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Towards Single Molecule Imaging - Understanding Structural Transitions Using Ultrafast X-ray Sources and Computer Simulations
Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
2007 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
Abstract [en]

X-ray lasers bring us into a new world in photon science by delivering extraordinarily intense beams of x-rays in very short bursts that can be more than ten billion times brighter than pulses from other x-ray sources. These lasers find applications in sciences ranging from astrophysics to structural biology, and could allow us to obtain images of single macromolecules when these are injected into the x-ray beam.

A macromolecule injected into vacuum in a microdroplet will be affected by evaporation and by the dynamics of the carrier liquid before being hit by the x-ray pulse. Simulations of neutral and charged water droplets were performed to predict structural changes and changes of temperature due to evaporation. The results are discussed in the aspect of single molecule imaging.

Further studies show ionization caused by the intense x-ray radiation. These simulations reveal the development of secondary electron cascades in water. Other studies show the development of these cascades in KI and CsI where experimental data exist. The results are in agreement with observation, and show the temporal, spatial and energetic evolution of secondary electron cascades in the sample.

X-ray diffraction is sensitive to structural changes on the length scale of chemical bonds. Using a short infrared pump pulse to trigger structural changes, and a short x-ray pulse for probing it, these changes can be studied with a temporal resolution similar to the pulse lengths. Time resolved diffraction experiments were performed on a phase transition during resolidification of a non-thermally molten InSb crystal. The experiment reveals the dynamics of crystal regrowth.

Computer simulations were performed on the infrared laser-induced melting of bulk ice, giving a comprehension of the dynamics and the wavelength dependence of melting. These studies form a basis for planning experiments with x-ray lasers.

Ort, förlag, år, upplaga, sidor
Uppsala: Acta Universitatis Upsaliensis , 2007. , s. 77
Serie
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 315
Nyckelord [en]
Molecular biophysics, XFEL, Ultrafast Melting, InSb, Molecular Dynamics, Water Cluster, Evaporation, Secondary Electron, Photo-cathode, Electron Scattering, Energy Loss Function, Single Particle Imaging, X-ray Diffraction, Water, Ice, KI, CsI
Nyckelord [sv]
Molekylär biofysik
Identifikatorer
URN: urn:nbn:se:uu:diva-7915ISBN: 978-91-554-6911-5 (tryckt)OAI: oai:DiVA.org:uu-7915DiVA, id: diva2:170359
Disputation
2007-06-07, B41, Biomedical Centre, Husargatan 3, Uppsala, 09:15 (Engelska)
Opponent
Handledare
Tillgänglig från: 2007-05-16 Skapad: 2007-05-16 Senast uppdaterad: 2010-03-16Bibliografiskt granskad
Delarbeten
1. Auger electron cascades in water and ice
Öppna denna publikation i ny flik eller fönster >>Auger electron cascades in water and ice
2004 (Engelska)Ingår i: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 299, s. 277-283Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Secondary electron cascades can induce significant ionisation in condensed matter due to electron–atom collisions. This is of interest in the context of diffraction and imaging using X-rays, where radiation damage is the main limiting factor for achieving high resolution data. Here we present new results on electron-induced damage on liquid water and ice, from the simulation of Auger electron cascades. We have compared our theoretical estimations to the available experimental data on elastic and inelastic electron–molecule interactions for water and found the theoretical results for elastic cross-sections to be in very good agreement with experiment. As a result of the cascade we find that the average number of secondary electrons after 100 fs in ice is about 25, slightly higher than in water, where it is about 20. The difference in damage between ice and water is discussed in the context of sample handling for biomolecular systems.

Nationell ämneskategori
Naturvetenskap
Identifikatorer
urn:nbn:se:uu:diva-95959 (URN)10.1016/j.chemphys.2003.10.011 (DOI)2004 (PubMedID)
Tillgänglig från: 2007-05-16 Skapad: 2007-05-16 Senast uppdaterad: 2017-12-14Bibliografiskt granskad
2. Studies if resolidification of non-thermally molten InSb using time-resolved X-ray diffraction
Öppna denna publikation i ny flik eller fönster >>Studies if resolidification of non-thermally molten InSb using time-resolved X-ray diffraction
Visa övriga...
2005 Ingår i: Applied Physics A, Vol. 81, s. 893-900Artikel i tidskrift (Refereegranskat) Published
Identifikatorer
urn:nbn:se:uu:diva-95960 (URN)
Tillgänglig från: 2007-05-16 Skapad: 2007-05-16 Senast uppdaterad: 2016-04-12Bibliografiskt granskad
3. Temperature and structural changes of water in vacuum due to evaporation
Öppna denna publikation i ny flik eller fönster >>Temperature and structural changes of water in vacuum due to evaporation
2006 Ingår i: Journal of Chemical Physics, Vol. 125, s. 154508-Artikel i tidskrift (Refereegranskat) Published
Identifikatorer
urn:nbn:se:uu:diva-95961 (URN)
Tillgänglig från: 2007-05-16 Skapad: 2007-05-16Bibliografiskt granskad
4. Picosecond Melting of Ice by an Infrared Laser Pulse
Öppna denna publikation i ny flik eller fönster >>Picosecond Melting of Ice by an Infrared Laser Pulse
2008 (Engelska)Ingår i: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 47, nr 8, s. 1417-1420Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Cold as ice: Molecular dynamics simulation provides snapshots of a melting ice crystal (see picture). The laser pulse heats up the system, and the energy is absorbed in the OH bonds. After a few picoseconds, the energy is transferred to rotational and translational energy, causing the crystal to melt. The melting starts as a nucleation process, and even long after the first melting is initialized, pockets of crystalline structures can be found.

Nyckelord
Computer Simulation, Crystallization, Ice, Infrared Rays, Kinetics, Lasers, Models; Molecular, Molecular Conformation, Phase Transition/*radiation effects, Temperature, Time Factors
Nationell ämneskategori
Biologiska vetenskaper
Identifikatorer
urn:nbn:se:uu:diva-95962 (URN)10.1002/anie.200703987 (DOI)000253345700010 ()18176920 (PubMedID)
Tillgänglig från: 2007-05-16 Skapad: 2007-05-16 Senast uppdaterad: 2017-12-14Bibliografiskt granskad
5. Secondary Electron Cascade Dynamics in KI and CsI
Öppna denna publikation i ny flik eller fönster >>Secondary Electron Cascade Dynamics in KI and CsI
2007 (Engelska)Ingår i: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 111, nr 46, s. 17442-17447Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

We present a study of the characteristics of secondary electron cascades in two photocathode materials, KI and CsI. To do so, we have employed a model that enables us to explicitly follow the electron trajectories once the dielectric properties have been derived semiempirically from the energy loss function. Furthermore, we introduce a modification to the model by which the energy loss function is calculated in a first-principle manner using the GW approximation for the self-energy of the electrons. We find good agreement between the two approaches. Our results show comparable saturation times and secondary electron yields for the cascades in the two materials, and a narrower electron energy distribution (51%) for KI compared to that for CsI.

Nationell ämneskategori
Fysik
Identifikatorer
urn:nbn:se:uu:diva-102110 (URN)10.1021/jp0736692 (DOI)000251024500041 ()
Tillgänglig från: 2009-05-06 Skapad: 2009-05-05 Senast uppdaterad: 2017-12-13Bibliografiskt granskad
6. Evaporation from water clusters containing singly charged ions
Öppna denna publikation i ny flik eller fönster >>Evaporation from water clusters containing singly charged ions
2007 (Engelska)Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 9, nr 37, s. 5105-5111Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Molecular dynamics simulations were used to study the evaporation from water clusterscontaining either ClÀ, H2PO4À, Na+ or NH4+ ions. The simulations ranged between 10 and500 ns, and were performed in vacuum starting at 275 K. A number of different models were usedincluding polarizable models. The clusters contain 216 or 512 molecules, 0, 4 or 8 of which wereions. The ions with hydrogen bonding properties do not affect evaporation, even though thephosphate ions have a pronounced ion–ion structure and tend to be inside the cluster whereasammonium shows little ion–ion structure and has a distribution within the cluster similar to thatof the water molecules. Since the individual ion–water interactions are much stronger in the caseof Na+–water and ClÀ–water clusters, evaporation is somewhat slower for clusters containingthese ions. It seems therefore that the main determinant of the evaporation rate in ion–waterclusters is the strength of the interaction. Fission of droplets that contain more ions than allowedaccording to the Rayleigh limit seems to occur more rapidly in clusters containing ammoniumand sodium ions.

Nyckelord
Sodium ion, Droplet, Aqueous solution, Distribution, Ammonium ion, Structure, Phosphates, Hydrogen bond, Models, Simulation, Molecular dynamics method, Ions, Water, Evaporation
Nationell ämneskategori
Biologiska vetenskaper
Identifikatorer
urn:nbn:se:uu:diva-95964 (URN)10.1039/b706243e (DOI)000249564300005 ()17878986 [ (PubMedID)
Tillgänglig från: 2007-05-16 Skapad: 2007-05-16 Senast uppdaterad: 2017-12-14Bibliografiskt granskad

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