Related papers: Accelerating Fermionic Molecular Dynamics
Perturbing a Go model towards a realistic protein Hamiltonian by adding non-native interactions, we find that the folding rate is in general enhanced as ruggedness is initially increased, as long as the protein is sufficiently large and…
A new approach for integration of motion in many-body systems of interacting polyatomic molecules is proposed. It is based on splitting time propagation of pseudo-variables in a modified phase space, while the real translational and…
An accurate treatment of the structures and dynamics that lead to enhanced chemical reactivity in enzymes requires explicit treatment of both electronic and nuclear quantum effects. The former can be captured in ab initio molecular dynamics…
We discuss nuclear dynamics at molecule-metal interfaces including non-equilibrium molecular junctions. Starting from the many-body states (pseudoparticle) formulation of the molecule-metal system in the molecular vibronic basis, we…
Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…
This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
One of the main computational bottlenecks when working with kernel based learning is dealing with the large and typically dense kernel matrix. Techniques dealing with fast approximations of the matrix vector product for these kernel…
Quantum mechanics based ab-initio molecular dynamics (MD) simulation schemes offer an accurate and direct means to monitor the time-evolution of materials. Nevertheless, the expensive and repetitive energy and force computations required in…
We have implemented a variant of the force gradient integrator proposed by Kennedy et.al. and are using it in our production 2+1 flavor DWF simulations with pion masses of 180 MeV in (4.5fm)3 volumes. We find modest speed-ups (\sim 20%)…
We show that accelerated optimization methods can be seen as particular instances of multi-step integration schemes from numerical analysis, applied to the gradient flow equation. In comparison with recent advances in this vein, the…
Including the effect of the molecular environment in the numerical modeling of time-resolved electronic spectroscopy remains an important challenge in computational spectroscopy. In this contribution, we present a general approach for the…
We present a novel approach for accelerating convolutions during inference for CPU-based architectures. The most common method of computation involves packing the image into the columns of a matrix (im2col) and performing general matrix…
Understanding the behavior of interacting fermions is of fundamental interest in many fields ranging from condensed matter to high energy physics. Developing numerically efficient and accurate simulation methods is an indispensable part of…
In this paper the modification of the method conventionally used for the modeling of the massive fermions production and decays is proposed. The step by step algorithm is presented. Under the strict conditions the proposed method of…
We introduce and explore an approach for constructing force fields for small molecules, which combines intuitive low body order empirical force field terms with the concepts of data driven statistical fits of recent machine learned…
The short-range modes of the fermionic determinant can be absorbed in the gauge action using the loop expansion. The coefficients of this expansion and the zeroes of the polynomial approximating the remainder can be optimized by a simple,…
An implementation of the fast multiple method (FMM) is performed for magnetic systems with long-ranged dipolar interactions. Expansion in spherical harmonics of the original FMM is replaced by expansion of polynomials in Cartesian…
Hasenbusch has proposed splitting the pseudo-fermionic action into two parts, in order to speed-up Hybrid Monte Carlo simulations of QCD. We have tested a different splitting, also using clover-improved Wilson fermions. An additional…
We introduce a dynamical fermion algorithm which is based on the hybrid Monte Carlo (HMC) algorithm, but without pseudofermions. The molecular dynamics steps in HMC are retained except the derivatives with respect to the gauge fields are…