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A charge-scaling implementation of the variational electrostatic projection method

Brent A. Gregersen, Darrin M. York
2006 Journal of Computational Chemistry  
The methods are extensions of the variational electrostatic projection (VEP) method, and allows a subset of atomic charges in the external environment to be adjusted to mimic, in the active dynamical region  ...  Two new charge-scaling methods for efficient modeling of the solvated macromolecular environment in hybrid QM/MM calculations of biological reactions are presented.  ...  Acknowledgments Computational resources were provided by the Minnesota Supercomputing Institute.  ... 
doi:10.1002/jcc.20318 pmid:16273506 fatcat:pdamwcrspjauzovgov7mqecr4u

A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations

Xiaoliang Pan, Kwangho Nam, Evgeny Epifanovsky, Andrew C. Simmonett, Edina Rosta, Yihan Shao
2021 Journal of Chemical Physics  
Here, a further simplification to the model is proposed, where the outer MM charges are projected onto inner MM atom positions (instead of ESP grid positions).  ...  This enables a representation of the long-range MM electrostatic potential via augmentary charges (AC) on inner MM atoms.  ...  the electrostatic field of QM electrons/nuclei at the position of the Bth MM atom and then scaling it by the charge value, q <,C B , and the charge derivatives, ∂q <,C B ∂x B is computed in a similar  ... 
doi:10.1063/5.0038120 pmid:33445891 pmcid:PMC7808763 fatcat:2jjebdd5f5bsrhf7pb6whctjni

Projected Potential Profiles across Intergranular Glassy Films

Somnath BHATTACHARYYA, Christoph T. KOCH, Manfred RÜHLE
2006 Journal of the Ceramic Society of Japan  
The electrostatic as well as the absorptive potentials were scaled with respect to vacuum.  ...  the electron exit face wave function from a series of defocused TEM images.  ...  Despite its potential the method as implemented for this work also suffers from the limited resolution of 8 Å imposed by the objective aperture.  ... 
doi:10.2109/jcersj.114.1005 fatcat:f3bp3kzdebf6dhr4ybgv7khgdi

Design and implementation of a Kelvin microprobe for contact potential measurements at the submicron scale

Walid Nabhan, Alexandre Broniatowski, Gilles de Rosny, Bernard Equer
1994 Microscopy Microanalysis Microstructures  
This instrument enables one to measure spatial variations in the electronic work function of a specimen on the submicron scale by a non-destructive technique, with a typical accuracy in the 10 meV range  ...  The high spatial resolution is achieved by means of an electrically guarded electrostatic probe.  ...  The authors are indebted to their colleagues in the near-field microscopy group of the Groupe de Physique des Solides for stimulating discussions and technical assistance.  ... 
doi:10.1051/mmm:0199400504-6050900 fatcat:wjn57ao3trdtxp2tjxgcxooriq

An efficient Monte Carlo method for calculating ab initio transition state theory reaction rates in solution

Radu Iftimie, Dennis Salahub, Jeremy Schofield
2003 Journal of Chemical Physics  
The method is applied to the study of the double proton transfer reaction that takes place between a molecule of acetic acid and a molecule of methanol in tetrahydrofuran.  ...  In the present method, the reaction is described by solving the electronic Schrödinger equation for the solute atoms in the presence of explicit solvent molecules.  ...  ACKNOWLEDGMENTS This work was supported by a grant from the Natural Sciences and Engineering Research Council of Canada.  ... 
doi:10.1063/1.1622653 fatcat:c2amr6ypqndy3mcqjggcu7yze4

Computing the Coulomb interaction in inhomogeneous dielectric media via a local electrostatics lattice algorithm

F. Fahrenberger, C. Holm
2014 Physical Review E  
We furthermore correct a problem of the original algorithm related to the correct treatment of the global dipole moment, provide an error estimate for the accuracy of the algorithm, and suggest a different  ...  form of the treatment of the self-energy problem.  ...  This work was supported by the DFG through the SFB 716, and the German Ministry of Science and Education (BMBF) under grant 01IH08001.  ... 
doi:10.1103/physreve.90.063304 pmid:25615219 fatcat:pjhmbphjjvcibetkpatpyc6gwq

Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods

Jana Khandogin, Darrin M. York
2004 Proteins: Structure, Function, and Bioinformatics  
This paper presents a set of macromolecular quantum descriptors for the characterization of biological macromolecules in solution that can be obtained with modest computational cost from linear-scaling  ...  The descriptors discussed include: solventpolarized electrostatic surface potential maps, equilibrated atomic charges, Fukui reactivity indices, approximate local hardness maps, and relative proton potentials  ...  D.Y. is grateful for financial support provided by the National Institutes of Health (grant 1R01-GM62248-01A1), and the Donors of The Petroleum Research Fund, administered by the American Chemical Society  ... 
doi:10.1002/prot.20171 pmid:15281126 fatcat:a2ks6jai2zeqtji76zsuhuyzpq

Comparing induced point-dipoles and Drude oscillators

Michael Schmollngruber, Volker Lesch, Christian Schröder, Andreas Heuer, Othmar Steinhauser
2015 Physical Chemistry, Chemical Physics - PCCP  
This work compares the two major methods to introduce polarisability in Molecular Dynamics simulations: induced point-dipoles and Drude oscillators.  ...  P23494,by the Cost Action CM 1206: "Exchange on ionic liquids" and the SafeBatt project of the BMBF (Project No. 03X4631N).  ...  This work was funded by the Austrian Science Fund FWF in the context of Project No.  ... 
doi:10.1039/c4cp04512b pmid:25425140 fatcat:uolquosg5zas3cxabknbtc6ywi

Jdpd: an open java simulation kernel for molecular fragment dissipative particle dynamics

Karina van den Broek, Hubert Kuhn, Achim Zielesny
2018 Journal of Cheminformatics  
It is characterized by an interface and factorypattern driven design for simple code changes and may help to avoid problems of polyglot programming.  ...  The new kernel may be utilized in different simulation environments ranging from flexible scripting solutions up to fully integrated "all-in-one" simulation systems.  ...  The support of GNWI -Gesellschaft für naturwissenschaftliche Informatik mbH, Oer-Erkenschwick, Germany, is gratefully acknowledged.  ... 
doi:10.1186/s13321-018-0278-7 pmid:29785513 pmcid:PMC5962482 fatcat:h7h6chnc6rhhdk4ynafoltmgcu

Which is better, electrostatic or piezoelectric energy harvesting systems?

A D T Elliott, L M Miller, E Halvorsen, P K Wright, P D Mitcheson
2015 Journal of Physics, Conference Series  
At very high accelerations using MEMS-scale devices the dielectric breakdown limit in piezoelectric energy harvesters severely decreases their performance thus electrostatics are again preferred.  ...  Using the insights gained in this comparison, the optimal transduction mechanism can be chosen as a function of harvesting operating frequency, acceleration and device size.  ...  Acknowledgements The authors would like to thank the California Energy Commission and Research Council of Norway grant number 229716 and for their support, and EPSRC for their sponsorship of this project  ... 
doi:10.1088/1742-6596/660/1/012128 fatcat:tjnptel5zbdcrgldlwwkjdi2ca

Classical Electrostatics for Biomolecular Simulations

G. Andrés Cisneros, Mikko Karttunen, Pengyu Ren, Celeste Sagui
2013 Chemical Reviews  
G.A.C. thanks Wayne State University, M.K. thanks the Natural Sciences and Engineering Research Council of Canada, P.R. thanks the Robert A.  ...  Duke for sharing with us his experience with truncation methods. We would like to thank the support we have received for this work.  ...  method scales as , where s is the number of charges per box at the finest level.  ... 
doi:10.1021/cr300461d pmid:23981057 pmcid:PMC3947274 fatcat:436zql6ojzgnbhd2q3hs7x5fhq

"Reverse-Schur" Approach to Optimization with Linear PDE Constraints: Application to Biomolecule Analysis and Design

Jaydeep P. Bardhan, Michael D. Altman, B. Tidor, Jacob K. White
2009 Journal of Chemical Theory and Computation  
The efficiency of the co-optimization approach may enhance the value of electrostatic optimization for ligand-design efforts-in such projects, it is often desirable to screen many candidate ligands for  ...  Model problems as well as realistic examples validate the reverse-Schur method, and demonstrate that our technique and alternative PDEconstrained methods scale very favorably compared to the standard approach  ...  Acknowledgments The authors thank J. Nocedal, J.-H. Lee  ... 
doi:10.1021/ct9001174 pmid:23055839 pmcid:PMC3465730 fatcat:cschrbj45bbyfaetp5innshcci

Multiscale analytic continuation approach to nanosystem simulation: Applications to virus electrostatics

Abhishek Singharoy, Anastasia M. Yesnik, Peter Ortoleva
2010 Journal of Chemical Physics  
Electrostatic effects in nanosystems are understood via a physical picture built on their multiscale character and the distinct behavior of mobile ions versus charge groups fixed to the nanostructure.  ...  The Poisson-Boltzmann equation is nondimensionalized to introduce a factor that measures the density of mobile ion charge versus that due to fixed charges; the diffusive smearing and volume exclusion effects  ...  This adds to the great efficiency of our methodology which retains both long-scale and short-scale variations, relegating the nonlinearity to a coarse-grained equation for ⌽ ‫ء‬ .  ... 
doi:10.1063/1.3424771 pmid:20459161 pmcid:PMC2878355 fatcat:to4vlrvs4jfr7atru5gmpgvpfu

Demonstration of a droplet electrohydrodynamic blower in aerosols [article]

Pramodt Srinivasula, Debabrat Biswal
2022 arXiv   pre-print
This is demonstrated through the deterioration of a strong electrostatic airborne particulate capture onto the droplet, when it is placed in an aerosol.  ...  Despite a rigorous analysis of nonlinear electrohydrodynamics of a liquid droplet deformation in air, its influence on the surrounding gas phase has received less attention.  ...  of projected area and a ± is the acceleration of the drop projected area in the forward (+) or backward (-) direction.  ... 
arXiv:2203.03210v1 fatcat:puwmqsfs6zb3thy24acxndd2ca

MEMS actuation for a continuously tunable optical buffer

N. Podoliak, W. H. Ng, H. Liu, A. J. Kenyon, W. Stewart, P. Horak
2014 2014 International Conference on Optical MEMS and Nanophotonics  
Up to 100% variation of the delay time with a driving voltage of 3 V is predicted.  ...  A continuously tunable delay in the propagation time can be achieved by varying the spacing between the waveguides using MEMS actuation.  ...  This work was supported by the EPSRC "Continuously tunable optical buffer" project (EP/J012874/1 and EP/J012823/1). Figure 1 . 1 Schematic of the optical buffer (top view, not to scale).  ... 
doi:10.1109/omn.2014.6924548 fatcat:eaty5kciubcjdaaqdvykchztla
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