Related papers: An Efficient Algorithm for Upper Bound on the Part…
In this study, a machine learning-based technique is developed to reduce the computational cost required to explore large design spaces of substitutional alloys. The first advancement is based on a neural network approach to predict the…
In this work, we develop a fast hierarchical solver for solving large, sparse least squares problems. We build upon the algorithm, spaQR (sparsified QR), that was developed by the authors to solve large sparse linear systems. Our algorithm…
In probability theory, the partition function is a factor used to reduce any probability function to a density function with total probability of one. Among other statistical models used to represent joint distribution, Markov random fields…
We study a population of $N$ particles, which evolve according to a diffusion process and interact through a dynamical network. In turn, the evolution of the network is coupled to the particles' positions. In contrast with the mean-field…
We formulate the RNA folding problem as an $N\times N$ matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is…
In this paper, we give a faster width-dependent algorithm for mixed packing-covering LPs. Mixed packing-covering LPs are fundamental to combinatorial optimization in computer science and operations research. Our algorithm finds a $1+\eps$…
We consider the problem of doing fast and reliable estimation of the number of non-zero entries in a sparse boolean matrix product. This problem has applications in databases and computer algebra. Let n denote the total number of non-zero…
Stacking fault energy (SFE) is of the most critical microstructure attribute for controlling the deformation mechanism and optimizing mechanical properties of austenitic steels, while there are no accurate and straightforward computational…
The cross section of a given process fundamentally quantifies the probability for that given process to occur. In the quantum regime of low energies, the cross section can vary strongly with collision energy due to quantum effects. Here, we…
Schedulability is a fundamental problem in real-time scheduling, but it has to be approximated due to the intrinsic computational hardness. As the most popular algorithm for deciding schedulability on multiprocess platforms, the speedup…
The so-called matrix-element method (MEM) has long been used successfully as a classification tool in particle physics searches. In the presence of invisible final state particles, the traditional MEM typically assigns probabilities to an…
We develop Random Batch Methods for interacting particle systems with large number of particles. These methods use small but random batches for particle interactions, thus the computational cost is reduced from $O(N^2)$ per time step to…
A linear external perturbation is introduced in the action of the partition function of the random matrix model of RNA [G. Vernizzi, H. Orland and A. Zee, Phys. Rev. Lett. 94, 168103 (2005)]. It is seen that (i). the perturbation…
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.…
The ever increasing number and complexity of energy-bound devices (such as the ones used in Internet of Things applications, smart phones, and mission critical systems) pose an important challenge on techniques to optimize their energy…
Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be…
Traditional multiconfiguration Hartree-Fock (MCHF) and configuration interaction (CI) methods are based on a single orthonormal orbital basis (OB). For atoms with complicated shell structures, a large OB is needed to saturate all the…
Accurate prediction of mRNA secondary structure is critical for understanding gene expression, translation efficiency, and advancing mRNA-based therapeutics. However, the combinatorial complexity of possible foldings, especially in long…
Superlevel partitioning is combined with a simple relaxation procedure to construct an iterative technique for solving equations of statistical equilibrium. In treating an $N$-level model atom, the technique avoids the $N^{3}$ scaling in…
RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary…