Related papers: Fast Surface Based Electrostatics for biomolecules…
Electrostatic interactions play crucial roles in biophysical processes such as protein folding and molecular recognition. Poisson-Boltzmann equation (PBE)-based models have emerged as widely used in modeling these important processes.…
Despite the well-established presence of amorphous compounds on planetary bodies such as the Moon and Mercury due to space weathering, the direct effect of atomic arrangement on the surface binding energies (SBEs) of elements on these…
The structure and dynamics of a molecular system is governed by its potential energy surface (PES), representing the total energy as a function of the nuclear coordinates. Obtaining accurate potential energy surfaces is limited by the…
Closed-form, analytical approximations for electrostatic properties of molecules are of unique value, as these can provide computational speed, versatility, and physical insight. Here, we derive a simple, closed-form formula for the…
Molecular beam experiments that use low-temperature bolometers as (energy-) detectors are well suited to the study of physisorption and recombination of hydrogen on low-temperature surfaces. Experiments where this technique is combined with…
Accurate and fast calculations of localized surface plasmon resonances (LSPR) in metallic nanoparticles is essential for applications in sensing, nano-optics, and energy harvesting. Although full-wave numerical techniques such as the…
We present a highly efficient method to directly simulate the photodissociation followed by Coulomb explosion of methyl iodide. In order to achieve statistical reliability, more than 40,000 trajectories are calculated on accurate potential…
Rapid and accurate assessment of protein structural models is essential for protein structure prediction and design. Great progress has been made in this regard, especially by recent development of ``knowledge-based'' potentials. Various…
One of the goals in the development of large scale electronic structure methods is to perform calculations explicitly for a localised region of a system, while still taking into account the rest of the system outside of this region. An…
The recent developments of quantum computing present potential novel pathways for quantum chemistry, as the increased computational power of quantum computers could be harnessed to naturally encode and solve electronic structure problems.…
We develop a random batch Ewald (RBE) method for molecular dynamics simulations of particle systems with long-range Coulomb interactions, which achieves an $O(N)$ complexity in each step of simulating the $N$-body systems. The RBE method is…
The Poisson-Boltzmann equation (PBE) is a relevant partial differential equation commonly used in biophysical applications to estimate the electrostatic energy of biomolecular systems immersed in electrolytic solutions. A conventional mean…
Solid-liquid interfaces are at the heart of many modern-day technologies and provide a challenge to many materials simulation methods. A realistic first-principles computational study of such systems entails the inclusion of solvent…
A family of fast sampling methods is introduced here for molecular simulations of systems having rugged free energy landscapes. The methods represent a generalization of a strategy consisting of adjusting a model for the free energy as a…
Molecular dynamics simulations of biomolecules have been widely adopted in biomedical studies. As classical point-charge models continue to be used in routine biomolecular applications, there have been growing demands on developing…
The determination of the solvation free energy of ions and molecules holds profound importance across a spectrum of applications spanning chemistry, biology, energy storage, and the environment. Molecular dynamics simulations are a powerful…
We present an energy-specific Bethe-Salpeter equation (BSE) implementation for efficient core and valence optical spectrum calculations. In energy-specific BSE, high-lying excitation energies are obtained by constructing trial vectors and…
Modeling electronic systems is an important application for quantum computers. In the context of materials science, an important open problem is the computational description of chemical reactions on surfaces. In this work, we outline a…
Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the…
In the given paper we describe methods finding analytical gradients (derivatives) of solvation energy over atomic coordinates. It is made both for not polar energy and for the polar energy found by methods PCM, COSMO and SGB. These…