or do not take into account the ubiquitous sparsity in the underlying functional networks. When applied to spike recordings from neuronal ensembles undergoing rapid task-dependent dynamics, they thus hinder a precise statistical characterization of the dynamic neuronal functional networks underlying adaptive behavior. We develop a dynamic estimation and inference paradigm for extracting functional neuronal network dynamics in the sense of Granger, by integrating techniques from adaptive filtering, compressed sensing, point process theory, and high-dimensional statistics. We demonstrate the utility of our proposed paradigm through theoretical analysis, algorithm development, and application to synthetic and real data. Application of our techniques to two-photon Ca 2+ imaging experiments from the mouse auditory cortex reveals unique features of the functional neuronal network structures underlying spontaneous activity at unprecedented spatiotemporal resolution. Our analysis of simultaneous recordings from the ferret auditory and prefrontal cortical areas suggests evidence for the role of rapid top-down and bottom-up functional dynamics across these areas involved in robust attentive behavior.

Dynamic Analysis of Money Demand Function: Case of Turkey*

OpenAIRE

doğru, bülent

2013-01-01

In this paper, the dynamic determinants of money demand function and the long-run and short-run relationships between money demand, income and nominal interest rates are examined in Turkey for the time period 1980-2012. In particular we estimate a dynamic specification of a log money demand function based on Keynesian liquidity preference theory to ascertain the relevant elasticity of money demand. The empirical results of the study show that in Turkey inflation, exchange rate and money deman...

Clinical applications of dynamic functional musculoskeletal ultrasound

Directory of Open Access Journals (Sweden)

Petscavage-Thomas J

2014-02-01

Full Text Available Jonelle Petscavage-Thomas Department of Radiology, Penn State Hershey Medical Center, Hershey, PA, USA Abstract: There is an increasing trend in medicine to utilize ultrasound for diagnosis of musculoskeletal pathology. Although magnetic resonance imaging provides excellent spatial resolution of musculoskeletal structures in multiple imaging planes and is generally the cross-sectional modality of choice, it does not provide dynamic functional assessment of muscles, tendons, and ligaments. Dynamic maneuvers with ultrasound provide functional data and have been shown to be accurate for diagnosis. Ultrasound is also less expensive, portable, and more readily available. This article will review the common snapping, impingement, and friction syndromes imaged with dynamic ultrasound. It will also discuss future areas of research, including musculoskeletal sonoelastography. Keywords: snapping, dynamic, ultrasound, functional, musculoskeletal

A Comparative Study on Optimal Structural Dynamics Using Wavelet Functions

Directory of Open Access Journals (Sweden)

Seyed Hossein Mahdavi

2015-01-01

Full Text Available Wavelet solution techniques have become the focus of interest among researchers in different disciplines of science and technology. In this paper, implementation of two different wavelet basis functions has been comparatively considered for dynamic analysis of structures. For this aim, computational technique is developed by using free scale of simple Haar wavelet, initially. Later, complex and continuous Chebyshev wavelet basis functions are presented to improve the time history analysis of structures. Free-scaled Chebyshev coefficient matrix and operation of integration are derived to directly approximate displacements of the corresponding system. In addition, stability of responses has been investigated for the proposed algorithm of discrete Haar wavelet compared against continuous Chebyshev wavelet. To demonstrate the validity of the wavelet-based algorithms, aforesaid schemes have been extended to the linear and nonlinear structural dynamics. The effectiveness of free-scaled Chebyshev wavelet has been compared with simple Haar wavelet and two common integration methods. It is deduced that either indirect method proposed for discrete Haar wavelet or direct approach for continuous Chebyshev wavelet is unconditionally stable. Finally, it is concluded that numerical solution is highly benefited by the least computation time involved and high accuracy of response, particularly using low scale of complex Chebyshev wavelet.

Functional System Dynamics

OpenAIRE

Ligterink, N.E.

2007-01-01

Functional system dynamics is the analysis, modelling, and simulation of continuous systems usually described by partial differential equations. From the infinite degrees of freedom of such systems only a finite number of relevant variables have to be chosen for a practical model description. The proper input and output of the system are an important part of the relevant variables.

Functional integral approach to classical statistical dynamics

International Nuclear Information System (INIS)

Jensen, R.V.

1980-04-01

A functional integral method is developed for the statistical solution of nonlinear stochastic differential equations which arise in classical dynamics. The functional integral approach provides a very natural and elegant derivation of the statistical dynamical equations that have been derived using the operator formalism of Martin, Siggia, and Rose

Crossing the entropy barrier of dynamical zeta functions

International Nuclear Information System (INIS)

Aurich, R.; Bolte, J.; Matthies, C.; Sieber, M.; Steiner, F.

1992-01-01

Dynamical zeta functions are an important tool to quantize chaotic dynamical systems. The basic quantization rules require the computation of the zeta functions on the real energy axis, where the Euler product representations running over the classical periodic orbits usually do not converge due to the existence of the so-called entropy barrier determined by the topological entropy of the classical system. We shown that the convergence properties of the dynamical zeta functions rewritten as Dirichlet series are governed not only by the well-known topological and metric entropy, but depend crucially on subtle statistical properties of the Maslow indices and of the multiplicities of the periodic orbits that are measured by a new parameter for which we introduce the notion of a third entropy. If and only if the third entropy is nonvanishing, one can cross the entropy barrier; if it exceeds a certain value, one can even compute the zeta function in the physical region by means of a convergent Dirichlet series. A simple statistical model is presented which allows to compute the third entropy. Four examples of chaotic systems are studied in detail to test the model numerically. (orig.)

Crossing the entropy barrier of dynamical zeta functions

Energy Technology Data Exchange (ETDEWEB)

Aurich, R.; Bolte, J.; Matthies, C.; Sieber, M.; Steiner, F. (Hamburg Univ. (Germany). 2. Inst. fuer Theoretische Physik)

1992-01-01

Dynamical zeta functions are an important tool to quantize chaotic dynamical systems. The basic quantization rules require the computation of the zeta functions on the real energy axis, where the Euler product representations running over the classical periodic orbits usually do not converge due to the existence of the so-called entropy barrier determined by the topological entropy of the classical system. We shown that the convergence properties of the dynamical zeta functions rewritten as Dirichlet series are governed not only by the well-known topological and metric entropy, but depend crucially on subtle statistical properties of the Maslow indices and of the multiplicities of the periodic orbits that are measured by a new parameter for which we introduce the notion of a third entropy. If and only if the third entropy is nonvanishing, one can cross the entropy barrier; if it exceeds a certain value, one can even compute the zeta function in the physical region by means of a convergent Dirichlet series. A simple statistical model is presented which allows to compute the third entropy. Four examples of chaotic systems are studied in detail to test the model numerically. (orig.).

Function and dynamics of aptamers: A case study on the malachite green aptamer

Energy Technology Data Exchange (ETDEWEB)

Wang, Tianjiao [Iowa State Univ., Ames, IA (United States)

2008-01-01

Aptamers are short single-stranded nucleic acids that can bind to their targets with high specificity and high affinity. To study aptamer function and dynamics, the malachite green aptamer was chosen as a model. Malachite green (MG) bleaching, in which an OH- attacks the central carbon (C1) of MG, was inhibited in the presence of the malachite green aptamer (MGA). The inhibition of MG bleaching by MGA could be reversed by an antisense oligonucleotide (AS) complementary to the MGA binding pocket. Computational cavity analysis of the NMR structure of the MGA-MG complex predicted that the OH^- is sterically excluded from the C1 of MG. The prediction was confirmed experimentally using variants of the MGA with changes in the MG binding pocket. This work shows that molecular reactivity can be reversibly regulated by an aptamer-AS pair based on steric hindrance. In addition to demonstrate that aptamers could control molecular reactivity, aptamer dynamics was studied with a strategy combining molecular dynamics (MD) simulation and experimental verification. MD simulation predicted that the MG binding pocket of the MGA is largely pre-organized and that binding of MG involves reorganization of the pocket and a simultaneous twisting of the MGA terminal stems around the pocket. MD simulation also provided a 3D-structure model of unoccupied MGA that has not yet been obtained by biophysical measurements. These predictions were consistent with biochemical and biophysical measurements of the MGA-MG interaction including RNase I footprinting, melting curves, thermodynamic and kinetic constants measurement. This work shows that MD simulation can be used to extend our understanding of the dynamics of aptamer-target interaction which is not evident from static 3D-structures. To conclude, I have developed a novel concept to control molecular reactivity by an aptamer based on steric protection and a strategy to study the dynamics of aptamer-target interaction by combining MD

Fractal diffusion coefficient from dynamical zeta functions

Energy Technology Data Exchange (ETDEWEB)

Cristadoro, Giampaolo [Max Planck Institute for the Physics of Complex Systems, Noethnitzer Str. 38, D 01187 Dresden (Germany)

2006-03-10

Dynamical zeta functions provide a powerful method to analyse low-dimensional dynamical systems when the underlying symbolic dynamics is under control. On the other hand, even simple one-dimensional maps can show an intricate structure of the grammar rules that may lead to a non-smooth dependence of global observables on parameters changes. A paradigmatic example is the fractal diffusion coefficient arising in a simple piecewise linear one-dimensional map of the real line. Using the Baladi-Ruelle generalization of the Milnor-Thurnston kneading determinant, we provide the exact dynamical zeta function for such a map and compute the diffusion coefficient from its smallest zero. (letter to the editor)

Fractal diffusion coefficient from dynamical zeta functions

International Nuclear Information System (INIS)

Cristadoro, Giampaolo

2006-01-01

Dynamical zeta functions provide a powerful method to analyse low-dimensional dynamical systems when the underlying symbolic dynamics is under control. On the other hand, even simple one-dimensional maps can show an intricate structure of the grammar rules that may lead to a non-smooth dependence of global observables on parameters changes. A paradigmatic example is the fractal diffusion coefficient arising in a simple piecewise linear one-dimensional map of the real line. Using the Baladi-Ruelle generalization of the Milnor-Thurnston kneading determinant, we provide the exact dynamical zeta function for such a map and compute the diffusion coefficient from its smallest zero. (letter to the editor)

The dynamic adjoint as a Green’s function

International Nuclear Information System (INIS)

Pázsit, I.; Dykin, V.

2015-01-01

Highlight: • The relationship between the direct Green’s function and the dynamic adjoint function is discussed in two-group theory. • It is shown that the elements of the direct Greens’ function matrix are identical to those of the transpose of the adjoint Green’s function matrix, with an interchange of arguments. • It is also remarked how the dynamic adjoint function of van Dam can be given in terms of the direct Green’s function matrix. - Abstract: The concept of the dynamic adjoint was introduced by Hugo van Dam for calculating the in-core neutron noise in boiling water reactors in the mid-70’s. This successful approach found numerous applications for calculating the neutron noise in both PWRs and BWRs since then. Although the advantages and disadvantages of using the direct (forward) or the adjoint (backward) approach for the calculation of the neutron noise were analysed in a number of publications, the direct relationship between the forward Green’s function and the dynamic adjoint has not been discussed. On the other hand, in particle transport theory the relationship between the direct and adjoint Green’s function has been discussed in detail, in which Mike Williams has had many seminal contributions. In this note we analyse the relationship between the direct Green’s function and the dynamic adjoint in the spirit of Mike’s work in neutron transport and radiation damage theory. The paper is closed with some personal remarks and reminiscences.

Robust transient dynamics and brain functions

Directory of Open Access Journals (Sweden)

Mikhail I Rabinovich

2011-06-01

Full Text Available In the last few decades several concepts of Dynamical Systems Theory (DST have guided psychologists, cognitive scientists, and neuroscientists to rethink about sensory motor behavior and embodied cognition. A critical step in the progress of DST application to the brain (supported by modern methods of brain imaging and multi-electrode recording techniques has been the transfer of its initial success in motor behavior to mental function, i.e., perception, emotion, and cognition. Open questions from research in genetics, ecology, brain sciences, etc. have changed DST itself and lead to the discovery of a new dynamical phenomenon, i.e., reproducible and robust transients that are at the same time sensitive to informational signals. The goal of this review is to describe a new mathematical framework -heteroclinic sequential dynamics- to understand self-organized activity in the brain that can explain certain aspects of robust itinerant behavior. Specifically, we discuss a hierarchy of coarse-grain models of mental dynamics in the form of kinetic equations of modes. These modes compete for resources at three levels: (i within the same modality, (ii among different modalities from the same family (like perception, and (iii among modalities from different families (like emotion and cognition. The analysis of the conditions for robustness, i.e., the structural stability of transient (sequential dynamics, give us the possibility to explain phenomena like the finite capacity of our sequential working memory -a vital cognitive function-, and to find specific dynamical signatures -different kinds of instabilities- of several brain functions and mental diseases.

Dynamical Functional Theory for Compressed Sensing

DEFF Research Database (Denmark)

Cakmak, Burak; Opper, Manfred; Winther, Ole

2017-01-01

the Thouless-Anderson-Palmer (TAP) equations corresponding to the ensemble. Using a dynamical functional approach we are able to derive an effective stochastic process for the marginal statistics of a single component of the dynamics. This allows us to design memory terms in the algorithm in such a way...

Power functional theory for the dynamic test particle limit

International Nuclear Information System (INIS)

Brader, Joseph M; Schmidt, Matthias

2015-01-01

For classical Brownian systems both in and out of equilibrium we extend the power functional formalism of Schmidt and Brader (2013 J. Chem. Phys. 138 214101) to mixtures of different types of particles. We apply the framework to develop an exact dynamical test particle theory for the self and distinct parts of the van Hove function, which characterize tagged and collective particle motion. The memory functions that induce non-Markovian dynamics are related to functional derivatives of the excess (over ideal) free power dissipation functional. The method offers an alternative to the recently found nonequilibrium Ornstein–Zernike relation for dynamic pair correlation functions. (paper)

A functional-dynamic reflection on participatory processes in modeling projects.

Science.gov (United States)

Seidl, Roman

2015-12-01

The participation of nonscientists in modeling projects/studies is increasingly employed to fulfill different functions. However, it is not well investigated if and how explicitly these functions and the dynamics of a participatory process are reflected by modeling projects in particular. In this review study, I explore participatory modeling projects from a functional-dynamic process perspective. The main differences among projects relate to the functions of participation-most often, more than one per project can be identified, along with the degree of explicit reflection (i.e., awareness and anticipation) on the dynamic process perspective. Moreover, two main approaches are revealed: participatory modeling covering diverse approaches and companion modeling. It becomes apparent that the degree of reflection on the participatory process itself is not always explicit and perfectly visible in the descriptions of the modeling projects. Thus, the use of common protocols or templates is discussed to facilitate project planning, as well as the publication of project results. A generic template may help, not in providing details of a project or model development, but in explicitly reflecting on the participatory process. It can serve to systematize the particular project's approach to stakeholder collaboration, and thus quality management.

Dynamic response function and large-amplitude dissipative collective motion

International Nuclear Information System (INIS)

Wu Xizhen; Zhuo Yizhong; Li Zhuxia; Sakata, Fumihiko.

1993-05-01

Aiming at exploring microscopic dynamics responsible for the dissipative large-amplitude collective motion, the dynamic response and correlation functions are introduced within the general theory of nuclear coupled-master equations. The theory is based on the microscopic theory of nuclear collective dynamics which has been developed within the time-dependent Hartree-Fock (TDHF) theory for disclosing complex structure of the TDHF-manifold. A systematic numerical method for calculating the dynamic response and correlation functions is proposed. By performing numerical calculation for a simple model Hamiltonian, it is pointed out that the dynamic response function gives an important information in understanding the large-amplitude dissipative collective motion which is described by an ensemble of trajectories within the TDHF-manifold. (author)

Temperature dependent dynamics of DegP-trimer: A molecular dynamics study

Directory of Open Access Journals (Sweden)

Nivedita Rai

2015-01-01

Full Text Available DegP is a heat shock protein from high temperature requirement protease A family, which reacts to the environmental stress conditions in an ATP independent way. The objective of the present analysis emerged from the temperature dependent functional diversity of DegP between chaperonic and protease activities at temperatures below and above 28 °C, respectively. DegP is a multimeric protein and the minimal functional unit, DegP-trimer, is of great importance in understanding the DegP pathway. The structural aspects of DegP-trimer with respect to temperature variation have been studied using molecular dynamics simulations (for 100 ns and principal component analysis to highlight the temperature dependent dynamics facilitating its functional diversity. The DegP-trimer revealed a pronounced dynamics at both 280 and 320 K, when compared to the dynamics observed at 300 K. The LA loop is identified as the highly flexible region during dynamics and at extreme temperatures, the residues 46–80 of LA loop express a flip towards right (at 280 and left ( at 320 K with respect to the fixed β-sheet connecting the LA loop of protease for which Phe46 acts as one of the key residues. Such dynamics of LA loop facilitates inter-monomeric interaction with the PDZ1 domain of the neighbouring monomer and explains its active participation when DegP exists as trimer. Hence, the LA loop mediated dynamics of DegP-trimer is expected to provide further insight into the temperature dependent dynamics of DegP towards the understanding of its assembly and functional diversity in the presence of substrate.

Point defect dynamics in sodium aluminum hydrides - a combined quasielastic neutron scattering and density functional theory study

DEFF Research Database (Denmark)

Shi, Qing; Voss, Johannes; Jacobsen, H.S.

2007-01-01

we study hydrogen dynamics in undoped and TiCl3-doped samples of NaAlH4 and Na3AlH6 using a combination of density functional theory calculations and quasielastic neutron scattering. Hydrogen dynamics is found to be limited and mediated by hydrogen vacancies in both alanate phases, requiring......Understanding the catalytic role of titanium-based additives on the reversible hydrogenation of complex metal hydrides is an essential step towards developing hydrogen storage materials for the transport sector. Improved bulk diffusion of hydrogen is one of the proposed catalytic effects, and here...

Spatially heterogeneous dynamics investigated via a time-dependent four-point density correlation function

DEFF Research Database (Denmark)

Lacevic, N.; Starr, F. W.; Schrøder, Thomas

2003-01-01

correlation function g4(r,t) and corresponding "structure factor" S4(q,t) which measure the spatial correlations between the local liquid density at two points in space, each at two different times, and so are sensitive to dynamical heterogeneity. We study g4(r,t) and S4(q,t) via molecular dynamics......Relaxation in supercooled liquids above their glass transition and below the onset temperature of "slow" dynamics involves the correlated motion of neighboring particles. This correlated motion results in the appearance of spatially heterogeneous dynamics or "dynamical heterogeneity." Traditional...... two-point time-dependent density correlation functions, while providing information about the transient "caging" of particles on cooling, are unable to provide sufficiently detailed information about correlated motion and dynamical heterogeneity. Here, we study a four-point, time-dependent density...

A local dynamic correlation function from inelastic neutron scattering

International Nuclear Information System (INIS)

McQueeney, R.J.

1997-01-01

Information about local and dynamic atomic correlations can be obtained from inelastic neutron scattering measurements by Fourier transform of the Q-dependent intensity oscillations at a particular frequency. A local dynamic structure function, S(r,ω), is defined from the dynamic scattering function, S(Q,ω), such that the elastic and frequency-integrated limits correspond to the average and instantaneous pair-distribution functions, respectively. As an example, S(r,ω) is calculated for polycrystalline aluminum in a model where atomic motions are entirely due to harmonic phonons

Predicting individual brain maturity using dynamic functional connectivity

Directory of Open Access Journals (Sweden)

Jian eQin

2015-07-01

Full Text Available Neuroimaging-based functional connectivity (FC analyses have revealed significant developmental trends in specific intrinsic connectivity networks linked to cognitive and behavioral maturation. However, knowledge of how brain functional maturation is associated with FC dynamics at rest is limited. Here, we examined age-related differences in the temporal variability of FC dynamics with data publicly released by the Nathan Kline Institute (NKI (n=183, ages 7-30 and showed that dynamic inter-region interactions can be used to accurately predict individual brain maturity across development. Furthermore, we identified a significant age-dependent trend underlying dynamic inter-network FC, including increasing variability of the connections between the visual network, default mode network (DMN and cerebellum as well as within the cerebellum and DMN and decreasing variability within the cerebellum and between the cerebellum and DMN as well as the cingulo-opercular network. Overall, the results suggested significant developmental changes in dynamic inter-network interaction, which may shed new light on the functional organization of typical developmental brains.

TO STUDY THE EFFECT OF AGILITY AND PERTURBATION EXERCISES VERSUS DYNAMIC RESISTANCE EXERCISES TO IMPROVE KNEE FUNCTION IN KNEE OSTEOARTHRITIS A COMPARATIVE STUDY

Directory of Open Access Journals (Sweden)

Jeutishree Roy

2015-10-01

Full Text Available Background: Primary osteoarthritis is more commonly found in post menopausal women; Secondary osteoarthritis had an underlying cause such as trauma, obesity or inflammatory arthritis. It is characterized by a progressive degeneration of the articular cartilage with subsequent remodeling and hypertrophy of the bone at the joint margins. Muscle weakness is associated with increased functional limitation, disability. Muscle strengthening through resistance exercises increases physical function; decreases pain due to osteoarthritis and reduces self reported disability. Agility is the ability to change direction and maintain stability and is more often important in changing direction and speed; In order to train muscle to react quickly neuromuscular training is essential; Perturbation enhances the ability of the proprioceptor signals to the muscle and prevent injuries and enhances performance. The aim of this study is to compare the effectiveness of agility training and dynamic resistance training in patients with primary osteoarthritis. Methods: 50 subjects were assigned in two groups 25 each group and subjects were selected by convenient sampling method. Group A with agility training and Group B with dynamic resistance training. The treatment session was performed 3 days a week for 3 weeks lasting for 45minutes. Day 0 is the starting day of the session and Day-21 last day of the session. Each subject performed all the measurement with knee function assessed by Timed up and Go test (TUG and Lower extremity function Scale (LEFS. Both outcomes were tested at starting day and at the end of 21st day. Results: All the analysis was carried out in PASW version 21.0. An alpha level of 0.05 was used to determine statistical significance. The between group analysis of agility training and dynamic strengthening for LEFS and TUG in evaluation of knee function was done using independent ‘t’ test showed statistically very significant (P=0.000. Conclusions

Dynamical density functional theory for dense atomic liquids

International Nuclear Information System (INIS)

Archer, A J

2006-01-01

Starting from Newton's equations of motion, we derive a dynamical density functional theory (DDFT) applicable to atomic liquids. The theory has the feature that it requires as input the Helmholtz free energy functional from equilibrium density functional theory. This means that, given a reliable equilibrium free energy functional, the correct equilibrium fluid density profile is guaranteed. We show that when the isothermal compressibility is small, the DDFT generates the correct value for the speed of sound in a dense liquid. We also interpret the theory as a dynamical equation for a coarse grained fluid density and show that the theory can be used (making further approximations) to derive the standard mode coupling theory that is used to describe the glass transition. The present theory should provide a useful starting point for describing the dynamics of inhomogeneous atomic fluids

Differences in dynamic and static functional connectivity between young and elderly healthy adults

Energy Technology Data Exchange (ETDEWEB)

Park, Ji Eun; Jung, Seung Chai; Ryu, Kyeoung Hwa; Oh, Joo Young; Kim, Ho Sung; Choi, Choong-Gon; Kim, Sang Joon; Shim, Woo Hyun [University of Ulsan College of Medicine, Asan Medical Center, Department of Radiology and Research Institute of Radiology, Songpa-Gu, Seoul (Korea, Republic of)

2017-08-15

Brain connectivity is highly dynamic, but functional connectivity (FC) studies using resting-state functional magnetic resonance imaging (rs-fMRI) assume it to be static. This study assessed differences in dynamic FC between young healthy adults (YH) and elderly healthy adults (EH) compared to static FC. Using rs-fMRI data from 12 YH and 31 EH, FC was assessed in six functional regions (subcortical, auditory [AUD], sensorimotor [SM], visuospatial [VS], cognitive control [CC], and default mode network [DMN]). Static FC was calculated as Fisher's z-transformed correlation coefficient. The sliding time window correlation (window size 30 s, step size 3 s) was applied for dynamic FC, and the standard deviation across sliding windows was calculated. Differences in static and dynamic FC between EH and YH were calculated and compared by region. EH showed decreased static FC in the subcortical, CC, and DMN regions (FDR corrected p = 0.0013; 74 regions), with no regions showing static FC higher than that in YH. EH showed increased dynamic FC in the subcortical, CC, and DMN regions, whereas decreased dynamic FC in CC and DMN regions (p < 0.01). However, the regions showing differences between EH and YH did not overlap between static and dynamic FC. Dynamic FC exhibited differences from static FC in EH and YH, mainly in regions involved in cognitive control and the DMN. Altered dynamic FC demonstrated both qualitatively and quantitatively distinct patterns of transient brain activity and needs to be studied as an imaging biomarker in the aging process. (orig.)

An information theory framework for dynamic functional domain connectivity.

Science.gov (United States)

Vergara, Victor M; Miller, Robyn; Calhoun, Vince

2017-06-01

Dynamic functional network connectivity (dFNC) analyzes time evolution of coherent activity in the brain. In this technique dynamic changes are considered for the whole brain. This paper proposes an information theory framework to measure information flowing among subsets of functional networks call functional domains. Our method aims at estimating bits of information contained and shared among domains. The succession of dynamic functional states is estimated at the domain level. Information quantity is based on the probabilities of observing each dynamic state. Mutual information measurement is then obtained from probabilities across domains. Thus, we named this value the cross domain mutual information (CDMI). Strong CDMIs were observed in relation to the subcortical domain. Domains related to sensorial input, motor control and cerebellum form another CDMI cluster. Information flow among other domains was seldom found. Other methods of dynamic connectivity focus on whole brain dFNC matrices. In the current framework, information theory is applied to states estimated from pairs of multi-network functional domains. In this context, we apply information theory to measure information flow across functional domains. Identified CDMI clusters point to known information pathways in the basal ganglia and also among areas of sensorial input, patterns found in static functional connectivity. In contrast, CDMI across brain areas of higher level cognitive processing follow a different pattern that indicates scarce information sharing. These findings show that employing information theory to formally measured information flow through brain domains reveals additional features of functional connectivity. Copyright © 2017 Elsevier B.V. All rights reserved.

The preliminary study of quantitative evaluation of salivary gland function by dynamic imaging

International Nuclear Information System (INIS)

Han Chunqi; Li Yaming; Li Deshun; Wang Guoli; Bai Jingming; Luo Xigui

1999-01-01

Objective: To evaluate the function of salivary gland by quantitative dynamic imaging. Methods: In thirty normals and twenty patients with Sjogren's syndrome (SS), absorption rate (15 min) and excretion rate (30 min) were calculated using two quantitative software. Results: Parotid and submandibular absorption rates in normal subjects were (0.26 +- 0.09)% and (0.15 +- 0.08)%, respectively; those of SS patients were (0.07 +- 0.03)% and (0.05 +- 0.04)%, t = 5.3 and 4.1, both were P < 0.01. There were markedly relativity between the two groups (r = 0.85). Conclusions: Quantitative methods of analyzing salivary function is simple, sensitive, practical reliable for evaluating salivary function and also has important clinical significance

A study of the HEB longitudinal dynamics

International Nuclear Information System (INIS)

Larson, D.J.

1993-12-01

A study of the High Energy Booster (HEB) longitudinal dynamics is presented. Full derivations of ramp dependent longitudinal variables are given. The formulas assume that the input magnetic field and beam longitudinal emittance are known as a function of time, and that either the rf voltage or the rf bucket area are known as a function of time. Once these three inputs are specified, the formulas can be used to calculate values for all other longitudinal dynamics variables. The formulas have been incorporated into a single computer code named ELVIRA: Evaluation of Longitudinal Variables in Relativistic Accelerators. The ELVIRA code is documented here in detail. The ELVIRA code is used under two initial longitudinal emittance assumptions to plot ramp functions for the longitudinal dynamics design of the HEB as of May 5, 1992

Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes: Targeted quantification of functional enzyme dynamics

Energy Technology Data Exchange (ETDEWEB)

Li, Minjing [School of Environmental Studies, China University of Geosciences, Wuhan 430074 People' s Republic of China; Gao, Yuqian [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Qian, Wei-Jun [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Shi, Liang [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Liu, Yuanyuan [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Nelson, William C. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Nicora, Carrie D. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Resch, Charles T. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Thompson, Christopher [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Yan, Sen [School of Environmental Studies, China University of Geosciences, Wuhan 430074 People' s Republic of China; Fredrickson, James K. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Zachara, John M. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Liu, Chongxuan [Pacific Northwest National Laboratory, Richland, WA 99354 USA; School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055 People' s Republic of China

2017-07-13

Microbially mediated biogeochemical processes are catalyzed by enzymes that control the transformation of carbon, nitrogen, and other elements in environment. The dynamic linkage between enzymes and biogeochemical species transformation has, however, rarely been investigated because of the lack of analytical approaches to efficiently and reliably quantify enzymes and their dynamics in soils and sediments. Herein, we developed a signature peptide-based technique for sensitively quantifying dissimilatory and assimilatory enzymes using nitrate-reducing enzymes in a hyporheic zone sediment as an example. Moreover, the measured changes in enzyme concentration were found to correlate with the nitrate reduction rate in a way different from that inferred from biogeochemical models based on biomass or functional genes as surrogates for functional enzymes. This phenomenon has important implications for understanding and modeling the dynamics of microbial community functions and biogeochemical processes in environments. Our results also demonstrate the importance of enzyme quantification for the identification and interrogation of those biogeochemical processes with low metabolite concentrations as a result of faster enzyme-catalyzed consumption of metabolites than their production. The dynamic enzyme behaviors provide a basis for the development of enzyme-based models to describe the relationship between the microbial community and biogeochemical processes.

Optimised cut-off function for Tersoff-like potentials for a BN nanosheet: a molecular dynamics study

International Nuclear Information System (INIS)

Kumar, Rajesh; Rajasekaran, G; Parashar, Avinash

2016-01-01

In this article, molecular dynamics based simulations were carried out to study the tensile behaviour of boron nitride nanosheets (BNNSs). Four different sets of Tersoff potential parameters were used in the simulations for estimating the interatomic interactions between boron and nitrogen atoms. Modifications were incorporated in the Tersoff cut-off function to improve the accuracy of results with respect to fracture stress, fracture strain and Young’s modulus. In this study, the original cut-off function was optimised in such a way that small and large cut-off distances were made equal, and hence a single cut-off distance was used with all sets of Tersoff potential parameters. The single value of cut-off distance for the Tersoff potential was chosen after analysing the potential energy and bond forces experienced by boron and nitrogen atoms subjected to bond stretching. The simulations performed with the optimised cut-off function help in identifying the Tersoff potential parameters that reproduce the experimentally evaluated mechanical behaviour of BNNSs. (paper)

Predator-prey dynamics driven by feedback between functionally diverse trophic levels.

Directory of Open Access Journals (Sweden)

Katrin Tirok

Full Text Available Neglecting the naturally existing functional diversity of communities and the resulting potential to respond to altered conditions may strongly reduce the realism and predictive power of ecological models. We therefore propose and study a predator-prey model that describes mutual feedback via species shifts in both predator and prey, using a dynamic trait approach. Species compositions of the two trophic levels were described by mean functional traits--prey edibility and predator food-selectivity--and functional diversities by the variances. Altered edibility triggered shifts in food-selectivity so that consumers continuously respond to the present prey composition, and vice versa. This trait-mediated feedback mechanism resulted in a complex dynamic behavior with ongoing oscillations in the mean trait values, reflecting continuous reorganization of the trophic levels. The feedback was only possible if sufficient functional diversity was present in both trophic levels. Functional diversity was internally maintained on the prey level as no niche existed in our system, which was ideal under any composition of the predator level due to the trade-offs between edibility, growth and carrying capacity. The predators were only subject to one trade-off between food-selectivity and grazing ability and in the absence of immigration, one predator type became abundant, i.e., functional diversity declined to zero. In the lack of functional diversity the system showed the same dynamics as conventional models of predator-prey interactions ignoring the potential for shifts in species composition. This way, our study identified the crucial role of trade-offs and their shape in physiological and ecological traits for preserving diversity.

Connection between Dynamically Derived Initial Mass Function Normalization and Stellar Population Parameters

NARCIS (Netherlands)

McDermid, Richard M.; Cappellari, Michele; Alatalo, Katherine; Bayet, Estelle; Blitz, Leo; Bois, Maxime; Bournaud, Frédéric; Bureau, Martin; Crocker, Alison F.; Davies, Roger L.; Davis, Timothy A.; de Zeeuw, P. T.; Duc, Pierre-Alain; Emsellem, Eric; Khochfar, Sadegh; Krajnović, Davor; Kuntschner, Harald; Morganti, Raffaella; Naab, Thorsten; Oosterloo, Tom; Sarzi, Marc; Scott, Nicholas; Serra, Paolo; Weijmans, Anne-Marie; Young, Lisa M.

We report on empirical trends between the dynamically determined stellar initial mass function (IMF) and stellar population properties for a complete, volume-limited sample of 260 early-type galaxies from the ATLAS3D project. We study trends between our dynamically derived IMF normalization αdyn ≡

Dynamical Functional Theory for Compressed Sensing

DEFF Research Database (Denmark)

Cakmak, Burak; Opper, Manfred; Winther, Ole

2017-01-01

the Thouless Anderson-Palmer (TAP) equations corresponding to the ensemble. Using a dynamical functional approach we are able to derive an effective stochastic process for the marginal statistics of a single component of the dynamics. This allows us to design memory terms in the algorithm in such a way...... that the resulting fields become Gaussian random variables allowing for an explicit analysis. The asymptotic statistics of these fields are consistent with the replica ansatz of the compressed sensing problem....

Spatial-temporal-spectral EEG patterns of BOLD functional network connectivity dynamics

Science.gov (United States)

Lamoš, Martin; Mareček, Radek; Slavíček, Tomáš; Mikl, Michal; Rektor, Ivan; Jan, Jiří

2018-06-01

Objective. Growing interest in the examination of large-scale brain network functional connectivity dynamics is accompanied by an effort to find the electrophysiological correlates. The commonly used constraints applied to spatial and spectral domains during electroencephalogram (EEG) data analysis may leave part of the neural activity unrecognized. We propose an approach that blindly reveals multimodal EEG spectral patterns that are related to the dynamics of the BOLD functional network connectivity. Approach. The blind decomposition of EEG spectrogram by parallel factor analysis has been shown to be a useful technique for uncovering patterns of neural activity. The simultaneously acquired BOLD fMRI data were decomposed by independent component analysis. Dynamic functional connectivity was computed on the component’s time series using a sliding window correlation, and between-network connectivity states were then defined based on the values of the correlation coefficients. ANOVA tests were performed to assess the relationships between the dynamics of between-network connectivity states and the fluctuations of EEG spectral patterns. Main results. We found three patterns related to the dynamics of between-network connectivity states. The first pattern has dominant peaks in the alpha, beta, and gamma bands and is related to the dynamics between the auditory, sensorimotor, and attentional networks. The second pattern, with dominant peaks in the theta and low alpha bands, is related to the visual and default mode network. The third pattern, also with peaks in the theta and low alpha bands, is related to the auditory and frontal network. Significance. Our previous findings revealed a relationship between EEG spectral pattern fluctuations and the hemodynamics of large-scale brain networks. In this study, we suggest that the relationship also exists at the level of functional connectivity dynamics among large-scale brain networks when no standard spatial and spectral

Task-related Functional Connectivity Dynamics in a Block-designed Visual Experiment

Directory of Open Access Journals (Sweden)

Xin eDi

2015-09-01

Full Text Available Studying task modulations of brain connectivity using functional magnetic resonance imaging (fMRI is critical to understand brain functions that support cognitive and affective processes. Existing methods such as psychophysiological interaction (PPI and dynamic causal modelling (DCM usually implicitly assume that the connectivity patterns are stable over a block-designed task with identical stimuli. However, this assumption lacks empirical verification on high-temporal resolution fMRI data with reliable data-driven analysis methods. The present study performed a detailed examination of dynamic changes of functional connectivity (FC in a simple block-designed visual checkerboard experiment with a sub-second sampling rate (TR = 0.645 s by estimating time-varying correlation coefficient (TVCC between BOLD responses of different brain regions. We observed reliable task-related FC changes (i.e., FCs were transiently decreased after task onset and went back to the baseline afterward among several visual regions of the bilateral middle occipital gyrus (MOG and the bilateral fusiform gyrus (FuG. Importantly, only the FCs between higher visual regions (MOG and lower visual regions (FuG exhibited such dynamic patterns. The results suggested that simply assuming a sustained FC during a task block may be insufficient to capture distinct task-related FC changes. The investigation of FC dynamics in tasks could improve our understanding of condition shifts and the coordination between different activated brain regions.

The transfer function model for dynamic response of wet cooling coils

International Nuclear Information System (INIS)

Yao Ye; Liu Shiqing

2008-01-01

This paper mainly concerned about the dynamic response model of wet cooling coils that is developed by the Laplace transform method. The theoretic equations are firstly established based on the theory of energy conservation. Then, the transfer functions on the transient responses of wet cooling coils have been deduced using the method of Laplace transform. The transfer functions reveal the dynamic relationships between the inlet variables and the outlet ones of the cooling coils. Partial-fraction method and Newton-Raphson method are both used in the inversion of the transfer functions from the s-domain to τ-domain. To make the dynamic model of wet cooling coils more adaptive, RBFNN method is employed to determine the coefficients of heat and mass transfer. Experiments have been done and manifested that the coefficients of heat and mass transfer by RBFNN will be of great value to the validity of the transient response model of wet cooling coils in this study

Dynamical zeta functions for piecewise monotone maps of the interval

CERN Document Server

Ruelle, David

2004-01-01

Consider a space M, a map f:M\\to M, and a function g:M \\to {\\mathbb C}. The formal power series \\zeta (z) = \\exp \\sum ^\\infty _{m=1} \\frac {z^m}{m} \\sum _{x \\in \\mathrm {Fix}\\,f^m} \\prod ^{m-1}_{k=0} g (f^kx) yields an example of a dynamical zeta function. Such functions have unexpected analytic properties and interesting relations to the theory of dynamical systems, statistical mechanics, and the spectral theory of certain operators (transfer operators). The first part of this monograph presents a general introduction to this subject. The second part is a detailed study of the zeta functions associated with piecewise monotone maps of the interval [0,1]. In particular, Ruelle gives a proof of a generalized form of the Baladi-Keller theorem relating the poles of \\zeta (z) and the eigenvalues of the transfer operator. He also proves a theorem expressing the largest eigenvalue of the transfer operator in terms of the ergodic properties of (M,f,g).

Dynamic equations for gauge-invariant wave functions

International Nuclear Information System (INIS)

Kapshaj, V.N.; Skachkov, N.B.; Solovtsov, I.L.

1984-01-01

The Bethe-Salpeter and quasipotential dynamic equations for wave functions of relative quark motion, have been derived. Wave functions are determined by the gauge invariant method. The V.A. Fock gauge condition is used in the construction. Despite the transl tional noninvariance of the gauge condition the standard separation of variables has been obtained and wave function doesn't contain gauge exponents

Layered interfaces between immiscible liquids studied by density-functional theory and molecular-dynamics simulations.

Science.gov (United States)

Geysermans, P; Elyeznasni, N; Russier, V

2005-11-22

We present a study of the structure in the interface between two immiscible liquids by density-functional theory and molecular-dynamics calculations. The liquids are modeled by Lennard-Jones potentials, which achieve immiscibility by suppressing the attractive interaction between unlike particles. The density profiles of the liquids display oscillations only in a limited part of the simple liquid-phase diagram (rho,T). When approaching the liquid-vapor coexistence, a significant depletion appears while the layering behavior of the density profile vanishes. By analogy with the liquid-vapor interface and the analysis of the adsorption this behavior is suggested to be strongly related to the drying transition.

Structure and Dynamics of Hydroxyl-Functionalized Protic Ammonium Carboxylate Ionic Liquids.

Science.gov (United States)

Thummuru, Dhileep Nagi Reddy; Mallik, Bhabani S

2017-10-26

We performed classical molecular dynamics simulations to investigate the structure and dynamics of protic ionic liquids, 2-hydroxy ethylammonium acetate, ethylammonium hydroxyacetate, and 2-hydroxyethylammonium hydroxyacetate at ambient conditions. Structural properties such as density, radial distribution functions, spatial distribution functions, and structure factors have been calculated. Dynamic properties such as mean square displacements, as well as residence and hydrogen bond dynamics have also been calculated. Hydrogen bond lifetimes and residence times change with the addition of hydroxyl groups. We observe that when a hydroxyl group is present on the cation, dynamics become very slow and it forms a strong hydrogen bond with carboxylate oxygen atoms of the anion. The hydroxyl functionalized ILs show more dynamic diversity than structurally similar ILs.

Investigation of dynamic SPECT measurements of the arterial input function in human subjects using simulation, phantom and human studies

Science.gov (United States)

Winant, Celeste D.; Aparici, Carina Mari; Zelnik, Yuval R.; Reutter, Bryan W.; Sitek, Arkadiusz; Bacharach, Stephen L.; Gullberg, Grant T.

2012-01-01

Computer simulations, a phantom study and a human study were performed to determine whether a slowly rotating single-photon computed emission tomography (SPECT) system could provide accurate arterial input functions for quantification of myocardial perfusion imaging using kinetic models. The errors induced by data inconsistency associated with imaging with slow camera rotation during tracer injection were evaluated with an approach called SPECT/P (dynamic SPECT from positron emission tomography (PET)) and SPECT/D (dynamic SPECT from database of SPECT phantom projections). SPECT/P simulated SPECT-like dynamic projections using reprojections of reconstructed dynamic 94Tc-methoxyisobutylisonitrile (94Tc-MIBI) PET images acquired in three human subjects (1 min infusion). This approach was used to evaluate the accuracy of estimating myocardial wash-in rate parameters K1 for rotation speeds providing 180° of projection data every 27 or 54 s. Blood input and myocardium tissue time-activity curves (TACs) were estimated using spatiotemporal splines. These were fit to a one-compartment perfusion model to obtain wash-in rate parameters K1. For the second method (SPECT/D), an anthropomorphic cardiac torso phantom was used to create real SPECT dynamic projection data of a tracer distribution derived from 94Tc-MIBI PET scans in the blood pool, myocardium, liver and background. This method introduced attenuation, collimation and scatter into the modeling of dynamic SPECT projections. Both approaches were used to evaluate the accuracy of estimating myocardial wash-in parameters for rotation speeds providing 180° of projection data every 27 and 54 s. Dynamic cardiac SPECT was also performed in a human subject at rest using a hybrid SPECT/CT scanner. Dynamic measurements of 99mTc-tetrofosmin in the myocardium were obtained using an infusion time of 2 min. Blood input, myocardium tissue and liver TACs were estimated using the same spatiotemporal splines. The spatiotemporal maximum

Investigation of dynamic SPECT measurements of the arterial input function in human subjects using simulation, phantom and human studies

International Nuclear Information System (INIS)

Winant, Celeste D; Aparici, Carina Mari; Bacharach, Stephen L; Gullberg, Grant T; Zelnik, Yuval R; Reutter, Bryan W; Sitek, Arkadiusz

2012-01-01

Computer simulations, a phantom study and a human study were performed to determine whether a slowly rotating single-photon computed emission tomography (SPECT) system could provide accurate arterial input functions for quantification of myocardial perfusion imaging using kinetic models. The errors induced by data inconsistency associated with imaging with slow camera rotation during tracer injection were evaluated with an approach called SPECT/P (dynamic SPECT from positron emission tomography (PET)) and SPECT/D (dynamic SPECT from database of SPECT phantom projections). SPECT/P simulated SPECT-like dynamic projections using reprojections of reconstructed dynamic 94 Tc-methoxyisobutylisonitrile ( 94 Tc-MIBI) PET images acquired in three human subjects (1 min infusion). This approach was used to evaluate the accuracy of estimating myocardial wash-in rate parameters K 1 for rotation speeds providing 180° of projection data every 27 or 54 s. Blood input and myocardium tissue time-activity curves (TACs) were estimated using spatiotemporal splines. These were fit to a one-compartment perfusion model to obtain wash-in rate parameters K 1 . For the second method (SPECT/D), an anthropomorphic cardiac torso phantom was used to create real SPECT dynamic projection data of a tracer distribution derived from 94 Tc-MIBI PET scans in the blood pool, myocardium, liver and background. This method introduced attenuation, collimation and scatter into the modeling of dynamic SPECT projections. Both approaches were used to evaluate the accuracy of estimating myocardial wash-in parameters for rotation speeds providing 180° of projection data every 27 and 54 s. Dynamic cardiac SPECT was also performed in a human subject at rest using a hybrid SPECT/CT scanner. Dynamic measurements of 99m Tc-tetrofosmin in the myocardium were obtained using an infusion time of 2 min. Blood input, myocardium tissue and liver TACs were estimated using the same spatiotemporal splines. The spatiotemporal

Dynamics of inequalities in geometric function theory

Directory of Open Access Journals (Sweden)

Reich Simeon

2001-01-01

Full Text Available A domain in the complex plane which is star-like with respect to a boundary point can be approximated by domains which are star-like with respect to interior points. This approximation process can be viewed dynamically as an evolution of the null points of the underlying holomorphic functions from the interior of the open unit disk towards a boundary point. We trace these dynamics analytically in terms of the Alexander–Nevanlinna and Robertson inequalities by using the framework of complex dynamical systems and hyperbolic monotonicity.

Dynamic prediction of cumulative incidence functions by direct binomial regression.

Science.gov (United States)

Grand, Mia K; de Witte, Theo J M; Putter, Hein

2018-03-25

In recent years there have been a series of advances in the field of dynamic prediction. Among those is the development of methods for dynamic prediction of the cumulative incidence function in a competing risk setting. These models enable the predictions to be updated as time progresses and more information becomes available, for example when a patient comes back for a follow-up visit after completing a year of treatment, the risk of death, and adverse events may have changed since treatment initiation. One approach to model the cumulative incidence function in competing risks is by direct binomial regression, where right censoring of the event times is handled by inverse probability of censoring weights. We extend the approach by combining it with landmarking to enable dynamic prediction of the cumulative incidence function. The proposed models are very flexible, as they allow the covariates to have complex time-varying effects, and we illustrate how to investigate possible time-varying structures using Wald tests. The models are fitted using generalized estimating equations. The method is applied to bone marrow transplant data and the performance is investigated in a simulation study. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An optimal strategy for functional mapping of dynamic trait loci.

Science.gov (United States)

Jin, Tianbo; Li, Jiahan; Guo, Ying; Zhou, Xiaojing; Yang, Runqing; Wu, Rongling

2010-02-01

As an emerging powerful approach for mapping quantitative trait loci (QTLs) responsible for dynamic traits, functional mapping models the time-dependent mean vector with biologically meaningful equations and are likely to generate biologically relevant and interpretable results. Given the autocorrelation nature of a dynamic trait, functional mapping needs the implementation of the models for the structure of the covariance matrix. In this article, we have provided a comprehensive set of approaches for modelling the covariance structure and incorporated each of these approaches into the framework of functional mapping. The Bayesian information criterion (BIC) values are used as a model selection criterion to choose the optimal combination of the submodels for the mean vector and covariance structure. In an example for leaf age growth from a rice molecular genetic project, the best submodel combination was found between the Gaussian model for the correlation structure, power equation of order 1 for the variance and the power curve for the mean vector. Under this combination, several significant QTLs for leaf age growth trajectories were detected on different chromosomes. Our model can be well used to study the genetic architecture of dynamic traits of agricultural values.

Nonlinear generalized synchronization of chaotic systems by pure error dynamics and elaborate nondiagonal Lyapunov function

International Nuclear Information System (INIS)

Ge Zhengming; Chang Chingming

2009-01-01

By applying pure error dynamics and elaborate nondiagonal Lyapunov function, the nonlinear generalized synchronization is studied in this paper. Instead of current mixed error dynamics in which master state variables and slave state variables are presented, the nonlinear generalized synchronization can be obtained by pure error dynamics without auxiliary numerical simulation. The elaborate nondiagonal Lyapunov function is applied rather than current monotonous square sum Lyapunov function deeply weakening the powerfulness of Lyapunov direct method. Both autonomous and nonautonomous double Mathieu systems are used as examples with numerical simulations.

Functional magnetic resonance imaging phase synchronization as a measure of dynamic functional connectivity.

Science.gov (United States)

Glerean, Enrico; Salmi, Juha; Lahnakoski, Juha M; Jääskeläinen, Iiro P; Sams, Mikko

2012-01-01

Functional brain activity and connectivity have been studied by calculating intersubject and seed-based correlations of hemodynamic data acquired with functional magnetic resonance imaging (fMRI). To inspect temporal dynamics, these correlation measures have been calculated over sliding time windows with necessary restrictions on the length of the temporal window that compromises the temporal resolution. Here, we show that it is possible to increase temporal resolution by using instantaneous phase synchronization (PS) as a measure of dynamic (time-varying) functional connectivity. We applied PS on an fMRI dataset obtained while 12 healthy volunteers watched a feature film. Narrow frequency band (0.04-0.07 Hz) was used in the PS analysis to avoid artifactual results. We defined three metrics for computing time-varying functional connectivity and time-varying intersubject reliability based on estimation of instantaneous PS across the subjects: (1) seed-based PS, (2) intersubject PS, and (3) intersubject seed-based PS. Our findings show that these PS-based metrics yield results consistent with both seed-based correlation and intersubject correlation methods when inspected over the whole time series, but provide an important advantage of maximal single-TR temporal resolution. These metrics can be applied both in studies with complex naturalistic stimuli (e.g., watching a movie or listening to music in the MRI scanner) and more controlled (e.g., event-related or blocked design) paradigms. A MATLAB toolbox FUNPSY ( http://becs.aalto.fi/bml/software.html ) is openly available for using these metrics in fMRI data analysis.

Hydrogen dynamics in Na3AlH6: A combined density functional theory and quasielastic neutron scattering study

DEFF Research Database (Denmark)

Voss, Johannes; Shi, Qing; Jacobsen, Hjalte Sylvest

2007-01-01

alanate with TiCl3, and here we study hydrogen dynamics in doped and undoped Na3AlH6 using a combination of density functional theory calculations and quasielastic neutron scattering. The hydrogen dynamics is found to be vacancy mediated and dominated by localized jump events, whereas long-range bulk......Understanding the elusive catalytic role of titanium-based additives on the reversible hydrogenation of complex hydrides is an essential step toward developing hydrogen storage materials for the transport sector. Improved bulk diffusion of hydrogen is one of the proposed effects of doping sodium...... defect motion in sodium alanate could result from vacancy-mediated sodium diffusion....

Functional segmentation of dynamic PET studies: Open source implementation and validation of a leader-follower-based algorithm.

Science.gov (United States)

Mateos-Pérez, José María; Soto-Montenegro, María Luisa; Peña-Zalbidea, Santiago; Desco, Manuel; Vaquero, Juan José

2016-02-01

We present a novel segmentation algorithm for dynamic PET studies that groups pixels according to the similarity of their time-activity curves. Sixteen mice bearing a human tumor cell line xenograft (CH-157MN) were imaged with three different (68)Ga-DOTA-peptides (DOTANOC, DOTATATE, DOTATOC) using a small animal PET-CT scanner. Regional activities (input function and tumor) were obtained after manual delineation of regions of interest over the image. The algorithm was implemented under the jClustering framework and used to extract the same regional activities as in the manual approach. The volume of distribution in the tumor was computed using the Logan linear method. A Kruskal-Wallis test was used to investigate significant differences between the manually and automatically obtained volumes of distribution. The algorithm successfully segmented all the studies. No significant differences were found for the same tracer across different segmentation methods. Manual delineation revealed significant differences between DOTANOC and the other two tracers (DOTANOC - DOTATATE, p=0.020; DOTANOC - DOTATOC, p=0.033). Similar differences were found using the leader-follower algorithm. An open implementation of a novel segmentation method for dynamic PET studies is presented and validated in rodent studies. It successfully replicated the manual results obtained in small-animal studies, thus making it a reliable substitute for this task and, potentially, for other dynamic segmentation procedures. Copyright © 2016 Elsevier Ltd. All rights reserved.

Dynamic function MR of the cervical vertebral column

International Nuclear Information System (INIS)

Naegele, M.; Woell, B.; Reiser, M.; Koch, W.; Kaden, B.

1992-01-01

To obtain functional studies of the cervical spine, a device has been developed which allows MRI examinations to be carried out in five different degrees of flexion. T 1 and T 2 * weighted FFE sequences were used. Dynamic functional MRI was performed on 5 normals and 31 patients (5 disc herniation, 4 whiplash injuries, 6 spinal canal stenoses, 14 laminectomies and spinal fusions, 2 rheumatoid arthritis). The relationship of the spinal cord to the bony and ligamentous components in different degrees of flexion was particularly well shown in whiplash injury, spinal stenosis and postoperative situations. (orig.) [de

Functional clustering in hippocampal cultures: relating network structure and dynamics

International Nuclear Information System (INIS)

Feldt, S; Dzakpasu, R; Olariu, E; Żochowski, M; Wang, J X; Shtrahman, E

2010-01-01

In this work we investigate the relationship between gross anatomic structural network properties, neuronal dynamics and the resultant functional structure in dissociated rat hippocampal cultures. Specifically, we studied cultures as they developed under two conditions: the first supporting glial cell growth (high glial group), and the second one inhibiting it (low glial group). We then compared structural network properties and the spatio-temporal activity patterns of the neurons. Differences in dynamics between the two groups could be linked to the impact of the glial network on the neuronal network as the cultures developed. We also implemented a recently developed algorithm called the functional clustering algorithm (FCA) to obtain the resulting functional network structure. We show that this new algorithm is useful for capturing changes in functional network structure as the networks evolve over time. The FCA detects changes in functional structure that are consistent with expected dynamical differences due to the impact of the glial network. Cultures in the high glial group show an increase in global synchronization as the cultures age, while those in the low glial group remain locally synchronized. We additionally use the FCA to quantify the amount of synchronization present in the cultures and show that the total level of synchronization in the high glial group is stronger than in the low glial group. These results indicate an interdependence between the glial and neuronal networks present in dissociated cultures

Principal States of Dynamic Functional Connectivity Reveal the Link Between Resting-State and Task-State Brain: An fMRI Study.

Science.gov (United States)

Cheng, Lin; Zhu, Yang; Sun, Junfeng; Deng, Lifu; He, Naying; Yang, Yang; Ling, Huawei; Ayaz, Hasan; Fu, Yi; Tong, Shanbao

2018-01-25

Task-related reorganization of functional connectivity (FC) has been widely investigated. Under classic static FC analysis, brain networks under task and rest have been demonstrated a general similarity. However, brain activity and cognitive process are believed to be dynamic and adaptive. Since static FC inherently ignores the distinct temporal patterns between rest and task, dynamic FC may be more a suitable technique to characterize the brain's dynamic and adaptive activities. In this study, we adopted [Formula: see text]-means clustering to investigate task-related spatiotemporal reorganization of dynamic brain networks and hypothesized that dynamic FC would be able to reveal the link between resting-state and task-state brain organization, including broadly similar spatial patterns but distinct temporal patterns. In order to test this hypothesis, this study examined the dynamic FC in default-mode network (DMN) and motor-related network (MN) using Blood-Oxygenation-Level-Dependent (BOLD)-fMRI data from 26 healthy subjects during rest (REST) and a hand closing-and-opening (HCO) task. Two principal FC states in REST and one principal FC state in HCO were identified. The first principal FC state in REST was found similar to that in HCO, which appeared to represent intrinsic network architecture and validated the broadly similar spatial patterns between REST and HCO. However, the second FC principal state in REST with much shorter "dwell time" implied the transient functional relationship between DMN and MN during REST. In addition, a more frequent shifting between two principal FC states indicated that brain network dynamically maintained a "default mode" in the motor system during REST, whereas the presence of a single principal FC state and reduced FC variability implied a more temporally stable connectivity during HCO, validating the distinct temporal patterns between REST and HCO. Our results further demonstrated that dynamic FC analysis could offer unique

Function of dynamic models in systems biology: linking structure to behaviour.

Science.gov (United States)

Knüpfer, Christian; Beckstein, Clemens

2013-10-08

Dynamic models in Systems Biology are used in computational simulation experiments for addressing biological questions. The complexity of the modelled biological systems and the growing number and size of the models calls for computer support for modelling and simulation in Systems Biology. This computer support has to be based on formal representations of relevant knowledge fragments. In this paper we describe different functional aspects of dynamic models. This description is conceptually embedded in our "meaning facets" framework which systematises the interpretation of dynamic models in structural, functional and behavioural facets. Here we focus on how function links the structure and the behaviour of a model. Models play a specific role (teleological function) in the scientific process of finding explanations for dynamic phenomena. In order to fulfil this role a model has to be used in simulation experiments (pragmatical function). A simulation experiment always refers to a specific situation and a state of the model and the modelled system (conditional function). We claim that the function of dynamic models refers to both the simulation experiment executed by software (intrinsic function) and the biological experiment which produces the phenomena under investigation (extrinsic function). We use the presented conceptual framework for the function of dynamic models to review formal accounts for functional aspects of models in Systems Biology, such as checklists, ontologies, and formal languages. Furthermore, we identify missing formal accounts for some of the functional aspects. In order to fill one of these gaps we propose an ontology for the teleological function of models. We have thoroughly analysed the role and use of models in Systems Biology. The resulting conceptual framework for the function of models is an important first step towards a comprehensive formal representation of the functional knowledge involved in the modelling and simulation process

Semigroups of transcendental entire functions and their dynamics

Indian Academy of Sciences (India)

DINESH KUMAR

Abstract. We investigate the dynamics of semigroups of transcendental entire func- tions using Fatou–Julia theory. Several results of the dynamics associated with iteration of a transcendental entire function have been extended to transcendental semigroups. We provide some condition for connectivity of the Julia set of the ...

Role of quantitative and dynamic radioactive studies in renal testing

International Nuclear Information System (INIS)

Raynaud, C.

1977-01-01

Many dynamic and quantitative radioactive tests are at present used in studying renal function. Whether involving dynamic morphological tests such as sequential images, dynamic quantitative tests such as the renogram or quantitative static tests such as radioactive clearances, their effective and original contribution is rather unimportant. Only one provides original data, the Hg renal uptake test but it is generally avoided due to the radiation dose absorbed by the kidney in children. A study of the causes of this lack of effectiveness leads to the observation that such tests are not well adapted to the needs of kidneys specialists. They are for the most part based on replacing a 'cold' indicator by radioactive indicator and the advantages anticipated from using radionuclide are not evident. In fact, they are often cancelled by the shortcomings of external detection. For the future, it seems indispensable to abandon some traditional concepts which lead us to consider that the only exploitable renal function is represented by excretion. The kidney has other functions; one of the most interesting seems to be the function of uptake of heavy metals and toxic substances, a study of which is only possible using radionuclides. A new generation of radioactive tests based on a study of uptake and also on a study of other renal functions may provide dynamic or quantitative data which physician urgently need

Abnormal rich club organization and functional brain dynamics in schizophrenia.

Science.gov (United States)

van den Heuvel, Martijn P; Sporns, Olaf; Collin, Guusje; Scheewe, Thomas; Mandl, René C W; Cahn, Wiepke; Goñi, Joaquín; Hulshoff Pol, Hilleke E; Kahn, René S

2013-08-01

The human brain forms a large-scale structural network of regions and interregional pathways. Recent studies have reported the existence of a selective set of highly central and interconnected hub regions that may play a crucial role in the brain's integrative processes, together forming a central backbone for global brain communication. Abnormal brain connectivity may have a key role in the pathophysiology of schizophrenia. To examine the structure of the rich club in schizophrenia and its role in global functional brain dynamics. Structural diffusion tensor imaging and resting-state functional magnetic resonance imaging were performed in patients with schizophrenia and matched healthy controls. Department of Psychiatry, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, the Netherlands. Forty-eight patients and 45 healthy controls participated in the study. An independent replication data set of 41 patients and 51 healthy controls was included to replicate and validate significant findings. MAIN OUTCOME(S) AND MEASURES: Measures of rich club organization, connectivity density of rich club connections and connections linking peripheral regions to brain hubs, measures of global brain network efficiency, and measures of coupling between brain structure and functional dynamics. Rich club organization between high-degree hub nodes was significantly affected in patients, together with a reduced density of rich club connections predominantly comprising the white matter pathways that link the midline frontal, parietal, and insular hub regions. This reduction in rich club density was found to be associated with lower levels of global communication capacity, a relationship that was absent for other white matter pathways. In addition, patients had an increase in the strength of structural connectivity-functional connectivity coupling. Our findings provide novel biological evidence that schizophrenia is characterized by a selective

Molecular dynamics studies of the dynamics of supercooled Lennard-Jones liquids

International Nuclear Information System (INIS)

De Leeuw, S.W.; Brakkee, M.J.D.

1990-01-01

Results are presented of molecular dynamics experiments, in which the Lennard-Jones liquid is cooled isobarically into the metastable temperature region below the freezing temperature. The variation of the density-density and transverse current correlation functions with temperature is studied. We observed a power-law behaviour for the temperature dependence of dynamical properties (viscosity and coefficienty of self-diffusion) with an exponent in good agreement with prediction of mode coupling theories and recent experimental results. (author). 23 refs, 5 figs

Stochastic modeling and simulation of reaction-diffusion system with Hill function dynamics.

Science.gov (United States)

Chen, Minghan; Li, Fei; Wang, Shuo; Cao, Young

2017-03-14

Stochastic simulation of reaction-diffusion systems presents great challenges for spatiotemporal biological modeling and simulation. One widely used framework for stochastic simulation of reaction-diffusion systems is reaction diffusion master equation (RDME). Previous studies have discovered that for the RDME, when discretization size approaches zero, reaction time for bimolecular reactions in high dimensional domains tends to infinity. In this paper, we demonstrate that in the 1D domain, highly nonlinear reaction dynamics given by Hill function may also have dramatic change when discretization size is smaller than a critical value. Moreover, we discuss methods to avoid this problem: smoothing over space, fixed length smoothing over space and a hybrid method. Our analysis reveals that the switch-like Hill dynamics reduces to a linear function of discretization size when the discretization size is small enough. The three proposed methods could correctly (under certain precision) simulate Hill function dynamics in the microscopic RDME system.

Dynamic density functional theory of solid tumor growth: Preliminary models

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Arnaud Chauviere

2012-03-01

Full Text Available Cancer is a disease that can be seen as a complex system whose dynamics and growth result from nonlinear processes coupled across wide ranges of spatio-temporal scales. The current mathematical modeling literature addresses issues at various scales but the development of theoretical methodologies capable of bridging gaps across scales needs further study. We present a new theoretical framework based on Dynamic Density Functional Theory (DDFT extended, for the first time, to the dynamics of living tissues by accounting for cell density correlations, different cell types, phenotypes and cell birth/death processes, in order to provide a biophysically consistent description of processes across the scales. We present an application of this approach to tumor growth.

Assessment of input function distortions on kinetic model parameters in simulated dynamic 82Rb PET perfusion studies

International Nuclear Information System (INIS)

Meyer, Carsten; Peligrad, Dragos-Nicolae; Weibrecht, Martin

2007-01-01

Cardiac 82 rubidium dynamic PET studies allow quantifying absolute myocardial perfusion by using tracer kinetic modeling. Here, the accurate measurement of the input function, i.e. the tracer concentration in blood plasma, is a major challenge. This measurement is deteriorated by inappropriate temporal sampling, spillover, etc. Such effects may influence the measured input peak value and the measured blood pool clearance. The aim of our study is to evaluate the effect of input function distortions on the myocardial perfusion as estimated by the model. To this end, we simulate noise-free myocardium time activity curves (TACs) with a two-compartment kinetic model. The input function to the model is a generic analytical function. Distortions of this function have been introduced by varying its parameters. Using the distorted input function, the compartment model has been fitted to the simulated myocardium TAC. This analysis has been performed for various sets of model parameters covering a physiologically relevant range. The evaluation shows that ±10% error in the input peak value can easily lead to ±10-25% error in the model parameter K 1 , which relates to myocardial perfusion. Variations in the input function tail are generally less relevant. We conclude that an accurate estimation especially of the plasma input peak is crucial for a reliable kinetic analysis and blood flow estimation

Dynamic functional connectivity analysis reveals transient states of dysconnectivity in schizophrenia

Directory of Open Access Journals (Sweden)

E. Damaraju

2014-01-01

Full Text Available Schizophrenia is a psychotic disorder characterized by functional dysconnectivity or abnormal integration between distant brain regions. Recent functional imaging studies have implicated large-scale thalamo-cortical connectivity as being disrupted in patients. However, observed connectivity differences in schizophrenia have been inconsistent between studies, with reports of hyperconnectivity and hypoconnectivity between the same brain regions. Using resting state eyes-closed functional imaging and independent component analysis on a multi-site data that included 151 schizophrenia patients and 163 age- and gender matched healthy controls, we decomposed the functional brain data into 100 components and identified 47 as functionally relevant intrinsic connectivity networks. We subsequently evaluated group differences in functional network connectivity, both in a static sense, computed as the pairwise Pearson correlations between the full network time courses (5.4 minutes in length, and a dynamic sense, computed using sliding windows (44 s in length and k-means clustering to characterize five discrete functional connectivity states. Static connectivity analysis revealed that compared to healthy controls, patients show significantly stronger connectivity, i.e., hyperconnectivity, between the thalamus and sensory networks (auditory, motor and visual, as well as reduced connectivity (hypoconnectivity between sensory networks from all modalities. Dynamic analysis suggests that (1, on average, schizophrenia patients spend much less time than healthy controls in states typified by strong, large-scale connectivity, and (2, that abnormal connectivity patterns are more pronounced during these connectivity states. In particular, states exhibiting cortical–subcortical antagonism (anti-correlations and strong positive connectivity between sensory networks are those that show the group differences of thalamic hyperconnectivity and sensory hypoconnectivity

Protic ammonium carboxylate ionic liquids: insight into structure, dynamics and thermophysical properties by alkyl group functionalization.

Science.gov (United States)

Reddy, Th Dhileep N; Mallik, Bhabani S

2017-04-19

This study is aimed at characterising the structure, dynamics and thermophysical properties of five alkylammonium carboxylate ionic liquids (ILs) from classical molecular dynamics simulations. The structural features of these ILs were characterised by calculating the site-site radial distribution functions, g(r), spatial distribution functions and structure factors. The structural properties demonstrate that ILs show greater interaction between cations and anions when alkyl chain length increases on the cation or anion. In all ILs, spatial distribution functions show that the anion is close to the acidic hydrogen atoms of the ammonium cation. We determined the role of alkyl group functionalization of the charged entities, cations and anions, in the dynamical behavior and the transport coefficients of this family of ionic liquids. The dynamics of ILs are described by studying the mean square displacement (MSD) of the centres of mass of the ions, diffusion coefficients, ionic conductivities and hydrogen bonds as well as residence dynamics. The diffusion coefficients and ionic conductivity decrease with an increase in the size of the cation or anion. The effect of alkyl chain length on ionic conductivity calculated in this article is consistent with the findings of other experimental studies. Hydrogen bond lifetimes and residence times along with structure factors were also calculated, and are related to alkyl chain length.

Cumulant approach to dynamical correlation functions at finite temperatures

International Nuclear Information System (INIS)

Tran Minhtien.

1993-11-01

A new theoretical approach, based on the introduction of cumulants, to calculate thermodynamic averages and dynamical correlation functions at finite temperatures is developed. The method is formulated in Liouville instead of Hilbert space and can be applied to operators which do not require to satisfy fermion or boson commutation relations. The application of the partitioning and projection methods for the dynamical correlation functions is discussed. The present method can be applied to weakly as well as to strongly correlated systems. (author). 9 refs

Signals of dynamical and statistical process from IMF-IMF correlation function

Science.gov (United States)

Pagano, E. V.; Acosta, L.; Auditore, L.; Baran, V.; Cap, T.; Cardella, G.; Colonna, M.; De Luca, S.; De Filippo, E.; Dell'Aquila, D.; Francalanza, L.; Gnoffo, B.; Lanzalone, G.; Lombardo, I.; Maiolino, C.; Martorana, N. S.; Norella, S.; Pagano, A.; Papa, M.; Piasecki, E.; Pirrone, S.; Politi, G.; Porto, F.; Quattrocchi, L.; Rizzo, F.; Rosato, E.; Russotto, P.; Siwek-Wilczyńska, K.; Trifiro, A.; Trimarchi, M.; Verde, G.; Vigilante, M.; Wilczyńsky, J.

2017-11-01

In this paper we briefly discuss about a novel application of the IMF-IMF correlation function to the physical case of binary massive projectile-like (PLF) splitting for dynamical and statistical breakup/fission in heavy ion collisions at Fermi energy. Theoretical simulations are also shown for comparisons with the data. These preliminary results have been obtained for the reverse kinematics reaction 124Sn + 64Ni at 35 AMeV that was studied using the forward part of CHIMERA detector. In that reaction a strong competition between a dynamical and a statistical components and its evolution with the charge asymmetry of the binary break up was already shown. In this work we show that the IMF-IMF correlation function can be used to pin down the timescale of the fragments production in binary fission-like phenomena. We also made simulations with the CoMDII model in order to compare to the experimental IMF-IMF correlation function. In future we plan to extend these studies to different reaction mechanisms and nuclear systems and to compare with different theoretical transport simulations.

Social Dynamics Management and Functional Behavioral Assessment

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Lee, David L.

2018-01-01

Managing social dynamics is a critical aspect of creating a positive learning environment in classrooms. In this paper three key interrelated ideas, reinforcement, function, and motivating operations, are discussed with relation to managing social behavior.

General framework for fluctuating dynamic density functional theory

Science.gov (United States)

Durán-Olivencia, Miguel A.; Yatsyshin, Peter; Goddard, Benjamin D.; Kalliadasis, Serafim

2017-12-01

We introduce a versatile bottom-up derivation of a formal theoretical framework to describe (passive) soft-matter systems out of equilibrium subject to fluctuations. We provide a unique connection between the constituent-particle dynamics of real systems and the time evolution equation of their measurable (coarse-grained) quantities, such as local density and velocity. The starting point is the full Hamiltonian description of a system of colloidal particles immersed in a fluid of identical bath particles. Then, we average out the bath via Zwanzig’s projection-operator techniques and obtain the stochastic Langevin equations governing the colloidal-particle dynamics. Introducing the appropriate definition of the local number and momentum density fields yields a generalisation of the Dean-Kawasaki (DK) model, which resembles the stochastic Navier-Stokes description of a fluid. Nevertheless, the DK equation still contains all the microscopic information and, for that reason, does not represent the dynamical law of observable quantities. We address this controversial feature of the DK description by carrying out a nonequilibrium ensemble average. Adopting a natural decomposition into local-equilibrium and nonequilibrium contribution, where the former is related to a generalised version of the canonical distribution, we finally obtain the fluctuating-hydrodynamic equation governing the time-evolution of the mesoscopic density and momentum fields. Along the way, we outline the connection between the ad hoc energy functional introduced in previous DK derivations and the free-energy functional from classical density-functional theory. The resultant equation has the structure of a dynamical density-functional theory (DDFT) with an additional fluctuating force coming from the random interactions with the bath. We show that our fluctuating DDFT formalism corresponds to a particular version of the fluctuating Navier-Stokes equations, originally derived by Landau and Lifshitz

Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Vijaykumar, Adithya, E-mail: vijaykumar@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands); van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Bolhuis, Peter G. [van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Rein ten Wolde, Pieter, E-mail: p.t.wolde@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands)

2015-12-07

In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.

Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations

International Nuclear Information System (INIS)

Vijaykumar, Adithya; Bolhuis, Peter G.; Rein ten Wolde, Pieter

2015-01-01

In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level

Dynamic polarization in paramagnetic solids and microscopic correlation functions

International Nuclear Information System (INIS)

Boucher, Jean-Paul

1972-01-01

The different effects of Dynamic Nuclear Polarization in paramagnetic solids are described by means of a single thermodynamic formalism. In the case of large exchange interactions, the Overhauser effect correlated with nuclear relaxation time measurements can provide a way of studying correlation functions between electronic spins. This method is used to study the low-frequency behaviour of the microscopic spectral density which should diverge as ω → 0, in the case of a linear exchange chain. (author) [fr

Predictive assessment of models for dynamic functional connectivity

DEFF Research Database (Denmark)

Nielsen, Søren Føns Vind; Schmidt, Mikkel Nørgaard; Madsen, Kristoffer Hougaard

2018-01-01

represent functional brain networks as a meta-stable process with a discrete number of states; however, there is a lack of consensus on how to perform model selection and learn the number of states, as well as a lack of understanding of how different modeling assumptions influence the estimated state......In neuroimaging, it has become evident that models of dynamic functional connectivity (dFC), which characterize how intrinsic brain organization changes over time, can provide a more detailed representation of brain function than traditional static analyses. Many dFC models in the literature...... dynamics. To address these issues, we consider a predictive likelihood approach to model assessment, where models are evaluated based on their predictive performance on held-out test data. Examining several prominent models of dFC (in their probabilistic formulations) we demonstrate our framework...

Inferring the physical connectivity of complex networks from their functional dynamics

Directory of Open Access Journals (Sweden)

Holm Liisa

2010-05-01

background network to the observed change of the functional activities in the system. Conclusions The results presented in this study indicate a strong relationship between the structure and dynamics of complex network systems. As coupling strength increases, synchronization emerges among hub nodes and recruits small-degree nodes. The results show that the onset of global synchronization in the system hinders the reconstruction of an underlying complex structure. Our analysis helps to clarify how the synchronization is achieved in systems of different network topologies.

A Tensor Statistical Model for Quantifying Dynamic Functional Connectivity.

Science.gov (United States)

Zhu, Yingying; Zhu, Xiaofeng; Kim, Minjeong; Yan, Jin; Wu, Guorong

2017-06-01

Functional connectivity (FC) has been widely investigated in many imaging-based neuroscience and clinical studies. Since functional Magnetic Resonance Image (MRI) signal is just an indirect reflection of brain activity, it is difficult to accurately quantify the FC strength only based on signal correlation. To address this limitation, we propose a learning-based tensor model to derive high sensitivity and specificity connectome biomarkers at the individual level from resting-state fMRI images. First, we propose a learning-based approach to estimate the intrinsic functional connectivity. In addition to the low level region-to-region signal correlation, latent module-to-module connection is also estimated and used to provide high level heuristics for measuring connectivity strength. Furthermore, sparsity constraint is employed to automatically remove the spurious connections, thus alleviating the issue of searching for optimal threshold. Second, we integrate our learning-based approach with the sliding-window technique to further reveal the dynamics of functional connectivity. Specifically, we stack the functional connectivity matrix within each sliding window and form a 3D tensor where the third dimension denotes for time. Then we obtain dynamic functional connectivity (dFC) for each individual subject by simultaneously estimating the within-sliding-window functional connectivity and characterizing the across-sliding-window temporal dynamics. Third, in order to enhance the robustness of the connectome patterns extracted from dFC, we extend the individual-based 3D tensors to a population-based 4D tensor (with the fourth dimension stands for the training subjects) and learn the statistics of connectome patterns via 4D tensor analysis. Since our 4D tensor model jointly (1) optimizes dFC for each training subject and (2) captures the principle connectome patterns, our statistical model gains more statistical power of representing new subject than current state

Dynamics of functional failures and recovery in complex road networks

Science.gov (United States)

Zhan, Xianyuan; Ukkusuri, Satish V.; Rao, P. Suresh C.

2017-11-01

We propose a new framework for modeling the evolution of functional failures and recoveries in complex networks, with traffic congestion on road networks as the case study. Differently from conventional approaches, we transform the evolution of functional states into an equivalent dynamic structural process: dual-vertex splitting and coalescing embedded within the original network structure. The proposed model successfully explains traffic congestion and recovery patterns at the city scale based on high-resolution data from two megacities. Numerical analysis shows that certain network structural attributes can amplify or suppress cascading functional failures. Our approach represents a new general framework to model functional failures and recoveries in flow-based networks and allows understanding of the interplay between structure and function for flow-induced failure propagation and recovery.

The Dynamics of the Innovation System for Functional Foods in South Brazil

OpenAIRE

de Barcellos, Marcia Dutra; Pozzo, Daniele; Ferreira, Gabriela Cardozo; Lionello, Rafael Laitano

2011-01-01

This study aims at identifying the dynamics of the innovation system for functional foods (FF) in Rio Grande do Sul, Brazil. Functional food is any healthy food claimed to have a health-promoting or disease-preventing property beyond the basic function of supplying nutrients. Health has been named as the most significant trend and innovation driver in the global food and drinks market. Brazil is one of the leading countries in food production and consumption, and the market for functional foo...

Relevance of deterministic chaos theory to studies in functioning of dynamical systems

Science.gov (United States)

Glagolev, S. N.; Bukhonova, S. M.; Chikina, E. D.

2018-03-01

The paper considers chaotic behavior of dynamical systems typical for social and economic processes. Approaches to analysis and evaluation of system development processes are studies from the point of view of controllability and determinateness. Explanations are given for necessity to apply non-standard mathematical tools to explain states of dynamical social and economic systems on the basis of fractal theory. Features of fractal structures, such as non-regularity, self-similarity, dimensionality and fractionality are considered.

Quantitative evaluation of the reticuloendothelial system function with dynamic MRI.

Directory of Open Access Journals (Sweden)

Ting Liu

Full Text Available To evaluate the reticuloendothelial system (RES function by real-time imaging blood clearance as well as hepatic uptake of superparamagnetic iron oxide nanoparticle (SPIO using dynamic magnetic resonance imaging (MRI with two-compartment pharmacokinetic modeling.Kinetics of blood clearance and hepatic accumulation were recorded in young adult male 01b74 athymic nude mice by dynamic T2* weighted MRI after the injection of different doses of SPIO nanoparticles (0.5, 3 or 10 mg Fe/kg. Association parameter, Kin, dissociation parameter, Kout, and elimination constant, Ke, derived from dynamic data with two-compartment model, were used to describe active binding to Kupffer cells and extrahepatic clearance. The clodrosome and liposome were utilized to deplete macrophages and block the RES function to evaluate the capability of the kinetic parameters for investigation of macrophage function and density.The two-compartment model provided a good description for all data and showed a low sum squared residual for all mice (0.27±0.03. A lower Kin, a lower Kout and a lower Ke were found after clodrosome treatment, whereas a lower Kin, a higher Kout and a lower Ke were observed after liposome treatment in comparison to saline treatment (P<0.005.Dynamic SPIO-enhanced MR imaging with two-compartment modeling can provide information on RES function on both a cell number and receptor function level.

Biodiversity and ecosystem functioning in dynamic landscapes

Science.gov (United States)

Brose, Ulrich; Hillebrand, Helmut

2016-01-01

The relationship between biodiversity and ecosystem functioning (BEF) and its consequence for ecosystem services has predominantly been studied by controlled, short-term and small-scale experiments under standardized environmental conditions and constant community compositions. However, changes in biodiversity occur in real-world ecosystems with varying environments and a dynamic community composition. In this theme issue, we present novel research on BEF in such dynamic communities. The contributions are organized in three sections on BEF relationships in (i) multi-trophic diversity, (ii) non-equilibrium biodiversity under disturbance and varying environmental conditions, and (iii) large spatial and long temporal scales. The first section shows that multi-trophic BEF relationships often appear idiosyncratic, while accounting for species traits enables a predictive understanding. Future BEF research on complex communities needs to include ecological theory that is based on first principles of species-averaged body masses, stoichiometry and effects of environmental conditions such as temperature. The second section illustrates that disturbance and varying environments have direct as well as indirect (via changes in species richness, community composition and species' traits) effects on BEF relationships. Fluctuations in biodiversity (species richness, community composition and also trait dominance within species) can severely modify BEF relationships. The third section demonstrates that BEF at larger spatial scales is driven by different variables. While species richness per se and community biomass are most important, species identity effects and community composition are less important than at small scales. Across long temporal scales, mass extinctions represent severe changes in biodiversity with mixed effects on ecosystem functions. Together, the contributions of this theme issue identify new research frontiers and answer some open questions on BEF relationships

Inferring gene expression dynamics via functional regression analysis

Directory of Open Access Journals (Sweden)

Leng Xiaoyan

2008-01-01

Full Text Available Abstract Background Temporal gene expression profiles characterize the time-dynamics of expression of specific genes and are increasingly collected in current gene expression experiments. In the analysis of experiments where gene expression is obtained over the life cycle, it is of interest to relate temporal patterns of gene expression associated with different developmental stages to each other to study patterns of long-term developmental gene regulation. We use tools from functional data analysis to study dynamic changes by relating temporal gene expression profiles of different developmental stages to each other. Results We demonstrate that functional regression methodology can pinpoint relationships that exist between temporary gene expression profiles for different life cycle phases and incorporates dimension reduction as needed for these high-dimensional data. By applying these tools, gene expression profiles for pupa and adult phases are found to be strongly related to the profiles of the same genes obtained during the embryo phase. Moreover, one can distinguish between gene groups that exhibit relationships with positive and others with negative associations between later life and embryonal expression profiles. Specifically, we find a positive relationship in expression for muscle development related genes, and a negative relationship for strictly maternal genes for Drosophila, using temporal gene expression profiles. Conclusion Our findings point to specific reactivation patterns of gene expression during the Drosophila life cycle which differ in characteristic ways between various gene groups. Functional regression emerges as a useful tool for relating gene expression patterns from different developmental stages, and avoids the problems with large numbers of parameters and multiple testing that affect alternative approaches.

Abstraction of continuous dynamical systems utilizing lyapunov functions

DEFF Research Database (Denmark)

Sloth, Christoffer; Wisniewski, Rafael

2010-01-01

This paper considers the development of a method for abstracting continuous dynamical systems by timed automata. The method is based on partitioning the state space of dynamical systems with invariant sets, which form cells representing locations of the timed automata. To enable verification...... of the dynamical system based on the abstraction, conditions for obtaining sound, complete, and refinable abstractions are set up. It is proposed to partition the state space utilizing sub-level sets of Lyapunov functions, since they are positive invariant sets. The existence of sound abstractions for Morse......-Smale systems and complete and refinable abstractions for linear systems are shown....

LETTER TO THE EDITOR: Fractal diffusion coefficient from dynamical zeta functions

Science.gov (United States)

Cristadoro, Giampaolo

2006-03-01

Dynamical zeta functions provide a powerful method to analyse low-dimensional dynamical systems when the underlying symbolic dynamics is under control. On the other hand, even simple one-dimensional maps can show an intricate structure of the grammar rules that may lead to a non-smooth dependence of global observables on parameters changes. A paradigmatic example is the fractal diffusion coefficient arising in a simple piecewise linear one-dimensional map of the real line. Using the Baladi-Ruelle generalization of the Milnor-Thurnston kneading determinant, we provide the exact dynamical zeta function for such a map and compute the diffusion coefficient from its smallest zero.

Structural and functional analysis of glycoprotein butyrylcholinesterase using atomistic molecular dynamics

Science.gov (United States)

Bernardi, Austen; Faller, Roland

Atomistic molecular dynamics (MD) has proven to be a powerful tool for studying the structure and dynamics of biological systems on nanosecond to microsecond time scales and nanometer length scales. In this work we study the effects of modifying the glycan distribution on the structure and function of full length monomeric butyrylcholinesterase (BChE). BChE exists as a monomer, dimer, or tetramer, and is a therapeutic glycoprotein with nine asparagine glycosylation sites per monomer. Each monomer acts as a stoichiometric scavenger for organophosphorus (OP) nerve agents (e.g. sarin, soman). Glycan distributions are highly heterogeneous and have been shown experimentally to affect certain glycoproteins' stability and reactivity. We performed structural analysis of various biologically relevant glycoforms of BChE using classical atomistic MD. Functional analysis was performed through binding energy simulations using umbrella sampling with BChE and OP cofactors. Additionally, we assess the quality of the glycans' conformational sampling. We found that the glycan distribution has a significant effect on the structure and function of BChE on timescales available to atomistic MD. This project is funded by the DTRA Grant HDTRA1-15-1-0054.

Dynamics in Microbial Composition and Functionality over a Season in Two Contrasting Estuarine Systems

DEFF Research Database (Denmark)

Traving, Sachia; Bentzon-Tilia, Mikkel; Mantikci, Mustafa

2015-01-01

In aquatic microbial ecology it remains unclear how bacterial community composition and dynamics are coupled to functionality, and whether this putative coupling varies over the season. In this study we address the questions if bacterial community composition can be linked to community function, ...

Density functional theory based molecular dynamics study of hydration and electronic properties of aqueous La(3+).

Science.gov (United States)

Terrier, Cyril; Vitorge, Pierre; Gaigeot, Marie-Pierre; Spezia, Riccardo; Vuilleumier, Rodolphe

2010-07-28

Structural and electronic properties of La(3+) immersed in bulk water have been assessed by means of density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations. Correct structural properties, i.e., La(III)-water distances and La(III) coordination number, can be obtained within the framework of Car-Parrinello simulations providing that both the La pseudopotential and conditions of the dynamics (fictitious mass and time step) are carefully set up. DFT-MD explicitly treats electronic densities and is shown here to provide a theoretical justification to the necessity of including polarization when studying highly charged cations such as lanthanoids(III) with classical MD. La(3+) was found to strongly polarize the water molecules located in the first shell, giving rise to dipole moments about 0.5 D larger than those of bulk water molecules. Finally, analyzing Kohn-Sham orbitals, we found La(3+) empty 4f orbitals extremely compact and to a great extent uncoupled from the water conduction band, while the 5d empty orbitals exhibit mixing with unoccupied states of water.

Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics

Science.gov (United States)

Vijaykumar, Adithya; Ouldridge, Thomas E.; ten Wolde, Pieter Rein; Bolhuis, Peter G.

2017-03-01

The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.

Physical properties of Cu nanoparticles: A molecular dynamics study

International Nuclear Information System (INIS)

Kart, H.H.; Yildirim, H.; Ozdemir Kart, S.; Çağin, T.

2014-01-01

Thermodynamical, structural and dynamical properties of Cu nanoparticles are investigated by using Molecular Dynamics (MD) simulations at various temperatures. In this work, MD simulations of the Cu-nanoparticles are performed by means of the MPiSiM codes by utilizing from Quantum Sutton-Chen (Q-SC) many-body force potential to define the interactions between the Cu atoms. The diameters of the copper nanoparticles are varied from 2 nm to 10 nm. MD simulations of Cu nanoparticles are carried out at low and high temperatures to study solid and liquid properties of Cu nanoparticles. Simulation results such as melting point, radial distribution function are compared with the available experimental bulk results. Radial distribution function, mean square displacement, diffusion coefficient, Lindemann index and Honeycutt–Andersen index are also calculated for estimating the melting point of the Copper nanoparticles. - Highlights: • Solid and liquid properties of Cu nanoparticles are studied. • Molecular dynamics utilizing the Quantum Sutton Chen potential is used in this work. • Melting temperatures of nanoparticles are strongly depended on nanoparticle sizes. • Heat capacity, radial distribution function and diffusion coefficients are studied. • Structures of nanoparticles are analyzed by Lindemann and Honeycutt–Andersen index

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

Directory of Open Access Journals (Sweden)

Oyang Yen-Jen

2010-10-01

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

Unsteady locomotion: integrating muscle function with whole body dynamics and neuromuscular control

Science.gov (United States)

Biewener, Andrew A.; Daley, Monica A.

2009-01-01

Summary By integrating studies of muscle function with analysis of whole body and limb dynamics, broader appreciation of neuromuscular function can be achieved. Ultimately, such studies need to address non-steady locomotor behaviors relevant to animals in their natural environments. When animals move slowly they likely rely on voluntary coordination of movement involving higher brain centers. However, when moving fast, their movements depend more strongly on responses controlled at more local levels. Our focus here is on control of fast-running locomotion. A key observation emerging from studies of steady level locomotion is that simple spring-mass dynamics, which help to economize energy expenditure, also apply to stabilization of unsteady running. Spring-mass dynamics apply to conditions that involve lateral impulsive perturbations, sudden changes in terrain height, and sudden changes in substrate stiffness or damping. Experimental investigation of unsteady locomotion is challenging, however, due to the variability inherent in such behaviors. Another emerging principle is that initial conditions associated with postural changes following a perturbation define different context-dependent stabilization responses. Distinct stabilization modes following a perturbation likely result from proximo-distal differences in limb muscle architecture, function and control strategy. Proximal muscles may be less sensitive to sudden perturbations and appear to operate, in such circumstances, under feed-forward control. In contrast, multiarticular distal muscles operate, via their tendons, to distribute energy among limb joints in a manner that also depends on the initial conditions of limb contact with the ground. Intrinsic properties of these distal muscle–tendon elements, in combination with limb and body dynamics, appear to provide rapid initial stabilizing mechanisms that are often consistent with spring-mass dynamics. These intrinsic mechanisms likely help to simplify the

Integrating atomistic molecular dynamics simulations, experiments and network analysis to study protein dynamics: strength in unity

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Elena ePapaleo

2015-05-01

Full Text Available In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.

Functional coordination of muscles underlying changes in behavioural dynamics.

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Vernooij, Carlijn A; Rao, Guillaume; Perdikis, Dionysios; Huys, Raoul; Jirsa, Viktor K; Temprado, Jean-Jacques

2016-06-10

The dynamical systems approach addresses Bernstein's degrees of freedom problem by assuming that the neuro-musculo-skeletal system transiently assembles and dismantles its components into functional units (or synergies) to meet task demands. Strikingly, little is known from a dynamical point of view about the functioning of the muscular sub-system in this process. To investigate the interaction between the dynamical organisation at muscular and behavioural levels, we searched for specific signatures of a phase transition in muscular coordination when a transition is displayed at the behavioural level. Our results provide evidence that, during Fitts' task when behaviour switches to a different dynamical regime, muscular activation displays typical signatures of a phase transition; a reorganisation in muscular coordination patterns accompanied by a peak in the variability of muscle activation. This suggests that consistent changes occur in coordination processes across the different levels of description (i.e., behaviour and muscles). Specifically, in Fitts' task, target size acts as a control parameter that induces a destabilisation and a reorganisation of coordination patterns at different levels of the neuro-musculo-skeletal system.

Comparative study between 99Tcm-MDP renal dynamic imaging and measurement of serum cystatin C in evaluation of glomerular function

International Nuclear Information System (INIS)

Ji Zeqiang; Miao Weibing

2010-01-01

Objective: To compare the difference between 99 Tcm-diethylenetriaminepentaacetic acid ( 99 Tc m -DTPA) renal dynamic imaging and measurement of serum cystatin C in evaluation of glomerular filtration rate (GFR). Methods: One hundred patients were selected at random, 38 cases with hypertension, 35 with nephrosis, 10 with arteriosclerosis obliterans, 9 with diabetes and 8 with other diseases. Evaluation of patients' GFR was made separately by 99 Tc m -DTPA renal dynamic imaging and measurement of serum cystatin C. Results: No significant difference of GFR was found between the two methods (t=1.591, P>0.05 ), and linear correlation was showed as well (r=0.809, P 99 Tc m -DTPA renal dynamic imaging could reveal the individual renal function and provide a more comprehensive evaluation of renal function while the measurement of serum cystatin C was simple and convenient, timesaving, economic, and more suit-able for screening patients' renal function clinically. (authors)

Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily.

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Dong, Zheng; Zhou, Hongyu; Tao, Peng

2018-02-01

PAS domains are widespread in archaea, bacteria, and eukaryota, and play important roles in various functions. In this study, we aim to explore functional evolutionary relationship among proteins in the PAS domain superfamily in view of the sequence-structure-dynamics-function relationship. We collected protein sequences and crystal structure data from RCSB Protein Data Bank of the PAS domain superfamily belonging to three biological functions (nucleotide binding, photoreceptor activity, and transferase activity). Protein sequences were aligned and then used to select sequence-conserved residues and build phylogenetic tree. Three-dimensional structure alignment was also applied to obtain structure-conserved residues. The protein dynamics were analyzed using elastic network model (ENM) and validated by molecular dynamics (MD) simulation. The result showed that the proteins with same function could be grouped by sequence similarity, and proteins in different functional groups displayed statistically significant difference in their vibrational patterns. Interestingly, in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues. In addition, the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function. This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics. This is a new attempt to delineate functional evolution of proteins using the integrated information of sequence, structure, and dynamics. © 2017 The Protein Society.

Explicit symplectic algorithms based on generating functions for charged particle dynamics

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Zhang, Ruili; Qin, Hong; Tang, Yifa; Liu, Jian; He, Yang; Xiao, Jianyuan

2016-07-01

Dynamics of a charged particle in the canonical coordinates is a Hamiltonian system, and the well-known symplectic algorithm has been regarded as the de facto method for numerical integration of Hamiltonian systems due to its long-term accuracy and fidelity. For long-term simulations with high efficiency, explicit symplectic algorithms are desirable. However, it is generally believed that explicit symplectic algorithms are only available for sum-separable Hamiltonians, and this restriction limits the application of explicit symplectic algorithms to charged particle dynamics. To overcome this difficulty, we combine the familiar sum-split method and a generating function method to construct second- and third-order explicit symplectic algorithms for dynamics of charged particle. The generating function method is designed to generate explicit symplectic algorithms for product-separable Hamiltonian with form of H (x ,p ) =pif (x ) or H (x ,p ) =xig (p ) . Applied to the simulations of charged particle dynamics, the explicit symplectic algorithms based on generating functions demonstrate superiorities in conservation and efficiency.

Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes.

Science.gov (United States)

Wang, Jun; Tao, Feng; Marowsky, Nicholas C; Fan, Chuanzhu

2016-09-01

Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes. © 2016 American Society of Plant Biologists. All rights reserved.

Mode coupling theory analysis of electrolyte solutions: Time dependent diffusion, intermediate scattering function, and ion solvation dynamics.

Science.gov (United States)

Roy, Susmita; Yashonath, Subramanian; Bagchi, Biman

2015-03-28

A self-consistent mode coupling theory (MCT) with microscopic inputs of equilibrium pair correlation functions is developed to analyze electrolyte dynamics. We apply the theory to calculate concentration dependence of (i) time dependent ion diffusion, (ii) intermediate scattering function of the constituent ions, and (iii) ion solvation dynamics in electrolyte solution. Brownian dynamics with implicit water molecules and molecular dynamics method with explicit water are used to check the theoretical predictions. The time dependence of ionic self-diffusion coefficient and the corresponding intermediate scattering function evaluated from our MCT approach show quantitative agreement with early experimental and present Brownian dynamic simulation results. With increasing concentration, the dispersion of electrolyte friction is found to occur at increasingly higher frequency, due to the faster relaxation of the ion atmosphere. The wave number dependence of intermediate scattering function, F(k, t), exhibits markedly different relaxation dynamics at different length scales. At small wave numbers, we find the emergence of a step-like relaxation, indicating the presence of both fast and slow time scales in the system. Such behavior allows an intriguing analogy with temperature dependent relaxation dynamics of supercooled liquids. We find that solvation dynamics of a tagged ion exhibits a power law decay at long times-the decay can also be fitted to a stretched exponential form. The emergence of the power law in solvation dynamics has been tested by carrying out long Brownian dynamics simulations with varying ionic concentrations. The solvation time correlation and ion-ion intermediate scattering function indeed exhibit highly interesting, non-trivial dynamical behavior at intermediate to longer times that require further experimental and theoretical studies.

Application of generalized function to dynamic analysis of elasto-plastic thick plates

International Nuclear Information System (INIS)

Zheng, D.; Weng, Z.

1987-01-01

The elasto-plastic dynamic analysis of thick plates is of great significance to the research and the design on an anti-seismic structure and an anti-explosive structure. In this paper, the derivative of δ-function is handled by using the generalized function. The dynamic influence coefficient of thick plates in deduced. A dynamic response of elasto-plastic thick plates its material has hardening behaviour considered, is analysed by using known elastic solutions. The general expressions for the dynamic response of elasto-plastic rectangular thick plates subjected arbitrary loads are given. Detailed computations are performed for the square plates of various height-span ratios. The results are compared with those obtained from the improved theory and the classical theory of plates. The modification of the classical deflection theory for plates is employed. The increment analysis is used for calculations. The yield function is considered as a function of inplane and transverse shear stresses. (orig./GL)

The use of the partial coherence function technique for the investigation of BWR noise dynamics

International Nuclear Information System (INIS)

Kostic, Lj.

1983-01-01

The extensive experimental investigations, at the last time, indicate that the partial coherence function technique can be a powerful method of the investigation of BWR noise dynamics. Symple BWR noise dynamics model for the global noise study, based on different noise phenomena, is proposed in this paper. (author)

The Effectiveness of Limited Dynamic Wrist Splints on the Symptoms, Function, and Strength of Women with Carpal Tunnel Syndrome: A Controlled Trial Study

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Seyedeh Marjan Jaladat

2017-03-01

Full Text Available Background: Splinting is the most common conservative method of treating patients with mild and moderate Carpal Tunnel Syndrome (CTS. The aim of this study was to determine the effectiveness of the limited dynamic wrist splint on the symptoms, function, and strength of women with CTS. In this controlled trial study, the subjects wore a splint of a new design called the “limited dynamic wrist splint”, which allowed the wrist motion in the range (between 15-degree flexion and 15-degree extension that exerts minimum pressure on the median nerve and prevents extra pressure on the nerve by limiting the range of motions out of the allowed range. Methods: In this study, 24 women diagnosed with mild to moderate CTS were initially evaluated on the basis of the Boston questionnaire, the dexterity test of the Purdue pegboard, grip and pinch strength, distal sensory latency, and sensory nerve conduction velocity. The subjects were randomly divided into two groups, control and treatment. Both groups received routine rehabilitation treatment for six weeks. The treatment group received the limited dynamic wrist splint for about six to eight hours a day. After six weeks, the initial examinations were repeated. The SPSS-16, independent t, and paired t-tests were used for data analysis. Results: All the variables in the treatment and the control groups showed improvement. The function test of the Boston questionnaire, the Purdue pegboard test, and the pinch strength were significantly improved in the treatment group. The “severity of the symptoms” test of the Boston questionnaire and the pinch strength in the control group showed a statistically significant difference (P < 0.05. In a comparison of the two groups, the function test of the Boston questionnaire showed a significant difference. Conclusion: This study showed that the use of the limited dynamic wrist splint for about six weeks for six to eight hours a day could have a significant effect on the

Molecular-dynamics study of the dynamical excitations in commensurate monolayer films of nitrogen molecules on graphite: A test of the corrugation in the nitrogen-graphite potential

DEFF Research Database (Denmark)

Hansen, Flemming Yssing; Bruch, Ludwig Walter

1995-01-01

The dynamical excitations in a commensurate monolayer solid of N2 molecules adsorbed on graphite have been studied using molecular-dynamics simulations. Velocity and rotational correlation functions as well as coherent intermediate scattering functions and dynamical structure factors have been ca...

Dynamical rescaling, the EMC effect and universality of hadron structure functions

International Nuclear Information System (INIS)

Close, F.E.

1984-04-01

Data are compared on the EMC effect, with the hypothesis that the quark confinement size increases in going from a free nucleon to a nucleus. In QCD a dynamical rescaling is predicted: Q 2 variation of the distribution function in a given target parallels the dependence on confinement size, R, at fixed Q 2 . Thus a dynamical scale invariance obtains when both R and Q 2 are varied, yielding the dynamical rescaling relation F 2 sup(A)(x, Q 2 ) = F 2 sup(N)(x, zetaQ 2 ) where zeta > 1 is predicted for any nucleus and is a function of the confinement size. Data on 12 nuclei agree with this, implying that confinement size is governed by nuclear density. The formalism is tested by relating the pion and nucleon structure functions. (author)

Quantum fluid dynamics based current-density functional study of a helium atom in a strong time-dependent magnetic field

International Nuclear Information System (INIS)

Vikas

2011-01-01

Evolution of the helium atom in a strong time-dependent (TD) magnetic field (B) of strength up to 10 11 G is investigated through a quantum fluid dynamics (QFD) based current-density functional theory (CDFT). The TD-QFD-CDFT computations are performed through numerical solution of a single generalized nonlinear Schroedinger equation employing vector exchange-correlation potentials and scalar exchange-correlation density functionals that depend both on the electronic charge-density and the current-density. The results are compared with that obtained from a B-TD-QFD-DFT approach (based on conventional TD-DFT) under similar numerical constraints but employing only scalar exchange-correlation potential dependent on electronic charge-density only. The B-TD-QFD-DFT approach, at a particular TD magnetic field-strength, yields electronic charge- and current-densities as well as exchange-correlation potential resembling with that obtained from the time-independent studies involving static (time-independent) magnetic fields. However, TD-QFD-CDFT electronic charge- and current-densities along with the exchange-correlation potential and energy differ significantly from that obtained using B-TD-QFD-DFT approach, particularly at field-strengths >10 9 G, representing dynamical effects of a TD field. The work concludes that when a helium atom is subjected to a strong TD magnetic field of order >10 9 G, the conventional TD-DFT based approach differs 'dynamically' from the CDFT based approach under similar computational constraints. (author)

Default Mode Dynamics for Global Functional Integration.

Science.gov (United States)

Vatansever, Deniz; Menon, David K; Manktelow, Anne E; Sahakian, Barbara J; Stamatakis, Emmanuel A

2015-11-18

The default mode network (DMN) has been traditionally assumed to hinder behavioral performance in externally focused, goal-directed paradigms and to provide no active contribution to human cognition. However, recent evidence suggests greater DMN activity in an array of tasks, especially those that involve self-referential and memory-based processing. Although data that robustly demonstrate a comprehensive functional role for DMN remains relatively scarce, the global workspace framework, which implicates the DMN in global information integration for conscious processing, can potentially provide an explanation for the broad range of higher-order paradigms that report DMN involvement. We used graph theoretical measures to assess the contribution of the DMN to global functional connectivity dynamics in 22 healthy volunteers during an fMRI-based n-back working-memory paradigm with parametric increases in difficulty. Our predominant finding is that brain modularity decreases with greater task demands, thus adapting a more global workspace configuration, in direct relation to increases in reaction times to correct responses. Flexible default mode regions dynamically switch community memberships and display significant changes in their nodal participation coefficient and strength, which may reflect the observed whole-brain changes in functional connectivity architecture. These findings have important implications for our understanding of healthy brain function, as they suggest a central role for the DMN in higher cognitive processing. The default mode network (DMN) has been shown to increase its activity during the absence of external stimulation, and hence was historically assumed to disengage during goal-directed tasks. Recent evidence, however, implicates the DMN in self-referential and memory-based processing. We provide robust evidence for this network's active contribution to working memory by revealing dynamic reconfiguration in its interactions with other networks

DNA breathing dynamics: analytic results for distribution functions of relevant Brownian functionals.

Science.gov (United States)

Bandyopadhyay, Malay; Gupta, Shamik; Segal, Dvira

2011-03-01

We investigate DNA breathing dynamics by suggesting and examining several Brownian functionals associated with bubble lifetime and reactivity. Bubble dynamics is described as an overdamped random walk in the number of broken base pairs. The walk takes place on the Poland-Scheraga free-energy landscape. We suggest several probability distribution functions that characterize the breathing process, and adopt the recently studied backward Fokker-Planck method and the path decomposition method as elegant and flexible tools for deriving these distributions. In particular, for a bubble of an initial size x₀, we derive analytical expressions for (i) the distribution P(t{f}|x₀) of the first-passage time t{f}, characterizing the bubble lifetime, (ii) the distribution P(A|x₀) of the area A until the first-passage time, providing information about the effective reactivity of the bubble to processes within the DNA, (iii) the distribution P(M) of the maximum bubble size M attained before the first-passage time, and (iv) the joint probability distribution P(M,t{m}) of the maximum bubble size M and the time t{m} of its occurrence before the first-passage time. These distributions are analyzed in the limit of small and large bubble sizes. We supplement our analytical predictions with direct numericalsimulations of the related Langevin equation, and obtain a very good agreement in the appropriate limits. The nontrivial scaling behavior of the various quantities analyzed here can, in principle, be explored experimentally.

Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics

NARCIS (Netherlands)

Vijaykumar, A.; Ouldridge, T.E.; ten Wolde, P.R.; Bolhuis, P.G.

2017-01-01

The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic

Unveiling protein functions through the dynamics of the interaction network.

Directory of Open Access Journals (Sweden)

Irene Sendiña-Nadal

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

Evaluation of renal function with dynamic MRI-T2-weighted gradient echo technique

International Nuclear Information System (INIS)

Kato, Katsuya

1995-01-01

To evaluate the usefulness of dynamic MRI of kidneys in healthy volunteers and patients with different 24-hour creatinine clearance (Ccr) levels, a dynamic study that employed the T2 weighted gradient echo technique (FLASH: TR/TE=34/25 msec, flip angle= 20 degrees) with single images during breathhold was performed on 10 healthy volunteers and 35 patients, all examined for the Ccr and suspected of having renal parenchymal disease after a phantom study. T1-weighted and dynamic MR imagings were obtained with a 1.5T imager. I analyzed the time-intensity curve of renal cortex and medulla, and defined a cortex decreased ratio (CDR) and medulla decreased ratio (MDR) in comparison with the Ccr. The cortico-medullary difference ratio (CMDR) of T1WI was also compared with the Ccr. The parameters of the T2 dynamic MRI study (CDR, MDR) better correlated with the Ccr than CMDR. Renal function can be quantitatively evaluated with the T2 dynamic MRI and there is a possibility that we can qualitatively evaluate the renal dysfunction and estimate its cause. (author)

Root structural and functional dynamics in terrestrial biosphere models--evaluation and recommendations.

Science.gov (United States)

Warren, Jeffrey M; Hanson, Paul J; Iversen, Colleen M; Kumar, Jitendra; Walker, Anthony P; Wullschleger, Stan D

2015-01-01

There is wide breadth of root function within ecosystems that should be considered when modeling the terrestrial biosphere. Root structure and function are closely associated with control of plant water and nutrient uptake from the soil, plant carbon (C) assimilation, partitioning and release to the soils, and control of biogeochemical cycles through interactions within the rhizosphere. Root function is extremely dynamic and dependent on internal plant signals, root traits and morphology, and the physical, chemical and biotic soil environment. While plant roots have significant structural and functional plasticity to changing environmental conditions, their dynamics are noticeably absent from the land component of process-based Earth system models used to simulate global biogeochemical cycling. Their dynamic representation in large-scale models should improve model veracity. Here, we describe current root inclusion in models across scales, ranging from mechanistic processes of single roots to parameterized root processes operating at the landscape scale. With this foundation we discuss how existing and future root functional knowledge, new data compilation efforts, and novel modeling platforms can be leveraged to enhance root functionality in large-scale terrestrial biosphere models by improving parameterization within models, and introducing new components such as dynamic root distribution and root functional traits linked to resource extraction. No claim to original US Government works. New Phytologist © 2014 New Phytologist Trust.

Dynamic regulation of NMDAR function in the adult brain by the stress hormone corticosterone

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Yiu Chung eTse

2012-03-01

Full Text Available Stress and corticosteroids dynamically modulate the expression of synaptic plasticity at glutamatergic synapses in the developed brain. Together with alpha-amino-3-hydroxy-methyl-4-isoxazole propionic acid receptors (AMPAR, N-methyl-D-aspartate receptors (NMDAR are critical mediators of synaptic function and are essential for the induction of many forms of synaptic plasticity. Regulation of NMDAR function by cortisol/corticosterone (CORT may be fundamental to the effects of stress on synaptic plasticity. Recent reports of the efficacy of NMDAR antagonists in treating certain stress-associated psychopathologies further highlight the importance of understanding the regulation of NMDAR function by CORT. Knowledge of how corticosteroids regulate NMDAR function within the adult brain is relatively sparse, perhaps due to a common belief that NMDAR function is relatively stable in the adult brain. We review recent results from our laboratory and others demonstrating dynamic regulation of NMDAR function by CORT in the adult brain. In addition, we consider the issue of how differences in the early life environment may program differential sensitivity to modulation of NMDAR function by CORT and how this may influence synaptic function during stress. Findings from these studies demonstrate that NMDAR function in the adult hippocampus remains sensitive to even brief exposures to CORT and that the capacity for modulation of NMDAR may be programmed, in part, by the early life environment. Modulation of NMDAR function may contribute to dynamic regulation of synaptic plasticity and adaptation in the face of stress, however enhanced NMDAR function may be implicated in mechanisms of stress related psychopathologies including depression.

Riemann zeta function from wave-packet dynamics

DEFF Research Database (Denmark)

Mack, R.; Dahl, Jens Peder; Moya-Cessa, H.

2010-01-01

We show that the time evolution of a thermal phase state of an anharmonic oscillator with logarithmic energy spectrum is intimately connected to the generalized Riemann zeta function zeta(s, a). Indeed, the autocorrelation function at a time t is determined by zeta (sigma + i tau, a), where sigma...... index of JWKB. We compare and contrast exact and approximate eigenvalues of purely logarithmic potentials. Moreover, we use a numerical method to find a potential which leads to exact logarithmic eigenvalues. We discuss possible realizations of Riemann zeta wave-packet dynamics using cold atoms...

Structure and dynamics of photosynthetic proteins studied by neutron scattering and molecular dynamic simulation

International Nuclear Information System (INIS)

Dellerue, Serge

2000-01-01

Understand the structure-dynamics-function relation in the case of proteins is essential. But few experimental techniques allow to have access to knowledge of fast internal movements of biological macromolecules. With the neutron scattering method, it has been possible to study the reorientation dynamics of side chains and of polypeptide skeleton for two proteins in terms of water or detergent and of temperature. With the use of the molecular dynamics method, essential for completing and interpreting the experimental data, it has been possible to assess the different contributions of the whole structure of proteins to the overall dynamics. It has been shown that the polypeptide skeleton presents an energy relaxation comparable to those of the side chains. Moreover, it has been explained that the protein dynamics can only be understood in terms of relaxation time distribution. (author) [fr

The dynamic mechanism of presenilin-function: Sensitive gate dynamics and loop unplugging control protein access

DEFF Research Database (Denmark)

Somavarapu, Arun Kumar; Kepp, Kasper Planeta

2016-01-01

There is no molecular explanation for the many presenilin 1 (PSEN1) mutations causing Alzheimer's disease, but both gain of function relating to amyloid production and loss of isolated PSEN1 function have been implied. We report here the first detailed dynamic all-atom model of mature PSEN1 from ...

β-Cell Ca(2+) dynamics and function are compromised in aging.

Science.gov (United States)

Barker, Christopher J; Li, Luosheng; Köhler, Martin; Berggren, Per-Olof

2015-01-01

Defects in pancreatic β-cell function and survival are key components in type 2 diabetes (T2D). An age-dependent deterioration in β-cell function has also been observed, but little is known about the molecular mechanisms behind this phenomenon. Our previous studies indicate that the regulation of cytoplasmic free Ca(2+) concentration ([Ca(2+)]i) may be critical and that this is dependent on the proper function of the mitochondria. The [Ca(2+)]i dynamics of the pancreatic β-cell are driven by an interplay between glucose-induced influx of extracellular Ca(2+) via voltage-dependent Ca(2+) channels and the inositol 1,4,5-trisphosphate (Ins(1,4,5)P3)-mediated liberation of Ca(2+) from intracellular stores. Our previous work has indicated a direct relationship between disruption of Ins(1,4,5)P3-mediated Ca(2+) regulation and loss of β-cell function, including disturbed [Ca(2+)]i dynamics and compromised insulin secretion. To investigate these processes in aging we used three mouse models, a premature aging mitochondrial mutator mouse, a mature aging phenotype (C57BL/6) and an aging-resistant phenotype (129). Our data suggest that age-dependent impairment in mitochondrial function leads to modest changes in [Ca(2+)]i dynamics in mouse β-cells, particularly in the pattern of [Ca(2+)]i oscillations. These changes are driven by modifications in both PLC/Ins(1,4,5)P3-mediated Ca(2+) mobilization from intracellular stores and decreased β-cell Ca(2+) influx over the plasma membrane. Our findings underscore an important concept, namely that even relatively small, time-dependent changes in β-cell signal-transduction result in compromised insulin release and in a diabetic phenotype. Copyright © 2014 Elsevier Ltd. All rights reserved.

Functional network macroscopes for probing past and present Earth system dynamics (Invited)

Science.gov (United States)

Donges, J. F.

2013-12-01

The Earth, as viewed from a physicist's perspective, is a dynamical system of great complexity. Functional complex networks are inferred from observational data and model runs or constructed on the basis of theoretical considerations. Representing statistical interdependencies or causal interactions between objects (e.g., Earth system subdomains, processes, or local field variables), functional complex networks are conceptually well-suited for naturally addressing some of the fundamental questions of Earth system analysis concerning, among others, major dynamical patterns, teleconnections, and feedback loops in the planetary machinery, as well as critical elements such as thresholds, bottlenecks, and switches. The first part of this talk concerns complex network theory and network-based time series analysis. Regarding complex network theory, the novel contributions include consistent frameworks for analyzing the topology of (i) general networks of interacting networks and (ii) networks with vertices of heterogeneously distributed weights, as well as (iii) an analytical theory for describing spatial networks. In the realm of time series analysis, (i) recurrence network analysis is put forward as a theoretically founded, nonlinear technique for the study of single, but possibly multivariate time series. (ii) Coupled climate networks are introduced as an exploratory tool of data analysis for quantitatively characterizing the intricate statistical interdependency structure within and between several fields of time series. The second part presents applications for detecting dynamical transitions (tipping points) in time series and studying bottlenecks in the atmosphere's general circulation structure. The analysis of paleoclimate data reveals a possible influence of large-scale shifts in Plio-Pleistocene African climate variability on events in human evolution. This presentation summarizes the contents of the dissertation titled "Functional network macroscopes for

Alternating Dynamics of Segregation and Integration in Human EEG Functional Networks During Working-memory Task.

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Zippo, Antonio G; Della Rosa, Pasquale A; Castiglioni, Isabella; Biella, Gabriele E M

2018-02-10

Brain functional networks show high variability in short time windows but mechanisms governing these transient dynamics remain unknown. In this work, we studied the temporal evolution of functional brain networks involved in a working memory (WM) task while recording high-density electroencephalography (EEG) in human normal subjects. We found that functional brain networks showed an initial phase characterized by an increase of the functional segregation index followed by a second phase where the functional segregation faded after the prevailing the functional integration. Notably, wrong trials were associated with different or disrupted sequences of the segregation-integration profiles and measures of network centrality and modularity were able to identify crucial aspects of the oscillatory network dynamics. Additionally, computational investigations further supported the experimental results. The brain functional organization may respond to the information processing demand of a WM task following a 2-step atomic scheme wherein segregation and integration alternately dominate the functional configurations. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Simultaneous determination of dynamic cardiac metabolism and function using PET/MRI.

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Barton, Gregory P; Vildberg, Lauren; Goss, Kara; Aggarwal, Niti; Eldridge, Marlowe; McMillan, Alan B

2018-05-01

Cardiac metabolic changes in heart disease precede overt contractile dysfunction. However, metabolism and function are not typically assessed together in clinical practice. The purpose of this study was to develop a cardiac positron emission tomography/magnetic resonance (PET/MR) stress test to assess the dynamic relationship between contractile function and metabolism in a preclinical model. Following an overnight fast, healthy pigs (45-50 kg) were anesthetized and mechanically ventilated. 18 F-fluorodeoxyglucose ( 18 F-FDG) solution was administered intravenously at a constant rate of 0.01 mL/s for 60 minutes. A cardiac PET/MR stress test was performed using normoxic gas (F I O 2  = .209) and hypoxic gas (F I O 2  = .12). Simultaneous cardiac imaging was performed on an integrated 3T PET/MR scanner. Hypoxic stress induced a significant increase in heart rate, cardiac output, left ventricular (LV) ejection fraction (EF), and peak torsion. There was a significant decline in arterial SpO 2 , LV end-diastolic and end-systolic volumes in hypoxia. Increased LV systolic function was coupled with an increase in myocardial FDG uptake (Ki) during hypoxic stress. PET/MR with continuous FDG infusion captures dynamic changes in both cardiac metabolism and contractile function. This technique warrants evaluation in human cardiac disease for assessment of subtle functional and metabolic abnormalities.

MR-guided dynamic PET reconstruction with the kernel method and spectral temporal basis functions

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Novosad, Philip; Reader, Andrew J.

2016-06-01

Recent advances in dynamic positron emission tomography (PET) reconstruction have demonstrated that it is possible to achieve markedly improved end-point kinetic parameter maps by incorporating a temporal model of the radiotracer directly into the reconstruction algorithm. In this work we have developed a highly constrained, fully dynamic PET reconstruction algorithm incorporating both spectral analysis temporal basis functions and spatial basis functions derived from the kernel method applied to a co-registered T1-weighted magnetic resonance (MR) image. The dynamic PET image is modelled as a linear combination of spatial and temporal basis functions, and a maximum likelihood estimate for the coefficients can be found using the expectation-maximization (EM) algorithm. Following reconstruction, kinetic fitting using any temporal model of interest can be applied. Based on a BrainWeb T1-weighted MR phantom, we performed a realistic dynamic [18F]FDG simulation study with two noise levels, and investigated the quantitative performance of the proposed reconstruction algorithm, comparing it with reconstructions incorporating either spectral analysis temporal basis functions alone or kernel spatial basis functions alone, as well as with conventional frame-independent reconstruction. Compared to the other reconstruction algorithms, the proposed algorithm achieved superior performance, offering a decrease in spatially averaged pixel-level root-mean-square-error on post-reconstruction kinetic parametric maps in the grey/white matter, as well as in the tumours when they were present on the co-registered MR image. When the tumours were not visible in the MR image, reconstruction with the proposed algorithm performed similarly to reconstruction with spectral temporal basis functions and was superior to both conventional frame-independent reconstruction and frame-independent reconstruction with kernel spatial basis functions. Furthermore, we demonstrate that a joint spectral

Establishment of frame image in dynamic function renal studies

International Nuclear Information System (INIS)

Guedes, Germano P.; Brunetto, Sergio Q.

1996-01-01

Statistical procedures applied to a set of images of renal function study are described to define a region of interest (ROI) on the kidneys's contours. The kidneys geometry is considered to adapt to the emitting area in every frames

Thermal quantum time-correlation functions from classical-like dynamics

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Hele, Timothy J. H.

2017-07-01

Thermal quantum time-correlation functions are of fundamental importance in quantum dynamics, allowing experimentally measurable properties such as reaction rates, diffusion constants and vibrational spectra to be computed from first principles. Since the exact quantum solution scales exponentially with system size, there has been considerable effort in formulating reliable linear-scaling methods involving exact quantum statistics and approximate quantum dynamics modelled with classical-like trajectories. Here, we review recent progress in the field with the development of methods including centroid molecular dynamics , ring polymer molecular dynamics (RPMD) and thermostatted RPMD (TRPMD). We show how these methods have recently been obtained from 'Matsubara dynamics', a form of semiclassical dynamics which conserves the quantum Boltzmann distribution. We also apply the Matsubara formalism to reaction rate theory, rederiving t → 0+ quantum transition-state theory (QTST) and showing that Matsubara-TST, like RPMD-TST, is equivalent to QTST. We end by surveying areas for future progress.

Proteins with Novel Structure, Function and Dynamics

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Pohorille, Andrew

2014-01-01

Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828-831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81-83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha-helix or beta-sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

Comparison Criteria for Nonlinear Functional Dynamic Equations of Higher Order

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Taher S. Hassan

2016-01-01

Full Text Available We will consider the higher order functional dynamic equations with mixed nonlinearities of the form xnt+∑j=0Npjtϕγjxφjt=0, on an above-unbounded time scale T, where n≥2, xi(t≔ri(tϕαixi-1Δ(t,  i=1,…,n-1,   with  x0=x,  ϕβ(u≔uβsgn⁡u, and α[i,j]≔αi⋯αj. The function φi:T→T is a rd-continuous function such that limt→∞φi(t=∞ for j=0,1,…,N. The results extend and improve some known results in the literature on higher order nonlinear dynamic equations.

Dynamic studies of liver and thyroid function with the aid of a gamma camera and an on-line digital computer

International Nuclear Information System (INIS)

Raikar, U.R.; Ganatra, R.D.; Samuel, A.M.; Ramanathan, P.; Atmaram, S.H.

1975-01-01

Initial experience of dynamic studies with the use of a 16 K digital computer coupled to a scintillation camera is described. 1. A system for scoring bolus was developed taking into account peaking time, the ratio of counts at the peak and at 8 s after the peak and full width at half maximum. Various parameters affecting the boli are discussed. 2. A method is established for finding the slope of net early trapping of sup(99m)TcO 4 in the thyroid after subtraction of extrathyroidal vascular background. This value was found diagnostically useful in establishing the state of thyroid function in 26 patients. 3. Portal extraction half-times of various colloidal radiopharmaceuticals were studied in the first two-minute dynamic study of the liver. This determination provided a method of bioassay for the consistency of the production of colloid for liver scintigraphy. Differences were noted in the trapping time between the right and left lobes of the liver. 4. On the basis of portal extraction half-times, sup(99m)Tc phytate appeared to become colloidal instantaneously after injection into the circulation and its behavior in dynamic studies was more or less identical with that of the sup(99m)Tc-S-colloid. 5. Normal liver has a dual blood supply, while a malignancy in the liver derives blood from only the hepatic artery. Benign lesions such as abscesses and cysts are relatively avascular. This difference in the blood supply of benign and malignant space-occupying lesions in the liver was exploited in an early dynamic study of blood flow to offer a clue to the pathology of cold areas in 170 patients. (author)

Dynamic chest radiography: flat-panel detector (FPD) based functional X-ray imaging.

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Tanaka, Rie

2016-07-01

Dynamic chest radiography is a flat-panel detector (FPD)-based functional X-ray imaging, which is performed as an additional examination in chest radiography. The large field of view (FOV) of FPDs permits real-time observation of the entire lungs and simultaneous right-and-left evaluation of diaphragm kinetics. Most importantly, dynamic chest radiography provides pulmonary ventilation and circulation findings as slight changes in pixel value even without the use of contrast media; the interpretation is challenging and crucial for a better understanding of pulmonary function. The basic concept was proposed in the 1980s; however, it was not realized until the 2010s because of technical limitations. Dynamic FPDs and advanced digital image processing played a key role for clinical application of dynamic chest radiography. Pulmonary ventilation and circulation can be quantified and visualized for the diagnosis of pulmonary diseases. Dynamic chest radiography can be deployed as a simple and rapid means of functional imaging in both routine and emergency medicine. Here, we focus on the evaluation of pulmonary ventilation and circulation. This review article describes the basic mechanism of imaging findings according to pulmonary/circulation physiology, followed by imaging procedures, analysis method, and diagnostic performance of dynamic chest radiography.

Socio-functional dynamics of the mathematical contents

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Isabel Alonso-Berenguer

2018-01-01

Full Text Available The article presents a model of the socio-functional dynamics of the mathematical contents that offers a novel theoretical-methodological basement for the development of the process of teaching-learning of the mathematical one. The investigation, of theoretical character, used the methods of analysis-synthesis, inductive-deductive and historical-logical to elaborate the one mentioned model that leaves of considering that the future professors have appropriated previously of the mathematical contents, foreseen in the curriculum, and they are, therefore, under conditions of understanding the potentialities of the same ones to facilitate the formation of socio-functional values.   

Proton magnetic resonance imaging for assessment of lung function and respiratory dynamics

International Nuclear Information System (INIS)

Eichinger, Monika; Tetzlaff, Ralf; Puderbach, Michael; Woodhouse, Neil; Kauczor, H.-U.

2007-01-01

Since many pulmonary diseases present with a variable regional involvement, modalities for assessment of regional lung function gained increasing attention over the last years. Together with lung perfusion and gas exchange, ventilation, as a result of the interaction of the respiratory pump and the lungs, is an indispensable component of lung function. So far, this complex mechanism is still mainly assessed indirectly and globally. A differentiation between the individual determining factors of ventilation would be crucial for precise diagnostics and adequate treatment. By dynamic imaging of the respiratory pump, the mechanical components of ventilation can be assessed regionally. Amongst imaging modalities applicable to this topic, magnetic resonance imaging (MRI), as a tool not relying on ionising radiation, is the most attractive. Recent advances in MRI technology have made it possible to assess diaphragmatic and chest wall motion, static and dynamic lung volumes, as well as regional lung function. Even though existing studies show large heterogeneity in design and applied methods, it becomes evident that MRI is capable to visualise pulmonary function as well as diaphragmatic and thoracic wall movement, providing new insights into lung physiology. Partly contradictory results and conclusions are most likely caused by technical limitations, limited number of studies and small sample size. Existing studies mainly evaluate possible imaging techniques and concentrate on normal physiology. The few studies in patients with lung cancer and emphysema already give a promising outlook for these techniques from which an increasing impact on improved and quantitative disease characterization as well as better patient management can be expected

DEFINE: A Service-Oriented Dynamically Enabling Function Model

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Tan Wei-Yi

2017-01-01

In this paper, we introduce an innovative Dynamically Enable Function In Network Equipment (DEFINE to allow tenant get the network service quickly. First, DEFINE decouples an application into different functional components, and connects these function components in a reconfigurable method. Second, DEFINE provides a programmable interface to the third party, who can develop their own processing modules according to their own needs. To verify the effectiveness of this model, we set up an evaluating network with a FPGA-based OpenFlow switch prototype, and deployed several applications on it. Our results show that DEFINE has excellent flexibility and performance.

Time-resolved infrared studies of protein conformational dynamics

Energy Technology Data Exchange (ETDEWEB)

Woodruff, W.H.; Causgrove, T.P.; Dyer, R.B. [Los Alamos National Laboratory, NM (United States); Callender, R.H. [Univ. of New York, NY (United States)

1994-12-01

We have demonstrated that TRIR in the amide I region gives structural information regarding protein conformational changes in realtime, both on processes involved in the development of the functional structure (protein folding) and on protein structural changes that accompany the functional dynamics of the native structure. Assignment of many of the amide I peaks to specific amide or sidechain structures will require much additional effort. Specifically, the congestion and complexity of the protein vibrational spectra dictate that isotope studies are an absolute requirement for more than a qualitative notion of the structural interpretation of these measurements. It is clear, however, that enormous potential exists for elucidating structural relaxation dynamics and energetics with a high degree of structural specificity using this approach.

Computational Benchmarking for Ultrafast Electron Dynamics: Wave Function Methods vs Density Functional Theory.

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Oliveira, Micael J T; Mignolet, Benoit; Kus, Tomasz; Papadopoulos, Theodoros A; Remacle, F; Verstraete, Matthieu J

2015-05-12

Attosecond electron dynamics in small- and medium-sized molecules, induced by an ultrashort strong optical pulse, is studied computationally for a frozen nuclear geometry. The importance of exchange and correlation effects on the nonequilibrium electron dynamics induced by the interaction of the molecule with the strong optical pulse is analyzed by comparing the solution of the time-dependent Schrödinger equation based on the correlated field-free stationary electronic states computed with the equationof-motion coupled cluster singles and doubles and the complete active space multi-configurational self-consistent field methodologies on one hand, and various functionals in real-time time-dependent density functional theory (TDDFT) on the other. We aim to evaluate the performance of the latter approach, which is very widely used for nonlinear absorption processes and whose computational cost has a more favorable scaling with the system size. We focus on LiH as a toy model for a nontrivial molecule and show that our conclusions carry over to larger molecules, exemplified by ABCU (C10H19N). The molecules are probed with IR and UV pulses whose intensities are not strong enough to significantly ionize the system. By comparing the evolution of the time-dependent field-free electronic dipole moment, as well as its Fourier power spectrum, we show that TD-DFT performs qualitatively well in most cases. Contrary to previous studies, we find almost no changes in the TD-DFT excitation energies when excited states are populated. Transitions between states of different symmetries are induced using pulses polarized in different directions. We observe that the performance of TD-DFT does not depend on the symmetry of the states involved in the transition.

Adsorption of hairy particles with mobile ligands: Molecular dynamics and density functional study

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Borówko, M.; Sokołowski, S.; Staszewski, T.; Pizio, O.

2018-01-01

We study models of hairy nanoparticles in contact with a hard wall. Each particle is built of a spherical core with a number of ligands attached to it and each ligand is composed of several spherical, tangentially jointed segments. The number of segments is the same for all ligands. Particular models differ by the numbers of ligands and of segments per ligand, but the total number of segments is constant. Moreover, our model assumes that the ligands are tethered to the core in such a manner that they can "slide" over the core surface. Using molecular dynamics simulations we investigate the differences in the structure of a system close to the wall. In order to characterize the distribution of the ligands around the core, we have calculated the end-to-end distances of the ligands and the lengths and orientation of the mass dipoles. Additionally, we also employed a density functional approach to obtain the density profiles. We have found that if the number of ligands is not too high, the proposed version of the theory is capable to predict the structure of the system with a reasonable accuracy.

Out-of-equilibrium dynamics of repulsive Fermi gases in quasiperiodic potentials: A density functional theory study

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Ancilotto, Francesco; Rossini, Davide; Pilati, Sebastiano

2018-04-01

The dynamics of a one-dimensional two-component Fermi gas in the presence of a quasiperiodic optical lattice (OL) is investigated by means of a density functional theory approach. Inspired by the protocol implemented in recent cold-atom experiments—designed to identify the many-body localization transition—we analyze the relaxation of an initially prepared imbalance between the occupation number of odd and of even sites. For quasidisorder strength beyond the Anderson localization transition, the imbalance survives for long times, indicating the inability of the system to reach local equilibrium. The late-time value of the imbalance diminishes for increasing interaction strength. Close to the critical quasidisorder strength corresponding to the noninteracting (Anderson) transition, the interacting system displays an extremely slow relaxation dynamics, consistent with subdiffusive behavior. The amplitude of the imbalance fluctuations around its running average is found to decrease with time, and such damping is more effective with increasing interaction strengths. While our study addresses the setup with two equally intense OLs, very similar effects due to interactions have been observed also in recent cold-atom experiments performed in the tight-binding regime, i.e., where one of the two OLs is very deep and the other is much weaker.

Solvation and Aggregation of Meta-Aminobenzoic Acid in Water: Density Functional Theory and Molecular Dynamics Study

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Etienne Gaines

2018-01-01

Full Text Available Meta-aminobenzoic acid, an important model system in the study of polymorphism and crystallization of active pharmaceutical ingredients, exist in water in both the nonionic (mABA and zwitterionic (mABA± forms. However, the constituent molecules of the polymorph that crystallizes from aqueous solutions are zwitterionic. This study reports atomistic simulations of the events surrounding the early stage of crystal nucleation of meta-aminobenzoic acid from aqueous solutions. Ab initio molecular dynamics was used to simulate the hydration of mABA± and mABA and to quantify the interaction of these molecules with the surrounding water molecules. Density functional theory calculations were conducted to determine the low-lying energy conformers of meta-aminobenzoic acid dimers and to compute the Gibbs free energies in water of nonionic, (mABA2, zwitterionic, (mABA±2, and nonionic-zwitterionic, (mABA(mABA±, species. Classical molecular dynamics simulations of mixed mABA–mABA± aqueous solutions were carried out to examine the aggregation of meta-aminobenzoic acid. According to these simulations, the selective crystallization of the polymorphs whose constituent molecules are zwitterionic is driven by the formation of zwitterionic dimers in solution, which are thermodynamically more stable than (mABA2 and (mABA(mABA± pairs. This work represents a paradigm of the role of molecular processes during the early stages of crystal nucleation in affecting polymorph selection during crystallization from solution.

Multiscale simulations of patchy particle systems combining Molecular Dynamics, Path Sampling and Green's Function Reaction Dynamics

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Bolhuis, Peter

Important reaction-diffusion processes, such as biochemical networks in living cells, or self-assembling soft matter, span many orders in length and time scales. In these systems, the reactants' spatial dynamics at mesoscopic length and time scales of microns and seconds is coupled to the reactions between the molecules at microscopic length and time scales of nanometers and milliseconds. This wide range of length and time scales makes these systems notoriously difficult to simulate. While mean-field rate equations cannot describe such processes, the mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. The recently developed multiscale Molecular Dynamics Green's Function Reaction Dynamics (MD-GFRD) approach combines GFRD for simulating the system at the mesocopic scale where particles are far apart, with microscopic Molecular (or Brownian) Dynamics, for simulating the system at the microscopic scale where reactants are in close proximity. The association and dissociation of particles are treated with rare event path sampling techniques. I will illustrate the efficiency of this method for patchy particle systems. Replacing the microscopic regime with a Markov State Model avoids the microscopic regime completely. The MSM is then pre-computed using advanced path-sampling techniques such as multistate transition interface sampling. I illustrate this approach on patchy particle systems that show multiple modes of binding. MD-GFRD is generic, and can be used to efficiently simulate reaction-diffusion systems at the particle level, including the orientational dynamics, opening up the possibility for large-scale simulations of e.g. protein signaling networks.

Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes1[OPEN

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Wang, Jun; Tao, Feng; Marowsky, Nicholas C.; Fan, Chuanzhu

2016-01-01

Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella. Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes. PMID:27485883

Renal dynamic functional scintigraphy in children with congenital urinary tract anomalies

International Nuclear Information System (INIS)

Cui Ruixue; Zhou Qian

2000-01-01

Objective: To clarify the characteristics of renal scintigraphy in children with various congenital urinary tract anomalies and to evaluate their clinical significance. Methods: 51 children with congenital urinary tract anomalies were studied by 99 Tc m -DTPA renal dynamic functional scintigraphy (RDFS)). Among them, 8 cases were studied by diuretic renography in addition. Results: RDFS provided: 1) Both the morphological information of anomalies and the split renal function. 2) Localization of the site of urinary tract obstruction. In case of pelviureteric junction obstruction, the hydronephrosis was usually severe but with normal size ureter, whereas in ureterovesical junction obstruction the hydronephrosis was less severe but with dilatation of ureter. In case of lower urinary tract obstruction, the hydronephrosis and hydroureter were bilateral. Diuretic renography differentiated obstructive from non-obstructive hydronephrosis. By comparing pre-and post operative studies, it was easy to evaluate the recovery of renal function. Conclusions: RDFS is a valuable modality for giving both anatomical and functional information in children with congenital urinary tract anomalies and the authors suggest it should be used more popularly in Pediatrics

Challenges in microbial ecology: Building predictive understanding of community function and dynamics

DEFF Research Database (Denmark)

Widder, Stefanie; Allen, Rosalind J.; Pfeiffer, Thomas

2016-01-01

The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth's soil, oceans and the atmosphere, and perform ecosystem functions that impact plants, animals and humans. Yet our ability to predict and manage the function of these highly...... complex, dynamically changing communities is limited. Building predictive models that link MC composition to function is a key emerging challenge in microbial ecology. Here, we argue that addressing this challenge requires close coordination of experimental data collection and method development...... is needed to achieve significant progress in our understanding of MC dynamics and function, and we make specific practical suggestions as to how this could be achieved....

Dynamic density functional theory with hydrodynamic interactions: Theoretical development and application in the study of phase separation in gas-liquid systems

International Nuclear Information System (INIS)

Kikkinides, E. S.; Monson, P. A.

2015-01-01

Building on recent developments in dynamic density functional theory, we have developed a version of the theory that includes hydrodynamic interactions. This is achieved by combining the continuity and momentum equations eliminating velocity fields, so the resulting model equation contains only terms related to the fluid density and its time and spatial derivatives. The new model satisfies simultaneously continuity and momentum equations under the assumptions of constant dynamic or kinematic viscosity and small velocities and/or density gradients. We present applications of the theory to spinodal decomposition of subcritical temperatures for one-dimensional and three-dimensional density perturbations for both a van der Waals fluid and for a lattice gas model in mean field theory. In the latter case, the theory provides a hydrodynamic extension to the recently studied dynamic mean field theory. We find that the theory correctly describes the transition from diffusive phase separation at short times to hydrodynamic behaviour at long times

Discrete two-sex models of population dynamics: On modelling the mating function

Science.gov (United States)

Bessa-Gomes, Carmen; Legendre, Stéphane; Clobert, Jean

2010-09-01

Although sexual reproduction has long been a central subject of theoretical ecology, until recently its consequences for population dynamics were largely overlooked. This is now changing, and many studies have addressed this issue, showing that when the mating system is taken into account, the population dynamics depends on the relative abundance of males and females, and is non-linear. Moreover, sexual reproduction increases the extinction risk, namely due to the Allee effect. Nevertheless, different studies have identified diverse potential consequences, depending on the choice of mating function. In this study, we investigate the consequences of three alternative mating functions that are frequently used in discrete population models: the minimum; the harmonic mean; and the modified harmonic mean. We consider their consequences at three levels: on the probability that females will breed; on the presence and intensity of the Allee effect; and on the extinction risk. When we consider the harmonic mean, the number of times the individuals of the least abundant sex mate exceeds their mating potential, which implies that with variable sex-ratios the potential reproductive rate is no longer under the modeller's control. Consequently, the female breeding probability exceeds 1 whenever the sex-ratio is male-biased, which constitutes an obvious problem. The use of the harmonic mean is thus only justified if we think that this parameter should be re-defined in order to represent the females' breeding rate and the fact that females may reproduce more than once per breeding season. This phenomenon buffers the Allee effect, and reduces the extinction risk. However, when we consider birth-pulse populations, such a phenomenon is implausible because the number of times females can reproduce per birth season is limited. In general, the minimum or modified harmonic mean mating functions seem to be more suitable for assessing the impact of mating systems on population dynamics.

Simultaneous acquisition of dynamic PET-MRI: arterial input function using DSC-MRI and [18F]-FET

Energy Technology Data Exchange (ETDEWEB)

Caldeira, Liliana; Yun, Seong Dae; Silva, Nuno da; Filss, Christian; Scheins, Juergen; Telmann, Lutz; Herzog, Hans; Shah, Jon [Institute of Neuroscience and Medicine - 4, Forschungszentrum Juelich GmbH (Germany)

2015-05-18

This work focuses on the study of simultaneous dynamic MR-PET acquisition in brain tumour patients. MR-based perfusion-weighted imaging (PWI) and PET [18F]-FET are dynamic methods, which allow to evaluate tumour metabolism in a quantitative way. In both methods, arterial input function (AIF) is necessary for quantification. However, the AIF estimation is a challenging task. In this work, we explore the possibilities to combine dynamic MR and PET AIF.

Simultaneous acquisition of dynamic PET-MRI: arterial input function using DSC-MRI and [18F]-FET

International Nuclear Information System (INIS)

Caldeira, Liliana; Yun, Seong Dae; Silva, Nuno da; Filss, Christian; Scheins, Juergen; Telmann, Lutz; Herzog, Hans; Shah, Jon

2015-01-01

This work focuses on the study of simultaneous dynamic MR-PET acquisition in brain tumour patients. MR-based perfusion-weighted imaging (PWI) and PET [18F]-FET are dynamic methods, which allow to evaluate tumour metabolism in a quantitative way. In both methods, arterial input function (AIF) is necessary for quantification. However, the AIF estimation is a challenging task. In this work, we explore the possibilities to combine dynamic MR and PET AIF.

Soils in transition : dynamics and functioning of fungi

NARCIS (Netherlands)

Wal, Annemieke van der

2007-01-01

The focus of this thesis is on the dynamics and functions of saprotrophic soil fungi during conversion from an arable land into a natural ecosystem (heathland) and to asses their effects on soil ecosystem processes. Chapter 2 describes that fungal biomass in abandoned arable land is not increasing

Individual Differences in Dynamic Functional Brain Connectivity across the Human Lifespan.

Directory of Open Access Journals (Sweden)

Elizabeth N Davison

2016-11-01

Full Text Available Individual differences in brain functional networks may be related to complex personal identifiers, including health, age, and ability. Dynamic network theory has been used to identify properties of dynamic brain function from fMRI data, but the majority of analyses and findings remain at the level of the group. Here, we apply hypergraph analysis, a method from dynamic network theory, to quantify individual differences in brain functional dynamics. Using a summary metric derived from the hypergraph formalism-hypergraph cardinality-we investigate individual variations in two separate, complementary data sets. The first data set ("multi-task" consists of 77 individuals engaging in four consecutive cognitive tasks. We observe that hypergraph cardinality exhibits variation across individuals while remaining consistent within individuals between tasks; moreover, the analysis of one of the memory tasks revealed a marginally significant correspondence between hypergraph cardinality and age. This finding motivated a similar analysis of the second data set ("age-memory", in which 95 individuals, aged 18-75, performed a memory task with a similar structure to the multi-task memory task. With the increased age range in the age-memory data set, the correlation between hypergraph cardinality and age correspondence becomes significant. We discuss these results in the context of the well-known finding linking age with network structure, and suggest that hypergraph analysis should serve as a useful tool in furthering our understanding of the dynamic network structure of the brain.

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

International Nuclear Information System (INIS)

Aradi, Balint; Frauenheim, Thomas

2015-01-01

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materials science, chemistry, and biology

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids.

Science.gov (United States)

Aradi, Bálint; Niklasson, Anders M N; Frauenheim, Thomas

2015-07-14

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. For systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can be applied to a broad range of problems in materials science, chemistry, and biology.

Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics

DEFF Research Database (Denmark)

Papaleo, Elena

2015-01-01

that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....

Ab initio molecular dynamics study of temperature and pressure-dependent infrared dielectric functions of liquid methanol

Directory of Open Access Journals (Sweden)

C. C. Wang

2017-03-01

Full Text Available The temperature and pressure-dependent dielectric functions of liquids are of great importance to the thermal radiation transfer and the diagnosis and control of fuel combustion. In this work, we apply the state-of-the-art ab initio molecular dynamics (AIMD method to calculate the infrared dielectric functions of liquid methanol at 183–573 K and 0.1–160 MPa in the spectral range 10−4000 cm−1, and study the temperature and pressure effects on the dielectric functions. The AIMD approach is validated by the Infrared Variable Angle Spectroscopic Ellipsometry (IR-VASE experimental measurements at 298 K and 0.1 MPa, and the proposed IR-VASE method is verified by comparison with paper data of distilled water. The results of the AIMD approach agrees well with the experimental values of IR-VASE. The experimental and theoretical analyses indicate that the temperature and pressure exert a noticeable influence on the infrared dielectric functions of liquid methanol. As temperature increases, the average molecular dipole moment decreases. The amplitudes of dominant absorption peaks reduce to almost one half as temperature increases from 183 to 333 K at 0.1 MPa and from 273 to 573 K at 160 MPa. The absorption peaks below 1500 cm–1 show a redshift, while those centered around 3200 cm–1 show a blueshift. Moreover, larger average dipole moments are observed as pressure increases. The amplitudes of dominant absorption peaks increase to almost two times as pressure increases from 1 to 160 MPa at 373 K.

Dynamical study of liquid aluminium

International Nuclear Information System (INIS)

Dubey, G.S.; Chaturvedi, D.K.

1979-09-01

Recent molecular dynamics data of Ebbsjoe et al. in liquid aluminium have been analysed through the memory function formalism. Two forms of the memory functions which have correct asymptotic limit at large wavenumbers but accounts for interatomic correlations in a different manner are considered. The results for ω 2 s(q, ω) obtained from both models are compared with experimental data. (author)

A dynamically tunable plasmonic multi-functional device based on graphene nano-sheet pair arrays

Science.gov (United States)

Wang, Wei; Meng, Zhao; Liang, Ruisheng; Chen, Shijie; Ding, Li; Wang, Faqiang; Liu, Hongzhan; Meng, Hongyun; Wei, Zhongchao

2018-05-01

Dynamically tunable plasmonic multi-functional is particularly desirable for various nanotechnological applications. In this paper, graphene nano-sheet pair arrays separated by a substrate, which can act as a dynamically tunable plasmonic band stop filter with transmission at resonance wavelength lower than 1%, a high sensitivity refractive index sensor with sensitivity up to 4879 nm/RIU, figure of merit of 40.66 and a two circuit optical switch with the modulation depth up to 0.998, are proposed and numerically investigated. These excellent optical performances are calculated by using FDTD numerical modeling and theoretical deduction. Simulation results show that a slight variation of chemical potential of the graphene nano-sheet can achieve significant resonance wavelength shifts. In additional, the resonance wavelength and transmission of this plasmonic device can be tuned easily by two voltages owing to the simple patterned graphene. These studies may have great potential in fabrication of multi-functional and dynamically tunable optoelectronic integrated devices.

Numerical study of the initial dynamics in tormac

International Nuclear Information System (INIS)

Aydemir, A.Y.

1979-01-01

Using a single fluid magnetohydrodynamic (MHD) code, we study the initial plasma dynamics in Tormac, an experimental device which attempts to confine plasma in a toroidal, two-pole cusp field. The code is in two dimensions and includes classical electrical conductivity and a constant heat conductivity. The full set of nonlinear MHD equations for the mass density, fluid velocity, temperature, the poloidal flux function, and the poloidal current function are solved using a predictor-corrector method

Dynamic Sensor Management Algorithm Based on Improved Efficacy Function

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TANG Shujuan

2016-01-01

Full Text Available A dynamic sensor management algorithm based on improved efficacy function is proposed to solve the multi-target and multi-sensory management problem. The tracking task precision requirements (TPR, target priority and sensor use cost were considered to establish the efficacy function by weighted sum the normalized value of the three factors. The dynamic sensor management algorithm was accomplished through control the diversities of the desired covariance matrix (DCM and the filtering covariance matrix (FCM. The DCM was preassigned in terms of TPR and the FCM was obtained by the centralized sequential Kalman filtering algorithm. The simulation results prove that the proposed method could meet the requirements of desired tracking precision and adjust sensor selection according to target priority and cost of sensor source usage. This makes sensor management scheme more reasonable and effective.

Binary codes with impulse autocorrelation functions for dynamic experiments

International Nuclear Information System (INIS)

Corran, E.R.; Cummins, J.D.

1962-09-01

A series of binary codes exist which have autocorrelation functions approximating to an impulse function. Signals whose behaviour in time can be expressed by such codes have spectra which are 'whiter' over a limited bandwidth and for a finite time than signals from a white noise generator. These codes are used to determine system dynamic responses using the correlation technique. Programmes have been written to compute codes of arbitrary length and to compute 'cyclic' autocorrelation and cross-correlation functions. Complete listings of these programmes are given, and a code of 1019 bits is presented. (author)

Cosmological dynamics with non-minimally coupled scalar field and a constant potential function

International Nuclear Information System (INIS)

Hrycyna, Orest; Szydłowski, Marek

2015-01-01

Dynamical systems methods are used to investigate global behaviour of the spatially flat Friedmann-Robertson-Walker cosmological model in gravitational theory with a non-minimally coupled scalar field and a constant potential function. We show that the system can be reduced to an autonomous three-dimensional dynamical system and additionally is equipped with an invariant manifold corresponding to an accelerated expansion of the universe. Using this invariant manifold we find an exact solution of the reduced dynamics. We investigate all solutions for all admissible initial conditions using theory of dynamical systems to obtain a classification of all evolutional paths. The right-hand sides of the dynamical system depend crucially on the value of the non-minimal coupling constant therefore we study bifurcation values of this parameter under which the structure of the phase space changes qualitatively. We found a special bifurcation value of the non-minimal coupling constant which is distinguished by dynamics of the model and may suggest some additional symmetry in matter sector of the theory

Cosmological dynamics with non-minimally coupled scalar field and a constant potential function

Energy Technology Data Exchange (ETDEWEB)

Hrycyna, Orest [Theoretical Physics Division, National Centre for Nuclear Research, Hoża 69, 00-681 Warszawa (Poland); Szydłowski, Marek, E-mail: orest.hrycyna@ncbj.gov.pl, E-mail: marek.szydlowski@uj.edu.pl [Astronomical Observatory, Jagiellonian University, Orla 171, 30-244 Kraków (Poland)

2015-11-01

Dynamical systems methods are used to investigate global behaviour of the spatially flat Friedmann-Robertson-Walker cosmological model in gravitational theory with a non-minimally coupled scalar field and a constant potential function. We show that the system can be reduced to an autonomous three-dimensional dynamical system and additionally is equipped with an invariant manifold corresponding to an accelerated expansion of the universe. Using this invariant manifold we find an exact solution of the reduced dynamics. We investigate all solutions for all admissible initial conditions using theory of dynamical systems to obtain a classification of all evolutional paths. The right-hand sides of the dynamical system depend crucially on the value of the non-minimal coupling constant therefore we study bifurcation values of this parameter under which the structure of the phase space changes qualitatively. We found a special bifurcation value of the non-minimal coupling constant which is distinguished by dynamics of the model and may suggest some additional symmetry in matter sector of the theory.

Depression, disability and functional status among community-dwelling older adults in South Africa: evidence from the first South African National Income Dynamics Study.

Science.gov (United States)

Tomita, Andrew; Burns, Jonathan K

2013-12-01

This study examined the relationship between depression and functional status among a community-dwelling older population of 65 years and older in South Africa. Data from the first wave of the South African National Income Dynamics Study were used, this being the first longitudinal panel survey of a nationally representative sample of households. The study focused on the data for resident adults 65 years and older (n = 1,429). Depression was assessed using the 10-item version of the Center for Epidemiologic Studies Depression Scale. Functional status, pertaining to both difficulty and dependence in activities of daily living (ADL), instrumental activities of daily living (IADL), and physical functioning and mobility (PFM), were assessed using 11 items. Functional challenges were generally higher in the older age group. There was a significant association between depression and functional dependence in ADL (adjusted OR = 2.57 [CI: 1.03-6.41]), IADL (adjusted OR = 2.76 [CI: 1.89-4.04]), and PFM (adjusted OR = 1.66 [CI: 1.18-2.33]), but the relationship between depression and functional status, particularly PFM, appeared weaker in older age. The relationship between depression symptoms and function is complex. Functional characteristics between older and younger old populations are diverse, and caution is indicated against overgeneralizing the challenges related to depression and function among this target population. Copyright © 2013 John Wiley & Sons, Ltd.

One- and two-particle correlation functions in the dynamical quantum cluster approach

International Nuclear Information System (INIS)

Hochkeppel, Stephan

2008-01-01

This thesis is dedicated to a theoretical study of the 1-band Hubbard model in the strong coupling limit. The investigation is based on the Dynamical Cluster Approximation (DCA) which systematically restores non-local corrections to the Dynamical Mean Field approximation (DMFA). The DCA is formulated in momentum space and is characterised by a patching of the Brillouin zone where momentum conservation is only recovered between two patches. The approximation works well if k-space correlation functions show a weak momentum dependence. In order to study the temperature and doping dependence of the spin- and charge excitation spectra, we explicitly extend the Dynamical Cluster Approximation to two-particle response functions. The full irreducible two-particle vertex with three momenta and frequencies is approximated by an effective vertex dependent on the momentum and frequency of the spin and/or charge excitations. The effective vertex is calculated by using the Quantum Monte Carlo method on the finite cluster whereas the analytical continuation of dynamical quantities is performed by a stochastic version of the maximum entropy method. A comparison with high temperature auxiliary field quantum Monte Carlo data serves as a benchmark for our approach to two-particle correlation functions. Our method can reproduce basic characteristics of the spin- and charge excitation spectrum. Near and beyond optimal doping, our results provide a consistent overall picture of the interplay between charge, spin and single-particle excitations: a collective spin mode emerges at optimal doping and sufficiently low temperatures in the spin response spectrum and exhibits the energy scale of the magnetic exchange interaction J. Simultaneously, the low energy single-particle excitations are characterised by a coherent quasiparticle with bandwidth J. The origin of the quasiparticle can be quite well understood in a picture of a more or less antiferromagnetic ordered background in which holes

Monitoring renal function during biphosphonate treatment in patients with bone metastases - role of dynamic kidney scintigraphy

International Nuclear Information System (INIS)

Chavdarova, L.; Tzonevska, A.

2015-01-01

Full text: Biphosphonates (BP) are very effective in treatment of bone metastatic disease. Their renal excretion defines one of the major side effects - nephrotoxicity. Glomerular filtration rate (GFR) is a basic parameter for its early detection but clinical practice often uses only serum creatinine. Aim of our retrospective study is to assess the role of dynamic kidney scintigraphy (DKS) and the estimated during it GFR in BP-treated patients with bone metastatic disease. 61 patients (53 female, 8 male), aged 33-82, with biphosphonate-treated bone metastases from breast (n53), lung (n1) and prostate (n7) cancer were enrolled for the period 27.04.2012-14.04.2015. Overall 77 studies were made, in 13 patients more than one. GFR was assessed in 57 studies. Results were compared with serum creatinine. All patients with elevated creatinine showed low GFR and decreased renal function at DKS. With normal creatinine and decreased GFR: in 31 studies kidney function was reduced, in 14 function was normal but kidney scintigraphic appearance was disturbed- mostly as in diffuse parenchymal disease. In 5 studies GFR was normal and renal function decreased. In 3 studies both parameters were normal. Zoledronic acid was changed with denosumab in 2 patients because of worsened function and strongly reduced GFR, in one patient BP was stopped after DKS. In 3 patients the interval between BP was extended because of affected renal function. GFR is more sensitive than serum creatinine levels and changes in nephrographic curves. Dynamic kidney scintigraphy is a functional method directing clinical reaction to preserve renal function

Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps

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Stella Fabio

2011-05-01

Full Text Available Abstract Background Molecular dynamics (MD simulations are powerful tools to investigate the conformational dynamics of proteins that is often a critical element of their function. Identification of functionally relevant conformations is generally done clustering the large ensemble of structures that are generated. Recently, Self-Organising Maps (SOMs were reported performing more accurately and providing more consistent results than traditional clustering algorithms in various data mining problems. We present a novel strategy to analyse and compare conformational ensembles of protein domains using a two-level approach that combines SOMs and hierarchical clustering. Results The conformational dynamics of the α-spectrin SH3 protein domain and six single mutants were analysed by MD simulations. The Cα's Cartesian coordinates of conformations sampled in the essential space were used as input data vectors for SOM training, then complete linkage clustering was performed on the SOM prototype vectors. A specific protocol to optimize a SOM for structural ensembles was proposed: the optimal SOM was selected by means of a Taguchi experimental design plan applied to different data sets, and the optimal sampling rate of the MD trajectory was selected. The proposed two-level approach was applied to single trajectories of the SH3 domain independently as well as to groups of them at the same time. The results demonstrated the potential of this approach in the analysis of large ensembles of molecular structures: the possibility of producing a topological mapping of the conformational space in a simple 2D visualisation, as well as of effectively highlighting differences in the conformational dynamics directly related to biological functions. Conclusions The use of a two-level approach combining SOMs and hierarchical clustering for conformational analysis of structural ensembles of proteins was proposed. It can easily be extended to other study cases and to

Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps

Science.gov (United States)

2011-01-01

Background Molecular dynamics (MD) simulations are powerful tools to investigate the conformational dynamics of proteins that is often a critical element of their function. Identification of functionally relevant conformations is generally done clustering the large ensemble of structures that are generated. Recently, Self-Organising Maps (SOMs) were reported performing more accurately and providing more consistent results than traditional clustering algorithms in various data mining problems. We present a novel strategy to analyse and compare conformational ensembles of protein domains using a two-level approach that combines SOMs and hierarchical clustering. Results The conformational dynamics of the α-spectrin SH3 protein domain and six single mutants were analysed by MD simulations. The Cα's Cartesian coordinates of conformations sampled in the essential space were used as input data vectors for SOM training, then complete linkage clustering was performed on the SOM prototype vectors. A specific protocol to optimize a SOM for structural ensembles was proposed: the optimal SOM was selected by means of a Taguchi experimental design plan applied to different data sets, and the optimal sampling rate of the MD trajectory was selected. The proposed two-level approach was applied to single trajectories of the SH3 domain independently as well as to groups of them at the same time. The results demonstrated the potential of this approach in the analysis of large ensembles of molecular structures: the possibility of producing a topological mapping of the conformational space in a simple 2D visualisation, as well as of effectively highlighting differences in the conformational dynamics directly related to biological functions. Conclusions The use of a two-level approach combining SOMs and hierarchical clustering for conformational analysis of structural ensembles of proteins was proposed. It can easily be extended to other study cases and to conformational ensembles from

The study of correlation between neurological function rehabilitation and dynamic change of rCBF in patients with aphasia

International Nuclear Information System (INIS)

Liu Haibo; Song Debiao; Kong Jun; Lv Junfeng; Tian Jing

2004-01-01

Objective: To evaluate the result of SPECT and CT in the patients with acute cerebral infarction and further more, to study the correlation between aphasia and dynamic change of regional cerebral blood flow (rCBF) in patients. Methods: Thirty cases with cerebral infarction of left basal ganglia were divided into two groups according to the presence or absence of aphasia; the vision and semi-ration analysis were used in photograph reading and region of interest (ROI) technology, respectively. Results: 1) Group A: there was a low rCBF in left basal ganglia, the dimension was larger than that in CT. There was also a low rCBF in frontal lobe and temporal lobe. Group B: there was only a low rCBF in left basal ganglia. 2) There were 6 cases with crossed cerebellar diaschisis (CCD) in the patients with aphasia. 3) The comparison about aphasia: the rCBF was higher in language center in the patients with improved language function than that in the patients without language function improvement and the difference between them was significant. Conclusions: The neurological function can be indirectly reflected through the study of the rCBF. At the same time, it may conduce to the locating of the damage in the central nervous system and to the differentiation diagnosis. It may also conduce to the programming of the therapeutic course and prognostication. (authors)

Comparison of the Internal Dynamics of Metalloproteases Provides New Insights on Their Function and Evolution.

Directory of Open Access Journals (Sweden)

Henrique F Carvalho

Full Text Available Metalloproteases have evolved in a vast number of biological systems, being one of the most diverse types of proteases and presenting a wide range of folds and catalytic metal ions. Given the increasing understanding of protein internal dynamics and its role in enzyme function, we are interested in assessing how the structural heterogeneity of metalloproteases translates into their dynamics. Therefore, the dynamical profile of the clan MA type protein thermolysin, derived from an Elastic Network Model of protein structure, was evaluated against those obtained from a set of experimental structures and molecular dynamics simulation trajectories. A close correspondence was obtained between modes derived from the coarse-grained model and the subspace of functionally-relevant motions observed experimentally, the later being shown to be encoded in the internal dynamics of the protein. This prompted the use of dynamics-based comparison methods that employ such coarse-grained models in a representative set of clan members, allowing for its quantitative description in terms of structural and dynamical variability. Although members show structural similarity, they nonetheless present distinct dynamical profiles, with no apparent correlation between structural and dynamical relatedness. However, previously unnoticed dynamical similarity was found between the relevant members Carboxypeptidase Pfu, Leishmanolysin, and Botulinum Neurotoxin Type A, despite sharing no structural similarity. Inspection of the respective alignments shows that dynamical similarity has a functional basis, namely the need for maintaining proper intermolecular interactions with the respective substrates. These results suggest that distinct selective pressure mechanisms act on metalloproteases at structural and dynamical levels through the course of their evolution. This work shows how new insights on metalloprotease function and evolution can be assessed with comparison schemes that

Dynamic Biological Functioning Important for Simulating and Stabilizing Ocean Biogeochemistry

Science.gov (United States)

Buchanan, P. J.; Matear, R. J.; Chase, Z.; Phipps, S. J.; Bindoff, N. L.

2018-04-01

The biogeochemistry of the ocean exerts a strong influence on the climate by modulating atmospheric greenhouse gases. In turn, ocean biogeochemistry depends on numerous physical and biological processes that change over space and time. Accurately simulating these processes is fundamental for accurately simulating the ocean's role within the climate. However, our simulation of these processes is often simplistic, despite a growing understanding of underlying biological dynamics. Here we explore how new parameterizations of biological processes affect simulated biogeochemical properties in a global ocean model. We combine 6 different physical realizations with 6 different biogeochemical parameterizations (36 unique ocean states). The biogeochemical parameterizations, all previously published, aim to more accurately represent the response of ocean biology to changing physical conditions. We make three major findings. First, oxygen, carbon, alkalinity, and phosphate fields are more sensitive to changes in the ocean's physical state. Only nitrate is more sensitive to changes in biological processes, and we suggest that assessment protocols for ocean biogeochemical models formally include the marine nitrogen cycle to assess their performance. Second, we show that dynamic variations in the production, remineralization, and stoichiometry of organic matter in response to changing environmental conditions benefit the simulation of ocean biogeochemistry. Third, dynamic biological functioning reduces the sensitivity of biogeochemical properties to physical change. Carbon and nitrogen inventories were 50% and 20% less sensitive to physical changes, respectively, in simulations that incorporated dynamic biological functioning. These results highlight the importance of a dynamic biology for ocean properties and climate.

Assessment of renal function with 99Tcm-DTPA renal dynamic imaging in neonatal hydronephrosis

International Nuclear Information System (INIS)

Jiang Lixin; Guo Zongyuan; Wu Rongde; Yu Qihai; Liu Zhanfeng

2004-01-01

Objective: To assess the renal function in neonatal hydronephrosis with 99 Tc m -DTPA renal imaging. Methods: Eighteen unilateral hydronephrotic kidneys and 12 normal kidneys were studied by 99 Tc m -DTPA renal dynamic imaging , and glomerular filtration rate (GFR) quantitative analysis was also performed. Blood urea nitrogen (BUN), serum creatinine (SCr) and hemoglobin (Hb) were determined simultaneously and the correlations between GFR and each of these parameters were analyzed. Results: Positive correlation was discovered between GFR and Hb in neonates with moderate or severe hydronephrosis (r=0.414, 0.667, P 0.05). The renal function was decreased significantly in moderate and severe neonatal hydronephrosis (P 99 Tc m -DTPA renal dynamic imaging GFR is an ideal marker for estimating renal function in neonatal hydronephrosis; SCr could be a marker for renal damage especially in moderate and severe neonatal hydronephrosis; BUN could not be a marker for evaluating renal function in neonatal hydronephrosis. Neonates with hydronephrosis should be referred for surgical procedures as soon as possible in the early stage

The Impact of Family Violence, Family Functioning, and Parental Partner Dynamics on Korean Juvenile Delinquency

Science.gov (United States)

Kim, Hyun-Sil; Kim, Hun-Soo

2008-01-01

The present study was aimed at determining the family factors related to juvenile delinquency and identifying the effect of family violence, family functioning, parental partner dynamics, and adolescents' personality on delinquent behavior among Korean adolescents. A cross-sectional study was performed using an anonymous, self-reporting…

Static, dynamic balance and functional performance in subjects with and without plantar fasciitis

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Geiseane Aguiar Gonçalves

Full Text Available Abstract Introduction: Plantar fasciitis (PF is characterized by non-inflammatory degeneration and pain under the heel, and is one of the most common foot complaints. The compensations and adjustments made to decrease the discomfort caused by the disease are clinical findings and can be a factor that contributes to impaired balance and decreased functional performance. Objective: To compare functional performance as well as static and dynamic balance among subjects with and without PF. Methods: The sample consisted of 124 subjects of both sexes aged 20-60 years. Participants were divided into two groups: a bilateral PF group (PFG; n = 62 and a control group (CG, n = 62. The following outcomes were analyzed: static and dynamic balance (using functional tests and functional performance (using a questionnaire. We used Student’s t test for independent samples to compare variables between the groups. The alpha error was set at 0.05. Results: Subjects with PF showed greater impairment in their overall dynamic balance performance (p < 0.001 than the control group, except for left posteromedial movement (p = 0.19. The CG showed showed better functional performance (p < 0.001 than the PF group. There was no difference between groups for the variable static balance on stable (p = 0.160 and unstable surfaces (p = 0.085. Conclusion: Subjects with PF displayed smaller reach distances in the overall Star Excursion Balance Test (SEBT, demonstrating a deficit in dynamic balance and functional performance when compared with healthy subjects.

Dynamic behavior and functional integrity tests on RC shear walls

International Nuclear Information System (INIS)

Akino, Kinji; Nasuda, Toshiaki; Shibata, Akenori.

1991-01-01

A project consisting of seven subprojects has been conducted to study the dynamic behavior and functional integrity of reinforced concrete (RC) shear walls in reactor buildings. The objective of this project is to obtain the data to improve and prepare the seismic analysis code regarding the nonlinear structural behavior and integrity of reactor buildings during and after earthquakes. The project started in April, 1986, and will end in March, 1994. Seven subprojects are strain rate test, damping characteristic test, ultimate state response test and the verification test for the test of restoring force characteristics regarding dynamic restoring force characteristics and damping performance; the restoring force characteristic test on the shear walls with openings; and pull-out strength test and the test on air leakage through concrete cracks regarding the functional integrity. The objectives of respective subprojects, the test models and the interim results are reported. Three subprojects have been completed by March, 1990. The results of these projects will be used for the overall evaluation. The strain rate test showed that the ultimate strength of shear walls increased with strain rate. A formula for estimating air flow through the cracks in walls was given by the leakage test. (K.I.)

Simulation of Protein Structure, Dynamics and Function in Organic Media

National Research Council Canada - National Science Library

Daggett, Valerie

1998-01-01

The overall goal of our ONR-sponsored research is to pursue realistic molecular modeling strudies pertinnent to the related properties of protein stability, dynamics, structure, function, and folding in aqueous solution...

Visualizing functional motions of membrane transporters with molecular dynamics simulations.

Science.gov (United States)

Shaikh, Saher A; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad

2013-01-29

Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.

Recoil generated radiotracers in studies of molecular dynamics

International Nuclear Information System (INIS)

Spicer, L.D.

1981-01-01

This chapter summarizes many of the contributions that the recoil technique of generating excited radiotracer atoms in the presence of a thermal environment is making to the field of chemical dynamics. Specific topics discussed critically include characterization of the generation and behavior of excited molecules including fragmentation kinetics and energy transfer, measurement of thermal and hot kinetic parameters, and studies of reaction mechanisms and stereochemistry as a function of reaction energy. Distinctive features that provide unique approaches to dynamical problems are evaluated in detail and the complementarity with more conventional techniques is addressed. Prospects for future applications are also presented

Dynamical behaviors determined by the Lyapunov function in competitive Lotka-Volterra systems

Science.gov (United States)

Tang, Ying; Yuan, Ruoshi; Ma, Yian

2013-01-01

Dynamical behaviors of the competitive Lotka-Volterra system even for 3 species are not fully understood. In this paper, we study this problem from the perspective of the Lyapunov function. We construct explicitly the Lyapunov function using three examples of the competitive Lotka-Volterra system for the whole state space: (1) the general 2-species case, (2) a 3-species model, and (3) the model of May-Leonard. The basins of attraction for these examples are demonstrated, including cases with bistability and cyclical behavior. The first two examples are the generalized gradient system, where the energy dissipation may not follow the gradient of the Lyapunov function. In addition, under a new type of stochastic interpretation, the Lyapunov function also leads to the Boltzmann-Gibbs distribution on the final steady state when multiplicative noise is added.

Dynamic changes in protein functional linkage networks revealed by integration with gene expression data.

Directory of Open Access Journals (Sweden)

Shubhada R Hegde

2008-11-01

Full Text Available Response of cells to changing environmental conditions is governed by the dynamics of intricate biomolecular interactions. It may be reasonable to assume, proteins being the dominant macromolecules that carry out routine cellular functions, that understanding the dynamics of protein:protein interactions might yield useful insights into the cellular responses. The large-scale protein interaction data sets are, however, unable to capture the changes in the profile of protein:protein interactions. In order to understand how these interactions change dynamically, we have constructed conditional protein linkages for Escherichia coli by integrating functional linkages and gene expression information. As a case study, we have chosen to analyze UV exposure in wild-type and SOS deficient E. coli at 20 minutes post irradiation. The conditional networks exhibit similar topological properties. Although the global topological properties of the networks are similar, many subtle local changes are observed, which are suggestive of the cellular response to the perturbations. Some such changes correspond to differences in the path lengths among the nodes of carbohydrate metabolism correlating with its loss in efficiency in the UV treated cells. Similarly, expression of hubs under unique conditions reflects the importance of these genes. Various centrality measures applied to the networks indicate increased importance for replication, repair, and other stress proteins for the cells under UV treatment, as anticipated. We thus propose a novel approach for studying an organism at the systems level by integrating genome-wide functional linkages and the gene expression data.

The messenger matters: Pollinator functional group influences mating system dynamics.

Science.gov (United States)

Weber, Jennifer J

2017-08-01

The incredible diversity of plant mating systems has fuelled research in evolutionary biology for over a century. Currently, there is broad concern about the impact of rapidly changing pollinator communities on plant populations. Very few studies, however, examine patterns and mechanisms associated with multiple paternity from cross-pollen loads. Often, foraging pollinators collect a mixed pollen load that may result in the deposition of pollen from different sires to receptive stigmas. Coincident deposition of self- and cross-pollen leads to interesting mating system dynamics and has been investigated in numerous species. But, mixed pollen loads often consist of a diversity of cross-pollen and result in multiple sires of seeds within a fruit. In this issue of Molecular Ecology, Rhodes, Fant, and Skogen () examine how pollinator identity and spatial isolation influence multiple paternity within fruits of a self-incompatible evening primrose. The authors demonstrate that pollen pool diversity varies between two pollinator types, hawkmoths and diurnal solitary bees. Further, progeny from more isolated plants were less likely to have multiple sires regardless of the pollinator type. Moving forward, studies of mating system dynamics should consider the implications of multiple paternity and move beyond the self- and cross-pollination paradigm. Rhodes et al. () demonstrate the importance of understanding the roles that functionally diverse pollinators play in mating system dynamics. © 2017 John Wiley & Sons Ltd.

Dynamic changes in display architecture and function across environments revealed by a systems approach to animal communication.

Science.gov (United States)

Rosenthal, Malcolm F; Wilkins, Matthew R; Shizuka, Daizaburo; Hebets, Eileen A

2018-02-20

Animal communication is often structurally complex and dynamic, with signaler and receiver behavior varying in response to multiple environmental factors. To date, studies assessing signal dynamics have mostly focused on the relationships between select signaling traits and receiver responses in a single environment. We use the wolf spider Schizocosa floridana to explore the relationships between courtship display form and function across two social contexts (female presence vs absence) and two light environments (light vs dark). We use traditional analytical methods to determine predictors of copulation success (i.e., signal function) and examine these predictors in a structural context by overlaying them on signal phenotype networks (Wilkins et al. 2015). This allows us to explore system design principles (degeneracy, redundancy, pluripotentiality), providing insight into hypotheses regarding complex signal evolution. We found that both social context and light environment affect courtship structure, although the predictors of mating success remain similar across light environments, suggesting system degeneracy. Contrastingly, the same display traits may serve different functions across social environments, suggesting pluripotentiality. Ultimately, our network approach uncovers a complexity in display structure and function that is missed by functional analyses alone, highlighting the importance of systems-based methodologies for understanding the dynamic nature of complex signals. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Dynamic Response of Functionally Graded Carbon Nanotube Reinforced Sandwich Plate

Science.gov (United States)

Mehar, Kulmani; Panda, Subrata Kumar

2018-03-01

In this article, the dynamic response of the carbon nanotube-reinforced functionally graded sandwich composite plate has been studied numerically with the help of finite element method. The face sheets of the sandwich composite plate are made of carbon nanotube- reinforced composite for two different grading patterns whereas the core phase is taken as isotropic material. The final properties of the structure are calculated using the rule of mixture. The geometrical model of the sandwich plate is developed and discretized suitably with the help of available shell element in ANSYS library. Subsequently, the corresponding numerical dynamic responses computed via batch input technique (parametric design language code in ANSYS) of ANSYS including Newmark’s integration scheme. The stability of the sandwich structural numerical model is established through the proper convergence study. Further, the reliability of the sandwich model is checked by comparison study between present and available results from references. As a final point, some numerical problems have been solved to examine the effect of different design constraints (carbon nanotube distribution pattern, core to face thickness ratio, volume fractions of the nanotube, length to thickness ratio, aspect ratio and constraints at edges) on the time-responses of sandwich plate.

Molecular dynamics study of silver

International Nuclear Information System (INIS)

Akhter, J.I.; Yaldram, K.; Ahmad, W.; Khan, M.K.; Rehman, T.S.

1995-03-01

We present results of molecular dynamics study using the embedded atom potential to examine the equilibrium bulk properties of Ag. We calculate the total energy and the lattice parameters as a function of temperature. From these we determine the specific heat and linear coefficient of thermal expansion. The comparison with experimental results of these two quantities is found to be excellent. We have also calculated the mean square displacement of the atoms in the three directions. As expected because of symmetry the displacements in the three directions are comparable and increase with increasing temperature. (author) 5 figs

Molecular dynamics simulation studies of transmembrane transport of chemical components in Chinese herbs and the function of platycodin D in a biological membrane

Directory of Open Access Journals (Sweden)

Shufang Yang

2017-04-01

Conclusion: The Martini force field was successfully applied to the study of the interaction between herbal compounds and a biological membrane. By combining the dynamics equilibrium morphology, the distribution of drugs inside and outside the biomembrane, and the interaction sites of drugs on the DPPC bilayer, factors influencing transmembrane transport of drugs were elucidated and the function of platycodin D in a biological membrane was reproduced.

Molecular dynamics simulation study of the influence of the lattice atom potential function upon atom ejection processes

International Nuclear Information System (INIS)

Harrison, D.E. Jr.; Webb, R.P.

1982-01-01

A molecular dynamics simulation has been used to investigate the sensitivity of atom ejection processes from a single-crystal target to changes in the atom-atom potential function. Four functions, three constructed from the Gibson potentials with Anderman's attractive well, and a fouth specifically developed for this investigation, were investigated in the Cu/Ar/sup +/ system over a range of ion energies from 1.0 to 10.0 kev with the KSE-B ion-atom potential. Well depths and widths also were varied. The calculations were done at normal incidence on the fcc (111) crystal orientation. Computed values were compared with experimental data where they exist. Sputtering yields, multimer yield ratios, layer yield ratios, and the ejected atom energy distribution vary systematically with the parameters of the atom-atom potential function. Calculations also were done with the modified Moliere function. Yields and other properties fall exactly into the positions predicted from the Born-Mayer function analysis. Simultaneous analysis of the ejected atom energy distribution and the ion energy dependence of the sputtering yield curve provides information about the parameters of both the wall and well portions of the atom-atom potential function

Phase Structure and Dynamics of QCD–A Functional Perspective

International Nuclear Information System (INIS)

Strodthoff, Nils

2017-01-01

The understanding of the phase structure and the fundamental properties of QCD matter from its microscopic description requires appropriate first-principle approaches. Here I review the progress towards a quantitative first-principle continuum approach within the framework of the Functional Renormalization group established by the fQCD collaboration. I focus on recent quantitative results for quenched QCD and Yang-Mills in the vacuum before addressing the calculation of dynamical quantities such as spectral functions and transport coefficients in this framework. (paper)

Concentration dynamics in lakes and reservoirs. Studies using radioactive tracers

International Nuclear Information System (INIS)

Gilath, Ch.

1983-01-01

The use of radioactive tracers for the investigation of concentration dynamics of inert soluble matter in lakes and reservoirs is reviewed. Shallow and deep stratified lakes are considered. The mechanism of mixing in lakes, flow pattern and input - output response are discussed. The methodology of the use of radioactive tracers for concentration dynamic studies is described. Examples of various investigations are reviewed. The dynamics of shallow lakes can be found and expressed in terms of transfer functions, axial dispersion models, residence time distributions and sometimes only semiquantitative information about the flow pattern. The dynamics of deep, stratified lakes is more complex and difficult to investigate with tracers. Flow pattern, horizontal and vertical eddy diffusivities, mass transfer between the hypolimnion and epilimnion are tools used for describing this dynamics. (author)

Fundamental study of dynamic ECT by dual detector gammacamera system

International Nuclear Information System (INIS)

Kakegawa, M.; Matsui, S.; Maeda, H.; Takeda, K.; Nakagawa, T.

1982-01-01

The improvement of image quality of reconstructed image by the simple pre-processing of projections is studied. Using the improved algorithm and dual detector gammacamera system, the possibility of dynamic ECT is studied. As shown in clinical examples, renal flow study using Tc-99m-DTPA, dynamic ECT imaging is possible with measuring time of 1 or 2 minutes. By this method cortex and medulla are separately imaged and each function can be analyzed more precisely. Using high sensitive collimator it will be possible to take ECT images every 30 sec. with little resolution loss quantitative three dimensional time activity analysis is under study

Improvement of a new rotation function for molecular replacement by designing new scoring functions and dynamic correlation coefficient

Science.gov (United States)

Jiang, Fan; Ding, Wei

2010-10-01

A previously published new rotation function has been improved by using a dynamic correlation coefficient as well as two new scoring functions of relative entropy and mean-square-residues to make the rotation function more robust and independent of a specific set of weights for scoring and ranking. The previously described new rotation function calculates the rotation function of molecular replacement by matching the search model directly with the Patterson vector map. The signal-to-noise ratio for the correct match was increased by averaging all the matching peaks. Several matching scores were employed to evaluate the goodness of matching. These matching scores were then combined into a single total score by optimizing a set of weights using the linear regression method. It was found that there exists an optimal set of weights that can be applied to the global rotation search and the correct solution can be ranked in the top 100 or less. However, this set of optimal weights in general is dependent on the search models and the crystal structures with different space groups and cell parameters. In this work, we try to solve this problem by designing a dynamic correlation coefficient. It is shown that the dynamic correlation coefficient works for a variety of space groups and cell parameters in the global search of rotation function. We also introduce two new matching scores: relative entropy and mean-square-residues. Last but not least, we discussed a valid method for the optimization of the adjustable parameters for matching vectors.

Improvement of a new rotation function for molecular replacement by designing new scoring functions and dynamic correlation coefficient

International Nuclear Information System (INIS)

Fan, Jiang; Wei, Ding

2010-01-01

A previously published new rotation function has been improved by using a dynamic correlation coefficient as well as two new scoring functions of relative entropy and mean-square-residues to make the rotation function more robust and independent of a specific set of weights for scoring and ranking. The previously described new rotation function calculates the rotation function of molecular replacement by matching the search model directly with the Patterson vector map. The signal-to-noise ratio for the correct match was increased by averaging all the matching peaks. Several matching scores were employed to evaluate the goodness of matching. These matching scores were then combined into a single total score by optimizing a set of weights using the linear regression method. It was found that there exists an optimal set of weights that can be applied to the global rotation search and the correct solution can be ranked in the top 100 or less. However, this set of optimal weights in general is dependent on the search models and the crystal structures with different space groups and cell parameters. In this work, we try to solve this problem by designing a dynamic correlation coefficient. It is shown that the dynamic correlation coefficient works for a variety of space groups and cell parameters in the global search of rotation function. We also introduce two new matching scores: relative entropy and mean-square-residues. Last but not least, we discussed a valid method for the optimization of the adjustable parameters for matching vectors. (condensed matter: structure, thermal and mechanical properties)

Structural, Dynamic, and Vibrational Properties during Heat Transfer in Si/Ge Superlattices: A Car-Parrinello Molecular Dynamics Study

OpenAIRE

Ji, Pengfei; Zhang, Yuwen; Yang, Mo

2016-01-01

The structural, dynamic, and vibrational properties during the heat transfer process in Si/Ge superlattices, are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) ar...

Improved non-dimensional dynamic influence function method based on tow-domain method for vibration analysis of membranes

Directory of Open Access Journals (Sweden)

SW Kang

2015-02-01

Full Text Available This article introduces an improved non-dimensional dynamic influence function method using a sub-domain method for efficiently extracting the eigenvalues and mode shapes of concave membranes with arbitrary shapes. The non-dimensional dynamic influence function method (non-dimensional dynamic influence function method, which was developed by the authors in 1999, gives highly accurate eigenvalues for membranes, plates, and acoustic cavities, compared with the finite element method. However, it needs the inefficient procedure of calculating the singularity of a system matrix in the frequency range of interest for extracting eigenvalues and mode shapes. To overcome the inefficient procedure, this article proposes a practical approach to make the system matrix equation of the concave membrane of interest into a form of algebraic eigenvalue problem. It is shown by several case studies that the proposed method has a good convergence characteristics and yields very accurate eigenvalues, compared with an exact method and finite element method (ANSYS.

Pulmonary dynamics and functional imaging with krypton-81m as related to generator delivery characteristics

International Nuclear Information System (INIS)

Kaplan, E.

1985-01-01

Krypton-81m supplied from a generator by continuous elution with air is used with a gamma-camera computer system to produce a sequence of images from multiple breaths, which reconstructed the time-activity images of the breathing human lung. Functional images are produced by subsequent derivation to show specific variables of the dynamic sequences. The dynamic, quantitative, and regional aspects of the respiratory cycle are thus made available in a single study. The need for the delivery of a constant ratio of /sub 81m/Kr to air is required to accurately produce these various studies

Exploring protein dynamics space: the dynasome as the missing link between protein structure and function.

Directory of Open Access Journals (Sweden)

Ulf Hensen

Full Text Available Proteins are usually described and classified according to amino acid sequence, structure or function. Here, we develop a minimally biased scheme to compare and classify proteins according to their internal mobility patterns. This approach is based on the notion that proteins not only fold into recurring structural motifs but might also be carrying out only a limited set of recurring mobility motifs. The complete set of these patterns, which we tentatively call the dynasome, spans a multi-dimensional space with axes, the dynasome descriptors, characterizing different aspects of protein dynamics. The unique dynamic fingerprint of each protein is represented as a vector in the dynasome space. The difference between any two vectors, consequently, gives a reliable measure of the difference between the corresponding protein dynamics. We characterize the properties of the dynasome by comparing the dynamics fingerprints obtained from molecular dynamics simulations of 112 proteins but our approach is, in principle, not restricted to any specific source of data of protein dynamics. We conclude that: 1. the dynasome consists of a continuum of proteins, rather than well separated classes. 2. For the majority of proteins we observe strong correlations between structure and dynamics. 3. Proteins with similar function carry out similar dynamics, which suggests a new method to improve protein function annotation based on protein dynamics.

Functional Apparent Moduli (FAMs) as Predictors of Oral Implant Osseointegration Dynamics

OpenAIRE

Chang, Po-Chun; Seol, Yang-Jo; Kikuchi, Noboru; Goldstein, Steven A.; Giannobile, William V.

2010-01-01

At present, limited functional data exists regarding the application and use of biomechanical and imaging technologies for oral implant osseointegration assessment. The objective of this investigation was to determine the functional apparent moduli (FAMs) that could predict the dynamics of oral implant osseointegration. Using an in vivo dental implant osseous healing model, two FAMs, functional bone apparent modulus (FBAM) and composite tissue apparent modulus (FCAM), of the selected peri-imp...

Chronnectome fingerprinting: Identifying individuals and predicting higher cognitive functions using dynamic brain connectivity patterns.

Science.gov (United States)

Liu, Jin; Liao, Xuhong; Xia, Mingrui; He, Yong

2018-02-01

The human brain is a large, interacting dynamic network, and its architecture of coupling among brain regions varies across time (termed the "chronnectome"). However, very little is known about whether and how the dynamic properties of the chronnectome can characterize individual uniqueness, such as identifying individuals as a "fingerprint" of the brain. Here, we employed multiband resting-state functional magnetic resonance imaging data from the Human Connectome Project (N = 105) and a sliding time-window dynamic network analysis approach to systematically examine individual time-varying properties of the chronnectome. We revealed stable and remarkable individual variability in three dynamic characteristics of brain connectivity (i.e., strength, stability, and variability), which was mainly distributed in three higher order cognitive systems (i.e., default mode, dorsal attention, and fronto-parietal) and in two primary systems (i.e., visual and sensorimotor). Intriguingly, the spatial patterns of these dynamic characteristics of brain connectivity could successfully identify individuals with high accuracy and could further significantly predict individual higher cognitive performance (e.g., fluid intelligence and executive function), which was primarily contributed by the higher order cognitive systems. Together, our findings highlight that the chronnectome captures inherent functional dynamics of individual brain networks and provides implications for individualized characterization of health and disease. © 2017 Wiley Periodicals, Inc.

Vibrational signatures of cation-anion hydrogen bonding in ionic liquids: a periodic density functional theory and molecular dynamics study.

Science.gov (United States)

Mondal, Anirban; Balasubramanian, Sundaram

2015-02-05

Hydrogen bonding in alkylammonium based protic ionic liquids was studied using density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations. Normal-mode analysis within the harmonic approximation and power spectra of velocity autocorrelation functions were used as tools to obtain the vibrational spectra in both the gas phase and the crystalline phases of these protic ionic liquids. The hydrogen bond vibrational modes were identified in the 150-240 cm(-1) region of the far-infrared (far-IR) spectra. A blue shift in the far-IR mode was observed with an increasing number of hydrogen-bonding sites on the cation; the exact peak position is modulated by the cation-anion hydrogen bond strength. Sub-100 cm(-1) bands in the far-IR spectrum are assigned to the rattling motion of the anions. Calculated NMR chemical shifts of the acidic protons in the crystalline phase of these salts also exhibit the signature of cation-anion hydrogen bonding.

Kinesin-8 effects on mitotic microtubule dynamics contribute to spindle function in fission yeast

Science.gov (United States)

Gergely, Zachary R.; Crapo, Ammon; Hough, Loren E.; McIntosh, J. Richard; Betterton, Meredith D.

2016-01-01

Kinesin-8 motor proteins destabilize microtubules. Their absence during cell division is associated with disorganized mitotic chromosome movements and chromosome loss. Despite recent work studying effects of kinesin-8s on microtubule dynamics, it remains unclear whether the kinesin-8 mitotic phenotypes are consequences of their effect on microtubule dynamics, their well-established motor activity, or additional, unknown functions. To better understand the role of kinesin-8 proteins in mitosis, we studied the effects of deletion of the fission yeast kinesin-8 proteins Klp5 and Klp6 on chromosome movements and spindle length dynamics. Aberrant microtubule-driven kinetochore pushing movements and tripolar mitotic spindles occurred in cells lacking Klp5 but not Klp6. Kinesin-8–deletion strains showed large fluctuations in metaphase spindle length, suggesting a disruption of spindle length stabilization. Comparison of our results from light microscopy with a mathematical model suggests that kinesin-8–induced effects on microtubule dynamics, kinetochore attachment stability, and sliding force in the spindle can explain the aberrant chromosome movements and spindle length fluctuations seen. PMID:27146110

Construction of a fuel demand function portraying inter-fuel substitution, a system dynamics approach

International Nuclear Information System (INIS)

Abada, Ibrahim; Briat, Vincent; Massol, Olivier

2011-04-01

Most of the recent numerical market equilibrium models of natural gas markets use imperfect competition assumptions. These models are typically embedded with an oversimplified representation of the demand side, usually a single-variable affine function, that does not capture any dynamic adjustment to past prices. To remedy this, we report an effort to construct an enhanced functional specification using the system dynamics-based model of Moxnes (1987, 1990). Thanks to a vintage representation of capital stock, this putty-clay model captures the effect of both past and current energy prices on fuel consumption. Using a re-calibrated version of this model, we first confirm the pertinence of this modeling framework to represent inter-fuel substitutions at different fuel prices in the industrial sector. Building on these findings, a dynamic functional specification of the demand function for natural gas is then proposed and calibrated. (authors)

Dynamic Aperture Studies for the FCC-ee

CERN Document Server

Medina, L; Tomas, R; Zimmermann, F

2015-01-01

Dynamic aperture (DA) studies have been conducted on the latest Future Circular Collider – ee (FCC-ee) lattices as a function of momentum deviation.Two different schemes for the interaction region are used, which are connected to the main arcs: the crab waist approach, developed by BINP, and an update to the CERN design where the use of crab cavities is envisioned. The results presented show an improvement in the performance of both designs.

Functional dynamic factor models with application to yield curve forecasting

KAUST Repository

Hays, Spencer; Shen, Haipeng; Huang, Jianhua Z.

2012-01-01

resulted in a trade-off between goodness of fit and consistency with economic theory. To address this, herein we propose a novel formulation which connects the dynamic factor model (DFM) framework with concepts from functional data analysis: a DFM

The Functional Programming Language R and the Paradigm of Dynamic Scientific Programming

NARCIS (Netherlands)

Trancón y Widemann, B.; Bolz, C.F.; Grelck, C.; Loidl, H.-W.; Peña, R.

2013-01-01

R is an environment and functional programming language for statistical data analysis and visualization. Largely unknown to the functional programming community, it is popular and influential in many empirical sciences. Due to its integrated combination of dynamic and reflective scripting on one

Molecular dynamics studies of actinide nitrides

International Nuclear Information System (INIS)

Kurosaki, Ken; Uno, Masayoshi; Yamanaka, Shinsuke; Minato, Kazuo

2004-01-01

The molecular dynamics (MD) calculation was performed for actinide nitrides (UN, NpN, and PuN) in the temperature range from 300 to 2800 K to evaluate the physical properties viz., the lattice parameter, thermal expansion coefficient, compressibility, and heat capacity. The Morse-type potential function added to the Busing-Ida type potential was employed for the ionic interactions. The interatomic potential parameters were determined by fitting to the experimental data of the lattice parameter. The usefulness and applicability of the MD method to evaluate the physical properties of actinide nitrides were studied. (author)

New experimental possibilities for the study of the molecular structure and the dynamics of liquids

International Nuclear Information System (INIS)

Versmold, H.

1981-01-01

The general space-time-pair distribution function G(Rsub(A)(0), Ωsub(A)(0), Rsub(B)(t), Ωsub(B)(t) plays an important role for the theoretical description of liquids. In this report first the relationship between the space-time-pair distribution function and static pair distribution functions, which characterize the liquid structure, and time correlation functions, which can be used to comprehend the dynamics of liquids, will be introduced. As an experimental method, which is particularly suited to determine the static pair distribution function, coherent neutron scattering is discussed. The power of this method for the determination of the liquid structure is demonstrated by considering the examples of a fused salt and a molecular liquid. For investigations of the dynamics of liquids incoherent neutron scattering and several spectroscopic experiments have been in use during the last few years. The relationship between these experiments and time correlation functions is presented. A discussion concerning the possibility to study translational and rotational dynamics by incoherent neutron scattering follows. Finally, by referring to a depolarized Rayleigh experiment, the relationship between spectroscopic experiments and orientational correlation functions, which describe the reorientational dynamics in liquids, is illustrated. (orig.)

An experimental study on renal functional disturbance in rabbits after acute ureteral obstruction with dynamic Gd-DTPA enhanced MR imaging

Energy Technology Data Exchange (ETDEWEB)

Shin, Kyoung Ja [Seoul Red Cross Hospital, Seoul (Korea, Republic of); Chung, Eun Chul; Rlee, Chung Sik [Ewha Womans University College of Medicine, Seoul (Korea, Republic of)

1994-05-15

To evaluate the anatomic and functional change in acutely obstructed kidneys, and probability of functional recovery after resolving the obstruction. There were 5 animal groups (6 rabbits in each group)-normal control group, 4 acute ureteral obstruction group. Each of the latter group was imaged with Gd-DTPA enhanced dynamic MR 2, 6, 24, and 48 hours after ligation of the left proximal urter, respectively. We compared the findings of dynamic MR imaging and histopathological findings. We could observe centripetal movement of dark band pattern which could be defined as 3 phases renal cortex, outer medulla, and inner medulla in normal rabbits. The appearance of the dark band pattern was delayed or absent in ureteral obstruction group with linear relationship to the duration of the obstruction. Gd-DTPA enhanced MR can be used to differentiate acute obstructive nephropathy from other causes of nephropathy and foretell the prognosis of the obstruction.

An experimental study on renal functional disturbance in rabbits after acute ureteral obstruction with dynamic Gd-DTPA enhanced MR imaging

International Nuclear Information System (INIS)

Shin, Kyoung Ja; Chung, Eun Chul; Rlee, Chung Sik

1994-01-01

To evaluate the anatomic and functional change in acutely obstructed kidneys, and probability of functional recovery after resolving the obstruction. There were 5 animal groups (6 rabbits in each group)-normal control group, 4 acute ureteral obstruction group. Each of the latter group was imaged with Gd-DTPA enhanced dynamic MR 2, 6, 24, and 48 hours after ligation of the left proximal urter, respectively. We compared the findings of dynamic MR imaging and histopathological findings. We could observe centripetal movement of dark band pattern which could be defined as 3 phases renal cortex, outer medulla, and inner medulla in normal rabbits. The appearance of the dark band pattern was delayed or absent in ureteral obstruction group with linear relationship to the duration of the obstruction. Gd-DTPA enhanced MR can be used to differentiate acute obstructive nephropathy from other causes of nephropathy and foretell the prognosis of the obstruction

Proton structure functions in the dipole picture of BFKL dynamics

International Nuclear Information System (INIS)

Navelet, H.; Peschanski, R.; Wallon, S.; Royon, Ch.

1996-06-01

The proton structure functions are derived in the QCD dipole picture. Assuming k T and renormalization-group factorization, deep-inelastic proton scattering is related to deep-inelastic onium scattering. A three parameter fit of the 1994 H1 data in the low-x, moderate Q 2 range has been obtained. The dipole picture of BFKL dynamics is shown to provide a relevant model for quantitatively describing the proton structure functions at HERA. (author)

Investigation of dynamic fracture behavior in functionally graded materials

International Nuclear Information System (INIS)

Yang, X B; Qin, Y P; Zhuang, Z; You, X C

2008-01-01

The fast running crack in functionally graded materials (FGMs) is investigated through numerical simulations under impact loading. Some fracture characterizations such as crack propagation and arrest are evaluated by the criterion of the crack tip opening angle. Based on the experimental results, the whole propagation process of the fast running crack is simulated by the finite element program. Thus, the dynamic fracture parameters can be obtained during the crack growing process. In this paper, the crack direction is assumed to be the graded direction of the materials, and the property gradation in FGMs is considered by varying the elastic modulus exponentially along the graded direction and keeping the mass density and Poisson's ratio constant. The influences of the non-homogeneity, the loading ratio and the crack propagation speed on the dynamic fracture response of FGMs are analyzed through the test and numerical analysis. Considering the potential application of FGMs in natural-gas transmission engineering, a functionally graded pipeline is designed to arrest the fast running crack for a short period in high pressure large diameter natural-gas pipelines

Application of generalized function to dynamic analysis of thick plates

International Nuclear Information System (INIS)

Zheng, D.; Weng, Z.

1987-01-01

The structures with thick plates have been used extensively in national defence, mechanical engineering, chemical engineering, nuclear engineering, civil engineering, etc.. Various theories have been established to deal with the problems of elastic plates, which include the classical theory of thin plates, the improved theory of thick plates, three-dimensional elastical theory. In this paper, the derivative of δ-function is handled by using the generalized function. The dynamic analysis of thick plates subjected the concentrated load is presented. The improved Donnell's equation of thick plates is deduced and employed as the basic equation. The generalized coordinates are solved by using the method of MWR. The general expressions for the dynamic response of elastic thick plates subjected the concentrated load are given. The numerical results for rectangular plates are given herein. The results are compared with those obtained from the improved theory and the classical theory of plates. (orig./GL)

The interplay between dynamic heterogeneities and structure of bulk liquid water: A molecular dynamics simulation study

Energy Technology Data Exchange (ETDEWEB)

Demontis, Pierfranco; Suffritti, Giuseppe B. [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Gulín-González, Jorge [Grupo de Matemática y Física Computacionales, Universidad de las Ciencias Informáticas (UCI), Carretera a San Antonio de los Baños, Km 21/2, La Lisa, La Habana (Cuba); Masia, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Istituto Officina dei Materiali del CNR, UOS SLACS, Via Vienna 2, 07100 Sassari (Italy); Sant, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy)

2015-06-28

In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130–350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics. In particular, for temperatures higher than that of the dynamic crossover between “fragile” (at higher temperatures) and “strong” (at lower temperatures) liquid behaviors detected around 207 K, the rotational relaxation of supercooled water appears to be remarkably homogeneous. However, the structural parameters (number of NNs and of HBs, as well as q) do not show homogeneous distributions, and these distributions are different for the two water models. Another dynamic crossover between “fragile” (at lower temperatures) and “strong” (at higher temperatures) liquid behaviors, corresponding to the one found experimentally at T{sup ∗} ∼ 315 ± 5 K, was spotted at T{sup ∗} ∼ 283 K and T{sup ∗} ∼ 276 K for the TIP4P-Ew and the model developed in this laboratory, respectively. It was detected from the trend of Arrhenius plots of dynamic quantities and from the onset of a further heterogeneity in the rotational relaxation. To our best knowledge, it is the first time that this dynamical crossover is detected in computer simulations of bulk water. On the basis of the simulation results, the possible

Dynamic function MR of the cervical vertebral column. Dynamische Funktions-MRT der Halswirbelsaeule

Energy Technology Data Exchange (ETDEWEB)

Naegele, M.; Woell, B.; Reiser, M. (Radiologische Universitaetsklinik, Bonn (Germany)); Koch, W. (Orthopaedische Universitaetsklinik, Bonn (Germany)); Kaden, B. (Neurochirurgische Universitaetsklinik, Bonn (Germany))

1992-09-01

To obtain functional studies of the cervical spine, a device has been developed which allows MRI examinations to be carried out in five different degrees of flexion. T[sub 1] and T[sub 2][sup *] weighted FFE sequences were used. Dynamic functional MRI was performed on 5 normals and 31 patients (5 disc herniation, 4 whiplash injuries, 6 spinal canal stenoses, 14 laminectomies and spinal fusions, 2 rheumatoid arthritis). The relationship of the spinal cord to the bony and ligamentous components in different degrees of flexion was particularly well shown in whiplash injury, spinal stenosis and postoperative situations. (orig.).

Methodology to Support Dynamic Function Allocation Policies Between Humans and Flight Deck Automation

Science.gov (United States)

Johnson, Eric N.

2012-01-01

Function allocation assigns work functions to all agents in a team, both human and automation. Efforts to guide function allocation systematically have been studied in many fields such as engineering, human factors, team and organization design, management science, cognitive systems engineering. Each field focuses on certain aspects of function allocation, but not all; thus, an independent discussion of each does not address all necessary aspects of function allocation. Four distinctive perspectives have emerged from this comprehensive review of literature on those fields: the technology-centered, human-centered, team-oriented, and work-oriented perspectives. Each perspective focuses on different aspects of function allocation: capabilities and characteristics of agents (automation or human), structure and strategy of a team, and work structure and environment. This report offers eight issues with function allocation that can be used to assess the extent to which each of issues exist on a given function allocation. A modeling framework using formal models and simulation was developed to model work as described by the environment, agents, their inherent dynamics, and relationships among them. Finally, to validate the framework and metrics, a case study modeled four different function allocations between a pilot and flight deck automation during the arrival and approach phases of flight.

Direct assignment of molecular vibrations via normal mode analysis of the neutron dynamic pair distribution function technique

International Nuclear Information System (INIS)

Fry-Petit, A. M.; Sheckelton, J. P.; McQueen, T. M.; Rebola, A. F.; Fennie, C. J.; Mourigal, M.; Valentine, M.; Drichko, N.

2015-01-01

For over a century, vibrational spectroscopy has enhanced the study of materials. Yet, assignment of particular molecular motions to vibrational excitations has relied on indirect methods. Here, we demonstrate that applying group theoretical methods to the dynamic pair distribution function analysis of neutron scattering data provides direct access to the individual atomic displacements responsible for these excitations. Applied to the molecule-based frustrated magnet with a potential magnetic valence-bond state, LiZn 2 Mo 3 O 8 , this approach allows direct assignment of the constrained rotational mode of Mo 3 O 13 clusters and internal modes of MoO 6 polyhedra. We anticipate that coupling this well known data analysis technique with dynamic pair distribution function analysis will have broad application in connecting structural dynamics to physical properties in a wide range of molecular and solid state systems

Dynamic Studies with Radioisotopes in Medicine. Proceedings of the Symposium on Dynamics Studies with Radioisotopes in Clinical Medicine and Research

International Nuclear Information System (INIS)

1971-01-01

Observations on the temporal patterns of uptake, metabolism, clearance or excretion of administered radioactive materials form the basis of many important applications of radioisotopes in clinical medicine and research. Such applications include studies of organ function, of regional blood flow and of the turnover of various substances in the human body. Newly available radioisotopes, new instruments such as gamma came ras, new techniques and new methods of data analysis based on the use of analogue and digital computers are continually enlarging the scope of the applications. Progress in these matters was discussed at the Symposium on Dynamic Studies with Radioisotopes in Clinical Medicine and Research, organized by the lnternational Atomic Energy Agency and held in Rotterdam, The Netherlands, from 31 August to 4 September 1970. A total of 315 participants nominated by 39 countries and 4 international organizations attended, and the 70 papers presented cove r the theoretical aspects of dynamic studies, the development of techniques and instruments for such studies, and specific applications in studies of thyroid, renal, hepatic and splenic function, mineral metabolism, regional blood flow, and cardiac and pulmonary function. The proceedings include the full texts of all the papers presented together with the edited discussions. Invited review papers deal with the general aspects of the various main groups of applications covered. Many of the applications described have already reached the stage of routine use; others are still in the developmental stage. Of particular note in the latter connection are applications based on the quantitative analysis of scintillation camera data. The many papers presented on these topics and the ensuing discussions indicate the great interest now shown in this promising area of development. It is hoped that the proceedings will provide a valuable guide to the present status of the subject

Hash function construction using weighted complex dynamical networks

International Nuclear Information System (INIS)

Song Yu-Rong; Jiang Guo-Ping

2013-01-01

A novel scheme to construct a hash function based on a weighted complex dynamical network (WCDN) generated from an original message is proposed in this paper. First, the original message is divided into blocks. Then, each block is divided into components, and the nodes and weighted edges are well defined from these components and their relations. Namely, the WCDN closely related to the original message is established. Furthermore, the node dynamics of the WCDN are chosen as a chaotic map. After chaotic iterations, quantization and exclusive-or operations, the fixed-length hash value is obtained. This scheme has the property that any tiny change in message can be diffused rapidly through the WCDN, leading to very different hash values. Analysis and simulation show that the scheme possesses good statistical properties, excellent confusion and diffusion, strong collision resistance and high efficiency. (general)

Sea Surface Temperature Modeling using Radial Basis Function Networks With a Dynamically Weighted Particle Filter

KAUST Repository

Ryu, Duchwan; Liang, Faming; Mallick, Bani K.

2013-01-01

be modeled by a dynamic system which changes with time and location. In this article, we propose a radial basis function network-based dynamic model which is able to catch the nonlinearity of the data and propose to use the dynamically weighted particle

A modular open platform for systematic functional studies under physiological conditions

Science.gov (United States)

Mulholland, Christopher B.; Smets, Martha; Schmidtmann, Elisabeth; Leidescher, Susanne; Markaki, Yolanda; Hofweber, Mario; Qin, Weihua; Manzo, Massimiliano; Kremmer, Elisabeth; Thanisch, Katharina; Bauer, Christina; Rombaut, Pascaline; Herzog, Franz; Leonhardt, Heinrich; Bultmann, Sebastian

2015-01-01

Any profound comprehension of gene function requires detailed information about the subcellular localization, molecular interactions and spatio-temporal dynamics of gene products. We developed a multifunctional integrase (MIN) tag for rapid and versatile genome engineering that serves not only as a genetic entry site for the Bxb1 integrase but also as a novel epitope tag for standardized detection and precipitation. For the systematic study of epigenetic factors, including Dnmt1, Dnmt3a, Dnmt3b, Tet1, Tet2, Tet3 and Uhrf1, we generated MIN-tagged embryonic stem cell lines and created a toolbox of prefabricated modules that can be integrated via Bxb1-mediated recombination. We used these functional modules to study protein interactions and their spatio-temporal dynamics as well as gene expression and specific mutations during cellular differentiation and in response to external stimuli. Our genome engineering strategy provides a versatile open platform for efficient generation of multiple isogenic cell lines to study gene function under physiological conditions. PMID:26007658

Application of Solution NMR Spectroscopy to Study Protein Dynamics

Directory of Open Access Journals (Sweden)

Christoph Göbl

2012-03-01

Full Text Available Recent advances in spectroscopic methods allow the identification of minute fluctuations in a protein structure. These dynamic properties have been identified as keys to some biological processes. The consequences of this structural flexibility can be far‑reaching and they add a new dimension to the structure-function relationship of biomolecules. Nuclear Magnetic Resonance (NMR spectroscopy allows the study of structure as well as dynamics of biomolecules in a very broad range of timescales at atomic level. A number of new NMR methods have been developed recently to allow the measurements of time scales and spatial fluctuations, which in turn provide the thermodynamics associated with the biological processes. Since NMR parameters reflect ensemble measurements, structural ensemble approaches in analyzing NMR data have also been developed. These new methods in some instances can even highlight previously hidden conformational features of the biomolecules. In this review we describe several solution NMR methods to study protein dynamics and discuss their impact on important biological processes.

Aging effects on airflow dynamics and lung function in human bronchioles.

Science.gov (United States)

Kim, JongWon; Heise, Rebecca L; Reynolds, Angela M; Pidaparti, Ramana M

2017-01-01

The mortality rate for patients requiring mechanical ventilation is about 35% and this rate increases to about 53% for the elderly. In general, with increasing age, the dynamic lung function and respiratory mechanics are compromised, and several experiments are being conducted to estimate these changes and understand the underlying mechanisms to better treat elderly patients. Human tracheobronchial (G1 ~ G9), bronchioles (G10 ~ G22) and alveolar sacs (G23) geometric models were developed based on reported anatomical dimensions for a 50 and an 80-year-old subject. The aged model was developed by altering the geometry and material properties of the model developed for the 50-year-old. Computational simulations using coupled fluid-solid analysis were performed for geometric models of bronchioles and alveolar sacs under mechanical ventilation to estimate the airflow and lung function characteristics. The airway mechanical characteristics decreased with aging, specifically a 38% pressure drop was observed for the 80-year-old as compared to the 50-year-old. The shear stress on airway walls increased with aging and the highest shear stress was observed in the 80-year-old during inhalation. A 50% increase in peak strain was observed for the 80-year-old as compared to the 50-year-old during exhalation. The simulation results indicate that there is a 41% increase in lung compliance and a 35%-50% change in airway mechanical characteristics for the 80-year-old in comparison to the 50-year-old. Overall, the airway mechanical characteristics as well as lung function are compromised due to aging. Our study demonstrates and quantifies the effects of aging on the airflow dynamics and lung capacity. These changes in the aging lung are important considerations for mechanical ventilation parameters in elderly patients. Realistic geometry and material properties need to be included in the computational models in future studies.

Nonadiabatic Dynamics in Single-Electron Tunneling Devices with Time-Dependent Density-Functional Theory

Science.gov (United States)

Dittmann, Niklas; Splettstoesser, Janine; Helbig, Nicole

2018-04-01

We simulate the dynamics of a single-electron source, modeled as a quantum dot with on-site Coulomb interaction and tunnel coupling to an adjacent lead in time-dependent density-functional theory. Based on this system, we develop a time-nonlocal exchange-correlation potential by exploiting analogies with quantum-transport theory. The time nonlocality manifests itself in a dynamical potential step. We explicitly link the time evolution of the dynamical step to physical relaxation timescales of the electron dynamics. Finally, we discuss prospects for simulations of larger mesoscopic systems.

Functioning islet cell tumor of the pancreas. Localization with dynamic spiral CT

International Nuclear Information System (INIS)

Chung, M.J.; Choi, B.I.; Han, J.K.; Chung, J.W.; Han, M.C.; Bae, S.H.

1997-01-01

Purpose: The purpose of this study was to evaluate the usefulness of dynamic spiral CT, including multidimensional reformation, in the detection and localization of islet cell tumors of the pancreas. Material and Methods: Seven patients with histopathologically proven functioning islet cell tumors of the pancreas were studied with 2-phase contrast-enhanced spiral CT. Scanning of the arterial phase and late phase was started 30 s and 180 s, respectively, after injection of 100 ml of contrast medium at a rate of 3 ml/s. Results: Axial images in the arterial phase depicted the lesions in 5 patients, but in the late phase in only one patient. Multiplanar reformatted images of the arterial phase depicted the lesions in all 7 patients. Maximal intensity projection images demonstrated all lesions with information of their relationship to the vascular structure. Conclusion: Dynamic spiral CT with scanning during the arterial phase and retrospective multidimensional reformation is useful for preoperative detection and localization of small islet cell tumors of the pancreas. (orig.)

Instantons: Dynamical mass generation, chiral ward identities and the topological charge correlation function

International Nuclear Information System (INIS)

McDougall, N.A.

1983-01-01

When dynamical mass generation resulting from the breakdown of chiral symmetry is taken into account, instanton dynamics treated within the dilute gas approximation may satisfy the constraints on the quark condensates and the topological charge correlation function derived by Crewther from an analysis of the chiral Ward identities assuming the absence of a physical axial U(1) Goldstone boson. From a consideration of the contribution of the eta' to the topological charge correlation function, a relationship is derived in which msub(eta') 2 fsub(eta') 2 is proportional to the vacuum energy density. (orig.)

Molecular dynamics study of dynamic and structural properties of supercooled liquid and glassy iron in the rapid-cooling processes

Energy Technology Data Exchange (ETDEWEB)

Cao, Qi-Long; Huang, Duo-Hui; Yang, Jun-Sheng; Wan, Min-Jie; Wang, Fan-Hou, E-mail: eatonch@gmail.com

2014-10-01

Molecular dynamics simulations were applied to study the dynamic and structural properties of supercooled liquid and glassy iron in the rapid-cooling processes. The mean-square displacement and the non-Gaussian parameter were used to describe the dynamic properties. The evolution of structural properties was investigated using the pair distribution functions and bond-angle distribution functions. Results for dynamic and structural relaxations indicate that the dynamic features are consistently correlated with the structure evolution, and there are three temperature regions as the temperature decreases: (1) at higher temperatures (1500 K, 1300 K, and 1100 K), the system remains in the liquid characteristics during the overall relaxation process. (2) At medial temperatures (1050 K, 900 K, and 700 K), a fast β-relaxation is followed by a much slower α-relaxation. There is a little change in the structural properties in the β-relaxation region, while major configuration rearrangements occurred in the α-relaxation range and the crystallization process was completed at the end of α-relaxation region. (3) At lower temperature (500 K), the system shows glassy characteristics during the overall relaxation process. In addition, the melting temperature, glass transition temperature and diffusion coefficients of supercooled liquid iron are also computed.

Watching proteins function with picosecond X-ray crystallography and molecular dynamics simulations.

Science.gov (United States)

Anfinrud, Philip

2006-03-01

Time-resolved electron density maps of myoglobin, a ligand-binding heme protein, have been stitched together into movies that unveil with molecular dynamics (MD) calculations and picosecond time-resolved X-ray structures provides single-molecule insights into mechanisms of protein function. Ensemble-averaged MD simulations of the L29F mutant of myoglobin following ligand dissociation reproduce the direction, amplitude, and timescales of crystallographically-determined structural changes. This close agreement with experiments at comparable resolution in space and time validates the individual MD trajectories, which identify and structurally characterize a conformational switch that directs dissociated ligands to one of two nearby protein cavities. This unique combination of simulation and experiment unveils functional protein motions and illustrates at an atomic level relationships among protein structure, dynamics, and function. In collaboration with Friedrich Schotte and Gerhard Hummer, NIH.

Nonequilibrium self-energy functional theory. Accessing the real-time dynamics of strongly correlated fermionic lattice systems

Energy Technology Data Exchange (ETDEWEB)

Hofmann, Felix

2016-07-05

The self-energy functional theory (SFT) is extended to the nonequilibrium case and applied to the real-time dynamics of strongly correlated lattice-fermions. Exploiting the basic structure of the well established equilibrium theory the entire formalism is reformulated in the language of Keldysh-Matsubara Green's functions. To this end, a functional of general nonequilibrium self-energies is constructed which is stationary at the physical point where it moreover yields the physical grand potential of the initial thermal state. Nonperturbative approximations to the full self-energy can be constructed by reducing the original lattice problem to smaller reference systems and varying the functional on the space of the respective trial self-energies, which are parametrized by the reference system's one-particle parameters. Approximations constructed in this way can be shown to respect the macroscopic conservation laws related to the underlying symmetries of the original lattice model. Assuming thermal equilibrium, the original SFT is recovered from the extended formalism. However, in the general case, the nonequilibrium variational principle comprises functional derivatives off the physical parameter space. These can be carried out analytically to derive inherently causal conditional equations for the optimal physical parameters of the reference system and a computationally realizable propagation scheme is set up. As a benchmark for the numerical implementation the variational cluster approach is applied to the dynamics of a dimerized Hubbard model after fast ramps of its hopping parameters. Finally, the time-evolution of a homogeneous Hubbard model after sudden quenches and ramps of the interaction parameter is studied by means of a dynamical impurity approximation with a single bath site. Sharply separated by a critical interaction at which fast relaxation to a thermal final state is observed, two differing response regimes can be distinguished, where the

From dynamics to structure and function of model biomolecular systems

NARCIS (Netherlands)

Fontaine-Vive-Curtaz, F.

2007-01-01

The purpose of this thesis was to extend recent works on structure and dynamics of hydrogen bonded crystals to model biomolecular systems and biological processes. The tools that we have used are neutron scattering (NS) and density functional theory (DFT) and force field (FF) based simulation

Dynamical correlation functions of the quadratic coupling spin-Boson model

Science.gov (United States)

Zheng, Da-Chuan; Tong, Ning-Hua

2017-06-01

The spin-boson model with quadratic coupling is studied using the bosonic numerical renormalization group method. We focus on the dynamical auto-correlation functions {C}O(ω ), with the operator \\hat{O} taken as {\\hat{{{σ }}}}x, {\\hat{{{σ }}}}z, and \\hat{X}, respectively. In the weak-coupling regime α qualitatively, showing enhanced dephasing at the spin flip point. Project supported by the National Key Basic Research Program of China (Grant No. 2012CB921704), the National Natural Science Foundation of China (Grant No. 11374362), the Fundamental Research Funds for the Central Universities, China, and the Research Funds of Renmin University of China (Grant No. 15XNLQ03).

Allee’s dynamics and bifurcation structures in von Bertalanffy’s population size functions

Science.gov (United States)

Leonel Rocha, J.; Taha, Abdel-Kaddous; Fournier-Prunaret, D.

2018-03-01

The interest and the relevance of the study of the population dynamics and the extinction phenomenon are our main motivation to investigate the induction of Allee Effect in von Bertalanffy’s population size functions. The adjustment or correction factor of rational type introduced allows us to analyze simultaneously strong and weak Allee’s functions and functions with no Allee effect, whose classification is dependent on the stability of the fixed point x = 0. This classification is founded on the concepts of strong and weak Allee’s effects to the population growth rates associated. The transition from strong Allee effect to no Allee effect, passing through the weak Allee effect, is verified with the evolution of the rarefaction critical density or Allee’s limit. The existence of cusp points on a fold bifurcation curve is related to this phenomenon of transition on Allee’s dynamics. Moreover, the “foliated” structure of the parameter plane considered is also explained, with respect to the evolution of the Allee limit. The bifurcation analysis is based on the configurations of fold and flip bifurcation curves. The chaotic semistability and the nonadmissibility bifurcation curves are proposed to this family of 1D maps, which allow us to define and characterize the corresponding Allee effect region.

Effects of dynamic aspects on fusion excitation functions

International Nuclear Information System (INIS)

Hassan, G.S.

2008-01-01

As an extension of the macroscopic theory, the nucleus- nucleus fusion has been described in terms of the chaotic regime dynamics (liquid drop potential energy plus one body dissipation).Three milestone configurations are attended : the touching , the conditional saddle point and the unconditional saddle one. We would like to deduce the associated extra push and extra-extra push energy values required to carry the system between these configurations, respectively. The next step is to light on the effect of these limiting values on the fusion excitation functions and their significance for accurate fitting of the measured functions for larger values of the angular momentum. It is found that there is a limiting values of excitation energy and angular momentum for each interacting pair, over which these aspects must be considered to fit the excitation functions of different nucleus nucleus fusion .These values were found to be in relation with the limiting angular momentum for fusion in major cases

First passage Brownian functional properties of snowmelt dynamics

Science.gov (United States)

Dubey, Ashutosh; Bandyopadhyay, Malay

2018-04-01

In this paper, we model snow-melt dynamics in terms of a Brownian motion (BM) with purely time dependent drift and difusion and examine its first passage properties by suggesting and examining several Brownian functionals which characterize the lifetime and reactivity of such stochastic processes. We introduce several probability distribution functions (PDFs) associated with such time dependent BMs. For instance, for a BM with initial starting point x0, we derive analytical expressions for : (i) the PDF P(tf|x0) of the first passage time tf which specify the lifetime of such stochastic process, (ii) the PDF P(A|x0) of the area A till the first passage time and it provides us numerous valuable information about the total fresh water availability during melting, (iii) the PDF P(M) associated with the maximum size M of the BM process before the first passage time, and (iv) the joint PDF P(M; tm) of the maximum size M and its occurrence time tm before the first passage time. These P(M) and P(M; tm) are useful in determining the time of maximum fresh water availability and in calculating the total maximum amount of available fresh water. These PDFs are examined for the power law time dependent drift and diffusion which matches quite well with the available data of snowmelt dynamics.

A comparative study of density functional and density functional tight binding calculations of defects in graphene

Energy Technology Data Exchange (ETDEWEB)

Zobelli, Alberto [Laboratoire de Physique des Solides, Univ. Paris Sud, CNRS UMR, Orsay (France); Ivanovskaya, Viktoria; Wagner, Philipp; Yaya, Abu; Ewels, Chris P. [Institut des Materiaux Jean Rouxel (IMN), CNRS UMR, University of Nantes (France); Suarez-Martinez, Irene [Nanochemistry Research Institute, Curtin University of Technology, Perth, Western Australia (Australia)

2012-02-15

The density functional tight binding approach (DFTB) is well adapted for the study of point and line defects in graphene based systems. After briefly reviewing the use of DFTB in this area, we present a comparative study of defect structures, energies, and dynamics between DFTB results obtained using the dftb+ code, and density functional results using the localized Gaussian orbital code, AIMPRO. DFTB accurately reproduces structures and energies for a range of point defect structures such as vacancies and Stone-Wales defects in graphene, as well as various unfunctionalized and hydroxylated graphene sheet edges. Migration barriers for the vacancy and Stone-Wales defect formation barriers are accurately reproduced using a nudged elastic band approach. Finally we explore the potential for dynamic defect simulations using DFTB, taking as an example electron irradiation damage in graphene. DFTB-MD derived sputtering energy threshold map for a carbon atom in a graphene plane. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

BEYOND SOCIAL SKILLS: GROUP DYNAMICS AT SOCIAL SKILLS TRAINING FOR HIGH FUNCTIONING ADOLESCENTS WITH AUTISM SPECTRUM DISORDERS

Directory of Open Access Journals (Sweden)

Agnieszka Siedler

2015-06-01

Full Text Available The usefulness of group social skills training in Autism Spectrum Disorder therapy has been well established. However, little is known about the group dynamics of this kind of intervention. The current multiple case studies were conducted to demonstrate that, despite of the functioning specifics of participants with ASD, processes associated with the dynamics of the group during group social skills training session may be noticeable. Intervention groups consisted of fifteen adolescents and preadolescents with high functioning Autism Spectrum Disorders aged between 11 to 17 years old divided into three training groups. The social skills training sessions were conducted on a weekly basis. The observation lasted for six months and it included the formation of the group, the period of stability and unexpected changes. After each group session, the therapists filled in a detailed report about the participants’ behavior and interactions between participants. Collected data were carefully analyzed for group dynamic features. It was noticed that adolescents participating in group interventions are susceptible to the influence of the group, take different individual roles and are moderately sensitive to changes in the group structure. The influence of the disorder characteristics on group dynamics was also observed. Although the results show that group dynamics can be observed at a group training for ASD, the need for further structured observation should be emphasized as a current study constituted the first approach to the subject.

Probing molecular mechanisms of the Hsp90 chaperone: biophysical modeling identifies key regulators of functional dynamics.

Directory of Open Access Journals (Sweden)

Anshuman Dixit

Full Text Available Deciphering functional mechanisms of the Hsp90 chaperone machinery is an important objective in cancer biology aiming to facilitate discovery of targeted anti-cancer therapies. Despite significant advances in understanding structure and function of molecular chaperones, organizing molecular principles that control the relationship between conformational diversity and functional mechanisms of the Hsp90 activity lack a sufficient quantitative characterization. We combined molecular dynamics simulations, principal component analysis, the energy landscape model and structure-functional analysis of Hsp90 regulatory interactions to systematically investigate functional dynamics of the molecular chaperone. This approach has identified a network of conserved regions common to the Hsp90 chaperones that could play a universal role in coordinating functional dynamics, principal collective motions and allosteric signaling of Hsp90. We have found that these functional motifs may be utilized by the molecular chaperone machinery to act collectively as central regulators of Hsp90 dynamics and activity, including the inter-domain communications, control of ATP hydrolysis, and protein client binding. These findings have provided support to a long-standing assertion that allosteric regulation and catalysis may have emerged via common evolutionary routes. The interaction networks regulating functional motions of Hsp90 may be determined by the inherent structural architecture of the molecular chaperone. At the same time, the thermodynamics-based "conformational selection" of functional states is likely to be activated based on the nature of the binding partner. This mechanistic model of Hsp90 dynamics and function is consistent with the notion that allosteric networks orchestrating cooperative protein motions can be formed by evolutionary conserved and sparsely connected residue clusters. Hence, allosteric signaling through a small network of distantly connected

On Stabilizing the Variance of Dynamic Functional Brain Connectivity Time Series.

Science.gov (United States)

Thompson, William Hedley; Fransson, Peter

2016-12-01

Assessment of dynamic functional brain connectivity based on functional magnetic resonance imaging (fMRI) data is an increasingly popular strategy to investigate temporal dynamics of the brain's large-scale network architecture. Current practice when deriving connectivity estimates over time is to use the Fisher transformation, which aims to stabilize the variance of correlation values that fluctuate around varying true correlation values. It is, however, unclear how well the stabilization of signal variance performed by the Fisher transformation works for each connectivity time series, when the true correlation is assumed to be fluctuating. This is of importance because many subsequent analyses either assume or perform better when the time series have stable variance or adheres to an approximate Gaussian distribution. In this article, using simulations and analysis of resting-state fMRI data, we analyze the effect of applying different variance stabilization strategies on connectivity time series. We focus our investigation on the Fisher transformation, the Box-Cox (BC) transformation and an approach that combines both transformations. Our results show that, if the intention of stabilizing the variance is to use metrics on the time series, where stable variance or a Gaussian distribution is desired (e.g., clustering), the Fisher transformation is not optimal and may even skew connectivity time series away from being Gaussian. Furthermore, we show that the suboptimal performance of the Fisher transformation can be substantially improved by including an additional BC transformation after the dynamic functional connectivity time series has been Fisher transformed.

Instantons: Dynamical mass generation, chiral ward identities and the topological charge correlation function

Energy Technology Data Exchange (ETDEWEB)

McDougall, N.A. (Oxford Univ. (UK). Dept. of Theoretical Physics)

1983-01-10

When dynamical mass generation resulting from the breakdown of chiral symmetry is taken into account, instanton dynamics treated within the dilute gas approximation may satisfy the constraints on the quark condensates and the topological charge correlation function derived by Crewther from an analysis of the chiral Ward identities assuming the absence of a physical axial U(1) Goldstone boson. From a consideration of the contribution of the eta' to the topological charge correlation function, a relationship is derived in which msub(eta')/sup 2/fsub(eta')/sup 2/ is proportional to the vacuum energy density.

Multiscale functions, scale dynamics, and applications to partial differential equations

Science.gov (United States)

Cresson, Jacky; Pierret, Frédéric

2016-05-01

Modeling phenomena from experimental data always begins with a choice of hypothesis on the observed dynamics such as determinism, randomness, and differentiability. Depending on these choices, different behaviors can be observed. The natural question associated to the modeling problem is the following: "With a finite set of data concerning a phenomenon, can we recover its underlying nature? From this problem, we introduce in this paper the definition of multi-scale functions, scale calculus, and scale dynamics based on the time scale calculus [see Bohner, M. and Peterson, A., Dynamic Equations on Time Scales: An Introduction with Applications (Springer Science & Business Media, 2001)] which is used to introduce the notion of scale equations. These definitions will be illustrated on the multi-scale Okamoto's functions. Scale equations are analysed using scale regimes and the notion of asymptotic model for a scale equation under a particular scale regime. The introduced formalism explains why a single scale equation can produce distinct continuous models even if the equation is scale invariant. Typical examples of such equations are given by the scale Euler-Lagrange equation. We illustrate our results using the scale Newton's equation which gives rise to a non-linear diffusion equation or a non-linear Schrödinger equation as asymptotic continuous models depending on the particular fractional scale regime which is considered.

Generalized decompositions of dynamic systems and vector Lyapunov functions

Science.gov (United States)

Ikeda, M.; Siljak, D. D.

1981-10-01

The notion of decomposition is generalized to provide more freedom in constructing vector Lyapunov functions for stability analysis of nonlinear dynamic systems. A generalized decomposition is defined as a disjoint decomposition of a system which is obtained by expanding the state-space of a given system. An inclusion principle is formulated for the solutions of the expansion to include the solutions of the original system, so that stability of the expansion implies stability of the original system. Stability of the expansion can then be established by standard disjoint decompositions and vector Lyapunov functions. The applicability of the new approach is demonstrated using the Lotka-Volterra equations.

A STUDY ON DYNAMIC LOAD HISTORY RECONSTRUCTION USING PSEUDO-INVERSE METHODS

OpenAIRE

Santos, Ariane Rebelato Silva dos; Marczak, Rogério José

2017-01-01

Considering that the vibratory forces generally cannot be measured directly at the interface of two bodies, an inverse method is studied in the present work to recover the load history in such cases. The proposed technique attempts to reconstruct the dynamic loads history by using a frequency domain analysis and Moore-Penrose pseudo-inverses of the frequency response function (FRF) of the system. The methodology consists in applying discrete dynamic loads on a finite element model in the time...

Dynamic radioisotopic study of the salivary glands. Quantification test

International Nuclear Information System (INIS)

Estour, A.-B.

1976-01-01

Quantified dynamic radioisotopic exploration, a new and rational examination, should find its place in a thorough check-up of the salivary glands together with clinical, immunological, anatomopathological and sialographic investigations. The object of this work was to standardise the test procedure with a view to routine use on patients and to define certain quantified parameters representing objectively the different aspects of the salivary functions. Our procedure through reeding sophisticated equipment, is simple to perform and relies on use of: radiotechnetium employed at activities which allow repetitive exlorations whereby pathological changes may be followed; the gamma camera and its data processing system which records all radioactive information obtained on the patient's head. These results will supply the data needed to judge the salivary functions as a whole. The apparatus used provides a remarkable pictorial record made up not only of morphological and functional images at each stage of the examination but also of ciphered radioactivity versus time curves for each of the main salivary glands and for any other zone of interest. From these curves it is then possible to define quantified parameters, reproducible and expressing functional activity. This procedure, safe and painless, seems to suit the patients who lie still without complaint for 60 minutes, 45 minutes for the concentration study and 15 minutes for the post-stimulus excretion study. The dynamic radioisotopic examination of the salivary glands, by the comparison of concentration and excretion images and by the study of parameters, separately and as a whole, is thus a useful complement to other paraclinical examinations and contributes essential information in most salivary diseases [fr

Mining dynamic noteworthy functions in software execution sequences.

Science.gov (United States)

Zhang, Bing; Huang, Guoyan; Wang, Yuqian; He, Haitao; Ren, Jiadong

2017-01-01

As the quality of crucial entities can directly affect that of software, their identification and protection become an important premise for effective software development, management, maintenance and testing, which thus contribute to improving the software quality and its attack-defending ability. Most analysis and evaluation on important entities like codes-based static structure analysis are on the destruction of the actual software running. In this paper, from the perspective of software execution process, we proposed an approach to mine dynamic noteworthy functions (DNFM)in software execution sequences. First, according to software decompiling and tracking stack changes, the execution traces composed of a series of function addresses were acquired. Then these traces were modeled as execution sequences and then simplified so as to get simplified sequences (SFS), followed by the extraction of patterns through pattern extraction (PE) algorithm from SFS. After that, evaluating indicators inner-importance and inter-importance were designed to measure the noteworthiness of functions in DNFM algorithm. Finally, these functions were sorted by their noteworthiness. Comparison and contrast were conducted on the experiment results from two traditional complex network-based node mining methods, namely PageRank and DegreeRank. The results show that the DNFM method can mine noteworthy functions in software effectively and precisely.

Titanium Dioxide Nanoparticles Trigger Loss of Function and Perturbation of Mitochondrial Dynamics in Primary Hepatocytes.

Directory of Open Access Journals (Sweden)

Vaishaali Natarajan

Full Text Available Titanium dioxide (TiO2 nanoparticles are one of the most highly manufactured and employed nanomaterials in the world with applications in copious industrial and consumer products. The liver is a major accumulation site for many nanoparticles, including TiO2, directly through intentional exposure or indirectly through unintentional ingestion via water, food or animals and increased environmental contamination. Growing concerns over the current usage of TiO2 coupled with the lack of mechanistic understanding of its potential health risk is the motivation for this study. Here we determined the toxic effect of three different TiO2 nanoparticles (commercially available rutile, anatase and P25 on primary rat hepatocytes. Specifically, we evaluated events related to hepatocyte functions and mitochondrial dynamics: (1 urea and albumin synthesis using colorimetric and ELISA assays, respectively; (2 redox signaling mechanisms by measuring reactive oxygen species (ROS production, manganese superoxide dismutase (MnSOD activity and mitochondrial membrane potential (MMP; (3 OPA1 and Mfn-1 expression that mediates the mitochondrial dynamics by PCR; and (4 mitochondrial morphology by MitoTracker Green FM staining. All three TiO2 nanoparticles induced a significant loss (p < 0.05 in hepatocyte functions even at concentrations as low as 50 ppm with commercially used P25 causing maximum damage. TiO2 nanoparticles induced a strong oxidative stress in primary hepatocytes. TiO2 nanoparticles exposure also resulted in morphological changes in mitochondria and substantial loss in the fusion process, thus impairing the mitochondrial dynamics. Although this study demonstrated that TiO2 nanoparticles exposure resulted in substantial damage to primary hepatocytes, more in vitro and in vivo studies are required to determine the complete toxicological mechanism in primary hepatocytes and subsequently liver function.

Structure, dynamics, and function of biomolecules

International Nuclear Information System (INIS)

Frauenfelder, H.; Berendzen, J.R.; Garcia, A.; Gupta, G.; Olah, G.A.; Terwilliger, T.C.; Trewhella, J.; Wood, C.C.; Woodruff, W.H.

1998-01-01

This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The authors enhanced Los Alamos' core competency in Bioscience and Biotechnology by building on present strengths in experimental techniques, theory, high-performance computing, modeling, and simulation applied to biomolecular structure, dynamics, and function. Specifically, the authors strengthened their capabilities in neutron/x-ray scattering, x-ray crystallography, NMR, laser, and optical spectroscopies. Initially they focused on supporting the Los alamos Neutron Science Center (LANSCE) in the design and implementation of new neutron scattering instrumentation, they developed new methods for analysis of scattering data, and they developed new projects to study the structures of biomolecular complexes. The authors have also worked to strengthen interactions between theory and experiment, and between the biological and physical sciences. They sponsored regular meetings of members from all interested LANL technical divisions, and supported two lecture series: ''Biology for Physicists'' and ''Issues in Modern Biology''. They also supported the formation of interdisciplinary/inter-divisional teams to develop projects in science-based bioremediation and an integrated structural biology resource. Finally, they successfully worked with a multidisciplinary team to put forward the Laboratory's Genome and Beyond tactical goal

Computer Processing and Display of Positron Scintigrams and Dynamic Function Curves

Energy Technology Data Exchange (ETDEWEB)

Wilensky, S.; Ashare, A. B.; Pizer, S. M.; Hoop, B. Jr.; Brownell, G. L. [Massachusetts General Hospital, Boston, MA (United States)

1969-01-15

A computer processing and display system for handling radioisotope data is described. The system has been used to upgrade and display brain scans and to process dynamic function curves. The hardware and software are described, and results are presented. (author)

Instantaneous Transfer Entropy for the Study of Cardiovascular and Cardiorespiratory Nonstationary Dynamics.

Science.gov (United States)

Valenza, Gaetano; Faes, Luca; Citi, Luca; Orini, Michele; Barbieri, Riccardo

2018-05-01

Measures of transfer entropy (TE) quantify the direction and strength of coupling between two complex systems. Standard approaches assume stationarity of the observations, and therefore are unable to track time-varying changes in nonlinear information transfer with high temporal resolution. In this study, we aim to define and validate novel instantaneous measures of TE to provide an improved assessment of complex nonstationary cardiorespiratory interactions. We here propose a novel instantaneous point-process TE (ipTE) and validate its assessment as applied to cardiovascular and cardiorespiratory dynamics. In particular, heartbeat and respiratory dynamics are characterized through discrete time series, and modeled with probability density functions predicting the time of the next physiological event as a function of the past history. Likewise, nonstationary interactions between heartbeat and blood pressure dynamics are characterized as well. Furthermore, we propose a new measure of information transfer, the instantaneous point-process information transfer (ipInfTr), which is directly derived from point-process-based definitions of the Kolmogorov-Smirnov distance. Analysis on synthetic data, as well as on experimental data gathered from healthy subjects undergoing postural changes confirms that ipTE, as well as ipInfTr measures are able to dynamically track changes in physiological systems coupling. This novel approach opens new avenues in the study of hidden, transient, nonstationary physiological states involving multivariate autonomic dynamics in cardiovascular health and disease. The proposed method can also be tailored for the study of complex multisystem physiology (e.g., brain-heart or, more in general, brain-body interactions).

Dynamics of biopolymers on nanomaterials studied by quasielastic neutron scattering and MD simulations

Science.gov (United States)

Dhindsa, Gurpreet K.

Neutron scattering has been proved to be a powerful tool to study the dynamics of biological systems under various conditions. This thesis intends to utilize neutron scattering techniques, combining with MD simulations, to develop fundamental understanding of several biologically interesting systems. Our systems include a drug delivery system containing Nanodiamonds with nucleic acid (RNA), and two specific model proteins, beta-Casein and Inorganic Pyrophosphatase (IPPase). RNA and nanodiamond (ND) both are suitable for drug-delivery applications in nano-biotechnology. The architecturally flexible RNA with catalytic functionality forms nanocomposites that can treat life-threatening diseases. The non-toxic ND has excellent mechanical and optical properties and functionalizable high surface area, and thus actively considered for biomedical applications. In this thesis, we utilized two tools, quasielastic neutron scattering (QENS) and Molecular Dynamics Simulations to probe the effect of ND on RNA dynamics. Our work provides fundamental understanding of how hydrated RNA motions are affected in the RNA-ND nanocomposites. From the experimental and Molecular Dynamics Simulation (MD), we found that hydrated RNA motion is faster on ND surface than a freestanding one. MD Simulation results showed that the failure of Stokes Einstein relation results the presence of dynamic heterogeneities in the biomacromolecules. Radial pair distribution function from MD Simulation confirmed that the hydrophilic nature of ND attracts more water than RNA results the de-confinement of RNA on ND. Therefore, RNA exhibits faster motion in the presence of ND than freestanding RNA. In the second project, we studied the dynamics of a natively disordered protein beta-Casein which lacks secondary structures. In this study, the temperature and hydration effects on the dynamics of beta-Casein are explored by Quasielastic Neutron Scattering (QENS). We investigated the mean square displacement (MSD) of

Study of nuclear statics and dynamics using the Wigner transform

International Nuclear Information System (INIS)

Shlomo, S.

1983-01-01

The Wigner phase-space distribution function, given as the shifted Fourier transform of the density matrix, provides a framework for an exact reformulation of non-relativistic quantum mechanics in terms of classical concepts. The Wigner distribution function (WDF), f(r-vector, p-vector), is considered as a quantum mechanical generalization of the classical phase space distribution function. While basic observables, such as matter density and momentum density, are given by the same integrals over f(r-vector, p-vector) as in classical physics, f(r-vector, p-vector) differs from its classical analog by the fact that it can assume negative values in some regions. However, it is known that the WDF is a useful and convenient tool for the study of the static and the dynamical aspects of many-body quantum systems, and the equation of motion for f(r-vector, p-vector) serves as a starting point for semi-classical approximations. The aim of this talk is to present and discuss some recent results for static and dynamic properties of nuclei obtained by exact evaluation of the WDF

Using motor imagery to study the neural substrates of dynamic balance

NARCIS (Netherlands)

Ferraye, M.U.; Debû, B.H.G.; Heil, L.; Carpenter, M.; Bloem, B.R.; Toni, I.

2014-01-01

This study examines the cerebral structures involved in dynamic balance using a motor imagery (MI) protocol. We recorded cerebral activity with functional magnetic resonance imaging while subjects imagined swaying on a balance board along the sagittal plane to point a laser at target pairs of

Feedback dynamics and cell function: Why systems biology is called Systems Biology.

Science.gov (United States)

Wolkenhauer, Olaf; Mesarovic, Mihajlo

2005-05-01

A new paradigm, like Systems Biology, should challenge the way research has been conducted previously. This Opinion article aims to present Systems Biology, not as the application of engineering principles to biology but as a merger of systems- and control theory with molecular- and cell biology. In our view, the central dogma of Systems Biology is that it is system dynamics that gives rise to the functioning and function of cells. The concepts of feedback regulation and control of pathways and the coordination of cell function are emphasized as an important area of Systems Biology research. The hurdles and risks for this area are discussed from the perspective of dynamic pathway modelling. Most of all, the aim of this article is to promote mathematical modelling and simulation as a part of molecular- and cell biology. Systems Biology is a success if it is widely accepted that there is nothing more practical than a good theory.

The 3He spectral function in light-front dynamics

Directory of Open Access Journals (Sweden)

Rinaldi Matteo

2016-01-01

Full Text Available A distorted spin-dependent spectral function for 3He is considered for the extraction of the transverse-momentum dependent parton distributions in the neutron from semi-inclusive deep inelastic electron scattering off polarized 3He at finite momentum transfers, where final state interactions are taken into account. The generalization of the analysis to a Poincaré covariant framework within the light-front dynamics is outlined.

Estimation of the pulmonary input function in dynamic whole body PET

International Nuclear Information System (INIS)

Ho-Shon, K.; Buchen, P.; Meikle, S.R.; Fulham, M.J.; University of Sydney, Sydney, NSW

1998-01-01

Full text: Dynamic data acquisition in Whole Body PET (WB-PET) has the potential to measure the metabolic rate of glucose (MRGlc) in tissue in-vivo. Estimation of changes in tumoral MRGlc may be a valuable tool in cancer by providing an quantitative index of response to treatment. A necessary requirement is an input function (IF) that can be obtained from arterial, 'arterialised' venous or pulmonary arterial blood in the case of lung tumours. Our aim was to extract the pulmonary input function from dynamic WB-PET data using Principal Component Analysis (PCA), Factor Analysis (FA) and Maximum Entropy (ME) for the evaluation of patients undergoing induction chemotherapy for non-small cell lung cancer. PCA is first used as a method of dimension reduction to obtain a signal space, defined by an optimal metric and a set of vectors. FA is used together with a ME constraint to rotate these vectors to obtain 'physiological' factors. A form of entropy function that does not require normalised data was used. This enabled the introduction of a penalty function based on the blood concentration at the last time point which provides an additional constraint. Tissue functions from 10 planes through normal lung were simulated. The model was a linear combination of an IF and a tissue time activity curve (TAC). The proportion of the IF to TAC was varied over the planes to simulate the apical to basal gradient in vascularity of the lung and pseudo Poisson noise was added. The method accurately extracted the IF at noise levels spanning the expected range for dynamic ROI data acquired with the interplane septa extended. Our method is minimally invasive because it requires only 1 late venous blood sample and is applicable to a wide range of tracers since it does not assume a particular compartmental model. Pilot data from 2 patients have been collected enabling comparison of the estimated IF with direct blood sampling from the pulmonary artery

Wigner functions for angle and orbital angular momentum. Operators and dynamics

Energy Technology Data Exchange (ETDEWEB)

Kastrup, Hans A. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Gruppe Theorie

2017-02-15

Recently a paper on the construction of consistent Wigner functions for cylindrical phase spaces S{sup 1} x R, i.e. for the canonical pair angle and orbital angular momentum, was presented, main properties of those functions derived, discussed and their usefulness illustrated by examples. The present paper is a continuation which compares properties of the new Wigner functions for cylindrical phase spaces with those of the well-known Wigner functions on planar ones in more detail. Furthermore, the mutual (Weyl) correspondence between HIlbert space operators and their phase space functions is discussed. The * product formalism is shown to be completely implementable. In addition basic dynamical laws for Wigner and Moyal functions are derived as generalized Liouville and energy equations. They are very similar to those of the planar case, but also show characteristic differences.

Wigner functions for angle and orbital angular momentum. Operators and dynamics

International Nuclear Information System (INIS)

Kastrup, Hans A.

2017-02-01

Recently a paper on the construction of consistent Wigner functions for cylindrical phase spaces S"1 x R, i.e. for the canonical pair angle and orbital angular momentum, was presented, main properties of those functions derived, discussed and their usefulness illustrated by examples. The present paper is a continuation which compares properties of the new Wigner functions for cylindrical phase spaces with those of the well-known Wigner functions on planar ones in more detail. Furthermore, the mutual (Weyl) correspondence between HIlbert space operators and their phase space functions is discussed. The * product formalism is shown to be completely implementable. In addition basic dynamical laws for Wigner and Moyal functions are derived as generalized Liouville and energy equations. They are very similar to those of the planar case, but also show characteristic differences.

Quasi-particle excitations and dynamical structure function of trapped Bose-condensates in the WKB approximation

OpenAIRE

Csordás, András; Graham, Robert; Szépfalusy, Péter

1997-01-01

The Bogoliubov equations of the quasi-particle excitations in a weakly interacting trapped Bose-condensate are solved in the WKB approximation in an isotropic harmonic trap, determining the discrete quasi-particle energies and wave functions by torus (Bohr-Sommerfeld) quantization of the integrable classical quasi-particle dynamics. The results are used to calculate the position and strengths of the peaks in the dynamic structure function which can be observed by off-resonance inelastic light...

CONNECTION BETWEEN DYNAMICALLY DERIVED INITIAL MASS FUNCTION NORMALIZATION AND STELLAR POPULATION PARAMETERS

International Nuclear Information System (INIS)

McDermid, Richard M.; Cappellari, Michele; Bayet, Estelle; Bureau, Martin; Davies, Roger L.; Alatalo, Katherine; Blitz, Leo; Bois, Maxime; Bournaud, Frédéric; Duc, Pierre-Alain; Crocker, Alison F.; Davis, Timothy A.; De Zeeuw, P. T.; Emsellem, Eric; Kuntschner, Harald; Khochfar, Sadegh; Krajnović, Davor; Morganti, Raffaella; Oosterloo, Tom; Naab, Thorsten

2014-01-01

We report on empirical trends between the dynamically determined stellar initial mass function (IMF) and stellar population properties for a complete, volume-limited sample of 260 early-type galaxies from the ATLAS 3D project. We study trends between our dynamically derived IMF normalization α dyn ≡ (M/L) stars /(M/L) Salp and absorption line strengths, and interpret these via single stellar population-equivalent ages, abundance ratios (measured as [α/Fe]), and total metallicity, [Z/H]. We find that old and alpha-enhanced galaxies tend to have on average heavier (Salpeter-like) mass normalization of the IMF, but stellar population does not appear to be a good predictor of the IMF, with a large range of α dyn at a given population parameter. As a result, we find weak α dyn -[α/Fe] and α dyn –Age correlations and no significant α dyn –[Z/H] correlation. The observed trends appear significantly weaker than those reported in studies that measure the IMF normalization via the low-mass star demographics inferred through stellar spectral analysis

Connection between Dynamically Derived Initial Mass Function Normalization and Stellar Population Parameters

Science.gov (United States)

McDermid, Richard M.; Cappellari, Michele; Alatalo, Katherine; Bayet, Estelle; Blitz, Leo; Bois, Maxime; Bournaud, Frédéric; Bureau, Martin; Crocker, Alison F.; Davies, Roger L.; Davis, Timothy A.; de Zeeuw, P. T.; Duc, Pierre-Alain; Emsellem, Eric; Khochfar, Sadegh; Krajnović, Davor; Kuntschner, Harald; Morganti, Raffaella; Naab, Thorsten; Oosterloo, Tom; Sarzi, Marc; Scott, Nicholas; Serra, Paolo; Weijmans, Anne-Marie; Young, Lisa M.

2014-09-01

We report on empirical trends between the dynamically determined stellar initial mass function (IMF) and stellar population properties for a complete, volume-limited sample of 260 early-type galaxies from the ATLAS3D project. We study trends between our dynamically derived IMF normalization αdyn ≡ (M/L)stars/(M/L)Salp and absorption line strengths, and interpret these via single stellar population-equivalent ages, abundance ratios (measured as [α/Fe]), and total metallicity, [Z/H]. We find that old and alpha-enhanced galaxies tend to have on average heavier (Salpeter-like) mass normalization of the IMF, but stellar population does not appear to be a good predictor of the IMF, with a large range of αdyn at a given population parameter. As a result, we find weak αdyn-[α/Fe] and αdyn -Age correlations and no significant αdyn -[Z/H] correlation. The observed trends appear significantly weaker than those reported in studies that measure the IMF normalization via the low-mass star demographics inferred through stellar spectral analysis.

Dynamic PET of human liver inflammation: impact of kinetic modeling with optimization-derived dual-blood input function.

Science.gov (United States)

Wang, Guobao; Corwin, Michael T; Olson, Kristin A; Badawi, Ramsey D; Sarkar, Souvik

2018-05-30

The hallmark of nonalcoholic steatohepatitis is hepatocellular inflammation and injury in the setting of hepatic steatosis. Recent work has indicated that dynamic 18F-FDG PET with kinetic modeling has the potential to assess hepatic inflammation noninvasively, while static FDG-PET did not show a promise. Because the liver has dual blood supplies, kinetic modeling of dynamic liver PET data is challenging in human studies. The objective of this study is to evaluate and identify a dual-input kinetic modeling approach for dynamic FDG-PET of human liver inflammation. Fourteen human patients with nonalcoholic fatty liver disease were included in the study. Each patient underwent one-hour dynamic FDG-PET/CT scan and had liver biopsy within six weeks. Three models were tested for kinetic analysis: traditional two-tissue compartmental model with an image-derived single-blood input function (SBIF), model with population-based dual-blood input function (DBIF), and modified model with optimization-derived DBIF through a joint estimation framework. The three models were compared using Akaike information criterion (AIC), F test and histopathologic inflammation reference. The results showed that the optimization-derived DBIF model improved the fitting of liver time activity curves and achieved lower AIC values and higher F values than the SBIF and population-based DBIF models in all patients. The optimization-derived model significantly increased FDG K1 estimates by 101% and 27% as compared with traditional SBIF and population-based DBIF. K1 by the optimization-derived model was significantly associated with histopathologic grades of liver inflammation while the other two models did not provide a statistical significance. In conclusion, modeling of DBIF is critical for kinetic analysis of dynamic liver FDG-PET data in human studies. The optimization-derived DBIF model is more appropriate than SBIF and population-based DBIF for dynamic FDG-PET of liver inflammation. © 2018

Cochlear function tests in estimation of speech dynamic range.

Science.gov (United States)

Han, Jung Ju; Park, So Young; Park, Shi Nae; Na, Mi Sun; Lee, Philip; Han, Jae Sang

2016-10-01

The loss of active cochlear mechanics causes elevated thresholds, loudness recruitment, and reduced frequency selectivity. The problems faced by hearing-impaired listeners are largely related with reduced dynamic range (DR). The aim of this study was to determine which index of the cochlear function tests correlates best with the DR to speech stimuli. Audiological data on 516 ears with pure tone average (PTA) of ≤55 dB and word recognition score of ≥70% were analyzed. PTA, speech recognition threshold (SRT), uncomfortable loudness (UCL), and distortion product otoacoustic emission (DPOAE) were explored as the indices of cochlear function. Audiometric configurations were classified. Correlation between each index and the DR was assessed and multiple regression analysis was done. PTA and SRT demonstrated strong negative correlations with the DR (r = -0.788 and -0.860, respectively), while DPOAE sum was moderately correlated (r = 0.587). UCLs remained quite constant for the total range of the DR. The regression equation was Y (DR) = 75.238 - 0.719 × SRT (R(2 )=( )0.721, p equation.

Static versus Dynamic Disposition: The Role of GeoGebra in Representing Polynomial-Rational Inequalities and Exponential-Logarithmic Functions

Science.gov (United States)

Caglayan, Günhan

2014-01-01

This study investigates prospective secondary mathematics teachers' visual representations of polynomial and rational inequalities, and graphs of exponential and logarithmic functions with GeoGebra Dynamic Software. Five prospective teachers in a university in the United States participated in this research study, which was situated within a…

Periodic solutions of first-order functional differential equations in population dynamics

CERN Document Server

Padhi, Seshadev; Srinivasu, P D N

2014-01-01

This book provides cutting-edge results on the existence of multiple positive periodic solutions of first-order functional differential equations. It demonstrates how the Leggett-Williams fixed-point theorem can be applied to study the existence of two or three positive periodic solutions of functional differential equations with real-world applications, particularly with regard to the Lasota-Wazewska model, the Hematopoiesis model, the Nicholsons Blowflies model, and some models with Allee effects. Many interesting sufficient conditions are given for the dynamics that include nonlinear characteristics exhibited by population models. The last chapter provides results related to the global appeal of solutions to the models considered in the earlier chapters. The techniques used in this book can be easily understood by anyone with a basic knowledge of analysis. This book offers a valuable reference guide for students and researchers in the field of differential equations with applications to biology, ecology, a...

Dynamical interactions between solute and solvent studied by nonlinear infrared spectroscopy

International Nuclear Information System (INIS)

Ohta, K.; Tominaga, K.

2006-01-01

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

Dynamics of ligand exchange mechanism at Cu(II) in water: an ab initio quantum mechanical charge field molecular dynamics study with extended quantum mechanical region.

Science.gov (United States)

Moin, Syed Tarique; Hofer, Thomas S; Weiss, Alexander K H; Rode, Bernd M

2013-07-07

Ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) were successfully applied to Cu(II) embedded in water to elucidate structure and to understand dynamics of ligand exchange mechanism. From the simulation studies, it was found that using an extended large quantum mechanical region including two shells of hydration is required for a better description of the dynamics of exchanging water molecules. The structural features characterized by radial distribution function, angular distribution function and other analytical parameters were consistent with experimental data. The major outcome of this study was the dynamics of exchange mechanism and reactions in the first hydration shell that could not be studied so far. The dynamical data such as mean residence time of the first shell water molecules and other relevant data from the simulations are close to the results determined experimentally. Another major characteristic of hydrated Cu(II) is the Jahn-Teller distortion which was also successfully reproduced, leading to the final conclusion that the dominating aqua complex is a 6-coordinated species. The ab initio QMCF-MD formalism proved again its capabilities of unraveling even ambiguous properties of hydrated species that are far difficult to explore by any conventional quantum mechanics/molecular mechanics (QM/MM) approach or experiment.

Dynamics of ligand exchange mechanism at Cu(II) in water: An ab initio quantum mechanical charge field molecular dynamics study with extended quantum mechanical region

International Nuclear Information System (INIS)

Moin, Syed Tarique; Hofer, Thomas S.; Weiss, Alexander K. H.; Rode, Bernd M.

2013-01-01

Ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) were successfully applied to Cu(II) embedded in water to elucidate structure and to understand dynamics of ligand exchange mechanism. From the simulation studies, it was found that using an extended large quantum mechanical region including two shells of hydration is required for a better description of the dynamics of exchanging water molecules. The structural features characterized by radial distribution function, angular distribution function and other analytical parameters were consistent with experimental data. The major outcome of this study was the dynamics of exchange mechanism and reactions in the first hydration shell that could not be studied so far. The dynamical data such as mean residence time of the first shell water molecules and other relevant data from the simulations are close to the results determined experimentally. Another major characteristic of hydrated Cu(II) is the Jahn-Teller distortion which was also successfully reproduced, leading to the final conclusion that the dominating aqua complex is a 6-coordinated species. The ab initio QMCF-MD formalism proved again its capabilities of unraveling even ambiguous properties of hydrated species that are far difficult to explore by any conventional quantum mechanics/molecular mechanics (QM/MM) approach or experiment

Numerical tools for the study of defect dynamics in quasiperiodic structures

International Nuclear Information System (INIS)

Barak, G.; Lifshitz, R.

2004-01-01

Full Text:We have developed a set of numerical tools for the quantitative study of defect dynamics in quasiperiodic structures, with the intention of addressing in the near future some of the open questions regarding the dynamics of dislocations in quasicrystals. IS'e intend to apply these tools to study dislocation motion in the dynamical equation of Lifshitz and Petrich [1] whose steady-state solutions are quasiperiodic, exhibiting dodecagonal (12-fold) rotational symmetry. Here we demonstrate our ability to inject an arbitrary set of dislocations-parametrized by the homotopy group of the D-torus (here D=4)-and quantitatively follow the positions of these dislocations as the equation evolves in time. We measure dislocation velocities as a function of applied stress and shear, as well as the phonon and phason strains that accompany this motion as the system evolves in time

An open tool for input function estimation and quantification of dynamic PET FDG brain scans.

Science.gov (United States)

Bertrán, Martín; Martínez, Natalia; Carbajal, Guillermo; Fernández, Alicia; Gómez, Álvaro

2016-08-01

Positron emission tomography (PET) analysis of clinical studies is mostly restricted to qualitative evaluation. Quantitative analysis of PET studies is highly desirable to be able to compute an objective measurement of the process of interest in order to evaluate treatment response and/or compare patient data. But implementation of quantitative analysis generally requires the determination of the input function: the arterial blood or plasma activity which indicates how much tracer is available for uptake in the brain. The purpose of our work was to share with the community an open software tool that can assist in the estimation of this input function, and the derivation of a quantitative map from the dynamic PET study. Arterial blood sampling during the PET study is the gold standard method to get the input function, but is uncomfortable and risky for the patient so it is rarely used in routine studies. To overcome the lack of a direct input function, different alternatives have been devised and are available in the literature. These alternatives derive the input function from the PET image itself (image-derived input function) or from data gathered from previous similar studies (population-based input function). In this article, we present ongoing work that includes the development of a software tool that integrates several methods with novel strategies for the segmentation of blood pools and parameter estimation. The tool is available as an extension to the 3D Slicer software. Tests on phantoms were conducted in order to validate the implemented methods. We evaluated the segmentation algorithms over a range of acquisition conditions and vasculature size. Input function estimation algorithms were evaluated against ground truth of the phantoms, as well as on their impact over the final quantification map. End-to-end use of the tool yields quantification maps with [Formula: see text] relative error in the estimated influx versus ground truth on phantoms. The main

State-space model with deep learning for functional dynamics estimation in resting-state fMRI.

Science.gov (United States)

Suk, Heung-Il; Wee, Chong-Yaw; Lee, Seong-Whan; Shen, Dinggang

2016-04-01

Studies on resting-state functional Magnetic Resonance Imaging (rs-fMRI) have shown that different brain regions still actively interact with each other while a subject is at rest, and such functional interaction is not stationary but changes over time. In terms of a large-scale brain network, in this paper, we focus on time-varying patterns of functional networks, i.e., functional dynamics, inherent in rs-fMRI, which is one of the emerging issues along with the network modelling. Specifically, we propose a novel methodological architecture that combines deep learning and state-space modelling, and apply it to rs-fMRI based Mild Cognitive Impairment (MCI) diagnosis. We first devise a Deep Auto-Encoder (DAE) to discover hierarchical non-linear functional relations among regions, by which we transform the regional features into an embedding space, whose bases are complex functional networks. Given the embedded functional features, we then use a Hidden Markov Model (HMM) to estimate dynamic characteristics of functional networks inherent in rs-fMRI via internal states, which are unobservable but can be inferred from observations statistically. By building a generative model with an HMM, we estimate the likelihood of the input features of rs-fMRI as belonging to the corresponding status, i.e., MCI or normal healthy control, based on which we identify the clinical label of a testing subject. In order to validate the effectiveness of the proposed method, we performed experiments on two different datasets and compared with state-of-the-art methods in the literature. We also analyzed the functional networks learned by DAE, estimated the functional connectivities by decoding hidden states in HMM, and investigated the estimated functional connectivities by means of a graph-theoretic approach. Copyright © 2016 Elsevier Inc. All rights reserved.

Dynamics of two-phase interfaces and surface tensions: A density-functional theory perspective

Science.gov (United States)

Yatsyshin, Petr; Sibley, David N.; Duran-Olivencia, Miguel A.; Kalliadasis, Serafim

2016-11-01

Classical density functional theory (DFT) is a statistical mechanical framework for the description of fluids at the nanoscale, where the inhomogeneity of the fluid structure needs to be carefully accounted for. By expressing the grand free-energy of the fluid as a functional of the one-body density, DFT offers a theoretically consistent and computationally accessible way to obtain two-phase interfaces and respective interfacial tensions in a ternary solid-liquid-gas system. The dynamic version of DFT (DDFT) can be rigorously derived from the Smoluchowsky picture of the dynamics of colloidal particles in a solvent. It is generally agreed that DDFT can capture the diffusion-driven evolution of many soft-matter systems. In this context, we use DDFT to investigate the dynamic behaviour of two-phase interfaces in both equilibrium and dynamic wetting and discuss the possibility of defining a time-dependent surface tension, which still remains in debate. We acknowledge financial support from the European Research Council via Advanced Grant No. 247031 and from the Engineering and Physical Sciences Research Council of the UK via Grants No. EP/L027186 and EP/L020564.

Correlated electron dynamics and memory in time-dependent density functional theory

International Nuclear Information System (INIS)

Thiele, Mark

2009-01-01

Time-dependent density functional theory (TDDFT) is an exact reformulation of the time-dependent many-electron Schroedinger equation, where the problem of many interacting electrons is mapped onto the Kohn-Sham system of noninteracting particles which reproduces the exact electronic density. In the Kohn-Sham system all non-classical many-body effects are incorporated in the exchange-correlation potential which is in general unknown and needs to be approximated. It is the goal of this thesis to investigate the connection between memory effects and correlated electron dynamics in strong and weak fields. To this end one-dimensional two-electron singlet systems are studied. At the same time these systems include the onedimensional helium atom model, which is an established system to investigate the crucial effects of correlated electron dynamics in external fields. The studies presented in this thesis show that memory effects are negligible for typical strong field processes. Here the approximation of the spatial nonlocality is of primary importance. For the photoabsorption spectra on the other hand the neglect of memory effects leads to qualitative and quantitative errors, which are shown to be connected to transitions of double excitation character. To develop a better understanding of the conditions under which memory effects become important quantum fluid dynamics has been found to be especially suitable. It represents a further exact reformulation of the quantum mechanic many-body problem which is based on hydrodynamic quantities such as density and velocity. Memory effects are shown to be important whenever the velocity field develops strong gradients and dissipative effects contribute. (orig.)

Correlated electron dynamics and memory in time-dependent density functional theory

Energy Technology Data Exchange (ETDEWEB)

Thiele, Mark

2009-07-28

Time-dependent density functional theory (TDDFT) is an exact reformulation of the time-dependent many-electron Schroedinger equation, where the problem of many interacting electrons is mapped onto the Kohn-Sham system of noninteracting particles which reproduces the exact electronic density. In the Kohn-Sham system all non-classical many-body effects are incorporated in the exchange-correlation potential which is in general unknown and needs to be approximated. It is the goal of this thesis to investigate the connection between memory effects and correlated electron dynamics in strong and weak fields. To this end one-dimensional two-electron singlet systems are studied. At the same time these systems include the onedimensional helium atom model, which is an established system to investigate the crucial effects of correlated electron dynamics in external fields. The studies presented in this thesis show that memory effects are negligible for typical strong field processes. Here the approximation of the spatial nonlocality is of primary importance. For the photoabsorption spectra on the other hand the neglect of memory effects leads to qualitative and quantitative errors, which are shown to be connected to transitions of double excitation character. To develop a better understanding of the conditions under which memory effects become important quantum fluid dynamics has been found to be especially suitable. It represents a further exact reformulation of the quantum mechanic many-body problem which is based on hydrodynamic quantities such as density and velocity. Memory effects are shown to be important whenever the velocity field develops strong gradients and dissipative effects contribute. (orig.)

DNA functionalization by dynamic chemistry

Directory of Open Access Journals (Sweden)

Zeynep Kanlidere

2016-10-01

Full Text Available Dynamic combinatorial chemistry (DCC is an attractive method to efficiently generate libraries of molecules from simpler building blocks by reversible reactions under thermodynamic control. Here we focus on the chemical modification of DNA oligonucleotides with acyclic diol linkers and demonstrate their potential for the deoxyribonucleic acid functionalization and generation of libraries of reversibly interconverting building blocks. The syntheses of phosphoramidite building blocks derived from D-threoninol are presented in two variants with protected amino or thiol groups. The threoninol building blocks were successfully incorporated via automated solid-phase synthesis into 13mer oligonucleotides. The amino group containing phosphoramidite was used together with complementary single-strand DNA templates that influenced the Watson–Crick base-pairing equilibrium in the mixture with a set of aldehyde modified nucleobases. A significant fraction of all possible base-pair mismatches was obtained, whereas, the highest selectivity (over 80% was found for the guanine aldehyde templated by the complementary cytosine containing DNA. The elevated occurrence of mismatches can be explained by increased backbone plasticity derived from the linear threoninol building block as a cyclic deoxyribose analogue.

Dynamic mobility of functional GABAA receptors at inhibitory synapses.

Science.gov (United States)

Thomas, Philip; Mortensen, Martin; Hosie, Alastair M; Smart, Trevor G

2005-07-01

Importing functional GABAA receptors into synapses is fundamental for establishing and maintaining inhibitory transmission and for controlling neuronal excitability. By introducing a binding site for an irreversible inhibitor into the GABAA receptor alpha1 subunit channel lining region that can be accessed only when the receptor is activated, we have determined the dynamics of receptor mobility between synaptic and extrasynaptic locations in hippocampal pyramidal neurons. We demonstrate that the cell surface GABAA receptor population shows no fast recovery after irreversible inhibition. In contrast, after selective inhibition, the synaptic receptor population rapidly recovers by the import of new functional entities within minutes. The trafficking pathways that promote rapid importation of synaptic receptors do not involve insertion from intracellular pools, but reflect receptor diffusion within the plane of the membrane. This process offers the synapse a rapid mechanism to replenish functional GABAA receptors at inhibitory synapses and a means to control synaptic efficacy.

Dynamic functional connectivity and individual differences in emotions during social stress.

Science.gov (United States)

Tobia, Michael J; Hayashi, Koby; Ballard, Grey; Gotlib, Ian H; Waugh, Christian E

2017-12-01

Exposure to acute stress induces multiple emotional responses, each with their own unique temporal dynamics. Dynamic functional connectivity (dFC) measures the temporal variability of network synchrony and captures individual differences in network neurodynamics. This study investigated the relationship between dFC and individual differences in emotions induced by an acute psychosocial stressor. Sixteen healthy adult women underwent fMRI scanning during a social evaluative threat (SET) task, and retrospectively completed questionnaires that assessed individual differences in subjectively experienced positive and negative emotions about stress and stress relief during the task. Group dFC was decomposed with parallel factor analysis (PARAFAC) into 10 components, each with a temporal signature, spatial network of functionally connected regions, and vector of participant loadings that captures individual differences in dFC. Participant loadings of two networks were positively correlated with stress-related emotions, indicating the existence of networks for positive and negative emotions. The emotion-related networks involved the ventromedial prefrontal cortex, cingulate cortex, anterior insula, and amygdala, among other distributed brain regions, and time signatures for these emotion-related networks were uncorrelated. These findings demonstrate that individual differences in stress-induced positive and negative emotions are each uniquely associated with large-scale brain networks, and suggest that dFC is a mechanism that generates individual differences in the emotional components of the stress response. Hum Brain Mapp 38:6185-6205, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Genome organization in the nucleus: From dynamic measurements to a functional model.

Science.gov (United States)

Vivante, Anat; Brozgol, Eugene; Bronshtein, Irena; Garini, Yuval

2017-07-01

A biological system is by definition a dynamic environment encompassing kinetic processes that occur at different length scales and time ranges. To explore this type of system, spatial information needs to be acquired at different time scales. This means overcoming significant hurdles, including the need for stable and precise labeling of the required probes and the use of state of the art optical methods. However, to interpret the acquired data, biophysical models that can account for these biological mechanisms need to be developed. The structure and function of a biological system are closely related to its dynamic properties, thus further emphasizing the importance of identifying the rules governing the dynamics that cannot be directly deduced from information on the structure itself. In eukaryotic cells, tens of thousands of genes are packed in the small volume of the nucleus. The genome itself is organized in chromosomes that occupy specific volumes referred to as chromosome territories. This organization is preserved throughout the cell cycle, even though there are no sub-compartments in the nucleus itself. This organization, which is still not fully understood, is crucial for a large number of cellular functions such as gene regulation, DNA breakage repair and error-free cell division. Various techniques are in use today, including imaging, live cell imaging and molecular methods such as chromosome conformation capture (3C) methods to better understand these mechanisms. Live cell imaging methods are becoming well established. These include methods such as Single Particle Tracking (SPT), Continuous Photobleaching (CP), Fluorescence Recovery After Photobleaching (FRAP) and Fluorescence Correlation Spectroscopy (FCS) that are currently used for studying proteins, RNA, DNA, gene loci and nuclear bodies. They provide crucial information on its mobility, reorganization, interactions and binding properties. Here we describe how these dynamic methods can be used to

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

DEFF Research Database (Denmark)

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

2014-01-01

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

Dynamic neural network of insight: a functional magnetic resonance imaging study on solving Chinese 'chengyu' riddles.

Directory of Open Access Journals (Sweden)

Qingbai Zhao

Full Text Available The key components of insight include breaking mental sets and forming the novel, task-related associations. The majority of researchers have agreed that the anterior cingulate cortex may mediate processes of breaking one's mental set, while the exact neural correlates of forming novel associations are still debatable. In the present study, we used a paradigm of answer selection to explore brain activations of insight by using event-related functional magnetic resonance imaging during solving Chinese 'chengyu' (in Chinese pinyin riddles. Based on the participant's choice, the trials were classified into the insight and non-insight conditions. Both stimulus-locked and response-locked analyses are conducted to detect the neural activity corresponding to the early and late periods of insight solution, respectively. Our data indicate that the early period of insight solution shows more activation in the middle temporal gyrus, the middle frontal gyrus and the anterior cingulate cortex. These activities might be associated to the extensive semantic processing, as well as detecting and resolving cognitive conflicts. In contrast, the late period of insight solution produced increased activities in the hippocampus and the amygdala, possibly reflecting the forming of novel association and the concomitant "Aha" feeling. Our study supports the key role of hippocampus in forming novel associations, and indicates a dynamic neural network during insight solution.

Clinical studies of functional imaging of dynamic CT for chronic brain-damaged patients

International Nuclear Information System (INIS)

Inada, Haruo; Miyano, Satoshi

1995-01-01

The 311 brain-damaged patients, mostly of cerebrovascular disease (CVD) were examined by functional imaging to dynamic CT (FIDCT) at Tokyo Metropolitan Rehabilitation Hospital. The abnormal patterns of FIDCT were classified according to two categories, i.e. focal area where plain CT showed low density area (LDA), and extra-focal area where plain CT showed no abnormal findings. These patterns were diagnosed by using the two parameters, i.e. Corrected First Moment (CM) and Time to Peak (TP). Over 50% of the focal abnormal FIDCT revealed tha same area with LDA on plain CT. The extra-focal FIDCT showed various abnormal patterns, and only 11% of all the findings had no abnormalities. The correlation of the specific patterns of extra-focal FIDCT with the multiple CVD episodes was investigated, and the findings that had significant correlation were (a) delayed CM of bilateral white matter, (b) diffusely delayed TP of the affected hemisphere, and the patient group that showed no extra-focal abnormal FIDCT had significant low incidence of multiple CVD episodes. From these results, it is concluded that the high-risk group of stroke recurrence can be predicted by extra-focal findings of FIDCT. (author)

Clinical studies of functional imaging of dynamic CT for chronic brain-damaged patients

Energy Technology Data Exchange (ETDEWEB)

Inada, Haruo; Miyano, Satoshi [Jikei Univ., Tokyo (Japan). School of Medicine

1995-03-01

The 311 brain-damaged patients, mostly of cerebrovascular disease (CVD) were examined by functional imaging to dynamic CT (FIDCT) at Tokyo Metropolitan Rehabilitation Hospital. The abnormal patterns of FIDCT were classified according to two categories, i.e. focal area where plain CT showed low density area (LDA), and extra-focal area where plain CT showed no abnormal findings. These patterns were diagnosed by using the two parameters, i.e. Corrected First Moment (CM) and Time to Peak (TP). Over 50% of the focal abnormal FIDCT revealed tha same area with LDA on plain CT. The extra-focal FIDCT showed various abnormal patterns, and only 11% of all the findings had no abnormalities. The correlation of the specific patterns of extra-focal FIDCT with the multiple CVD episodes was investigated, and the findings that had significant correlation were (a) delayed CM of bilateral white matter, (b) diffusely delayed TP of the affected hemisphere, and the patient group that showed no extra-focal abnormal FIDCT had significant low incidence of multiple CVD episodes. From these results, it is concluded that the high-risk group of stroke recurrence can be predicted by extra-focal findings of FIDCT. (author).

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

Energy Technology Data Exchange (ETDEWEB)

Ji, Pengfei; Zhang, Yuwen, E-mail: zhangyu@missouri.edu [Department of Mechanical and Aerospace Engineering, University of Missouri, Columbia, Missouri 65211 (United States); Yang, Mo [College of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai 200093 (China)

2013-12-21

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

International Nuclear Information System (INIS)

Ji, Pengfei; Zhang, Yuwen; Yang, Mo

2013-01-01

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

Science.gov (United States)

Ji, Pengfei; Zhang, Yuwen; Yang, Mo

2013-12-01

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.

In Situ Test Study of Characteristics of Coal Mining Dynamic Load

Directory of Open Access Journals (Sweden)

Jiang He

2015-01-01

Full Text Available Combination of coal mining dynamic load and high static stress can easily induce such dynamic disasters as rock burst, coal and gas outburst, roof fall, and water inrush. In order to obtain the characteristic parameters of mining dynamic load and dynamic mechanism of coal and rock, the stress wave theory is applied to derive the relation of mining dynamic load strain rate and stress wave parameters. The in situ test was applied to study the stress wave propagation law of coal mine dynamic load by using the SOS microseismic monitoring system. An evaluation method for mining dynamic load strain rate was proposed, and the statistical evaluation was carried out for the range of strain rate. The research results show that the loading strain rate of mining dynamic load is in direct proportion to the seismic frequency of coal-rock mass and particle peak vibration velocity and is in inverse proportion to wave velocity. The high-frequency component damps faster than the low-frequency component in the shockwave propagating process; and the peak particle vibration velocity has a power functional relationship with the transmitting distance. The loading strain rate of mining dynamic load is generally less than class 10−1/s.

The dynamic functional capacity theory: A neuropsychological model of intense emotions

Directory of Open Access Journals (Sweden)

Philip C. Klineburger

2015-12-01

Full Text Available The music-evoked emotion literature implicates many brain regions involved in emotional processing but is currently lacking a model that specifically explains how they temporally and dynamically interact to produce intensely pleasurable emotions. A conceptual model, the dynamic functional capacity theory (DFCT, is proposed and provides a foundation for the further understanding of how brain regions interact to produce intensely pleasurable emotions. The DFCT claims that brain regions mediating emotion and arousal regulation have a limited functional capacity that can be exceeded by intense stimuli. The prefrontal cortex is hypothesized to abruptly deactivate when this happens, resulting in the inhibitory release of sensory cortices, the limbic system, the reward-circuit, and the brainstem reticular activating system, causing “unbridled” activation of these areas. This process is hypothesized to produce extremely intense emotions. This theory may provide—music-evoked emotion researchers and music therapy researchers—a theoretical foundation for continued research and complement current theories of emotion.

Dynamics of EEG functional connectivity during statistical learning.

Science.gov (United States)

Tóth, Brigitta; Janacsek, Karolina; Takács, Ádám; Kóbor, Andrea; Zavecz, Zsófia; Nemeth, Dezso

2017-10-01

Statistical learning is a fundamental mechanism of the brain, which extracts and represents regularities of our environment. Statistical learning is crucial in predictive processing, and in the acquisition of perceptual, motor, cognitive, and social skills. Although previous studies have revealed competitive neurocognitive processes underlying statistical learning, the neural communication of the related brain regions (functional connectivity, FC) has not yet been investigated. The present study aimed to fill this gap by investigating FC networks that promote statistical learning in humans. Young adults (N=28) performed a statistical learning task while 128-channels EEG was acquired. The task involved probabilistic sequences, which enabled to measure incidental/implicit learning of conditional probabilities. Phase synchronization in seven frequency bands was used to quantify FC between cortical regions during the first, second, and third periods of the learning task, respectively. Here we show that statistical learning is negatively correlated with FC of the anterior brain regions in slow (theta) and fast (beta) oscillations. These negative correlations increased as the learning progressed. Our findings provide evidence that dynamic antagonist brain networks serve a hallmark of statistical learning. Copyright © 2017 Elsevier Inc. All rights reserved.

Semiclassical dynamics

International Nuclear Information System (INIS)

Balazs, N.L.

1979-01-01

It is pointed out that in semiclassical dynamics one is encouraged to study the evolution of those curves in phase space which classically represent ensembles corresponding to wave functions. It is shown that the fixed points generate new time scales so that for times longer than the critical times, quantum dynamics will profoundly differ from classical dynamics. (P.L.)

Magnetic Dynamics of Fine Particles Studied by Inelastic Neutron Scattering

DEFF Research Database (Denmark)

Hansen, Mikkel Fougt; Bødker, Franz; Mørup, Steen

2000-01-01

We give an introduction to inelastic neutron scattering and the dynamic scattering function for magnetic nanoparticles. Differences between ferromagnetic and antiferromagnetic nanoparticles are discussed and we give a review of recent results on ferromagnetic Fe nanoparticles and canted antiferro......We give an introduction to inelastic neutron scattering and the dynamic scattering function for magnetic nanoparticles. Differences between ferromagnetic and antiferromagnetic nanoparticles are discussed and we give a review of recent results on ferromagnetic Fe nanoparticles and canted...

Alterations of Resting-State Static and Dynamic Functional Connectivity of the Dorsolateral Prefrontal Cortex in Subjects with Internet Gaming Disorder

Directory of Open Access Journals (Sweden)

Xu Han

2018-02-01

Full Text Available Internet gaming disorder (IGD, a major behavior disorder, has gained increasing attention. Recent studies indicate altered resting-state static functional connectivity (FC of the dorsolateral prefrontal cortex (DLPFC in subjects with IGD. Whereas static FC often provides information on functional changes in subjects with IGD, investigations of temporal changes in FC between the DLPFC and the other brain regions may shed light on the dynamic characteristics of brain function associated with IGD. Thirty subjects with IGD and 30 healthy controls (HCs matched for age, gender and education status were recruited. Using the bilateral DLPFC as seeds, static FC and dynamic FC maps were calculated and compared between groups. Correlations between alterations in static FC and dynamic FC and clinical variables were also investigated within the IGD group. The IGD group showed significantly lower static FC between the right DLPFC and the left rolandic operculum while higher static FC between the right DLPFC and the left pars triangularis when compared to HCs. The IGD group also had significantly decreased dynamic FC between the right DLPFC and the left insula, right putamen and left precentral gyrus, and increased dynamic FC in the left precuneus. Moreover, the dynamic FC between the right DLPFC and the left insula was negatively correlated with the severity of IGD. Dynamic FC can be used as a powerful supplement to static FC, helping us obtain a more comprehensive understanding of large-scale brain network activity in IGD and put forward new ideas for behavioral intervention therapy for it.

Imperialist Competitive Algorithm with Dynamic Parameter Adaptation Using Fuzzy Logic Applied to the Optimization of Mathematical Functions

Directory of Open Access Journals (Sweden)

Emer Bernal

2017-01-01

Full Text Available In this paper we are presenting a method using fuzzy logic for dynamic parameter adaptation in the imperialist competitive algorithm, which is usually known by its acronym ICA. The ICA algorithm was initially studied in its original form to find out how it works and what parameters have more effect upon its results. Based on this study, several designs of fuzzy systems for dynamic adjustment of the ICA parameters are proposed. The experiments were performed on the basis of solving complex optimization problems, particularly applied to benchmark mathematical functions. A comparison of the original imperialist competitive algorithm and our proposed fuzzy imperialist competitive algorithm was performed. In addition, the fuzzy ICA was compared with another metaheuristic using a statistical test to measure the advantage of the proposed fuzzy approach for dynamic parameter adaptation.

Tissue architecture and function: dynamic reciprocity via extra- and intra-cellular matrices

Energy Technology Data Exchange (ETDEWEB)

Xu, Ren; Boudreau, Aaron; Bissell, Mina J

2008-12-23

Mammary gland development, functional differentiation, and homeostasis are orchestrated and sustained by a balance of biochemical and biophysical cues from the organ's microenvironment. The three-dimensional microenvironment of the mammary gland, predominantly 'encoded' by a collaboration between the extracellular matrix (ECM), hormones, and growth factors, sends signals from ECM receptors through the cytoskeletal intracellular matrix to nuclear and chromatin structures resulting in gene expression; the ECM in turn is regulated and remodeled by signals from the nucleus. In this chapter, we discuss how coordinated ECM deposition and remodeling is necessary for mammary gland development, how the ECM provides structural and biochemical cues necessary for tissue-specific function, and the role of the cytoskeleton in mediating the extra - to intracellular dialogue occurring between the nucleus and the microenvironment. When operating normally, the cytoskeletal-mediated dynamic and reciprocal integration of tissue architecture and function directs mammary gland development, tissue polarity, and ultimately, tissue-specific gene expression. Cancer occurs when these dynamic interactions go awry for an extended time.

Locally optimal control under unknown dynamics with learnt cost function: application to industrial robot positioning

Science.gov (United States)

Guérin, Joris; Gibaru, Olivier; Thiery, Stéphane; Nyiri, Eric

2017-01-01

Recent methods of Reinforcement Learning have enabled to solve difficult, high dimensional, robotic tasks under unknown dynamics using iterative Linear Quadratic Gaussian control theory. These algorithms are based on building a local time-varying linear model of the dynamics from data gathered through interaction with the environment. In such tasks, the cost function is often expressed directly in terms of the state and control variables so that it can be locally quadratized to run the algorithm. If the cost is expressed in terms of other variables, a model is required to compute the cost function from the variables manipulated. We propose a method to learn the cost function directly from the data, in the same way as for the dynamics. This way, the cost function can be defined in terms of any measurable quantity and thus can be chosen more appropriately for the task to be carried out. With our method, any sensor information can be used to design the cost function. We demonstrate the efficiency of this method through simulating, with the V-REP software, the learning of a Cartesian positioning task on several industrial robots with different characteristics. The robots are controlled in joint space and no model is provided a priori. Our results are compared with another model free technique, consisting in writing the cost function as a state variable.

Structural connectivity in schizophrenia and its impact on the dynamics of spontaneous functional networks

International Nuclear Information System (INIS)

Cabral, Joana; Fernandes, Henrique M.; Van Hartevelt, Tim J.; Kringelbach, Morten L.; James, Anthony C.; Deco, Gustavo

2013-01-01

The neuropathology of schizophrenia remains unclear. Some insight has come from modern neuroimaging techniques, which offer an unparalleled opportunity to explore in vivo the structure and function of the brain. Using functional magnetic resonance imaging, it has been found that the large-scale resting-state functional connectivity (rsFC) in schizophrenia — measured as the temporal correlations of the blood-oxygen-level-dependent (BOLD) signal — exhibit altered network topology, with lower small-world index. The origin of these rsFC alterations and link with the underlying structural connectivity remain unclear. In this work, we used a computational model of spontaneous large-scale brain activity to explore the role of the structural connectivity in the large-scale dynamics of the brain in health and schizophrenia. The structural connectomes from 15 adolescent patients with early-onset schizophrenia and 15 age- and gender-matched controls were built from diffusion tensor imaging data to detect the white matter tracts between 90 brain areas. Brain areas, simulated using a reduced dynamic mean-field model, receive excitatory input from other areas in proportion to the number of fibre tracts between them. The simulated mean field activity was transformed into BOLD signal, and the properties of the simulated functional networks were analyzed. Our results suggest that the functional alterations observed in schizophrenia are not directly linked to alterations in the structural topology. Instead, subtly randomized and less small-world functional networks appear when the brain operates with lower global coupling, which shifts the dynamics from the optimal healthy regime

Structural connectivity in schizophrenia and its impact on the dynamics of spontaneous functional networks

Energy Technology Data Exchange (ETDEWEB)

Cabral, Joana [Theoretical and Computational Neuroscience Group, Center of Brain and Cognition, Universitat Pompeu Fabra, Barcelona 08018 (Spain); Department of Psychiatry, University of Oxford, Oxford OX3 7JX (United Kingdom); Fernandes, Henrique M.; Van Hartevelt, Tim J.; Kringelbach, Morten L. [Department of Psychiatry, University of Oxford, Oxford OX3 7JX (United Kingdom); Center of Functionally Integrative Neuroscience (CFIN), Aarhus University, Aarhus (Denmark); James, Anthony C. [Department of Psychiatry, University of Oxford, Oxford OX3 7JX (United Kingdom); Highfield Unit, Warneford Hospital, Oxford OX3 7JX (United Kingdom); Deco, Gustavo [Theoretical and Computational Neuroscience Group, Center of Brain and Cognition, Universitat Pompeu Fabra, Barcelona 08018 (Spain); Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010 (Spain)

2013-12-15

The neuropathology of schizophrenia remains unclear. Some insight has come from modern neuroimaging techniques, which offer an unparalleled opportunity to explore in vivo the structure and function of the brain. Using functional magnetic resonance imaging, it has been found that the large-scale resting-state functional connectivity (rsFC) in schizophrenia — measured as the temporal correlations of the blood-oxygen-level-dependent (BOLD) signal — exhibit altered network topology, with lower small-world index. The origin of these rsFC alterations and link with the underlying structural connectivity remain unclear. In this work, we used a computational model of spontaneous large-scale brain activity to explore the role of the structural connectivity in the large-scale dynamics of the brain in health and schizophrenia. The structural connectomes from 15 adolescent patients with early-onset schizophrenia and 15 age- and gender-matched controls were built from diffusion tensor imaging data to detect the white matter tracts between 90 brain areas. Brain areas, simulated using a reduced dynamic mean-field model, receive excitatory input from other areas in proportion to the number of fibre tracts between them. The simulated mean field activity was transformed into BOLD signal, and the properties of the simulated functional networks were analyzed. Our results suggest that the functional alterations observed in schizophrenia are not directly linked to alterations in the structural topology. Instead, subtly randomized and less small-world functional networks appear when the brain operates with lower global coupling, which shifts the dynamics from the optimal healthy regime.

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

Directory of Open Access Journals (Sweden)

Boris Dyatkin

2015-12-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2015-12-01

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

Lattice dynamics and molecular dynamics simulation of complex materials

International Nuclear Information System (INIS)

Chaplot, S.L.

1997-01-01

In this article we briefly review the lattice dynamics and molecular dynamics simulation techniques, as used for complex ionic and molecular solids, and demonstrate a number of applications through examples of our work. These computational studies, along with experiments, have provided microscopic insight into the structure and dynamics, phase transitions and thermodynamical properties of a variety of materials including fullerene, high temperature superconducting oxides and geological minerals as a function of pressure and temperature. The computational techniques also allow the study of the structures and dynamics associated with disorder, defects, surfaces, interfaces etc. (author)

Dynamical equations for time-ordered Green’s functions: from the Keldysh time-loop contour to equilibrium at finite and zero temperature

International Nuclear Information System (INIS)

Ness, H; Dash, L K

2012-01-01

We study the dynamical equation of the time-ordered Green’s function at finite temperature. We show that the time-ordered Green’s function obeys a conventional Dyson equation only at equilibrium and in the limit of zero temperature. In all other cases, i.e. finite temperature at equilibrium or non-equilibrium, the time-ordered Green’s function obeys instead a modified Dyson equation. The derivation of this result is obtained from the general formalism of the non-equilibrium Green’s functions on the Keldysh time-loop contour. At equilibrium, our result is fully consistent with the Matsubara temperature Green’s function formalism and also justifies rigorously the correction terms introduced in an ad hoc way with Hedin and Lundqvist. Our results show that one should use the appropriate dynamical equation for the time-ordered Green’s function when working beyond the equilibrium zero-temperature limit.

Investigation of Balance Function Using Dynamic Posturography under Electrical-Acoustic Stimulation in Cochlear Implant Recipients

Directory of Open Access Journals (Sweden)

B. Schwab

2010-01-01

Full Text Available Introduction. The purpose of the present study is to investigate the effect of electrical-acoustic stimulation on vestibular function in CI patients by using the EquiTest and to help answer the question of whether electrically stimulating the inner ear using a cochlear implant influences the balance system in any way. Material and Methods. A test population (=50 was selected at random from among the cochlear implant recipients. Dynamic posturography (using the EquiTest was performed with the device switched off an switched on. Results. In summary, it can be said that an activated cochlear implant affects the function of the vestibular system and may, to an extent, even lead to a stabilization of balance function under the static conditions of dynamic posturography, but nevertheless also to a significant destabilization. Significant improvements in vestibular function were seen mainly in equilibrium scores under conditions 4 and 5, the composite equilibrium score, and the vestibular components as revealed by sensory analysis. Conclusions. Only under the static conditions are significantly poorer scores achieved when stimulation is applied. It may be that the explanation for any symptoms of dizziness lies precisely in the fact that they occur in supposedly noncritical situations, since, when the cochlear implant makes increased demands on the balance system, induced disturbances can be centrally suppressed.

Extended dynamic oligopolies with flexible workforce and isoelastic price function

Directory of Open Access Journals (Sweden)

Akio Matsumoto

2016-11-01

Full Text Available Single-product oligopolies without product differentiation are examined with linear production, production adjustment, flexible workforce and investment costs. The price function is assumed to be hyperbolic which makes the nonlinearity of the model much stronger than in the case of linear price function examined earlier in the literature. The best responses of the firms are determined which are not monotonic in contrast to the linear case. The set of all steady states is then characterized and in the case of a duopoly it is illustrated. The asymptotical behavior of the steady states is examined by using simulation. We analyze the effects of such costs on the industry dynamics and compare them to the prediction by the well known model with hyperbolic price function and no product adjustment and investments costs.

High-speed AFM for Studying Dynamic Biomolecular Processes

Science.gov (United States)

Ando, Toshio

2008-03-01

Biological molecules show their vital activities only in aqueous solutions. It had been one of dreams in biological sciences to directly observe biological macromolecules (protein, DNA) at work under a physiological condition because such observation is straightforward to understanding their dynamic behaviors and functional mechanisms. Optical microscopy has no sufficient spatial resolution and electron microscopy is not applicable to in-liquid samples. Atomic force microscopy (AFM) can visualize molecules in liquids at high resolution but its imaging rate was too low to capture dynamic biological processes. This slow imaging rate is because AFM employs mechanical probes (cantilevers) and mechanical scanners to detect the sample height at each pixel. It is quite difficult to quickly move a mechanical device of macroscopic size with sub-nanometer accuracy without producing unwanted vibrations. It is also difficult to maintain the delicate contact between a probe tip and fragile samples. Two key techniques are required to realize high-speed AFM for biological research; fast feedback control to maintain a weak tip-sample interaction force and a technique to suppress mechanical vibrations of the scanner. Various efforts have been carried out in the past decade to materialize high-speed AFM. The current high-speed AFM can capture images on video at 30-60 frames/s for a scan range of 250nm and 100 scan lines, without significantly disturbing week biomolecular interaction. Our recent studies demonstrated that this new microscope can reveal biomolecular processes such as myosin V walking along actin tracks and association/dissociation dynamics of chaperonin GroEL-GroES that occurs in a negatively cooperative manner. The capacity of nanometer-scale visualization of dynamic processes in liquids will innovate on biological research. In addition, it will open a new way to study dynamic chemical/physical processes of various phenomena that occur at the liquid-solid interfaces.

CONNECTION BETWEEN DYNAMICALLY DERIVED INITIAL MASS FUNCTION NORMALIZATION AND STELLAR POPULATION PARAMETERS

Energy Technology Data Exchange (ETDEWEB)

McDermid, Richard M. [Department of Physics and Astronomy, Macquarie University, Sydney NSW 2109 (Australia); Cappellari, Michele; Bayet, Estelle; Bureau, Martin; Davies, Roger L. [Sub-Department of Astrophysics, Department of Physics, University of Oxford, Denys Wilkinson Building, Keble Road, Oxford, OX1 3RH (United Kingdom); Alatalo, Katherine [Infrared Processing and Analysis Center, California Institute of Technology, Pasadena, CA 91125 (United States); Blitz, Leo [Department of Astronomy, Campbell Hall, University of California, Berkeley, CA 94720 (United States); Bois, Maxime [Observatoire de Paris, LERMA and CNRS, 61 Av. de l' Observatoire, F-75014 Paris (France); Bournaud, Frédéric; Duc, Pierre-Alain [Laboratoire AIM Paris-Saclay, CEA/IRFU/SAp- CNRS-Université Paris Diderot, F-91191 Gif-sur-Yvette Cedex (France); Crocker, Alison F. [Ritter Astrophysical Observatory, University of Toledo, Toledo, OH 43606 (United States); Davis, Timothy A.; De Zeeuw, P. T.; Emsellem, Eric; Kuntschner, Harald [European Southern Observatory, Karl-Schwarzschild-Str. 2, D-85748 Garching (Germany); Khochfar, Sadegh [Institute for Astronomy, University of Edinburgh, Royal Observatory, Edinburgh, EH9 3HJ (United Kingdom); Krajnović, Davor [Leibniz-Institut für Astrophysik Potsdam (AIP), An der Sternwarte 16, D-14482 Potsdam (Germany); Morganti, Raffaella; Oosterloo, Tom [Netherlands Institute for Radio Astronomy (ASTRON), Postbus 2, 7990 AA Dwingeloo (Netherlands); Naab, Thorsten, E-mail: richard.mcdermid@mq.edu.au [Max-Planck-Institut für Astrophysik, Karl-Schwarzschild-Str. 1, D-85741 Garching (Germany); and others

2014-09-10

We report on empirical trends between the dynamically determined stellar initial mass function (IMF) and stellar population properties for a complete, volume-limited sample of 260 early-type galaxies from the ATLAS{sup 3D} project. We study trends between our dynamically derived IMF normalization α{sub dyn} ≡ (M/L){sub stars}/(M/L){sub Salp} and absorption line strengths, and interpret these via single stellar population-equivalent ages, abundance ratios (measured as [α/Fe]), and total metallicity, [Z/H]. We find that old and alpha-enhanced galaxies tend to have on average heavier (Salpeter-like) mass normalization of the IMF, but stellar population does not appear to be a good predictor of the IMF, with a large range of α{sub dyn} at a given population parameter. As a result, we find weak α{sub dyn}-[α/Fe] and α{sub dyn} –Age correlations and no significant α{sub dyn} –[Z/H] correlation. The observed trends appear significantly weaker than those reported in studies that measure the IMF normalization via the low-mass star demographics inferred through stellar spectral analysis.

Collagenolytic Matrix Metalloproteinase Structure-Function Relationships: Insights From Molecular Dynamics Studies.

Science.gov (United States)

Karabencheva-Christova, Tatyana G; Christov, Christo Z; Fields, Gregg B

2017-01-01

Several members of the zinc-dependent matrix metalloproteinase (MMP) family catalyze collagen degradation. Experimental data reveal a collaboration between different MMP domains in order to achieve efficient collagenolysis. Molecular dynamics (MD) simulations have been utilized to provide atomistic details of the collagenolytic process. The triple-helical structure of collagen exhibits local regions of flexibility, with modulation of interchain salt bridges and water bridges contributing to accessibility of individual chains by the enzyme. In turn, the hemopexin-like (HPX) domain of the MMP initially binds the triple helix and facilitates the presentation of individual strands to active site in the catalytic (CAT) domain. Extensive positive and negative correlated motions are observed between the CAT and HPX domains when collagen is bound. Ultimately, the MD simulation studies have complemented structural (NMR spectroscopy, X-ray crystallography) and kinetic analyses to provide a more detailed mechanistic view of MMP-catalyzed collagenolysis. © 2017 Elsevier Inc. All rights reserved.

Dissociation of polycyclic aromatic hydrocarbons: molecular dynamics studies

Science.gov (United States)

Simon, A.; Rapacioli, M.; Rouaut, G.; Trinquier, G.; Gadéa, F. X.

2017-03-01

We present dynamical studies of the dissociation of polycyclic aromatic hydrocarbon (PAH) radical cations in their ground electronic states with significant internal energy. Molecular dynamics simulations are performed, the electronic structure being described on-the-fly at the self-consistent-charge density functional-based tight binding (SCC-DFTB) level of theory. The SCC-DFTB approach is first benchmarked against DFT results. Extensive simulations are achieved for naphthalene , pyrene and coronene at several energies. Such studies enable one to derive significant trends on branching ratios, kinetics, structures and hints on the formation mechanism of the ejected neutral fragments. In particular, dependence of branching ratios on PAH size and energy were retrieved. The losses of H and C2H2 (recognized as the ethyne molecule) were identified as major dissociation channels. The H/C2H2 ratio was found to increase with PAH size and to decrease with energy. For , which is the most interesting PAH from the astrophysical point of view, the loss of H was found as the quasi-only channel for an internal energy of 30 eV. Overall, in line with experimental trends, decreasing the internal energy or increasing the PAH size will favour the hydrogen loss channels with respect to carbonaceous fragments. This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.

Q-angle in patellofemoral pain: relationship with dynamic knee valgus, hip abductor torque, pain and function

Directory of Open Access Journals (Sweden)

Gabriel Peixoto Leão Almeida

2016-04-01

Full Text Available OBJECTIVE: To investigate the relationship between the q-angle and anterior knee pain severity, functional capacity, dynamic knee valgus and hip abductor torque in women with patellofemoral pain syndrome (PFPS. METHODS: This study included 22 women with PFPS. The q-angle was assessed using goniometry: the participants were positioned in dorsal decubitus with the knee and hip extended, and the hip and foot in neutral rotation. Anterior knee pain severity was assessed using a visual analog scale, and functional capacity was assessed using the anterior knee pain scale. Dynamic valgus was evaluated using the frontal plane projection angle (FPPA of the knee, which was recorded using a digital camera during step down, and hip abductor peak torque was recorded using a handheld dynamometer. RESULTS: The q-angle did not present any significant correlation with severity of knee pain (r = -0.29; p = 0.19, functional capacity (r = -0.08; p = 0.72, FPPA (r = -0.28; p = 0.19 or isometric peak torque of the abductor muscles (r = -0.21; p = 0.35. CONCLUSION: The q-angle did not present any relationship with pain intensity, functional capacity, FPPA, or hip abductor peak torque in the patients with PFPS.

Direct Quantum Dynamics Using Grid-Based Wave Function Propagation and Machine-Learned Potential Energy Surfaces.

Science.gov (United States)

Richings, Gareth W; Habershon, Scott

2017-09-12

We describe a method for performing nuclear quantum dynamics calculations using standard, grid-based algorithms, including the multiconfiguration time-dependent Hartree (MCTDH) method, where the potential energy surface (PES) is calculated "on-the-fly". The method of Gaussian process regression (GPR) is used to construct a global representation of the PES using values of the energy at points distributed in molecular configuration space during the course of the wavepacket propagation. We demonstrate this direct dynamics approach for both an analytical PES function describing 3-dimensional proton transfer dynamics in malonaldehyde and for 2- and 6-dimensional quantum dynamics simulations of proton transfer in salicylaldimine. In the case of salicylaldimine we also perform calculations in which the PES is constructed using Hartree-Fock calculations through an interface to an ab initio electronic structure code. In all cases, the results of the quantum dynamics simulations are in excellent agreement with previous simulations of both systems yet do not require prior fitting of a PES at any stage. Our approach (implemented in a development version of the Quantics package) opens a route to performing accurate quantum dynamics simulations via wave function propagation of many-dimensional molecular systems in a direct and efficient manner.

COPEWELL: A Conceptual Framework and System Dynamics Model for Predicting Community Functioning and Resilience After Disasters.

Science.gov (United States)

Links, Jonathan M; Schwartz, Brian S; Lin, Sen; Kanarek, Norma; Mitrani-Reiser, Judith; Sell, Tara Kirk; Watson, Crystal R; Ward, Doug; Slemp, Cathy; Burhans, Robert; Gill, Kimberly; Igusa, Tak; Zhao, Xilei; Aguirre, Benigno; Trainor, Joseph; Nigg, Joanne; Inglesby, Thomas; Carbone, Eric; Kendra, James M

2018-02-01

Policy-makers and practitioners have a need to assess community resilience in disasters. Prior efforts conflated resilience with community functioning, combined resistance and recovery (the components of resilience), and relied on a static model for what is inherently a dynamic process. We sought to develop linked conceptual and computational models of community functioning and resilience after a disaster. We developed a system dynamics computational model that predicts community functioning after a disaster. The computational model outputted the time course of community functioning before, during, and after a disaster, which was used to calculate resistance, recovery, and resilience for all US counties. The conceptual model explicitly separated resilience from community functioning and identified all key components for each, which were translated into a system dynamics computational model with connections and feedbacks. The components were represented by publicly available measures at the county level. Baseline community functioning, resistance, recovery, and resilience evidenced a range of values and geographic clustering, consistent with hypotheses based on the disaster literature. The work is transparent, motivates ongoing refinements, and identifies areas for improved measurements. After validation, such a model can be used to identify effective investments to enhance community resilience. (Disaster Med Public Health Preparedness. 2018;12:127-137).

Applied systems theory as a means for studying the function and dynamics of living space used for agro-silviculture

Energy Technology Data Exchange (ETDEWEB)

Grossmann, W D; Schneider, T W

1980-09-01

Applied systems theories are sensitive tools for analysing the functions and dynamics of agrosilvicultural systems. Major interactions within and between agrosilvicultural systems and the natural and socio-economic environment are represented by corresponding interactions within a hierarchy of system models. A new meta-criteria analysis quantifies the variables of agrosilvicultural systems and produces indicators for assessing the stability or instability of the whole system complex. Two highly disaggregated models predict growth and yield and analyse structure and floristic variation of forest systems.

Studying Membrane Protein Structure and Function Using Nanodiscs

DEFF Research Database (Denmark)

Huda, Pie

The structure and dynamic of membrane proteins can provide valuable information about general functions, diseases and effects of various drugs. Studying membrane proteins are a challenge as an amphiphilic environment is necessary to stabilise the protein in a functionally and structurally relevant...... form. This is most typically achieved through the use of detergent based reconstitution systems. However, time and again such systems fail to provide a suitable environment causing aggregation and inactivation. Nanodiscs are self-assembled lipoproteins containing two membrane scaffold proteins...... and a lipid bilayer in defined nanometer size, which can act as a stabiliser for membrane proteins. This enables both functional and structural investigation of membrane proteins in a detergent free environment which is closer to the native situation. Understanding the self-assembly of nanodiscs is important...

Study on dynamic behavior analysis of towed line array sensor

Directory of Open Access Journals (Sweden)

Hyun Kyoung Shin

2012-03-01

Full Text Available A set of equations of motion is derived for vibratory motions of an underwater cable connected to a moving vehicle at one end and with drogues at the other end. From the static analysis, cable configurations are obtained for different vehicle speeds and towing pretensions are determined by fluid resistance of drogues. Also the dynamic analysis is required to predict its vibratory motion. Nonlinear fluid drag forces greatly influence the dynamic tension. In this study, a numerical analysis program was developed to find out the characteristic of cable behaviour. The motion is described in terms of space and time coordinates based on Chebyshev polynomial expansions. For the spatial integration the collocation method is employed and the Newmark method is applied for the time integration. Dynamic tensions, displacements, velocities, accelerations were predicted in the time domain while natural frequencies and transfer functions were obtained in the frequency domain.

Dynamic Graphics in Excel for Teaching Statistics: Understanding the Probability Density Function

Science.gov (United States)

Coll-Serrano, Vicente; Blasco-Blasco, Olga; Alvarez-Jareno, Jose A.

2011-01-01

In this article, we show a dynamic graphic in Excel that is used to introduce an important concept in our subject, Statistics I: the probability density function. This interactive graphic seeks to facilitate conceptual understanding of the main aspects analysed by the learners.

Functional dynamic MR imaging and pharmacokinetics of Gd-DTPA in patients with renal failure

International Nuclear Information System (INIS)

Krestin, G.P.; Neufang, K.F.R.; Friedmann, G.; Clauss, W.; Schuhmann-Giampieri, G.; Stoeckl, B.

1989-01-01

This paper reports excretion of Gd-DTPA analyzed in 20 patients with renal parenchymal disease and decreased creatinine clearance (20-80 mL/min) and compared with excretion in five patients with normal renal function. All 25 underwent a dynamic MR study that employed fast gradient-echo sequences with single images during breath holding. The time between appearance of the contrast agent in the renal cortex and signal intensity drop in the medulla was an indicator of glomerular filtration rate and correlated well with creatinine clearance values. Fractionate urine collection and serum analysis up to 120 hours showed a prolonged but complete (98%) elimination of Gd-DTPA. Renal functional parameters did not change after administration of Gd-DTPA, and no nephrotoxic effects were observed. Thus, MR imaging provides a good quantitative evaluation of the glomerular filtration rate; moreover, administration of Gd-DTPA in patients with renal failure does not impair excretory function and can therefore be safely applied in patients with reduced excretory function

Aquaporin-4 Functionality and Virchow-Robin Space Water Dynamics: Physiological Model for Neurovascular Coupling and Glymphatic Flow.

Science.gov (United States)

Nakada, Tsutomu; Kwee, Ingrid L; Igarashi, Hironaka; Suzuki, Yuji

2017-08-18

The unique properties of brain capillary endothelium, critical in maintaining the blood-brain barrier (BBB) and restricting water permeability across the BBB, have important consequences on fluid hydrodynamics inside the BBB hereto inadequately recognized. Recent studies indicate that the mechanisms underlying brain water dynamics are distinct from systemic tissue water dynamics. Hydrostatic pressure created by the systolic force of the heart, essential for interstitial circulation and lymphatic flow in systemic circulation, is effectively impeded from propagating into the interstitial fluid inside the BBB by the tightly sealed endothelium of brain capillaries. Instead, fluid dynamics inside the BBB is realized by aquaporin-4 (AQP-4), the water channel that connects astrocyte cytoplasm and extracellular (interstitial) fluid. Brain interstitial fluid dynamics, and therefore AQP-4, are now recognized as essential for two unique functions, namely, neurovascular coupling and glymphatic flow, the brain equivalent of systemic lymphatics.

Reconstruction of tissue dynamics in the compressed breast using multiplexed measurements and temporal basis functions

Science.gov (United States)

Boverman, Gregory; Miller, Eric L.; Brooks, Dana H.; Fang, Qianqian; Carp, S. A.; Selb, J. J.; Boas, David A.

2007-02-01

In the course of our experiments imaging the compressed breast in conjunction with digital tomosynthesis, we have noted that significant changes in tissue optical properties, on the order of 5%, occur during our imaging protocol. These changes seem to consistent with changes both in total Hemoglobin concentration as well as in oxygen saturation, as was the case for our standalone breast compression study, which made use of reflectance measurements. Simulation experiments show the importance of taking into account the temporal dynamics in the image reconstruction, and demonstrate the possibility of imaging the spatio-temporal dynamics of oxygen saturation and total Hemoglobin in the breast. In the image reconstruction, we make use of spatio-temporal basis functions, specifically a voxel basis for spatial imaging, and a cubic spline basis in time, and we reconstruct the spatio-temporal images using the entire data set simultaneously, making use of both absolute and relative measurements in the cost function. We have modified the sequence of sources used in our imaging acquisition protocol to improve our temporal resolution, and preliminary results are shown for normal subjects.

Studying Dynamics in Business Networks

DEFF Research Database (Denmark)

Andersen, Poul Houman; Anderson, Helen; Havila, Virpi

1998-01-01

This paper develops a theory on network dynamics using the concepts of role and position from sociological theory. Moreover, the theory is further tested using case studies from Denmark and Finland......This paper develops a theory on network dynamics using the concepts of role and position from sociological theory. Moreover, the theory is further tested using case studies from Denmark and Finland...

Studies of dynamics of electron clouds in STAR silicon drift detectors

CERN Document Server

Bellwied, R; Brandon, N; Caines, H; Chen, W; Dimassimo, D; Dyke, H; Hall, J R; Hardtke, D; Hoffmann, G W; Humanic, T J; Kotova, A I; Kotov, I V; Kraner, H W; Li, Z; Lynn, D; Middelkamp, P; Ott, G; Pandey, S U; Pruneau, C A; Rykov, V L; Schambach, J; Sedlmeir, J; Sugarbaker, E R; Takahashi, J; Wilson, W K

2000-01-01

The dynamics of electrons generated in silicon drift detectors was studied using an IR LED. Electrons were generated at different drift distances. In this way, the evolution of the cloud as a function of drift time was measured. Two methods were used to measure the cloud size. The method of cumulative functions was used to extract the electron cloud profiles. Another method obtains the cloud width from measurements of the charge collected on a single anode as a function of coordinate of the light spot. The evolution of the electron cloud width with drift time is compared with theoretical calculations. Experimental results agreed with theoretical expectations.

Trimethylamine-N-oxide: its hydration structure, surface activity, and biological function, viewed by vibrational spectroscopy and molecular dynamics simulations.

Science.gov (United States)

Ohto, Tatsuhiko; Hunger, Johannes; Backus, Ellen H G; Mizukami, Wataru; Bonn, Mischa; Nagata, Yuki

2017-03-08

The osmolyte molecule trimethylamine-N-oxide (TMAO) stabilizes the structure of proteins. As functional proteins are generally found in aqueous solutions, an important aspect of this stabilization is the interaction of TMAO with water. Here, we review, using vibrational spectroscopy and molecular dynamics simulations, recent studies on the structure and dynamics of TMAO with its surrounding water molecules. This article ends with an outlook on the open questions on TMAO-protein and TMAO-urea interactions in aqueous environments.

Information sensitivity functions to assess parameter information gain and identifiability of dynamical systems.

Science.gov (United States)

Pant, Sanjay

2018-05-01

A new class of functions, called the 'information sensitivity functions' (ISFs), which quantify the information gain about the parameters through the measurements/observables of a dynamical system are presented. These functions can be easily computed through classical sensitivity functions alone and are based on Bayesian and information-theoretic approaches. While marginal information gain is quantified by decrease in differential entropy, correlations between arbitrary sets of parameters are assessed through mutual information. For individual parameters, these information gains are also presented as marginal posterior variances, and, to assess the effect of correlations, as conditional variances when other parameters are given. The easy to interpret ISFs can be used to (a) identify time intervals or regions in dynamical system behaviour where information about the parameters is concentrated; (b) assess the effect of measurement noise on the information gain for the parameters; (c) assess whether sufficient information in an experimental protocol (input, measurements and their frequency) is available to identify the parameters; (d) assess correlation in the posterior distribution of the parameters to identify the sets of parameters that are likely to be indistinguishable; and (e) assess identifiability problems for particular sets of parameters. © 2018 The Authors.

Molecular beam studies of adsorption dynamics

International Nuclear Information System (INIS)

Arumainayagam, C.R.; McMaster, M.C.; Madix, R.J.

1991-01-01

We have investigated the trapping dynamics of C 1 -C 3 alkanes and Xe on Pt(111) using supersonic molecular beams and a direct technique to measure trapping probabilities. We have extended a one-dimensional model based on classical mechanics to include trapping and have found semiquantitative agreement with experimental results for the dependence of the initial trapping probability on incident translational energy at normal incidence. Our measurements of the initial trapping probability as a function of incident translational energy at normal incidence are in agreement with previous mean translational energy measurements for Xe and CH 4 desorbing near the surface normal, in accordance with detailed balance. However, the angular dependence of the initial trapping probability shows deviations from normal energy scaling, demonstrating the importance of parallel momentum in the trapping process and the inadequacy of one-dimensional models. The dependence of the initial trapping probability of Xe on incident translational energy and angle is quite well fit by three-dimensional stochastic classical trajectory calculations utilizing a Morse potential. Angular distributions of the scattered molecules indicate that the trapping probability is not a sensitive function of surface temperature. The trapping probability increases with surface coverage in quantitative agreement with a modified Kisliuk model which incorporates enhanced trapping onto the monolayer. We have also used the direct technique to study trapping onto a saturated monolayer state to investigate the dynamics of extrinsic precursor adsorption and find that the initial trapping probability onto the monolayer is higher than on the clean surface. The initial trapping probability onto the monolayer scales with total energy, indicating a highly corrugated interaction potential

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

Science.gov (United States)

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

2017-12-01

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

Stability of dynamical systems on the role of monotonic and non-monotonic Lyapunov functions

CERN Document Server

Michel, Anthony N; Liu, Derong

2015-01-01

The second edition of this textbook provides a single source for the analysis of system models represented by continuous-time and discrete-time, finite-dimensional and infinite-dimensional, and continuous and discontinuous dynamical systems.  For these system models, it presents results which comprise the classical Lyapunov stability theory involving monotonic Lyapunov functions, as well as corresponding contemporary stability results involving non-monotonicLyapunov functions.Specific examples from several diverse areas are given to demonstrate the applicability of the developed theory to many important classes of systems, including digital control systems, nonlinear regulator systems, pulse-width-modulated feedback control systems, and artificial neural networks.   The authors cover the following four general topics:   -          Representation and modeling of dynamical systems of the types described above -          Presentation of Lyapunov and Lagrange stability theory for dynamical sy...

Tuning of electronic properties and dynamical stability of graphene oxide with different functional groups

Science.gov (United States)

Dabhi, Shweta D.; Jha, Prafulla K.

2017-09-01

The structural, electronic and vibrational properties of graphene oxide (GO) with varying proportion of epoxy and hydroxyl functional groups have been studied using density functional theory. The functional groups and oxygen density have an obvious influence on the electronic and vibrational properties. The dependence of band gap on associated functional groups and oxygen density shows a possibility of tuning the band gap of graphene by varying the functional groups as well as oxidation level. The absorption of high oxygen content in graphene leads to the gap opening and resulting in a transition from semimetal to semiconductor. Phonon dispersion curves show no imaginary frequency or no softening of any phonon mode throughout the Brillouin zone which confirms the dynamical stability of all considered GO models. Different groups and different oxygen density result into the varying characteristics of phonon modes. The computed results show good agreement with the experimental observations. Our results present interesting possibilities for engineering the electronic properties of graphene and GO and impact the fabrication of new electronics.

NMR studies of organic liquids confined in mesoporous materials: (1) Pore size distribution and (2) Phase behaviour and dynamic studies in restricted geometry

International Nuclear Information System (INIS)

Foerland, Kjersti

2005-01-01

In the thesis NMR spectroscopy is used for studying liquids confined in various porous materials. In the first part, pore size distributions of mesoporous silicas and controlled pore glasses were determined by measuring the 1H NMR signal from the non-frozen fraction of the confined liquid as a function of temperature, using benzene, acetonitrile and HMDS as probe molecules. In the second part, the molecular dynamics of acetonitrile, hexamethyldisilane, cyclohexane and cyclopentane confined in mesoporous materials were studied as a function of temperature. 6 papers are included with titles: 1) Pore-size determination of mesoporous materials by 1H NMR spectroscopy. 2) Pore-size distribution in mesoporous materials as studied by 1H NMR. 3) Dynamic 1H and 2H NMR investigations of acetonitrile confined in porous silica. 4) NMR investigations of hexamethyldisilane confined in controlled pore glasses: Pore size distribution and molecular dynamics studies. 5) 1H and 2H NMR studies of cyclohexane nano crystals in controlled pore glasses. 6) 1H NMR relaxation and diffusion studies of cyclohexane and cyclopentane confined in MCM-41

NMR studies of organic liquids confined in mesoporous materials: (1) Pore size distribution and (2) Phase behaviour and dynamic studies in restricted geometry

Energy Technology Data Exchange (ETDEWEB)

Foerland, Kjersti

2005-07-01

In the thesis NMR spectroscopy is used for studying liquids confined in various porous materials. In the first part, pore size distributions of mesoporous silicas and controlled pore glasses were determined by measuring the 1H NMR signal from the non-frozen fraction of the confined liquid as a function of temperature, using benzene, acetonitrile and HMDS as probe molecules. In the second part, the molecular dynamics of acetonitrile, hexamethyldisilane, cyclohexane and cyclopentane confined in mesoporous materials were studied as a function of temperature. 6 papers are included with titles: 1) Pore-size determination of mesoporous materials by 1H NMR spectroscopy. 2) Pore-size distribution in mesoporous materials as studied by 1H NMR. 3) Dynamic 1H and 2H NMR investigations of acetonitrile confined in porous silica. 4) NMR investigations of hexamethyldisilane confined in controlled pore glasses: Pore size distribution and molecular dynamics studies. 5) 1H and 2H NMR studies of cyclohexane nano crystals in controlled pore glasses. 6) 1H NMR relaxation and diffusion studies of cyclohexane and cyclopentane confined in MCM-41.

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

Directory of Open Access Journals (Sweden)

Yosef Y Kuttner

2013-04-01

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

The dynamic functional connectome: State-of-the-art and perspectives.

Science.gov (United States)

Preti, Maria Giulia; Bolton, Thomas Aw; Van De Ville, Dimitri

2017-10-15

Resting-state functional magnetic resonance imaging (fMRI) has highlighted the rich structure of brain activity in absence of a task or stimulus. A great effort has been dedicated in the last two decades to investigate functional connectivity (FC), i.e. the functional interplay between different regions of the brain, which was for a long time assumed to have stationary nature. Only recently was the dynamic behaviour of FC revealed, showing that on top of correlational patterns of spontaneous fMRI signal fluctuations, connectivity between different brain regions exhibits meaningful variations within a typical resting-state fMRI experiment. As a consequence, a considerable amount of work has been directed to assessing and characterising dynamic FC (dFC), and several different approaches were explored to identify relevant FC fluctuations. At the same time, several questions were raised about the nature of dFC, which would be of interest only if brought back to a neural origin. In support of this, correlations with electroencephalography (EEG) recordings, demographic and behavioural data were established, and various clinical applications were explored, where the potential of dFC could be preliminarily demonstrated. In this review, we aim to provide a comprehensive description of the dFC approaches proposed so far, and point at the directions that we see as most promising for the future developments of the field. Advantages and pitfalls of dFC analyses are addressed, helping the readers to orient themselves through the complex web of available methodologies and tools. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Energetics and Dynamics of GaAs Epitaxial Growth via Quantum Wave Packet Studies

Science.gov (United States)

Dzegilenko, Fedor N.; Saini, Subhash (Technical Monitor)

1998-01-01

The dynamics of As(sub 2) molecule incorporation into the flat Ga-terminated GaAs(100) surface is studied computationally. The time-dependent Schrodinger equation is solved on a two-dimensional potential energy surface obtained using density functional theory calculations. The probabilities of trapping and subsequent dissociation of the molecular As(sub 2) bond are calculated as a function of beam translational energy and vibrational quantum number of As(sub 2).

Vibrational characteristics of diethyltoluenediamines (DETDA) functionalized carbon nanotubes using molecular dynamics simulations

International Nuclear Information System (INIS)

Ajori, S.; Ansari, R.

2015-01-01

Functionalization of carbon nanotubes (CNTs) can be viewed as an important process by which the dispersion and solubility of CNTs in the matrices of nanocomposites are improved. Covalent functionalization can affect the mechanical behavior of CNTs. In this paper, the vibrational behavior of diethyltoluenediamines (DETDA) functionalized CNTs is investigated utilizing molecular dynamics simulations in canonical ensemble at room temperature. The models of simulations are divided into two categories of functionalized CNTs with regular and random distributions of DETDA polymers. The results demonstrate that natural frequency of functionalized CNTs is lower than that of pristine ones. Also, it is observed that buckling phenomenon occurs during vibration for functionalized CNTs with regular distribution of polymers. It is further observed that polymer mass and van der Waals (vdW) forces are responsible for frequency changes in functionalized CNTs with random and regular distribution patterns of CNTs, respectively

deFUME: Dynamic exploration of functional metagenomic sequencing data

DEFF Research Database (Denmark)

van der Helm, Eric; Geertz-Hansen, Henrik Marcus; Genee, Hans Jasper

2015-01-01

is time consuming and constitutes a major bottleneck for experimental researchers in the field. Here we present the deFUME web server, an easy-to-use web-based interface for processing, annotation and visualization of functional metagenomics sequencing data, tailored to meet the requirements of non......-bioinformaticians. The web-server integrates multiple analysis steps into one single workflow: read assembly, open reading frame prediction, and annotation with BLAST, InterPro and GO classifiers. Analysis results are visualized in an online dynamic web-interface. The deFUME webserver provides a fast track from raw sequence...

Simultaneous functional photoacoustic microscopy and electrocorticography reveal the impact of rtPA on dynamic neurovascular functions after cerebral ischemia.

Science.gov (United States)

Bandla, Aishwarya; Liao, Lun-De; Chan, Su Jing; Ling, Ji Min; Liu, Yu-Hang; Shih, Yen-Yu Ian; Pan, Han-Chi; Wong, Peter Tsun-Hon; Lai, Hsin-Yi; King, Nicolas Kon Kam; Chen, You-Yin; Ng, Wai Hoe; Thakor, Nitish V

2018-06-01

The advance of thrombolytic therapy has been hampered by the lack of optimization of the therapy during the hyperacute phase of focal ischemia. Here, we investigate neurovascular dynamics using a custom-designed hybrid electrocorticography (ECoG)-functional photoacoustic microscopy (fPAM) imaging system during the hyperacute phase (first 6 h) of photothrombotic ischemia (PTI) in male Wistar rats following recombinant tissue plasminogen activator (rtPA)-mediated thrombolysis. We reported, for the first time, the changes in neural activity and cerebral hemodynamic responses following rtPA infusion at different time points post PTI. Interestingly, very early administration of rtPA ( 4 h post PTI) resulted in the deterioration of neurovascular function. A therapeutic window between 1 and 3 h post PTI was found to improve recovery of neurovascular function (i.e. significant restoration of neural activity to 93 ± 4.2% of baseline and hemodynamics to 81 ± 2.1% of baseline, respectively). The novel combination of fPAM and ECoG enables direct mapping of neurovascular dynamics and serves as a platform to evaluate potential interventions for stroke.

Towards the dynamical study of heavy-flavor quarks in the Quark-Gluon-Plasma

International Nuclear Information System (INIS)

Berrehrah, H; Bratkovskaya, E; Cassing, W; Gossiaux, P B; Aichelin, J

2014-01-01

Within the aim of a dynamical study of on- and off-shell heavy quarks Q in the quark gluon plasma (QGP) – as produced in relativistic nucleus-nucleus collisions – we study the heavy quark collisional scattering on partons of the QGP. The elastic cross sections σ q,g−Q are evaluated for perturbative partons (massless on-shell particles) and for dynamical quasi-particles (massive off-shell particles as described by the dynamical quasi-particles model D QPM ) using the leading order Born diagrams. We demonstrate that the finite width of the quasi-particles in the DQPM has little influence on the cross sections σ q,g−Q except close to thresholds. We, furthermore, calculate the heavy quark relaxation time as a function of temperature T within the different approaches using these cross sections

Response Functions for the Two-Dimensional Ultracold Fermi Gas: Dynamical BCS Theory and Beyond

Science.gov (United States)

Vitali, Ettore; Shi, Hao; Qin, Mingpu; Zhang, Shiwei

2017-12-01

Response functions are central objects in physics. They provide crucial information about the behavior of physical systems, and they can be directly compared with scattering experiments involving particles such as neutrons or photons. Calculations of such functions starting from the many-body Hamiltonian of a physical system are challenging and extremely valuable. In this paper, we focus on the two-dimensional (2D) ultracold Fermi atomic gas which has been realized experimentally. We present an application of the dynamical BCS theory to obtain response functions for different regimes of interaction strengths in the 2D gas with zero-range attractive interaction. We also discuss auxiliary-field quantum Monte Carlo (AFQMC) methods for the calculation of imaginary time correlations in these dilute Fermi gas systems. Illustrative results are given and comparisons are made between AFQMC and dynamical BCS theory results to assess the accuracy of the latter.

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

International Nuclear Information System (INIS)

Heyderman, L J; Stamps, R L

2013-01-01

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

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

Science.gov (United States)

Heyderman, L J; Stamps, R L

2013-09-11

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

A Case Study on Air Combat Decision Using Approximated Dynamic Programming

Directory of Open Access Journals (Sweden)

Yaofei Ma

2014-01-01

Full Text Available As a continuous state space problem, air combat is difficult to be resolved by traditional dynamic programming (DP with discretized state space. The approximated dynamic programming (ADP approach is studied in this paper to build a high performance decision model for air combat in 1 versus 1 scenario, in which the iterative process for policy improvement is replaced by mass sampling from history trajectories and utility function approximating, leading to high efficiency on policy improvement eventually. A continuous reward function is also constructed to better guide the plane to find its way to “winner” state from any initial situation. According to our experiments, the plane is more offensive when following policy derived from ADP approach other than the baseline Min-Max policy, in which the “time to win” is reduced greatly but the cumulated probability of being killed by enemy is higher. The reason is analyzed in this paper.

Review of selected dynamic material control functions for international safeguards

International Nuclear Information System (INIS)

Lowry, L.L.

1980-09-01

With the development of Dynamic Special Nuclear Material Accounting and Control systems used in nuclear manufacturing and reprocessing plants, there arises the question as to how these systems affect the IAEA inspection capabilities. The systems in being and under development provide information and control for a variety of purposes important to the plant operator, the safeguards purpose being one of them. This report attempts to judge the usefulness of these dynamic systems to the IAEA and have defined 12 functions that provide essential information to it. If the information acquired by these dynamic systems is to be useful to the IAEA, the inspectors must be able to independently verify it. Some suggestions are made as to how this might be done. But, even if it should not be possible to verify all the data, the availability to the IAEA of detailed, simultaneous, and plant-wide information would tend to inhibit a plant operator from attempting to generate a floating or fictitious inventory. Suggestions are made that might be helpful in the design of future software systems, an area which has proved to be fatally deficient in some systems and difficult in all

Trajectory-based nonadiabatic dynamics with time-dependent density functional theory.

Science.gov (United States)

Curchod, Basile F E; Rothlisberger, Ursula; Tavernelli, Ivano

2013-05-10

Understanding the fate of an electronically excited molecule constitutes an important task for theoretical chemistry, and practical implications range from the interpretation of atto- and femtosecond spectroscopy to the development of light-driven molecular machines, the control of photochemical reactions, and the possibility of capturing sunlight energy. However, many challenging conceptual and technical problems are involved in the description of these phenomena such as 1) the failure of the well-known Born-Oppenheimer approximation; 2) the need for accurate electronic properties such as potential energy surfaces, excited nuclear forces, or nonadiabatic coupling terms; and 3) the necessity of describing the dynamics of the photoexcited nuclear wavepacket. This review provides an overview of the current methods to address points 1) and 3) and shows how time-dependent density functional theory (TDDFT) and its linear-response extension can be used for point 2). First, the derivation of Ehrenfest dynamics and nonadiabatic Bohmian dynamics is discussed and linked to Tully's trajectory surface hopping. Second, the coupling of these trajectory-based nonadiabatic schemes with TDDFT is described in detail with special emphasis on the derivation of the required electronic structure properties. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular dynamics study of lubricant depletion by pulsed laser heating

Science.gov (United States)

Seo, Young Woo; Rosenkranz, Andreas; Talke, Frank E.

2018-05-01

In this study, molecular dynamics simulations were performed to numerically investigate the effect of pulsed laser heating on lubricant depletion. The maximum temperature, the lubricant depletion width, the number of evaporated lubricant beads and the number of fragmented lubricant chains were studied as a function of laser peak power, pulse duration and repetition rate. A continuous-wave laser and a square pulse laser were simulated and compared to a Gaussian pulse laser. With increasing repetition rate, pulsed laser heating was found to approach continuous-wave laser heating.

Non-parametric Bayesian models of response function in dynamic image sequences

Czech Academy of Sciences Publication Activity Database

Tichý, Ondřej; Šmídl, Václav

2016-01-01

Roč. 151, č. 1 (2016), s. 90-100 ISSN 1077-3142 R&D Projects: GA ČR GA13-29225S Institutional support: RVO:67985556 Keywords : Response function * Blind source separation * Dynamic medical imaging * Probabilistic models * Bayesian methods Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 2.498, year: 2016 http://library.utia.cas.cz/separaty/2016/AS/tichy-0456983.pdf

Dynamic alterations of hepatocellular function by on-demand elasticity and roughness modulation.

Science.gov (United States)

Uto, K; Aoyagi, T; DeForest, C A; Ebara, M

2018-05-01

Temperature-responsive cell culture substrates reported here can be dynamically programmed to induce bulk softening and surface roughness changes in the presence of living cells. Alterations in hepatocellular function following temporally controlled substrate softening depend on the extent of stiff mechanical priming prior to user-induced material transition.

Measures of static postural control moderate the association of strength and power with functional dynamic balance.

Science.gov (United States)

Forte, Roberta; Boreham, Colin A G; De Vito, Giuseppe; Ditroilo, Massimiliano; Pesce, Caterina

2014-12-01

Age-related reductions in strength and power are considered to negatively impact balance control, but the existence of a direct association is still an issue of debate. This is possibly due to the fact that balance assessment is complex, reflects different underlying physiologic mechanisms and involves quantitative measurements of postural sway or timing of performance during balance tasks. The present study evaluated the moderator effect of static postural control on the association of power and strength with dynamic balance tasks. Fifty-seven healthy 65-75 year old individuals performed tests of dynamic functional balance (walking speed under different conditions) and of strength, power and static postural control. Dynamic balance performance (walking speed) was associated with lower limb strength and power, as well as postural control under conditions requiring postural adjustments (narrow surface walking r(2) = 0.31, p balance tasks. Practical implications for assessment and training are discussed.

Algebraic dynamics solutions and algebraic dynamics algorithm for nonlinear partial differential evolution equations of dynamical systems

Institute of Scientific and Technical Information of China (English)

2008-01-01

Using functional derivative technique in quantum field theory, the algebraic dy-namics approach for solution of ordinary differential evolution equations was gen-eralized to treat partial differential evolution equations. The partial differential evo-lution equations were lifted to the corresponding functional partial differential equations in functional space by introducing the time translation operator. The functional partial differential evolution equations were solved by algebraic dynam-ics. The algebraic dynamics solutions are analytical in Taylor series in terms of both initial functions and time. Based on the exact analytical solutions, a new nu-merical algorithm—algebraic dynamics algorithm was proposed for partial differ-ential evolution equations. The difficulty of and the way out for the algorithm were discussed. The application of the approach to and computer numerical experi-ments on the nonlinear Burgers equation and meteorological advection equation indicate that the algebraic dynamics approach and algebraic dynamics algorithm are effective to the solution of nonlinear partial differential evolution equations both analytically and numerically.

Bayesian Inference for Functional Dynamics Exploring in fMRI Data

Directory of Open Access Journals (Sweden)

Xuan Guo

2016-01-01

Full Text Available This paper aims to review state-of-the-art Bayesian-inference-based methods applied to functional magnetic resonance imaging (fMRI data. Particularly, we focus on one specific long-standing challenge in the computational modeling of fMRI datasets: how to effectively explore typical functional interactions from fMRI time series and the corresponding boundaries of temporal segments. Bayesian inference is a method of statistical inference which has been shown to be a powerful tool to encode dependence relationships among the variables with uncertainty. Here we provide an introduction to a group of Bayesian-inference-based methods for fMRI data analysis, which were designed to detect magnitude or functional connectivity change points and to infer their functional interaction patterns based on corresponding temporal boundaries. We also provide a comparison of three popular Bayesian models, that is, Bayesian Magnitude Change Point Model (BMCPM, Bayesian Connectivity Change Point Model (BCCPM, and Dynamic Bayesian Variable Partition Model (DBVPM, and give a summary of their applications. We envision that more delicate Bayesian inference models will be emerging and play increasingly important roles in modeling brain functions in the years to come.

Dynamic studies of poly(di-n-alkyl itaconate)s

CERN Document Server

Arrighi, V; Gagliardi, S; McEwen, I J; Telling, M T F

2002-01-01

We report a preliminary dynamic study of poly(di-n-alkyl itaconate)s with varying side chain length n. QENS measurements were carried out on two backscattering spectrometers, IRIS at ISIS and IN10 at the ILL in the temperature range of 4 to 350 K. We show that molecular motion can be detected well below the polymer glass transition for all samples. It is possible to distinguish different dynamic processes. The temperature range over which these are observed is dependent on the length of the side chain, n. The intermediate scattering function, I(Q,t), was determined from the IRIS and found to obey time-temperature superposition. We show that the I(Q,t) data at different temperatures can be overlapped using the same time-scale shift factors, indicating that the relaxation process is common to all the polymers investigated. (orig.)

Frequency response function-based explicit framework for dynamic identification in human-structure systems

Science.gov (United States)

Wei, Xiaojun; Živanović, Stana

2018-05-01

The aim of this paper is to propose a novel theoretical framework for dynamic identification in a structure occupied by a single human. The framework enables the prediction of the dynamics of the human-structure system from the known properties of the individual system components, the identification of human body dynamics from the known dynamics of the empty structure and the human-structure system and the identification of the properties of the structure from the known dynamics of the human and the human-structure system. The novelty of the proposed framework is the provision of closed-form solutions in terms of frequency response functions obtained by curve fitting measured data. The advantages of the framework over existing methods are that there is neither need for nonlinear optimisation nor need for spatial/modal models of the empty structure and the human-structure system. In addition, the second-order perturbation method is employed to quantify the effect of uncertainties in human body dynamics on the dynamic identification of the empty structure and the human-structure system. The explicit formulation makes the method computationally efficient and straightforward to use. A series of numerical examples and experiments are provided to illustrate the working of the method.

Threshold defect production in silicon determined by density functional theory molecular dynamics simulations

International Nuclear Information System (INIS)

Holmstroem, E.; Kuronen, A.; Nordlund, K.

2008-01-01

We studied threshold displacement energies for creating stable Frenkel pairs in silicon using density functional theory molecular dynamics simulations. The average threshold energy over all lattice directions was found to be 36±2 STAT ±2 SYST eV, and thresholds in the directions and were found to be 20±2 SYST eV and 12.5±1.5 SYST eV, respectively. Moreover, we found that in most studied lattice directions, a bond defect complex is formed with a lower threshold than a Frenkel pair. The average threshold energy for producing either a bond defect or a Frenkel pair was found to be 24±1 STAT ±2 SYST eV

NVU dynamics. II. Comparing to four other dynamics

DEFF Research Database (Denmark)

Ingebrigtsen, Trond; Toxværd, Søren; Schrøder, Thomas

2011-01-01

-potential-energy hypersurface. Here, simulations of NVU dynamics are compared to results for four other dynamics, both deterministic and stochastic. First, NVU dynamics is compared to the standard energy-conserving Newtonian NVE dynamics by simulations of the Kob-Andersen binary Lennard-Jones liquid, its WCA version (i.......e., with cut-off's at the pair potential minima), and the Lennard-Jones Gaussian liquid. We find identical results for all quantities probed: radial distribution functions, incoherent intermediate scattering functions, and mean-square displacement as function of time. Arguments are presented...... on the constant-potential-energy hypersurface, and to Nos-Hoover NVT dynamics. If time is scaled for the two stochastic dynamics to make single-particle diffusion constants identical to that of NVE dynamics, the simulations show that all five dynamics are equivalent at low temperatures except at short times....

Proton structure functions in the dipole picture of BFKL dynamics

International Nuclear Information System (INIS)

Navelet, H.; Wallon, S.

1996-06-01

The F 2 , F G , R=F L /F T proton structure functions are derived in the QCD dipole picture. Assuming k T and renormalization-group factorization, we relate deep-inelastic proton scattering to deep-inelastic onium scattering. We get a three-parameter fit of the 1994 H1 data in the low-x, moderate Q 2 range. The ratios F G /F 2 and R are predicted without further adjustment. The dipole picture of BFKL dynamics is shown to provide a relevant model for quantitatively describing the proton structure functions at HERA. The predictions for F 2 and F G are compatible with next-to-leading DGLAP analysis, while R is expected to be significantly lower at very small x. (orig.)

Using transfer functions to quantify El Niño Southern Oscillation dynamics in data and models.

Science.gov (United States)

MacMartin, Douglas G; Tziperman, Eli

2014-09-08

Transfer function tools commonly used in engineering control analysis can be used to better understand the dynamics of El Niño Southern Oscillation (ENSO), compare data with models and identify systematic model errors. The transfer function describes the frequency-dependent input-output relationship between any pair of causally related variables, and can be estimated from time series. This can be used first to assess whether the underlying relationship is or is not frequency dependent, and if so, to diagnose the underlying differential equations that relate the variables, and hence describe the dynamics of individual subsystem processes relevant to ENSO. Estimating process parameters allows the identification of compensating model errors that may lead to a seemingly realistic simulation in spite of incorrect model physics. This tool is applied here to the TAO array ocean data, the GFDL-CM2.1 and CCSM4 general circulation models, and to the Cane-Zebiak ENSO model. The delayed oscillator description is used to motivate a few relevant processes involved in the dynamics, although any other ENSO mechanism could be used instead. We identify several differences in the processes between the models and data that may be useful for model improvement. The transfer function methodology is also useful in understanding the dynamics and evaluating models of other climate processes.

Femtosecond X-Ray Scattering Study of Ultrafast Photoinduced Structural Dynamics in Solvated [Co(terpy)2]2+

DEFF Research Database (Denmark)

Biasin, Elisa; Brandt van Driel, Tim; Kjær, Kasper Skov

2016-01-01

We study the structural dynamics of photoexcited [Co(terpy)2]2+ in an aqueous solution with ultrafast x-ray diffuse scattering experiments conducted at the Linac Coherent Light Source. Through direct comparisons with density functional theory calculations, our analysis shows that the photoexcitat......We study the structural dynamics of photoexcited [Co(terpy)2]2+ in an aqueous solution with ultrafast x-ray diffuse scattering experiments conducted at the Linac Coherent Light Source. Through direct comparisons with density functional theory calculations, our analysis shows...... find that the equilibrium bond-elongated structure of the high spin state is established on a single-picosecond time scale and that this state has a lifetime of ∼7 ps....

Molecular dynamic simulation study of molten cesium

Directory of Open Access Journals (Sweden)

Yeganegi Saeid

2017-01-01

Full Text Available Molecular dynamics simulations were performed to study thermodynamics and structural properties of expanded caesium fluid. Internal pressure, radial distribution functions (RDFs, coordination numbers and diffusion coefficients have been calculated at temperature range 700–1600 K and pressure range 100–800 bar. We used the internal pressure to predict the metal–non-metal transition occurrence region. RDFs were calculated at wide ranges of temperature and pressure. The coordination numbers decrease and positions of the first peak of RDFs slightly increase as the temperature increases and pressure decreases. The calculated self-diffusion coefficients at various temperatures and pressures show no distinct boundary between Cs metallic fluid and its expanded fluid where it continuously increases with temperature.

Finding the best density functional approximation to describe interaction energies and structures of ionic liquids in molecular dynamics studies

Science.gov (United States)

Perlt, Eva; Ray, Promit; Hansen, Andreas; Malberg, Friedrich; Grimme, Stefan; Kirchner, Barbara

2018-05-01

Ionic liquids raise interesting but complicated questions for theoretical investigations due to the fact that a number of different inter-molecular interactions, e.g., hydrogen bonding, long-range Coulomb interactions, and dispersion interactions, need to be described properly. Here, we present a detailed study on the ionic liquids ethylammonium nitrate and 1-ethyl-3-methylimidazolium acetate, in which we compare different dispersion corrected density functional approximations to accurate local coupled cluster data in static calculations on ionic liquid clusters. The efficient new composite method B97-3c is tested and has been implemented in CP2K for future studies. Furthermore, tight-binding based approaches which may be used in large scale simulations are assessed. Subsequently, ab initio as well as classical molecular dynamics simulations are conducted and structural analyses are presented in order to shed light on the different short- and long-range structural patterns depending on the method and the system size considered in the simulation. Our results indicate the presence of strong hydrogen bonds in ionic liquids as well as the aggregation of alkyl side chains due to dispersion interactions.

The Effects of Core Stabilization Exercise on Dynamic Balance and Gait Function in Stroke Patients

OpenAIRE

Chung, Eun-Jung; Kim, Jung-Hee; Lee, Byoung-Hee

2013-01-01

[Purpose] The purpose of this study was to determine the effects of core stabilization exercise on dynamic balance and gait function in stroke patients. [Subjects] The subjects were 16 stroke patients, who were randomly divided into two groups: a core stabilization exercise group of eight subjects and control group of eight subjects. [Methods] Subjects in both groups received general training five times per week. Subjects in the core stabilization exercise group practiced an additional core s...

Improved non-dimensional dynamic influence function method for vibration analysis of arbitrarily shaped plates with clamped edges

Directory of Open Access Journals (Sweden)

Sang-Wook Kang

2016-03-01

Full Text Available A new formulation for the non-dimensional dynamic influence function method, which was developed by the authors, is proposed to efficiently extract eigenvalues and mode shapes of clamped plates with arbitrary shapes. Compared with the finite element and boundary element methods, the non-dimensional dynamic influence function method yields highly accurate solutions in eigenvalue analysis problems of plates and membranes including acoustic cavities. However, the non-dimensional dynamic influence function method requires the uneconomic procedure of calculating the singularity of a system matrix in the frequency range of interest for extracting eigenvalues because it produces a non-algebraic eigenvalue problem. This article describes a new approach that reduces the problem of free vibrations of clamped plates to an algebraic eigenvalue problem, the solution of which is straightforward. The validity and efficiency of the proposed method are illustrated through several numerical examples.

Density-functional study of photoinduced water splitting

International Nuclear Information System (INIS)

Martínez Mesa, Aliezer; Rodríguez Hernández, Fermín; Seifert, Gotthard; Tranca, Diana

2015-01-01

We investigate the dynamics of water splitting on dye-sensitized metal (Ti, Cu) oxide surfaces, induced by direct sunlight excitation. In this study, we will consider the typical photoexcitation-followed-by-injection scheme, treating electron-injection and water splitting dynamics as independent events. The simultaneous modeling of the molecular motion and the quantum nonadiabatic transitions is achieved via the computation of the low-lying electronic states along several alternative reaction paths. Electronic structure calculations are based on a B3LYP-DFT Hamiltonian. The proposed approach combines an atomistic description of the reactants and of the immediate region of the surface, while the vibrational dynamics of the substrate is modeled as an effective bath leading to dissipation effects. The use of density-functional theory to solve the many- body electronic problem allows investigating the atomic motion of the water molecules and of a representative part of the substrate, thereby providing a theoretical and computational model capable to account simultaneously for the molecular character of the dye molecule and for the bulk properties of the surface. Furthermore, the insight emerging from this fundamental modeling can be used to optimize the chemical composition of the system to attain high incident-photon-flux-to-hydrogen-yield ratios. (full text)

Nuclear energy density functional from chiral pion-nucleon dynamics revisited

Science.gov (United States)

Kaiser, N.; Weise, W.

2010-05-01

We use a recently improved density-matrix expansion to calculate the nuclear energy density functional in the framework of in-medium chiral perturbation theory. Our calculation treats systematically the effects from 1 π-exchange, iterated 1 π-exchange, and irreducible 2 π-exchange with intermediate Δ-isobar excitations, including Pauli-blocking corrections up to three-loop order. We find that the effective nucleon mass M(ρ) entering the energy density functional is identical to the one of Fermi-liquid theory when employing the improved density-matrix expansion. The strength F(ρ) of the ( surface-term as provided by the pion-exchange dynamics is in good agreement with that of phenomenological Skyrme forces in the density region ρ/2short-range spin-orbit interaction. The strength function F(ρ) multiplying the square of the spin-orbit density comes out much larger than in phenomenological Skyrme forces and it has a pronounced density dependence.

Dynamics of tropomyosin in muscle fibers as monitored by saturation transfer EPR of bi-functional probe.

Directory of Open Access Journals (Sweden)

Roni F Rayes

Full Text Available The dynamics of four regions of tropomyosin was assessed using saturation transfer electron paramagnetic resonance in the muscle fiber. In order to fully immobilize the spin probe on the surface of tropomyosin, a bi-functional spin label was attached to i,i+4 positions via cysteine mutagenesis. The dynamics of bi-functionally labeled tropomyosin mutants decreased by three orders of magnitude when reconstituted into "ghost muscle fibers". The rates of motion varied along the length of tropomyosin with the C-terminus position 268/272 being one order of magnitude slower then N-terminal domain or the center of the molecule. Introduction of troponin decreases the dynamics of all four sites in the muscle fiber, but there was no significant effect upon addition of calcium or myosin subfragment-1.

Every storage function is a state function

NARCIS (Netherlands)

Trentelman, H.L.; Willems, J.C.

1997-01-01

It is shown that for linear dynamical systems with quadratic supply rates, a storage function can always be written as a quadratic function of the state of an associated linear dynamical system. This dynamical system is obtained by combining the dynamics of the original system with the dynamics of

The effects of core stabilization exercise on dynamic balance and gait function in stroke patients.

Science.gov (United States)

Chung, Eun-Jung; Kim, Jung-Hee; Lee, Byoung-Hee

2013-07-01

[Purpose] The purpose of this study was to determine the effects of core stabilization exercise on dynamic balance and gait function in stroke patients. [Subjects] The subjects were 16 stroke patients, who were randomly divided into two groups: a core stabilization exercise group of eight subjects and control group of eight subjects. [Methods] Subjects in both groups received general training five times per week. Subjects in the core stabilization exercise group practiced an additional core stabilization exercise program, which was performed for 30 minutes, three times per week, during a period of four weeks. All subjects were evaluated for dynamic balance (Timed Up and Go test, TUG) and gait parameters (velocity, cadence, step length, and stride length). [Results] Following intervention, the core exercise group showed a significant change in TUG, velocity, and cadence. The only significant difference observed between the core group and control group was in velocity. [Conclusion] The results of this study suggest the feasibility and suitability of core stabilization exercise for stroke patients.

The dynamics of a harvested predator-prey system with Holling type IV functional response.

Science.gov (United States)

Liu, Xinxin; Huang, Qingdao

2018-05-31

The paper aims to investigate the dynamical behavior of a predator-prey system with Holling type IV functional response in which both the species are subject to capturing. We mainly consider how the harvesting affects equilibria, stability, limit cycles and bifurcations in this system. We adopt the method of qualitative and quantitative analysis, which is based on the dynamical theory, bifurcation theory and numerical simulation. The boundedness of solutions, the existence and stability of equilibrium points of the system are further studied. Based on the Sotomayor's theorem, the existence of transcritical bifurcation and saddle-node bifurcation are derived. We use the normal form theorem to analyze the Hopf bifurcation. Simulation results show that the first Lyapunov coefficient is negative and a stable limit cycle may bifurcate. Numerical simulations are performed to make analytical studies more complete. This work illustrates that using the harvesting effort as control parameter can change the behaviors of the system, which may be useful for the biological management. Copyright © 2018 Elsevier B.V. All rights reserved.

Dynamic Analysis of an Impulsively Controlled Predator-Prey Model with Holling Type IV Functional Response

Directory of Open Access Journals (Sweden)

Yanzhen Wang

2012-01-01

Full Text Available The dynamic behavior of a predator-prey model with Holling type IV functional response is investigated with respect to impulsive control strategies. The model is analyzed to obtain the conditions under which the system is locally asymptotically stable and permanent. Existence of a positive periodic solution of the system and the boundedness of the system is also confirmed. Furthermore, numerical analysis is used to discover the influence of impulsive perturbations. The system is found to exhibit rich dynamics such as symmetry-breaking pitchfork bifurcation, chaos, and nonunique dynamics.

A generalized Wigner function for quantum systems with the SU(2) dynamical symmetry group

International Nuclear Information System (INIS)

Klimov, A B; Romero, J L

2008-01-01

We introduce a Wigner-like quasidistribution function to describe quantum systems with the SU(2) dynamic symmetry group. This function is defined in a three-dimensional group manifold and can be used to represent the states defined in several SU(2) invariant subspaces. The explicit differential Moyal-like form of the star product is found and analyzed in the semiclassical limit

Dynamical study of DBI-essence in loop quantum cosmology and brane world

International Nuclear Information System (INIS)

Bhadra, Jhumpa; Debnath, Ujjal

2012-01-01

We have studied homogeneous isotropic FRW model having dynamical dark energy DBI-essence with scalar field. Existence of cosmological scaling solutions restricts the Lagrangian of the scalar field φ. Choosing p=Xg(Xe λφ ), where X=-g μν ∂ μ φ∂ ν φ/2 with g any function of Xe λφ and defining some suitable transformations, we have constructed the dynamical system in different models of gravity: (i) Loop Quantum Cosmology (LQC), (ii) DGP brane world and (iii) RS II brane world. We have investigated stability of this dynamical system around the critical point for three gravity models and investigated the scalar-field dominated attractor solution in support of accelerated universe. The roles of the physical parameters have also been shown graphically during the accelerating phase of the universe. (orig.)

Study of dynamic strain aging in dual phase steel

International Nuclear Information System (INIS)

Queiroz, R.R.U.; Cunha, F.G.G.; Gonzalez, B.M.

2012-01-01

Highlights: ► Characterization of the high temperature mechanical behavior of a dual phase steel. ► Determination of the effect of dynamic strain aging on the strain hardening rate. ► Identification of the mechanism associated with dynamic strain aging. ► The value of the interaction energy carbon–dislocation in ferrite was confirmed. - Abstract: The susceptibility to dynamic strain aging of a dual phase steel was evaluated by the variation of mechanical properties in tension with the temperature and the strain rate. The tensile tests were performed at temperatures varying between 25 °C and 600 °C and at strain rates ranging from 10 −2 to 5 × 10 −4 s −1 . The studied steel presented typical manifestations related to dynamic strain aging: serrated flow (the Portevin–Le Chatelier effect) for certain combinations of temperature and strain rates; the presence of a plateau in the variation of yield stress with temperature; a maximum in the curves of tensile strength, flow stress, and work hardening exponent as a function of temperature; and a minimum in the variation of total elongation with temperature. The determined apparent activation energy values, associated with the beginning of the Portevin–Le Chatelier effect and the maximum in the variation of flow stress with temperature, were 83 kJ/mol and 156 kJ/mol, respectively. These values suggest that the mechanism responsible for dynamic strain aging in the dual phase steel is the locking of dislocations by carbon atoms in ferrite and that the formation of clusters and/or transition carbides and carbide precipitation in martensite do not interfere with the dynamic strain aging process.

Dynamic functional connectivity using state-based dynamic community structure: method and application to opioid analgesia.

Science.gov (United States)

Robinson, Lucy F; Atlas, Lauren Y; Wager, Tor D

2015-03-01

We present a new method, State-based Dynamic Community Structure, that detects time-dependent community structure in networks of brain regions. Most analyses of functional connectivity assume that network behavior is static in time, or differs between task conditions with known timing. Our goal is to determine whether brain network topology remains stationary over time, or if changes in network organization occur at unknown time points. Changes in network organization may be related to shifts in neurological state, such as those associated with learning, drug uptake or experimental conditions. Using a hidden Markov stochastic blockmodel, we define a time-dependent community structure. We apply this approach to data from a functional magnetic resonance imaging experiment examining how contextual factors influence drug-induced analgesia. Results reveal that networks involved in pain, working memory, and emotion show distinct profiles of time-varying connectivity. Copyright © 2014 Elsevier Inc. All rights reserved.

Functional Dynamics of Hexameric Helicase Probed by Hydrogen Exchange and Simulation

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Radou, Gaël; Dreyer, Frauke N.; Tuma, Roman; Paci, Emanuele

2014-01-01

The biological function of large macromolecular assemblies depends on their structure and their dynamics over a broad range of timescales; for this reason, it is a significant challenge to investigate these assemblies using conventional experimental techniques. One of the most promising experimental techniques is hydrogen-deuterium exchange detected by mass spectrometry. Here, we describe to our knowledge a new computational method for quantitative interpretation of deuterium exchange kinetics and apply it to a hexameric viral helicase P4 that unwinds and translocates RNA into a virus capsid at the expense of ATP hydrolysis. Room-temperature dynamics probed by a hundred nanoseconds of all-atom molecular dynamics simulations is sufficient to predict the exchange kinetics of most sequence fragments and provide a residue-level interpretation of the low-resolution experimental results. The strategy presented here is also a valuable tool to validate experimental data, e.g., assignments, and to probe mechanisms that cannot be observed by x-ray crystallography, or that occur over timescales longer than those that can be realistically simulated, such as the opening of the hexameric ring. PMID:25140434

Experimental Waterflow Determination of the Dynamic Hydraulic Transfer Function for the J-2X Oxidizer Turbopump. Part Two; Results and Interpretation

Science.gov (United States)

Zoladz, Tom; Patel, Sandeep; Lee, Erik; Karon, Dave

2011-01-01

Experimental results describing the hydraulic dynamic pump transfer matrix (Yp) for a cavitating J-2X oxidizer turbopump inducer+impeller tested in subscale waterflow are presented. The transfer function is required for integrated vehicle pogo stability analysis as well as optimization of local inducer pumping stability. Dynamic transfer functions across widely varying pump hydrodynamic inlet conditions are extracted from measured data in conjunction with 1D-model based corrections. Derived Dynamic transfer functions are initially interpreted relative to traditional Pogo pump equations. Water-to-liquid oxygen scaling of measured cavitation characteristics are discussed. Comparison of key dynamic transfer matrix terms derived from waterflow testing are made with those implemented in preliminary Ares Upper Stage Pogo stability modeling. Alternate cavitating pump hydraulic dynamic equations are suggested which better reflect frequency dependencies of measured transfer matrices.

A qualitative numerical study of high dimensional dynamical systems

Science.gov (United States)

Albers, David James

Since Poincare, the father of modern mathematical dynamical systems, much effort has been exerted to achieve a qualitative understanding of the physical world via a qualitative understanding of the functions we use to model the physical world. In this thesis, we construct a numerical framework suitable for a qualitative, statistical study of dynamical systems using the space of artificial neural networks. We analyze the dynamics along intervals in parameter space, separating the set of neural networks into roughly four regions: the fixed point to the first bifurcation; the route to chaos; the chaotic region; and a transition region between chaos and finite-state neural networks. The study is primarily with respect to high-dimensional dynamical systems. We make the following general conclusions as the dimension of the dynamical system is increased: the probability of the first bifurcation being of type Neimark-Sacker is greater than ninety-percent; the most probable route to chaos is via a cascade of bifurcations of high-period periodic orbits, quasi-periodic orbits, and 2-tori; there exists an interval of parameter space such that hyperbolicity is violated on a countable, Lebesgue measure 0, "increasingly dense" subset; chaos is much more likely to persist with respect to parameter perturbation in the chaotic region of parameter space as the dimension is increased; moreover, as the number of positive Lyapunov exponents is increased, the likelihood that any significant portion of these positive exponents can be perturbed away decreases with increasing dimension. The maximum Kaplan-Yorke dimension and the maximum number of positive Lyapunov exponents increases linearly with dimension. The probability of a dynamical system being chaotic increases exponentially with dimension. The results with respect to the first bifurcation and the route to chaos comment on previous results of Newhouse, Ruelle, Takens, Broer, Chenciner, and Iooss. Moreover, results regarding the high

A density-functional and molecular-dynamics study on the physical properties of yttrium-doped tantalum oxynitride

International Nuclear Information System (INIS)

Wolff, H.; Schilling, H.; Lerch, M.; Dronskowski, R.

2006-01-01

Fluorite-type phases in the system Y-Ta-O-N have been studied using both first-principle electronic-structure calculations and molecular-dynamic simulations to validate the structural data and to explain unusual asymmetric reflection profiles observed in the experimental X-ray diffraction patterns. We provide evidence that the compounds may be macroscopically described as to represent cubic fluorite-type defect structures despite the fact that DFT calculations clearly show that all crystallographic unit cells appear as triclinically distorted. Additionally, we find that there is a minute (but hardly significant) tendency for anionic ordering at absolute zero temperature but none under reaction conditions. - Graphical abstract: Structural result of a room-temperature molecular-dynamic simulation of a supercell of Y 0.125 Ta 0.875 O 0.875 N□ 0.125

The density functional theory and the charged fluid molecular dynamics

International Nuclear Information System (INIS)

Hansen, J.P.; Zerah, G.

1993-01-01

Car and Parrinello had the idea of combining the density functional theory (Hohenberg, Kohn and Sham) to the 'molecular dynamics' numerical modelling method, in order to simulate metallic or co-valent solids and liquids from the first principles. The objective of this paper is to present a simplified version of this method ab initio, applicable to classical and quantal charged systems. The method is illustrated with recent results on charged colloidal suspensions and highly correlated electron-proton plasmas. 1 fig., 21 refs

Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid.

Science.gov (United States)

Babbitt, Gregory A; Alawad, Mohammed A; Schulze, Katharina V; Hudson, André O

2014-01-01

While mRNA stability has been demonstrated to control rates of translation, generating both global and local synonymous codon biases in many unicellular organisms, this explanation cannot adequately explain why codon bias strongly tracks neighboring intergene GC content; suggesting that structural dynamics of DNA might also influence codon choice. Because minor groove width is highly governed by 3-base periodicity in GC, the existence of triplet-based codons might imply a functional role for the optimization of local DNA molecular dynamics via GC content at synonymous sites (≈GC3). We confirm a strong association between GC3-related intrinsic DNA flexibility and codon bias across 24 different prokaryotic multiple whole-genome alignments. We develop a novel test of natural selection targeting synonymous sites and demonstrate that GC3-related DNA backbone dynamics have been subject to moderate selective pressure, perhaps contributing to our observation that many genes possess extreme DNA backbone dynamics for their given protein space. This dual function of codons may impose universal functional constraints affecting the evolution of synonymous and non-synonymous sites. We propose that synonymous sites may have evolved as an 'accessory' during an early expansion of a primordial genetic code, allowing for multiplexed protein coding and structural dynamic information within the same molecular context. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Human Skin Barrier Structure and Function Analyzed by Cryo-EM and Molecular Dynamics Simulation.

Science.gov (United States)

Lundborg, Magnus; Narangifard, Ali; Wennberg, Christian L; Lindahl, Erik; Daneholt, Bertil; Norlén, Lars

2018-04-24

In the present study we have analyzed the molecular structure and function of the human skin's permeability barrier using molecular dynamics simulation validated against cryo-electron microscopy data from near native skin. The skin's barrier capacity is located to an intercellular lipid structure embedding the cells of the superficial most layer of skin - the stratum corneum. According to the splayed bilayer model (Iwai et al., 2012) the lipid structure is organized as stacked bilayers of ceramides in a splayed chain conformation with cholesterol associated with the ceramide sphingoid moiety and free fatty acids associated with the ceramide fatty acid moiety. However, knowledge about the lipid structure's detailed molecular organization, and the roles of its different lipid constituents, remains circumstantial. Starting from a molecular dynamics model based on the splayed bilayer model, we have, by stepwise structural and compositional modifications, arrived at a thermodynamically stable molecular dynamics model expressing simulated electron microscopy patterns matching original cryo-electron microscopy patterns from skin extremely closely. Strikingly, the closer the individual molecular dynamics models' lipid composition was to that reported in human stratum corneum, the better was the match between the models' simulated electron microscopy patterns and the original cryo-electron microscopy patterns. Moreover, the closest-matching model's calculated water permeability and thermotropic behaviour were found compatible with that of human skin. The new model may facilitate more advanced physics-based skin permeability predictions of drugs and toxicants. The proposed procedure for molecular dynamics based analysis of cellular cryo-electron microscopy data might be applied to other biomolecular systems. Copyright © 2018. Published by Elsevier Inc.

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

International Nuclear Information System (INIS)

Thompson, K.; Martinez, T.J.

1999-01-01

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

Granulometry use for the study of dynamics speckles patterns

International Nuclear Information System (INIS)

Mavilioa, Adriana; Fernandez, Margarita; Trivi, Marcelo; Rabal, Hector; Arizaga, Ricardo

2009-01-01

Dynamic speckle patterns are generated by laser light scattering on surfaces that exhibit some kind of activity, due to physical or biological processes that take place in the illuminated object. The characterization of this dynamic process is carried out by studying the texture changes of auxiliary images: temporal history of the speckle pattern (THSP) obtained from this speckles patterns. The drying process of water borne paint is studied through a method based on mathematical morphology applied to the THSP image processing. It is based on obtaining the granulometry of these images and their characteristic granulometric spectrum. From the granulometric size distribution of each THSP image four parameters are obtained: mean length, standard deviation, asymmetry and kurtosis. These parameters are found to be suitable as texture features. The Mahalanobis distance is calculated between the texture features of the THSP images representative of the temporary stages of the drying process and the features of the final stage or pattern texture. The behavior of the distance function describes satisfactorily the drying process of the water borne paint. Finally, these results are compared with the obtained by other methods. Compared with others, the granulometric method reported in this work distinguished by its simplicity and easy implementation and can be used to characterize the evolution of any process recorded through dynamic speckles. (Author)

A Quasi-Dynamic Optimal Control Strategy for Non-Linear Multivariable Processes Based upon Non-Quadratic Objective Functions

Directory of Open Access Journals (Sweden)

Jens G. Balchen

1984-10-01

Full Text Available The problem of systematic derivation of a quasi-dynamic optimal control strategy for a non-linear dynamic process based upon a non-quadratic objective function is investigated. The wellknown LQG-control algorithm does not lead to an optimal solution when the process disturbances have non-zero mean. The relationships between the proposed control algorithm and LQG-control are presented. The problem of how to constrain process variables by means of 'penalty' - terms in the objective function is dealt with separately.

Gentlest ascent dynamics for calculating first excited state and exploring energy landscape of Kohn-Sham density functionals.

Science.gov (United States)

Li, Chen; Lu, Jianfeng; Yang, Weitao

2015-12-14

We develop the gentlest ascent dynamics for Kohn-Sham density functional theory to search for the index-1 saddle points on the energy landscape of the Kohn-Sham density functionals. These stationary solutions correspond to excited states in the ground state functionals. As shown by various examples, the first excited states of many chemical systems are given by these index-1 saddle points. Our novel approach provides an alternative, more robust way to obtain these excited states, compared with the widely used ΔSCF approach. The method can be easily generalized to target higher index saddle points. Our results also reveal the physical interest and relevance of studying the Kohn-Sham energy landscape.

A Dynamic Simulation of Musculoskeletal Function in the Mouse Hindlimb During Trotting Locomotion

Directory of Open Access Journals (Sweden)

James P. Charles

2018-05-01

Full Text Available Mice are often used as animal models of various human neuromuscular diseases, and analysis of these models often requires detailed gait analysis. However, little is known of the dynamics of the mouse musculoskeletal system during locomotion. In this study, we used computer optimization procedures to create a simulation of trotting in a mouse, using a previously developed mouse hindlimb musculoskeletal model in conjunction with new experimental data, allowing muscle forces, activation patterns, and levels of mechanical work to be estimated. Analyzing musculotendon unit (MTU mechanical work throughout the stride allowed a deeper understanding of their respective functions, with the rectus femoris MTU dominating the generation of positive and negative mechanical work during the swing and stance phases. This analysis also tested previous functional inferences of the mouse hindlimb made from anatomical data alone, such as the existence of a proximo-distal gradient of muscle function, thought to reflect adaptations for energy-efficient locomotion. The results do not strongly support the presence of this gradient within the mouse musculoskeletal system, particularly given relatively high negative net work output from the ankle plantarflexor MTUs, although more detailed simulations could test this further. This modeling analysis lays a foundation for future studies of the control of vertebrate movement through the development of neuromechanical simulations.

Neutrophil programming dynamics and its disease relevance.

Science.gov (United States)

Ran, Taojing; Geng, Shuo; Li, Liwu

2017-11-01

Neutrophils are traditionally considered as first responders to infection and provide antimicrobial host defense. However, recent advances indicate that neutrophils are also critically involved in the modulation of host immune environments by dynamically adopting distinct functional states. Functionally diverse neutrophil subsets are increasingly recognized as critical components mediating host pathophysiology. Despite its emerging significance, molecular mechanisms as well as functional relevance of dynamically programmed neutrophils remain to be better defined. The increasing complexity of neutrophil functions may require integrative studies that address programming dynamics of neutrophils and their pathophysiological relevance. This review aims to provide an update on the emerging topics of neutrophil programming dynamics as well as their functional relevance in diseases.

Neuropsychiatric dynamics: the study of mental illness using functional magnetic resonance imaging

International Nuclear Information System (INIS)

Callicott, Joseph H.; Weinberger, Daniel R.

1999-01-01

Functional magnetic resonance imaging (fMRI) is poised to make significant contributions to the study of neuropsychiatric illnesses. Whatever neural pathology attends such illnesses has proven subtle at best. By identifying predictable, regionally specific deficits in brain function, fMRI can suggest brain regions for detailed cellular analyses, provide valuable in vivo data regarding effective connectivity, provide a means to model the effects of various drug challenge paradigms, and characterize intermediate phenotypes in the search for the genes underlying mental illness. Nonetheless, as promising as fMRI appears to be in terms of its relative safety, repeatability, ability to generate individual brain maps and widespread availability, it is still subject to a number of unresolved conceptual conundrums inherited from earlier neuroimaging work. For example, functional neuroimaging has not generated any pathognomic findings in mental illness, has not established a clear link between neurophysiology and observable behavior, and has not resolved the potential confounds of medication. In this article, we will review the relevant historical background preceding fMRI, address methodological considerations in fMRI, and summarize recent fMRI findings in psychiatry. Finally, fMRI is being used to simplify the complex genetics of neuropsychiatric illness by generating quantitative and qualitative brain phenotypes

Neuropsychiatric dynamics: the study of mental illness using functional magnetic resonance imaging

Energy Technology Data Exchange (ETDEWEB)

Callicott, Joseph H. E-mail: callicoj@intra.nimh.nih.gov; Weinberger, Daniel R

1999-05-01

Functional magnetic resonance imaging (fMRI) is poised to make significant contributions to the study of neuropsychiatric illnesses. Whatever neural pathology attends such illnesses has proven subtle at best. By identifying predictable, regionally specific deficits in brain function, fMRI can suggest brain regions for detailed cellular analyses, provide valuable in vivo data regarding effective connectivity, provide a means to model the effects of various drug challenge paradigms, and characterize intermediate phenotypes in the search for the genes underlying mental illness. Nonetheless, as promising as fMRI appears to be in terms of its relative safety, repeatability, ability to generate individual brain maps and widespread availability, it is still subject to a number of unresolved conceptual conundrums inherited from earlier neuroimaging work. For example, functional neuroimaging has not generated any pathognomic findings in mental illness, has not established a clear link between neurophysiology and observable behavior, and has not resolved the potential confounds of medication. In this article, we will review the relevant historical background preceding fMRI, address methodological considerations in fMRI, and summarize recent fMRI findings in psychiatry. Finally, fMRI is being used to simplify the complex genetics of neuropsychiatric illness by generating quantitative and qualitative brain phenotypes.

Dynamics modeling and modal experimental study of high speed motorized spindle

International Nuclear Information System (INIS)

Li, Yunsong; Chen, Xiaoan; Zhang, Peng; Zhou, Jinming

2017-01-01

This paper presents a dynamical model of high speed motorized spindles in free state and work state. In the free state, the housing is modeled as a rotor with equivalent masses including bearing pedestals, motor stator and rear end cover. As a consequence, a double rotor dynamics can be modeled for high speed motorized spindles by a bearing element which connects the housing and bearing pedestals. In the work state, the housing is fixed and the system becomes a bearing-rotor dynamical model. An excitation-measurement test in the free state is designed to analyze the cross spectral density and auto spectral density of input and output signals. Then the frequency response function of system and coherence function of input and output signals which are used to analyze the inherent characteristics of the double- rotor model can be obtained. The other vibration test in the work state is designed to research the dynamical supporting characteristics of bearings and the effects from bearings on the inherent characteristics of the system. The good agreement between the experimental data and theoretical results indicates that the dynamical model in two states is capable of accurately predicting the dynamic behavior of high speed motorized spindles

Dynamics modeling and modal experimental study of high speed motorized spindle

Energy Technology Data Exchange (ETDEWEB)

Li, Yunsong; Chen, Xiaoan; Zhang, Peng; Zhou, Jinming [Chongqing Univ., Chongqing (China)

2017-03-15

This paper presents a dynamical model of high speed motorized spindles in free state and work state. In the free state, the housing is modeled as a rotor with equivalent masses including bearing pedestals, motor stator and rear end cover. As a consequence, a double rotor dynamics can be modeled for high speed motorized spindles by a bearing element which connects the housing and bearing pedestals. In the work state, the housing is fixed and the system becomes a bearing-rotor dynamical model. An excitation-measurement test in the free state is designed to analyze the cross spectral density and auto spectral density of input and output signals. Then the frequency response function of system and coherence function of input and output signals which are used to analyze the inherent characteristics of the double- rotor model can be obtained. The other vibration test in the work state is designed to research the dynamical supporting characteristics of bearings and the effects from bearings on the inherent characteristics of the system. The good agreement between the experimental data and theoretical results indicates that the dynamical model in two states is capable of accurately predicting the dynamic behavior of high speed motorized spindles.

The Virtual Mouse Brain: A Computational Neuroinformatics Platform to Study Whole Mouse Brain Dynamics.

Science.gov (United States)

Melozzi, Francesca; Woodman, Marmaduke M; Jirsa, Viktor K; Bernard, Christophe

2017-01-01

Connectome-based modeling of large-scale brain network dynamics enables causal in silico interrogation of the brain's structure-function relationship, necessitating the close integration of diverse neuroinformatics fields. Here we extend the open-source simulation software The Virtual Brain (TVB) to whole mouse brain network modeling based on individual diffusion magnetic resonance imaging (dMRI)-based or tracer-based detailed mouse connectomes. We provide practical examples on how to use The Virtual Mouse Brain (TVMB) to simulate brain activity, such as seizure propagation and the switching behavior of the resting state dynamics in health and disease. TVMB enables theoretically driven experimental planning and ways to test predictions in the numerous strains of mice available to study brain function in normal and pathological conditions.

Comparison of relative renal function measured with either 99m Tc-DTPA or 99m Tc-EC dynamic scintigraphies with that measured with 99m Tc-DMSA static scintigraphy

Energy Technology Data Exchange (ETDEWEB)

Domingues, F.C.; Fujikawa, G.Y.; Decker, H.; Alonso, G.; Pereira, J.C.; Duarte, P.S. [Centro de Diagnostico Fleury, Sao Paulo, SP (Brazil). Secao de Medicina Nuclear; Sao Paulo Univ. (USP), SP (Brazil). Escola de Saude Publica. Dept. de Epidemiologia]. E-mail: paulo.duarte@fleury.com.br

2006-07-15

Objective: The aim of this study was to compare the renal function measured with either {sup 99m}Tc-DTPA or {sup 99m}Tc-EC dynamic scintigraphies with that measured using {sup 99m}Tc-DMSA static scintigraphy. Methods: the values of relative renal function measured in 111 renal dynamic scintigraphies performed either with {sup 99m}Tc-DTPA (55 studies) or with {sup 99m}Tc-EC (56 studies) were compared with the relative function measured using {sup 99m}Tc-DMSA static scintigraphy performed within a 1-month period. The comparisons were performed using Wilcoxon signed rank test. The number of {sup 99m}Tc-DTPA and {sup 99m}Tc-EC studies that presented relative renal function different by more than 5% from that measured with {sup 99m}Tc-DMSA, using chi square test were also compared. Results: the relative renal function measured with {sup 99m}Tc-EC is not statistically different from that measured with {sup 99m}Tc-DMSA (p = 0.97). The relative renal function measured with {sup 99m}Tc-DTPA was statistically different from that measured using {sup 99m}Tc-DMSA, but with a borderline statistical significance (p = 0.05). The number of studies with relative renal function different by more than 5% from that measured with {sup 99m}Tc-DMSA is higher for the {sup 99m}Tc-DTPA scintigraphy (p 0.04) than for {sup 99m}Tc-EC. Conclusion: the relative renal function measured with {sup 99m}Tc-EC dynamic scintigraphy is comparable with that measured with {sup 99m}Tc-DMSA static scintigraphy, while the relative renal function measured with {sup 99m}Tc-DTPA dynamic scintigraphy presents a significant statistical difference from that measured with {sup 99m}Tc-DMSA static scintigraphy. (author)

Comparison of relative renal function measured with either 99m Tc-DTPA or 99m Tc-EC dynamic scintigraphies with that measured with 99m Tc-DMSA static scintigraphy

International Nuclear Information System (INIS)

Domingues, F.C.; Fujikawa, G.Y.; Decker, H.; Alonso, G.; Pereira, J.C.; Duarte, P.S.; Sao Paulo Univ.

2006-01-01

Objective: The aim of this study was to compare the renal function measured with either 99m Tc-DTPA or 99m Tc-EC dynamic scintigraphies with that measured using 99m Tc-DMSA static scintigraphy. Methods: the values of relative renal function measured in 111 renal dynamic scintigraphies performed either with 99m Tc-DTPA (55 studies) or with 99m Tc-EC (56 studies) were compared with the relative function measured using 99m Tc-DMSA static scintigraphy performed within a 1-month period. The comparisons were performed using Wilcoxon signed rank test. The number of 99m Tc-DTPA and 99m Tc-EC studies that presented relative renal function different by more than 5% from that measured with 99m Tc-DMSA, using chi square test were also compared. Results: the relative renal function measured with 99m Tc-EC is not statistically different from that measured with 99m Tc-DMSA (p = 0.97). The relative renal function measured with 99m Tc-DTPA was statistically different from that measured using 99m Tc-DMSA, but with a borderline statistical significance (p = 0.05). The number of studies with relative renal function different by more than 5% from that measured with 99m Tc-DMSA is higher for the 99m Tc-DTPA scintigraphy (p 0.04) than for 99m Tc-EC. Conclusion: the relative renal function measured with 99m Tc-EC dynamic scintigraphy is comparable with that measured with 99m Tc-DMSA static scintigraphy, while the relative renal function measured with 99m Tc-DTPA dynamic scintigraphy presents a significant statistical difference from that measured with 99m Tc-DMSA static scintigraphy. (author)

Reconstruction of an input function from a dynamic PET water image using multiple tissue curves

Science.gov (United States)

Kudomi, Nobuyuki; Maeda, Yukito; Yamamoto, Yuka; Nishiyama, Yoshihiro

2016-08-01

Quantification of cerebral blood flow (CBF) is important for the understanding of normal and pathologic brain physiology. When CBF is assessed using PET with {{\\text{H}}2} 15O or C15O2, its calculation requires an arterial input function, which generally requires invasive arterial blood sampling. The aim of the present study was to develop a new technique to reconstruct an image derived input function (IDIF) from a dynamic {{\\text{H}}2} 15O PET image as a completely non-invasive approach. Our technique consisted of using a formula to express the input using tissue curve with rate constant parameter. For multiple tissue curves extracted from the dynamic image, the rate constants were estimated so as to minimize the sum of the differences of the reproduced inputs expressed by the extracted tissue curves. The estimated rates were used to express the inputs and the mean of the estimated inputs was used as an IDIF. The method was tested in human subjects (n  =  29) and was compared to the blood sampling method. Simulation studies were performed to examine the magnitude of potential biases in CBF and to optimize the number of multiple tissue curves used for the input reconstruction. In the PET study, the estimated IDIFs were well reproduced against the measured ones. The difference between the calculated CBF values obtained using the two methods was small as around  PET imaging. This suggests the possibility of using a completely non-invasive technique to assess CBF in patho-physiological studies.

Brownian dynamics and dynamic Monte Carlo simulations of isotropic and liquid crystal phases of anisotropic colloidal particles: a comparative study.

Science.gov (United States)

Patti, Alessandro; Cuetos, Alejandro

2012-07-01

We report on the diffusion of purely repulsive and freely rotating colloidal rods in the isotropic, nematic, and smectic liquid crystal phases to probe the agreement between Brownian and Monte Carlo dynamics under the most general conditions. By properly rescaling the Monte Carlo time step, being related to any elementary move via the corresponding self-diffusion coefficient, with the acceptance rate of simultaneous trial displacements and rotations, we demonstrate the existence of a unique Monte Carlo time scale that allows for a direct comparison between Monte Carlo and Brownian dynamics simulations. To estimate the validity of our theoretical approach, we compare the mean square displacement of rods, their orientational autocorrelation function, and the self-intermediate scattering function, as obtained from Brownian dynamics and Monte Carlo simulations. The agreement between the results of these two approaches, even under the condition of heterogeneous dynamics generally observed in liquid crystalline phases, is excellent.

Examination of the esophageal function with dynamic scintigraphy in diabetic patients

Energy Technology Data Exchange (ETDEWEB)

Tornoczky, J.; Pasztarak, E.; Muth, L.; Sziladi, E.; Simon, L.; Kiss, M.

1985-05-19

The disturbance of the esophageal function in diabetes was demonstrated earlier with radiological examination and intraluminal manometry. In the present paper the results of examinations carried out in 130 diabetic cases by a novel, non-invasive method, the dynamic scintigraphy for studying the function of esophagus, i.e. transit time and retention, are presented. The method is highly sensitive, harmless for the patients, inexpensive, and easily reproducible. The sup(99m)Tc-DTPA used for labelling is not absorbed, has no harmful side-effects and does not influence the results of other isotopic examinations. Based on the results, it was stated, that the esophageal function decreased significantly in patients suffering from diabetes for a longer period as compared to the controls or to patients with newly detected and still untreated diabetes. The role of instable state of equilibrium and neuropathy in the background is stressed. Stable carbohydrate metabolism has favourable effect especially in the insulin-treated group. Gastrointestinal complications such as the simultaneous occurrence of reflux esophagitis and peptic esophageal ulcer are also more frequent in cases with instable metabolism. The method is considered to be suitable for the demonstration of neuropathy and for the determination of the efficiency of the treatment. Its performance is recommended in the up-to-date treatment of diabetic patients. (author). 33 refs.; 7 figs.

Fluids density functional theory and initializing molecular dynamics simulations of block copolymers

Science.gov (United States)

Brown, Jonathan R.; Seo, Youngmi; Maula, Tiara Ann D.; Hall, Lisa M.

2016-03-01

Classical, fluids density functional theory (fDFT), which can predict the equilibrium density profiles of polymeric systems, and coarse-grained molecular dynamics (MD) simulations, which are often used to show both structure and dynamics of soft materials, can be implemented using very similar bead-based polymer models. We aim to use fDFT and MD in tandem to examine the same system from these two points of view and take advantage of the different features of each methodology. Additionally, the density profiles resulting from fDFT calculations can be used to initialize the MD simulations in a close to equilibrated structure, speeding up the simulations. Here, we show how this method can be applied to study microphase separated states of both typical diblock and tapered diblock copolymers in which there is a region with a gradient in composition placed between the pure blocks. Both methods, applied at constant pressure, predict a decrease in total density as segregation strength or the length of the tapered region is increased. The predictions for the density profiles from fDFT and MD are similar across materials with a wide range of interfacial widths.

Beam Dynamics Simulation Platform and Studies of Beam Breakup in Dielectric Wakefield Structures

International Nuclear Information System (INIS)

Schoessow, P.; Kanareykin, A.; Jing, C.; Kustov, A.; Altmark, A.; Gai, W.

2010-01-01

A particle-Green's function beam dynamics code (BBU-3000) to study beam breakup effects is incorporated into a parallel computing framework based on the Boinc software environment, and supports both task farming on a heterogeneous cluster and local grid computing. User access to the platform is through a web browser.

Neutron scattering studies of the dynamics of biological systems as a function of hydration, temperature and pressure

International Nuclear Information System (INIS)

Trapp, Marcus

2010-01-01

Incoherent elastic and quasi-elastic neutron scattering were used to measure membrane and protein dynamics in the nano- to picosecond time and Angstrom length scale. The hydration dependent dynamics of DMPC model membranes was studied using elastic and quasi-elastic neutron scattering. The elastic experiments showed a clear shift of the temperature of the main phase transition to higher temperatures with decreasing hydration level. The performed quasi-elastic measurements demonstrated nicely the influence, hydration has on the diffusive motions of the head lipid groups. Different models are necessary to fit the Q-dependence of the elastic incoherent structure factor and show therefore the reduced mobility as a result of reduced water content. In addition to temperature, pressure as a second thermodynamic variable was used to explore dynamics of DMPC membranes. The ordering introduced by applying pressure has similar effect to decreased hydration, therefore both approaches are complementary. Covering three orders of magnitude in observation time, the dynamics of native AChE and its complexed counterpart in presence of Huperzin A was investigated in the range from 1 ns to 100 ps. The mean square displacements obtained from the elastic data allowed the determination of activation energies and gave evidence that a hierarchy of motions contributes to the enzymatic activity. Diffusion constants and residence times were extracted from the quasi-elastic broadening. (author) [fr

A New Theoretical Approach to Single-Molecule Fluorescence Optical Studies of RNA Dynamics

International Nuclear Information System (INIS)

Zhao Xinghai; Shan Guangcun; Bao Shuying

2011-01-01

Single-molecule fluorescence spectroscopy in condensed phases has many important chemical and biological applications. The single-molecule fluorescence measurements contain information about conformational dynamics on a vast range of time scales. Based on the data analysis protocols methodology proposed by X. Sunney Xie, the theoretical study here mainly focuses on the single-molecule studies of single RNA with interconversions among different conformational states, to with a single FRET pair attached. We obtain analytical expressions for fluorescence lifetime correlation functions that relate changes in fluorescence lifetime to the distance-dependent FRET mechanism within the context of the Smoluchowski diffusion model. The present work establishes useful guideline for the single-molecule studies of biomolecules to reveal the complicated folding dynamics of single RNA molecules at nanometer scale.

Noninvasive investigation of exocrine pancreatic function: Feasibility of cine dynamic MRCP with a spatially selective inversion-recovery pulse.

Science.gov (United States)

Yasokawa, Kazuya; Ito, Katsuyoshi; Tamada, Tsutomu; Yamamoto, Akira; Hayashida, Minoru; Tanimoto, Daigo; Higaki, Atsushi; Noda, Yasufumi; Kido, Ayumu

2015-11-01

To investigate the feasibility of noncontrast-enhanced cine dynamic magnetic resonance cholangiopancreatography (MRCP) with a spatially selective inversion-recovery (IR) pulse for evaluating exocrine pancreatic function in comparison with the N-benzoyl-L-tyrosyl-p-aminobenzoic acid (BT-PABA) test as a pancreatic exocrine function test. Twenty subjects with or without chronic pancreatitis were included. MRCP with a spatially selective IR pulse was repeated every 15 seconds for 5 minutes to acquire a total of 20 images (cine-dynamic MRCP). The median and mean frequency of the observation (the number of times) and the moving distance (mean secretion grading scores) of pancreatic juice inflow on cine-dynamic MRCP were compared with a BT-PABA test. The urinary PABA excretion rate (%) had significant positive correlations with both the mean secretion grade (r = 0.66, P = 0.002) and frequency of secretory inflow (r = 0.62, P = 0.004) in cine dynamic MRCP. Both the mean frequency of observations of pancreatic secretory inflow (1.4 ± 1.6 times vs. 14.3 ± 4.2 times, P Cine dynamic MRCP with a spatially selective IR pulse may have potential for estimating the pancreatic exocrine function noninvasively as a substitute for the BT-PABA test. © 2015 Wiley Periodicals, Inc.

Towards automatic analysis of dynamic radionuclide studies using principal-components factor analysis

International Nuclear Information System (INIS)

Nigran, K.S.; Barber, D.C.

1985-01-01

A method is proposed for automatic analysis of dynamic radionuclide studies using the mathematical technique of principal-components factor analysis. This method is considered as a possible alternative to the conventional manual regions-of-interest method widely used. The method emphasises the importance of introducing a priori information into the analysis about the physiology of at least one of the functional structures in a study. Information is added by using suitable mathematical models to describe the underlying physiological processes. A single physiological factor is extracted representing the particular dynamic structure of interest. Two spaces 'study space, S' and 'theory space, T' are defined in the formation of the concept of intersection of spaces. A one-dimensional intersection space is computed. An example from a dynamic 99 Tcsup(m) DTPA kidney study is used to demonstrate the principle inherent in the method proposed. The method requires no correction for the blood background activity, necessary when processing by the manual method. The careful isolation of the kidney by means of region of interest is not required. The method is therefore less prone to operator influence and can be automated. (author)