Related papers: Using the Fast Fourier Transform in Binding Free E…
An improved approach to updating the electric field in simulations of Coulomb gases using the local lattice technique introduced by Maggs and Rossetto, is described and tested. Using the Fast Fourier Transform (FFT) an independent…
We present a method for determining the free energy of coexisting states from irreversible work measurements. Our approach is based on a fluctuation relation that is valid for dissipative transformations in partially equilibrated systems.…
The Casimir energy for the transverse oscillations of a piecewise uniform closed string is calculated. The great adaptibility of this string model with respect to various regularization methods is pointed out. We survey several…
Herein, we present a new method to efficiently calculate electronically excited states in large molecular assemblies, consisting of hundreds of molecules. For this purpose, we combine the long-range corrected tight-binding…
Interactions between negatively charged aluminosilicate species and positively charged metal cations are critical to many important engineering processes and applications, including sustainable cements and aluminosilicate glasses. In an…
Using concepts from classical density functional theory (DFT) we investigate the freezing of a two-dimensional (2D) system of ultra-soft particles in a one-dimensional (1D) external potential; a phenomenon often called laser-induced…
Energy efficiency has emerged as a critical challenge in modern base stations (BSs), as the power amplifier (PA) consumes a substantial portion of the total power due to its limited efficiency. We investigate waveform and mode adaptation to…
A recent tight-binding scheme provides a method for extending the results of first principles calculations to regimes involving $10^2 - 10^3$ atoms in a unit cell. The method uses an analytic set of two-center, non-orthogonal tight-binding…
Accurate prediction of protein-ligand binding affinities is crucial in drug discovery, particularly during hit-to-lead and lead optimization phases, however, limitations in ligand force fields continue to impact prediction accuracy. In this…
I present the mathematical structure of classical phonon theory in a general form, which emphasizes the wave natures of phonons, and which can serve as a robust foundation for further development of the theory of strongly interacting…
We propose a new method of calculating electronically excited states that combines a density functional theory (DFT) based ground state calculation with a linear response treatment that employs approximations used in the time-dependent…
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 $O(n\log n)$. From a…
Orbital-free density functional theory (OF-DFT) provides an alternative approach for calculating the molecular electronic energy, relying solely on the electron density. In OF-DFT, both the ground-state density is optimized variationally to…
The development of machine-learning (ML) potentials offers significant accuracy improvements compared to molecular mechanics (MM) because of the inclusion of quantum-mechanical effects in molecular interactions. However, ML simulations are…
We develop a fluctuation framework to quantify the free energy difference between two equilibrium states connected by nonequilibrium processes under arbitrary dynamics and system-environment coupling. For an open system described by the…
In the molecular dynamics calculations for the free energy of ions and ionic molecules, we often encounter wet charged molecular systems where electrical neutrality condition is broken. This causes a problem in the evaluation of…
Binding free energies are a key element in understanding and predicting the strength of protein--drug interactions. While classical free energy simulations yield good results for many purely organic ligands, drugs including transition metal…
A new reference state for density functional theory, termed the independent atom ansatz, is introduced in this work. This ansatz allows for the exact representation of electron density in terms of non-interacting, atom-localized orbitals.…
Hydrogen bonding is an important non-covalent interaction that plays a major role in molecular self-organization and supramolecular structures. It can be described accurately with ab initio quantum chemical wave function methods, which…
Quantum algorithms are well-suited to calculate estimates of the energy spectra for spin lattice systems. These algorithms are based on the efficient calculation of the discrete Fourier components of the density of states. The efficiency of…