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816 results on '"Jacobs, Donald"'

152. An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions.

Author

Yuchun Lin, Baumketner, Andrij, Shaozhong Deng, Zhenli Xu, Jacobs, Donald, and Wei Cai

Subjects
MOLECULAR dynamics, ELECTROSTATICS, ELECTROLYTE solutions, MOLECULES, SOLUTION (Chemistry), SIMULATION methods & models
Abstract

In this paper, a new solvation model is proposed for simulations of biomolecules in aqueous solutions that combines the strengths of explicit and implicit solvent representations. Solute molecules are placed in a spherical cavity filled with explicit water, thus providing microscopic detail where it is most needed. Solvent outside of the cavity is modeled as a dielectric continuum whose effect on the solute is treated through the reaction field corrections. With this explicit/implicit model, the electrostatic potential represents a solute molecule in an infinite bath of solvent, thus avoiding unphysical interactions between periodic images of the solute commonly used in the lattice-sum explicit solvent simulations. For improved computational efficiency, our model employs an accurate and efficient multiple-image charge method to compute reaction fields together with the fast multipole method for the direct Coulomb interactions. To minimize the surface effects, periodic boundary conditions are employed for nonelectrostatic interactions. The proposed model is applied to study liquid water. The effect of model parameters, which include the size of the cavity, the number of image charges used to compute reaction field, and the thickness of the buffer layer, is investigated in comparison with the particle-mesh Ewald simulations as a reference. An optimal set of parameters is obtained that allows for a faithful representation of many structural, dielectric, and dynamic properties of the simulated water, while maintaining manageable computational cost. With controlled and adjustable accuracy of the multiple-image charge representation of the reaction field, it is concluded that the employed model achieves convergence with only one image charge in the case of pure water. Future applications to pKa calculations, conformational sampling of solvated biomolecules and electrolyte solutions are briefly discussed. [ABSTRACT FROM AUTHOR]

Published
2009
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154. The polymerization of actin: Extent of polymerization under pressure, volume change of polymerization, and relaxation after temperature jumps.

Author

Matthews, Jermey N. A., Yim, Peter B., Jacobs, Donald T., Forbes, Jeffrey G., Peters, Neçois D., and Greer, Sandra C.

Subjects
ACTIN, POLYMERIZATION, MUSCLES, POTASSIUM chloride, PYRENE, CHEMICAL reactions
Abstract

The protein actin can polymerize from monomeric globular G-actin to polymeric filamentary F-actin, under the regulation of thermodynamic variables such as temperature, pressure, and compositions of G-actin and salts. We present here new measurements of the extent of polymerization ([lowercase_phi_synonym]) of actin under pressure (P), for rabbit skeletal muscle actin in H2O buffer in the presence of adenosine triposphate and calcium ions and at low (5–15 mM) KCl concentrations. We measured [lowercase_phi_synonym] using pyrene-labeled actin, as a function of time (t) and temperature (T), for samples of fixed concentrations of initial G-actin and KCl and at fixed pressure. The [lowercase_phi_synonym](T,P) measurements at equilibrium have the same form as reported previously at 1 atm: low levels of polymerization at low temperatures, representing dimerization of the actin; an increase in [lowercase_phi_synonym] at the polymerization temperature (Tp); a maximum in [lowercase_phi_synonym](T) above Tp with a decrease in [lowercase_phi_synonym](T) beyond the maximum, indicating a depolymerization at higher T. From [lowercase_phi_synonym](T,P) at temperatures below Tp, we estimate the change in volume for the dimerization of actin, ΔVdim, to be -307±10 ml/mol at 279 K. The change of Tp with pressure dTp/dP=(0.3015±0.0009) K/MPa=(30.15±0.09) mK/atm. The [lowercase_phi_synonym](T,P) data at higher T indicate the change in volume on propagation, ΔVprop, to be +401±48 ml/mol at 301 K. The [lowercase_phi_synonym](t) measurements yield initial relaxation times rp(T) that reflect the behavior of [lowercase_phi_synonym](T) and support the presence of a depolymerization temperature. We also measured the density of polymerizing actin with a vibrating tube density meter, the results of which confirm that the data from this instrument are affected by viscosity changes and can be erroneous. [ABSTRACT FROM AUTHOR]

Published
2005
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164. Key Concepts in Critical Limb Ischemia: Selected Proceedings from the 2015 Vascular Interventional Advances Meeting

Author

Rundback, John H., primary, Armstrong, Ehrin J., additional, Contos, Brian, additional, Iida, Osamu, additional, Jacobs, Donald, additional, Jaff, Michael R., additional, Matsumoto, Alan H., additional, Mills, Joseph L., additional, Montero-Baker, Miguel, additional, Pena, Constantino, additional, Tallian, Alexander, additional, Uematsu, Masaaki, additional, Wilkins, Luke R., additional, and Shishehbor, Mehdi H., additional

Published
2017
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165. The impact of youth's use of the Internet on their use of the public library

Author

D'Ella, George, Abbas, June, Bishop, Kay, Jacobs, Donald, and Rodger, Eleanor Jo

Subjects
Library use studies -- Research, Elementary school students -- Behavior, High school students -- Behavior, Information-seeking behavior -- Research, Internet access -- Influence, Internet access, Computers, Library and information science, Mathematics
Abstract

The effect of Internet use among youth on their use of the public library is investigated using a survey of students from grades 5-12. Youths with Internet access at home used the library less frequently than those without Internet access, but use of both information sources complement each other .

Published
2007

184. Candid Comments on Wireless

Author

Jacobs, Donald M.

Subjects
Wireless network, Health care industry, Wireless LAN/WAN system, Wireless technology, Market trend/market analysis, Telecommunications equipment industry, Telecommunication systems -- Usage -- Product information, Wireless communication systems -- Usage -- Product information, Telecommunications equipment industry -- Product information -- Forecasts and trends, Health care industry -- Product information -- Forecasts and trends, Mobile communication systems -- Usage -- Product information, Wireless local area networks (Computer networks) -- Usage -- Product information, Medical care -- Product information
Abstract

Constructive advice on wireless. A new definition of ROI for technology. Until major vendors embrace wireless technology as an integrated part of their product line, it's going to be an […]

Published
1999

189. FrontMatter.

Author

Schauland, Derek and Jacobs, Donald

Published
2016

199. Current trends in the treatment of the Section 501(c)(6) business league exemption.

Author

Jacobs, Donald F.

Subjects
trade and professional associations -- Taxation, Tax exemption, Nonprofit organizations -- Taxation, Associated Master Barbers & Beauticians of America, Inc. v. Commissioner (69 T.C. 53 (1977)), National Muffler Dealers Ass'n v. United States (440 U.S. 472 (1979)), Internal Revenue Code (I.R.C. 501(c)(6))
Published
1980

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