相关论文: Mathematical Analysis of the BIBEE Approximation f…
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…
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…
Understanding the behavior of biomolecules such as proteins requires understanding the critical influence of the surrounding fluid (solvent) environment--water with mobile salt ions such as sodium. Unfortunately, for many studies, fully…
Surface integral equation (SIE) methods are of great interest for the numerical solution of Maxwell's equations in the presence of homogeneous objects. However, existing SIE algorithms have limitations, either in terms of scalability,…
The analytical solution of the recently proposed ideal chain polymer mean-spherical approximation (Yu.Kalyuzhnyi, Mol.Phys., 94, 735(1998)) is presented for the multicomponent mixture of charged hard-sphere linear chain flexible molecules.…
In this paper, we present an analytical solution to nonlocal continuum electrostatics for an arbitrary charge distribution in a spherical solute. Our approach relies on two key steps: (1) re-formulating the PDE problem using…
We consider the common problem setting of an elastic sphere impacting on a flexible beam. In contrast to previous studies, we analyze the modal energy distribution induced by the impact, having in mind the particular application of impact…
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…
The size-modified Poisson-Boltzmann equation (SMPBE) is one important variant of the popular dielectric model, the Poisson-Boltzmann equation (PBE), to reflect ionic size effects in the prediction of electrostatics for a biomolecule in an…
Diffusion coefficients are key thermophysical properties for modeling mass transport in liquids, but experimental data are scarce, making reliable prediction methods indispensable. In the present work, we introduce a new method for…
This paper presents a re-formulation of the boundary integral method (BIM) for the Debye-Huckel model of molecular and colloidal electrostatics that removes the mathematical singularities that have been accepted as an intrinsic part of the…
The long-ranged nature of the Coulomb potential requires a proper accounting for the influence of even distant electrostatic boundaries in the determination of the solvation free energy of a charged solute. We introduce an exact rewriting…
The solvation model proposed by Fattebert and Gygi [Journal of Computational Chemistry 23, 662 (2002)] and Scherlis et al. [Journal of Chemical Physics 124, 074103 (2006)] is reformulated, overcoming some of the numerical limitations…
The Bethe-Salpeter equation (BSE) is currently the state of the art in the description of neutral electron excitations in both solids and large finite systems. It is capable of accurately treating charge-transfer excitations that present…
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…
The Poisson-Boltzmann equation offers an efficient way to study electrostatics in molecular settings. Its numerical solution with the boundary element method is widely used, as the complicated molecular surface is accurately represented by…
A surface integral equation (SIE) formulation under the magneto-quasi-static assumption is proposed to efficiently and accurately model arbitrarily shaped interconnects in packages. Through decently transferring all electromagnetic…
We develop an immersed-boundary approach to modeling reaction-diffusion processes in dispersions of reactive spherical particles, from the diffusion-limited to the reaction-limited setting. We represent each reactive particle with a…
This paper tests a dielectric model for variation of hydration free energy with geometry of complex solutes in water. It works out some basic aspects of the theory of boundary integral methods for these problems. One aspect of the…
The interaction of fibers in a viscous (Stokes) fluid plays a crucial role in industrial and biological processes, such as sedimentation, rheology, transport, cell division, and locomotion. Numerical simulations generally rely on slender…