Related papers: Using the Fast Fourier Transform in Binding Free E…
Understanding design principles of biomolecular recognition is a key question of molecular biology. Yet the enormous complexity and diversity of biological molecules hamper the efforts to gain a predictive ability for the free energy of…
The standard particle-in-cell algorithm suffers from grid heating. There exists a gridless alternative which bypasses the deposition step and calculates each Fourier mode of the charge density directly from the particle positions. We show…
The surface free energies, interfacial tensions and correlation lengths of the Andrews-Baxter-Forrester models in regimes III and IV are calculated with fixed boundary conditions. The interfacial tensions are calculated between arbitrary…
The Fourier Transform is one of the most important linear transformations used in science and engineering. Cooley and Tukey's Fast Fourier Transform (FFT) from 1964 is a method for computing this transformation in time $O(n\log n)$.…
Living systems at the molecular scale are composed of many constituents with strong and heterogeneous interactions, operating far from equilibrium, and subject to strong fluctuations. These conditions pose significant challenges to…
We study universal bosonic few-body systems within the framework of effective field theory at leading order (LO). We calculate binding energies of systems of up to six particles and the atom-dimer scattering length. Convergence to the limit…
We present a methodology for accelerating the estimation of the free energy from path integral Monte Carlo simulations by considering an intermediate artificial reference system where interactions are inexpensive to evaluate numerically.…
Radio interferometers consisting of identical antennas arranged on a regular lattice permit fast Fourier transform beamforming, which reduces the correlation cost from $\mathcal{O}(n^2)$ in the number of antennas to $\mathcal{O}(n\log n)$.…
Structure factor twist averaging (sfTA) is a newer method that has been shown to reproduce twist-averaged (TA) CCSD energies for bulk systems at a low computational cost. In this work, we extend this method for the treatment of…
The molecular distributions obtained from canonical Monte Carlo simulations can be used to find an approximate interaction energy. This serves as the basis of a method for estimating the binding free energy for a ligand to a protein which…
Ab initio molecular dynamics (AIMD) simulations employing density functional theory (DFT) and plane waves are routinely carried out using density functionals at the level of Generalized Gradient Approximation (GGA). AIMD simulations…
This letter gives results on improving protein-ligand binding affinity predictions based on molecular dynamics simulations using machine learning potentials with a hybrid neural network potential and molecular mechanics methodology…
The discrete Fourier transform is approximated by summing over part of the terms with corresponding weights. The approximation reduces significantly the requirement for computer memory storage and enhances the numerical computation…
The impact of leading collective electronic fluctuations on a free energy of a prototype 1D model for molecular systems is considered within the recently developed Fluctuating Local Field (FLF) approach. The FLF method is a non-perturbative…
When described by a low-dimensional reaction coordinate, the rates of protein folding are determined by a subtle interplay between free-energy barriers and friction. While it is commonplace to extract free-energy profiles from molecular…
The exciton binding energy, the energy required to dissociate an excited electron-hole pair into free charge carriers, is one of the key factors to the optoelectronic performance of organic materials. However, it remains unclear whether…
The bandgap and band bowing parameter of semiconductor alloys are calculated with a fast and realistic approach. The method is a dielectric scaling approximation that is based on a scissor approximation. It adds an energy shift to the…
Alchemical free energy calculations via molecular dynamics have been widely used to obtain thermodynamic properties related to protein-ligand binding and solute-solvent interactions. Although soft-core modeling is the most common approach,…
The current investigation focuses on detailed analysis of the anchor based optimization approach (ABOA), its comparison with alternative global fitting protocols and on the global analysis of the truncation of basis effects in the…
We describe a simple method to determine, from ab initio calculations, the complete orientation-dependence of interfacial free energies in solid-state crystalline systems. We illustrate the method with an application to precipitates in the…