相关论文: Identification of simple reaction coordinates from…
In the study of rare events in complex systems with many degrees of freedom, a key element is to identify the reaction coordinates of a given process. Over recent years, a number of methods and protocols have been developed to extract the…
Reaction coordinates (RCs) are the few essential coordinates of a protein that control its functional processes, such as allostery, enzymatic reaction, and conformational change. They are critical for understanding protein function and…
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,…
Finding optimal reaction coordinates and predicting accurate kinetic rates for activated processes are two of the foremost challenges of molecular simulations. We introduce an algorithm that tackles the two problems at once: starting from a…
Understanding mechanisms of rare but important events in complex molecular systems, such as protein folding or ligand (un)binding, requires accurately mapping transition paths from an initial to a final state. The committor is the ideal…
Reaction Coordinates (RCs) are indicators of hidden, low-dimensional mechanisms that govern the long-term behavior of high-dimensional stochastic processes. We present a novel and general variational characterization of optimal RCs and…
We consider a class of nonequilibrium systems of interacting agents with pairwise interactions and quenched disorder in the dynamics featuring, in the thermodynamic limit, phase transitions. We provide conditions on the microscopic…
Reaction systems are discrete dynamical systems inspired by bio-chemical processes, whose dynamical behaviour is expressed by set-theoretic operations on finite sets. Reaction systems thus provide a description of bio-chemical phenomena…
Complex biochemical pathways or regulatory enzyme kinetics can be reduced to chains of elementary reactions, which can be described in terms of chemical kinetics. This discipline provides a set of tools for quantifying and understanding the…
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…
Effective dynamics using conditional expectation was proposed in [F. Legoll and T. Leli\`evre, Nonlinearity, 2010] to approximate the essential dynamics of high-dimensional diffusion processes along a given reaction coordinate. The…
Interpretable reaction coordinates are essential for understanding rare conformational transitions in molecular dynamics. The Atomistic Mechanism Of Rare Events in Molecular Dynamics (AMORE-MD) framework enhances interpretability of…
The identification of meaningful reaction coordinates plays a key role in the study of complex molecular systems whose essential dynamics is characterized by rare or slow transition events. In a recent publication, precise defining…
In this work, we demonstrate that Linear Discriminant Analysis (LDA) applied to atomic positions in two different states of a biomolecule produces a good reaction coordinate between those two states. Atomic coordinates of a macromolecule…
A new self-learning algorithm for accelerated dynamics, reconnaissance metadynamics, is proposed that is able to work with a very large number of collective coordinates. Acceleration of the dynamics is achieved by constructing a bias…
Local interactions among biomolecules, and the role played by their environment, have gained increasing attention in modelling biochemical reactions. By defining the automaton of molecular perceptions, we explore an agent-based…
Reaction-diffusion equations are widely used as the governing evolution equations for modeling many physical, chemical, and biological processes. Here we derive reaction-diffusion equations to model transport with reactions on a…
Reaction rate equations are ordinary differential equations that are frequently used to describe deterministic chemical kinetics at the macroscopic scale. At the microscopic scale, the chemical kinetics is stochastic and can be captured by…
We investigate and provide optimal sets of reaction coordinates for mixed pairs of molecules displaying polar, uniaxial, or spherical symmetry in two and three dimensions. These coordinates are non-redundant, i.e., they implicitly involve…
The construction of a reaction network containing all relevant intermediates and elementary reactions is necessary for the accurate description of chemical processes. In the case of a complex chemical reaction (involving, for instance, many…