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Articles by Harry M. Quiney in JoVE

Measurements of Longrange Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene
Rebecca A. Ryan^{1}, Sophie Williams^{1}, Andrew V. Martin^{1}, Ruben A. Dilanian^{1}, Connie Darmanin^{2}, Corey T. Putkunz^{1}, David Wood^{3}, Victor A. Streltsov^{4}, Michael W.M. Jones^{5}, Naylyn Gaffney^{6}, Felix Hofmann^{7}, Garth J. Williams^{8}, Sebastien Boutet^{9}, Marc Messerschmidt^{10}, M. Marvin Seibert^{11}, Evan K. Curwood^{11}, Eugeniu Balaur^{2}, Andrew G. Peele^{5}, Keith A. Nugent^{2}, Harry M. Quiney^{1}, Brian Abbey^{2}
^{1}ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, ^{2}Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, ^{3}Department of Physics, Imperial College London, ^{4}Florey Institute of Neuroscience and Mental Health, ^{5}Science and Engineering Faculty, Queensland University of Technology, ^{6}Swinburne University of Technology, ^{7}Department of Engineering Science, University of Oxford, ^{8}Brookhaven National Laboratory, ^{9}Linac Coherent Light Source, SLAC National Accelerator Laboratory, ^{10}BioXFEL Science and Technology Center, ^{11}Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, ^{12}Australian Synchrotron
We describe an experiment designed to probe the electronic damage induced in nanocrystals of Buckminsterfullerene (C60) by intense, femtosecond pulses of Xrays. The experiment found that, surprisingly, rather than being stochastic, the Xray induced electron dynamics in C60 are highly correlated, extending over hundreds of unit cells within the crystals^{1}.
Other articles by Harry M. Quiney on PubMed


The Electronic Structure of Alkali Aurides. A Fourcomponent DiracKohnSham Study
The Journal of Physical Chemistry. A.
Apr, 2006 
Pubmed ID: 16571062 Spectroscopic constants, including dissociation energies, harmonic and anharmonic vibrational frequencies, and dipole moments, are calculated for the complete alkali auride series (LiAu, NaAu, KAu, RbAu, CsAu). The fourcomponent formulation of relativistic density functional theory has been employed in this study, using the Gspinor basis sets implemented recently in the program BERTHA. The performance of four standard nonrelativistic density functionals employed is investigated by comparing the results with the best available theoretical and experimental data. The present work provides the first theoretical predictions on the molecular properties of RbAu. The intermetallic bond that occurs in the alkali auride series is highly polar and is characterized by a large charge transfer from the alkali metals to gold. The extent of this electron transfer has been investigated using several different charge analysis methods, enabling us to reach some general conclusions on their relative performance. We further report a detailed analysis of the topological properties of relativistic electron density in the bonding region, discussing the features of this approach which characterize the nature of the chemical bond. We have also computed the fully relativistic density for the alkali halides MBr and MI (M = Li, Na, K, Rb, and Cs). The comparative study shows that, on the basis of several topological properties and the variation in bond lengths, the gold atom behaves similarly to a halogen intermediate between Br and I.

Electron Density Fitting for the Coulomb Problem in Relativistic Densityfunctional Theory
The Journal of Chemical Physics.
Mar, 2006 
Pubmed ID: 16599659 A density fitting approach for the Coulomb matrix representation within the fourcomponent formulation of relativistic densityfunctional theory is presented. Our implementation, which uses Gspinor basis sets, shares all the advantages of those found in nonrelativistic quantum chemistry. We show that very accurate Coulomb energies may be obtained using a modest number of scalar auxiliary basis functions for molecules containing heavy atoms. The efficiency of this new implementation is demonstrated in a detailed study of the spectroscopic properties of the gold dimer, and its scaling behavior has been tested by calculations of some closedshell gold clusters (Au2, Au3+, Au4, Au5+). The algorithm is found to scale as O(N3), just as it does in the nonrelativistic case, and represents a dramatic improvement in efficiency over the conventional approach in the calculation of the Coulomb matrix, with computation times that are reduced to less than 3% for Au2 and up to 1% in the case of Au5+.

Nuclear Electric Quadrupole Moment of Gold
The Journal of Chemical Physics.
Feb, 2007 
Pubmed ID: 17313222 The nuclear quadrupole moment for (197)Au has been determined on the base of the stateofart relativistic molecular calculations. The experimental shifts in the nuclear coupling constants in the series of molecules AuF, XeAuF, KrAuF, ArAuF, (OC)AuF, and AuH have been combined with highly accurate determinations of the electric field gradient (EFG) at the gold nucleus, obtained by molecular relativistic DiracCoulombGaunt HartreeFock calculations. The electronic correlation contribution to the EFG is included with the CCSD(T) and CCSDT approaches, also in the fourcomponent framework, using a finitedifference method. In order to estimate the accuracy of their approach the authors have thoroughly investigated the convergence of the results with respect to the basis set employed and the size of the correlated orbital space. The effect of the full Breit electronelectron interaction on the nuclear quadrupole moment of gold has also been considered explicitly for the AuF molecule. They obtain for (197)Au a nuclear quadrupole moment of 510+/15 mb, which deviates by about 7% from the currently accepted muonic value.

Poissontransformed Density Fitting in Relativistic Fourcomponent DiracKohnSham Theory
The Journal of Chemical Physics.
Mar, 2008 
Pubmed ID: 18376909 We present recent developments in the implementation of the density fitting approach for the Coulomb interaction within the fourcomponent formulation of relativistic density functional theory [Belpassi et al., J. Chem. Phys. 124, 124104 (2006)]. In particular, we make use of the Poisson equation to generate suitable auxiliary basis sets and simplify the electron repulsion integrals [Manby and Knowles, Phys. Rev. Lett. 87, 163001 (2001)]. We propose a particularly simple and efficient method for the generation of accurate Poisson auxiliary basis sets, based on already available standard Coulomb fitting sets. Just as is found in the nonrelativistic case, we show that the number of standard auxiliary fitting functions that need to be added to the Poissongenerated functions in order to achieve a fitting accuracy equal or, in some cases, better than that of the standard procedure is remarkably small. The efficiency of the present implementation is demonstrated in a detailed study of the spectroscopic properties and energetics of several gold containing systems, including the Au dimer and the CsAu molecule. The extraction reaction of a H(2)O molecule from a Au(H(2)O)(9) (+) cluster is also calculated as an example of mixed heavylightatom molecular systems. The scaling behavior of the algorithm implemented is illustrated for some closed shell gold clusters up to Au(5) (+). The increased sparsity of the Coulomb matrices involved in the Poisson fitting is identified, as are potential computational applications and the use of the Poisson fitting for the relativistic exchangecorrelation problem.







Efficient Parallel AllElectron FourComponent DiracKohnSham Program Using a Distributed Matrix Approach II
Journal of Chemical Theory and Computation.
Dec, 2013 
Pubmed ID: 26592273 We propose a new complete memorydistributed algorithm, which significantly improves the parallel implementation of the allelectron fourcomponent DiracKohnSham (DKS) module of BERTHA (J. Chem. Theory Comput. 2010, 6, 384). We devised an original procedure for mapping the DKS matrix between an efficient integraldriven distribution, guided by the structure of specific Gspinor basis sets and by density fitting algorithms, and the twodimensional blockcyclic distribution scheme required by the ScaLAPACK library employed for the linear algebra operations. This implementation, because of the efficiency in the memory distribution, represents a leap forward in the applicability of the DKS procedure to arbitrarily large molecular systems and its porting on lastgeneration massively parallel systems. The performance of the code is illustrated by some test calculations on several gold clusters of increasing size. The DKS selfconsistent procedure has been explicitly converged for two representative clusters, namely Au20 and Au34, for which the density of electronic states is reported and discussed. The largest gold cluster uses more than 39k basis functions and DKS matrices of the order of 23 GB.

Singlemolecule Imaging with Longer Xray Laser Pulses
IUCrJ.
Nov, 2015 
Pubmed ID: 26594374 During the last five years, serial femtosecond crystallography using Xray laser pulses has been developed into a powerful technique for determining the atomic structures of protein molecules from micrometre and submicrometresized crystals. One of the key reasons for this success is the 'selfgating' pulse effect, whereby the Xray laser pulses do not need to outrun all radiation damage processes. Instead, Xrayinduced damage terminates the Bragg diffraction prior to the pulse completing its passage through the sample, as if the Bragg diffraction were generated by a shorter pulse of equal intensity. As a result, serial femtosecond crystallography does not need to be performed with pulses as short as 510 fs, but can succeed for pulses 50100 fs in duration. It is shown here that a similar gating effect applies to singlemolecule diffraction with respect to spatially uncorrelated damage processes like ionization and ion diffusion. The effect is clearly seen in calculations of the diffraction contrast, by calculating the diffraction of the average structure separately to the diffraction from statistical fluctuations of the structure due to damage ('damage noise'). The results suggest that subnanometre singlemolecule imaging with 3050 fs pulses, like those produced at currently operating facilities, should not yet be ruled out. The theory presented opens up new experimental avenues to measure the impact of damage on singleparticle diffraction, which is needed to test damage models and to identify optimal imaging conditions.



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