Related papers: Explicit-Solute Implicit-Solvent Molecular Simulat…
The presence of solvent tunes many properties of a molecule, such as its ground and excited state geometry, dipole moment, excitation energy, and absorption spectrum. Because the energy of the system will vary depending on the solvent…
The structure and function of biological molecules are strongly influenced by the water and dissolved ions that surround them. This aqueous solution (solvent) exerts significant electrostatic forces in response to the biomolecule's…
Dimensionality reduction methods have found vast application as visualization tools in diverse areas of science. Although many different methods exist, their performance is often insufficient for providing quick insight into many…
Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet, no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such…
Computing has revolutionised the study of complex nonlinear systems, both by allowing us to solve previously intractable models and through the ability to visualise solutions in different ways. Using ubiquitous computing infrastructure, we…
We present GridFF, an efficient method for simulating molecules on rigid substrates, derived from techniques used in protein-ligand docking in biochemistry. By projecting molecule-substrate interactions onto precomputed spatial grids with…
Recent efforts in open-source GPU research are opening new avenues in a domain that has long been tightly coupled with a few commercial vendors. Emerging open GPU architectures define SIMT functionality through their own ISAs, but executing…
Vertical equilibrium models have proven to be well suited for simulating fluid flow in subsurface porous media such as saline aquifers with caprocks. However, in most cases the dimensionally reduced model lacks the accuracy to capture the…
Recently, graphics processors (GPUs) have been increasingly leveraged in a variety of scientific computing applications. However, architectural differences between CPUs and GPUs necessitate the development of algorithms that take advantage…
Implicit particle-in-cell codes offer advantages over their explicit counterparts in that they suffer weaker stability constraints on the need to resolve the higher frequency modes of the system. This feature may prove particularly valuable…
The solution for non-linear, complex partial differential Equations (PDEs) is achieved through numerical approximations, which yield a linear system of equations. This approach is prevalent in Computational Fluid Dynamics (CFD), but it…
Many solid mechanics problems on complex geometries are conventionally solved using discrete boundary methods. However, such an approach can be cumbersome for problems involving evolving domain boundaries due to the need to track boundaries…
Mobile robots operating indoors must be prepared to navigate challenging scenes that contain transparent surfaces. This paper proposes a novel method for the fusion of acoustic and visual sensing modalities through implicit neural…
Multi-solid systems are foundational to a wide range of real-world applications, yet modeling their complex interactions remains challenging. Existing deep learning methods predominantly rely on implicit modeling, where the factors…
This paper presents a Graphics Processing Units (GPUs) acceleration method of an iterative scheme for gas-kinetic model equations. Unlike the previous GPU parallelization of explicit kinetic schemes, this work features a fast converging…
We discuss the use of the Discrete Element Method (DEM) to simulate the dynamics of granular systems made up of elements with nontrivial geometries. The DEM simulator is GPU accelerated and can handle elements whose shape is defined as the…
Coupled nonlinear system of reaction-diffusion equations describing multi-component (species) interactions with heterogeneous coefficients is considered. Finite volume method based approximation for the space is used to construct…
We introduce a particle-based simulation method for granular material in interactive frame rates. We divide the simulation into two decoupled steps. In the first step, a relatively small number of particles is accurately simulated with a…
With the development of artificial intelligence techniques, transportation system optimization is evolving from traditional methods relying on expert experience to simulation and learning-based decision and optimization methods.…
All-atom, force field-based molecular dynamics simulations are essential tools in computational chemistry, enabling the prediction and analysis of biomolecular systems with atomic-level resolution. However, as system sizes and simulation…