Related papers: Exploring the Protein G Helix Free Energy Surface …
We perform a generalized-ensemble simulation of a small peptide taking the interactions among all atoms into account. From this simulation we obtain thermodynamic quantities over a wide range of temperatures. In particular, we show that the…
Phase-separated biomolecular condensates exhibit a wide range of dynamical properties, which depend on the sequences of the constituent proteins and RNAs. However, it is unclear to what extent condensate dynamics can be tuned without also…
The aqueous solvent profoundly influences protein folding, yet its effects are relatively poorly understood. In this study, we investigate the impact of solvation on the folding of lattice proteins by using Monte Carlo simulations. The…
Understanding the impact of extractant functionalization in solvent extraction is essential to guide the development of better separations processes. Traditionally, computational extractant design uses electronic structure calculations to…
High-temperature reactions widely exist in nature. However, they are difficult to be characterized either experimentally or computationally. The routinely used minimum energy path (MEP) model in computational modeling of chemical reactions…
Water and glycerol are well-known to facilitate the structural relaxation of amorphous protein matrices. However, several studies evidenced that they may also limit fast ($\sim$ pico-nanosecond, ps-ns) and small-amplitude ($\sim$ \AA )…
We explore the consequences of very high dimensionality in the dynamical landscape of protein folding. Consideration of both typical range of stabilising interactions, and folding rates themselves, leads to a model of the energy…
Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free…
Cellular decision-making under stress involves rapid pathway selection despite energy scarcity. Here we demonstrate that thermodynamic constraints actively drive energy-efficient sporulation, where continuous metabolic sources enable system…
We study the relation of the potential energy landscape (PEL) topography to relaxation dynamics of a small model glass former of Lennard-Jones type. The mechanism under investigation is the hopping betweem superstructures of PEL mimima,…
Previous research focused on two different mechanisms of microstructure stabilization in alloys: thermodynamic stabilization by reducing the grain boundary (GB) free energy and kinetic stabilization by suppressing the GB mobility by solute…
Using Monte Carlo simulations we study the dynamics of three-dimensional Ising models with nearest-, next-nearest-, and four-spin (plaquette) interactions. During coarsening, such models develop growing energy barriers, which leads to very…
Protein sequences are believed to have been selected to provide the stability of, and reliable renaturation to, an encoded unique spatial fold. In recently proposed theoretical schemes, this selection is modeled as ``minimal frustration,''…
We carried out dynamic force manipulations $in$ $silico$ on a variety of superhelical protein fragments from myosin, chemotaxis receptor, vimentin, fibrin, and phenylalanine zippers that vary in size and topology of their $\alpha$-helical…
Molecular dynamics simulations are often used to provide feedback in the design workflow of DNA nanostructures. However, even with coarse-grained models, convergence of distributions from unbiased simulation is slow, limiting applications…
The folding kinetics of a number of sequences for off-lattice continuum model of proteins is studied using Langevin simulations at two values of the friction coefficient. We show that there is a remarkable correlation between folding times,…
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…
In this paper we describe a new model for solidification with heat flux using the phase field crystal (PFC) framework. The equations are thermodynamically consistent, in the sense that the time rate of change of the entropy density is…
Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground…
Using a variant of parallel tempering, we study the changes in sampling within a simulation when the all-atom model is coupled to a Go-like potential. We find that the native structure is not the lowest-energy configuration in the all-atom…