Related papers: Biomolecular electrostatics using a fast multipole…
In this work we propose an accelerated stochastic learning system for very large-scale applications. Acceleration is achieved by mapping the training algorithm onto massively parallel processors: we demonstrate a parallel, asynchronous GPU…
Simulation of atomic resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated…
A surface integral representation of Maxwell's equations allows the efficient electromagnetic (EM) modeling of three-dimensional structures with a two-dimensional discretization, via the boundary element method (BEM). However, existing BEM…
We demonstrate a GPU-accelerated nested sampling framework for efficient high-dimensional Bayesian inference in cosmology. Using JAX-based neural emulators and likelihoods for cosmic microwave background and cosmic shear analyses, our…
The complex regulatory dynamics of a biological network can be succinctly captured using discrete logic models. Given even sparse time-course data from the system of interest, previous work has shown that global optimization schemes are…
Simulating charged many-body systems has been a computational demanding task due to the long-range nature of electrostatic interaction. For the multi-scale model of electrolytes which combines the strengths of atomistic/continuum…
Immersed boundary-lattice Boltzmann method (IB-LBM) has been widely used for simulation of particle-laden flows recently. However, it was limited to small-scale simulations with no more than O(103) particles. Here, we expand IB-LBM for…
We present a design through analysis workflow that enables virtual prototyping of electric devices. A CAD plugin establishes the interaction between design and analysis, allowing the preparation of analysis models and the visualization of…
We analyze deficiencies of commonly used Coulomb approximations in Generalized Born solvation energy calculation models and report a development of a new fast surface-based method (FSBE) for numerical calculations of the solvation energy of…
Branch-and-Bound (B&B) algorithms are time intensive tree-based exploration methods for solving to optimality combinatorial optimization problems. In this paper, we investigate the use of GPU computing as a major complementary way to speed…
In this and the associated article 'BioBlender: Fast and Efficient All Atom Morphing of Proteins Using Blender Game Engine', by Zini et al., we present BioBlender, a complete instrument for the elaboration of motion (Zini et al.) and the…
Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones.…
We present a novel multi-scale embedding scheme that links conventional QM/MM embedding and bootstrap embedding (BE) to allow simulations of large chemical systems on limited quantum devices. We also propose a mixed-basis BE scheme that…
In boundary element methods (BEM) in $\mathbb{R}^3$, matrix elements and right hand sides are typically computed via analytical or numerical quadrature of the layer potential multiplied by some function over line, triangle and tetrahedral…
Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
There exists an increasing interest for using immersed boundary methods (IBMs) (Peskin 2000) to model moving objects in computational fluid dynamics. Indeed, this approach is particularly efficient, because the fluid mesh does not require…
GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
We present a novel technique by which highly-segmented electrostatic configurations can be solved. The Robin Hood method is a matrix-inversion algorithm optimized for solving high density boundary element method (BEM) problems. We…
Large-scale molecular dynamics simulations with high accuracy have been increasingly popular for their capability to bridge the gap between atomistic modeling and mesoscale phenomena. Both machine learning potentials and enhanced sampling…