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PubMed2005

Statistical mechanics of combinatorial optimization problems with site disorder.

We study the statistical mechanics of a class of problems whose phase space is the set of permutations of an ensemble of quenched random positions. Specific examples analyzed are the finite-temperature traveling salesman problem on several different domains and various problems in one dimension such as the so-called descent problem. We first motivate our method by analyzing these problems using the annealed approximation. Then in the limit of a large number of points we develop a formalism to carry out the quenched calculation. This formalism does not require the replica method, and its predictions are found to agree with Monte Carlo simulations. In addition our method reproduces an exact mathematical result for the maximum traveling salesman problem in two dimensions and suggests its generalization to higher dimensions. The general approach may provide an alternative method to study certain systems with quenched disorder.

Journal Article↗
PubMed2004

Canonical Bose gas simulations with stochastic gauges.

A technique to simulate the grand canonical ensembles of interacting Bose gases is presented. Results are generated for many temperatures by averaging over energy-weighted stochastic paths, each corresponding to a solution of coupled Gross-Pitaevskii equations with phase noise. The stochastic gauge method used relies on an off-diagonal coherent-state expansion, thus taking into account all quantum correlations. As an example, the second-order spatial correlation function and momentum distribution for an interacting 1D Bose gas are calculated.

Journal Article↗
PubMed2001

Real-time single-molecule imaging of the infection pathway of an adeno-associated virus.

We describe a method, based on single-molecule imaging, that allows the real-time visualization of the infection pathway of single viruses in living cells, each labeled with only one fluorescent dye molecule. The tracking of single viruses removes ensemble averaging. Diffusion trajectories with high spatial and time resolution show various modes of motion of adeno-associated viruses (AAV) during their infection pathway into living HeLa cells: (i) consecutive virus touching at the cell surface and fast endocytosis; (ii) free and anomalous diffusion of the endosome and the virus in the cytoplasm and the nucleus; and (iii) directed motion by motor proteins in the cytoplasm and in nuclear tubular structures. The real-time visualization of the infection pathway of single AAVs shows a much faster infection than was generally observed so far.

Adsorption↗
PubMed2003

Positional clustering of differentially expressed genes on human chromosomes 20, 21 and 22.

BACKGROUND: Clusters of genes co-expressed are known in prokaryotes (operons) and were recently described in several eukaryote organisms, including Human. According to some studies, these clusters consist of housekeeping genes, whereas other studies suggest that these clustered genes exhibit similar tissue specificity. Here we further explore the relationship between co-expression and chromosomal co-localization in the human genome by analyzing the expression status of the genes along the best-annotated chromosomes 20, 21 and 22. METHODS: Gene expression levels were estimated according to their publicly available ESTs and gene differential expressions were assessed using a previously described and validated statistical test. Gene sequences for chromosomes 20, 21 and 22 were taken from the Ensembl annotation. RESULTS: We identified clusters of genes specifically expressed in similar tissues along chromosomes 20, 21 and 22. These co-expression clusters occurred more frequently than expected by chance and may thus be biologically significant. CONCLUSION: The co-expression of co-localized genes might be due to higher chromatin structures influencing the gene availability for transcription in a given tissue or cell type.

Chromosomes, Human, Pair 20↗
PubMed2006

Contamination: a comparison of 2 personal protective systems.

BACKGROUND: The purpose of this study was to examine the difference in self-contamination rates and levels of contact and droplet protection associated with enhanced respiratory and contact precautions (E-RCP) and a personal protective system that included a full body suit, personal protective equipment and a powered air-purifying respirator (PAPR). METHODS: In this prospective, randomized, controlled crossover study, 50 participants donned and removed E-RCP and PAPR in random order. Surrogate contamination consisted of fluorescein solution and ultraviolet (UV) light- detectable paste, which was applied after each ensemble was donned. A blinded evaluator inspected participants for contamination using a UV lamp after removal of each ensemble. Areas of contamination were counted and measured in square centimetres. Donning and removal violations were recorded. The primary end point was the presence of any contamination on the skin or base clothing layer. RESULTS: Participants wearing E-RCP were more likely to experience skin and base-clothing contamination; their contamination episodes measuring > or = 1 cm2 were more frequent, and they had larger total areas of contamination (all p < 0.0001). The anterior neck, forearms, wrists and hands were the likeliest zones for contamination. Participants donning PAPR committed more donning procedure violations (p = 0.0034). Donning and removing the PAPR system took longer than donning and removing E-RCP garments (p < 0.0001). INTERPRETATION: Participants wearing E-RCP were more likely to experience contamination of their skin and base clothing layer. Those wearing PAPR required significantly more time to don and remove the ensemble and violated donning procedures more frequently.

Cross-Over Studies↗
PubMed2003

Absolute measurements of total target strength from reverberation in a cavity.

A new method was developed to acoustically measure the density and total scattering cross-section (sigma(t)) or total target strength [TTS = 10log10(sigma(t)/4pi)] of objects in motion in a highly reflective cavity [J. De Rosny and P. Roux, J. Acoust. Soc. Am. 109, 2587-2597 (2001)]. From an ensemble of pulse-echo recordings, the average contribution of the scatterer(s) to the reverberation within the cavity provides a measurement of the scattering mean free path. The latter was shown through theory and experiment to be proportional to the volume of the cavity and inversely proportional the product of the mean sigma(t) and number of scatterers. Here, the TTS measurement uncertainty is characterized using standard metal spheres as references. Theoretical TTS was calculated for multiple copper and tungsten carbide standard spheres (Cu: 60.0 30.05 and 23 mm and WC: 38.1 and 33.4 mm diameters, respectively), using well-described theory for scattering from elastic spheres and the optical theorem. Measurements of TTS were made over a wide bandwidth (30-120 kHz) and compared to their theoretical values. Measurements were made in a corrugated, cylindrical, galvanized-steel tank with 25 or 50 l of fresh water at a temperature of 21 +/- 1 degrees C. The results indicate the method can provide TTS measurements that are accurate to at least 0.4 dB with an average precision of +/-0.7 dB (95% confidence interval). Discussed are the requisite cavity volumes and signal-to-noise ratios for quality measurements of TTS, tank volume, and/or numerical abundance of mobile targets. Also discussed are multiple potential applications of this technique in bioacoustical oceanography.

Journal Article↗
PubMed2005

Molecular mechanism for stabilizing a short helical peptide studied by generalized-ensemble simulations with explicit solvent.

We study the folding mechanism of an analog of the C-peptide of ribonuclease A in explicit water by a replica-exchange multicanonical molecular dynamics simulation based on all-atom models. The multicanonical weight factor was determined by the combined use of the multicanonical replica-exchange method and the replica-exchange multicanonical algorithm. Using statistically reliable data thus obtained, we have examined the free-energy landscape of the peptide system. The global-minimum free-energy state in the landscape at room temperature has an alpha-helix structure with a distortion near the N-terminus. The state also has a salt bridge between Glu(-)-2 and Arg(+)-10 and an aromatic-aromatic interaction between Phe-8 and His(+)-12, both of which have been observed in x-ray and other experimental measurements. Principal component analysis clearly shows the different roles of these side-chain interactions in the peptide folding. The side-chain interaction between Phe-8 and His(+)-12 greatly enhances the stability of helical structure toward the C-terminal end, whereas the salt bridge between Glu(-)-2 and Arg(+)-10 mainly works as a restraint to prevent the alpha-helix structure from extending to the N-terminus. The free-energy landscape of C-peptide reveals a funnel-like shape where all of these interactions consistently exist only in the global-minimum state. This is the major reason why the native structure of the short helical peptide shows significant stability at low temperatures.

Algorithms↗
PubMed1994

Activation of single cardiac and skeletal ryanodine receptor channels by flash photolysis of caged Ca2+.

Single ryanodine-sensitive sarcoplasmic reticulum (SR) Ca2+ release channels isolated from rabbit skeletal and canine cardiac muscle were reconstituted in planar lipid bilayers. Single channel activity was measured in simple solutions (no ATP or Mg2+) with 250 mM symmetrical Cs+ as charge carrier. A laser flash was used to photolyze caged-Ca2+ (DM-nitrophen) in a small volume directly in front of the bilayer. The free [Ca2+] in this small volume and in the bulk solution was monitored with Ca2+ electrodes. This setup allowed fast, calibrated free [Ca2+] stimuli to be applied repetitively to single SR Ca2+ release channels. A standard photolytically induced free [Ca2+] step (pCa 7-->6) was applied to both the cardiac and skeletal release channels. The rate of channel activation was determined by fitting a single exponential to ensemble currents generated from at least 50 single channel sweeps. The time constants of activation were 1.43 +/- 0.65 ms (mean +/- SD; n = 5) and 1.28 +/- 0.61 ms (n = 5) for cardiac and skeletal channels, respectively. This study presents a method for defining the fast Ca2+ regulation kinetics of single SR Ca2+ release channels and shows that the activation rate of skeletal SR Ca2+ release channels is consistent with a role for CICR in skeletal muscle excitation-contraction coupling.

Acetates↗
PubMed2004

Event-related electroencephalographic correlations between isolated human subjects.

OBJECTIVE: To examine electroencephalograms (EEG) in pairs of people to see if event-related potentials evoked in one person's brain are correlated with concurrent responses in the brain of a distant, isolated person. DESIGN: Simultaneously record EEGs using independent physiologic monitoring systems. One person relaxes in a double steel-walled, electromagnetically and acoustically shielded room while a second, located in a dimly lit room 20 meters away, is stimulated at random times by the live video image of the first person. SUBJECTS: Thirteen (13) pairs of volunteers. Eleven (11) pairs of adult friends and 2 mother-daughter pairs. OUTCOME MEASURES: Epochs of interest were the moments of stimulus onset and offset, +/- 5 seconds, in both participants' EEGs. A positive correlation was postulated to appear between the ensemble variance of the stimulated subjects' EEGs versus an identical measure in the nonstimulated subjects. Control data using the same equipment and test conditions, but without humans present, was collected to check for equipment and analytical artifacts. Nonparametric bootstrap methods were used to assess statistical significance of the observed correlations. RESULTS: The control test resulted in a correlation of r =-0.03, p = 0.61; the experimental test resulted in r = 0.20, p = 0.0005. Three (3) of the 13 pairs of participants showed independently significant correlations. Examination of the stimulated subjects' event-related potentials showed that the stronger their responses, the larger the corresponding responses in the nonstimulated subjects (p = 0.0008). CONCLUSION: Under certain conditions, the EEG of a sensorially isolated human subject can become correlated with event-related potentials in a distant person's EEG. This suggests the presence of an unknown form of energetic or informational interaction.

Adolescent↗
PubMed2000

Symbolic dynamics of event-related brain potentials.

We apply symbolic dynamics techniques such as word statistics and measures of complexity to nonstationary and noisy multivariate time series of electroencephalograms (EEG) in order to estimate event-related brain potentials (ERP). Their significance against surrogate data as well as between different experimental conditions is tested. These methods are validated by simulations using stochastic dynamical systems with time-dependent control parameters and compared with traditional ERP-analysis techniques. Continuous EEG data are cut into epochs according to stimuli events presented to the subjects. These ensembles of time series can be considered as ensembles of trajectories given by some dynamical systems. We employ a statistical mechanics approach motivated by the Frobenius-Perron equation and apply it to coarse-grained symbolic descriptions of the dynamics. We develop time-dependent measures of complexity founded on running cylinder sets and show that these quantities are able to distinguish simulated data obtained by different control parameters as well as experimental data between different experimental conditions. As a first finding, our approach restores the well-known ERP components and it reveals additionally qualitative changes in the EEG that cannot be detected by means of the traditional techniques. We criticize the prerequisites of the traditional approach to ERP analysis and propose to consider ERP instead in terms of dynamical system theory and information theory.

Brain↗
PubMed2002

Design of an optimal Chebyshev-expanded discrimination function for globular proteins.

We describe the construction of a scoring function designed to model the free energy of protein folding. An optimization technique is used to determine the best functional forms of the hydrophobic, residue-residue and hydrogen-bonding components of the potential. The scoring function is expanded by use of Chebyshev polynomials, the coefficients of which are determined by minimizing the score, in units of standard deviation, of native structures in the ensembles of alternate decoy conformations. The derived effective potential is then tested on decoy sets used conventionally in such studies. Using our scoring function, we achieve a high level of discrimination between correct and incorrect folds. In addition, our method is able to represent functions of arbitrary shape with fewer parameters than the usual histogram potentials of similar resolution. Finally, our representation can be combined easily with many optimization methods, because the total energy is a linear function of the parameters. Our results show that the techniques of Z-score optimization and Chebyshev expansion work well.

Amino Acids↗
PubMed2005

High-frequency ultrasound scattering from microspheres and single cells.

Assessing the proportion of biological cells in a volume of interest undergoing structural changes, such as cell death, using high-frequency ultrasound (20-100 MHz), requires the development of a theoretical model of scattering by any arbitrary cell ensemble. A prerequisite to building such a model is to know the scattering by a single cell in different states. In this paper, a simple model for the high-frequency acoustic scattering by one cell is proposed. A method for deducing the backscatter transfer function from a single, subresolution scatterer is also devised. Using this method, experimental measurements of backscatter from homogeneous, subresolution polystyrene microspheres and single, viable eukaryotic cells, acquired across a broad, continuous range of frequencies were compared with elastic scattering theory and the proposed cell scattering model, respectively. The resonant features observed in the backscatter transfer function of microspheres were found to correspond accurately to theoretical predictions. Using the spacing of the major spectral peaks in the transfer functions obtained experimentally, it is possible to predict microsphere diameters with less than 4% error. Such good agreement was not seen between the cell model and the measured backscatter from cells. Possible reasons for this discrepancy are discussed.

Apoptosis↗
PubMed2006

RNAKinetics: a web server that models secondary structure kinetics of an elongating RNA.

The RNAKinetics server (http://www.ig-msk.ru/RNA/kinetics) is a web interface for the newly developed RNAKinetics software. The software models the dynamics of RNA secondary structure by the means of kinetic analysis of folding transitions of a growing RNA molecule. The result of the modeling is a kinetic ensemble, i.e. a collection of RNA structures that are endowed with probabilities, which depend on time. This approach gives comprehensive probabilistic description of RNA folding pathways, revealing important kinetic details that are not captured by the traditional structure prediction methods. The access to the RNAKinetics server is free.

Base Sequence↗
PubMedDate not supplied

[Modeling of the 3D structure of the HIV-Haiti immunodominant epitope].

The 3D structure for the HIV-Haiti immunodominant epitope was computed in terms of NMR spectroscopy data using the theoretical procedure including a probabilistic approach in conjunction with molecular mechanics algorithms and quantum chemical methods. The immunogenic crown of the virus protein gp120 was shown to form in solution a prevalent conformation whose geometric parameters match the double beta-turn IV-IV. Two structures observed in crystal were found in the ensemble of the best-energy conformations of the HIV-Haiti principal neutralizing epitope. From a comparison of simulated structures with those computed previously for the HIV-Thailand and HIV-MN isolates, it was concluded that the immunogenic tip of gp120 gives rise to similar spatial backbone forms in different HIV-1 strains but has some inherent conformational flexibility of its individual amino acid residues. The differences in local fragment structures revealed in three isolates of HIV-1 are supposed to be important for the specificity of its binding with neutralizing antibodies.

Computational Biology↗
PubMed2025

The Effect of Alcohol Intake on Brain White Matter Microstructural Integrity: A New Causal Inference Framework for Incomplete Phenomic Data.

Although substance use, such as alcohol intake, is known to be associated with cognitive decline during aging, its direct influence on the central nervous system remains incompletely understood. In this study, we investigate the influence of alcohol intake frequency on reduction of brain white matter microstructural integrity in the fornix, a brain region considered a promising marker of age-related microstructural degeneration, using a large UK Biobank (UKB) cohort with extensive phenomic data reflecting a comprehensive lifestyle profile. Two major challenges arise: (a) potentially nonlinear confounding effects from phenomic variables and (b) a limited proportion of participants with complete phenomic data. To address these challenges, we develop a novel ensemble learning framework tailored for robust causal inference and introduce a data integration step to incorporate information from UKB participants with incomplete phenomic data, improving estimation efficiency. Our analysis reveals that daily alcohol intake may significantly reduce fractional anisotropy, a neuroimaging-derived measure of white matter structural integrity, in the fornix and increase systolic and diastolic blood pressure levels. Moreover, extensive numerical studies demonstrate the superiority of our method over competing approaches in terms of estimation bias, while outcome regression-based estimators may be preferred when minimizing mean squared error is prioritized. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.

Brain aging↗
PubMed2003

Spanning set defines variability in locomotive patterns.

The purpose of the investigation was to use the spanning set methodology to quantify variability in locomotive patterns and to compare this method with traditional measures of variability. Subjects ran on a treadmill while sagittal plane kinematic data were collected with a high-speed (180 Hz) camera. Changes in variability were evaluated as the subject ran barefoot and in shoes. Mean ensemble curves for the knee angle during the stance period were created for each condition. From these curves, traditional measures of variability were calculated using the coefficients of variation (CVs), and the mean deviation (MD). Spanning set vectors were defined from the coefficients of polynomials that were fitted to the respective standard deviation curves. The magnitude of the spanning set was determined by calculating the norm of the difference between the two vectors. The normalised difference between the two conditions was 6.6%, 6.9% and 98%, for the MD, CV and spanning sets, respectively. The results indicated that the spanning set was capable of statistically (p < 0.05) determining differences in variability between the two conditions. CV and MD measures were unable to detect statistical differences (p > 0.05) between the two conditions. The spanning set provides an alternative, and sensitive measure for evaluating differences in variability from the mean ensemble curve.

Adult↗
PubMed2006

Extended multicanonical method combined with thermodynamically optimized potential: application to the liquid-crystal transition of silicon.

A novel method is proposed to study first-order phase transition in real materials. It is applied to the liquid-crystal transition of silicon successfully. It consists of two parts: a direct simulation of the transition by an extended multicanonical ensemble with an order parameter defined with structure factors that characterize the transition, and optimization of a model interatomic potential in terms of the ensemble from an accurate one. These provide a principle to project a first-principles approach on a model-based approach conserving thermodynamic properties of multiple phases.

Journal Article↗
PubMed1999

Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures.

Guided by recent experimental results suggesting that protein-folding rates and mechanisms are determined largely by native-state topology, we develop a simple model for protein folding free-energy landscapes based on native-state structures. The configurations considered by the model contain one or two contiguous stretches of residues ordered as in the native structure with all other residues completely disordered; the free energy of each configuration is the difference between the entropic cost of ordering the residues, which depends on the total number of residues ordered and the length of the loop between the two ordered segments, and the favorable attractive interactions, which are taken to be proportional to the total surface area buried by the ordered residues in the native structure. Folding kinetics are modeled by allowing only one residue to become ordered/disordered at a time, and a rigorous and exact method is used to identify free-energy maxima on the lowest free-energy paths connecting the fully disordered and fully ordered configurations. The distribution of structure in these free-energy maxima, which comprise the transition-state ensemble in the model, are reasonably consistent with experimental data on the folding transition state for five of seven proteins studied. Thus, the model appears to capture, at least in part, the basic physics underlying protein folding and the aspects of native-state topology that determine protein-folding mechanisms.

Models, Theoretical↗