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At least 721 records · Page 40Linked to original sources

Stochastic calculus: application to dynamic bifurcations and threshold crossings

For the dynamic pitchfork bifurcation in the presence of white noise, the statistics of the last time at zero are calculated as a function of the noise level and the rate of change of the parameter. The threshold crossing problem used, for example, to model the firing of a single cortical neuron is considered, concentrating on quantities that may be experimentally measurable but have so far received little attention. Expressions for the statistics of pre-threshold excursions, occupation density and last crossing time of zero are compared with results from numerical generation of paths.

adap-org↗

The Mathematical Theory of Molecular Motor Movement and Chemomechanical Energy Transduction

The mathematical formulation of the model for molecular movement of single motor proteins driven by cyclic biochemical reactions in an aqueous environment leads to a drifted Brownian motion characterized by coupled diffusion equations. In this article, we introduce the basic notion for the continuous model and review some asymptotic solutions for the problem. Stochastic, nonequilibrium thermodynamic interpretations of the mathematical equations and their solutions are presented. Some relevant mathematics, mainly in the field of stochastic processes, are discussed.

cond-mat.stat-mech↗

Extremely Dilute Modular Neuronal Networks: Neocortical Memory Retrieval Dynamics

A model of the columnar functional organization of neocortical association areas is studied. The neuronal network is composed of many Hebbian autoassociators, or modules, each of which interacts with a relatively small number of the others. Every module encodes and stores a number of elementary percepts, or features. Memory items, or patterns, are peculiar combinations of features sparsely distributed over the multi-modular network. Any feature stored in any module can be involved in several of the stored patterns; feature-sharing is in fact source of local ambiguities and, consequently, a potential cause of erroneous memory retrieval activity spreading through the model network. The memory retrieval dynamics of the large multi-modular autoassociator is investigated by means of quantitative analysis and numerical simulations. An oscillatory retrieval process is found to be very efficient in overcoming feature-sharing drawbacks; it requires a mechanism that modulates the robustness of local attractors to noise, and neuronal activity sparseness such that quiescent and active modules are about equally noisy. Correlated activation of interconnected modules and extramodular neuronal contacts more effective than the intramodular ones seem to be general requirements in order to efficiently achieve satisfactory quality of memory retrieval. It is also shown that, even in ideal conditions, some spots of the network cannot be reached by retrieval activity spread. The locations of these activity isles depend on the pattern to retrieve and on the cue, while their extension only depends on architecture of the graph and statistics of the stored patterns. The existence of these isles determines an upper-bound to retrieval quality that does not depend on the specific retrieval dynamics adopted, nor on whether feature-sharing is permitted. The oscillatory retrieval process nearly saturates this bound.

cond-mat.dis-nn↗

Poland-Scheraga models and the DNA denaturation transition

Poland-Scheraga models were introduced to describe the DNA denaturation transition. We give a rigorous and refined discussion of a family of these models. We derive possible scaling functions in the neighborhood of the phase transition point and review common examples. We introduce a self-avoiding Poland-Scheraga model displaying a first order phase transition in two and three dimensions. We also discuss exactly solvable directed examples. This complements recent suggestions as to how the Poland-Scheraga class might be extended in order to display a first order transition, which is observed experimentally.

cond-mat.stat-mech↗

Multifractality in Human Heartbeat Dynamics

Recent evidence suggests that physiological signals under healthy conditions may have a fractal temporal structure. We investigate the possibility that time series generated by certain physiological control systems may be members of a special class of complex processes, termed multifractal, which require a large number of exponents to characterize their scaling properties. We report on evidence for multifractality in a biological dynamical system --- the healthy human heartbeat. Further, we show that the multifractal character and nonlinear properties of the healthy heart rate are encoded in the Fourier phases. We uncover a loss of multifractality for a life-threatening condition, congestive heart failure.

cond-mat.stat-mech↗

The Web of Human Sexual Contacts

Many ``real-world'' networks are clearly defined while most ``social'' networks are to some extent subjective. Indeed, the accuracy of empirically-determined social networks is a question of some concern because individuals may have distinct perceptions of what constitutes a social link. One unambiguous type of connection is sexual contact. Here we analyze data on the sexual behavior of a random sample of individuals, and find that the cumulative distributions of the number of sexual partners during the twelve months prior to the survey decays as a power law with similar exponents $α\approx 2.4$ for females and males. The scale-free nature of the web of human sexual contacts suggests that strategic interventions aimed at preventing the spread of sexually-transmitted diseases may be the most efficient approach.

cond-mat.stat-mech↗

Interactions between Membrane Inclusions on Fluctuating Membranes

We model membrane proteins as anisotropic objects characterized by symmetric-traceless tensors and determine the coupling between these order-parameters and membrane curvature. We consider the interactions between transmembrane proteins that respect up-down (reflection) symmetry of bilayer membranes and that have circular or non-circular cross-sectional areas in the tangent-plane of membranes. Using a field theoretic approach, we find non-entropic $1/R^{4}$ interactions between reflection-symmetry-breaking transmembrane proteins with circular cross-sectional area and entropic $1/R^{4}$ interactions between transmembrane proteins with circular cross-section that do not break up-down symmetry in agreement with previous calculations. We also find anisotropic $1/R^{4}$ interactions between reflection-symmetry-conserving transmembrane proteins with non-circular cross-section, anisotropic $1/R^{2}$ interactions between reflection-symmetry-breaking transmembrane proteins with non-circular cross-section, and non-entropic $1/R^{4}$ many-particle interactions among non-transmembrane proteins. For large $R$, these interactions might provide the dominant force inducing aggregation of the membrane proteins.

cond-mat↗

A Self-Assembled Microlensing Rotational Probe

A technique to measure microscopic rotational motion is presented. When a small fluorescent polystyrene microsphere is attached to a larger polystyrene microsphere, the larger sphere acts as a lens for the smaller microsphere and provides an optical signal that is a strong function of the azimuthal angle. We demonstrate the technique by measuring the rotational diffusion constant of the microsphere in solutions of varying viscosity and discuss the feasibility of using this probe to measure rotational motion of biological systems.

cond-mat.soft↗

Geometry Selects Highly Designable Structures

By enumerating all sequences of length 20, we study the designability of structures in a two-dimensional Hydrophobic-Polar (HP) lattice model in a wide range of inter-monomer interaction parameters. We find that although the histogram of designability depends on interaction parameters, the set of highly designable structures is invariant. So in the HP lattice model the High Designability should be a purely geometrical feature. Our results suggest two geometrical properties for highly designable structures, they have maximum number of contacts and unique neighborhood vector representation. Also we show that contribution of perfectly stable sequences in designability of structures plays a major role to make them highly designable.

cond-mat.soft↗

Designer Gene Networks: Towards Fundamental Cellular Control

The engineered control of cellular function through the design of synthetic genetic networks is becoming plausible. Here we show how a naturally occurring network can be used as a parts list for artificial network design, and how model formulation leads to computational and analytical approaches relevant to nonlinear dynamics and statistical physics.

physics.bio-ph↗

Population dynamics advected by chaotic flows: a discrete-time map approach

A discrete-time model of reacting evolving fields, transported by a bidimensional chaotic fluid flow, is studied. Our approach is based on the use of a Lagrangian scheme where {\it fluid particles} are advected by a $2d$ symplectic map possibly yielding Lagrangian chaos. Each {\it fluid particle} carries concentrations of active substances which evolve according to its own reaction dynamics. This evolution is also modeled in terms of maps. Motivated by the question, of relevance in marine ecology, of how a localized distribution of nutrients or preys affects the spatial structure of predators transported by a fluid flow, we study a specific model in which the population dynamics is given by a logistic map with space-dependent coefficient, and advection is given by the standard map. Fractal and random patterns in the Eulerian spatial concentration of predators are obtained under different conditions. Exploiting the analogies of this coupled-map (advection plus reaction) system with a random map, some features of these patterns are discussed.

nlin.CD↗

Thermodynamics and Kinetics of Folding of a Small Peptide

We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at suitable temperatures. The results of these canonical simulations are compared with that of a generalized-ensemble simulation. Our work demonstrates that concepts of folding which were developed in the past for minimalist models hold also for this peptide when simulated with an all-atom force field.

cond-mat↗

A model for predation pressure in colonial birds

Different explanations have been proposed for the existence of colonial breeding behavior in birds, but field studies offer no conclusive results. We analyze the interplay between learning habits and predation pressure by means of numerical simulations. Our analysis suggests that extremely simple learning processes and equally simplistic models of predation pressure lead to the formation of stable colonies.

nlin.AO↗

New mechanism of membrane fusion

We have carried out Monte Carlo simulation of the fusion of bilayers of single chain amphiphiles which show phase behavior similar to that of biological lipids. The fusion mechanism we observe is very different from the ``stalk'' hypothesis. Stalks do form on the first stage of fusion, but they do not grow radially to form a hemifused state. Instead, stalk formation destabilizes the membranes and results in hole formation in the vicinity of the stalks. When holes in each bilayer nucleate spontaneously next to the same stalk, an incomplete fusion pore is formed. The fusion process is completed by propagation of the initial connection, the stalk, along the edges of the aligned holes.

cond-mat.soft↗

Thermodynamic control and dynamical regimes in protein folding

Monte Carlo simulations of a simple lattice model of protein folding show two distinct regimes depending on the chain length. The first regime well describes the folding of small protein sequences and its kinetic counterpart appears to be single exponential in nature, while the second regime is typical of sequences longer than 80 amino acids and the folding performance achievable is sensitive to target conformation. The extent to which stability, as measured by the energy of a sequence in the target, is an essential requirement and affects the folding dynamics of protein molecules in the first regime is investigated. The folding dynamics of sequences whose design stage was restricted to a certain fraction of randomly selected amino acids shows that while some degree of stability is a necessary and sufficient condition for successful folding, designing sequences that provide the lowest energy in the target seems to be a superfluous constraint. By studying the dynamics of under annealed but otherwise freely designed sequences we explore the relation between stability and kinetic accessibility. We find that there is no one-to-one correspondence between having low energy and folding quickly to the target, as only a small fraction of the most stable sequences were also found to fold relatively quickly.

cond-mat.soft↗

Small-scale structure of nonlinearly interacting species advected by chaotic flows

We study the spatial patterns formed by interacting biological populations or reacting chemicals under the influence of chaotic flows. Multiple species and nonlinear interactions are explicitly considered, as well as cases of smooth and nonsmooth forcing sources. The small-scale structure can be obtained in terms of characteristic Lyapunov exponents of the flow and of the chemical dynamics. Different kinds of morphological transitions are identified. Numerical results from a three-component plankton dynamics model support the theory, and they serve also to illustrate the influence of asymmetric couplings.

nlin.CD↗

Molecular theory of hydrophobic mismatch between lipids and peptides

Effects of the mismatch between the hydrophobic length, d, of transmembrane alpha helices of integral proteins and the hydrophobic thickness, D_h, of the membranes they span are studied theoretically utilizing a microscopic model of lipids. In particular, we examine the dependence of the period of a lamellar phase on the hydrophobic length and volume fraction of a rigid, integral, peptide. We find that the period decreases when a short peptide, such that d D_h, is inserted. The effect is due to the replacement of extensible lipid tails by rigid peptide. As the peptide length is increased, the lamellar period continues to increase, but at a slower rate, and can eventually decrease. The amount of peptide which fails to incorporate and span the membrane increases with the magnitude of the hydrophobic mismatch |d-D_h|. We explicate these behaviors which are all in accord with experiment. Predictions are made for the dependence of the tilt of a single trans-membrane alpha helix on hydrophobic mismatch and helix density.

cond-mat.soft↗

Helix Formation and Folding in an Artificial Peptide

We study the relation between $α$-helix formation and folding for a simple artificial peptide, Ala$_{10}$-Gly$_5$-Ala$_{10}$. Our data rely on multicanonical Monte Carlo simulations where the interactions among all atoms are taken into account. The free-energy landscape of the peptide is evaluated for various temperatures. Our data indicate that folding of this peptide is a two-step process: in a first step two $α$-helices are formed which afterwards re-arrange themselves into a U-like structure.

cond-mat.stat-mech↗