| 1. |
- Caleman, Carl, et al.
(author)
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Evaporation from water clusters containing singly charged ions
- 2007
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In: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 9:37, s. 5105-5111
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Journal article (peer-reviewed)abstract
- 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.
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| 2. |
- Caleman, Carl, et al.
(author)
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Picosecond Melting of Ice by an Infrared Laser Pulse
- 2008
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In: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 47:8, s. 1417-1420
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Journal article (peer-reviewed)abstract
- 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.
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| 3. |
- Caleman, Carl, et al.
(author)
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Radiation damage in biological material : electronic properties and electron impact ionization in urea
- 2009
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In: Europhysics letters. - : IOP. - 0295-5075 .- 1286-4854. ; 85:1, s. 18005-
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Journal article (peer-reviewed)abstract
- Radiation damage is an unavoidable process when performing structural investigations of biological macromolecules with X-rays. In crystallography this process can be limited through damage distribution in a crystal, while for single molecular imaging it can be outrun by employing short intense pulses. Secondary electron generation is crucial during damage formation and we present a study of urea, as model for biomaterial. From first principles we calculate the band structure and energy loss function, and subsequently the inelastic electron cross-section in urea. Using Molecular Dynamics simulations, we quantify the damage and study the magnitude and spatial extent of the electron cloud coming from an incident electron, as well as the dependence with initial energy.
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| 4. |
- Caleman, Carl, et al.
(author)
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Temperature and structural changes of water clusters in vacuum due to evaporation
- 2006
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In: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 125:15, s. 154508-
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Journal article (peer-reviewed)abstract
- This paper presents a study on evaporation of pure water clusters. Molecular dynamics simulations between 20 ns and 3 mu s of clusters ranging from 125 to 4096 molecules in vacuum were performed. Three different models (SPC, TIP4P, and TIP5P) were used to simulate water, starting at temperatures of 250, 275, and 300 K. We monitored the temperature, the number of hydrogen bonds, the tetrahedral order, the evaporation, the radial distribution functions, and the diffusion coefficients. The three models behave very similarly as far as temperature and evaporation are concerned. Clusters starting at a higher temperature show a higher initial evaporation rate and therefore reach the point where evaporation stop (around 240 K) sooner. The radius of the clusters is decreased by 0.16-0.22 nm after 0.5 mu s (larger clusters tend to decrease their radius slightly more), which corresponds to around one evaporated molecule per nm(2). The cluster temperature seems to converge towards 215 K independent of cluster size, when starting at 275 K. We observe only small structural changes, but the clusters modeled by TIP5P show a larger percentage of molecules with low diffusion coefficient as t ->infinity, than those using the two other water models. TIP4P seems to be more structured and more hydrogen bonds are formed than in the other models as the temperature falls. The cooling rates are in good agreement with experimental results, and evaporation rates agree well with a phenomenological expression based on experimental observations.
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| 5. |
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| 6. |
- Caleman, Carl, 1975-
(author)
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Towards Single Molecule Imaging - Understanding Structural Transitions Using Ultrafast X-ray Sources and Computer Simulations
- 2007
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Doctoral thesis (other academic/artistic)abstract
- 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.
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| 7. |
- Chalupsky, J., et al.
(author)
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Characteristics of focused soft X-ray free-electron laser beam determined by ablation of organic molecular solids
- 2007
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In: Optics Express. - 1094-4087. ; 15:10, s. 6036-6043
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Journal article (peer-reviewed)abstract
- A linear accelerator based source of coherent radiation, FLASH (Free-electron LASer in Hamburg) provides ultra-intense femtosecond radiation pulses at wavelengths from the extreme ultraviolet (XUV; lambda< 100nm) to the soft X-ray (SXR; lambda<30nm) spectral regions. 25-fs pulses of 32-nm FLASH radiation were used to determine the ablation parameters of PMMA - poly ( methyl methacrylate). Under these irradiation conditions the attenuation length and ablation threshold were found to be (56.9 +/- 7.5) nm and similar to 2 mJ center dot cm(-2), respectively. For a second wavelength of 21.7 nm, the PMMA ablation was utilized to image the transverse intensity distribution within the focused beam at mu m resolution by a method developed here.
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| 8. |
- Chapman, Henry N., et al.
(author)
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Femtosecond diffractive imaging with a soft-X-ray free-electron laser
- 2006
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In: Nature Physics. - : Springer Science and Business Media LLC. - 1745-2473 .- 1745-2481. ; 2:12, s. 839-843
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Journal article (peer-reviewed)abstract
- Theory predicts(1-4) that, with an ultrashort and extremely bright coherent X-ray pulse, a single diffraction pattern may be recorded from a large macromolecule, a virus or a cell before the sample explodes and turns into a plasma. Here we report the first experimental demonstration of this principle using the FLASH soft-X-ray free-electron laser. An intense 25 fs, 4 x 10(13) W cm(-2) pulse, containing 10(12) photons at 32 nm wavelength, produced a coherent diffraction pattern from a nanostructured non-periodic object, before destroying it at 60,000 K. A novel X-ray camera assured single-photon detection sensitivity by filtering out parasitic scattering and plasma radiation. The reconstructed image, obtained directly from the coherent pattern by phase retrieval through oversampling(5-9), shows no measurable damage, and is reconstructed at the diffraction-limited resolution. A three-dimensional data set may be assembled from such images when copies of a reproducible sample are exposed to the beam one by one(10).
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| 9. |
- Chapman, Henry N, et al.
(author)
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Femtosecond time-delay X-ray holography
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 448:7154, s. 676-679
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Journal article (peer-reviewed)abstract
- Extremely intense and ultrafast X-ray pulses from free-electron lasers offer unique opportunities to study fundamental aspects of complex transient phenomena in materials. Ultrafast time-resolved methods usually require highly synchronized pulses to initiate a transition and then probe it after a precisely defined time delay. In the X-ray regime, these methods are challenging because they require complex optical systems and diagnostics. Here we propose and apply a simple holographic measurement scheme, inspired by Newton's 'dusty mirror' experiment1, to monitor the X-ray-induced explosion of microscopic objects. The sample is placed near an X-ray mirror; after the pulse traverses the sample, triggering the reaction, it is reflected back onto the sample by the mirror to probe this reaction. The delay is encoded in the resulting diffraction pattern to an accuracy of one femtosecond, and the structural change is holographically recorded with high resolution. We apply the technique to monitor the dynamics of polystyrene spheres in intense free-electron-laser pulses, and observe an explosion occurring well after the initial pulse. Our results support the notion that X-ray flash imaging2, 3 can be used to achieve high resolution, beyond radiation damage limits for biological samples4. With upcoming ultrafast X-ray sources we will be able to explore the three-dimensional dynamics of materials at the timescale of atomic motion.
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| 10. |
- Gabrysch, Markus, et al.
(author)
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Formation of secondary electron cascades in single-crystalline plasma-deposited diamond upon exposure to femtosecond x-ray pulses
- 2008
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In: Journal of Applied Physics. - : AIP Publishing. - 0021-8979 .- 1089-7550. ; 103:6
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Journal article (peer-reviewed)abstract
- Secondary electron cascades were measured in high purity single-crystalline chemical vapor deposition (CVD) diamond, following exposure to ultrashort hard x-ray pulses (140 fs full width at half maximum, 8.9 keV energy) from the Sub-Picosecond Pulse Source at the Stanford Linear Accelerator Center. We report measurements of the pair creation energy and of drift mobility of carriers in two CVD diamond crystals. This was done for the first time using femtosecond x-ray excitation. Values for the average pair creation energy were found to be 12.17 +/- 0.57 and 11.81 +/- 0.59 eV for the two crystals, respectively. These values are in good agreement with recent theoretical predictions. The average drift mobility of carriers, obtained by the best fit to device simulations, was mu(h)= 2750 cm(2)/V s for holes and was mu(e)= 2760 cm(2) / V s for electrons. These mobility values represent lower bounds for charge mobilities due to possible polarization of the samples. The results demonstrate outstanding electric properties and the enormous potential of diamond in ultrafast x-ray detectors.
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| 11. |
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| 12. |
- Hau-Riege, S. P., et al.
(author)
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Damage threshold of inorganic solids under free-electron-laser irradiation at 32.5 nm wavelength
- 2007
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In: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 90:17, s. 173128-
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Journal article (peer-reviewed)abstract
- Samples of B4C, amorphous C, chemical-vapor-deposition-diamond C, Si, and SiC were exposed to single 25 fs long pulses of 32.5 nm free-electron-laser radiation at fluences of up to 2.2 J/cm(2). The samples were chosen as candidate materials for x-ray free-electron-laser optics. It was found that the threshold for surface damage is on the order of the fluence required for thermal melting. For larger fluences, the crater depths correspond to temperatures on the order of the critical temperature, suggesting that the craters are formed by two-phase vaporization.
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| 13. |
- Hau-Riege, S. P., et al.
(author)
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Force Field Benchmark of Organic Liquids : Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant
- 2007
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In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 98:14, s. 145502-
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Journal article (peer-reviewed)abstract
- At the recently built FLASH x-ray free-electron laser, we studied the reflectivity of Si/C multilayers with fluxes up to 3×1014W/cm2. Even though the nanostructures were ultimately completely destroyed, we found that they maintained their integrity and reflectance characteristics during the 25-fs-long pulse, with no evidence for any structural changes over lengths greater than 3Å. This experiment demonstrates that with intense ultrafast pulses, structural damage does not occur during the pulse, giving credence to the concept of diffraction imaging of single macromolecules.
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| 14. |
- Larsson, Jörgen, et al.
(author)
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Opportunities and challenges using short-pulse X-ray sources.
- 2005
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In: Second International Conference on Photo-Induced Phase Transitions: Cooperative, Nonlinear and Functional Properties. - : IOP Publishing. - 1742-6588 .- 1742-6596. ; 21, s. 87-94
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Conference paper (peer-reviewed)abstract
- Free-electron lasers will change the way we carry out time-resolved X-ray experiments. At present date, we use laser-produced plasma sources or synchrotron radiation. Laser-produced plasma sources have short pulses, but unfortunately large pulse-to-pulse fluctuations and large divergence. Synchrotron radiation from third generation source provide collimated and stable beams, but unfortunately long pulses. This means that either the time-resolution is limited to 100 ps or rather complex set-ups involving slicing or streak cameras are needed. Hard X-ray free-electron lasers will combine the best properties of present-day sources and increase the number of photons by many orders of magnitude. Already today, a precursor to the free-electron lasers has been built at Stanford Linear Accelerator Centre (SLAC). The Sub-Picosecond Photon Source (SPPS) has already shown the opportunities and challenges of using short-pulse X-ray sources.
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| 15. |
- Lindenberg, A.M., et al.
(author)
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Ultrafast x-ray measurements of inertial atomic-scale motion
- 2005
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In: Quantum Electronics and Laser Science Conference. ; , s. 742-744
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Conference paper (peer-reviewed)abstract
- Using a new, accelerator-based source of femtosecond x-rays, we directly measure atomic displacements on an optically-modified potential energy surface. It is shown that the short time dynamics are predominantly inertial in character.
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| 16. |
- Marklund, Erik G., et al.
(author)
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Structural stability of electrosprayed proteins : temperature and hydration effects
- 2009
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In: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 11:36, s. 8069-8078
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Journal article (peer-reviewed)abstract
- Electrospray ionization is a gentle method for sample delivery, routinely used in gas-phase studies of proteins. It is crucial for structural investigations that the protein structure is preserved, and a good understanding of how structure is affected by the transition to the gas phase is needed for the tuning of experiments to meet that requirement. Small amounts of residual solvent have been shown to protect the protein, but temperature is important too, although it is not well understood how the latter affects structural details. Using molecular dynamics we have simulated four sparingly hydrated globular proteins (Trp-cage; Ctf, a C-terminal fragment of a bacterial ribosomal protein; ubiquitin; and lysozyme) in vacuum starting at temperatures ranging from 225 K to 425 K. For three of the proteins, our simulations show that a water layer corresponding to 3 angstrom preserves the protein structure in vacuum, up to starting temperatures of 425 K. Only Ctf shows minor secondary structural changes at lower starting temperatures. The structural conservation stems mainly from interactions with the surrounding water. Temperature scales in simulations are not directly translatable into experiments, but the wide temperature range in which we find the proteins to be stable is reassuring for the success of future single particle imaging experiments. The water molecules aggregate in clusters and form patterns on the protein surface, maintaining a reproducible hydrogen bonding network. The simulations were performed mainly using OPLS-AA/L, with cross checks using AMBER03 and GROMOS96 53a6. Only minor differences between the results from the three different force fields were observed.
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| 17. |
- Ortiz, Carlos, 1976-, et al.
(author)
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Secondary Electron Cascade Dynamics in KI and CsI
- 2007
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In: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 111:46, s. 17442-17447
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Journal article (peer-reviewed)abstract
- 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.
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| 18. |
- van der Spoel, David, et al.
(author)
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Structural studies of melting on the picosecond time scale
- 2008
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In: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 10:42, s. 6344-6349
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Research review (peer-reviewed)abstract
- Ultrafast structural studies of laser-induced melting have demonstrated that the solid-liquid phase transition can take place on a picosecond time scale in a variety of materials. Experimental studies using ångström wavelength X-rays from the sub-picosecond pulse source at Stanford (now retired) on non-thermal melting of semi-conductors, such as indium antimonide, employed the decay of a single Bragg-peak to measure the time component of the phase transition. These materials were found to start melting within one picosecond after the laser pulse. Recent computer simulations have described the thermal melting of ice induced by an infrared laser pulse. Here it was shown that melting can happen within a few picoseconds, somewhat slower than non-thermal melting in semi-conductors. These computer simulations are compatible with spectroscopy experiments on ice-melting, demonstrating that simulations form a very powerful complement to experiments targeting the process of phase-transitions. Here we present an overview of recent experimental and theoretical studies of melting, as well as new simulations of ice-melting where the effect of the size of the crystal on scattering is studied. Based on simulations of a near-macroscopic crystal, we predict the decay of the most intense Bragg peaks of ice following heating by laser pulse, by modeling the scattering from the melting sample in the simulations.
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