uu.seUppsala University Publications
Change search
Link to record
Permanent link

Direct link
BETA
Caleman, C
Alternative names
Publications (10 of 63) Show all publications
Jönsson, O., Östlin, C., Scott, H. A., Chapman, H., Aplin, S. J., Timneanu, N. & Caleman, C. (2018). FreeDam – A Webtool for Free-Electron Laser-Induced Damage in Femtosecond X-ray Crystallography. High Energy Density Physics, 26, 93-98
Open this publication in new window or tab >>FreeDam – A Webtool for Free-Electron Laser-Induced Damage in Femtosecond X-ray Crystallography
Show others...
2018 (English)In: High Energy Density Physics, ISSN 1574-1818, Vol. 26, p. 93-98Article in journal (Refereed) Published
Abstract [en]

Over the last decade X-ray free-electron laser (XFEL) sources have been made available to the scientific community. One of the most successful uses of these new machines has been protein crystallography. When samples are exposed to the intense short X-ray pulses provided by the XFELs, the sample quickly becomes highly ionized and the atomic structure is affected. Here we present a webtool dubbed FreeDam based on non-thermal plasma simulations, for estimation of radiation damage in free-electron laser experiments in terms of ionization, temperatures and atomic displacements. The aim is to make this tool easily accessible to scientists who are planning and performing experiments at XFELs.

Keywords
FreeDam, non-local thermodynamic equilibrium, x-ray free-electron laser, radiation damage, serial femtosecond x-ray crystallography, Cretin, simulation, database
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-329499 (URN)
Available from: 2017-09-17 Created: 2017-09-17 Last updated: 2018-06-26
Östlin, C., Timneanu, N., Jönsson, H. O., Ekeberg, T., Martin, A. V. & Caleman, C. (2018). Reproducibility of Single Protein Explosions Induced by X-ray Lasers. Physical Chemistry, Chemical Physics - PCCP, 20(18), 12381-12389
Open this publication in new window or tab >>Reproducibility of Single Protein Explosions Induced by X-ray Lasers
Show others...
2018 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 18, p. 12381-12389Article in journal (Refereed) Published
Abstract [en]

Single particle imaging (SPI) using X-ray pulses has become increasingly attainable with the advent of high-intensity free electron lasers. Eliminating the need for crystallized samples enables structural studies of molecules previously inaccessible by conventional crystallography. While this emerging technique already demonstrates substantial promise, some obstacles need to be overcome before SPI can reach its full potential. One such problem is determining the spatial orientation of the sample at the time of X-ray interaction. Existing solutions rely on diffraction data and are computationally demanding and sensitive to noise. In this in silico study, we explore the possibility of aiding these methods by mapping the ion distribution as the sample undergoes a Coulomb explosion following the intense ionization. By detecting the ions ejected from the fragmented sample, the orientation of the original sample should be possible to determine. Knowledge of the orientation has been shown earlier to be of substantial advantage in the reconstruction of the original structure. 150 explosions of each of twelve separate systems – four polypeptides with different amounts of surface bound water – were simulated with molecular dynamics (MD) and the average angular distribution of carbon and sulfur ions was investigated independently. The results show that the explosion maps are reproducible in both cases, supporting the idea that orientation information is preserved. Additional water seems to restrict the carbon ion trajectories further through a shielding mechanism, making the maps more distinct. For sulfurs, water has no significant impact on the trajectories, likely due to their higher mass and greater ionization cross section, indicating that they could be of particular interest. Based on these findings, we conclude that explosion data can aid spatial orientation in SPI experiments and could substantially improve the capabilities of the novel technique.

Keywords
XFEL, Single-particle imaging, Coulomb explosion, ultrafast, GROMACS, simulation.
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-329340 (URN)10.1039/C7CP07267H (DOI)000431825300006 ()
Funder
Swedish Research Council, 2013-3940Swedish Foundation for Strategic Research Carl Tryggers foundation
Available from: 2017-09-13 Created: 2017-09-13 Last updated: 2018-08-16Bibliographically approved
Beyerlein, K., Jönsson, O., Alonso-Mori, R., Aquila, A., Bajt, S., Barty, A., . . . Caleman, C. (2018). Ultrafast non-thermal heating of water initiated by an X-ray laser. Proceedings of the National Academy of Sciences of the United States of America, 115(22), 5652-5657
Open this publication in new window or tab >>Ultrafast non-thermal heating of water initiated by an X-ray laser
Show others...
2018 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 22, p. 5652-5657Article in journal (Refereed) Published
Abstract [en]

X-ray Free-Electron Lasers have opened the door to a new era in structural biology, enabling imaging of biomolecules and dynamics that were impossible to access with conventional methods. A vast majority of imaging experiments, including Serial Femtosecond Crystallography, use a liquid jet to deliver the sample into the interaction region. We have observed structural changes in the carrying water during X-ray exposure, showing how it transforms from the liquid phase to a plasma. This ultrafast phase transition observed in water provides evidence that any biological structure exposed to these X-ray pulses is destroyed during the X-ray exposure.The bright ultrafast pulses of X-ray Free-Electron Lasers allow investigation into the structure of matter under extreme conditions. We have used single pulses to ionize and probe water as it undergoes a phase transition from liquid to plasma. We report changes in the structure of liquid water on a femtosecond time scale when irradiated by single 6.86 keV X-ray pulses of more than 106 J/cm2. These observations are supported by simulations based on molecular dynamics and plasma dynamics of a water system that is rapidly ionized and driven out of equilibrium. This exotic ionic and disordered state with the density of a liquid is suggested to be structurally different from a neutral thermally disordered state.

National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-294554 (URN)10.1073/pnas.1711220115 (DOI)000433283700046 ()29760050 (PubMedID)
Funder
Swedish Foundation for Strategic Research Swedish Research Council, 2013-3940The Swedish Foundation for International Cooperation in Research and Higher Education (STINT)Swedish National Infrastructure for Computing (SNIC)Carl Tryggers foundation
Note

De två första författarna delar förstaförfattarskapet

Available from: 2016-05-24 Created: 2016-05-24 Last updated: 2018-08-20Bibliographically approved
Marklund, E., Ekeberg, T., Moog, M., Benesch, J. L. P. & Caleman, C. (2017). Controlling Protein Orientation in Vacuum Using Electric Fields. Journal of Physical Chemistry Letters, 8(18), 4540-4544
Open this publication in new window or tab >>Controlling Protein Orientation in Vacuum Using Electric Fields
Show others...
2017 (English)In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 8, no 18, p. 4540-4544Article in journal (Refereed) Published
Abstract [en]

Single-particle imaging using X-ray free-electron lasers is an emerging technique that could provide high-resolution structures of macromolecules in the gas phase. One of the largest difficulties in realizing this goal is the unknown orientation of the individual sample molecules at the time of exposure. Preorientation of the molecules has been identified as a possible solution to this problem. Using molecular dynamics simulations, we identify a range of electric field strengths where proteins become oriented without losing their structure. For a number of experimentally relevant cases we show that structure determination is possible only when orientation information is included in the orientation-recovery process. We conclude that nondestructive field orientation of intact proteins is feasible and that it enables a range of new structural investigations with single particle imaging.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2017
National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-336478 (URN)10.1021/acs.jpclett.7b02005 (DOI)000411781900033 ()28862456 (PubMedID)
Available from: 2017-12-20 Created: 2017-12-20 Last updated: 2017-12-20Bibliographically approved
Jönsson, H. O., Caleman, C., Andreasson, J. & Timneanu, N. (2017). Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission. IUCrJ, 4(6), 778-784
Open this publication in new window or tab >>Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission
2017 (English)In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 4, no 6, p. 778-784Article in journal (Refereed) Published
Abstract [en]

Serial femtosecond crystallography is an emerging and promising method for determining protein structures, making use of the ultrafast and bright X-ray pulses from X-ray free-electron lasers. The upcoming X-ray laser sources will produce well above 1000pulses per second and will pose a new challenge: how to quickly determine successful crystal hits and avoid a high-rate data deluge. Proposed here is a hit-finding scheme based on detecting photons from plasma emission after the sample has been intercepted by the X-ray laser. Plasma emission spectra are simulated for systems exposed to high-intensity femtosecond pulses, for both protein crystals and the liquid carrier systems that are used for sample delivery. The thermal radiation from the glowing plasma gives a strong background in the XUV region that depends on the intensity of the pulse, around the emission lines from light elements (carbon, nitrogen, oxygen). Sample hits can be reliably distinguished from the carrier liquid based on the characteristic emission lines from heavier elements present only in the sample, such as sulfur. For buffer systems with sulfur present, selenomethionine substitution is suggested, where the selenium emission lines could be used both as an indication of a hit and as an aid in phasing and structural reconstruction of the protein.

Keywords
hit detection, plasma emission spectra, serial femtosecond crystallography, protein structure
National Category
Biophysics
Research subject
Physics with specialization in Biophysics
Identifiers
urn:nbn:se:uu:diva-331934 (URN)10.1107/S2052252517014154 (DOI)000414266200011 ()29123680 (PubMedID)
Funder
Swedish Research CouncilSwedish National Infrastructure for Computing (SNIC), 2016-7-61Swedish Foundation for Strategic Research The Swedish Foundation for International Cooperation in Research and Higher Education (STINT)ÅForsk (Ångpanneföreningen's Foundation for Research and Development)
Available from: 2017-10-25 Created: 2017-10-25 Last updated: 2018-02-05Bibliographically approved
Bergh, M. & Caleman, C. (2016). A Validation Study of the General Amber Force Field Applied to Energetic Molecular Crystals. Journal of Energetic Materials, 34(1), 62-75
Open this publication in new window or tab >>A Validation Study of the General Amber Force Field Applied to Energetic Molecular Crystals
2016 (English)In: Journal of Energetic Materials, ISSN 0737-0652, E-ISSN 1545-8822, Vol. 34, no 1, p. 62-75Article in journal (Refereed) Published
Abstract [en]

Molecula dynamics is a well-established tool to computationally study molecules. However, to reach predictive capability at the level required for applied research and design, extensive validation of the available force fields is pertinent. Here we present a study of density, isothermal compressibility and coefficients of thermal expansion of four energetic materials (FOX-7, RDX, CL-20 and HMX) based on molecular dynamics simulations with the General Amber Force Field (GAFF), and compare the results to experimental measurements from the literature. Furthermore, we quantify the accuracy of the calculated properties through hydrocode simulation of a typical impact scenario. We find that molecular dynamics simulations with generic and computationally efficient force fields may be used to understand and estimate important physical properties of nitramine-like energetic materials.

Keywords
energetic materials, GAFF, General Amber Force Field, molecular dynamics
National Category
Materials Engineering Materials Chemistry
Identifiers
urn:nbn:se:uu:diva-268756 (URN)10.1080/07370652.2014.998797 (DOI)000364779700006 ()
Funder
Swedish Research Council FormasSwedish Research Council
Available from: 2015-12-15 Created: 2015-12-09 Last updated: 2017-12-01Bibliographically approved
Galli, L., Son, S.-K. -., Klinge, M., Bajt, S., Barty, A., Bean, R., . . . Chapman, H. N. (2015). Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse. STRUCTURAL DYNAMICS, 2(4), Article ID 041703.
Open this publication in new window or tab >>Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse
Show others...
2015 (English)In: STRUCTURAL DYNAMICS, ISSN 2329-7778, Vol. 2, no 4, article id 041703Article in journal (Refereed) Published
Abstract [en]

Current hard X-ray free-electron laser (XFEL) sources can deliver doses to biological macromolecules well exceeding 1 GGy, in timescales of a few tens of femtoseconds. During the pulse, photoionization can reach the point of saturation in which certain atomic species in the sample lose most of their electrons. This electronic radiation damage causes the atomic scattering factors to change, affecting, in particular, the heavy atoms, due to their higher photoabsorption cross sections. Here, it is shown that experimental serial femtosecond crystallography data collected with an extremely bright XFEL source exhibit a reduction of the effective scattering power of the sulfur atoms in a native protein. Quantitative methods are developed to retrieve information on the effective ionization of the damaged atomic species from experimental data, and the implications of utilizing new phasing methods which can take advantage of this localized radiation damage are discussed.

National Category
Chemical Sciences Physical Sciences
Identifiers
urn:nbn:se:uu:diva-263539 (URN)10.1063/1.4919398 (DOI)000360649200005 ()
Funder
Swedish Research CouncilSwedish Foundation for Strategic Research
Available from: 2015-10-05 Created: 2015-10-02 Last updated: 2015-10-05Bibliographically approved
Nass, K., Foucar, L., Barends, T. R. M., Hartmann, E., Botha, S., Shoeman, R. L., . . . Schlichting, I. (2015). Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams. Journal of Synchrotron Radiation, 22(2), 225-238
Open this publication in new window or tab >>Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams
Show others...
2015 (English)In: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 22, no 2, p. 225-238Article in journal (Refereed) Published
Abstract [en]

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 influence of the molecular bonding and geometry on the atomic displacement dynamics following initial photoionization. The experiments are complemented by plasma code calculations.

Keywords
free-electron laser, SFX, serial femtosecond crystallography, radiation damage, protein crystallography, metalloprotein
National Category
Structural Biology
Identifiers
urn:nbn:se:uu:diva-245011 (URN)10.1107/S1600577515002349 (DOI)000350641100004 ()
Available from: 2015-02-23 Created: 2015-02-23 Last updated: 2017-12-04Bibliographically approved
Jönsson, H. O., Timneanu, N., Östlin, C., Scott, H. A. & Caleman, C. (2015). Simulations of Radiation Damage as a Function of the Temporal Pulse Profile in Femtosecond X-ray Protein Crystallography. Journal of Synchrotron Radiation, 22(2), 256-266
Open this publication in new window or tab >>Simulations of Radiation Damage as a Function of the Temporal Pulse Profile in Femtosecond X-ray Protein Crystallography
Show others...
2015 (English)In: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 22, no 2, p. 256-266Article in journal (Refereed) Published
Abstract [en]

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$\sp 4$ to 10$\sp 7$Jcm$\sp $-$2$ with photon energies from 2 to 12keV, up to 100fs long. Radiation damage in the form of sample heating that will lead to a loss of crystalline periodicity and changes in scattering factor due to electronic reconfigurations of ionized atoms are considered here. The simulations show differences in the dynamics of the radiation damage processes for different temporal pulse profiles and intensities, where ionization or atomic motion could be predominant. The different dynamics influence the recorded diffracted signal in any given resolution and will affect the subsequent structure determination.

Keywords
X-ray free-electron laser, serial femtosecond crystallography, radiation damage, plasma simulations
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-245210 (URN)10.1107/S1600577515002878 (DOI)000350641100007 ()
Available from: 2015-02-25 Created: 2015-02-25 Last updated: 2018-06-26
Martin, A. V., Corso, J. K., Caleman, C., Timneanu, N. & Quiney, H. M. (2015). Single-molecule imaging with longer X-ray laser pulses. IUCrJ, 2, 661-674
Open this publication in new window or tab >>Single-molecule imaging with longer X-ray laser pulses
Show others...
2015 (English)In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 2, p. 661-674Article in journal (Refereed) Published
Abstract [en]

During the last five years, serial femtosecond crystallography using X-ray laser pulses has been developed into a powerful technique for determining the atomic structures of protein molecules from micrometre- and sub-micrometre-sized crystals. One of the key reasons for this success is the ‘self-gating’ pulse effect, whereby the X-ray laser pulses do not need to outrun all radiation damage processes. Instead, X-ray-induced 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 5–10fs, but can succeed for pulses 50–100fs in duration. It is shown here that a similar gating effect applies to single-molecule 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 sub-nanometre single-molecule imaging with 30–50fs 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 single-particle diffraction, which is needed to test damage models and to identify optimal imaging conditions.

Keywords
coherent diffractive imaging, single-molecule imaging, radiation damage, ‘self-gated’ pulses, XFELs
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-267778 (URN)10.1107/S2052252515016887 (DOI)000364415900011 ()
Funder
Swedish Foundation for Strategic Research Swedish Research Council
Available from: 2015-11-26 Created: 2015-11-26 Last updated: 2017-12-01Bibliographically approved
Organisations

Search in DiVA

Show all publications