Related papers: CSAW: a dynamical model of protein folding
We consider Activated Random Walk (ARW), a model which generalizes the Stochastic Sandpile, one of the canonical examples of self organized criticality. Informally ARW is a particle system on $\mathbb{Z}$ with mass conservation. One starts…
The HP model of protein folding, where the chain exists in a free medium, is investigated using a parallel Monte Carlo scheme based upon Wang-Landau sampling. Expanding on the work of Wust and Landau by introducing a lesser known replica…
A complex network approach to protein folding is proposed. The graph object is the network of shortcut edges present in a native-state protein (SCN0). Although SCN0s are found via an intuitive message passing algorithm (S. Milgram,…
We show that if the three dimensional self-avoiding walk (SAW) is conformally invariant, then one can compute the hitting densities for the SAW in a half space and in a sphere. We test these predictions by Monte Carlo simulations and find…
We review some recent results obtained in the framework of the 2-dimensional Interacting Self-Avoiding Walk (ISAW). After a brief presentation of the rigorous results that have been obtained so far for ISAW we focus on the Interacting…
We consider self-assembly of proteins into a virus capsid by the methods of molecular dynamics. The capsid corresponds either to SPMV or CCMV and is studied with and without the RNA molecule inside. The proteins are flexible and described…
The question of whether proteins originate from random sequences of amino acids is addressed. A statistical analysis is performed in terms of blocked and random walk values formed by binary hydrophobic assignments of the amino acids along…
In the present paper, we investigate the collapsed phase of the interacting partially-directed self-avoiding walk (IPDSAW) that was introduced in Zwanzig and Lauritzen (1968). We provide sharp asymptotics of the partition function inside…
We study numerically a disordered version of the model for DNA denaturation transition (DSAW-DNA) consisting of two interacting SAWs in 3d, which undergoes a first order transition in the homogeneous case. The two possible values eAT and…
We present a theoretical study of the folding of small proteins inside confining potentials. Proteins are described in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom and does not…
Carbon Atomic Wires (CAWs) are finite linear chains of sp-hybridized carbon atoms. Here the electrochemical reduction of CAWs in the form of polyynes (i.e. with alternated single-triple bonds) is reported. Upon applying a reducing potential…
Although deep learning techniques show promising results for many neuroimaging tasks in research settings, they have not yet found widespread use in clinical scenarios. One of the reasons for this problem is that many machine learning…
Although the title seems self-contradictory, it does not contain a misprint. The model we study is a seemingly minor modification of the "true self-avoiding walk" (TSAW) model of Amit, Parisi, and Peliti in two dimensions. The walks in it…
The scaling behavior of linear polymers in disordered media, modelled by self-avoiding walks (SAWs) on the backbone of percolation clusters in two, three and four dimensions is studied by numerical simulations. We apply the pruned-enriched…
Folklore has, that the universal scaling properties of linear polymers in disordered media are well described by the statistics of self-avoiding walks Folklore has, that the universal scaling properties of linear polymers in disordered…
A correlated Gaussian random walk(CGRW) model is proposed as a simple model of animal dispersal. The general features of CGRW is described. We will discuss how from this single model a number of different kinds of correlated random walk can…
A first principles machine learning model has been developed aimed at studying the formation of calcium carbonate from aqueous solution using molecular dynamics simulations. The model, dubbed SCAN-ML, reproduces accurately the potential…
Single linear polymer chains in dilute solutions under good solvent conditions are studied by Monte Carlo simulations with the pruned-enriched Rosenbluth method up to the chain length $N \sim {\cal O}(10^4)$. Based on the standard simple…
Long-distance characteristics of small-world networks have been studied by means of self-avoiding walks (SAW's). We consider networks generated by rewiring links in one- and two-dimensional regular lattices. The number of SAW's $u_n$ was…
The dynamics of contact pair formation between various hydrophobic residues during folding of a model protein Hp-36 is investigated by Brownian dynamics simulation. Hydropathy scale and non-local helix propensity of amino acids are used to…