Relevant bibliographies by topics / Poisson-Boltzmann calculations

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers

Academic literature on the topic 'Poisson-Boltzmann calculations'

Author: Grafiati
Published: 3 June 2025
Last updated: 20 July 2025

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Journal articles on the topic "Poisson-Boltzmann calculations"

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Friedrichs, Mark, Ruhong Zhou, Shlomit R. Edinger, and Richard A. Friesner. "Poisson−Boltzmann Analytical Gradients for Molecular Modeling Calculations." Journal of Physical Chemistry B 103, no. 16 (1999): 3057–61. http://dx.doi.org/10.1021/jp982513m.

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Tjong, Harianto, and Huan-Xiang Zhou. "On the Dielectric Boundary in Poisson−Boltzmann Calculations." Journal of Chemical Theory and Computation 4, no. 3 (2008): 507–14. http://dx.doi.org/10.1021/ct700319x.

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Lo, Wai Yin, and Kwong‐Yu Chan. "Poisson–Boltzmann calculations of ions in charged capillaries." Journal of Chemical Physics 101, no. 2 (1994): 1431–34. http://dx.doi.org/10.1063/1.467767.

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Ivanović, Miloš T., Linda K. Bruetzel, Roman Shevchuk, Jan Lipfert, and Jochen S. Hub. "Quantifying the influence of the ion cloud on SAXS profiles of charged proteins." Physical Chemistry Chemical Physics 20, no. 41 (2018): 26351–61. http://dx.doi.org/10.1039/c8cp03080d.

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Pang, Xiaodong, and Huan-Xiang Zhou. "Poisson-Boltzmann Calculations: van der Waals or Molecular Surface?" Communications in Computational Physics 13, no. 1 (2013): 1–12. http://dx.doi.org/10.4208/cicp.270711.140911s.

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AbstractThe Poisson-Boltzmann equation is widely used for modeling the electro-statics of biomolecules, but the calculation results are sensitive to the choice of the boundary between the low solute dielectric and the high solvent dielectric. The default choice for the dielectric boundary has been the molecular surface, but the use of the van der Waals surface has also been advocated. Here we review recent studies in which the two choices are tested against experimental results and explicit-solvent calculations. The assignment of the solvent high dielectric constant to interstitial voids in th
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Wang, Jun, Qin Cai, Ye Xiang, and Ray Luo. "Reducing Grid Dependence in Finite-Difference Poisson–Boltzmann Calculations." Journal of Chemical Theory and Computation 8, no. 8 (2012): 2741–51. http://dx.doi.org/10.1021/ct300341d.

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Luo, Ray, Laurent David, and Michael K. Gilson. "Accelerated Poisson-Boltzmann calculations for static and dynamic systems." Journal of Computational Chemistry 23, no. 13 (2002): 1244–53. http://dx.doi.org/10.1002/jcc.10120.

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Morais, Pablo A., Francisco Franciné Maia, Christian Solis-Calero, Ewerton Wagner Santos Caetano, Valder Nogueira Freire, and Hernandes F. Carvalho. "The urokinase plasminogen activator binding to its receptor: a quantum biochemistry description within an in/homogeneous dielectric function framework with application to uPA–uPAR peptide inhibitors." Physical Chemistry Chemical Physics 22, no. 6 (2020): 3570–83. http://dx.doi.org/10.1039/c9cp06530j.

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DFT calculations using the MFCC fragment-based model considering a spatial-dependent dielectric function based on the Poisson–Boltzmann approximation were performed to describe the uPA–uPAR interactions.
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Li, Chuan, Lin Li, Marharyta Petukh, and Emil Alexov. "Progress in developing Poisson-Boltzmann equation solvers." Computational and Mathematical Biophysics 1 (March 21, 2013): 42–62. http://dx.doi.org/10.2478/mlbmb-2013-0002.

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AbstractThis review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nanoobjects, the last one referring to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules. The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task provided the specific definition of the system to be modeled and as a physical problem aiming to bett
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Lamm, Gene, and George R. Pack. "Induced Coalescence of Cations through Low-Temperature Poisson-Boltzmann Calculations." Biophysical Journal 87, no. 2 (2004): 764–67. http://dx.doi.org/10.1529/biophysj.104.040220.

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Dissertations / Theses on the topic "Poisson-Boltzmann calculations"

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Ritchie, Andrew William. "Quantifying electrostatic fields at protein interfaces using classical electrostatics calculations." Thesis, 2015. http://hdl.handle.net/2152/31346.

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The functional aspects of proteins are largely dictated by highly selective protein- protein and protein-ligand interactions, even in situations of high structural homology, where electrostatic factors are the major contributors to selectivity. The vibrational Stark effect (VSE) allows us to measure electrostatic fields in complex environments, such as proteins, by the introduction of a vibrational chromophore whose vibrational absorption energy is linearly sensitive to changes in the local electrostatic field. The works presented here seek to computationally quantify electrostatic fields meas
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Book chapters on the topic "Poisson-Boltzmann calculations"

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Ilin, Andrew, Babak Bagheri, L. Ridgway Scott, James M. Briggs, and J. Andrew McCammon. "Parallelization of Poisson—Boltzmann and Brownian Dynamics Calculations." In Parallel Computing in Computational Chemistry. American Chemical Society, 1995. http://dx.doi.org/10.1021/bk-1995-0592.ch012.

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"FIG. 15 Model of a spherical SDS micelle devised by Israelachvili (J.Israelachvili, Intermolecular and Surface Forces, 2nd Ed.; Academic Press: London, 1991.) displaying a fairly well-defined hydrocarbon-water interface. The hydrocarbon chains packed inside the core to normal density are subject to geometrical constraints, which are taken into account in the (mean field) calculations of their configurational state due to Gruen and de Lacey [55] and others. The sodium counterions have been omitted. Besides, in the standard Poisson-Boltzmann treatment of the curved electrostatic double layer, the." In Surface and Interfacial Tension. CRC Press, 2004. http://dx.doi.org/10.1201/9780203021262-178.

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Conference papers on the topic "Poisson-Boltzmann calculations"

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Machuqueiro, Miguel, Pedro Reis, Diogo Vila-Viçosa, and Walter Rocchia. "PypKa: a python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism." In MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition. MDPI, 2018. http://dx.doi.org/10.3390/mol2net-04-06101.

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Horwitz, Jeremy A. K., S. P. Vanka, and P. Kumar. "LBM Simulations of Dispersed Multiphase Flows in a Channel: Role of a Pressure Poisson Equation." In ASME-JSME-KSME 2019 8th Joint Fluids Engineering Conference. American Society of Mechanical Engineers, 2019. http://dx.doi.org/10.1115/ajkfluids2019-4943.

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Abstract In recent years, Lattice Boltzmann Methods (LBM’s) have emerged as a popular class of paradigms for the simulation of multiphase flows. These methods rely on discretized Boltzmann equations to represent the individual multiphase species. Among LBM’s advantages is its ability to explicitly account for interfacial physics and its local streaming/collision operations which make it ideally suited for parallelization. However, one drawback of LBM is in the simulation of incompressible multiphase flow, whereby the density should remain constant along material characteristics. Because LBM us
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Zhao, Cunlu, and Chun Yang. "Electroosmotic Flow of Power-Law Fluids in a Slit Microchannel." In ASME 2009 7th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2009. http://dx.doi.org/10.1115/icnmm2009-82182.

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Electroosmotic flow of power-law fluids in a slit channel is analyzed. The governing equations including the linearized Poisson–Boltzmann equation, the Cauchy momentum equation and the continuity equation are solved to seek analytical expressions for the shear stress, dynamic viscosity and velocity distributions. Specifically, exact solutions of the velocity distributions are explicitly found for several special values of the flow behavior index. Furthermore, with the implementation of an approximate scheme for the hyperbolic cosine function, approximate solutions of the velocity distributions
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Su, Shanshan, and Jeong Ho You. "Conducting Heterointerface of Polar-Nonpolar Band Gap Insulators." In ASME 2012 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/imece2012-88089.

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Recently, the heterointerface between two band insulators, LaAlO3 and SrTiO3 has received much attention due to its high conducting behavior. The origin of conducting carriers at the LaAlO3/SrTiO3 heterointerface has been mainly explained by two distinct models: the polar catastrophe model and the atomic inter-diffusion model. The polar catastrophe model is based on a half electron transferred from polar LaAlO3 to nonpolar SrTiO3 to avoid the divergence of electric field without any atomic diffusions. The atomic inter-diffusion model is based on the transfer of dopants from LaAlO3 to SrTiO3 ne
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Zhou, Yi, Chun Yang, and Cunlu Zhao. "Thermal Effect on Electroosmotic Flow in a Slit Microchannel." In ASME 2013 11th International Conference on Nanochannels, Microchannels, and Minichannels. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/icnmm2013-73055.

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Electroosmotic flow (EOF) in microfluidic systems is frequently subjected to thermal effect because of temperature-dependent material properties. Boltzmann equation is usually used to describe the ion distribution in EOF. This study will compare the ion distribution under the thermal effect with the Boltzmann distribution. Moreover, for thin electrical double layer (EDL), constant potential model always be used to simplify the calculation of EOF at constant charge. In this study, the thermal effects on EOF at both constant potential and constant charge are analyzed. In addition, as the surface
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Zakeri, Ramin, and Eon Soo Lee. "Similar Region in Electroosmotic Flow Rate for Newtonian and Non-Newtonian Fluids Using Dissipative Particle Dynamics (DPD)." In ASME 2014 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/imece2014-37836.

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In this paper, analysis of electroosmotic flow in Newtonian and non Newtonian fluids in nanochannel with dissipative particle dynamics (DPD) method is presented and our results are validated with analytical solutions. Our aim is that which region or regions, based on the volumetric flow rates, in non-Newtonian fluids are similar with comparison to Newtonian ones in regards to various effective EOF parameters. For numerical simulation, the linearized Poisson Boltzmann for external force calculation is used and DPD method is applied for power law fluids to predict non-Newtonian fluids behavior i
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