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: 13 July 2025

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles

Select a source type:

Consult the lists of relevant articles, books, theses, conference reports, and other scholarly sources on the topic 'Poisson-Boltzmann calculations.'

Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.

You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.

Journal articles on the topic "Poisson-Boltzmann calculations"

1

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.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

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.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

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.

Full text
APA, Harvard, Vancouver, ISO, and other styles
4

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.

Full text
APA, Harvard, Vancouver, ISO, and other styles
5

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.

Full text
Abstract:
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 the solute is often used as a criticism against the van der Waals surface. However, this assignment may not be as unrealistic as previously thought, since hydrogen exchange and other NMR experiments have firmly established that all interior parts of proteins are transiently accessible to the solvent.
APA, Harvard, Vancouver, ISO, and other styles
6

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.

Full text
APA, Harvard, Vancouver, ISO, and other styles
7

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.

Full text
APA, Harvard, Vancouver, ISO, and other styles
8

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.

Full text
Abstract:
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.
APA, Harvard, Vancouver, ISO, and other styles
9

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.

Full text
Abstract:
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 better capture the phenomena occurring in the real experiments. In addition, specific attention is paid to methods to extend the capabilities of the existing solvers to model large systems toward applications of calculations of the electrostatic potential and energies in molecular motors, mitochondria complex, photosynthetic machinery and systems involving large nanoobjects.
APA, Harvard, Vancouver, ISO, and other styles
10

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.

Full text
APA, Harvard, Vancouver, ISO, and other styles
More sources

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

1

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

Full text
Abstract:
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 measured via VSE, with the eventual goal of being able to quantitatively predict electrostatic fields, and therefore Stark shifts, for any given protein-interaction. This is done using extensive molecular dynamics in the Amber03 and AMOEBA force fields to generate large ensembles the GTPase Rap1a docked to RalGDS and [superscript p]²¹Ras docked to RalGDS. We discuss how side chain orientations contribute to the differential binding of different mutations of Rap1a binding to RalGDS, where it was found that a hydrogen-bonding pocket is disrupted by the mutation of position 31 from lysine to glutamic acid. We then show that multi-dimensional umbrella sampling of the probe orientations yields a wider range of accessible structures, increasing the quality of the ensembles generated. A large variety of methods for calculating electrostatic fields are presented, with Poisson- Boltzmann electrostatics yielding the most consistent, reliable results. Finally, we explore using AMOEBA for both ensemble-generation as well as the electrostatic description of atoms for field calculations, where early results suggest that the electrostatic field due to the induce dipole moment of the probe is responsible for predicting qualitatively correct Stark shifts.
APA, Harvard, Vancouver, ISO, and other styles

Book chapters on the topic "Poisson-Boltzmann calculations"

1

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.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

"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.

Full text
APA, Harvard, Vancouver, ISO, and other styles

Conference papers on the topic "Poisson-Boltzmann calculations"

1

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.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

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.

Full text
Abstract:
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 uses a state equation to relate pressure and density, incompressibility cannot be enforced directly. This is true even for incompressible single-phase LBM calculations, in which a finite density drop is needed to drive through the flow. This is also the case for compressible Navier-Stokes algorithms when applied to low Mach number flow. To mitigate compressibility effects, LBM can be used in low Mach regimes which should keep material density variation small. In this work, we demonstrate that the assumption of low Mach number is not sufficient in multiphase internal flows. In such flows, in the absence of a Pressure Poisson constraint to enforce incompressibility, LBM predicts a compressible solution whereby a density gradient must develop to conserve mass. Imposition of inflow/outflow boundary conditions or a mean body force can ensure that mass is conserved globally, thereby quelling density variation. The primary numerical problem we study is the deformation of a liquid droplet immersed in another fluid. Though LBM is not typically conducted with a pressure Poisson equation, we incorporate one in this work and demonstrate that its inclusion can significantly lower the density variation in view of maintaining an incompressible flow.
APA, Harvard, Vancouver, ISO, and other styles
3

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.

Full text
Abstract:
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 are obtained. In addition, a mathematical expression for the average electroosmotic velocity is derived for large values of the dimensionless electrokinetic parameter, κH, in a fashion similar to the Smoluchowski equation. Hence, a generalized Smoluchowski velocity is introduced by taking into account contributions due to the finite thickness of the electric double layer and the flow behavior index of power-law fluids. Finally, calculations are performed to examine the effects of κH, flow behavior index, double layer thickness, and applied electric field on the shear stress, dynamic viscosity, velocity distribution, and average velocity/flow rate of the electroosmotic flow of power-law fluids.
APA, Harvard, Vancouver, ISO, and other styles
4

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.

Full text
Abstract:
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 near the interface. However, the origin of the conducting carriers is still under debate and needs to be investigated further. In this study, we have examined the origin of conducting carriers at the LaAlO3/SrTiO3 heterointerface using the self-consistency calculations of Schrödinger equation and Poisson equation. We have studied the LaAlO3/SrTiO3 heterointerfaces with and without atomic diffusions. From the self-consistency calculations, carrier distributions, band structures, energy levels, and wavefunctions have been obtained. It has been found that the majority of electron is localized within a few nm from the interface forming two-dimensional electron gas, and multi-subbands are occupied indicating a multi-channel conducting behavior. We also calculated the electron mobility at the interface using the linearized Boltzmann equation including various scattering mechanisms, such as acoustic phonon, polar optical phonon, and remote charged layers in LaAlO3. The calculated mobility has been compared with available experimental data as a function of temperature and thickness of LaAlO3.
APA, Harvard, Vancouver, ISO, and other styles
5

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.

Full text
Abstract:
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 charge density increases largely with higher temperature, in this study efforts are also made to address the thermal effect on EOF induced by the temperature-dependent charge density. In particular, a numerical model is presented for investigating the steady EOF under the thermal effect. The proposed model involves several coupled governing equations including the Nernst-Planck equations, the Poisson equation, the modified Navier-Stokes equations, and the energy equation. The simulation results show that the Boltzmann equation cannot fully describe the ionic concentration distributions under the large thermal effect when EDL overlap. Moreover, for thin EDL, the electroosmotic velocity under the thermal effect at constant potential is lower than that at constant charge, due to the negative electrothermal force at constant potential. Furthermore, it is revealed that the temperature-dependence of surface charge can significantly modify the characteristics of EOF.
APA, Harvard, Vancouver, ISO, and other styles
6

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.

Full text
Abstract:
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 in electroosmotic in various conditions such as different zeta potential, external electric fields, kh parameter (mainly Debye length and channel height), and flow behavior index. Based on the our results, for certain values of effective parameters, there are regions for volumetric flow rates which both Newtonian and non Newtonian electroosmotic flows have similar behavior while out of these regions, there are obviously significant differences and it is not possible to take Newtonian assumption for these regions. Based on our results validated with analytical solution, simplified assumption of taking non Newtonian fluid as Newtonians ones, in different EOF conditions in most cases, have a clearly inaccuracy and presented method can predict which EOF rates in both cases are correctly similar.
APA, Harvard, Vancouver, ISO, and other styles
You might also be interested in the extended bibliographies on the topic 'Poisson-Boltzmann calculations' for particular source types:
Journal articles
We offer discounts on all premium plans for authors whose works are included in thematic literature selections. Contact us to get a unique promo code!

To the bibliography