Carl Caleman - Academia.edu (original) (raw)
Papers by Carl Caleman
Springer Proceedings in Physics, 2007
The first soft X-ray free-electron laser has recently been put into operation at DESY in Hamburg.... more The first soft X-ray free-electron laser has recently been put into operation at DESY in Hamburg. Tunable soft X-ray coherent radiation can be generated at the FLASH (Free-electron LASer in Hamburg; formerly known as VUV FEL or TTF2 FEL). In the interaction experiments reported here, the laser system provided ~ 25-fs, ~ 10-μ J pulses of 32-nm radiation. We irradiated
Journal of synchrotron radiation, 2015
Serial femtosecond X-ray crystallography of protein nanocrystals using ultrashort and intense pul... more Serial femtosecond X-ray crystallography of protein nanocrystals using ultrashort and intense pulses from an X-ray free-electron laser has proved to be a successful method for structural determination. However, due to significant variations in diffraction pattern quality from pulse to pulse only a fraction of the collected frames can be used. Experimentally, the X-ray temporal pulse profile is not known and can vary with every shot. This simulation study describes how the pulse shape affects the damage dynamics, which ultimately affects the biological interpretation of electron density. The instantaneously detected signal varies during the pulse exposure due to the pulse properties, as well as the structural and electronic changes in the sample. Here ionization and atomic motion are simulated using a radiation transfer plasma code. Pulses with parameters typical for X-ray free-electron lasers are considered: pulse energies ranging from 10(4) to 10(7) J cm(-2) with photon energies fr...
Philosophical transactions of the Royal Society of London. Series B, Biological sciences, Jan 17, 2014
X-ray free-electron lasers have opened up the possibility of structure determination of protein c... more X-ray free-electron lasers have opened up the possibility of structure determination of protein crystals at room temperature, free of radiation damage. The femtosecond-duration pulses of these sources enable diffraction signals to be collected from samples at doses of 1000 MGy or higher. The sample is vaporized by the intense pulse, but not before the scattering that gives rise to the diffraction pattern takes place. Consequently, only a single flash diffraction pattern can be recorded from a crystal, giving rise to the method of serial crystallography where tens of thousands of patterns are collected from individual crystals that flow across the beam and the patterns are indexed and aggregated into a set of structure factors. The high-dose tolerance and the many-crystal averaging approach allow data to be collected from much smaller crystals than have been examined at synchrotron radiation facilities, even from radiation-sensitive samples. Here, we review the interaction of intense...
Optics Express, 2015
In structural determination of crystalline proteins using intense femtosecond X-ray lasers, damag... more In structural determination of crystalline proteins using intense femtosecond X-ray lasers, damage processes lead to loss of structural coherence during the exposure. We use a nonthermal description for the damage dynamics to calculate the ultrafast ionization and the subsequent atomic displacement. These effects degrade the Bragg diffraction on femtosecond time scales and gate the ultrafast imaging. This process is intensity and resolution dependent. At high intensities the signal is gated by the ionization affecting low resolution information first. At lower intensities, atomic displacement dominates the loss of coherence affecting high-resolution information. We find that pulse length is not a limiting factor as long as there is a high enough X-ray flux to measure a diffracted signal.
Journal of synchrotron radiation, 2015
Proteins that contain metal cofactors are expected to be highly radiation sensitive since the deg... more Proteins that contain metal cofactors are expected to be highly radiation sensitive since the degree of X-ray absorption correlates with the presence of high-atomic-number elements and X-ray energy. To explore the effects of local damage in serial femtosecond crystallography (SFX), Clostridium ferredoxin was used as a model system. The protein contains two [4Fe-4S] clusters that serve as sensitive probes for radiation-induced electronic and structural changes. High-dose room-temperature SFX datasets were collected at the Linac Coherent Light Source of ferredoxin microcrystals. Difference electron density maps calculated from high-dose SFX and synchrotron data show peaks at the iron positions of the clusters, indicative of decrease of atomic scattering factors due to ionization. The electron density of the two [4Fe-4S] clusters differs in the FEL data, but not in the synchrotron data. Since the clusters differ in their detailed architecture, this observation is suggestive of an influ...
Chemical Science, 2014
ABSTRACT The concentration of hydronium and hydroxide at the water-air interface has been debated... more ABSTRACT The concentration of hydronium and hydroxide at the water-air interface has been debated for a long time. Recent evidence from a range of experiments and theoretical calculations strongly suggests the water surface to be somewhat acidic. Using novel polarizable models we have performed potential of mean force calculations of a hydronium ion, a hydroxide ion and a water molecule in a water droplet and a water slab and we were able to rationalize that hydronium, but not hydroxide, is slightly enriched at the surface for two reasons. First, because the hydrogen bond acceptance capacity of hydronium is weaker than water and it is more favorable to have the hydronium oxygen on the surface. Second, hydroxide ions are expelled from the surface of the droplets, due to the entropy being lower when a hydroxide ion is hydrated on the surface. As a result, the water dissociation constant pKw increases slightly near the surface. The results are corroborated by calculations of surface tension of NaOH solutions that are in reasonable agreement with the experiment. The structural and thermodynamic interpretation of hydronium and hydroxide hydration provided by these calculations opens the route to a better understanding of atmospheric and surface chemistry.
The Journal of Physical Chemistry C, 2007
We present a study of the characteristics of secondary electron cascades in two photocathode mate... more 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 ...
Proceedings of SPIE - The International Society for Optical Engineering, 2011
Powerful free electron lasers (FELs) operating in the soft X-ray regime are offering new possibil... more Powerful free electron lasers (FELs) operating in the soft X-ray regime are offering new possibilities for creating and probing materials under extreme conditions. We describe here simulations to model the interaction of a focused FEL pulse with metallic solids (niobium, vanadium, and their deuterides) at 13.5 nm wavelength (92 eV) with peak intensities between 10 15 to 10 18 W/cm 2 and a fixed pulse length of 15 femtoseconds (full width at half maximum). The interaction of the pulse with the metallic solids was modeled with a non-local thermodynamic equilibrium code that included radiation transfer. The calculations also made use of a self-similar isothermal fluid model for plasma expansion into vacuum. We find that the time-evolution of the simulated critical charge density in the sample results in a critical depth that approaches the observed crater depths in an earlier experiment performed at the FLASH free electron laser in Hamburg. The results show saturation in the ablation process at intensities exceeding 10 16 W/cm 2 . Furthermore, protons and deuterons with kinetic energies of several keV have been measured, and these concur with predictions from the plasma expansion model. The results indicate that the temperature of the plasma reached almost 5 million K after the pulse has passed.
Advances in X-ray Free-Electron Lasers: Radiation Schemes, X-ray Optics, and Instrumentation, 2011
... and Karol Nass“ and Dusko Odie“ and Emanuele Pedersoli“ and Christian Reich“ and Daniel Rolle... more ... and Karol Nass“ and Dusko Odie“ and Emanuele Pedersoli“ and Christian Reich“ and Daniel Rollesci“ and Benedikt Rudek“'“ and Artem Rudenko“'“ and Carlo Schmidt“'“ and Joachim Schulz“ and M. Marvin Seibert“ and Robert L. Shoeman“ and Raymond G. Sierra“ and Heike ...
Optics Express, 2012
We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to... more We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 s after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.
Physical Review Letters, 2014
We report experimental results on x-ray diffraction of quantum-state-selected and strongly aligne... more We report experimental results on x-ray diffraction of quantum-state-selected and strongly aligned ensembles of the prototypical asymmetric rotor molecule 2,5-diiodobenzonitrile using the Linac Coherent Light Source. The experiments demonstrate first steps toward a new approach to diffractive imaging of distinct structures of individual, isolated gas-phase molecules. We confirm several key ingredients of single molecule diffraction experiments: the abilities to detect and count individual scattered x-ray photons in single shot diffraction data, to deliver state-selected, e. g., structural-isomer-selected, ensembles of molecules to the x-ray interaction volume, and to strongly align the scattering molecules. Our approach, using ultrashort x-ray pulses, is suitable to study ultrafast dynamics of isolated molecules. 33.15.Dj, 37.10.-x X-ray Free-Electron Lasers (XFELs) hold the promise to determine atomically resolved structures and to trace structural dynamics of individual molecules and nanoparticles [1]. Over the last decade, ground-breaking experiments were performed at the Free-Electron Laser at DESY in Hamburg (FLASH) [2-5] and the Linac Coherent Light Source (LCLS) at the SLAC National Accelerator Laboratory . These experiments already begin to provide new insights into fundamental aspects of matter, such as hitherto unobserved structures of noncrystallizable mesoscopic objects or the radiation damage induced by the short and very strong x-ray pulses . However, the path to actual determination of atomically resolved structures and dynamics of single molecules is still long . Nevertheless, related experiments on the investigation of small-molecule structures and their dynamics utilizing molecular ensembles are within reach .
Physical review letters, Jan 6, 2007
At the recently built FLASH x-ray free-electron laser, we studied the reflectivity of Si/C multil... more At the recently built FLASH x-ray free-electron laser, we studied the reflectivity of Si/C multilayers with fluxes up to 3 x 10(14) W/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 3 A. 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.
Nature, 2014
Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energ... more Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth's oxygenic atmosphere. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S0 to S4, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S1 state and after double laser excitation (putative S3 state) at 5 and 5.5 Å resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn4CaO5 core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the 'dangler' Mn) and the Mn3CaOx cubane in the S2 to S3 transition, as predicted by spectroscopic and computational studies. This…
Science, 2005
The motion of atoms on interatomic potential energy surfaces is fundamental to the dynamics of li... more The motion of atoms on interatomic potential energy surfaces is fundamental to the dynamics of liquids and solids. An accelerator-based source of femtosecond x-ray pulses allowed us to follow directly atomic displacements on an optically modified energy landscape, leading eventually to the transition from crystalline solid to disordered liquid. We show that, to first order in time, the dynamics are inertial, and we place constraints on the shape and curvature of the transition-state potential energy surface. Our measurements point toward analogies between this nonequilibrium phase transition and the short-time dynamics intrinsic to equilibrium liquids.
Proceedings of the National Academy of Sciences, 2011
Water is a demanding partner. It strongly attracts ions, yet some halide anions-chloride, bromide... more Water is a demanding partner. It strongly attracts ions, yet some halide anions-chloride, bromide, and iodide-are expelled to the air/water interface. This has important implications for chemistry in the atmosphere, including the ozone cycle. We present a quantitative analysis of the energetics of ion solvation based on molecular simulations of all stable alkali and halide ions in water droplets. The potentials of mean force for Cl − ,Br − , and I − have shallow minima near the surface. We demonstrate that these minima derive from more favorable water-water interaction energy when the ions are partially desolvated. Alkali cations are on the inside because of the favorable ion-water energy, whereas F − is driven inside by entropy. Models attempting to explain the surface preference based on one or more ion properties such as polarizability or size are shown to lead to qualitative and quantitative errors, prompting a paradigm shift in chemistry away from such simplifications.
Physical Review Letters, 2005
Linear-accelerator-based sources will revolutionize ultrafast x-ray science due to their unpreced... more Linear-accelerator-based sources will revolutionize ultrafast x-ray science due to their unprecedented brightness and short pulse duration. However, time-resolved studies at the resolution of the x-ray pulse duration are hampered by the inability to precisely synchronize an external laser to the accelerator. At the Sub-Picosecond Pulse Source at the Stanford Linear-Accelerator Center we solved this problem by measuring the arrival time of each high energy electron bunch with electro-optic sampling. This measurement indirectly determined the arrival time of each x-ray pulse relative to an external pump laser pulse with a time resolution of better than 60 fs rms.
Physical Review Letters, 2005
The melting dynamics of laser excited InSb have been studied with femtosecond x-ray diffraction. ... more The melting dynamics of laser excited InSb have been studied with femtosecond x-ray diffraction. These measurements observe the delayed onset of diffusive atomic motion, signaling the appearance of liquidlike dynamics. They also demonstrate that the root-mean-squared displacement in the [111] direction increases faster than in the [110] direction after the first 500 fs. This structural anisotropy indicates that the initially generated fluid differs significantly from the equilibrium liquid.
Physical Review E, 2011
Studies of materials under extreme conditions have relevance to a broad area of research, includi... more Studies of materials under extreme conditions have relevance to a broad area of research, including planetary physics, fusion research, materials science, and structural biology with x-ray lasers. We study such extreme conditions and experimentally probe the interaction between ultrashort soft x-ray pulses and solid targets (metals and their deuterides) at the FLASH free-electron laser where power densities exceeding 10 17 W/cm 2 were reached. Time-of-flight ion spectrometry and crater analysis were used to characterize the interaction. The results show the onset of saturation in the ablation process at power densities above 10 16 W/cm 2 . This effect can be linked to a transiently induced x-ray transparency in the solid by the femtosecond x-ray pulse at high power densities. The measured kinetic energies of protons and deuterons ejected from the surface reach several keV and concur with predictions from plasma-expansion models. Simulations of the interactions were performed with a nonlocal thermodynamic equilibrium code with radiation transfer. These calculations return critical depths similar to the observed crater depths and capture the transient surface transparency at higher power densities.
Springer Proceedings in Physics, 2007
The first soft X-ray free-electron laser has recently been put into operation at DESY in Hamburg.... more The first soft X-ray free-electron laser has recently been put into operation at DESY in Hamburg. Tunable soft X-ray coherent radiation can be generated at the FLASH (Free-electron LASer in Hamburg; formerly known as VUV FEL or TTF2 FEL). In the interaction experiments reported here, the laser system provided ~ 25-fs, ~ 10-μ J pulses of 32-nm radiation. We irradiated
Journal of synchrotron radiation, 2015
Serial femtosecond X-ray crystallography of protein nanocrystals using ultrashort and intense pul... more Serial femtosecond X-ray crystallography of protein nanocrystals using ultrashort and intense pulses from an X-ray free-electron laser has proved to be a successful method for structural determination. However, due to significant variations in diffraction pattern quality from pulse to pulse only a fraction of the collected frames can be used. Experimentally, the X-ray temporal pulse profile is not known and can vary with every shot. This simulation study describes how the pulse shape affects the damage dynamics, which ultimately affects the biological interpretation of electron density. The instantaneously detected signal varies during the pulse exposure due to the pulse properties, as well as the structural and electronic changes in the sample. Here ionization and atomic motion are simulated using a radiation transfer plasma code. Pulses with parameters typical for X-ray free-electron lasers are considered: pulse energies ranging from 10(4) to 10(7) J cm(-2) with photon energies fr...
Philosophical transactions of the Royal Society of London. Series B, Biological sciences, Jan 17, 2014
X-ray free-electron lasers have opened up the possibility of structure determination of protein c... more X-ray free-electron lasers have opened up the possibility of structure determination of protein crystals at room temperature, free of radiation damage. The femtosecond-duration pulses of these sources enable diffraction signals to be collected from samples at doses of 1000 MGy or higher. The sample is vaporized by the intense pulse, but not before the scattering that gives rise to the diffraction pattern takes place. Consequently, only a single flash diffraction pattern can be recorded from a crystal, giving rise to the method of serial crystallography where tens of thousands of patterns are collected from individual crystals that flow across the beam and the patterns are indexed and aggregated into a set of structure factors. The high-dose tolerance and the many-crystal averaging approach allow data to be collected from much smaller crystals than have been examined at synchrotron radiation facilities, even from radiation-sensitive samples. Here, we review the interaction of intense...
Optics Express, 2015
In structural determination of crystalline proteins using intense femtosecond X-ray lasers, damag... more In structural determination of crystalline proteins using intense femtosecond X-ray lasers, damage processes lead to loss of structural coherence during the exposure. We use a nonthermal description for the damage dynamics to calculate the ultrafast ionization and the subsequent atomic displacement. These effects degrade the Bragg diffraction on femtosecond time scales and gate the ultrafast imaging. This process is intensity and resolution dependent. At high intensities the signal is gated by the ionization affecting low resolution information first. At lower intensities, atomic displacement dominates the loss of coherence affecting high-resolution information. We find that pulse length is not a limiting factor as long as there is a high enough X-ray flux to measure a diffracted signal.
Journal of synchrotron radiation, 2015
Proteins that contain metal cofactors are expected to be highly radiation sensitive since the deg... more Proteins that contain metal cofactors are expected to be highly radiation sensitive since the degree of X-ray absorption correlates with the presence of high-atomic-number elements and X-ray energy. To explore the effects of local damage in serial femtosecond crystallography (SFX), Clostridium ferredoxin was used as a model system. The protein contains two [4Fe-4S] clusters that serve as sensitive probes for radiation-induced electronic and structural changes. High-dose room-temperature SFX datasets were collected at the Linac Coherent Light Source of ferredoxin microcrystals. Difference electron density maps calculated from high-dose SFX and synchrotron data show peaks at the iron positions of the clusters, indicative of decrease of atomic scattering factors due to ionization. The electron density of the two [4Fe-4S] clusters differs in the FEL data, but not in the synchrotron data. Since the clusters differ in their detailed architecture, this observation is suggestive of an influ...
Chemical Science, 2014
ABSTRACT The concentration of hydronium and hydroxide at the water-air interface has been debated... more ABSTRACT The concentration of hydronium and hydroxide at the water-air interface has been debated for a long time. Recent evidence from a range of experiments and theoretical calculations strongly suggests the water surface to be somewhat acidic. Using novel polarizable models we have performed potential of mean force calculations of a hydronium ion, a hydroxide ion and a water molecule in a water droplet and a water slab and we were able to rationalize that hydronium, but not hydroxide, is slightly enriched at the surface for two reasons. First, because the hydrogen bond acceptance capacity of hydronium is weaker than water and it is more favorable to have the hydronium oxygen on the surface. Second, hydroxide ions are expelled from the surface of the droplets, due to the entropy being lower when a hydroxide ion is hydrated on the surface. As a result, the water dissociation constant pKw increases slightly near the surface. The results are corroborated by calculations of surface tension of NaOH solutions that are in reasonable agreement with the experiment. The structural and thermodynamic interpretation of hydronium and hydroxide hydration provided by these calculations opens the route to a better understanding of atmospheric and surface chemistry.
The Journal of Physical Chemistry C, 2007
We present a study of the characteristics of secondary electron cascades in two photocathode mate... more 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 ...
Proceedings of SPIE - The International Society for Optical Engineering, 2011
Powerful free electron lasers (FELs) operating in the soft X-ray regime are offering new possibil... more Powerful free electron lasers (FELs) operating in the soft X-ray regime are offering new possibilities for creating and probing materials under extreme conditions. We describe here simulations to model the interaction of a focused FEL pulse with metallic solids (niobium, vanadium, and their deuterides) at 13.5 nm wavelength (92 eV) with peak intensities between 10 15 to 10 18 W/cm 2 and a fixed pulse length of 15 femtoseconds (full width at half maximum). The interaction of the pulse with the metallic solids was modeled with a non-local thermodynamic equilibrium code that included radiation transfer. The calculations also made use of a self-similar isothermal fluid model for plasma expansion into vacuum. We find that the time-evolution of the simulated critical charge density in the sample results in a critical depth that approaches the observed crater depths in an earlier experiment performed at the FLASH free electron laser in Hamburg. The results show saturation in the ablation process at intensities exceeding 10 16 W/cm 2 . Furthermore, protons and deuterons with kinetic energies of several keV have been measured, and these concur with predictions from the plasma expansion model. The results indicate that the temperature of the plasma reached almost 5 million K after the pulse has passed.
Advances in X-ray Free-Electron Lasers: Radiation Schemes, X-ray Optics, and Instrumentation, 2011
... and Karol Nass“ and Dusko Odie“ and Emanuele Pedersoli“ and Christian Reich“ and Daniel Rolle... more ... and Karol Nass“ and Dusko Odie“ and Emanuele Pedersoli“ and Christian Reich“ and Daniel Rollesci“ and Benedikt Rudek“'“ and Artem Rudenko“'“ and Carlo Schmidt“'“ and Joachim Schulz“ and M. Marvin Seibert“ and Robert L. Shoeman“ and Raymond G. Sierra“ and Heike ...
Optics Express, 2012
We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to... more We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 s after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.
Physical Review Letters, 2014
We report experimental results on x-ray diffraction of quantum-state-selected and strongly aligne... more We report experimental results on x-ray diffraction of quantum-state-selected and strongly aligned ensembles of the prototypical asymmetric rotor molecule 2,5-diiodobenzonitrile using the Linac Coherent Light Source. The experiments demonstrate first steps toward a new approach to diffractive imaging of distinct structures of individual, isolated gas-phase molecules. We confirm several key ingredients of single molecule diffraction experiments: the abilities to detect and count individual scattered x-ray photons in single shot diffraction data, to deliver state-selected, e. g., structural-isomer-selected, ensembles of molecules to the x-ray interaction volume, and to strongly align the scattering molecules. Our approach, using ultrashort x-ray pulses, is suitable to study ultrafast dynamics of isolated molecules. 33.15.Dj, 37.10.-x X-ray Free-Electron Lasers (XFELs) hold the promise to determine atomically resolved structures and to trace structural dynamics of individual molecules and nanoparticles [1]. Over the last decade, ground-breaking experiments were performed at the Free-Electron Laser at DESY in Hamburg (FLASH) [2-5] and the Linac Coherent Light Source (LCLS) at the SLAC National Accelerator Laboratory . These experiments already begin to provide new insights into fundamental aspects of matter, such as hitherto unobserved structures of noncrystallizable mesoscopic objects or the radiation damage induced by the short and very strong x-ray pulses . However, the path to actual determination of atomically resolved structures and dynamics of single molecules is still long . Nevertheless, related experiments on the investigation of small-molecule structures and their dynamics utilizing molecular ensembles are within reach .
Physical review letters, Jan 6, 2007
At the recently built FLASH x-ray free-electron laser, we studied the reflectivity of Si/C multil... more At the recently built FLASH x-ray free-electron laser, we studied the reflectivity of Si/C multilayers with fluxes up to 3 x 10(14) W/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 3 A. 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.
Nature, 2014
Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energ... more Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth's oxygenic atmosphere. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S0 to S4, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S1 state and after double laser excitation (putative S3 state) at 5 and 5.5 Å resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn4CaO5 core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the 'dangler' Mn) and the Mn3CaOx cubane in the S2 to S3 transition, as predicted by spectroscopic and computational studies. This…
Science, 2005
The motion of atoms on interatomic potential energy surfaces is fundamental to the dynamics of li... more The motion of atoms on interatomic potential energy surfaces is fundamental to the dynamics of liquids and solids. An accelerator-based source of femtosecond x-ray pulses allowed us to follow directly atomic displacements on an optically modified energy landscape, leading eventually to the transition from crystalline solid to disordered liquid. We show that, to first order in time, the dynamics are inertial, and we place constraints on the shape and curvature of the transition-state potential energy surface. Our measurements point toward analogies between this nonequilibrium phase transition and the short-time dynamics intrinsic to equilibrium liquids.
Proceedings of the National Academy of Sciences, 2011
Water is a demanding partner. It strongly attracts ions, yet some halide anions-chloride, bromide... more Water is a demanding partner. It strongly attracts ions, yet some halide anions-chloride, bromide, and iodide-are expelled to the air/water interface. This has important implications for chemistry in the atmosphere, including the ozone cycle. We present a quantitative analysis of the energetics of ion solvation based on molecular simulations of all stable alkali and halide ions in water droplets. The potentials of mean force for Cl − ,Br − , and I − have shallow minima near the surface. We demonstrate that these minima derive from more favorable water-water interaction energy when the ions are partially desolvated. Alkali cations are on the inside because of the favorable ion-water energy, whereas F − is driven inside by entropy. Models attempting to explain the surface preference based on one or more ion properties such as polarizability or size are shown to lead to qualitative and quantitative errors, prompting a paradigm shift in chemistry away from such simplifications.
Physical Review Letters, 2005
Linear-accelerator-based sources will revolutionize ultrafast x-ray science due to their unpreced... more Linear-accelerator-based sources will revolutionize ultrafast x-ray science due to their unprecedented brightness and short pulse duration. However, time-resolved studies at the resolution of the x-ray pulse duration are hampered by the inability to precisely synchronize an external laser to the accelerator. At the Sub-Picosecond Pulse Source at the Stanford Linear-Accelerator Center we solved this problem by measuring the arrival time of each high energy electron bunch with electro-optic sampling. This measurement indirectly determined the arrival time of each x-ray pulse relative to an external pump laser pulse with a time resolution of better than 60 fs rms.
Physical Review Letters, 2005
The melting dynamics of laser excited InSb have been studied with femtosecond x-ray diffraction. ... more The melting dynamics of laser excited InSb have been studied with femtosecond x-ray diffraction. These measurements observe the delayed onset of diffusive atomic motion, signaling the appearance of liquidlike dynamics. They also demonstrate that the root-mean-squared displacement in the [111] direction increases faster than in the [110] direction after the first 500 fs. This structural anisotropy indicates that the initially generated fluid differs significantly from the equilibrium liquid.
Physical Review E, 2011
Studies of materials under extreme conditions have relevance to a broad area of research, includi... more Studies of materials under extreme conditions have relevance to a broad area of research, including planetary physics, fusion research, materials science, and structural biology with x-ray lasers. We study such extreme conditions and experimentally probe the interaction between ultrashort soft x-ray pulses and solid targets (metals and their deuterides) at the FLASH free-electron laser where power densities exceeding 10 17 W/cm 2 were reached. Time-of-flight ion spectrometry and crater analysis were used to characterize the interaction. The results show the onset of saturation in the ablation process at power densities above 10 16 W/cm 2 . This effect can be linked to a transiently induced x-ray transparency in the solid by the femtosecond x-ray pulse at high power densities. The measured kinetic energies of protons and deuterons ejected from the surface reach several keV and concur with predictions from plasma-expansion models. Simulations of the interactions were performed with a nonlocal thermodynamic equilibrium code with radiation transfer. These calculations return critical depths similar to the observed crater depths and capture the transient surface transparency at higher power densities.