Related papers: Dominant folding pathways of a peptide chain, from…
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…
We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…
We study the role of quantum fluctuations of atomic nuclei in the real-time dynamics of non-equilibrium macro-molecular transitions. To this goal we introduce an extension of the Dominant Reaction Pathways (DRP) formalism, in which the…
We use the Dominant Reaction Pathway (DRP) approach to study the dynamics of the folding of a beta-hairpin, within a model which accounts for both native and non-native interactions. We compare the most probable folding pathways calculated…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
We investigate the folding mechanism of the WW domain Fip35 using a realistic atomistic force field by applying the Dominant Reaction Pathways (DRP) approach. We find evidence for the existence of two folding pathways, which differ by the…
We assess the reliability of the recently developed approach denominated Dominant Reaction Pathways (DRP) by studying the folding of a 16-residue beta-hairpin, within a coarse-grained Go-type model. We show that the DRP predictions are in…
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…
A new simulation approach of field evaporation is presented. The model combines classical electrostatics with molecular dynamics (MD) simulations. Unlike previous atomic-level simulation approaches, our method does not rely on an…
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…
Ultrafast non-equilibrium dynamics offer a route to study the microscopic interactions that govern macroscopic behavior. In particular, photo-induced phase transitions (PIPTs) in solids provide a test case for how forces, and the resulting…
Characterizing thermally activated transitions in high-dimensional rugged energy surfaces is a very challenging task for classical computers. Here, we develop a quantum annealing scheme to solve this problem. First, the task of finding the…
Spontaneous structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, physics-based computer simulations like Molecular Dynamics (MD) enable us to investigate these…
We expand iterative numerically-exact influence functional path-integral tools and present a method capable of following the nonequilibrium time evolution of subsystems coupled to multiple bosonic and fermionic reservoirs simultaneously.…
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…
This paper is devoted to the development of a theoretical and computational framework to efficiently sample the statistically significant thermally activated reaction pathways, in multi-dimensional systems obeying Langevin dynamics. We show…
We study the dynamics of quantum excitations inside macromolecules which can undergo conformational transitions. In the first part of the paper, we use the path integral formalism to rigorously derive a set of coupled equations of motion…
The discovery of topological phases in condensed matter systems has changed the modern conception of phases of matter. The global nature of topological ordering makes these phases robust and hence promising for applications. However, the…
Natural proteins fold to a unique, thermodynamically dominant state. Modeling of the folding process and prediction of the native fold of proteins are two major unsolved problems in biophysics. Here, we show successful all-atom ab initio…
We develop a new fermionic path-integral formalism to analyze the phase diagram of open nonequilibrium systems. The formalism is applied to analyze an ensemble of two-level atoms interacting with a single-mode optical cavity, described by…