Related papers: Linear scaling computation of forces for the domai…
The past years have witnessed impressive advances in electronic structure calculation, especially in the complexity and size of the systems studied, as well as in computation time. Linear scaling methods based on empirical tight-binding…
We present an implementation of the fast multipole method for computing coulombic electrostatic and polarization forces from polarizable force-fields based on induced point dipole moments. We demonstrate the expected $O(N)$ scaling of that…
With a sufficiently fine discretisation, the Lattice Boltzmann Method (LBM) mimics a second order Crank-Nicolson scheme for certain types of balance laws (Farag et al. [2021]). This allows the explicit, highly parallelisable LBM to…
In this paper, we propose a lattice Boltzmann (LB) model for the generalized coupled cross-diffusion-fluid system. Through the direct Taylor expansion method, the proposed LB model can correctly recover the macroscopic equations. The cross…
State of the art domain decomposition algorithms for large-scale boundary value problems (with $M\gg 1$ degrees of freedom) suffer from bounded strong scalability because they involve the synchronisation and communication of workers…
We present a fast direct solver for structured linear systems based on multilevel matrix compression. Using the recently developed interpolative decomposition of a low-rank matrix in a recursive manner, we embed an approximation of the…
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 consider the nonlinear Poisson-Boltzmann equation in the context of electrostatic models for a biological macromolecule, embedded in a bounded domain containing a solution of an arbitrary number of ionic species which is not necessarily…
Nonlinear balanced truncation is a model order reduction technique that reduces the dimension of nonlinear systems in a manner that accounts for either open- or closed-loop observability and controllability aspects of the system. A…
A domain decomposition method for the solution of general variable-coefficient elliptic partial differential equations on regular domains is introduced. The method is based on tessellating the domain into overlapping thin slabs or shells,…
At higher altitudes, for high temperature gases, for instance near space shuttles moving at hypersonic speed, not only mechanical collisions are affecting the gas flow, but also chemical reactions have an impact on such hypersonic flows. In…
An accurate force calculation with the Poisson-Boltzmann equation is challenging, as it requires the electric field on the molecular surface. Here, we present a calculation of the electric field on the solute-solvent interface that is exact…
To accurately model the electron density and polarization, a polarizable multipole (PM) model using the AMOEBA force field has been introduced \cite{Ren:2003, Shi:2013} recently. In the AMOEBA force field, the traditional point atomic…
The modern design of industrial structures leads to very complex simulations characterized by nonlinearities, high heterogeneities, tortuous geometries... Whatever the modelization may be, such an analysis leads to the solution to a family…
Matrix acidization simulation is a challenging task in the study of flows in porous media, due to the changing porosity in the procedure. The improved DBF framework is one model to do this simulation, and its numerical scheme discretises…
The Poisson-Boltzmann equation is widely used to model molecular electrostatics; however, it is usually solved in linearised form because the sinh nonlinearity is challenging, limiting its applicability in highly charged systems such as…
We present an efficient approach for simulating Coulomb systems confined by planar polarizable surfaces. The method is based on the solution of Poisson equation using periodic Green functions. It is shown that the electrostatic energy…
Electrostatics is of paramount importance to chemistry, physics, biology, and medicine. The Poisson-Boltzmann (PB) theory is a primary model for electrostatic analysis. However, it is highly challenging to compute accurate PB electrostatic…
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…
Inference scaling methods for LLMs often rely on decomposing problems into steps (or groups of tokens), followed by sampling and selecting the best next steps. However, these steps and their sizes are often predetermined or manually…