arXiv subjects

Jose A. Rodriguez

Publications and source records attributed to Jose A. Rodriguez.

10 recordsLinked to original sources

arXiv2024

Mapping electron beam-induced radiolytic damage in molecular crystals

Every electron crystallography experiment is fundamentally limited by radiation damage. Nevertheless, little is known about the onset and progression of radiolysis in beam-sensitive molecular crystals. Here we apply ambient-temperature scanning nanobeam electron diffraction to record simultaneous dual-space snapshots of organic and organometallic nanocrystals at sequential stages of beam-induced radiolytic decay. We show that the underlying mosaic of coherently diffracting zones (CDZs) continuously undergoes spatial reorientation as a function of accumulating electron exposure, causing the intensities of many Bragg reflections to fade nonmonotonically. Furthermore, we demonstrate that repeated irradiation at a single probe position leads to the concentric propagation of delocalized radiolytic damage well beyond the initial point of impact. These results sharpen our understanding of molecular crystals as conglomerates of CDZs whose complex lattice structure deteriorates through a series of dynamic internal changes during exposure to ionizing radiation.

cond-mat.mtrl-sci↗

arXiv2022

Parsimonious Argument Annotations for Hate Speech Counter-narratives

We present an enrichment of the Hateval corpus of hate speech tweets (Basile et. al 2019) aimed to facilitate automated counter-narrative generation. Comparably to previous work (Chung et. al. 2019), manually written counter-narratives are associated to tweets. However, this information alone seems insufficient to obtain satisfactory language models for counter-narrative generation. That is why we have also annotated tweets with argumentative information based on Wagemanns (2016), that we believe can help in building convincing and effective counter-narratives for hate speech against particular groups. We discuss adequacies and difficulties of this annotation process and present several baselines for automatic detection of the annotated elements. Preliminary results show that automatic annotators perform close to human annotators to detect some aspects of argumentation, while others only reach low or moderate level of inter-annotator agreement.

cs.CL↗

arXiv2021

Symmetry of magnetic correlations in spin-triplet superconductor UTe2

The temperature dependence of the low-energy magnetic excitations in the spin-triplet superconductor UTe$_2$ was measured via inelastic neutron scattering in the normal and superconducting states. The imaginary part of the dynamic susceptibility follows the behavior of interband correlations in a hybridized Kondo lattice with an appropriate characteristic energy. These excitations are a lower-dimensional analogue of phenomena observed in other Kondo lattice materials, such that their presence is not necessarily due to dominance of ferromagnetic or antiferromagnetic correlations. The onset of superconductivity alters the magnetic excitations noticeably on the same energy scales, suggesting that these changes originate from additional electronic structure modification.

cond-mat.str-el↗

arXiv2020

Incommensurate magnetism mediated by Weyl fermions in NdAlSi

Emergent relativistic quasiparticles in Weyl semimetals are the source of exotic electronic properties such as surface Fermi arcs, the anomalous Hall effect, and negative magnetoresistance, all observed in real materials. Whereas these phenomena highlight the effect of Weyl fermions on the electronic transport properties, less is known about what collective phenomena they may support. Here, we report a new Weyl semimetal, NdAlSi that offers an example. Using neutron diffraction, we report a long-wavelength magnetic order in NdAlSi whose periodicity is linked to the nesting vector between two topologically non-trivial Fermi pockets, which we characterize using density functional theory and quantum oscillation measurements. Our work provides a rare example of Weyl fermions driving collective magnetism.

cond-mat.str-el↗

arXiv2018

Lattice nano-ripples revealed in peptide microcrystals by scanning electron nanodiffraction

Changes in lattice structure across sub-regions of protein crystals are challenging to assess when relying on whole crystal measurements. Because of this difficulty, macromolecular structure determination from protein micro and nano crystals requires assumptions of bulk crystallinity and domain block substructure. To evaluate the fidelity of these assumptions in protein nanocrystals we map lattice structure across micron size areas of cryogenically preserved three-dimensional peptide crystals using a nano-focused electron beam. This approach produces diffraction from as few as 1,500 molecules in a crystal, is sensitive to crystal thickness and three-dimensional lattice orientation. Real-space maps reconstructed from unsupervised classification of diffraction patterns across a crystal reveal regions of crystal order/disorder and three-dimensional lattice reorientation on a 20nm scale. The lattice nano-ripples observed in micron-sized macromolecular crystals provide a direct view of their plasticity. Knowledge of these features is a first step to understanding crystalline macromolecular self-assembly and improving the determination of structures from protein nano and microcrystals from single or serial crystal diffraction.

cond-mat.soft↗

arXiv2017

GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging

Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. In many scientific applications, however, the number of projections that can be measured is limited due to geometric constraints, tolerable radiation dose and/or acquisition speed. Thus it becomes an important problem to obtain the best-possible reconstruction from a limited number of projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE). By iterating between real and reciprocal space, GENFIRE searches for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques by numerical simulations, and by experimentally by reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. Equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines.

physics.comp-ph↗

arXiv2017

Single-Shot 3D Diffractive Imaging of Core-Shell Nanoparticles with Elemental Specificity

We report 3D coherent diffractive imaging of Au/Pd core-shell nanoparticles with 6 nm resolution on 5-6 femtosecond timescales. We measured single-shot diffraction patterns of core-shell nanoparticles using very intense and short x-ray free electron laser pulses. By taking advantage of the curvature of the Ewald sphere and the symmetry of the nanoparticle, we reconstructed the 3D electron density of 34 core-shell structures from single-shot diffraction patterns. We determined the size of the Au core and the thickness of the Pd shell to be 65.0 +/- 1.0 nm and 4.0 +/- 0.5 nm, respectively, and identified the 3D elemental distribution inside the nanoparticles with an accuracy better than 2%. We anticipate this method can be used for quantitative 3D imaging of symmetrical nanostructures and virus particles.

physics.ins-det↗

arXiv2014

Three-dimensional coherent X-ray diffraction imaging of a whole, frozen-hydrated cell

A structural understanding of whole cells in three dimensions at high spatial resolution remains a significant challenge and, in the case of X-rays, has been limited by radiation damage. By alleviating this limitation, cryogenic coherent diffraction imaging (cryo-CDI) could bridge the important resolution gap between optical and electron microscopy in bio-imaging. Here, we report for the first time 3D cryo-CDI of a whole, frozen-hydrated cell - in this case a Neospora caninum tachyzoite - using 8 keV X-rays. Our 3D reconstruction reveals the surface and internal morphology of the cell, including its complex, polarized sub-cellular architecture with a 3D resolution of ~75-100 nm, which is presently limited by the coherent X-ray flux and detector size. Given the imminent improvement in the coherent X-ray flux at the facilities worldwide, our work forecasts the possibility of routine 3D imaging of frozen-hydrated cells with spatial resolutions in the tens of nanometres.

physics.bio-ph↗

arXiv2013

Single-shot 3D structure determination of nanocrystals with femtosecond X-ray free electron laser pulses

Coherent diffraction imaging (CDI) using synchrotron radiation, X-ray free electron lasers (X-FELs), high harmonic generation, soft X-ray lasers, and optical lasers has found broad applications across several disciplines. An active research direction in CDI is to determine the structure of single particles with intense, femtosecond X-FEL pulses based on diffraction-before-destruction scheme. However, single-shot 3D structure determination has not been experimentally realized yet. Here we report the first experimental demonstration of single-shot 3D structure determination of individual nanocrystals using ~10 femtosecond X-FEL pulses. Coherent diffraction patterns are collected from high-index-faceted nanocrystals, each struck by a single X-FEL pulse. Taking advantage of the symmetry of the nanocrystal, we reconstruct the 3D structure of each nanocrystal from a single-shot diffraction pattern at ~5.5 nm resolution. As symmetry exists in many nanocrystals and virus particles, this method can be applied to 3D structure studies of such particles at nanometer resolution on femtosecond time scales.

physics.optics↗

arXiv2009

Three-dimensional structure determination from a single view

The ability to determine the structure of matter in three dimensions has profoundly advanced our understanding of nature. Traditionally, the most widely used schemes for 3D structure determination of an object are implemented by acquiring multiple measurements over various sample orientations, as in the case of crystallography and tomography (1,2), or by scanning a series of thin sections through the sample, as in confocal microscopy (3). Here we present a 3D imaging modality, termed ankylography (derived from the Greek words ankylos meaning 'curved' and graphein meaning 'writing'), which enables complete 3D structure determination from a single exposure using a monochromatic incident beam. We demonstrate that when the diffraction pattern of a finite object is sampled at a sufficiently fine scale on the Ewald sphere, the 3D structure of the object is determined by the 2D spherical pattern. We confirm the theoretical analysis by performing 3D numerical reconstructions of a sodium silicate glass structure at 2 Angstrom resolution and a single poliovirus at 2 - 3 nm resolution from 2D spherical diffraction patterns alone. Using diffraction data from a soft X-ray laser, we demonstrate that ankylography is experimentally feasible by obtaining a 3D image of a test object from a single 2D diffraction pattern. This approach of obtaining complete 3D structure information from a single view is anticipated to find broad applications in the physical and life sciences. As X-ray free electron lasers (X-FEL) and other coherent X-ray sources are under rapid development worldwide, ankylography potentially opens a door to determining the 3D structure of a biological specimen in a single pulse and allowing for time-resolved 3D structure determination of disordered materials.

cond-mat.mtrl-sci↗