TABI-PB 2.0: An Improved Version of the Treecode-Accelerated Boundary Integral Poisson-Boltzmann Solver

Wilson, Leighton; Geng, Weihua; Krasny, Robert

doi:10.1021/acs.jpcb.2c04604

Cited by 13 publications

(6 citation statements)

References 57 publications

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“…This, however, does not diminish the importance of studying the behavior of the LPBE also in the case of highly charged objects: their electrostatics may still be correctly described at sufficiently long distances (as compared to the Debye length) by the usual DH approximation provided that the sources of the electric field are properly renormalized. − (See also the recent ref for additional comments concerning the ranges of applicability of the DH theory.) This once again emphasizes the importance of a thorough study of the DH approximations, both theoretically and numerically, and justifies the constant stream of works related to the LPBE (see recent refs , , and − , and references therein).…”

Section: Introductionsupporting

confidence: 63%

Arbitrary-Shape Dielectric Particles Interacting in the Linearized Poisson–Boltzmann Framework: An Analytical Treatment

Siryk

Rocchia

2022

J. Phys. Chem. B

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This work considers the interaction of two dielectric particles of arbitrary shape immersed into a solvent containing a dissociated salt and assuming that the linearized Poisson–Boltzmann equation holds. We establish a new general spherical re-expansion result which relies neither on the conventional condition that particle radii are small with respect to the characteristic separating distance between particles nor on any symmetry assumption. This is instrumental in calculating suitable expansion coefficients for the electrostatic potential inside and outside the objects and in constructing small-parameter asymptotic expansions for the potential, the total electrostatic energy, and forces in ascending order of Debye screening. This generalizes a recent result for the case of dielectric spheres to particles of arbitrary shape and builds for the first time a rigorous (exact at the Debye–Hückel level) analytical theory of electrostatic interactions of such particles at arbitrary distances. Numerical tests confirm that the proposed theory may also become especially useful in developing a new class of grid-free, fast, highly scalable solvers.

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Section: Introductionsupporting

confidence: 63%

Arbitrary-Shape Dielectric Particles Interacting in the Linearized Poisson–Boltzmann Framework: An Analytical Treatment

Siryk

Rocchia

2022

J. Phys. Chem. B

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“…The HOBI code 51 ( https://sourceforge.net/projects/hobipb/ ) can be implemented with MPI. The C++ TABI code 53 ( https://github.com/Treecodes/TABI-PB ) can be implemented with MPI and GPU in a hybrid parallelization. The Fortran TABI code 30 ( https://github.com/gengwh/TABI-PB ) can be implemented in MPI (in preparation 64 ) utilizing the parallel algorithm developed recently.…”

Section: Resultsmentioning

confidence: 99%

“…The integrals in Equations (11a) and (11b) can be discretized by centroid collocation, which is popular due to its simplicity. 30 Alternatively, it can also be discretized using other more complicated approaches such as node-patch collocation, 52 , 53 curved triangles, 51 or Galerkin’s method 54 with a trade-off of accuracy and efficiency. Here we provide the centroid collocation approach.…”

Section: Methodsmentioning

confidence: 99%

Bridging Eulerian and Lagrangian Poisson–Boltzmann solvers by ESES

Ullah,

Yang,

Jones

et al. 2023

J Comput Chem

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The Poisson–Boltzmann (PB) model is a widely used electrostatic model for biomolecular solvation analysis. Formulated as an elliptic interface problem, the PB model can be numerically solved on either Eulerian meshes using finite difference/finite element methods or Lagrangian meshes using boundary element methods. Molecular surface generators, which produce the discretized dielectric interfaces between solutes and solvents, are critical factors in determining the accuracy and efficiency of the PB solvers. In this work, we investigate the utility of the Eulerian Solvent Excluded Surface (ESES) software for rendering conjugated Eulerian and Lagrangian surface representations, which enables us to numerically validate and compare the quality of Eulerian PB solvers, such as the MIBPB solver, and the Lagrangian PB solvers, such as the TABI‐PB solver. Furthermore, with the ESES software and its associated PB solvers, we are able to numerically validate an interesting and useful but often neglected source‐target symmetric property associated with the linearized PB model.

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“…18 The same solvent model was assumed in the development of an improved version of the TABI-PB solver. 19 Along the same lines, but following a different model, a coarse-grained version of ddCOSMO was presented as an efficient way to compute the solvation energy of large solutes within a polarizable continuum medium in a linear scaling computational time. 20 The computational advantages of using a simplified model such as Generalized Born (GB) are leveraged by enriching the CHARMM-GUI toolkit of the functionality to set up calculations with different GB flavors for different MD engines.…”

mentioning

confidence: 99%

“…Improvements to continuum models were discussed regarding a better prediction of water molecule distribution around negatively charged solutes, and introducing better analytical estimates of the interaction energy of dielectric particles in a solvent obeying the linearized Poisson–Boltzmann equation . The same solvent model was assumed in the development of an improved version of the TABI-PB solver . Along the same lines, but following a different model, a coarse-grained version of ddCOSMO was presented as an efficient way to compute the solvation energy of large solutes within a polarizable continuum medium in a linear scaling computational time .…”

mentioning

confidence: 99%