相关论文: Structural Feature in Dynamical Processes Accelera…
The minimum energy path (MEP) describes the mechanism of reaction, and the energy barrier along the path can be used to calculate the reaction rate in thermal systems. The nudged elastic band (NEB) method is one of the most commonly used…
Characterizing conformational transitions in physical systems remains a fundamental challenge, as traditional sampling methods struggle with the high-dimensional nature of molecular systems and high-energy barriers between stable states.…
The minimum energy path (MEP) is the most probable transition path that connects two equilibrium states of a potential energy landscape. It has been widely used to study transition mechanisms as well as transition rates in the fields of…
We describe a robust and efficient chain-of-states method for computing Minimum Energy Paths~(MEPs) associated to barrier-crossing events in poly-atomic systems. The path is parametrized in terms of a continuous variable $t \in [0,1]$ that…
The Chain-of-states(CoS) methods like nudge elastic band(NEB) method can be used to determine the minimum energy path (MEP) and transition state (TS) between two end local minima. However, the CoS methods are inefficient for difficult cases…
We present an efficient algorithm for calculating the minimum energy path (MEP) and energy barriers between local minima on a multidimensional potential energy surface (PES). Such paths play a central role in the understanding of transition…
The discovery of a minimum energy pathway (MEP) between metastable states is crucial for scientific tasks including catalyst and biomolecular design. However, the standard nudged elastic band (NEB) algorithm requires hundreds to tens of…
Stochastic electronic structure theories, e.g., Quantum Monte Carlo methods, enable highly accurate total energy calculations which in principle can be used to construct highly accurate potential energy surfaces. However, their stochastic…
Identifying minimum-energy paths (MEPs) is crucial for understanding chemical reaction mechanisms but remains computationally demanding. We introduce MEPIN, a scalable machine-learning method for efficiently predicting MEPs from reactant…
Accurate determination of transition states is central to an understanding of reaction kinetics. Double-endpoint methods where both initial and final states are specified, such as the climbing image nudged elastic band (CI-NEB), identify…
We present a new method that enables the identification and analysis of both transition and metastable conformational states from atomistic or coarse-grained molecular dynamics (MD) trajectories. Our algorithm is presented and studied by…
Efficient and reliable identification and optimization of transition state structures is a longstanding challenge in computational chemistry. Popular chain-of-states methods require hundreds if not thousands of ab initio calculations to…
The modeling of solid-state transformations, such as polymorphic transitions and chemical reactions in molecular crystals, is vital for many applications including drug design or the development of new synthesis methods. However, a…
In finite systems, such as nanoparticles and gas-phase molecules, calculations of minimum energy paths (MEPs) connecting initial and final states of transitions as well as searches for saddle points are complicated by the presence of…
Popular methods for identifying transition paths between energy minima, such as the nudged elastic band and string methods, typically do not incorporate potential energy curvature information, leading to slow relaxation to the minimum…
Under certain conditions, the dynamics of coarse-grained models of solvated proteins can be described using a Markov state model, which tracks the evolution of populations of configurations. The transition rates among states that appear in…
We show that neural networks can be optimized to represent minimum energy paths as continuous functions, offering a flexible alternative to discrete path-search methods such as Nudged Elastic Band (NEB). Our approach parameterizes reaction…
We apply the minimum energy paths (MEPs) approach to study the helix unwinding transition in chiral nematic liquid crystals. A mechanism of the transition is determined by a MEP passing through a first order saddle point on the free energy…
Minimum energy paths for transitions such as atomic and/or spin rearrangements in thermalized systems are the transition paths of largest statistical weight. Such paths are frequently calculated using the nudged elastic band method, where…
MAB phases (MABs) are atomically-thin laminates of ceramic/metallic-like layers, having made a breakthrough in the development of 2D materials. Though theoretically offering a vast chemical and phase space, relatively few MABs have yet been…