All posts under category "Condensed Matter / Cond-Mat.stat-Mech"
We present an improved parallel algorithm for the enumeration of fixed benzenoids B_h containing h hexagonal cells. We can thus extend the enumeration of B_h from the previous best h=35 up to h=50. Analysis of the associated generating function confirms to a very high degree of certainty that $B_h s
Futures trading is the core of futures business, and it is considered as one of the typical complex systems. To investigate the complexity of futures trading, we employ the analytical method of complex networks. First, we use real trading records from the Shanghai Futures Exchange to construct futur
We examine the effective counterion-mediated electrostatic interaction between two like-charged dielectric cylinders immersed in a continuous dielectric medium containing neutralizing mobile counterions. We focus on the effects of image charges induced as a result of the dielectric mismatch between
The focus of this article is on entropy and Markov processes. We study the properties of functionals which are invariant with respect to monotonic transformations and analyze two invariant 'additivity' properties: (i) existence of a monotonic transformation which makes the functional additive with r
We study a directed flipping process that underlies the performance of the random edge simplex algorithm. In this stochastic process, which takes place on a one-dimensional lattice whose sites may be either occupied or vacant, occupied sites become vacant at a constant rate and simultaneously cause
The kinetics of the transformation from the hexagonal packed cylinder (HEX) phase to the face-centered-cubic (FCC) phase was simulated using Brownian Dynamics for an ABA triblock copolymer in a selective solvent for the A block. The kinetics was obtained by instantaneously changing either the temper
We propose a biologically motivated quantity, twinness, to evaluate local similarity between nodes in a network. The twinness of a pair of nodes is the number of connected, labeled subgraphs of size n in which the two nodes possess identical neighbours. The graph animal algorithm is used to estimate
We investigate the problem of growing clusters, which is modeled by two dimensional disks and three dimensional droplets. In this model we place a number of seeds on random locations on a lattice with an initial occupation probability, $p$. The seeds simultaneously grow with a constant velocity to f
We study synchronization in the context of network traffic on a $2-d$ communication network with local clustering and geographic separations. The network consists of nodes and randomly distributed hubs where the top five hubs ranked according to their coefficient of betweenness centrality (CBC) are
A dramatic increase in the number of computing devices with wireless communication capability has resulted in the emergence of a new class of computer worms which specifically target such devices. The most striking feature of these worms is that they do not require Internet connectivity for their pr
A multicanonical update relation for calculation of the microcanonical entropy $S_{micro}(E)$ by means of the estimates of the inverse statistical temperature $beta_S$, is proposed. This inverse temperature is obtained from the recently proposed statistical temperature weighted histogram analysis me
Recently, Imambekov and Glazman [Phys. Rev. Lett. 100, 206805 (2008)] showed that the dynamic structure factor (DSF) of the 1D Bose gas demonstrates power-law behaviour along the limiting dispersion curve of the collective modes and calculated the corresponding exponents exactly. Combining these rec
We use quantum quenches to study the dynamics and thermalization of hardcore bosons in finite one-dimensional lattices. We perform exact diagonalizations and find that, far away from integrability, few-body observables thermalize. We then study the breakdown of thermalization as one approaches an in
We describe an effective landscape introduced in [1] for the analysis of Constraint Satisfaction problems, such as Sphere Packing, K-SAT and Graph Coloring. This geometric construction reexpresses these problems in the more familiar terms of optimization in rugged energy landscapes. In particular, i
Counting problems, determining the number of possible states of a large system under certain constraints, play an important role in many areas of science. They naturally arise for complex disordered systems in physics and chemistry, in mathematical graph theory, and in computer science. Counting pro
We set up a structural model to study credit risk for a portfolio containing several or many credit contracts. The model is based on a jump--diffusion process for the risk factors, i.e. for the company assets. We also include correlations between the companies. We discuss that models of this type ha
We show that heterogeneous degree distributions in observed scale-free topologies of complex networks can emerge as a consequence of the exponential expansion of hidden hyperbolic space. Fermi-Dirac statistics provides a physical interpretation of hyperbolic distances as energies of links. The hidde
We extend the event-chain Monte Carlo algorithm from hard-sphere interactions to the micro-canonical ensemble (constant potential energy) for general potentials. This event-driven Monte Carlo algorithm is non-local, rejection-free, and allows for the breaking of detailed balance. The algorithm uses
We investigate in detail the model of a trophic web proposed by Amaral and Meyer [Phys. Rev. Lett. 82, 652 (1999)]. We focused on small-size systems that are relevant for real biological food webs and for which the fluctuations are playing an important role. We show, using Monte Carlo simulations, t
The effects of the finite size of the network on the evolutionary dynamics of a Boolean network are analyzed. In the model considered, Boolean networks evolve via a competition between nodes that punishes those in the majority. It is found that finite size networks evolve in a fundamentally differen
Motivated by stochastic models of climate phenomena, the steady-state of a linear stochastic model with additive Gaussian white noise is studied. Fluctuation theorems for nonequilibrium steady-states provide a constraint on the character of these fluctuations. The properties of the fluctuations whic
By exerting mechanical force it is possible to unfold/refold RNA molecules one at a time. In a small range of forces, an RNA molecule can hop between the folded and the unfolded state with force-dependent kinetic rates. Here, we introduce a mesoscopic model to analyze the hopping kinetics of RNA hai
Soft-constraint affinity propagation (SCAP) is a new statistical-physics based clustering technique. First we give the derivation of a simplified version of the algorithm and discuss possibilities of time- and memory-efficient implementations. Later we give a detailed analysis of the performance of
We point out the connection between mathematical knot theory and spin glass/search problem. In particular, we present a statistical mechanical formulation of the problem of computing a knot invariant; p-colorability problem, which provides an algorithm to find the solution. The method also allows on
PDZ domains are typical examples of binding motifs mediating the formation of protein-protein assemblies in many different cells. A quantitative characterization of the mechanisms intertwining structure, chemistry and dynamics with the PDZ function represent a challenge in molecular biology. Here we
Experiments in many fields of science and engineering yield data in the form of time series. The Fourier and wavelet transform-based nonparametric methods are used widely to study the spectral characteristics of these time series data. Here, we extend the framework of nonparametric spectral methods
In contrast to the conventional wisdom that scale-free networks are prone to epidemic propagation, in the paper we present that disease spreading is inhibited in fractal scale-free networks. We first propose a novel network model and show that it simultaneously has the following rich topological pro
The existence of a phase transition with diverging susceptibility in batch Minority Games (MGs) is the mark of informationally efficient regimes and is linked to the specifics of the agents' learning rules. Here we study how the standard scenario is affected in a mixed population game in which agent
We propose a fluctuation analysis to quantify spatial correlations in complex networks. The approach considers the sequences of degrees along shortest paths in the networks and quantifies the fluctuations in analogy to time series. In this work, the Barabasi-Albert (BA) model, the Cayley tree at the
We prove exponential decay of the off-diagonal correlation function in the two-dimensional homogeneous Bose gas when a^2 rho is small and the temperature T satisfies T > 4 pi rho / ln |ln(a^2rho). Here, a is the scattering length of the repulsive interaction potential and rho is the density. To lead
The critical behavior of the three-dimensional n-vector model in the presence of an external field is investigated. Mathematical description is performed with the collective variables (CV) method in the framework of the $rho^4$ model approximation at the microscopic level without any adjustable para
By assuming that a particle of energy hbar.omega is actually a dissipative system maintained in a nonequilibrium steady state by a constant throughput of energy (heat flow), the exact Schroedinger equation is derived, both for conservative and nonconservative systems. Thereby, only universal propert
Species extinction occurs regularly and unavoidably in ecological systems. The time scales for extinction can broadly vary and inform on the ecosystem's stability. We study the spatio-temporal extinction dynamics of a paradigmatic population model where three species exhibit cyclic competition. The
Two important aspects of the Internet, namely the properties of its topology and the characteristics of its data traffic, have attracted growing attention of the physics community. My thesis has considered problems of both aspects. First I studied the stochastic behavior of TCP, the primary algorith
KIF1A kinesins are single-headed motor proteins which move on cylindrical nano-tubes called microtubules (MT). A normal MT consists of 13 protofilaments on which the equispaced motor binding sites form a periodic array. The collective movement of the kinesins on a MT is, therefore, analogous to vehi
The early stages of the collective invasion may occur by single mesenchymal cells or hybrid epithelial-mesenchymal cell groups that detach from cancerous tissue. Tumors may also emit invading protrusions of epithelial cells, which could be led (or not) by a basal cell. Here we devise a fractional st
We study analytically and numerically the mean fastest first-passage time (fFPT) to an immobile target for an ensemble of $N$ independent finite-speed random searchers driven by dichotomous noise and described by the telegrapher's equation. In stark contrast to the well-studied case of Brownian part
As collective states of animal groups go, swarms of midge insects pose a number of puzzling questions. Their ordering polarization parameter is quite small and the insects are weakly coupled among themselves but strongly coupled to the swarm. In laboratory studies (free of external perturbations), t
We present a dynamical model of DNA mechanical unzipping under the action of a force. The model includes the motion of the fork in the sequence-dependent landscape, the trap(s) acting on the bead(s), and the polymeric components of the molecular construction (unzipped single strands of DNA, and link
During the synthesis of integral membrane proteins (IMPs), the hydrophobic amino acids of the polypeptide sequence are partitioned mostly into the membrane interior and hydrophilic amino acids mostly into the aqueous exterior. We analyze the minimum free energy state of polypeptide sequences partiti
We investigate the slow time scales that arise from aging of the paths during the process of path aggregation. This is studied using Monte-Carlo simulations of a model aiming to describe the formation of fascicles of axons mediated by contact axon-axon interactions. The growing axons are represented
Experimental variables of optical tweezers instrumentation that affect RNA folding/unfolding kinetics were investigated. A model RNA hairpin, P5ab, was attached to two micron-sized beads through hybrid RNA/DNA handles; one bead was trapped by dual-beam lasers and the other was held by a micropipette
Biodiversity is essential to the viability of ecological systems. Species diversity in ecosystems is promoted by cyclic, non-hierarchical interactions among competing populations. Such non-transitive relations lead to an evolution with central features represented by the `rock-paper-scissors' game,
Irreversible opinion spreading phenomena are studied on small-world networks generated from 2D regular lattices by means of the magnetic Eden model, a nonequilibrium kinetic model for the growth of binary mixtures in contact with a thermal bath. In this model, the opinion or decision of an individua
RNA polymerase (RNAP) is a mobile molecular workshop that polymerizes a RNA molecule by adding monomeric subunits one by one, while moving step by step on the DNA template itself. Here we develop a theoretical model by incorporating the steric interactions of the RNAPs and their mechanochemical cycl
We report experimental results on unidirectional traffic-like collective movement of ants on trails. Our work is primarily motivated by fundamental questions on the collective spatio-temporal organization in systems of interacting motile constituents driven far from equilibrium. Making use of the an
In this paper we present a new approach to control variates for improving computational efficiency of Ensemble Monte Carlo. We present the approach using simulation of paths of a time-dependent nonlinear stochastic equation. The core idea is to extract information at one or more nominal model parame
We introduce a minimal Agent Based Model with two classes of agents, fundamentalists (stabilizing) and chartists (destabilizing) and we focus on the essential features which can generate the stylized facts. This leads to a detailed understanding of the origin of fat tails and volatility clustering a
We propose a method to reduce the relaxation time towards equilibrium in stochastic sampling of complex energy landscapes in statistical systems with discrete degrees of freedom by generalizing the platform previously developed for continuous systems. The method starts from a master equation, in con
Social networks are not static but rather constantly evolve in time. One of the elements thought to drive the evolution of social network structure is homophily - the need for individuals to connect with others who are similar to them. In this paper, we study how the spread of a new opinion, idea, o
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