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At least 1,351 records · Page 75Linked to original sources

arXiv2002

Morphology of axisymmetric vesicles with encapsulated filaments and impurities

The shape deformation of a three-dimensional axisymmetric vesicle with encapsulated filaments or impurities is analyzed by integrating a dissipation dynamics. This method can incorporate systematically the constraint of a fixed surface area and/or a fixed volume. The filament encapsulated in a vesicle is assumed to take a form of a rod or a ring so as to imitate cytoskeletons. In both cases, results of the shape transition of the vesicle are summarized in phase diagrams in the phase space of the vesicular volume and a rod length or a ring radius. We also study the dynamics of a vesicle with impurities coupled to the membrane curvature. The phase separation and the associated shape deformation in the early stage of the dynamical evolution can well be explained by the linear stability analysis. Long runs of simulation demonstrate the nonlinear coarsening of the wavy deformation of the vesicle in the late stage.

cond-mat.soft↗

arXiv2000

Analysis of immune network dynamical system model with small number of degrees of freedom

We numerically study a dynamical system model of an idiotypic immune network with a small number of degrees of freedom. The model was originally introduced by Varela et.al., and describes antibodies interacting in a body in order to prepare for the invasion of external antigens. The main purpose of this paper is to investigate the direction of change in the network system when antigens invade it. We investigate three models, original model, a modified model and a modified model with a threshold of concentration over which each antibody can recognize other antibodies. In all these models, both chaotic and periodic states exist. In particular, we find peculiar states organized in the network, the clustering state.

nlin.CD↗

arXiv2001

Response to Invasion by Antigen and Effects of Threshold in an Immune Network Dynamical System Model with a Small Number of Degrees of Freedom

We study a dynamical system model of an idiotypic immune network with a small number of degrees of freedom, mainly focusing on the effect of a threshold above which antibodies can recognise antibodies. The response of the system to invasions by antigens is investigated in the both models with and without the threshold and it turns out that the system changes in a desirable direction for moderate magnitude of perturbation. direction for moderate magnitude of perturbation. Also, the propagation of disturbance by an antigen is investigated in the system of one-dimensionally connected basic units taking the closed 3-clone system as a unit, and it is clarified that the threshold of the system has effects to enhance the stability of the network and to localise the immune response.

cond-mat↗

arXiv2003

Spectral Statistics of RR Intervals in ECG

The statistical properties (fluctuations) of heartbeat intervals (RR intervals) in ECG are studied and compared with the predictions of Random Matrix Theory (RMT). It is found that heartbeat intervals only locally exhibit the fluctuation patterns (universality) predicted by the RMT. This finding shows that heartbeat dynamics is of the mixed type where regular and irregular (chaotic) regimes coexist and the Berry-Robnik theory can be applied. It is also observed that the distribution of heartbeat intervals is well described by the one-parameter Brody distribution. The parameter $β$ of the Brody distribution is seen to be connected with the dynamical state of the heart.

physics.med-ph↗

arXiv2001

Molecular Theory of Hydrophobic Effects: ``She is too mean to have her name repeated.''

This paper reviews the molecular theory of hydrophobic effects relevant to biomolecular structure and assembly in aqueous solution. Recent progress has resulted in simple, validated molecular statistical thermodynamic theories and clarification of confusing theories of decades ago. Current work is resolving effects of wider variations of thermodynamic state, e.g. pressure denaturation of soluble proteins, and more exotic questions such as effects of surface chemistry in treating stability of macromolecular structures in aqueous solution

physics.chem-ph↗

arXiv2002

Individual-based lattice model for spatial spread of epidemics

We present a lattice gas cellular automaton (LGCA) to study spatial and temporal dynamics of an epidemic of SIR (susceptible-infected-removed) type. The automaton is fully discrete, i.e. space, time and number of individuals are discrete variables. The automaton can be applied to study spread of epidemics in both human and animal populations. We investigate effects of spatial inhomogeneities in initial distribution of infected and vaccinated populations on the dynamics of epidemic of SIR type. We discuss vaccination strategies which differ only in spatial distribution of vaccinated individuals. Also, we derive an approximate, mean-field type description of the automaton, and discuss differences between the mean-field dynamics and the results of LGCA simulation.

nlin.CG↗

arXiv1996

Direct Determination of DNA Twist-Stretch Coupling

The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this important material parameter. We extract its value from a recent experiment of Strick et al. [Science 271 (1996) 1835] and find rough agreement with an independent experimental estimate recently given by Marko. We also present a very simple microscopic theory predicting a value comparable to the one observed.

cond-mat.soft↗

arXiv1997

Stochastic Feedback and the Regulation of Biological Rhythms

We propose a general approach to the question of how biological rhythms spontaneously self-regulate, based on the concept of ``stochastic feedback''. We illustrate this approach by considering the neuroautonomic regulation of the heart rate. The model generates complex dynamics and successfully accounts for key characteristics of cardiac variability, including the $1/f$ power spectrum, the functional form and scaling of the distribution of variations, and correlations in the Fourier phases. Our results suggest that in healthy systems the control mechanisms operate to drive the system away from extreme values while not allowing it to settle down to a constant output.

cond-mat.stat-mech↗

arXiv1999

The role of long-range forces in the phase behavior of colloids and proteins

The phase behavior of colloid-polymer mixtures, and of solutions of globular proteins, is often interpreted in terms of a simple model of hard spheres with short-ranged attraction. While such a model yields a qualitative understanding of the generic phase diagrams of both colloids and proteins, it fails to capture one important difference: the model predicts fluid-fluid phase separation in the metastable regime below the freezing curve. Such demixing has been observed for globular proteins, but for colloids it appears to be pre-empted by the appearance of a gel. In this paper, we study the effect of additional long-range attractions on the phase behavior of spheres with short-ranged attraction. We find that such attractions can shift the (metastable) fluid-fluid critical point out of the gel region. As this metastable critical point may be important for crystal nucleation, our results suggest that long-ranged attractive forces may play an important role in the crystallization of globular proteins. However, in colloids, where refractive index matching is often used to switch off long-ranged dispersion forces, gelation is likely to inhibit phase separation.

cond-mat.soft↗

arXiv1999

Evolution dynamics in terraced NK landscapes

We study populations of agents evolving in fitness landscapes constructed according to the rules of a modified NK model with a tunable amount of neutral paths. In the `punctuated equilibrium' regime evolutionary events are identified as jumps in the mean population fitness, and the statistics of these jumps in an ensemble of independently evolving populations is analyzed. We show that, for a wide range of landscapes parameters, the number of events in time t is Poisson distributed, with the time parameter replaced by the logarithm of time. This simple log-Poisson statistics likewise describes the number n of records in any sequence of t independently generated random numbers. The implications of this behavior for evolution dynamics are discussed.

adap-org↗

arXiv1999

Sleep-Wake Differences in Scaling Behavior of the Human Heartbeat: Analysis of Terrestrial and Long-Term Space Flight Data

We compare scaling properties of the cardiac dynamics during sleep and wake periods for healthy individuals, cosmonauts during orbital flight, and subjects with severe heart disease. For all three groups, we find a greater degree of anticorrelation in the heartbeat fluctuations during sleep compared to wake periods. The sleep-wake difference in the scaling exponents for the three groups is comparable to the difference between healthy and diseased individuals. The observed scaling differences are not accounted for simply by different levels of activity, but appear related to intrinsic changes in the neuroautonomic control of the heartbeat.

cond-mat.stat-mech↗

arXiv1999

Modelling Molecular Motors as Folding-Unfolding Cycles

We propose a model for motor proteins based on a hierarchical Hamiltonian that we have previously introduced to describe protein folding. The proposed motor model has high efficiency and is consistent with a linear load-velocity response. The main improvement with respect to previous models is that this description suggests a connection between folding and function of allosteric proteins.

cond-mat↗

arXiv2001

Warm and Cold Denaturation in the Phase Diagram of a Protein Lattice Model

Studying the properties of the solvent around proteins, we propose a much more sophisticated model of solvation than temperature-independent pairwise interactions between monomers, as is used commonly in lattice representations. We applied our model of solvation to a 16-monomer chain constrained on a two-dimensional lattice. We compute a phase diagram function of the temperature and a solvent parameter which is related to the pH of the solution. It exhibits a native state in which the chain coalesces into a unique compact conformation as well as a denatured state. Under certain solvation conditions, both warm and cold denaturations occur between the native and the denatured states. A good agreement is found with the data obtained from calorimetric experiments, thereby validating the proposed model.

cond-mat.soft↗

arXiv2001

A simple model for DNA denaturation

Following Poland and Scheraga, we consider a simplified model for the denaturation transition of DNA. The two strands are modeled as interacting polymer chains. The attractive interactions, which mimic the pairing between the four bases, are reduced to a single short range binding term. Furthermore, base-pair misalignments are forbidden, implying that this binding term exists only for corresponding (same curvilinear abscissae) monomers of the two chains. We take into account the excluded volume repulsion between monomers of the two chains, but neglect intra-chain repulsion. We find that the excluded volume term generates an effective repulsive interaction between the chains, which decays as $1/r^{d-2}$. Due to this long-range repulsion between the chains, the denaturation transition is first order in any dimension, in agreement with previous studies.

cond-mat.soft↗

arXiv2001

Stochastic resonance as a collective property of ion channel assemblies

By use of a stochastic generalization of the Hodgkin-Huxley model we investigate both the phenomena of stochastic resonance (SR) and coherence resonance (CR) in variable size patches of an excitable cell membrane. Our focus is on the challenge how internal noise stemming from individual ion channels does affect collective properties of the whole ensemble. We investigate both an unperturbed situation with no applied stimuli and one in which the membrane is stimulated externally by a periodic signal and additional external noise. For the nondriven case, we demonstrate the existence of an optimal size of the membrane patch for which the internal noise causes a most regular spike activity. This phenomenon shall be termed intrinsic CR. In presence of an applied periodic stimulus we demonstrate that the signal-to-noise ratio (SNR) exhibits SR vs. decreasing patch size, or vs. increasing internal noise strength, respectively. Moreover, we demonstrate that conventional SR vs. the external noise intensity occurs only for sufficiently large membrane patches, when the intensity of internal noise is below its optimal level. Thus, biological SR seemingly is rooted in the collective properties of large ion channel ensembles rather than in the individual stochastic dynamics of single ion channels.

physics.bio-ph↗

arXiv2001

Differentiation and Replication of Spots in a Reaction Diffusion System with Many Chemicals

The replication and differentiation of spots in reaction diffusion equations are studied by extending the Gray-Scott model with self-replicating spots to include many degrees of freedom needed to model systems with many chemicals. By examining many possible reaction networks, the behavior of this model is categorized into three types: replication of homogeneous fixed spots, replication of oscillatory spots, and differentiation from `m ultipotent spots'. These multipotent spots either replicate or differentiate into other types of spots with different fixed-point dynamics, and as a result, an inhomogeneous pattern of spots is formed. This differentiation process of spots is analyzed in terms of the loss of chemical diversity and decrease of the local Kolmogorov-Sinai entropy. The relevance of the results to developmental cell biology and stem cells is also discussed.

nlin.PS↗

arXiv2001

Relaxation kinetics of biological dimer adsorption models

We discuss the relaxation kinetics of a one-dimensional dimer adsorption model as recently proposed for the binding of biological dimers like kinesin on microtubules. The non-equilibrium dynamics shows several regimes: irreversible adsorption on short time scales, an intermediate plateau followed by a power-law regime and finally exponential relaxation towards equilibrium. In all four regimes we give analytical solutions. The algebraic decay and the scaling behaviour can be explained by mapping onto a simple reaction-diffusion model. We show that there are several possibilities to define the autocorrelation function and that they all asymptotically show exponential decay, however with different time constants. Our findings remain valid if there is an attractive interaction between bound dimers.

cond-mat.soft↗

arXiv2002

Folding dynamics of the helical structures in a minimal model

The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial denatured state. The Monte Carlo implementation of a recent helix-forming model enables us to study the entire folding process dynamically. As shown by the computer simulations, the foldability and helical propagation are both strongly correlated to the nucleation properties of the sequence.

cond-mat.soft↗