Related papers: Sequence Dependence of Self-Interacting Random Cha…
We study the behaviour of a hydrophobic chain near a hydrophobic boundary in two dimensions, using the decorated lattice model of Berkema and Widom [G.T. Barkema and B. Widom, J. Chem. Phys. 113, 2349 (2000)] to obtain effective,…
In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…
We study the stochastic thermodynamics of an overdamped harmonic chain, which can be viewed equivalently as a 1D Rouse chain or as an approximate model of single file diffusion. We discuss mainly two levels of description of this system:…
Records of social interactions provide us with new sources of data for understanding how interaction patterns affect collective dynamics. Such human activity patterns are often bursty, i.e., they consist of short periods of intense activity…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
The phase structure of self-avoiding polymerized membranes is studied by extensive Hybrid Monte Carlo simulations. Several folding transitions from the flat to a collapsed state are found. Using a suitable order parameter and finite size…
We investigate the stability of an Anderson localized chain to the inclusion of a single finite interacting thermal seed. This system models the effects of rare low-disorder regions on many-body localized chains. Above a threshold value of…
We discuss simulations of a simple model for polymer blends in the framework of the Rouse model. At odds with standard predictions, large dynamic asymmetry between the two components induces strong non-exponentiality of the Rouse modes for…
Non-equilibrium selection pressures were proposed for the formation of oligonucleotides with rich functionalities encoded in their sequences, such as catalysis. Since phase separation was shown to direct various chemical processes, we ask…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
In this paper we investigate the role of native geometry on the kinetics of protein folding based on simple lattice models and Monte Carlo simulations. Results obtained within the scope of the Miyazawa-Jernigan indicate the existence of two…
We investigate thermalization in a tight-binding chain with an on-site defect subject to local dephasing noise implemented as random phase kicks. For a single linear defect of strength $\epsilon$, we obtain an exact analytical description…
The phase diagram and the thermodynamics of the random field Ising model (RFIM) defined on a family of diamond hierarchical lattices of arbitrary dimension and scaling factor $b=2$ is investigated. The phase diagram is studied considering…
We reconsider the structure-based route to coarse graining in which the coarse-grained model is defined in such a way to reproduce some distributions functions of the original system as accurately as possible. We consider standard…
We consider a statistical mechanical model of a generic flexible polyelectrolyte, comprised of identically charged monomers with long range electrostatic interactions, and short-range interactions quantified by a disorder field along the…
We develop a path-based approach to continuous-time random walks on networks with arbitrarily weighted edges. We describe an efficient numerical algorithm for calculating statistical properties of the stochastic path ensemble. After…
This paper presents ``randomized SINDy", a sequential machine learning algorithm designed for dynamic data that has a time-dependent structure. It employs a probabilistic approach, with its PAC learning property rigorously proven through…
We consider the adsorption of a random heteropolymer onto an interface within the model by Garel et al. [1] by taking into account self-interactions between the monomers. Within the replica trick and by using a self-consistent preaveraging…
We develop dependent hierarchical normalized random measures and apply them to dynamic topic modeling. The dependency arises via superposition, subsampling and point transition on the underlying Poisson processes of these measures. The…
We investigate interaction networks that we derive from multivariate time series with methods frequently employed in diverse scientific fields such as biology, quantitative finance, physics, earth and climate sciences, and the…