Finding mesoscopic communities in sparse networks

We suggest a fast method to find possibly overlapping network communities of a desired size and link density. Our method is a natural generalization of the finite-$T$ superparamegnetic Potts clustering introduced by Blatt, Wiseman, and Domany (Phys. Rev. Lett. v.76, 3251 (1996) and the recently suggested by Reichard and Bornholdt (Phys. Rev. Lett. v.93, 21870 (2004)) annealing of Potts model with global antiferromagnetic term. Similarly to both preceding works, the proposed generalization is based on ordering of ferromagnetic Potts model; the novelty of the proposed approach lies in the adjustable dependence of the antiferromagnetic term on the population of each Potts state, which interpolates between the two previously considered cases. This adjustability allows to empirically tune the algorithm to detect the maximum number of communities of the given size and link density. We illustrate the method by detecting protein complexes in high-throughput protein binding networks.Comment: 8 pages, 2 figure, typos corrected, 1 figure adde

Cliques and duplication-divergence network growth

A population of complete subgraphs or cliques in a network evolving via duplication-divergence is considered. We find that a number of cliques of each size scales linearly with the size of the network. We also derive a clique population distribution that is in perfect agreement with both the simulation results and the clique statistic of the protein-protein binding network of the fruit fly. In addition, we show that such features as fat-tail degree distribution, various rates of average degree growth and non-averaging, revealed recently for only the particular case of a completely asymmetric divergence, are present in a general case of arbitrary divergence.Comment: 7 pages, 6 figure

Pigmented purpuric dermatosis: a review of the literature

The pigmented purpuric dermatoses (PPDs) are a group of benign, chronic diseases. The variants described to date represent different clinical presentations of the same entity, all having similar histopathologic characteristics. We provide an overview of the most common PPDs and describe their clinical, dermatopathologic, and epiluminescence features. PPDs are both rare and benign, and this, together with an as yet poor understanding of the pathogenic mechanisms involved, means that no standardized treatments exist. We review the treatments described to date. However, because most of the descriptions are based on isolated cases or small series, there is insufficient evidence to support the use of any of these treatments as first-line therapy

Brownian motion of a charged particle driven internally by correlated noise

We give an exact solution to the generalized Langevin equation of motion of a charged Brownian particle in a uniform magnetic field that is driven internally by an exponentially-correlated stochastic force. A strong dissipation regime is described in which the ensemble-averaged fluctuations of the velocity exhibit transient oscillations that arise from memory effects. Also, we calculate generalized diffusion coefficients describing the transport of these particles and briefly discuss how they are affected by the magnetic field strength and correlation time. Our asymptotic results are extended to the general case of internal driving by correlated Gaussian stochastic forces with finite autocorrelation times.Comment: 10 pages, 4 figures with subfigures, RevTeX, v2: revise

Heat conductivity of DNA double helix

Thermal conductivity of isolated single molecule DNA fragments is of importance for nanotechnology, but has not yet been measured experimentally. Theoretical estimates based on simplified (1D) models predict anomalously high thermal conductivity. To investigate thermal properties of single molecule DNA we have developed a 3D coarse-grained (CG) model that retains the realism of the full all-atom description, but is significantly more efficient. Within the proposed model each nucleotide is represented by 6 particles or grains; the grains interact via effective potentials inferred from classical molecular dynamics (MD) trajectories based on a well-established all-atom potential function. Comparisons of 10 ns long MD trajectories between the CG and the corresponding all-atom model show similar root-mean-square deviations from the canonical B-form DNA, and similar structural fluctuations. At the same time, the CG model is 10 to 100 times faster depending on the length of the DNA fragment in the simulation. Analysis of dispersion curves derived from the CG model yields longitudinal sound velocity and torsional stiffness in close agreement with existing experiments. The computational efficiency of the CG model makes it possible to calculate thermal conductivity of a single DNA molecule not yet available experimentally. For a uniform (polyG-polyC) DNA, the estimated conductivity coefficient is 0.3 W/mK which is half the value of thermal conductivity for water. This result is in stark contrast with estimates of thermal conductivity for simplified, effectively 1D chains ("beads on a spring") that predict anomalous (infinite) thermal conductivity. Thus, full 3D character of DNA double-helix retained in the proposed model appears to be essential for describing its thermal properties at a single molecule level.Comment: 16 pages, 12 figure

Equilibrium properties of a Josephson junction ladder with screening effects

In this paper we calculate the ground state phase diagram of a Josephson Junction ladder when screening field effects are taken into account. We study the ground state configuration as a function of the external field, the penetration depth and the anisotropy of the ladder, using different approximations to the calculation of the induced fields. A series of tongues, characterized by the vortex density $\omega$, is obtained. The vortex density of the ground state, as a function of the external field, is a Devil's staircase, with a plateau for every rational value of $\omega$. The width of each of these steps depends strongly on the approximation made when calculating the inductance effect: if the self-inductance matrix is considered, the $\omega=0$ phase tends to occupy all the diagram as the penetration depth decreases. If, instead, the whole inductance matrix is considered, the width of any step tends to a non-zero value in the limit of very low penetration depth. We have also analyzed the stability of some simple metastable phases: screening fields are shown to enlarge their stability range.Comment: 16 pp, RevTex. Figures available upon request at [email protected] To be published in Physical Review B (01-Dec-96

Mesoscopic Model for Free Energy Landscape Analysis of DNA sequences

A mesoscopic model which allows us to identify and quantify the strength of binding sites in DNA sequences is proposed. The model is based on the Peyrard-Bishop-Dauxois model for the DNA chain coupled to a Brownian particle which explores the sequence interacting more importantly with open base pairs of the DNA chain. We apply the model to promoter sequences of different organisms. The free energy landscape obtained for these promoters shows a complex structure that is strongly connected to their biological behavior. The analysis method used is able to quantify free energy differences of sites within genome sequences.Comment: 7 pages, 5 figures, 1 tabl

Discrete breathers in nonlinear lattices: Experimental detection in a Josephson array

We present an experimental study of discrete breathers in an underdamped Josephson-junction array. Breathers exist under a range of dc current biases and temperatures, and are detected by measuring dc voltages. We find the maximum allowable bias current for the breather is proportional to the array depinning current while the minimum current seems to be related to a junction retrapping mechanism. We have observed that this latter instability leads to the formation of multi-site breather states in the array. We have also studied the domain of existence of the breather at different values of the array parameters by varying the temperature.Comment: 5 pages, 5 figures, submitted to Physical Revie

Chicken egg white — characteristics of its properties and the prospects for functional foods development

The overview presents the literature data and the results of our own research on prospects of using the chicken eggs as the basis of functional foods. The composition of chicken eggs and their components, characteristics of egg white proteins properties are presented thereto. The biologically active compounds included into egg composition are analyzed. The data on the biological value of egg white are given. The characteristic of egg white foaming ability is presented. It has been shown that the ability of proteins to form stable intermolecular structures, especially with partially denaturated proteins, allows them forming viscoelastic superficial films that ensure foam stability. The high foaming ability of chicken egg protein macromolecules is directly related to their interphase properties, i. e. the ability to form interphase layers at the “liquid —  gas” interface. The foaming properties of the various egg proteins are not equal, and therefore they contribute to foaming properties at various extents. The model of egg white proteins gelation is considered and the factors influencing the gelation process are described. It has been shown that very important changes in proteins properties are caused by denaturation. The proteins lose their ability to hydrate; the protective aqueous shell around the globules disappears, the proteins stick together, grow larger and lose solubility. This process is called coagulation. The influence of denaturation and aggregation on variations of protein properties is described below. Data on protein fortification with functional ingredients (calcium, iodine, plant polyphenols) and creation of functional egg and meat foods are presented here