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At least 1,153 records · Page 64Linked to original sources

arXiv2003

Recoverable prevalence in growing scale-free networks and the effective immunization

We study the persistent recoverable prevalence and the extinction of computer viruses via e-mails on a growing scale-free network with new users, which structure is estimated form real data. The typical phenomenon is simulated in a realistic model with the probabilistic execution and detection of viruses. Moreover, the conditions of extinction by random and targeted immunizations for hubs are derived through bifurcation analysis for simpler models by using a mean-field approximation without the connectivity correlations. We can qualitatively understand the mechanisms of the spread in linearly growing scale-free networks.

cond-mat.stat-mech↗

arXiv2003

Recurrent biological neural networks: The weak and noisy limit

A perturbative method is developed for calculating the effects of recurrent synaptic interactions between neurons embedded in a network. A series expansion is constructed that converges for networks with noisy membrane potential and weak synaptic connectivity. The terms of the series can be interpreted as loops of interactions between neurons, so the technique is called a loop-expansion. A diagrammatic method is introduced that allows for construction of analytic expressions for the parameter dependencies of the spike probability function and correlation functions. An analytic expression is obtained to predict the effect of the surrounding network on a neuron during an intracellular current injection. The analytic results are compared with simulations to test the range of their validity and significant effects of the the recurrent connections in network are accurately predicted by the loop-expansion.

cond-mat.dis-nn↗

arXiv2003

Electrokinetic behavior of two touching inhomogeneous biological cells and colloidal particles: Effects of multipolar interactions

We present a theory to investigate electro-kinetic behavior, namely, electrorotation and dielectrophoresis under alternating current (AC) applied fields for a pair of touching inhomogeneous colloidal particles and biological cells. These inhomogeneous particles are treated as graded ones with physically motivated model dielectric and conductivity profiles. The mutual polarization interaction between the particles yields a change in their respective dipole moments, and hence in the AC electrokinetic spectra. The multipolar interactions between polarized particles are accurately captured by the multiple images method. In the point-dipole limit, our theory reproduces the known results. We find that the multipolar interactions as well as the spatial fluctuations inside the particles can affect the AC electrokinetic spectra significantly.

cond-mat.soft↗

arXiv2005

Analytical description of finite size effects for RNA secondary structures

The ensemble of RNA secondary structures of uniform sequences is studied analytically. We calculate the partition function for very long sequences and discuss how the cross-over length, beyond which asymptotic scaling laws apply, depends on thermodynamic parameters. For realistic choices of parameters this length can be much longer than natural RNA molecules. This has to be taken into account when applying asymptotic theory to interpret experiments or numerical results.

physics.bio-ph↗

arXiv2005

Systematic identification of statistically significant network measures

We present a novel graph embedding space (i.e., a set of measures on graphs) for performing statistical analyses of networks. Key improvements over existing approaches include discovery of "motif-hubs" (multiple overlapping significant subgraphs), computational efficiency relative to subgraph census, and flexibility (the method is easily generalizable to weighted and signed graphs). The embedding space is based on {\it scalars}, functionals of the adjacency matrix representing the network. {\it Scalars} are global, involving all nodes; although they can be related to subgraph enumeration, there is not a one-to-one mapping between scalars and subgraphs. Improvements in network randomization and significance testing--we learn the distribution rather than assuming gaussianity--are also presented. The resulting algorithm establishes a systematic approach to the identification of the most significant scalars and suggests machine-learning techniques for network classification.

cond-mat.dis-nn↗

arXiv2004

A Complex Network Approach to Topographical Connections

The neuronal networks in the mammals cortex are characterized by the coexistence of hierarchy, modularity, short and long range interactions, spatial correlations, and topographical connections. Particularly interesting, the latter type of organization implies special demands on the evolutionary and ontogenetic systems in order to achieve precise maps preserving spatial adjacencies, even at the expense of isometry. Although object of intensive biological research, the elucidation of the main anatomic-functional purposes of the ubiquitous topographical connections in the mammals brain remains an elusive issue. The present work reports on how recent results from complex network formalism can be used to quantify and model the effect of topographical connections between neuronal cells over a number of relevant network properties such as connectivity, adjacency, and information broadcasting. While the topographical mapping between two cortical modules are achieved by connecting nearest cells from each module, three kinds of network models are adopted for implementing intracortical connections (ICC), including random, preferential-attachment, and short-range networks. It is shown that, though spatially uniform and simple, topographical connections between modules can lead to major changes in the network properties, fostering more effective intercommunication between the involved neuronal cells and modules. The possible implications of such effects on cortical operation are discussed.

cond-mat.dis-nn↗

arXiv2005

A steepest descent calculation of RNA pseudoknots

We enumerate possible topologies of pseudoknots in single-stranded RNA molecules. We use a steepest-descent approximation in the large N matrix field theory, and a Feynman diagram formalism to describe the resulting pseudoknot structure.

physics.bio-ph↗

arXiv1995

Elasticity of Semiflexible Biopolymer Networks

We develop a model for gels and entangled solutions of semiflexible biopolymers such as F-actin. Such networks play a crucial structural role in the cytoskeleton of cells. We show that the rheologic properties of these networks can result from nonclassical rubber elasticity. This model can explain a number of elastic properties of such networks {\em in vitro}, including the concentration dependence of the storage modulus and yield strain.

cond-mat↗

arXiv1996

Competing Patterns of Signaling Activity in Dictyostelium discoideum

Quantitative experiments are described on spatio-temporal patterns of coherent chemical signaling activity in populations of {\it Dictyostelium discoideum} amoebae. We observe competition between spontaneously firing centers and rotating spiral waves that depends strongly on the overall cell density. At low densities, no complete spirals appear and chemotactic aggregation is driven by periodic concentric waves, whereas at high densities the firing centers seen at early times nucleate and are apparently entrained by spiral waves whose cores ultimately serve as aggregation centers. Possible mechanisms for these observations are discussed.

cond-mat↗

arXiv1995

A New Algorithm for Protein Design

We apply a new approach to the reverse protein folding problem. Our method uses a minimization function in the design process which is different from the energy function used for folding. For a lattice model, we show that this new approach produces sequences that are likely to fold into desired structures. Our method is a significant improvement over previous attempts which used the energy function for designing sequences.

cond-mat↗

arXiv1996

Is Heteropolymer Freezing Well Described by the Random Energy Model?

It is widely held that the Random Energy Model (REM) describes the freezing transition of a variety of types of heteropolymers. We demonstrate that the hallmark property of REM, statistical independence of the energies of states over disorder, is violated in different ways for models commonly employed in heteropolymer freezing studies. The implications for proteins are also discussed.

cond-mat↗

arXiv1996

Reply to Comment on "Criterion that Determines the Foldability of Proteins"

We point out that the correlation between folding times and $σ= (T_{θ} - T_{f})/T_{θ}$ in protein-like heteropolymer models where $T_{θ}$ and $T_{f}$ are the collapse and folding transition temperatures was already established in 1993 before the other presumed equivalent criterion (folding times correlating with $T_{f}$ alone) was suggested. We argue that the folding times for these models show no useful correlation with the energy gap even if restricted to the ensemble of compact structures as suggested by Karplus and Shakhnovich (cond-mat/9606037).

cond-mat↗

arXiv1996

Branching Processes and Evolution at the Ends of a Food Chain

In a critically self--organized model of punctuated equilibrium, boundaries determine peculiar scaling of the size distribution of evolutionary avalanches. This is derived by an inhomogeneous generalization of standard branching processes, extending previous mean field descriptions and yielding $ν=1/2$ together with $τ'=7/4$, as distribution exponent of avalanches starting from species at the ends of a food chain. For the nearest neighbor chain one obtains numerically $τ'=1.25 \pm 0.01$, and $τ'_{first}=1.35 \pm 0.01$ for the first return times of activity, again distinct from bulk exponents.

cond-mat↗

arXiv1995

Entropic Barriers, Frustration and Order: Basic Ingredients in Protein Folding

We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this state is reached in a time that scales as $M^λ$, with $λ\simeq 3$. This scaling is limited by the amount of frustration which leads to the dynamical selectivity of proteins: foldable proteins are limited to $\sim 300$ monomers; and they are stable in {\it one} range of temperatures, independent of size and structure. These predictions explain generic properties of {\it in vivo} proteins.

cond-mat↗

arXiv1996

Freezing Transition of Compact Polyampholytes

Polyampholytes (PAs) are heteropolymers with long range Coulomb interactions. Unlike polymers with short range forces, PA energy levels have non-vanishing correlations and are thus very different from the Random Energy Model (REM). Nevertheless, if charges in the PA globule are screened as in a regular plasma, PAs freeze in REM fashion. Our results shed light on the potential role of Coulomb interactions in folding and evolution of {\it proteins}, which are weakly charged PAs, in particular making connection with the finding that sequences of charged amino acids in proteins are not random.

cond-mat↗

arXiv1996

Chain length scaling of protein folding time

Folding of protein-like heteropolymers into unique 3D structures is investigated using Monte Carlo simulations on a cubic lattice. We found that folding time of chains of length $N$ scales as $N^λ$ at temperature of fastest folding. For chains with random sequences of monomers $λ\approx 6$, and for chains with sequences designed to provide a pronounced minimum of energy to their ground state conformation $λ\approx 4$. Folding at low temperatures exhibits an Arrhenius-like behavior with the energy barrier $E_b \approx ϕ|E_n|$, where $E_n$ is the energy of the native conformation. $ϕ\approx 0.18$ both for random and designed sequences.

cond-mat↗

arXiv1996

Traveling-Wave Chemotaxis

A simple model is studied for the chemotactic movement of biological cells in the presence of a periodic chemical wave. It incorporates the feature of adaptation that may play an important role in allowing for ``rectified" chemotaxis: motion opposite the direction of wave propagation. The conditions under which such rectification occurs are elucidated in terms of the form and speed of the chemical wave, the velocity of chemotaxis, and the time scale for adaptation. An experimental test of the adaptation dynamics is proposed.

cond-mat↗

arXiv1997

Stability Threshold as a Selection Principle for Protein Design

The sensitivity of the native states of protein-like heteropolymers to mutations modelled as perturbations in the interaction potential between amino acids is studied. The stability threshold against mutations is shown to be zero for random heteropolymers on a lattice in two dimensions, whereas a design procedure modelling evolution produces a non-zero threshold. We introduce an evolution-like protein design procedure based on an optimization of the stability threshold that is shown to naturally ensure thermodynamic stability as well.

cond-mat.soft↗