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142
Community detection in graphs
, 2009
"... The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices of th ..."
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Cited by 801 (1 self)
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The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices of the same cluster and comparatively few edges joining vertices of different clusters. Such
Models of the small world
 J. Stat. Phys
, 2000
"... It is believed that almost any pair of people in the world can be connected to one another by a short chain of intermediate acquaintances, of typical length about six. This phenomenon, colloquially referred to as the ``six degrees of separation,' ' has been the subject of considerable rece ..."
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Cited by 131 (1 self)
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It is believed that almost any pair of people in the world can be connected to one another by a short chain of intermediate acquaintances, of typical length about six. This phenomenon, colloquially referred to as the ``six degrees of separation,' ' has been the subject of considerable recent interest within the physics community. This paper provides a short review of the topic. KEY WORDS: social networks. Small world; networks; disordered systems; graph theory;
Criticality in diluted ferromagnets
, 2008
"... We perform a detailed study of the critical behavior of the mean field diluted Ising ferromagnet by analytical and numerical tools. We obtain selfaveraging for the magnetization and write down an expansion for the free energy close to the critical line. The scaling of the magnetization is also rigo ..."
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Cited by 14 (13 self)
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We perform a detailed study of the critical behavior of the mean field diluted Ising ferromagnet by analytical and numerical tools. We obtain selfaveraging for the magnetization and write down an expansion for the free energy close to the critical line. The scaling of the magnetization is also rigorously obtained and compared with extensive Monte Carlo simulations. We explain the transition from an ergodic region to a non trivial phase by commutativity breaking of the infinite volume limit and a suitable vanishing field. We find full agreement among theory, simulations and previous results.
Sequence dependence of transcription factormediated DNA looping
 Nucleic Acids Res
, 2012
"... S1 Modeling the Looping Probability. 2 S1.1 Tuning the simple titration curve................................. 2 S1.2 The case of multiple looped states................................. 6 S1.3 Effect of an “inactive fraction ” of repressor............................ 6 ..."
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Cited by 12 (4 self)
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S1 Modeling the Looping Probability. 2 S1.1 Tuning the simple titration curve................................. 2 S1.2 The case of multiple looped states................................. 6 S1.3 Effect of an “inactive fraction ” of repressor............................ 6
Multiscale Advanced Raster Map Analysis System
 Definition, Design, and Development. Invited Plenary Address at the Brazilian Ecological Congress
"... of the Agency and no official endorsement should be inferred. ..."
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Cited by 11 (3 self)
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of the Agency and no official endorsement should be inferred.
Computation of strained epitaxial growth in three dimensions by kinetic Monte
, 2006
"... A numerical method for computation of heteroepitaxial growth in the presence of strain is presented. The model used is based on a solidonsolid model with a cubic lattice. Elastic effects are incorporated using a ball and spring type model. The growing film is evolved using Kinetic Monte Carlo (KMC ..."
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Cited by 10 (0 self)
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A numerical method for computation of heteroepitaxial growth in the presence of strain is presented. The model used is based on a solidonsolid model with a cubic lattice. Elastic effects are incorporated using a ball and spring type model. The growing film is evolved using Kinetic Monte Carlo (KMC) and it is assumed that the film is in mechanical equilibrium. The strain field in the substrate is computed by an exact solution which is efficiently evaluated using the fast Fourier transform. The strain field in the growing film is computed directly. The resulting coupled system is solved iteratively using the conjugate gradient method. Finally we introduce various approximations in the implementation of KMC to improve the computation speed. Numerical results show that layerbylayer growth is unstable if the misfit is large enough resulting in the formation of three dimensional islands. 1
Simulation of wettinglayer and island formation in heteroepitaxial growth
 Europhys. Lett
"... PACS. 07.05.Tp – Computer modeling and simulation. PACS. 68.55.Ac – Nucleation and growth: microscopic aspects. PACS. 81.10.Aj – Theory and models of crystal growth; physics of crystal growth, crystal morphology and orientation. Abstract. – We investigate various phenomena of strained heteroepitaxia ..."
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Cited by 9 (4 self)
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PACS. 07.05.Tp – Computer modeling and simulation. PACS. 68.55.Ac – Nucleation and growth: microscopic aspects. PACS. 81.10.Aj – Theory and models of crystal growth; physics of crystal growth, crystal morphology and orientation. Abstract. – We investigate various phenomena of strained heteroepitaxial growth. To this end, we study a model in 1 + 1 dimension by means of offlattice kinetic Monte Carlo simulations. We observe the appearance of straininduced mounds upon a wetting layer, i.e. StranskiKrastanov growth. The transition from 2d to 3d islands occurs at a critical layer thickness and its dependence on the growth parameters is studied quantitatively. We find that for large enough deposition rates the layer thickness as well as the size and density of islands depend on the misfit between substrate and adsorbate, only. Introduction. – In recent years, the importance of semiconductor and optoelectronic devices fabricated in strainedlayer epitaxy has increased continuously. As a consequence, heteroepitaxial growth has been a matter of significant interest in both experimental and theoretical studies (see, e.g., [1,2] for an overview). In particular, the straininduced formation
Intracluster Moves for Constrained DiscreteSpace MCMC
"... This paper addresses the problem of sampling from binary distributions with constraints. In particular, it proposes an MCMC method to draw samples from a distribution of the set of all states at a specified distance from some reference state. For example, when the reference state is the vector of ze ..."
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Cited by 6 (4 self)
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This paper addresses the problem of sampling from binary distributions with constraints. In particular, it proposes an MCMC method to draw samples from a distribution of the set of all states at a specified distance from some reference state. For example, when the reference state is the vector of zeros, the algorithm can draw samples from a binary distribution with a constraint on the number of active variables, say the number of 1’s. We motivate the need for this algorithm with examples from statistical physics and probabilistic inference. Unlike previous algorithms proposed to sample from binary distributions with these constraints, the new algorithm allows for large moves in state space and tends to propose them such that they are energetically favourable. The algorithm is demonstrated on three Boltzmann machines of varying difficulty: A ferromagnetic Ising model (with positive potentials), a restricted Boltzmann machine with learned Gaborlike filters as potentials, and a challenging threedimensional spinglass (with positive and negative potentials). 1
A simple lattice model that exhibits a proteinlike cooperative allornone folding transition. Biopolymers 69:399–405
, 2003
"... we applied a simple combination of the Replica Exchange Monte Carlo and the Histogram methods in the computational studies of a simplified protein lattice model containing hydrophobic and polar units and sequencedependent local stiffness. A welldefined, relatively complex Greekkey topology, groun ..."
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Cited by 5 (2 self)
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we applied a simple combination of the Replica Exchange Monte Carlo and the Histogram methods in the computational studies of a simplified protein lattice model containing hydrophobic and polar units and sequencedependent local stiffness. A welldefined, relatively complex Greekkey topology, ground (native) conformations was found; however, the cooperativity of the folding transition was very low. Here we describe a modified minimal model of the same Greekkey motif for which the folding transition is very cooperative and has all the features of the “allornone ” transition typical of real globular proteins. It is demonstrated that the allornone transition arises from the interplay between local stiffness and properly defined tertiary interactions. The tertiary interactions are directional, mimicking the packing preferences seen in proteins. The model properties are compared with other minimal proteinlike models, and we argue that the model presented here captures essential physics of protein folding (structurally welldefined proteinlike native conformation and cooperative allornone folding
A new mathematical representation of game theory. arXiv: quantph/0404159
"... In this paper, we introduce a framework of new mathematical representation of Game Theory, including static classical game and static quantum game. The idea is to find a set of base vectors in strategy space and to define their inner product so as to form them as a Hilbert space, and then form a Hil ..."
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Cited by 5 (4 self)
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In this paper, we introduce a framework of new mathematical representation of Game Theory, including static classical game and static quantum game. The idea is to find a set of base vectors in strategy space and to define their inner product so as to form them as a Hilbert space, and then form a Hilbert space of system state. Basic ideas and formulas in Game Theory have been reexpressed in such a space of system state. This space provides more possible strategies than traditional classical game and quantum game. All the games have been unified in the new representation and their relation has been discussed. It seems that if the quantized classical game has some independent meaning other than traditional classical, a payoff matrix with nonzero offdiagonal elements is required. On the other hand, when such new representation is applied onto quantum game, the payoff matrix gives nonzero offdiagonal elements. Also in the new representation of quantum games, a set of base vectors are naturally given from the quantum strategy (operator) space. This gives a kind of support for our approach in classical game. Ideas and technics from Statistical Physics can be easily incorporated into Game Theory through such a representation. This incorporation gives an endogenous method for refinement of Equilibrium State and some hits to simplify the calculation of Equilibrium State. Kinetics Equation and thermal equilibrium has been introduced as an efficient way to calculate the Equilibrium State. Although we have gotten some successful experience on some trivially cases, the progress of such a dynamical equation for the general case is still waiting for more exploration.