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The dynamics of contact networks and epidemics of infectious diseases often occur on comparable time scales. Ignoring one of these time scales may provide an incomplete understanding of the population dynamics of the infection process. We…
We investigate global phase coherence in a system of coupled oscillators on a small-world networks constructed from a ring with nearest-neighbor edges. The effects of both thermal noise and quenched randomness on phase ordering are examined…
In this paper, we mathematically describe the time evolution of protein folding features via Iori et al.'s heteropolymer model. More specifically, we identify that the folding amino acid chain evolve according to a power law $D \sim…
Sinai's model of diffusion in one-dimension with random local bias is studied by a real space renormalization group which yields asymptotically exact long time results. The distribution of the position of a particle and the probability of…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
A generic algorithm for the extraction of probabilistic (Bayesian) information about model parameters from data is presented. The algorithm propagates an ensemble of particles in the product space of model parameters and outputs. Each…
Drawing inspiration from real world interacting systems we study a system consisting of two networks that exhibit antagonistic and dependent interactions. By antagonistic and dependent interactions, we mean, that a proportion of functional…
The neural network techniques are developed for artificial sequences based on approximate models of proteins. We only encode the hydrophobicity of the amino acid side chains without attempting to model the secondary structure. We use our…
We present a simple model that recalls two different patterns depending on the temperature. To realize a change in recall pattern due to temperature change, we embed two patterns to different graphs: the first pattern into a fully connected…
We present the results of a self-consistent, unified molecular dynamics study of simple model heteropolymers in the continuum with emphasis on folding, sequence design and the determination of the interaction parameters of the effective…
The paper presents a new numerical approach for studying the thermodynamical and dynamical properties of finite spin-$\frac{1}{2}$ $XY$ chains. Special attention is given to examining the influence of disorder on the average transverse…
The interaction of distinct units in physical, social, biological and technological systems naturally gives rise to complex network structures. Networks have constantly been in the focus of research for the last decade, with considerable…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
In this Letter, we investigate the effects of a time-dependent, short-ranged interaction on the long-time expansion dynamics of Fermi gases. We show that the effects of the interaction on the dynamics is dictated by how it changes under a…
Virtually all real-world networks are dynamical entities. In social networks, the propensity of nodes to engage in social interactions (activity) and their chances to be selected by active nodes (attractiveness) are heterogeneously…
Simulated annealing is an effective and general means of optimization. It is in fact inspired by metallurgy, where the temperature of a material determines its behavior in thermodynamics. Likewise, in simulated annealing, the actions that…
We study a generic model of self-assembling chains which can branch and form networks with branching points (junctions) of arbitrary functionality. The physical realizations include physical gels, wormlike micells, dipolar fluids and…
Through large-scale numerical simulations, we study the phase ordering kinetics of the $2d$ Ising Model after a zero-temperature quench from a high-temperature homogeneous initial condition. Analysing the behaviour of two important…
In this work we employ various methods of analysis (unfolding simulations and comparative analysis of structures and sequences of proteomes of thermophilic organisms) to show that organisms can follow two major strategies of thermophilic…
Strategic test allocation plays a major role in the control of both emerging and existing pandemics (e.g., COVID-19, HIV). Widespread testing supports effective epidemic control by (1) reducing transmission via identifying cases, and (2)…