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At least 1,243 records · Page 69Linked to original sources
arXiv2001

The shape of ecological networks

We study the statistics of ecosystems with a variable number of co-evolving species. The species interact in two ways: by prey-predator relationships and by direct competition with similar kinds. The interaction coefficients change slowly through successful adaptations and speciations. We treat them as quenched random variables. These interactions determine long-term topological features of the species network, which are found to agree with those of biological systems.

nlin.AO↗
arXiv2001

Mutual Information of Population Codes and Distance Measures in Probability Space

We studied the mutual information between a stimulus and a large system consisting of stochastic, statistically independent elements that respond to a stimulus. The Mutual Information (MI) of the system saturates exponentially with system size. A theory of the rate of saturation of the MI is developed. We show that this rate is controlled by a distance function between the response probabilities induced by different stimuli. This function, which we term the {\it Confusion Distance} between two probabilities, is related to the Renyi $α$-Information.

cond-mat.stat-mech↗
arXiv2001

Behavioral-Independent Features of Complex Heartbeat Dynamics

We test whether the complexity of cardiac interbeat interval time series is simply a consequence of the wide range of scales characterizing human behavior, especially physical activity, by analyzing data taken from healthy adult subjects under three conditions with controls: (i) a ``constant routine'' protocol where physical activity and postural changes are kept to a minimum, (ii) sympathetic blockade, and (iii) parasympathetic blockade. We find that when fluctuations in physical activity and other behavioral modifiers are minimized, a remarkable level of complexity of heartbeat dynamics remains, while for neuroautonomic blockade the multifractal complexity decreases.

cond-mat.stat-mech↗
arXiv2001

The future is noisy: on the role of spatial fluctuations in genetic switching

A genetic switch may be realised by a certain operator sector on the DNA strand from which either genetic code, to the left or to the right of this operator sector, can be transcribed and the corresponding information processed. This switch is controlled by messenger molecules, i.e., they determine to which side the switch is flipped. Recently, it has been realised that noise plays an elementary role in genetic switching, and the effect of number fluctuations of the messenger molecules have been explored. Here we argue that the assumption of well-stirredness taken in the previous models may not be sufficient to characterise the influence of noise: {\em spatial} fluctuations play a non-negligible part in cellular genetic switching processes.

cond-mat.stat-mech↗
arXiv2001

Noise Effects on the Complex Patterns of Abnormal Heartbeats

Patients at high risk for sudden death often exhibit complex heart rhythms in which abnormal heartbeats are interspersed with normal heartbeats. We analyze such a complex rhythm in a single patient over a 12-hour period and show that the rhythm can be described by a theoretical model consisting of two interacting oscillators with stochastic elements. By varying the magnitude of the noise, we show that for an intermediate level of noise, the model gives best agreement with key statistical features of the dynamics.

cond-mat.stat-mech↗
arXiv2001

Free Energy Self-Averaging in Protein-Sized Random Heteropolymers

Current theories of heteropolymers are inherently macrpscopic, but are applied to folding proteins which are only mesoscopic. In these theories, one computes the averaged free energy over sequences, always assuming that it is self-averaging -- a property well-established only if a system with quenched disorder is macroscopic. By enumerating the states and energies of compact 18, 27, and 36mers on a simplified lattice model with an ensemble of random sequences, we test the validity of the self-averaging approximation. We find that fluctuations in the free energy between sequences are weak, and that self-averaging is a valid approximation at the length scale of real proteins. These results validate certain sequence design methods which can exponentially speed up computational design and greatly simplify experimental realizations.

cond-mat.soft↗
arXiv2001

Active Fusion and Fission Processes on a Fluid Membrane

We investigate the steady states and dynamical instabilities resulting from ``particles'' depositing on (fusion) and pinching off (fission) a fluid membrane. These particles could be either small lipid vesicles or isolated proteins. In the stable case, such fusion/fission events suppress long wavelength fluctuations of the membrane. In the unstable case, the membrane shoots out long tubular structures reminiscent of endosomal compartments or folded structures as in internal membranes like the endoplasmic reticulum or Golgi. We argue that these fusion/fission events should be strongly affected by tension.

cond-mat.soft↗
arXiv2001

Swarming ring patterns in bacterial colonies exposed to ultraviolet radiation

We report a novel morphological transition in a Bacillus subtilis colony initially growing under ambient conditions, after ultraviolet radiation exposure. The bacteria in the central regions of the colonies are observed to migrate towards the colony edge forming a ring during uniform spatial exposure. When the radiation is switched off, the colonies were observed to grow both inward into the evacuated regions as well as outward indicating that the pattern is not formed due to depletion of nutrients at the center of the colony. We also propose a reaction-diffusion model in which waste-limited chemotaxis initiated by the UV radiation leads to the observed phenomenology.

cond-mat↗
arXiv2000

On the Dynamics of the Evolution of the HIV Infection

We use a cellular automata model to study the evolution of HIV infection and the onset of AIDS. The model takes into account the global features of the immune response to any pathogen, the fast mutation rate of the HIV and a fair amount of spatial localization. Our results reproduce quite well the three-phase pattern observed in T cell and virus counts of infected patients, namely, the primary response, the clinical latency period and the onset of AIDS. We have also found that the infected cells may organize themselves into special spatial structures since the primary infection, leading to a decrease on the concentration of uninfected cells. Our results suggest that these cell aggregations, which can be associated to syncytia, leads to AIDS.

cond-mat.stat-mech↗
arXiv2000

Scale Invariance in the Nonstationarity of Physiological Signals

We introduce a segmentation algorithm to probe temporal organization of heterogeneities in human heartbeat interval time series. We find that the lengths of segments with different local values of heart rates follow a power-law distribution. This scale-invariant structure is not a simple consequence of the long-range correlations present in the data. We also find that the differences in mean heart rates between consecutive segments display a common functional form, but with different parameters for healthy individuals and for patients with heart failure. This finding may provide information into the way heart rate variability is reduced in cardiac disease.

cond-mat.stat-mech↗
arXiv2001

Predictability of large future changes in a competitive evolving population

The dynamical evolution of many economic, sociological, biological and physical systems tends to be dominated by a relatively small number of unexpected, large changes (`extreme events'). We study the large, internal changes produced in a generic multi-agent population competing for a limited resource, and find that the level of predictability actually increases prior to a large change. These large changes hence arise as a predictable consequence of information encoded in the system's global state.

cond-mat.dis-nn↗
arXiv2001

Dynamical scaling of the DNA unzipping transition

We report studies of the equilibrium and the dynamics of a general set of lattice models which capture the essence of the force-induced or mechanical DNA unzipping transition. Besides yielding the whole equilibrium phase diagram in the force vs temperature plane, which reveals the presence of an interesting re-entrant unzipping transition for low T, these models enable us to characterize the dynamics of the process starting from a non-equilibrium initial condition. The thermal melting of the DNA strands displays a model dependent time evolution. On the contrary, our results suggest that the dynamical mechanism for the unzipping by force is very robust and the scaling behaviour does not depend on the details of the description we adopt.

cond-mat.soft↗
arXiv2001

Epigenetics as a first exit problem

We develop a framework to discuss stability of epigenetic states as first exit problems in dynamical systems with noise. We consider in particular the stability of the lysogenic state of the lambda prophage, which is known to exhibit exceptionally large stability. The formalism defines a quantative measure of robustness of inherited states. In contrast to Kramers' well-known problem of escape from a potential well, the stability of inherited states in our formulation is not a numerically trivial problem. The most likely exit path does not go along a steepest decent of a potential -- there is no potential. Instead, such a path can be described as a zero-energy trajectory between two equilibria in an auxiliary classical mechanical system. Finding it is similar to e.g. computing heteroclinic orbits in celestial mechanics. The overall lesson of this study is that an examination of equilibria and their bifurcations with changing parameter values allow us to quantify both the stability and the robustness of particular states of a genetic control system.

cond-mat.soft↗
arXiv2001

Tilt Texture Domains on a Membrane and Chirality induced Budding

We study the equilibrium conformations of a lipid domain on a planar fluid membrane where the domain is decorated by a vector field representing the tilt of the stiff fatty acid chains of the lipid molecules, while the surrounding membrane is fluid and structureless. The inclusion of chirality in the bulk of the domain induces a novel budding of the membrane, which preempts the budding induced by a decrease in interfacial tension.

cond-mat.soft↗
arXiv2002

Neural Network Model for Apparent Deterministic Chaos in Spontaneously Bursting Hippocampal Slices

A neural network model that exhibits stochastic population bursting is studied by simulation. First return maps of inter-burst intervals exhibit recurrent unstable periodic orbit (UPO)-like trajectories similar to those found in experiments on hippocampal slices. Applications of various control methods and surrogate analysis for UPO-detection also yield results similar to those of experiments. Our results question the interpretation of the experimental data as evidence for deterministic chaos and suggest caution in the use of UPO-based methods for detecting determinism in time-series data.

cond-mat.dis-nn↗
arXiv2002

Roles of stiffness and excluded volume in DNA denaturation

The nature and the universal properties of DNA thermal denaturation are investigated by Monte Carlo simulations. For suitable lattice models we determine the exponent c describing the decay of the probability distribution of denaturated loops of length l, $P \sim l^{-c}$. If excluded volume effects are fully taken into account, c= 2.10(4) is consistent with a first order transition. The stiffness of the double stranded chain has the effect of sharpening the transition, if it is continuous, but not of changing its order and the value of the exponent c, which is also robust with respect to inclusion of specific base-pair sequence heterogeneities.

cond-mat.stat-mech↗
arXiv2002

Robust Patterns in Food Web Structure

We analyze the properties of seven community food webs from a variety of environments--including freshwater, marine-freshwater interfaces and terrestrial environments. We uncover quantitative unifying patterns that describe the properties of the diverse trophic webs considered and suggest that statistical physics concepts such as scaling and universality may be useful in the description of ecosystems. Specifically, we find that several quantities characterizing these diverse food webs obey functional forms that are universal across the different environments considered. The empirical results are in remarkable agreement with the analytical solution of a recently proposed model for food webs.

cond-mat.dis-nn↗