相关论文: Enlarged Surface Meshes and Normalization Conditio…

Several implicit (continuum) solvent models are considered: the Polarized Continuum Model (PCM), the Surface Generalized Born model (SGB), and the COnductor-like Screening model (COSMO) as well as their implementation in the form of the…

The Surface Cauchy-Born (SCB) method is a computational multi-scale method for the simulation of surface-dominated crystalline materials. We present an error analysis of the SCB method, focused on the role of surface relaxation. In a…

In this paper the full and exhaustive algorithm of formation of a smooth molecular Solvent Excluded Surface- SES, and also Solvent Accessible Surface- SAS is presented. These surfaces are a boundary between molecule and solvent. The basis…

We introduce a novel concept, the minimal molecular surface (MMS), as a new paradigm for the theoretical modeling of biomolecule-solvent interfaces. When a less polar macromolecule is immersed in a polar environment, the surface free energy…

Modeling of spherical metasurfaces using Generalized Sheet Transition Conditions (GSTCs) and Vector Wave Function (VWF) expansion is presented. The fields internal and external to the metasurface is expanded in terms of spherical VWFs and…

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…

Quantum Mechanics/Molecular Mechanics (QM/MM) simulations are a popular approach to study various features of large systems. A common application of QM/MM calculations is in the investigation of reaction mechanisms in condensed-phase and…

Recovering the polarized cosmic microwave background (CMB) is essential for shedding light on the exponential expansion of the very early Universe, known as cosmic inflation. Achieving this goal requires not only improved instrumental…

Estimation of the sky signal from sequences of time ordered data is one of the key steps in Cosmic Microwave Background (CMB) data analysis, commonly referred to as the map-making problem. Some of the most popular and general methods…

Recent developments for mathematical modeling and numerical simulation of biomolecular systems raise new demands for qualified, stable, and efficient surface meshing, especially in implicit-solvent modeling. In our former work, we have…

The modeling and removal of foregrounds poses a major challenge to searches for signals from inflation using the cosmic microwave background (CMB). In particular, the modeling of CMB foregrounds including various spatial averaging effects…

Image modeling and simulation are critical to extending the limits of leading edge lithography technologies used for IC making. Simultaneous source mask optimization (SMO) has become an important objective in the field of computational…

Polarimetry of the Cosmic Microwave Background (CMB) represents one of the possible diagnostics aimed at testing large-scale magnetism at the epoch of the photon decoupling. The propagation of electromagnetic disturbances in a magnetized…

The general approach in metasurface design is to find the unit-cell properties required to achieve a given functionality. This is usually done by modeling the metasurface as a combination of surface electric and magnetic polarization…

Obtaining the set of cosmological parameters consistent with observational data is an important exercise in current cosmological research. It involves finding the global maximum of the likelihood function in the multi-dimensional parameter…

Microscopic processes on surfaces such as adsorption, desorption, diffusion and reaction of interacting particles can be simulated using kinetic Monte Carlo (kMC) algorithms. Even though kMC methods are accurate, they are computationally…

This paper develops column partition based distributed schemes for a class of large-scale convex sparse optimization problems, e.g., basis pursuit (BP), LASSO, basis pursuit denosing (BPDN), and their extensions, e.g., fused LASSO. We are…

This paper concerns the use of sequential Monte Carlo methods (SMC) for smoothing in general state space models. A well-known problem when applying the standard SMC technique in the smoothing mode is that the resampling mechanism introduces…

Continuum solvation models are becoming increasingly relevant in condensed matter simulations, allowing to characterize materials interfaces in the presence of wet electrified environments at a reduced computational cost with respect to all…

An extension of the Method of Regularized Stokeslets (MRS) in three dimensions is developed for triangulated surfaces with a piecewise linear force distribution. The method extends the regularized Stokeslet segment methodology used for…