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At least 343 records · Page 19Linked to original sources

arXiv1999

Self-Organization of Complex Systems

The basic laws of physics are simple, so why is the world complex? The theory of self-organized criticality posits that complex behavior in nature emerges from the dynamics of extended, dissipative systems that evolve through a sequence of meta-stable states into a critical state, with long range spatial and temporal correlations. Minor disturbances lead to intermittent events of all sizes. These events organize the system into a complex state that cannot be reduced to a few degrees of freedom. This type of ``punctuated equilibrium'' dynamics has been observed in astrophysical, geophysical, and biological processes, as well as in human social activity.

cond-mat.stat-mech↗

arXiv1999

Simulation and Experimental Investigation of Cellular Material Breakage Using the Pulsed Electric Field Treatment

We consider the simplified dielectric breakage model used for simulation of the kinetics of cellular material breakage under the pulsed electric field (PEF) treatment. The model is based on an effective media approximation, which includes equations with the same morphology parameters as in percolation theory. The probability of a whole cell breakage by the pulse with $t_{i}$ duration is estimated on the basis of electroporation theory. We account for the bridging effect resulting from the deviations of the local conductivity near the selected cell from the average effective media conductivity. The most important feature of the proposed model is the existence of the ``jamming'' behaviour occurring sometimes in experimental observations of the biological tissue breakage. The different transitions corresponding to the ``jamming'' steps are identified. The experimental results are obtained for thin apple slices treated with electric pulses at field strengths $E=0.2-2.2$ kV cm$^{-1}$, pulse durations $t_{i}=10-100$ $μ$s, pulse repetition times $t=10-100$ ms and the number of pulses $N=1-100000$. The model gives results consistent in general with the experimental observations. We discuss the correlation between the degree of cellular material destruction, field strength, time of PEF treatment and power consumption.

cond-mat.stat-mech↗

arXiv1999

Ocular dominance patterns in mammalian visual cortex: A wire length minimization approach

We propose a theory for ocular dominance (OD) patterns in mammalian primary visual cortex. This theory is based on the premise that OD pattern is an adaptation to minimize the length of intra-cortical wiring. Thus we can understand the existing OD patterns by solving a wire length minimization problem. We divide all the neurons into two classes: left-eye dominated and right-eye dominated. We find that segregation of neurons into monocular regions reduces wire length if the number of connections with the neurons of the same class differs from that with the other class. The shape of the regions depends on the relative fraction of neurons in the two classes. If the numbers are close we find that the optimal OD pattern consists of interdigitating stripes. If one class is less numerous than the other, the optimal OD pattern consists of patches of the first class neurons in the sea of the other class neurons. We predict the transition from stripes to patches when the fraction of neurons dominated by the ipsilateral eye is about 40%. This prediction agrees with the data in macaque and Cebus monkeys. This theory can be applied to other binary cortical systems.

cond-mat.soft↗

arXiv1999

Optimal sizes of dendritic and axonal arbors in a topographic projection

I consider a topographic projection between two neuronal layers with different densities of neurons. Given the number of output neurons connected to each input neuron (divergence) and the number of input neurons synapsing on each output neuron (convergence) I determine the widths of axonal and dendritic arbors which minimize the total volume of axons and dendrites. Analytical results for one-dimensional and two-dimensional projections can be summarized qualitatively in the following rule: neurons of the sparser layer should have arbors wider than those of the denser layer. This agrees with the anatomical data from retinal and cerebellar neurons whose morphology and connectivity are known. The rule may be used to infer connectivity of neurons from their morphology.

cond-mat.dis-nn↗

arXiv1999

Binocular disparity can explain the orientation of ocular dominance stripes in primate V1

In the primate primary visual area (V1), the ocular dominance pattern consists of alternating monocular stripes. Stripe orientation follows systematic trends preserved across several species. I propose that these trends result from minimizing the length of intra-cortical wiring needed to recombine information from the two eyes in order to achieve the perception of depth. I argue that the stripe orientation at any point of V1 should follow the direction of binocular disparity in the corresponding point of the visual field. The optimal pattern of stripes determined from this argument agrees with the ocular dominance pattern of macaque and Cebus monkeys. This theory predicts that for any point in the visual field the limits of depth perception are greatest in the direction along the ocular dominance stripes at that point.

cond-mat.dis-nn↗

arXiv1999

From Car Parking to Protein Adsorption: An Overview of Sequential Adsorption Processes

The adsorption or adhesion of large particles (proteins, colloids, cells, >...) at the liquid-solid interface plays an important role in many diverse applications. Despite the apparent complexity of the process, two features are particularly important: 1) the adsorption is often irreversible on experimental time scales and 2) the adsorption rate is limited by geometric blockage from previously adsorbed particles. A coarse-grained description that encompasses these two properties is provided by sequential adsorption models whose simplest example is the random sequential adsorption (RSA) process. In this article, we review the theoretical formalism and tools that allow the systematic study of kinetic and structural aspects of these sequential adsorption models. We also show how the reference RSA model may be generalized to account for a variety of experimental features including particle anisotropy, polydispersity, bulk diffusive transport, gravitational effects, surface-induced conformational and orientational change, desorption, and multilayer formation. In all cases, the significant theoretical results are presented and their accuracy (compared to computer simulation) and applicability (compared to experiment) are discussed.

cond-mat.stat-mech↗

arXiv1999

Monte Carlo procedure for protein folding in lattice model. Conformational rigidity

A rigourous Monte Carlo method for protein folding simulation on lattice model is introduced. We show that a parameter which can be seen as the rigidity of the conformations has to be introduced in order to satisfy the detailed balance condition. Its properties are discussed and its role during the folding process is elucidated. This method is applied on small chains on two-dimensional lattice. A Bortz-Kalos-Lebowitz type algorithm which allows to study the kinetic of the chains at very low temperature is implemented in the presented method. We show that the coefficients of the Arrhenius law are in good agreement with the value of the main potential barrier of the system.

cond-mat.soft↗

arXiv1999

Generic growth instabilities in one-layered tissue sheets

Growth and folding in one-layered model tissue sheets are studied in a stochastic, lattice-free single cell model which considers the discrete cellular structure of the tissue, and a coarse grained analytical approach. The polarity of the tissue sheet is considered by a bending term. Cell division gives rise to a locally increasing metric. An exponential and a power-law growth regime are identified. In both regimes folding occurs as soon as the bending contribution becomes too small to compensate the destabilizing effect of the cell proliferation. The potential biological relevance is discussed.

cond-mat.stat-mech↗

arXiv1999

Can pulling cause right- to left-handed structural transitions in negatively supercoiled DNA double-helix?

The folding angle distribution of stretched and negatively supercoiled DNA double-helix is investigated based on a theoretical model we proposed earlier [H. Zhou et al., Phys. Rev. Lett. 82, 4560 (1999)]. It is shown that pulling can transit a negatively supercoiled DNA double-helix from the right-handed B-form to a left-handed configuration which resembles DNA Z-form in some important respects. The energetics of this possible transition is calculated and the comparison with recent experimental observations are qualitatively discussed.

cond-mat.soft↗

arXiv1999

Stable integration of isolated cell membrane patches in a nanomachined aperture: a step towards a novel device for membrane physiology

We investigate the microscopic contact of a cell/semiconductor hybrid. The semiconductor is nanostructured with the aim of single channel recording of ion channels in cell membranes. This approach will overcome many limitations of the classical patch-clamp technique. The integration of silicon-based devices 'on-chip' promises novel types of experiments on single ion channels.

cond-mat.soft↗

arXiv1999

Evolution of Fragments Formed at the Rupture of a Knotted Alkane Molecule

Common experience tells us that a knot significantly weakens the polymer strand in which it is tied, which in turn leads to more facile chain rupture under tensile loading. Using first-principles molecular dynamics calculations we describe the dynamical evolution of the radicals that form after chain rupture of a single knotted alkane molecule in their very early stages of life. They are able to recombine, to form cyclic alkanes and to undergo disproportionation phenomena with nearby chain segments. The breaking of a single knotted polymer chain under mechanical loading is thus predicted to reveal phenomena falling in the domain of ultrafast spectroscopy.

cond-mat.mtrl-sci↗

arXiv1999

Generalization in the Hopfield Model

In the Hopfield model the ability of the network to generalization is studied in the case of the network trained by one input image ({\it the standard}).

cond-mat.dis-nn↗

arXiv1999

Conformation changes and folding of proteins mediated by Davidov's soliton

We suggest that Davidov's solitons, propagating through the backbone of a protein, can mediate conformational transition and folding of a protein to its native state. A simple toy model is presented in which a Non Linear Schrodinger (NLS) field interacts with another field phi, corresponding to the conformation angles of the protein. The interaction provides the conformation field with the energy needed in order to overcome energy barriers for folding, thus avoiding the need for stochastic thermal activation. Such a transition is therefore a deterministic controled process.The soliton is compensated for its energy loss by absorption of the energy gained in the folding process. This scenario does not change significantly even in the presence of imposed disorder, provided that the initial momentum of the soliton is large enough.

cond-mat↗

arXiv1999

Instantons in the working memory: implications for schizophrenia

The influence of the synaptic channel properties on the stability of delayed activity maintained by recurrent neural network is studied. The duration of excitatory post-synaptic current (EPSC) is shown to be essential for the global stability of the delayed response. NMDA receptor channel is a much more reliable mediator of the reverberating activity than AMPA receptor, due to a longer EPSC. This allows to interpret the deterioration of working memory observed in the NMDA channel blockade experiments. The key mechanism leading to the decay of the delayed activity originates in the unreliability of the synaptic transmission. The optimum fluctuation of the synaptic conductances leading to the decay is identified. The decay time is calculated analytically and the result is confirmed computationally.

cond-mat.dis-nn↗

arXiv1999

A Model for Double-Stranded Excitations of DNA

We calculate the spectrum of torsional vibrations of a double-stranded structure that models the double helix of the DNA. We come to the conclusion that within the framework of the model elementary excitations may display an asymmetry as regards their winding and direction of the propagation, depending on initial polarization. The asymmetry could have a bearing on processes that take place in molecules of the DNA.

cond-mat.soft↗

arXiv1999

Self-localization of directed polymers and oppressive population control

We construct a phenomenological theory of self-localization of directed polymers in d+1 dimensions. In d=1 we show that the polymer is always self-localized, whereas in d=2 there is a phase transition between localized and free states. We also map this system to a model of population dynamics with fixed total population. Our previous results translate to static and expanding population clusters, depending on the birth and death rates. A novel ``pseudo-travelling wave'' is observed in some sectors of parameter space.

cond-mat.stat-mech↗

arXiv1999

Mixed state on a sparsely encoded associative memory model

In the present paper, we analyze symmetric mixed states corresponding to the so-called concept formation on a sparsely encoded associative memory model with 0-1 neurons. Three types of mixed states, OR, AND and a majority decision mixed state are described as typical examples. Each element of the OR mixed state is composed of corresponding memory pattern elements by means of the OR-operation. The other two types are similarly defined. By analyzing their stabilities through the SCSNA and the computer simulation, we found that the storage capacity of the OR mixed state diverges in the sparse limit, but that the other states do not diverge. In addition, we found that the optimal threshold values, which maximize the storage capacity, for the memory pattern and the OR mixed state coincide with each other in the spare limit. Thus, we conclude that the OR mixed state is a reasonable representative of the mixed state in the spare limit. Finally, the paper examines the relationship between our results and recently reported physiological findings regarding face-responsive neurons in the inferior temporal cortex.

cond-mat.dis-nn↗

arXiv1999

The Penna model for biological ageing on a lattice: spatial consequences of child-care

We introduce a square lattice into the Penna bit-string model for biological ageing and study the evolution of the spatial distribution of the population considering different strategies of child-care. Two of the strategies are related to the movements of a whole family on the lattice: in one case the mother cannot move if she has any child younger than a given age, and in the other case if she moves, she brings these young children with her. A stronger condition has also been added to the second case, considering that young children die with a higher probability if their mothers die, this probability decreasing with age. We show that a highly non uniform occupation can be obtained when child-care is considered, even for an uniform initial occupation per site. We also compare the standard survival rate of the model with that obtained when the spacial lattice is considered (without any kind of child-care).

cond-mat.stat-mech↗