相关论文: PASTA: Python Algorithms for Searching Transition …
Chemical reactions inside cells are generally considered to happen within fixed-size compartments. Needless to say, cells and their compartments are highly dynamic. Thus, such stringent assumptions may not reflect biochemical reality, and…
The essence of a chemical reaction lies in the redistribution and reorganization of electrons, which is often manifested through electron transfer or the migration of electron pairs. These changes are inherently discrete and abrupt in the…
Density functional theory (DFT) underpins modern atomistic simulations of transition-metal surfaces. It can predict key properties linked to catalytic performance, such as adsorption energies and barrier heights, enabling new paradigms in…
The fold recognition methods are promissing tools for capturing the structure of a protein by its amino acid residues sequence but their use is still restricted by the needs of huge computational resources and suitable efficient algorithms…
The simulated tempering (ST) is an important method to deal with systems whose phase spaces are hard to sample ergodically. However, it uses accepting probabilities weights which often demand involving and time consuming calculations. Here…
Leveraging Transformer attention has led to great advancements in HDR deghosting. However, the intricate nature of self-attention introduces practical challenges, as existing state-of-the-art methods often demand high-end GPUs or exhibit…
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…
The formation of complex nonuniform phases of nuclear matter, known as nuclear pasta, is studied with molecular dynamics simulations containing 51200 nucleons. A phenomenological nuclear interaction is used that reproduces the saturation…
The Minima Hopping global optimization method uses physically realizable molecular dynamics moves in combination with an energy feedback that guarantees the escape from any potential energy funnel. For the purpose of finding reactions…
Shortcuts to adiabaticity (STA) are techniques allowing rapid variation of the system Hamiltonian without inducing excess heating. Fast optical transfer of atoms between different locations is a prime example of an STA application. We show…
The recrossing correction to the transition state theory estimate of a thermal rate can be difficult to calculate when the energy barrier is flat. This problem arises, for example, in polymer escape if the polymer is long enough to stretch…
Excited state proton transfer is an ubiquitous phenomenon in biology and chemistry, spanning from the ultrafast reactions of photo-bases and acids to light-driven, enzymatic catalysis and photosynthesis. However, the simulation of such…
As computational chemistry methods evolve, dynamic effects have been increasingly recognized to govern chemical reaction pathways in both organic and inorganic systems. Here, we introduce a committor-based workflow that integrates a…
Transition Path Theory (TPT) provides a rigorous framework to investigate the dynamics of rare thermally activated transitions. In this theory, a central role is played by the forward committor function q^+(x), which provides the ideal…
Mechanistic models are important tools to describe and understand biological processes. However, they typically rely on unknown parameters, the estimation of which can be challenging for large and complex systems. We present pyPESTO, a…
We introduce a path sampling method for obtaining statistical properties of an arbitrary stochastic dynamics. The method works by decomposing a trajectory in time, estimating the probability of satisfying a progress constraint, modifying…
We describe PyRaTE, a new, non-local thermodynamic equilibrium (non-LTE) line radiative transfer code developed specifically for post-processing astrochemical simulations. Population densities are estimated using the escape probability…
Sensitivity analysis of biochemical reactions aims at quantifying the dependence of the reaction dynamics on the reaction rates. The computation of the parameter sensitivities, however, poses many computational challenges when taking…
The study of complex many-body systems via analysis of the trajectories of the units that dynamically move and interact within them is a non-trivial task. The workflow for extracting meaningful information from the raw trajectory data is…
An open-source and modular Python package, Catalight, is developed and demonstrated to automate (photo)catalysis measurements. (Photo)catalysis experiments require studying several parameters to evaluate performance, including temperature,…