Related papers: Constraint methods for determining pathways and fr…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
In many systems, the time scales of the microscopic dynamics and macroscopic dynamics of interest are separated by many orders of magnitude. Examples abound, for instance nucleation, protein folding, and chemical reactions. For these…
The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics…
The evaluation of nucleation rates from molecular dynamics trajectories is hampered by the slow nucleation time scale and impact of finite size effects. Here, we show that accurate nucleation rates can be obtained in a very general fashion…
We present an overview of the reaction coordinate approach to handling strong system-reservoir interactions in quantum thermodynamics. This technique is based on incorporating a collective degree of freedom of the reservoir (the reaction…
In this study, we introduce a training protocol for developing machine learning force fields (MLFFs), capable of accurately determining energy barriers in catalytic reaction pathways. The protocol is validated on the extensively explored…
We propose an efficient novel path sampling-based framework designed to accelerate the investigation of rare events in complex molecular systems. A key innovation is the shift from sampling restricted path ensemble distributions, as in…
Identifying reaction coordinates(RCs) is an active area of research, given the crucial role RCs play in determining the progress of a chemical reaction. The choice of the reaction coordinate is often based on heuristic knowledge. However,…
Many physical systems have underlying safety considerations that require that the policy employed ensures the satisfaction of a set of constraints. The analytical formulation usually takes the form of a Constrained Markov Decision Process…
We propose algorithms for determining both lower and upper bounds for the energy barriers encountered by a flux line in moving through a two-dimensional random potential. Analytical arguments, supported by numerical simulations, suggest…
When a chemical reaction is driven by an external field, the transition state that the system must pass through as it changes from reactant to product -for example, an energy barrier- becomes time-dependent. We show that for periodic…
We extend the non-parametric framework of reaction coordinate optimization to non-equilibrium ensembles of (short) trajectories. For example, we show how, starting from such an ensemble, one can obtain an equilibrium free energy profile…
Mathematical and computational tools have proven to be reliable in decision-making processes. In recent times, in particular, machine learning-based methods are becoming increasingly popular as advanced support tools. When dealing with…
A modification of the Adaptive Biasing Force method is introduced, in which the free energy is approximated by a sum of tensor products of one-dimensional functions. This enables to handle a larger number of reaction coordinates than the…
A novel mechanism for the appearance of oriented processes is investigated with a flexible dynamical system overcoming barriers. Under non-equilibrium condition with external driving, reaction paths deviate from that at equilibrium with an…
Moment dynamics in stochastic chemical kinetics often involve an infinite chain of coupled equations, where lower-order moments depend on higher-order ones, making them analytically intractable. Moment bounding via semidefinite programming…
Deep reinforcement learning algorithms typically act on the same set of actions. However, this is not sufficient for a wide range of real-world applications where different subsets are available at each step. In this thesis, we consider the…
Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…
We investigate whether making the friction spatially dependent on the reaction coordinate introduces quantum effects into the thermal reaction rates for dissipative reactions. Quantum rates are calculated using the numerically exact…
During a crossover via a switching mechanism from one 2-body potential to another as might be applied in modeling (chemical) reactions in the vicinity of bond formation, energy violations would occur due to finite step size which determines…