Christopher D. Cooper, Lorena A. Barba
Interactions between surfaces and proteins occur in many vital processes and are crucial in biotechnology: the ability to control specific interactions is essential in fields like biomaterials, biomedical implants and biosensors. In the latter case, biosensor sensitivity hinges on ligand proteins adsorbing on bioactive surfaces with a favorable orientation, exposing reaction sites to target molecules. […]
Jose Colmenares, Antonella Galizia, Jesus Ortiz, Andrea Clematis, Walter Rocchia
The Poisson-Boltzmann equation models the electrostatic potential generated by fixed charges on a polarizable solute immersed in an ionic solution. This approach is often used in computational Structural Biology to estimate the electrostatic energetic component of the assembly of molecular biological systems. In the last decades the amount of structural data concerning proteins and other […]
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Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba
The continuum theory applied to bimolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like solvent-filled cavities or ion-exclusion (Stern) layers, due to the added difficulty of treating multiple boundary surfaces. This has hindered meaningful comparisons with volume-based methods, and […]
Christopher Cooper, Lorena A. Barba
The PyGBe code solves the linearized Poisson-Boltzmann equation using a boundary-integral formulation. We use a boundary element method with a collocation approach, and solve it via a Krylov-subspace method. To do this efficiently, the matrix-vector multiplications in the Krylov iterations are accelerated with a treecode, achieving O(N log N) complexity. The code presents a Python […]
Weihua Geng, Ferosh Jacob
In this paper, we present a GPU-accelerated direct-sum boundary integral method to solve the linear Poisson-Boltzmann (PB) equation. In our method, a well-posed boundary integral formulation is used to ensure the fast convergence of Krylov subspace based linear algebraic solver such as the GMRES. The molecular surfaces are discretized with flat triangles and centroid collocation. […]
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Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Francesco Zerbetto, Siegfried Hofinger
Electrostatic potentials (ESPs) are frequently used in structural biology for the characterization of biomolecules. Here we study the potential employment of hardware accelerators like the graphics processing unit or the application-specific integrated circuit MD-GRAPE-3 for the purpose of efficient computation of ESPs. An algorithm closely coupled to the general description of molecular surfaces is ported […]
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Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Siegfried Hofinger
Scientific applications do frequently suffer from limited compute performance. In this article, we investigate the suitability of specialized computer chips to overcome this limitation. An enhanced Poisson Boltzmann program is ported to the graphics processing unit and the application specific integrated circuit MDGRAPE-3 and resulting execution times are compared to the conventional performance obtained on […]

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