arXiv subjects

Andrew V. Martin

Publications and source records attributed to Andrew V. Martin.

9 recordsLinked to original sources

arXiv2025

Heavy-element damage seeding in proteins under XFEL illumination

Serial femtosecond X-ray crystallography (SFX) captures the structure and dynamics of biological macromolecules at high spatial and temporal resolutions. The ultrashort pulse produced by an X-ray free electron laser (XFEL) 'outruns' much of the radiation damage that impairs conventional crystallography. However, the rapid onset of 'electronic damage' due to ionization limits this benefit. Here, we distinguish the influence of different atomic species on the ionization of protein crystals by employing a plasma code that tracks the unbound electrons as a continuous energy distribution. The simulations show that trace quantities of heavy atoms (Z > 10) contribute a substantial proportion of global radiation damage by rapidly seeding electron ionization cascades. In a typical protein crystal, sulfur atoms and solvated salts induce a substantial fraction of light-atom ionization. In further modeling of various targets, global ionization peaks at photon energies roughly 2 keV above inner-shell absorption edges, as sub-2 keV photoelectrons ejected from these shells initiate ionization cascades that are briefer than the XFEL pulse. These results indicate that relatively small quantities of heavy elements can substantially affect global radiation damage in XFEL experiments.

physics.plasm-ph↗

arXiv2023

The pypadf package: computing the pair-angle distribution function from fluctuation scattering data

The pair-angle distribution function (PADF) is a three- and four-atom correlation function that can characterise the local angular structure of disordered materials, particles or nanocrystalline materials. The PADF can be measured by x-ray or electron fluctuation diffraction experiments, which can be collected by scanning a small beam across a structurally disordered sample or flowing a sample across the beam path. It is a natural generalisation of the established pair-distribution methods, which do not provide angular information. This software package provides tools to calculate the PADF from from fluctuation diffraction data. The package includes tools for calculating the intensity correlation function, which is a necessary step in the PADF calculation and also the basis for other fluctuation scattering techniques.

cond-mat.dis-nn↗

arXiv2021

Numerical investigation of the logarithmic Schrödinger model of quantum decoherence

A logarithmic Schrödinger equation with time-dependent coupling to the non-linearity is presented as a model of collisional decoherence of the wavefunction of a quantum particle in position-space. The particular mathematical form of the logarithmic Schrödinger equation has been shown to follow from conditional wave theory, but the validity of the logarithmic Schrödinger equation has not yet been investigated numerically for general initial conditions. Using an operator-splitting approach, we solve the non-linear equation of motion for the wavefunction numerically and compare it it to the solution of the standard Joos-Zeh master equation for the density matrix. We find good agreement for the time-dependent behaviour of the ensemble widths between the two approaches, but note curious `zero-pinning' behaviour of the logarithmic Schrödinger equation, whereby the zeros of the wavefunction are not erased by continued propagation. By examining the derivation of the logarithmic Schrödinger equation from conditional wave theory, we indicate possible avenues of resolution to this zero-pinning problem.

quant-ph↗

arXiv2021

Conditional wave theory of environmental interactions with a quantum particle

We present an alternative formulation of quantum decoherence theory using conditional wave theory (CWT), which was originally developed in molecular physics (also known as exact factorisation methods). We formulate a CWT of a classic model of collisional decoherence of a free particle with environmental particles treated in a long-wavelength limit. In general, the CWT equation of motion for the particle is non-linear, where the non-linearity enters via the CWT gauge fields. For Gaussian wave packets the analytic solutions of the CWT equations are in exact agreement with those from the density matrix formalism. We show that CWT gauge terms that determine the dynamics of the particle's marginal wave function are related to a Taylor series expansion of the particle's reduced density matrix. Approximate solutions to these equations lead to a linear-time approximation that reproduces the ensemble width in the limits of both short and long times, in addition to reproducing the long-term behaviour of the coherence length. With this approximation, the non-linear equation of motion for the particle's marginal wave function can be written in the form of the logarithmic Schrödinger equation. The CWT formalism may lead to computationally efficient calculations of quantum decoherence, since it involves working with wave-function level terms instead of evolving a density matrix via a master equation.

quant-ph↗

arXiv2016

Expansion-maximization-compression algorithm with spherical harmonics for single particle imaging with X-ray lasers

In 3D single particle imaging with X-ray free-electron lasers, particle orientation is not recorded during measurement but is instead recovered as a necessary step in the reconstruction of a 3D image from the diffraction data. Here we use harmonic analysis on the sphere to cleanly separate the angu- lar and radial degrees of freedom of this problem, providing new opportunities to efficiently use data and computational resources. We develop the Expansion-Maximization-Compression algorithm into a shell-by-shell approach and implement an angular bandwidth limit that can be gradually raised during the reconstruction. We study the minimum number of patterns and minimum rotation sampling required for a desired angular and radial resolution. These extensions provide new av- enues to improve computational efficiency and speed of convergence, which are critically important considering the very large datasets expected from experiment.

physics.data-an↗

arXiv2015

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.

physics.optics↗

arXiv2014

Toward atomic resolution diffractive imaging of isolated molecules with x-ray free-electron lasers

We give a detailed account of the theoretical analysis and the experimental results of an x-ray-diffraction experiment on quantum-state selected and strongly laser-aligned gas-phase ensembles of the prototypical large asymmetric rotor molecule 2,5-diiodobenzonitrile, performed at the Linac Coherent Light Source [Phys. Rev. Lett. 112, 083002 (2014)]. This experiment is the first step toward coherent diffractive imaging of structures and structural dynamics of isolated molecules at atomic resolution, i. e., picometers and femtoseconds, using x-ray free-electron lasers.

physics.atom-ph↗

arXiv2014

X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser

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.

physics.atom-ph↗

arXiv2012

Femtosecond X-ray Laser induced transient electronic phase change observed in fullerene C60

X-ray Free-Electron Lasers (XFELs) deliver X-ray pulses with a coherent flux that is approximately eight orders of magnitude greater than that available from a modern third generation synchrotron source. The power density in an XFEL pulse may be so high that it can modify the electronic properties of a sample on a femtosecond timescale. Exploration of the interaction of intense coherent X-ray pulses and matter is of both intrinsic scientific interest, and of critical importance to the interpretation of experiments that probe the structures of materials using high-brightness femtosecond XFEL pulses. In this letter, we report observations of the diffraction of an extremely intense 32 fs nanofocused X-ray pulses by a powder sample of crystalline C60. We find that the diffraction pattern at the highest available incident power exhibits significant structural signatures that are absent in data obtained at both third-generation synchrotron sources or from XFEL sources operating at low output power. These signatures are consistent with a highly ordered structure that does not correspond with any previously known phase of crystalline C60. We argue that these data indicate the formation of a transient phase that is formed by a dynamic electronic distortion induced by inner-shell ionisation of at least one carbon atom in each C60 molecule.

cond-mat.mtrl-sci↗