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Recent developments for mathematical modeling and numerical simulation of biomolecular systems raise new demands for qualified, stable, and efficient surface meshing, especially in implicit-solvent modeling. In our former work, we have…
Maximum weight matching is one of the most fundamental combinatorial optimization problems with a wide range of applications in data mining and bioinformatics. Developing distributed weighted matching algorithms is challenging due to the…
Mining dense subgraphs on multi-layer graphs is an interesting problem, which has witnessed lots of applications in practice. To overcome the limitations of the quasi-clique-based approach, we propose d-coherent core (d-CC), a new notion of…
Owing to the computational complexity of electronic structure algorithms running on classical digital computers, the range of molecular systems amenable to simulation remains tightly circumscribed even after many decades of work. Quantum…
In this paper, we present a surface remeshing method with high approximation quality based on Principal Component Analysis. Given a triangular mesh and a user assigned polygon/vertex budget, traditional methods usually require the extra…
What particle shape will generate the highest packing fraction when randomly poured into a container? In order to explore and navigate the enormous search space efficiently, we pair molecular dynamics simulations with artificial evolution.…
In Multiple-Input Multiple-Output (MIMO) systems, Sphere Decoding (SD) can achieve performance equivalent to full search Maximum Likelihood (ML) decoding, with reduced complexity. Several researchers reported techniques that reduce the…
Determining whether two particle systems are similar is a common problem in particle simulations. When the comparison should be invariant under permutations, orthogonal transformations, and translations of the systems, special techniques…
There is increasing demand for automated systems that can fabricate 3D structures. Robotic spatial extrusion has become an attractive alternative to traditional layer-based 3D printing due to a manipulator's flexibility to print large,…
In this paper, the surface of revolution discrete element method (SR-DEM) is introduced to simulate systems of particles with closed surfaces of revolution. Due to the cylindrical symmetry of a surface of revolution, the geometry of any…
An effective technique for solving optimization problems over massive data sets is to partition the data into smaller pieces, solve the problem on each piece and compute a representative solution from it, and finally obtain a solution…
We study the classical scheduling problem on parallel machines %with precedence constraints where the precedence graph has the bounded depth $h$. Our goal is to minimize the maximum completion time. We focus on developing approximation…
In the first part of a series of two papers, we present in considerable detail a collision-driven molecular dynamics algorithm for a system of nonspherical particles, within a parallelepiped simulation domain, under both periodic or…
We initiate the algorithmic study of the Quantum Max-$d$-Cut problem, a quantum generalization of the well-known Max-$d$-Cut problem. The Quantum Max-$d$-Cut problem involves finding a quantum state that maximizes the expected energy…
We develop an algorithm capable of imaging a three-dimensional object given a collection of two-dimensional images of that object that are significantly influenced by the curvature of the Ewald sphere. These two-dimensional images cannot be…
We present an efficient algorithm for twirling a multi-qudit quantum state. The algorithm can be used for approximating the twirling operation in an ensemble of physical systems in which the systems cannot be individually accessed. It can…
Given a set of $n$ vectors in $\mathbb{R}^d$, the goal of the \emph{determinant maximization} problem is to pick $k$ vectors with the maximum volume. Determinant maximization is the MAP-inference task for determinantal point processes (DPP)…
In this paper, a color edge detection strategy based on collaborative filtering combined with multiscale gradient fusion is proposed. The block-matching and 3D (BM3D) filter are used to enhance the sparse representation in the transform…
Disordered molecular systems such as amorphous catalysts, organic thin films, electrolyte solutions, and water are at the cutting edge of computational exploration today. Traditional simulations of such systems at length-scales relevant to…
Edge computing has emerged as an alternative to reduce transmission and processing delay and preserve privacy of the video streams. However, the ever-increasing complexity of Deep Neural Networks (DNNs) used in video-based applications…