Related papers: Exact analytical algorithm for solvent accessible …
Sequential robot manipulation tasks require finding collision-free trajectories that satisfy geometric constraints across multiple object interactions in potentially high-dimensional configuration spaces. Solving these problems in real-time…
We report an efficient algorithm for calculating momentum-space integrals in solid state systems on modern graphics processing units (GPUs). Our algorithm is based on the tetrahedron method, which we demonstrate to be ideally suited for…
Open-source 3D data processing libraries originally developed for computer vision and pattern recognition are used to align and compare molecular shapes and sub-shapes. Here, a shape is represented by a set of points distributed on the van…
We introduce Soft Anisotropic Diagrams (SAD), an explicit and differentiable image representation parameterized by a set of adaptive sites in the image plane. In SAD, each site specifies an anisotropic metric and an additively weighted…
In recent years, several particle-based stochastic simulation algorithms (PSSA) have been developed to study the spatially resolved dynamics of biochemical networks at a molecular scale. A challenge all these approaches have to address is…
The alpha complex, a subset of the Delaunay triangulation, has been extensively used as the underlying representation for biomolecular structures. We propose a GPU-based parallel algorithm for the computation of the alpha complex, which…
Global sensitivity analysis of complex numerical simulators is often limited by the small number of model evaluations that can be afforded. In such settings, surrogate models built from a limited set of simulations can substantially reduce…
We consider the problem of efficiently simulating stochastic models of chemical kinetics. The Gillespie Stochastic Simulation algorithm (SSA) is often used to simulate these models, however, in many scenarios of interest, the computational…
The relative solvent accessibility (RSA) of a residue in a protein measures the extent of burial or exposure of that residue in the 3D structure. RSA is frequently used to describe a protein's biophysical or evolutionary properties. To…
Global Sensitivity Analysis (GSA) methods are useful tools to rank input parameters uncertainties regarding their impact on result variability. In practice, such type of approach is still at an exploratory level for studies relying on 2D…
Yukawa systems have drawn widespread interest across various applications. In this paper, we introduce a novel random batch sum-of-Gaussians (RBSOG) algorithm for molecular dynamics simulations of 3D Yukawa systems with periodic boundary…
We propose MESA and DMESA as novel feature matching methods, which utilize Segment Anything Model (SAM) to effectively mitigate matching redundancy. The key insight of our methods is to establish implicit-semantic area matching prior to…
This paper presents a practical GPU-accelerated convex hull algorithm and a novel Sorting-based Preprocessing Approach (SPA) for planar point sets. The proposed algorithm consists of two stages: (1) two rounds of preprocessing performed on…
In the self-consistent continuum solvation (SCCS) approach ($\textit{J. Chem. Phys.}$ 136, 064102 (2012)), the analytical expressions of the local solute-solvent interface functions determine the interface function and dielectric function…
Deep learning methods have gained popularity in high energy physics for fast modeling of particle showers in detectors. Detailed simulation frameworks such as the gold standard Geant4 are computationally intensive, and current deep…
Treating realistically the ambient water is one of the main difficulties in applying Monte Carlo methods to protein folding. The solvent-accessible area method, a popular method for treating water implicitly, is investigated by means of…
Matrix decompositions are ubiquitous in machine learning, including applications in dimensionality reduction, data compression and deep learning algorithms. Typical solutions for matrix decompositions have polynomial complexity which…
The recent trend of using Graphics Processing Units (GPU's) for high performance computations is driven by the high ratio of price performance for these units, complemented by their cost effectiveness. At first glance, computational fluid…
Comprehensive simulations of the entire biochemistry of cells have great potential to help physicians treat disease and help engineers design biological machines. But such simulations must model networks of millions of molecular species and…
Performing high accuracy hybrid functional calculations for condensed matter systems containing a large number of atoms is at present computationally very demanding - when not out of reach - if high quality basis sets are used. We present a…