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SpecSwap-RMC: A novel reverse Monte Carlo approach using a discrete set of local configurations and pre-computed properties
Stockholm University, Faculty of Science, Department of Physics. (Kvantkemi)
Stockholm University, Faculty of Science, Department of Physics. (Kvantkemi)
Stockholm University, Faculty of Science, Department of Physics. (Kvantkemi)
2010 (English)In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 22, no 13, 135001- p.Article in journal (Refereed) Published
Abstract [en]

We present a novel approach to reverse Monte Carlo (RMC) modeling, SpecSwap-RMC, specifically applicable to structure modeling based on properties that require significant computer time to evaluate. In this approach pre-computed property data from a discrete set of local configurations are used and the configuration space is expressed in this basis. Atomistic moves are replaced with swap moves of contributions to a sample set representing the state of the simulated system. We demonstrate the approach by fitting jointly and separately the EXAFS signal and x-ray absorption spectrum (XAS) of ice Ih using a SpecSwap sample set of 80 configurations from a library of 1382 local structures with associated pre-computed spectra. As an additional demonstration we compare SpecSwap and FEFFIT fits of EXAFS data on crystalline copper, finding excellent agreement. SpecSwap-RMC thus extends RMC structure modeling to any property that can be computed from a structure irrespective of computational expense, but at the cost of a reduced configuration space. The method is general enough that it can be applied to any sets of computed properties, not necessarily limited to structure determination.

Place, publisher, year, edition, pages
2010. Vol. 22, no 13, 135001- p.
National Category
Physical Sciences
Identifiers
URN: urn:nbn:se:su:diva-47088DOI: 10.1088/0953-8984/22/13/135001OAI: oai:DiVA.org:su-47088DiVA: diva2:372989
Available from: 2010-11-29 Created: 2010-11-29 Last updated: 2017-12-12Bibliographically approved
In thesis
1. Structure Modeling with X-ray Absorption and Reverse Monte Carlo: Applications to Water
Open this publication in new window or tab >>Structure Modeling with X-ray Absorption and Reverse Monte Carlo: Applications to Water
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Water is an important substance. It is part of us, of our environment, and is a fundamental prerequisite for the existence of life as we know it. The structure of water is still, after over 100 years of research on the subject, however under debate. In this thesis x-ray absorption spectroscopy (XAS) and reverse Monte Carlo (RMC) modeling are used to search for structural solutions of water consistent with many different experimental data sets, with emphasis on the combination of different experimental techniques for a reliable structure determination. Neutron and x-ray diffraction are analyzed in combination with the more recent synchrotron radiation based XAS. Geometrical criteria for H-bonding are implemented in RMC to drive the fits and allow to evaluate differently H-bonded structure models against the data. It is shown that the available diffraction data put little constraints on the type of H-bond topology or O-O-O tetrahedrality for the structure of liquid water. It is also demonstrated that classical MD simulations, using some of the most common interaction potentials for water, give rise to O-O and O-H pair-correlation functions with too sharp first peaks at too short distances to be in agreement with diffraction, and furthermore that requiring a large fraction of broken H-bonds is not in itself enough for a structure model to reproduce the experimental XAS. A contribution to the theoretical description of XAS is made by an in-depth investigation of important technical aspects of the TP-DFT spectrum calculations. A novel approach to RMC, applicable also to data that require a significant amount of computer time to evaluate, is developed which makes use of pre-computed properties from a large set of local geometries allowing RMC simulations directly on data from core-level spectroscopies such as XAS.

Place, publisher, year, edition, pages
Stockholm: Department of Physics, Stockholm University, 2009. 83 p.
Keyword
water structure, x-ray absorption, spectroscopy, diffraction, reverse monte carlo, XAS, EXAFS, XANES, RMC, TP-DFT spectrum calculations
National Category
Physical Sciences
Research subject
Chemical Physics
Identifiers
urn:nbn:se:su:diva-31475 (URN)978-91-7155-972-2 (ISBN)
Public defence
2009-12-11, FB53 AlbaNova universitetscentrum, Roslagstullsbacken 21, Stockholm, 10:00 (English)
Opponent
Supervisors
Note
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4, 5 and 6: SubmittedAvailable from: 2009-11-19 Created: 2009-11-16 Last updated: 2011-04-26Bibliographically approved
2. Structure, Dynamics and Thermodynamics of Liquid Water: Insights from Molecular Simulations
Open this publication in new window or tab >>Structure, Dynamics and Thermodynamics of Liquid Water: Insights from Molecular Simulations
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Water is a complex liquid with many unusual properties. Our understanding of its physical, chemical and biological properties is greatly advanced after a century of dedicated research but there are still many unresolved questions. If answered, they could have important long-term consequences for practical applications ranging from drug design to water purification. This thesis presents results on the structure, dynamics and thermodynamics of liquid water. The focus is on theoretical simulations applied to interpret experimental data from mainly x-ray and neutron scattering and spectroscopy techniques. The structural sensitivity of x-ray and neutron diffraction is investigated using reverse Monte Carlo simulations and information on the pair-correlation functions of water is derived. A new method for structure modeling of computationally demanding data sets is presented and used to resolve an inconsistency between experimental extended x-ray absorption fine-structure and diffraction data regarding oxygen-oxygen pair-correlations. Small-angle x-ray scattering data are modeled using large-scale classical molecular dynamics simulations, and the observed enhanced scattering at supercooled temperatures is connected to the presence of a Widom line emanating from a liquid-liquid critical point in the deeply supercooled high pressure regime. An investigation of inherent structures reveals an underlying structural bimodality in the simulations connected to disordered high-density and ordered low-density molecules, providing a clearer interpretation of experimental small-angle scattering data. Dynamical anomalies in supercooled water observed in inelastic neutron scattering experiments, manifested by low-frequency collective excitations resembling a boson peak, are investigated and found to be connected to the thermodynamically defined Widom line. Finally, x-ray absorption spectra are calculated for simulated water structures using density functional theory. An approximation of intra-molecular zero-point vibrational effects is found to significantly improve the relative spectral intensities but a structural investigation indicates that the classical simulations underestimate the amount of broken hydrogen bonds.

Abstract [sv]

Vatten är en komplex vätska med flera ovanliga egenskaper. Vår förståelse av dess fysiska, kemiska och biologiska egenskaper har utvecklats mycket sedan systematiska vetenskapliga studier började genomföras för mer än ett sekel sedan, men många viktiga frågor är fortfarande obesvarade. En ökad förståelse skulle på sikt kunna leda till framsteg inom viktiga områden så som medicinutveckling och vattenrening. Denna avhandling presenterar resultat kring vattnets struktur, dynamik och termodynamik. Fokusen ligger på teoretiska simuleringar som använts för att tolka experimentella data från huvudsakligen röntgen- och neutronspridning samt spektroskopier. Den strukturella känsligheten i röntgen- och neutrondiffraktionsdata undersöks via reverse Monte Carlo metoden och information om de partiella parkorrelationsfunktionerna erhålls. En ny metod för strukturmodellering av beräkningsintensiva data presenteras och används för att lösa en motsägelse mellan experimentell diffraktion och EXAFS angående syre- syre parkorrelationsfunktionen. Data från röntgensmåvinkelspridning modelleras med storskaliga klassiska molekyldynamiksimuleringar, och den observerade förhöjda småvinkelspridningen vid underkylda temperaturer kopplas till existensen av en Widomlinje härrörande från en vätske- vätske kritisk punkt i det djupt underkylda området vid höga tryck. En undersökning av inherenta strukturer i simuleringarna påvisar en underliggande strukturell bimodalitet mellan molekyler i oordnade högdensitetsregioner respektive ordnade lågdensitetsregioner, vilket ger en tydligare tolkning av den experimentella småvinkelspridningen. Dynamiska anomalier i underkylt vatten som har observerats i inelastisk neutronspridning, speciellt förekomsten av lågfrekventa excitationer som liknar en bosontopp, undersöks och kopplas till den termodynamiskt definierade Widomlinjen. Slutligen presenteras densitetsfunktionalberäkningar av röntgenabsorptionsspektra för simulerade vattenstrukturer. En approximation av intramolekylära nollpunktsvibrationseffekter förbättrar relativa intensiteteri spektrumen avsevärt, men en strukturanalys visar att klassiska simuleringar av vatten underskattar andelen brutna vätebindningar.

Place, publisher, year, edition, pages
Stockholm: Department of Physics, Stockholm University, 2011. 102 p.
Keyword
Liquid water, supercooled water, diffraction, structure modeling, molecular dynamics, x-ray spectroscopy, EXAFS, SAXS
National Category
Physical Sciences
Research subject
Theoretical Physics
Identifiers
urn:nbn:se:su:diva-56711 (URN)978-91-7447-287-5 (ISBN)
Public defence
2011-05-27, lecture room FA31, AlbaNova universitetscentrum, Roslagstullsbacken 21, Stockholm, 13:00 (English)
Opponent
Supervisors
Note
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 6: Submitted. Paper 7: Submitted. Paper 8: Manuscript. Paper 9: Submitted. Available from: 2011-05-05 Created: 2011-04-22 Last updated: 2011-04-26Bibliographically approved

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