| 1. |
- Sinelnikova, Anna, et al.
(författare)
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Protein orientation in time-dependent electric fields : orientation before destruction
- 2021
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Ingår i: Biophysical Journal. - : Cell Press. - 0006-3495 .- 1542-0086. ; 120:17, s. 3709-3717
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Tidskriftsartikel (refereegranskat)abstract
- Proteins often have nonzero electric dipole moments, making them interact with external electric fields and offering a means for controlling their orientation. One application that is known to benefit from orientation control is single-particle imaging with x-ray free-electron lasers, in which diffraction is recorded from proteins in the gas phase to determine their structures. To this point, theoretical investigations into this phenomenon have assumed that the field experienced by the proteins is constant or a perfect step function, whereas any real-world pulse will be smooth. Here, we explore the possibility of orienting gas-phase proteins using time-dependent electric fields. We performed ab initio simulations to estimate the field strength required to break protein bonds, with 45 V/nm as a breaking point value. We then simulated ubiquitin in time-dependent electric fields using classical molecular dynamics. The minimal field strength required for orientation within 10 ns was on the order of 0.5 V/nm. Although high fields can be destructive for the structure, the structures in our simulations were preserved until orientation was achieved regardless of field strength, a principle we denote "orientation before destruction."
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| 2. |
- Sinelnikova, Anna, et al.
(författare)
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Reproducibility in the unfolding process of protein induced by an external electric field
- 2021
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Ingår i: Chemical Science. - : Royal Society of Chemistry. - 2041-6520 .- 2041-6539. ; 12:6, s. 2030-2038
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Tidskriftsartikel (refereegranskat)abstract
- The dynamics of proteins are crucial for their function. However, commonly used techniques for studying protein structures are limited in monitoring time-resolved dynamics at high resolution. Combining electric fields with existing techniques to study gas phase proteins, such as Single Particle Imaging using Free-electron Lasers and gas phase Small Angle X-ray Scattering, has the potential to open up a new era in time-resolved studies of gas phase protein dynamics. Using molecular dynamics simulations, we identify well-defined unfolding pathways of a protein, induced by experimentally achievable external electric fields. Our simulations show that strong electric fields in conjunction with short pulsed X-ray sources such as Free-electron Lasers can be a new path for imaging dynamics of gas-phase proteins at high spatial and temporal resolution.
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| 3. |
- Akiyama, Tomoko
(författare)
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Ionization Influence on the Dynamics of Simple Organic Molecules
- 2023
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This licentiate thesis is devoted to the investigation of how bonding in simple organic molecules are affected by X-ray beam irradiation. The investigation targets molecules with three carbons as their main-chain structure. The stability of the bonds under ionization are simulated using the SIESTA package. SIESTA is a simulation package that provides molecular dynamics simulations based on density functional theory within the Born-Oppenheimer approximation. The aim of this study is to understand statistically the damaging process and selectivity among different types of bond. As the first targets, 4 hydrocarbons are investigated. They are propane, propene, propyne and propadiene, which have different combinations of single, double and triple bonds as their main-chain structures. Depending on the combinations, the structures can be either symmetric around the central atom or not. The structure of the symmetric molecules propane and propadiene are stable until charge +3. In contrast, the asymmetric molecules propene and propyne, the main-chain bonds show a tendency towards a more similar bond-distance as the level of ionization increases. In addition, hydrogens relocation occurs in propene, leading to a symmetric structure. Secondly, the bond fluctuations are investigated among 4 types of three-carbon molecules which have functional parts. Alcohol and carboxyl groups molecules show the stable bond integrities at charging 0 to +2. On the other hand, the carbon-carbon bonds in molecules with acetyl and ketone groups are broken by ionization. Comparing the 8 kinds of bond breaking processes in these molecules, this statistical study gives an insight to organic molecules bonding systems.
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| 4. |
- Björnson, Kristofer, et al.
(författare)
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In Situ Pseudopotentials for Electronic Structure Theory
- 2021
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 125:27, s. 15103-15111
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Tidskriftsartikel (refereegranskat)abstract
- We present a general method of constructing in situ pseodopotentials from first-principles, all-electron, and full-potential electronic structure calculations of a solid. The method is applied to bcc Na, at low-temperature equilibrium volume. The essential steps of the method involve (i) calculating an all-electron Kohn-Sham eigenstate, (ii) replacing the oscillating part of the wave function (inside the muffin-tin spheres) of this state, with a smooth function, (iii) representing the smooth wave function in a Fourier series, and (iv) inverting the Kohn-Sham equation, to extract the pseudopotential that produces the state generated in steps i-iii. It is shown that an in situ pseudopotential can reproduce an all-electron full-potential eigenvalue up to the sixth significant digit. A comparison of the all-electron theory, in situ pseudopotential theory, and the standard nonlocal pseudopotential theory demonstrates good agreement, e.g., in the energy dispersion of the 3s band state of bcc Na.
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| 5. |
- Caleman, Carl, et al.
(författare)
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A Perspective on Molecular Structure and Bond-Breaking in Radiation Damage in Serial Femtosecond Crystallography
- 2020
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Ingår i: Crystals. - : MDPI. - 2073-4352. ; 10:7
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Tidskriftsartikel (refereegranskat)abstract
- X-ray free-electron lasers (XFELs) have a unique capability for time-resolved studies of protein dynamics and conformational changes on femto- and pico-second time scales. The extreme intensity of X-ray pulses can potentially cause significant modifications to the sample structure during exposure. Successful time-resolved XFEL crystallography depends on the unambiguous interpretation of the protein dynamics of interest from the effects of radiation damage. Proteins containing relatively heavy elements, such as sulfur or metals, have a higher risk for radiation damage. In metaloenzymes, for example, the dynamics of interest usually occur at the metal centers, which are also hotspots for damage due to the higher atomic number of the elements they contain. An ongoing challenge with such local damage is to understand the residual bonding in these locally ionized systems and bond-breaking dynamics. Here, we present a perspective on radiation damage in XFEL experiments with a particular focus on the impacts for time-resolved protein crystallography. We discuss recent experimental and modelling results of bond-breaking and ion motion at disulfide bonding sites in protein crystals.
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| 6. |
- Droulias, S. A., et al.
(författare)
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Influence of deuterium-induced volume changes on optical transmission in Fe/V (001) and Cr/V (001) superlattices
- 2022
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Ingår i: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 105:19
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Tidskriftsartikel (refereegranskat)abstract
- The deuterium-induced changes of the optical transmission in Fe/V (001) and Cr/V (001) superlattices are found experimentally to be dominated by the volume changes of the vanadium layers and thus indirectly linked to concentration. The deuterium-induced expansion is 67% larger in Cr/V 2/14 monolayers (ML) as compared to Fe/V 2/14 ML. This large difference can be explained by a difference in the site of deuterium from tetrahedral in Fe/V to octahedral in Cr/V. First-principles calculations based on this assumption give quantitative agreement with both the measured optical transmission and the deuterium-induced expansion coefficient. Placing hydrogen in the middle of the vanadium layers results in total energies at 0 K that favor tetrahedral occupancy at low concentrations, although the energy difference is of the order of the thermal energy available in the experiments. Hence small changes in strain, defect concentration, and/or vibrational spectrum of the superlattices may tip the balance to octahedral occupancy at low concentrations. Given this link to concentration and the linear scaling, optical transmission can, therefore, be used in a straightforward way to obtain pressure-composition isotherms also in thin metal films that do not undergo metal-insulator transitions upon hydrogenation.
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| 7. |
- Elhanoty, Mohamed F., et al.
(författare)
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Different fingerprints for the OISTR mechanism in the magnetic alloys experiments
- 2022
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Ingår i: ADVANCES IN ULTRAFAST CONDENSED PHASE PHYSICS III. - : SPIE - The International Society for Optics and Photonics. - 9781510651418 - 9781510651401
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Konferensbidrag (refereegranskat)abstract
- The interplay between various degrees of freedom in laser induced ultrafast magnetization dynamics (LIUMD) of magnetic alloys is intricate due to the competition between different mechanisms and processes. In this work, we resolve the element specific magnetization dynamics of FePd alloy and further elucidate the dependency of the OISTR mechanism on the laser pulse parameters using ultrashort, short and relatively longer pulse duration with weak and strong fluence. Remarkably, our results illustrate potential discrepancies in experiments measuring the optical inter site spin transfer (OISTR) effect in magnetic alloys.
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| 8. |
- Elhanoty, Mohamed F., et al.
(författare)
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Element-selective ultrafast magnetization dynamics of hybrid Stoner-Heisenberg magnets
- 2022
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Ingår i: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 105:10
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Tidskriftsartikel (refereegranskat)abstract
- Stoner and Heisenberg excitations in magnetic materials are inherently different. The first involves an effective reduction of the exchange splitting, whereas the second comprises excitation of spin waves. In this work, we test the impact of these two excitations in the hybrid Stoner-Heisenberg system of FePd. We present a microscopic picture of ultrafast demagnetization dynamics in this alloy, which represents both components of strong local exchange splitting in Fe and induced polarization in Pd. We identify the spin-orbit coupling (SOC) and the optical intersite spin transfer (OISTR) as the two dominant factors for demagnetization at ultrashort timescales. Remarkably, the drastic difference in the origin of the magnetic moment of the Fe and Pd species is not deciding the initial magnetization dynamics in this alloy. By tuning the external laser pulse, the extrinsic OISTR can be manipulated for site-selective demagnetization on femtosecond timescales providing the fastest way for optical and selective control of the magnetization dynamics in alloys. Saliently, our results signify why various experiments demonstrating OISTR might obtain conflicting results.
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| 9. |
- Eliah Dawod, Ibrahim, et al.
(författare)
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Imaging of femtosecond bond breaking and charge dynamics in ultracharged peptides
- 2022
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 24:3, s. 1532-1543
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Tidskriftsartikel (refereegranskat)abstract
- X-ray free-electrons lasers have revolutionized the method of imaging biological macromolecules such as proteins, viruses and cells by opening the door to structural determination of both single particles and crystals at room temperature. By utilizing high intensity X-ray pulses on femtosecond timescales, the effects of radiation damage can be reduced. Achieving high resolution structures will likely require knowledge of how radiation damage affects the structure on an atomic scale, since the experimentally obtained electron densities will be reconstructed in the presence of radiation damage. Detailed understanding of the expected damage scenarios provides further information, in addition to guiding possible corrections that may need to be made to obtain a damage free reconstruction. In this work, we have quantified the effects of ionizing photon-matter interactions using first principles molecular dynamics. We utilize density functional theory to calculate bond breaking and charge dynamics in three ultracharged molecules and two different structural conformations that are important to the structural integrity of biological macromolecules, comparing to our previous studies on amino acids. The effects of the ultracharged states and subsequent bond breaking in real space are studied in reciprocal space using coherent diffractive imaging of an ensemble of aligned biomolecules in the gas phase.
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| 10. |
- Esteban-Puyuelo, Raquel, et al.
(författare)
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Tailoring the opto-electronic response of graphene nanoflakes by size and shape optimization
- 2020
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : ROYAL SOC CHEMISTRY. - 1463-9076 .- 1463-9084. ; 22:15, s. 8212-8218
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Tidskriftsartikel (refereegranskat)abstract
- The long spin-diffusion length, spin-lifetime and excellent optical absorption coefficient of graphene provide an excellent platform for building opto-electronic devices and spin-based logic in a nanometer regime. In this study, by using density functional theory and its time-dependent version, we provide a detailed analysis of how the size and shape of graphene nanoflakes can be used to alter their magnetic structures and optical properties. As the edges of zigzag graphene nanoribbons are known to align anti-ferromagnetically and armchair nanoribbons are typically non-magnetic, a combination of both in a nanoflake geometry can be used to optimize the ground-state magnetic structure and tailor the exchange coupling decisive for ferro- or anti-ferromagnetic edge magnetism, thereby offering the possibility to optimize the external fields needed to switch magnetic ordering. Most importantly, we show that the magnetic state alters the optical response of the flake leading to the possibility of opto-spintronic applications.
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