The case for data science in experimental chemistry: examples and recommendations.

The physical sciences community is increasingly taking advantage of the possibilities offered by modern data science to solve problems in experimental chemistry and potentially to change the way we design, conduct and understand results from experiments. Successfully exploiting these opportunities involves considerable challenges. In this Expert Recommendation, we focus on experimental co-design and its importance to experimental chemistry.

Insights from high-fidelity modeling of industrial rotary bell atomization.

The global automotive industry sprayed over 2.6 billion liters of paint in 2018, much of which through electrostatic rotary bell atomization, a highly complex process involving the fluid mechanics of rapidly rotating thin films tearing apart into micrometer-thin filaments and droplets. Coating operations account for 65% of the energy usage in a typical automotive assembly plant, representing 10,000s of gigawatt-hours each year in the United States alone.

Cryo-electron tomography with mixed-scale dense neural networks reveals key steps in deployment of invasion machinery.

Host cell invasion by intracellular, eukaryotic parasites within the phylum Apicomplexa is a remarkable and active process involving the coordinated action of apical organelles and other structures. To date, capturing how these structures interact during invasion has been difficult to observe in detail. Here, we used cryogenic electron tomography to image the apical complex of tachyzoites under conditions that mimic resting parasites and those primed to invade through stimulation with calcium ionophore.

Cross-correlation analysis of X-ray photon correlation spectroscopy to extract rotational diffusion coefficients.

Coefficients for translational and rotational diffusion characterize the Brownian motion of particles. Emerging X-ray photon correlation spectroscopy (XPCS) experiments probe a broad range of length scales and time scales and are well-suited for investigation of Brownian motion. While methods for estimating the translational diffusion coefficients from XPCS are well-developed, there are no algorithms for measuring the rotational diffusion coefficients based on XPCS, even though the required raw data are accessible from such experiments.

A Kriging-Based Approach to Autonomous Experimentation with Applications to X-Ray Scattering.

Modern scientific instruments are acquiring data at ever-increasing rates, leading to an exponential increase in the size of data sets. Taking full advantage of these acquisition rates will require corresponding advancements in the speed and efficiency of data analytics and experimental control. A significant step forward would come from automatic decision-making methods that enable scientific instruments to autonomously explore scientific problems-that is, to intelligently explore parameter spaces without human intervention, selecting high-value measurements to perform based on the continually growing experimental data set.

Xi-cam: a versatile interface for data visualization and analysis.

Xi-cam is an extensible platform for data management, analysis and visualization. Xi-cam aims to provide a flexible and extensible approach to synchrotron data treatment as a solution to rising demands for high-volume/high-throughput processing pipelines. The core of Xi-cam is an extensible plugin-based graphical user interface platform which provides users with an interactive interface to processing algorithms.

A mixed-scale dense convolutional neural network for image analysis.

Deep convolutional neural networks have been successfully applied to many image-processing problems in recent works. Popular network architectures often add additional operations and connections to the standard architecture to enable training deeper networks. To achieve accurate results in practice, a large number of trainable parameters are often required.

Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase.

Free-electron lasers now have the ability to collect X-ray diffraction patterns from individual molecules; however, each sample is delivered at unknown orientation and may be in one of several conformational states, each with a different molecular structure. Hit rates are often low, typically around 0.1%, limiting the number of useful images that can be collected.

Nanosurveyor: a framework for real-time data processing.

Background: The ever improving brightness of accelerator based sources is enabling novel observations and discoveries with faster frame rates, larger fields of view, higher resolution, and higher dimensionality.

Results: Here we present an integrated software/algorithmic framework designed to capitalize on high-throughput experiments through efficient kernels, load-balanced workflows, which are scalable in design. We describe the streamlined processing pipeline of ptychography data analysis.

Iterative phasing for fluctuation X-ray scattering.

Fluctuation X-ray scattering (FXS) is an extension of small- and wide-angle X-ray scattering in which the X-ray snapshots are taken below rotational diffusion times. This technique, performed using a free electron laser or ultrabright synchrotron source, provides significantly more experimental information compared with traditional solution scattering methods. We develop a multitiered iterative phasing algorithm to determine the underlying structure of the scattering object from FXS data.

Multicellular architecture of malignant breast epithelia influences mechanics.

Cell-matrix and cell-cell mechanosensing are important in many cellular processes, particularly for epithelial cells. A crucial question, which remains unexplored, is how the mechanical microenvironment is altered as a result of changes to multicellular tissue structure during cancer progression. In this study, we investigated the influence of the multicellular tissue architecture on mechanical properties of the epithelial component of the mammary acinus.

Rapid disorganization of mechanically interacting systems of mammary acini.

Cells and multicellular structures can mechanically align and concentrate fibers in their ECM environment and can sense and respond to mechanical cues by differentiating, branching, or disorganizing. Here we show that mammary acini with compromised structural integrity can interconnect by forming long collagen lines. These collagen lines then coordinate and accelerate transition to an invasive phenotype.

Algorithmic framework for X-ray nanocrystallographic reconstruction in the presence of the indexing ambiguity.

X-ray nanocrystallography allows the structure of a macromolecule to be determined from a large ensemble of nanocrystals. However, several parameters, including crystal sizes, orientations, and incident photon flux densities, are initially unknown and images are highly corrupted with noise. Autoindexing techniques, commonly used in conventional crystallography, can determine orientations using Bragg peak patterns, but only up to crystal lattice symmetry.

Multiscale modeling of membrane rearrangement, drainage, and rupture in evolving foams.

Modeling the physics of foams and foamlike materials, such as soapy froths, fire retardants, and lightweight crash-absorbent structures, presents challenges, because of the vastly different time and space scales involved. By separating and coupling these disparate scales, we have designed a multiscale framework to model dry foam dynamics. This leads to a predictive and flexible computational methodology linking, with a few simplifying assumptions, foam drainage, rupture, and topological rearrangement, to coupled interface-fluid motion under surface tension, gravity, and incompressible fluid dynamics.

The Voronoi Implicit Interface Method for computing multiphase physics.

We introduce a numerical framework, the Voronoi Implicit Interface Method for tracking multiple interacting and evolving regions (phases) whose motion is determined by complex physics (fluids, mechanics, elasticity, etc.), intricate jump conditions, internal constraints, and boundary conditions. The method works in two and three dimensions, handles tens of thousands of interfaces and separate phases, and easily and automatically handles multiple junctions, triple points, and quadruple points in two dimensions, as well as triple lines, etc.

Automatic Structure Analysis in High-Throughput Characterization of Porous Materials.

Inspection of the structure and the void space of a porous material is a critical step in most computational studies involving guest molecules. Some sections of the void space, like inaccessible pockets, have to be identified and blocked in molecular simulations. These pockets are typically detected by visual analysis of the geometry, potential or free energy landscapes, or a histogram of an initial molecular simulation.

Exact subgrid interface correction schemes for elliptic interface problems.

We introduce a nonconforming finite-element method for second order elliptic interface problems. Our approach applies to problems in which discontinuous coefficients and singular sources on the interface may give rise to jump discontinuities in either the solution or its normal derivative. Given a standard background mesh and an interface that passes between elements, the key idea is to construct a singular correction function that satisfies the prescribed jump conditions, providing accurate subgrid resolution of the discontinuities.

Simulating complex tumor dynamics from avascular to vascular growth using a general level-set method.

A comprehensive continuum model of solid tumor evolution and development is investigated in detail numerically, both under the assumption of spherical symmetry and for arbitrary two-dimensional growth. The level set approach is used to obtain solutions for a recently developed multi-cell transport model formulated as a moving boundary problem for the evolution of the tumor. The model represents both the avascular and the vascular phase of growth, and is able to simulate when the transition occurs; progressive formation of a necrotic core and a rim structure in the tumor during the avascular phase are also captured.