Related papers: Fast Surface Based Electrostatics for biomolecules…
The evaluation of electrostatic energy for a set of point charges in a periodic lattice is a computationally expensive part of molecular dynamics simulations (and other applications) because of the long-range nature of the Coulomb…
We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coarse grained (CG) potential and test it for a biomolecular…
This work further improves the pseudo-transient approach for the Poisson Boltzmann equation (PBE) in the electrostatic analysis of solvated biomolecules. The numerical solution of the nonlinear PBE is known to involve many difficulties,…
Ab initio modeling of electrochemical systems is becoming a key tool for understanding and predicting electrochemical behavior. Development and careful benchmarking of computational electrochemical methods are essential to ensure their…
The continuum theory applied to bimolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like…
Experimental determination of absolute surface energies remains a challenge. We propose a simple method based on two independent measurements on 3D and 2D equilibrium shapes completed by the analysis of the thermal fluctuation of an…
We report an ab initio evaluation of the surface energy of a simple metal, performed via a coupling-constant integration over the dynamical density-response function. The rapid rate of change of the electron density at the surface is…
Free energy calculations are widely used tools in computational chemistry, but their dependence on the assignment of partial charges during force field parametrization reduces their accuracy and reproducibility. In this work, we highlight…
Lipid vesicles appear ubiquitously in biological systems. Understanding how the mechanical and intermolecular interations deform vesicle membrane is a fundamental question in biophysics. In this article we developed a fast algorithm to…
Molecules in equilibrium follow a Boltzmann distribution, making the underlying energy landscape a physically grounded modeling objective. However, such landscapes are difficult to learn from data and, once learned, hard to sample from.…
We present an efficient approach for simulating Coulomb systems confined by planar polarizable surfaces. The method is based on the solution of Poisson equation using periodic Green functions. It is shown that the electrostatic energy…
The $GW$-Bethe-Salpeter Equation (BSE) method is promising for calculating the low-lying excited states of molecular systems. So far, it has only been applied to rather small molecules, and in the commonly implemented diagonal…
Free energies govern the behavior of soft and liquid matter, and improving their predictions could have a large impact on the development of drugs, electrolytes or homogeneous catalysts. Unfortunately, it is challenging to devise an…
Predicting the binding affinity between small molecules and target macromolecules while combining both speed and accuracy, is a cornerstone of modern computational drug discovery which is critical for accelerating therapeutic development.…
The presence of solvent tunes many properties of a molecule, such as its ground and excited state geometry, dipole moment, excitation energy, and absorption spectrum. Because the energy of the system will vary depending on the solvent…
Coulomb interactions are present in a wide variety of all-atom force fields. Spherical truncations of these interactions permit fast simulations but are problematic due to their incorrect thermodynamics. Herein we demonstrate that simple…
An accurate and efficient numerical electromagnetic model for superconducting qubits is essential for characterizing and minimizing design-dependent dielectric losses. The energy participation ratio (EPR) is the commonly adopted metric used…
We present a new method for calculating CMB anisotropies in a non-flat Friedmann universe, relying on a very stable algorithm for the calculation of hyperspherical Bessel functions, that can be pushed to arbitrary precision levels. We also…
The effect of solvent on the free energy of reaction intermediates adsorbed on electrocatalyst surfaces can significantly change the thermochemical overpotential, but accurate calculations of this are challenging. Here, we present…
Considering recent advancements and successes in the development of efficient quantum algorithms for electronic structure calculations --- alongside impressive results using machine learning techniques for computation --- hybridizing…