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.
Grouleff, Julie; Irudayam, Sheeba Jem; Skeby, Katrine K; Schiøtt, Birgit
2015-09-01
The plasma membrane, which encapsulates human cells, is composed of a complex mixture of lipids and embedded proteins. Emerging knowledge points towards the lipids as having a regulating role in protein function. Furthermore, insight from protein crystallography has revealed several different types of lipids intimately bound to membrane proteins and peptides, hereby possibly pointing to a site of action for the observed regulation. Cholesterol is among the lipid membrane constituents most often observed to be co-crystallized with membrane proteins, and the cholesterol levels in cell membranes have been found to play an essential role in health and disease. Remarkably little is known about the mechanism of lipid regulation of membrane protein function in health as well as in disease. Herein, we review molecular dynamics simulation studies aimed at investigating the effect of cholesterol on membrane protein and peptide properties. This article is part of a Special Issue entitled: Lipid-protein interactions. Copyright © 2015. Published by Elsevier B.V.
Discrete Wigner function dynamics
Energy Technology Data Exchange (ETDEWEB)
Klimov, A B; Munoz, C [Departamento de Fisica, Universidad de Guadalajara, Revolucion 1500, 44410, Guadalajara, Jalisco (Mexico)
2005-12-01
We study the evolution of the discrete Wigner function for prime and the power of prime dimensions using the discrete version of the star-product operation. Exact and semiclassical dynamics in the limit of large dimensions are considered.
Simulation study and function analysis of the dynamic aortic valve
Institute of Scientific and Technical Information of China (English)
XIA Dongdong; BAI Jing
2006-01-01
The dynamic aortic valve (DAV) is a new left ventricular assist device, a micro-axial blood pump implemented at the position of the aortic valve, pumping blood from the left ventricle into the aortic artery. The present dynamic aortic valve operates at 7 different rotation speeds, ranging from 3000 r/min (speed 1) to 9000 r/min (speed 7). Because in vivo experiments need a lot of live animals and take a long period of time, modeling and simulation have been widely used to simulate and analyze hydra-dynamic property of the DAV and its assisting effects. With the measurements from the mock circulatory loop, a mathematic model of the DAV is established and embedded into the previously developed canine circulatory system. Using this model, the effect of the DAV on the failing heart at each rotation speed level is investigated. The vital cardiac variables are computed and compared with in vivo experimental results, which are in good agreement with an acceptable difference mostly 15 %. The establishment of the DAV model and its simulation are useful for further improvement of the DAV device.
Indian Academy of Sciences (India)
Shubin Liu
2005-09-01
Dynamic behaviors of chemical concepts in density functional theory such as frontier orbitals (HOMO/LUMO), chemical potential, hardness, and electrophilicity index have been investigated in this work in the context of Bohn-Oppenheimer quantum molecular dynamics in association with molecular conformation changes. Exemplary molecular systems like CH$^{+}_{5}$ , Cl- (H2O)30 and Ca2+ (H2O)15 are studied at 300 K in the gas phase, demonstrating that HOMO is more dynamic than LUMO, chemical potential and hardness often fluctuate concurrently. It is argued that DFT concepts and indices may serve as a good framework to understand molecular conformation changes as well as other dynamic phenomena.
Roccatano, Danilo
2015-07-01
The monooxygenase P450 BM-3 is a NADPH-dependent fatty acid hydroxylase enzyme isolated from soil bacterium Bacillus megaterium. As a pivotal member of cytochrome P450 superfamily, it has been intensely studied for the comprehension of structure-dynamics-function relationships in this class of enzymes. In addition, due to its peculiar properties, it is also a promising enzyme for biochemical and biomedical applications. However, despite the efforts, the full understanding of the enzyme structure and dynamics is not yet achieved. Computational studies, particularly molecular dynamics (MD) simulations, have importantly contributed to this endeavor by providing new insights at an atomic level regarding the correlations between structure, dynamics, and function of the protein. This topical review summarizes computational studies based on MD simulations of the cytochrome P450 BM-3 and gives an outlook on future directions.
STUDY ON DYNAMICS, STABILITY AND CONTROL OF MULTI-BODY FLEXIBLE STRUCTURE SYSTEM IN FUNCTIONAL SPACE
Institute of Scientific and Technical Information of China (English)
徐建国; 贾军国
2001-01-01
The dynamics, stability and control problem of a kind of infinite dimensional system are studied in the functional space with the method of modern mathematics. First,the dynamical control model of the distributed parameter system with multi-body flexible and multi-topological structure was established which has damping, gyroscopic parts and constrained damping. Secondly, the necessary and sufficient condition of controllability and observability, the stability theory and asymptotic property of the system were obtained.These results expand the theory of the field about the dynamics and control of the system with multi-body flexible structure, and have important engineering significance.
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...... and epoxy resin increases....
The Influence of Dynamic Orthosis Training on Upper Extremity Function after Stroke: A Pilot Study
Directory of Open Access Journals (Sweden)
Rodrigo Cappato de Araújo
2014-01-01
Full Text Available The goal of this study was to assess the use of a dynamic orthosis on upper extremity function in chronic stroke patients. A case series approach was utilized, with provision of a training program (3x/week, 50 minutes/session for 8 weeks and employment of a dynamic orthosis. Six volunteers with persistent hemiparesis due to a single, unilateral stroke performed task-oriented movements with the aid of a dynamic orthosis. Tests were administered before and after training. Functional capacity was assessed using the TEMPA (Test d'Évaluation des Membres Supérieurs de Personnes Âgées test. The Wilcoxon test was used for pre-training and post-training comparisons of TEMPA scores. The volunteers showed significant improvement of upper extremity function in the performance of a bilateral task (p = 0.01 and three unilateral tasks (p = 0.04. This pilot study suggests that the dynamic orthosis associated with the performance of functional tasks can have positive outcomes regarding the improvement of functional capacity of upper extremity.
Shedding light on protein folding, structural and functional dynamics by single molecule studies
DEFF Research Database (Denmark)
Bavishi, Krutika; Hatzakis, Nikos
2014-01-01
The advent of advanced single molecule measurements unveiled a great wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways unattainable by conventional bulk assays. Equipped with the ability to record distribution of behaviors rather than the mean...... property of a population, single molecule measurements offer observation and quantification of the abundance, lifetime and function of multiple protein states. They also permit the direct observation of the transient and rarely populated intermediates in the energy landscape that are typically averaged out...... in non-synchronized ensemble measurements. Single molecule studies have thus provided novel insights about how the dynamic sampling of the free energy landscape dictates all aspects of protein behavior; from its folding to function. Here we will survey some of the state of the art contributions...
Ghasemi, Hamid; Rajabpour, Ali
2017-01-01
In this paper, we studied the thermal expansion coefficient (TEC) of pristine graphene sheets (GSs) using molecular dynamics (MD) simulation. We validated our model with previous studies employing AIREBO potential function and repeated the same simulation with the optimized Tersoff potential function. We also discussed the differences of the results and the corresponding reasons: evaluating the negative TEC of graphene by measuring the C-C bond length and out-of-plane vibrations of the GS. We finally showed that the ripples and wrinkles are more represented over the GS during the simulation with the AIREBO potential function rather than the optimized Tersoff. Comparing the results of both potential functions; it is seen that the results obtained by AIREBO potential function are in better agreement with those reported by previous scholars.
A molecular dynamics study on the interaction between epoxy and functionalized graphene sheets
Melro, L. S.; Pyrz, R.; Jensen, L. R.
2016-07-01
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 and epoxy resin increases.
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
A dynamical study of the chirally rotated Schr\\"odinger functional in QCD
Brida, Mattia Dalla
2014-01-01
The chirally rotated Schr\\"odinger functional for Wilson-fermions allows for finite-volume, mass-independent renormalization schemes compatible with automatic O($a$) improvement. So far, in QCD, the set-up has only been studied in the quenched approximation. Here we present first results for $N_{\\rm f} = 2$ dynamical quark-flavours for several renormalization factors of quark-bilinears. We discuss how these renormalization factors can be easily obtained from simple ratios of two-point functions, and show how automatic O($a$) improvement is at work. As a by-product of this investigation the renormalization of the non-singlet axial current, $Z_A$, is determined very precisely.
A dynamical study of the chirally rotated Schroedinger functional in QCD
Energy Technology Data Exchange (ETDEWEB)
Dalla Brida, Mattia; Sint, Stefan [Trinity College, Dublin (Ireland). School of Mathematics; Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany). John von Neumann-Inst. fuer Computing NIC
2014-12-15
The chirally rotated Schroedinger functional for Wilson-fermions allows for finite-volume, mass-independent renormalization schemes compatible with automatic O(a) improvement. So far, in QCD, the set-up has only been studied in the quenched approximation. Here we present first results for N{sub f}=2 dynamical quark-flavours for several renormalization factors of quark-bilinears. We discuss how these renormalization factors can be easily obtained from simple ratios of two-point functions, and show how automatic O(a) improvement is at work. As a by-product of this investigation the renormalization of the non-singlet axial current, Z{sub A}, is determined very precisely.
Vasil'ev, Sergej; Bruce, Doug
2006-05-01
Molecular dynamics simulations have been performed to study photosystem II structure and function. Structural information obtained from simulations was combined with ab initio computations of chromophore excited states. In contrast to calculations based on the x-ray structure, the molecular-dynamics-based calculations accurately predicted the experimental absorbance spectrum. In addition, our calculations correctly assigned the energy levels of reaction-center (RC) chromophores, as well as the lowest-energy antenna chlorophyll. The primary and secondary quinone electron acceptors, Q(A) and Q(B), exhibited independent changes in position over the duration of the simulation. Q(B) fluctuated between two binding sites similar to the proximal and distal sites previously observed in light- and dark-adapted RC from purple bacteria. Kinetic models were used to characterize the relative influence of chromophore geometry, site energies, and electron transport rates on RC efficiency. The fluctuating energy levels of antenna chromophores had a larger impact on quantum yield than did their relative positions. Variations in electron transport rates had the most significant effect and were sufficient to explain the experimentally observed multi-component decay of excitation in photosystem II. The implications of our results are discussed in the context of competing evolutionary selection pressures for RC structure and function.
Energy Technology Data Exchange (ETDEWEB)
Urbina, A; Miguel, C [Departamento Electronica, Universidad Politecnica de Cartagena, Plaza Hospital 1, 30202 Cartagena (Spain); Delgado, J L; Langa, F [Facultad de Ciencias del Medio Ambiente, Universidad de Castilla-La Mancha, 45071, Toledo (Spain); DIaz-Paniagua, C [Centro Espanol de MetrologIa, 28760 Madrid (Spain); Jimenez, M [Institut Laue-Langevin, 39042 Grenoble Cedex (France); Batallan, F [Instituto de Ciencia de Materiales de Madrid, CSIC, 28049 Madrid (Spain)], E-mail: antonio.urbina@upct.es
2008-03-12
We have studied, by incoherent neutron scattering experiments, the dynamics of a colloidal suspension of functionalized single wall carbon nanotubes (SWNTs). The nanotubes have been functionalized with pentyl ester groups attached at the ends and suspended in deuterated toluene with a concentration of 2.6 mg SWNT/1 ml of deuterated toluene. The experimental techniques were incoherent elastic neutron scattering (IENS) and incoherent quasielastic neutron scattering (IQNS). In the temperature range between 4 K and 300 K, three phases were observed by IENS measurements: a solid phase for T
Image derived input functions for dynamic High Resolution Research Tomograph PET brain studies.
Mourik, Jurgen E M; van Velden, Floris H P; Lubberink, Mark; Kloet, Reina W; van Berckel, Bart N M; Lammertsma, Adriaan A; Boellaard, Ronald
2008-12-01
The High Resolution Research Tomograph (HRRT) is a dedicated human brain positron emission tomography (PET) scanner. The aim of the present study was to validate the use of image derived input functions (IDIF) as an alternative for arterial sampling for HRRT human brain studies. To this end, IDIFs were extracted from 3D ordinary Poisson ordered subsets expectation maximization (OP-OSEM) and reconstruction based partial volume corrected (PVC) OP-OSEM images. IDIFs, either derived directly from regions of interest or further calibrated using manual samples taken during scans, were evaluated for dynamic [(11)C]flumazenil data (n=6). Results obtained with IDIFs were compared with those obtained using blood sampler input functions (BSIF). These comparisons included areas under the curve (AUC) for peak (0-3.3 min) and tail (3.3-55.0 min). In addition, slope, intercept and Pearson's correlation coefficient of tracer kinetic analysis results based on IDIF and BSIF were calculated for each subject. Good peak AUC ratios (0.83+/-0.21) between IDIF and BSIF were found for calibrated IDIFs extracted from OP-OSEM images. This combination of IDIFs and images also provided good slope values (1.07+/-0.11). Improved resolution, as obtained with PVC OP-OSEM, changed AUC ratios to 1.14+/-0.35 and, for tracer kinetic analysis, slopes changed to 0.95+/-0.13. For all reconstructions, non-calibrated IDIFs gave poorer results (>61+/-34% higher slopes) compared with calibrated IDIFs. The results of this study indicate that the use of IDIFs, extracted from OP-OSEM or PVC OP-OSEM images, is feasible for dynamic HRRT data, thereby obviating the need for online arterial sampling.
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.
Liu, Jia; Yan, Zhengzheng; Pu, Yuehua; Shiu, Wen-Shin; Wu, Jianhuang; Chen, Rongliang; Leng, Xinyi; Qin, Haiqiang; Liu, Xin; Jia, Baixue; Song, Ligang; Wang, Yilong; Miao, Zhongrong; Wang, Yongjun; Liu, Liping; Cai, Xiao-Chuan
2016-10-04
The fractional pressure ratio is introduced to quantitatively assess the hemodynamic significance of severe intracranial stenosis. A computational fluid dynamics-based method is proposed to non-invasively compute the FPRCFD and compared against fractional pressure ratio measured by an invasive technique. Eleven patients with severe intracranial stenosis considered for endovascular intervention were recruited and an invasive procedure was performed to measure the distal and the aortic pressure (Pd and Pa). The fractional pressure ratio was calculated as [Formula: see text] The computed tomography angiography was used to reconstruct three-dimensional (3D) arteries for each patient. Cerebral hemodynamics was then computed for the arteries using a mathematical model governed by Navier-Stokes equations and with the outflow conditions imposed by a model of distal resistance and compliance. The non-invasive [Formula: see text], [Formula: see text], and FPRCFD were then obtained from the computational fluid dynamics calculation using a 16-core parallel computer. The invasive and non-invasive parameters were tested by statistical analysis. For this group of patients, the computational fluid dynamics method achieved comparable results with the invasive measurements. The fractional pressure ratio and FPRCFD are very close and highly correlated, but not linearly proportional, with the percentage of stenosis. The proposed computational fluid dynamics method can potentially be useful in assessing the functional alteration of cerebral stenosis.
Reyt, Sébastien; Picq, Chloé; Sinniger, Valérie; Clarençon, Didier; Bonaz, Bruno; David, Olivier
2010-10-01
Dynamic Causal Modelling (DCM) has been proposed to estimate neuronal connectivity from functional magnetic resonance imaging (fMRI) using a biophysical model that links synaptic activity to hemodynamic processes. However, it is well known that fMRI is sensitive not only to neuronal activity, but also to many other psychophysiological responses which may be task-related, such as changes in cardio-respiratory activity. They are not explicitly taken into account in the generative models of DCM and their effects on estimated neuronal connectivity are not known. The main goal of this study was to report the face validity of DCM in the presence of strong physiological confounds that presumably cannot be corrected for, using an fMRI experiment of vagus nerve stimulation (VNS) performed in rats. First, a simple simulation was used to evaluate the principled ability of DCM to recover directed connectivity in the presence of a confounding factor. Second, we tested the experimental validity using measures of the BOLD correlates of left 5Hz VNS. Because VNS mostly activates the central autonomic regulation system, fMRI signals were likely to represent both direct and indirect vascular responses to such activation. In addition to the inference of standard statistical parametric maps, DCM was thus used to estimate directed neural connectivity in a small brain network including the nucleus tractus solitarius (NTS) known to receive vagal afferents. Though blood pressure changes may constitute a major physiological confound in this dataset, model comparison of DCMs still allowed the identification of the NTS as the input station of the VNS pathway to the brain. Our study indicates that current developments of DCM are robust to psychophysiological responses to some extent, but does not exclude the need to develop specific models of brain - body interactions within the DCM framework to better estimate neuronal connectivity from fMRI time series. Copyright 2010 Elsevier Inc. All
Energy Technology Data Exchange (ETDEWEB)
Miller, J.; Miaskiewicz, K. [Pacific Northwest Lab., Richland, WA (United States); Osman, R. [Mount Sinai School of Medicine, New York, NY (United States). Dept. of Physiology and Biophysics
1993-12-01
Studies of ring-saturated pyrimidine base lesions are used to illustrate an integrated modeling approach that combines quantum-chemical calculations with molecular dynamics simulation. Electronic-structure calculations on the lesions in Isolation reveal strong conformational preferences due to interactions between equatorial substituents to the pyrimidine ring. Large distortions of DNA should result when these interactions force the methyl group of thymine to assume an axial orientation, as is the case for thymine glycol but not for dihydrothymine. Molecular dynamics simulations of the dodecamer d(CGCGAATTCGCG){sub 2} with and without a ring-saturated thymine lesion at position T7 support this conclusion. Implications of these studies for recognition of thymine lesions by endonuclease III are also discussed.
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...
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...
Nouri Kadijani, M.; Abbasi, H.
2016-09-01
Dynamics of a dust layer suspending in a plasma and interacting through a Yukawa-type potential is considered. In the small affinity limit, the influence of an external white noise on the formation of Tsallis' velocity distribution function is studied through molecular dynamics simulation. The characteristic length of the noise is much smaller than the system size that causes a number of subsystems (islands) to be formed with the size similar to the noise one. The external noise leads to the temperature fluctuation in each island. Therefore, a stochastic formalism based on a Langevin equation for the fluctuating temperature is presented. The approach provides a dynamical reason how a fluctuating temperature takes a system to a unique class of quasi-equilibrium states. In particular, the dependence of the model systems on the noise parameters is explained. The non-extensive parameter is obtained through which the small affinity limit can be defined.
Dynamic Monte Carlo study on the probability distribution functions of tail-like polymer chain
Institute of Scientific and Technical Information of China (English)
CHEN Ying-cai; LUO Meng-bo
2005-01-01
The configurational properties of tail-like polymer chains with one end attached to a flat surface are studied by using p(z) can be scaled approximately by a factor β to be a length independent function for both random walking (RW) and scaled P(Rz) of the SAW chain roughly overlaps that of the RW chain, but the scaled p(z) of the SAW chain locates at smaller βz than that of the RW chain.
Methods of studying the functional ecology of protein and organ dynamics in birds
Piersma, Theunis; Klaassen, Marcel; Adams, N.J.; Slotow, R.H.
1999-01-01
Birds are capable of adaptive responses to ecological challenges involving changes in body composition, including both body stores and functional tissues. These physiological adjustments may affect aspects of the birds’ ecology, such as choice of diet and microhabitat or susceptibility to aerial predators. Carcass analysis provides accurate data on body composition; however, ethical considerations apart, this method neither enables studies of temporal changes within individuals nor allows com...
Dynamics and computation in functional shifts
Namikawa, Jun; Hashimoto, Takashi
2004-07-01
We introduce a new type of shift dynamics as an extended model of symbolic dynamics, and investigate the characteristics of shift spaces from the viewpoints of both dynamics and computation. This shift dynamics is called a functional shift, which is defined by a set of bi-infinite sequences of some functions on a set of symbols. To analyse the complexity of functional shifts, we measure them in terms of topological entropy, and locate their languages in the Chomsky hierarchy. Through this study, we argue that considering functional shifts from the viewpoints of both dynamics and computation gives us opposite results about the complexity of systems. We also describe a new class of shift spaces whose languages are not recursively enumerable.
Spatial-Temporal Study of Rab1b Dynamics and Function at the ER-Golgi Interface.
Martinez, Hernán; García, Iris A; Sampieri, Luciana; Alvarez, Cecilia
2016-01-01
The GTPase Rab1b is involved in ER to Golgi transport, with multiple Rab1b effectors (located at ERES, VTCs and the Golgi complex) being required for its function. In this study, we performed live-cell dual-expression studies to analyze the dynamics of Rab1b and some effectors located at the ERES-Golgi interface. Rab1b occupied widely distributed mobile punctate and tubular structures, displaying a transient overlaps with its effectors and showing that these overlaps occurred at the same time in spatially distinct steps of ER to Golgi transport. In addition, we assessed Rab1b dynamics during cargo sorting by analyzing the concentration at ERES of a Golgi protein (SialT2-CFP) during Brefeldin A washout (BFA WO). Rab1b was associated to most of the ERES structures, but at different times during BFA WO, and recurrently SialT2-CFP was sorted in the ERES-Rab1b positive structures. Furthermore, we reveal for first time that Rab1b localization time at ERES depended on GBF1, a Rab1b effector that acts as the guanine nucleotide exchange factor of Arf1, and that Rab1b membrane association/dissociation dynamics at ERES was dependent on the GBF1 membrane association and activity, which strongly suggests that GBF1 activity modulates Rab1b membrane cycling dynamic.
Spatial-Temporal Study of Rab1b Dynamics and Function at the ER-Golgi Interface
Martinez, Hernán; García, Iris A.; Sampieri, Luciana
2016-01-01
The GTPase Rab1b is involved in ER to Golgi transport, with multiple Rab1b effectors (located at ERES, VTCs and the Golgi complex) being required for its function. In this study, we performed live-cell dual-expression studies to analyze the dynamics of Rab1b and some effectors located at the ERES-Golgi interface. Rab1b occupied widely distributed mobile punctate and tubular structures, displaying a transient overlaps with its effectors and showing that these overlaps occurred at the same time in spatially distinct steps of ER to Golgi transport. In addition, we assessed Rab1b dynamics during cargo sorting by analyzing the concentration at ERES of a Golgi protein (SialT2-CFP) during Brefeldin A washout (BFA WO). Rab1b was associated to most of the ERES structures, but at different times during BFA WO, and recurrently SialT2-CFP was sorted in the ERES-Rab1b positive structures. Furthermore, we reveal for first time that Rab1b localization time at ERES depended on GBF1, a Rab1b effector that acts as the guanine nucleotide exchange factor of Arf1, and that Rab1b membrane association/dissociation dynamics at ERES was dependent on the GBF1 membrane association and activity, which strongly suggests that GBF1 activity modulates Rab1b membrane cycling dynamic. PMID:27500526
Large-Field Multicolor Study of Abell 168 Subclusters, Dynamics and Luminosity Functions
Yang, Y; Yuan, Q; Jiang, Z; Ma, J; Wu, H; Chen, J; Yang, Yanbin; Zhou, Xu; Yuan, Qirong; Jiang, Zhaoji; Ma, Jun; Wu, Hong; Chen, Jiansheng
2004-01-01
This paper presents a multicolor study of the nearby cluster of galaxies Abell 168 (z=0.045) with 13 intermediate-band filters in the Beijing-Arizona-Taiwan-Connecticut (BATC) filter system. After a cross-identification between the photometric data obtained from the BATC and the Sloan Digital Sky Survey (SDSS), a catalog containing 1553 galaxies down to r'<20.0 mag is achieved, which includes 121 spectroscopically confirmed member galaxies. The technique of photometric redshift has been applied to all these galaxies with combined 18-band (13 from BATC and 5 from SDSS) spectral energy distributions (SEDs), in order to perform a faint membership selection in Abell 168. As a result, 255 galaxies are newly selected as the member candidates. Based on the enlarged sample of cluster galaxies, the spatial distribution and dynamics of Abell 168 are investigated. In the light of the spatial distribution of the member galaxies and the 0.2-3.5 keV X-ray image by Einstein observatory, it seems that Abell 168 consists o...
Ogorodova, L M; Kulikov, E S; Deev, I A; Cherniak, B A; Fassakhov, R S
2011-01-01
Different strategies for disease control in real clinical practice are compared in terms of dynamics of functional parameters in patients with persistent bronchial asthma. This prospective multicentre surveillance study was carried out in 19 Russian clinics using the common protocol. The patients were divided in 3 groups in accordance with the changes of basal antiinflammatory therapy during the study period. Group A--stepwise increase in the extent of combined salmoterol/fluticason therapy, group B--long-term stable-dose salmoterol/fluticason therapy, group C--salmoterol/fluticason therapy with gradual decrease of the dose and/or transition to an alternative variant. Statistical analysis using Statistica 6.0 program included data from 543 patients. The results suggest that the two first modalities increased the level of control (ACT test) and improved characteristics of external respiration throughout the study period. Strategy 3 was associated with a decrease in the external respiration function and the level of control.
The application of psoralens to the study of DNA structure, function and dynamics
Energy Technology Data Exchange (ETDEWEB)
Spielmann, P.H. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry]|[Lawrence Berkeley Lab., CA (United States)
1991-04-01
A series of six nitroxide spin-labeled psoralens were designed, synthesized and tested as probes for DNA dynamics. The synthesis of these spin-labeled psoralen derivatives and their photoreactivity with double-stranded DNA fragments is described. The spin labels (nitroxides) were demonstrated to survive the uv irradiation required to bind the probe to the target DNA. EPR spectra of the photobound spin-labels indicate that they do not wobble with respect to the DNA on the time-scales investigated. The author has used psoralen modified DNA as a model for the study of DNA repair enzyme systems in human cell free extracts. He has shown that damage-induced DNA synthesis is associated with removal of psoralen adducts and therefore is {open_quotes}repair synthesis{close_quotes} and not an aberrant DNA synthesis reaction potentiated by deformation of the DNA by adducts. He has found that all DNA synthesis induced by psoralen monoadducts is the consequence of removal of these adducts. By the same approach he has obtained evidence that this in vitro system is capable of removing psoralen cross-links as well. Reported here are synthetic methods that make use of high intensity lasers coupled with HPLC purification to make homogeneous and very pure micromole quantities of furan-side monoadducted, cross-linked, and pyrone-side monoadducted DNA oligonucleotide. These molecules are currently being studied by NMR and X-ray crystallography. The application of the site-specifically psoralen modified oligonucleotide synthesized by these methods to the construction of substrates for the investigation of DNA repair is also discussed.
Molecular Dynamics Studies of Structure and Functions of Water-Membrane Interfaces
Pohorille, Andrew; Wilson, Michael A.; DeVincenzi, Donald L. (Technical Monitor)
2001-01-01
A large number of essential cellular processes occur at the interfaces between water and membranes. The selectivity and dynamics of these processes are largely determined by the structural and electrical properties of the water-membrane interface. We investigate these properties by the molecular dynamics method. Over the time scales of the simulations, the membrane undergoes fluctuations described by the capillary wave model. These fluctuations produce occasional thinning defects in the membrane which provide effective pathways for passive transport of ions and small molecules across the membrane. Ions moving through the membrane markedly disrupt its structure and allow for significant water penetration into the membrane interior. Selectivity of transport, with respect to ionic charge, is determined by the interfacial electrostatic potential. Many small molecules. of potential significance in catalysis, bioenergetics and pharmacology, are shown to bind to the interface. The energetics and dynamics of this process will be discussed.
Molecular Dynamics Studies of Structure and Functions of Water-Membrane Interfaces
Pohorille, Andrew; Wilson, Michael A.; DeVincenzi, Donald L. (Technical Monitor)
2001-01-01
A large number of essential cellular processes occur at the interfaces between water and membranes. The selectivity and dynamics of these processes are largely determined by the structural and electrical properties of the water-membrane interface. We investigate these properties by the molecular dynamics method. Over the time scales of the simulations, the membrane undergoes fluctuations described by the capillary wave model. These fluctuations produce occasional thinning defects in the membrane which provide effective pathways for passive transport of ions and small molecules across the membrane. Ions moving through the membrane markedly disrupt its structure and allow for significant water penetration into the membrane interior. Selectivity of transport, with respect to ionic charge, is determined by the interfacial electrostatic potential. Many small molecules. of potential significance in catalysis, bioenergetics and pharmacology, are shown to bind to the interface. The energetics and dynamics of this process will be discussed.
Molecular Dynamics Studies of Self-Assembling Biomolecules and DNA-functionalized Gold Nanoparticles
Cho, Vince Y.
This thesis is organized as following. In Chapter 2, we use fully atomistic MD simulations to study the conformation of DNA molecules that link gold nanoparticles to form nanoparticle superlattice crystals. In Chapter 3, we study the self-assembly of peptide amphiphiles (PAs) into a cylindrical micelle fiber by using CGMD simulations. Compared to fully atomistic MD simulations, CGMD simulations prove to be computationally cost-efficient and reasonably accurate for exploring self-assembly, and are used in all subsequent chapters. In Chapter 4, we apply CGMD methods to study the self-assembly of small molecule-DNA hybrid (SMDH) building blocks into well-defined cage-like dimers, and reveal the role of kinetics and thermodynamics in this process. In Chapter 5, we extend the CGMD model for this system and find that the assembly of SMDHs can be fine-tuned by changing parameters. In Chapter 6, we explore superlattice crystal structures of DNA-functionalized gold nanoparticles (DNA-AuNP) with the CGMD model and compare the hybridization.
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
Winant, Celeste D; Aparici, Carina Mari; Zelnik, Yuval R; Reutter, Bryan W; Sitek, Arkadiusz; Bacharach, Stephen L; Gullberg, Grant T
2012-01-21
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
Energy Technology Data Exchange (ETDEWEB)
Zaminpayma, Esmaeil, E-mail: zaminpayma@qiau.ac.ir [Physics Group, Qazvin Branch, Islamic Azad University, Qazvin (Iran, Islamic Republic of); Nayebi, Payman [Physics Department, Saveh Branch, Islamic Azad University, Saveh (Iran, Islamic Republic of)
2015-02-15
Graphene has novel electronic structure, such as unusual transport properties, high carrier mobility and excellent mechanical properties like high Young's modulus. These properties can be modified by many methods, such as functionalized with adding chemical groups, cutting graphene as a nanoribbon and Appling a stress along graphene. In this work, we studied the mechanical and electrical properties of functionalized graphene nanoribbon with –NH{sub 2}, –CH{sub 3}, –OH, –C{sub 5}H{sub 6} groups. In mechanical section, we calculated Young's modulus of functionalized graphene nanoribbon as a function of temperature by method of reactive molecular dynamic simulation. Our results show that Young's modulus decrease by increasing temperature. Also we studied the effect of functionalized groups on Young's modulus. We show that Young's modulus decreases by adding these groups. It is in the order of Y (nanoribbon)>Y (NH{sub 2})>Y (C{sub 6}H{sub 5})>Y (OH)>Y (CH{sub 3}). In electrical section, we calculated current–voltage curve for functionalized nanoribbon with density functional tight-binding method at two different 0% and 5% strain. We found for both strains, the functionalized groups decrease the electrical resistance of nanoribbon and increase its current. The relationship of the current is in the order of I(CH{sub 3}) >I(C{sub 5}H{sub 6}) >I(NH{sub 2}) >I(OH) >I (nanoribbon)
Methods of studying the functional ecology of protein and organ dynamics in birds
Piersma, Theunis; Klaassen, Marcel; Adams, N.J.; Slotow, R.H.
1999-01-01
Birds are capable of adaptive responses to ecological challenges involving changes in body composition, including both body stores and functional tissues. These physiological adjustments may affect aspects of the birds’ ecology, such as choice of diet and microhabitat or susceptibility to aerial pre
Directory of Open Access Journals (Sweden)
Amado Geroge Stefan
2008-01-01
Full Text Available The paper contains data regarding the processes that occur art normal pressure and the variations of enthalpy, entropy, molar isobar heat, isobar potential. The variations of enthalpy and molar isobar heat are useful in the calculation of the thermic balance-sheet, and those in connection with the isobar potential are useful for the calculation of the balances. The enthalpy and entropy are linear combinations of the temperature functions and, being taken as a basis for the calculation of isobar potential. The indicated proprieties for each component can be calculated, if we know the approximation function for the isobar molar heat and the known value of the propriety at a temperature. In order to find the, coefficients we consider known the values of the molar isobar heat at five values of absolute temperature, after which we apply the linear algebra method.
Directory of Open Access Journals (Sweden)
N.V. Karlovich
2014-03-01
Full Text Available In 92 patients with end-stage chronic kidney disease we have evaluated serum levels of parathyroid hormone (PTH, vitamin D3, indicators of phosphorus and calcium metabolism and markers of bone metabolism: at baseline and at the end of dynamic follow-up period lasting from 6 to 24 months. In the whole group the mean PTH level and incidence of secondary hyperparathyroidism (SHPT have not changed significantly. Phosphorus levels decreased significantly, but did not reach the target level, indicating the lack of patients’ adherence to medical recommendations on hyperphosphatemia correction. It was found that the persistence of high levels of PTH during follow-up is determined by high baseline levels of PTH, alkaline phosphatase, osteocalcin and beta-cross-laps, as well as the young age of the patients. Persistence of hypercalcemia and hyperphosphatemia has the greatest impact on SHPT aggravation. The findings allow us to conclude that in patients with stable parameters of phosphorus and calcium metabolism, with the absence of correction for calcium and phosphorus metabolism or use of diet in combination with calcium and vitamin D3 preparations, the measurement of PTH once a year in most cases is enough to control its levels.
Time-dependent density functional studies of nuclear quantum dynamics in large amplitudes
Wen, Kai; Fang, Ni; Nakatsukasa, Takashi
2015-01-01
The time-dependent density functional theory (TDDFT) provides a unified description of the structure and reaction. The linear approximation leads to the random-phase approximation (RPA) which is capable of describing a variety of collective motion in a harmonic regime. Beyond the linear regime, we present applications of the TDDFT to nuclear fusion and fission reaction. In particular, the extraction of the internuclear potential and the inertial mass parameter is performed using two different methods. A fusion hindrance mechanism for heavy systems is investigated from the microscopic point of view. The canonical collective variables are determined by the adiabatic self-consistent collective coordinate method. Preliminary results of the spontaneous fission path, the potential, and the collective mass parameter are shown for 8Be --> alpha+alpha.
Dynamics of cavitating cascades. [transfer functions
Brennen, C. E.; Acosta, A. J.
1980-01-01
The unsteady dynamics of cavitating cascades and inducer pumps were studied with a view to understanding (and possibly predicting) the dynamic characteristics of these devices. The chronology of the research is summarized as well as the final conculsions for each task. The construction of a dynamic pump test facility and its use in making experimental measurements of the transfer function is described as well as tests conducted using a scale model of the low pressure liquid oxygen turbopump inducer in the shuttle main engine. Auto-oscillation and unsteady inlet flow characteristics are discussed in addition to blade cavity influence and bubbly cavitation.
Shityakov, Sergey; Salvador, Ellaine; Pastorin, Giorgia; Förster, Carola
2015-01-01
In this study, the ability of a multiwalled carbon nanotube functionalized with fluorescein isothiocyanate (MWCNT-FITC) was assessed as a prospective central nervous system-targeting drug delivery system to permeate the blood-brain barrier. The results indicated that the MWCNT-FITC conjugate is able to penetrate microvascular cerebral endothelial monolayers; its concentrations in the Transwell(®) system were fully equilibrated after 48 hours. Cell viability test, together with phase-contrast and fluorescence microscopies, did not detect any signs of MWCNT-FITC toxicity on the cerebral endothelial cells. These microscopic techniques also revealed presumably the intracellular localization of fluorescent MWCNT-FITCs apart from their massive nonfluorescent accumulation on the cellular surface due to nanotube lipophilic properties. In addition, the 1,000 ps molecular dynamics simulation in vacuo discovered the phenomenon of carbon nanotube aggregation driven by van der Waals forces via MWCNT-FITC rapid dissociation as an intermediate phase.
Dynamic Blowout Risk Analysis Using Loss Functions.
Abimbola, Majeed; Khan, Faisal
2017-08-11
Most risk analysis approaches are static; failing to capture evolving conditions. Blowout, the most feared accident during a drilling operation, is a complex and dynamic event. The traditional risk analysis methods are useful in the early design stage of drilling operation while falling short during evolving operational decision making. A new dynamic risk analysis approach is presented to capture evolving situations through dynamic probability and consequence models. The dynamic consequence models, the focus of this study, are developed in terms of loss functions. These models are subsequently integrated with the probability to estimate operational risk, providing a real-time risk analysis. The real-time evolving situation is considered dependent on the changing bottom-hole pressure as drilling progresses. The application of the methodology and models are demonstrated with a case study of an offshore drilling operation evolving to a blowout. © 2017 Society for Risk Analysis.
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
A functional calculus for the magnetization dynamics
Tranchida, Julien; Nicolis, Stam
2016-01-01
A functional calculus approach is applied to the derivation of evolution equations for the moments of the magnetization dynamics of systems subject to stochastic fields. It allows us to derive a general framework for obtaining the master equation for the stochastic magnetization dynamics, that is applied to both, Markovian and non-Markovian dynamics. The formalism is applied for studying different kinds of interactions, that are of practical relevance and hierarchies of evolution equations for the moments of the distribution of the magnetization are obtained. In each case, assumptions are spelled out, in order to close the hierarchies. These closure assumptions are tested by extensive numerical studies, that probe the validity of Gaussian or non--Gaussian closure Ans\\"atze.
Energy Technology Data Exchange (ETDEWEB)
Kobayashi, Shigeki; Kawaguchi, Tatsuya; Takano, Katsuhiro; Tanaka, Naoshi; Nishide, Yoshiya; Takeda, Kan; Hioki, Takuichi; Kawamura, Hisaichi; Nakagawa, Tsuyoshi (Mie Univ., Tsu (Japan). School of Medicine)
1994-02-01
A Phase III clinical study compared Tc-99m mercaptoacetylglycylglycylglycine (Tc-99m MAG3) with I-123 orthoiodohippurate (I-123 OIH) in functional radionuclide renal study using deconvolution analysis. The subjects were six patients with diabetic nephropathy, four with renal transplants and seven healthy volunteers. Tc-99m MAG3 tended to give a prolonger transit time than I-123 OIH, although there was no significant correlation between the two radiopharmaceuticals. The shape of the transfer function showed the same distribution pattern of the transit time in Tc-99m MAG3 and I-123 OIH, revealing that both radiopharmaceuticals had the analogous renal dynamics. Regarding effective renal plasma flow, there was a good correlation between the two drug, especially for those with renal transplants. In all patients with renal transplants, defects were seen on functional images when using I-123 OIH, but not seen when using Tc-99m MAG3. This may be attributable to artifacts caused by insufficient dosage of I-123 OIH. Thus Tc-99m MAG3 is considered more useful for evaluating renal function in functional radionuclide imaging because its dosage can be adjusted voluntarily. (N.K.).
Actin dynamics shape microglia effector functions.
Uhlemann, Ria; Gertz, Karen; Boehmerle, Wolfgang; Schwarz, Tobias; Nolte, Christiane; Freyer, Dorette; Kettenmann, Helmut; Endres, Matthias; Kronenberg, Golo
2016-06-01
Impaired actin filament dynamics have been associated with cellular senescence. Microglia, the resident immune cells of the brain, are emerging as a central pathophysiological player in neurodegeneration. Microglia activation, which ranges on a continuum between classical and alternative, may be of critical importance to brain disease. Using genetic and pharmacological manipulations, we studied the effects of alterations in actin dynamics on microglia effector functions. Disruption of actin dynamics did not affect transcription of genes involved in the LPS-triggered classical inflammatory response. By contrast, in consequence of impaired nuclear translocation of phospho-STAT6, genes involved in IL-4 induced alternative activation were strongly downregulated. Functionally, impaired actin dynamics resulted in reduced NO secretion and reduced release of TNFalpha and IL-6 from LPS-stimulated microglia and of IGF-1 from IL-4 stimulated microglia. However, pathological stabilization of the actin cytoskeleton increased LPS-induced release of IL-1beta and IL-18, which belong to an unconventional secretory pathway. Reduced NO release was associated with decreased cytoplasmic iNOS protein expression and decreased intracellular arginine uptake. Furthermore, disruption of actin dynamics resulted in reduced microglia migration, proliferation and phagocytosis. Finally, baseline and ATP-induced [Ca(2+)]int levels were significantly increased in microglia lacking gelsolin, a key actin-severing protein. Together, the dynamic state of the actin cytoskeleton profoundly and distinctly affects microglia behaviours. Disruption of actin dynamics attenuates M2 polarization by inhibiting transcription of alternative activation genes. In classical activation, the role of actin remodelling is complex, does not relate to gene transcription and shows a major divergence between cytokines following conventional and unconventional secretion.
Directory of Open Access Journals (Sweden)
Nagasundaram N
Full Text Available The cyclin-dependent kinase 4 (CDK4-cyclin D1 complex plays a crucial role in the transition from the G1 phase to S phase of the cell cycle. Among the CDKs, CDK4 is one of the genes most frequently affected by somatic genetic variations that are associated with various forms of cancer. Thus, because the abnormal function of the CDK4-cyclin D1 protein complex might play a vital role in causing cancer, CDK4 can be considered a genetically validated therapeutic target. In this study, we used a systematic, integrated computational approach to identify deleterious nsSNPs and predict their effects on protein-protein (CDK4-cyclin D1 and protein-ligand (CDK4-flavopiridol interactions. This analysis resulted in the identification of possible inhibitors of mutant CDK4 proteins that bind the conformations induced by deleterious nsSNPs. Using computational prediction methods, we identified five nsSNPs as highly deleterious: R24C, Y180H, A205T, R210P, and R246C. From molecular docking and molecular dynamic studies, we observed that these deleterious nsSNPs affected CDK4-cyclin D1 and CDK4-flavopiridol interactions. Furthermore, in a virtual screening approach, the drug 5_7_DIHYDROXY_ 2_ (3_4_5_TRI HYDROXYPHENYL _4H_CHROMEN_ 4_ONE displayed good binding affinity for proteins with the mutations R24C or R246C, the drug diosmin displayed good binding affinity for the protein with the mutation Y180H, and the drug rutin displayed good binding affinity for proteins with the mutations A205T and R210P. Overall, this computational investigation of the CDK4 gene highlights the link between genetic variation and biological phenomena in human cancer and aids in the discovery of molecularly targeted therapies for personalized treatment.
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.
Langueur, H.; Kassali, K.
2017-03-01
Using a density functional scheme, for the first time the carbon dependence on the structural, dynamic, thermodynamic, and dynamic properties of Si_{1-x}Cx alloys (x=0.0 to 1.0 in steps of 0.125) has been investigated. The structural properties of these materials, in particular, the composition dependence of the lattice parameter and bulk modulus, are in excellent agreement with experimental data and follow a quadratic law in ( x). A nonlinear relationship is found between the elastic constants C_{11}, C_{12}, and C_{44} and the carbon concentration ( x). The behavior of the acoustical and optical phonon frequencies at high-symmetry points Γ, X, and L is predicted. Through the quasi-harmonic Debye model, in which the photonic effects are taken into account, the Debye temperature, the heat capacity, the Helmholtz free energy, the internal energy, and the entropy are determined for the Si_{1-x}C_{x } compounds.
Molecular Dynamics and Protein Function
National Research Council Canada - National Science Library
M. Karplus; J. Kuriyan; Bruce J. Berne
2005-01-01
.... Molecular dynamics simulations provide powerful tools for the exploration of the conformational energy landscape accessible to these molecules, and the rapid increase in computational power coupled...
Dynamics and zeta functions on conformally compact manifolds
Rowlett, Julie; Tapie, Samuel
2011-01-01
In this note, we study the dynamics and associated zeta functions of conformally compact manifolds with variable negative sectional curvatures. We begin with a discussion of a larger class of manifolds known as convex co-compact manifolds with variable negative curvature. Applying results from dynamics on these spaces, we obtain optimal meromorphic extensions of weighted dynamical zeta functions and asymptotic counting estimates for the number of weighted closed geodesics. A meromorphic extension of the standard dynamical zeta function and the prime orbit theorem follow as corollaries. Finally, we investigate interactions between the dynamics and spectral theory of these spaces.
Institute of Scientific and Technical Information of China (English)
Chen Sheng; Li Shiting; Fang Youping
2014-01-01
Objective: To explore the systemic and local cellular immune function of patients with esophageal carcinoma or cardiac cancer. Methods: The distribution of tumor-infiltrating lymphocyte (TIL) and cancer-associated macrophage (TAM) in local tumor tissues of 52 patients with esophageal cancer or cardiac cancer were observed by immunehistochemical method. The level of peripheral SIL-2R and TNF-α of preoperative and postoperative 1, 2, 3 weeks were detected by ELISA and ABC-ELISA methods respectively, then the acquired results were compared with 30 cases of normal control group. Results:The peritumor inifltration densities of TIL and TAM was greater than that of cancer nest stroma (P<0.05). Compared with the normal control group, the levels of sIL-2R and TNF-α increased signiifcantly (P<0.01). Immune function could be suppressed by operative wound in a short time of post-operation, whose damage severity was closely associated with tumor TNM stages. Conclusion: Patients with esophageal or cardiac cancer have cellular immune function disorders. Dynamic testing of peripheral sIL-2R and TNT-α level in patients with esophageal or cardiac cancer has positive clinical signiifcance in the evaluation of cellular immune function, tumor lesion degree and curative effect.
GPU accelerated dynamic functional connectivity analysis for functional MRI data.
Akgün, Devrim; Sakoğlu, Ünal; Esquivel, Johnny; Adinoff, Bryon; Mete, Mutlu
2015-07-01
Recent advances in multi-core processors and graphics card based computational technologies have paved the way for an improved and dynamic utilization of parallel computing techniques. Numerous applications have been implemented for the acceleration of computationally-intensive problems in various computational science fields including bioinformatics, in which big data problems are prevalent. In neuroimaging, dynamic functional connectivity (DFC) analysis is a computationally demanding method used to investigate dynamic functional interactions among different brain regions or networks identified with functional magnetic resonance imaging (fMRI) data. In this study, we implemented and analyzed a parallel DFC algorithm based on thread-based and block-based approaches. The thread-based approach was designed to parallelize DFC computations and was implemented in both Open Multi-Processing (OpenMP) and Compute Unified Device Architecture (CUDA) programming platforms. Another approach developed in this study to better utilize CUDA architecture is the block-based approach, where parallelization involves smaller parts of fMRI time-courses obtained by sliding-windows. Experimental results showed that the proposed parallel design solutions enabled by the GPUs significantly reduce the computation time for DFC analysis. Multicore implementation using OpenMP on 8-core processor provides up to 7.7× speed-up. GPU implementation using CUDA yielded substantial accelerations ranging from 18.5× to 157× speed-up once thread-based and block-based approaches were combined in the analysis. Proposed parallel programming solutions showed that multi-core processor and CUDA-supported GPU implementations accelerated the DFC analyses significantly. Developed algorithms make the DFC analyses more practical for multi-subject studies with more dynamic analyses.
Topilsky, Yan; Vaturi, Ori; Watanabe, Nozomi; Bichara, Valentina; Nkomo, Vuyisile T.; Michelena, Hector; Le Tourneau, Thierry; Mankad, Sunil V.; Park, Soon; Capps, Mary Ann; Suri, Rakesh; Pislaru, Sorin V.; Maalouf, Joseph; Yoshida, Kiyoshi; Enriquez‐Sarano, Maurice
2013-01-01
Background Three‐dimensional transthoracic echocardiography (3D‐TTE) with dedicated software permits quantification of mitral annulus dynamics and papillary muscle motion throughout the cardiac cycle. Methods and Results Mitral apparatus 3D‐TTE was acquired in controls (n=42), patients with left ventricle dysfunction and functional mitral regurgitation (LVD‐FMR; n=43) or without FMR (LVD‐noMR, n=35). Annulus in both normal and LVD‐noMR subjects displayed saddle shape accentuation in early‐systole (ratio of height to intercommissural diameter, 10.6±3.7 to 13.5±4.0 in normal and 9.1±4.3 to 12.6±3.6 in LVD‐noMR; PPtAR) throughout systole. In LVD‐FMR patients midsystolic posterior papillary tip to anterior annulus distance was increased, resulting in higher PtAR (P=0.05 compared to both other groups). Mechanisms of early‐ and midsystolic FMR differed between different etiologies of LV dysfunction. In patients with anterior MI and global dysfunction annular function and dilatation were the dominant parameters, while papillary muscle motion was the predominant determinant of FMR in patients with inferior MI. Conclusions Inadequate early‐systolic annular contraction and saddle‐shape accentuation in patients with impaired LV contribute to early–mitral incompetency. Asymmetric papillary tip movement towards the midanterior annulus is a major determinant of mid‐ and late‐systolic functional mitral regurgitation. PMID:23727698
Electronic structure of CeRu4Sn6: a density functional plus dynamical mean field theory study
Wissgott, Philipp; Held, Karsten
2016-01-01
The Kondo system CeRu4Sn6 shows a strong anisotropy in its electric, optic and magnetic properties. We employ density functional theory plus dynamical mean field theory and show that the predominant Ce-f state has total angular moment J = 5 / 2 and z-component mJ = ± 1 / 2 in agreement with recent X-ray absorption experiments. There is also an admixture of mJ = ± 3 / 2 which is reduced in favor of mJ = ± 1 / 2 with the onset of the Kondo effect. Even though CeRu4Sn6 has the direct gap of a Kondo insulator through most of the Brillouin zone it remains weakly metallic. This is because of (i) a band crossing in the z-direction and (ii) a negative indirect gap.
Density functional and molecular dynamics studies of solid electrolyte Li7La3Zr2O12
Johannes, Michelle; Hoang, Khang; Bernstein, Noam
2012-02-01
Garnet-type structured Li7La3Zr2O12(LLZO) is considered as a promising candidate for Li-ion battery solid electrolytes because of its high ionic conductivity and electrochemical and chemical stability. We use first-principles density-functional theory calculations and molecular dynamics simulations to reveal the underlying mechanism that drives a tetragonal to cubic transition at elevated temperatures, and also to explain why the cubic phase can be stabilized with the incorporation of a certain amount of impurities such as Al. We show that the relationship between the observance of a cubic phase and the measurement of a substantially higher ionic conductivity is a secondary effect not directly attributable to the presence of Al in the crystal structure. Suggestions for enhancing the ionic conductivity in LLZO will also be discussed.
Functional evolutions for homogeneous stationary death-immigration spatial dynamics
Finkelshtein, Dmitri
2011-01-01
We discover death-immigration non-equilibrium stochastic dynamics in the continuum also known as the Surgailis process. Explicit expression for the correlation functions is presented. Dynamics of states and their generating functionals are studied. Ergodic properties for the evolutions are considered.
Elements and modulation of functional dynamics.
Gibbs, Alan C
2014-10-09
The existing structure-function paradigm of drug discovery has been evolving toward the essential incorporation of dynamics data. This new functional dynamics paradigm emphasizes conformational entropy as a driving force of protein function and intermolecular recognition. Conformational dynamics (a proxy of conformational entropy) impacts the degree of protein (dis)order and the constitution of the conformational ensemble, the mechanisms of allostery and drug resistance, and the free energy of ligand binding. Specific protein and ligand conformations facilitate favorable, reciprocal interactions. The number of protein and ligand conformers that exhibit favorable binding interactions will vary from system to system. All binding scenarios can modulate protein dynamics by various levels of enthalpic and entropic contribution, with significant influence on the functional dynamics of the system. Analysis and consideration of resulting changes of activity, signaling, catalysis, and subsequent phenotypic outcome are powerful motivations in the drug design process.
Time evolution of the autocorrelation function in dynamical replica theory
Sakata, A.
2013-04-01
Asynchronous dynamics given by the master equation in the Sherrington-Kirkpatrick (SK) spin-glass model is studied based on dynamical replica theory (DRT) with an extension to take into account the autocorrelation function. The dynamical behaviour of the system is approximately described by dynamical equations of the macroscopic quantities: magnetization, energy contributed by randomness and the autocorrelation function. The dynamical equations under the replica symmetry assumption are derived by introducing the subshell equipartitioning assumption and exploiting the replica method. The obtained dynamical equations are compared with Monte Carlo simulations, and it is demonstrated that the proposed formula describes well the time evolution of the autocorrelation function in some parameter regions. The study offers a reasonable description of the autocorrelation function in the SK spin-glass system.
Pérez, Alejandro; Tuckerman, Mark E.; Müser, Martin H.
2009-05-01
The problems of ergodicity and internal consistency in the centroid and ring-polymer molecular dynamics methods are addressed in the context of a comparative study of the two methods. Enhanced sampling in ring-polymer molecular dynamics (RPMD) is achieved by first performing an equilibrium path integral calculation and then launching RPMD trajectories from selected, stochastically independent equilibrium configurations. It is shown that this approach converges more rapidly than periodic resampling of velocities from a single long RPMD run. Dynamical quantities obtained from RPMD and centroid molecular dynamics (CMD) are compared to exact results for a variety of model systems. Fully converged results for correlations functions are presented for several one dimensional systems and para-hydrogen near its triple point using an improved sampling technique. Our results indicate that CMD shows very similar performance to RPMD. The quality of each method is further assessed via a new χ2 descriptor constructed by transforming approximate real-time correlation functions from CMD and RPMD trajectories to imaginary time and comparing these to numerically exact imaginary time correlation functions. For para-hydrogen near its triple point, it is found that adiabatic CMD and RPMD both have similar χ2 error.
Zeng, Dong; Gong, Changfei; Bian, Zhaoying; Huang, Jing; Zhang, Xinyu; Zhang, Hua; Lu, Lijun; Niu, Shanzhou; Zhang, Zhang; Liang, Zhengrong; Feng, Qianjin; Chen, Wufan; Ma, Jianhua
2016-11-01
Dynamic myocardial perfusion computed tomography (MPCT) is a promising technique for quick diagnosis and risk stratification of coronary artery disease. However, one major drawback of dynamic MPCT imaging is the heavy radiation dose to patients due to its dynamic image acquisition protocol. In this work, to address this issue, we present a robust dynamic MPCT deconvolution algorithm via adaptive-weighted tensor total variation (AwTTV) regularization for accurate residue function estimation with low-mA s data acquisitions. For simplicity, the presented method is termed ‘MPD-AwTTV’. More specifically, the gains of the AwTTV regularization over the original tensor total variation regularization are from the anisotropic edge property of the sequential MPCT images. To minimize the associative objective function we propose an efficient iterative optimization strategy with fast convergence rate in the framework of an iterative shrinkage/thresholding algorithm. We validate and evaluate the presented algorithm using both digital XCAT phantom and preclinical porcine data. The preliminary experimental results have demonstrated that the presented MPD-AwTTV deconvolution algorithm can achieve remarkable gains in noise-induced artifact suppression, edge detail preservation, and accurate flow-scaled residue function and MPHM estimation as compared with the other existing deconvolution algorithms in digital phantom studies, and similar gains can be obtained in the porcine data experiment.
Directory of Open Access Journals (Sweden)
Akihiro T Sasaki
2012-08-01
Full Text Available Automatic mimicry is based on the tight linkage between motor and perception action representations in which internal models play a key role. Based on the anatomical connection, we hypothesized that the direct effective connectivity from the posterior superior temporal sulcus (pSTS to the ventral premotor area (PMv formed an inverse internal model, converting visual representation into a motor plan, and that reverse connectivity formed a forward internal model, converting the motor plan into a sensory outcome of action. To test this hypothesis, we employed dynamic causal-modeling analysis with functional magnetic-resonance imaging. Twenty-four normal participants underwent a change-detection task involving two visually-presented balls that were either manually rotated by the investigator’s right hand (‘Hand’ or automatically rotated. The effective connectivity from the pSTS to the PMv was enhanced by hand observation and suppressed by execution, corresponding to the inverse model. Opposite effects were observed from the PMv to the pSTS, suggesting the forward model. Additionally, both execution and hand observation commonly enhanced the effective connectivity from the pSTS to the inferior parietal lobule (IPL, the IPL to the primary sensorimotor cortex (S/M1, the PMv to the IPL, and the PMv to the S/M1. Representation of the hand action therefore was implemented in the motor system including the S/M1. During hand observation, effective connectivity toward the pSTS was suppressed whereas that toward the PMv and S/M1 was enhanced. Thus the action-representation network acted as a dynamic feedback-control system during action observation.
Kikkinides, E S; Monson, P A
2015-03-07
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.
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...
Symbolic Tensor Calculus -- Functional and Dynamic Approach
Woszczyna, A; Czaja, W; Golda, Z A
2016-01-01
In this paper, we briefly discuss the dynamic and functional approach to computer symbolic tensor analysis. The ccgrg package for Wolfram Language/Mathematica is used to illustrate this approach. Some examples of applications are attached.
Understanding Microbial Communities: Function, Structure and Dynamics
2015-02-11
microbial communities: Function, structure and dynamics’, at the Isaac Newton Institute, University of Cambridge, United Kingdom, from August to...dynamics’, at the Isaac Newton Institute, University of Cambridge, United Kingdom, from August to December 2014. The programme involved over 150...Communities: Function, Structure and Dynamics’, at the Isaac Newton Institute, Cambridge University, UK, from 19th August 2014 – 19th December 2014
Pohorille, Andrew; Wilson, Michael A.
1995-01-01
Molecular dynamics computer simulations of the structure and functions of a simple membrane are performed in order to examine whether membranes provide an environment capable of promoting protobiological evolution. Our model membrane is composed of glycerol 1-monooleate. It is found that the bilayer surface fluctuates in time and space, occasionally creating thinning defects in the membrane. These defects are essential for passive transport of simple ions across membranes because they reduce the Born barrier to this process by approximately 40%. Negative ions are transferred across the bilayer more readily than positive ions due to favorable interactions with the electric field at the membrane-water interface. Passive transport of neutral molecules is, in general, more complex than predicted by the solubility-diffusion model. In particular, molecules which exhibit sufficient hydrophilicity and lipophilicity concentrate near membrane surfaces and experience 'interfacial resistance' to transport. The membrane-water interface forms an environment suitable for heterogeneous catalysis. Several possible mechanisms leading to an increase of reaction rates at the interface are discussed. We conclude that vesicles have many properties that make them very good candidates for earliest protocells. Some potentially fruitful directions of experimental and theoretical research on this subject are proposed.
Pohorille, Andrew; Wilson, Michael A.
1995-01-01
Molecular dynamics computer simulations of the structure and functions of a simple membrane are performed in order to examine whether membranes provide an environment capable of promoting protobiological evolution. Our model membrane is composed of glycerol 1-monooleate. It is found that the bilayer surface fluctuates in time and space, occasionally creating thinning defects in the membrane. These defects are essential for passive transport of simple ions across membranes because they reduce the Born barrier to this process by approximately 40%. Negative ions are transferred across the bilayer more readily than positive ions due to favorable interactions with the electric field at the membrane-water interface. Passive transport of neutral molecules is, in general, more complex than predicted by the solubility-diffusion model. In particular, molecules which exhibit sufficient hydrophilicity and lipophilicity concentrate near membrane surfaces and experience 'interfacial resistance' to transport. The membrane-water interface forms an environment suitable for heterogeneous catalysis. Several possible mechanisms leading to an increase of reaction rates at the interface are discussed. We conclude that vesicles have many properties that make them very good candidates for earliest protocells. Some potentially fruitful directions of experimental and theoretical research on this subject are proposed.
Semigroups of transcendental entire functions and their dynamics
Indian Academy of Sciences (India)
DINESH KUMAR; SANJAY KUMAR
2017-04-01
We investigate the dynamics of semigroups of transcendental entire functions 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 transcendental semigroups. We also study finitely generated transcendental semigroups, abelian transcendental semigroups and limit functions of transcendental semigroups on its invariant Fatou components.
Directory of Open Access Journals (Sweden)
Wan-Ying Lin
2014-01-01
Full Text Available Compressive stimulation can modulate articular chondrocyte functions. Nevertheless, the relevant studies are not comprehensive. This is primarily due to the lack of cell culture apparatuses capable of conducting the experiments in a high throughput, precise, and cost-effective manner. To address the issue, we demonstrated the use of a perfusion microcell culture system to investigate the stimulating frequency (0.5, 1.0, and 2.0 Hz effect of compressive loading (20% and 40% strain on the functions of articular chondrocytes. The system mainly integrates the functions of continuous culture medium perfusion and the generation of pneumatically-driven compressive stimulation in a high-throughput micro cell culture system. Results showed that the compressive stimulations explored did not have a significant impact on chondrocyte viability and proliferation. However, the metabolic activity of chondrocytes was significantly affected by the stimulating frequency at the higher compressive strain of 40% (2 Hz, 40% strain. Under the two compressive strains studied, the glycosaminoglycans (GAGs synthesis was upregulated when the stimulating frequency was set at 1 Hz and 2 Hz. However, the stimulating frequencies explored had no influence on the collagen production. The results of this study provide useful fundamental insights that will be helpful for cartilage tissue engineering and cartilage rehabilitation.
Directory of Open Access Journals (Sweden)
Magnus Lindwall
2012-01-01
Full Text Available The present study used a coordinated analyses approach to examine the association of physical activity and cognitive change in four longitudinal studies. A series of multilevel growth models with physical activity included both as a fixed (between-person and time-varying (within-person predictor of four domains of cognitive function (reasoning, memory, fluency, and semantic knowledge was used. Baseline physical activity predicted fluency, reasoning and memory in two studies. However, there was a consistent pattern of positive relationships between time-specific changes in physical activity and time-specific changes in cognition, controlling for expected linear trajectories over time, across all four studies. This pattern was most evident for the domains of reasoning and fluency.
Biodiversity and ecosystem functioning in dynamic landscapes.
Brose, Ulrich; Hillebrand, Helmut
2016-05-19
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
Particle conservation in dynamical density functional theory.
de Las Heras, Daniel; Brader, Joseph M; Fortini, Andrea; Schmidt, Matthias
2016-06-22
We present the exact adiabatic theory for the dynamics of the inhomogeneous density distribution of a classical fluid. Erroneous particle number fluctuations of dynamical density functional theory are absent, both for canonical and grand canonical initial conditions. We obtain the canonical free energy functional, which yields the adiabatic interparticle forces of overdamped Brownian motion. Using an exact and one of the most advanced approximate hard core free energy functionals, we obtain excellent agreement with simulations. The theory applies to finite systems in and out of equilibrium.
Adsorption of Zn2+ on the (110) surface of TiO2: A density functional molecular dynamics study.
Energy Technology Data Exchange (ETDEWEB)
Bandura, Andrei V. [St. Petersburg State University, St. Petersburg, Russia; Sofo, Jorge O. [Pennsylvania State University; Kubicki, James D. [Pennsylvania State University
2011-01-01
Adsorption of Zn2 at the rutile TiO2 (110)-aqueous interface was studied with BornOppenheimer molecular dynamics at 300 K. Simulations were carried out using the periodically repeated slab model with vacuum gap of 15 filled with 72 H2O molecules. Two possible adsorption sites, monodentate above bridging oxygen (TiOTi or Obr) and bidentate above terminal oxygens (TiO), were investigated. Sites with different coordination environment for adsorbed Zn2 differ from each other by the position of Zn2 above surface level and by characteristic ZnOdistances. Obtained results gave evidence that 4-fold coordination of adsorbed Zn2 is more probable than the 6-fold coordination found for aqueous species. The hydrolysis of H2O molecules was observed in the first coordination shell of adsorbed ion, resulting in formation of OH groups attached to Zn2 . Calculated energies favor the tetrahedral bidentate structure of hydrated Zn2 on the rutile surface. The model structures are compared to observed positions of Zn2 above the rutile (110) surface using X-ray scattering techniques.
Energy Technology Data Exchange (ETDEWEB)
Díaz-Paniagua, Carlos [Instituto de Ciencia de Materiales de Madrid, CSIC, 28049 Madrid (Spain); Urbina, Antonio, E-mail: a.urbina@imperial.ac.uk [Department of Physics, Imperial College London, London SW7 2AZ (United Kingdom); Universidad Politécnica de Cartagena, Plaza del Hospital 1, 30202 Cartagena (Spain); García-Sakai, Victoria [ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX (United Kingdom); Seydel, Tilo [Institut Laue-Langevin, 39042 Grenoble Cedex (France); Abad, José; Padilla, Javier; García-Valverde, Rafael; Espinosa, Nieves [Universidad Politécnica de Cartagena, Plaza del Hospital 1, 30202 Cartagena (Spain); Gómez-Escalonilla, Marí a-José; Langa, Fernando [Instituto de Nanociencia, Nanotecnología y Materiales Moleculares (INAMOL), Universidad de Castilla-La Mancha, 45071 Toledo (Spain); Batallán, Francisco [Instituto de Ciencia de Materiales de Madrid, CSIC, 28049 Madrid (Spain)
2013-12-12
Highlights: • P3OT diffusion characteristic times in toluene solution at different temperatures have been obtained. • Gelation process for P3OT in solution has been demonstrated. • A methodology for elastic and quasielastic neutron scattering data analysis for liquids has been developed. - Abstract: Using both quasielastic and elastic window neutron spectroscopy, we study the molecular dynamics of poly-3-octyl-thiophene and of mixtures of carbon nanotube derivatives and poly-3-octyl-thiophene, both in deuterated toluene solutions. From the analysis of the experimental results of solutions for a broad range of concentrations, from very diluted to concentrated, different regimes of molecular motions are established, and a critical concentration between 2 and 3 wt% for the overlapping of macromolecules is obtained, including evidence of gelation processes for the higher concentrations driven by the entanglement of the macromolecules. Additionally, the temperature and momentum dependence of the characteristic times of the motions are obtained from the fit of the experimental data to stretched exponential models, delivering temperature dependent subnanosecond timescales for the diffusion of the macromolecule (0.02–0.5 ns)
Tanaka, Rie; Matsuda, Hiroaki; Sanada, Shigeru
2017-03-01
The density of lung tissue changes as demonstrated on imagery is dependent on the relative increases and decreases in the volume of air and lung vessels per unit volume of lung. Therefore, a time-series analysis of lung texture can be used to evaluate relative pulmonary function. This study was performed to assess a time-series analysis of lung texture on dynamic chest radiographs during respiration, and to demonstrate its usefulness in the diagnosis of pulmonary impairments. Sequential chest radiographs of 30 patients were obtained using a dynamic flat-panel detector (FPD; 100 kV, 0.2 mAs/pulse, 15 frames/s, SID = 2.0 m; Prototype, Konica Minolta). Imaging was performed during respiration, and 210 images were obtained over 14 seconds. Commercial bone suppression image-processing software (Clear Read Bone Suppression; Riverain Technologies, Miamisburg, Ohio, USA) was applied to the sequential chest radiographs to create corresponding bone suppression images. Average pixel values, standard deviation (SD), kurtosis, and skewness were calculated based on a density histogram analysis in lung regions. Regions of interest (ROIs) were manually located in the lungs, and the same ROIs were traced by the template matching technique during respiration. Average pixel value effectively differentiated regions with ventilatory defects and normal lung tissue. The average pixel values in normal areas changed dynamically in synchronization with the respiratory phase, whereas those in regions of ventilatory defects indicated reduced variations in pixel value. There were no significant differences between ventilatory defects and normal lung tissue in the other parameters. We confirmed that time-series analysis of lung texture was useful for the evaluation of pulmonary function in dynamic chest radiography during respiration. Pulmonary impairments were detected as reduced changes in pixel value. This technique is a simple, cost-effective diagnostic tool for the evaluation of regional
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.
Vikas, Hash(0x125f4490)
2011-02-01
Evolution of the helium atom in a strong time-dependent (TD) magnetic field ( B) of strength up to 1011 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 Schrödinger 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 >109 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 >109 G, the conventional TD-DFT based approach differs "dynamically" from the CDFT based approach under similar computational constraints.
Cardiac mitochondria exhibit dynamic functional clustering
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Felix Tobias Kurz
2014-09-01
Full Text Available Multi-oscillatory behavior of mitochondrial inner membrane potential ΔΨm in self-organized cardiac mitochondrial networks can be triggered by metabolic or oxidative stress. Spatio-temporal analyses of cardiac mitochondrial networks have shown that mitochondria are heterogeneously organized in synchronously oscillating clusters in which the mean cluster frequency and size are inversely correlated, thus suggesting a modulation of cluster frequency through local inter-mitochondrial coupling. In this study, we propose a method to examine the mitochondrial network's topology through quantification of its dynamic local clustering coefficients. Individual mitochondrial ΔΨm oscillation signals were identified for each cardiac myocyte and cross-correlated with all network mitochondria using previously described methods (Kurz et al., 2010. Time-varying inter-mitochondrial connectivity, defined for mitochondria in the whole network whose signals are at least 90% correlated at any given time point, allowed considering functional local clustering coefficients. It is shown that mitochondrial clustering in isolated cardiac myocytes changes dynamically and is significantly higher than for random mitochondrial networks that are constructed using the Erdös-Rényi model based on the same sets of vertices. The network's time-averaged clustering coefficient for cardiac myocytes was found to be 0.500 ± 0.051 (N=9 versus 0.061 ± 0.020 for random networks, respectively. Our results demonstrate that cardiac mitochondria constitute a network with dynamically connected constituents whose topological organization is prone to clustering. Cluster partitioning in networks of coupled oscillators has been observed in scale-free and chaotic systems and is therefore in good agreement with previous models of cardiac mitochondrial networks (Aon et al., 2008.
LOCAL ENTROPY FUNCTION OF DYNAMICAL SYSTEM
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İsmail TOK
2013-05-01
Full Text Available In this work, we first,define the entropy function of the topological dynamical system and investigate basic properties of this function without going into details. Let (X,A,T be a probability measure space and consider P = { pl5p2,...,pn} a finite measurable partition of all sub-sets of topological dynamical system (X,T.Then,the quantity H (P = ^ zpt is called the i=1 entropy function of finite measurable partition P.Where f-1 log t if 0 0.If diam(P < s,then the quantity L^ (T = h^ (T - h^ (T,P is called a local entropy function of topological dynamical system (X,T . In conclusion, Let (X,T and (Y,S be two topological dynamical system. If TxS is a transformation defined on the product space (XxY,TxS with (TxS(x , y = (Tx,Sy for all (x,y X x Y.Then L ^^ (TxS = L^d(T + L (S .and, we prove some fundamental properties of this function.
Rahko, Jukka S.; Paakki, Jyri-Johan; Starck, Tuomo H.; Nikkinen, Juha; Pauls, David L.; Katsyri, Jari V.; Jansson-Verkasalo, Eira M.; Carter, Alice S.; Hurtig, Tuula M.; Mattila, Marja-Leena; Jussila, Katja K.; Remes, Jukka J.; Kuusikko-Gauffin, Sanna A.; Sams, Mikko E.; Bolte, Sven; Ebeling, Hanna E.; Moilanen, Irma K.; Tervonen, Osmo; Kiviniemi, Vesa
2012-01-01
FMRI was performed with the dynamic facial expressions fear and happiness. This was done to detect differences in valence processing between 25 subjects with autism spectrum disorders (ASDs) and 27 typically developing controls. Valence scaling was abnormal in ASDs. Positive valence induces lower deactivation and abnormally strong activity in ASD…
Banerjee, Tanmay; Biswas, Abul Kalam; Sahu, Tuhin Subhra; Ganguly, Bishwajit; Das, Amitava; Ghosh, Hirendra Nath
2014-09-28
New Ru(ii)- and Os(ii)-polypyridyl complexes have been synthesized with pendant acetylacetone (acac) functionality for anchoring on nanoparticulate TiO2 surfaces with a goal of developing an alternate sensitizer that could be utilized for designing an efficient dye-sensitized solar cell (DSSC). Time-resolved transient absorption spectroscopic studies in the femtosecond time domain have been carried out. The charge recombination rates are observed to be very slow, compared with those for strongly coupled dye molecules having catechol as the anchoring functionality. The results of such studies reveal that electron-injection rates from the metal complex-based LUMO to the conduction band of TiO2 are faster than one would expect for an analogous complex in which the chromophoric core and the anchoring moiety are separated with multiple saturated C-C linkages. Such an observation is rationalized based on computational studies, and a relatively smaller spatial distance between the dye LUMO and the TiO2 surface accounted for this. Results of this study are compared with those for analogous complexes having a gem-dicarboxy group as the anchoring functionality for covalent binding to the TiO2 surface to compare the role of binding functionalities on electron-transfer dynamics.
Dynamic reorganization of intrinsic functional networks in the mouse brain.
Grandjean, Joanes; Preti, Maria Giulia; Bolton, Thomas A W; Buerge, Michaela; Seifritz, Erich; Pryce, Christopher R; Van De Ville, Dimitri; Rudin, Markus
2017-03-14
Functional connectivity (FC) derived from resting-state functional magnetic resonance imaging (rs-fMRI) allows for the integrative study of neuronal processes at a macroscopic level. The majority of studies to date have assumed stationary interactions between brain regions, without considering the dynamic aspects of network organization. Only recently has the latter received increased attention, predominantly in human studies. Applying dynamic FC (dFC) analysis to mice is attractive given the relative simplicity of the mouse brain and the possibility to explore mechanisms underlying network dynamics using pharmacological, environmental or genetic interventions. Therefore, we have evaluated the feasibility and research potential of mouse dFC using the interventions of social stress or anesthesia duration as two case-study examples. By combining a sliding-window correlation approach with dictionary learning, several dynamic functional states (dFS) with a complex organization were identified, exhibiting highly dynamic inter- and intra-modular interactions. Each dFS displayed a high degree of reproducibility upon changes in analytical parameters and across datasets. They fluctuated at different degrees as a function of anesthetic depth, and were sensitive indicators of pathology as shown for the chronic psychosocial stress mouse model of depression. Dynamic functional states are proposed to make a major contribution to information integration and processing in the healthy and diseased brain.
Chang, Yu-Kai; Alderman, Brandon L; Chu, Chien-Heng; Wang, Chun-Chih; Song, Tai-Fen; Chen, Feng-Tzu
2017-02-01
This study examined whether acute moderate intensity exercise results in a general or selective improvement in cognitive function. In addition, multiple stimulus-locked ERP components and serum BDNF levels were assessed to investigate potential neurobiological mechanisms underlying acute exercise effects on select aspects of cognitive performance. Thirty young adults were recruited and participated in exercise and reading control sessions in a counterbalanced order. Following treatments, the Stroop task was administrated, and N1, N2, P3, and N450 components of the ERP waveform were recorded and analyzed. Additionally, blood samples were withdrawn immediately following exercise or rest conditions prior to administration of the Stroop task. Acute exercise facilitated response times for both Stroop congruent and incongruent task conditions, with a similar magnitude of improvement. Larger P3 and reduced N450 amplitudes as well as decreased N450 latency were observed following exercise, but no effects on N1 and N2 components were found. This dose of exercise also did not influence serum BDNF levels. These findings suggest that moderate intensity acute exercise results in a generalized rather than selective improvement in cognition. The facilitation may be related to an increase in attentional or neural resource allocation and conflict detection processes reflected by longer latency endogenous components (P3, N450), but is not influenced by earlier sensory and monitoring processes revealed by earlier ERP components or by serum levels of BDNF.
Microtransitions and the dynamics of family functioning.
Everri, Marina; Fruggeri, Laura; Molinari, Luisa
2014-03-01
This paper presents a qualitative observational study aimed at exploring microtransitions in the relational dynamics of family functioning when the children are adolescents. Three concurrent levels were considered central for family functioning in this period: the acknowledgment of emerging competences, the redefinition of the power structure, and the regulation of interpersonal distances. Twenty-eight non-clinical Italian families with at least one adolescent child were interviewed and video-recorded in their homes. A stance-taking process analysis was carried out on the family interactive sequences arising in the course of the interviews. This analysis was based on the stances taken by all family members in relation to their reciprocal evaluations, positions, and alignments, which allowed us to point out the interlocking of competences, power and distances. Out of all the possible theoretical combinations of these three dimensions, we identified four forms of interaction. In two forms, the emerging changes were not incorporated in the families' interactive repertoires by either reconfirming family stability or resisting family changes. In these ways of interacting competences, power, and distances were not reorganized. In the other two forms, instead, family microtransitions were observable in the extent to which family members either explored family changes or legitimated family reorganizations. In these processes, they could redefine and readdress their ways of interacting.
Analysis of Uncertainty in Dynamic Processes Development of Banks Functioning
Directory of Open Access Journals (Sweden)
Aleksei V. Korovyakovskii
2013-01-01
Full Text Available The paper offers the approach to measure of uncertainty estimation in dynamic processes of banks functioning, using statistic data of different banking operations indicators. To calculate measure of uncertainty in dynamic processes of banks functioning the phase images of relevant sets of statistic data are considered. Besides, it is shown that the form of phase image of the studied sets of statistic data can act as a basis of measure of uncertainty estimation in dynamic processes of banks functioning. The set of analytical characteristics are offered to formalize the form of phase image definition of the studied sets of statistic data. It is shown that the offered analytical characteristics consider inequality of changes in values of the studied sets of statistic data, which is one of the ways of uncertainty display in dynamic processes development. The invariant estimates of measure of uncertainty in dynamic processes of banks functioning, considering significant changes in absolute values of the same indicators for different banks were obtained. The examples of calculation of measure of uncertainty in dynamic processes of concrete banks functioning were cited.
Exact four-spinon dynamical correlation function
Abada, A; Si-Lakhal, B; Seba, S; Abada, As
1998-01-01
We discuss some properties of the exact four-spinon dynamical correlation function in the antiferromagnetic spin 1/2 XXX-model the expression of which we derived recently. We show that the region in which it is not identically zero is different from and larger than the spin-wave continuum. We discuss its behavior as a function of the neutron momentum transfer $k$ for fixed values of the neutron energy $\\omega$ and compare it to the one corresponding to the exact two-spinon dynamical correlation function. We show that the overall shapes are quite similar but there are differences that we discuss. Particular is the fact that the symmetry about the axis $k=\\pi$ present in the two-spinon case seems to be lost in the four-spinon one. We finish with concluding remarks.
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.
Mörl, Falk; Siebert, Tobias; Häufle, Daniel
2016-02-01
Experimental studies show different muscle-tendon complex (MTC) functions (e.g. motor or spring) depending on the muscle fibre-tendon length ratio. Comparing different MTC of different animals examined experimentally, the extracted MTC functions are biased by, for example, MTC-specific pennation angle and fibre-type distribution or divergent experimental protocols (e.g. influence of temperature or stimulation on MTC force). Thus, a thorough understanding of variation of these inner muscle fibre-tendon length ratios on MTC function is difficult. In this study, we used a hill-type muscle model to simulate MTC. The model consists of a contractile element (CE) simulating muscle fibres, a serial element (SE) as a model for tendon, and a parallel elastic element (PEE) modelling tissue in parallel to the muscle fibres. The simulation examines the impact of length variations of these components on contraction dynamics and MTC function. Ensuring a constant overall length of the MTC by L(MTC) = L(SE) + L(CE), the SE rest length was varied over a broad physiological range from 0.1 to 0.9 MTC length. Five different MTC functions were investigated by simulating typical physiological experiments: the stabilising function with isometric contractions, the motor function with contractions against a weight, the capability of acceleration with contractions against a small inertial mass, the braking function by decelerating a mass, and the spring function with stretch-shortening cycles. The ratio of SE and CE mainly determines the MTC function. MTC with comparably short tendon generates high force and maximal shortening velocity and is able to produce maximal work and power. MTC with long tendon is suitable to store and release a maximum amount of energy. Variation of muscle fibre-tendon ratio yielded two peaks for MTC's force response for short and long SE lengths. Further, maximum work storage capacity of the SE is at long relL(SE,0). Impact of fibre-tendon length ratio on MTC
Kim, Changsun; Cha, Hyunmin; Kang, Bo Seung; Choi, Hyuk Joong; Lim, Tae Ho; Oh, Jaehoon
2016-06-01
Our aim was to prove the feasibility of the remote interpretation of real-time transmitted ultrasound videos of dynamic and static organs using a smartphone with control of the image quality given a limited internet connection speed. For this study, 100 cases of echocardiography videos (dynamic organ)-50 with an ejection fraction (EF) of ≥50 s and 50 with EF smartphone, to which the images were transmitted from the ultrasound machine. The resolution of the transmitted echocardiography videos was reduced by approximately 20 % to increase the frame rate of transmission given the limited internet speed. The differences in diagnostic performance between the two devices when evaluating left ventricular (LV) systolic function by measuring the EF and when evaluating the presence of acute appendicitis were investigated using a five-point Likert scale. The average areas under the receiver operating characteristic curves for each reviewer's interpretations using the LCD monitor and smartphone were respectively 0.968 (0.949-0.986) and 0.963 (0.945-0.982) (P = 0.548) for echocardiography and 0.972 (0.954-0.989) and 0.966 (0.947-0.984) (P = 0.175) for abdominal ultrasonography. We confirmed the feasibility of remotely interpreting ultrasound images using smartphones, specifically for evaluating LV function and diagnosing pediatric acute appendicitis; the images were transferred from the ultrasound machine using image quality-controlled telesonography.
Cardamone, Francesca; Iacovelli, Federico; Chillemi, Giovanni; Falconi, Mattia; Desideri, Alessandro
2017-03-01
The human sterile alpha motif SAM and HD domain-containing protein 1 (SAMHD1) restricts in non-cycling cells type the infection of a large range of retroviruses including HIV-1, reducing the intracellular pool concentration of deoxynucleoside triphosphates (dNTPs) required for the reverse transcription of the viral genome. The enzyme is in equilibrium between different forms depending on bound cofactors and substrate. In this work, two SAMHD1 three-dimensional models have been investigated through classical molecular dynamics simulation, to define the role of cofactors and metal ions in the association of the tetrameric active form. A detailed analysis of the inter-subunit interactions, taking place at the level of helix 13, indicates that removal of metal ions and cofactors induces an asymmetric loosening of the monomer-monomer interface leading to the formation of a loose tetramer where the two dimeric interfaces are weakened in different way.
Cardamone, Francesca; Iacovelli, Federico; Chillemi, Giovanni; Falconi, Mattia; Desideri, Alessandro
2017-05-01
The human sterile alpha motif SAM and HD domain-containing protein 1 (SAMHD1) restricts in non-cycling cells type the infection of a large range of retroviruses including HIV-1, reducing the intracellular pool concentration of deoxynucleoside triphosphates (dNTPs) required for the reverse transcription of the viral genome. The enzyme is in equilibrium between different forms depending on bound cofactors and substrate. In this work, two SAMHD1 three-dimensional models have been investigated through classical molecular dynamics simulation, to define the role of cofactors and metal ions in the association of the tetrameric active form. A detailed analysis of the inter-subunit interactions, taking place at the level of helix 13, indicates that removal of metal ions and cofactors induces an asymmetric loosening of the monomer-monomer interface leading to the formation of a loose tetramer where the two dimeric interfaces are weakened in different way.
Snaar-Jagalska, B.E.; Cambi, A.; Schmidt, T.; Keijzer, S. de
2013-01-01
The lateral diffusion of a G-protein-coupled receptor (GPCR) in the plasma membrane determines its interaction capabilities with downstream signaling molecules and critically modulates its function. Mechanisms that control GPCR mobility, like compartmentalization, enable a cell to fine-tune its
Energy Technology Data Exchange (ETDEWEB)
Vikas [Quantum Chemistry Group, Department of Chemistry and Centre of Advanced Studies in Chemistry, Panjab University, 160014 Chandigrah (India)
2011-02-15
Evolution of the helium atom in a strong time-dependent (TD) magnetic field (B) of strength up to 10{sup 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{sup 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{sup 9} G, the conventional TD-DFT based approach differs 'dynamically' from the CDFT based approach under similar computational constraints. (author)
Dynamics of biomolecules, ligand binding & biological functions
Yi, Myunggi
Proteins are flexible and dynamic. One static structure alone does not often completely explain biological functions of the protein, and some proteins do not even have high resolution structures. In order to provide better understanding to the biological functions of nicotinic acetylcholine receptor, Diphtheria toxin repressor and M2 proton channel, the dynamics of these proteins are investigated using molecular modeling and molecular dynamics (MD) simulations. With absence of high resolution structure of alpha7 receptor, the homology models of apo and cobra toxin bound forms have been built. From the MD simulations of these model structures, we observed one subunit of apo simulation moved away from other four subunits. With local movement of flexible loop regions, the whole subunit tilted clockwise. These conformational changes occurred spontaneously, and were strongly correlated with the conformational change when the channel is activated by agonists. Unlike other computational studies, we directly compared our model of open conformation with the experimental data. However, the subunits of toxin bound form were stable, and conformational change is restricted by the bound cobra toxin. These results provide activation and inhibition mechanisms of alpha7 receptors and a possible explanation for intermediate conductance of the channel. Intramolecular complex of SH3-like domain with a proline-rich (Pr) peptide segment in Diphtheria toxin repressor (DtxR) is stabilized in inactive state. Upon activation of DtxR by transition metal binding, this intramolecular complex should be dissociated. The dynamics of this intramolecular complex is investigated using MD simulations and NMR spectroscopy. We observed spontaneous opening and closing motions of the Pr segment binding pockets in both Pr-SH3 and SH3 simulations. The MD simulation results and NMR relaxation data suggest that the Pr segment exhibits a binding ↔ unbinding equilibrium. Despite a wealth of experimental
Qin, Tao; Hofstetter, Walter
2017-08-01
We present a systematic study of the spectral functions of a time-periodically driven Falicov-Kimball Hamiltonian. In the high-frequency limit, this system can be effectively described as a Harper-Hofstadter-Falicov-Kimball model. Using real-space Floquet dynamical mean-field theory (DMFT), we take into account the interaction effects and contributions from higher Floquet bands in a nonperturbative way. Our calculations show a high degree of similarity between the interacting driven system and its effective static counterpart with respect to spectral properties. However, as also illustrated by our results, one should bear in mind that Floquet DMFT describes a nonequilibrium steady state, while an effective static Hamiltonian describes an equilibrium state. We further demonstrate the possibility of using real-space Floquet DMFT to study edge states on a cylinder geometry.
Maurer, Reinhard J; 10.1063/1.3664305
2012-01-01
We present a detailed comparison of the S0, S1 (n -> \\pi*) and S2 (\\pi -> \\pi*) potential energy surfaces (PESs) of the prototypical molecular switch azobenzene as obtained by Delta-self-consistent-field (Delta-SCF) Density-Functional Theory (DFT), time-dependent DFT (TD-DFT) and approximate Coupled Cluster Singles and Doubles (RI-CC2). All three methods unanimously agree in terms of the PES topologies, which are furthermore fully consistent with existing experimental data concerning the photo-isomerization mechanism. In particular, sum-method corrected Delta-SCF and TD-DFT yield very similar results for S1 and S2, when based on the same ground-state exchange-correlation (xc) functional. While these techniques yield the correct PES topology already on the level of semi-local xc functionals, reliable absolute excitation energies as compared to RI-CC2 or experiment require an xc treatment on the level of long-range corrected hybrids. Nevertheless, particularly the robustness of Delta-SCF with respect to state c...
Measuring Dynamic Transfer Functions of Cavitating Pumps
Baun, Daniel
2007-01-01
A water-flow test facility has been built to enable measurement of dynamic transfer functions (DTFs) of cavitating pumps and of inducers in such pumps. Originally, the facility was intended for use in an investigation of the effects of cavitation in a rocket-engine low-pressure oxygen turbopump. The facility can also be used to measure DTFs of cavitating pumps in general
Boek, E. S.; Briels, W. J.
1993-01-01
Molecular dynamics simulations have been performed in order to study the structure of two molal urea solutions in D2O. Several initial dimer configurations were considered for an adequate sampling of phase space. Eventually all of them appeared to be unstable, when system size and periodic boundary conditions are chosen properly, even after a very careful equilibration. The total nitrogen scattering function GN(r), calculated from these simulations, is in good agreement with neutron scattering experiments when both intra- and intermolecular correlations are considered and the experimental truncation ripples are introduced by a Fourier transform of GN(r) back and forth. The simple pair potential model that we used gives results in good agreement with experiments and with a much more involved potential model, recently described in the literature [J. Chem. Phys. 95, 8419 (1991)].
Yang, Shu-Jing; Qin, Xiao-Ya; He, Rongxing; Shen, Wei; Li, Ming; Zhao, Liu-Bin
2017-05-21
Organic redox compounds have become the emerging electrode materials for rechargeable lithium ion batteries. The high electrochemical performance provides organic electrode materials with great opportunities to be applied in electric energy storage devices. Among the different types of organic materials, conjugated carbonyl compounds are the most promising type at present, because only they can simultaneously achieve, high energy density, high cycling stability, and high power density. In this research, a series of heteroatom substituted anthraquinone (AQ) derivatives were designed theoretically so that the high theoretical capacity of AQ remained. The discharge and charge mechanism as well as the thermodynamic and dynamic properties of AQ and its derivatives were investigated using first-principles density functional theory. Using heteroatom substitution, both the thermodynamic and dynamic properties of AQ as cathode materials could be largely improved. Among these conjugated carboxyl compounds, BDOZD and BDIOZD with a simultaneously high theoretical capacity and high working potential exhibit the largest energy density of about 780 W h kg(-1), which is 41% larger than that of AQ. The PQD with the smallest value of λ gives the largest charge transfer rate constant, which is about four times as large as the prototype molecule, AQ. The most interesting finding is that the lithium ion transfer plays a very important role in influencing both the discharge potential and electrochemical charge transfer rate. The present study illustrates that theoretical calculations provide a highly effective way to discover potential materials for use with rechargeable lithium ion batteries.
Ma, W.C.
1972-01-01
The present study of contact chemoreception in Pieris brassicae L. is divided into three major parts, viz. 1. behavioural analyses, 2. the identification and description of sense organs and 3. investigations concerning the sensory physiology. In a separate section some of the results were put into a
Dynamic Responsive Systems for Catalytic Function.
Vlatković, Matea; Collins, Beatrice S L; Feringa, Ben L
2016-11-21
Responsive systems have recently gained much interest in the scientific community in attempts to mimic dynamic functions in biological systems. One of the fascinating potential applications of responsive systems lies in catalysis. Inspired by nature, novel responsive catalytic systems have been built that show analogy with allosteric regulation of enzymes. The design of responsive catalytic systems allows control of catalytic activity and selectivity. In this Review, advances in the field over the last four decades are discussed and a comparison is made amongst the dynamic responsive systems based on the principles underlying their catalytic mechanisms. The catalyst systems are sorted according to the triggers used to achieve control of the catalytic activity and the distinct catalytic reactions illustrated. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Proteins with Novel Structure, Function and Dynamics
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.
Dynamics and function of compact nucleosome arrays.
Poirier, Michael G; Oh, Eugene; Tims, Hannah S; Widom, Jonathan
2009-09-01
The packaging of eukaryotic DNA into chromatin sterically occludes polymerases, recombinases and repair enzymes. How chromatin structure changes to allow their actions is unknown. We constructed defined fluorescently labeled trinucleosome arrays, allowing analysis of chromatin conformational dynamics via fluorescence resonance energy transfer (FRET). The arrays undergo reversible Mg2+-dependent folding similar to that of longer arrays studied previously. We define two intermediate conformational states in the reversible folding of the nucleosome arrays and characterize the microscopic rate constants. Nucleosome arrays are highly dynamic even when compact, undergoing conformational fluctuations on timescales in the second to microsecond range. Compact states of the arrays allow binding to DNA within the central nucleosome via site exposure. Protein binding can also drive decompaction of the arrays. Thus, our results reveal multiple modes by which spontaneous chromatin fiber dynamics allow for the invasion and action of DNA-processing protein complexes.
2014-01-01
There is evidence that having a stronger sense of positive well-being may be a potential resource for healthier aging as represented by slower physical decline, reduced risk of frailty and longer survival. However, it is unclear whether positive well-being is protective of another crucial component of healthy aging, cognitive function, or whether it has a bidirectional relationship with cognitive function. We use multilevel models with within-person centering to estimate the within- and between-person association between cognitive function and positive well-being in 4 waves of data from the English Longitudinal Study of Ageing (ELSA), (N = 10985, aged 50–90 years at wave 1). Our findings show that, although most variation in cognitive function was explained by age, and most variation in well-being was explained by depression, small but significant associations between cognition and well-being remained after variation in age and depression were controlled. In models where cognition was the outcome, the association was mainly because of variation in mean levels of well-being between persons. In models where well-being was the outcome, the association was mainly because of within-person fluctuation in cognitive test performance. Exercise and depression were the most important moderating influences on the association between cognition and positive well-being. Depression had greater effect upon this association for those with higher well-being, but exercise protected cognitive performance against the adverse effects of lower well-being. PMID:24955999
Combining Molecular Dynamics and Density Functional Theory
Kaxiras, Efthimios
2015-03-01
The time evolution of a system consisting of electrons and ions is often treated in the Born-Oppenheimer approximation, with electrons in their instantaneous ground state. This approach cannot capture many interesting processes that involved excitation of electrons and its effects on the coupled electron-ion dynamics. The time scale needed to accurately resolve the evolution of electron dynamics is atto-seconds. This poses a challenge to the simulation of important chemical processes that typically take place on time scales of pico-seconds and beyond, such as reactions at surfaces and charge transport in macromolecules. We will present a methodology based on time-dependent density functional theory for electrons, and classical (Ehrenfest) dynamics for the ions, that successfully captures such processes. We will give a review of key features of the method and several applications. These illustrate how the atomic and electronic structure evolution unravels the elementary steps that constitute a chemical reaction. In collaboration with: G. Kolesov, D. Vinichenko, G. Tritsaris, C.M. Friend, Departments of Physics and of Chemistry and Chemical Biology.
Directory of Open Access Journals (Sweden)
Long-Biao eCui
2015-11-01
Full Text Available Understanding the neural basis of schizophrenia (SZ is important for shedding light on the neurobiological mechanisms underlying this mental disorder. Structural and functional alterations in the anterior cingulate cortex (ACC, dorsolateral prefrontal cortex (DLPFC, hippocampus, and medial prefrontal cortex (MPFC have been implicated in the neurobiology of SZ. However, the effective connectivity among them in SZ remains unclear. The current study investigated how neuronal pathways involving these regions were affected in first-episode SZ using functional magnetic resonance imaging (fMRI. Forty-nine patients with a first-episode of psychosis and diagnosis of SZ—according to the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, Text Revision—were studied. Fifty healthy controls (HCs were included for comparison. All subjects underwent resting state fMRI. We used spectral dynamic causal modeling (DCM to estimate directed connections among the bilateral ACC, DLPFC, hippocampus, and MPFC. We characterized the differences using Bayesian parameter averaging (BPA in addition to classical inference (t-test. In addition to common effective connectivity in these two groups, HCs displayed widespread significant connections predominantly involved in ACC not detected in SZ patients, but SZ showed few connections. Based on BPA results, SZ patients exhibited anterior cingulate cortico-prefrontal-hippocampal hyperconnectivity, as well as ACC-related and hippocampal-dorsolateral prefrontal-medial prefrontal hypoconnectivity. In summary, sDCM revealed the pattern of effective connectivity involving ACC in patients with first-episode SZ. This study provides a potential link between SZ and dysfunction of ACC, creating an ideal situation to associate mechanisms behind SZ with aberrant connectivity among these cognition and emotion-related regions.
Meel-van den Abeelen, Aisha S S; Simpson, David M; Wang, Lotte J Y; Slump, Cornelis H; Zhang, Rong; Tarumi, Takashi; Rickards, Caroline A; Payne, Stephen; Mitsis, Georgios D; Kostoglou, Kyriaki; Marmarelis, Vasilis; Shin, Dae; Tzeng, Yu-Chieh; Ainslie, Philip N; Gommer, Erik; Müller, Martin; Dorado, Alexander C; Smielewski, Peter; Yelicich, Bernardo; Puppo, Corina; Liu, Xiuyun; Czosnyka, Marek; Wang, Cheng-Yen; Novak, Vera; Panerai, Ronney B; Claassen, Jurgen A H R
2014-05-01
Transfer function analysis (TFA) is a frequently used method to assess dynamic cerebral autoregulation (CA) using spontaneous oscillations in blood pressure (BP) and cerebral blood flow velocity (CBFV). However, controversies and variations exist in how research groups utilise TFA, causing high variability in interpretation. The objective of this study was to evaluate between-centre variability in TFA outcome metrics. 15 centres analysed the same 70 BP and CBFV datasets from healthy subjects (n=50 rest; n=20 during hypercapnia); 10 additional datasets were computer-generated. Each centre used their in-house TFA methods; however, certain parameters were specified to reduce a priori between-centre variability. Hypercapnia was used to assess discriminatory performance and synthetic data to evaluate effects of parameter settings. Results were analysed using the Mann-Whitney test and logistic regression. A large non-homogeneous variation was found in TFA outcome metrics between the centres. Logistic regression demonstrated that 11 centres were able to distinguish between normal and impaired CA with an AUC>0.85. Further analysis identified TFA settings that are associated with large variation in outcome measures. These results indicate the need for standardisation of TFA settings in order to reduce between-centre variability and to allow accurate comparison between studies. Suggestions on optimal signal processing methods are proposed.
Institute of Scientific and Technical Information of China (English)
无
2002-01-01
In the forming of the Dynamic System of Tourism Development (DSTD) in developed regions from theview of supply side, the Delphi Method and the Analytical Hierarchy Process(AHP) are used to count the weight of eachcomponent of the DSTD. It has been found that the attraction subsystem is the most important one of the three subsystemsat the firt hierarchical level of DSTD, which means that tourist attractions are always the principal factors for regionaltourism development, even in developed regions. But it is also noteworthy that the significance of the attraction subsystemis not dominant in the DSTD. At the second hierarchical level, the physical attraction subsystem rank No. 1, while theweight of the non-physical attraction subsystem is just a little larger than the weight of the hardware subsystem and that ofsoftware subsystem. And the weights of the three components in the medium subsystem are similar. The top 3 factors atthe third hierarchical level are scenic spot, location and regional economic impact. The result verifies the conclusions ofqualitative analysis, which depends on the market research and the study of historical date, that the most important component of the DSTD in Feshan is the impact of the developed economy. Knowing the weight of each component of the DSTDcan be helpful to make out the most useful force, furthermore to determine the future orientation for regional tourism development.
Institute of Scientific and Technical Information of China (English)
ZHONGYun; PENGHua
2002-01-01
In the forming of the Dynamic System of Tourism Development(DSTD)in developed regions from the view of supply side,the Dhlphi Method and the Analytical Hierarchy Process (AHP) are used to count the weight of each component of the DSTD.It has been found that the attraction subsystem is the most important one of the three subsystems at the first hierarchical level of DSTD,which means that tourist attractions are always the principal factors for regional tourism development,even in developed regions.But it is also noteworthy that the significance of the attraction subsystem is not dominant in the DSTD.At the second hierarchical level,the physical attraction subsystem rand No.1,while the weight of the non-physical attraction subsystem is just a little larger than the weight of the hardware subsystem and that of software subsystem.And the weights of the three components in the medium subsystem are similar.The top 3 factors at the third hierarchical level are scenic spot,location and regional economic impact.The result verifies the conclusions of qualitative analysis,which depends on the market research and the study of historical date,that the most important compo-nent of the DSTD in Foshan is the impact of the developed economy.Knowing the weight of each component of the DSTD can be helpful to make out the most useful force,furthermore to determine the future orientation for regional tourism develop-ment.
Anero, Jesús G; Español, Pep; Tarazona, Pedro
2013-07-21
We present a generalization of Density Functional Theory (DFT) to non-equilibrium non-isothermal situations. By using the original approach set forth by Gibbs in his consideration of Macroscopic Thermodynamics (MT), we consider a Functional Thermo-Dynamics (FTD) description based on the density field and the energy density field. A crucial ingredient of the theory is an entropy functional, which is a concave functional. Therefore, there is a one to one connection between the density and energy fields with the conjugate thermodynamic fields. The connection between the three levels of description (MT, DFT, FTD) is clarified through a bridge theorem that relates the entropy of different levels of description and that constitutes a generalization of Mermin's theorem to arbitrary levels of description whose relevant variables are connected linearly. Although the FTD level of description does not provide any new information about averages and correlations at equilibrium, it is a crucial ingredient for the dynamics in non-equilibrium states. We obtain with the technique of projection operators the set of dynamic equations that describe the evolution of the density and energy density fields from an initial non-equilibrium state towards equilibrium. These equations generalize time dependent density functional theory to non-isothermal situations. We also present an explicit model for the entropy functional for hard spheres.
Relativistic dynamics, Green function and pseudodifferential operators
Cirilo-Lombardo, Diego Julio
2016-01-01
The central role played by pseudodifferential operators in relativistic dynamics is very well know. In this work, operators as the Schrodinger one (e.g: square root) are treated from the point of view of the non-local pseudodifferential Green functions. Starting from the explicit construction of the Green (semigroup) theoretical kernel, a theorem linking the integrability conditions and their dependence on the spacetime dimensions is given. Relativistic wave equations with arbitrary spin and the causality problem are discussed with the algebraic interpretation of the radical operator and their relation with coherent and squeezed states. Also we perform by mean of pure theoretical procedures (based in physical concepts and symmetry) the relativistic position operator which satisfies the conditions of integrability : it is non-local, Lorentz invariant and does not have the same problems as the "local"position operator proposed by Newton and Wigner. Physical examples, as Zitterbewegung and rogue waves, are prese...
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...
Population dynamics and mutualism: Functional responses of benefits and costs
Holland, J. Nathaniel; DeAngelis, Donald L.; Bronstein, Judith L.
2002-01-01
We develop an approach for studying population dynamics resulting from mutualism by employing functional responses based on density‐dependent benefits and costs. These functional responses express how the population growth rate of a mutualist is modified by the density of its partner. We present several possible dependencies of gross benefits and costs, and hence net effects, to a mutualist as functions of the density of its partner. Net effects to mutualists are likely a monotonically saturating or unimodal function of the density of their partner. We show that fundamental differences in the growth, limitation, and dynamics of a population can occur when net effects to that population change linearly, unimodally, or in a saturating fashion. We use the mutualism between senita cactus and its pollinating seed‐eating moth as an example to show the influence of different benefit and cost functional responses on population dynamics and stability of mutualisms. We investigated two mechanisms that may alter this mutualism's functional responses: distribution of eggs among flowers and fruit abortion. Differences in how benefits and costs vary with density can alter the stability of this mutualism. In particular, fruit abortion may allow for a stable equilibrium where none could otherwise exist.
Functional connectivity change as shared signal dynamics
Cole, Michael W.; Yang, Genevieve J.; Murray, John D.; Repovš, Grega; Anticevic, Alan
2015-01-01
Background An increasing number of neuroscientific studies gain insights by focusing on differences in functional connectivity – between groups, individuals, temporal windows, or task conditions. We found using simulations that additional insights into such differences can be gained by forgoing variance normalization, a procedure used by most functional connectivity measures. Simulations indicated that these functional connectivity measures are sensitive to increases in independent fluctuations (unshared signal) in time series, consistently reducing functional connectivity estimates (e.g., correlations) even though such changes are unrelated to corresponding fluctuations (shared signal) between those time series. This is inconsistent with the common notion of functional connectivity as the amount of inter-region interaction. New Method Simulations revealed that a version of correlation without variance normalization – covariance – was able to isolate differences in shared signal, increasing interpretability of observed functional connectivity change. Simulations also revealed cases problematic for non-normalized methods, leading to a “covariance conjunction” method combining the benefits of both normalized and non-normalized approaches. Results We found that covariance and covariance conjunction methods can detect functional connectivity changes across a variety of tasks and rest in both clinical and non-clinical functional MRI datasets. Comparison with Existing Method(s) We verified using a variety of tasks and rest in both clinical and non-clinical functional MRI datasets that it matters in practice whether correlation, covariance, or covariance conjunction methods are used. Conclusions These results demonstrate the practical and theoretical utility of isolating changes in shared signal, improving the ability to interpret observed functional connectivity change. PMID:26642966
Dynamical density functional theory with hydrodynamic interactions in confined geometries
Goddard, B. D.; Nold, A.; Kalliadasis, S.
2016-12-01
We study the dynamics of colloidal fluids in both unconfined geometries and when confined by a hard wall. Under minimal assumptions, we derive a dynamical density functional theory (DDFT) which includes hydrodynamic interactions (HI; bath-mediated forces). By using an efficient numerical scheme based on pseudospectral methods for integro-differential equations, we demonstrate its excellent agreement with the full underlying Langevin equations for systems of hard disks in partial confinement. We further use the derived DDFT formalism to elucidate the crucial effects of HI in confined systems.
Bastos-Leite, António J; Ridgway, Gerard R; Silveira, Celeste; Norton, Andreia; Reis, Salomé; Friston, Karl J
2015-01-01
We report the first stochastic dynamic causal modeling (sDCM) study of effective connectivity within the default mode network (DMN) in schizophrenia. Thirty-three patients (9 women, mean age = 25.0 years, SD = 5) with a first episode of psychosis and diagnosis of schizophrenia--according to the Diagnostic and Statistic Manual of Mental Disorders, 4th edition, revised criteria--were studied. Fifteen healthy control subjects (4 women, mean age = 24.6 years, SD = 4) were included for comparison. All subjects underwent resting state functional magnetic resonance imaging (fMRI) interspersed with 2 periods of continuous picture viewing. The anterior frontal (AF), posterior cingulate (PC), and the left and right parietal nodes of the DMN were localized in an unbiased fashion using data from 16 independent healthy volunteers (using an identical fMRI protocol). We used sDCM to estimate directed connections between and within nodes of the DMN, which were subsequently compared with t tests at the between subject level. The excitatory effect of the PC node on the AF node and the inhibitory self-connection of the AF node were significantly weaker in patients (mean values = 0.013 and -0.048 Hz, SD = 0.09 and 0.05, respectively) relative to healthy subjects (mean values = 0.084 and -0.088 Hz, SD = 0.15 and 0.77, respectively; P < .05). In summary, sDCM revealed reduced effective connectivity to the AF node of the DMN--reflecting a reduced postsynaptic efficacy of prefrontal afferents--in patients with first-episode schizophrenia.
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
@@ Genomics is a biology term appeared ten years ago, used to describe the researches of genomic mapping, sequencing, and structure analysis, etc. Genomics, the first journal for publishing papers on genomics research was born in 1986. In the past decade, the concept of genomics has been widely accepted by scientists who are engaging in biology research. Meanwhile, the research scope of genomics has been extended continuously, from simple gene mapping and sequencing to function genomics study. To reflect the change, genomics is divided into two parts now, the structure genomics and the function genomics.
Boek, E.S.; Briels, W.J.
1993-01-01
Molecular dynamics simulations have been performed in order to study the structure of two molal urea solutions in D2O. Several initial dimer configurations were considered for an adequate sampling of phase space. Eventually all of them appeared to be unstable, when system size and periodic boundary
DEFF Research Database (Denmark)
Hak, Sjoerd; Cebulla, Jana; Huuse, Else Marie
2014-01-01
kinetics. These kinetics will not only depend on nanoparticle characteristics, but also on receptor binding and recycling. In this study, we monitored the in vivo targeting kinetics of αvβ3-integrin specific nanoparticles with intravital microscopy and dynamic contrast enhanced magnetic resonance imaging...... in the accumulation kinetics of αvβ3-integrin targeted nanoparticles and hypothesize that this periodicity is caused by receptor binding, internalization and recycling dynamics. Taken together, this demonstrates that our experimental approach provides new insights in in vivo nanoparticle targeting, which may proof...
Institute of Scientific and Technical Information of China (English)
Jianguo Wang; Yulin Guo; Xiaojuan Guo; Min Liu; Youmin Guo; Chen Wang; Yuanhua Yang; Zhenguo Zhai; Li Zhu; Hongxia Ma
2008-01-01
Objective: To analyze the value of CTPA in assessing the dissolve of embolus and the function of the fight ventricle dynamically.Methods:Twenty-three cases of massive pulmonary embolism were analyzed retrospectively. The pulmonary artery obstruction index and the fight ventricular function parameters were collected and analyzed on CTPA before thrombolytic therapy, 24 hours and 14 days after therapy, respectively. Results:The pulmonary artery obstruction index decreased gradually, and there was significant difference before therapy, 24 hours and 2 weeks after therapy. Twenty-four hours after therapy, the maximal short axes diameter and the maximal transverse area of fight ventricle(RVd, RVs) decreased significantly, the maximal short axes diameter and the maximal transverse area of left ventricle(LVd, LVs) increased significantly, and the RVd/LVd, RVs/LVs decreased apparently. The pulmonary artery symbolic pressure before and 24 hours after therapy were apparently different. There was no significant difference between azygos vein, the super vena cava, the main pulmonary artery and vein reflux before and after therapy. Conclusion:CTPA can evaluate the pulmonary artery obstruction degree and right ventricular function dynamically.
Kita, Soma; Oshima, Marie; Shimazaki, Kazuo; Iwai, Toshinori; Omura, Susumu; Ono, Takashi
2016-11-01
This study aimed to evaluate the influence of maxillary impaction orthognathic surgery on nasal respiratory function and the efficacy of bone trimming at the inferior edge of the pyriform aperture. The participants were 10 patients (3 male and 7 female patients) with mandibular prognathism who underwent bimaxillary orthognathic surgery with maxillary impaction. The surgical procedures performed were Le Fort I osteotomy with bone trimming at the inferior edge of the pyriform aperture and bilateral sagittal split osteotomy. Three-dimensional models of the nasal cavity were reconstructed from preoperative and postoperative computed tomography images. Furthermore, we remodeled the nasal valve region based on the postoperative models by adding a 1-mm and 2-mm stenosis to investigate the effects of bone trimming at the inferior edge of the pyriform aperture on the pressure effort. The 3-dimensional models were simulated with computational fluid dynamics, and the results of the pressure effort and the cross-sectional area (CSA) were compared for the anterior, middle, and posterior parts of the nasal cavity. The Wilcoxon signed rank test and Spearman rank correlation coefficients were used for statistical comparisons (P < .05). In the preoperative and postoperative models, there were considerable correlations between the CSA and the pressure effort in each part of the nasal cavity. The postoperative pressure effort showed a tendency to decrease and the CSA showed a tendency to increase in each part of the nasal cavity. In four 2-mm stenosis models, the pressure effort in the anterior nasal cavity was larger than the preoperative pressure effort and the CSA of the anterior nasal cavity was smaller than the preoperative CSA. Bone trimming at the inferior edge of the pyriform aperture appears to be useful for avoiding nasal respiratory complications with maxillary impaction. Copyright © 2016 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc
A Bayesian Algorithm for Functional Mapping of Dynamic Complex Traits
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Rongling Wu
2009-04-01
Full Text Available Functional mapping of dynamic traits measured in a longitudinal study was originally derived within the maximum likelihood (ML context and implemented with the EM algorithm. Although ML-based functional mapping possesses many favorable statistical properties in parameter estimation, it may be computationally intractable for analyzing longitudinal data with high dimensions and high measurement errors. In this article, we derive a general functional mapping framework for quantitative trait locus mapping of dynamic traits within the Bayesian paradigm. Markov chain Monte Carlo techniques were implemented for functional mapping to estimate biologically and statistically sensible parameters that model the structures of time-dependent genetic effects and covariance matrix. The Bayesian approach is useful to handle difficulties in constructing confidence intervals as well as the identifiability problem, enhancing the statistical inference of functional mapping. We have undertaken simulation studies to investigate the statistical behavior of Bayesian-based functional mapping and used a real example with F2 mice to validate the utilization and usefulness of the model.
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.
Shkrob, Ilya A; Glover, William J; Larsen, Ross E; Schwartz, Benjamin J
2007-06-21
Adiabatic mixed quantum/classical (MQC) molecular dynamics (MD) simulations were used to generate snapshots of the hydrated electron in liquid water at 300 K. Water cluster anions that include two complete solvation shells centered on the hydrated electron were extracted from the MQC MD simulations and embedded in a roughly 18 Ax18 Ax18 A matrix of fractional point charges designed to represent the rest of the solvent. Density functional theory (DFT) with the Becke-Lee-Yang-Parr functional and single-excitation configuration interaction (CIS) methods were then applied to these embedded clusters. The salient feature of these hybrid DFT(CIS)/MQC MD calculations is significant transfer (approximately 18%) of the excess electron's charge density into the 2p orbitals of oxygen atoms in OH groups forming the solvation cavity. We used the results of these calculations to examine the structure of the singly occupied and the lower unoccupied molecular orbitals, the density of states, the absorption spectra in the visible and ultraviolet, the hyperfine coupling (hfcc) tensors, and the infrared (IR) and Raman spectra of these embedded water cluster anions. The calculated hfcc tensors were used to compute electron paramagnetic resonance (EPR) and electron spin echo envelope modulation (ESEEM) spectra for the hydrated electron that compared favorably to the experimental spectra of trapped electrons in alkaline ice. The calculated vibrational spectra of the hydrated electron are consistent with the red-shifted bending and stretching frequencies observed in resonance Raman experiments. In addition to reproducing the visible/near IR absorption spectrum, the hybrid DFT model also accounts for the hydrated electron's 190-nm absorption band in the ultraviolet. Thus, our study suggests that to explain several important experimentally observed properties of the hydrated electron, many-electron effects must be accounted for: one-electron models that do not allow for mixing of the excess
Energy Technology Data Exchange (ETDEWEB)
Shkrob, I. A.; Glover, W. J.; Larsen, R. E.; Schwartz, B. J.; Chemistry; Univ. of California at Los Angeles
2007-06-21
Adiabatic mixed quantum/classical (MQC) molecular dynamics (MD) simulations were used to generate snapshots of the hydrated electron in liquid water at 300 K. Water cluster anions that include two complete solvation shells centered on the hydrated electron were extracted from the MQC MD simulations and embedded in a roughly 18 Angstrom x 18 Angstrom x 18 Angstrom matrix of fractional point charges designed to represent the rest of the solvent. Density functional theory (DFT) with the Becke-Lee-Yang-Parr functional and single-excitation configuration interaction (CIS) methods were then applied to these embedded clusters. The salient feature of these hybrid DFT(CIS)/MQC MD calculations is significant transfer ({approx}18%) of the excess electron's charge density into the 2p orbitals of oxygen atoms in OH groups forming the solvation cavity. We used the results of these calculations to examine the structure of the singly occupied and the lower unoccupied molecular orbitals, the density of states, the absorption spectra in the visible and ultraviolet, the hyperfine coupling (hfcc) tensors, and the infrared (IR) and Raman spectra of these embedded water cluster anions. The calculated hfcc tensors were used to compute electron paramagnetic resonance (EPR) and electron spin echo envelope modulation (ESEEM) spectra for the hydrated electron that compared favorably to the experimental spectra of trapped electrons in alkaline ice. The calculated vibrational spectra of the hydrated electron are consistent with the red-shifted bending and stretching frequencies observed in resonance Raman experiments. In addition to reproducing the visible/near IR absorption spectrum, the hybrid DFT model also accounts for the hydrated electron's 190-nm absorption band in the ultraviolet. Thus, our study suggests that to explain several important experimentally observed properties of the hydrated electron, many-electron effects must be accounted for: one-electron models that do not
Directory of Open Access Journals (Sweden)
Lam Wynnie WM
2007-11-01
Full Text Available Abstract Background Restrictive impairment is the commonest reported pulmonary deficit in AIS, which improves following surgical operation. However, exact mechanism of how improvement is brought about is unknown. Dynamic fast breath-hold (BH-MR imaging is a recent advance which provides direct quantitative visual assessment of pulmonary function. By using above technique, change in lung volume, chest wall and diaphragmatic motion in AIS patients before and six months after posterior spinal fusion surgery were measured. Methods 16 patients with severe right-sided predominant thoracic scoliosis (standing Cobb's angle 50° -82°, mean 60° received posterior spinal fusion without thoracoplasty were recruited into this study. BH-MR sequences were used to obtain coronal images of the whole chest during full inspiration and expiration. The following measurements were assessed: (1 inspiratory, expiratory and change in lung volume; (2 change in anteroposterior (AP and transverse (TS diameter of the chest wall at two levels: carina and apex (3 change in diaphragmatic heights. The changes in parameters before and after operation were compared using Wilcoxon signed ranks test. Patients were also asked to score their breathing effort before and after operation using a scale of 1–9 with ascending order of effort. The degree of spinal surgical correction at three planes was also assessed by reformatted MR images and correction rate of Cobb's angle was calculated. Results The individual or total inspiratory and expiratory volume showed slight but insignificant increase after operation. There was significantly increase in bilateral TS chest wall movement at carina level and increase in bilateral diaphragmatic movements between inspiration and expiration. The AP chest wall movements, however, did not significantly change. The median breathing effort after operation was lower than that before operation (p There was significant reduction in coronal Cobb's angle
Crossing the entropy barrier of dynamical zeta functions
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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.).
Enzymes: An integrated view of structure, dynamics and function
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Agarwal Pratul K
2006-01-01
Full Text Available Abstract Microbes utilize enzymes to perform a variety of functions. Enzymes are biocatalysts working as highly efficient machines at the molecular level. In the past, enzymes have been viewed as static entities and their function has been explained on the basis of direct structural interactions between the enzyme and the substrate. A variety of experimental and computational techniques, however, continue to reveal that proteins are dynamically active machines, with various parts exhibiting internal motions at a wide range of time-scales. Increasing evidence also indicates that these internal protein motions play a role in promoting protein function such as enzyme catalysis. Moreover, the thermodynamical fluctuations of the solvent, surrounding the protein, have an impact on internal protein motions and, therefore, on enzyme function. In this review, we describe recent biochemical and theoretical investigations of internal protein dynamics linked to enzyme catalysis. In the enzyme cyclophilin A, investigations have lead to the discovery of a network of protein vibrations promoting catalysis. Cyclophilin A catalyzes peptidyl-prolyl cis/trans isomerization in a variety of peptide and protein substrates. Recent studies of cyclophilin A are discussed in detail and other enzymes (dihydrofolate reductase and liver alcohol dehydrogenase where similar discoveries have been reported are also briefly discussed. The detailed characterization of the discovered networks indicates that protein dynamics plays a role in rate-enhancement achieved by enzymes. An integrated view of enzyme structure, dynamics and function have wide implications in understanding allosteric and co-operative effects, as well as protein engineering of more efficient enzymes and novel drug design.
Dynamic Behavior of Axially Functionally Graded Pipes Conveying Fluid
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Chen An
2017-01-01
Full Text Available Dynamic behavior of axially functionally graded (FG pipes conveying fluid was investigated numerically by using the generalized integral transform technique (GITT. The transverse vibration equation was integral transformed into a coupled system of second-order differential equations in the temporal variable. The Mathematica’s built-in function, NDSolve, was employed to numerically solve the resulting transformed ODE system. Excellent convergence of the proposed eigenfunction expansions was demonstrated for calculating the transverse displacement at various points of axially FG pipes conveying fluid. The proposed approach was verified by comparing the obtained results with the available solutions reported in the literature. Moreover, parametric studies were performed to analyze the effects of Young’s modulus variation, material distribution, and flow velocity on the dynamic behavior of axially FG pipes conveying fluid.
The Dynamics of Semigroups of Transcendental Meromorphic Functions
Institute of Scientific and Technical Information of China (English)
黄志刚
2004-01-01
This paper considers the dynamics associated with an arbitrary semigroup of transcendental meromorphic functions.Fatou-Julia theory was used to investigate the dynamics of these semigroups.Some results of the dynamics of a rational mapping on the Riemann sphere were extended to the case.
Unveiling protein functions through the dynamics of the interaction network.
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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.
Subdiffusive dynamics of bump attractors: mechanisms and functional roles.
Qi, Yang; Breakspear, Michael; Gong, Pulin
2015-02-01
Bump attractors are localized activity patterns that can self-sustain after stimulus presentation, and they are regarded as the neural substrate for a host of perceptual and cognitive processes. One of the characteristic features of bump attractors is that they are neutrally stable, so that noisy inputs cause them to drift away from their initial locations, severely impairing the accuracy of bump location-dependent neural coding. Previous modeling studies of such noise-induced drifting activity of bump attractors have focused on normal diffusive dynamics, often with an assumption that noisy inputs are uncorrelated. Here we show that long-range temporal correlations and spatial correlations in neural inputs generated by multiple interacting bumps cause them to drift in an anomalous subdiffusive way. This mechanism for generating subdiffusive dynamics of bump attractors is further analyzed based on a generalized Langevin equation. We demonstrate that subdiffusive dynamics can significantly improve the coding accuracy of bump attractors, since the variance of the bump displacement increases sublinearly over time and is much smaller than that of normal diffusion. Furthermore, we reanalyze existing psychophysical data concerning the spread of recalled cue position in spatial working memory tasks and show that its variance increases sublinearly with time, consistent with subdiffusive dynamics of bump attractors. Based on the probability density function of bump position, we also show that the subdiffusive dynamics result in a long-tailed decay of firing rate, greatly extending the duration of persistent activity.
Infimal convolution of total generalized variation functionals for dynamic MRI.
Schloegl, Matthias; Holler, Martin; Schwarzl, Andreas; Bredies, Kristian; Stollberger, Rudolf
2017-07-01
To accelerate dynamic MR applications using infimal convolution of total generalized variation functionals (ICTGV) as spatio-temporal regularization for image reconstruction. ICTGV comprises a new image prior tailored to dynamic data that achieves regularization via optimal local balancing between spatial and temporal regularity. Here it is applied for the first time to the reconstruction of dynamic MRI data. CINE and perfusion scans were investigated to study the influence of time dependent morphology and temporal contrast changes. ICTGV regularized reconstruction from subsampled MR data is formulated as a convex optimization problem. Global solutions are obtained by employing a duality based non-smooth optimization algorithm. The reconstruction error remains on a low level with acceleration factors up to 16 for both CINE and dynamic contrast-enhanced MRI data. The GPU implementation of the algorithm suites clinical demands by reducing reconstruction times of one dataset to less than 4 min. ICTGV based dynamic magnetic resonance imaging reconstruction allows for vast undersampling and therefore enables for very high spatial and temporal resolutions, spatial coverage and reduced scan time. With the proposed distinction of model and regularization parameters it offers a new and robust method of flexible decomposition into components with different degrees of temporal regularity. Magn Reson Med 78:142-155, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.
Real-time estimation of dynamic functional connectivity networks.
Monti, Ricardo Pio; Lorenz, Romy; Braga, Rodrigo M; Anagnostopoulos, Christoforos; Leech, Robert; Montana, Giovanni
2017-01-01
Two novel and exciting avenues of neuroscientific research involve the study of task-driven dynamic reconfigurations of functional connectivity networks and the study of functional connectivity in real-time. While the former is a well-established field within neuroscience and has received considerable attention in recent years, the latter remains in its infancy. To date, the vast majority of real-time fMRI studies have focused on a single brain region at a time. This is due in part to the many challenges faced when estimating dynamic functional connectivity networks in real-time. In this work, we propose a novel methodology with which to accurately track changes in time-varying functional connectivity networks in real-time. The proposed method is shown to perform competitively when compared to state-of-the-art offline algorithms using both synthetic as well as real-time fMRI data. The proposed method is applied to motor task data from the Human Connectome Project as well as to data obtained from a visuospatial attention task. We demonstrate that the algorithm is able to accurately estimate task-related changes in network structure in real-time. Hum Brain Mapp 38:202-220, 2017. © 2016 Wiley Periodicals, Inc.
Theoretical studies of combustion dynamics
Energy Technology Data Exchange (ETDEWEB)
Bowman, J.M. [Emory Univ., Atlanta, GA (United States)
1993-12-01
The basic objectives of this research program are to develop and apply theoretical techniques to fundamental dynamical processes of importance in gas-phase combustion. There are two major areas currently supported by this grant. One is reactive scattering of diatom-diatom systems, and the other is the dynamics of complex formation and decay based on L{sup 2} methods. In all of these studies, the authors focus on systems that are of interest experimentally, and for which potential energy surfaces based, at least in part, on ab initio calculations are available.
Dynamic requirements for a functional protein hinge.
Kempf, James G; Jung, Ju-Yeon; Ragain, Christina; Sampson, Nicole S; Loria, J Patrick
2007-04-20
The enzyme triosephosphate isomerase (TIM) is a model of catalytic efficiency. The 11 residue loop 6 at the TIM active site plays a major role in this enzymatic prowess. The loop moves between open and closed states, which facilitate substrate access and catalysis, respectively. The N and C-terminal hinges of loop 6 control this motion. Here, we detail flexibility requirements for hinges in a comparative solution NMR study of wild-type (WT) TIM and a quintuple mutant (PGG/GGG). The latter contained glycine substitutions in the N-terminal hinge at Val167 and Trp168, which follow the essential Pro166, and in the C-terminal hinge at Lys174, Thr175, and Ala176. Previous work demonstrated that PGG/GGG has a tenfold higher Km value and 10(3)-fold reduced k(cat) relative to WT with either d-glyceraldehyde 3-phosphate or dihyrdroxyacetone phosphate as substrate. Our NMR results explain this in terms of altered loop-6 dynamics in PGG/GGG. In the mutant, loop 6 exhibits conformational heterogeneity with corresponding motional rates hinge design in proteins: structural rigidity is essential for focused motional freedom of active-site loops.
Automatically Discovering Relaxed Lyapunov Functions for Polynomial Dynamical Systems
Liu, Jiang; Zhao, Hengjun
2011-01-01
The notion of Lyapunov function plays a key role in design and verification of dynamical systems, as well as hybrid and cyber-physical systems. In this paper, to analyze the asymptotic stability of a dynamical system, we generalize standard Lyapunov functions to relaxed Lyapunov functions (RLFs), by considering higher order Lie derivatives of certain functions along the system's vector field. Furthermore, we present a complete method to automatically discovering polynomial RLFs for polynomial dynamical systems (PDSs). Our method is complete in the sense that it is able to discover all polynomial RLFs by enumerating all polynomial templates for any PDS.
Directory of Open Access Journals (Sweden)
Hai-Xiao Jin
Full Text Available The current paradigm of cyclin-dependent kinase (CDK regulation based on the well-established CDK2 has been recently expanded. The determination of CDK9 crystal structures suggests the requirement of an additional regulatory protein, such as human immunodeficiency virus type 1 (HIV-1 Tat, to exert its physiological functions. In most kinases, the exact number and roles of the cofactor metal ions remain unappreciated, and the repertoire has thus gained increasing attention recently. Here, molecular dynamics (MD simulations were implemented on CDK9 to explore the functional roles of HIV-1 Tat and the second Mg2+ ion at site 1 (Mg12+. The simulations unveiled that binding of HIV-1 Tat to CDK9 not only stabilized hydrogen bonds (H-bonds between ATP and hinge residues Asp104 and Cys106, as well as between ATP and invariant Lys48, but also facilitated the salt bridge network pertaining to the phosphorylated Thr186 at the activation loop. By contrast, these H-bonds cannot be formed in CDK9 owing to the absence of HIV-1 Tat. MD simulations further revealed that the Mg12+ ion, coupled with the Mg22+ ion, anchored to the triphosphate moiety of ATP in its catalytic competent conformation. This observation indicates the requirement of the Mg12+ ion for CDK9 to realize its function. Overall, the introduction of HIV-1 Tat and Mg12+ ion resulted in the active site architectural characteristics of phosphorylated CDK9. These data highlighted the functional roles of HIV-1 Tat and Mg12+ ion in the regulation of CDK9 activity, which contributes an important complementary understanding of CDK molecular underpinnings.
Dynamic inventory models: an illustrative case study
Directory of Open Access Journals (Sweden)
Adendorff, Kris
2014-10-01
Full Text Available The study revisits the subject matter of inventory control, a continual part of the activities of wide-ranging organisations internationally. The mathematical model is presented of a particular situation that deals with the regular acquisition of a material required for a production process in a volatile environment of varying demand and fluctuating price. The usual process dynamics are demonstrated against a background of diverse choices of probability density function. The model makes use of Normal and Weibull distributions.
Dynamical zeta functions for piecewise monotone maps of the interval
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).
Lattice dynamics and disorder-induced contraction in functionalized graphene
Feng Huang, Liang; Zeng, Zhi
2013-02-01
The lattice dynamics and disorder-induced contraction in hydrogenated, fluorinated, and chlorinated graphene are studied by first-principles simulation. The effects of the functionalization on the phonon dispersions, Grüneissen constants, vibrational thermodynamic functions (free energy, internal energy, entropy, and heat capacity), thermal-expansion coefficients, and bulk moduli are systematically investigated. Functionalization changes the chemical-bond length, mass, thickness, vibrational-mode symmetry, and mode number, and subsequently has significant effects on the phonon dispersions and Grüneissen constants. Functionalization generally increases the vibrational thermodynamic functions, and their temperature dependences all present conventional isotope effects. Functionalization suppresses (enhances) the thermal contraction (expansion) of the lattice, due to the increases in the system mass, membrane thickness, and the compressibility of the phonons. Both the lattice-constant variation and the phonon thermalization contribute to the temperature dependence of the bulk modulus. Both pristine and hydrogenated graphene can be viewed as two kinds of materials having the Invar and Elinvar properties. The contribution to the lattice contraction in functionalized graphene from the conformation disorder (about 2.0%) is much larger than that by thermalization (<0.1% at 300 K), which explains the mismatch between the experimental and theoretical lattice constants.
Functional data analysis for dynamical system identification of behavioral processes.
Trail, Jessica B; Collins, Linda M; Rivera, Daniel E; Li, Runze; Piper, Megan E; Baker, Timothy B
2014-06-01
Efficient new technology has made it straightforward for behavioral scientists to collect anywhere from several dozen to several thousand dense, repeated measurements on one or more time-varying variables. These intensive longitudinal data (ILD) are ideal for examining complex change over time but present new challenges that illustrate the need for more advanced analytic methods. For example, in ILD the temporal spacing of observations may be irregular, and individuals may be sampled at different times. Also, it is important to assess both how the outcome changes over time and the variation between participants' time-varying processes to make inferences about a particular intervention's effectiveness within the population of interest. The methods presented in this article integrate 2 innovative ILD analytic techniques: functional data analysis and dynamical systems modeling. An empirical application is presented using data from a smoking cessation clinical trial. Study participants provided 42 daily assessments of pre-quit and post-quit withdrawal symptoms. Regression splines were used to approximate smooth functions of craving and negative affect and to estimate the variables' derivatives for each participant. We then modeled the dynamics of nicotine craving using standard input-output dynamical systems models. These models provide a more detailed characterization of the post-quit craving process than do traditional longitudinal models, including information regarding the type, magnitude, and speed of the response to an input. The results, in conjunction with standard engineering control theory techniques, could potentially be used by tobacco researchers to develop a more effective smoking intervention.
Dynamic fracture of functionally graded magnetoelectroelastic composite materials
Energy Technology Data Exchange (ETDEWEB)
Stoynov, Y. [Faculty of Applied Mathematics and Informatics, Technical University of Sofia (Bulgaria); Dineva, P. [Institute of Mechanics, Bulgarian Academy of Sciences, Sofia (Bulgaria)
2014-11-12
The stress, magnetic and electric field analysis of multifunctional composites, weakened by impermeable cracks, is of fundamental importance for their structural integrity and reliable service performance. The aim is to study dynamic behavior of a plane of functionally graded magnetoelectroelastic composite with more than one crack. The coupled material properties vary exponentially in an arbitrary direction. The plane is subjected to anti-plane mechanical and in-plane electric and magnetic load. The boundary value problem described by the partial differential equations with variable coefficients is reduced to a non-hypersingular traction boundary integral equation based on the appropriate functional transform and frequency-dependent fundamental solution derived in a closed form by Radon transform. Software code based on the boundary integral equation method (BIEM) is developed, validated and inserted in numerical simulations. The obtained results show the sensitivity of the dynamic stress, magnetic and electric field concentration in the cracked plane to the type and characteristics of the dynamic load, to the location and cracks disposition, to the wave-crack-crack interactions and to the magnitude and direction of the material gradient.
Kim, Dongchul; Chin, Mian; Kemp, Eric M.; Tao, Zhining; Peters-Lidard, Christa D.; Ginoux, Paul
2017-06-01
A high-resolution dynamic dust source has been developed in the NASA Unified-Weather Research and Forecasting (NU-WRF) model to improve the existing coarse static dust source. In the new dust source map, topographic depression is in 1-km resolution and surface bareness is derived using the Normalized Difference Vegetation Index (NDVI) data from Moderate Resolution Imaging Spectroradiometer (MODIS). The new dust source better resolves the complex topographic distribution over the Western United States where its magnitude is higher than the existing, coarser resolution static source. A case study is conducted with an extreme dust storm that occurred in Phoenix, Arizona in 02-03 UTC July 6, 2011. The NU-WRF model with the new high-resolution dynamic dust source is able to successfully capture the dust storm, which was not achieved with the old source identification. However the case study also reveals several challenges in reproducing the time evolution of the short-lived, extreme dust storm events.
Magnetoencephalography in the study of brain dynamics.
Pizzella, Vittorio; Marzetti, Laura; Della Penna, Stefania; de Pasquale, Francesco; Zappasodi, Filippo; Romani, Gian Luca
2014-01-01
To progress toward understanding of the mechanisms underlying the functional organization of the human brain, either a bottom-up or a top-down approach may be adopted. The former starts from the study of the detailed functioning of a small number of neuronal assemblies, while the latter tries to decode brain functioning by considering the brain as a whole. This review discusses the top-down approach and the use of magnetoencephalography (MEG) to describe global brain properties. The main idea behind this approach is that the concurrence of several areas is required for the brain to instantiate a specific behavior/functioning. A central issue is therefore the study of brain functional connectivity and the concept of brain networks as ensembles of distant brain areas that preferentially exchange information. Importantly, the human brain is a dynamic device, and MEG is ideally suited to investigate phenomena on behaviorally relevant timescales, also offering the possibility of capturing behaviorally-related brain connectivity dynamics.
Dynamically Consistent Nonlinear Evaluations with Their Generating Functions in Lp
Institute of Scientific and Technical Information of China (English)
Feng HU
2013-01-01
In this paper,we study dynamically consistent nonlinear evaluations in Lp (1 ＜ p ＜ 2).One of our aim is to obtain the following result:under a domination condition,an Ft-consistent evaluation is an ∑g-evaluation in Lp.Furthermore,without the assumption that the generating function g(t,ω,y,z) is continuous with respect to t,we provide some useful characterizations of an εg-evaluation by g and give some applications.These results include and extend some existing results.
Dynamic critical phenomena from spectral functions on the lattice
Berges, J; Sexty, D
2009-01-01
We investigate spectral functions in the vicinity of the critical temperature of a second-order phase transition. Since critical phenomena in quantum field theories are governed by classical dynamics, universal properties can be computed using real-time lattice simulations. For the example of a relativistic single-component scalar field theory in 2+1 dimensions, we compute the spectral function described by universal scaling functions and extract the dynamic critical exponent z. Together with exactly known static properties of this theory, we obtain a verification from first principles that the relativistic theory is well described by the dynamic universality class of relaxational models with conserved density (Model C).
Dynamic optimization case studies in DYNOPT tool
Ozana, Stepan; Pies, Martin; Docekal, Tomas
2016-06-01
Dynamic programming is typically applied to optimization problems. As the analytical solutions are generally very difficult, chosen software tools are used widely. These software packages are often third-party products bound for standard simulation software tools on the market. As typical examples of such tools, TOMLAB and DYNOPT could be effectively applied for solution of problems of dynamic programming. DYNOPT will be presented in this paper due to its licensing policy (free product under GPL) and simplicity of use. DYNOPT is a set of MATLAB functions for determination of optimal control trajectory by given description of the process, the cost to be minimized, subject to equality and inequality constraints, using orthogonal collocation on finite elements method. The actual optimal control problem is solved by complete parameterization both the control and the state profile vector. It is assumed, that the optimized dynamic model may be described by a set of ordinary differential equations (ODEs) or differential-algebraic equations (DAEs). This collection of functions extends the capability of the MATLAB Optimization Tool-box. The paper will introduce use of DYNOPT in the field of dynamic optimization problems by means of case studies regarding chosen laboratory physical educational models.
Hak, Sjoerd; Cebulla, Jana; Huuse, Else Marie; Davies, Catharina de L; Mulder, Willem J M; Larsson, Henrik B W; Haraldseth, Olav
2014-01-01
In the past two decades advances in the development of targeted nanoparticles have facilitated their application as molecular imaging agents and targeted drug delivery vehicles. Nanoparticle-enhanced molecular imaging of the angiogenic tumor vasculature has been of particular interest. Not only because angiogenesis plays an important role in various pathologies, but also since endothelial cell surface receptors are directly accessible for relatively large circulating nanoparticles. Typically, nanoparticle targeting towards these receptors is studied by analyzing the contrast distribution on tumor images acquired before and at set time points after administration. Although several exciting proof-of-concept studies demonstrated qualitative assessment of relative target concentration and distribution, these studies did not provide quantitative information on the nanoparticle targeting kinetics. These kinetics will not only depend on nanoparticle characteristics, but also on receptor binding and recycling. In this study, we monitored the in vivo targeting kinetics of αvβ3-integrin specific nanoparticles with intravital microscopy and dynamic contrast enhanced magnetic resonance imaging, and using compartment modeling we were able to quantify nanoparticle targeting rates. As such, this approach can facilitate optimization of targeted nanoparticle design and it holds promise for providing more quantitative information on in vivo receptor levels. Interestingly, we also observed a periodicity in the accumulation kinetics of αvβ3-integrin targeted nanoparticles and hypothesize that this periodicity is caused by receptor binding, internalization and recycling dynamics. Taken together, this demonstrates that our experimental approach provides new insights in in vivo nanoparticle targeting, which may proof useful for vascular targeting in general.
Intrinsically disordered proteins: structural and functional dynamics
Directory of Open Access Journals (Sweden)
Wallin S
2017-02-01
Full Text Available Stefan Wallin Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John’s, NL, Canada Abstract: The classical view holds that proteins fold into essentially unique three-dimensional structures before becoming biologically active. However, studies over the last several years have provided broad and convincing evidence that some proteins do not adopt a single structure and yet are fully functional. These intrinsically disordered proteins (IDPs have been found to be highly prevalent in many genomes, including human, and play key roles in central cellular processes, such as regulation of transcription and translation, cell cycle, and cell signaling. Moreover, IDPs are overrepresented among proteins implicated in disease, including various cancers and neurodegenerative disorders. Intense efforts, by using both experimental and computational approaches, are consequently under way to uncover the molecular mechanisms that underpin the roles of IDPs in biology and disease. This review provides an introduction to the general biophysical properties of IDPs and discusses some of the recent emerging areas in IDP research, including the roles of IDPs in allosteric regulation, regulatory unfolding, and formation of intracellular membrane-less organelles. In addition, recent attempts at therapeutic targeting of IDPs by small molecules, noting in particular that IDPs represent a potentially important source of new drug targets in light of their central role in protein–protein interaction networks, are also reviewed. Keywords: natively unfolded proteins, unstructured proteins, protein folding, protein–protein interaction, cell regulation, signaling, drug development, inhibitors
Saha, Sourav Kr.; Ghosh, Pritam; Hens, Abhiram; Murmu, Naresh Chandra; Banerjee, Priyabrata
2015-02-01
Corrosion inhibition mechanism of two mercapto-quinoline Schiff bases, eg., 3-((phenylimino)methyl)quinoline-2-thiol (PMQ) and 3-((5-methylthiazol-2-ylimino)methyl) quinoline-2-thiol (MMQT) on mild steel surface is investigated by quantum chemical calculation and molecular dynamics simulation. Quantum chemical parameters such as EHOMO, ELUMO, energy gap (ΔE), dipolemoment (μ), electronegativity (χ), global hardness (η) and fraction of electron transfers from the inhibitor molecule to the metallic atom surface (ΔN) have been studied to investigate their relative corrosion inhibition performance. Parameters like local reactive sites of the present molecule have been analyzed through Fukui indices. Moreover, adsorption behavior of the inhibitor molecules on Fe (1 1 0) surface have been analyzed using molecular dynamics simulation. The binding strength of the concerned inhibitor molecules on mild steel surface follows the order MMQT>PMQ, which is in good agreement with the experimentally determined inhibition efficiencies. In view of the above, our approach will be helpful for quick prediction of a potential inhibitor from a lot of similar inhibitors and subsequently in their rational designed synthesis for corrosion inhibition application following a wet chemical synthetic route.
Shkrob, I A; Larsen, R E; Schwartz, B J; Glover, William J.; Larsen, Ross E.; Schwartz, Benjamin J.; Shkrob, Ilya A.
2006-01-01
Adiabatic mixed quantum/classical molecular dynamics simulations were used to generate snapshots of the hydrated electron (e-) in liquid water at 300 K. Water cluster anions that include two complete solvation shells centered on the e- were extracted from these simulations and embedded in a matrix of fractional point charges designed to represent the rest of the solvent. Density functional theory and single-excitation configuration interaction methods were then applied to these embedded clusters. The salient feature of these hybrid calculations is significant transfer (ca. 0.18) of the excess electron's charge density into the O 2p orbitals in OH groups forming the solvation cavity. We used the results of these calculations to examine the structure of the molecular orbitals, the density of states, the absorption spectra in the visible and ultraviolet, the hyperfine coupling (hfc) tensors, and the IR and Raman spectra of the e-. The calculated hfc tensors were used to compute the EPR and ESEEM spectra for the ...
Functional Loop Dynamics of the Streptavidin-Biotin Complex
Song, Jianing; Li, Yongle; Ji, Changge; Zhang, John Z. H.
2015-01-01
Accelerated molecular dynamics (aMD) simulation is employed to study the functional dynamics of the flexible loop3-4 in the strong-binding streptavidin-biotin complex system. Conventional molecular (cMD) simulation is also performed for comparison. The present study reveals the following important properties of the loop dynamics: (1) The transition of loop3-4 from open to closed state is observed in 200 ns aMD simulation. (2) In the absence of biotin binding, the open-state streptavidin is more stable, which is consistent with experimental evidences. The free energy (ΔG) difference is about 5 kcal/mol between two states. But with biotin binding, the closed state is more stable due to electrostatic and hydrophobic interactions between the loop3-4 and biotin. (3) The closure of loop3-4 is concerted to the stable binding of biotin to streptavidin. When the loop3-4 is in its open-state, biotin moves out of the binding pocket, indicating that the interactions between the loop3-4 and biotin are essential in trapping biotin in the binding pocket. (4) In the tetrameric streptavidin system, the conformational change of the loop3-4 in each monomer is independent of each other. That is, there is no cooperative binding for biotin bound to the four subunits of the tetramer.
Yue, Jeffrey; Du, Zheng; Shao, Minhua
2016-08-01
The effect of surfactants on the synthesis of shape-controlled palladium (Pd) nanocrystals was studied using computational simulation methods. We found that the functional groups in surfactant molecules played an important role in the specific adsorption on Pd surfaces. Citric acid and ascorbic acid were found to be preferentially adsorbed onto Pd(1 1 1) and (1 0 0) planes resulting in the formation of octahedral and cubic nanocrystals, respectively.
Energy Technology Data Exchange (ETDEWEB)
Duan, Yuhua; Parlinski, K.
2011-01-01
The structural, electronic, lattice dynamical, optical, thermodynamic, and CO{sub 2} capture properties of monoclinic and triclinic phases of Li{sub 4}SiO{sub 4} are investigated by combining density functional theory with phonon lattice dynamics calculations. We found that these two phases have some similarities in their bulk and thermodynamic properties. The calculated bulk modulus and the cohesive energies of these two phases are close to each other. Although both of them are insulators, the monoclinic phase of Li{sub 4}SiO{sub 4} has a direct band gap of 5.24 eV while the triclinic Li{sub 4}SiO{sub 4} phase has an indirect band gap of 4.98 eV. In both phases of Li{sub 4}SiO{sub 4}, the s orbital of O mainly contributes to the lower-energy second valence band (VB{sub 2}) and the p orbitals contribute to the fist valence band (VB{sub 1}) and the conduction bands (CBs). The s orbital of Si mainly contributes to the lower portions of the VB1 and VB{sub 2}, and Si p orbitals mainly contribute to the higher portions of the VB{sub 1} and VB{sub 2}. The s and p orbitals of Li contribute to both VBs and to CBs, and Li p orbitals have a higher contribution than the Li s orbital. There is possibly a phonon soft mode existing in triclinic {gamma}-Li{sub 4}SiO{sub 4}; in the monoclinic Li{sub 4}SiO{sub 4}, there are three phonon soft modes, which correspond to the one type of Li disordered over a few sites. Their LO-TO splitting indicates that both phases of Li{sub 4}SiO{sub 4} are polar anisotropic materials. The calculated infrared absorption spectra for LO and TO modes are different for these two phases of Li{sub 4}SiO{sub 4}. The calculated relationships of the chemical potential versus temperature and CO{sub 2} pressure for reaction of Li{sub 4}SiO{sub 4} with CO{sub 2} shows that Li{sub 4}SiO{sub 4} could be a good candidate for a high-temperature CO{sub 2} sorbent while used for postcombustion capture technology.
Time-dependent density-functional description of nuclear dynamics
Nakatsukasa, Takashi; Matsuo, Masayuki; Yabana, Kazuhiro
2016-01-01
We present the basic concepts and recent developments in the time-dependent density functional theory (TDDFT) for describing nuclear dynamics at low energy. The symmetry breaking is inherent in nuclear energy density functionals (EDFs), which provides a practical description of important correlations at the ground state. Properties of elementary modes of excitation are strongly influenced by the symmetry breaking and can be studied with TDDFT. In particular, a number of recent developments in the linear response calculation have demonstrated their usefulness in description of collective modes of excitation in nuclei. Unrestricted real-time calculations have also become available in recent years, with new developments for quantitative description of nuclear collision phenomena. There are, however, limitations in the real-time approach; for instance, it cannot describe the many-body quantum tunneling. Thus, we treat the quantum fluctuations associated with slow collective motions assuming that time evolution of...
Ceylan, Ümit; Çapan, Ali; Yalçın, Şerife Pınar; Sönmez, Mehmet; Aygün, Muhittin
2017-05-01
This study covers the synthesis, structural characterization by experimental FT-IR, 1H NMR and 13C NMR, UV-Vis and single crystal XRD and comparison with theoretical calculations of a Schiff base compound bearing phenoxy group, C34H28N2O4 by using the DFT method 6-311G(d,p) basis set. The molecular geometry, the dipole moments, electrostatic potential, vibrational frequencies, HOMO-LUMO energy were calculated. NBO, NLO, thermodynamic properties and Fukui function were studied. In this work, theoretical values show good agreement with experimental values.
Directory of Open Access Journals (Sweden)
Massimo Bionaz
Full Text Available The overrepresented approach (ORA is the most widely-accepted method for functional analysis of microarray datasets. The ORA is computationally-efficient and robust; however, it suffers from the inability of comparing results from multiple gene lists particularly with time-course experiments or those involving multiple treatments. To overcome such limitation a novel method termed Dynamic Impact Approach (DIA is proposed. The DIA provides an estimate of the biological impact of the experimental conditions and the direction of the impact. The impact is obtained by combining the proportion of differentially expressed genes (DEG with the log2 mean fold change and mean -log P-value of genes associated with the biological term. The direction of the impact is calculated as the difference of the impact of up-regulated DEG and down-regulated DEG associated with the biological term. The DIA was validated using microarray data from a time-course experiment of bovine mammary gland across the lactation cycle. Several annotation databases were analyzed with DIA and compared to the same analysis performed by the ORA. The DIA highlighted that during lactation both BTA6 and BTA14 were the most impacted chromosomes; among Uniprot tissues those related with lactating mammary gland were the most positively-impacted; within KEGG pathways 'Galactose metabolism' and several metabolism categories related to lipid synthesis were among the most impacted and induced; within Gene Ontology "lactose biosynthesis" among Biological processes and "Lactose synthase activity" and "Stearoyl-CoA 9-desaturase activity" among Molecular processes were the most impacted and induced. With the exception of the terms 'Milk', 'Milk protein' and 'Mammary gland' among Uniprot tissues and SP_PIR_Keyword, the use of ORA failed to capture as significantly-enriched (i.e., biologically relevant any term known to be associated with lactating mammary gland. Results indicate the DIA is a
Structural dynamics flexibility informs function and evolution at a proteome scale
Nevin Gerek, Zeynep; Kumar, Sudhir; Banu Ozkan, Sefika
2013-01-01
Protein structures are dynamic entities with a myriad of atomic fluctuations, side-chain rotations, and collective domain movements. Although the importance of these dynamics to proper functioning of proteins is emerging in the studies of many protein families, there is a lack of broad evidence for the critical role of protein dynamics in shaping the biological functions of a substantial fraction of residues for a large number of proteins in the human proteome. Here, we propose a novel dynamic flexibility index (dfi) to quantify the dynamic properties of individual residues in any protein and use it to assess the importance of protein dynamics in 100 human proteins. Our analyses involving functionally critical positions, disease-associated and putatively neutral population variations, and the rate of interspecific substitutions per residue produce concordant patterns at a proteome scale. They establish that the preservation of dynamic properties of residues in a protein structure is critical for maintaining the protein/biological function. Therefore, structural dynamics needs to become a major component of the analysis of protein function and evolution. Such analyses will be facilitated by the dfi, which will also enable the integrative use of structural dynamics with evolutionary conservation in genomic medicine as well as functional genomics investigations. PMID:23745135
DEFF Research Database (Denmark)
Moses, Matias Emil; Hedegård, Per; Hatzakis, Nikos
2016-01-01
and quantification of the activity, abundance, and lifetime of multiple states and transient intermediates in the energy landscape that are typically averaged out in nonsynchronized ensemble measurements. Studying the function of membrane proteins at the single-molecule level remains a formidable challenge......, and to date there is limited number of available functional assays. In this chapter, we describe in detail our recently developed methodology to reconstitute membrane proteins such as the integral membrane protein cytochrome P450 oxidoreductase on membrane systems such as Nanodiscs and study their functional...... dynamics by recordings at the fundamental resolution of individual catalytic turnovers using prefluorescent substrate analogues. We initially describe the methodology for reconstitution, surface immobilization, and data acquisition of individual enzyme catalytic turnovers. We then explain in detail...
Study of the structure and dynamics of complex biological networks
Samal, Areejit
2008-12-01
In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large scale metabolic networks inside three organisms, Escherichia coli, Saccharomyces cerevisiae and Staphylococcus aureus. We also study the dynamics of the large scale genetic network controlling E. coli metabolism. We have tried to explain the observed system level dynamical properties of these networks in terms of their underlying structure. Our studies of the system level dynamics of these large scale biological networks provide a different perspective on their functioning compared to that obtained from purely structural studies. Our study also leads to some new insights on features such as robustness, fragility and modularity of these large scale biological networks. We also shed light on how different networks inside the cell such as metabolic networks and genetic networks are interrelated to each other.
Measurement of dynamic efficiency: a directional distance function parametric approach
Serra, T.; Oude Lansink, A.G.J.M.; Stefanou, S.E.
2011-01-01
This research proposes a parametric estimation of the structural dynamic efficiency measures proposed by Silva and Oude Lansink (2009). Overall, technical and allocative efficiency measurements are derived based on a directional distance function and the duality between this function and the optimal
Directory of Open Access Journals (Sweden)
Fabian M Stuby
Full Text Available This study was conducted according to GCP criteria as a prospective randomized cross-over study. The primary goal of the study was to determine clinical findings and patient satisfaction with postoperative treatment. 29 patients with a distal radius fracture that was surgically stabilized from volar and who met the inclusion criteria were enrolled over a 12-month period. Each patient randomly received either a dorsal plaster splint or a vacuum-fit flexible but blocked orthosis applied postoperatively in the operating theatre to achieve postoperative immobilization. After one week all patients were crossed over to the complementary device maintaining the immobilization until end of week 2. After week 2 both groups were allowed to exercise wrist mobility with a physiotherapist, in the orthosis group the device was deblocked, thus allowing limited wrist mobility. After week 4 the devices were removed in both groups. Follow-up exams were performed after postoperative weeks 1, 2, 4 and 12.Results were determined after week 1 and 2 using SF 36 and a personally compiled questionnaire; after weeks 4 and 12 with a clinical check-up, calculation of ROM and the DASH Score. Comparison of the two groups showed a significant difference in ROM for volar flexion after 4 weeks, but no significant differences in DASH Score, duration of disability or x-ray findings. With regard to satisfaction with comfort and hygiene, patients were significantly more satisfied with the dynamic orthosis, and 23 of the 29 patients would prefer the flexible vacuum orthosis in future.German Clinical Trials Register (DRKS DRKS00006097.
Multi-functional stage-scanning fluorescence micro/nanoscope for single-lipid dynamics
Yang, Li-Ling; Hsieh, Chia-Fen; Chang, Yi-Ren; Shen, Jie-Pan; Chang, Yu-Chung; Chou, Chia-Fu
2012-02-01
We combine pulsed laser, supercontinuum radiation source and fast single-photon counting peripherals to obtain a multifunctional micro/nano-scope. This provides us with better spatial and temporal resolution to observe fast dynamics. Performing fluorescence correlation spectroscopy for fast dynamics (lipid dynamics in supported lipid bilayers and living cells is our goal. Lipid raft serves as a platform for recruiting signaling components of effective signal transduction. However, the dynamics of sub-200nm rapidly aggregated lipid rafts are still not elucidated in living cells. We here report our recent progress on the construction of this multi-functional stage-scanning fluorescence micro/nanoscope for single-lipid dynamics study.
Wood, E H
1977-10-01
Major segments of the biologic sciences and the practice of medicine are based on study and knowledge of the relationships of anatomic structure to biologic function. Traditionally, this knowledge has been gained by indirect means, inference, or by direct surgical vivisection or postmortem examination. The revolutionary capability of nondestructive, operator interactive, mathematical vivisection provided by synchronous cylindrical scanning tomography to obtain similar information non-invasively and painlessly will provide these data to the internist for individual patients. Furthermore, this information will be in a computerized format which can be subjected to myriad types of objective measurements and display. These developments promise beneficial effects of clinical diagnosis and health care which may approach those associated with the discoveries of the biomedical investigative and clinical diagnostic value of X-rays and cardiac catheterization.
Optical imaging of fast, dynamic neurophysiological function.
Energy Technology Data Exchange (ETDEWEB)
Rector, D. M. (David M.); Carter, K. M. (Kathleen M.); Yao, X. (Xincheng); George, J. S. (John S.)
2002-01-01
Fast evoked responses were imaged from rat dorsal medulla and whisker barrel cortex. To investigate the biophysical mechanisms involved, fast optical responses associated with isolated crustacean nerve stimulation were recorded using birefringence and scattered light. Such studies allow optimization of non-invasive imaging techniques being developed for use in humans.
Abstraction of Continuous Dynamical Systems Utilizing Lyapunov Functions
DEFF Research Database (Denmark)
Sloth, Christoffer; Wisniewski, Rafal
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....
The dynamic transfer function for a cavitating inducer
Brennen, C.; Acosta, A. J.
1975-01-01
Knowledge of the dynamic performance of pumps is essential for the prediction of transient behavior and instabilities in hydraulic systems; the necessary information is in the form of a transfer function which relates the instantaneous or fluctuating pressure and mass flow rate at inlet to the same quantities in the discharge from the pump. The presence of cavitation within the pump can have a major effect on this transfer function since dynamical changes in the volume of cavitation contribute to the difference in the instantaneous inlet and discharge mass flow rates. The present paper utilizes results from free streamline cascade theory to evaluate the elements in the transfer function for a cavitating inducer and shows that the numerical results are consistent with the characteristics observed in some dynamic tests on rocket engine turbopumps.
Differences in dynamic and static functional connectivity between young and elderly healthy adults.
Park, Ji Eun; Jung, Seung Chai; Ryu, Kyeoung Hwa; Oh, Joo Young; Kim, Ho Sung; Choi, Choong-Gon; Kim, Sang Joon; Shim, Woo Hyun
2017-08-01
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 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.
Structure/Function/Dynamics of Photosystem II Plastoquinone Binding Sites
Lambreva, Maya D.; Russo, Daniela; Polticelli, Fabio; Scognamiglio, Viviana; Antonacci, Amina; Zobnina, Veranika; Campi, Gaetano; Rea, Giuseppina
2014-01-01
Photosystem II (PSII) continuously attracts the attention of researchers aiming to unravel the riddle of its functioning and efficiency fundamental for all life on Earth. Besides, an increasing number of biotechnological applications have been envisaged exploiting and mimicking the unique properties of this macromolecular pigment-protein complex. The PSII organization and working principles have inspired the design of electrochemical water splitting schemes and charge separating triads in energy storage systems as well as biochips and sensors for environmental, agricultural and industrial screening of toxic compounds. An intriguing opportunity is the development of sensor devices, exploiting native or manipulated PSII complexes or ad hoc synthesized polypeptides mimicking the PSII reaction centre proteins as bio-sensing elements. This review offers a concise overview of the recent improvements in the understanding of structure and function of PSII donor side, with focus on the interactions of the plastoquinone cofactors with the surrounding environment and operational features. Furthermore, studies focused on photosynthetic proteins structure/function/dynamics and computational analyses aimed at rational design of high-quality bio-recognition elements in biosensor devices are discussed. PMID:24678671
Function-valued adaptive dynamics and optimal control theory.
Parvinen, Kalle; Heino, Mikko; Dieckmann, Ulf
2013-09-01
In this article we further develop the theory of adaptive dynamics of function-valued traits. Previous work has concentrated on models for which invasion fitness can be written as an integral in which the integrand for each argument value is a function of the strategy value at that argument value only. For this type of models of direct effect, singular strategies can be found using the calculus of variations, with singular strategies needing to satisfy Euler's equation with environmental feedback. In a broader, more mechanistically oriented class of models, the function-valued strategy affects a process described by differential equations, and fitness can be expressed as an integral in which the integrand for each argument value depends both on the strategy and on process variables at that argument value. In general, the calculus of variations cannot help analyzing this much broader class of models. Here we explain how to find singular strategies in this class of process-mediated models using optimal control theory. In particular, we show that singular strategies need to satisfy Pontryagin's maximum principle with environmental feedback. We demonstrate the utility of this approach by studying the evolution of strategies determining seasonal flowering schedules.
An information theory framework for dynamic functional domain connectivity.
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.
Structural and Dynamic Process Family Risk Factors: Consequences for Holistic Adolescent Functioning
Matjasko, Jennifer L.; Grunden, Leslie N.; Ernst, Jody L.
2007-01-01
This study utilized a dynamic cumulative family risk model to explain changes in adolescent functioning. We used a person-centered approach to detect patterns of academic, emotional, and behavioral functioning and the stability of these patterns using two waves of the National Longitudinal Study of Adolescent Health (N = 10,173). Four adjustment…
Crystallization induced by multiple seeds: dynamical density functional approach.
Neuhaus, T; Schmiedeberg, M; Löwen, H
2013-12-01
Using microscopic dynamical density functional theory, we calculate the dynamical formation of polycrystals by following the crystal growth around multiple crystalline seeds imposed to an undercooled fluid. Depending on the undercooling and the size ratio as well as the relative crystal orientation of two neighboring seeds, three possibilities of the final state emerge, namely no crystallization at all, formation of a monocrystal, or two crystallites separated by a curved grain boundary. Our results, which are obtained for two-dimensional hard disk systems using a fundamental-measure density functional, shed new light on the particle-resolved structure and growth of polycrystalline material in general.
Quantitative evaluation of the reticuloendothelial system function with dynamic MRI.
Directory of Open Access Journals (Sweden)
Ting Liu
Full Text Available PURPOSE: 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. MATERIALS AND METHODS: 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. RESULTS: 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. CONCLUSION: Dynamic SPIO-enhanced MR imaging with two-compartment modeling can provide information on RES function on both a cell number and receptor function level.
Ab initio molecular dynamics using hybrid density functionals
Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; Vandevondele, Joost
2008-06-01
Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.
Stability studies of Solar Optical Telescope dynamics
Gullapalli, Sarma N.; Pal, Parimal K.; Ruthven, Gregory P.
1987-01-01
The Solar Optical Telescope (SOT) is designed to operate as an attached payload mounted on the Instrument Pointing System (IPS) in the cargo bay of the Shuttle Orbiter. Pointing and control of SOT is accomplished by an active Articulated Primary Mirror (APM), an active Tertiary Mirror (TM), an elaborate set of optical sensors, electromechanical actuators and programmable controllers. The structural interactions of this complex control system are significant factors in the stability of the SOT. The preliminary stability study results of the SOT dynamical system are presented. Structural transfer functions obtained from the NASTRAN model of the structure were used. These studies apply to a single degree of freedom (elevation). Fully integrated model studies will be conducted in the future.
Experimental study on dynamic gas adsorption
Institute of Scientific and Technical Information of China (English)
Qin Yueping; Wang Yaru; Yang Xiaobin; Liu Wei; Luo Wei
2012-01-01
In order to predict the actual adsorption amount as gas adsorption reaches the equilibrium,this research designed a dynamic gas adsorption experiment under constant temperature and pressure,and also studied the isopiestic adsorption characteristics of coal samples with same quality but different sizes.Through the experiment,the study found the adsorption-time changing relationships under different pressures of four different size samples.After regression analysis,we obtained the functional relationship between adsorption and time.According to this,the research resulted in the actual adsorption amount when gas adsorption reaches the equilibrium.In addition,the current study obtained the relationship between adsorption and pressure as well as the effect of the coal size to the adsorption rate.These results have great theoretical and practical significance for the prediction of gas amount in coal seam and gas adsorption process.
Molecular Dynamics Studies of Nanofluidic Devices
DEFF Research Database (Denmark)
Zambrano Rodriguez, Harvey Alexander
in opposite direction to the imposed thermal gradient also we measure higher velocities as higher thermal gradients are imposed. Secondly, we present an atomistic analysis of a molecular linear motor fabricated of coaxial carbon nanotubes and powered by thermal gradients. The MD simulation results indicate...... in transport caused by the walls become more dominant and the fluid consists of fewer molecules. Carbon nanotubes are tubular graphite molecules which can be imagined to function as nanoscale pipes or conduits. Another important material for nanofluidics applications is silica. Nowadays, silica nanochannels...... of such devices. Computational nanofluidics complements experimental studies by providing detailed spatial and temporal information of the nanosystem. In this thesis, we conduct molecular dynamics simulations to study basic nanoscale devices. We focus our studies on the understanding of transport mechanism...
Directory of Open Access Journals (Sweden)
Zhiyu Zhou
2014-01-01
Full Text Available Hydrogel injection has been recently proposed as a novel therapy for disc degenerative diseases, with the potential to restore the spine motion and the intervertebral disc height. However, it remains unknown whether the new technique could also maintain the shock absorbing property of the treated intervertebral disc. In this study, 18 porcine lumbar bone-disc-bone specimens were collected and randomly divided into three groups: the normal with intact intervertebral discs, the mimic for the injection of disulfide cross-linked hyaluronan hydrogels following discectomy, and the control disc with discectomy only. In the static compression test, specimens in the mimic group exhibited displacements similar to those in the normal discs, whereas the control group showed a significantly larger displacement range in the first two steps (P<0.05. With the frequency increasing, all specimens generally displayed an increasing storage modulus, decreasing loss modulus, and tanδ. At any frequency point, the control group exhibited the largest value in all the three parameters among three groups while the normal group was the lowest, with the mimic group being mostly close to the normal group. Therefore, the hydrogel injection into the intervertebral discs greatly restored their shock absorbing function, suggesting that the technique could serve as an effective approach to maintaining biomechanical properties of the degenerative intervertebral disc.
Development of a transfer function method for dynamic stability measurement
Johnson, W.
1977-01-01
Flutter testing method based on transfer function measurements is developed. The error statistics of several dynamic stability measurement methods are reviewed. It is shown that the transfer function measurement controls the error level by averaging the data and correlating the input and output. The method also gives a direct estimate of the error in the response measurement. An algorithm is developed for obtaining the natural frequency and damping ratio of low damped modes of the system, using integrals of the transfer function in the vicinity of a resonant peak. Guidelines are given for selecting the parameters in the transfer function measurement. Finally, the dynamic stability measurement technique is applied to data from a wind tunnel test of a proprotor and wing model.
Dynamics Model Abstraction Scheme Using Radial Basis Functions
Directory of Open Access Journals (Sweden)
Silvia Tolu
2012-01-01
Full Text Available This paper presents a control model for object manipulation. Properties of objects and environmental conditions influence the motor control and learning. System dynamics depend on an unobserved external context, for example, work load of a robot manipulator. The dynamics of a robot arm change as it manipulates objects with different physical properties, for example, the mass, shape, or mass distribution. We address active sensing strategies to acquire object dynamical models with a radial basis function neural network (RBF. Experiments are done using a real robot’s arm, and trajectory data are gathered during various trials manipulating different objects. Biped robots do not have high force joint servos and the control system hardly compensates all the inertia variation of the adjacent joints and disturbance torque on dynamic gait control. In order to achieve smoother control and lead to more reliable sensorimotor complexes, we evaluate and compare a sparse velocity-driven versus a dense position-driven control scheme.
Light-Front Dynamics and the 3He Spectral Function
Pace, Emanuele; Kaptari, Leonid; Rinaldi, Matteo; Salme', Giovanni; Scopetta, Sergio
2016-01-01
Two topics are presented. The first one is a novel approach for a Poincare' covariant description of nuclear dynamics based on light-front Hamiltonian dynamics. The key quantity is the light-front spectral function, where both normalization and momentum sum rule can be satisfied at the same time. Preliminary results are discussed for an initial analysis of the role of relativity in the EMC effect in 3He. A second issue, very challenging, is considered in a non-relativistic framework, namely a distorted spin-dependent spectral function for 3He in order to take care of the final state interaction between the observed pion and the remnant in semi-inclusive deep inelastic electron scattering off polarized 3He. The generalization of the analysis within the light-front dynamics is outlined.
Hopkins, Paul; Fortini, Andrea; Archer, Andrew J; Schmidt, Matthias
2010-12-14
We describe a test particle approach based on dynamical density functional theory (DDFT) for studying the correlated time evolution of the particles that constitute a fluid. Our theory provides a means of calculating the van Hove distribution function by treating its self and distinct parts as the two components of a binary fluid mixture, with the "self " component having only one particle, the "distinct" component consisting of all the other particles, and using DDFT to calculate the time evolution of the density profiles for the two components. We apply this approach to a bulk fluid of Brownian hard spheres and compare to results for the van Hove function and the intermediate scattering function from Brownian dynamics computer simulations. We find good agreement at low and intermediate densities using the very simple Ramakrishnan-Yussouff [Phys. Rev. B 19, 2775 (1979)] approximation for the excess free energy functional. Since the DDFT is based on the equilibrium Helmholtz free energy functional, we can probe a free energy landscape that underlies the dynamics. Within the mean-field approximation we find that as the particle density increases, this landscape develops a minimum, while an exact treatment of a model confined situation shows that for an ergodic fluid this landscape should be monotonic. We discuss possible implications for slow, glassy, and arrested dynamics at high densities.
Atomic dynamics of alumina melt: A molecular dynamics simulation study
Directory of Open Access Journals (Sweden)
S.Jahn
2008-03-01
Full Text Available The atomic dynamics of Al2O3 melt are studied by molecular dynamics simulation. The particle interactions are described by an advanced ionic interaction model that includes polarization effects and ionic shape deformations. The model has been shown to reproduce accurately the static structure factors S(Q from neutron and x-ray diffraction and the dynamic structure factor S(Q,ω from inelastic x-ray scattering. Analysis of the partial dynamic structure factors shows inelastic features in the spectra up to momentum transfers, Q, close to the principal peaks of partial static structure factors. The broadening of the Brillouin line widths is discussed in terms of a frequency dependent viscosity η(ω.
Moscarello, Justin M.; Ben-Shahar, Osnat; Ettenberg, Aaron
2007-01-01
This study examined the effects of simultaneous variations in motivational state (food deprivation) and reinforcer magnitude (food presentation) on c-Fos immunoreactivity in the pre-and infralimbic medial prefrontal cortex (mPFC), nucleus accumbens (NAcc) core and shell, and dorsal striatum. In the first experiment, c-Fos was reliably increased in pre- and infralimbic mPFC of animals 12- and 36-h compared to 0-h deprived. In the second experiment, a small meal (2.5g) selectively increased c-Fos immunoreactivity in both mPFC subdivisions of 36-h deprived animals, as well as in both NAcc subdivisions of 12-h deprived animals. Correlational analyses revealed a changing relationship between mPFC subregions and the NAcc compartments to which they project. In subjects 12-h deprived and allowed a small meal, c-Fos counts in prelimbic mPFC and NAcc core were positively correlated, as were those in infralimbic mPFC and NAcc shell (r = . 83 and .76, respectively). The opposite was true of animals 36-h deprived, with prelimbic mPFC/NAcc core and infralimbic mPFC/NAcc shell negatively correlated (r = -.85 and -.82, respectively). The third experiment examined the effects of unrestricted feeding (presentation of 20g food) after 0, 12, or 36-h deprivation. No differences between mean c-Fos counts were found, though prelimbic mPFC/NAcc core, and mPFC/NAcc shell were positively correlated in animals 36-h deprived (r = .76 and .89, respectively). These data suggest that the activity within the mPFC and NAcc, as well as the interaction between the two, change as a complex combinatorial function of motivational state and reinforcer magnitude. Section: Cognitive and Behavioral Neuroscience PMID:17706947
McCormick, Benjamin J J; Lee, Gwenyth O; Seidman, Jessica C; Haque, Rashidul; Mondal, Dinesh; Quetz, Josiane; Lima, Aldo A M; Babji, Sudhir; Kang, Gagandeep; Shrestha, Sanjaya K; Mason, Carl J; Qureshi, Shahida; Bhutta, Zulfiqar A; Olortegui, Maribel Paredes; Yori, Pablo Peñataro; Samie, Amidou; Bessong, Pascal; Amour, Caroline; Mduma, Estomih; Patil, Crystal L; Guerrant, Richard L; Lang, Dennis R; Gottlieb, Michael; Caulfield, Laura E; Kosek, Margaret N
2017-02-08
Growth and development shortfalls that are disproportionately prevalent in children living in poor environmental conditions are postulated to result, at least in part, from abnormal gut function. Using data from The Etiology, Risk Factors, and Interactions of Enteric Infections and Malnutrition and the Consequences for Child Health and Development (MAL-ED) longitudinal cohort study, we examine biomarkers of gut inflammation and permeability in relation to environmental exposures and feeding practices. Trends in the concentrations of three biomarkers, myeloperoxidase (MPO), neopterin (NEO), and α-1-antitrypsin (AAT), are described from fecal samples collected during the first 2 years of each child's life. A total of 22,846 stool samples were processed during the longitudinal sampling of 2,076 children 0-24 months of age. Linear mixed models were constructed to examine the relationship between biomarker concentrations and recent food intake, symptoms of illness, concurrent enteropathogen infection, and socioeconomic status. Average concentrations of MPO, NEO, and AAT were considerably higher than published references for healthy adults. The concentration of each biomarker tended to decrease over the first 2 years of life and was highly variable between samples from each individual child. Both MPO and AAT were significantly elevated by recent breast milk intake. All three biomarkers were associated with pathogen presence, although the strength and direction varied by pathogen. The interpretation of biomarker concentrations is subject to the context of their collection. Herein, we identify that common factors (age, breast milk, and enteric infection) influence the concentration of these biomarkers. Within the context of low- and middle-income communities, we observe concentrations that indicate gut abnormalities, but more appropriate reference standards are needed.
McCormick, Benjamin J. J.; Lee, Gwenyth O.; Seidman, Jessica C.; Haque, Rashidul; Mondal, Dinesh; Quetz, Josiane; Lima, Aldo A. M.; Babji, Sudhir; Kang, Gagandeep; Shrestha, Sanjaya K.; Mason, Carl J.; Qureshi, Shahida; Bhutta, Zulfiqar A.; Olortegui, Maribel Paredes; Yori, Pablo Peñataro; Samie, Amidou; Bessong, Pascal; Amour, Caroline; Mduma, Estomih; Patil, Crystal L.; Guerrant, Richard L.; Lang, Dennis R.; Gottlieb, Michael; Caulfield, Laura E.; Kosek, Margaret N.
2017-01-01
Growth and development shortfalls that are disproportionately prevalent in children living in poor environmental conditions are postulated to result, at least in part, from abnormal gut function. Using data from The Etiology, Risk Factors, and Interactions of Enteric Infections and Malnutrition and the Consequences for Child Health and Development (MAL-ED) longitudinal cohort study, we examine biomarkers of gut inflammation and permeability in relation to environmental exposures and feeding practices. Trends in the concentrations of three biomarkers, myeloperoxidase (MPO), neopterin (NEO), and α-1-antitrypsin (AAT), are described from fecal samples collected during the first 2 years of each child's life. A total of 22,846 stool samples were processed during the longitudinal sampling of 2,076 children 0–24 months of age. Linear mixed models were constructed to examine the relationship between biomarker concentrations and recent food intake, symptoms of illness, concurrent enteropathogen infection, and socioeconomic status. Average concentrations of MPO, NEO, and AAT were considerably higher than published references for healthy adults. The concentration of each biomarker tended to decrease over the first 2 years of life and was highly variable between samples from each individual child. Both MPO and AAT were significantly elevated by recent breast milk intake. All three biomarkers were associated with pathogen presence, although the strength and direction varied by pathogen. The interpretation of biomarker concentrations is subject to the context of their collection. Herein, we identify that common factors (age, breast milk, and enteric infection) influence the concentration of these biomarkers. Within the context of low- and middle-income communities, we observe concentrations that indicate gut abnormalities, but more appropriate reference standards are needed. PMID:27994110
From dynamics to structure and function of model biomolecular systems
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 method
Green’s function molecular dynamics meets discrete dislocation plasticity
Venugopalan, Syam P.; Müser, Martin H.; Nicola, Lucia
2017-09-01
Metals deform plastically at the asperity level when brought in contact with a counter body even when the nominal contact pressure is small. Modeling the plasticity of solids with rough surfaces is challenging due to the multi-scale nature of surface roughness and the length-scale dependence of plasticity. While discrete-dislocation plasticity (DDP) simulations capture size-dependent plasticity by keeping track of the motion of individual dislocations, only simple two-dimensional surface geometries have so far been studied with DDP. The main computational bottleneck in contact problems modeled by DDP is the calculation of the dislocation image fields. We address this issue by combining two-dimensional DDP with Green’s function molecular dynamics. The resulting method allows for an efficient boundary-value-method based treatment of elasticity in the presence of dislocations. We demonstrate that our method captures plasticity quantitatively from single to many dislocations and that it scales more favorably with system size than conventional methods. We also derive the relevant Green’s functions for elastic slabs of finite width allowing arbitrary boundary conditions on top and bottom surface to be simulated.
Papaleo, Elena
2015-01-01
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.
A Frame Work for Frequent Pattern Mining Using Dynamic Function
Directory of Open Access Journals (Sweden)
Sunil Joshi
2011-05-01
Full Text Available Discovering frequent objects (item sets, sequential patterns is one of the most vital fields in data mining. It is well understood that it require running time and memory for defining candidates and this is the motivation for developing large number of algorithm. Frequent patterns mining is the paying attention research issue in association rules analysis. Apriori algorithm is a standard algorithm of association rules mining. Plenty of algorithms for mining association rules and their mutations are projected on the foundation of Apriori Algorithm. Most of the earlier studies adopted Apriori-like algorithms which are based on generate-and-test candidates theme and improving algorithm approach and formation but no one give attention to the structure of database. Several modifications on apriori algorithms are focused on algorithm Strategy but no one-algorithm emphasis on least transaction and more attribute representation of database. We presented a new research trend on frequent pattern mining in which generate Transaction pair to lighten current methods from the traditional blockage, providing scalability to massive data sets and improving response time. In order to mine patterns in database with more columns than rows, we proposed a complete framework for the frequent pattern mining. A simple approach is if we generate pair of transaction instead of item id where attributes are much larger then transaction so result is very fast. Newly, different works anticipated a new way to mine patterns in transposed databases where there is a database with thousands of attributes but merely tens of stuff. We suggest a novel dynamic algorithm for frequent pattern mining in which generate transaction pair and for generating frequent pattern we find out by longest common subsequence using dynamic function. Our solutions give result more rapidly. A quantitative investigation of these tradeoffs is conducted through a wide investigational study on artificial and
Dynamics of homegarden structure and function in Kerala, India
Peyre, A.; Guidal, A.; Wiersum, K.F.; Bongers, F.J.J.M.
2006-01-01
Homegardens in Kerala have long been important multi-purpose agroforestry systems that combine ecological and socioeconomical sustainability. However, traditional homegardens are subject to different conversion processes linked to socioeconomic changes. These dynamics were studied in a survey of 30
Dynamical model for biological functions of DNA molecules
Institute of Scientific and Technical Information of China (English)
PANGXiao-fengI; YANGYao
2004-01-01
We proposed a dynamic model of DNA to study its nonlinear excitation and duplication and transcription in the basis of molecular structure and changes of conformation of DNA under influence of bioenergy.
Directory of Open Access Journals (Sweden)
Yongkun Li
2011-01-01
Full Text Available Firstly, we propose a concept of uniformly almost periodic functions on almost periodic time scales and investigate some basic properties of them. When time scale T=ℝ or ℤ, our definition of the uniformly almost periodic functions is equivalent to the classical definitions of uniformly almost periodic functions and the uniformly almost periodic sequences, respectively. Then, based on these, we study the existence and uniqueness of almost periodic solutions and derive some fundamental conditions of admitting an exponential dichotomy to linear dynamic equations. Finally, as an application of our results, we study the existence of almost periodic solutions for an almost periodic nonlinear dynamic equations on time scales.
Quantum Dynamics in Classical Time Evolution of Correlation Functions
Wetterich, C
1997-01-01
The time-dependence of correlation functions under the influence of cla= ssical equations of motion is described by an exact evolution equation. For conservative systems thermodynamic equilibrium is a fixed point of these equations. We show that this fixed point is not universally stable, since infinitely many conserved correlation functions obstruct the approach to equilibrium. Equilibrium can therefore be reached at most for suitably av= eraged quantities or for subsystems, similar to quantum statistics. The classica= l time evolution of correlation functions shows many dynamical features of quant= um mechanics.
Comparison Criteria for Nonlinear Functional Dynamic Equations of Higher Order
Directory of Open Access Journals (Sweden)
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≔uβsgnu, 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.
DEFF Research Database (Denmark)
Papaleo, Elena
2015-01-01
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 pos......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...... 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....
Modeling dynamic functional information flows on large-scale brain networks.
Lv, Peili; Guo, Lei; Hu, Xintao; Li, Xiang; Jin, Changfeng; Han, Junwei; Li, Lingjiang; Liu, Tianming
2013-01-01
Growing evidence from the functional neuroimaging field suggests that human brain functions are realized via dynamic functional interactions on large-scale structural networks. Even in resting state, functional brain networks exhibit remarkable temporal dynamics. However, it has been rarely explored to computationally model such dynamic functional information flows on large-scale brain networks. In this paper, we present a novel computational framework to explore this problem using multimodal resting state fMRI (R-fMRI) and diffusion tensor imaging (DTI) data. Basically, recent literature reports including our own studies have demonstrated that the resting state brain networks dynamically undergo a set of distinct brain states. Within each quasi-stable state, functional information flows from one set of structural brain nodes to other sets of nodes, which is analogous to the message package routing on the Internet from the source node to the destination. Therefore, based on the large-scale structural brain networks constructed from DTI data, we employ a dynamic programming strategy to infer functional information transition routines on structural networks, based on which hub routers that most frequently participate in these routines are identified. It is interesting that a majority of those hub routers are located within the default mode network (DMN), revealing a possible mechanism of the critical functional hub roles played by the DMN in resting state. Also, application of this framework on a post trauma stress disorder (PTSD) dataset demonstrated interesting difference in hub router distributions between PTSD patients and healthy controls.
Students' Conceptions of Function Transformation in a Dynamic Mathematical Environment
Daher, Wajeeh; Anabousy, Ahlam
2015-01-01
The study of function transformations helps students understand the function concept which is a basic and main concept in mathematics, but this study is problematic to school students as well as college students, especially when transformations are performed on non-basic functions. The current research tried to facilitate grade 9 students'…
Dynamic Regulation and Function of Histone Monoubiquitination in Plants
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Jing eFeng
2014-03-01
Full Text Available Polyubiquitin chain deposition on a target protein frequently leads to proteasome-mediated degradation whereas monoubiquitination modifies target protein property and function independent of proteolysis. Histone monoubiquitination occurs in chromatin and is in nowadays recognized as one critical type of epigenetic marks in eukaryotes. While H2A monoubiquitination (H2Aub1 is generally associated with transcription repression mediated by the Polycomb pathway, H2Bub1 is involved in transcription activation. H2Aub1 and H2Bub1 levels are dynamically regulated via deposition and removal by specific enzymes. We review knows and unknowns of dynamic regulation of H2Aub1 and H2Bub1 deposition and removal in plants and highlight the underlying crucial functions in gene transcription, cell proliferation/differentiation, and plant growth and development. We also discuss crosstalks existing between H2Aub1 or H2Bub1 and different histone methylations for an ample mechanistic understanding.
DEFF Research Database (Denmark)
Somavarapu, Arun Kumar; Kepp, Kasper Planeta
2016-01-01
molecular dynamics in an explicit membrane with particular account of the as yet unexplored loop dynamics. We find that mature PSEN1 contains multiple distinct conformational states whereas non-mature PSEN1 is a typical one-state protein. We confirm a previously suggested gating mechanism, and find......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...... that the 106-131 loop acts as a "hinge" for the TM2 and TM6 "doors". More importantly, we identify an unplugging mechanism of the Exon 9 loop associated only with mature PSEN1. Proper opening of both the "gate" and "plug" in the membrane produces channel-like morphologies and access to the catalytic aspartates...
Molecular dynamics studies of entangled polymer chains
Bulacu, Monica Iulia
2008-01-01
The thesis presents three molecular dynamics studies of polymeric ensembles in which the chain entanglement plays the major role in the internal dynamics of the system. A coarse-grained model is used for representing the polymer chains as strings of beads connected by finite-extensible springs. In a
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.
The 3He spectral function in light-front dynamics
Rinaldi, Matteo; Kaptari, Leonid; Pace, Emanuele; Salmè, Giovanni; Scopetta, Sergio
2016-01-01
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 Poincar\\'e covariant framework within the light-front dynamics is outlined.
Energy Technology Data Exchange (ETDEWEB)
Saito, Kazuhiro; Hashimoto, Tsuyoshi; Araki, Yoichi; Akata, Soichi; Tokuuye, Koichi [Tokyo Medical University, Department of Radiology, Tokyo (Japan); Ledsam, Joseph; Sourbron, Steven [University of Leeds, Division of Medical Physics, Leeds (United Kingdom)
2014-01-15
To investigate if tracer kinetic modelling of low temporal resolution dynamic contrast-enhanced (DCE) MRI with Gd-EOB-DTPA could replace technetium-99 m galactosyl human serum albumin (GSA) single positron emission computed tomography (SPECT) and indocyanine green (ICG) retention for the measurement of liver functional reserve. Twenty eight patients awaiting liver resection for various cancers were included in this retrospective study that was approved by the institutional review board. The Gd-EOB-DTPA MRI sequence acquired five images: unenhanced, double arterial phase, portal phase, and 4 min after injection. Intracellular contrast uptake rate (UR) and extracellular volume (Ve) were calculated from DCE-MRI, along with the ratio of GSA radioactivity of liver to heart-plus-liver and per cent of cumulative uptake from 15-16 min (LHL15 and LU15, respectively) from GSA-scintigraphy. ICG retention at 15 min, Child-Pugh cirrhosis score (CPS) and postoperative Inuyama fibrosis criteria were also recorded. Statistical analysis was with Spearman rank correlation analysis. Comparing MRI parameters with the reference methods, significant correlations were obtained for UR and LHL15, LU15, ICG15 (all 0.4-0.6, P < 0.05); UR and CPS (-0.64, P < 0.001); Ve and Inuyama (0.44, P < 0.05). Measures of liver function obtained by routine Gd-EOB-DTPA DCE-MRI with tracer kinetic modelling may provide a suitable method for the evaluation of liver functional reserve. (orig.)
Preliminary report: Dynamic stereopsis in patients with impaired binocular function.
Mollenhauer, K A; Haase, W
2000-12-01
In this study, 46 strabismic patients aged between 9 and 58 years were tested for dynamic stereopsis in the peripheral visual field with up to 20 degrees eccentricity. Squint angles ranged from +30 to -36 degrees. The effect of surgical realignment of the visual axes on dynamic stereopsis was tested before and after surgery in 40 of these patients. Of the 46 patients, 23 had esotropia and 23 exotropia. A test device was used which presented two projected squares in polarized light (each square being perceived monocularly through a polarization filter) in horizontal motion, thus creating a three-dimensional impression. Patients were tested qualitatively for dynamically stereoactive fields of vision and quantitatively for the threshold value needed to create a three-dimensional impression. We found residual dynamic stereopsis in 30% of patients who had no central static stereopsis. 56% of the patients improved after surgery, either through a significant (p traffic and sports medicine, regardless of the effect on classical tests.
Dynamic density functional theory of protein adsorption on polymer-coated nanoparticles
Angioletti-Uberti, Stefano; Dzubiella, Joachim
2014-01-01
We present a theoretical model for the description of the adsorption kinetics of globular proteins onto charged core-shell microgel particles based on Dynamic Density Functional Theory (DDFT). This model builds on a previous description of protein adsorption thermodynamics [Yigit \\textit{et al}, Langmuir 28 (2012)], shown to well interpret the available calorimetric experimental data of binding isotherms. In practice, a spatially-dependent free-energy functional including the same physical interactions is built, and used to study the kinetics via a generalised diffusion equation. To test this model, we apply it to the case study of Lysozyme adsorption on PNIPAM coated nanoparticles, and show that the dynamics obtained within DDFT is consistent with that extrapolated from experiments. We also perform a systematic study of the effect of various parameters in our model, and investigate the loading dynamics as a function of proteins' valence and hydrophobic adsorption energy, as well as their concentration and th...
Stratum corneum dynamic function measurements after moisturizer or irritant application.
Treffel, P; Gabard, B
1995-01-01
Two simple tests were conducted which allowed the quantification of parameters that characterize the stratum corneum (SC) dynamic functions in vivo under physiological conditions after moisturizer applications for 1 h and after irritation with different concentrations of sodium lauryl sulphate (SLS; 0.5-4%) applied under occlusion for 15 min or 24 h. Both tests, the sorption-desorption test (SDT) and the moisture accumulation test (MAT), were performed with a Nova Dermal Phase Meter 9003. The following parameters were quantified: prehydration state (SDT, MAT), hygroscopicity, water-holding capacity (SDT), water accumulation velocity and water accumulation (MAT). These procedures allowed the demonstration of the water-holding effect of urea contained in moisturizers. Differences between the long and the short application time of SLS were characterized by differences in SC dynamic functions while the hydration state was not changed. An effect on transepidermal water loss (TEWL) was noted only after the long application time, although the MAT clearly showed dynamic parameters to be changed after 15 min of treatment. These tests were simple in practice and allowed the demonstration of functional modifications of the SC while other parameters remained unchanged. They gave insight into possible action mechanisms of urea and SLS in the SC.
Dynamic reorganization of brain functional networks during cognition.
Bola, Michał; Sabel, Bernhard A
2015-07-01
How does cognition emerge from neural dynamics? The dominant hypothesis states that interactions among distributed brain regions through phase synchronization give basis for cognitive processing. Such phase-synchronized networks are transient and dynamic, established on the timescale of milliseconds in order to perform specific cognitive operations. But unlike resting-state networks, the complex organization of transient cognitive networks is typically not characterized within the graph theory framework. Thus, it is not known whether cognitive processing merely changes the strength of functional connections or, conversely, requires qualitatively new topological arrangements of functional networks. To address this question, we recorded high-density EEG while subjects performed a visual discrimination task. We conducted an event-related network analysis (ERNA) where source-space weighted functional networks were characterized with graph measures. ERNA revealed rapid, transient, and frequency-specific reorganization of the network's topology during cognition. Specifically, cognitive networks were characterized by strong clustering, low modularity, and strong interactions between hub-nodes. Our findings suggest that dense and clustered connectivity between the hub nodes belonging to different modules is the "network fingerprint" of cognition. Such reorganization patterns might facilitate global integration of information and provide a substrate for a "global workspace" necessary for cognition and consciousness to occur. Thus, characterizing topology of the event-related networks opens new vistas to interpret cognitive dynamics in the broader conceptual framework of graph theory. Copyright © 2015 Elsevier Inc. All rights reserved.
Dynamics of learning near singularities in radial basis function networks.
Wei, Haikun; Amari, Shun-Ichi
2008-09-01
The radial basis function (RBF) networks are one of the most widely used models for function approximation in the regression problem. In the learning paradigm, the best approximation is recursively or iteratively searched for based on observed data (teacher signals). One encounters difficulties in such a process when two component basis functions become identical, or when the magnitude of one component becomes null. In this case, the number of the components reduces by one, and then the reduced component recovers as the learning process proceeds further, provided such a component is necessary for the best approximation. Strange behaviors, especially the plateau phenomena, have been observed in dynamics of learning when such reduction occurs. There exist singularities in the space of parameters, and the above reduction takes place at the singular regions. This paper focuses on a detailed analysis of the dynamical behaviors of learning near the overlap and elimination singularities in RBF networks, based on the averaged learning equation that is applicable to both on-line and batch mode learning. We analyze the stability on the overlap singularity by solving the eigenvalues of the Hessian explicitly. Based on the stability analysis, we plot the analytical dynamic vector fields near the singularity, which are then compared to those real trajectories obtained by a numeric method. We also confirm the existence of the plateaus in both batch and on-line learning by simulation.
Operators versus functions: from quantum dynamical semigroups to tomographic semigroups
Aniello, Paolo
2013-11-01
Quantum mechanics can be formulated in terms of phase-space functions, according to Wigner's approach. A generalization of this approach consists in replacing the density operators of the standard formulation with suitable functions, the so-called generalized Wigner functions or (group-covariant) tomograms, obtained by means of group-theoretical methods. A typical problem arising in this context is to express the evolution of a quantum system in terms of tomograms. In the case of a (suitable) open quantum system, the dynamics can be described by means of a quantum dynamical semigroup 'in disguise', namely, by a semigroup of operators acting on tomograms rather than on density operators. We focus on a special class of quantum dynamical semigroups, the twirling semigroups, that have interesting applications, e.g., in quantum information science. The 'disguised counterparts' of the twirling semigroups, i.e., the corresponding semigroups acting on tomograms, form a class of semigroups of operators that we call tomographic semigroups. We show that the twirling semigroups and the tomographic semigroups can be encompassed in a unique theoretical framework, a class of semigroups of operators including also the probability semigroups of classical probability theory, so achieving a deeper insight into both the mathematical and the physical aspects of the problem.
Fallah, Zohreh; Jamali, Yousef; Rafii-Tabar, Hashem
2016-01-01
Dopamine as a neurotransmitter plays a critical role in the functioning of the central nervous system. The structure of D3 receptor as a member of class A G-protein coupled receptors (GPCRs) has been reported. We used MD simulation to investigate the effect of an oscillating electric field, with frequencies in the range 0.6–800 GHz applied along the z-direction, on the dopamine-D3R complex. The simulations showed that at some frequencies, the application of an external oscillating electric field along the z-direction has a considerable effect on the dopamine-D3R. However, there is no enough evidence for prediction of changes in specific frequency, implying that there is no order in changes. Computing the correlation coefficient parameter showed that increasing the field frequency can weaken the interaction between dopamine and D3R and may decrease the Arg128{3.50}-Glu324{6.30} distance. Because of high stability of α helices along the z-direction, applying an oscillating electric field in this direction with an amplitude 10-time higher did not have a considerable effect. However, applying the oscillating field at the frequency of 0.6 GHz along other directions, such as X-Y and Y-Z planes, could change the energy between the dopamine and the D3R, and the number of internal hydrogen bonds of the protein. This can be due to the effect of the direction of the electric field vis-à-vis the ligands orientation and the interaction of the oscillating electric field with the dipole moment of the protein. PMID:27832207
Temperature dependent dynamics of DegP-trimer: A molecular dynamics study.
Rai, Nivedita; Ramaswamy, Amutha
2015-01-01
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.
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.
Institute of Scientific and Technical Information of China (English)
Wenjuan Qiu; Bin Yan; Hongjian He; Li Tong; Jianxin Li
2012-01-01
The present study conducted a multi-scale dynamic functional connectivity analysis to evaluate dynamic behavior of acupuncture at Taichong (LR3) and sham acupoints surrounding Taichong. Results showed differences in wavelet transform coherence characteristic curves in the declive, precuneus, postcentral gyrus, supramarginal gyrus, and occipital lobe between acupuncture at Taichong and acupuncture at sham acupoints. The differences in characteristic curves revealed that the specific effect of acupuncture existed during the post-acupuncture rest state and lasted for 5 minutes.
Dynamics of Microbial Functional Groups in Rhizosphere of Spring Barley
Directory of Open Access Journals (Sweden)
Vlad Stoian
2016-11-01
Full Text Available Plant rhizosphere is the portion of soil which is in direct contact with the plant roots. From the microbiological point of view, this area is characterized by strong dynamic of functional groups with high specificity towards the substrate available. Spring barley is a crop with high requirements to the composition of the microflora in the rhizosphere, disturbances produced by agronomic inputs affecting the stability of rhizospheric contact interfaces and ultimately the plant growth. Analysis of changes within the microbial community was carried out with the purpose of defining the disruptive impact of mineral inputs and potential of zeolite to reduce these disruptions. Microbial functional groups were analyzed on the basis of the CO2 export under the specific conditions of soil inoculation on specific substrates over a time period of incubation. Microresp detection plates allow evaluation of a large number of samples under identical conditions of inoculation and the establishment of dynamics of the entire microbial community. The dynamics of the entire microbial communities (basal respiration is stimulated to increase in case of unilateral application of zeolite and zeolite as a buffer for urea fertilization. General growth trend of microbial communities follows proportional the associated application of zeolite with urea, the most powerful non-symbiotic nitrogen fixation processes being stimulated by this combination of fertilizers. Simultaneously, an increase in the dynamics of denitrifiers was observed, also the decomposition of lignin and cellulose and biological crust formation due to the proliferation of cyanobacteria. Rhizosphere of barley plants is characterized by the presence of actinomycetes as dominant in functional microbial community of all experimental variants analyzed with a high capacity for biological degradation and raised mineralization of organic matter.
Spontaneous Functional Network Dynamics and Associated Structural Substrates in the Human Brain
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Xuhong eLiao
2015-09-01
Full Text Available Recent imaging connectomics studies have demonstrated that the spontaneous human brain functional networks derived from resting-state functional MRI (R-fMRI include many non-trivial topological properties, such as highly efficient small-world architecture and densely connected hub regions. However, very little is known about dynamic functional connectivity (D-FC patterns of spontaneous human brain networks during rest and about how these spontaneous brain dynamics are constrained by the underlying structural connectivity. Here, we combined sub-second multiband R-fMRI data with graph-theoretical approaches to comprehensively investigate the dynamic characteristics of the topological organization of human whole-brain functional networks, and then employed diffusion imaging data in the same participants to further explore the associated structural substrates. At the connection level, we found that human whole-brain D-FC patterns spontaneously fluctuated over time, while homotopic D-FC exhibited high connectivity strength and low temporal variability. At the network level, dynamic functional networks exhibited time-varying but evident small-world and assortativity architecture, with several regions (e.g., insula, sensorimotor cortex and medial prefrontal cortex emerging as functionally persistent hubs (i.e., highly connected regions while possessing large temporal variability in their degree centrality. Finally, the temporal characteristics (i.e., strength and variability of the connectional and nodal properties of the dynamic brain networks were significantly associated with their structural counterparts. Collectively, we demonstrate the economical, efficient and flexible characteristics of dynamic functional coordination in large-scale human brain networks during rest, and highlight their relationship with underlying structural connectivity, which deepens our understandings of spontaneous brain network dynamics in humans.
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…
The Panel Study of Income Dynamics (PSID)
U.S. Department of Health & Human Services — The Panel Study of Income Dynamics (PSID) began in 1968 with a nationally representative sample of over 18,000 individuals living in 5,000 families in the United...
Brownian dynamics without Green's functions
Energy Technology Data Exchange (ETDEWEB)
Delong, Steven; Donev, Aleksandar, E-mail: donev@courant.nyu.edu [Courant Institute of Mathematical Sciences, New York University, New York, New York 10012 (United States); Usabiaga, Florencio Balboa; Delgado-Buscalioni, Rafael [Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Univeridad Autónoma de Madrid, Madrid 28049 (Spain); Griffith, Boyce E. [Courant Institute of Mathematical Sciences, New York University, New York, New York 10012 (United States); Leon H. Charney Division of Cardiology, Department of Medicine, New York University School of Medicine, New York, New York 10016 (United States)
2014-04-07
We develop a Fluctuating Immersed Boundary (FIB) method for performing Brownian dynamics simulations of confined particle suspensions. Unlike traditional methods which employ analytical Green's functions for Stokes flow in the confined geometry, the FIB method uses a fluctuating finite-volume Stokes solver to generate the action of the response functions “on the fly.” Importantly, we demonstrate that both the deterministic terms necessary to capture the hydrodynamic interactions among the suspended particles, as well as the stochastic terms necessary to generate the hydrodynamically correlated Brownian motion, can be generated by solving the steady Stokes equations numerically only once per time step. This is accomplished by including a stochastic contribution to the stress tensor in the fluid equations consistent with fluctuating hydrodynamics. We develop novel temporal integrators that account for the multiplicative nature of the noise in the equations of Brownian dynamics and the strong dependence of the mobility on the configuration for confined systems. Notably, we propose a random finite difference approach to approximating the stochastic drift proportional to the divergence of the configuration-dependent mobility matrix. Through comparisons with analytical and existing computational results, we numerically demonstrate the ability of the FIB method to accurately capture both the static (equilibrium) and dynamic properties of interacting particles in flow.
Multiscale functions, scale dynamics, and applications to partial differential equations
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.
Dynamic network participation of functional connectivity hubs assessed by resting-state fMRI
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Alexander eSchaefer
2014-05-01
Full Text Available Network studies of large-scale brain connectivity have demonstrated that highly connected areas, or ‘hubs’, are a key feature of human functional and structural brain organization. We use resting-state functional MRI data and connectivity clustering to identify multi network hubs and show that while hubs can belong to multiple networks their degree of integration into these different networks varies dynamically over time. In addition, we found that these network dynamics were inversely related to positive self-generated thoughts reported by individuals and were further decreased with older age. Moreover, the left caudate varied its degree of participation between a default mode subnetwork and a limbic network. This variation was predictive of individual differences in the reports of past-related thoughts. These results support an association between ongoing thought processes and network dynamics and offer a new approach to investigate the brain dynamics underlying mental experience.
Ab initio molecular dynamics study of liquid methanol
Handgraaf, J W; Meijer, E J; Handgraaf, Jan-Willem; Erp, Titus S. van; Meijer, Evert Jan
2003-01-01
We present a density-functional theory based molecular-dynamics study of the structural, dynamical, and electronic properties of liquid methanol under ambient conditions. The calculated radial distribution functions involving the oxygen and hydroxyl hydrogen show a pronounced hydrogen bonding and compare well with recent neutron diffraction data, except for an underestimate of the oxygen-oxygen correlation. We observe that, in line with infrared spectroscopic data, the hydroxyl stretching mode is significantly red-shifted in the liquid. A substantial enhancement of the dipole moment is accompanied by significant fluctuations due to thermal motion. Our results provide valuable data for improvement of empirical potentials.
Dynamic functional connectivity and brain metastability during altered states of consciousness.
Cavanna, Federico; Vilas, Martina G; Palmucci, Matías; Tagliazucchi, Enzo
2017-10-03
The scientific study of human consciousness has greatly benefited from the development of non-invasive brain imaging methods. The quest to identify the neural correlates of consciousness combined psychophysical experimentation with neuroimaging tools such as functional magnetic resonance imaging (fMRI) to map the changes in neural activity associated with conscious vs. unconscious percepts. Different neuroimaging methods have also been applied to characterize spontaneous brain activity fluctuations during altered states of consciousness, and to develop quantitative metrics for the level of consciousness. Most of these studies, however, have not explored the dynamic nature of the whole-brain imaging data provided by fMRI. A series of empirical and computational studies strongly suggests that the temporal fluctuations observed in this data present a non-trivial structure, and that this structure is compatible with the exploration of a discrete repertoire of states. In this review we focus on how dynamic neuroimaging can be used to address theoretical accounts of consciousness based on the hypothesis of a dynamic core, i.e. a constantly evolving and transiently stable set of coordinated neurons that constitute an integrated and differentiated physical substrate for each conscious experience. We review work exploring the possibility that metastability in brain dynamics leads to a repertoire of dynamic core states, and discuss how it might be modified during altered states of consciousness. This discussion prompts us to review neuroimaging studies aimed to map the dynamic exploration of the repertoire of states as a function of consciousness. Complementary studies of the dynamic core hypothesis using perturbative methods are also discussed. Finally, we propose that a link between metastability in brain dynamics and the level of consciousness could pave the way towards a mechanistic understanding of altered states of consciousness using tools from dynamical systems
Hash function construction using weighted complex dynamical networks
Institute of Scientific and Technical Information of China (English)
Song Yu-Rong; Jiang Guo-Ping
2013-01-01
A novel scheme to construct a hash function based on a weighted complex dynamical network (WCDN) generated from an original message is proposed in this paper.First,the original message is divided into blocks.Then,each block is divided into components,and the nodes and weighted edges are well defined from these components and their relations.Namely,the WCDN closely related to the original message is established.Furthermore,the node dynamics of the WCDN are chosen as a chaotic map.After chaotic iterations,quantization and exclusive-or operations,the fixed-length hash value is obtained.This scheme has the property that any tiny change in message can be diffused rapidly through the WCDN,leading to very different hash values.Analysis and simulation show that the scheme possesses good statistical properties,excellent confusion and diffusion,strong collision resistance and high efficiency.
Córdova-Sintjago, Tania; Villa, Nancy; Fang, Lijuan; Booth, Raymond G.
2014-02-01
The serotonin (5-hydroxytryptamine, 5-HT) 5-HT2 G protein-coupled receptor (GPCR) family consists of types 2A, 2B, and 2C that share ∼75% transmembrane (TM) sequence identity. Agonists for 5-HT2C receptors are under development for psychoses; whereas, at 5-HT2A receptors, antipsychotic effects are associated with antagonists - in fact, 5-HT2A agonists can cause hallucinations and 5-HT2B agonists cause cardiotoxicity. It is known that 5-HT2A TM6 residues W6.48, F6.51, and F6.52 impact ligand binding and function; however, ligand interactions with these residues at the 5-HT2C receptor have not been reported. To predict and validate molecular determinants for 5-HT2C-specific activation, results from receptor homology modelling, ligand docking, and molecular dynamics simulation studies were compared with experimental results for ligand binding and function at wild type and W6.48A, F6.51A, and F6.52A point-mutated 5-HT2C receptors.
Vijaykumar, Adithya; Wolde, Pieter Rein ten; Bolhuis, Peter G
2016-01-01
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 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. {\\bf 43}, 21: 214102 (2015)]. Here we extend this multiscale BD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm we discuss its performance. The rotational BD-GFRD multiscale method will open up the possibility for large scale simulations of e.g. protein signalling networks.
Dynamics of localized particles from density functional theory
Reinhardt, J.; Brader, J. M.
2012-01-01
A fundamental assumption of the dynamical density functional theory (DDFT) of colloidal systems is that a grand-canonical free-energy functional may be employed to generate the thermodynamic driving forces. Using one-dimensional hard rods as a model system, we analyze the validity of this key assumption and show that unphysical self-interactions of the tagged particle density fields, arising from coupling to a particle reservoir, are responsible for the excessively fast relaxation predicted by the theory. Moreover, our findings suggest that even employing a canonical functional would not lead to an improvement for many-particle systems, if only the total density is considered. We present several possible schemes to suppress these effects by incorporating tagged densities. When applied to confined systems, we demonstrate, using a simple example, that DDFT necessarily leads to delocalized tagged particle density distributions, which do not respect the fundamental geometrical constraints apparent in Brownian dynamics simulation data. The implication of these results for possible applications of DDFT to treat the glass transition are discussed.
Dynamic density functional theory with hydrodynamic interactions and fluctuations
Energy Technology Data Exchange (ETDEWEB)
Donev, Aleksandar, E-mail: donev@courant.nyu.edu; Vanden-Eijnden, Eric, E-mail: eve2@courant.nyu.edu [Courant Institute of Mathematical Sciences, New York University, New York, New York 10012 (United States)
2014-06-21
We derive a closed equation for the empirical concentration of colloidal particles in the presence of both hydrodynamic and direct interactions. The ensemble average of our functional Langevin equation reproduces known deterministic Dynamic Density Functional Theory (DDFT) [M. Rex and H. Löwen, “Dynamical density functional theory with hydrodynamic interactions and colloids in unstable traps,” Phys. Rev. Lett. 101(14), 148302 (2008)], and, at the same time, it also describes the microscopic fluctuations around the mean behavior. We suggest separating the ideal (non-interacting) contribution from additional corrections due to pairwise interactions. We find that, for an incompressible fluid and in the absence of direct interactions, the mean concentration follows Fick's law just as for uncorrelated walkers. At the same time, the nature of the stochastic terms in fluctuating DDFT is shown to be distinctly different for hydrodynamically-correlated and uncorrelated walkers. This leads to striking differences in the behavior of the fluctuations around Fick's law, even in the absence of pairwise interactions. We connect our own prior work [A. Donev, T. G. Fai, and E. Vanden-Eijnden, “A reversible mesoscopic model of diffusion in liquids: from giant fluctuations to Fick's law,” J. Stat. Mech.: Theory Exp. (2014) P04004] on fluctuating hydrodynamics of diffusion in liquids to the DDFT literature, and demonstrate that the fluid cannot easily be eliminated from consideration if one wants to describe the collective diffusion in colloidal suspensions.
Bacterial dynamics in steady-state biofilters: beyond functional stability.
Cabrol, Léa; Malhautier, Luc; Poly, Franck; Lepeuple, Anne-Sophie; Fanlo, Jean-Louis
2012-01-01
The spatial and temporal dynamics of microbial community structure and function were surveyed in duplicated woodchip-biofilters operated under constant conditions for 231 days. The contaminated gaseous stream for treatment was representative of composting emissions, included ammonia, dimethyl disulfide and a mixture of five oxygenated volatile organic compounds. The community structure and diversity were investigated by denaturing gradient gel electrophoresis on 16S rRNA gene fragments. During the first 42 days, microbial acclimatization revealed the influence of operating conditions and contaminant loading on the biofiltration community structure and diversity, as well as the limited impact of inoculum compared to the greater persistence of the endogenous woodchip community. During long-term operation, a high and stable removal efficiency was maintained despite a highly dynamic microbial community, suggesting the probable functional redundancy of the community. Most of the contaminant removal occurred in the first compartment, near the gas inlet, where the microbial diversity was the highest. The stratification of the microbial structures along the filter bed was statistically correlated to the longitudinal distribution of environmental conditions (selective pressure imposed by contaminant concentrations) and function (contaminant elimination capacity), highlighting the central role of the bacterial community. The reproducibility of microbial succession in replicates suggests that the community changes were presumably driven by a deterministic process.
Toe functions have little effect on dynamic balance ability in elderly people.
Yoshimoto, Yoshinobu; Oyama, Yukitsuna; Tanaka, Mamoru; Sakamoto, Asuka
2017-01-01
[Purpose] The purpose of this study was to examine the toe function of elderly people and the association with the dynamic balance ability for the developing effective fall-prevention measures. [Subjects and Methods] Seventy-eight participants in a community health service were included in this cross-sectional study. The Timed Up and Go Test and Four Square Step Test were used to test dynamic balance ability. The toe functions related to dynamic balance ability were toe flexion strength, presence or absence of restricted range of motion of the hallux, presence or absence of hallux pain, and hallux valgus angle. [Results] Factors related to the Timed Up and Go Test results were toe flexion strength, age, and presence or absence of hallux pain. Their standard partial regression coefficients were -0.400, 0.277, and -0.218, respectively. Factors related to the Four Square Step Test results were toe flexion strength and age. Their standard partial regression coefficients were -0.334 and 0.277, respectively. [Conclusion] Toe functions appear to have little impact on dynamic balance ability in elderly people who have mild toe dysfunction. Approaches that address not only the toes, but trunk functions, and other leg joints should be investigated for improving the dynamic balance ability.
Ab initio molecular dynamics study of Fe-containing smectites
Liu, X.; Meijer, E.J.; Lu, X.; Wang, R.
2010-01-01
In order to identify the influences imposed by Fe substitution, density functional theory-based Car-Parrinello molecular dynamics simulations were employed to study both oxidized and reduced Fe-bearing smectites. The following basic properties were investigated: local structures in the clay layer, h
Dynamic heart phantom with functional mitral and aortic valves
Vannelli, Claire; Moore, John; McLeod, Jonathan; Ceh, Dennis; Peters, Terry
2015-03-01
Cardiac valvular stenosis, prolapse and regurgitation are increasingly common conditions, particularly in an elderly population with limited potential for on-pump cardiac surgery. NeoChord©, MitraClipand numerous stent-based transcatheter aortic valve implantation (TAVI) devices provide an alternative to intrusive cardiac operations; performed while the heart is beating, these procedures require surgeons and cardiologists to learn new image-guidance based techniques. Developing these visual aids and protocols is a challenging task that benefits from sophisticated simulators. Existing models lack features needed to simulate off-pump valvular procedures: functional, dynamic valves, apical and vascular access, and user flexibility for different activation patterns such as variable heart rates and rapid pacing. We present a left ventricle phantom with these characteristics. The phantom can be used to simulate valvular repair and replacement procedures with magnetic tracking, augmented reality, fluoroscopy and ultrasound guidance. This tool serves as a platform to develop image-guidance and image processing techniques required for a range of minimally invasive cardiac interventions. The phantom mimics in vivo mitral and aortic valve motion, permitting realistic ultrasound images of these components to be acquired. It also has a physiological realistic left ventricular ejection fraction of 50%. Given its realistic imaging properties and non-biodegradable composition—silicone for tissue, water for blood—the system promises to reduce the number of animal trials required to develop image guidance applications for valvular repair and replacement. The phantom has been used in validation studies for both TAVI image-guidance techniques1, and image-based mitral valve tracking algorithms2.
Li, X P; Xia, Q; Qu, D; Wu, T C; Yang, D G; Hao, W D; Jiang, X; Li, X M
2014-11-04
Functional brain imaging has tremendous applications. The existing methods for functional brain imaging include functional Magnetic Resonant Imaging (fMRI), scalp electroencephalography (EEG), implanted EEG, magnetoencephalography (MEG) and Positron Emission Tomography (PET), which have been widely and successfully applied to various brain imaging studies. To develop a new method for functional brain imaging, here we show that the dielectric at a brain functional site has a dynamic nature, varying with local neuronal activation as the permittivity of the dielectric varies with the ion concentration of the extracellular fluid surrounding neurons in activation. Therefore, the neuronal activation can be sensed by a radiofrequency (RF) electromagnetic (EM) wave propagating through the site as the phase change of the EM wave varies with the permittivity. Such a dynamic nature of the dielectric at a brain functional site provides the basis for an RF EM wave approach to detecting and imaging neuronal activation at brain functional sites, leading to an RF EM wave approach to functional brain imaging.
Chen, Jinfan; Sit, Patrick H-L
2017-05-11
The catalytic hydrogen-producing processes of two prototypical cobaloxime catalysts, Co(dmgBF2)2 (dmgBF2 = difluoroboryl-dimethylglyoxime) and Co(dmgH)2 (dmgH = dimethylglyoxime), were studied by density functional theory (DFT) and Car-Parrinello molecular dynamics (CPMD) simulations in the explicit acetonitrile-water solvent. Our study demonstrates the key role of water molecules as shuttles to deliver protons to the cobalt active centers of these catalysts. However, the transfer of protons to the cobalt centers also competes with the diffusion of the proton away from the complex via the hydrogen bond network of water. Protons were found to react with the oxygen of the side group of Co(dmgH)2, while a similar reaction was not observed for Co(dmgBF2)2. This explains the experimentally observed relative instability of Co(dmgH)2 in the acidic medium. The rate-limiting step of the hydrogen-producing process was found to be the first proton transfer to the cobalt center for both cobaloxime complexes. Structural and electron population analysis was carried out to provide insight into the origin of the difference of the proton transfer free-energy barriers of these two cobalt complexes. Our study has contributed to the key microscopic understanding of the hydrogen-producing process by this class of catalysts.
Moments of meson distribution functions with dynamical twisted mass fermions
Baron, R; Carbonell, J; Jansen, K; Liu, Z; Pène, O; Urbach, C
2007-01-01
We present our preliminary results on the lowest moment of quark distribution functions of the pion using two flavor dynamical simulations with Wilson twisted mass fermions at maximal twist. The calculation is done in a range of pion masses from 300 to 500 MeV. A stochastic source method is used to reduce inversions in calculating propagators. Finite volume effects at the lowest quark mass are examined by using two different lattice volumes. Our results show that we achieve statistical errors of only a few percent. We plan to compute renormalization constants non-perturbatively and extend the calculation to two more lattice spacings and to the nucleons.
Nonlinear dynamics in the study of birdsong
Mindlin, Gabriel B.
2017-09-01
Birdsong, a rich and complex behavior, is a stellar model to understand a variety of biological problems, from motor control to learning. It also enables us to study how behavior emerges when a nervous system, a biomechanical device and the environment interact. In this review, I will show that many questions in the field can benefit from the approach of nonlinear dynamics, and how birdsong can inspire new directions for research in dynamics.
Dynamic study of milling low depth channels
Directory of Open Access Journals (Sweden)
Rosca Dorin Mircea
2017-01-01
Full Text Available This paper presents a study of dynamic aspects of the milling cutters used in particular case of low depth channels. A new calculation method was developed, taking into account the high variations of cutting forces during milling small depth channels with peripheral cutting tools. A new formula was established for the minimal value of channel depth that allows cutting process to be performed in conditions of dynamic stability.
Ab initio molecular dynamics study of collective dynamics in liquid Tl: Thermo-viscoelastic analysis
Bryk, Taras; Demchuk, Taras
2017-08-01
We studied collective dynamics of pure liquid metal Tl using a combination of ab initio molecular dynamics (AIMD) simulations and a thermoviscoelastic model applied to calculations of dynamic eigenmodes and dispersion of collective excitations in particular. We found that for liquid Tl at ambient pressure the transverse current spectral functions obtained directly in ab initio simulations for wave numbers larger than first pseudo-Brillouin-zone boundary contain two low-and high-frequency peaks that is an evidence of emergence of the unusually high-frequency transverse modes as it was observed before in liquid Li at very high pressures. The thermo-viscoelastic dynamic model shows perfect reproduction of the simulation-derived longitudinal current autocorrelation functions, and the acoustic eigenmodes are in nice agreement with the peaks of the longitudinal current spectral functions up to the first pseudo-Brillouin-zone boundary. The deviation of the dynamic eigenmodes from peak positions at higher wave numbers gives evidence of L-T coupling effects.
Cine CT technique for dynamic airway studies
Energy Technology Data Exchange (ETDEWEB)
Ell, S.R.; Jolles, H.; Keyes, W.D.; Galvin, J.R.
1985-07-01
The advent of cine CT scanning with its 50-msec data acquisition time promises a much wider range of dynamic CT studies. The authors describe a method for dynamic evaluation of the extrathoracic airway, which they believe has considerable potential application in nonfixed upper-airway disease, such as sleep apnea and stridor of unknown cause. Conventional CT is limited in such studies by long data acquisition time and can be used to study only prolonged maneuvers such as phonation. Fluoroscopy and digital subtraction studies are limited by relatively high radiation dose and inability to image all wall motions simultaneously.
Mining dynamic noteworthy functions in software execution sequences.
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.
Mining dynamic noteworthy functions in software execution sequences
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. PMID:28278276
Mindfulness and dynamic functional neural connectivity in children and adolescents.
Marusak, Hilary A; Elrahal, Farrah; Peters, Craig A; Kundu, Prantik; Lombardo, Michael V; Calhoun, Vince D; Goldberg, Elimelech K; Cohen, Cindy; Taub, Jeffrey W; Rabinak, Christine A
2017-09-05
Interventions that promote mindfulness consistently show salutary effects on cognition and emotional wellbeing in adults, and more recently, in children and adolescents. However, we lack understanding of the neurobiological mechanisms underlying mindfulness in youth that should allow for more judicious application of these interventions in clinical and educational settings. Using multi-echo multi-band fMRI, we examined dynamic (i.e., time-varying) and conventional static resting-state connectivity between core neurocognitive networks (i.e., salience/emotion, default mode, central executive) in 42 children and adolescents (ages 6-17). We found that trait mindfulness in youth relates to dynamic but not static resting-state connectivity. Specifically, more mindful youth transitioned more between brain states over the course of the scan, spent overall less time in a certain connectivity state, and showed a state-specific reduction in connectivity between salience/emotion and central executive networks. The number of state transitions mediated the link between higher mindfulness and lower anxiety, providing new insights into potential neural mechanisms underlying benefits of mindfulness on psychological health in youth. Our results provide new evidence that mindfulness in youth relates to functional neural dynamics and interactions between neurocognitive networks, over time. Copyright © 2017. Published by Elsevier B.V.
Functional clustering algorithm for the analysis of dynamic network data
Feldt, S.; Waddell, J.; Hetrick, V. L.; Berke, J. D.; Żochowski, M.
2009-05-01
We formulate a technique for the detection of functional clusters in discrete event data. The advantage of this algorithm is that no prior knowledge of the number of functional groups is needed, as our procedure progressively combines data traces and derives the optimal clustering cutoff in a simple and intuitive manner through the use of surrogate data sets. In order to demonstrate the power of this algorithm to detect changes in network dynamics and connectivity, we apply it to both simulated neural spike train data and real neural data obtained from the mouse hippocampus during exploration and slow-wave sleep. Using the simulated data, we show that our algorithm performs better than existing methods. In the experimental data, we observe state-dependent clustering patterns consistent with known neurophysiological processes involved in memory consolidation.
Ephemeral penalty functions for contact-impact dynamics
De La Fuente, Horacio M.; Felippa, Carlos A.
1991-01-01
The use of penalty functions to treat a class of structural contact-impact problems is investigated, with emphasis on ones in which the impact phenomena are primarily nondestructive in nature and in which only the gross characterization of the response is required. The dynamic equations of motion are integrated by the difference method. The penalty is represented as an ephemeral fictitious nonlinear spring that is inserted on anticipation of contact. The magnitude and variation of the penalty force is determined through energy balancing considerations. The 'bell shape' of the penalty force function for positive gap was found to be satisfactory, as it depends on only two parameters that can be directly assigned the physical meaning of force and distance. The determination of force law parameters by energy balance worked well. The incorporation of restitution coefficients by the area balancing method yielded excellent results, and no substantial modifications are anticipated. Extensional penalty springs are obviously sufficient for the simple examples treated.
Diffusion of innovations dynamics, biological growth and catenary function
Guseo, Renato
2016-12-01
The catenary function has a well-known role in determining the shape of chains and cables supported at their ends under the force of gravity. This enables design using a specific static equilibrium over space. Its reflected version, the catenary arch, allows the construction of bridges and arches exploiting the dual equilibrium property under uniform compression. In this paper, we emphasize a further connection with well-known aggregate biological growth models over time and the related diffusion of innovation key paradigms (e.g., logistic and Bass distributions over time) that determine self-sustaining evolutionary growth dynamics in naturalistic and socio-economic contexts. Moreover, we prove that the 'local entropy function', related to a logistic distribution, is a catenary and vice versa. This special invariance may be explained, at a deeper level, through the Verlinde's conjecture on the origin of gravity as an effect of the entropic force.
Scale effects in the dynamic transfer functions for cavitating inducers
Brennen, C. E.; Meissner, C.; Lo, E. Y.; Hoffman, G. S.
1980-01-01
Dynamic transfer functions for two cavitating inducers of the same geometry but different size are presented, compared and discussed. The transfer functions for each inducer indicate similar trends as the cavitation number is decreased; only minor changes are noted with changes in the flow coefficient, the uniformity of the inlet flow or the temperature of the water (21-74 C). The non-dimensional results for the two sizes are compared with themselves and with theoretical calculations based on the bubbly flow model. All three sets of results compare well and lend further credence to the theoretical model. The best values of the two parameters in the model are evaluated and recommended for use in applications.
Westinskow, Dwayne (Inventor); Agutter, James (Inventor); Syroid, Noah (Inventor); Strayer, David (Inventor); Albert, Robert (Inventor); Wachter, S. Blake (Inventor); Drews, Frank (Inventor)
2010-01-01
A method, system, apparatus and device for the monitoring, diagnosis and evaluation of the state of a dynamic pulmonary system is disclosed. This method and system provides the processing means for receiving sensed and/or simulated data, converting such data into a displayable object format and displaying such objects in a manner such that the interrelationships between the respective variables can be correlated and identified by a user. This invention provides for the rapid cognitive grasp of the overall state of a pulmonary critical function with respect to a dynamic system.
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 relevan...
Trinh, Hung-Cuong; Kwon, Yung-Keun
2015-11-01
Efficiently identifying functionally important genes in order to understand the minimal requirements of normal cellular development is challenging. To this end, a variety of structural measures have been proposed and their effectiveness has been investigated in recent literature; however, few studies have shown the effectiveness of dynamics-based measures. This led us to investigate a dynamic measure to identify functionally important genes, and the effectiveness of which was verified through application on two large-scale human signaling networks. We specifically consider Boolean sensitivity-based dynamics against an update-rule perturbation (BSU) as a dynamic measure. Through investigations on two large-scale human signaling networks, we found that genes with relatively high BSU values show slower evolutionary rate and higher proportions of essential genes and drug targets than other genes. Gene-ontology analysis showed clear differences between the former and latter groups of genes. Furthermore, we compare the identification accuracies of essential genes and drug targets via BSU and five well-known structural measures. Although BSU did not always show the best performance, it effectively identified the putative set of genes, which is significantly different from the results obtained via the structural measures. Most interestingly, BSU showed the highest synergy effect in identifying the functionally important genes in conjunction with other measures. Our results imply that Boolean-sensitive dynamics can be used as a measure to effectively identify functionally important genes in signaling networks.
Fluorescence spectroscopic studies of DNA dynamics
Energy Technology Data Exchange (ETDEWEB)
Scalettar, B.A.
1987-04-01
Random solvent induced motions of DNA are manifest as nanosecond torsional oscillations of the helix backbone, nanosecond through millisecond bending deformations and overall rotational and translational diffusion of the polymer. Fluorescence spectroscopy is used to study this spectrum of DNA motions while ethidium monoazide was covalently bounded. The steady state fluorescence depolarization data indicate that the covalent monoazide/DNA complex exhibits internal motions characterized by an average angular amplitude of 26 degrees confirming reports of fast torsional oscillations in noncovalent ethidium bromide/DNA systems. Data obtained by use of a new polarized photobleaching recovery technique (FPR) reflect both the rotational dynamics of the polymer and the reversible photochemistry of the dye. To isolate the reorientational motion of the DNA, the FPR experiments were ran in two modes that differ only in the polarization of the bleaching light. A quotient function constructed from the data obtained in these two modes monitors only the rotational component of the FPR recovery. In specific applications those bending deformations of long DNA molecules that have characteristic relaxation times on the order of 100 microseconds have been resolved. A fluorescence correlation technique that relates fluctuations in particle number to center-of-mass motion was used to measure translational diffusion on coefficients of the plasmid PBR322 and a short oligomeric DNA. A theory that describes angular correlation in systems exhibiting cyclic, biologically directed reorientation and random Brownian rotation is developed.
Multiscale functions, Scale dynamics and Applications to partial differential equations
Cresson, Jacky
2015-01-01
Modeling phenomena from experimental data, always begin with a \\emph{choice of hypothesis} on the observed dynamics such as \\emph{determinism}, \\emph{randomness}, \\emph{derivability} etc. Depending on these choices, different behaviors can be observed. The natural question associated to the modeling problem is the following : \\emph{"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 \\emph{multi-scale functions}, \\emph{scale calculus} and \\emph{scale dynamics} based on the \\emph{time-scale calculus} (see \\cite{bohn}). These definitions will be illustrated on the \\emph{multi-scale Okamoto's functions}. The introduced formalism explains why there exists different continuous models associated to an equation with different \\emph{scale regimes} whereas the equation is \\emph{scale invariant}. A typical example of such an equation, is the \\emph{Euler-Lagrange equation} and particularly the \\emph{Newton's equation} ...
Institute of Scientific and Technical Information of China (English)
秦长锋; 李伟; 康建东; 吴国辉; 陈继林
2014-01-01
Oline dynamic security assessment system using real-time operating data and model parameters, track and analyze power flow,power system stability,short circuit current,etc.,and advanced assessment of total transfer capacity(TTC).Real-time alarm information of power grid is shown which reflect weak points of the grid.However,with the development of grid structure and data model,only displaying current alarm results that is unable to meet dispatchers’ demands through pre-allocation fixed parameters mechanism adopted. This paper introduced combination of dynamic security assessment system and offline system, not only view Online historical data and online information of grid,but also achieve online monitoring, assessment and early warning for power grid at all levels,which ensure the system's flexibility and stability,improve work efficiency,and provide convenient means for operator.%在线动态安全评估系统利用实时运行数据和模型参数，进行电力系统潮流、电力系统稳定性、短路电流等进行跟踪分析，并进行高级的稳定裕度评估，给出电网实时的告警信息，反应电网的薄弱点。然而随着电网结构的发展，数据模型的变化，采用预分配的固定参数设置，显示当前告警结果已无法满足调度自动化的需求。本文将动态安全评估的在线与离线结合起来，不但能提供电网的历史数据和在线信息查看，而且实现了对各级电网的在线监视、评估和预警，保证了系统的灵活性和稳定性，提高了工作效率，为运行人员提供了便捷手段。
Dynamics of homegarden structure and function in Kerala, India
PEYRE, A.; Guidal, A.; Wiersum, K.F.; Bongers, F.J.J.M.
2006-01-01
Homegardens in Kerala have long been important multi-purpose agroforestry systems that combine ecological and socioeconomical sustainability. However, traditional homegardens are subject to different conversion processes linked to socioeconomic changes. These dynamics were studied in a survey of 30 homegardens. On the basis of a cluster analysis of tree/shrub species density and subsequent further grouping using homegarden size as additional characteristic, six homegarden types were different...
An empirical study of dynamic graph algorithms
Energy Technology Data Exchange (ETDEWEB)
Alberts, D. [Freie Universitaet Berlin (Germany); Cattaneo, G. [Universita di Salerno (Italy); Italiano, G.F. [Universita Ca Forscari di Venezia (Italy)
1996-12-31
We conduct an empirical study on some dynamic graph algorithms which where developed recently. The following implementations were tested and compared with simple algorithms: dynamic connectivity, and dynamic minimum 1 spanning tree based on sparsification by Eppstein et al.; dynamic connectivity based on a very recent paper by Henzinger and King. In our experiments, we considered both random and non-random inputs. Moreover, we present a simplified variant of the algorithm by Henzinger and King, which for random inputs was always faster than the original implementation. Indeed, this variant was among the fastest implementations for random inputs. For non-random inputs, sparsification was the fastest algorithm for small sequences of updates; for medium and large sequences of updates, the original algorithm by Henzinger and King was faster. Perhaps one of the main practical results of this paper is that our implementations of the sophisticated dynamic graph algorithms were faster than simpler algorithms for most practical values of the graph parameters, and competitive with simpler algorithms even in case of very small graphs (say graphs with less than a dozen vertices and edges). From the theoretical point of view, we analyze the average case running time of sparsification and prove that the logarithmic overhead for simple sparsification vanishes for dynamic random graphs.
Interplay between functional connectivity and scale-free dynamics in intrinsic fMRI networks.
Ciuciu, Philippe; Abry, Patrice; He, Biyu J
2014-07-15
Studies employing functional connectivity-type analyses have established that spontaneous fluctuations in functional magnetic resonance imaging (fMRI) signals are organized within large-scale brain networks. Meanwhile, fMRI signals have been shown to exhibit 1/f-type power spectra - a hallmark of scale-free dynamics. We studied the interplay between functional connectivity and scale-free dynamics in fMRI signals, utilizing the fractal connectivity framework - a multivariate extension of the univariate fractional Gaussian noise model, which relies on a wavelet formulation for robust parameter estimation. We applied this framework to fMRI data acquired from healthy young adults at rest and while performing a visual detection task. First, we found that scale-invariance existed beyond univariate dynamics, being present also in bivariate cross-temporal dynamics. Second, we observed that frequencies within the scale-free range do not contribute evenly to inter-regional connectivity, with a systematically stronger contribution of the lowest frequencies, both at rest and during task. Third, in addition to a decrease of the Hurst exponent and inter-regional correlations, task performance modified cross-temporal dynamics, inducing a larger contribution of the highest frequencies within the scale-free range to global correlation. Lastly, we found that across individuals, a weaker task modulation of the frequency contribution to inter-regional connectivity was associated with better task performance manifesting as shorter and less variable reaction times. These findings bring together two related fields that have hitherto been studied separately - resting-state networks and scale-free dynamics, and show that scale-free dynamics of human brain activity manifest in cross-regional interactions as well.
VUV studies of molecular photofragmentation dynamics
Energy Technology Data Exchange (ETDEWEB)
White, M.G. [Brookhaven National Laboratory, Upton, NY (United States)
1993-12-01
State-resolved, photoion and photoelectron methods are used to study the neutral fragmentation and ionization dynamics of small molecules relevant to atmospheric and combustion chemistry. Photodissociation and ionization are initiated by coherent VUV radiation and the fragmentation dynamics are extracted from measurements of product rovibronic state distributions, kinetic energies and angular distributions. The general aim of these studies is to investigate the multichannel interactions between the electronic and nuclear motions which determine the evolution of the photoexcited {open_quotes}complex{close_quotes} into the observed asymptotic channels.
In vivo Dynamic Studies of Brain Metabolism
Institute of Scientific and Technical Information of China (English)
LUO Xuechun; JIANG Yufeng; ZHANG Riqing
2005-01-01
Nuclear magnetic resonance (NMR) can noninvasively monitor intracellular concentrations and kinetic properties of numerous inorganic and organic compounds. A 31P NMR surface coil was used in vivo to dynamically measure phosphocreatine (PCr), adenosine triphosphate (ATP), and intracellular inorganic phosphate (Pi) levels in mouse brain during ischemia-reperfusion to study the damage of cerebral tissues caused by ischemia and effects of herbs on cerebral energy metabolism during ischemia-reperfusion. The study provides dynamic brain energy metabolism data during different periods. The data show that some herbs more rapidly increase the PCr level during the recovery phase than in the control group.
Amaro-Estrada, J I; Maron, L; Ramírez-Solís, A
2013-09-19
A systematic study of the hydration of Hg(OH)2 by the stepwise solvation approach is reported. The optimized structures, solvation energies, and incremental free energies of 1-24 water molecules interacting with the solute have been computed at the B3PW91 level using 6-31G(d,p) basis sets for the O and H atoms. The mercury atom was treated with the Stuttgart-Köln relativistic core potential in combination with an extended optimized valence basis set. One to three direct Hg-water interactions appear along the solvation process. The first solvation shell is fully formed with 24 water molecules. A stable pentacoordinated Hg trigonal bipyramid structure appears for n > 15. Density functional theory (DFT) Born-Oppenheimer molecular dynamics simulations showed the thermal stability of the Hg(OH)2-(H2O)24 structure at room temperature and the persistence of the trigonal bipyramid coordination around Hg. The Gibbs free energy for the first solvation shell is significantly larger for the fully solvated Hg(OH)2 than the one previously obtained for the HgCl2 case, due to σ-acceptor and π-donor properties involving the hydroxyl groups of the solute. This suggests that the transmembrane passage of Hg(OH)2 into the cell via simple diffusion is less favorable compared to the case when the metal is coordinated with two Cl groups.
Contributions to the Study of Dynamic Absorbers, a Case Study
Directory of Open Access Journals (Sweden)
Monica Balcau
2012-01-01
Full Text Available Dynamic absorbers are used to reduce torsional vibrations. This paper studies the effect of a dynamic absorber attached to a mechanical system formed of three reduced masses which are acted on by one, two or three order x harmonics of a disruptive force.
Functional dynamic factor models with application to yield curve forecasting
Hays, Spencer
2012-09-01
Accurate forecasting of zero coupon bond yields for a continuum of maturities is paramount to bond portfolio management and derivative security pricing. Yet a universal model for yield curve forecasting has been elusive, and prior attempts often 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 with functional factor loading curves. This results in a model capable of forecasting functional time series. Further, in the yield curve context we show that the model retains economic interpretation. Model estimation is achieved through an expectation- maximization algorithm, where the time series parameters and factor loading curves are simultaneously estimated in a single step. Efficient computing is implemented and a data-driven smoothing parameter is nicely incorporated. We show that our model performs very well on forecasting actual yield data compared with existing approaches, especially in regard to profit-based assessment for an innovative trading exercise. We further illustrate the viability of our model to applications outside of yield forecasting.
Aircraft path planning for optimal imaging using dynamic cost functions
Christie, Gordon; Chaudhry, Haseeb; Kochersberger, Kevin
2015-05-01
Unmanned aircraft development has accelerated with recent technological improvements in sensing and communications, which has resulted in an "applications lag" for how these aircraft can best be utilized. The aircraft are becoming smaller, more maneuverable and have longer endurance to perform sensing and sampling missions, but operating them aggressively to exploit these capabilities has not been a primary focus in unmanned systems development. This paper addresses a means of aerial vehicle path planning to provide a realistic optimal path in acquiring imagery for structure from motion (SfM) reconstructions and performing radiation surveys. This method will allow SfM reconstructions to occur accurately and with minimal flight time so that the reconstructions can be executed efficiently. An assumption is made that we have 3D point cloud data available prior to the flight. A discrete set of scan lines are proposed for the given area that are scored based on visibility of the scene. Our approach finds a time-efficient path and calculates trajectories between scan lines and over obstacles encountered along those scan lines. Aircraft dynamics are incorporated into the path planning algorithm as dynamic cost functions to create optimal imaging paths in minimum time. Simulations of the path planning algorithm are shown for an urban environment. We also present our approach for image-based terrain mapping, which is able to efficiently perform a 3D reconstruction of a large area without the use of GPS data.
Dynamic regulation of NMDAR function in the adult brain by the stress hormone corticosterone
Directory of Open Access Journals (Sweden)
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.
Dynamic study of synchronous machine electric drive
Directory of Open Access Journals (Sweden)
Dimitar Spirov
2005-10-01
Full Text Available The dynamic behaviour of the fan blower synchoronous machine drive have been studied in the paper. The equations for the voltages of the synchoronous machine windings are presented in a coordinate system which rotates at the angular speed of the rotor. The mechanical equipment is presented by means of a single-mass dynamic model. The derived system of differential equations is transformed and solved using suitable software product. The results obtained for rotation frequency and electromagnetic torque motor in the courses of different values of rated supply voltage and of different initial resistant moment of the mechanism have been graphically presented. Conclusions from the results obtained have been done.
Wu, Yan; Misra, Sambit; Karacor, M Basar; Prakash, Shaurya; Shannon, Mark A
2010-11-16
The dynamic response of an oscillating microcantilever with a gold-coated tip interacting with dissimilar functionalized silica surfaces was studied in electrolyte solutions with pH ranging from 4 to 9. Silica surfaces were chemically modified, yielding dissimilar surfaces with -Br, -NH(2), and -CH(3) functional group terminations. The relative hydrophobicity of the surfaces was characterized by contact angle measurements. The surface charge of the functionalized surfaces was first probed with commonly used static AFM measurements and serves as a reference to the dynamic response data. The amplitude and phase of the cantilever oscillation were monitored and used to calculate the effective interaction stiffness and damping coefficient, which relate to the electrical double layer interactions and also to distance-dependent hydrodynamic damping at the solid/water interface. The data for the dynamic response of the AFM over silica surfaces as a function of chemical functionalization and electrolyte pH show that the effective stiffness has a distinctive dependence on the surface charge of functionalized silica surfaces. The hydrodynamic damping also correlates strongly with the relative hydrophobicity of the surface. The data reported here indicate that interfacial properties can be strongly affected by changing the chemical composition of surfaces.
Molecular Dynamics Studies of Matrix Metalloproteases.
Díaz, Natalia; Suárez, Dimas
2017-01-01
Matrix metalloproteases are multidomain enzymes with a remarkable proteolytic activity located in the extracellular environment. Their catalytic activity and structural properties have been intensively studied during the last few decades using both experimental and theoretical approaches, but many open questions still remain. Extensive molecular dynamics simulations enable the sampling of the configurational space of a molecular system, thus contributing to the characterization of the structure, dynamics, and ligand binding properties of a particular MMP. Based on previous computational experience, we provide in this chapter technical and methodological guidelines that may be useful to and stimulate other researchers to perform molecular dynamics simulations to help address unresolved questions concerning the molecular mode of action of MMPs.
Analysis of dynamic pulmonary functions in air conditioned work environment
Directory of Open Access Journals (Sweden)
Anu T. E.
2016-07-01
Conclusions: The results of the study indicate that the subjects working in AC environment for a long duration are prone to develop restrictive lung diseases. Hence, study concludes that periodic pulmonary function assessment should be made mandatory. Further, regular maintenance of ACs is also recommended. [Int J Res Med Sci 2016; 4(7.000: 2661-2664
A molecular density functional theory to study solvation in water
Jeanmairet, Guillaume
2014-01-01
A classical density functional theory is applied to study solvation of solutes in water. An approx- imate form of the excess functional is proposed for water. This functional requires the knowledge of pure solvent direct correlation functions. Those functions can be computed by using molecular simulations such as molecular dynamic or Monte Carlo. It is also possible to use functions that have been determined experimentally. The functional minimization gives access to the solvation free energy and to the equilibrium solvent density. Some correction to the functional are also proposed to get the proper tetrahedral order of solvent molecules around a charged solute and to reproduce the correct long range hydrophobic behavior of big apolar solutes. To proceed the numerical minimization of the functional, the theory has been discretized on two tridimensional grids, one for the space coordinates, the other for the angular coordinates, in a functional minimization code written in modern Fortran, mdft. This program i...
A molecular dynamics study of structure and dynamics in high-density liquids
Variyar, Jayasankar E.; Noro, Massimo; Kivelson, Daniel
By means of molecular dynamics simulations we have investigated increasing configurational ordering and decreasing particle mobility with increasing density ρ of a three-dimensional equilibrated liquid composed of soft discs. The equal-time correlation function h(n)3 (0) which includes two-, three- and four-body correlations is introduced as a measure of structural order; this function is related to the dipole-induced-dipole equal-time correlation function and its sensitivity to structural order in the liquid is associated with the cancellation effect, i.e. the cancellation of the positive contributions of the two- and four- body correlations by the negative contribution of the three-body correlations. The analogous time-dependent correlation function h(4)3 (t) is also studied. The possible implications of these results to the study of supercooled liquids and glasses is discussed.
Dynamic Study of Bicycle Frame Structure
Sani, M. S. M.; Nazri, N. A.; Zahari, S. N.; Abdullah, N. A. Z.; Priyandoko, G.
2016-11-01
Bicycle frames have to bear variety of loads and it is needed to ensure the frame can withstand dynamic loads to move. This paper focusing on dynamic study for bicycle frame structure with a purpose to avoid the problem regarding loads on the structure and to ensure the structure is safe when multiple loads are applied on it. The main objectives of dynamic study are to find the modal properties using two method; finite element analysis (FEA) and experimental modal analysis (EMA). The correlation between two studies will be obtained using percentage error. Firstly, 3D model of mountain bike frame structure has been draw using computer-aided design (CAD) software and normal mode analysis using MSC Nastran Patran was executed for numerical method meanwhile modal testing using impact hammer was performed for experimental counterpart. From the correlation result, it show that percentage error between FEA and EMA were below 10% due to noise, imperfect experiment setup during perform EMA and imperfect modeling of mountain bike frame structure in CAD software. Small percentage error differences makes both of the method can be applied to obtain the dynamic characteristic of structure. It is essential to determine whether the structure is safe or not. In conclusion, model updating method is required to reduce more percentage error between two results.
Study of the nonlinear longitudinal dynamics of a stochastic system
Directory of Open Access Journals (Sweden)
Cunha Americo
2014-01-01
Full Text Available This paper deals with the theoretical study of how discrete elements attached to a continuous stochastic systems can affect their dynamical behavior. For this, it is studied the nonlinear longitudinal dynamics of an elastic bar, attached to springs and a lumped mass, with a random elastic modulus and subjected to a Gaussian white-noise distributed external force. Numerical simulations are conducted and their results are analyzed in function of the ratio between the masses of the discrete and the continuous parts of the system. This analysis reveals that the dynamic behavior of the bar is significantly altered when the lumped mass is varied, being more inﬂuenced by the randomness for small values of the lumped mass.
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.
Rathleff, M S; Nielsen, R G; Simonsen, O; Olesen, C G; Kersting, U G
2010-02-01
Several studies have investigated if static posture assessments qualify to predict dynamic function of the foot showing diverse outcomes. However, it was suggested that dynamic measures may be better suited to predict foot-related overuse problems. The purpose of this study was to establish the reliability for dynamic measures of longitudinal arch angle (LAA) and navicular height (NH) and to examine to what extent static and dynamic measures thereof are related. Intra-rater reliability of LAA and NH measures was tested on a sample of 17 control subjects. Subsequently, 79 subjects were tested while walking on a treadmill. The ranges and minimum values for LAA and NH during ground contact were identified over 20 consecutive steps. A geometric error model was used to simulate effects of marker placement uncertainty and skin movement artifacts. Results demonstrated the highest reliability for the minimum NH (MinNH), followed by the minimum LAA (MinLAA), the dynamic range of navicular height (DeltaNH) and the range of LAA (DeltaLAA) while all measures were highly reliable. Marker location uncertainty and skin movement artifacts had the smallest effects on measures of NH. The use of an alignment device for marker placement was shown to reduce error ranges for NH measures. Therefore, DeltaNH and MinNH were recommended for functional dynamic foot characterization in the sagittal plane. There is potential for such measures to be a suitable predictor for overuse injuries while being obtainable in clinical settings. Future research needs to include such dynamic but simple foot assessments in large-scale clinical studies.
Demontis, Pierfranco; Gulín-González, Jorge; Masia, Marco; Sant, Marco; Suffritti, Giuseppe B
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(∗) ∼ 315 ± 5 K, was spotted at T(∗) ∼ 283 K and T(∗) ∼ 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 mechanisms of the two
LOW-x Dynamics Through Jet Studies
Ferencei, Jozef; H1; ZEUS Collaborations
One of the most challenging aspects of low x proton structure is the study of QCD dynamics - the evolution of partons between different kinematic regimes. In electron-proton deep-inelastic scattering, this can be investigated by studying processes in the target region of the proton - forward going jets. In this paper various measurements made at HERA by the H1 and ZEUS experiments are presented and compared to Monte Carlo models and fixed-order QCD calculations.
Study of Nanowires Using Molecular Dynamics Simulations
Monk, Joshua D
2007-01-01
In this dissertation I present computational studies that focus on the unique characteristics of metallic nanowires. We generated virtual nanowires of nanocrystalline nickel (nc-Ni) and single crystalline silver (Ag) in order to investigate particular nanoscale effects. Three-dimensional atomistic molecular dynamics studies were performed for each sample using the super computer System X located at Virginia Tech. Thermal grain growth simulations were performed on 4 nm grain size nc-Ni by o...
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.
DYNAMIC SCALING OF GROWING SURFACES WITH GROWTH INHOMOGENEITIES OF SCREENED COULOMBIC FUNCTION
Institute of Scientific and Technical Information of China (English)
TANG GANG; MA BEN-KUN
2000-01-01
The dynamic scaling properties of growing surfaces with growth inhomogeneities are studied by applying a dy namic renormalization-group analysis to the generalized Kardar-Parisi-Zhang(hereafter abbreviated to KPZ) equation, which contains an additional term of growth inhomogeneities. In a practical crystal growth process, these growth inho mogeneities can be induced by surface impurities and defects and are modeled by a screened Coulomb function in this paper. Our results show that the existence of the growth inhomogeneities can significantly change the dynamic scaling properties of a growing surface and can lead to a rougher surface.
Animal diversity and ecosystem functioning in dynamic food webs
Schneider, Florian D.; Brose, Ulrich; Rall, Björn C.; Guill, Christian
2016-10-01
Species diversity is changing globally and locally, but the complexity of ecological communities hampers a general understanding of the consequences of animal species loss on ecosystem functioning. High animal diversity increases complementarity of herbivores but also increases feeding rates within the consumer guild. Depending on the balance of these counteracting mechanisms, species-rich animal communities may put plants under top-down control or may release them from grazing pressure. Using a dynamic food-web model with body-mass constraints, we simulate ecosystem functions of 20,000 communities of varying animal diversity. We show that diverse animal communities accumulate more biomass and are more exploitative on plants, despite their higher rates of intra-guild predation. However, they do not reduce plant biomass because the communities are composed of larger, and thus energetically more efficient, plant and animal species. This plasticity of community body-size structure reconciles the debate on the consequences of animal species loss for primary productivity.
Functional diversity and evolutionary dynamics of thermoTRP channels.
Saito, Shigeru; Tominaga, Makoto
2015-03-01
Animals have evolved sophisticated physiological systems for sensing ambient temperature since changes in environmental temperatures affect various biological processes. Thermosensitive transient receptor potential (thermoTRP) channels serve as thermal sensors in diverse animal species. They are multimodal receptors that are activated by temperature as well as other physical and chemical stimuli. Since thermoTRP channels are calcium permeable non-selective cation channels, their activation leads to an influx of calcium and sodium ions into the cell and triggers downstream signal transduction. ThermoTRP channels have been characterized in diverse animal species over the past several years, illuminating the diversification of thermoTRP channels in the course of evolution. The gene repertoires of thermoTRP channels differ among animal species. Additionally, in some cases, the temperature and chemical sensitivities among orthologous thermoTRP channels vary among species. The evolutionary flexibility of thermoTRP channels enabled them to contribute to unique physiological systems such as infrared sensation in snakes and bats and seasonal adaptation in silk moth. On the other hand, the functional differences of thermoTRP channels among species have been utilized for understanding the molecular basis for their activation (or inhibition) mechanisms, and amino acid residues (or domains) responsible for the respective channel properties have been identified in various thermoTRP channels. Here we summarize the current understanding of the functional diversity and evolutionary dynamics of thermoTRP channels.
Family dynamics and psychosocial functioning in children with SCI/D from Colombia, South America
Nicolais, Christina J.; Perrin, Paul B.; Panyavin, Ivan; Nicholls, Elizabeth G.; Olivera Plaza, Silvia Leonor; Quintero, Lorena Medina; Arango-Lasprilla, Juan Carlos
2016-01-01
Objective The purpose of this study was to examine the connections between family dynamics and the psychosocial functioning of children with spinal cord injuries and disorders (SCI/D). Design Cross-sectional. Setting Participants were recruited from communities in Neiva, Colombia. Participants Thirty children with SCI/D and their primary caregiver participated. Children were between 8 and 17 years of age, and had sustained their injury at least six months prior to data collection. Interventions NA. Outcome measures Participating children completed measures assessing their own psychosocial functioning (Children's Depression Inventory, Revised Children's Manifest Anxiety Scale-2, Pediatric Quality of Life Inventory), and their primary caregiver completed measures of family dynamics (Family Adaptability and Cohesion Evaluation Scale- Fourth Edition, Family Communication Scale, Family Assessment Device- General Functioning, Family Satisfaction Scale, Relationship-Focused Coping Scale). Results A correlation matrix showed a number of significant bivariate correlations between child and family variables, and three multiple regressions showed that family satisfaction, empathy, and flexibility significantly explained 27% of the variance in child worry; family satisfaction and communication explained 18% of the variance in child social anxiety; and family cohesion and communication explained 23% of the variance in child emotional functioning. Conclusions These findings highlight the importance of rehabilitation professionals considering the association between family dynamics and the psychosocial functioning of children with SCI/D when working with this population. PMID:25582185
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
Dynamic Aperture Studies for the FCC-ee
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.
A functional-dynamic reflection on participatory processes in modeling projects.
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 MRI study for breast tumors
Energy Technology Data Exchange (ETDEWEB)
Seki, Tsuneaki (Kyorin Univ., Mitaka, Tokyo (Japan). School of Medicine)
1990-10-01
Application of MRI for diagnosis of breast tumors was retrospectively examined in 103 consecutive cases. Contrast enhancement, mostly by dynamic study, was performed in 83 cases using Gd-DTPA and 0.5 T superconductive apparatus. Results were compared to those of mammography and sonography. On dynamic study, carcinoma showed abrupt rise of signal intensity with clear-cut peak formation in early phase, while benign fibroadenoma showed slow rise of signal intensity and prolonged enhancement without peak formation. In 12 of 33 carcinomas (33%), peripheral ring enhancement was noted reflecting vascular stroma of histologic sections. All fibroadenomas showed homogenous enhancement without peripheral ring. In MRI, sensitivity, specificity, and accuracy were 86%, 96%, 91%. In mammography 82%, 95%, 87% and in ultrasonography 91%, 95%, 93%. Although MRI should not be regarded as routine diagnostic procedure because of expense and limited availability, it may afford useful additional information when standard mammographic findings are not conclusive. (author).
Sakschewski, B.; Bloh, von W.; Boit, A.; Rammig, A.; Kattge, J.; Poorter, L.; Peñualeas, J.; Thonicke, K.
2015-01-01
Functional diversity is critical for ecosystem dynamics, stability and productivity. However, dynamic global vegetation models (DGVMs) which are increasingly used to simulate ecosystem functions under global change, condense functional diversity to plant functional types (PFTs) with constant paramet
Functional Disorders in Neurology : Case Studies
Stone, Jon; Hoeritzauer, Ingrid; Gelauff, Jeannette; Lehn, Alex; Gardiner, Paula; van Gils, Anne; Carson, Alan
Functional, often called psychogenic, disorders are common in neurological practice. We illustrate clinical issues and highlight some recent research findings using six case studies of functional neurological disorders. We discuss dizziness as a functional disorder, describing the relatively new
A Density Functional Theory Study
Lim, XiaoZhi
2011-12-11
Complexes with pincer ligand moieties have garnered much attention in the past few decades. They have been shown to be highly active catalysts in several known transition metal-catalyzed organic reactions as well as some unprecedented organic transformations. At the same time, the use of computational organometallic chemistry to aid in the understanding of the mechanisms in organometallic catalysis for the development of improved catalysts is on the rise. While it was common in earlier studies to reduce computational cost by truncating donor group substituents on complexes such as tertbutyl or isopropyl groups to hydrogen or methyl groups, recent advancements in the processing capabilities of computer clusters and codes have streamlined the time required for calculations. As the full modeling of complexes become increasingly popular, a commonly overlooked aspect, especially in the case of complexes bearing isopropyl substituents, is the conformational analysis of complexes. Isopropyl groups generate a different conformer with each 120 ° rotation (rotamer), and it has been found that each rotamer typically resides in its own potential energy well in density functional theory studies. As a result, it can be challenging to select the most appropriate structure for a theoretical study, as the adjustment of isopropyl substituents from a higher-energy rotamer to the lowest-energy rotamer usually does not occur during structure optimization. In this report, the influence of the arrangement of isopropyl substituents in pincer complexes on calculated complex structure energies as well as a case study on the mechanism of the isomerization of an iPrPCP-Fe complex is covered. It was found that as many as 324 rotamers can be generated for a single complex, as in the case of an iPrPCP-Ni formato complex, with the energy difference between the global minimum and the highest local minimum being as large as 16.5 kcalmol-1. In the isomerization of a iPrPCP-Fe complex, it was found
Molecular dynamics simulation of doxorubicin adsorption on a bundle of functionalized CNT.
Izadyar, Akram; Farhadian, Nafiseh; Chenarani, Naser
2016-08-01
In this study, molecular dynamics simulation is used to investigate the adsorption of an anticancer drug, doxorubicin, on bundles of functionalized single-walled carbon nanotubes (SWNTs) in an aqueous solution. Carboxylic group has been selected as the functional group. Molecular dynamics (MD) simulations are performed for both separated systems containing a SWNT bundle and a functionalized carbon nanotube bundle, and results are compared with existing experimental data. MD results show that doxorubicin can be adsorbed on CNTs using different methods such as entrapment within CNT bundle, attachment to the side wall of the CNT, and adsorption on the CNT inner cavity. For functionalized CNT, the adsorption of drugs on the functional groups is essential for predicting the enhancement of drug loading on the functionalized nanotubes. Furthermore, the adsorption behavior of doxorubicin on CNTs is fitted with Langmuir and Freundlich isotherm models. The results show that Langmuir model can predict the adsorption behavior of doxorubicin on CNTs more accurately than Freundlich model does. As predicted by this isotherm model, the adsorption process of doxorubicin on CNTs is relatively difficult, but it can be improved by increasing the functional groups on the CNTs surface.
London, Gábor; Chen, Kuang-Yen; Carroll, Gregory T; Feringa, Ben L
2013-08-05
We report the synthesis of altitudinal molecular motors that contain functional groups in their rotor part. In an approach to achieve dynamic control over the properties of solid surfaces, a hydrophobic perfluorobutyl chain and a relatively hydrophilic cyano group were introduced to the rotor part of the motors. Molecular motors were attached to quartz surfaces by using interfacial 1,3-dipolar cycloadditions. To test the effect of the functional groups on the rotary motion, photochemical and thermal isomerization studies of the motors were performed both in solution and when attached to the surface. We found that the substituents have no significant effect on the thermal and photochemical processes, and the functionalized motors preserved their rotary function both in solution and on a quartz surface. Preliminary results on the influence of the functional groups on surface wettability are also described.
Season physical functioning dynamic of men with different physical condition
Directory of Open Access Journals (Sweden)
Prushva O.B.
2015-10-01
Full Text Available Purpose: study season peculiarities of physical functioning of men with different physical condition. Material: in the research 53 men of 41-55 years’ age without chronic disease, who practiced healthy life style, participated. It was assessed: daily physical functioning of different intensity with the help of bio-register BASIS B1; body mass index; adaptation potential of Bayevskiy. Results: we determined that men with normal adaptation potential have less quantity of highly intensive steps than men with excessively tensed adaptation potential of cardio-vascular system. Men with tensed adaptation potential have less expressed season changes in physical functioning. Conclusions: We found the following optimal correlations: total quantity of steps per day; quantity of steps with average intensity (80-86 steps per min.; total run steps of high intensity (140-145 steps per min.; quantity of low intensity steps (8-10 steps per min..
Theoretical studies of chemical reaction dynamics
Energy Technology Data Exchange (ETDEWEB)
Schatz, G.C. [Argonne National Laboratory, IL (United States)
1993-12-01
This collaborative program with the Theoretical Chemistry Group at Argonne involves theoretical studies of gas phase chemical reactions and related energy transfer and photodissociation processes. Many of the reactions studied are of direct relevance to combustion; others are selected they provide important examples of special dynamical processes, or are of relevance to experimental measurements. Both classical trajectory and quantum reactive scattering methods are used for these studies, and the types of information determined range from thermal rate constants to state to state differential cross sections.
Fast dynamics perturbation analysis for prediction of protein functional sites
Directory of Open Access Journals (Sweden)
Cohn Judith D
2008-01-01
Full Text Available Abstract Background We present a fast version of the dynamics perturbation analysis (DPA algorithm to predict functional sites in protein structures. The original DPA algorithm finds regions in proteins where interactions cause a large change in the protein conformational distribution, as measured using the relative entropy Dx. Such regions are associated with functional sites. Results The Fast DPA algorithm, which accelerates DPA calculations, is motivated by an empirical observation that Dx in a normal-modes model is highly correlated with an entropic term that only depends on the eigenvalues of the normal modes. The eigenvalues are accurately estimated using first-order perturbation theory, resulting in a N-fold reduction in the overall computational requirements of the algorithm, where N is the number of residues in the protein. The performance of the original and Fast DPA algorithms was compared using protein structures from a standard small-molecule docking test set. For nominal implementations of each algorithm, top-ranked Fast DPA predictions overlapped the true binding site 94% of the time, compared to 87% of the time for original DPA. In addition, per-protein recall statistics (fraction of binding-site residues that are among predicted residues were slightly better for Fast DPA. On the other hand, per-protein precision statistics (fraction of predicted residues that are among binding-site residues were slightly better using original DPA. Overall, the performance of Fast DPA in predicting ligand-binding-site residues was comparable to that of the original DPA algorithm. Conclusion Compared to the original DPA algorithm, the decreased run time with comparable performance makes Fast DPA well-suited for implementation on a web server and for high-throughput analysis.
Osmosis : a molecular dynamics computer simulation study
Lion, Thomas
Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..
Boltzmann-conserving classical dynamics in quantum time-correlation functions: Matsubara dynamics
Hele, Timothy J H; Muolo, Andrea; Althorpe, Stuart C
2015-01-01
We show that a single change in the derivation of the linearized semiclassical-initial value representation (LSC-IVR or classical Wigner approximation) results in a classical dynamics which conserves the quantum Boltzmann distribution. We rederive the (standard) LSC-IVR approach by writing the (exact) quantum time-correlation function in terms of the normal modes of a free ring-polymer (i.e. a discrete imaginary-time Feynman path), taking the limit that the number of polymer beads $N \\to \\infty$, such that the lowest normal-mode frequencies take their Matsubara values. The change we propose is to truncate the quantum Liouvillian, not explicitly in powers of $\\hbar^2$ at $\\hbar^0$ (which gives back the standard LSC-IVR approximation), but in the normal-mode derivatives corresponding to the lowest Matsubara frequencies. The resulting Matsubara dynamics is inherently classical (since all terms $\\mathcal{O}\\left(\\hbar^{2}\\right)$ disappear from the Matsubara Liouvillian in the limit $N \\to \\infty$), and conserves...
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.
Predator-prey dynamics driven by feedback between functionally diverse trophic levels.
Tirok, Katrin; Bauer, Barbara; Wirtz, Kai; Gaedke, Ursula
2011-01-01
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.
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.
A lagrangian dynamical theory for the mass function of cosmic structures; 1, dynamics
Monaco, P
1996-01-01
A new theory for determining the mass function of cosmic structures is presented. It relies on a realistic treatment of collapse dynamics. Gravitational collapse is analyzed in the Lagrangian perturbative framework. Lagrangian perturbations provide an approximation of truncated type, i.e. small-scale structure is filtered out. The collapse time is suitably defined as the instant at which orbit crossing takes place. The convergence of the Lagrangian series in predicting the collapse time of a homogeneous ellipsoid is demonstrated; it is also shown that third-order calculations are necessary in predicting collapse. Then, the Lagrangian prediction, with a correction for quasi-spherical perturbations, can be used to determine the collapse time of a homogeneous ellipsoid in a very fast and precise way. Furthermore, ellipsoidal collapse can be considered as a particular truncation of the Lagrangian series. Gaussian fields with scale-free power spectra are then considered. The Lagrangian series for the collapse time...
Solar dynamic power system definition study
Wallin, Wayne E.; Friefeld, Jerry M.
1988-01-01
The solar dynamic power system design and analysis study compared Brayton, alkali-metal Rankine, and free-piston Stirling cycles with silicon planar and GaAs concentrator photovoltaic power systems for application to missions beyond the Phase 2 Space Station level of technology for all power systems. Conceptual designs for Brayton and Stirling power systems were developed for 35 kWe and 7 kWe power levels. All power systems were designed for 7-year end-of-life conditions in low Earth orbit. LiF was selected for thermal energy storage for the solar dynamic systems. Results indicate that the Stirling cycle systems have the highest performance (lowest weight and area) followed by the Brayton cycle, with photovoltaic systems considerably lower in performance. For example, based on the performance assumptions used, the planar silicon power system weight was 55 to 75 percent higher than for the Stirling system. A technology program was developed to address areas wherein significant performance improvements could be realized relative to the current state-of-the-art as represented by Space Station. In addition, a preliminary evaluation of hardenability potential found that solar dynamic systems can be hardened beyond the hardness inherent in the conceptual designs of this study.
Energy Technology Data Exchange (ETDEWEB)
Kan, Yongjin; Shinozuka, Akira; Takenaka, Hiroki; Munechika, Hirotsugu [Showa Univ., Tokyo (Japan). School of Medicine
2001-08-01
A lung dynamic SPECT study using {sup 133}Xe gas was performed a functional map created be region. The time activity curve (TAC) of each voxel was obtained from subsequent SPECT data. Washout rate (K) was calculated from TAC. The product of K and counter weighted voxel volume was defined as the lung function index (LFI). Using these 3 parameters (functional volume, K, and LFI) a function map was created. The sum of LFI was defined as total lung functional index (TLFI). Five healthy volunteers and 20 patients with various lung diseases were investigated. TLFI correlated well with FEV{sub 1.0} and MMF, and mean K with FEV{sub 1.0}%. The results indicate that a functional map obtained from lung dynamic SPECT is useful in estimating both resional and whole lung function. (author)
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.
Mithen, James P; Gregori, G
2011-01-01
The complementarity of the liquid and plasma descriptions of the classical one-component plasma (OCP) is explored by studying wavevector and frequency dependent dynamical quantities: the dynamical structure factor (DSF), and the dynamic local field correction (LFC). Accurate Molecular Dynamics (MD) simulations are used to validate/test models of the DSF and LFC. Our simulations, which span the entire fluid regime ($\\Gamma = 0.1 - 175$), show that the DSF is very well represented by a simple and well known memory function model of generalized hydrodynamics. On the other hand, the LFC, which we have computed using MD for the first time, is not well described by existing models.
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.).
NMR studies of nucleic acid dynamics
Al-Hashimi, Hashim M.
2013-12-01
Nucleic acid structures have to satisfy two diametrically opposite requirements; on one hand they have to adopt well-defined 3D structures that can be specifically recognized by proteins; on the other hand, their structures must be sufficiently flexible to undergo very large conformational changes that are required during key biochemical processes, including replication, transcription, and translation. How do nucleic acids introduce flexibility into their 3D structure without losing biological specificity? Here, I describe the development and application of NMR spectroscopic techniques in my laboratory for characterizing the dynamic properties of nucleic acids that tightly integrate a broad set of NMR measurements, including residual dipolar couplings, spin relaxation, and relaxation dispersion with sample engineering and computational approaches. This approach allowed us to obtain fundamental new insights into directional flexibility in nucleic acids that enable their structures to change in a very specific functional manner.
Van Raemdonck, Mario; Alcoba, Diego R; Poelmans, Ward; De Baerdemacker, Stijn; Torre, Alicia; Lain, Luis; Massaccesi, Gustavo E; Van Neck, Dimitri; Bultinck, Patrick
2015-09-14
A class of polynomial scaling methods that approximate Doubly Occupied Configuration Interaction (DOCI) wave functions and improve the description of dynamic correlation is introduced. The accuracy of the resulting wave functions is analysed by comparing energies and studying the overlap between the newly developed methods and full configuration interaction wave functions, showing that a low energy does not necessarily entail a good approximation of the exact wave function. Due to the dependence of DOCI wave functions on the single-particle basis chosen, several orbital optimisation algorithms are introduced. An energy-based algorithm using the simulated annealing method is used as a benchmark. As a computationally more affordable alternative, a seniority number minimising algorithm is developed and compared to the energy based one revealing that the seniority minimising orbital set performs well. Given a well-chosen orbital basis, it is shown that the newly developed DOCI based wave functions are especially suitable for the computationally efficient description of static correlation and to lesser extent dynamic correlation.
Abnormal dynamics of cortical resting state functional connectivity in chronic headache patients.
Wang, Zewei; Yang, Qing; Chen, Li Min
2017-02-01
The goals of this study are to characterize the temporal dynamics of inter-regional connectivity of the brain in chronic headache (CH) patients versus their age/gender matched controls (CONCH, n=28 pairs), and to determine whether dynamic measures reveal additional features to static functional connectivity and correlate with psychometric scores. Cortical thickness and inter-regional resting state fMRI connectivity were quantified and compared between CH and CONCH groups. Six cortical regions of interest (ROI) pairs that exhibited correlated cortical thickness and static functional connectivity abnormalities were selected for temporal dynamic analysis. Two methods were used: temporal sliding-window (SW) and wavelet transformation coherence (WTC). SW analyses using three temporal windows of 30, 60, 120s revealed that all six ROI pairs of CH exhibited higher percentage of strong connectivity (high r values), and smaller fast Fourier transform (FFT) amplitudes at a very low frequency range (i.e., 0.002-0.01Hz), compared to those of CONCH. These features were particularly prevalent in the 120s window analysis. Less variable dynamic fluctuation (i.e., smaller standard deviation of r values) was identified in two out of six ROI pairs in CH. WTC analysis revealed that time-averaged coherence was generally greater in CH than CONCH between wavelet decomposition scales 20 to 55 (0.018-0.05Hz), and was statistically significant in three out of six ROI pairs. Together, the most robust and significant differences in temporal dynamics between CH and CONCH were detected in two ROI pairs: left medial-orbitofrontal-left posterior-cingulate and left medial-orbitofrontal-left inferior-temporal. The high degrees of sleep disturbance (high PSQI score), depression (high HRSD score) and fatigue (low SF-36 score) were associated with high degree of inter-regional temporal coherence in CH. In summary, these dynamic functional connectivity (dFC) measures uncovered a temporal "lock
Levy-Bencheton, D; Terras, V
2015-01-01
We pursue our study of the antiperiodic dynamical 6-vertex model using Sklyanin's separation of variables approach, allowing in the model new possible global shifts of the dynamical parameter. We show in particular that the spectrum and eigenstates of the antiperiodic transfer matrix are completely characterized by a system of discrete equations. We prove the existence of different reformulations of this characterization in terms of functional equations of Baxter's type. We notably consider the homogeneous functional $T$-$Q$ equation which is the continuous analog of the aforementioned discrete system and show, in the case of a model with an even number of sites, that the complete spectrum and eigenstates of the antiperiodic transfer matrix can equivalently be described in terms of a particular class of its $Q$-solutions, hence leading to a complete system of Bethe equations. Finally, we compute the form factors of local operators for which we obtain determinant representations in finite volume.
Awrejcewicz, J.; Krysko, A. V.; Pavlov, S. P.; Zhigalov, M. V.; Krysko, V. A.
2017-09-01
Chaotic dynamics of microbeams made of functionally graded materials (FGMs) is investigated in this paper based on the modified couple stress theory and von Kármán geometric nonlinearity. We assume that the beam properties are graded along the thickness direction. The influence of size-dependent and functionally graded coefficients on the vibration characteristics, scenarios of transition from regular to chaotic vibrations as well as a series of static problems with an emphasis put on the load-deflection behavior are studied. Our theoretical/numerical analysis is supported by methods of nonlinear dynamics and the qualitative theory of differential equations supplemented by Fourier and wavelet spectra, phase portraits, and Lyapunov exponents spectra estimated by different algorithms, including Wolf's, Rosenstein's, Kantz's, and neural networks. We have also detected and numerically validated a general scenario governing transition into chaotic vibrations, which follows the classical Ruelle-Takens-Newhouse scenario for the considered values of the size-dependent and grading parameters.
Extreme value laws for fractal intensity functions in dynamical systems: Minkowski analysis
Mantica, Giorgio; Perotti, Luca
2016-09-01
Typically, in the dynamical theory of extremal events, the function that gauges the intensity of a phenomenon is assumed to be convex and maximal, or singular, at a single, or at most a finite collection of points in phase-space. In this paper we generalize this situation to fractal landscapes, i.e. intensity functions characterized by an uncountable set of singularities, located on a Cantor set. This reveals the dynamical rôle of classical quantities like the Minkowski dimension and content, whose definition we extend to account for singular continuous invariant measures. We also introduce the concept of extremely rare event, quantified by non-standard Minkowski constants and we study its consequences to extreme value statistics. Limit laws are derived from formal calculations and are verified by numerical experiments. Dedicated to the memory of Joseph Ford, on the twentieth anniversary of his departure.
DEFF Research Database (Denmark)
Lacevic, N.; Starr, F. W.; Schrøder, Thomas
2003-01-01
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...... simulations of a binary Lennard-Jones mixture approaching the mode coupling temperature from above. We find that the correlations between particles measured by g4(r,t) and S4(q,t) become increasingly pronounced on cooling. The corresponding dynamical correlation length xi4(t) extracted from the small......-q behavior of S4(q,t) provides an estimate of the range of correlated particle motion. We find that xi4(t) has a maximum as a function of time t, and that the value of the maximum of xi4(t) increases steadily from less than one particle diameter to a value exceeding nine particle diameters in the temperature...
Proton magnetic resonance imaging for assessment of lung function and respiratory dynamics
Energy Technology Data Exchange (ETDEWEB)
Eichinger, Monika [Deutsches Krebsforschungszentrum (DKFZ), Department of Radiology (E010), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany)], E-mail: m.eichinger@dkfz.de; Tetzlaff, Ralf; Puderbach, Michael [Deutsches Krebsforschungszentrum (DKFZ), Department of Radiology (E010), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany); Woodhouse, Neil [Unit of Academic Radiology, University of Sheffield (United Kingdom); Kauczor, H.-U. [Deutsches Krebsforschungszentrum (DKFZ), Department of Radiology (E010), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany)
2007-12-15
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.
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.
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
Qian, Jing-Guang; Rong, Ke; Qian, Zhenyun; Wen, Chen; Zhang, Songning
2015-11-01
[Purpose] The purpose of the study was to design and implement a multichannel dynamic functional electrical stimulation system and investigate acute effects of functional electrical stimulation of the tibialis anterior and rectus femoris on ankle and knee sagittal-plane kinematics and related muscle forces of hemiplegic gait. [Subjects and Methods] A multichannel dynamic electrical stimulation system was developed with 8-channel low frequency current generators. Eight male hemiplegic patients were trained for 4 weeks with electric stimulation of the tibia anterior and rectus femoris muscles during walking, which was coupled with active contraction. Kinematic data were collected, and muscle forces of the tibialis anterior and rectus femoris of the affected limbs were analyzed using a musculoskelatal modeling approach before and after training. A paired sample t-test was used to detect the differences between before and after training. [Results] The step length of the affected limb significantly increased after the stimulation was applied. The maximum dorsiflexion angle and maximum knee flexion angle of the affected limb were both increased significantly during stimulation. The maximum muscle forces of both the tibia anterior and rectus femoris increased significantly during stimulation compared with before functional electrical stimulation was applied. [Conclusion] This study established a functional electrical stimulation strategy based on hemiplegic gait analysis and musculoskeletal modeling. The multichannel functional electrical stimulation system successfully corrected foot drop and altered circumduction hemiplegic gait pattern.
Connizzo, Brianne K; Adams, Sheila M; Adams, Thomas H; Jawad, Abbas F; Birk, David E; Soslowsky, Louis J
2016-06-14
Recent advances in technology have allowed for the measurement of dynamic processes (re-alignment, crimp, deformation, sliding), but only a limited number of studies have investigated their relationship with mechanical properties. The overall objective of this study was to investigate the role of composition, structure, and the dynamic response to load in predicting tendon mechanical properties in a multi-level fashion mimicking native hierarchical collagen structure. Multiple linear regression models were investigated to determine the relationships between composition/structure, dynamic processes, and mechanical properties. Mediation was then used to determine if dynamic processes mediated structure-function relationships. Dynamic processes were strong predictors of mechanical properties. These predictions were location-dependent, with the insertion site utilizing all four dynamic responses and the midsubstance responding primarily with fibril deformation and sliding. In addition, dynamic processes were moderately predicted by composition and structure in a regionally-dependent manner. Finally, dynamic processes were partial mediators of the relationship between composition/structure and mechanical function, and results suggested that mediation is likely shared between multiple dynamic processes. In conclusion, the mechanical properties at the midsubstance of the tendon are controlled primarily by fibril structure and this region responds to load via fibril deformation and sliding. Conversely, the mechanical function at the insertion site is controlled by many other important parameters and the region responds to load via all four dynamic mechanisms. Overall, this study presents a strong foundation on which to design future experimental and modeling efforts in order to fully understand the complex structure-function relationships present in tendon.
Linearization models for parabolic dynamical systems via Abel's functional equation
Elin, Mark; Reich, Simeon; Shoikhet, David
2009-01-01
We study linearization models for continuous one-parameter semigroups of parabolic type. In particular, we introduce new limit schemes to obtain solutions of Abel's functional equation and to study asymptotic behavior of such semigroups. The crucial point is that these solutions are univalent functions convex in one direction. In a parallel direction, we find analytic conditions which determine certain geometric properties of those functions, such as the location of their images in either a half-plane or a strip, and their containing either a half-plane or a strip. In the context of semigroup theory these geometric questions may be interpreted as follows: is a given one-parameter continuous semigroup either an outer or an inner conjugate of a group of automorphisms? In other words, the problem is finding a fractional linear model of the semigroup which is defined by a group of automorphisms of the open unit disk. Our results enable us to establish some new important analytic and geometric characteristics of t...
Dynamic network participation of functional connectivity hubs assessed by resting-state fMRI
Schaefer, Alexander; Margulies, Daniel S.; Lohmann, Gabriele; Gorgolewski, Krzysztof J.; Smallwood, Jonathan; Kiebel, Stefan J.; Villringer, Arno
2014-01-01
Network studies of large-scale brain connectivity have demonstrated that highly connected areas, or “hubs,” are a key feature of human functional and structural brain organization. We use resting-state functional MRI data and connectivity clustering to identify multi-network hubs and show that while hubs can belong to multiple networks their degree of integration into these different networks varies dynamically over time. The extent of the network variation was related to the connectedness of the hub. In addition, we found that these network dynamics were inversely related to positive self-generated thoughts reported by individuals and were further decreased with older age. Moreover, the left caudate varied its degree of participation between a default mode subnetwork and a limbic network. This variation was predictive of individual differences in the reports of past-related thoughts. These results support an association between ongoing thought processes and network dynamics and offer a new approach to investigate the brain dynamics underlying mental experience. PMID:24860458
Izvekov, Sergei
2017-03-01
We consider the generalized Langevin equations of motion describing exactly the particle-based coarse-grained dynamics in the classical microscopic ensemble that were derived recently within the Mori-Zwanzig formalism based on new projection operators [S. Izvekov, J. Chem. Phys. 138(13), 134106 (2013)]. The fundamental difference between the new family of projection operators and the standard Zwanzig projection operator used in the past to derive the coarse-grained equations of motion is that the new operators average out the explicit irrelevant trajectories leading to the possibility of solving the projected dynamics exactly. We clarify the definition of the projection operators and revisit the formalism to compute the projected dynamics exactly for the microscopic system in equilibrium. The resulting expression for the projected force is in the form of a "generalized additive fluctuating force" describing the departure of the generalized microscopic force associated with the coarse-grained coordinate from its projection. Starting with this key expression, we formulate a new exact formula for the memory function in terms of microscopic and coarse-grained conservative forces. We conclude by studying two independent limiting cases of practical importance: the Markov limit (vanishing correlations of projected force) and the limit of weak dependence of the memory function on the particle momenta. We present computationally affordable expressions which can be efficiently evaluated from standard molecular dynamics simulations.
Abstraction of Continuous Dynamical Systems Utilizing Lyapunov Functions
DEFF Research Database (Denmark)
Sloth, Christoffer; Wisniewski, Rafal
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 t...
Directory of Open Access Journals (Sweden)
Garvita Gupta
Full Text Available Dengue genome encodes a two component protease complex (NS2B-NS3pro essential for the viral maturation/infectivity, thus representing a key drug target. Previously, due to its "complete insolubility", the isolated NS3pro could not be experimentally studied and it remains elusive what structure it adopts without NS2B and why NS2B is indispensable. Here as facilitated by our previous discovery, the isolated NS3pro has been surprisingly deciphered by NMR to be the first intrinsically-disordered chymotrypsin-like fold, which exists in a loosely-packed state with non-native long-range interactions as revealed by paramagnetic relaxation enhancement (PRE. The disordered NS3pro appears to be needed for binding a human host factor to trigger the membrane remodeling. Moreover, we have in vitro refolded the NS3pro in complex with either NS2B (48-100 or the full-length NS2B (1-130 anchored into the LMPC micelle, and the two complexes have similar activities but different dynamics. We also performed molecular dynamics (MD simulations and the results revealed that NS2B shows the highest structural fluctuations in the complex, thus providing the dynamic basis for the observation on its conformational exchange between open and closed states. Remarkably, the NS2B cofactor plays a central role in maintaining the correlated motion network required for the catalysis as we previously decoded for the SARS 3CL protease. Indeed, a truncated NS2B (48-100;Δ77-84 with the flexible loop deleted is able to trap the NS2B-NS3pro complex in a highly dynamic and catalytically-impotent state. Taken together, our study implies potential strategies to perturb the NS2B-NS3pro interface for design of inhibitors for treating dengue infection.
Mirhosseini, Mohammad Masoud; Rahmati, Mahmoud; Zargarian, Seyed Shahrooz; Khordad, Reza
2017-08-01
Molecular dynamics simulations are performed to study the design and optimization of nanocarriers with high drug loading capacity. Functionalized graphene is considered as the nominated high capacity drug carrier and Dox as the drug model. The graphene surface functionalized with hydroxyl (- OH), carboxyl (- COOH), methyl (- CH3) and amine (- NH2) groups and their associated properties are investigated. The simulation results are illustrated that G - COOH surface absorbs Dox more effectively in comparison to other functionalized graphene surfaces due to the higher binding energy of carboxylic groups and the model drug. The effect of hydrogen bonding, temperature and surface porosity are also evaluated. The results show that binding energy and the solubility parameter are temperature-dependent. The simulation results in this present work reveal the underlying mechanisms of Dox loading on neat and functionalized graphene surfaces may be employed to design better graphene-based nanocarriers for the Dox delivery applications.
Dynamical behaviors determined by the Lyapunov function in competitive Lotka-Volterra systems.
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.
Kresh, J Y; Izrailtyan, I
1998-09-01
The capacity of self-organized systems to adapt is embodied in the functional organization of intrinsic control mechanisms. Evolution in functional complexity of heart rate variability (HRV) was used as measure of the capacity of the transplanted heart to express newly emergent regulatory order. In a cross-sectional study of 100 patients after (0-10 yr) heart transplantation (HTX), heart rate dynamics were assessed using pointwise correlation dimension (PD2) analysis. A new observation is that, commencing with the acute event of allograft transplantation, the dynamics of rhythm formation proceed through complex phase transitions. At implantation, the donor heart manifested metronome-like chronotropic behavior (PD2 approximately 1.0). At 11-100 days, dimensional complexity of HRV reached a peak (PD2 approximately 2.0) associated with resurgence in the high-frequency component (0.15-0.5 Hz) of the power spectral density. Subsequent dimensional loss to PD2 approximately 1.0 at 20-30 mo after HTX was followed by a progressive near-linear gain in system complexity, reaching PD2 approximately 3.0 7-10 yr after HTX. The "dynamic reorganization" in the allograft rhythm-generating system, seen in the first 100 days, is a manifestation of the adaptive capacity of intrinsic control mechanisms. The loss of HRV 2 yr after HTX implies a withdrawal of intrinsic autonomic control and/or development of an entrained dynamic pattern characteristic of extrinsic sympathetic input. The subsequent long-term progressive rise in dimensional complexity of HRV can be attributed to the restoration of a functional order patterning parasympathetic control. The recognition that the decentralized heart can restitute the multidimensional state space of HR generator dynamics independent of external autonomic signaling may provide a new perspective on principles that constitute homeodynamic regulation.
Time-varying coupling functions: Dynamical inference and cause of synchronization transitions.
Stankovski, Tomislav
2017-02-01
Interactions in nature can be described by their coupling strength, direction of coupling, and coupling function. The coupling strength and directionality are relatively well understood and studied, at least for two interacting systems; however, there can be a complexity in the interactions uniquely dependent on the coupling functions. Such a special case is studied here: synchronization transition occurs only due to the time variability of the coupling functions, while the net coupling strength is constant throughout the observation time. To motivate the investigation, an example is used to present an analysis of cross-frequency coupling functions between delta and alpha brain waves extracted from the electroencephalography recording of a healthy human subject in a free-running resting state. The results indicate that time-varying coupling functions are a reality for biological interactions. A model of phase oscillators is used to demonstrate and detect the synchronization transition caused by the varying coupling functions during an invariant coupling strength. The ability to detect this phenomenon is discussed with the method of dynamical Bayesian inference, which was able to infer the time-varying coupling functions. The form of the coupling function acts as an additional dimension for the interactions, and it should be taken into account when detecting biological or other interactions from data.
Estimation of Response Functions Based on Variational Bayes Algorithm in Dynamic Images Sequences
Directory of Open Access Journals (Sweden)
Bowei Shan
2016-01-01
Full Text Available We proposed a nonparametric Bayesian model based on variational Bayes algorithm to estimate the response functions in dynamic medical imaging. In dynamic renal scintigraphy, the impulse response or retention functions are rather complicated and finding a suitable parametric form is problematic. In this paper, we estimated the response functions using nonparametric Bayesian priors. These priors were designed to favor desirable properties of the functions, such as sparsity or smoothness. These assumptions were used within hierarchical priors of the variational Bayes algorithm. We performed our algorithm on the real online dataset of dynamic renal scintigraphy. The results demonstrated that this algorithm improved the estimation of response functions with nonparametric priors.
2016-01-01
A review of studies performed using the R-functions theory to solve problems of nonlinear dynamics of plates and shallow shells is presented. The systematization of results and studies for the problems of free and parametric vibrations and for problems of static and dynamic stability is fulfilled. Expansion of the developed original method of discretization for nonlinear movement equations on new classes of nonlinear problems is shown. These problems include researches of vibratio...
MR-guided dynamic PET reconstruction with the kernel method and spectral temporal basis functions.
Novosad, Philip; Reader, Andrew J
2016-06-21
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 [(18)F]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
MR-guided dynamic PET reconstruction with the kernel method and spectral temporal basis functions
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
Directory of Open Access Journals (Sweden)
Minky Son
Full Text Available Porcine testicular carbonyl reductase, PTCR which is one of the short chain dehydrogenases/reductases (SDR superfamily catalyzes the NADPH-dependent reduction of carbonyl compounds including steroids and prostaglandins. Previously we reported C-terminal tail of PTCR was deleted due to a nonsynonymous single nucleotide variation (nsSNV. Here we identified from kinetic studies that the enzymatic properties for 5α-dihydrotestosterone (5α-DHT were different between wild-type and C-terminal-deleted PTCRs. Compared to wild-type PTCR, C-terminal-deleted PTCR has much higher reduction rate. To investigate structural difference between wild-type and C-terminal-deleted PTCRs upon 5α-DHT binding, we performed molecular dynamics simulations for two complexes. Using trajectories, molecular interactions including hydrogen bonding patterns, distance between 5α-DHT and catalytic Tyr193, and interaction energies are analyzed and compared. During the MD simulation time, the dynamic behavior of C-terminal tail in wild-type PTCR is also examined using essential dynamics analysis. The results of our simulations reveal that the binding conformation of 5α-DHT in C-terminal-deleted PTCR is more favorable for reduction reaction in PTCR, which shows strong agreement with kinetic data. These structural findings provide valuable information to understand substrate specificity of PTCR and further kinetic properties of enzymes belonging to the SDR superfamily.
Allosteric dynamics of SAMHD1 studied by molecular dynamics simulations
Patra, K. K.; Bhattacharya, A.; Bhattacharya, S.
2016-10-01
SAMHD1 is a human cellular enzyme that blocks HIV-1 infection in myeloid cells and non-cycling CD4+T cells. The enzyme is an allosterically regulated triphosphohydrolase that modulates the level of cellular dNTP. The virus restriction is attributed to the lowering of the pool of dNTP in the cell to a point where reverse-transcription is impaired. Mutations in SAMHD1 are also implicated in Aicardi-Goutieres syndrome. A mechanistic understanding of the allosteric activation of the enzyme is still elusive. We have performed molecular dynamics simulations to examine the allosteric site dynamics of the protein and to examine the connection between the stability of the tetrameric complex and the Allosite occupancy.
Molecular dynamics study of naturally existing cavity couplings in proteins.
Barbany, Montserrat; Meyer, Tim; Hospital, Adam; Faustino, Ignacio; D'Abramo, Marco; Morata, Jordi; Orozco, Modesto; de la Cruz, Xavier
2015-01-01
Couplings between protein sub-structures are a common property of protein dynamics. Some of these couplings are especially interesting since they relate to function and its regulation. In this article we have studied the case of cavity couplings because cavities can host functional sites, allosteric sites, and are the locus of interactions with the cell milieu. We have divided this problem into two parts. In the first part, we have explored the presence of cavity couplings in the natural dynamics of 75 proteins, using 20 ns molecular dynamics simulations. For each of these proteins, we have obtained two trajectories around their native state. After applying a stringent filtering procedure, we found significant cavity correlations in 60% of the proteins. We analyze and discuss the structure origins of these correlations, including neighbourhood, cavity distance, etc. In the second part of our study, we have used longer simulations (≥100 ns) from the MoDEL project, to obtain a broader view of cavity couplings, particularly about their dependence on time. Using moving window computations we explored the fluctuations of cavity couplings along time, finding that these couplings could fluctuate substantially during the trajectory, reaching in several cases correlations above 0.25/0.5. In summary, we describe the structural origin and the variations with time of cavity couplings. We complete our work with a brief discussion of the biological implications of these results.
NMR Dynamic Studies in Living Systems
Institute of Scientific and Technical Information of China (English)
闫永彬; 范明杰; 罗雪春; 张日清
2002-01-01
Nuclear magnetic resonance (NMR) can noninvasively monitor the intracellular concentrations and kinetic properties of numerous inorganic and organic compounds. These characteristics have made NMR a useful tool for dynamic studies of living systems. Applications of NMR to living systems have successfully extended to many areas, including studies of metabolic regulation, ion transport, and intracellular reaction rates in vivo. The major purpose of this review is to summarize the results that can be obtained by modern NMR techniques in living systems. With the advances of new techniques, NMR measurements of various nuclides have been performed for specific physiological purposes. Although some technical problems still remain and there are still discrepancies between NMR and traditional biochemical results, the abundant and unique information obtained from NMR spectra suggests that NMR will be more extensively applied in future studies of living systems. The fast development of these new techniques is providing many new NMR applications in living systems, as well as in structural biology.
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...... demonstrated from the time dependence of the mean-square displacement of the molecules and the two-dimensional diffusion coefficient is estimated to be 2–3×10-5 cm2/s at 75–80 K.......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...
Institute of Scientific and Technical Information of China (English)
王志萍; 朱云; 吴亚敏; 张秀梅
2014-01-01
采用将含时密度泛函理论和分子动力学非绝热耦合的方法，研究了不同入射速度下质子与羟基碰撞的反应动力学。计算了碰撞前后质子动能和羟基动能的变化及羟基电子和质子的运动。计算结果表明，质子沿垂直羟基分子轴方向入射时，质子与羟基碰撞后，质子被反弹且动能损失并俘获了羟基中氧的一部分电子，而丢失部分电子的羟基则获得动能以伸缩振动的形式向计算边界平动。随着入射质子的初动能增加，质子从羟基中俘获的电子增多，碰撞后羟基的键长变长，羟基振动变强而伸缩振动频率降低。此外，还发现质子的入射方向对碰撞过程的激发动力学有很大的影响。质子从不同的方向入射时，质子的入射初动能越大，其损失的动能越多且损失的动能与入射初动能呈线性关系，而入射方向对质子动能损失的影响很小。在质子入射初动能较低(小于25 eV)的情况下，羟基获得的动能与质子入射初动能呈线性关系且与入射方向无关；在质子入射初动能较高(大于25 eV)时，当质子沿羟基分子轴方向入射时，羟基动能的增量远大于质子沿垂直于羟基分子轴方向入射时羟基动能的增量。%Using the time-dependent density functional theory and non-adiabatic coupling in molecular dynamics, the reaction dynamics of collisions between energetic proton and hydroxy is studied. The variations in kinetic energy of proton and hydroxy and the motions of electron of hydroxyl and ion before and after collisions are investigated. It is found that when a proton is incident in the direction perpendicular to the molecular axis, it that has lose kinetic energy rebounds, and captures electrons from hydroxy, while the hydroxy that has lost part of electrons gains kinetic energy , and thus translates toward the calculating boundary in the manner of contracting vibration. The larger the
Dynamical Study of 3D Boson Stars
Choi, Dae-Il; Choptuik, M. W.
1998-10-01
We study the dynamical evolution of ``boson stars'' in 3D numerical relativity. Boson stars are equilibrium states of a self-gravitating, complex Klein-Gordon field: a resurgence of interest in scalar fields in the context of astroparticle physics and quantum cosmology has prompted investigation of their dynamics, particularly since they are possible dark matter candidates. In addition, even though any direct physical relevance has yet to be demonstrated, boson star systems provide excellent numerical laboratories in which to study strong gravitational fields. Specifically, the boson star model provides an ideal vehicle with which to implement and evaluate (1) various coordinate conditions in the context of the ADM formalism, and (2) multi-dimensional adaptive mesh refinement techniques which appear crucial for many problems in 3D numerical relativity. We first consider boson stars in the Newtonian regime, where the (numerical) stability of single stars is shown and the interaction of multiple-star-systems is simulated. We also discuss issues which hamper progress towards a stable evolution of general relativistic boson stars, and then show some preliminary results for the general relativistic case.
Functional verification of dynamically reconfigurable FPGA-based systems
Gong, Lingkan
2015-01-01
This book analyzes the challenges in verifying Dynamically Reconfigurable Systems (DRS) with respect to the user design and the physical implementation of such systems. The authors describe the use of a simulation-only layer to emulate the behavior of target FPGAs and accurately model the characteristic features of reconfiguration. Readers are enabled with this simulation-only layer to maintain verification productivity by abstracting away the physical details of the FPGA fabric. Two implementations of the simulation-only layer are included: Extended ReChannel is a SystemC library that can be used to check DRS designs at a high level; ReSim is a library to support RTL simulation of a DRS reconfiguring both its logic and state. Through a number of case studies, the authors demonstrate how their approach integrates seamlessly with existing, mainstream DRS design flows and with well-established verification methodologies such as top-down modeling and coverage-driven verification. Provides researchers with an i...
Roondhe, Basant; Upadhyay, Deepak; Som, Narayan; Pillai, Sharad B.; Shinde, Satyam; Jha, Prafulla K.
2017-03-01
The structural, electronic, dynamical and thermodynamical properties of CmX (X = N, P, As, Sb, and Bi) compounds are studied using first principles calculations within density functional theory. The Perdew-Burke-Ernzerhof spin polarized generalized gradient approximation and Perdew-Wang (PW) spin polarized local density approximation as the exchange correlational functionals are used in these calculations. There is a good agreement between the present and previously reported data. The calculated electronic density of states suggests that the curium monopnictides are metallic in nature, which is consistent with earlier studies. The significant values of magnetic moment suggest their magnetic nature. The phonon dispersion curves and phonon density of states are also calculated, which depict the dynamical stability of these compounds. There is a significant separation between the optical and acoustical phonon branches. The temperature dependence of the thermodynamical functions are also calculated and discussed. Internal energy and vibrational contribution to the Helmholtz free energy increases and decreases, respectively, with temperature. The entropy increases with temperature. The specific heat at constant volume and Debye temperature obey Debye theory. The temperature variation of the considered thermodynamical functions is in line with those of other crystalline solids.
Max-Sum Diversification, Monotone Submodular Functions and Dynamic Updates
Borodin, Allan; Ye, Yuli
2012-01-01
Result diversification has many important applications in databases, operations research, information retrieval, and finance. In this paper, we study and extend a particular version of result diversification, known as max-sum diversification. More specifically, we consider the setting where we are given a set of elements in a metric space and a set valuation function $f$ defined on every subset. For any given subset $S$, the overall objective is a linear combination of $f(S)$ and the sum of the distances induced by $S$. The goal is to find a subset $S$ satisfying some constraints that maximizes the overall objective. This problem is first studied by Gollapudi and Sharma for modular set functions and for sets satisfying a cardinality constraint. We consider an extension of the modular case to the monotone submodular case, for which the previous algorithm no longer applies. Interestingly, we are able to match the 2-approximation using a natural, but different greedy algorithm. We then further extend the problem...
Dynamic functional brain networks involved in simple visual discrimination learning.
Fidalgo, Camino; Conejo, Nélida María; González-Pardo, Héctor; Arias, Jorge Luis
2014-10-01
Visual discrimination tasks have been widely used to evaluate many types of learning and memory processes. However, little is known about the brain regions involved at different stages of visual discrimination learning. We used cytochrome c oxidase histochemistry to evaluate changes in regional brain oxidative metabolism during visual discrimination learning in a water-T maze at different time points during training. As compared with control groups, the results of the present study reveal the gradual activation of cortical (prefrontal and temporal cortices) and subcortical brain regions (including the striatum and the hippocampus) associated to the mastery of a simple visual discrimination task. On the other hand, the brain regions involved and their functional interactions changed progressively over days of training. Regions associated with novelty, emotion, visuo-spatial orientation and motor aspects of the behavioral task seem to be relevant during the earlier phase of training, whereas a brain network comprising the prefrontal cortex was found along the whole learning process. This study highlights the relevance of functional interactions among brain regions to investigate learning and memory processes. Copyright © 2014 Elsevier Inc. All rights reserved.
Functional network macroscopes for probing past and present Earth system dynamics (Invited)
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
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.
Microbial Diversity Indexes Can Explain Soil Carbon Dynamics as a Function of Carbon Source
Maron, Pierre-Alain; Menasseri-Aubry, Safya; Sarr, Amadou; Lévêque, Jean; Mathieu, Olivier; Jolivet, Claudy; Leterme, Philippe; Viaud, Valérie
2016-01-01
Mathematical models do not explicitly represent the influence of soil microbial diversity on soil organic carbon (SOC) dynamics despite recent evidence of relationships between them. The objective of the present study was to statistically investigate relationships between bacterial and fungal diversity indexes (richness, evenness, Shannon index, inverse Simpson index) and decomposition of different pools of soil organic carbon by measuring dynamics of CO2 emissions under controlled conditions. To this end, 20 soils from two different land uses (cropland and grassland) were incubated with or without incorporation of 13C-labelled wheat-straw residue. 13C-labelling allowed us to study residue mineralisation, basal respiration and the priming effect independently. An innovative data-mining approach was applied, based on generalized additive models and a predictive criterion. Results showed that microbial diversity indexes can be good covariates to integrate in SOC dynamics models, depending on the C source and the processes considered (native soil organic carbon vs. fresh wheat residue). Specifically, microbial diversity indexes were good candidates to help explain mineralisation of native soil organic carbon, while priming effect processes seemed to be explained much more by microbial composition, and no microbial diversity indexes were found associated with residue mineralisation. Investigation of relationships between diversity and mineralisation showed that higher diversity, as measured by the microbial diversity indexes, seemed to be related to decreased CO2 emissions in the control soil. We suggest that this relationship can be explained by an increase in carbon yield assimilation as microbial diversity increases. Thus, the parameter for carbon yield assimilation in mathematical models could be calculated as a function of microbial diversity indexes. Nonetheless, given limitations of the methods used, these observations should be considered with caution and
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
Study of dynamic strain aging in dual phase steel
Energy Technology Data Exchange (ETDEWEB)
Queiroz, R.R.U. [Instituto Federal de Minas Gerais. Rua Pandia Calogeras, 898, Bauxita, Ouro Preto, MG (Brazil); Cunha, F.G.G. [Department of Metallurgical and Materials Engineering, Universidade Federal de Minas Gerais, Av. Antonio Carlos, 6627, Pampulha, Belo Horizonte, MG (Brazil); Gonzalez, B.M., E-mail: gonzalez@demet.ufmg.br [Department of Metallurgical and Materials Engineering, Universidade Federal de Minas Gerais, Av. Antonio Carlos, 6627, Pampulha, Belo Horizonte, MG (Brazil)
2012-05-01
Highlights: Black-Right-Pointing-Pointer Characterization of the high temperature mechanical behavior of a dual phase steel. Black-Right-Pointing-Pointer Determination of the effect of dynamic strain aging on the strain hardening rate. Black-Right-Pointing-Pointer Identification of the mechanism associated with dynamic strain aging. Black-Right-Pointing-Pointer 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 Degree-Sign C and 600 Degree-Sign C and at strain rates ranging from 10{sup -2} to 5 Multiplication-Sign 10{sup -4} s{sup -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.
Prakash, T.; Sundararajan, N.; Ganapathi, M.
2007-01-01
Here, the dynamic thermal buckling behavior of functionally graded spherical caps is studied considering geometric nonlinearity based on von Karman's assumptions. The formulation is based on first-order shear deformation theory and it includes the in-plane and rotary inertia effects. The material properties are graded in the thickness direction according to the power-law distribution in terms of volume fractions of the material constituents. The effective material properties are evaluated using homogenization method. The governing equations obtained using finite element approach are solved employing the Newmark's integration technique coupled with a modified Newton-Raphson iteration scheme. The pressure load corresponding to a sudden jump in the maximum average displacement in the time history of the shell structure is taken as the dynamic buckling load. The present model is validated against the available isotropic case. A detailed numerical study is carried out to highlight the influences of shell geometries, power law index of functional graded material and boundary conditions on the dynamic buckling load of shallow spherical shells.
Tools for the study of dynamical spacetimes
Zhang, Fan
This thesis covers a range of topics in numerical and analytical relativity, centered around introducing tools and methodologies for the study of dynamical spacetimes. The scope of the studies is limited to classical (as opposed to quantum) vacuum spacetimes described by Einstein's general theory of relativity. The numerical works presented here are carried out within the Spectral Einstein Code (SpEC) infrastructure, while analytical calculations extensively utilize Wolfram's Mathematica program. We begin by examining highly dynamical spacetimes such as binary black hole mergers, which can be investigated using numerical simulations. However, there are difficulties in interpreting the output of such simulations. One difficulty stems from the lack of a canonical coordinate system (henceforth referred to as gauge freedom) and tetrad, against which quantities such as Newman-Penrose Psi4 (usually interpreted as the gravitational wave part of curvature) should be measured. We tackle this problem in Chapter 2 by introducing a set of geometrically motivated coordinates that are independent of the simulation gauge choice, as well as a quasi-Kinnersley tetrad, also invariant under gauge changes in addition to being optimally suited to the task of gravitational wave extraction. Another difficulty arises from the need to condense the overwhelming amount of data generated by the numerical simulations. In order to extract physical information in a succinct and transparent manner, one may define a version of gravitational field lines and field strength using spatial projections of the Weyl curvature tensor. Introduction, investigation and utilization of these quantities will constitute the main content in Chapters 3 through 6. For the last two chapters, we turn to the analytical study of a simpler dynamical spacetime, namely a perturbed Kerr black hole. We will introduce in Chapter 7 a new analytical approximation to the quasi-normal mode (QNM) frequencies, and relate various
Molecular beam studies of reaction dynamics
Energy Technology Data Exchange (ETDEWEB)
Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)
1993-12-01
The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.
Ultrasonic Study of Dislocation Dynamics in Lithium -
Han, Myeong-Deok
1987-09-01
Experimental studies of dislocation dynamics in LiF single crystals, using ultrasonic techniques combined with dynamic loading, were performed to investigate the time evolution of the plastic deformation process under a short stress pulse at room temperature, and the temperature dependence of the dislocation damping mechanism in the temperature range 25 - 300(DEGREES)K. From the former, the time dependence of the ultrasonic attenuation was understood as resulting from dislocation multiplication followed by the evolution of mobile dislocations to immobile ones under large stress. From the latter, the temperature dependence of the ultrasonic attenuation was interpreted as due to the motion of the dislocation loops overcoming the periodic Peierls potential barrier in a manner analogous to the motion of a thermalized sine-Gordon chain under a small stress. The Peierls stress obtained from the experimental results by application of Seeger's relaxation model with exponential dislocation length distribution was 4.26MPa, which is consistent with the lowest stress for the linear relation between the dislocation velocity and stress observed by Flinn and Tinder.
Partial volume effects in dynamic contrast magnetic resonance renal studies
Energy Technology Data Exchange (ETDEWEB)
Gutierrez, D. Rodriguez, E-mail: drodriguez@biotronics3d.co [CVSSP, Faculty of Engineering and Physical Sciences, University of Surrey (United Kingdom); Wells, K., E-mail: k.wells@surrey.ac.u [CVSSP, Faculty of Engineering and Physical Sciences, University of Surrey (United Kingdom); Diaz Montesdeoca, O., E-mail: o.diaz.montesdeoca@gmail.co [EUITT, Universidad de Las Palmas de Gran Canaria (Spain); Moran Santana, A. [EUITT, Universidad de Las Palmas de Gran Canaria (Spain); Mendichovszky, I.A., E-mail: iosifm@hotmail.co [Radiology and Physics Unit, UCL Institute of Child Health, London WC1N 1EH (United Kingdom); Gordon, I., E-mail: i.gordon@ich.ucl.ac.u [Radiology and Physics Unit, UCL Institute of Child Health, London WC1N 1EH (United Kingdom)
2010-08-15
This is the first study of partial volume effect in quantifying renal function on dynamic contrast enhanced magnetic resonance imaging. Dynamic image data were acquired for a cohort of 10 healthy volunteers. Following respiratory motion correction, each voxel location was assigned a mixing vector representing the 'overspilling' contributions of each tissue due to the convolution action of the imaging system's point spread function. This was used to recover the true intensities associated with each constituent tissue. Thus, non-renal contributions from liver, spleen and other surrounding tissues could be eliminated from the observed time-intensity curves derived from a typical renal cortical region of interest. This analysis produced a change in the early slope of the renal curve, which subsequently resulted in an enhanced glomerular filtration rate estimate. This effect was consistently observed in a Rutland-Patlak analysis of the time-intensity data: the volunteer cohort produced a partial volume effect corrected mean enhancement of 36% in relative glomerular filtration rate with a mean improvement of 7% in r{sup 2} fitting of the Rutland-Patlak model compared to the same analysis undertaken without partial volume effect correction. This analysis strongly supports the notion that dynamic contrast enhanced magnetic resonance imaging of kidneys is substantially affected by the partial volume effect, and that this is a significant obfuscating factor in subsequent glomerular filtration rate estimation.
NATO Advanced Study Institute on Hamiltonian Dynamical Systems and Applications
2008-01-01
Physical laws are for the most part expressed in terms of differential equations, and natural classes of these are in the form of conservation laws or of problems of the calculus of variations for an action functional. These problems can generally be posed as Hamiltonian systems, whether dynamical systems on finite dimensional phase space as in classical mechanics, or partial differential equations (PDE) which are naturally of infinitely many degrees of freedom. This volume is the collected and extended notes from the lectures on Hamiltonian dynamical systems and their applications that were given at the NATO Advanced Study Institute in Montreal in 2007. Many aspects of the modern theory of the subject were covered at this event, including low dimensional problems as well as the theory of Hamiltonian systems in infinite dimensional phase space; these are described in depth in this volume. Applications are also presented to several important areas of research, including problems in classical mechanics, continu...
A quantum molecular dynamics study of aqueous solvation dynamics
Videla, Pablo E.; Rossky, Peter J.; Laria, D.
2013-10-01
Ring polymer molecular dynamics experiments have been carried out to examine effects derived from nuclear quantum fluctuations at ambient conditions on equilibrium and non-equilibrium dynamical characteristics of charge solvation by a popular simple, rigid, water model, SPC/E, and for a more recent, and flexible, q-TIP4P/F model, to examine the generality of conclusions. In particular, we have recorded the relaxation of the solvent energy gap following instantaneous, ±e charge jumps in an initially uncharged Lennard-Jones-like solute. In both charge cases, quantum effects are reflected in sharper decays at the initial stages of the relaxation, which produce up to a ˜20% reduction in the characteristic timescales describing the solvation processes. For anionic solvation, the magnitude of polarization fluctuations controlling the extent of the water proton localization in the first solvation shell is somewhat more marked than for cations, bringing the quantum solvation process closer to the classical case. Effects on the solvation response from the explicit incorporation of flexibility in the water Hamiltonian are also examined. Predictions from linear response theories for the overall relaxation profile and for the corresponding characteristic timescales are reasonably accurate for the solvation of cations, whereas we find that they are much less satisfactory for the anionic case.
Molecular dynamics studies of aromatic hydrocarbon liquids
Energy Technology Data Exchange (ETDEWEB)
McLaughlin, E.; Gupta, S.
1990-01-01
This project mainly involves a molecular dynamics and Monte Carlo study of the effect of molecular shape on thermophysical properties of bulk fluids with an emphasis on the aromatic hydrocarbon liquids. In this regard we have studied the modeling, simulation methodologies, and predictive and correlating methods for thermodynamic properties of fluids of nonspherical molecules. In connection with modeling we have studied the use of anisotropic site-site potentials, through a modification of the Gay-Berne Gaussian overlap potential, to successfully model the aromatic rings after adding the necessary electrostatic moments. We have also shown these interaction sites should be located at the geometric centers of the chemical groups. In connection with predictive methods, we have shown two perturbation type theories to work well for fluids modeled using one-center anisotropic potentials and the possibility exists for extending these to anisotropic site-site models. In connection with correlation methods, we have studied, through simulations, the effect of molecular shape on the attraction term in the generalized van der Waals equation of state for fluids of nonspherical molecules and proposed a possible form which is to be studied further. We have successfully studied the vector and parallel processing aspects of molecular simulations for fluids of nonspherical molecules.
Small-world topology of functional connectivity in randomly connected dynamical systems.
Hlinka, J; Hartman, D; Paluš, M
2012-09-01
Characterization of real-world complex systems increasingly involves the study of their topological structure using graph theory. Among global network properties, small-world property, consisting in existence of relatively short paths together with high clustering of the network, is one of the most discussed and studied. When dealing with coupled dynamical systems, links among units of the system are commonly quantified by a measure of pairwise statistical dependence of observed time series (functional connectivity). We argue that the functional connectivity approach leads to upwardly biased estimates of small-world characteristics (with respect to commonly used random graph models) due to partial transitivity of the accepted functional connectivity measures such as the correlation coefficient. In particular, this may lead to observation of small-world characteristics in connectivity graphs estimated from generic randomly connected dynamical systems. The ubiquity and robustness of the phenomenon are documented by an extensive parameter study of its manifestation in a multivariate linear autoregressive process, with discussion of the potential relevance for nonlinear processes and measures.
Behavior of the Escape Rate Function in Hyperbolic Dynamical Systems
Demers, Mark
2011-01-01
For a fixed initial reference measure, we study the dependence of the escape rate on the hole for a smooth or piecewise smooth hyperbolic map. First, we prove the existence and Holder continuity of the escape rate for systems with small holes admitting Young towers. Then we consider general holes for Anosov diffeomorphisms, without size or Markovian restrictions. We prove bounds on the upper and lower escape rates using the notion of pressure on the survivor set and show that a variational principle holds under generic conditions. However, we also show that the escape rate function forms a devil's staircase with jumps along sequences of regular holes and present examples to elucidate some of the difficulties involved in formulating a general theory.
Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps
Directory of Open Access Journals (Sweden)
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
Stauch, Kelly L; Purnell, Phillip R; Fox, Howard S
2014-04-01
Aging correlates with a progressive impairment of mitochondrial homeostasis and is an influential factor for several forms of neurodegeneration. However, the mechanisms underlying age-related alterations in synaptosomal mitochondria, a neuronal mitochondria population highly susceptible to insults and critical for brain function, remain incompletely understood. Therefore this study investigates the synaptic mitochondrial proteomic and bioenergetic alterations that occur with age. The utilization of a state of the art quantitative proteomics approach allowed for the comparison of protein expression levels in synaptic mitochondria isolated from 5 (mature), 12 (old), and 24 (aged) month old mice. During the process of aging we find that dynamic proteomic alterations occur in synaptic mitochondria. Despite direct (mitochondrial DNA deletions) and indirect (increased antioxidant protein levels) signs of mitochondrial damage in the aged mice, there was an overall maintenance of mitochondrial function. Therefore the synaptic mitochondrial proteomic changes that occur with aging correlate with preservation of synaptic mitochondrial function.
Changes in functional connectivity dynamics associated with vigilance network in taxi drivers.
Shen, Hui; Li, Zhenfeng; Qin, Jian; Liu, Qiang; Wang, Lubin; Zeng, Ling-Li; Li, Hong; Hu, Dewen
2016-01-01
An increasing number of neuroimaging studies have suggested that the fluctuations of low-frequency resting-state functional connectivity (FC) are not noise but are instead linked to the shift between distinct cognitive states. However, there is very limited knowledge about whether and how the fluctuations of FC at rest are influenced by long-term training and experience. Here, we investigated how the dynamics of resting-state FC are linked to driving behavior by comparing 20 licensed taxi drivers with 20 healthy non-drivers using a sliding window approach. We found that the driving experience could be effectively decoded with 90% (ptaxi. Furthermore, temporally quasi-stable functional connectivity segmentation revealed significant differences between the drivers and non-drivers in the dwell time of specific vigilance-related transient brain states, although the brain's repertoire of functional states was preserved. Overall, these results suggested a significant link between the changes in the time-dependent aspects of resting-state FC within the vigilance network and long-term driving experiences. The results not only improve our understanding of how the brain supports driving behavior but also shed new light on the relationship between the dynamics of functional brain networks and individual behaviors. Copyright © 2015 Elsevier Inc. All rights reserved.
Thermodynamic functions from lattice dynamic of KMgH{sub 3} for hydrogen storage applications
Energy Technology Data Exchange (ETDEWEB)
Bouhadda, Youcef, E-mail: bouhadda@yahoo.com [Unite de Recherche Appliquee en Energies Renouvelables, BP 88, Ghardaia (Algeria); Kheloufi, Nawal; Bentabet, Abdelouahab [Centre universistaire Bordj Bouariej (Algeria); Boudouma, Youcef [Faculte de Physique USTHB, Alger (Algeria); Fenineche, Noureddine [LERMPS, UTBM, Belfort (France); Benyalloul, Kamel [Unite de Recherche Appliquee en Energies Renouvelables, BP 88, Ghardaia (Algeria)
2011-09-15
Highlights: > The dynamical and thermodynamic properties of KMgH{sub 3} are presented. > The density of state is calculated and shows that the KMgH{sub 3} is an insulator. > Formation energy of the KMgH{sub 3} is calculated for different possible reaction pathways. > The phonon frequencies at gamma point for the infrared and Raman modes are assigned. > The thermodynamic functions of KMgH{sub 3} are determined for the first time in this study. - Abstract: The dynamic and the thermodynamic properties of KMgH{sub 3} have been investigated by density functional theory (DFT). We have found that the calculated lattice parameters differ from the experimental data by less than 0.6% and the electronic density of states (DOS) reveals that the KMgH{sub 3} is an insulator. The formation energy of KMgH{sub 3} from binary hydrides (MgH{sub 2} and KH) has been calculated. Using density-functional perturbation theory, we have calculated the phonon dispersion curves, the phonon density of states, the Born effective charge tensors, the dielectric permittivity tensors and the phonon frequencies at the center of the Brillouin zone of KMgH{sub 3}. Also we have assigned the calculated phonon frequencies at the gamma point for Infrared-active and Raman-active modes. For the first time, the thermodynamic functions are computed using the phonon density of states.
Indian Academy of Sciences (India)
Y Pathania; P K Ahluwalla
2005-09-01
We have carried out a molecular dynamics simulation of two- and three- dimensional double Yukawa fluids near the triple point. We have compared some of the static and dynamic correlation functions with those of Lennard{Jones, when parameters occurring in double Yukawa potential are chosen to fit Lennard-Jones potential. The results are in good agreement. However, when repulsive and attractive parameters occurring in double Yukawa potential are varied, we found distinct differences in static and dynamic correlation functions. We have also compared the two-dimensional correlation functions with those of three-dimensional to study the effect of dimensionality, near the triple point region.
Dynamic speckle study of microbial growth
Vincitorio, F. M.; Mulone, C.; Marcuzzi, P. A.; Budini, N.; Freyre, C.; Lopez, A. J.; Ramil, A.
2015-08-01
In this work we present a characterization of yeast dynamic speckle activity during growth in an isolated agar culture medium. We found that it is possible to detect the growth of the microorganisms even before they turn out to be visible. By observing the time evolution of the speckle activity at different regions of the culture medium we could extract a map of the growth process, which served to analyze how the yeast develops and spreads over the agar's medium. An interesting point of this study concerns with the influence of the laser light on the yeast growth rate. We have found that yeast finds hard to develop at regions with higher laser light illumination, although we used a synchronous system to capture the speckle pattern. The results obtained in this work would serve us as a starting point to fabricate a detector of growing microorganism colonies, with obvious interesting applications in diverse areas.
Monte Carlo study of real time dynamics
Alexandru, Andrei; Bedaque, Paulo F; Vartak, Sohan; Warrington, Neill C
2016-01-01
Monte Carlo studies involving real time dynamics are severely restricted by the sign problem that emerges from highly oscillatory phase of the path integral. In this letter, we present a new method to compute real time quantities on the lattice using the Schwinger-Keldysh formalism via Monte Carlo simulations. The key idea is to deform the path integration domain to a complex manifold where the phase oscillations are mild and the sign problem is manageable. We use the previously introduced "contraction algorithm" to create a Markov chain on this alternative manifold. We substantiate our approach by analyzing the quantum mechanical anharmonic oscillator. Our results are in agreement with the exact ones obtained by diagonalization of the Hamiltonian. The method we introduce is generic and in principle applicable to quantum field theory albeit very slow. We discuss some possible improvements that should speed up the algorithm.
Molecular dynamics study of ice structural evolution
Institute of Scientific and Technical Information of China (English)
Wang Yan; Dong Shun-Le
2008-01-01
Molecular dynamics simulation is employed to study the structural evolution of low density amorphous ice during its compression from one atmosphere to 2.5 GPa. Calculated results show that high density amorphous ice is formed at an intermediate pressure of～1.0GPa; the O-O-O bond angle ranges from 83° to 113°, and the O-H...O bond is bent from 112° to 160°. Very high density amorphous ice is obtained by quenching to 80K and decompressing the ice to ambient pressure from 160 K/1.3 GPa or 160 K/1.7 GPa; and the next-nearest O-O length is found to be 0.310 nm, just 0.035 nm beyond the nearest O-O distance of 0.275 nm.
GROUP DYNAMICS AND TEAM FUNCTIONING IN ORGANIZATIONAL CONTEXT
Directory of Open Access Journals (Sweden)
Raluca ZOLTAN
2015-07-01
Full Text Available In all kind of organization many activities are done by groups and teams. But how are they formed? What factors influence their existence and development? How members of groups and teams are selected? Which are the consequences in organizational context? In order to answer these questions, in the present paper we describe and analyze the main approaches regarding the formation of work groups and work teams (sociometric approach and group dynamics approach, the main factors that affects group dynamics and the FIRO model for evaluation the team members’ needs.
Dynamic modelling of pectin extraction describing yield and functional characteristics
DEFF Research Database (Denmark)
Andersen, Nina Marianne; Cognet, T.; Santacoloma, P. A.
2017-01-01
A dynamic model of pectin extraction is proposed that describes pectin yield, degree of esterification and intrinsic viscosity. The dynamic model is one dimensional in the peel geometry and includes mass transport of pectin by diffusion and reaction kinetics of hydrolysis, degradation and de-esterification....... The model takes into account the effects of the process conditions such as temperature and acid concentration on extraction kinetics. It is shown that the model describes pectin bulk solution concentration, degree of esterification and intrinsic viscosity in pilot scale extractions from lime peel...
Oxidation dynamics of nanophase aluminum clusters : a molecular dynamics study.
Energy Technology Data Exchange (ETDEWEB)
Ogata, S.
1998-01-27
Oxidation of an aluminum nanocluster (252,158 atoms) of radius 100{angstrom} placed in gaseous oxygen (530,727 atoms) is investigated by performing molecular-dynamics simulations on parallel computers. The simulation takes into account the effect of charge transfer between Al and O based on the electronegativity equalization principles. We find that the oxidation starts at the surface of the cluster and the oxide layer grows to a thickness of {approximately}28{angstrom}. Evolutions of local temperature and densities of Al and O are investigated. The surface oxide melts because of the high temperature resulting from the release of energy associated with Al-O bondings. Amorphous surface-oxides are obtained by quenching the cluster. Vibrational density-of-states for the surface oxide is analyzed through comparisons with those for crystalline Al, Al nanocluster, and {alpha}-Al{sub 2}O{sub 3}.
Dissociation of polycyclic aromatic hydrocarbons: molecular dynamics studies
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'.
Directory of Open Access Journals (Sweden)
Wladyslaw A. Krajewski
2016-03-01
Full Text Available Evidence is emerging that many diseases result from defects in gene functions, which, in turn, depend on the local chromatin environment of a gene. However, it still remains not fully clear how chromatin activity code is ‘translated’ to the particular ‘activating’ or ‘repressing’ chromatin structural transition. Commonly, chromatin remodeling in vitro was studied using mononucleosomes as a model. However, recent data suggest that structural reorganization of a single mononucleosome is not equal to remodeling of a nucleosome particle under multinucleosomal content – such as, interaction of nucleosomes via flexible histone termini could significantly alter the mode (and the resulting products of nucleosome structural transitions. It is becoming evident that a nucleosome array does not constitute just a ‘polymer’ of individual ‘canonical’ nucleosomes due to multiple inter-nucleosomal interactions which affect nucleosome dynamics and structure. It could be hypothesized, that inter-nucleosomal interactions could act in cooperation with nucleosome inherent dynamics to orchestrate DNA-based processes and promote formation and stabilization of highly-dynamic, accessible structure of a nucleosome array. In the proposed paper we would like to discuss the nucleosome dynamics within the chromatin fiber mainly as it pertains to the roles of the structural changes mediated by inter-nucleosomal interactions.
Hernández, Antonio; Dhaher, Yasin; Thelen, Darryl G
2008-01-01
Forward dynamic models suggest that muscle-induced joint motions depend on dynamic coupling between body segments. As a result, biarticular muscles may exhibit non-intuitive behavior in which the induced joint motion is opposite to that assumed based on anatomy. Empirical validation of such predictions is important for models to be relied upon to characterize muscle function. In this study, we measured, in vivo, the hip and knee accelerations induced by electrical stimulation of the rectus femoris (RF) and the vastus medialis (VM) at postures representatives of the toe-off and early swing phases of the gait cycle. Seven healthy young subjects were positioned side-lying with their lower limb supported on air bearings while a 90 ms pulse train stimulated each muscle separately or simultaneously. Lower limb kinematics were measured and compared to predictions from a similarly configured dynamic model of the lower limb. We found that both RF and VM, when stimulated independently, accelerated the hip and knee into extension at these postures, consistent with model predictions. Predicted ratios of hip acceleration to knee acceleration were generally within 1 s.d. of average values. In addition, measured responses to simultaneous RF and VM stimulation were within 13% of predictions based on the assumption that joint accelerations induced by activating two muscles simultaneously can be found by adding the joint accelerations induced by activating the same muscles independently. These results provide empirical evidence of the importance of considering dynamic effects when interpreting the role of muscles in generating movement.
Probabilistic density function method for nonlinear dynamical systems driven by colored noise
Energy Technology Data Exchange (ETDEWEB)
Barajas-Solano, David A.; Tartakovsky, Alexandre M.
2016-05-01
We present a probability density function (PDF) method for a system of nonlinear stochastic ordinary differential equations driven by colored noise. The method provides an integro-differential equation for the temporal evolution of the joint PDF of the system's state, which we close by means of a modified Large-Eddy-Diffusivity-type closure. Additionally, we introduce the generalized local linearization (LL) approximation for deriving a computable PDF equation in the form of the second-order partial differential equation (PDE). We demonstrate the proposed closure and localization accurately describe the dynamics of the PDF in phase space for systems driven by noise with arbitrary auto-correlation time. We apply the proposed PDF method to the analysis of a set of Kramers equations driven by exponentially auto-correlated Gaussian colored noise to study the dynamics and stability of a power grid.
Dynamics in the Kuramoto model with a bi-harmonic coupling function
Yuan, Di; Cui, Haitao; Tian, Junlong; Xiao, Yi; Zhang, Yingxin
2016-09-01
We study a variant of the Kuramoto model with a bi-harmonic coupling function, in which oscillators with positive first harmonic coupling strength are conformists and oscillators with negative first harmonic coupling strength are contrarians. We show that the model displays different synchronous dynamics and different dynamics may be characterized by the phase distributions of oscillators. There exist stationary synchronous states, travelling wave states, π state and, most interestingly, another type of nonstationary state: an oscillating π state. The phase distribution oscillates in a confined region and the phase difference between conformists and contrarians oscillates around π with a constant amplitude and a constant period in oscillating π state. Finally, the bifurcation diagram of the model in the parameter space is presented.
Nonparametric modeling of dynamic functional connectivity in fmri data
DEFF Research Database (Denmark)
Nielsen, Søren Føns Vind; Madsen, Kristoffer H.; Røge, Rasmus
2015-01-01
in Bayesian statistical modeling we use the predictive likelihood to investigate if the model can discriminate between a motor task and rest both within and across subjects. We further investigate what drives dynamic states using the model on the entire data collated across subjects and task/rest. We find...
Simultaneous dynamic electrical and structural measurements of functional materials
Energy Technology Data Exchange (ETDEWEB)
Vecchini, C.; Stewart, M.; Muñiz-Piniella, A.; Wooldridge, J. [National Physical Laboratory, Hampton Road, Teddington TW11 0LW (United Kingdom); Thompson, P.; McMitchell, S. R. C.; Bouchenoire, L.; Brown, S.; Wermeille, D.; Lucas, C. A. [XMaS, The UK-CRG, ESRF-The European Synchrotron, CS40220, F-38043, Grenoble Cedex 09 (France); Department of Physics, University of Liverpool, Liverpool L69 3BX (United Kingdom); Lepadatu, S. [National Physical Laboratory, Hampton Road, Teddington TW11 0LW (United Kingdom); Jeremiah Horrocks Institute, University of Central Lancashire, Preston PR1 2HE (United Kingdom); Bikondoa, O.; Hase, T. P. A. [XMaS, The UK-CRG, ESRF-The European Synchrotron, CS40220, F-38043, Grenoble Cedex 09 (France); Department of Physics, University of Warwick, Coventry CV4 7AL (United Kingdom); Lesourd, M. [ESRF-The European Synchrotron, CS40220, F-38043, Grenoble Cedex 09 (France); Dontsov, D. [SIOS Meßtechnik GmbH, Am Vogelherd 46, 98693 Ilmenau (Germany); Cain, M. G. [National Physical Laboratory, Hampton Road, Teddington TW11 0LW (United Kingdom); Electrosciences Ltd., Farnham, Surrey GU9 9QT (United Kingdom)
2015-10-15
A new materials characterization system developed at the XMaS beamline, located at the European Synchrotron Radiation Facility in France, is presented. We show that this new capability allows to measure the atomic structural evolution (crystallography) of piezoelectric materials whilst simultaneously measuring the overall strain characteristics and electrical response to dynamically (ac) applied external stimuli.
Modeling dynamic functional connectivity using a wishart mixture model
DEFF Research Database (Denmark)
Nielsen, Søren Føns Vind; Madsen, Kristoffer Hougaard; Schmidt, Mikkel Nørgaard
2017-01-01
.e. the window length. In this work we use the Wishart Mixture Model (WMM) as a probabilistic model for dFC based on variational inference. The framework admits arbitrary window lengths and number of dynamic components and includes the static one-component model as a special case. We exploit that the WMM...
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.
Valenza, Gaetano; Citi, Luca; Barbieri, Riccardo
2014-01-01
Measures of nonlinearity and complexity, and in particular the study of Lyapunov exponents, have been increasingly used to characterize dynamical properties of a wide range of biological nonlinear systems, including cardiovascular control. In this work, we present a novel methodology able to effectively estimate the Lyapunov spectrum of a series of stochastic events in an instantaneous fashion. The paradigm relies on a novel point-process high-order nonlinear model of the event series dynamics. The long-term information is taken into account by expanding the linear, quadratic, and cubic Wiener-Volterra kernels with the orthonormal Laguerre basis functions. Applications to synthetic data such as the Hénon map and Rössler attractor, as well as two experimental heartbeat interval datasets (i.e., healthy subjects undergoing postural changes and patients with severe cardiac heart failure), focus on estimation and tracking of the Instantaneous Dominant Lyapunov Exponent (IDLE). The novel cardiovascular assessment demonstrates that our method is able to effectively and instantaneously track the nonlinear autonomic control dynamics, allowing for complexity variability estimations.
Kandasamy, Ramkumar; Cui, Fangsen
2016-04-01
In the traditional layered piezoelectric structures, high stress concentrations could cause the structural failure in interlayer surfaces due to repeated strain reversals. To overcome the performance limitations of these structures, the concept of Functionally Graded Materials (FGMs) has been introduced to improve the lifetime, integrity, and reliability of these structures. In this paper, the free and forced vibration of radially polarized Functionally Graded Piezoelectric (FGP) cylinders under different sets of loading are studied. Material properties such as piezoelectric, elastic and permittivity are assumed to change along its thickness, based on a specific gradation function. Four-parameter power law distribution is used to grade the volume fraction of the constituents comprising of PZT-5A and PZT-5H. Material property is assumed to be temperature dependent for a few numerical studies. The present modeling approach is validated by comparing the free and forced vibration of radially polarized Functionally Graded Piezoelectric (FGP) cylinders with those reported in the literature. The effects of material composition, loading and boundary conditions on the dynamic behavior of FGP cylinder are described. Since the modeling of functionally graded piezoelectric systems is challenging, the present study can help in the design and analysis of FGP cylinders.
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
Lung function assessment using Xe-133 dynamic SPECT in dual-camera system
Energy Technology Data Exchange (ETDEWEB)
Sakaji, Katsuyuki; Akiyama, Masayuki; Nakazawa, Yasuo [Showa Univ., Tokyo (Japan). Hospital; Umeda, Hirotaka; Takenaka, Haruki; Shinozuka, Akira
2001-09-01
The purpose of this study was to estimate lung regional function using Xe-133 dynamic SPECT. SPECT equipment with a dual camera was used. Fourteen rotation acquisitions were obtained beginning immediately after Xe-133 gas inhalation. The time activity curve of each pixel was obtained, and T{sub 1/2} of the washout phase was calculated and mapped. Residual radioactivity was evaluated. Adequate images could be obtained at 30 seconds per rotation even with the dual-camera system. Mapping of T{sub 1/2} allowed temporal changes on one image. Three-dimensional evaluation could be made on a SPECT system using our method. (author)
Institute of Scientific and Technical Information of China (English)
李卫华; 诸蔚朝; 马红孺
2003-01-01
One component hard-sphere fluid confined in two planar hard walls is studied by means of density functional theory with Rosenfeld functional and molecular dynamics simulation. The validity of the Rosenfeld functional is examined. Chemical potential, grand potential and free energy as functions of the wall separation are obtained.
Functional Nanostructures and Dynamic Materials through Self-Organization
Institute of Scientific and Technical Information of China (English)
Jean-Marie; LEHN
2007-01-01
1 Results Supramolecular chemistry is actively exploring systems undergoing self-organization.The design of molecular information controlled,"programmed"and functional self-organizing systems provides an original approach to nanoscience and nanotechnology.The spontaneous but controlled generation of well-defined,functional molecular and supramolecular architectures of nanometric size through self-organization represents a means of performing programmed engineering and processing of functional nanostruct...
Molecular Dynamics Study of Helicobacter pylori Urease.
Minkara, Mona S; Ucisik, Melek N; Weaver, Michael N; Merz, Kenneth M
2014-05-13
Helicobacter pylori have been implicated in an array of gastrointestinal disorders including, but not limited to, gastric and duodenal ulcers and adenocarcinoma. This bacterium utilizes an enzyme, urease, to produce copious amounts of ammonia through urea hydrolysis in order to survive the harsh acidic conditions of the stomach. Molecular dynamics (MD) studies on the H. pylori urease enzyme have been employed in order to study structural features of this enzyme that may shed light on the hydrolysis mechanism. A total of 400 ns of MD simulation time were collected and analyzed in this study. A wide-open flap state previously observed in MD simulations on Klebsiella aerogenes [Roberts et al. J. Am. Chem. Soc.2012, 134, 9934] urease has been identified in the H. pylori enzyme that has yet to be experimentally observed. Critical distances between residues on the flap, contact points in the closed state, and the separation between the active site Ni(2+) ions and the critical histidine α322 residue were used to characterize flap motion. An additional flap in the active site was elaborated upon that we postulate may serve as an exit conduit for hydrolysis products. Finally we discuss the internal hollow cavity and present analysis of the distribution of sodium ions over the course of the simulation.
Path Integral Monte Carlo and Density Functional Molecular Dynamics Simulations of Warm Dense Matter
Militzer, Burkhard; Driver, Kevin
2011-10-01
We analyze the applicability of two first-principles simulation techniques, path integral Monte Carlo (PIMC) and density functional molecular dynamics (DFT-MD), to study the regime of warm dense matter. We discuss the advantages as well as the limitations of each method and propose directions for future development. Results for dense, liquid helium, where both methods have been applied, demonstrate the range of each method's applicability. Comparison of the equations of state from simulations with analytical theories and free energy models show that DFT is useful for temperatures below 100000 K and then PIMC provides accurate results for all higher temperatures. We characterize the structure of the liquid in terms of pair correlation functions and study the closure of the band gap with increasing density and temperature. Finally, we discuss simulations of heavier elements and demonstrate the reliability are both methods in such cases with preliminary results.
Institute of Scientific and Technical Information of China (English)
王建国; 王振伟
2013-01-01
动载荷作用引起岩石边坡失稳破坏,尤其力幅突变激扰作用对边坡稳定影响很大.对动、静载荷作用下岩石力学性质进行了分析,建立了岩石边坡非线性运动方程,分析了岩石边坡动力变形模型及非线性动力响应,得出当扰动频率增加到一定程度,滑体振幅突然增加,产生向上突跳并随力幅的增加继续增加:反之,当力幅较大并逐渐减小时,滑体振幅也随之减小,当扰动的振幅减小至一定程度,滑体振幅突然降低,产生向下突跳减小.对初始条件和力幅突变激扰对岩石力学非线性振动系统的影响进行了分析,得到初始条件的微小变化可引起系统响应的巨大差异,当振幅A极小时,线性系统的振荡很弱,它对非线性系统的作用也很弱,整个系统的运动便可看作两运动的独立叠加.当振幅A再加大到使其幅值超过非线性系统三奇点之间的间隔时,系统可以在这些奇点之间来回跃迁振荡,从而运动复杂化,随振幅A的增加,系统从倍周期运动向混运动变化,研究结果可为岩石边坡的动力稳定提供指导.%The dynamic loading leads to instability and failure of rock slope.Especially,the role of force increase mutation has a great influence on slope stability.The rock mechanical properties are analyzed under static and dynamic loadings.And then,the nonlinear equation of rock slope is established.The dynamic deformation model of rock slope and the nonlinear dynamic response are studied.The amplitude of the sliding body suddenly increase,resulting in the sudden jump up and continue to increasing with the increase of the force,when the disturbance frequency to a certain extent.Conversely,the amplitude of the landslide suddenly reduces,resulting in the sudden decreases when the perturbation amplitude reduces to a certain extent.Tiny changes in initial conditions can cause a huge difference of the system response.The movement of the entire system can
Tornador, Cristian; Falcón, Carles; López‐Solà, Marina; Hernández‐Ribas, Rosa; Pujol, Jesús; Menchón, José M.; Ritter, Petra; Cardoner, Narcis; Soriano‐Mas, Carles; Deco, Gustavo
2016-01-01
Abstract Resting‐state fMRI (RS‐fMRI) has become a useful tool to investigate the connectivity structure of mental health disorders. In the case of major depressive disorder (MDD), recent studies regarding the RS‐fMRI have found abnormal connectivity in several regions of the brain, particularly in the default mode network (DMN). Thus, the relevance of the DMN to self‐referential thoughts and ruminations has made the use of the resting‐state approach particularly important for MDD. The majority of such research has relied on the grand averaged functional connectivity measures based on the temporal correlations between the BOLD time series of various brain regions. We, in our study, investigated the variations in the functional connectivity over time at global and local level using RS‐fMRI BOLD time series of 27 MDD patients and 27 healthy control subjects. We found that global synchronization and temporal stability were significantly increased in the MDD patients. Furthermore, the participants with MDD showed significantly increased overall average (static) functional connectivity (sFC) but decreased variability of functional connectivity (vFC) within specific networks. Static FC increased to predominance among the regions pertaining to the default mode network (DMN), while the decreased variability of FC was observed in the connections between the DMN and the frontoparietal network. Hum Brain Mapp 37:2918–2930, 2016. © 2016 Wiley Periodicals, Inc. PMID:27120982
[Functional magnetic resonance imaging and dynamic neuroanatomy of addictive disorders].
Mel'nikov, M E; Shtark, M B
2014-01-01
Research into the cerebral patterns that govern the formation and development of addictive behavior is one of the most interesting goals of neurophysiology. Authors of contemporary papers on the matter define a number of symptoms that are all part of substance or non-substance dependence, each one of them leading to abnormalities in the corresponding system of the brain. During the last twenty years the functional magnetic resonance imaging (fMR1) technology has been instrumental in locating such abnormalities, identifying specific parts of the brain that, when dysfunctional, may enhance addiction and cause its positive or negative symptoms. This article reviews fMRI studies aimed toward locating areas in the brain that are responsible for cognitive, emotional, and motivational dysfunction. Cerebral correlatives of impulsiveness, behavior control, and drug cravings are reviewed separately. The article also contains an overview of possibilities to further investigate the Selves of those dependent on substances, identify previously unknown diagnostic markers of substance dependence, and evaluate the effectiveness of therapy. The research under review in this article provides data that points to a special role of the nucleus caudatus as well as the nucleus accumbens, the thalamus, the insular cortex (IC), the anterior cingulate, prefrontal and orbitofrontal areas in psychological disorders that are part of substance dependence. General findings of the article are in accordance with contemporary models of addictive pattern.
Dynamic Colour Possibilities and Functional Properties of Thermochromic Printing Inks
Directory of Open Access Journals (Sweden)
Rahela Kulcar
2012-07-01
Full Text Available Thermochromic printing inks change their colour regarding the change in temperature and they are one of the major groups of colour-changing inks. One of the most frequently used thermochromic material in printing inks are leuco dyes. The colour of thermochromic prints is dynamic, it is not just temperature-dependent, but it also depends on thermal history. The effect is described by colour hysteresis. This paper aims at discussing general aspects of thermochromic inks, dynamic colorimetric properties of leuco dye-based thermochromic inks, their stability and principle of variable-temperature colour measurement. Thermochromic material is protected in round-shaped capsules. They are much larger than pigments in conventional inks. The polymer envelopes of pigment capsules are more stable against oxidation than the binder. If these envelopes are damaged, the dynamic colour is irreversibly lost. Our aim is to analyse the colorimetric properties of several reversible screen-printed UV-curing leuco dye thermochromic inks with different activation temperatures printed on paper. A small analysis of irreversible thermochromic inks will be presented for comparison with reversible thermochromic inks. Moreover, so as to show interesting possibilities, a combination of different inks was made, an irreversible thermochromic ink was printed on top of the red and blue reversible thermochromic inks. Special attention was given to the characterization of colour hysteresis and the meaning of activation temperature.
Bioreactor Studies and Computational Fluid Dynamics
Singh, H.; Hutmacher, D. W.
The hydrodynamic environment “created” by bioreactors for the culture of a tissue engineered construct (TEC) is known to influence cell migration, proliferation and extra cellular matrix production. However, tissue engineers have looked at bioreactors as black boxes within which TECs are cultured mainly by trial and error, as the complex relationship between the hydrodynamic environment and tissue properties remains elusive, yet is critical to the production of clinically useful tissues. It is well known in the chemical and biotechnology field that a more detailed description of fluid mechanics and nutrient transport within process equipment can be achieved via the use of computational fluid dynamics (CFD) technology. Hence, the coupling of experimental methods and computational simulations forms a synergistic relationship that can potentially yield greater and yet, more cohesive data sets for bioreactor studies. This review aims at discussing the rationale of using CFD in bioreactor studies related to tissue engineering, as fluid flow processes and phenomena have direct implications on cellular response such as migration and/or proliferation. We conclude that CFD should be seen by tissue engineers as an invaluable tool allowing us to analyze and visualize the impact of fluidic forces and stresses on cells and TECs.
Using computational fluid dynamics to test functional and ecological hypotheses in fossil taxa
Rahman, Imran
2016-04-01
Reconstructing how ancient organisms moved and fed is a major focus of study in palaeontology. Traditionally, this has been hampered by a lack of objective data on the functional morphology of extinct species, especially those without a clear modern analogue. However, cutting-edge techniques for characterizing specimens digitally and in three dimensions, coupled with state-of-the-art computer models, now provide a robust framework for testing functional and ecological hypotheses even in problematic fossil taxa. One such approach is computational fluid dynamics (CFD), a method for simulating fluid flows around objects that has primarily been applied to complex engineering-design problems. Here, I will present three case studies of CFD applied to fossil taxa, spanning a range of specimen sizes, taxonomic groups and geological ages. First, I will show how CFD enabled a rigorous test of hypothesized feeding modes in an enigmatic Ediacaran organism with three-fold symmetry, revealing previously unappreciated complexity of pre-Cambrian ecosystems. Second, I will show how CFD was used to evaluate hydrodynamic performance and feeding in Cambrian stem-group echinoderms, shedding light on the probable feeding strategy of the latest common ancestor of all deuterostomes. Third, I will show how CFD allowed us to explore the link between form and function in Mesozoic ichthyosaurs. These case studies serve to demonstrate the enormous potential of CFD for addressing long-standing hypotheses for a variety of fossil taxa, opening up an exciting new avenue in palaeontological studies of functional morphology.
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...
Wang, Xiangpeng; Zhang, Wenwen; Sun, Yujing; Hu, Min; Chen, Antao
2016-12-01
Aberrant functional interactions between several large-scale networks, especially the central executive network (CEN), the default mode network (DMN) and the salience network (SN), have been postulated as core pathophysiologic features of schizophrenia; however, the attributing factors of which remain unclear. The study employed resting-state fMRI with 77 participants (42 patients and 35 controls). We performed dynamic functional connectivity (DFC) and functional connectivity (FC) analyses to explore the connectivity patterns of these networks. Furthermore, we performed a structural equation model (SEM) analysis to explore the possible role of the SN in modulating network interactions. The results were as follows: (1) The inter-network connectivity showed decreased connectivity strength and increased time-varying instability in schizophrenia; (2) The SN manifested schizophrenic intra-network dysfunctions in both the FC and DFC patterns; (3) The connectivity properties of the SN were effective in discriminating controls from patients; (4) In patients, the dynamic intra-SN connectivity negatively predicted the inter-network FC, and this effect was mediated by intra-SN connectivity strength. These findings suggest that schizophrenia show systematic deficits in temporal stability of large-scale network connectivity. Furthermore, aberrant network interactions in schizophrenia could be attributed to instable intra-SN connectivity and the dysfunction of the SN may be an intrinsic biomarker of the disease. Copyright © 2016 Elsevier Ltd. All rights reserved.
Institute of Scientific and Technical Information of China (English)
Lou Zhi-Mei; Chen Zi-Dong; Wang Wen-Long
2005-01-01
In this paper, we express the differential equations of a noncentral dynamical system in Ermakov formalism to obtain the Ermakov invariant. In term of Hamiltonian theories and using the Ermakov invariant as the Hamiltonian,the Poisson structure of a noncentral dynamical system in four-dimensional phase space are constructed. The result indicates that the Poisson structure is degenerate and the noncentral dynamical system possesses four invariants: the Hamiltonian, the Ermakov invariant and two Casimir functions.
Abel Bombasaro, Jose; Barrera Guisasola, Exequiel Ernesto; Masman, Marcelo Fabricio; Angel Zamora, Miguel; Maria Rodriguez, Ana
2013-01-01
Acetogenins are among the most potent of the known inhibitors of complex I (NADH-ubiquinone oxidoreductase) in mitochondrial electron transfer system. Elucidation of the dynamic function of the alkyl spacer linking the two toxophores (i.e., the hydroxylated tetrahydrofuran and the gamma-lactone
Effect of a 6-week dynamic neuromuscular training programme on ankle joint function: A Case report
LENUS (Irish Health Repository)
O'Driscoll, Jeremiah
2011-06-09
Abstract Background Ankle joint sprain and the subsequent development of chronic ankle instability (CAI) are commonly encountered by clinicians involved in the treatment and rehabilitation of musculoskeletal injuries. It has recently been advocated that ankle joint post-sprain rehabilitation protocols should incorporate dynamic neuromuscular training to enhance ankle joint sensorimotor capabilities. To date no studies have reported on the effects of dynamic neuromuscular training on ankle joint positioning during landing from a jump, which has been reported as one of the primary injury mechanisms for ankle joint sprain. This case report details the effects of a 6-week dynamic neuromuscular training programme on ankle joint function in an athlete with CAI. Methods The athlete took part in a progressive 6-week dynamic neuromuscular training programme which incorporated postural stability, strengthening, plyometric, and speed\\/agility drills. The outcome measures chosen to assess for interventional efficacy were: 1 Cumberland Ankle Instability Tool (CAIT) scores, 2 Star Excursion Balance Test (SEBT) reach distances, 3 ankle joint plantar flexion during drop landing and drop vertical jumping, and 4 ground reaction forces (GRFs) during walking. Results CAIT and SEBT scores improved following participation in the programme. The angle of ankle joint plantar flexion decreased at the point of initial contact during the drop landing and drop vertical jumping tasks, indicating that the ankle joint was in a less vulnerable position upon landing following participation in the programme. Furthermore, GRFs were reduced whilst walking post-intervention. Conclusions The 6-week dynamic neuromuscular training programme improved parameters of ankle joint sensorimotor control in an athlete with CAI. Further research is now required in a larger cohort of subjects to determine the effects of neuromuscular training on ankle joint injury risk factors.
Directory of Open Access Journals (Sweden)
Lockie Robert G.
2015-09-01
Full Text Available Dynamic stability is an essential physical component for team sport athletes. Certain Functional Movement Screen (FMS exercises (deep squat; left- and right-leg hurdle step; left- and right-leg in-line lunge [ILL]; left- and right-leg active straight-leg raise; and trunk stability push-up [TSPU] have been suggested as providing an indication of dynamic stability. No research has investigated relationships between these screens and an established test of dynamic stability such as the modified Star Excursion Balance Test (mSEBT, which measures lower-limb reach distance in posteromedial, medial, and anteromedial directions, in team sport athletes. Forty-one male and female team sport athletes completed the screens and the mSEBT. Participants were split into high-, intermediate-, and low-performing groups according to the mean of the excursions when both the left and right legs were used for the mSEBT stance. Any between-group differences in the screens and mSEBT were determined via a one-way analysis of variance with Bonferroni post hoc adjustment (p < 0.05. Data was pooled for a correlation analysis (p < 0.05. There were no between-group differences in any of the screens, and only two positive correlations between the screens and the mSEBT (TSPU and right stance leg posteromedial excursion, r = 0.37; left-leg ILL and left stance leg posteromedial excursion, r = 0.46. The mSEBT clearly indicated participants with different dynamic stability capabilities. In contrast to the mSEBT, the selected FMS exercises investigated in this study have a limited capacity to identify dynamic stability in team sport athletes.
Effect of a 6-week dynamic neuromuscular training programme on ankle joint function: A Case report
Directory of Open Access Journals (Sweden)
O'Driscoll Jeremiah
2011-06-01
Full Text Available Abstract Background Ankle joint sprain and the subsequent development of chronic ankle instability (CAI are commonly encountered by clinicians involved in the treatment and rehabilitation of musculoskeletal injuries. It has recently been advocated that ankle joint post-sprain rehabilitation protocols should incorporate dynamic neuromuscular training to enhance ankle joint sensorimotor capabilities. To date no studies have reported on the effects of dynamic neuromuscular training on ankle joint positioning during landing from a jump, which has been reported as one of the primary injury mechanisms for ankle joint sprain. This case report details the effects of a 6-week dynamic neuromuscular training programme on ankle joint function in an athlete with CAI. Methods The athlete took part in a progressive 6-week dynamic neuromuscular training programme which incorporated postural stability, strengthening, plyometric, and speed/agility drills. The outcome measures chosen to assess for interventional efficacy were: 1 Cumberland Ankle Instability Tool (CAIT scores, 2 Star Excursion Balance Test (SEBT reach distances, 3 ankle joint plantar flexion during drop landing and drop vertical jumping, and 4 ground reaction forces (GRFs during walking. Results CAIT and SEBT scores improved following participation in the programme. The angle of ankle joint plantar flexion decreased at the point of initial contact during the drop landing and drop vertical jumping tasks, indicating that the ankle joint was in a less vulnerable position upon landing following participation in the programme. Furthermore, GRFs were reduced whilst walking post-intervention. Conclusions The 6-week dynamic neuromuscular training programme improved parameters of ankle joint sensorimotor control in an athlete with CAI. Further research is now required in a larger cohort of subjects to determine the effects of neuromuscular training on ankle joint injury risk factors.
Dynamic stiffness matrix of a poroelastic multi-layered site and its Green's functions
Institute of Scientific and Technical Information of China (English)
梁建文; 尤红兵
2004-01-01
Few studies of wave propagation in layered saturated soils have been reported in the literature. In this paper, a general solution of the equation of wave motion in saturated soils, based on one kind of practical Biot's equation,was deduced by introducing wave potentials. Then exact dynamic-stiffness matrices for a poroelastic soil layer and halfspace were derived, which extended Wolf's theory for an elastic layered site to the case of poroelasticity, thus resolving a fundamental problem in the field of wave propagation and soil-structure interaction in a poroelastic layered soil site. By using the integral transform method, Green's functions of horizontal and vertical uniformly distributed loads in a poroelastic layered soil site were given. Finally, the theory was verified by numerical examples and dynamic responses by comparing three different soil sites. This study has the following advantages: all parameters in the dynamic-stiffness matrices have explicitly physical meanings and the thickness of the sub-layers does not affect the precision of the calculation which is very convenient for engineering applications. The present theory can degenerate into Wolf's theory and yields numerical results approaching those for an ideal elastic layered site when porosity tends to zero.
Liu, Y. Z.; Hao, Y. X.; Zhang, W.; Chen, J.; Li, S. B.
2015-07-01
The nonlinear vibration of a simply supported FGM cylindrical shell with small initial geometric imperfection under complex loads is studied. The effects of radial harmonic excitation, compressive in-plane force combined with supersonic aerodynamic and thermal loads are considered. The small initial geometric imperfection of the cylindrical shell is characterized in the form of the sine-type trigonometric functions. The effective material properties of this FGM cylindrical shell are graded in the radial direction according to a simple power law in terms of the volume fractions. Based on Reddy's third-order shear deformation theory, von Karman-type nonlinear kinematics and Hamilton's principle, the nonlinear partial differential equation that controls the shell dynamics is derived. Both axial symmetric and driven modes of the cylindrical shell deflection pattern are included. Furthermore, the equations of motion can be reduced into a set of coupled nonlinear ordinary differential equations by applying Galerkin's method. In the study of the nonlinear dynamics responses of small initial geometric imperfect FGM cylindrical shell under complex loads, the 4th order Runge-Kutta method is used to obtain time history, phase portraits, bifurcation diagrams and Poincare maps with different parameters. The effects of external loads, geometric imperfections and volume fractions on the nonlinear dynamics of the system are discussed.
Impacts of soil tillage and cover crops on soil carbon (C) dynamics and microbiological function were investigated in a vineyard grown in California’s Mediterranean climate. We 1) compared soil organic matter (SOM), C dynamics and microbiological activity of two cover crops [Trios 102 (Triticale x T...
Gündüç, Semra; Dilaver, Mehmet; Aydın, Meral; Gündüç, Yiğit
2005-02-01
In this work we have studied the dynamic scaling behavior of two scaling functions and we have shown that scaling functions obey the dynamic finite size scaling rules. Dynamic finite size scaling of scaling functions opens possibilities for a wide range of applications. As an application we have calculated the dynamic critical exponent (z) of Wolff's cluster algorithm for 2-, 3- and 4-dimensional Ising models. Configurations with vanishing initial magnetization are chosen in order to avoid complications due to initial magnetization. The observed dynamic finite size scaling behavior during early stages of the Monte Carlo simulation yields z for Wolff's cluster algorithm for 2-, 3- and 4-dimensional Ising models with vanishing values which are consistent with the values obtained from the autocorrelations. Especially, the vanishing dynamic critical exponent we obtained for d=3 implies that the Wolff algorithm is more efficient in eliminating critical slowing down in Monte Carlo simulations than previously reported.
Transfer function analysis of dynamic cerebral autoregulation in humans
Zhang, R.; Zuckerman, J. H.; Giller, C. A.; Levine, B. D.; Blomqvist, C. G. (Principal Investigator)
1998-01-01
To test the hypothesis that spontaneous changes in cerebral blood flow are primarily induced by changes in arterial pressure and that cerebral autoregulation is a frequency-dependent phenomenon, we measured mean arterial pressure in the finger and mean blood flow velocity in the middle cerebral artery (VMCA) during supine rest and acute hypotension induced by thigh cuff deflation in 10 healthy subjects. Transfer function gain, phase, and coherence function between changes in arterial pressure and VMCA were estimated using the Welch method. The impulse response function, calculated as the inverse Fourier transform of this transfer function, enabled the calculation of transient changes in VMCA during acute hypotension, which was compared with the directly measured change in VMCA during thigh cuff deflation. Beat-to-beat changes in VMCA occurred simultaneously with changes in arterial pressure, and the autospectrum of VMCA showed characteristics similar to arterial pressure. Transfer gain increased substantially with increasing frequency from 0.07 to 0.20 Hz in association with a gradual decrease in phase. The coherence function was > 0.5 in the frequency range of 0.07-0.30 Hz and transfer function with the quality of a high-pass filter in the frequency range of 0.07-0.30 Hz.
Riemann zeta function from wave-packet dynamics
DEFF Research Database (Denmark)
Mack, R.; Dahl, Jens Peder; Moya-Cessa, H.
2010-01-01
is governed by the temperature of the thermal phase state and tau is proportional to t. We use the JWKB method to solve the inverse spectral problem for a general logarithmic energy spectrum; that is, we determine a family of potentials giving rise to such a spectrum. For large distances, all potentials...... 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...
Institute of Scientific and Technical Information of China (English)
李思殿; 金志浩; 等
2002-01-01
A many-body potential energy function has been employed to investigate the dynamical properties, surface energies and reconstruc-tions, and melting behavior of face-centered cubic (FCC) lead. Experimental phonon dispersion curves along (q00), (qq0) and (qqq) highsymmetry directions are well reproduced. Surface energy calculations indicate that Pb(110) undergoes a severe surface relaxation. A large in-ward relaxation up to - 18 % relative to FCC lattice is predicted for the top-most layer of Pb(110) surface and an expansion-contraction alter-nation for the top 7 interlayer spaces is observed. Monte Carlo simulation indicates that FCC lead melt above 425K with this potential, an esti-mation about 25K lower than the observed melting point of Pb nano-particles.%采用优化的多体展开势能函数研究面心立方(FCC)晶体铅的动力学和表面性质.在(q00),(qq0)及(qqq)高对称方向,计算声子散射频率与实验曲线良好吻合.Pb(110)表面驰豫严重,其最外层原子向内压缩率达18%,表面7层存在压缩-膨胀交替现象.蒙特卡罗模拟表明,FCC铅在425K开始熔化,模拟结果比纳米铅低约25K.
Dynamics of crowd disasters: An empirical study
Helbing, Dirk; Johansson, Anders; Al-Abideen, Habib Zein
2007-04-01
Many observations of the dynamics of pedestrian crowds, including various self-organization phenomena, have been successfully described by simple many-particle models. For ethical reasons, however, there is a serious lack of experimental data regarding crowd panic. Therefore, we have analyzed video recordings of the crowd disaster in Mina/Makkah during the Hajj in 1426H on 12 January 2006. They reveal two subsequent, sudden transitions from laminar to stop-and-go and “turbulent” flows, which question many previous simulation models. While the transition from laminar to stop-and-go flows supports a recent model of bottleneck flows [D. Helbing , Phys. Rev. Lett. 97, 168001 (2006)], the subsequent transition to turbulent flow is not yet well understood. It is responsible for sudden eruptions of pressure release comparable to earthquakes, which cause sudden displacements and the falling and trampling of people. The insights of this study into the reasons for critical crowd conditions are important for the organization of safer mass events. In particular, they allow one to understand where and when crowd accidents tend to occur. They have also led to organizational changes, which have ensured a safe Hajj in 1427H.
Dynamic remodeling of microbial biofilms by functionally distinct exopolysaccharides.
Chew, Su Chuen; Kundukad, Binu; Seviour, Thomas; van der Maarel, Johan R C; Yang, Liang; Rice, Scott A; Doyle, Patrick; Kjelleberg, Staffan
2014-08-05
Biofilms are densely populated communities of microbial cells protected and held together by a matrix of extracellular polymeric substances. The structure and rheological properties of the matrix at the microscale influence the retention and transport of molecules and cells in the biofilm, thereby dictating population and community behavior. Despite its importance, quantitative descriptions of the matrix microstructure and microrheology are limited. Here, particle-tracking microrheology in combination with genetic approaches was used to spatially and temporally study the rheological contributions of the major exopolysaccharides Pel and Psl in Pseudomonas aeruginosa biofilms. Psl increased the elasticity and effective cross-linking within the matrix, which strengthened its scaffold and appeared to facilitate the formation of microcolonies. Conversely, Pel reduced effective cross-linking within the matrix. Without Psl, the matrix becomes more viscous, which facilitates biofilm spreading. The wild-type biofilm decreased in effective cross-linking over time, which would be advantageous for the spreading and colonization of new surfaces. This suggests that there are regulatory mechanisms to control production of the exopolysaccharides that serve to remodel the matrix of developing biofilms. The exopolysaccharides were also found to have profound effects on the spatial organization and integration of P. aeruginosa in a mixed-species biofilm model of P. aeruginosa-Staphylococcus aureus. Pel was required for close association of the two species in mixed-species microcolonies. In contrast, Psl was important for P. aeruginosa to form single-species biofilms on top of S. aureus biofilms. Our results demonstrate that Pel and Psl have distinct physical properties and functional roles during biofilm formation. Importance: Most bacteria grow as biofilms in the environment or in association with eukaryotic hosts. Removal of biofilms that form on surfaces is a challenge in clinical
Single-molecule conformational dynamics of a biologically functional hydroxocobalamin riboswitch.
Holmstrom, Erik D; Polaski, Jacob T; Batey, Robert T; Nesbitt, David J
2014-12-03
Riboswitches represent a family of highly structured regulatory elements found primarily in the leader sequences of bacterial mRNAs. They function as molecular switches capable of altering gene expression; commonly, this occurs via a conformational change in a regulatory element of a riboswitch that results from ligand binding in the aptamer domain. Numerous studies have investigated the ligand binding process, but little is known about the structural changes in the regulatory element. A mechanistic description of both processes is essential for deeply understanding how riboswitches modulate gene expression. This task is greatly facilitated by studying all aspects of riboswitch structure/dynamics/function in the same model system. To this end, single-molecule fluorescence resonance energy transfer (smFRET) techniques have been used to directly observe the conformational dynamics of a hydroxocobalamin (HyCbl) binding riboswitch (env8HyCbl) with a known crystallographic structure.1 The single-molecule RNA construct studied in this work is unique in that it contains all of the structural elements both necessary and sufficient for regulation of gene expression in a biological context. The results of this investigation reveal that the undocking rate constant associated with the disruption of a long-range kissing-loop (KL) interaction is substantially decreased when the ligand is bound to the RNA, resulting in a preferential stabilization of the docked conformation. Notably, the formation of this tertiary KL interaction directly sequesters the Shine-Dalgarno sequence (i.e., the ribosome binding site) via base-pairing, thus preventing translation initiation. These results reveal that the conformational dynamics of this regulatory switch are quantitatively described by a four-state kinetic model, whereby ligand binding promotes formation of the KL interaction. The results of complementary cell-based gene expression experiments conducted in Escherichia coli are highly
Vacuum energy as a c-function for theories with dynamically generated masses
Energy Technology Data Exchange (ETDEWEB)
Aguilar, A.C., E-mail: arlene.aguilar@ufabc.edu.b [Federal University of ABC, CCNH, Rua Santa Adelia 166, 09210-170, Santo Andre (Brazil); Doff, A. [Universidade Tecnologica Federal do Parana - UTFPR, COMAT, Via do Conhecimento Km 01, 85503-390, Pato Branco, PR (Brazil); Natale, A.A. [Instituto de Fisica Teorica, UNESP - Universidade Estadual Paulista, Rua Dr. Bento T. Ferraz, 271, Bloco II, 01140-070, Sao Paulo (Brazil)
2011-01-24
We argue that in asymptotically free non-Abelian gauge theories possessing the phenomenon of dynamical mass generation the {beta} function is negative up to a value of the coupling constant that corresponds to a non-trivial fixed point, in agreement with recent AdS/QCD analysis. This fixed point happens at the minimum of the vacuum energy ({Omega}), which, as a characteristic of theories with dynamical mass generation, has the properties of a c-function.
Nomura, K; Otsuka, T; Shimizu, N; Vretenar, D
2011-01-01
Microscopic energy density functionals (EDF) have become a standard tool for nuclear structure calculations, providing an accurate global description of nuclear ground states and collective excitations. For spectroscopic applications this framework has to be extended to account for collective correlations related to restoration of symmetries broken by the static mean field, and for fluctuations of collective variables. In this work we compare two approaches to five-dimensional quadrupole dynamics: the collective Hamiltonian for quadrupole vibrations and rotations, and the Interacting Boson Model. The two models are compared in a study of the evolution of non-axial shapes in Pt isotopes. Starting from the binding energy surfaces of $^{192,194,196}$Pt, calculated with a microscopic energy density functional, we analyze the resulting low-energy collective spectra obtained from the collective Hamiltonian, and the corresponding IBM-2 Hamiltonian. The calculated excitation spectra and transition probabilities for t...
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.
Periodic solutions of first-order functional differential equations in population dynamics
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...
Dynamics of stochastic predator-prey models with Holling II functional response
Liu, Qun; Zu, Li; Jiang, Daqing
2016-08-01
In this paper, we consider the dynamics of stochastic predator-prey models with Holling II functional response. For the stochastic systems, we firstly establish sufficient conditions for the existence of the globally positive solutions. Then we investigate the asymptotic moment estimations of the positive solutions and study the ultimately bounded in the mean of them. Thirdly, by constructing some suitable Lyapunov functions, we verify that there are unique stationary distributions and they are ergodic. The obtained results show that the systems still retain some stability in the sense of weak stability provided that the intensity of the white noise is relatively small. Finally, some numerical simulations are introduced to illustrate our main results.
Kunert, James M.; Maia, Pedro D.; Kutz, J. Nathan
2017-01-01
Using a model for the dynamics of the full somatic nervous system of the nematode C. elegans, we address how biological network architectures and their functionality are degraded in the presence of focal axonal swellings (FAS) arising from neurodegenerative disease and/or traumatic brain injury. Using biophysically measured FAS distributions and swelling sizes, we are able to simulate the effects of injuries on the neural dynamics of C. elegans, showing how damaging the network degrades its low-dimensional dynamical responses. We visualize these injured neural dynamics by mapping them onto the worm’s low-dimensional postures, i.e. eigenworm modes. We show that a diversity of functional deficits arise from the same level of injury on a connectomic network. Functional deficits are quantified using a statistical shape analysis, a procrustes analysis, for deformations of the limit cycles that characterize key behaviors such as forward crawling. This procrustes metric carries information on the functional outcome of injuries in the model. Furthermore, we apply classification trees to relate injury structure to the behavioral outcome. This makes testable predictions for the structure of an injury given a defined functional deficit. More critically, this study demonstrates the potential role of computational simulation studies in understanding how neuronal networks process biological signals, and how this processing is impacted by network injury. PMID:28056097
Lęski, Szymon; Kublik, Ewa; Swiejkowski, Daniel A; Wróbel, Andrzej; Wójcik, Daniel K
2010-12-01
Local field potentials have good temporal resolution but are blurred due to the slow spatial decay of the electric field. For simultaneous recordings on regular grids one can reconstruct efficiently the current sources (CSD) using the inverse Current Source Density method (iCSD). It is possible to decompose the resultant spatiotemporal information about the current dynamics into functional components using Independent Component Analysis (ICA). We show on test data modeling recordings of evoked potentials on a grid of 4 × 5 × 7 points that meaningful results are obtained with spatial ICA decomposition of reconstructed CSD. The components obtained through decomposition of CSD are better defined and allow easier physiological interpretation than the results of similar analysis of corresponding evoked potentials in the thalamus. We show that spatiotemporal ICA decompositions can perform better for certain types of sources but it does not seem to be the case for the experimental data studied. Having found the appropriate approach to decomposing neural dynamics into functional components we use the technique to study the somatosensory evoked potentials recorded on a grid spanning a large part of the forebrain. We discuss two example components associated with the first waves of activation of the somatosensory thalamus. We show that the proposed method brings up new, more detailed information on the time and spatial location of specific activity conveyed through various parts of the somatosensory thalamus in the rat.
Energy Technology Data Exchange (ETDEWEB)
Lee, C.C.; Ku, W.; Hsueh, H.C.
2010-08-30
Within the framework of time-dependent density-functional theory (TDDFT), we derive the dynamical linear response of local-density approximation plus U functional and benchmark it on NiO, a prototypical Mott insulator. Formulated using real-space Wannier functions, our computationally inexpensive framework gives detailed insights into the formation of tightly bound Frenkel excitons with reasonable accuracy. Specifically, a strong hybridization of multiple excitons is found to significantly modify the exciton properties. Furthermore, our study exposes a significant generic limitation of adiabatic approximation in TDDFT with hybrid functionals and in existing Bethe-Salpeter-equation approaches, advocating the necessity of strongly energy-dependent kernels in future development.
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.
Energy Technology Data Exchange (ETDEWEB)
Krestin, G.P. [Dept. of Medical Radiology, University Hospital Zurich (Switzerland); Fischbach, R. [Dept. of Radiology, Univ. of Cologne (Germany); Vorreuther, R. [Dept. of Urology, Univ. of Cologne (Germany); Schulthess, G.K. von [Dept. of Medical Radiology, University Hospital Zurich (Switzerland)
1993-06-01
Contrast-enhanced gradient-echo MRI was used to evaluate morphological and functional alterations in the kidneys after extracorporeal shock wave lithotripsy (ESWL). Dynamic MRI with a temporal resolution of 10 s per image was performed by repeated imaging in the coronal plane after administration of gadolinium-DTPA (0.1 mmol/kg) before and after ESWL for renal calculi in 25 patients. Before ESWL 22 patients had normally functioning kidneys, characterised by a marked decrease in signal intensity in the renal medulla 30-40 s after the onset of cortical perfusion. After ESWL 8 patients had functional abnormalities: in 2 cases the medullary signal decrease was disturbed throughout the whole organ, while 6 kidneys demonstrated regional loss of concentrating ability in the medulla. Morphological alterations (oedema with blurred contours and loss of corticomedullary differentiation; parenchymal haemorrhage and haemorrhage in a cortical cyst; subcapsular, perirenal and pararenal haematoma) were detected in 9 cases. Haemorrhage was encountered more often after administration of more than 2500 shock waves; however, no such correlation was seen in the kidneys with functional disturbances following ESWL therapy. MRI proved to be a sensitive method for the assessment of morphological and functional alterations after ESWL, but longer follow-up studies are required to identify the clinical impact of these early changes. (orig.)
Communication: Dynamical density functional theory for dense suspensions of colloidal hard spheres.
Stopper, Daniel; Roth, Roland; Hansen-Goos, Hendrik
2015-11-14
We study structural relaxation of colloidal hard spheres undergoing Brownian motion using dynamical density functional theory. Contrary to the partial linearization route [D. Stopper et al., Phys. Rev. E 92, 022151 (2015)] which amounts to using different free energy functionals for the self and distinct part of the van Hove function G(r, t), we put forward a unified description employing a single functional for both components. To this end, interactions within the self part are removed via the zero-dimensional limit of the functional with a quenched self component. In addition, we make use of a theoretical result for the long-time mobility in hard-sphere suspensions, which we adapt to the inhomogeneous fluid. Our results for G(r, t) are in excellent agreement with numerical simulations even in the dense liquid phase. In particular, our theory accurately yields the crossover from free diffusion at short times to the slower long-time diffusion in a crowded environment.
Studies of dynamical processes affecting global climate
Energy Technology Data Exchange (ETDEWEB)
Keller, C.; Cooper, D.; Eichinger, W. [and others
1998-12-31
This is the final report of a three-year, Laboratory Directed Research and Development project at the Los Alamos National Laboratory (LANL). The main objective was, by a combined theoretical and observational approach, to develop improved models of dynamic processes in the oceans and atmosphere and to incorporate them into large climate codes, chiefly in four main areas: numerical physics, chemistry, water vapor, and ocean-atmosphere interactions. Main areas of investigation included studies of: cloud parameterizations for global climate codes, Lidar and the planetary boundary layer, chemistry, climate variability using coupled ocean-atmospheric models, and numerical physical methods. This project employed a unique approach that included participation of a number of University of California faculty, postdoctoral fellows and graduate students who collaborated with Los Alamos research staff on specific tasks, thus greatly enhancing the research output. Overall accomplishments during the sensing of the atmospheric planetary were: (1) first two- and three-dimensional remote sensing of the atmospheric planetary boundary layer using Lidars, (2) modeling of 20-year cycle in both pressure and sea surface temperatures in North Pacific, (3) modeling of low frequency internal variability, (4) addition of aerosols to stratosphere to simulate Pinatubo effect on ozone, (5) development of fast, comprehensive chemistry in the troposphere for urban pollution studies, (6) new prognostic cloud parameterization in global atmospheric code remedied problems with North Pacific atmospheric circulation and excessive equatorial precipitation, (7) development of a unique aerosol analysis technique, the aerosol time-of-flight mass spectrometer (ATOFMS), which allows real-time analysis of the size and chemical composition of individual aerosol particles, and (8) numerical physics applying Approximate Inertial Manifolds to ocean circulation. 14 refs., 6 figs.
The nucleon wave function in light-front dynamics
Karmanov, V A
1998-01-01
The general spin structure of the relativistic nucleon wave function in the $3q$-model is found. It contains 16 spin components, in contrast to 8 ones known previously, since in a many-body system the parity conservation does not reduce the number of the components. The explicitly covariant form of the wave function automatically takes into account the relativistic spin rotations, without introducing any Melosh rotation matrices. It also reduces the calculations to the standard routine of the Dirac matrices and of the trace techniques. In examples of the proton magnetic moment and of the axial nucleon form factor, with a particular wave function, we reproduce the results of the standard approach. Calculations beyond the standard assumptions give different results.
Strong semiclassical approximation of Wigner functions for the Hartree dynamics
Athanassoulis, Agissilaos
2011-01-01
We consider the Wigner equation corresponding to a nonlinear Schrödinger evolution of the Hartree type in the semiclassical limit h → 0. Under appropriate assumptions on the initial data and the interaction potential, we show that the Wigner function is close in L 2 to its weak limit, the solution of the corresponding Vlasov equation. The strong approximation allows the construction of semiclassical operator-valued observables, approximating their quantum counterparts in Hilbert-Schmidt topology. The proof makes use of a pointwise-positivity manipulation, which seems necessary in working with the L 2 norm and the precise form of the nonlinearity. We employ the Husimi function as a pivot between the classical probability density and the Wigner function, which - as it is well known - is not pointwise positive in general.
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
Functional metagenomic selections represent a powerful technique that is widely applied for identification of novel genes from complex metagenomic sources. However, whereas hundreds to thousands of clones can be easily generated and sequenced over a few days of experiments, analyzing the data...... to a comprehensive visual data overview that facilitates effortless inspection of gene function, clustering and distribution. The webserver is available at cbs.dtu.dk/services/deFUME/and the source code is distributed at github.com/EvdH0/deFUME....
Quantum power functional theory for many-body dynamics
Energy Technology Data Exchange (ETDEWEB)
Schmidt, Matthias, E-mail: Matthias.Schmidt@uni-bayreuth.de [Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95440 Bayreuth (Germany)
2015-11-07
We construct a one-body variational theory for the time evolution of nonrelativistic quantum many-body systems. The position- and time-dependent one-body density, particle current, and time derivative of the current act as three variational fields. The generating (power rate) functional is minimized by the true current time derivative. The corresponding Euler-Lagrange equation, together with the continuity equation for the density, forms a closed set of one-body equations of motion. Space- and time-nonlocal one-body forces are generated by the superadiabatic contribution to the functional. The theory applies to many-electron systems.
A study of a curious arithmetic function
Farhi, Bakir
2010-01-01
In this note, we study the arithmetic function $f : \\mathbb{Z}_+^* \\to \\mathbb{Q}_+^*$ defined by $f(2^k \\ell) = \\ell^{1 - k}$ ($\\forall k, \\ell \\in \\mathbb{N}$, $\\ell$ odd). We show several important properties about that function and then we use them to obtain some curious results involving the 2-adic valuation.
Recent Studies in Functional Analytic Psychotherapy
Garcia, Rafael Ferro
2008-01-01
Functional Analytic Psychotherapy (FAP), based on the principles of radical behaviorism, emphasizes the impact of eventualities that occur during therapeutic sessions, the therapist-client interaction context, functional equivalence between environments, natural reinforcement and shaping by the therapist. This paper reviews recent studies of FAP…
Ensuring safety and functionality of electroglottography measurements during dynamic pulmonary MRI.
Özen, Ali Caglar; Traser, Louisa; Echternach, Matthias; Dadakova, Tetiana; Burdumy, Michael; Richter, Bernhard; Bock, Michael
2016-11-01
To combine vocal tract measurements with dynamic MRI of the lungs to provide fundamental insights into the lung physiology during singing. To analyze vocal fold oscillatory patterns during dynamic lung MRI, an electroglottography (EGG) system was modified to allow for simultaneous EGG measurements during MR image acquisitions. A low-pass filter was introduced to suppress residual radiofrequency (RF) coupling into the EGG signal. RF heating was tested in a gel phantom to ensure MR safety, and functionality of the EGG device was assessed in a volunteer experiment at singing frequencies from A5 to A3. In the recorded EGG signals, remaining RF interferences were removed by independent component analysis post processing, and standard EGG parameters such as fundamental frequency, contact quotient and jitter were calculated. In a second volunteer experiment, EGG recordings were compared with lung diameter measurements from 2D time-resolved trueFISP acquisitions. RF heating measurements resulted in less than 1.2°C temperature increase in the gel phantom. EGG parameters measured during MR imaging are within the range of ideal values. In the lung measurement, both the lung diameter and the EGG recordings could be successfully performed with only minimal interference. EGG recording is pos sible during dynamic lung MRI, and glottal activity can be studied safely at 1.5T. Magn Reson Med 76:1629-1635, 2016. © 2015 International Society for Magnetic Resonance in Medicine. © 2015 International Society for Magnetic Resonance in Medicine.
Zou, Peng; Dalfovo, Franco; Sharma, Rishi; Liu, Xia-Ji; Hu, Hui
2016-11-01
We theoretically investigate the dynamic structure factor of a strongly interacting Fermi gas at the crossover from Bardeen-Cooper-Schrieffer superfluids to Bose-Einstein condensates, by developing an improved random phase approximation within the framework of a density functional theory (DFT)—the so-called superfluid local density approximation. Compared with the previous random-phase-approximation studies based on the standard Bogoliubov-de Gennes equations, the use of the DFT greatly improves the accuracy of the equation of state at the crossover, and leads to a better description of both collective Bogoliubov-Anderson-Goldstone phonon mode and single-particle fermionic excitations at small transferred momentum. Near unitarity, where the s-wave scattering length diverges, we show that the single-particle excitations start to significantly contribute to the spectrum of dynamic structure factor once the frequency is above a threshold of the energy gap at 2{{Δ }}. The sharp rise in the spectrum at this threshold can be utilized to measure the pairing gap Δ. Together with the sound velocity determined from the phonon branch, the dynamic structure factor provides us some key information of the crossover Fermi superfluid. Our predictions could be examined in experiments with 6Li or 40K atoms using Bragg spectroscopy.
Directory of Open Access Journals (Sweden)
Yang Liu
2015-01-01
Full Text Available An electric oil pump (EOP was integrated into the hydraulic system and an automatic transmission (AT mechanical oil pump (MOP was downsized. These processes were performed to combine a start-stop function with the AT and further improve the transmission efficiency. Furthermore, this study established a dynamics model of power loss and leakage of an 8-speed AT; a flow-based control algorithm of the EOP was then developed to realize the start-stop function and support the MOP to meet the flow requirement of the system. Based on a driving simulation method, sizes of the MOP and EOP that ensured optimal fuel economy were selected. A control strategy for the starting clutch was also developed to minimize the starting delay of the test vehicle. A test environment on a rig and prototype vehicle was established to verify the feasibility of the proposed control strategies. The test results indicated that the transmission functioned favorably with the novel two-pump system presented, and a quick and smooth starting performance was achieved when the engine was restarted. The findings in this study are extremely valuable for forward designs of an AT for realizing start-stop function and improving efficiency.
Organizational dynamics, functions, and pathobiological dysfunctions of neurofilaments.
Shea, Thomas B; Chan, Walter K-H; Kushkuley, Jacob; Lee, Sangmook
2009-01-01
Neurofilament phosphorylation has long been considered to regulate their axonal transport rate, and in doing so it provides stability to mature axons. We evaluate the collective evidence to date regarding how neurofilament C-terminal phosphorylation may regulate axonal transport. We present a few suggestions for further experimentation in this area, and expand upon previous models for axonal NF dynamics. We present evidence that the NFs that display extended residence along axons are critically dependent upon the surrounding microtubules, and that simultaneous interaction with multiple microtubule motors provides the architectural force that regulates their distribution. Finally, we address how C-terminal phosphorylation is regionally and temporally regulated by a balance of kinase and phosphatase activities, and how misregulation of this balance might contribute to motor neuron disease.
Anderst, William J; Donaldson, William F; Lee, Joon Y; Kang, James D
2015-05-01
The objective of this study was to determine the intervertebral kinematics of the young, healthy cervical spine during dynamic, three-dimensional, functional loading. Intervertebral motion was characterized by the range of motion (ROM) and the helical axis of motion (HAM). Biplane radiographs of the cervical spine were collected at 30 images/s as 29 participants (20-35 yr) performed dynamic flexion\\extension, axial rotation, and lateral bending. Vertebral motion (C1-T1 in flexion\\extension, C3-T1 in lateral bending and axial rotation) was tracked with sub-millimeter accuracy using a validated volumetric model-based tracking process that matched subject-specific CT-based bone models to the radiographs. Flexion\\extension ROM was smallest at the C2-C3 motion segment (12.7±2.6°) and largest at the C5-C6 motion segment (19.7±3.7°). During head lateral bending and axial rotation, the intervertebral bending ROM was greater than the rotation ROM at every motion segment. The HAM demonstrated differences among motion segments and among movements. During flexion\\extension, the helical axis of motion was directed nearly perpendicular to the sagittal plane for the C2-C3 through C7-T1 motion segments. During lateral bending, the angle between the HAM and the transverse plane progressively increased from the C6-C7 motion segment (approximately ±22°) to the C3-C4 motion segment (approximately ±40°). During axial rotation, the angle between the transverse plane and the HAM was approximately ±42° at the C3-C4 through C5-C6 motion segments, and approximately ±32° at the C6-C7 motion segment. This study provides valuable reference data for evaluating the effects of age, degeneration, and surgical procedures on cervical spine kinematics during three-dimensional dynamic functional loading.
Measuring Dynamic Kidney Function in an Undergraduate Physiology Laboratory
Medler, Scott; Harrington, Frederick
2013-01-01
Most undergraduate physiology laboratories are very limited in how they treat renal physiology. It is common to find teaching laboratories equipped with the capability for high-resolution digital recordings of physiological functions (muscle twitches, ECG, action potentials, respiratory responses, etc.), but most urinary laboratories still rely on…
Assessing Sensorimotor Function Following ISS with Computerized Dynamic Posturography.
Wood, Scott J; Paloski, William H; Clark, Jonathan B
2015-12-01
Postflight postural ataxia reflects both the control strategies adopted for movement in microgravity and the direct effects of deconditioning. Computerized dynamic posturography (CDP) has been used during the first decade of the International Space Station (ISS) expeditions to quantify the initial postflight decrements and recovery of postural stability. The CDP data were obtained on 37 crewmembers as part of their pre- and postflight medical examinations. Sensory organization tests evaluated the ability to make effective use of (or suppress inappropriate) visual, vestibular, and somatosensory information for balance control. This report focuses on eyes closed conditions with either a fixed or sway-referenced base of support, with the head erect or during pitch-head tilts (± 20° at 0.33 Hz). Equilibrium scores were derived from peak-to-peak anterior-posterior sway. Motor-control tests were also used to evaluate a crewmember's ability to automatically recover from unexpected support-surface perturbations. The standard Romberg condition was the least sensitive. Dynamic head tilts led to increased incidence of falls and revealed significantly longer recovery than head-erect conditions. Improvements in postflight postural performance during the later expeditions may be attributable to higher preflight baselines and/or advanced exercise capabilities aboard the ISS. The diagnostic assessment of postural instability is more pronounced during unstable-support conditions requiring active head movements. In addition to supporting return-to-duty decisions by flight surgeons, the CDP provides a standardized sensorimotor measure that can be used to evaluate the effectiveness of countermeasures designed to either minimize deconditioning on orbit or promote reconditioning upon return to Earth.
Final report for NIF chamber dynamics studies
Energy Technology Data Exchange (ETDEWEB)
Burnham, A; Peterson, P F; Scott, J M
1998-09-01
The National Ignition Facility (NIF), a 1.8 MJ, 192 laser beam facility, will have anticipated fusion yields of up to 20 MJ from D-T pellets encased in a gold hohlraum target. The energy emitted from the target in the form of x rays, neutrons, target debris kinetic energy, and target shrapnel will be contained in a 5 m. radius spherical target chamber. various diagnostics will be stationed around the target at varying distances from the target. During each shot, the target will emit x rays that will vaporize nearby target facing surfaces including those of the diagnostics, the target positioner, and other chamber structures. This ablated vapor will be transported throughout the chamber, and will eventually condense and deposit on surfaces in the chamber, including the final optics debris shields. The research at the University of California at Berkeley relates primarily to the NIF chamber dynamics. The key design issues are the ablation of the chamber structures, transport of the vapor through the chamber and the condensation or deposition processes of those vaporized materials. An understanding of these processes is essential in developing a concept for protecting the fina optics debris shields from an excessive coating (> 10 A) of target debris and ablated material, thereby prolonging their lifetime between change-outs. At Berkeley, we have studied the physical issues of the ablation process and the effects of varying materials, the condensation process of the vaporized material, and design schemes that can lower the threat posed to the debris shields by these processes. The work or portions of the work completed this year have been published in several papers and a dissertation [l-5].
Bhadra, Pratiti; Pal, Debnath
2017-02-24
Dynamics is integral to the function of proteins, yet the use of molecular dynamics (MD) simulation as a technique remains under-explored for molecular function inference. This is more important in the context of genomics projects where novel proteins are determined with limited evolutionary information. Recently we developed a method to match the query protein's flexible segments to infer function using a novel approach combining analysis of residue fluctuation-graphs and auto-correlation vectors derived from coarse-grained (CG) MD trajectory. The method was validated on a diverse dataset with sequence identity between proteins as low as 3%, with high function-recall rates. Here we share its implementation as a publicly accessible web service, named DynFunc (Dynamics Match for Function) to query protein function from ≥1 µs long CG dynamics trajectory information of protein subunits. Users are provided with the custom-developed coarse-grained molecular mechanics (CGMM) forcefield to generate the MD trajectories for their protein of interest. On upload of trajectory information, the DynFunc web server identifies specific flexible regions of the protein linked to putative molecular function. Our unique application does not use evolutionary information to infer molecular function from MD information and can, therefore, work for all proteins, including moonlighting and the novel ones, whenever structural information is available. Our pipeline is expected to be of utility to all structural biologists working with novel proteins and interested in moonlighting functions.
Interacting relativistic quantum dynamics for multi-time wave functions
Directory of Open Access Journals (Sweden)
Lienert Matthias
2016-01-01
Full Text Available In this paper, we report on recent progress about a rigorous and manifestly covariant interacting model for two Dirac particles in 1+1 dimensions [9, 10]. It is formulated using the multi-time formalism of Dirac, Tomonaga and Schwinger. The mechanism of interaction is a relativistic generalization of contact interactions, and it is achieved going beyond the usual functional-analytic Hamiltonian method.
Interacting relativistic quantum dynamics for multi-time wave functions
Lienert, Matthias
2016-11-01
In this paper, we report on recent progress about a rigorous and manifestly covariant interacting model for two Dirac particles in 1+1 dimensions [9, 10]. It is formulated using the multi-time formalism of Dirac, Tomonaga and Schwinger. The mechanism of interaction is a relativistic generalization of contact interactions, and it is achieved going beyond the usual functional-analytic Hamiltonian method.
López, Dardo R.; Cavallero, Laura
2017-02-01
In arid ecosystems, recruitment dynamics are limited by harsh environmental conditions and greatly depend on the net outcome of the balance between facilitation and competition. This outcome can change as a consequence of degradation caused by livestock overgrazing. Also, distinct plant species may show a differential response to a common neighbour under the same environmental conditions. Therefore, ecosystem degradation could affect the net balance of plant-plant interactions, which can also depend on the functional traits of potential nurse species. The aim of this study is to assess the influence of alternative degradation states on (i) the density of seedlings of perennial species emerging in four microsite types, and on (ii) the relative interaction intensity (RII) between seedlings and potential nurses belonging to three functional types (deep- and shallow-rooted shrubs, and tussock grasses). During three years, we recorded seedling density of perennial species in four alternative degradation states in grass-shrubby steppes from northwestern Patagonia. The density of emerged seedlings of perennial species decreased sharply as degradation increased, showing non-linear responses in most microsites. Seedling density underneath deep-rooted shrubs was higher than underneath shallow-rooted shrubs and tussock grasses. Also, deep-rooted shrubs were the only functional type that recorded seedling emergence in highly degraded states. Deep-rooted shrubs had facilitative effects on the seedlings emerging and surviving underneath them, independently of ecosystem degradation. In contrast, RII between shallow-rooted shrubs and recently emerged seedlings, switched from positive effects in the less degraded states, to negative effects in the most degraded state. Tussock grasses recorded the weakest intensity of facilitative interactions with recently emerged seedlings, switching to competitive interactions as degradation increased. Our results suggest that species with key
New perspectives of studying gastrointestinal muscle function
Institute of Scientific and Technical Information of China (English)
Hans Gregersen; Donghua Liao
2006-01-01
The motor function of the gastrointestinal tract has primarily been studied using manometry and radiography,though more indirect tests have also been applied. Manometry and radiography do not provide detailed information about the muscle properties as can be assessed from studies of muscle properties in muscle strips in vitro. In recent years a technique based on impedance planimetric mEasurement of pressure-cross-sectional area relations in a distending bag has proven to provide more detailed information about the muscle function in vivo. This review shows examples of new muscle function analysis such as length-tension diagrams, forcevelocity curves and preload-afterload diagrams.
Recovery of methanotrophs from disturbance: population dynamics, evenness and functioning.
Ho, Adrian; Lüke, Claudia; Frenzel, Peter
2011-04-01
Biodiversity is claimed to be essential for ecosystem functioning, but is threatened by anthropogenic disturbances. Prokaryotes have been assumed to be functionally redundant and virtually inextinguishable. However, recent work indicates that microbes may well be sensitive to environmental disturbance. Focusing on methane-oxidizing bacteria as model organisms, we simulated disturbance-induced mortality by mixing native with sterilized paddy soil in two ratios, 1:4 and 1:40, representing moderate and severe die-offs. Disturbed microcosms were compared with an untreated control. Recovery of activity and populations was followed over 4 months by methane uptake measurements, pmoA-qPCR, pmoA-based terminal restriction fragment length polymorphism and a pmoA-based diagnostic microarray. Diversity and evenness of methanotrophs decreased in disturbed microcosms, but functioning was not compromised. We consistently observed distinctive temporal shifts between type I and type II methanotrophs, and a rapid population growth leading to even higher cell numbers comparing disturbed microcosms with the control. Overcompensating mortality suggested that population size in the control was limited by competition with other bacteria. Overall, methanotrophs showed a remarkable ability to compensate for die-offs.
Vortex Dynamics Studies in Type II Superconductors
Xu, Zhigang
1993-03-01
Vibrating reed, ac susceptibility and resistance measurements have been used to study the dynamics of vortices in type II superconductors. In Nb measurements, in spite of the low T _{c}'s and long coherence lengths compared to the high T_{c} superconductors, we find an extended region of temperature and field over which reversible flux line motion occurs when the Nb reed is oriented with its long dimension perpendicular to the applied field. We observe a strong, frequency-independent depression of the "irreversibility temperature" T _{Q}(H) below the resistively determined critical temperature T_{R}. The results of the ac susceptibility measurements also support these results. We concluded that observation of an extended region of magnetic reversibility is not restricted to high T_{c} or extremely anisotropic materials, and depends upon the geometry of samples with respect to the applied field direction. In NbSe_2 measurements, vibrating reed measurements were performed with the hexagonal c-axis approximately parallel or perpendicular to an applied magnetic field. Field-cooling data revealed an unusual peak in the frequency shift of the reed, accompanied by two peaks in reed dissipation. The upper peak occurs near the temperature where R~ 0, and the lower peak is very sample and amplitude dependent and hysteretic. The ac susceptibility results also show that corresponding features. The interplay of superconductivity and density waves were investigated by comparing data for NbSe _2 with the results for NbS_2 , which has a comparable superconducting T _{c } and crystal structure. In NbS_2 measurements, we did not see such a peak in the frequency shift nor the double peak feature in the dissipation in either vibrating reed measurements or ac susceptibility measurements. We have also studied the (Ba,K)BiO_3 system. It is cubic at its superconducting composition, but exhibits a moderately high T_{c }=30 K that is intermediate between conventional and high T_{rm c
Analysis of in vitro and in vivo function of total knee replacements using dynamic contact models
Zhao, Dong
Despite the high incidence of osteoarthritis in human knee joint, its causes remain unknown. Total knee replacement (TKR) has been shown clinically to be effective in restoring the knee function. However, wear of ultra-high molecular weight polyethylene has limited the longevity of TKRs. To address these important issues, it is necessary to investigate the in vitro and in vivo function of total knee replacements using dynamic contact models. A multibody dynamic model of an AMTI knee simulator was developed. Incorporating a wear prediction model into the contact model based on elastic foundation theory enables the contact surface to take into account creep and wear during the dynamic simulation. Comparisons of the predicted damage depth, area, and volume lost with worn retrievals from a physical machine were made to validate the model. In vivo tibial force distributions during dynamic and high flexion activities were investigated using the dynamic contact model. In vivo medial and lateral contact forces experienced by a well-aligned instrumented knee implant, as well as upper and lower bounds on contact pressures for a variety of activities were studied. For all activities, the predicted medial and lateral contact forces were insensitive to the selected material model. For this patient, the load split during the mid-stance phase of gait and during stair is more equal than anticipated. The external knee adduction torque has been proposed as a surrogate measure for medial compartment load during gait. However, a direct link between these two quantities has not been demonstrated using in vivo measurement of medial compartment load. In vivo data collected from a subject with an instrumented knee implant were analyzed to evaluate this link. The subject performed five different overground gait motions (normal, fast, slow, wide, and toe out) while instrumented implant, video motion, and ground reaction data were simultaneously collected. The high correlation coefficient
Microfluidic strategy to investigate dynamics of small blood vessel function
Yasotharan, Sanjesh; Bolz, Steffen-Sebastian; Guenther, Axel
2010-11-01
Resistance arteries (RAs, 30-300 microns in diameter) that are located within the terminal part of the vascular tree regulate the laminar perfusion of tissue with blood, via the peripheral vascular resistance, and hence controls the systemic blood pressure. The structure of RAs is adapted to actively controlling flow resistance by dynamically changing their diameter, which is non-linearly dependent on the temporal variation of the transmural pressure, perfusion flow rate and spatiotemporal changes in the chemical environment. Increases in systemic blood pressure (hypertension) resulting from pathologic changes in the RA response represent the primary risk factor for cardiovascular diseases. We use a microfluidic strategy to investigate small blood vessels by quantifying structural variations within the arterial wall, RA outer contour and diameter over time. First, we document the artery response to vasomotor drugs that were homogeneously applied at step-wise increasing concentration. Second, we investigate the response in the presence of well-defined axial and circumferential heterogeneities. Artery per- and superfusion is discussed based on microscale PIV measurements of the fluid velocity on both sides of the arterial wall. Structural changes in the arterial wall are quantified using cross-correlation and proper orthogonal decomposition analyses of bright-field micrographs.
Beam Dynamics Studies for the SPARC Project
Energy Technology Data Exchange (ETDEWEB)
Ferrario, M.; Biagini, Maria E.; Boscolo, M.; Fusco, V.; Guiducci, S.; Migliorati, M.; Serafini, L.; Vaccarezza, C.; Bartolini, R.; Giannessi, L.; Quattromini, M.; Ronsivalle, C.; Limborg, C.G.; /Unlisted /Unlisted /ENEA, Frascati /SLAC
2008-03-17
The aim of the SPARC project, is to promote an R&D activity oriented to the development of a high brightness photoinjector to drive SASE-FEL experiments. We discuss in this paper the status of the beam dynamics simulation activities.
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
Localized Template-Driven Functionalization of Nanoparticles by Dynamic Combinatorial Chemistry
Nowak, Piotr; Saggiomo, Vittorio; Salehian, Fatemeh; Colomb-Delsuc, Mathieu; Han, Yang; Otto, Sijbren
2015-01-01
We have developed a method for the localized functionalization of gold nanoparticles using imine-based dynamic combinatorial chemistry. By using DNA templates, amines were grafted on the aldehyde-functionalized nanoparticles only if and where the nanoparticles interacted with the template molecules.
Localized Template-Driven Functionalization of Nanoparticles by Dynamic Combinatorial Chemistry
Nowak, Piotr; Saggiomo, Vittorio; Salehian, Fatemeh; Colomb-Delsuc, Mathieu; Han, Yang; Otto, Sijbren
2015-01-01
We have developed a method for the localized functionalization of gold nanoparticles using imine-based dynamic combinatorial chemistry. By using DNA templates, amines were grafted on the aldehyde-functionalized nanoparticles only if and where the nanoparticles interacted with the template molecules.
Structural and functional dynamics of Excitatory Amino Acid Transporters (EAAT
Directory of Open Access Journals (Sweden)
Thomas Rauen
2014-09-01
Full Text Available Glutamate transporters control the glutamate homeostasis in the central nervous system, and, thus, are not only crucial for physiological excitatory synaptic signaling, but also for the prevention of a large number of neurodegenerative diseases that are associated with excessive and prolonged presence of the neurotransmitter glutamate in the extracellular space. Until now, five subtypes of high-affinity glutamate transporters (excitatory amino acid transporters, EAATs 1–5 have been identified. These 5 high-affinity glutamate transporter subtypes belong to the solute carrier 1 (SLC1 family of transmembrane proteins: EAAT1/GLAST (SLC1A3, EAAT2/GLT1 (SLC1A2, EAAT3/EAAC1 (SLC1A1, EAAT4 (SLC1A6 and EAAT5 (SLC1A7. EAATs are secondary-active transporters, taking up glutamate into the cell against a substantial concentration gradient. The driving force for concentrative uptake is provided by the co-transport of Na+ ions and the counter-transport of one K+ in a step independent of the glutamate translocation step. Due to the electrogenicity of transport, the transmembrane potential can also act as driving force. Glutamate transporters are also able to run in reverse, resulting in glutamate release from cells. Due to these important physiological functions, glutamate transporter expression and, therefore, the transport rate, are tightly regulated. The EAAT protein family are structurally expected to be highly similar, however, these transporters show a functional diversity that ranges from high capacity glutamate uptake systems (EAATs 1–3 to receptor-like glutamate activated anion channels (EAATs 4–5. Here, we provide an update on most recent progress made on EAAT’s molecular transport mechanism, structure-function relationships, pharmacology, and will add recent insights into mechanism of rapid membrane trafficking of glutamate transporters.
Hakun, Jonathan G; Johnson, Nathan F
2017-11-01
Older adults tend to over-activate regions throughout frontoparietal cortices and exhibit a reduced range of functional modulation during WM task performance compared to younger adults. While recent evidence suggests that reduced functional modulation is associated with poorer task performance, it remains unclear whether reduced range of modulation is indicative of general WM capacity-limitations. In the current study, we examined whether the range of functional modulation observed over multiple levels of WM task difficulty (N-Back) predicts in-scanner task performance and out-of-scanner psychometric estimates of WM capacity. Within our sample (60-77years of age), age was negatively associated with frontoparietal modulation range. Individuals with greater modulation range exhibited more accurate N-Back performance. In addition, despite a lack of significant relationships between N-Back and complex span task performance, range of frontoparietal modulation during the N-Back significantly predicted domain-general estimates of WM capacity. Consistent with previous cross-sectional findings, older individuals with less modulation range exhibited greater activation at the lowest level of task difficulty but less activation at the highest levels of task difficulty. Our results are largely consistent with existing theories of neurocognitive aging (e.g. CRUNCH) but focus attention on dynamic range of functional modulation asa novel marker of WM capacity-limitations in older adults. Copyright © 2017 Elsevier Inc. All rights reserved.
Lee, K. E.; Lee, J. W.
2006-03-01
We study a simple model for a neuron function in a collective brain system. The neural network is composed of an uncorrelated configuration model (UCM) for eliminating the degree correlation of dynamical processes. The interaction of neurons is assumed to be isotropic and idealized. These neuron dynamics are similar to biological evolution in extremal dynamics with locally isotropic interaction but has a different time scale. The functioning of neurons takes place as punctuated patterns based on avalanche dynamics. In our model, the avalanche dynamics of neurons exhibit self-organized criticality which shows power-law behavior of the avalanche sizes. For a given network, the avalanche dynamic behavior is not changed with different degree exponents of networks, γ≥2.4 and various refractory periods referred to the memory effect, Tr. Furthermore, the avalanche size distributions exhibit power-law behavior in a single scaling region in contrast to other networks. However, return time distributions displaying spatiotemporal complexity have three characteristic time scaling regimes Thus, we find that UCM may be inefficient for holding a memory.
Energy Technology Data Exchange (ETDEWEB)
Fry-Petit, A. M., E-mail: mcqueen@jhu.edu, E-mail: afry@fullerton.edu; Sheckelton, J. P.; McQueen, T. M., E-mail: mcqueen@jhu.edu, E-mail: afry@fullerton.edu [Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218 (United States); Institute for Quantum Matter and Department of Physics and Astronomy, The Johns Hopkins University, Baltimore, Maryland 21218 (United States); Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Rebola, A. F.; Fennie, C. J. [Department of Applied Physics, Cornell University, Ithaca, New York 14853 (United States); Mourigal, M.; Valentine, M.; Drichko, N. [Institute for Quantum Matter and Department of Physics and Astronomy, The Johns Hopkins University, Baltimore, Maryland 21218 (United States)
2015-09-28
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{sub 2}Mo{sub 3}O{sub 8}, this approach allows direct assignment of the constrained rotational mode of Mo{sub 3}O{sub 13} clusters and internal modes of MoO{sub 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.
Molecular Dynamics Study of Polyethylene under Extreme Confinement
Kritikos, G.; Sgouros, A.; Vogiatzis, G. G.; Theodorou, D. N.
2016-08-01
We present results concerning the dynamics and the structure of adsorbed layers of molten polyethylene (PE) between two graphite surfaces. The molecular weight of the monodisperse PE chains reaches the entanglement regime. We study three cases of interwall distances, equal to two, three and four times the unperturbed radius of gyration (Rg ) of PE chains. The confined system is equilibrated by use of efficient Monte Carlo (MC) algorithms. Conducting molecular dynamics (MD) simulations, we reveal the distribution of relaxation times as a function of distance from the graphite walls at the temperature of 450 K. From the atomic-level stresses we calculate a realistic estimate of the adhesion tension, which is not affected significantly by the width of the pore. Although the distance between the two walls is comparable to the width of the adsorbed layer, we do not record the formation of ‘glassy bridges’ under the studied conditions. The diffusion of polymer chains in the middle layer is not inhibited by the existence of the two adsorbed layers. Extreme confinement conditions imposed by the long range wall potentials bring about an increase in both the adsorption and desorption rates of chains. The presented results seem to cohere with a reduction in the calorimetric (heat capacity step) glass transition temperature (Tg ).
Effective model hierarchies for dynamic and static classical density functional theories
Energy Technology Data Exchange (ETDEWEB)
Majaniemi, S [Department of Applied Physics, Aalto University School of Science and Technology, PO Box 11100, FI-00076 Aalto (Finland); Provatas, N [Department of Materials Science and Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S-4L7 (Canada); Nonomura, M, E-mail: maj@fyslab.hut.f [Department of Physics, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522 (Japan)
2010-09-15
The origin and methodology of deriving effective model hierarchies are presented with applications to solidification of crystalline solids. In particular, it is discussed how the form of the equations of motion and the effective parameters on larger scales can be obtained from the more microscopic models. It will be shown that tying together the dynamic structure of the projection operator formalism with static classical density functional theories can lead to incomplete (mass) transport properties even though the linearized hydrodynamics on large scales is correctly reproduced. To facilitate a more natural way of binding together the dynamics of the macrovariables and classical density functional theory, a dynamic generalization of density functional theory based on the nonequilibrium generating functional is suggested.
Arnold, Aiden E G F; Iaria, Giuseppe; Goghari, Vina M
2016-02-28
Schizophrenia is associated with deficits in face perception and emotion recognition. Despite consistent behavioural results, the neural mechanisms underlying these cognitive abilities have been difficult to isolate, in part due to differences in neuroimaging methods used between studies for identifying regions in the face processing system. Given this problem, we aimed to validate a recently developed fMRI-based dynamic functional localizer task for use in studies of psychiatric populations and specifically schizophrenia. Previously, this functional localizer successfully identified each of the core face processing regions (i.e. fusiform face area, occipital face area, superior temporal sulcus), and regions within an extended system (e.g. amygdala) in healthy individuals. In this study, we tested the functional localizer success rate in 27 schizophrenia patients and in 24 community controls. Overall, the core face processing regions were localized equally between both the schizophrenia and control group. Additionally, the amygdala, a candidate brain region from the extended system, was identified in nearly half the participants from both groups. These results indicate the effectiveness of a dynamic functional localizer at identifying regions of interest associated with face perception and emotion recognition in schizophrenia. The use of dynamic functional localizers may help standardize the investigation of the facial and emotion processing system in this and other clinical populations.
STRUCTURE AND DYNAMICS OF ALKALI BORATE GLASSES - A MOLECULAR-DYNAMICS STUDY
VERHOEF, AH; DENHARTOG, HW
1995-01-01
Structural and dynamical properties of lithium, cesium and mixed alkali (i.e., lithium and cesium) borate glasses have been studied by the molecular dynamics method. The calculations yield glass structures consisting of planar BO3 triangles and BO4 tetrahedrons with no sixfold ring structures at all
Framework to study dynamic dependencies in networks of interacting processes.
Chicharro, Daniel; Ledberg, Anders
2012-10-01
The analysis of dynamic dependencies in complex systems such as the brain helps to understand how emerging properties arise from interactions. Here we propose an information-theoretic framework to analyze the dynamic dependencies in multivariate time-evolving systems. This framework constitutes a fully multivariate extension and unification of previous approaches based on bivariate or conditional mutual information and Granger causality or transfer entropy. We define multi-information measures that allow us to study the global statistical structure of the system as a whole, the total dependence between subsystems, and the temporal statistical structure of each subsystem. We develop a stationary and a nonstationary formulation of the framework. We then examine different decompositions of these multi-information measures. The transfer entropy naturally appears as a term in some of these decompositions. This allows us to examine its properties not as an isolated measure of interdependence but in the context of the complete framework. More generally we use causal graphs to study the specificity and sensitivity of all the measures appearing in these decompositions to different sources of statistical dependence arising from the causal connections between the subsystems. We illustrate that there is no straightforward relation between the strength of specific connections and specific terms in the decompositions. Furthermore, causal and noncausal statistical dependencies are not separable. In particular, the transfer entropy can be nonmonotonic in dependence on the connectivity strength between subsystems and is also sensitive to internal changes of the subsystems, so it should not be interpreted as a measure of connectivity strength. Altogether, in comparison to an analysis based on single isolated measures of interdependence, this framework is more powerful to analyze emergent properties in multivariate systems and to characterize functionally relevant changes in the
Reconstruction of an input function from a dynamic PET water image using multiple tissue curves
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 <8% and the calculated CBF values showed a tight correlation (r = 0.97). The simulation showed that errors associated with the assumed parameters were <10%, and that the optimal number of tissue curves to be used was around 500. Our results demonstrate that IDIF can be reconstructed directly from tissue curves obtained through {{\\text{H}}2} 15O PET imaging. This suggests the possibility of using a completely non-invasive technique to assess CBF in patho-physiological studies.
One- and two-particle correlation functions in the dynamical quantum cluster approach
Energy Technology Data Exchange (ETDEWEB)
Hochkeppel, Stephan
2008-07-25
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
The dynamical system generated by the 3n+1 function
Wirsching, Günther J
1998-01-01
The 3n+1 function T is defined by T(n)=n/2 for n even, and T(n)=(3n+1)/2 for n odd. The famous 3n+1 conjecture, which remains open, states that, for any starting number n>0, iterated application of T to n eventually produces 1. After a survey of theorems concerning the 3n+1 problem, the main focus of the book are 3n+1 predecessor sets. These are analyzed using, e.g., elementary number theory, combinatorics, asymptotic analysis, and abstract measure theory. The book is written for any mathematician interested in the 3n+1 problem, and in the wealth of mathematical ideas employed to attack it.
Neural network design for J function approximation in dynamic programming
Pang, X
1998-01-01
This paper shows that a new type of artificial neural network (ANN) -- the Simultaneous Recurrent Network (SRN) -- can, if properly trained, solve a difficult function approximation problem which conventional ANNs -- either feedforward or Hebbian -- cannot. This problem, the problem of generalized maze navigation, is typical of problems which arise in building true intelligent control systems using neural networks. (Such systems are discussed in the chapter by Werbos in K.Pribram, Brain and Values, Erlbaum 1998.) The paper provides a general review of other types of recurrent networks and alternative training techniques, including a flowchart of the Error Critic training design, arguable the only plausible approach to explain how the brain adapts time-lagged recurrent systems in real-time. The C code of the test is appended. As in the first tests of backprop, the training here was slow, but there are ways to do better after more experience using this type of network.
Evaluation of dynamic renal function by nuclear medicine using Tc-99m DTPA
Energy Technology Data Exchange (ETDEWEB)
Ishibashi, M.
1987-01-01
Dynamic renal function was nucleomedically evaluated using Tc-99m DTPA, and its value was assessed in various renal diseases. In addition to RI angiography, sequential image and renogram curve which were traditionally used as routine studies, Renal First Blood Flow (RFBF) by aortic blood flow exactly at the entrance of the renal artery, GFR (DTPA-GFR) by renal uptake and mean transit time (MTT) of the tracer by deconvolution analysis were measured. RFBF was useful to evaluate the stricture at the confluence of the renal artery and renal circulation, particularly cortical circulation. DTPA-GFR enabled the simple and rapid measurement of Total-GFR and Split-GFR. MTT was considered to be valuable in diagnosing obstructive nephropathy. In particular, RFBF was useful for assessment of renovascular hypertension. The measurement of the above-mentioned parameters made it possible to evaluate renal function objectively and quantitatively in addition to imaging and semiquantitative studies obtained by traditional routine examination. The major advantage of this procedure includes its possible performance along with routine renal function tests without any special preparation.
Studying Human Dynamics Through Web Analytics
Ramasco, Jose; Goncalves, Bruno
2008-03-01
When Tim Berners Lee, a physicist at the European Center for Nuclear Research (CERN) first conceived the World Wide Web (WWW) in 1990 as a way to facilitate the sharing of scientific information and results among the centers different researchers and groups, even the most ingenious of science fiction writers could not have imagined the role it would come to play in the following decades. The increasing ubiquitousness of Internet access and the frequency with which people interact with it raise the possibility of using it to better observe, understand, and even monitor several aspects of human social behavior. Websites with large numbers of frequently returning users, such as search engines, company or university websites, are ideal for this task. The properly anonymized logs detailing the access history to Emory University's website is studied. We find that a small number of users is responsible for a finite fraction of the total activity. A saturation phenomenon is observed where, certain connections age, becoming less attractive to new activity over time. Finally, by measuring the average activity as a function of the day of the week, we find that productivity seems to be higher on Tuesdays and Wednesdays, with Sundays being the least active day.
Density functional theory studies of etoricoxib
Sachdeva, Ritika; Kaur, Prabhjot; Singh, V. P.; Saini, G. S. S.
2016-05-01
Etoricoxib is a COX-2 selective inhibitor drug with molecular formula C18H15ClN2O2S. It is primarily used for the treatment of arthritis(rheumatoid, psoriatic, osteoarthritis), ankylosing spondylitis, gout and chronic low back pain. Theoretical studies of the molecule including geometry optimization and vibrational frequency calculations were carried out with the help of density functional theory calculations using 6-311++ g (d, p) basis set and B3LYP functional.
Excess water dynamics in hydrotalcite: QENS study
Indian Academy of Sciences (India)
S Mitra; A Pramanik; D Chakrabarty; R Mukhopadhyay
2004-08-01
Results of the quasi-elastic neutron scattering (QENS) measurements on the dynamics of excess water in hydrotalcite sample with varied content of excess water are reported. Translational motion of excess water can be best described by random translational jump diffusion model. The observed increase in translational diffusivity with increase in the amount of excess water is attributed to the change in binding of the water molecules to the host layer.
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.
Tribological Studies of Dynamic Thermal Seal Materials
DeMange, Jeffrey J.; Taylor, Shawn C.
2016-01-01
Thermal seals are required on high-speed vehicles in many dynamic applications such as variable inlets in propulsion systems and control surfaces. These seals, often referred to as dynamic thermal seals, must not only mitigate inboard heat transfer, but must also exhibit sufficient durability when scrubbed against mating surfaces. For high-temperature high-speed vehicle applications, the mating surfaces are often made from thermal protection system (TPS) materials, which are typically rougher and more abrasive than TPS materials used at lower temperatures. The high-temperature TPS materials used can include non-ablative (e.g., lightweight porous oxides, ceramic matrix composites) andor ablative systems (e.g., phenolic systems). Due to the increased need for durable high-temperature dynamic seals, researchers working with the NASA Glenn Research Center embarked on an effort to (a) characterize the tribological performance of state-of-the-art thermal seal materials against a variety of TPS materials and (b) develop approaches for improved wear resistance. Tests were conducted using a recently upgraded high-temperature tribometer to assess wear resistance for a variety of tribopairs under multiple conditions. This data will begin to frame the challenges of using these materials and eventually permit an improved ability to design and implement these critical TPS components.
Functional studies on the phosphatidychloride transfer protein
Brouwer, A.P.M. de
2002-01-01
The phosphatidylcholine transfer protein (PC-TP) has been studied for over 30 years now. Despite extensive research concerning the biochemical, biophysical and structural properties of PC-TP, the function of this protein is still elusive. We have studied in vitro the folding and the mechanism of PC
A nonlinear correlation function for selecting the delay time in dynamical reconstructions
Aguirre, Luis Antonio
1995-02-01
Numerical results discussed in this paper suggest that a function which detects nonlinear correlations in time series usually indicates shorter correlation times than the linear autocorrelation function which is often used for this purpose. The nonlinear correlation function can also detect changes in the data which cannot be distinguished by the linear counterpart. This affects a number of approaches for the selection of the delay time used in the reconstruction of nonlinear dynamics from a single time series based on time delay coordinates.
Ramírez-García, Gonzalo; d'Orlyé, Fanny; Gutiérrez-Granados, Silvia; Martínez-Alfaro, Minerva; Mignet, Nathalie; Richard, Cyrille; Varenne, Anne
2015-12-01
Zinc gallate nanoparticles doped with chromium (III) (ZnGa1.995O4:Cr0.005) are innovative persistent luminescence materials with particular optical properties allowing their use for in vivo imaging. They can be excited in the tissue transparency window by visible photons and emit light for hours after the end of the excitation. This allows to observe the probe without any time constraints and without autofluorescence signals produced by biological tissues. Modification of the surface of these nanoparticles is essential to be colloidally stable not only for cell targeting applications but also for proper distribution in living organisms. The use of different methods for controlling and characterizing the functionalization process is imperative to better understand the subsequent interactions with biological elements. This work explores for the first time the characterization and optimization of a classic functionalization sequence, starting with hydroxyl groups (ZGO-OH) at the nanoparticle surface, followed by an aminosilane-functionalization intermediate stage (ZGO-NH2) before PEGylation (ZGO-PEG). Dynamic light scattering and laser doppler electrophoresis were used in combination with capillary electrophoresis to characterize the nanoparticle functionalization processes and control their colloidal and chemical stability. The hydrodynamic diameter, zeta potential, electrophoretic mobility, stability over time and aggregation state of persistent luminescence nanoparticles under physiological-based solution conditions have been studied for each functional state. Additionally, a new protocol to improve ZGO-NH2 stability based on a thermal treatment to complete covalent binding of (3-aminopropyl) triethoxysilane onto the particle surface has been optimized. This thorough control increases our knowledge on these nanoparticles for subsequent toxicological studies and ultimately medical application.
Evaluation of renal function using Gd-DTPA dynamic MR imaging
Energy Technology Data Exchange (ETDEWEB)
Furukawa, Akira; Murata, Kiyoshi; Morita, Rikushi [Shiga Univ., Otsu (Japan). Medical Science
1996-04-01
To establish a new method for evaluating renal function using MRI, we performed dynamic Gd-DTPA enhanced MR imaging at 1.5 T in 68 subjects (71 examinations), including 23 normal volunteers, 19 patients with chronic renal failure, 22 with hydronephrosis, and 7 with renal vascular disorders. Thirty GRASS images [35/9/20deg/1 (TR/TE/Flip Angle/NEX)] were obtained after a bolus injection of Gd-DTPA (0.2 mmol/Kg) in each case, and were evaluated in the following respects. Whether or not the initial signal increase and/or the following signal drop in cortex was observed. Whether or not the signal drop in medulla and/or calyces was observed. Time between initial signal increase in cortex and signal drop in medulla (Ta). Time between signal drop in medulla and calyces (Tb). Time between signal increase in cortex and signal drop in calyces (Tc). Maximum ratio of signal intensity between cortex and medulla(Max. C/M). In normal subjects, the initial signal increase and the following signal drop in cortex, and the signal drop in medulla and calyces were observed. In patients with abnormal renal function, the characteristic signal changes discribed above were not seen clearly or disappeared in many cases. In normal subjects, Ta, Tb, Tc, and Max. C/M were 41.9{+-}6.9 sec, 53.2{+-}10.6 sec, 95.0{+-}9.5 sec, and 1.10{+-}0.05, respectively. In the patients, time parameters were significantly larger than those of normal subjects and C/M ratios were lower. This study suggested that dynamic Gd-DTPA renal MR imaging can serve as a new method for the evaluation of renal function. (author).
The effects of core stabilization exercise on dynamic balance and gait function in stroke patients.
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.
Ryu, Duchwan
2013-03-01
The sea surface temperature (SST) is an important factor of the earth climate system. A deep understanding of SST is essential for climate monitoring and prediction. In general, SST follows a nonlinear pattern in both time and location and can 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 filter to estimate the parameters of the dynamic model. We analyze the SST observed in the Caribbean Islands area after a hurricane using the proposed dynamic model. Comparing to the traditional grid-based approach that requires a supercomputer due to its high computational demand, our approach requires much less CPU time and makes real-time forecasting of SST doable on a personal computer. Supplementary materials for this article are available online. © 2013 American Statistical Association.
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.)
A study of tachyon dynamics for broad classes of potentials
Energy Technology Data Exchange (ETDEWEB)
Quiros, Israel [Division de Ciencias e Ingenieria de la Universidad de Guanajuato, AP 150, 37150, Leon, Guanajuato (Mexico); Gonzalez, Tame [Departamento de Fisica, Universidad Central de Las Villas, 54830 Santa Clara (Cuba); Gonzalez, Dania; Napoles, Yunelsy [Departamento de Matematica, Universidad Central de Las Villas, 54830 Santa Clara (Cuba); GarcIa-Salcedo, Ricardo [Centro de Investigacion en Ciencia Aplicada y Tecnologia Avanzada-Legaria del IPN, Mexico DF (Mexico); Moreno, Claudia, E-mail: iquiros@Fisica.ugto.m, E-mail: tame@uclv.edu.c, E-mail: dgm@uclv.edu.c, E-mail: yna@uclv.edu.c, E-mail: rigarcias@ipn.m, E-mail: claudia.moreno@cucei.udg.m [Departamento de Fisica y Matematicas, Centro Universitario de Ciencias Exactas e IngenierIas, Av. Revolucion 1500 SR, Universidad de Guadalajara, 44430 Guadalajara, Jalisco (Mexico)
2010-11-07
We investigate in detail the asymptotic properties of tachyon cosmology for a broad class of self-interaction potentials. The present approach relies on an appropriate re-definition of the tachyon field, which, in conjunction with a method formerly applied in the bibliography in a different context allows us to generalize the dynamical systems study of tachyon cosmology to a wider class of self-interaction potentials beyond the (inverse) square-law one. It is revealed that independent of the functional form of the potential, the matter-dominated solution and the ultra-relativistic (also matter-dominated) solution are always associated with equilibrium points in the phase space of the tachyon models. The latter is always the past attractor, while the former is a saddle critical point. For inverse power-law potentials V{proportional_to}{phi}{sup -2{lambda}} the late-time attractor is always the de Sitter solution, while for sinh-like potentials V{proportional_to}sinh {sup -{alpha}}({lambda}{sup {phi}}), depending on the region of parameter space, the late-time attractor can be either the inflationary tachyon-dominated solution or the matter-scaling (also inflationary) phase. In general, for most part of known quintessential potentials, the late-time dynamics will be associated either with de Sitter inflation, or with matter-scaling, or with scalar field-dominated solutions.
Ji, Pengfei; 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) 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 quant...
Nuclear magnetic resonance studies of macroscopic morphology and dynamics
Energy Technology Data Exchange (ETDEWEB)
Barrall, Geoffrey Alden [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry
1995-09-01
Nuclear magnetic resonance techniques are traditionally used to study molecular level structure and dynamics with a noted exception in medically applied NMR imaging (MRI). In this work, new experimental methods and theory are presented relevant to the study of macroscopic morphology and dynamics using NMR field gradient techniques and solid state two-dimensional exchange NMR. The goal in this work is not to take some particular system and study it in great detail, rather it is to show the utility of a number of new and novel techniques using ideal systems primarily as a proof of principle. By taking advantage of the analogy between NMR imaging and diffraction, one may simplify the experiments necessary for characterizing the statistical properties of the sample morphology. For a sample composed of many small features, e.g. a porous medium, the NMR diffraction techniques take advantage of both the narrow spatial range and spatial isotropy of the sample`s density autocorrelation function to obtain high resolution structural information in considerably less time than that required by conventional NMR imaging approaches. The time savings of the technique indicates that NMR diffraction is capable of finer spatial resolution than conventional NMR imaging techniques. Radio frequency NMR imaging with a coaxial resonator represents the first use of cylindrically symmetric field gradients in imaging. The apparatus as built has achieved resolution at the micron level for water samples, and has the potential to be very useful in the imaging of circularly symmetric systems. The study of displacement probability densities in flow through a random porous medium has revealed the presence of features related to the interconnectedness of the void volumes. The pulsed gradient techniques used have proven successful at measuring flow properties for time and length scales considerably shorter than those studied by more conventional techniques.
Modeling Dynamic Functional Neuroimaging Data Using Structural Equation Modeling
Price, Larry R.; Laird, Angela R.; Fox, Peter T.; Ingham, Roger J.
2009-01-01
The aims of this study were to present a method for developing a path analytic network model using data acquired from positron emission tomography. Regions of interest within the human brain were identified through quantitative activation likelihood estimation meta-analysis. Using this information, a "true" or population path model was then…
DYNAMICS AND FUNCTION OF THE INOSITOLCYCLE IN DICTYOSTELIUM-DISCOIDEUM
BOMINAAR, AA; VANDERKAAY, J; VANHAASTERT, PJM
1991-01-01
The inositolcycle in Dictyostelium discoideum was studied under several conditions both in vitro and in vivo. The results are compared with the inositolcycle as it is known from higher eukaryotes: although there is a strong resemblance both cycles are different at some essential points.
Xu, Song; Li, Yang; Guo, Qi; Yang, Xiao-Feng; Chan, Rosa H M
2017-02-15
Tracking the changes of neural dynamics based on neuronal spiking activities is a critical step to understand the neurobiological basis of learning from behaving animals. These dynamical neurobiological processes associated with learning are also time-varying, which makes the modeling problem challenging. We developed a novel multiwavelet-based time-varying generalized Laguerre-Volterra (TVGLV) modeling framework to study the time-varying neural dynamical systems using natural spike train data. By projecting the time-varying parameters in the TVGLV model onto a finite sequence of multiwavelet basis functions, the time-varying identification problem is converted into a time invariant linear-in-the-parameters one. An effective forward orthogonal regression (FOR) algorithm aided by mutual information (MI) criterion is then applied for the selection of significant model regressors or terms and the refinement of model structure. A generalized linear model fit approach is finally employed for parameter estimation from spike train data. The proposed multiwavelet-based TVGLV approach is used to identify both synthetic input-output spike trains and spontaneous retinal spike train recordings. The proposed method gives excellent the performance of tracking either sharply or slowly changing parameters with high sensitivity and accuracy regardless of the a priori knowledge of spike trains, which these results indicate that the proposed method is shown to deal well with spike train data. The proposed multiwavelet-based TVGLV approach was compared with several state-of-art parametric estimation methods like the steepest descent point process filter (SDPPF) or Chebyshev polynomial expansion method. The conventional SDPPF algorithm, or SDPPF with B-splines wavelet expansion method was shown to have the poor performance of tracking the time-varying system changes with the synthetic spike train data due to the slow convergence of the adaptive filter methods. Although the Chebyshev
Kaltashov, Igor A; Zhang, Mingxuan; Eyles, Stephen J; Abzalimov, Rinat R
2006-10-01
Electrospray ionization mass spectrometry (ESI MS) has emerged recently as a powerful tool for analyzing many structural and behavioral aspects of metalloproteins in great detail. In this review we discuss recent developments in the field, placing particular emphasis on the unique features of ESI MS that lend themselves to metalloprotein characterization at a variety of levels. Direct mass measurement enables the determination of protein-metal ion binding stoichiometry in solution and metalloprotein higher order structure in the case of multi-subunit proteins. MS techniques have been developed for determining the locations of metal-binding centers, metal oxidation states and reaction intermediates of metal-containing enzymes. Other ESI MS techniques are also discussed, such as protein ion charge state distributions and hydrogen/deuterium exchange studies, which can be used to measure metal binding affinities and to shed light on vital dynamic aspects of the functional properties of metalloproteins endowed by metal binding.
Takaba, Hiromitsu; Kimura, Shou; Alam, Md. Khorshed
2017-03-01
Durability of organo-lead halide perovskite are important issue for its practical application in a solar cells. In this study, using density functional theory (DFT) and molecular dynamics, we theoretically investigated a crystal structure, electronic structure, and ionic diffusivity of the partially substituted cubic MA0.5X0.5PbI3 (MA = CH3NH3+, X = NH4+ or (NH2)2CH+ or Cs+). Our calculation results indicate that a partial substitution of MA induces a lattice distortion, resulting in preventing MA or X from the diffusion between A sites in the perovskite. DFT calculations show that electronic structures of the investigated partially substituted perovskites were similar with that of MAPbI3, while their bandgaps slightly decrease compared to that of MAPbI3. Our results mean that partial substitution in halide perovskite is effective technique to suppress diffusion of intrinsic ions and tune the band gap.
Molecular Dynamics Investigation of Efficient SO₂ Absorption by Anion-Functionalized Ionic Liquids
Indian Academy of Sciences (India)
ANIRBAN MONDAL; SUNDARAM BALASUBRAMANIAN
2017-07-01
Ionic liquids are appropriate candidates for the absorption of acid gases such as SO₂. Six anion functionalized ionic liquids with different basicities have been studied for SO₂ absorption capacity by employing quantum chemical calculations and molecular dynamics (MD) simulations. Gas phase quantum calculations unveil that the high uptake of SO₂ in these ionic liquids originates from the basicity of the anions and the consequent enhanced anion-SO₂ interactions. MD simulations of SO₂–IL mixtures reveal the crucial role of both cations and anions in SO₂ dissolution. Multiple-site interactions of SO₂ with the anions have been identified. The calculated solvation free energy substantiates these observations. The order of computed Henry’s law constant values with change in the anion is in fair agreement with experimentally determined SO₂ solubility order.
Andrade, Xavier; Botti, Silvana; Marques, Miguel A. L.; Rubio, Angel
2007-05-01
The authors present an efficient perturbative method to obtain both static and dynamic polarizabilities and hyperpolarizabilities of complex electronic systems. This approach is based on the solution of a frequency-dependent Sternheimer equation, within the formalism of time-dependent density functional theory, and allows the calculation of the response both in resonance and out of resonance. Furthermore, the excellent scaling with the number of atoms opens the way to the investigation of response properties of very large molecular systems. To demonstrate the capabilities of this method, they implemented it in a real-space (basis-set-free) code and applied it to benchmark molecules, namely, CO, H2O, and para-nitroaniline. Their results are in agreement with experimental and previous theoretical studies and fully validate their approach.
Lattice dynamical studies of HTSC materials
Energy Technology Data Exchange (ETDEWEB)
Pintschovius, L.; Pyka, N.; Reichardt, W. (Kernforschungszentrum Karlsruhe, INFP (Germany)); Rumiantsev, A.Yu.; Mitrofanov, N.L.; Ivanov, A.S. (I.V. Kurchatov-Inst. of Atomic Energy, Moscow (USSR)); Collin, G.; Bourges, P. (Lab. Leon Brillouin, CEA-CNRS, CEN Saclay, 91 - Gif-sur-Yvette (France))
1991-12-01
A survey is presented on recent progress in the understanding of the lattice dynamics in Nd{sub 2}CuO{sub 4}, (La,Sr){sub 2}CuO{sub 4} and YBa{sub 2}Cu{sub 3}O{sub 6/7}. Classical anharmonicity and twinning were found to be major complications for the interpretation of the data. The lattice vibrations of the cuprates can now largely be described within the framework of shell models for strongly ionic compounds. Phonon anomalies inferred from a comparison of doped and undoped compounds resemble those found in classical superconductors. (orig.).
Pouplin, Samuel; Robertson, Johanna; Antoine, Jean-Yves; Blanchet, Antoine; Kahloun, Jean Loup; Volle, Philippe; Bouteille, Justine; Lofaso, Frédéric; Bensmail, Djamel
2014-01-01
Information technology plays a very important role in society. People with disabilities are often limited by slow text input speed despite the use of assistive devices. This study aimed to evaluate the effect of a dynamic on-screen keyboard (Custom Virtual Keyboard) and a word-prediction system (Sibylle) on text input speed in participants with functional tetraplegia. Ten participants tested four modes at home (static on-screen keyboard with and without word prediction and dynamic on-screen keyboard with and without word prediction) for 1 mo before choosing one mode and then using it for another month. Initial mean text input speed was around 23 characters per minute with the static keyboard and 12 characters per minute with the dynamic keyboard. The results showed that the dynamic keyboard reduced text input speed by 37% compared with the standard keyboard and that the addition of word prediction had no effect on text input speed. We suggest that current forms of dynamic keyboards and word prediction may not be suitable for increasing text input speed, particularly for subjects who use pointing devices. Future studies should evaluate the optimal ergonomic design of dynamic keyboards and the number and position of words that should be predicted.
Abney, Drew H; Paxton, Alexandra; Dale, Rick; Kello, Christopher T
2015-11-01
Successful interaction requires complex coordination of body movements. Previous research has suggested a functional role for coordination and especially synchronization (i.e., time-locked movement across individuals) in different types of human interaction contexts. Although such coordination has been shown to be nearly ubiquitous in human interaction, less is known about its function. One proposal is that synchrony supports and facilitates communication (Topics Cogn Sci 1:305-319, 2009). However, questions still remain about what the properties of coordination for optimizing communication might look like. In the present study, dyads worked together to construct towers from uncooked spaghetti and marshmallows. Using cross-recurrence quantification analysis, we found that dyads with loosely coupled gross body movements performed better, supporting recent work suggesting that simple synchrony may not be the key to effective performance (Riley et al. 2011). We also found evidence that leader-follower dynamics-when sensitive to the specific role structure of the interaction-impact task performance. We discuss our results with respect to the functional role of coordination in human interaction.
Blondel, Claire; Briset, Loïc; Legay, Nicolas; Arnoldi, Cindy; Poly, Franck; Clément, Jean-Christophe; Raveton, Muriel
2017-06-05
The persistent organochlorine pesticides (OCPs) in soils are suspected to disturb soil biogeochemical cycles. This study addressed the dynamic changes in soil functionality under lindane and chlordecone exposures with or without maize plant. Decreases in soil ammonium concentration, potential nitrogen mineralization and microbial biomass were only OCP-influenced in bulk soils. OCPs appeared to inhibit the ammonification step. With plants, soil functionality under OCP stress was similar to controls demonstrating the plant influence to ensure the efficiency of C- and N-turnover in soils. Moreover, OCPs did not impact the microbial community physiological profile in all tested conditions. However, microbial community structure was OCP-modified only in the presence of plants. Abundances of gram-negative and saprophytic fungi increased (up to +93% and +55%, respectively) suggesting a plant stimulation of nutrient turnover and rhizodegradation processes. Nevertheless, intimate microbial/plant interactions appeared to be OCP-impacted with depletions in mycorrhizae and micro/meso-fauna abundances (up to -53% and -56%, respectively) which might have adverse effects on more long-term plant growth (3-4 months). In short-term experiment (28days), maize growth was similar to the control ones, indicating an enhanced plasticity of the soil functioning in the presence of plants, which could efficiently participate to the remediation of OCP-contaminated soils. Copyright © 2017 Elsevier B.V. All rights reserved.
Effect of the environment on the protein dynamical transition: a neutron scattering study.
Paciaroni, Alessandro; Cinelli, Stefania; Onori, Giuseppe
2002-01-01
We performed an elastic neutron scattering investigation of the molecular dynamics of lysozyme solvated in glycerol, at different water contents h (grams of water/grams of lysozyme). The marked non-Gaussian behavior of the elastic intensity was studied in a wide experimental momentum transfer range, as a function of the temperature. The internal dynamics is well described in terms of the double-well jump model. At low temperature, the protein total mean square displacements exhibit an almost ...
Molecular dynamics study of nitrobenzene and 2-nitrophenyloctyl ether saturated with water
Jorge, Miguel; Gulaboski, Rubin; Pereira, Carlos M.; Cordeiro, M. Natália D. S.
2006-01-01
In this paper, results obtained from molecular dynamics (MD) simulations on the watersaturated organic liquids nitrobenzene (NB) and 2-nitrophenyloctyl ether (NPOE) are presented. Both solvents are extremely important in many areas of chemistry, and they are seen as the most promising successors of n-octanol for ion transfer studies at the liquid–liquid interface. Thermodynamic (mass density, enthalpy of vaporization), structural (radial distribution functions) and dynamic (dif...
Sojoudi, Alireza; Goodyear, Bradley G
2016-12-01
Spontaneous fluctuations of blood-oxygenation level-dependent functional magnetic resonance imaging (BOLD fMRI) signals are highly synchronous between brain regions that serve similar functions. This provides a means to investigate functional networks; however, most analysis techniques assume functional connections are constant over time. This may be problematic in the case of neurological disease, where functional connections may be highly variable. Recently, several methods have been proposed to determine moment-to-moment changes in the strength of functional connections over an imaging session (so called dynamic connectivity). Here a novel analysis framework based on a hierarchical observation modeling approach was proposed, to permit statistical inference of the presence of dynamic connectivity. A two-level linear model composed of overlapping sliding windows of fMRI signals, incorporating the fact that overlapping windows are not independent was described. To test this approach, datasets were synthesized whereby functional connectivity was either constant (significant or insignificant) or modulated by an external input. The method successfully determines the statistical significance of a functional connection in phase with the modulation, and it exhibits greater sensitivity and specificity in detecting regions with variable connectivity, when compared with sliding-window correlation analysis. For real data, this technique possesses greater reproducibility and provides a more discriminative estimate of dynamic connectivity than sliding-window correlation analysis. Hum Brain Mapp 37:4566-4580, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
Molecular-dynamic study of liquid ethylenediamine
Balabaev, N. K.; Kraevskii, S. V.; Rodnikova, M. N.; Solonina, I. A.
2016-10-01
Models of liquid ethylenediamine (ED) are built using the molecular dynamics approach at temperatures of 293-363 K and a size of 1000 molecules in a basic cell as a cuboid. The structural and dynamic characteristics of liquid ED versus temperature are derived. The gauche conformation of the ED molecule that is characteristic of the gas phase is shown to transition easily into the trans conformation of the molecules in the liquid. NH···N hydrogen bonds are analyzed in liquid ED. The number of H-bonds per ED molecule is found to vary from 5.02 at 293 K to 3.86 at 363 K. The lifetimes in the range of the temperatures and dissociation activation energy for several H-bonds in liquid ED are found to range from 0.574 to 4.524 ps at 293 K; the activation energies are 8.8 kJ/mol for 50% of the H-bonds and 16.3 kJ/mol for 6.25% of them. A weaker and more mobile spatial grid of H-bonds in liquid ED is observed, compared to data calculated earlier for monoethanolamine.
High transition frequencies of dynamic functional connectivity states in the creative brain
Li, Junchao; Zhang, Delong; Liang, Aiying; Liang, Bishan; Wang, Zengjian; Cai, Yuxuan; Gao, Mengxia; Gao, Zhenni; Chang, Song; Jiao, Bingqing; Huang, Ruiwang; Liu, Ming
2017-01-01
Creativity is thought to require the flexible reconfiguration of multiple brain regions that interact in transient and complex communication patterns. In contrast to prior emphases on searching for specific regions or networks associated with creative performance, we focused on exploring the association between the reconfiguration of dynamic functional connectivity states and creative ability. We hypothesized that a high frequency of dynamic functional connectivity state transitions will be associated with creative ability. To test this hypothesis, we recruited a high-creative group (HCG) and a low-creative group (LCG) of participants and collected resting-state fMRI (R-fMRI) data and Torrance Tests of Creative Thinking (TTCT) scores from each participant. By combining an independent component analysis with a dynamic network analysis approach, we discovered the HCG had more frequent transitions between dynamic functional connectivity (dFC) states than the LCG. Moreover, a confirmatory analysis using multiplication of temporal derivatives also indicated that there were more frequent dFC state transitions in the HCG. Taken together, these results provided empirical evidence for a linkage between the flexible reconfiguration of dynamic functional connectivity states and creative ability. These findings have the potential to provide new insights into the neural basis of creativity. PMID:28383052
High transition frequencies of dynamic functional connectivity states in the creative brain.
Li, Junchao; Zhang, Delong; Liang, Aiying; Liang, Bishan; Wang, Zengjian; Cai, Yuxuan; Gao, Mengxia; Gao, Zhenni; Chang, Song; Jiao, Bingqing; Huang, Ruiwang; Liu, Ming
2017-04-06
Creativity is thought to require the flexible reconfiguration of multiple brain regions that interact in transient and complex communication patterns. In contrast to prior emphases on searching for specific regions or networks associated with creative performance, we focused on exploring the association between the reconfiguration of dynamic functional connectivity states and creative ability. We hypothesized that a high frequency of dynamic functional connectivity state transitions will be associated with creative ability. To test this hypothesis, we recruited a high-creative group (HCG) and a low-creative group (LCG) of participants and collected resting-state fMRI (R-fMRI) data and Torrance Tests of Creative Thinking (TTCT) scores from each participant. By combining an independent component analysis with a dynamic network analysis approach, we discovered the HCG had more frequent transitions between dynamic functional connectivity (dFC) states than the LCG. Moreover, a confirmatory analysis using multiplication of temporal derivatives also indicated that there were more frequent dFC state transitions in the HCG. Taken together, these results provided empirical evidence for a linkage between the flexible reconfiguration of dynamic functional connectivity states and creative ability. These findings have the potential to provide new insights into the neural basis of creativity.
Archer, A J
2009-01-07
In recent years, a number of dynamical density functional theories (DDFTs) have been