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Generating a superposition of spin states in an atomic ensemble.

A method for generating a mesoscopic superposition state of the collective spin variable of a gas of atoms is proposed. The state consists of a superposition of the atomic spins pointing in two slightly different directions. It is obtained by using off resonant light to carry out quantum nondemolition measurements of the spins. The relevant experimental conditions, which require very dense atomic samples, can be realized with presently available techniques. Long-lived atomic superposition states may become useful as an off-line resource for quantum computing with otherwise linear operations.

Journal Article↗

Toward generating simpler QSAR models: nonlinear multivariate regression versus several neural network ensembles and some related methods.

In this study we want to test whether a simple modeling procedure used in the field of QSAR/QSPR can produce simple models that will be, at the same time, as accurate as robust Neural Network Ensemble (NNE) ones. We present results of application of two procedures for generating/selecting simple linear and nonlinear multiregression (MR) models: (1) method for selecting the best possible MR models (named as CROMRsel) and (2) Genetic Function Approximation (GFA) method from the Cerius2 program package. The obtained MR models are strictly compared with several NNE models. For the comparison we selected four QSAR data sets previously studied by NNE (Tetko et al. J. Chem. Inf. Comput. Sci. 1996, 36, 794-803. Kovalishyn et al. J. Chem. Inf. Comput. Sci. 1998, 38, 651-659.): (1) 51 benzodiazepine derivatives, (2) 37 carboquinone derivatives, (3) 74 pyrimidines, and (4) 31 antimycin analogues. These data sets were parameterized with 7, 6, 27, and 53 descriptors, respectively. Modeled properties were anti-pentylenetetrazole activity, antileukemic activity, inhibition constants to dihydrofolate reductase from MB1428 E. coli, and antifilarial activity, respectively. Nonlinearities were introduced into the MR models through 2-fold and/or 3-fold cross-products of initial (linear) descriptors. Then, using the CROMRsel and GFA programs (J. Chem. Inf. Comput. Sci. 1999, 39, 121-132) the sets of I (I < or = 8, in this paper) the best descriptors (according to the fit and leave-one-out correlation coefficients) were selected for multiregression models. Two classes of models were obtained: (1) linear or nonlinear MR models which were generated starting from the complete set of descriptors, and (2) nonlinear MR models which were generated starting from the same set of descriptors that was used in the NNE modeling. In addition, the descriptor selection method from CROMRsel was compared with the GFA method included in the QSAR module of the Cerius2 program. For each data set it has been found that the MR models have better cross-validated statistical parameters than the corresponding NNE models and that CROMRsel selects somewhat better MR models than the GFA method. MR models are also much simpler than NNEs, which is the important surprising fact, and, additionally, express calculated dependencies in a functional form. Moreover, MR models were shown to be better than all other models obtained by different methods on the same data sets ("old" multivariate regressions, functional-link-net models, back-propagation neural networks, genetic algorithm, and partial least squares models). This study also indicated that the robust NNE models cannot generate good models when applied on small data sets, suggesting that it is perhaps better to apply robust methods (like NNE ones) on larger data sets.

Journal Article↗

Improved method for measuring the ensemble average of strand breaks in genomic DNA.

The cis-syn cyclobutane pyrimidine dimer (CPD) is the major photoproduct induced in DNA by low wavelength ultraviolet radiation. An improved method was developed to detect CPD formation and removal in genomic DNA that avoids the problems encountered with the standard method of endonuclease detection of these photoproducts. Since CPD-specific endonucleases make single-strand cuts at CPD sites, quantification of the frequency of CPDs in DNA is usually done by denaturing gel electrophoresis. The standard method of ethidium bromide staining and gel photography requires more than 10 microg of DNA per gel lane, and correction of the photographic signal for the nonlinear film response. To simplify this procedure, a standard Southern blot protocol, coupled with phosphorimage analysis, was developed. This method uses random hybridization probes to detect genomic sequences with minimal sequence bias. Because of the vast linearity range of phosphorimage detection, scans of the signal profiles for the heterogeneous population of DNA fragments can be integrated directly to determine the number-average size of the population.

Animals↗

Phase coexistence in heterogeneous porous media: a new extension to Gibbs ensemble Monte Carlo simulation method.

The effect of confinement on phase behavior of simple fluids is still an area of intensive research. In between experiment and theory, molecular simulation is a powerful tool to study the effect of confinement in realistic porous materials, containing some disorder. Previous simulation works aiming at establishing the phase diagram of a confined Lennard-Jones-type fluid, concentrated on simple pore geometries (slits or cylinders). The development of the Gibbs ensemble Monte Carlo technique by Panagiotopoulos [Mol. Phys. 61, 813 (1987)], greatly favored the study of such simple geometries for two reasons. First, the technique is very efficient to calculate the phase diagram, since each run (at a given temperature) converges directly to an equilibrium between a gaslike and a liquidlike phase. Second, due to volume exchange procedure between the two phases, at least one invariant direction of space is required for applicability of this method, which is the case for slits or cylinders. Generally, the introduction of some disorder in such simple pores breaks the initial invariance in one of the space directions and prevents to work in the Gibbs ensemble. The simulation techniques for such disordered systems are numerous (grand canonical Monte Carlo, molecular dynamics, histogram reweighting, N-P-T+test method, Gibbs-Duhem integration procedure, etc.). However, the Gibbs ensemble technique, which gives directly the coexistence between phases, was never generalized to such systems. In this work, we focus on two weakly disordered pores for which a modified Gibbs ensemble Monte Carlo technique can be applied. One of the pores is geometrically undulated, whereas the second is cylindrical but presents a chemical variation which gives rise to a modulation of the wall potential. In the first case almost no change in the phase diagram is observed, whereas in the second strong modifications are reported.

Journal Article↗

Firemaster 550 differentially alters gene expression underlying synaptic function in amygdala of prairie voles after gestational or lactational exposure.

Neurodevelopmental disorders often share similar behavioral diagnostic criteria including socioemotional and cognitive deficits. The prairie vole is a uniquely suitable model to study these deficits because they demonstrate strong social affiliation, bi-parental care, and partner attachment. Previously, we have shown that developmental exposure to the flame-retardant mixture Firemaster 550 (FM 550) impairs socioemotional behavior in the prairie vole and alters underlying neuroanatomy and function. However, the mechanisms for impaired pair bonding in males and increased anxiety in females remain unknown, along with the specific critical window(s) of vulnerability. Herein, we exposed prairie vole dams to FM 550 during gestation or lactation, and performed bulk RNA-seq on the amygdala, a hub of socioemotional processing, in their adult offspring. Two mathematically orthogonal methods were utilized for analysis, a linear statistical method and an ensemble machine learning method, incorporating sex as a biological variable. Gene ontology (GO) pathway analysis was performed following both and results compared to identify potential mechanisms of toxicity. GO results indicated consistent expression changes in the Synapse cellular component in all conditions, and implicated glutamatergic signaling specifically. Additionally, gestational exposure (GE) altered genes underlying modulation of synaptic transmission and neural development, while lactational exposure (LE) impacted genes underlying synaptic plasticity, axon guidance, and mitophagy. Machine learning identified disruption of endocrine system development, regulation of biosynthetic processes in GE animals, and suppression of various neuroinflammatory genes across multiple groups. Finally, we performed RNA expression analysis using Nanostring and demonstrated stronger correlation with the differentially expressed genes (DEG) of interest in females than males. Overall, this study demonstrates both the intersecting and distinct impacts of FM 550 exposure on amygdalar gene expression depending on sex and timing of exposure.

Animals↗

Minimal repetition evoked potentials by modified adaptive line enhancement.

A new method called modified adaptive line enhancement (MALE) to obtain evoked potentials with minimum stimulus repetitions is described. The theory of MALE is developed and the assumptions made are tested and shown to be adequate in the case of brain-stem auditory evoked potential. The signal distortion are characterized and methods to alleviate the problem are developed. Using the weighted exact least squares lattice algorithm, the MALE method is implemented and applied to real data. It is shown that brainstem auditory evoked potential can be obtained with less than 40 repetitions using MALE method compared to 2000 required if conventional ensemble averaging method is used.

Algorithms↗

Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles.

We describe a novel method to generate ensembles of conformations of the main-chain atoms [N, C(alpha), C, O, Cbeta] for a sequence of amino acids within the context of a fixed protein framework. Each conformation satisfies fundamental stereo-chemical restraints such as idealized geometry, favorable phi/psi angles, and excluded volume. The ensembles include conformations both near and far from the native structure. Algorithms for effective conformational sampling and constant time overlap detection permit the generation of thousands of distinct conformations in minutes. Unlike previous approaches, our method samples dihedral angles from fine-grained phi/psi state sets, which we demonstrate is superior to exhaustive enumeration from coarse phi/psi sets. Applied to a large set of loop structures, our method samples consistently near-native conformations, averaging 0.4, 1.1, and 2.2 A main-chain root-mean-square deviations for four, eight, and twelve residue long loops, respectively. The ensembles make ideal decoy sets to assess the discriminatory power of a selection method. Using these decoy sets, we conclude that quality of anchor geometry cannot reliably identify near-native conformations, though the selection results are comparable to previous loop prediction methods. In a subsequent study (de Bakker et al.: Proteins 2003;51:21-40), we demonstrate that the AMBER forcefield with the Generalized Born solvation model identifies near-native conformations significantly better than previous methods.

Algorithms↗

BAEP dynamic estimation in case of endocochlear pathologies using a time delay correction method.

Extraction of Brainstem Auditory Evoked Potentials (BAEPs) from the electroencephalogram (EEG) is generally difficult when both BAEP and EEG are non-stationary. In this paper we focus on the problem of BAEP non-stationarities, in particular those observed in some endocochlear pathologies assumed causing random delays of BAEPs due to an abnormal behaviour of the cochlea. The technique developed in this paper, called the Time Delay Correction (TDC) method, allows us to estimate the averaged BAEP by an optimal alignment of responses based on a correlation criterion. We demonstrate that the TDC method avoids wave smoothness, generally produced with the classical ensemble averaging method, especially in the case when the hypothesis of the time delay non-stationarity is verified. The TDC method is performed using simulated annealing (SA) algorithm, since the criterion to be optimized is nonlinear. Real signals recorded from pathological subjects are used to validate the model of non-stationarity.

Adult↗

Dynamic and structural analysis of isotropically distributed molecular ensembles.

An efficient new method is presented for the characterization of motional correlations derived from a set of protein structures without requiring the separation of overall and internal motion. In this method, termed isotropically distributed ensemble (IDE) analysis, each structure is represented by an ensemble of isotropically distributed replicas corresponding to the situation found in an isotropic protein solution. This leads to a covariance matrix of the cartesian atomic positions with elements proportional to the ensemble average of scalar products of the position vectors with respect to the center of mass. Diagonalization of the covariance matrix yields eigenmodes and amplitudes that describe concerted motions of atoms, including overall rotational and intramolecular dynamics. It is demonstrated that this covariance matrix naturally distinguishes between "rigid" and "mobile" parts without necessitating a priori selection of a reference structure and an atom set for the orientational alignment process. The method was applied to the analysis of a 5-ns molecular dynamics trajectory of native ubiquitin and a 40-ns trajectory of a partially folded state of ubiquitin. The results were compared with essential dynamics analysis. By taking advantage of the spherical symmetry of the IDE covariance matrix, more than a 10-fold speed up is achieved for the computation of eigenmodes and mode amplitudes. IDE analysis is particularly suitable for studying the correlated dynamics of flexible and large molecules.

Computer Simulation↗

The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins.

While reliable procedures for determining the conformations of proteins are available, methods for generating ensembles of structures that also reflect their flexibility are much less well established. Here we present a systematic assessment of the ability of ensemble-averaged molecular dynamics simulations with ensemble-averaged NMR restraints to simultaneously reproduce the average structure of proteins and their associated dynamics. We discuss the effects that under-restraining (overfitting) and over-restraining (underfitting) have on the structures generated in ensemble-averaged molecular simulations. We then introduce the MUMO (minimal under-restraining minimal over-restraining) method, a procedure in which different observables are averaged over a different number of molecules. As both over-restraining and under-restraining are significantly reduced in the MUMO method, it is possible to generate ensembles of conformations that accurately characterize both the structure and the dynamics of native states of proteins. The application of the MUMO method to the protein ubiquitin yields a high-resolution structural ensemble with an RDC Q-factor of 0.19.

Amino Acid Sequence↗

Comparison of photophysical and colloidal properties of biocompatible semiconductor nanocrystals using fluorescence correlation spectroscopy.

A number of different surface chemistries have been developed in recent years to render semiconductor nanocrystals (NCs) stable in water and biocompatible. However, most of these surface modifications affect NCs' photophysical properties, calling for a method to simultaneously monitor colloidal and fluorescence properties. Fluorescence correlation spectroscopy (FCS) combined with ensemble spectroscopic methods and Monte Carlo simulations were used to interpret and derive photophysical as well as colloidal properties of four different NC surface treatments. Using a novel FCS scheme with alternating laser excitation at two different intensities, we first ruled out influences from optical gradient forces (optical trapping). We then compared concentration of emitting particles, brightness per particle, saturation intensity, blinking (intermittency), hydrodynamic radius, and propensity for aggregation of the different bioconjugated NCs. This approach was successfully applied during the development and optimization of peptide-coated NCs.

Biocompatible Materials↗

Weighted-ensemble Brownian dynamics simulations for protein association reactions.

A new method, weighted-ensemble Brownian dynamics, is proposed for the simulation of protein-association reactions and other events whose frequencies of outcomes are constricted by free energy barriers. The method features a weighted ensemble of trajectories in configuration space with energy levels dictating the proper correspondence between "particles" and probability. Instead of waiting a very long time for an unlikely event to occur, the probability packets are split, and small packets of probability are allowed to diffuse almost immediately into regions of configuration space that are less likely to be sampled. The method has been applied to the Northrup and Erickson (1992) model of docking-type diffusion-limited reactions and yields reaction rate constants in agreement with those obtained by direct Brownian simulation, but at a fraction of the CPU time (10(-4) to 10(-3), depending on the model). Because the method is essentially a variant of standard Brownian dynamics algorithms, it is anticipated that weighted-ensemble Brownian dynamics, in conjunction with biophysical force models, can be applied to a large class of association reactions of interest to the biophysics community.

Algorithms↗

Convective rolls and heat transfer in finite-length rayleigh-Benard convection: A two-dimensional numerical study

A two-dimensional (2D) numerical study using a single-point algebraic k-straight theta;(2)-varepsilon-varepsilon(straight theta) turbulence closure was performed to detect the existence, origin, creation and behavior of convective rolls and associated wall Nusselt (Nu) number variation in thermal convection in 2D horizontal slender enclosures heated from below. The study covered the Rayleigh (Ra) numbers from 10(5) to 10(12) and aspect ratios from 4:1 to 32:1. The time evolution of the convective rolls and the formation of the corner vortices were analyzed using numerical flow visualization, and the correlation between roll structures and heat transfer established. A major consequence of the imposed two dimensionality appeared in the persistence of regular roll structures at higher Ra numbers that approach a steady state for all configurations considered. This finding contradicts the full three-dimensional direct numerical simulations (DNS), large eddy simulations (LES), and three-dimensional transient Reynolds-averaged Navier-Stokes (TRANS) computations, which all show continuously changing unsteady patterns. However, the final-stage roll structures, long-term averaged mean temperature and turbulence moments, and the Nusselt number (both local and integral), are all reproduced in good agreement with the ensemble-averaged 3D DNS, TRANS, and several recent experimental results. These findings justified the 2D approach as an acceptable method for ensemble average analysis of fully 3D flows with at least one homogeneous direction. Based on our 2D computations and adopting the low and high Ra number asymptotic power laws of Grossmann and Lohse [J. Fluid Mech. 407, 27 (2000)], new prefactors in the Nu-Ra correlation for Pr=O(1) were proposed that fit better several sets of data over a wide range of Ra numbers and aspect ratios: Nu=0.1Ra(1/4)+0.05Ra(1/3). Even better agreement of our computations was achieved with the new correlation Nu=0.124 Ra0.309 proposed recently by Niemela et al. [Nature (London) 404, 837 (2000)] for 10(6)</=Ra</=10(17).

Journal Article↗

Overcoming selective ensemble averaging: unsupervised identification of event-related brain potentials.

We present a novel approach to the problem of event-related potential (ERP) identification, based on a competitive artificial neural network (ANN) structure. Our method uses ensembled electroencephalogram (EEG) data just as used in conventional averaging, however without the need for a priori data subgrouping into distinct categories (e.g., stimulus- or event-related), and thus avoids conventional assumptions on response invariability. The competitive ANN, often described as a winner takes all neural structure, is based on dynamic competition among the net neurons where learning takes place only with the winning neuron. Using a simple single-layered structure, the proposed scheme results in convergence of the actual neural weights to the embedded ERP patterns. The method is applied to real event-related potential data recorded during a common odd-ball type paradigm. For the first time, within-session variable signal patterns are automatically identified, dismissing the strong and limiting requirement of a priori stimulus-related selective grouping of the recorded data. The results present new possibilities in ERP research.

Artifacts↗

A method for analysis of encoding of stimulus separation in ensembles of afferents.

This paper describes a new method for the analysis of ensemble coding in populations of receptor afferents. The method is based on principal component analysis (PCA) combined with algorithms for calculation of stimulus separation (discrimination). It allows a quantification of the ability of ensembles of afferents to discriminate between stimuli of different intensity, and it can also be used to calculate to which extent each afferent in an ensemble contributes to the discrimination. Since the emphasis is put on discrimination of stimuli rather than on similarities between the representations of the stimulus in the ensemble response and the stimulus itself, it involves no implicit assumption about the unknown decoding mechanisms in the CNS. Examples of results obtained with analysis of and comparison of simultaneously recorded and pooled sequentially recorded populations of primary muscle spindle afferents are given. These results support some of the general arguments in favour of the ensemble coding theory, and indicate that the results of studies made on populations of simultaneously recorded receptor afferents may differ considerably from results obtained in studies on pooled sequentially recorded afferents. In contrast to when ensemble responses are based on parallel recordings, population responses constructed from sequential recordings will be distorted as a result of unavoidable temporal variations in physiological conditions.

Algorithms↗

A posteriori time-varying filtering of averaged evoked potentials. II. Mathematical and computational aspects.

The problem of estimating an unknown transient signal, given an ensemble of waveforms, in which this signal appears as a nonrandom component in the presence of additive noise is considered. This problem is solved by generalizing the method of "a posteriori 'Wiener' filtering". In the new method, the ensemble average is filtered by a time-varying system which is based on estimated time-varying power spectra of signal and noise. The nature of this system, and the computational procedures involved, are discussed in detail. A software package for time-varying filtering is briefly described. Application of the method is illustrated by a simulation example, which also provides a comparison to time-invariant a posteriori "Wiener" filtering.

Brain↗