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At least 253 records · Page 14Linked to original sources
PubMed2004

Potential of mean force between a spherical particle suspended in a nematic liquid crystal and a substrate: sphere size effects.

The expanded ensemble density of states method (ExEDOS) is used to investigate the effective interaction of a spherical colloidal particle suspended in a confined liquid crystal (LC) with a substrate. The potential of mean force (PMF) is determined as a function of the normal distance between the particle and the substrate's surface. The presence of the substrate induces a layered structure of the LC, which in turn greatly influences the PMF. We analyze the structure of the Saturn ring defect that accompanies the colloidal sphere, and find that the ring is displaced slightly towards the surface when the sphere is within the first LC surface layer. A transition occurs from an overall attraction of the colloid to the substrate to a global repulsion when the sphere's radius is roughly twice the length of the LC molecules.

Journal Article↗
PubMed1990

An evaluation of the ensemble averaged impedance cardiogram.

The ensemble averaged impedance cardiogram was evaluated during rest and during vocal mental arithmetic stress in samples of female (n = 17) and male (n = 40) undergraduates. Measures of myocardial performance determined from ensemble averaged signals were compared to those determined by simple beat-to-beat averaging over 60-s and 20-s sampling intervals. In addition, the influence of cardiac interval variability on dZ/dt amplitude measures was assessed. As expected, measures derived by the two averaging techniques corresponded closely, with correlations ranging from r = 0.882 to r = 1.000 for the 60-s sampling intervals, and from r = 0.726 to r = 1.000 for the 20-s sampling intervals. Inverse relationships of comparable magnitude were found between cardiac interval variability and dZ/dt amplitude measures determined by both averaging techniques, suggesting that these relationships did not result simply from artifacts introduced by the ensemble averaging technique. The results support the validity of ensemble averaging as a method for deriving impedance cardiographic measures of myocardial performance.

Adolescent↗
PubMed2003

Coding of sensory signals by neuronal populations: the role of correlated activity.

How is sensory information encoded by the patterns of action potentials emitted by ensembles of neurons? Computational methods have recently been applied to this fundamental question and have found, both in the somatosensory and visual system, that the basic unit of information transmission is the timing of individual spikes. In systems studied to date, the neuronal population codes appear to be simple ones that do not rely on complex patterns of correlated spikes.

Action Potentials↗
PubMed2006

Monte Carlo study of the screening effect of carriers on terahertz radiation from InAs with high excitation intensity.

The dynamics of terahertz radiation from InAs were investigated by the ensemble Monte Carlo simulation method. Our simulations indicated that under high-intensity excitation it is the ratio of carrier screening to the carrier-polar optical phonon scattering that has an obvious influence in high-frequency components of terahertz pulses; that is, the amplitudes of high-frequency spectra are reduced with increased excitation intensity. Our calculated results qualitatively reproduce recently published experimental data.

Journal Article↗
PubMed2000

Spectral-temporal receptive fields of nonlinear auditory neurons obtained using natural sounds.

The stimulus-response function of many visual and auditory neurons has been described by a spatial-temporal receptive field (STRF), a linear model that for mathematical reasons has until recently been estimated with the reverse correlation method, using simple stimulus ensembles such as white noise. Such stimuli, however, often do not effectively activate high-level sensory neurons, which may be optimized to analyze natural sounds and images. We show that it is possible to overcome the simple-stimulus limitation and then use this approach to calculate the STRFs of avian auditory forebrain neurons from an ensemble of birdsongs. We find that in many cases the STRFs derived using natural sounds are strikingly different from the STRFs that we obtained using an ensemble of random tone pips. When we compare these two models by assessing their predictions of neural response to the actual data, we find that the STRFs obtained from natural sounds are superior. Our results show that the STRF model is an incomplete description of response properties of nonlinear auditory neurons, but that linear receptive fields are still useful models for understanding higher level sensory processing, as long as the STRFs are estimated from the responses to relevant complex stimuli.

Acoustic Stimulation↗
PubMed2006

Decision forest analysis of large-scale sib-pair identical-by-decent profiles for locating the underlying disease genes for alcoholism in human.

OBJECTIVE: To extract the relevant SNPs for alcoholism using sib-pair IBD profiles of pedigrees. METHODS: We used the ensemble decision approach, a supervised learning approach based on decision forests, to locate alcoholism relevant SNPs using genome-wide SNP data. RESULTS: Application to a publicly available large dataset of 100 simulated replicates for three American populations (http://www.gaworkshop.org/) demonstrates that the proposed approach has successfully located all of the simulated true loci. CONCLUSION: The numerical results establish the proposed decision forest analysis to be a powerful and practical alternative for large-scale family-based association study.

Alcoholism↗
PubMed2003

Large-scale ensemble averaging of ambulatory impedance cardiograms.

Impedance cardiography has been used increasingly to measure human physiological responses to emotional and mentally engaging stimuli. The validity of large-scale ensemble averaging of ambulatory impedance cardiograms was evaluated for preejection period (PEP), interbeat interval, and dZ/dt(min) amplitude. We tested whether the average of "classical" 60-sec ensemble averages across periods with fixed activity, posture, physical load, social situation, and location could be accurately estimated from a single large-scale ensemble average spanning these entire periods. Impedance and electrocardiograms were recorded for about 24-h from 21 subjects. Recordings were scored by seven raters, using both methods for each subject. Good agreement (average intraclass correlation coefficient was .91) between both ensemble averaging methods was found for all three cardiac function measures. The results indicate that for unambiguous ambulatory impedance cardiograms, large-scale ensemble averaging is valid, which makes measuring prolonged changes in cardiac sympathetic activity by measuring ambulatory PEP feasible even in large epidemiological samples.

Activity Cycles↗
PubMed2003

Hybrid global optimization algorithms for protein structure prediction: alternating hybrids.

Hybrid global optimization methods attempt to combine the beneficial features of two or more algorithms, and can be powerful methods for solving challenging nonconvex optimization problems. In this paper, novel classes of hybrid global optimization methods, termed alternating hybrids, are introduced for application as a tool in treating the peptide and protein structure prediction problems. In particular, these new optimization methods take the form of hybrids between a deterministic global optimization algorithm, the alphaBB, and a stochastically based method, conformational space annealing (CSA). The alphaBB method, as a theoretically proven global optimization approach, exhibits consistency, as it guarantees convergence to the global minimum for twice-continuously differentiable constrained nonlinear programming problems, but can benefit from computationally related enhancements. On the other hand, the independent CSA algorithm is highly efficient, though the method lacks theoretical guarantees of convergence. Furthermore, both the alphaBB method and the CSA method are found to identify ensembles of low-energy conformers, an important feature for determining the true free energy minimum of the system. The proposed hybrid methods combine the desirable features of efficiency and consistency, thus enabling the accurate prediction of the structures of larger peptides. Computational studies for met-enkephalin and melittin, employing sequential and parallel computing frameworks, demonstrate the promise for these proposed hybrid methods.

Algorithms↗
PubMed2006

Protein folding kinetics and thermodynamics from atomistic simulations.

Determining protein folding kinetics and thermodynamics from all-atom molecular dynamics (MD) simulations without using experimental data represents a formidable scientific challenge because simulations can easily get trapped in local minima on rough free energy landscapes. This necessitates the computation of multiple simulation trajectories, which can be independent from each other or coupled in some manner, as, for example, in the replica exchange MD method. Here we present results obtained with a new analysis tool that allows the deduction of faithful kinetics data from a heterogeneous ensemble of simulation trajectories. The method is demonstrated on the decapeptide Chignolin for which we predict folding and unfolding time constants of 1.0 +/- 0.3 and 2.6 +/- 0.4 micros, respectively. We also derive the energetics of folding, and calculate a realistic melting curve for Chignolin.

Computer Simulation↗
PubMed2003

Calculation of mutational free energy changes in transition states for protein folding.

Recent advances in experimental and computational methods have made it possible to determine with considerable accuracy the structures whose formation is rate limiting for the folding of some small proteins-the transition state ensemble, or TSE. We present a method to analyze and validate all-atom models of such structures. The method is based on the comparison of experimental data with the computation of the change in free energy of the TSE resulting from specific mutations. Each mutation is modeled individually in all members of an ensemble of transition state structures using a method originally developed to predict mutational changes in the stability of native proteins. We first apply this method to six proteins for which we have determined the TSEs with a technique that uses experimental mutational data (Phi-values) as restraints in the structure determination and find a highly significant correlation between the calculated free energy changes and those derived from experimental kinetic data. We then use the procedure to analyze transition state structures determined by molecular dynamics simulations of unfolding, again finding a high correlation. Finally, we use the method to estimate changes in folding rates of several hydrophobic core mutants of Fyn SH3. Taken together, these results show that the procedure developed here is a tool of general validity for analyzing, assessing, and improving the quality of the structures of transition states for protein folding.

Amino Acid Sequence↗
PubMed2006

Methodological considerations on the use of template matching to study long-lasting memory trace replay.

Replay of behaviorally induced neural activity patterns during subsequent sleep has been suggested to play an important role in memory consolidation. Many previous studies, mostly involving familiar experiences, suggest that such reactivation occurs, but decays quickly (approximately 1 h). Recently, however, long-lasting (up to approximately 48 h) "reverberation" of neural activity patterns induced by a novel experience was reported on the basis of a template-matching analysis. Because detection and quantification of memory-trace replay depends critically on analysis methods, we investigated the statistical properties of the template-matching method and analyzed rodent neural ensemble activity patterns after a novel experience. For comparison, we also analyzed the same data with an independent analysis technique, the explained variance method. Contrary to the recent report, we did not observe significant long-lasting reverberation using either the template matching or the explained variance approaches. The latter, however, did reveal short-lasting reactivation in the hippocampus and prefrontal cortex. In addition, detailed analysis of the template-matching method shows that, in the present study, coarse mean firing rate differences among neurons, but not fine temporal spike structures, dominate the results of template matching. Most importantly, it is also demonstrated that partial comparisons of template-matching correlations, such as used in the recent paper, may lead to erroneous conclusions. These investigations indicate that the outcome of template-matching analysis is very sensitive to the conditions of how it is applied, and should be interpreted cautiously, and that the existence of long-lasting reverberation after a novel experience requires additional verification.

Action Potentials↗
PubMed2003

Normalisation of gait EMGs: a re-examination.

The purpose of this study was to compare four different methods of normalising electromyograms (EMGs) recorded during normal gait. Comparisons were made between the amplitude, intra-individual variability and inter-individual variability of EMGs. Surface EMGs were recorded from the biceps femoris, semitendinosus, vastus lateralis and vastus medialis of ten males and two females while they walked on a treadmill at a self-selected speed. EMGs from the same muscles were subsequently recorded during isometric maximal voluntary contractions (MVCs) and concentric, isokinetic MVCs that were performed between 0.52 and 7.85 rad x s(-1) on a BIODEX dynamometer. EMGs were also recorded during eccentric, isokinetic MVCs between 0.52 and 2.62 rad x s(-1). Gait EMGs were then normalised at 2% intervals of the gait cycle by expressing them as a percentage of the following reference values: the mean (mean dynamic method) and the peak (peak dynamic method) EMG from the intra-individual ensemble average; the EMG from an isometric MVC (isometric MVC method); and the EMG from an isokinetic MVC that occurred with the same muscle action, length and velocity of musculotendinous unit as the gait EMGs (isokinetic MVC method). The isokinetic MVC method produced significantly greater (P<0.05) intra-individual variability compared to the other methods when it was measured using the variance ratio. Inter-individual variability of gait EMGs, again measured using the variance ratio, was also greatest when they were normalised using the isokinetic MVC method. The pattern and amplitude of EMGs normalised using the isometric MVC method and the isokinetic MVC method were very similar (root mean square difference and absolute difference both less than 3%). It was concluded that the isokinetic MVC method should not be adopted by gait researchers or clinicians as it does not reduce intra- or inter-individual variability anymore than existing normalisation methods, nor does it provide a more representative measure of muscle activation during gait than the isometric MVC method.

Adult↗
PubMed2004

Calculation of the near field of aggregates of arbitrary spheres.

We study a numerical method of calculating the near field of ensembles of arbitrary spheres by extending Mie theory. A recursive method based on the orders of scattering is presented. This method represents a concise way to calculate the near field of aggregates of any number of arbitrary spheres, Numerical examples are given to show its validity.

Journal Article↗
PubMed2004

Membrane surface dynamics of DNA-threaded nanopores revealed by simultaneous single-molecule optical and ensemble electrical recording.

We describe a method for simultaneous single-molecule optical and electrical characterization of membrane-based sensors that contain ion-channel nanopores. The technique is used to study the specific and nonspecific interactions of streptavidin-capped DNA polymers with lipid bilayers composed of diphytanoyl phosphatidylcholine and diphytanoyl phosphatidylglycerol. Biotinylated DNA that is bound to fluorescently labeled streptavidin is electrophoretically driven into, or away from, the lumen of alpha hemolysin (alphaHL) ion channels by an external electric field. Confocal microscopy simultaneously captures single-molecule fluorescence dynamics from the membrane interface at different applied potentials. Fluorescence correlation analysis is used to determine the surface number density and diffusion constant of membrane-associated complexes. The dual optical and electrical approach can detect membrane-associated species at a surface coverage below 10(-5) monolayers of streptavidin, a sensitivity that surpasses most other in vitro surface analysis techniques. By comparing the change in transmembrane current to the number of fluorescent molecules leaving the bilayer when the electrical potential is reversed, we demonstrate the general utility of the approach within the context of nanopore-based sensing and discuss a mechanism by which DNA-streptavidin complexes can be nonspecifically retained at the membrane interface.

Biotinylation↗
PubMed2004

Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations.

In complex systems with many degrees of freedom such as spin glass and biomolecular systems, conventional simulations in canonical ensemble suffer from the quasi-ergodicity problem. A simulation in generalized ensemble performs a random walk in potential energy space and overcomes this difficulty. From only one simulation run, one can obtain canonical ensemble averages of physical quantities as functions of temperature by the single-histogram and/or multiple-histogram reweighting techniques. In this article we review the generalized ensemble algorithms. Three well-known methods, namely, multicanonical algorithm (MUCA), simulated tempering (ST), and replica-exchange method (REM), are described first. Both Monte Carlo (MC) and molecular dynamics (MD) versions of the algorithms are given. We then present five new generalized-ensemble algorithms which are extensions of the above methods.

Algorithms↗
PubMed2026

Cleavage region organizes the structural architecture of the SINE-derived B2 repressive ribozyme.

The SINE-encoded B2 retrotransposon is an RNA Polymerase III (POL-III)-derived transcript whose expression is substantially upregulated during various cellular stress responses. Beyond retrotransposition, the B2 non-coding RNA can directly bind and repress the activity of RNA Polymerase II (POL-II), leading to a significant downregulation of transcripts during stress. Notably, our recent findings have shown that B2 is a self-cleaving ribozyme whose activity can be induced by interactions with chromatin-modifying factors through non-canonical epigenetic mechanisms that co-regulate its function across distinct chromatin-binding target loci. Here, by integrating RNA chemical probing, small-angle X-ray scattering, and 3D motif modeling, we determine structural ensemble-to-function relations for the B2 SINE ribozyme RNA. Genetic perturbations of the RNA suggest that the B2 SINE ribozyme has a well-defined secondary and dynamic tertiary structure that depends on the integrity of the critical region, which confers ribozymatic activity and repressive extent by POL-II. Using an RNA engineering approach, we examine the effects of point mutations, deletions of the main cleavage site, and deletions of the cleavage domain on the structural ensemble of the RNA. Combining this approach with in vitro and in vivo functional perturbation methods highlights the relationships between structural ensembles and various biologically relevant functional outcomes.

RNA, Catalytic↗
PubMed2006

Simulation of the density of states in isothermal and adiabatic ensembles.

This paper provides a unified treatment of the fundamental methods used to obtain the density of states via molecular simulations with isothermal ensembles (IEs) and adiabatic ensembles (AEs). Our analysis and results show that provides a natural bridge to go back and forth between IE and AE simulation data. They also underline the difference between the density of states of potential energy macrostates and that of total energy macrostates Omega, even though both provide access to the thermodynamic properties of the system. Visited-states approaches and transition matrix methods are described and applied to the Lennard-Jones fluid to target omega and Omega as functions of energy and volume macrostates. It is shown that one can obtain omega via a generalized acceptance-ratio formula that is applicable regardless of the conditions at which the ensemble is simulated. In this way, one can obtain while performing conventional IE or AE simulations, and do it at no extra cost and with a higher accuracy than is achievable with histogram methods.

Journal Article↗
PubMed2005

DFT-based chemical reactivity indices in the Hartree-Fock method. II. Fukui function, chemical potential, and hardness.

A derivation of the density-functional-theory- (DFT) based reactivity indices in the ensemble unrestricted Hartree-Fock (eUHF) method is presented. The comparison between the properties of the reactivity indices evaluated in one and two sets of spin-orbital approach of the eUHF and hyper-unrestricted Hartree-Fock (UHF) methods are shown. All approaches give similar Fukui function irrespective of methodology used, but significantly differ for the global indices, containing important chemical information, and so their interpretation in terms of DFT- based indices can be questionable. The calculation scheme for the indices using the first- and second-order coupled perturbed eHF equations is proposed. A method for the identification of the spinorbitals involved in the change of the total number of electrons is included. The illustrative examples (water and hydrogen cyanide) show that the ground-state (GS) properties of the (Z +/- 1)-electron systems can be predicted from the GS properties of the Z-electron systems with an accuracy comparable with the UHF calculations. The relaxation effect, important for the HCN system in which a change in the symmetry of the highest-occupied spin-orbital occurs, is effectively predicted.

Journal Article↗