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Electron Microscopy Studies of Soft Nanomaterials

This review highlights recent efforts on applying electron microscopy (EM) to soft (including biological) nanomaterials. We will show how developments of both the hardware and software of EM have enabled new insights into the formation, assembly, and functioning (e.g., energy conversion and storage, phonon/photon modulation) of these materials by providing shape, size, phase, structural, and chemical information at the nanometer or higher spatial resolution. Specifically, we first discuss standard real-space two-dimensional imaging and analytical techniques which are offered conveniently by microscopes without special holders or advanced beam technology. The discussion is then extended to recent advancements, including visualizing three-dimensional morphology of soft nanomaterials using electron tomography and its variations, identifying local structure and strain by electron diffraction, and recording motions and transformation by in situ EM. On these advancements, we cover state-of-the-art technologies designed for overcoming the technical barriers for EM to characterize soft materials as well as representative application examples. Here, the even more recent integration of machine learning and its impacts on EM are also discussed in detail. With our perspectives of future opportunities offered at the end, we expect this review to inspire and stimulate more efforts in developing and utilizing EM-based characterization methods for soft nanomaterials at the atomic to nanometer length scales in academic research and industrial applications.

Imaging↗

The International Virus Bioinformatics Meeting 2020

The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8–9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of RNA viruses, (2) viral metagenomics and ecology, (3) virus evolution and classification and (4) viral infections and immunology. Further, the meeting featured 20 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting.

59 BASIC BIOLOGICAL SCIENCES↗

Photoenzymatic Catalysis in a New Light: Gluconobacter “Ene”-Reductase Conjugates Possessing High-Energy Reactivity with Tunable Low-Energy Excitation

Non-natural light-driven enzymatic reactivity was recently developed to perform the highly stereoselective reactions required for pharmaceutical synthesis. However, photoenzymes require high-intensity light to function because of the poor absorption properties of their photoactive intermediates. Inspired by the modular architecture of photosynthesis, we designed a conjugate composed of a covalently linked photoenzyme and a light antenna to separate light capture from catalysis. Spectroscopic characterization of the conjugate showed the presence of efficient energy transfer from the light-harvesting components to the photoenzyme. In the presence of energy transfer, a ~4-fold increase in product yield was observed for intramolecular hydroalkylation of alkenes, and reactivity was enabled for intermolecular hydroalkylation of alkenes. As a result, these improvements establish the power of incorporating nature’s design into non-natural photoenzymatic catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Drone flight visible images, digital elevation maps, and geotiffs, Council, Seward Peninsula, Alaska, USA, July 2017

Remote sensing data collected from Lawrence Berkeley National Laboratory’s (LBNL) unmanned aerial system (UAS) quadcopter platform – Inspire-1 – operated by the Ameriflux Management Project (ameriflux.lbl.gov) Technical Team. The Insprire-1 is a visible imagery UAS platform that simultaneously measures very high spatial resolution optical red/green/blue (RGB) at regular intervals along each flight path. This package includes data from four flight paths over the NGEE Arctic Council Road Site near mile marker 71 in the Seward Peninsula, Alaska in July 2017. Derived image products for each flight include ortho-mosaiced RGB, an RGB-based digital surface model (DSM) using the structure from motion (SfM) technique, and a digital terrain model (DTM). Ancillary aircraft data, flight mission parameters, and general flight conditions are also included. Unprocessed and processed data products are included in this package (processing levels 0-2). This metadata document contains flight campaign, instrument and file metadata, along with a description of data processing levels, data products and file naming scheme.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic) was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy’s Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy’s Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Drone flight visible images, digital elevation maps, and geotiffs, Teller, Seward Peninsula, Alaska, USA, July 2017

Remote sensing data collected from Lawrence Berkeley National Laboratory’s (LBNL) unmanned aerial system (UAS) quadcopter platform – Inspire-1 – operated by the Ameriflux Management Project (ameriflux.lbl.gov) Technical Team. The Insprire-1 is a visible imagery UAS platform that simultaneously measures very high spatial resolution optical red/green/blue (RGB) at regular intervals along the flight path. This package includes data from a flight path over the NGEE Arctic Teller Site, west of mile marker 27 Bob Blodgett Highway in the Seward Peninsula, Alaska in July 2017. Derived image products include ortho-mosaiced RGB, an RGB-based digital surface model (DSM) using the structure from motion (SfM) technique, and a digital terrain model (DTM). Ancillary aircraft data, flight mission parameters, and general flight conditions are also included. Unprocessed and processed data products are included in this package (processing levels 0-2). This metadata document contains flight campaign, instrument and file metadata, along with a description of data processing levels, data products and file naming scheme.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic) was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy’s Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy’s Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Drone flight visible images, digital elevation maps, and geotiffs, Kougarok, Seward Peninsula, Alaska, USA, July 2017

Remote sensing data collected from Lawrence Berkeley National Laboratory’s (LBNL) unmanned aerial system (UAS) quadcopter platform – Inspire-1 – operated by the Ameriflux Management Project (ameriflux.lbl.gov) Technical Team. The Insprire-1 is a visible imagery UAS platform that simultaneously measures very high spatial resolution optical red/green/blue (RGB) at regular intervals along each flight path. This package includes data from four flight paths over the NGEE Arctic Kougarok Site, west of mile marker 64 on Kuzitrin Road in the Seward Peninsula, Alaska in July 2017. Derived image products include ortho-mosaiced RGB, an RGB-based digital surface model (DSM) using the structure from motion (SfM) technique, and a digital terrain model (DTM). Ancillary aircraft data, flight mission parameters, and general flight conditions are also included. Unprocessed and processed data products are included in this package (processing levels 0-2). This metadata document contains flight campaign, instrument and file metadata, along with a description of data processing levels, data products and file naming scheme.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic) was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy’s Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy’s Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

RDPP: Accelerating Diversity in DOE Climate Science and Resilience Research (Final Report)

The scope of the project was set out to accelerate the inclusion of diversity into the Department of Energy (DOE) Earth and Environmental Systems Sciences Division (EESSD) relevant climate science and resilience research to inclusively advance solutions. The Project Objectives were to usher in equitable use-inspired climate-related research with underrepresented Minorities of which this project helped fund 7 HU graduate students work with the DOE (three of which will graduate in Spring 2025). The two key aims underpinning that core goal were AIM1: developing partnerships (18 organized engaged, see partners list) and AIM2: Developing capabilities (3 visits to DOE facilities, 5 DOE partners visits to HU, increased visiting faculty participation in BNL-DOE lab, secured 5 grants together totaling 1.2 million in funds for HU). The project objectives were highly successful as they were designed to ambitiously pull together DOE lab researchers with the long-standing and successful transdisciplinary climate science research programs of the PI and local DC groups. The major outcomes of this RDPP program will be in the new fundamentally inclusive partnerships with DOE and HU tasked to understand the urban-rural impacts due to climate change in the US, Eastern South Atlantic (ESA) Region, related to energy issues driven by heat stress and the water cycle. Overall, this project contributes to the DOE and science community vision for catalyze connections for project-ready underrepresented minorities (URMs) at a prominent HBCU to DOE projects supported by the Biological and Environmental research (BER) Program; particularly, the Earth and Environmental Systems Sciences Division (EESSD).

54 ENVIRONMENTAL SCIENCES↗

Perspectives on improving photosynthesis to increase crop yield

Abstract Improving photosynthesis, the fundamental process by which plants convert light energy into chemical energy, is a key area of research with great potential for enhancing sustainable agricultural productivity and addressing global food security challenges. This perspective delves into the latest advancements and approaches aimed at optimizing photosynthetic efficiency. Our discussion encompasses the entire process, beginning with light harvesting and its regulation and progressing through the bottleneck of electron transfer. We then delve into the carbon reactions of photosynthesis, focusing on strategies targeting the enzymes of the Calvin–Benson–Bassham (CBB) cycle. Additionally, we explore methods to increase carbon dioxide (CO2) concentration near the Rubisco, the enzyme responsible for the first step of CBB cycle, drawing inspiration from various photosynthetic organisms, and conclude this section by examining ways to enhance CO2 delivery into leaves. Moving beyond individual processes, we discuss two approaches to identifying key targets for photosynthesis improvement: systems modeling and the study of natural variation. Finally, we revisit some of the strategies mentioned above to provide a holistic view of the improvements, analyzing their impact on nitrogen use efficiency and on canopy photosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗

Supramolecular and Hybrid Bonding Polymers

Staudinger established a century ago the existence of covalent macromolecules, work that led to the development of transformative materials of great benefit to society and a “quantum leap” in our understanding of biological systems. Over the past few decades the concept of supramolecular polymers has emerged–chemical systems in which structural units bond strongly to each other non-covalently. Herein, we discuss how these dynamic systems actually exist in the natural world and can create soft materials with structures, properties, and functions beyond the ones we know in Staudinger polymers. We reflect here on the potential of novel systems in which covalent and supramolecular polymers are chemically integrated and describe them as hybrid bonding polymers. This paper describes the concept with recent examples from the Stupp laboratory, and discusses their potential functions as robotic materials that mimic living matter and structures that offer new ideas on how to recycle and reuse soft materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Selective hydrogenation via precise hydrogen bond interactions on catalytic scaffolds

Abstract The active site environment in enzymes has been known to affect catalyst performance through weak interactions with a substrate, but precise synthetic control of enzyme inspired heterogeneous catalysts remains challenging. Here, we synthesize hyper-crosslinked porous polymer (HCPs) with solely -OH or -CH 3 groups on the polymer scaffold to tune the environment of active sites. Reaction rate measurements, spectroscopic techniques, along with DFT calculations show that HCP-OH catalysts enhance the hydrogenation rate of H-acceptor substrates containing carbonyl groups whereas hydrophobic HCP- CH 3 ones promote non-H bond substrate activation. The functional groups go beyond enhancing substrate adsorption to partially activate the C = O bond and tune the catalytic sites. They also expose selectivity control in the hydrogenation of multifunctional substrates through preferential substrate functional group adsorption. The proposed synthetic strategy opens a new class of porous polymers for selective catalysis.

59 BASIC BIOLOGICAL SCIENCES↗

Neuromorphic scaling advantages for energy-efficient random walk computations

Computing stands to be radically improved by neuromorphic computing (NMC) approaches inspired by the brain's incredible efficiency and capabilities. Most NMC research, which aims to replicate the brain's computational structure and architecture in man-made hardware, has focused on artificial intelligence; however, less explored is whether this brain-inspired hardware can provide value beyond cognitive tasks. We demonstrate that high-degree parallelism and configurability of spiking neuromorphic architectures makes them well-suited to implement random walks via discrete time Markov chains. Such random walks are useful in Monte Carlo methods, which represent a fundamental computational tool for solving a wide range of numerical computing tasks. Additionally, we show how the mathematical basis for a probabilistic solution involving a class of stochastic differential equations can leverage those simulations to provide solutions for a range of broadly applicable computational tasks. Despite being in an early development stage, we find that NMC platforms, at a sufficient scale, can drastically reduce the energy demands of high-performance computing platforms.

59 BASIC BIOLOGICAL SCIENCES↗

A biohybrid strategy for enabling photoredox catalysis with low-energy light

Natural systems drive the high-energy reactions of photosynthesis with efficient and broadband energy capture. Transition-metal photocatalysts similarly convert light into chemical reactivity, and yet suffer from light-limited operation and require blue-to-UV excitation. In photosynthesis, both light capture and reactivity have been optimized by separation into distinct sites. In this work, inspired by this modular architecture, we synthesized a biohybrid photocatalyst by covalent attachment of the photosynthetic light-harvesting protein R-phycoerythrin (RPE) to the transition-metal photocatalyst tris(2,2'-bipyridine)ruthenium(II) ([Ru(bpy) 3 ] 2+ ). Spectroscopic investigation found that absorbed photoenergy was efficiently funneled from RPE to [Ru(bpy) 3 ] 2+ . The utility of the biohybrid photocatalyst was demonstrated via an increase in yields for a thiol-ene coupling reaction and a cysteinyl-desulfurization reaction, including recovered reactivity at red wavelengths where [Ru(bpy) 3 ] 2+ alone does not absorb.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Space‐Time Causal Discovery in Earth System Science: A Local Stencil Learning Approach

Causal discovery tools enable scientists to infer meaningful relationships from observational data, spurring advances in fields as diverse as biology, economics, and climate science. Despite these successes, the application of causal discovery to space-time systems remains immensely challenging due to the high-dimensional nature of the data. For example, in climate sciences, modern observational temperature records over the past few decades regularly measure thousands of locations around the globe. To address these challenges, we introduce Causal Space-Time Stencil Learning (CaStLe), a novel meta-algorithm for discovering causal structures in complex space-time systems. CaStLe leverages regularities in local space-time dependencies to learn governing global dynamics. This local perspective eliminates spurious confounding and drastically reduces sample complexity, making space-time causal discovery practical and effective. For causal discovery, CaStLe flexibly accepts any appropriately adapted time series causal discovery algorithm to recover local causal structures. These advances enable causal discovery of geophysical phenomena that were previously unapproachable, including non-periodic, transient phenomena such as volcanic eruption plumes. Regularities in local space-time dependencies are transformed into informative spatial replicates, which actually improve CaStLe's performance when applied to ever-larger spatial grids. We successfully apply CaStLe to discover the atmospheric dynamics governing the climate response to the 1991 Mount Pinatubo volcanic eruption. We provide validation experiments to demonstrate the effectiveness of CaStLe over existing causal-discovery frameworks on a range of geophysics-inspired benchmarks while identifying the method's limitations and domains where its assumptions may not hold.

Nichol, J. Jake [Univ. of New Mexico, Albuquerque,↗

Interfacing DNA nanotechnology and biomimetic photonic complexes: advances and prospects in energy and biomedicine

Abstract Self-assembled photonic systems with well-organized spatial arrangement and engineered optical properties can be used as efficient energy materials and as effective biomedical agents. The lessons learned from natural light-harvesting antennas have inspired the design and synthesis of a series of biomimetic photonic complexes, including those containing strongly coupled dye aggregates with dense molecular packing and unique spectroscopic features. These photoactive components provide excellent features that could be coupled to multiple applications including light-harvesting, energy transfer, biosensing, bioimaging, and cancer therapy. Meanwhile, nanoscale DNA assemblies have been employed as programmable and addressable templates to guide the formation of DNA-directed multi-pigment complexes, which can be used to enhance the complexity and precision of artificial photonic systems and show the potential for energy and biomedical applications. This review focuses on the interface of DNA nanotechnology and biomimetic photonic systems. We summarized the recent progress in the design, synthesis, and applications of bioinspired photonic systems, highlighted the advantages of the utilization of DNA nanostructures, and discussed the challenges and opportunities they provide. Graphical Abstract

59 BASIC BIOLOGICAL SCIENCES↗

Lifelike behavior of chemically oscillating mobile capsules

Inspired by the self-organization of unicellular species into multicellular organisms, we use theory and simulation to design a system of mobile, active microcapsules that produce chemicals according to a catalytic reaction network (CRN). In solution, the catalytic reactions generate a force that drives the flow of the surrounding fluid. The convective flow, in turn, transports the capsules to new chemical surroundings with each successive translation. Consequently, the chemical signal produced by a cluster of capsules is critically dependent on the proximity and spatial configuration of the neighboring capsules. If all of the capsules and chemical products involved in the CRN lie within sufficient proximity, then the system develops oscillatory behavior that drives the dynamic self-assembly of capsules into larger clusters that are capable of collective action. Finally, these simulations indicate potential chemo-mechanic mechanisms that enable single cellular units, such as ameba, to organize into multicellular life forms.

59 BASIC BIOLOGICAL SCIENCES↗

Sequence Design of Random Heteropolymers as Protein Mimics

Random heteropolymers (RHPs) have been computationally designed and experimentally shown to recapitulate protein-like phase behavior and function. However, unlike proteins, RHP sequences are only statistically defined and cannot be sequenced. Recent developments in reversible-deactivation radical polymerization allowed simulated polymer sequences based on the well-established Mayo–Lewis equation to more accurately reflect ground-truth sequences that are experimentally synthesized. This led to opportunities to perform bioinformatics-inspired analysis on simulated sequences to guide the design, synthesis, and interpretation of RHPs. We compared batches on the order of 10000 simulated RHP sequences that vary by synthetically controllable and measurable RHP characteristics such as chemical heterogeneity and average degree of polymerization. Our analysis spans across 3 levels: segments along a single chain, sequences within a batch, and batch-averaged statistics. We discuss simulator fidelity and highlight the importance of robust segment definition. Examples are presented that demonstrate the use of simulated sequence analysis for in-silico iterative design to mimic protein hydrophobic/hydrophilic segment distributions in RHPs and compare RHP and protein sequence segments to explain experimental results of RHPs that mimic protein function. To facilitate the community use of this workflow, the simulator and analysis modules have been made available through an open source toolkit, the RHPapp.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters

Protein structure and dynamics can be probed using x-ray crystallography. Whereas the Bragg peaks are only sensitive to the average unit-cell electron density, the signal between the Bragg peaks—diffuse scattering—is sensitive to spatial correlations in electron-density variations. Although diffuse scattering contains valuable information about protein dynamics, the diffuse signal is more difficult to isolate from the background compared to the Bragg signal, and the reproducibility of diffuse signal is not yet well understood. We present a systematic study of the reproducibility of diffuse scattering from isocyanide hydratase in three different protein forms. Both replicate diffuse datasets and datasets obtained from different mutants were similar in pairwise comparisons (Pearson correlation coefficient ≥0.8). The data were processed in a manner inspired by previously published methods using custom software with modular design, enabling us to perform an analysis of various data processing choices to determine how to obtain the highest quality data as assessed using unbiased measures of symmetry and reproducibility. The diffuse data were then used to characterize atomic mobility using a liquid-like motions (LLM) model. This characterization was able to discriminate between distinct anisotropic atomic displacement parameter (ADP) models arising from different anisotropic scaling choices that agreed comparably with the Bragg data. Our results emphasize the importance of data reproducibility as a model-free measure of diffuse data quality, illustrate the ability of LLM analysis of diffuse scattering to select among alternative ADP models, and offer insights into the design of successful diffuse scattering experiments.

59 BASIC BIOLOGICAL SCIENCES↗

CRCNS21 Computational Models of Multisensory Integration by Upper Limb in Humanoids and Amputees

This international collaborative research project between Johns Hopkins University (JHU) and the Technical University of Munich (TUM) investigated how the human brain processes and integrates multiple types of sensory information, such as touch and force, with the goal of improving prosthetic limbs for amputees and advancing sensory capabilities in humanoid robots. The research advanced our understanding of how the brain responds to sensory feedback in upper-limb amputees. Through experiments in which amputees received electrical stimulation while performing phantom hand movements, we demonstrated that sensory feedback activates the cortical sensorimotor and multisensory regions, and that these regions communicate dynamically during stimulation. Experiments with intact-limb participants explored the integration of visual, haptic, and force feedback, as well as in virtual reality motor training, further showing how the brain processes multimodal sensory information. In addition, this research inspired work on examining the reliability of where amputees perceive sensations over time, which contributed to a successful doctoral fellowship for continued investigation. Our collaborators at TUM improved multimodal sensor technology combining tactile and thermal feedback for humanoid robots, demonstrating the feasibility of integrating multiple sensor types into a unified system for detecting and responding to environmental stimuli. The experimental methods and analysis techniques developed across both teams, including functional network analysis and multimodal sensor integration, provide a foundation for future research in prosthetics and robotics. This research benefits the public by generating knowledge about how amputees process restored sensory information. Advances in humanoid sensing contribute to safer human-robot interaction. The project also fostered international collaboration and cross-disciplinary training: one TUM doctoral student spent a summer at JHU working on multimodal sensor integration, while two JHU students traveled to TUM to host workshops on neuromorphic sensory encoding and sensory integration.

42 ENGINEERING↗