Related papers: Soliton driven relaxation dynamics and universalit…
We present a method to investigate the kinetics of protein folding on a long time-scale and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. The approach is based on the formal analogy…
In this study we evaluate, at full atomic detail, the folding processes of two small helical proteins, the B domain of protein A and the Villin headpiece. Folding kinetics are studied by performing a large number of ab initio Monte Carlo…
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…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
A novel approach to protein folding dynamics is presented. We suggest that folding of protein may be mediated via interaction with solitons which propagate along the molecular chain. A simple toy model is presented in which a Sine-Gordon…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical…
We introduce a powerful iterative algorithm to compute protein folding pathways, with realistic all-atom force fields. Using the path integral formalism, we explicitly derive a modified Langevin equation which samples directly the ensemble…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
Modeling and simulating the protein folding process overall remains a grand challenge in computational biology. We systematically investigate end-to-end quantum algorithms for simulating various protein dynamics with effects, such as…
We introduce a novel generalization of the discrete nonlinear Schr\"odinger equation. It supports solitons that describe how proteins fold. As an example we scrutinize the villin headpiece HP35, an archetypal protein for testing both…
Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…
We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding - all sidechain and backbone torsions - and…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
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…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…