Dynamics and intrinsic statistical fluctuations of a gene switch

We studied a simple gene regulatory network, the toggle switch. Specifically, we examined the means and statistical fluctuations in numbers of proteins. We found that when omega, the ratio of rates of protein-gene unbinding to protein degradation, was between similar to 10(-3) and similar to 10, the fluctuations were much larger than those we would have expected from Poisson statistics. In addition, we examined characteristic time values for system relaxation and found both that they increased with omega and that they have significant phase transition effects, with a secondary time scale appearing near the boundary between bistable and other phases. Last, we discuss the bistability of the toggle switch.

Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding

We study the nature of biomolecular binding. We found that in general there exists several thermodynamic phases: a native binding phase, a non-native phase, and a glass or local trapping phase. The quantitative optimal criterion for the binding specificity is found to be the maximization of the ratio of the binding transition temperature versus the trapping transition temperature, or equivalently the ratio of the energy gap of binding between the native state and the average non-native states versus the dispersion or variance of the non-native states. This leads to a funneled binding energy landscape.

Statistical thermodynamics of polydisperse polymer systems in the framework of lattice fluid model: Effect of molecular weight and its distribution on the spinodal in polymer solution

With the aid of thermodynamics of Gibbs, the expression of the spinodal was derived for the polydisperse polymer-solvent system in the framework of Sanchez-Lacombe Lattice Fluid Theory (SLLFT). For convenience, we considered that a model polydisperse polymer contains three sub-components. According to our calculation, the spinodal depends on both weight-average ((M) over bar (w)) and number-average ((M) over bar (n)) molecular weights of the polydisperse polymer, but the z-average molecular weight ((M) over bar (z)) dependence on the spinodal is invisible. The dependence of free volume on composition, temperature, molecular weight, and its distribution results in the effect of (M) over bar (n) on the spinodal. Moreover, it has been found that the effect of changing (M) over bar (w) on the spinodal is much bigger than that of changing (M) over bar (n) and the extrema of the spinodal increases with the rise of the weight-average molecular weight of the polymer in the solutions with upper critical solution temperature (UCST). However, the effect of polydispersity on the spinodal can be neglected for the polymer with a considerably high weight-average molecular weight. A more simple expression of the spinodal for the polydisperse polymer solution in the framework of SLLFT was also derived under the assumption of upsilon(*)=upsilon(1)(*)=upsilon(2)(*) and (1/r(1)(0))-(1/r(2i)(0))-->(1/r(1)(0)).

Thermodynamics of blends of PEO with PVAc: application of the Sanchez-Lacombe lattice-fluid theory

Sanchez-Lacombe (SL) lattice-fluid theory was used to predict the miscibility of the PEO/PVAc blending system. Integral interaction parameters, g of this polymer pair were calculated by using SL theory. And the effect of the temperature, composition of blends and molecular weight of PVAc on the extent of their miscibility has been discussed. (C) 2000 Elsevier Science Ltd. All rights reserved.

STATISTICAL THERMODYNAMICS IN THE FRAMEWORK OF THE LATTICE FLUID MODEL .1. POLYDISPERSE POLYMERS OF SPECIAL DISTRIBUTION

The Gibbs free energies and equations of state of polymers with special molar mass distributions, e.g., Flory distribution, uniform distribution and Schulz distribution, are derived based on a lattice fluid model. The influence of the polydispersity (or t

STATISTICAL THERMODYNAMICS IN THE FRAMEWORK OF THE LATTICE FLUID MODEL .2. BINARY MIXTURE OF POLYDISPERSE POLYMERS OF SPECIAL DISTRIBUTION

In this paper, the Gibbs free energy, the equation of state and the chemical potentials of polydisperse multicomponent polymer mixtures are derived. For general binary mixtures of polydisperse polymers, we also give the Gibbs free energy, the equation of

STATISTICAL THERMODYNAMICS IN THE FRAMEWORK OF THE LATTICE FLUID MODEL .3. BINARY MIXTURE OF POLYDISPERSE POLYMERS OF SPECIAL DISTRIBUTION WITH STRONG-INTERACTIONS

For a binary mixture of polydisperse polymers with strong interactions, the free energy, the equation of state, the chemical potentials and the spinodal are formulated on the basis of the lattice fluid model. Further, the spinodal curves for the system wi

STATISTICAL THERMODYNAMICS OF POLYDISPERSE POLYMER MIXTURES

A statistical thermodynamics theory of polydisperse polymer blends based on a lattice model description of a fluid is formulated. Characterization of a binary polydisperse polymer mixture requires a knowledge of the pure polymer system and the interaction energy. It is assumed that the intrinsic and interactive properties of polymer (for example, T*, P*, rho*, and epsilon(ij)*) are independent of molecular size. Thermodynamic properties of ternary and higher order mixtures are completely defined in terms of the pure fluid polymer parameters and the binary interaction energies. Thermodynamic stability criteria for the phase transitions of a binary mixture are shown. The binodal and spinodal of general binary systems and of special binary systems are discussed.

STATISTICAL THERMODYNAMICS OF POLYDISPERSE POLYMER BLENDS WITH STRONG INTERACTION

A statistical thermodynamics theory of polydisperse polymer mixtures with strong interaction between dissimilar components based on a lattice fluid model is formulated. Expressions for the free energy, equation of state, phase stability and spinodal for a polydisperse, binary polymer mixture with strong interaction are derived.

STATISTICAL THERMODYNAMICS OF POLYDISPERSE POLYMERS

A statistical thermodynamics theory of polydisperse polymers based on a lattice model of fluids is formulated. Pure polydisperse polymer can be completely characterized by three scale factors and the molecular weight distribution of the system. The equation of state does not satisfy a simple corresponding-states principle, except for a polymer fluid of sufficiently high molecular weight. The relationships between thermal expansion coefficient alpha and isothermal compressibility beta with reduced variables are also predicted.

STATISTICAL THERMODYNAMICS OF A LATTICE FLUID - PURE POLYMER

A statistical thermodynamics theory of a polydisperse polymer based on a lattice model of a fluid is formulated. The pure polydisperse polymer is completely characterized by three scale factors and the distribution law of the system. The equation of state does not satisfy a simple corresponding state principle, except for the polymer fluid with sufficiently high molecular weight.

Outer wave number spectrum and statistical distribution of apparent wave number vector

Based on the ray theory and Longuet-Higgins's linear,model of sea waves, the joint distribution of wave envelope and apparent wave number vector is established. From the joint distribution, we define a new concept, namely the outer wave number spectrum, to describe the outer characteristics of ocean waves. The analytical form of the outer wave number spectrum, the probability distributions of the apparent wave number vector and its components are then derived. The outer wave number spectrum is compared with the inner wave number spectrum for the average status of wind-wave development corresponding to a peakness factor P = 3. Discussions on the similarity and difference between the outer wave number spectrum and inner one are also presented in the paper. (C) 2002 Elsevier Science Ltd. All rights reserved.

Statistical distribution of nonlinear random wave height

A statistical model of random wave is developed using Stokes wave theory of water wave dynamics. A new nonlinear probability distribution function of wave height is presented. The results indicate that wave steepness not only could be a parameter of the distribution function of wave height but also could reflect the degree of wave height distribution deviation from the Rayleigh distribution. The new wave height distribution overcomes the problem of Rayleigh distribution that the prediction of big wave is overestimated and the general wave is underestimated. The prediction of small probability wave height value of new distribution is also smaller than that of Rayleigh distribution. Wave height data taken from East China Normal University are used to verify the new distribution. The results indicate that the new distribution fits the measurements much better than the Rayleigh distribution.

Mean Field Theory for Sigmoid Belief Networks

We develop a mean field theory for sigmoid belief networks based on ideas from statistical mechanics. Our mean field theory provides a tractable approximation to the true probability distribution in these networks; it also yields a lower bound on the likelihood of evidence. We demonstrate the utility of this framework on a benchmark problem in statistical pattern recognition -- the classification of handwritten digits.

A Unified Statistical and Information Theoretic Framework for Multi-modal Image Registration

We formulate and interpret several multi-modal registration methods in the context of a unified statistical and information theoretic framework. A unified interpretation clarifies the implicit assumptions of each method yielding a better understanding of their relative strengths and weaknesses. Additionally, we discuss a generative statistical model from which we derive a novel analysis tool, the "auto-information function", as a means of assessing and exploiting the common spatial dependencies inherent in multi-modal imagery. We analytically derive useful properties of the "auto-information" as well as verify them empirically on multi-modal imagery. Among the useful aspects of the "auto-information function" is that it can be computed from imaging modalities independently and it allows one to decompose the search space of registration problems.