Related papers: An implicit boundary integral method for computing…
We present new, practical algorithms for the hypersurface implicitization problem: namely, given a parametric description (in terms of polynomials or rational functions) of the hypersurface, find its implicit equation. Two of them are for…
In the calculation of thermodynamic properties and three dimensional structures of macromolecules, such as proteins, it is important to have a good algorithm for computing solvent accessible surface area of macromolecules. Here we propose a…
An algorithm is proposed to implement unsteady jump boundary conditions, presenting discontinuity in physical quantities, within the lattice Boltzmann method (LBM). This is useful to tackle problems involving mass or heat transfer through…
This paper presents a general and robust method for the fluid-structure interaction of membranes and shells undergoing large displacement and large added-mass effects by coupling an immersed-boundary method with a shell finite-element…
The Poisson-Boltzmann equation (PBE) is a nonlinear elliptic PDE that arises in biomolecular modeling and is a fundamental tool for structural biology. It is used to calculate electrostatic potentials around an ensemble of fixed charges…
We present a simple modification of the direct-forcing immersed boundary method (IBM) proposed by Uhlmann [J. Comput. Phys, 2005] in order to enable it to be applied to particulate flows with solid-to-fluid density ratios around unity. The…
Recent studies on the solvation of atomistic and nanoscale solutes indicate that a strong coupling exists between the hydrophobic, dispersion, and electrostatic contributions to the solvation free energy, a facet not considered in current…
The Poisson-Boltzmann (PB) equation provides a mean-field theory of electrolyte solutions at interfaces and in confinement, describing how ions reorganize close to charged surfaces to form the so-called electrical double layer (EDL), with…
The Poisson-Boltzmann equation is a widely used model to study the electrostatics in molecular solvation. Its numerical solution using a boundary integral formulation requires a mesh on the molecular surface only, yielding accurate…
The Poisson-Boltzmann (PB) model governs the electrostatics of solvated biomolecules, i.e., potential, field, energy, and force. These quantities can provide useful information about protein properties, functions, and dynamics. By…
An electrostatic, implicit particle-in-cell (PIC) model for collisionless, fully magnetized, paraxial plasma expansions in a magnetic nozzle is introduced with exact charge, energy, and magnetic moment conservation properties. The approach…
We propose implicit integrators for solving stiff differential equations on unit spheres. Our approach extends the standard backward Euler and Crank-Nicolson methods in Cartesian space by incorporating the geometric constraint inherent to…
Implicit shape representation, such as SDFs, is a popular approach to recover the surface of a 3D shape as the level sets of a scalar field. Several methods approximate SDFs using machine learning strategies that exploit the knowledge that…
We present and analyze a new iterative solver for implicit discretizations of a simplified Boltzmann-Poisson system. The algorithm builds on recent work that incorporated a sweeping algorithm for the Vlasov-Poisson equations as part of…
Implicit-solvent models are widely used to study the electrostatics in dissolved biomolecules, which are parameterized using force fields. Standard force fields treat the charge distribution with point charges, however, other force fields…
We propose an immersed boundary scheme for the numerical resolution of the Complete Electrode Model in Electrical Impedance Tomography, that we use as a main ingredient in the resolution of inverse problems in medical imaging. Such method…
Multiperforated plates exhibit high gradients and a loss of regularity concentrated in a boundary layer for which a direct numerical simulation becomes very expensive. For elliptic equations the solution at some distance of the boundary is…
Continuum solvation methods can provide an accurate and inexpensive embedding of quantum simulations in liquid or complex dielectric environments. Notwithstanding a long history and manifold applications to isolated systems in open boundary…
In this paper, the Immersed Boundary Method (IBM) proposed by Pinelli is implemented for finite volume approximations of incompressible Navier-Stokes equations solutions in the open source toolbox OpenFOAM version 2.2. Solid obstacles are…
The Immersed Interface Method is employed to solve the time-varying electric field equations around a three-dimensional vesicle. To achieve second-order accuracy the implicit jump conditions for the electric potential, up to the second…