Base excision repair enzymes (BERs) detect and repair oxidative DNA damage with efficacy despite the small size of the defects and their often only minor structural impact. A charge transfer (CT) model for rapid scanning of DNA stretches has been evoked to ...
Data-driven approaches have been applied to reduce the cost of accurate computational studies on materials, by using only a small number of expensive reference electronic structure calculations for a representative subset of the materials space, and using ...
Statistical (machine-learning, ML) models are more and more often used in computational chemistry as a substitute to more expensive ab initio and parametrizable methods. While the ML algorithms are capable of learning physical laws implicitly from data, ad ...
Accessing the thermal transport properties of glasses is a major issue for the design of production strategies of glass industry, as well as for the plethora of applications and devices where glasses are employed. From the computational standpoint, the che ...
We propose a novel approach to evaluating the ionic Seebeck coefficient in electrolytes from relatively short equilibrium molecular dynamics simulations, based on the Green-Kubo theory of linear response and Bayesian regression analysis. By exploiting the ...
Molecular quantum dynamics simulations are essential for understanding many fundamental phenomena in physics and chemistry. They often require solving the time-dependent Schrödinger equation for molecular nuclei, which is challenging even for medium-sized ...
In aqueous solutions, a charged surface causes the redistribution of nearby ions. The ion layers formed are known as the electrical double layer (EDL), and are widespread in many systems involving electrochemistry, colloidal science, biomedicine, and energ ...
Transmembrane protein 16 F (TMEM16F) is a Ca2+-activated homodimer which functions as an ion channel and a phospholipid scramblase. Despite the availability of several TMEM16F cryogenic electron microscopy (cryo-EM) structures, the mechanism of activation ...
Hydrogen clathrate hydrates are ice-like crystalline substances in which hydrogen molecules are trapped inside polyhedral cages formed by the water molecules. Small cages can host only a single H-2 molecule, while each large cage can be occupied by up to f ...
The design and discovery of potential novel materials is critical for the advancement of climate change mitigation technologies. In this respect, metal-organic frameworks (MOFs) have received considerable attention over the last two decades. The combinatio ...
Machine learned interatomic interaction potentials have enabled efficient and accurate molecular simulations of closed systems. However, external fields, which can greatly change the chemical structure and/or reactivity, have been seldom included in curren ...
Computational chemistry aims to simulate reactions and molecular properties at the atomic scale, advancing the design of novel compounds and materials with economic, environmental, and societal implications. However, the field relies on approximate quantum ...
We present an efficient method to compute diffusion coefficients of multiparticle systems with strong interactions directly from the geometry and topology of the potential energy field of the migrating particles. The approach is tested on Li-ion diffusion ...
The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments sp ...
Molecular dynamics (MD) simulations have emerged as a transformative approach to analyse molecular systems at the atomic level, offering valuable insights into complex biological processes. Many biological phenomena can only accurately be described by inco ...
At present, there is no general standard automated method for engineering metalloenzymes, industrially-relevant systems able to catalyze environmentally friendly reactions. One of the most studied natural metalloenzymes is the second isoform of human carbo ...
A long-standing goal of science is to accurately simulate large molecular systems using quantum mechanics. The poor scaling of current quantum chemistry algorithms on classical computers, however, imposes an effective limit of about a few dozen atoms on tr ...
. High-resolution simulations of particle-based kinetic plasma models typically require a high number of particles and thus often become computationally intractable. This is exacerbated in multi-query simulations, where the problem depends on a set of para ...
We introduce two new approximation methods for the numerical evaluation of the long-range component of the range-separated Coulomb potential and the approximation of the resulting high dimensional Two-Electron Integrals tensor (TEI) with long-range interac ...
Metal plasticity is an inherently multiscale phenomenon due to the complex long-range field of atomistic dislocations that are the primary mechanism for plastic deformation in metals. Atomistic/Continuum (A/C) coupling methods are computationally efficient ...
