Related papers: An Efficient Particle-Field Algorithm with Neural …
A novel electromagnetic particle-in-cell algorithm has been developed for fully kinetic plasma simulations on unstructured (irregular) meshes in complex body-of-revolution geometries. The algorithm, implemented in the BORPIC++ code,…
Mathematical modeling and simulation is a promising approach to personalized cancer medicine. Yet, the complexity, heterogeneity and multi-scale nature of cancer pose significant computational challenges. Coupling discrete cell-based models…
Meshfree particle methods, such as Smoothed Particle Hydrodynamics (SPH) and the Moving Particle Semi-Implicit (MPS) method, are widely used to simulate complex free-surface and multiphase flows. A key challenge in these methods is the…
Obtaining high-quality particle distributions for stable and accurate particle-based simulations poses significant challenges, especially for complex geometries. We introduce a preprocessing technique for 2D and 3D geometries, optimized for…
The hybrid particle-field molecular dynamics method is an efficient alternative to standard particle-based coarse grained approaches. In this work, we propose an automated protocol for optimisation of the effective parameters that define…
Predicting the three-dimensional (3D) structure of a protein from its primary sequence of amino acids is known as the protein folding (PF) problem. Due to the central role of proteins' 3D structures in chemistry, biology and medicine…
Angiogenesis, the formation of new vessels, is one of the key mechanisms in tumor development and an appealing target for therapy. Non-invasive, high-resolution, high sensitivity, quantitative 3D imaging techniques are required to correctly…
When modeling of tumor-driven angiogenesis, a major source of analytical and computational complexity is the strong coupling between the kinetic parameters of the relevant stochastic branching-and-growth of the capillary network, and the…
This article presents a novel computational model to study the selective filtering of biological hydrogels due to the surface charge and size of diffusing particles. It is the first model that includes the random 3D fiber orientation and…
In this paper, we study a semilinear parabolic PDE system which describes the interaction of normal cells, tumor cells, immune cells, with a chemotherapeutic drug. The model extends the previous model with incorporating strong Allee affects…
This article presents new hexagonal and pentagonal PEM fuel cell models. The models have been optimized after achieving improved cell performance. The input parameters of the multi-objective optimization algorithm were pressure and…
We propose an autofocusing algorithm to obtain, relatively accurately, the 3D position of each particle, particularly its axial location, and particle number of a dense transparent particle solution via its hologram. First, morphological…
Bacterial cancer therapy exploits anaerobic bacteria's ability to target hypoxia tumor regions, yet the interactions among tumor growth, bacterial colonization, oxygen levels, immunosuppressive cytokines, and bacterial communication remain…
To evaluate electrostatics interactions, Molecular dynamics (MD) simulations rely on Particle Mesh Ewald (PME), an O(Nlog(N)) algorithm that uses Fast Fourier Transforms (FFTs) or, alternatively, on O(N) Fast Multipole Methods (FMM)…
There are many interesting physical processes which involve the generation of high density plasmas in large volumes. However, when modeling these systems numerically, the large densities and volumes present a significant computational…
We introduce a fast mesh-based method for computing N-body interactions that is both scalable and accurate. The method is founded on a particle-particle--particle-mesh P3M approach, which decomposes a potential into rapidly decaying…
Using a Deep Neuronal Network model (DNN) trained on the large ANI-1 data set of small organic molecules, we propose a transferable density-free many-body dispersion model (DNN-MBD). The DNN strategy bypasses the explicit Hirshfeld…
In this work, we propose efficient and accurate numerical algorithms based on Difference Potentials Method for numerical solution of chemotaxis systems and related models in 3D. The developed algorithms handle 3D irregular geometry with the…
We present a new scheme to compensate for the small-scales approximations resulting from Particle-Mesh (PM) schemes for cosmological N-body simulations. This kind of simulations are fast and low computational cost realizations of the large…
When the effects of relative motion at the solid object interfaces are not negligible, the contact method is required in the smoothed particle hydrodynamics (SPH) method to prevent virtual shear and tensile stresses. However, there is still…