Related papers: CSAW: a dynamical model of protein folding
Quantum walk (QW) provides a versatile tool to study fundamental physics and also to make a variety of practical applications. We here start with the recent idea of {\it nonlinear} QW and show that introducing {\it nonlinearity} to QW can…
The high computational cost of carrying out molecular dynamics simulations of even small-size proteins is a major obstacle in the study, at atomic detail and in explicit solvent, of the physical mechanism which is at the basis of the…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…
Motion planning failures during autonomous navigation often occur when safety constraints are either too conservative, leading to deadlocks, or too liberal, resulting in collisions. To improve robustness, a robot must dynamically adapt its…
Approaches to continual learning aim to successfully learn a set of related tasks that arrive in an online manner. Recently, several frameworks have been developed which enable deep learning to be deployed in this learning scenario. A key…
We theoretically investigate the effects of surface acoustic waves (SAWs) on an electric-field-driven sliding motion of a one-dimensional charge density wave (CDW), which is initially pinned by impurities. By numerically analyzing an…
A novel version of the Continuous-Time Random Walk (CTRW) model with memory is developed. This memory means the dependence between arbitrary number of successive jumps of the process, while waiting times between jumps are considered as…
The scalar auxiliary variable (SAV) approach is a highly efficient method widely used for solving gradient flow systems. This approach offers several advantages, including linearity, unconditional energy stability, and ease of…
This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free…
We introduce CAFLOW, a new diverse image-to-image translation model that simultaneously leverages the power of auto-regressive modeling and the modeling efficiency of conditional normalizing flows. We transform the conditioning image into a…
We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each…
We study the Brownian motion of a charged colloid, confined between two charged walls, for small separation between the colloid and the walls. The system is embedded in an ionic solution. The combined effect of electrostatic repulsion and…
The atomistic characterization of the transition state is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations…
We analyse the metastable behaviour of the disordered Curie-Weiss-Potts (DCWP) model subject to a Glauber dynamics. The model is a randomly disordered version of the mean-field $q$-spin Potts model (CWP), where the interaction coefficients…
Annual maximum temperature data provides crucial insights into the impacts of climate change, especially for regions like India, where temperature variations have significant implications for agriculture, health, and infrastructure. In this…
We use a three dimensional cubic lattice model of proteins to study their properties that determine folding to the native state. The protein chain is modeled as a sequence of $N$ beads. The interactions between beads are taken from a…
Protein folding is a phenomenon that has been studied for about 50 years and still remains as an unsolved problem. The main feature of this process is that it occurs as an all or none process, so a protein, can jump directly between folded…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
We develop a multi-scale approach to simulate hydrated nanobio systems under realistic condi- tions (e.g., nanoparticles and protein solutions at physiological conditions over time-scales up to hours). We combine atomistic simulations of…
While the fat tailed jump size and the waiting time distributions characterizing individual human trajectories strongly suggest the relevance of the continuous time random walk (CTRW) models of human mobility, no one seriously believes that…