Single molecule imaging with longer x-ray laser pulses

During the last five years, serial femtosecond crystallography using x-ray laser pulses has developed into a powerful technique for determining the atomic structures of protein molecules from micrometer and sub-micrometer 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 was 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--10 fs, as once thought, but can succeed for pulses 50--100 fs in duration. We show 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 average structure separately to the diffraction from statistical fluctuations of the structure due to damage ("damage noise"). Our results suggest that sub-nanometer single molecule imaging with 30--50 fs pulses, like those produced at currently operating facilities, should not yet be ruled out. The theory we present 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.Comment: 23 pages; 5 figure

MolDStruct: modelling the dynamics and structure of matter exposed to ultrafast X-ray lasers with hybrid collisional-radiative/molecular dynamics

We describe a method to compute photon-matter interaction and atomic dynamics with X-ray lasers using a hybrid code based on classical molecular dynamics and collisional-radiative calculations. The forces between the atoms are dynamically computed based on changes to their electronic occupations and the free electron cloud created due to the irradiation of photons in the X-ray spectrum. The rapid transition from neutral solid matter to dense plasma phase allows the use of screened potentials, which reduces the number of non-bonded interactions required to compute. In combination with parallelisation through domain decomposition, large-scale molecular dynamics and ionisation induced by X-ray lasers can be followed. This method is applicable for large enough samples (solids, liquids, proteins, viruses, atomic clusters and crystals) that when exposed to an X-ray laser pulse turn into a plasma in the first few femtoseconds of the interaction. We show several examples of the applicability of the method and we quantify the sizes that the method is suitable for. For large systems, we investigate non-thermal heating and scattering of bulk water, which we compare to previous experiments. We simulate molecular dynamics of a protein crystal induced by an X-ray pump, X-ray probe scheme, and find good agreement of the damage dynamics with experiments. For single particle imaging, we simulate ultrafast dynamics of a methane cluster exposed to a femtosecond X-ray laser. In the context of coherent diffractive imaging we study the fragmentation as given by an X-ray pump X-ray probe setup to understand the evolution of radiation damage.Comment: 12 pages, 11 figures, 50 reference

Proton dynamics in molecular solvent clusters as an indicator for hydrogen bond network strength in confined geometries

Hydrogen bonding leads to the formation of strong, extended intermolecular networks in molecular liquids such as water. However, it is less well-known how robust the network is to environments in which surface formation or confinement effects become prominent, such as in clusters or droplets. Such systems provide a useful way to probe the robustness of the network, since the degree of confinement can be tuned by altering the cluster size, changing both the surface-to-volume ratio and the radius of curvature. To explore the formation of hydrogen bond networks in confined geometries, here we present O 1s Auger spectra of small and large clusters of water, methanol, and dimethyl ether, as well as their deuterated equivalents. The Auger spectra of the clusters and the corresponding macroscopic liquids are compared and evaluated for an isotope effect, which is due to proton dynamics within the lifetime of the core hole (proton-transfer-mediated charge-separation, PTM-CS), and can be linked to the formation of a hydrogen bond network in the system. An isotope effect is observed in water and methanol but not for dimethyl ether, which cannot donate a hydrogen bond at its oxygen site. The isotope effect, and therefore the strength of the hydrogen bond network, is more pronounced in water than in methanol. Its value depends on the average size of the cluster, indicating that confinement effects change proton dynamics in the core ionised excited state

Auger Electron Cascades in Water and Ice

Secondary electron cascades can induce significant ionisation in condensed matter due to electron-atom collisions. This is of interest in the context of diffraction and imaging using X-rays, where radiation damage is the main limiting factor for achieving high resolution data. Here we present new results on electron-induced damage on liquid water and ice, from the simulation of Auger electron cascades. We have compared our theoretical estimations to the available experimental data on elastic and inelastic electron-molecule interactions for water and found the theoretical results for elastic cross sections to be in very good agreement with experiment. As a result of the cascade we find that the average number of secondary electrons after 100 fs in ice is about 25, slightly higher than in water, where it is about 20. The difference in damage between ice and water is discussed in the context of sample handling for biomolecular systems.Comment: 19 pages, 8 figures. Includes slight corrections to the version submitted for publicatio

Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser

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

Procesos de organización política de las mujeres indígenas en el movimiento amplio de mujeres en Argentina. Consideraciones sobre el feminismo desde la perspectiva indígena

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

A Validation Study of the General Amber Force Field Applied to Energetic Molecular Crystals

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

Secondary Electron Cascade Dynamics in KI and CsI

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

Charge State Dependence of Amino Acid Propensity at Water Surface : Mechanisms Elucidated by Molecular Dynamics Simulations

Atmospheric aerosols contain a variety of compounds, among them free amino acids and salt ions. The pH of the aerosol droplets depends on their origin and environment. Consequently, compounds like free amino acids found in the droplets will be at different charge states, since these states to a great extent depend on the surrounding pH condition. In droplets of marine origin, amino acids are believed to drive salt ions to the water surface and a pH-dependent amino acid surface propensity will, therefore, indirectly affect many processes in atmospheric chemistry and physics such as for instance cloud condensation. To understand the surface propensity of glycine, valine, and phenylalanine at acidic, neutral, and basic pH, we used molecular dynamics (MD) simulations to investigate them at three different charge states in water. Their respective surface propensities were obtained by the means of a potential of mean force (PMF) in an umbrella sampling approach. Glycine was found to have no preference for the surface, while both valine and phenylalanine showed high propensities. Among the charge states of the surface-enriched ones, the cation, representing the amino acids at low pH, was found to have the highest affinity. Free energy decomposition revealed that the driving forces depend strongly on the nature of the amino acid and its charge state. In phenylalanine, the main factor was found to be a substantial entropy gain, likely related to the side chain, whereas in valine, hydrogen bonding to the functional groups leads to favorable energies and, in turn, affects the surface propensity. A significant gain in water-water enthalpy was seen for both valine and phenylalanine

Distinguishing between Similar Miniproteins with Single-Molecule Nanopore Sensing : A Computational Study

A nanopore is a tool in single-molecule sensing biotechnology that offers label-free identification with high throughput. Nanopores have been successfully applied to sequence DNA and show potential in the study of proteins. Nevertheless, the task remains challenging due to the large variability in size, charges, and folds of proteins. Miniproteins have a small number of residues, limited secondary structure, and stable tertiary structure, which can offer a systematic way to reduce complexity. In this computational work, we theoretically evaluated sensing two miniproteins found in the human body using a silicon nitride nanopore. We employed molecular dynamics methods to compute occupied-pore ionic current magnitudes and electronic structure calculations to obtain interaction strengths between pore wall and miniprotein. From the interaction strength, we derived dwell times using a mix of combinatorics and numerical solutions. This latter approach circumvents typical computational demands needed to simulate translocation events using molecular dynamics. We focused on two miniproteins potentially difficult to distinguish owing to their isotropic geometry, similar number of residues, and overall comparable structure. We found that the occupied-pore current magnitudes not to vary significantly, but their dwell times differ by 1 order of magnitude. Together, these results suggest a successful identification protocol for similar miniproteins