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en>Addbot: Bot: Migrating 2 interwiki links, now provided by Wikidata on d:q2549576

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Bot: Migrating 2 interwiki links, now provided by Wikidata on d:q2549576

← Older revision		Revision as of 14:32, 16 March 2013
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	~~Golda~~ is ~~what~~'~~s created~~ on ~~my beginning certification even though it is not~~ [~~http~~:/~~/www~~.~~khuplaza~~.~~com/dent/14869889 tarot readings~~] the name ~~on my birth certification~~. ~~To climb is something I really appreciate performing~~. ~~My working day job is an invoicing officer but I~~'~~ve already applied for an additional one~~. ~~For years he's~~ been ~~residing in Alaska~~ [~~http~~:/~~/www~~.~~chk~~.~~woobi~~.co.kr/xe/~~?document_srl~~=~~346069 best psychics]~~ and ~~he doesn't plan on changing it~~.<br><br>~~Here~~ is ~~my weblog~~ [~~http~~://~~www~~.~~prograd~~.~~uff~~.br/~~novo~~/~~facts~~-~~about~~-~~growing~~-~~greater-organic-garden psychic readings~~]		'''Drude particles''' are model [[oscillator]]s used to simulate the effects of electronic [[polarizability]] in the context of a classical [[molecular mechanics]] [[force field (chemistry)\|force field]]. They are inspired by the [[Drude model]] of mobile electrons and are used in the computational study of [[protein]]s, [[nucleic acid]]s, and other [[biomolecule]]s.

			==Classical Drude Oscillator==
			Most force fields in current practice represent individual [[atoms]] as hard spheres interacting according to the laws of [[Newtonian mechanics]]. To each [[atom]], a single electric charge is assigned that doesn't change during the course of the simulation. However, such models cannot have induced [[dipoles]] or other [[electronic effects]] due to a changing local environment.

			Classical Drude particles are massless virtual sites carrying a partial electric charge, attached to individual atoms via a [[harmonic]] spring. The [[spring constant]] and relative partial charges on the atom and associated Drude particle determine its response to the local [[Electrostatics\|electrostatic]] field, serving as a proxy<ref name="MacKerell">MacKerell AD. (2004). Empirical force fields for biological macromolecules: Overview and issues. ''J Comp Chem'' 25(13): 1584-1604.</ref> for the changing distribution of the electronic charge of the atom or molecule. However, this response is limited to a changing dipole moment. This response is not enough to model interactions in environments with large [[Electric field gradient\|field gradients]], which interact with higher order moments.

			===Efficiency of simulation===
			The major computational cost of simulating classical Drude Oscillators is the calculation of the local electrostatic field and the repositioning of the Drude particle at each step. Traditionally, this repositioning is done [[Self consistent field\|self consistently]]. This cost can be reduced by assigning a small mass to each Drude particle, applying a [[Lagrangian mechanics\|Lagrangian transformation]]<ref name="Lamoureux">Lamoureux G, Roux B. (2003). Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm. ''J Chem Phys'' 119(6):3025-3039.</ref> and evolving the simulation in the generalised coordinates. This method of simulation has been used to create [[water model]]s incorporating classical Drude Oscillators.<ref name="Lamoureux2">Lamoureux G, MacKerell AD, Roux B. (2003). A simple polarizable model of water based on classical Drude oscillators. ''J Chem Phys'' 119(3):5185-97.</ref><ref name="Lamoureux3">Lamoureux G, Harder E, Vorobyov IV, Roux B, MacKerell AD. (2006). A polarizable model of water for molecular dynamics simulations of biomolecules. ''Chem Phys Lett'' 418:245-9.</ref>

			==Quantum Drude Oscillator==
			Since the response of a classical Drude oscillator is limited, it is not enough to model interactions in heterogeneous media with large field gradients, where higher order electronic responses have significant contributions to the interaction energy.{{Citation needed\|date=September 2013}} A Quantum Drude Oscillator (QDO)<ref name="jones-thesis">A. Jones, “Quantum Drude Oscillators for Accurate Many-body Intermolecular Forces,” The University of Edinburgh, 2010.</ref><ref name="prb-xenonn">A. Jones, A. Thompson, J. Crain, M. Müser, and G. Martyna, “Norm-conserving diffusion Monte Carlo method and diagrammatic expansion of interacting Drude oscillators: Application to solid xenon,” Physical Review B, vol. 79, no. 14, pp. 1–17, Apr. 2009.</ref><ref name="prl-water">A. Jones, F. Cipcigan, V. P. Sokhan, J. Crain, and G. J. Martyna, “Electronically Coarse-Grained Model for Water,” Physical Review Letters, vol. 110, no. 22, p. 227801, May 2013.</ref> is a natural extension to the classical Drude Oscillator. Instead of a classical point particle serving as a proxy for the charge distribution, a QDO uses a [[quantum harmonic oscillator]], in the form of a pseudoelectron connected to an oppositely charged pseudonucleus by a harmonic spring.

			A QDO has three free parameters: the spring's [[frequency]] <math>\omega</math>, the pseudoelectron's charge <math>q</math> and the system's reduced mass <math>\mu</math>. The ground state of a QDO is a gaussian of width <math>\sigma = 1/\sqrt{2 \mu \omega}</math>. Adding an external field [[Perturbation theory (quantum mechanics)\|perturbs]] the ground state of a QDO, which allows us to calculate its [[polarizability]].<ref name="jones-thesis"/> To second order, the change in energy relative to the ground state is given by the following series:
			:<math>E^{(2)} = \sum_{l=1}^{\infty} E_l^{(2)} = \sum_{l=1}^{\infty} - \frac{Q^2 \alpha_l}{2 R^{2l + 2}}</math>
			where the polarizabilities <math>\alpha_l</math> are
			:<math>\alpha_l = \left[ \frac{q^2}{\mu \omega^2} \right] \left[ \frac{(2 l - 1)!!}{l} \right] \left( \frac{\hbar}{2 \mu \omega} \right)^{l-1}</math>

			Furthermore, since QDOs are quantum mechanical objects, their electrons can [[electronic correlation\|correlate]], giving rise to [[London dispersion force\|dispersion forces]] between them. The second order change in energy corresponding to such an interaction is:
			:<math>E^{(2)} = \sum_{l=3}^{\infty} C_{2 l} R^{-2 l}</math>
			with the first three dispersion coefficients being (in the case of identical QDOs):
			:<math>C_6 = \frac{3}{4} \alpha_1 \alpha_1 \hbar \omega</math>
			:<math>C_8 = 5 \alpha_1 \alpha_2 \hbar \omega</math>
			:<math>C_{10} = \left( \frac{21}{2} \alpha_1 \alpha_3 + \frac{70}{4} \alpha_2 \alpha_2 \right) \hbar \omega</math>

			Since the response coefficients of QDOs depend on three parameters only, they are all related. Thus, these response coefficients can combine into four dimensionless constants, all equal to unity:
			:<math>\sqrt{\frac{20}{9}} \frac{\alpha_2}{\sqrt{\alpha_1 \alpha_3}} = 1</math>
			:<math>\sqrt{\frac{49}{40}} \frac{C_8}{\sqrt{C_6 C_{10}}} = 1</math>
			:<math>\frac{C_6 \alpha_1}{4 C_9} = 1</math>

			==References==
			<references />

			[[Category:Computational chemistry]]

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2012-05-08T04:03:51Z

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Golda is what's created on my beginning certification even though it is not [http://www.khuplaza.com/dent/14869889 tarot readings] the name on my birth certification. To climb is something I really appreciate performing. My working day job is an invoicing officer but I've already applied for an additional one. For years he's been residing in Alaska [http://www.chk.woobi.co.kr/xe/?document_srl=346069 best psychics] and he doesn't plan on changing it.<br><br>Here is my weblog [http://www.prograd.uff.br/novo/facts-about-growing-greater-organic-garden psychic readings]

Warnock algorithm - Revision history

en>Monkbot: Task 5: Fix CS1 deprecated coauthor parameter errors

en>BG19bot: WP:CHECKWIKI error fix for #02. Fix br tag, Do general fixes if a problem exists. - using AWB (9949)

en>Addbot: Bot: Migrating 2 interwiki links, now provided by Wikidata on d:q2549576

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