A methodology to calculate the decay rates of normal and resonant Auger processes in atoms and molecules based on the One-Center Approximation (OCA), using atomic radial Auger integrals, is implemented within the restricted-active-space self-consistent-field (RASSCF) and the multistate restricted-active-space perturbation theory of second order (MS-RASPT2) frameworks, as part of the OpenMolcas project

The recently introduced multisite tensor network path integral (MS-TNPI) allows simulation of extended quantum systems coupled to dissipative media. We use MS-TNPI to simulate the exciton transport and the absorption spectrum of a B850 bacteriochlorophyll (BChl) ring. The MS-TNPI network is extended to account for the ring topology of the B850 system. Accurate molecular-dynamics-based description of

We introduce perturbation and coupled-cluster theories based on a cluster mean-field reference for describing the ground state of strongly correlated spin systems. In cluster mean-field, the ground state wave function is written as a simple tensor product of optimized cluster states. The cluster language and the mean-field nature of the ansatz allow for a straightforward improvement which uses perturbation

In the original paper focusing on the unexpected and strong dependency of noncovalent interaction energy differences on isotropic Jastrow cutoff radii (rcut) setting within 1-determinant fixed-node diffusion Monte Carlo (FNDMC) computations involving effective core potentials (ECPs), wrong data and conclusions regarding the determinant localization approximation (DLA) (1) method were presented. The

Atomistic Molecular Dynamics (MD) simulations provide researchers the ability to model biomolecular structures such as proteins and their interactions with drug-like small molecules with greater spatiotemporal resolution than is otherwise possible using experimental methods. MD simulations are notoriously expensive computational endeavors that have traditionally required massive investment in specialized

In biological systems, proteins can be attracted to curved or stretched regions of lipid bilayers by sensing hydrophobic defects in the lipid packing on the membrane surface. Here, we present an efficient end-state free energy calculation method to quantify such sensing in molecular dynamics simulations. We illustrate that lipid packing defect sensing can be defined as the difference in mechanical

Co-crystals are a highly interesting material class as varying their components and stoichiometry in principle allows tuning supramolecular assemblies toward desired physical properties. The in silico prediction of co-crystal structures represents a daunting task, however, as they span a vast search space and usually feature large unit cells. This requires theoretical models that are accurate and fast

Constrained density functional theory (CDFT) is a powerful tool for the prediction of electron transfer parameters in condensed phase simulations at a reasonable computational cost. In this work we present an extension to CDFT in the popular mixed Gaussian/plane wave electronic structure package CP2K, implementing the additional force terms arising from a constraint based on Hirshfeld charge partitioning

The capability of current force fields to reproduce RNA structural dynamics is limited. Several methods have been developed to take advantage of experimental data in order to enforce agreement with experiments. Here, we extend an existing framework which allows arbitrarily chosen force-field correction terms to be fitted by quantification of the discrepancy between observables back-calculated from

High harmonic generation (HHG) takes place in all phases of matter. In gaseous atomic and molecular media, it has been extensively studied and is very well understood. In solids, research is ongoing, but a consensus is forming for the dominant microscopic HHG mechanisms. In liquids, on the other hand, no established theory yet exists, and approaches developed for gases and solids are generally inapplicable

We derive a formulation of molecular dynamics that generates only symmetric configurations. We implement it for all 2D planar and 3D space groups. An atlas of 2D Lennard-Jones crystals under all planar groups is created with symmetric molecular dynamics.

Identifying low-energy conformers with quantum mechanical accuracy for molecules with many degrees of freedom is challenging. In this work, we use the molecular dihedral angles as features and explore the possibility of performing molecular conformer search in a latent space with a generative model named variational auto-encoder (VAE). We bias the VAE towards low-energy molecular configurations to

We test a range of standard generalized Born (GB) models and protein force fields for a set of five experimentally characterized, designed peptides comprising alternating blocks of glutamate and lysine, which have been shown to differ significantly in α-helical content. Sixty-five combinations of force fields and GB models are evaluated in >800 μs of molecular dynamics simulations. GB models generally

The rapid progress in quantum-optical experiments, especially in the field of cavity quantum electrodynamics and nanoplasmonics, allows one to substantially modify and control chemical and physical properties of atoms, molecules, and solids by strongly coupling to the quantized field. Alongside such experimental advances has been the recent development of ab initio approaches such as quantum electrodynamical

In the initially published version of this article, the potential for the disulfide dihedral CαCβSS was incorrect in Figure 4E, with a sign error in A_{2,CαCβSS} from equation S11. Here is the corrected figure panel: We thank Claiborne W. Tydings, Dr. Oanh T. Vu, and Prof. Jens Meiler of Vanderbilt University for identifying this error. This article has not yet been cited by other publications.

Molecular dynamics (MD) simulations are coming of age in the study of nucleic acids, including specific tertiary structures such as G-quadruplexes. While being precious for providing structural and dynamic information inaccessible to experiments at the atomistic level of resolution, MD simulations in this field may still be limited by several factors. These include the force fields used, different

An emerging class of therapeutic molecules are cyclic peptides with over 40 cyclic peptide drugs currently in clinical use. Their mode of action is, however, not fully understood, impeding rational drug design. Computational techniques could positively impact their design, but modeling them and their interactions remains challenging due to their cyclic nature and their flexibility. This study presents

In the context of advanced hit-to-lead drug design based on atomistic molecular dynamics simulations, we propose a dual topology alchemical approach for calculating the relative binding free energy (RBFE) between two chemically distant compounds. The method (termed NE-RBFE) relies on the enhanced sampling of the end-states in bulk and in the bound state via Hamiltonian Replica Exchange, alchemically

In adaptive-bias enhanced sampling methods, a bias potential is added to the system to drive transitions between metastable states. The bias potential is a function of a few collective variables and is gradually modified according to the underlying free energy surface. We show that when the collective variables are suboptimal, there is an exploration–convergence tradeoff, and one must choose between