Related papers: Poisson-Boltzmann model for protein-surface electr…
Protein surface fingerprint encodes chemical and geometric features that govern protein-protein interactions and can be used to predict changes in binding affinity between two protein complexes. Current state-of-the-art models for…
In this paper we develop a methodology for the mesoscale simulation of strong electrolytes. The methodology is an extension of the Fluctuating Immersed Boundary (FIB) approach that treats a solute as discrete Lagrangian particles that…
Despite tremendous potential of highly sensitive electronic detection of bio-molecules by nanoscale biosensors for genomics and proteomic applications, many aspects of experimentally observed sensor response (S) are unexplained within…
The standard Poisson-Boltzmann model for molecular electrostatics assumes a sharp variation of the permittivity and salt concentration along the solute-solvent interface. The discontinuous field parameters are not only difficult…
Binding processes are difficult to sample with molecular-dynamics (MD) simulations. In particular, the state space exploration is often incomplete. Evaluating the molecular interaction energy on a grid circumvents this problem but is…
Despite the recognized importance of the multi-scale spatio-temporal organization of proteins, most computational tools can only access a limited spectrum of time and spatial scales, thereby ignoring the effects on protein behavior of the…
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…
Implicit solvent models, such as Poisson-Boltzmann models, play important roles in computational studies of biomolecules. A vital step in almost all implicit solvent models is to determine the solvent-solute interface, and the solvent…
Accurate identification of protein binding sites is crucial for understanding biomolecular interaction mechanisms and for the rational design of drug targets. Traditional predictive methods often struggle to balance prediction accuracy with…
We consider the Poisson-Boltzmann equation in a periodic cell, representative of a porous medium. It is a model for the electrostatic distribution of $N$ chemical species diluted in a liquid at rest, occupying the pore space with charged…
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…
The Poisson-Boltzmann model is an effective and popular approach for modeling solvated biomolecules in continuum solvent with dissolved electrolytes. In this paper, we report our recent work in developing a Galerkin boundary integral method…
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…
Optical molecular sensing techniques are often limited by the refractive index change associated with the probed interactions. In this work, we present a closed form analytical model to estimate the magnitude of optical refractive index…
Enhanced sampling and free energy calculation algorithms of the Thermodynamic Integration family (such as the Adaptive Biasing Force method, ABF) are not based on the direct computation of a free energy surface, but rather of its gradient.…
We propose a method to model metallic surfaces in Lattice Boltzmann Electrokinetics simulations (LBE), a lattice-based algorithm rooted in kinetic theory which captures the coupled solvent and ion dynamics in electrolyte solutions. This is…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
The work reviews on a general level various modified Poisson-Boltzmann equations and demonstrates their use on the specific system of charged particles at an interface. This system is special, first, because it exhibits the long-range…
The Poisson-Boltzmann (PB) model is a widely used implicit solvent model in protein simulations. Although variants, such as the size modified PB and nonlocal modified PB models, have been developed to account for ionic size effects and…
Predicting interactions between proteins is one of the most important yet challenging problems in structural bioinformatics. Intrinsically, potential function sites in protein surfaces are determined by both geometric and chemical features.…