Related papers: Using the Fast Fourier Transform in Binding Free E…
Given a time series vector, how can we efficiently compute a specified part of Fourier coefficients? Fast Fourier transform (FFT) is a widely used algorithm that computes the discrete Fourier transform in many machine learning applications.…
Free energy perturbation (FEP) is considered the gold-standard simulation method for estimating small molecule binding affinity, a quantity of vital importance to drug discovery. The accuracy of FEP critically depends on an accurate model…
The bond dissociation energies of a set of 44 3d transition metal-containing diatomics are computed with phaseless auxiliary-field quantum Monte Carlo (ph-AFQMC) utilizing a correlated sampling technique. We investigate molecules with H, N,…
Ultra-fast electronic phenomena originating from finite temperature, such as nonlinear optical excitation, can be simulated with high fidelity via real-time time dependent density functional theory (rt-TDDFT) calculations with hybrid…
We present a new and highly efficient algorithm for computing a power spectrum made from evenly spaced data which combines the noise-reducing advantages of the weighted fit with the computational advantages of the Fast Fourier Transform…
Optical processes in insulators and semiconductors, including excitonic effects, can be described in principle exactly using time-dependent density-functional theory (TDDFT). Starting from a linearization of the TDDFT semiconductor Bloch…
Recent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while other systems remain problematic for others. In paper I…
Density functional theory (DFT) is an exact alternative formulation of quantum mechanics, in which it is possible to calculate the total energy, the spin and the charge density of many-electron systems in the ground state. In practice, it…
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…
The theory of receptor-ligand binding equilibria has long been well-established in biochemistry, and was primarily constructed to describe dilute aqueous solutions. Accordingly, few computational approaches have been developed for making…
We consider a system of spinless fermions in a nearly one-dimensional cylindrical trap. We introduce four-fermion interaction terms through which particles in low-lying modes of the trap may interact with particles in radially or angularly…
We present an analytical description of the Alchemical Transfer Method (ATM) for molecular binding using the Potential Distribution Theory (PDT) formalism. ATM models the binding free energy by mapping the bound and unbound states of the…
This paper describes a low-power processor tailored for fast Fourier transform computations where transport triggering template is exploited. The processor is software-programmable while retaining an energy-efficiency comparable to existing…
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.…
Traditional force fields commonly use a combination of bonded torsional terms and empirically scaled non-bonded interactions to capture 1-4 energies and forces of atoms separated by three bonds in a molecule. While this approach can yield…
This paper considers the discrete Fourier transform (DFT) based hybrid beamforming multiuser system and studies the use of analog beam selection schemes. We first analyze the uplink ergodic achievable rates of the zero-forcing (ZF) receiver…
Pseudo-spectral method is one of the most accurate techniques for simulating turbulent flows. Fast Fourier transform (FFT) is an integral part of this method. In this paper, we present a new procedure to compute FFT in which we save…
We present an efficient Monte-Carlo method for long-range interacting systems to calculate free energy as a function of an order parameter. In this method, a variant of the Wang-Landau method regarding the order parameter is combined with…
For the theoretical understanding of the reactivity of complex chemical systems accurate relative energies between intermediates and transition states are required. Despite its popularity, density functional theory (DFT) often fails to…
Real-time time-dependent density functional theory (TDDFT) is widely considered to be the most accurate available method for calculating electronic stopping powers from first principles, but there have been relatively few assessments of the…