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At least 613 records · Page 34Linked to original sources

arXiv1999

Force and Motion Generation of Molecular Motors: A Generic Description

We review the properties of biological motor proteins which move along linear filaments that are polar and periodic. The physics of the operation of such motors can be described by simple stochastic models which are coupled to a chemical reaction. We analyze the essential features of force and motion generation and discuss the general properties of single motors in the framework of two-state models. Systems which contain large numbers of motors such as muscles and flagella motivate the study of many interacting motors within the framework of simple models. In this case, collective effects can lead to new types of behaviors such as dynamic instabilities of the steady states and oscillatory motion.

physics.bio-ph↗

arXiv1999

Population Dynamics and Non-Hermitian Localization

We review localization with non-Hermitian time evolution as applied to simple models of population biology with spatially varying growth profiles and convection. Convection leads to a constant imaginary vector potential in the Schroedinger-like operator which appears in linearized growth models. We illustrate the basic ideas by reviewing how convection affects the evolution of a population influenced by a simple square well growth profile. Results from discrete lattice growth models in both one and two dimensions are presented. A set of similarity transformations which lead to exact results for the spectrum and winding numbers of eigenfunctions for random growth rates in one dimension is described in detail. We discuss the influence of boundary conditions, and argue that periodic boundary conditions lead to results which are in fact typical of a broad class of growth problems with convection.

cond-mat.dis-nn↗

arXiv1999

Collective Motion

With the aim of understanding the emergence of collective motion from local interactions of organisms in a "noisy" environment, we study biologically inspired, inherently non-equilibrium models consisting of self-propelled particles. In these models particles interact with their neighbors by turning towards the local average direction of motion. In the limit of vanishing velocities this behavior results in a dynamics analogous to some Monte Carlo realization of equilibrium ferromagnets. However, numerical simulations indicate the existence of new types of phase transitions which are not present in the corresponding ferromagnets. In particular, here we demonstrate both numerically and analytically that even in certain one dimensional self-propelled particle systems an ordered phase exists for finite noise levels.

physics.bio-ph↗

arXiv1997

The topological structure of 2D disordered cellular systems

We analyze the structure of two dimensional disordered cellular systems generated by extensive computer simulations. These cellular structures are studied as topological trees rooted on a central cell or as closed shells arranged concentrically around a germ cell. We single out the most significant parameters that characterize statistically the organization of these patterns. Universality and specificity in disordered cellular structures are discussed.

cond-mat.dis-nn↗

arXiv1998

Elastically coupled molecular motors

We study the influence of filament elasticity on the motion of collective molecular motors. It is found that for a backbone flexibility exceeding a characteristic value (motor stiffness divided through the mean displacement between attached motors), the ability of motors to produce force reduces as compared to rigidly coupled motors, while the maximum velocity remains unchanged. The force-velocity-relation in two different analytic approximations is calculated and compared with Monte-Carlo simulations. Finally, we extend our model by introducing motors with a strain-dependent detachment rate. A remarkable crossover from the nearly hyperbolic shape of the Hill curve for stiff backbones to a linear force-velocity relation for very elastic backbones is found. With realistic model parameters we show that the backbone flexibility plays no role under physiological conditions in muscles, but it should be observable in certain in vitro assays.

cond-mat.soft↗

arXiv1998

Competing Species Dynamics: Qualitative Advantage versus Geography

A simple cellular automata model for a two-group war over the same territory is presented. It is shown that a qualitative advantage is not enough for a minority to win. A spatial organization as well a definite degree of aggressiveness are instrumental to overcome a less fitted majority. The model applies to a large spectrum of competing groups: smoker-non smoker war, epidemic spreading, opinion formation, competition for industrial standards and species evolution. In the last case, it provides a new explanation for punctuated equilibria.

cond-mat.dis-nn↗

arXiv1998

Levy-flight spreading of epidemic processes leading to percolating clusters

We consider two stochastic processes, the Gribov process and the general epidemic process, that describe the spreading of an infectious disease. In contrast to the usually assumed case of short-range infections that lead, at the critical point, to directed and isotropic percolation respectively, we consider long-range infections with a probability distribution decaying in d dimensions with the distance as 1/R^{d+σ}. By means of Wilson's momentum shell renormalization-group recursion relations, the critical exponents characterizing the growing fractal clusters are calculated to first order in an ε-expansion. It is shown that the long-range critical behavior changes continuously to its short-range counterpart for a decay exponent of the infection σ=σ_c>2.

cond-mat.stat-mech↗

arXiv1999

Stochastic group selection model for the evolution of altruism

We study numerically and analytically a stochastic group selection model in which a population of asexually reproducing individuals, each of which can be either altruist or non-altruist, is subdivided into $M$ reproductively isolated groups (demes) of size $N$. The cost associated with being altruistic is modelled by assigning the fitness $1- τ$, with $τ\in [0,1]$, to the altruists and the fitness 1 to the non-altruists. In the case that the altruistic disadvantage $τ$ is not too large, we show that the finite $M$ fluctuations are small and practically do not alter the deterministic results obtained for $M \to \infty$. However, for large $τ$ these fluctuations greatly increase the instability of the altruistic demes to mutations. These results may be relevant to the dynamics of parasite-host systems and, in particular, to explain the importance of mutation in the evolution of parasite virulence.

adap-org↗

arXiv1999

N-body Study of Anisotropic Membrane Inclusions: Membrane Mediated Interactions and Ordered Aggregation

We study the collective behavior of inclusions inducing local anisotropic curvatures in a flexible fluid membrane. The N-body interaction energy for general anisotropic inclusions is calculated explicitly, including multi-body interactions. Long-range attractive interactions between inclusions are found to be sufficiently strong to induce aggregation. Monte Carlo simulations show a transition from compact clusters to aggregation on lines or circles. These results might be relevant to proteins in biological membranes or colloidal particles bound to surfactant membranes.

cond-mat.soft↗

arXiv1999

Attractive forces between anisotropic inclusions in the membrane of a vesicle

The fluctuation-induced interaction between two rod-like, rigid inclusions in a fluid vesicle is studied by means of canonical ensemble Monte Carlo simulations. The vesicle membrane is represented by a triangulated network of hard spheres. Five rigidly connected hard spheres form rod-like inclusions that can leap between sites of the triangular network. Their effective interaction potential is computed as a function of mutual distance and angle of the inclusions. On account of the hard-core potential among these, the nature of the potential is purely entropic. Special precaution is taken to reduce lattice artifacts and the influence of finite-size effects due to the spherical geometry. Our results show that the effective potential is attractive and short-range compared with the rod length L. Its well depth is of the order of κ/10, where κis the bending modulus.

cond-mat.soft↗

arXiv2000

Protein Folding Simulations in a Deformed Energy Landscape

A modified version of stochastic tunneling, a recently introduced global optimization technique, is introduced as a new generalized-ensemble technique and tested for a benchmark peptide, Met-enkephalin. It is demonstrated that the new technique allows to evaluate folding properties of this peptide

physics.comp-ph↗

arXiv2000

Is there a universality of the helix-coil transition in protein models?

The similarity in the thermodynamic properties of two completely different theoretical models for the helix-coil transition is examined critically. The first model is an all-atomic representation for a poly-alanine chain, while the second model is a minimal helix-forming model that contains no system specifics. Key characteristics of the helix-coil transition, in particular, the effective critical exponents of these two models agree with each other, within a finite-size scaling analysis.

physics.chem-ph↗

arXiv2001

A simple atomistic model for the simulation of the gel phase of lipid bilayers

In this paper we present the results of a large-scale numerical investigation of structural properties of a model of cell membrane, simulated as a bilayer of flexible molecules in vacuum. The study was performed by carrying out extensive Molecular Dynamics simulations, in the (NVE) micro-canonical ensemble, of two systems of different sizes (2x32 and 2x256 molecules), over a fairly large set of temperatures and densities, using parallel platforms and more standard serial computers. Depending on the dimension of the system, the dynamics was followed for physical times that go from few hundred of picoseconds for the largest system to 5--10 nanoseconds for the smallest one. We find that the bilayer remains stable even in the absence of water and neglecting Coulomb interactions in the whole range of temperatures and densities we have investigated. The extension of the region of physical parameters that we have explored has allowed us to study significant points in the phase diagram of the bilayer and to expose marked structural changes as density and temperature are varied, which are interpreted as the system passing from a crystal to a gel phase.

physics.bio-ph↗

arXiv1999

Estimation of light transport parameters in biological media using coherent backscattering

The suitability of using the angular peak shape of the coherent backscattered light for estimating the light transport parameters of biological media has been investigated. Milk and methylene blue doped milk were used as tissue phantoms for the measurements carried out with a He-Ne laser (632.8nm). Results indicate that while the technique accurately estimates the transport length, it can determine the absorption coefficient only when the absorption is moderately high ($α> 1 cm^{-1}$) for the long transport lengths typical of tissues. Further, the possibility of determining the anisotropy factor by estimating the single scattering contribution to the diffuse background is examined.

physics.med-ph↗

arXiv1994

Learning and Complexity in Genetic Auto-Adaptive Systems

We describe and investigate the learning capablities displayed by a population of self-replicating segments of computer-code subject to random mutation: the tierra environment. We find that learning is achieved through phase transitions that adapt the population to whichever environment it encounters, with a learning rate characterized by the environmental variables. Our results suggest that most effective learning is achieved close to the edge of chaos.

adap-org↗

arXiv1994

Self-organized Critical Model Of Biological Evolution

A punctuated equilibrium model of biological evolution with relative fitness between different species being the fundamental driving force of evolution is introduced. Mutation is modeled as a fitness updating cellular automaton process where the change in fitness after mutation follows a Gaussian distribution with mean $x>0$ and standard deviation $σ$. Scaling behaviors are observed in our numerical simulation, indicating that the model is self-organized critical. Besides, the numerical experiment suggests that models with different $x$ and $σ$ belong to the same universality class. PACS numbers: 87.10.+e, 05.40.+j

cond-mat↗

arXiv1995

Protein Folding and Spin Glass

We explicitly show the connection between the protein folding problem and spin glass transition. This is then used to identify appropriate quantities that are required to describe the transition. A possible way of observing the spin glass transition is proposed.

cond-mat↗

arXiv1996

Monte Carlo Simulations of Sexual Reproduction

Modifying the Redfield model of sexual reproduction and the Penna model of biological aging, we compare reproduction with and without recombination in age-structured populations. In contrast to Redfield and in agreement with Bernardes we find sexual reproduction to be preferred to asexual one. In particular, the presence of old but still reproducing males helps the survival of younger females beyond their reproductive age.

cond-mat↗