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At least 415 records · Page 23Linked to original sources
PubMed1997

On the registration of time and the patterning of speech movements.

In order to study speech coordination we frequently average kinematic and other physiological signals. The averages are assumed to be more representative of the underlying patterns of production than individual records. In this note we outline different approaches to averaging and present a new nonlinear normalization technique that offers better information than ensemble averaging, linear normalization, or feature alignment methods. We suggest that this technique provides a clear estimation of pattern shape while preserving information on the variation over time.

Humans↗
PubMed2004

On the use of Bennett's acceptance ratio method in multi-canonical-type simulations.

A common strategy for mapping coexistence curves is to employ multi-canonical (MUCA) sampling to simulate along a macrostate path connecting two phases. Central to this approach is the task of accurately calculating the importance weights used in the MUCA procedure, which are needed for both effective sampling and accurate determination of phase boundaries. The purpose of this study is to develop a strategy for determining the importance weights that is built upon Bennett's optimized acceptance ratio method. This approach is shown to be closely related to transition matrix schemes, and is used to compute the vapor-liquid equilibrium of a Lennard-Jones fluid and the liquid-liquid equilibrium of a n-hexane/n-perfluorohexane mixture. For the Lennard-Jones system, the importance weights as a function of the number of particles "N" (at fixed temperature and volume) are obtained by using Bennett's method to estimate free energy differences between N and N+1 particle systems over the desired range of N values. In this application, the method is found to perform slightly better than a related transition matrix scheme. For the n-hexane/n-perfluorohexane liquid mixture, the method is designed to obtain weights as a function of composition (for fixed temperature, pressure, and total number of particles); in this case, the method is found to outperform the Gibbs ensemble approach.

Journal Article↗
PubMed2004

Synchronization of trajectories in canonical molecular-dynamics simulations: observation, explanation, and exploitation.

For two methods commonly used to achieve canonical-ensemble sampling in a molecular-dynamics simulation, the Langevin thermostat and the Andersen [H. C. Andersen, J. Chem. Phys. 72, 2384 (1980)] thermostat, we observe, as have others, synchronization of initially independent trajectories in the same potential basin when the same random number sequence is employed. For the first time, we derive the time dependence of this synchronization for a harmonic well and show that the rate of synchronization is proportional to the thermostat coupling strength at weak coupling and inversely proportional at strong coupling with a peak in between. Explanations for the synchronization and the coupling dependence are given for both thermostats. Observation of the effect for a realistic 97-atom system indicates that this phenomenon is quite general. We discuss some of the implications of this effect and propose that it can be exploited to develop new simulation techniques. We give three examples: efficient thermalization (a concept which was also noted by Fahy and Hamann [S. Fahy and D. R. Hamann, Phys. Rev. Lett. 69, 761 (1992)]), time-parallelization of a trajectory in an infrequent-event system, and detecting transitions in an infrequent-event system.

Algorithms↗
PubMed2005

The birth of a bubble: a molecular simulation study.

We study the nucleation of a bubble in a metastable Lennard-Jones (LJ) fluid, confined to a spherical pore with wetting walls, by a combination of grand canonical, canonical ensemble, and gauge cell Monte Carlo simulation methods complemented by the Voronoi-Delaunay tessellation analysis of statistical geometry of intermolecular cavities. We construct the isotherm of confined fluid in the form of a continuous van der Waals' loop, in which the unstable backward trajectory between the spinodals corresponds to bubble states. We show that as the degree of metastability increases and the fluid becomes progressively stretched, the decrease of fluid density is associated with the evolution of a population of interstitial intermolecular cavities. At the spinodal, the fluid becomes mechanically unstable: Interstitial cavities partly coalesce into a larger cavity located due to the system symmetry around the pore center. This cavity represents a bubble embryo, which grows at the expense of interstitial cavities. The nucleation barrier is calculated by direct thermodynamic integration along the isotherm. We compare our simulation results to the predictions of the classical nucleation theory and experiments on capillary condensation-evaporation of nitrogen in pores of hybrid organic-inorganic mesoporous molecular sieve HMM-3.

Journal Article↗
PubMed2005

Convergence of replica exchange molecular dynamics.

Replica exchange molecular dynamics (REMD) method is one of the generalized-ensemble algorithms which performs random walk in energy space and helps a system to escape from local energy traps. In this work, we studied the accuracy and efficiency of REMD by examining its ability to reproduce the results of multiple extended conventional molecular dynamics (MD) simulations and to enhance conformational sampling. Two sets of REMD simulations with different initial configurations, one from the fully extended and the other from fully helical conformations, were conducted on a fast-folding 21-amino-acid peptide with a continuum solvent model. Remarkably, the two REMD simulation sets started to converge even within 1.0 ns, despite their dramatically different starting conformations. In contrast, the conventional MD within the same time and with identical starting conformations did not show obvious signs of convergence. Excellent convergence between the REMD sets for T>300 K was observed after 14.0 ns REMD simulations as measured by the average helicity and free-energy profiles. We also conducted a set of 45 MD simulations at nine different temperatures with each trajectory simulated to 100.0 and 200.0 ns. An excellent agreement between the REMD and the extended MD simulation results was observed for T>300 K, showing that REMD can accurately reproduce long-time MD results with high efficiency. The autocorrelation times of the calculated helicity demonstrate that REMD can significantly enhance the sampling efficiency by 14.3+/-6.4, 35.1+/-0.2, and 71.5+/-20.4 times at, respectively, approximately 360, approximately 300, and approximately 275 K in comparison to the regular MD. Convergence was less satisfactory at low temperatures (T<300 K) and a slow oscillatory behavior suggests that longer simulation time was needed to reach equilibrium. Other technical issues, including choice of exchange frequency, were also examined.

Algorithms↗
PubMed2001

Kinetics of duplex formation for individual DNA strands within a single protein nanopore.

A single oligonucleotide was covalently attached to a genetically engineered subunit of the heptameric protein pore, alpha-hemolysin, to allow DNA duplex formation inside the pore lumen. Single-channel current recording was used to study the properties of the modified pore. On addition of an oligonucleotide 8 bases in length and with a sequence complementary to the tethered DNA strand, current blockades with durations of hundreds of milliseconds occurred, representing hybridization events of individual oligonucleotides to the tethered DNA strand. Kinetic constants for DNA duplex formation at the single molecule level were derived and found to be consistent with established literature values for macroscopic duplex formation. The resultant equilibrium constant for duplex formation in the nanopore was found to be close to the experimentally derived constant for duplex formation in solution. A good agreement between the equilibrium constants for duplex formation in the nanopore and in solution was also found for two other oligonucleotide pairs. In addition, the nanopore recordings revealed details of the kinetics difficult to obtain by conventional methods, like surface plasmon resonance, which measure ensemble properties. By investigating the temperature dependence of DNA duplex formation at the single molecule level, the standard enthalpy and entropy of the interaction could be obtained.

DNA↗
PubMed2002

Numerical study of a first-order irreversible phase transition in a CO+NO catalyzed reaction model.

The first-order irreversible phase transition (IPT) of the Yaldran-Khan model [Yaldran-Khan, J. Catal. 131, 369 (1991)] for the CO+NO reaction is studied using the constant-coverage (CC) ensemble and performing epidemic simulations. The CC method allows the study of hysteretic effects close to coexistence as well as the location of both the upper spinodal point and the coexistence point. Epidemic studies show that at coexistence the number of active sites decreases according to a (short-time) power law followed by a (long-time) exponential decay. It is concluded that first-order IPT's share many characteristics of their reversible counterparts, such as the development of short-ranged correlations, hysteretic effects, metastabilities, etc.

Journal Article↗
PubMed2003

Phase shift experiments identifying Kramers doublets in a chaotic superconducting microwave billiard of threefold symmetry.

The spectral properties of a two-dimensional microwave billiard showing threefold symmetry have been studied with a new experimental technique. This method is based on the behavior of the eigenmodes under variation of a phase shift between two input channels, which strongly depends on the symmetries of the eigenfunctions. Thereby a complete set of 108 Kramers doublets has been identified by a simple and purely experimental method. This set clearly shows Gaussian unitary ensemble statistics, although the system is time-reversal invariant.

Journal Article↗
PubMed2005

Correcting the use of ensemble averages in the calculation of harmonics to noise ratios in voice signals (L).

A correcting formula for the estimation of harmonics-to-noise ratios (HNR) based on ensemble-averaging techniques is derived. The original method yields a biased approximation which is more accurate as the number of averaged pulses (N) increases. However, the method treats gradual waveform changes incorrectly as noise, which is worsened for large values of N. The obtained formula allows the use of as few averaged pulses as desired, while allowing the complete removal of the bias from the estimate of HNR.

Algorithms↗
PubMed2003

Thermal insulation and evaporative resistance of football uniforms.

PURPOSE: To measure the thermal resistance (R(t)) and evaporative resistance (R(e,t)) of five different configurations of football uniforms commonly worn for American football practices and games. METHODS: The R(t) (insulation) of the ensembles was measured using an electrically heated manikin in thermal equilibrium with its surroundings. For the R(e,t) determinations, the manikin was covered with a cotton knit "skin" and sprayed with distilled water to simulate sweat-saturated skin. RESULTS: Compared with reference values for a T-shirt and shorts ensemble (R(t) = 0.140 m2. degrees C.W-1, R(e,t) = 0.020 m2.kPa-1.W-1), the R(t) of football uniforms ranged from 0.178 m2. degrees C.W-1 (1.15 clo) for a practice configuration of shorts, shoulder pads, practice jersey, and helmet to 0.233 m2. degrees C.W-1 (1.50 clo) for a full cold-weather uniform. Associated R(e,t) values ranged from 0.027 to 0.039 m2.kPa-1.W-1. CONCLUSION: Football uniforms contribute significantly to the heat load on a player. The thermal and evaporative resistance data presented in this paper can be used in the solution of heat balance equations to predict physiological responses of football players.

Body Temperature Regulation↗
PubMed1978

Objective specification of the incremental weight variable in weanling diarrhoeal disease of infants.

The objective specification of the second variable (body weight) measured in an epidemiological field study of weanling diarrhoeal disease of infants has been approached by computer-based pattern analysis, complementing previous studies of the diarrhoeal signal of daily defaecation count (DS). The weight data are available for 64 weeks in a subset of 50 out of 139 infants in the study. A weekly incremental weight signal (IWE) was estimated by successively differencing each new observed weight with a smoothed version of the previous value. Variable latency of the different features of this variable precludes the formation of an average-profile by coherent averaging the ensemble of records; a feature-analysis method based on statistical trend analysis was therefore developed. Features of the resulting IWE average profile can be linked to weanling events, transient diarrhoeal episodes, and typical post-neonatal shifts in level of the diarrhoeal signal. The results are consistent with the view that both nutritional and infectious factors operate in most deviations from typical behaviour seen in individual IWE records. In all the infants having an abnormally low (64 week) weight gain, a sustained abnormal DS elevation can be recognized in the 7-15 week period, with recurrent diarrhoeal episodes (type P2, as previously classified) during the 45-60 week period; both abnormalities were associated with substantial effects on weight gain. But individual P2-diarrhoeal episodes occurring before about 40 weeks of age could be linked only to small, quickly-compensated effects on incremental weight.

Body Weight↗
PubMed2002

Nonlinear spectrotemporal sound analysis by neurons in the auditory midbrain.

The auditory system of humans and animals must process information from sounds that dynamically vary along multiple stimulus dimensions, including time, frequency, and intensity. Therefore, to understand neuronal mechanisms underlying acoustic processing in the central auditory pathway, it is essential to characterize how spectral and temporal acoustic dimensions are jointly processed by the brain. We use acoustic signals with a structurally rich time-varying spectrum to study linear and nonlinear spectrotemporal interactions in the central nucleus of the inferior colliculus (ICC). Our stimuli, the dynamic moving ripple (DMR) and ripple noise (RN), allow us to systematically characterize response attributes with the spectrotemporal receptive field (STRF) methods to a rich and dynamic stimulus ensemble. Theoretically, we expect that STRFs derived with DMR and RN would be identical for a linear integrating neuron, and we find that approximately 60% of ICC neurons meet this basic requirement. We find that the remaining neurons are distinctly nonlinear; these could either respond selectively to DMR or produce no STRFs despite selective activation to spectrotemporal acoustic attributes. Our findings delineate rules for spectrotemporal integration in the ICC that cannot be accounted for by conventional linear-energy integration models.

Acoustic Stimulation↗
PubMed1993

Simultaneous derivation of clothing-specific heat exchange coefficients.

Clothing adds resistance to heat exchange between the wearer and the environment. If clothing-specific heat exchange coefficients are known, a combined rational/empirical approach can be used to describe thermal exchange between clothed humans and the environment. However, during exercise these coefficients--typically calculated using thermal manikins--change, primarily due to wetting of the fabric during intense sweating and body movement. A procedure is described that allows for the simultaneous determination of both total insulation (IT) and resistance to water vapor permeation (Re) on exercising clothed subjects without the need to directly measure skin water vapor pressure or continuously weigh the subjects. Two tests are performed by each subject in each clothing ensemble. In one test, ambient water vapor pressure (Pa) is systematically increased in stepwise fashion while dry-bulb temperature (Tdb) is held constant; in the second test protocol Pa is held constant while Tdb is increased. Heat exchange data are collected at the time at which core temperature is forced out of equilibrium by the environment (according to the assumption that heat production is balanced by heat loss immediately prior to this critical environmental limit). Previous studies using similar approaches have typically estimated IT a priori and used this value in the subsequent derivation of Re for each clothing ensemble or condition tested. In the proposed method, IT and Re are derived from the solution of two simultaneous equations based on heat balance data from both tests. This paper describes and critiques this methodology via an error analysis, and compares the coefficients obtained with those from similar trials using other physiological and nonphysiological approaches.

Clothing↗
PubMed1996

[Carbohydrate-carbohydrate interaction].

The review deals with the new area in biorecognition--the carbohydrate-carbohydrate interaction. Seven experimental approaches are described that were used for detecting and investigating this phenomenon, with special reference to its mechanism and peculiarities, particularly, in comparison with other types of molecular interactions; some historical aspects are also considered. The whole body of experimental evidence published on carbohydrate-carbohydrate interaction by the end of 1995, is reviewed. A special chapter is dedicated to intercellular adhesion mediated or initiated by carbohydrate-carbohydrate recognition. The main peculiarities of carbohydrate-carbohydrate interaction are as follows. Monovalent interaction is so low affinity that it cannot be recorded by routine physical methods, such as NMR. However, if polyvalent ensembles of oligosaccharides (e.g., two membranes with a high density of built-in glycolipids) come in contact, one can observe a specific Ca(2+)-dependent interaction which is inhibited by either EDTA antibodies against carbohydrates or by oligosaccharides. The carbohydrate/carbohydrate-mediated cell adhesion is a rapid primary process which immediately precedes carbohydrate-lectin (selective) and protein-protein (integrin) adhesion. Le(x)/Le(x)-Mediated compactization of embrions and Gm3/Gg3 mediated adhesion of tumour cells provide illustrative examples of such intercellular contacts.

Animals↗
PubMed2005

Theoretical study of the transfer integral and density of states in spiro-linked triphenylamine derivatives.

We present a method for calculating the parameters that control hopping transport in disordered molecular solids, i.e., the transfer integrals and the distribution of transport site energies. Average values of these parameters are obtained by performing quantum-chemical calculations on a large ensemble of bimolecular complexes in random relative orientations. The method is applied to triphenylamine (TPA) and three differently substituted spiro-linked phenylamine compounds, 2,2',7,7'-tetrakis-(N,N-di-4-methoxyphenylamino)-9,9'-spirobifluorene (spiro-MeOTAD), 2,2'7,7'-tetrakis-(N,N-diphenylhenylamino)-9,9'-spirobifluorene (spiro-TAD), and 2,2',7,7'-tetrakis-(N,N-di-m-methylphenylamino)-9,9'-spirobifluorene (spiro-m-TTB). In the case of TPA, the dependence of the root-mean-square hole transfer integral J on intermolecular separation r for the ensemble of relative orientations is compared with that obtained by performing the same calculations for a fixed, approximately cofacial, orientation of the two TPA molecules. The calculation for the disordered geometry predicts a larger localization radius r0, where J approximately exp(-r/r0), than the calculation for the fixed orientation and is in better agreement with experiment. In the case of the spiro-linked compounds, results from our method are compared with parameters extracted from time-of-flight mobility measurements analyzed with the Gaussian disorder model (GDM). We find that the highest occupied molecular-orbital (HOMO) energies of the bimolecular complexes are distributed on an asymmetric peak, whose width varies in qualitative agreement with the value of the energetic disorder sigma obtained from experimental data using the GDM. The mean-square hole transfer integral varies in accordance with the experimentally determined value of the mobility prefactor micro0. The differences between the differently substituted compounds are interpreted in terms of differences in the spatial extent of the wave function. Spiro-MeOTAD was found to have a greater localization radius, which leads to both a larger transfer integral and a broader distribution of HOMO energies than either of the other compounds. For these compounds, differences in energetic disorder could not be explained in terms of differences in the permanent dipole moment. Our method is proposed as an approximate means of predicting the effect of chemical structure on the values of transport parameters in disordered molecular films.

Journal Article↗
PubMed1997

Time-frequency plane Wiener filtering of the high-resolution ECG: development and application.

The time-frequency plane Wiener (TFPW) filter is a new method, based on a posteriori Wiener filtering principles, to enhance the performance of ensemble averaging. This paper develops the mathematical aspects of the TFPW filter, and assesses its performance with elementary signals, such as sine waves and chirps, and authentic high-resolution electrocardiogram (HRECG) ensembles. The principal feature of the TFPW filter is its use of the time-frequency plane to accommodate signal nonstationarity. Using a posteriori computed statistics of the ensemble, the filter matches itself to the time-frequency structure of the signals to be estimated. The method is sufficiently general to be applicable to any class of repetitive signal with a deterministic time-frequency structure and additive noise in the ensemble. It is concluded that significant improvements in both estimated signal fidelity and noise reduction are possible with the TFPW filter, compared to conventional ensemble averaging.

Electrocardiography↗
PubMed2006

On the characterization of protein native state ensembles.

Describing and understanding the biological function of a protein requires a detailed structural and thermodynamic description of the protein's native state ensemble. Obtaining such a description often involves characterizing equilibrium fluctuations that occur beyond the nanosecond timescale. Capturing such fluctuations remains nontrivial even for very long molecular dynamics and Monte Carlo simulations. We propose a novel multiscale computational method to exhaustively characterize, in atomistic detail, the protein conformations constituting the native state with no inherent timescale limitations. Applications of this method to proteins of various folds and sizes show that thermodynamic observables measured as averages over the native state ensembles obtained by the method agree remarkably well with nuclear magnetic resonance data that span multiple timescales. By characterizing equilibrium fluctuations at atomistic detail over a broad range of timescales, from picoseconds to milliseconds, our method offers to complement current simulation techniques and wet-lab experiments and can impact our understanding and description of the relationship between protein flexibility and function.

Amino Acids↗
PubMed1995

Travelling on the potential energy surfaces of carbohydrates: comparative application of an exhaustive systematic conformational search with an heuristic search.

The calculated ensembles found by a heuristic conformational search algorithm, CICADA, for three small carbohydrates, ethyl beta-lactoside, methyl alpha-D-galactoside, and methyl beta-D-galactoside, are evaluated in terms of their ability to reproduce time-averaged optical rotation and NMR data. A unique dynamic model for methyl beta-D-galactoside has been obtained by fitting experimental NOESY volumes to the theoretical ones elaborated from the CICADA ensemble internuclear distances with the model-free formalism. In the case of ethyl beta-lactoside, the CICADA ensemble is compared to that of an exhaustive systematic grid-search method. The CICADA algorithm proved to be a very efficient method to find most of the important minima on even very complex potential energy surfaces, and the spectral quality of the CICADA ensemble was found to be of equal quality, if not superior, to that of the exhaustive systematic grid-search method. The CICADA algorithm has several advantages over other conformational search algorithms: (1) It has polynomial dependence of dimensions on computer time in contrast to the grid search, which has exponential dependence, (2) the conformations found are free of artificial harmonic constraint potentials, (3) it passes all barriers amongst families of conformations on conformational hypersurface but spends almost all its time in the essential highly populated areas, (4) the inherent properties of the algorithm make rigorous minimization criteria superfluous and provide good convergence behavior, and (5) as an important spin-off, it provides low-energy interconversion pathways that can, amongst others, be used for estimating adiabatic rotational barriers.

Algorithms↗