相关论文: Entropy and Energy Profiles of Chemical Reactions
Chemical reaction sampling critically depends on collective variables (CVs) that capture the slow degrees of freedom governing reactive transformations. However, existing reaction CVs are often defined in geometric space or learned in a…
Enhanced sampling methods typically require predefined collective variables (CVs) that presuppose knowledge of reaction coordinates, restricting the discovery of unanticipated transition mechanisms or intermediates. Here, we show that a…
Enhanced sampling techniques such as umbrella sampling and metadynamics are now routinely used to provide information on how the thermodynamic potential, or free energy, depends on a small number of collective variables. The free energy…
Understanding the long-time dynamics of complex physical processes depends on our ability to recognize patterns. To simplify the description of these processes, we often introduce a set of reaction coordinates, customarily referred to as…
High-dimensional metastable molecular system can often be characterised by a few features of the system, i.e. collective variables (CVs). Thanks to the rapid advance in the area of machine learning and deep learning, various deep…
Chemical reactions involve the movement of charges, and this work presents a mathematical model for describing chemical reactions in electrolytes. The model is developed using an energy variational method that aligns with classical…
We consider viscous, heat conducting mixtures of molecularly miscible chemical species forming a fluid in which the constituents can undergo chemical reactions. Assuming a common temperature for all components, we derive a closed system of…
Generating a data set that is representative of the accessible configuration space of a molecular system is crucial for the robustness of machine learned interatomic potentials (MLIP). However, the complexity of molecular systems,…
In molecular dynamics (MD) simulations, transitions between states are often rare events due to energy barriers that exceed the thermal temperature. Because of their infrequent occurrence and the huge number of degrees of freedom in…
Like any fluid heated from below, the atmosphere is subject to vertical instability which triggers convection. Convection occurs on small time and space scales, which makes it a challenging feature to include in climate models. Usually…
Collective variables (CVs) are low-dimensional projections of high-dimensional system states. They are used to gain insights into complex emergent dynamical behaviors of processes on networks. The relation between CVs and network measures…
Since molecular energy transformations are responsible for chemical reaction rates at the most fundamental level, chemical kinetics should provide some information about molecular energies. This is the premise and objective of this note. We…
The dynamics of physical systems that require high-dimensional representation can often be captured in a few meaningful degrees of freedom called collective variables (CVs). However, identifying CVs is challenging and constitutes a…
Given a chemical reaction going from reactant (R) to the product (P) on a potential energy surface (PES) and a collective variable (CV) that discriminates between R and P, one can define a free-energy profile (FEP) as the logarithm of the…
The long-time behavior of many complex molecular systems is often governed by slow relaxation dynamics that can be described by a few reaction coordinates referred to as collective variables (CVs). However, identifying CVs hidden in a…
For a single enzyme or molecular motor operating in an aqueous solution of non-equilibrated solute concentrations, a thermodynamic description is developed on the level of an individual trajectory of transitions between states. The concept…
Understanding the behavior of complex molecular systems is a fundamental problem in physical chemistry. To describe the long-time dynamics of such systems, which is responsible for their most informative characteristics, we can identify a…
The bottleneck in enhanced sampling lies in finding collective variables (CVs) that can effectively accelerate protein conformational changes. True reaction coordinates (tRCs) that can predict the committor are considered the optimal CVs,…
We use local diffusion maps to assess the quality of two types of collective variables (CVs) for a recently published hydrogen combustion benchmark dataset~\cite{guan2022benchmark} that contains ab initio molecular dynamics trajectories and…
The evolution of chemical reaction networks is often analyzed through kinetic models and energy landscapes, but these approaches fail to capture the deeper structural constraints governing complexity growth. In chemical reaction networks,…