Related papers: An Efficient Algorithm for Upper Bound on the Part…
We propose and justify a new approach for fast calculation of the electrostatic interaction energy of clusters of charged particles in constrained energy minimization in the framework of rigid protein-ligand docking. Our ``blind search''…
Partition functions of a canonical ensemble of non-interacting bound electrons are a key ingredient of the super-transition-array approach to the computation of radiative opacity. A few years ago, we published a robust and stable recursion…
The localized operator partitioning method [Y. Khan and P. Brumer, J. Chem. Phys. 137, 194112 (2012)] rigorously defines the electronic energy on any subsystem within a molecule and gives a precise meaning to the subsystem ground and…
In this paper we study the effect of energy parameters on minimum free energy (mfe) RNA secondary structures. Employing a simplified combinatorial energy model, that is only dependent on the diagram representation and that is not sequence…
We describe a simple and fast algorithm for identifying friends-of-friends features and prove its correctness. The algorithm avoids unnecessary expensive neighbor queries, uses minimal memory overhead, and rejects slowdown in high…
We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling…
We present FIRE, Fast Interpretable Rule Extraction, an optimization-based framework to extract a small but useful collection of decision rules from tree ensembles. FIRE selects sparse representative subsets of rules from tree ensembles,…
Large classes of materials systems in physics and engineering are governed by magnetic and electrostatic interactions. Continuum or mesoscale descriptions of such systems can be cast in terms of integral equations, whose direct…
Recent research on mutual exclusion for shared-memory systems has focused on "local spin" algorithms. Performance is measured using the "remote memory references" (RMRs) metric. As common in recent literature, we consider a standard…
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,…
Geometry optimization is an important part of both computational materials and surface science because it is the path to finding ground state atomic structures and reaction pathways. These properties are used in the estimation of…
Blocking is a mechanism to improve the efficiency of Entity Resolution (ER) which aims to quickly prune out all non-matching record pairs. However, depending on the distributions of entity cluster sizes, existing techniques can be either…
We aim to investigate relationships between select processing parameters or inputs (composition, temperature, annealing time) and two structural parameters, specifically, the mean radius and volume fraction of the Fe$_3$Si nanocrystals. To…
We present the novel algorithmically regularised integration method MSTAR for high accuracy ($|\Delta E/E| \gtrsim 10^{-14}$) integrations of N-body systems using minimum spanning tree coordinates. The two-fold parallelisation of the…
A low-latency and energy-efficient tensor algebra accelerator design must optimize how data movement and operations are scheduled (i.e., mapped) in the accelerator architecture. A key mapping optimization is fusion, meaning holding data…
Quantum phase estimation (QPE) is a promising quantum algorithm for obtaining molecular ground-state energies with chemical accuracy. However, its computational cost, dominated by the Hamiltonian 1-norm $\lambda$ and the cost of the block…
We present an efficient algorithm for computing the exact exchange contributions in the Hartree-Fock and hybrid density functional theory models on the basis of the fast multipole method (FMM). Our algorithm is based on the observation that…
In this paper, we present a finite element method (FEM) framework enhanced by an operator-adapted wavelet decomposition algorithm designed for the efficient analysis of multiscale electromagnetic problems. Usual adaptive FEM approaches,…
A new linked cluster expansion for the calculation of ground state observables of complex nuclei with realistic interactions has been developed [1-3]; using the V8' potential [4] the ground state energy, density and momentum distribution of…
We consider the algorithm by Ferson et al. (Reliable computing 11(3), p. 207-233, 2005) designed for solving the NP-hard problem of computing the maximal sample variance over interval data, motivated by robust statistics (in fact, the…