Related papers: Using the Fast Fourier Transform in Binding Free E…
As minimal cells or protocells are dramatically simpler than modern unicells it is possible to quantitatively estimate free energy changes for every process in the lifecycle of a protocell and compare these with estimates of the free energy…
Large language models (LLMs) require substantial compute, and thus energy, at inference time. While quantizing weights and activations is effective at improving efficiency, naive quantization of LLMs can significantly degrade performance…
We compute the isotope shifts of the \emph{total} electron binding energy of neutral atoms and singly charged ions up to element $Z=120$, using relativistic Hartree-Fock method including the Breit interaction. Field shift coefficients are…
The nonlinear Fourier transform (NFT) decomposes waveforms propagating through optical fiber into nonlinear degrees of freedom, which are preserved during transmission. By encoding information on the nonlinear spectrum, a transmission…
A method for generating angular forces around $\sigma$-bonded transition metal ions is generalized to treat $\pi$-bonded configurations. The theoretical approach is based on an analysis of a ligand-field Hamiltonian based on the moments of…
We introduce the self-Relative Binding Free Energy (self-RBFE) approach to evaluate the intrinsic statistical variance of dual-topology alchemical binding free energy estimators. The self-RBFE is the relative binding free energy between a…
Molecular motors fulfill critical functions within all living beings. Understanding their underlying working principles is therefore of great interest. Here we develop a simple model inspired by the two-component biomolecular motor Fo-F1…
Interatomic pairwise methods are currently among the most popular and accurate ways to include dispersion energy in density functional theory (DFT) calculations. However, when applied to more than two atoms, these methods are still…
A recently proposed "DFT+dispersion" treatment (Rajchel et al., Phys. Rev. Lett., 2010, 104, 163001) is described in detail and illustrated by more examples. The formalism derives the dispersion-free density functional theory (DFT)…
The Targeted Free Energy Perturbation (TFEP) method aims to overcome the time-consuming and computer-intensive stratification process of standard methods for estimating the free energy difference between two states. To achieve this, TFEP…
The experimental solubility limit of Zr in Al is well-known. Al3Zr has a stable structure DO23 and a metastable one L12. Consequently there is a metastable solubility limit for which only few experimental data are available. The purpose of…
This work proposes a new precoded filter bank (FB) system via a two-dimensional (2D) fast Fourier transform (2D-FFT). Its structure is similar to Orthogonal Time Frequency Space (OTFS) systems, where the OFDM transmitter is changed to a…
Different computational techniques in combination with molecular dynamics computer simulation are used to to determine the wall-liquid and the wall-crystal interfacial free energies of a modified Lennard-Jones (LJ) system in contact with a…
Calculating relative free energies is a topic of substantial interest and has many applications including solvation and binding free energies, which are used in computational drug discovery. However, there remain the challenges of accuracy,…
This thesis report deals with the 1D Hubbard model and the quantum objects that diagonalize the normal ordered Hubbard hamiltonian, among those the so called PseudoFermions (PFs). These PFs have no residual energy interactions, are eta-spin…
An accurate description of nonadiabatic energy relaxation is crucial for modeling atomistic dynamics at metal surfaces. Interfacial energy transfer due to electron-hole pair excitations coupled to motion of molecular adsorbates is often…
Accurately predicting protein-ligand binding free energies (BFEs) remains a central challenge in drug discovery, particularly because the most reliable methods, such as free energy perturbation (FEP), are computationally intensive and…
Free energies are fundamental quantities governing phase behavior and thermodynamic stability in polymer systems, yet their accurate computation often requires extensive simulations and post-processing techniques such as the Bennett…
Efficient estimators of Fourier-space statistics for large number of objects rely on Fast Fourier Transforms (FFTs), which are affected by aliasing from unresolved small scale modes due to the finite FFT grid. Aliasing takes the form of a…
We demonstrate an efficient and accurate, general-purpose first-principles blueprint for calculating anharmonic vibrational free energy and predicting structural phase transition temperatures of solids. Thermodynamic integration is…