Related papers: Soliton driven relaxation dynamics and universalit…
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
Among the unsolved problems in computational biology, protein folding is one of the most interesting challenges. To study this folding, tools like neural networks and genetic algorithms have received a lot of attention, mainly due to the…
We theoretically investigate the kinetics of the folding transition of a single semiflexible polymer. In the folding transition, the growth rate decrease with an increase in the number of monomers in a collapsed domain, suggesting that the…
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely,…
Many processes of scientific importance are characterized by time scales that extend far beyond the reach of standard simulation techniques. To circumvent this impediment a plethora of enhanced sampling methods has been developed. One…
We discuss general thermodynamic properties of molecular structure formation processes like protein folding by means of simplified, coarse-grained models. The conformational transitions accompanying these processes exhibit similarities to…
Machine learning (ML) is rapidly transforming the way molecular dynamics simulations are performed and analyzed, from materials modeling to studies of protein folding and function. ML algorithms are often employed to learn low-dimensional…
In this study, we explore nucleation and the transition state ensemble of the ribosomal protein S6 using a Monte Carlo Go model in conjunction with restraints from experiment. The results are analyzed in the context of extensive…
Methods of local topology are introduced to the field of protein physics. This is achieved by explaining how the folding and unfolding processes of a globular protein alter the local topology of the protein's C-alpha backbone through…
Biomolecular folding and function are often coupled. During molecular recognition events, one of the binding partners may transiently or partially unfold, allowing more rapid access to a binding site. We describe a simple model for this…
A rigourous Monte Carlo method for protein folding simulation on lattice model is introduced. We show that a parameter which can be seen as the rigidity of the conformations has to be introduced in order to satisfy the detailed balance…
Molecular-scale computation is crucial for smart materials and nanoscale devices, yet creating single-molecule systems capable of complex computations remains challenging. We present a theoretical framework for a single-molecule computer…
We have performed a multicanonical molecular dynamics simulation on a simple model protein.We have studied a model protein composed of charged, hydrophobic, and neutral spherical bead monomers.Since the hydrophobic interaction is considered…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
Performing full-resolution atomistic simulations of nucleic acid folding has remained a challenge for biomolecular modeling. Understanding how nucleic acids fold and how they transition between different folded structures as they unfold and…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
The quantitative description of model protein folding kinetics using a diffusive collective reaction coordinate is examined. Direct folding kinetics, diffusional coefficients and free energy profiles are determined from Monte Carlo…