Related papers: Accurate biomolecular simulations account for elec…
The inclusion of electronic polarization is of crucial importance in molecular simulations of systems containing charged moieties. When neglected, as often done in force field simulations, charge-charge interactions in solution may become…
The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER,…
The quality of biomolecular simulations critically depends on the accuracy of the force field used to calculate the potential energy of the molecular configurations. Currently, most simulations employ non-polarisable force fields, which…
In X-ray photoelectron spectroscopy (XPS), the injected hole interacts with the electronic polarization cloud induced by the hole itself, ultimately resulting in a lower binding energy. Such polarization effect can shift the core-level…
Quasi-optical experiments are emerging as a powerful technique to probe magnetic transitions in molecular spin systems. However, the simultaneous presence of the electric- and magnetic-dipole induced transitions poses the challenge of…
We present an approach to electronic polarization in molecular solids treated as a set of quantum systems interacting classically. Individual molecules are dealt with rigorously as quantum-mechanical systems subject to classical external…
The method has been developed to calculate effects of polarization not only for a atomic core in a field of valent electron, but also polarization of atom as a whole in the electron-hole formalism. A secondary quantized density matrix for…
Electrostatic interactions involving proteins depend not just on the ionic charges involved but also on their chemical identities. Here we examine the origins of incompletely understood differences in the strength of association of…
Accurate prediction of binding free energies is critical to streamlining the drug development and protein design process. With the advent of GPU acceleration, absolute alchemical methods, which simulate the removal of ligand electrostatics…
Cell polarity and movement are fundamental to many biological functions. Experimental and theoretically studies have indicated that interactions of certain proteins lead to the cell polarization which plays a key role in controlling the…
A better understanding of interfacial mechanisms is needed to improve the performances of electrochemical devices. Yet, simulating an electrode surface at fixed electrolyte composition remains a challenge. Here we apply a finite electric…
We employ the exact factorization of a multi-component wavefunction to analyze the dynamics of interacting photons, electrons and nuclei. We consider physical situations emerging in the regime of strong coupling between light excitations…
Exposing a molecule to intense light pulses may bring this molecule to a nonstationary quantum state, thus launching correlated dynamics of electronic and nuclear subsystems. Although much had been achieved in the understanding of…
One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise…
When it is polarised, a cell develops an asymmetric distribution of specific molecular markers, cytoskeleton and cell membrane shape. Polarisation can occur spontaneously or be triggered by external signals, like gradients of signalling…
It has been long recognized that the spatial polarization of the electronic clouds in molecules, and the spatial arrangements of atoms into chiral molecular structures, play crucial roles in physics, chemistry and biology. However, these…
In this paper, a review on dielectric mixtures and the importance of the numerical simulations of dielectric mixtures are presented. It stresses on the interfacial polarization observed in mixtures. It is shown that this polarization can…
We present a detailed study of the effect of the double core polarization (the polarization of the core electrons due to the simultaneous action of the electric dipole and parity-violating weak fields) for amplitudes of the s-s and s-d…
Machine learning force fields offer the ability to simulate biomolecules with quantum mechanical accuracy while significantly reducing computational costs, attracting growing attention in biophysics. Meanwhile, leveraging the efficiency of…
In heavy atoms and ions, nuclear structure effects are significantly enhanced due to the overlap of the electron wave functions with the nucleus. This overlap rapidly increases with the nuclear charge $Z$. We study the energy level shifts…