Electrostatic interactions play a central role in biological processes. Development of fast computational methods to solve the underlying Poisson-Boltzmann equation (PBE) is vital for biomolecular modeling and simulation package. In this paper, we propose new methods for efficiently computing the electrostatic potentials for large molecules by using the geometry of the molecular shapes to guide...

Abstract. The mathematical modelling of the dynamics of particle suspension is based on the population balance equation (PBE). PBE is an integro-differential equation for the population density that is a function of time t, space coordinates and internal parameters. Usually, the particle is characterized by a unique parameter, e.g. the matter volume v. PBE consists of several terms: for instanc...

Electrostatic potential as well as the local volume charge density are computed for a macromolecule by solving the Poisson-Boltzmann equation (PBE) using the finite element method (FEM). As a verification, our numerical results for a one dimensional PBE, which corresponds to an infinite-length macromolecule, are compared with the existing analytical solution and good agreement is found. As a ma...

manipulate the sources or their information, such as the location of their files on a haed drive or the emails in their in-boxes. End-user programming is emerging as a crucial instrument in the daily informationprocessing struggle [8]. Such programming allows customized personal information processing. But few end users have the background, motivation, or time to use traditional programming app...

The Poisson–Boltzmann equation (PBE) is an establishedmodel for the electrostatic analysis of biomolecules. The development of advanced computational techniques for the solution of the PBE has been an important topic in the past two decades. This article presents a matched interface and boundary (MIB)-based PBE software package, theMIBPB solver, for electrostatic analysis. The MIBPB has a uniqu...

In yeast, resolution of chiasmata in meiosis I requires proteolytic cleavage along chromosome arms of cohesin's Rec8 subunit by separase. Since activation of separase by the anaphase-promoting complex (APC/C) is supposedly not required for meiosis I in Xenopus oocytes, it has been suggested that animal cells might resolve chiasmata by a separase-independent mechanism related to the so-called "p...

We show the existing solution of Poisson-Boltzmann equation (PBE) to violate charge conservation principle, and then derive the correct formula for charge density distribution (ρe) in a fluid. We replaced unphysical old boundary conditions with some conditions that have never been used. Our result demonstrates that PBE cannot explain the formation of ‘Electric Double Layer’ (EDL); it follows th...

Programming by example (PBE), or inductive synthesis is a subfield of program synthesis where specification on a target program is provided in a form of input-output examples or, more generally, constraints on the output [9]. While research in PBE dates back as far as 1980s [8], its mass-market applications only appeared in the last decade. PBE has gained prominence due to its applicability in ...

The nonlinear Poisson-Boltzmann equation (PBE) has been successfully used for the prediction of numerous electrostatic properties of highly charged biopolyelectrolytes immersed in aqueous salt solutions. While numerous numerical solvers for the 3D PBE have been developed, the formulation of the outer boundary treatments used in these methods has only been loosely addressed, especially in the no...

The concept of policy-based cryptography (PBC) is a promising paradigm for trust establishment and authorization in large-scale open environments. A policy-based encryption scheme (PBE) allows to encrypt a message according to a policy so that only entities fulfilling the policy are able to perform the decryption of the message. Symmetrically, a policy-based signature scheme (PBS) assures that ...