Searcharxiv⌕ Search

SEARCH · Searcharxiv

Results for “q-bio”

Search indexed arXiv papers on artificial intelligence, large language models, computer vision and robotics. Read source abstracts and follow links to arXiv.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,333 records · Page 74Linked to original sources
arXiv1997

A simple ansatz to describe thermodynamic quantities of peptides and proteins at low temperatures

We describe a simple ansatz to approximate the low temperature behavior of proteins and peptides by a mean-field-like model which is analytically solvable. For a small peptide some thermodynamic quantities are calculated and compared with numerical results of an all-atoms simulation. Our approach can be used to determine the weights for a multicanonical simulation of the molecule under consideration.

cond-mat↗
arXiv1998

Species Formation in Simple Ecosystems

In this paper we consider a microscopic model of a simple ecosystem. The basic ingredients of this model are individuals, and both the phenotypic and genotypic levels are taken in account. The model is based on a long range cellular automaton (CA); introducing simple interactions between the individuals, we get some of the complex collective behaviors observed in a real ecosystem. Since our fitness function is smooth, the model does not exhibit the error threshold transition; on the other hand the size of total population is not kept constant, and the mutational meltdown transition is present. We study the effects of competition between genetically similar individuals and how it can lead to species formation. This speciation transition does not depend on the mutation rate. We present also an analytical approximation of the model.

cond-mat.stat-mech↗
arXiv1999

Eigen's Error Threshold and Mutational Meltdown in a Quasispecies Model

We introduce a toy model for interacting populations connected by mutations and limited by a shared resource. We study the presence of Eigen's error threshold and mutational meltdown. The phase diagram of the system shows that the extinction of the whole population due to mutational meltdown can occur well before an eventual error threshold transition.

cond-mat.stat-mech↗
arXiv1999

Lattice three-species models of the spatial spread of rabies among foxes

Lattice models describing the spatial spread of rabies among foxes are studied. In these models, the fox population is divided into three-species: susceptible, infected or incubating, and infectious or rabid. They are based on the fact that susceptible and incubating foxes are territorial while rabid foxes have lost their sense of direction and move erratically. Two different models are investigated: a one-dimensional coupled-map lattice model, and a two-dimensional automata network model. Both models take into account the short-range character of the infection process and the diffusive motion of rabid foxes. Numerical simulations show how the spatial distribution of rabies, and the speed of propagation of the epizootic front depend upon the carrying capacity of the environment and diffusion of rabid foxes out of their territory.

adap-org↗
arXiv2000

Condensed Matter Physics - Biology Resonance

The field of condensed matter physics had its genesis this century and it has had a remarkable evolution. A closer look at its growth reveals a hidden aim in the collective consciousness of the field - a part of the development this century is a kind of warm up exercise to understand the nature of living condensed matter, namely the field of biology, by a growing new breed of scientists in the coming century. Through some examples the vitality of this interaction will be pointed out.

cond-mat↗
arXiv1998

Diversity, Stability, Recursivity, and Rule Generation in Biological System: Intra-inter Dynamics Approach

Basic problems for the construction of a scenario for the Life are discussed. To study the problems in terms of dynamical systems theory, a scheme of intra-inter dynamics is presented. It consists of internal dynamics of a unit, interaction among the units, and the dynamics to change the dynamics itself, for example by replication (and death) of units according to their internal states. Applying the dynamics to cell differentiation, isologous diversification theory is proposed. According to it, orbital instability leads to diversified cell behaviors first. At the next stage, several cell types are formed, first triggered by clustering of oscillations, and then as attracting states of internal dynamics stabilized by the cell-to-cell interaction. At the third stage, the differentiation is determined as a recursive state by cell division. At the last stage, hierarchical differentiation proceeds, with the emergence of stochastic rule for the differentiation to sub-groups, where regulation of the probability for the differentiation provides the diversity and stability of cell society. Relevance of the theory to cell biology is discussed.

adap-org↗
arXiv1997

Evolution and extinction dynamics in rugged fitness landscapes

Macroevolution is considered as a problem of stochastic dynamics in a system with many competing agents. Evolutionary events (speciations and extinctions) are triggered by fitness records found by random exploration of the agents' fitness landscapes. As a consequence, the average fitness in the system increases logarithmically with time, while the rate of extinction steadily decreases. This dynamics is studied by numerical simulations and, in a simpler mean field version, analytically. We also study the effect of externally added `mass' extinctions. The predictions for various quantities of paleontological interest (life-time distributions, distribution of event sizes and behavior of the rate of extinction) are robust and in good agreement with available data. Brief version of parts of this work have been published as Letters. (PRL 75, 2055, (1995) and PRL, 79, 1413, (1997))

adap-org↗
arXiv2000

Controlling chaos in diluted networks with continuous neurons

Diluted neural networks with continuous neurons and nonmonotonic transfer function are studied, with both fixed and dynamic synapses. A noisy stimulus with periodic variance results in a mechanism for controlling chaos in neural systems with fixed synapses: a proper amount of external perturbation forces the system to behave periodically with the same period as the stimulus.

cond-mat.dis-nn↗
arXiv1997

Testing the helix model for protein folding on four simple proteins

We test a simplified, local version of the helix model on two synthetic and two natural proteins, to study its efficiency in predicting the native secondary structure. The results we obtain are very good for the synthetic sequences, poorer for the two natural ones. This suggests that non-local terms play a fundamental role in determining the secondary structure, even if in some cases local terms alone may be sufficient.

cond-mat.soft↗
arXiv1997

Kinetics, Hydrodynamics and Stochastodynamics of Cellular Structure Coarsening

For the first time the phenomenon of cellular structure coarsening are consistently analysed from the positions of kinetic, hydrodynamic and stochastodynamic theories of nonequilibrium statistical systems. Thereby micro-, meso- and macroscopic levels of approach are distinguished. At the microscopic level the cellular structure is describe by a probability distribution function in a phase space of cell coordinates and of cell sizes. A kinetic equation for the function is written and a development to a hydrodynamic equation of a mesoscopic cell medium is realised. It has the form of a diffusion-reaction equation with a negative "diffusion" coefficient and with a cell interface density playing the role of concentration. Its analysis reveals a new effect of macroscopic patterning in the cell medium: existence of space-correlated stochastic fluctuations of the cell interface density.

cond-mat↗
arXiv1999

Capture on High Curvature Region: Aggregation of Colloidal Particle Bound to Giant Phospholipid Vesicles

A very recent observation on the membrane mediated attraction and ordered aggregation of colloidal particles bound to giant phospholipid vesicles (I. Koltover, J. O. Rädler, C. R. Safinya, Phys. Rev. Lett. {\bf 82}, 1991(1999)) is investigated theoretically within the frame of Helfrich curvature elasticity theory of lipid bilayer fluid membrane. Since the concave or waist regions of the vesicle possess the highest local bending energy density, the aggregation of colloidal beads on these places can reduce the elastic energy in maximum. Our calculation shows that a bead in the concave region lowers its energy $\sim 20 k_B T$. For an axisymmetrical dumbbell vesicle, the local curvature energy density along the waist is equally of maximum, the beads can thus be distributed freely with varying separation distance.

cond-mat.soft↗
arXiv1997

Theory for Characterization of Hippocampal Long-Term Potentiation Induced by Time-Structured Stimuli

We theoretically investigate long-term potentiation (LTP) in the hippocampus using a simple model of a neuron stimulated by three different time-structured input signals (regular, Markov, and chaotic). The synaptic efficacy change is described taking into account both N-methyl-D-aspartate (NMDA) and non-NMDA receptors. The experimental results are successfully explained by our neuron model, and the remarkable fact that the chaotic stimuli in the nonstationary regime produce the largest LTP is discussed.

cond-mat.dis-nn↗
arXiv1998

Coupled Oscillators with Chemotaxis

A simple coupled oscillator system with chemotaxis is introduced to study morphogenesis of cellular slime molds. The model successfuly explains the migration of pseudoplasmodium which has been experimentally predicted to be lead by cells with higher intrinsic frequencies. Results obtained predict that its velocity attains its maximum value in the interface region between total locking and partial locking and also suggest possible roles played by partial synchrony during multicellular development.

adap-org↗
arXiv1997

Equilibrium Chemical Engines

An equilibrium reversible cycle with a certain engine to transduce the energy of any chemical reaction into mechanical energy is proposed. The efficiency for chemical energy transduction is also defined so as to be compared with Carnot efficiency. Relevance to the study of protein motors is discussed. KEYWORDS: Chemical thermodynamics, Engine, Efficiency, Molecular machine.

cond-mat.soft↗
arXiv2000

Energy Storage in a Hamiltonian System in Partial Contact with a Heat Bath

To understand the mechanism allowing for the long-term storage of excess energy in proteins, we study a Hamiltonian system consisting of several coupled pendula in partial contact with a heat bath. It is found that energy storage is possible when the motion of each pendulum switches between oscillatory (vibrational) and rotational (phase-slip) modes. The storage time increases almost exponentially to the square root of the injected energy. The relevance of our mechanism to protein motors is discussed.

cond-mat.stat-mech↗
arXiv2001

A Multicanonical Molecular Dynamics Study on a Simple Bead-Spring Model for Protein Folding

We have performed a multicanonical molecular dynamics simulation on a simple model protein.We have studied a model protein composed of charged, hydrophobic, and neutral spherical bead monomers.Since the hydrophobic interaction is considered to significantly affect protein folding, we particularly focus on the competition between effects of the Coulomb interaction and the hydrophobic interaction. We found that the transition which occurs upon decreasing the temperature is markedly affected by the change in both parameters and forms of the hydrophobic potential function, and the transition changes from first order to second order, when the Coulomb interaction becomes weaker.

cond-mat.stat-mech↗
arXiv2001

Topological entropy of a stiff ring polymer and its connection to DNA knots

We discuss the entropy of a circular polymer under a topological constraint. We call it the {\it topological entropy} of the polymer, in short. A ring polymer does not change its topology (knot type) under any thermal fluctuations. Through numerical simulations using some knot invariants, we show that the topological entropy of a stiff ring polymer with a fixed knot is described by a scaling formula as a function of the thickness and length of the circular chain. The result is consistent with the viewpoint that for stiff polymers such as DNAs, the length and diameter of the chains should play a central role in their statistical and dynamical properties. Furthermore, we show that the new formula extends a known theoretical formula for DNA knots.

cond-mat.stat-mech↗