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At least 1,171 records · Page 65Linked to original sources

arXiv1997

A soluble model of evolution and extinction dynamics in a rugged fitness landscape

We consider a continuum version of a previously introduced and numerically studied model of macroevolution (PRL 75, 2055, (1995)) in which agents evolve by an optimization process in a rugged fitness landscape and die due to their competitive interactions. We first formulate dynamical equations for the fitness distribution and the survival probability. Secondly we analytically derive the $t^{-2}$ law which characterizes the life time distribution of biological genera. Thirdly we discuss other dynamical properties of the model such as the rate of extinction and conclude with a brief discussion.

physics.bio-ph↗

arXiv1997

Denaturation of Heterogeneous DNA

The effect of heterogeneous sequence composition on the denaturation of double stranded DNA is investigated. The resulting pair-binding energy variation is found to have a negligible effect on the critical properties of the smooth second order melting transition in the simplest (Peyrard-Bishop) model. However, sequence heterogeneity is dramatically amplified upon adopting a more realistic treatment of the backbone stiffness. The model yields features of ``multi-step melting'' similar to those observed in experiments.

cond-mat.stat-mech↗

arXiv1997

Parisi Phase in a Neuron

Pattern storage by a single neuron is revisited. Generalizing Parisi's framework for spin glasses we obtain a variational free energy functional for the neuron. The solution is demonstrated at high temperature and large relative number of examples, where several phases are identified by thermodynamical stability analysis, two of them exhibiting spontaneous full replica symmetry breaking. We give analytically the curved segments of the order parameter function and in representative cases compute the free energy, the storage error, and the entropy.

cond-mat.dis-nn↗

arXiv1996

Morphological Instabilities in a growing Yeast Colony: Experiment and Theory

We study the growth of colonies of the yeast Pichia membranaefaciens on agarose film. The growth conditions are controlled in a setup where nutrients are supplied through an agarose film suspended over a solution of nutrients. As the thickness of the agarose film is varied, the morphology of the front of the colony changes. The growth of the front is modeled by coupling it to a diffusive field of inhibitory metabolites. Qualitative agreement with experiments suggests that such a coupling is responsible for the observed instability of the front.

cond-mat↗

arXiv1997

Viscosity Dependence of the Folding Rates of Proteins

The viscosity dependence of the folding rates for four sequences (the native state of three sequences is a beta-sheet, while the fourth forms an alpha-helix) is calculated for off-lattice models of proteins. Assuming that the dynamics is given by the Langevin equation we show that the folding rates increase linearly at low viscosities η, decrease as 1/ηat large ηand have a maximum at intermediate values. The Kramers theory of barrier crossing provides a quantitative fit of the numerical results. By mapping the simulation results to real proteins we estimate that for optimized sequences the time scale for forming a four turn α-helix topology is about 500 nanoseconds, whereas the time scale for forming a beta-sheet topology is about 10 microseconds.

cond-mat.soft↗

arXiv1997

Evolution on a Rugged Landscape:Pinning and Aging

Population dynamics on a rugged landscape is studied analytically and numerically within a simple discrete model for evolution of N individuals in one-dimensional fitness space. We reduce the set of master equations to a single Fokker-Plank equation which allows us to describe the dynamics of the population in terms of thermo-activated Langevin diffusion of a single particle in a specific random potential. We found that the randomness in the mutation rate leads to pinning of the population and on average to a logarithmic slowdown of the evolution, resembling aging phenomenon in spin glass systems. In contrast, the randomness in the replication rate turns out to be irrelevant for evolution in the long-time limit as it is smoothed out by increasing ``evolution temperature''. The analytic results are in a good agreement with numerical simulations.

adap-org↗

arXiv1997

Speciation as Pattern Formation by Competition in a Smooth Fitness Landscape

We investigate the problem of speciation and coexistence in simple ecosystems when the competition among individuals is included in the Eigen model for quasi-species. By suggesting an analogy between the competition among strains and the diffusion of a chemical inhibitor in a reaction-diffusion system, the speciation phenomenon is considered the analogous of chemical pattern formation in genetic space. In the limit of vanishing mutation rate we obtain analytically the conditions for speciation. Using different forms of the competition interaction we show that the speciation is absent for the genetic equivalent of a normal diffusing inhibitor, and is present for shorter-range interactions. The comparison with numerical simulations is very good.

cond-mat.stat-mech↗

arXiv1997

Thermodynamic stability of folded proteins against mutations

By balancing the average energy gap with its typical change due to mutations for protein-like heteropolymers with M residues, we show that native states are unstable to mutations on a scale M* ~ (lambda/sigma_mu)^(1/zeta_s), where lambda is the dispersion in the interaction free energies and sigma_mu their typical change. Theoretical bounds and numerical estimates (based on complete enumeration on four lattices) of the instability exponent zeta_s are given. Our analysis suggests that a limiting size of single-domain proteins should exist, and leads to the prediction that small proteins are insensitive to random mutations.

cond-mat.soft↗

arXiv1997

Unicellular algal growth: A biomechanical approach to cell wall dynamics

We present a model for unicellular algal growth as motivated by several experiments implicating the importance of calcium ions and ``loosening'' enzymes in morphogenesis. A growing cell at rest in a diffusive calcium solution is viewed as an elastic shell on short timescales. For a given turgor pressure, we calculate the stressed shapes of the wall elements whose elastic properties are determined by Young's modulus and the thickness of the wall. The local enzyme concentration then determines the rate at which the unstressed shape of a wall element relaxes toward its stressed shape. The local wall thickness is calculated from the calcium-mediated addition of material and thinning due to elongation. We use this model to calculate growth rates for small perturbations to a circular cell. We find an instability related to modulations of the wall thickness, leading to growth rates which peak at a finite wave number.

patt-sol↗

arXiv1997

Multiresolution wavelet analysis of heartbeat intervals discriminates healthy patients from those with cardiac pathology

We applied multiresolution wavelet analysis to the sequence of times between human heartbeats (R-R intervals) and have found a scale window, between 16 and 32 heartbeats, over which the widths of the R-R wavelet coefficients fall into disjoint sets for normal and heart-failure patients. This has enabled us to correctly classify every patient in a standard data set as either belonging to the heart-failure or normal group with 100% accuracy, thereby providing a clinically significant measure of the presence of heart-failure from the R-R intervals alone. Comparison is made with previous approaches, which have provided only statistically significant measures.

adap-org↗

arXiv1997

Elasticity model of a supercoiled DNA molecule

Within a simple elastic theory, we study the elongation versus force characteristics of a supercoiled DNA molecule at thermal equilibrium in the regime of small supercoiling. The partition function is mapped to the path integral representation for a quantum charged particle in the field of a magnetic monopole with unquantized charge. We show that the theory is singular in the continuum limit and must be regularised at an intermediate length scale. We find good agreement with existing experimental data, and point out how to measure the twist rigidity accurately.

cond-mat.soft↗

arXiv1997

Shape Changes of Self-Assembled Actin Bilayer Composite Membranes

We report the self-assembly of thin actin shells beneath the membranes of giant vesicles. Ion-carrier mediated influx of Mg2+ induces actin polymerization in the initially spherical vesicles. Buckling of the vesicles and the formation of blisters after thermally induced bilayer expansion is demonstrated. Bilayer flickering is dominated by tension generated by its coupling to the actin cortex. Quantitative flicker analysis suggests the bilayer and the actin cortex are separated by 0.4 \mum to 0.5 \mum due to undulation forces.

physics.bio-ph↗

arXiv1997

Comment on "Chain Length Scaling of Protein Folding Time", PRL 77, 5433 (1996)

In a recent Letter, Gutin, Abkevich, and Shakhnovich (GAS) reported on a series of dynamical Monte Carlo simulations on lattice models of proteins. Based on these highly simplified models, they found that four different potential energies lead to four different folding time scales tau_f, where tau_f scales with chain length as N^lambda (see, also, Refs. [2-4]), with lambda varying from 2.7 to 6.0. However, due to the lack of microscopic models of protein folding dynamics, the interpretation and origin of the data have remained somewhat speculative. It is the purpose of this Comment to point out that the application of a simple "mesoscopic" model (cond-mat/9512019, PRL 77, 2324, 1996) of protein folding provides a full account of the data presented in their paper. Moreover, we find a major qualitative disagreement with the argumentative interpretation of GAS. Including, the origin of the dynamics, and size of the critical folding nucleus.

cond-mat.stat-mech↗

arXiv1998

Self-control in Sparsely Coded Networks

A complete self-control mechanism is proposed in the dynamics of neural networks through the introduction of a time-dependent threshold, determined in function of both the noise and the pattern activity in the network. Especially for sparsely coded models this mechanism is shown to considerably improve the storage capacity, the basins of attraction and the mutual information content of the network.

cond-mat.stat-mech↗

arXiv1998

A New Monte Carlo Algorithm for Protein Folding

We demonstrate that the recently proposed pruned-enriched Rosenbluth method (P. Grassberger, Phys. Rev. E 56 (1997) 3682) leads to extremely efficient algorithms for the folding of simple model proteins. We test them on several models for lattice heteropolymers, and compare to published Monte Carlo studies. In all cases our algorithms are faster than all previous ones, and in several cases we find new minimal energy states. In addition to ground states, our algorithms give estimates for the partition sum at finite temperatures.

cond-mat.stat-mech↗

arXiv1998

Master equation approach to protein folding and kinetic traps

The master equation for 12-monomer lattice heteropolymers is solved numerically and the time evolution of the occupancy of the native state is determined. At low temperatures, the median folding time follows the Arrhenius law and is governed by the longest relaxation time. For good folders, significant kinetic traps appear in the folding funnel whereas for bad folders, the traps also occur in non-native energy valleys.

cond-mat.stat-mech↗

arXiv1997

Flexive and Propulsive Dynamics of Elastica at Low Reynolds Numbers

A stiff one-armed swimmer in glycerine goes nowhere, but if its arm is elastic, exerting a restorative torque proportional to local curvature, the swimmer can go on its way. Considering this happy consequence and the principles of elasticity, we study a hyperdiffusion equation for the shape of the elastica in viscous flow, find solutions for impulsive or oscillatory forcing, and elucidate relevant aspects of propulsion. These results have application in a variety of physical and biological contexts, from dynamic biopolymer bending experiments to instabilities of elastic filaments.

cond-mat.soft↗

arXiv1997

Hard Spheres in Vesicles: Curvature-Induced Forces and Particle-Induced Curvature

We explore the interplay of membrane curvature and nonspecific binding due to excluded-volume effects among colloidal particles inside lipid bilayer vesicles. We trapped submicron spheres of two different sizes inside a pear-shaped, multilamellar vesicle and found the larger spheres to be pinned to the vesicle's surface and pushed in the direction of increasing curvature. A simple model predicts that hard spheres can induce shape changes in flexible vesicles. The results demonstrate an important relationship between the shape of a vesicle or pore and the arrangement of particles within it.

cond-mat.soft↗