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Results for “statistical physics”

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At least 73 records · Page 4Linked to original sources

PubMed2025

Repeats mimic pathogen-associated patterns across a vast evolutionary landscape.

An emerging hallmark of many human diseases is transcription of typically silenced repetitive DNA containing pathogen-associated molecular patterns (PAMPs). These PAMPs engage the innate immune system via pattern recognition receptors (PRRs)-a phenomenon known as viral mimicry. We propose a statistical physics framework to quantify viral mimicry by measuring "selective forces" that enrich PAMPs compared to a genome-wide reference distribution. We validate our predictions by identifying repeats that bind different PRRs and show potential viral mimics in different repeat families across eukaryotic genomes, suggesting shared mechanisms drive emergence and retention. We propose two non-exclusive evolutionary hypotheses. The first "repeat-centric" hypothesis posits PAMPs are integral to the repeat life cycle and are therefore enriched as they mediate repeat expansion. The second "organism-centric" hypothesis proposes viral mimicry functions as a cell-intrinsic feedback mechanism for sensing and reacting to transcriptional dysregulation, which provides a selective pressure to maintain PAMPs in genomes.

Humans↗

PubMed1994

ODS_BOOTSTRAP: assessing the statistical reliability of physical maps by bootstrap resampling.

In the program ODS_BOOTSTRAP we provide a methodology for quickly ordering clones in a genomic library into a physical map and for applying a statistical tool known as the bootstrap to assess the statistical reliability of a clonal ordering. Each clone is assigned a binary fingerprint by one of a variety of experimental approaches to physical mapping. For example, the binary fingerprints might be generated by hybridizing a panel of m probes to a library of n clones. The resulting n x m binary data matrix, X, is input to ODS_BOOTSTRAP, which utilizes the similarity in binary fingerprints of clones to construct a physical map. Under this particular implementation of bootstrap resampling, the m probes (or columns of the data matrix) are sampled randomly with replacement in the computer to generate a new n x m data matrix, X*, from which a second physical map is constructed. The resampling process is repeated 100 or more times to generate 100 or more X* matrices. The resulting 100 or more physical maps are compared with the original physical map based on the original data matrix X by counting how often links in the original physical map reappear. Three confidence statistics are introduced for each link in a physical map. The statistic C1 is defined as the percentage of time two neighboring clones on the original map reappear as neighbors under resampling. The statistic C2 is defined as the percentage of time that two neighboring clones i and j on the original map reappear as neighbors or that a clone with an identical binary fingerprint to clone i reappears as a neighbor to clone j. The statistic C3 is defined as the percentage of time that two neighboring clones on the original map reappear in the same contig under resampling.

Algorithms↗

PubMed2004

Replica model for an unusual directed polymer in 1+1 dimensions and prediction of the extremal parameter of gapped sequence alignment statistics.

Sequence alignment is one of the most important bioinformatics tools for modern molecular biology. The statistical characterization of gapped alignment scores has been a long-standing problem in sequence alignment research. In this paper, we provide a self-contained exposition of sequence alignment, a short review about how this problem is related to the directed polymer problem in statistical physics, and some analytical results that can be used for predicting alignment score statistics. Basically, we present two classes of solutions for the gapped alignment statistics by explicitly calculating the evolution of the few-replica partition function in 1+1 dimensions. We have obtained the conditions under which the more important extremal parameter lambda, characterizing the alignment score statistics, becomes predictable.

Algorithms↗

PubMedDate not supplied

[Mathematical model of microorganism biomass growth in the absence of a limiting substrate and inhibiting agents].

A mathematical model for the growth of microbial cells upon submerged cultivation was constructed. The model describes the growth phases of the biomass of microorganisms in the absence of inhibiting agents and limitation by substrate in the medium. At the basis of model is the requirement that cells should not be in physical contact during some time in order that they can divide. The model involves the known concepts of statistical physics. The consequences of the model are discussed.

Biomass↗

PubMed1998

A molar entropy model of age differences in spatial memory.

Two very-short-term-memory, spatial scanning aging experiments were conducted involving a graphics character as a target stimulus. On the probe portion of a trial, the stimulus was presented in the same position as it was on the target portion of the trial (i.e., a same trial) 50% of the time. However, on the remaining 50% of the trials, the probe stimulus was shifted (or transposed) 1, 2, or 3 positions to the right or left of the original presentation (target) position. In Experiment 1, exposure duration was manipulated. In Experiment 2, the number of potential target display positions was manipulated. For both experiments, older adults showed larger transposition distance effects than younger adults for errors. In the past (e.g., P.A. Allen, 1990, 1991), this effect has been attributed to higher levels of internal noise (entropy) in older than younger adults. This research provides converging operations to this contention by using statistical physics methods to rigorously compute the entropy in a molar neural network across age groups. After successfully fitting the statistical mechanics model to the data, the model is proved to have external validity by fitting a simplified version of it to an earlier spatial memory aging experiment reported by P. R. Bruce and J. F. Herman (1986). The results of both traditional reaction time and error rate analyses, as well as the entropy modeling analyses, indicated that older adults exhibited higher levels of entropy than did the younger adults and that this effect appeared to be generalized across processing stage.

Adolescent↗

PubMed2004

Patterns in syntactic dependency networks.

Many languages are spoken on Earth. Despite their diversity, many robust language universals are known to exist. All languages share syntax, i.e., the ability of combining words for forming sentences. The origin of such traits is an issue of open debate. By using recent developments from the statistical physics of complex networks, we show that different syntactic dependency networks (from Czech, German, and Romanian) share many nontrivial statistical patterns such as the small world phenomenon, scaling in the distribution of degrees, and disassortative mixing. Such previously unreported features of syntax organization are not a trivial consequence of the structure of sentences, but an emergent trait at the global scale.

Czech Republic↗

PubMed2004

Resonance overlap, secular effects, and nonintegrability: an approach from ensemble theory.

The time evolution of a classical multiresonance nonintegrable Hamiltonian system with few degrees of freedom is analyzed on the ensemble level. Time-dependent perturbation analysis is applied to the Liouville equation to determine the most secular series for the time evolution of the expectation value of some physical observables. In contrast to the so-called lambda(2) t expansion for thermodynamic systems, which is well known in nonequilibrium statistical physics, we find a square root of lambda t expansion in small nonintegrable systems with few degrees of freedom. This asymptotic expansion exists only on the level of ensemble but not on the level of trajectories. Moreover, the time symmetry of this expansion is broken as in nonequilibrium statistical mechanics. The relation of the Chirikov overlapping criterion to our approach is discussed.

Journal Article↗

PubMed2003

Parameter estimation in a model for multidimensional recording of neuronal data: a Gibbsian approximation approach.

This article proposes improved numerical procedures for estimating parameters in a spatiotemporal lattice model introduced for the analysis of cortical activities monitored from arrays of diodes. The numerical algorithms are based on approximations inspired by statistical physics. Both Gibbsian and mean-field approximations are used; they allow for computing local conditional probabilities inside the lattice. The statistical procedures rely on the computation of pseudomaximum-likelihood estimators. The estimators are evaluated on the basis of Monte Carlo simulations. These simulations show that mean-field approximations are useful for reducing the variance of estimators when the data are recorded from arrays of 144 diodes (which are in accordance with standard practice). In light of these improved methods, we give new interpretations for a data set obtained from optical recording of a Guinea pig's auditory cortex in response to pure tone stimulations.

Algorithms↗

PubMed2001

Headways in traffic flow: remarks from a physical perspective.

Traffic flow can be understood as a realization of a broad class of one dimensional physical systems, where a hard core repulsive interaction competes with a longer ranged attraction between the particles. It can be shown rigorously that the statistical properties of such systems in thermal equilibrium are well described by a family of distributions that stems from the random matrix theory. Analyzing the traffic data from different sources, we show that traffic on real roads belongs to that class of random matrix distributions. Also, various traffic simulation models show a similar behavior. It is demonstrated in such a way that the headway distribution of a highway traffic, that serves usually as a paradigm of systems driven far from equilibrium, is reasonably well described by a distribution originating from equilibrium statistical physics.

Journal Article↗

PubMed2004

Physical properties of aqueous suspensions of goethite (alpha-FeOOH) nanorods. Part II: In the nematic phase.

At volume fractions larger than 8.5%, aqueous suspensions of lath-like goethite (alpha-FeOOH) nanorods form a lyotropic nematic phase. In this article, we first discuss the nematic ordering within statistical-physics models of the isotropic/nematic phase transition. We then describe the influence of a magnetic field on the nematic phase. Because the nanorods bear permanent magnetic moments, the nematic suspensions have dipolar order and very low Frederiks thresholds. Moreover, the nematic phase aligns parallel to a small magnetic field but realigns perpendicular to a high field because of a competition between the permanent moments of the nanorods and their negative anisotropy of magnetic susceptibility. This magneto-optical study of the nematic phase is completely consistent with that of the isotropic phase of the same suspensions published in Part I (this issue, p. 291). Besides, we demonstrate the field-induced biaxiality of a nematic single domain aligned perpendicular to the field. We also describe here preliminary experiments where an a.c. electric field is applied to the nematic phase. Both field amplitude and frequency were found to control the alignment direction and homeotropic-to-planar alignment transitions were observed. From this data, simple models were used to estimate some physical constants of the nematic phase.

Journal Article↗

PubMed2004

A new approach to define dynamics of the ion channel gates.

Voltage-gated ion channels are of great importance in the generation and propagation of electrical signals in the excitable cell membranes. How these channels respond to changes in the potential across the membrane has been a challenging problem, and different approaches have been proposed to address the mechanism of voltage sensing and gating in these channels. In this study, we attempt a new approach by considering a simple two-state gate system and applying the path probability method to construct a nonequilibrium statistical mechanical model of the system. The model which is based on the principles of statistical physics provides a firm physical basis for ion channel gating.

Cell Membrane↗

PubMed2002

Emerging measurement and statistical methods in physical activity research.

Although many studies have attempted to identify mediators and moderators of changes in physical activity involvement, the literature is inconclusive regarding which variable(s) relate to physical activity behavior change. The Cooper 2001 Conference series dedicated a session to discussing measurement and statistical methods that could contribute to advancing this research agenda. This article focuses on four such methodologic approaches: qualitative; psychometric; latent-variable, structural equation modeling; and multilevel modeling. The article presents a brief overview of these methods and discusses potential advantages and limitations of using them.

Factor Analysis, Statistical↗

PubMed2002

Fractional Langevin model of memory in financial markets.

The separation of the microscopic and macroscopic time scales is necessary for the validity of ordinary statistical physics and the dynamical description embodied in the Langevin equation. When the microscopic time scale diverges, the differential equations on the macroscopic level are no longer valid and must be replaced with fractional differential equations of motion; in particular, we obtain a fractional-differential stochastic equation of motion. After decades of statistical analysis of financial time series certain "stylized facts" have emerged, including the statistics of stock price fluctuations having "fat tails" and their linear correlations in time being exceedingly short lived. On the other hand, the magnitude of these fluctuations and other such measures of market volatility possess temporal correlations that decay as an inverse power law. One explanation of this long-term memory is that it is a consequence of the time-scale separation between "microscopic" and "macroscopic" economic variables. We propose a fractional Langevin equation as a dynamical model of the observed memory in financial time series.

Journal Article↗

PubMed1984

Physician knowledge and utilization of physical therapy procedures.

The purpose of this study was to assess physician knowledge and utilization of physical therapy procedures. We sent a questionnaire to 600 physicians in three medical specialties (neurology, orthopedic surgery, and physical medicine and rehabilitation), in four geographic regions of the United States. The usable return was 41 percent. Overall knowledge, technical knowledge, and professional knowledge scores were compared by medical specialty, region of the country, years in practice, and three measures of utilization using analysis of variance, student's t, and chi-square statistics. Physical medicine and rehabilitation specialists and physicians in practice 10 years or more had the most knowledge of physical therapy procedures. Respondents preferred a prescriptive relationship when referring patients to physical therapists, and they most often selected "technical" procedures traditionally associated with the profession rather than "professional" procedures when referring patients to physical therapy. Those practicing medicine in their specialty 10 years or more were more conservative in their referral preferences than those in practice less than 10 years. The implications for educational intervention concerning the professional role of the physical therapist are briefly discussed.

Attitude of Health Personnel↗

PubMed2002

Statistical mechanics of learning: a variational approach for real data.

Using a variational technique, we generalize the statistical physics approach of learning from random examples to make it applicable to real data. We demonstrate the validity and relevance of our method by computing approximate estimators for generalization errors that are based on training data alone.

Models, Theoretical↗

PubMed1999

Information theoretical approach to the storage capacity of neural networks with binary weights.

The storage capacity of the perceptron with binary weights w(i)in[0,1] is derived by introducing the minimum distance d between input patterns. The approach presented in this paper is based on some results in the information theory, and the obtained storage capacity 0.585 is in good agreement with the well-known value 0.59 by the replica method in statistical physics. A strength of the present information theoretical approach is that it provides an easier and more intuitive understanding for the storage capacity than the replica method, which is believed to be more reliable and informative than the Vapnik-Chervonenkis procedure.

Biophysical Phenomena↗

PubMedDate not supplied

[Information capacity of the nucleotide sequences and their fragments].

The problem of determining the information content of nucleotide sequences is discussed. Exact expressions for the reconstitution of higher-order frequency dictionaries from lower-order once were obtained by the maximum entropy method. In form, they are analogous to superpositional approximations known in statistical physics. The features of entropy characteristics of real nucleotide sequences are described that reliably distinguish them from random texts. Methods for comparing the information content of frequency dictionaries and assessing the residual uncertainty of the text at the known frequency dictionary are proposed.

Base Sequence↗

PubMed2000

Statistical analysis of genealogical trees for polygamic species.

Repetitions within a given genealogical tree provide some information about the degree of consanguinity of a population. They can be analyzed with techniques usually employed in statistical physics when dealing with fixed point transformations. In particular, we show that the tree features strongly depend on the fractions of males and females in the population, and also on the offspring probability distribution. We check different possibilities, some of them relevant to human groups, and compare them with simulations.

Animals↗