Streaming Large-Scale Microscopy Data to a Supercomputing Facility.

Data management is a critical component of modern experimental workflows. As data generation rates increase, transferring data from acquisition servers to processing servers via conventional file-based methods is becoming increasingly impractical. The 4D Camera at the National Center for Electron Microscopy generates data at a nominal rate of 480 Gbit s-1 (87,000 frames s-1), producing a 700 GB dataset in 15 s.

Quantum-parallel vectorized data encodings and computations on trapped-ion and transmon QPUs.

Compact data representations in quantum systems are crucial for the development of quantum algorithms for data analysis. In this study, we present two innovative data encoding techniques, known as QCrank and QBArt, which exhibit significant quantum parallelism via uniformly controlled rotation gates. The QCrank method encodes a series of real-valued data as rotations on data qubits, resulting in increased storage capacity.

A bacterial sensor taxonomy across earth ecosystems for machine learning applications.

Microbial communities have evolved to colonize all ecosystems of the planet, from the deep sea to the human gut. Microbes survive by sensing, responding, and adapting to immediate environmental cues. This process is driven by signal transduction proteins such as histidine kinases, which use their sensing domains to bind or otherwise detect environmental cues and "transduce" signals to adjust internal processes.

Interpreting macromolecular diffraction through simulation.

This chapter discusses the use of diffraction simulators to improve experimental outcomes in macromolecular crystallography, in particular for future experiments aimed at diffuse scattering. Consequential decisions for upcoming data collection include the selection of either a synchrotron or free electron laser X-ray source, rotation geometry or serial crystallography, and fiber-coupled area detector technology vs. pixel-array detectors.

XFEL Microcrystallography of Self-Assembling Silver -Alkanethiolates.

New synthetic hybrid materials and their increasing complexity have placed growing demands on crystal growth for single-crystal X-ray diffraction analysis. Unfortunately, not all chemical systems are conducive to the isolation of single crystals for traditional characterization. Here, small-molecule serial femtosecond crystallography (smSFX) at atomic resolution (0.

Remembering the Work of Phillip L. Geissler: A Coda to His Scientific Trajectory.

Phillip L. Geissler made important contributions to the statistical mechanics of biological polymers, heterogeneous materials, and chemical dynamics in aqueous environments. He devised analytical and computational methods that revealed the underlying organization of complex systems at the frontiers of biology, chemistry, and materials science.

Chemical crystallography by serial femtosecond X-ray diffraction.

Inorganic-organic hybrid materials represent a large share of newly reported structures, owing to their simple synthetic routes and customizable properties. This proliferation has led to a characterization bottleneck: many hybrid materials are obligate microcrystals with low symmetry and severe radiation sensitivity, interfering with the standard techniques of single-crystal X-ray diffraction and electron microdiffraction. Here we demonstrate small-molecule serial femtosecond X-ray crystallography (smSFX) for the determination of material crystal structures from microcrystals.

Room temperature XFEL crystallography reveals asymmetry in the vicinity of the two phylloquinones in photosystem I.

Photosystem I (PS I) has a symmetric structure with two highly similar branches of pigments at the center that are involved in electron transfer, but shows very different efficiency along the two branches. We have determined the structure of cyanobacterial PS I at room temperature (RT) using femtosecond X-ray pulses from an X-ray free electron laser (XFEL) that shows a clear expansion of the entire protein complex in the direction of the membrane plane, when compared to previous cryogenic structures. This trend was observed by complementary datasets taken at multiple XFEL beamlines.

X-ray linear dichroic ptychography.

Biominerals such as seashells, coral skeletons, bone, and tooth enamel are optically anisotropic crystalline materials with unique nanoscale and microscale organization that translates into exceptional macroscopic mechanical properties, providing inspiration for engineering new and superior biomimetic structures. Using coral skeleton as a model, here, we experimentally demonstrate X-ray linear dichroic ptychography and map the -axis orientations of the aragonite (CaCO) crystals. Linear dichroic phase imaging at the oxygen K-edge energy shows strong polarization-dependent contrast and reveals the presence of both narrow (<35°) and wide (>35°) -axis angular spread in the coral samples.

An ultrahigh-resolution soft x-ray microscope for quantitative analysis of chemically heterogeneous nanomaterials.

The analysis of chemical states and morphology in nanomaterials is central to many areas of science. We address this need with an ultrahigh-resolution scanning transmission soft x-ray microscope. Our instrument provides multiple analysis tools in a compact assembly and can achieve few-nanometer spatial resolution and high chemical sensitivity via x-ray ptychography and conventional scanning microscopy.

MAGI: A Method for Metabolite Annotation and Gene Integration.

Metabolomics is a widely used technology for obtaining direct measures of metabolic activities from diverse biological systems. However, ambiguous metabolite identifications are a common challenge and biochemical interpretation is often limited by incomplete and inaccurate genome-based predictions of enzyme activities (that is, gene annotations). Metabolite Annotation and Gene Integration (MAGI) generates a metabolite-gene association score using a biochemical reaction network.

Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes.

Background: As microbiome research becomes increasingly prevalent in the fields of human health, agriculture and biotechnology, there exists a need for a resource to better link organisms and environmental chemistries. Exometabolomics experiments now provide assertions of the metabolites present within specific environments and how the production and depletion of metabolites is linked to specific microbes. This information could be broadly useful, from comparing metabolites across environments, to predicting competition and exchange of metabolites between microbes, and to designing stable microbial consortia.

Methods for Specifying Scientific Data Standards and Modeling Relationships with Applications to Neuroscience.

Neuroscience continues to experience a tremendous growth in data; in terms of the volume and variety of data, the velocity at which data is acquired, and in turn the veracity of data. These challenges are a serious impediment to sharing of data, analyses, and tools within and across labs. Here, we introduce BRAINformat, a novel data standardization framework for the design and management of scientific data formats.

GW100: Benchmarking G0W0 for Molecular Systems.

We present the GW100 set. GW100 is a benchmark set of the ionization potentials and electron affinities of 100 molecules computed with the GW method using three independent GW codes and different GW methodologies. The quasi-particle energies of the highest-occupied molecular orbitals (HOMO) and lowest-unoccupied molecular orbitals (LUMO) are calculated for the GW100 set at the G0W0@PBE level using the software packages TURBOMOLE, FHI-aims, and BerkeleyGW.

Analysis of Metabolomics Datasets with High-Performance Computing and Metabolite Atlases.

Even with the widespread use of liquid chromatography mass spectrometry (LC/MS) based metabolomics, there are still a number of challenges facing this promising technique. Many, diverse experimental workflows exist; yet there is a lack of infrastructure and systems for tracking and sharing of information. Here, we describe the Metabolite Atlas framework and interface that provides highly-efficient, web-based access to raw mass spectrometry data in concert with assertions about chemicals detected to help address some of these challenges.

Helium superfluidity. Shapes and vorticities of superfluid helium nanodroplets.

Helium nanodroplets are considered ideal model systems to explore quantum hydrodynamics in self-contained, isolated superfluids. However, exploring the dynamic properties of individual droplets is experimentally challenging. In this work, we used single-shot femtosecond x-ray coherent diffractive imaging to investigate the rotation of single, isolated superfluid helium-4 droplets containing ~10(8) to 10(11) atoms.

From voxels to knowledge: a practical guide to the segmentation of complex electron microscopy 3D-data.

Modern 3D electron microscopy approaches have recently allowed unprecedented insight into the 3D ultrastructural organization of cells and tissues, enabling the visualization of large macromolecular machines, such as adhesion complexes, as well as higher-order structures, such as the cytoskeleton and cellular organelles in their respective cell and tissue context. Given the inherent complexity of cellular volumes, it is essential to first extract the features of interest in order to allow visualization, quantification, and therefore comprehension of their 3D organization. Each data set is defined by distinct characteristics, e.

Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy.

The dioxygen we breathe is formed by light-induced oxidation of water in photosystem II. O2 formation takes place at a catalytic manganese cluster within milliseconds after the photosystem II reaction centre is excited by three single-turnover flashes. Here we present combined X-ray emission spectra and diffraction data of 2-flash (2F) and 3-flash (3F) photosystem II samples, and of a transient 3F' state (250 μs after the third flash), collected under functional conditions using an X-ray free electron laser.

A computational approach to identify genes for functional RNAs in genomic sequences.

Currently there is no successful computational approach for identification of genes encoding novel functional RNAs (fRNAs) in genomic sequences. We have developed a machine learning approach using neural networks and support vector machines to extract common features among known RNAs for prediction of new RNA genes in the unannotated regions of prokaryotic and archaeal genomes. The Escherichia coli genome was used for development, but we have applied this method to several other bacterial and archaeal genomes.

Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing.

Alternative pre-mRNA splicing is a major cellular process by which functionally diverse proteins can be generated from the primary transcript of a single gene, often in tissue-specific patterns. The current study investigates the hypothesis that splicing of tissue-specific alternative exons is regulated in part by control sequences in adjacent introns and that such elements may be recognized via computational analysis of exons sharing a highly specific expression pattern. We have identified 25 brain-specific alternative cassette exons, compiled a dataset of genomic sequences encompassing these exons and their adjacent introns and used word contrast algorithms to analyze key features of these nucleotide sequences.

VISTA : visualizing global DNA sequence alignments of arbitrary length.

Summary: VISTA is a program for visualizing global DNA sequence alignments of arbitrary length. It has a clean output, allowing for easy identification of similarity, and is easily configurable, enabling the visualization of alignments of various lengths at different levels of resolution. It is currently available on the web, thus allowing for easy access by all researchers.