Related papers: Using the Fast Fourier Transform in Binding Free E…
We develop an efficient sampling and free energy calculation technique within the adaptive biasing potential (ABP) framework. By mollifying the density of states we obtain an approximate free energy and an adaptive bias potential that is…
The Fast Fourier Transform (FFT) correlation approach to protein-protein docking can evaluate the energies of billions of docked conformations on a grid if the energy is described in the form of a correlation function. Here, this…
Fourier transform methods are used to analyze functions and data sets to provide frequencies, amplitudes, and phases of underlying oscillatory components. Fast Fourier transform (FFT) methods offer speed advantages over evaluation of…
Quantum--Mechanical methods that are both computationally fast and accurate are not yet available for electronic excitations having charge transfer character. In this work, we present a significant step forward towards this goal for those…
We have carried out a thorough benchmark of the FDE-ET method for calculating hole transfer couplings. We have considered 10 exchange-correlation functionals, 3 non-additive kinetic energy functionals and 3 basis sets. Overall, we conclude…
It has recently been shown that a free energy for Baxter's sticky hard sphere fluid is uniquely defined within the framework of fundamental measure theory (FMT) for the inhomogeneous hard sphere fluid, provided that it obeys scaled-particle…
In this paper, a new fast and low complexity transform is introduced for orthogonal frequency division multiplexing (OFDM) wireless systems. The new transform combines the effects of fast complex-Walsh-Hadamard transform (CHT) and the fast…
In this contribution I critically revise the alchemical reversible approach in the context of the statistical mechanics theory of non covalent bonding in drug receptor systems. I show that most of the pitfalls and entanglements for the…
The Discrete Fourier Transform (DFT) is essential for various applications ranging from signal processing to convolution and polynomial multiplication. The groundbreaking Fast Fourier Transform (FFT) algorithm reduces DFT time complexity…
We study the free energy of a heavy quark-antiquark pair in a thermal medium using the AdS/CFT correspondence. We point out that a commonly used prescription for calculating this quantity leads to a temperature dependence in conflict with…
The fast Fourier transform, FFT, is a useful and prevalent algorithm in signal processing. It characterizes the spectral components of a signal, or is used in combination with other operations to perform more complex computations such as…
Applying the previously developed systematic thermal (imaginary time) perturbative expansion to the relevant effective field theory we compute the free energy $F$ of the diluted gas of (nonrelativistic) spin $1/2$ fermions interacting…
We present an effective field theory (EFT) at leading order to describe light single-$\Lambda$ hypernuclei. Owing to the weak $\Lambda$ binding and to the $\Lambda N$ short interaction range, meson exchange forces are approximated by…
The energy minimization involved in density functional calculations of electronic systems can be carried out using an exponential transformation that preserves the orthonormality of the orbitals. The energy of the system is then represented…
Tight-binding models provide great insight and are a low-cost alternative to \emph{ab initio} methods for calculation of a material's electronic structure. These models are used to calculate optical responses, including nonlinear optical…
This paper describes the development of the Four Model Tree Ensemble (FMTE). The FMTE is a composite of machine learning models trained on experimental binding energies from the Atomic Mass Evaluation (AME) 2012. The FMTE predicts binding…
In this article we present an algorithm to efficiently evaluate the exchange matrix in periodic systems when Gaussian basis set with pseudopotentials are used. The usual algorithm for evaluating exchange matrix scales cubically with the…
We consider membranes adhered through specific receptor-ligand bonds. Thermal undulations of the membrane induce effective interactions between adhesion sites. We derive an upper bound to the free energy that is independent of interaction…
We propose a method, Temperature Integration, which allows an efficient calculation of free energy differences between two systems of interest, with the same degrees of freedom, which may have rough energy landscapes. The method is based on…
We propose a Fast Fourier Transform based Periodic Interpolation Method (FFT-PIM), a flexible and computationally efficient approach for computing the scalar potential given by a superposition sum in a unit cell of an infinitely periodic…