Distance, dissimilarity index, and network community structure

We address the question of finding the community structure of a complex network. In an earlier effort [H. Zhou, {\em Phys. Rev. E} (2003)], the concept of network random walking is introduced and a distance measure defined. Here we calculate, based on this distance measure, the dissimilarity index between nearest-neighboring vertices of a network and design an algorithm to partition these vertices into communities that are hierarchically organized. Each community is characterized by an upper and a lower dissimilarity threshold. The algorithm is applied to several artificial and real-world networks, and excellent results are obtained. In the case of artificially generated random modular networks, this method outperforms the algorithm based on the concept of edge betweenness centrality. For yeast's protein-protein interaction network, we are able to identify many clusters that have well defined biological functions.Comment: 10 pages, 7 figures, REVTeX4 forma

Global regularity criterion for the 3D Navier-Stokes equations involving one entry of the velocity gradient tensor

In this paper we provide a sufficient condition, in terms of only one of the nine entries of the gradient tensor, i.e., the Jacobian matrix of the velocity vector field, for the global regularity of strong solutions to the three-dimensional Navier-Stokes equations in the whole space, as well as for the case of periodic boundary conditions

Scattering mechanism in a step-modulated subwavelength metal slit: a multi-mode multi-reflection analysis

In this paper, the scattering/transmission inside a step-modulated subwavelength metal slit is investigated in detail. We firstly investigate the scattering in a junction structure by two types of structural changes. The variation of transmission and reflection coefficients depending on structural parameters are analyzed. Then a multi-mode multi-reflection model based on ray theory is proposed to illustrate the transmission in the step-modulated slit explicitly. The key parts of this model are the multi-mode excitation and the superposition procedure of the scatterings from all possible modes, which represent the interference and energy transfer happened at interfaces. The method we use is an improved modal expansion method (MEM), which is a more practical and efficient version compared with the previous one [Opt. Express 19, 10073 (2011)]. In addition, some commonly used methods, FDTD, scattering matrix method, and improved characteristic impedance method, are compared with MEM to highlight the preciseness of these methods.Comment: 25 pages, 9 figure

Growing carbon nanotubes by microwave plasma-enhanced chemical vapor deposition

A processing route has been developed to grow bundles of carbon nanotubes on substrates from methane and hydrogen mixtures by microwave plasma-enhanced chemical vapor deposition, catalyzed by iron particles reduced from ferric nitrate. Growth takes place at about 900°C leading to nanotubes with lengths of more than 20 μm and diameters on the nanometer scale

Resistance distance, information centrality, node vulnerability and vibrations in complex networks

We discuss three seemingly unrelated quantities that have been introduced in different fields of science for complex networks. The three quantities are the resistance distance, the information centrality and the node displacement. We first prove various relations among them. Then we focus on the node displacement, showing its usefulness as an index of node vulnerability.We argue that the node displacement has a better resolution as a measure of node vulnerability than the degree and the information centrality

Network Landscape from a Brownian Particle's Perspective

Given a complex biological or social network, how many clusters should it be decomposed into? We define the distance $d_{i,j}$ from node $i$ to node $j$ as the average number of steps a Brownian particle takes to reach $j$ from $i$. Node $j$ is a global attractor of $i$ if $d_{i,j}\leq d_{i,k}$ for any $k$ of the graph; it is a local attractor of $i$, if $j\in E_i$ (the set of nearest-neighbors of $i$) and $d_{i,j}\leq d_{i,l}$ for any $l\in E_i$. Based on the intuition that each node should have a high probability to be in the same community as its global (local) attractor on the global (local) scale, we present a simple method to uncover a network's community structure. This method is applied to several real networks and some discussion on its possible extensions is made.Comment: 5 pages, 4 color-figures. REVTeX 4 format. To appear in PR

Two-Boson Exchange Physics: A Brief Review

Current status of the two-boson exchange contributions to elastic electron-proton scattering, both for parity conserving and parity-violating, is briefly reviewed. How the discrepancy in the extraction of elastic nucleon form factors between unpolarized Rosenbluth and polarization transfer experiments can be understood, in large part, by the two-photon exchange corrections is discussed. We also illustrate how the measurement of the ratio between positron-proton and electron-proton scattering can be used to differentiate different models of two-photon exchange. For the parity-violating electron-proton scattering, the interest is on how the two-boson exchange (TBE), \gamma Z-exchange in particular, could affect the extraction of the long-sought strangeness form factors. Various calculations all indicate that the magnitudes of effect of TBE on the extraction of strangeness form factors is small, though can be large percentage-wise in certain kinematics.Comment: 6 pages, 5 figures, prepared for Proceedings of the fifth Asia-Pacific Conference on Few-Body Problems in Physics (APFB2011), Seoul, Korea, August 22-26, 2011, to appear in Few-Body Systems, November 201

Approach to the semiconductor cavity QED in high-Q regimes with q-deformed boson

The high density Frenkel exciton which interacts with a single mode microcavity field is dealed with in the framework of the q-deformed boson. It is shown that the q-defomation of bosonic commutation relations is satisfied naturally by the exciton operators when the low density limit is deviated. An analytical expression of the physical spectrum for the exciton is given by using of the dressed states of the cavity field and the exciton. We also give the numerical study and compare the theoretical results with the experimental resultsComment: 6 pages, 2 figure

Colon carcinoma cells harboring PIK3CA mutations display resistance to growth factor deprivation induced apoptosis.

PIK3CA, encoding the p110alpha catalytic subunit of phosphatidylinositol 3-kinase (PI3K), is mutated in a variety of human cancers. We screened the colon cancer cell lines previously established in our laboratory for PIK3CA mutations and found that four of them harbored gain of function mutations. We have now compared a panel of mutant and wild-type cell lines for cell proliferation and survival in response to stress. There was little difference in PI3K activity between mutant PIK3CA-bearing cells (mutant cells) and wild-type PIK3CA-bearing cells (wild-type cells) under optimal growth conditions. However, the mutant cells showed constitutive PI3K activity during growth factor deprivation stress (GFDS), whereas PI3K activity decayed rapidly in the wild-type cells. Importantly, constitutively active PI3K rendered the mutant cells resistant to GFDS-induced apoptosis relative to the wild-type cells, indicating a biological advantage under stress conditions that is imparted by the mutant enzymes. Compared with the wild-type cells, the mutant cells were hypersensitive to the apoptosis induced by the PI3K inhibitor LY294002. In addition, PIK3CA small interfering RNA significantly decreased DNA synthesis and/or induced apoptosis in the mutant cells but not in the wild-type cells. Furthermore, ecotopic expression of a mutant PIK3CA in a nontumorigenic PIK3CA wild-type cell line resulted in resistance to GFDS-induced apoptosis, whereas transfection of wild-type PIK3CA or empty vector had little effect. Taken together, our studies show that mutant PIK3CA increases the capacity for proliferation and survival under environmental stresses, such as GFDS while also imparting greater dependency on the PI3K pathway for proliferation and survival

Discrete molecular dynamics simulations of peptide aggregation

We study the aggregation of peptides using the discrete molecular dynamics simulations. At temperatures above the alpha-helix melting temperature of a single peptide, the model peptides aggregate into a multi-layer parallel beta-sheet structure. This structure has an inter-strand distance of 0.48 nm and an inter-sheet distance of 1.0 nm, which agree with experimental observations. In this model, the hydrogen bond interactions give rise to the inter-strand spacing in beta-sheets, while the Go interactions among side chains make beta-strands parallel to each other and allow beta-sheets to pack into layers. The aggregates also contain free edges which may allow for further aggregation of model peptides to form elongated fibrils.Comment: 15 pages, 8 figure