Paper-Biologically Inspired Acquisition Function for Training and Optimizing Fourier Neural Operator Surrogates of Physical Phenomena
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River Geomorphology Affects Biogeochemical Responses to Hydrologic Events in a Large River Ecosystem
Shifts in the frequency and intensity of high discharge events due to climate change may have important consequences for the hydrology and biogeochemistry of rivers. However, our understanding of event-scale biogeochemical dynamics in large rivers lags that of small streams. To fill this gap, we used high-frequency sensor data collected during four consecutive summers from a main channel and backwater site of the Upper Mississippi River. We identified high discharge events and calculated event concentration-discharge responses for both physical-chemical (nitrate, turbidity, and fluorescent dissolved organic matter) and biological (chlorophyll-a and cyanobacteria) constituents using metrics of hysteresis and slope. We found a range of responses across events, particularly for nitrate. Although fluorescent dissolved organic matter (FDOM) and turbidity exhibited more consistent responses across events, contrasting hysteresis metrics indicated that FDOM was flushed to the river from more distant sources than turbidity. Biological responses (chlorophyll a and cyanobacteria) differed more between sites than physical and chemical constituents. Lastly, we found that the event characteristics best explaining concentration responses differed between sites, with event magnitude more frequently related to responses in the main channel, and antecedent wetness conditions associated with response variation in the backwater. Furthermore, our results indicate that event responses in large rivers are distinct across the diverse habitats and biogeochemical components of a large floodplain river, which has implications for local and downstream ecosystems as the climate shifts.
54 ENVIRONMENTAL SCIENCES↗
Separation Process of Plant Fibers for Textile and Composite Application: A Review of Recent Advances
Plant fiber resources have gained significant attention for value-added utilization due to their renewability, sustainability, abundance, and widely acknowledged physical properties. The efficient and pragmatic separation of plant fibers is a critical process for their efficient utilization, yet a substantial gap persists between laboratory research advancements and their commercialization. To increase the possibility of research advancements for industrial application, this review summarizes the recent advances in different extraction methodologies of plant fiber research in textile and composite fields. It systematically outlines, compares, and contrasts physical (cryogenic, supercritical carbon dioxide, ultrasonic, steam explosion and microwave heating treatment), chemical (alkali, oxidation, organic solvents and deep eutectic solvents methods), and biological (natural retting, enzymatic and microorganism approaches) methods, addressing their respective mechanisms, strengths, limitations, research progress, and future prospects. In general, traditional chemical approaches have proven significantly effective but are accompanied by high pollution. Conversely, novel chemical treatments such as deep eutectic solvents and organic solvents offer a promising blend of efficiency and environmental friendliness but require deeper studies currently. Meanwhile, physical and biological treatments, though largely eco-friendly, tend to suffer from lower separation efficiencies. The research needs and future direction are also addressed to bridge the gap between scientific advancements and their widespread industrial application.
60 APPLIED LIFE SCIENCES↗
Biotropic liquid crystal phase transformations in cellulose-producing bacterial communities
Biological functionality is often enabled by a fascinating variety of physical phenomena that emerge from orientational order of building blocks, a defining property of nematic liquid crystals that is also pervasive in nature. Out-of-equilibrium, “living” analogs of these technological materials are found in biological embodiments ranging from myelin sheath of neurons to extracellular matrices of bacterial biofilms and cuticles of beetles. However, physical underpinnings behind manifestations of orientational order in biological systems often remain unexplored. For example, while nematiclike birefringent domains of biofilms are found in many bacterial systems, the physics behind their formation is rarely known. Here, using cellulose-synthesizing Acetobacter xylinum bacteria, we reveal how biological activity leads to orientational ordering in fluid and gel analogs of these soft matter systems, both in water and on solid agar, with a topological defect found between the domains. Furthermore, the nutrient feeding direction plays a role like that of rubbing of confining surfaces in conventional liquid crystals, turning polydomain organization within the biofilms into a birefringent monocrystal-like order of both the extracellular matrix and the rod-like bacteria within it. We probe evolution of scalar orientational order parameters of cellulose nanofibers and bacteria associated with fluid-gel and isotropic-nematic transformations, showing how highly ordered active nematic fluids and gels evolve with time during biological-activity-driven, disorder-order transformation. In conclusion, with fluid and soft-gel nematics observed in a certain range of biological activity, this mesophase-exhibiting system is dubbed “biotropic,” analogously to thermotropic nematics that exhibit solely orientational order within a temperature range, promising technological and fundamental-science applications.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Short-lived metal-centered excited state initiates iron-methionine photodissociation in ferrous cytochrome c
Abstract The dynamics of photodissociation and recombination in heme proteins represent an archetypical photochemical reaction widely used to understand the interplay between chemical dynamics and reaction environment. We report a study of the photodissociation mechanism for the Fe(II)-S bond between the heme iron and methionine sulfur of ferrous cytochrome c . This bond dissociation is an essential step in the conversion of cytochrome c from an electron transfer protein to a peroxidase enzyme. We use ultrafast X-ray solution scattering to follow the dynamics of Fe(II)-S bond dissociation and 1 s 3 p (Kβ) X-ray emission spectroscopy to follow the dynamics of the iron charge and spin multiplicity during bond dissociation. From these measurements, we conclude that the formation of a triplet metal-centered excited state with anti-bonding Fe(II)-S interactions triggers the bond dissociation and precedes the formation of the metastable Fe high-spin quintet state.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Nanoscale cooperative adsorption for materials control
Abstract Adsorption plays vital roles in many processes including catalysis, sensing, and nanomaterials design. However, quantifying molecular adsorption, especially at the nanoscale, is challenging, hindering the exploration of its utilization on nanomaterials that possess heterogeneity across different length scales. Here we map the adsorption of nonfluorescent small molecule/ion and polymer ligands on gold nanoparticles of various morphologies in situ under ambient solution conditions, in which these ligands are critical for the particles’ physiochemical properties. We differentiate at nanometer resolution their adsorption affinities among different sites on the same nanoparticle and uncover positive/negative adsorption cooperativity, both essential for understanding adsorbate-surface interactions. Considering the surface density of adsorbed ligands, we further discover crossover behaviors of ligand adsorption between different particle facets, leading to a strategy and its implementation in facet-controlled synthesis of colloidal metal nanoparticles by merely tuning the concentration of a single ligand.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Nasa program planning in space sciences
Experiments & research in astronomy, solar physics, planetary atmospheres, ionospheres & radio physics, particles & fields, and biosciences
SPACE BIOLOGY↗
A multilayer network analysis of Alzheimer's disease pathogenesis: Roles for p‐tau, synaptic peptides, and physical activity
INTRODUCTION: In the aging brain, cognitive abilities emerge from the coordination of complex pathways arising from a balance between protective lifestyle and environmental factors and accumulation of neuropathologies. METHODS: As part of the Rush Memory and Aging Project (n = 440), we measured accelerometer-based actigraphy, cognitive performance, and after brain autopsy, selected reaction monitoring mass spectrometry. Multilevel network analysis was used to examine the relationships among the molecular machinery of vesicular neurotransmission, Alzheimer's disease (AD) neuropathology, cognition, and late-life physical activity. RESULTS: Synaptic peptides involved in neuronal secretory function were the most influential contributors to the multilayer network, reflecting the complex interdependencies among AD pathology, synaptic processes, and late-life cognition. Older adults with lower physical activity evidenced stronger adverse relationships among phosphorylated tau peptides, markers of synaptic integrity, and tangle pathology. DISCUSSION: Network-based approaches simultaneously model interdependent biological processes and advance understanding of the role of physical activity in age-associated cognitive impairment. Highlights: Network-based approaches simultaneously model interdependent biological processes. Secretory synaptic peptides were influential contributors to the multilayer network. Older adults with lower physical activity had adverse relationships among pathology. There was interdependence among phosphorylated tau, synaptic integrity, and tangles. Network methods elucidate the role of physical activity in cognitive impairment.
60 APPLIED LIFE SCIENCES↗
Confinement Controls the Bend Instability of Three-Dimensional Active Liquid Crystals
Spontaneous growth of long-wavelength deformations is a defining feature of active liquid crystals. We investigate the effect of confinement on the instability of 3D active liquid crystals in the isotropic phase composed of extensile microtubule bundles and kinesin molecular motors. When shear aligned, such fluids exhibit finite-wavelength self-amplifying bend deformations. By systematically changing the channel size we elucidate how the instability wavelength and its growth rate depend on the channel dimensions. Experimental findings are qualitatively consistent with a minimal hydrodynamic model, where the fastest growing deformation is set by a balance of active driving and elastic relaxation. Furthermore, our results demonstrate that confinement determines the structure and dynamics of active fluids on all experimentally accessible length scales.
59 BASIC BIOLOGICAL SCIENCES↗
LDRD FY25 Program Overview
As Lawrence Livermore National Laboratory’s (LLNL’s) Laboratory Directed Research and Development (LDRD) program enters its fifth decade of leading-edge research and development, its impact and importance have never been stronger. The program continues to advance strategic investments in pioneering science, technology, and engineering, ensuring LLNL will be ready to deliver on our mission as it evolves over the coming decades. Investing in LDRD research, and the people who perform this critical work, gives LLNL the ability to sustain our role as a leader in the Department of Energy and National Nuclear Security Administration enterprise. The LDRD program enables high-risk, high-payoff research that anticipates emerging threats and future mission needs. By nurturing the ingenuity of the Lab’s greatest asset, its people, LDRD funding advances not only our research but also grows and nurtures our workforce: engaging future innovators with student mentoring, challenging postdoctoral researchers to apply their skills to support national security, and strengthening the leadership skills of early career staff. This annual report documents how LDRD investments advance LLNL’s science, technology, and engineering across our mission space. To assess LDRD’s impact we track both short and long-term metrics such as peer-reviewed publications, number of students, or professional fellows. In addition to reviewing these metrics, I encourage you to delve deeper into the breadth of science and technology that illustrate the strategic value of this research portfolio. For instance, a recent exploratory research project used advanced manufacturing to construct miniaturized three-dimensional ion traps for a quantum computer with reduced quantum error rates to enable applications that address national security missions and support basic science. Another project has delved into studying detonation by examining deflagration to enhance the safety and security of the nuclear weapons stockpile. LDRD researchers are also deploying AI agents on two of the world’s most powerful supercomputers to automate and accelerate inertial confinement fusion experiments. Other teams are delivering more accurate optical constants to enable improved validation for aluminum to advance atomic and molecular physics models. LDRD-driven discoveries of how metals deform under extreme conditions strengthen our ability to model and design materials for demanding national security environments. National security challenges are increasingly complex and continuously evolving. LDRD focuses our most innovative science and technology on these challenges, ensuring the Laboratory is developing creative, forward-leaning solutions for our nation and the world. The following pages feature highlights of published scientific advances, patents, and honors that stem from LDRD investments. As you read this report, I hope you will understand how these investments position the Laboratory, and our partners, to meet the demands of the decades ahead.
36 MATERIALS SCIENCE↗
Dynamic response of biological materials.
Effect of varying strain rate on physical properties of bone and muscle tissue, measuring load and time displacement with constant-velocity compression test machine
STRAIN RATE↗
Mass mortality and extraterrestrial impacts
The discovery of iridium enrichment at the Cretaceous/Tertiary boundary resulted in formulation of hypothesis of a cometary or asteroid impact as the cause of the biological extinctions at this boundary. Subsequent discoveries of geochemical anomalies at major stratigraphic boundaries like the Precambrian/Cambrian, Permian/Triassic, Middle/Late Jurassic, resulted in the application of similar extraterrestrial impact theories to explain biological changes at these boundaries. Until recently the major physical evidence, as is the location of the impact crater site, to test the impact induced biological extinction was lacking. The diameter of such a crater would be in the range of 60 to 100 km. The recent discovery of the first impact crater in the ocean provide the first opportunity to test the above theory. The crater, named Montagnais and located on the outer shelf off Nova Scotia, Canada, has a minimum diameter of 42 km, with some evidence to a diameter of more than 60 km. At the Montagnais impact site, micropaleontological analysis of the uppermost 80 m of the fall-back breccia represented by a mixture of pre-impact sediments and basement rocks which fills the crater and of the basal 50 m of post-impact marine sediments which overly the impact deposits, revealed presence of diversified foraminiferal and nannoplankton assemblages. The sediments which are intercalated within the uppermost part of the fall-back breccia, had to be deposited before the meteorite impact. The post-impact deposits were laid down almost immediately after the impact as also supported by the micropaleontological data. In conclusion, micropaleontological studies of sediments from the first submarine impact crater site identified in the ocean did not reveal any mass extinction or significant biological changes at the impact site or in the proximal deep ocean basin.
Jansa, L. F.↗
Radiation dosimetry and biophysical models of space radiation effects
Estimating the biological risks from space radiation remains a difficult problem because of the many radiation types including protons, heavy ions, and secondary neutrons, and the absence of epidemiology data for these radiation types. Developing useful biophysical parameters or models that relate energy deposition by space particles to the probabilities of biological outcomes is a complex problem. Physical measurements of space radiation include the absorbed dose, dose equivalent, and linear energy transfer (LET) spectra. In contrast to conventional dosimetric methods, models of radiation track structure provide descriptions of energy deposition events in biomolecules, cells, or tissues, which can be used to develop biophysical models of radiation risks. In this paper, we address the biophysical description of heavy particle tracks in the context of the interpretation of both space radiation dosimetry and radiobiology data, which may provide insights into new approaches to these problems.
Review↗
Cosmic heavy ion tracks in mesoscopic biological test objects
Since more than 20 years ago, when the National Academy of Sciences and the National Research Council of the U.S.A. released their report on 'HZE particle effects in manned spaced flight', it has been emphasized how difficult - if not even impossible - it is to assess their radiobiological impact on man from conventional studies where biological test organisms are stochastically exposed to 'large' fluences of heavy ions. An alternative, competing approach had been realized in the BIOSTACK experiments, where the effects of single cosmic as well as accelerator - heavy ions on individual biological test organisms could be investigated. Although presented from the beginning as the preferable approach for terrestrial investigations with accelerator heavy ions too ('The BIOSTACK as an approach to high LET radiation research'), only recently this insight is gaining more widespread recognition. In space flight experiments, additional constraints imposed by the infrastructure of the vehicle or satellite further impede such investigations. Restrictions concern the physical detector systems needed for the registration of the cosmic heavy ions' trajectories as well as the biological systems eligible as test organisms. Such optimized procedures and techniques were developed for the investigations on chromosome aberrations induced by cosmic heavy ions in cells of the stem meristem of lettuce seeds (Lactuca sativa) and for the investigation of the radiobiological response of Wolffia arriza, which is the smallest flowering (water) plant. The biological effects were studied by the coworkers of the Russian Institute of Biomedical Problems (IBMP) which in cooperation with the European Space Agency ESA organized the exposure in the Biosatellites of the Cosmos series. Since biological investigations and physical measurements of particle tracks had to be performed in laboratories widely separated, the preferred fixed contact between biological test objects and the particle detectors until the geometrical correlation between tracks and organisms has been established could not be maintained. This gave rise to half a dozen of coordinate systems for different measurements which finally had to be related to a single stack reference system.
Facius, R.↗
Biosentinel: Developing a Space Radiation Biosensor
Ionizing radiation presents a major challenge to human exploration and long-term residence in space. The deep-space radiation spectrum includes highly energetic particles that generate double strand breaks (DSBs), deleterious DNA lesions that are usually repaired without errors via homologous recombination (HR), a conserved pathway in all eukaryotes. While progress identifying and characterizing biological radiation effects using Earth-based facilities has been significant, no terrestrial source duplicates the unique space radiation environment.We are developing a biosensor-based nanosatellite to fly aboard NASAs Space Launch System Exploration Mission 1, expected to launch in 2017 and reach a 1AU (astronomic unit) heliocentric orbit. Our biosensor (called BioSentinel) uses the yeast S. cerevisiae to measure DSBs in response to ambient space radiation. The BioSentinel strain contains engineered genetic defects that prevent growth until and unless a radiation-induced DSB near a reporter gene activates the yeasts HR repair mechanisms. Thus, culture growth and metabolic activity directly indicate a successful DSB-and-repair event. In parallel, HR-defective and wild type strains will provide survival data. Desiccated cells will be carried within independent culture microwells, built into 96-well microfluidic cards. Each microwell set will be activated by media addition at different time points over 18 months, and cell growth will be tracked continuously via optical density. One reserve set will be activated only in the occurrence of a solar particle event. Biological measurements will be compared to data provided by onboard physical dosimeters and to Earth-based experiments.BioSentinel will conduct the first study of biological response to space radiation outside Low Earth Orbit in over 40 years. BioSentinel will thus address strategic knowledge gaps related to the biological effects of space radiation and will provide an adaptable platform to perform human-relevant measurements in multiple space environments. We hope that it can therefore be used on the ISS, on and around other planetary bodies as well as other exploration platforms as a self-contained system that will allow us to compare and calibrate different radiation environments.BioSentinels results will be critical for improving interpretation of the effects of space radiation exposure, and for reducing the risk associated with long-term human exploration.
space radiation↗
Microbial Extremophiles for Earth and Beyond: Pushing the Boundaries with Synthetic Biology
All organisms live in a multi-dimensional physical and chemical niche space. Discoveries in the 20th century enormously expanded the range of what was considered "habitable." However, the current diversity of life on Earth begs the question of what terrestrial life - or indeed, another life form - would be capable of. With the needs of both modern laboratory science and the burgeoning field of biotechnology, as well as our deeply held desire to answer the question "are we alone in the universe?, we are exploiting the tools of synthetic biology to probe the question of whether we can create "synthetic extremophiles" or, as our lab has dubbed them, "Hell Cells."
synthetic extremophiles↗
Sanford Underground Research Facility’s approach to school education, community activities, and public outreach
The Sanford Underground Research Facility (SURF) is the deepest underground science facility in the United States. SURF hosts world-leading experiments in neutrino, astroparticle and nuclear physics, as well as projects in biology, geology, and engineering, and is home to a major excavation project making space for Fermi National Accelerator Laboratory’s Long-Baseline Neutrino Facility (LBNF), which will power the Deep Underground Neutrino Experiment (DUNE). An emphasis on outreach and education is embedded in SURF’s mission statement: “to advance world-class science and inspire learning across generations.” To achieve this mission, SURF goes beyond established science communication methods, including operating an open-to-the-public visitor center, hosting multiple public outreach events per month, and an annual city-wide science festival. Furthermore, SURF is training K-12 science educators, developing school curriculum units, and providing classroom materials, based on science researched at the laboratory. The strategic approach, specific methods, and successful outcomes of these programs, which are based on SURF’s science, location, and community, may serve as examples for effective science education, public outreach, and community engagement.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Biological rhythms
An overview is given of basic features of biological rhythms. The classification of periodic behavior of physical and psychological characteristics as circadian, circannual, diurnal, and ultradian is discussed, and the notion of relativistic time as it applies in biology is examined. Special attention is given to circadian rhythms which are dependent on the adrenocortical cycle. The need for adequate understanding of circadian variations in the basic physiological indicators of an individual (heart rate, body temperature, systolic and diastolic blood pressure, etc.) to ensure the effectiveness of prophylactic and therapeutic measures is stressed.
Halberg, F.↗