Related papers: Optimal modularity for nucleation in network-organ…
We investigate the nucleation of Ising model on complex networks and focus on the role played by the heterogeneity of degree distribution on nucleation rate. Using Monte Carlo simulation combined with forward flux sampling, we find that for…
Identifying nucleation pathway is important for understanding the kinetics of first-order phase transitions in natural systems. In the present work, we study nucleation pathway of the Ising model in homogeneous and heterogeneous networks…
We study the heterogeneous nucleation of Ising model on complex networks under a non-equilibrium situation where the impurities perform degree-biased motion controlled by a parameter \alpha. Through the forward flux sampling and detailed…
We compute rates and pathways for nucleation in a sheared two dimensional Ising model with Metropolis spin flip dynamics, using Forward Flux Sampling (FFS). We find a peak in the nucleation rate at intermediate shear rate. We analyse the…
We have studied nucleation dynamics of the Ising model in scale-free networks with degree distribution $P(k)\sim k^{-\gamma}$ by using forward flux sampling method, focusing on how the network topology would influence the nucleation rate…
Nucleation phenomena are ubiquitous in nature and the presence of impurities in every real and experimental system is unavoidable. Yet numerical studies of nucleation are nearly always conducted for entirely pure systems. We have studied…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
A theoretical framework is presented for the estimation of nucleation times in systems with Brownian type dynamics. This framework is applied to a prototype system: the two-dimensional Ising model with spin-flip dynamics in an external…
Reactive pathways to nucleation in a three-dimensional Ising model at 60% of the critical temperature are studied using transition path sampling of single spin flip Monte Carlo dynamics. Analysis of the transition state ensemble (TSE)…
Several networks occurring in real life have modular structures that are arranged in an hierarchical fashion. In this paper, we have proposed a model for such networks, using a stochastic generation method. Using this model we show that,…
Now that spike trains from many neurons can be recorded simultaneously, there is a need for methods to decode these data to learn about the networks that these neurons are part of. One approach to this problem is to adjust the parameters of…
In this paper, we propose an evolving network model growing fast in units of module, based on the analysis of the evolution characteristics in real complex networks. Each module is a small-world network containing several interconnected…
We develop a model in the framework of nuclear fragmentation at thermodynamic equilibrium which can be mapped onto an Ising model with constant magnetization. We work out the thermodynamic properties of the model as well as the properties…
The central question of systems biology is to understand how individual components of a biological system such as genes or proteins cooperate in emerging phenotypes resulting in the evolution of diseases. As living cells are open systems in…
Network reliability is the probability that a dynamical system composed of discrete elements interacting on a network will be found in a configuration that satisfies a particular property. We introduce a new reliability property, Ising…
[Background] Several studies have mentioned network modularity -- that a network can easily be decomposed into subgraphs that are densely connected within and weakly connected between each other -- as a factor affecting metabolic…
Simulations using the Forward Flux Sampling method have shown a nonmonotonic de- pendence of the homogeneous nucleation rate on the shear rate for a sheared two dimensional Ising model [R. J. Allen et al, arXiv cond-mat/0805.3029]. For…
In this paper we study a simple cascading process in a structured heterogeneous population, namely, a network composed of two loosely coupled communities. We demonstrate that under certain conditions the cascading dynamics in such a network…
Many works have studied the Internet topology, but few have investigated the question of how it evolves over time. This paper focuses on the Internet routing IP-level topology and proposes a first step towards realistic modeling of its…
Modularity has been widely studied as a mechanism to improve the capabilities of neural networks through various techniques such as hand-crafted modular architectures and automatic approaches. While these methods have sometimes shown…