Related papers: CSAW: a dynamical model of protein folding
Slow waves (SWs) are spatio-temporal patterns of cortical activity that occur both during natural sleep and anesthesia and are preserved across species. Even though electrophysiological recordings have been largely used to characterize…
L\'evy walks are continuous time random walks with spatio-temporal coupling of jump lengths and waiting times, often used to model superdiffusive spreading processes such as animals searching for food, tracer motion in weakly chaotic…
Understanding protein conformational dynamics is essential for elucidating biological function but remains challenging due to the wide range of timescales and the complexity of collective motions. Enhanced sampling methods overcome…
The Activated Random Walk (ARW) model is a promising candidate for demonstrating self-organized criticality due to its potential for universality. Recent studies have shown that the ARW model exhibits a well-defined critical density in one…
As humanoid robots transition from labs to real-world environments, it is essential to democratize robot control for non-expert users. Recent human-robot imitation algorithms focus on following a reference human motion with high precision,…
A lattice model of the directed self-avoiding walk is used to estimate the possibility on the formation of an infinitely long linear semi-flexible copolymer chain. The copolymer chain is assumed to composed of four different types of the…
We present here a detailed numerical study of the dynamical behaviour of `soft' uncompressed grains in a granular chain where the grains interact via the intrinsically nonlinear Hertz force. It is well known that such a chain supports the…
Protein collapse can be viewed as a dynamical phase transition, during which new scales and collective variables become excited while the old ones recede and fade away. This causes formidable computational bottle-necks in approaches that…
We study the asymptotic shape of self-avoiding random walks (SAW) on the backbone of the incipient percolation cluster in d-dimensional lattices analytically. It is generally accepted that the configurational averaged probability…
Many small proteins fold via a first-order "all-or-none" transition directly from an expanded coil to a compact native state. Here we study an analogous direct freezing transition from an expanded coil to a compact crystallite for a simple…
The analysis of single particle trajectories plays an important role in elucidating dynamics within complex environments such as those found in living cells. However, the characterization of intracellular particle motion is often confounded…
We study the thermodynamics of an exactly solvable model of a self-interacting partially directed self-avoiding walk (DSAW) in two dimensions, when a force is applied on one end of the chain. The critical force for the unfolding is…
Self Consistent Normal Mode Analysis (SCNMA) is applied to heme c type cytochrome f to study temperature dependent protein motion. Classical Normal Mode Analysis (NMA) assumes harmonic behavior and the protein Mean Square Displacement (MSD)…
In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the…
Random walk (RW)-based algorithms have long been popular in distributed systems due to low overheads and scalability, with recent growing applications in decentralized learning. However, their reliance on local interactions makes them…
Polymer chains with hard-core interaction on a two-dimensional lattice are modeled by directed random walks. Two models, one with intersecting walks (IW) and another with non-intersecting walks (NIW) are presented, solved and compared. The…
Continuous Time Random Walks (CTRWs) are jump processes with random waiting times between jumps. We study scaling limits for CTRWs where the distribution of jumps and waiting times is coupled and varies in space and time. Such processes…
A multi-state version of an animal movement analysis method based on conditional logistic regression, called Step Selection Function (SSF), is proposed. In ecology SSF is developed from a comparison between the observed location of an…
The scaling behavior of linear polymers in disordered media modelled by self-avoiding random walks (SAWs) on the backbone of two- and three-dimensional percolation clusters at their critical concentrations p_c is studied. All possible SAW…
Contact matrices provide a coarse grained description of the configuration omega of a linear chain (polymer or random walk) on Z^n: C_{ij}(omega)=1 when the distance between the position of the i-th and j-th step are less than or equal to…