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Journal articles on the topic 'Continuum electrostatics'

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Published: 4 June 2021
Last updated: 28 January 2023

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1

Rashin, Alexander A. "Continuum electrostatics and hydration phenomena." International Journal of Quantum Chemistry 34, S15 (March 12, 1988): 103–18. http://dx.doi.org/10.1002/qua.560340711.

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2

Smart, Jason L., and J. Andrew McCammon. "Surface Titration: A Continuum Electrostatics Model." Journal of the American Chemical Society 118, no. 9 (January 1996): 2283–84. http://dx.doi.org/10.1021/ja953878c.

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3

Truchon, Jean-François, Anthony Nicholls, Radu I. Iftimie, Benoît Roux, and Christopher I. Bayly. "Accurate Molecular Polarizabilities Based on Continuum Electrostatics." Journal of Chemical Theory and Computation 4, no. 9 (August 13, 2008): 1480–93. http://dx.doi.org/10.1021/ct800123c.

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4

Schaefer, Michael, and Martin Karplus. "A Comprehensive Analytical Treatment of Continuum Electrostatics." Journal of Physical Chemistry 100, no. 5 (January 1996): 1578–99. http://dx.doi.org/10.1021/jp9521621.

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5

Couch, Vernon, and Alexei Stuchebrukhov. "Histidine in continuum electrostatics protonation state calculations." Proteins: Structure, Function, and Bioinformatics 79, no. 12 (August 30, 2011): 3410–19. http://dx.doi.org/10.1002/prot.23114.

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6

Simonson, Thomas. "Electrostatic Free Energy Calculations for Macromolecules: A Hybrid Molecular Dynamics/Continuum Electrostatics Approach." Journal of Physical Chemistry B 104, no. 28 (July 2000): 6509–13. http://dx.doi.org/10.1021/jp0014317.

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7

WANG, ZHEN-GANG. "VARIATIONAL ELECTROSTATICS FOR CHARGE SOLVATION." Journal of Theoretical and Computational Chemistry 07, no. 03 (June 2008): 397–419. http://dx.doi.org/10.1142/s0219633608003824.

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We show that the equations of continuum electrostatics can be obtained entirely and simply from a variational free energy comprising the Coulomb interactions among all charged species and a spring-like term for the polarization of the dielectric medium. In this formulation, the Poisson equation, the constitutive relationship between polarization and the electric field, as well as the boundary conditions across discontinuous dielectric boundaries, are all natural consequences of the extremization of the free energy functional. This formulation thus treats the electrostatic equations and the energetics within a single unified framework, avoiding some of the pitfalls in the study of electrostatic problems. Application of this formalism to the nonequilbrium solvation free energy in electron transfer is illustrated. Our calculation reaffirms the well-known result of Marcus. We address the recent criticisms by Li and coworkers who claim that the Marcus result is incorrect, and expose some key mistakes in their approach.
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8

Zhou, Baojing, Manish Agarwal, and Chung F. Wong. "Variable atomic radii for continuum-solvent electrostatics calculation." Journal of Chemical Physics 129, no. 1 (July 7, 2008): 014509. http://dx.doi.org/10.1063/1.2949821.

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9

Mandell, Jeffrey G., Victoria A. Roberts, Michael E. Pique, Vladimir Kotlovyi, Julie C. Mitchell, Erik Nelson, Igor Tsigelny, and Lynn F. Ten Eyck. "Protein docking using continuum electrostatics and geometric fit." Protein Engineering, Design and Selection 14, no. 2 (February 2001): 105–13. http://dx.doi.org/10.1093/protein/14.2.105.

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10

Simonson, Thomas. "Macromolecular electrostatics: continuum models and their growing pains." Current Opinion in Structural Biology 11, no. 2 (April 2001): 243–52. http://dx.doi.org/10.1016/s0959-440x(00)00197-4.

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11

Potter, Michael J., Michael K. Gilson, and J. Andrew McCammon. "Small Molecule pKa Prediction with Continuum Electrostatics Calculations." Journal of the American Chemical Society 116, no. 22 (November 1994): 10298–99. http://dx.doi.org/10.1021/ja00101a059.

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12

Liu, Liping. "On energy formulations of electrostatics for continuum media." Journal of the Mechanics and Physics of Solids 61, no. 4 (April 2013): 968–90. http://dx.doi.org/10.1016/j.jmps.2012.12.007.

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13

Miteva, M. A., P. Tuffery, and B. O. Villoutreix. "PCE: web tools to compute protein continuum electrostatics." Nucleic Acids Research 33, Web Server (July 1, 2005): W372—W375. http://dx.doi.org/10.1093/nar/gki365.

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14

Scarsi, Marco, and Amedeo Caflisch. "Comment on the validation of continuum electrostatics models." Journal of Computational Chemistry 20, no. 14 (November 15, 1999): 1533–36. http://dx.doi.org/10.1002/(sici)1096-987x(19991115)20:14<1533::aid-jcc6>3.0.co;2-3.

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15

Zhou, Y. C., Michael Feig, and G. W. Wei. "Highly accurate biomolecular electrostatics in continuum dielectric environments." Journal of Computational Chemistry 29, no. 1 (2007): 87–97. http://dx.doi.org/10.1002/jcc.20769.

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16

Merlo, Manuele, Fabio Negretto, Monica Soncini, and Franco Maria Montevecchi. "Electrostatic Nanomechanics of Cantilever Biosensors." Materials Science Forum 539-543 (March 2007): 595–601. http://dx.doi.org/10.4028/www.scientific.net/msf.539-543.595.

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Interest in microcantilever based biosensors in the biomedical field has largely increased during the last years. Potentially, this kind of sensor can provide a considerable contribution to complex disease diagnosis, which requires the detection of biological molecules. Microcantilever biosensors allow the detection of complementary DNA fragment hybridization or specific antibody-antigen binding; it is known that adsorption of specific biological molecules upon the microcantilever surface induces cantilever deflection due to the interaction of the molecules with the surface. To date, the phenomena which determine the deflection mechanism are not completely known. The present work investigates the electrostatic field within the molecules and the forces consequently acting on the molecules and on the cantilever in order to provide a description of the deflection mechanism. The electrostatic potential of arrays of double strand DNA molecules immersed in an ionic solution was modelled by means of cylinders negatively charged at the surface and a FE (Finite Element) continuum electrostatics analysis was implemented in order to numerically solve the second order non-linear Poisson-Boltzmann equation. Then, a FE structural analysis of the cantilever was performed coupled with the continuum electrostatics analysis. In this way, the effects of the molecules’ electrostatic interactions on the cantilever deflection were taken into account. The model was run to describe the microcantilever deflection due to the electrostatic field under different design and operating conditions, and it was also set to compare hexagonal and square disposition of double strand DNA molecules.
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17

Farafonov, Vladimir, Alexander Lebed, and Nikolay Mchedlov-Petrossyan. "CONTINUUM ELECTROSTATICS INVESTIGATION OF IONIC MICELLES USING ATOMISTIC MODELS." Ukrainian Chemistry Journal 87, no. 6 (July 26, 2021): 55–69. http://dx.doi.org/10.33609/2708-129x.87.06.2021.55-69.

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The key parameter related to the structure of the electric double layer of ionic surfactant micelles – electrostatic potential – is considered. A brief overview of experimental methods and theoretical models for estimating electrostatic potential- is given. The calculating method for the electrostatic potential based on a numerical solution of the Poisson-Boltzmann equation using an atomistic model of anionic surfactant micelle - is proposed. The parameters necessary for the construction of atomistic models - are obtained from molecular dynamic modeling. The electrostatic potentials for the micelles of sodium dodecyl sulfate and cetyltrimethylammonium bromide at different ionic strengths - were calculated by this method. The results are discussed in comparison with the values calculated in the simplified model, the Ohshima – Healy – White equation.
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18

Choe, Seungho, Karen A. Hecht, and Michael Grabe. "A Continuum Method for Determining Membrane Protein Insertion Energies and the Problem of Charged Residues." Journal of General Physiology 131, no. 6 (May 12, 2008): 563–73. http://dx.doi.org/10.1085/jgp.200809959.

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Continuum electrostatic approaches have been extremely successful at describing the charged nature of soluble proteins and how they interact with binding partners. However, it is unclear whether continuum methods can be used to quantitatively understand the energetics of membrane protein insertion and stability. Recent translation experiments suggest that the energy required to insert charged peptides into membranes is much smaller than predicted by present continuum theories. Atomistic simulations have pointed to bilayer inhomogeneity and membrane deformation around buried charged groups as two critical features that are neglected in simpler models. Here, we develop a fully continuum method that circumvents both of these shortcomings by using elasticity theory to determine the shape of the deformed membrane and then subsequently uses this shape to carry out continuum electrostatics calculations. Our method does an excellent job of quantitatively matching results from detailed molecular dynamics simulations at a tiny fraction of the computational cost. We expect that this method will be ideal for studying large membrane protein complexes.
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19

Banavali, Nilesh K., and Benoıt Roux. "Atomic Radii for Continuum Electrostatics Calculations on Nucleic Acids." Journal of Physical Chemistry B 106, no. 42 (October 2002): 11026–35. http://dx.doi.org/10.1021/jp025852v.

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20

Nina, Mafalda, Wonpil Im, and Benoı̂t Roux. "Optimized atomic radii for protein continuum electrostatics solvation forces." Biophysical Chemistry 78, no. 1-2 (April 1999): 89–96. http://dx.doi.org/10.1016/s0301-4622(98)00236-1.

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21

Ullmann, G. Matthias, Edda Kloppmann, Timm Essigke, Eva-Maria Krammer, Astrid R. Klingen, Torsten Becker, and Elisa Bombarda. "Investigating the mechanisms of photosynthetic proteins using continuum electrostatics." Photosynthesis Research 97, no. 1 (May 14, 2008): 33–53. http://dx.doi.org/10.1007/s11120-008-9306-1.

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22

Pan, Cong, Shasha Yi, and Zhonghan Hu. "The effect of electrostatic boundaries in molecular simulations: symmetry matters." Physical Chemistry Chemical Physics 19, no. 6 (2017): 4861–76. http://dx.doi.org/10.1039/c6cp07406e.

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23

Botello-Smith, Wesley M., Qin Cai, and Ray Luo. "Biological applications of classical electrostatics methods." Journal of Theoretical and Computational Chemistry 13, no. 03 (May 2014): 1440008. http://dx.doi.org/10.1142/s0219633614400082.

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Continuum electrostatics modeling of solvation based on the Poisson–Boltzmann (PB) equation has gained wide acceptance in biomolecular applications such as energetic analysis and structural visualization. Successful application of the PB solvent models requires careful calibration of the solvation parameters. Extensive testing and validation is also important to ensure accuracy in their applications. Limitation in the continuum modeling of solvation is also a known issue in certain biomolecular applications. Growing interest in membrane systems has further spurred developmental efforts to allow inclusion of membrane in the PB solvent models. Despite their past successes due to careful parameterization, algorithm development and parallel implementation, there is still much to be done to improve their transferability from the small molecular systems upon which they were developed and validated to complex macromolecular systems as advances in technology continue to push forward, providing ever greater computational resources to researchers to study more interesting biological systems of higher complexity.
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24

Li, Bo. "Continuum electrostatics for ionic solutions with non-uniform ionic sizes." Nonlinearity 22, no. 4 (February 26, 2009): 811–33. http://dx.doi.org/10.1088/0951-7715/22/4/007.

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25

Huang, Danzhi, and Amedeo Caflisch. "Efficient Evaluation of Binding Free Energy Using Continuum Electrostatics Solvation." Journal of Medicinal Chemistry 47, no. 23 (November 2004): 5791–97. http://dx.doi.org/10.1021/jm049726m.

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26

Bennett, Gerald E., Peter J. Rossky, and Keith P. Johnston. "Continuum Electrostatics Model for an SN2 Reaction in Supercritical Water." Journal of Physical Chemistry 99, no. 43 (October 1995): 16136–43. http://dx.doi.org/10.1021/j100043a065.

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27

Bardhan, Jaydeep P. "BIBEE: a Rigorous and Computationally Efficient Approximation to Continuum Electrostatics." Biophysical Journal 98, no. 3 (January 2010): 392a. http://dx.doi.org/10.1016/j.bpj.2009.12.2111.

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28

Partenskii, Michael B., and Peter C. Jordan. "Theoretical perspectives on ion-channel electrostatics: continuum and microscopic approaches." Quarterly Reviews of Biophysics 25, no. 4 (November 1992): 477–510. http://dx.doi.org/10.1017/s0033583500004388.

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Peter Läuger introduced me (P.C.J.) to the field of ion-channel electrostatics while I was a sabbatical visitor at Konstanz in 1978–79. Läuger pointed out that the relative conductance of hydrophobic ions through phosphatidyl choline (PC) and glyceryl monooleate (GMO) membranes differed by a factor of about 100 (Hladky & Haydon, 1973), quite consistent with the difference in the water-membrane potential differences in the two systems (Pickar & Benz, 1978). However, cation conductance through gramicidin channels spanning these membranes only differs by a factor of 2–3 (Bamberg et al. 1976). Why? It is the pursuit of an answer to this question which led me into my researches in this field.
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29

Rashin, Alexander A. "Continuum electrostatics of the C-peptide: Anatomy of the problem." Proteins: Structure, Function, and Genetics 13, no. 2 (June 1992): 120–31. http://dx.doi.org/10.1002/prot.340130205.

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30

Edwards, Scott, Ben Corry, Serdar Kuyucak, and Shin-Ho Chung. "Continuum Electrostatics Fails to Describe Ion Permeation in the Gramicidin Channel." Biophysical Journal 83, no. 3 (September 2002): 1348–60. http://dx.doi.org/10.1016/s0006-3495(02)73905-2.

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31

Georgescu, Roxana E., Emil G. Alexov, and Marilyn R. Gunner. "Combining Conformational Flexibility and Continuum Electrostatics for Calculating pKas in Proteins." Biophysical Journal 83, no. 4 (October 2002): 1731–48. http://dx.doi.org/10.1016/s0006-3495(02)73940-4.

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32

Purisima, Enrico O., and Traian Sulea. "Restoring Charge Asymmetry in Continuum Electrostatics Calculations of Hydration Free Energies." Journal of Physical Chemistry B 113, no. 24 (June 18, 2009): 8206–9. http://dx.doi.org/10.1021/jp9020799.

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33

Alagona, Giuliano, and Caterina Ghio. "The role of electrostatics in solute-solvent interactions with the continuum." Journal of Molecular Structure: THEOCHEM 256 (April 1992): 187–216. http://dx.doi.org/10.1016/0166-1280(92)87167-x.

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34

Ritchie, Andrew W., and Lauren J. Webb. "Understanding and Manipulating Electrostatic Fields at the Protein–Protein Interface Using Vibrational Spectroscopy and Continuum Electrostatics Calculations." Journal of Physical Chemistry B 119, no. 44 (October 6, 2015): 13945–57. http://dx.doi.org/10.1021/acs.jpcb.5b06888.

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35

Juffer, André H. "Theoretical calculations of acid-dissociation constants of proteins." Biochemistry and Cell Biology 76, no. 2-3 (May 1, 1998): 198–209. http://dx.doi.org/10.1139/o98-034.

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The purpose of this review is to introduce several computational procedures for the determination of acid-dissociation constants (pKa) of titratable groups in proteins. Several concepts, such as continuum electrostatics and the exact meaning of intrinsic and apparent pKas, will be explained in some detail. Each of the methods will be judged on its merits, and some comparisons between the methods will be presented. While the emphasis of this review will be on theoretical formulations, the experimental determination by means of nuclear magnetic resonance will be briefly explained. The determination of individual pKa values by nuclear magnetic resonance in combination with computationally determined pKas can provide unique information about the pH-dependent properties of proteins and their complexes with peptides, DNA, and ligands.Key words: acid-dissociation constants, NMR, continuum electrostatics, dielectric constant of proteins, Monte Carlo, molecular dynamics.
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36

Schaefer, Michael, Christian Bartels, and Martin Karplus. "Solution conformations of structured peptides: continuum electrostatics versus distance-dependent dielectric functions." Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) 101, no. 1-3 (February 15, 1999): 194–204. http://dx.doi.org/10.1007/s002140050429.

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37

Pokala, Navin, and Tracy M. Handel. "Energy functions for protein design I: Efficient and accurate continuum electrostatics and solvation." Protein Science 13, no. 4 (April 2004): 925–36. http://dx.doi.org/10.1110/ps.03486104.

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38

McAliley, James H., Christopher P. O’Brien,, and David A. Bruce. "Continuum Electrostatics for Electronic Structure Calculations in Bulk Amorphous Polymers: Application to Polylactide." Journal of Physical Chemistry A 112, no. 31 (August 2008): 7244–49. http://dx.doi.org/10.1021/jp712114q.

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39

Nina, Mafalda, Dmitri Beglov, and Benoît Roux. "Atomic Radii for Continuum Electrostatics Calculations Based on Molecular Dynamics Free Energy Simulations." Journal of Physical Chemistry B 101, no. 26 (June 1997): 5239–48. http://dx.doi.org/10.1021/jp970736r.

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40

Kutteh, Ramzi, Jamie I. Vandenberg, and Serdar Kuyucak. "Molecular Dynamics and Continuum Electrostatics Studies of Inactivation in the HERG Potassium Channel." Journal of Physical Chemistry B 111, no. 5 (February 2007): 1090–98. http://dx.doi.org/10.1021/jp066294d.

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41

Sulea, Traian, Duangporn Wanapun, Sheldon Dennis, and Enrico O. Purisima. "Prediction of SAMPL-1 Hydration Free Energies Using a Continuum Electrostatics-Dispersion Model†." Journal of Physical Chemistry B 113, no. 14 (April 9, 2009): 4511–20. http://dx.doi.org/10.1021/jp8061477.

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42

Cortis, Christian M., Jean‐Marc Langlois, Michael D. Beachy, and Richard A. Friesner. "Quantum mechanical geometry optimization in solution using a finite element continuum electrostatics method." Journal of Chemical Physics 105, no. 13 (October 1996): 5472–84. http://dx.doi.org/10.1063/1.472388.

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43

Aleksandrov, Alexey, Linda Schuldt, Winfried Hinrichs, and Thomas Simonson. "Tet Repressor Induction by Tetracycline: A Molecular Dynamics, Continuum Electrostatics, and Crystallographic Study." Journal of Molecular Biology 378, no. 4 (May 2008): 898–912. http://dx.doi.org/10.1016/j.jmb.2008.03.022.

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44

Zauhar, R. J. "The incorporation of hydration forces determined by continuum electrostatics into molecular mechanics simulations." Journal of Computational Chemistry 12, no. 5 (June 1991): 575–83. http://dx.doi.org/10.1002/jcc.540120507.

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45

Rankin, Kathryn N., Traian Sulea, and Enrico O. Purisima. "On the transferability of hydration-parametrized continuum electrostatics models to solvated binding calculations." Journal of Computational Chemistry 24, no. 8 (June 2003): 954–62. http://dx.doi.org/10.1002/jcc.10261.

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46

Ma, Chiansan, Nathan A. Baker, Simpson Joseph, and J. Andrew McCammon. "Binding of Aminoglycoside Antibiotics to the Small Ribosomal Subunit: A Continuum Electrostatics Investigation." Journal of the American Chemical Society 124, no. 7 (February 2002): 1438–42. http://dx.doi.org/10.1021/ja016830+.

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47

Johnston, Keith P., Gerald E. Bennett, Perla B. Balbuena, and Peter J. Rossky. "Continuum Electrostatics Model for Ion Solvation and Relative Acidity of HCl in Supercritical Water." Journal of the American Chemical Society 118, no. 28 (January 1996): 6746–52. http://dx.doi.org/10.1021/ja953558t.

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48

Basilevsky, M. V., and D. F. Parsons. "An advanced continuum medium model for treating solvation effects: Nonlocal electrostatics with a cavity." Journal of Chemical Physics 105, no. 9 (September 1996): 3734–46. http://dx.doi.org/10.1063/1.472193.

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49

Fowler, Nicholas J., Christopher F. Blanford, Jim Warwicker, and Sam P. de Visser. "Prediction of Reduction Potentials of Copper Proteins with Continuum Electrostatics and Density Functional Theory." Chemistry - A European Journal 23, no. 61 (September 21, 2017): 15436–45. http://dx.doi.org/10.1002/chem.201702901.

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50

ROTKIN, SLAVA V., VAISHALI SHRIVASTAVA, KIRILL A. BULASHEVICH, and N. R. ALURU. "ATOMISTIC CAPACITANCE OF A NANOTUBE ELECTROMECHANICAL DEVICE." International Journal of Nanoscience 01, no. 03n04 (June 2002): 337–46. http://dx.doi.org/10.1142/s0219581x02000279.

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An atomistic capacitance is derived for a single-wall carbon nanotube in a nano-electromechanical device. Multi-scale calculation is performed using a continuum model for the geometrical capacitance, and statistical and quantum mechanical approaches for the quantum capacitance of the nanotube. The geometrical part of the capacitance is studied in detail using full three-dimensional electrostatics. Results reported in this paper are useful for compact modeling of the electronic and electromechanical nanotube devices.
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