Results for “biological processing” — Page 47

NASA NTRS1984

Inland Aquatic Resources and Biogeochemical Cycles

The biosphere is the entire planetary system that includes, sustains and is influenced by life. The central issue of the science of the biosphere is the extent to which the Earth's surface, atmosphere and hydrosphere is the result of biological rather than abiotic processes. Space science and technology accelerates the understanding of global biological processes by providing repetive synoptic observations on large spatial scales once the relationships between the processes and the remotely sensed quantities are established. Especially promising applications of space technology are the measurement of biological productivity and portions of geochemical cycles in aquatic ecosystems and the evaluation and management of the quality of freshwater resources.

Melack, J. M.↗

NASA NTRS2008

Growth Control and Disease Mechanisms in Computational Embryogeny

This paper presents novel approach to applying growth control and diseases mechanisms in computational embryogeny. Our method, which mimics fundamental processes from biology, enables individuals to reach maturity in a controlled process through a stochastic environment. Three different mechanisms were implemented; disease mechanisms, gene suppression, and thermodynamic balancing. This approach was integrated as part of a structural evolutionary model. The model evolved continuum 3-D structures which support an external load. By using these mechanisms we were able to evolve individuals that reached a fixed size limit through the growth process. The growth process was an integral part of the complete development process. The size of the individuals was determined purely by the evolutionary process where different individuals matured to different sizes. Individuals which evolved with these characteristics have been found to be very robust for supporting a wide range of external loads.

Genetic algorithm↗

DOE OSTI2026

Divergent carbon use efficiency-growth rate tradeoff in popular biological growth models

Carbon use efficiency (CUE) is an important trait emerging from processes regulating biological growth. CUE can be computed either based on the growth of structural biomass or total biomass divided by substrate uptake rate. Nonequilibrium thermodynamics and observations suggest that, for an exponentially growing population of cells, structural biomass CUE should first increase, then peak, and finally decrease with specific growth rate; meanwhile, total biomass CUE increases asymptotically with specific growth rate. We compared predictions from six popular models that are often used for plant and microbial growth in existing ecosystem models. We found that, for an exponentially growing population of biological cells, (1) the source-driven Pirt and Compromise models predict that structural biomass CUE increase asymptotically with growth rate; (2) the apparent sink-driven modified Droop model predicts that structural biomass CUE decreases with growth rate; and (3) the sink-driven variable internal storage model and two dynamic energy budget models predict that structural biomass CUE first increases, then peaks, and finally decreases with growth rate. Moreover, the modified Droop model predicts that total biomass CUE is constant with growth rate, while all other five models predict that total biomass CUE increases with growth rate asymptotically. For non-exponential biological growth, we show that there is no static relationship between total biomass CUE or structural biomass CUE with respect to either growth rate or temperature. Therefore, we contend that biological growth models should explicitly represent interactions between substrate acquisition, substate transformation, and maintenance respiration to better capture observed CUE dynamics, and the sink-driven model should be preferred for general ecosystem biogeochemistry modeling.

Tang, Jinyun [Lawrence Berkeley National Laborator↗

DOE OSTI2016

WE-DE-202-00: Connecting Radiation Physics with Computational Biology

Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are the most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological processes are too complex for a mechanistic approach. Can computer simulations be used to guide future biological research? We will debate the feasibility of explaining biology from a physicists’ perspective. Learning Objectives: Understand the potential applications and limitations of computational methods for dose-response modeling at the molecular, cellular and tissue levels Learn about mechanism of action underlying the induction, repair and biological processing of damage to DNA and other constituents Understand how effects and processes at one biological scale impact on biological processes and outcomes on other scales J. Schuemann, NCI/NIH grantsS. McMahon, Funding: European Commission FP7 (grant EC FP7 MC-IOF-623630)

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

WE-DE-202-01: Connecting Nanoscale Physics to Initial DNA Damage Through Track Structure Simulations

Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are the most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological processes are too complex for a mechanistic approach. Can computer simulations be used to guide future biological research? We will debate the feasibility of explaining biology from a physicists’ perspective. Learning Objectives: Understand the potential applications and limitations of computational methods for dose-response modeling at the molecular, cellular and tissue levels Learn about mechanism of action underlying the induction, repair and biological processing of damage to DNA and other constituents Understand how effects and processes at one biological scale impact on biological processes and outcomes on other scales J. Schuemann, NCI/NIH grantsS. McMahon, Funding: European Commission FP7 (grant EC FP7 MC-IOF-623630)

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

WE-DE-202-02: Are Track Structure Simulations Truly Needed for Radiobiology at the Cellular and Tissue Levels?

Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are the most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological processes are too complex for a mechanistic approach. Can computer simulations be used to guide future biological research? We will debate the feasibility of explaining biology from a physicists’ perspective. Learning Objectives: Understand the potential applications and limitations of computational methods for dose-response modeling at the molecular, cellular and tissue levels Learn about mechanism of action underlying the induction, repair and biological processing of damage to DNA and other constituents Understand how effects and processes at one biological scale impact on biological processes and outcomes on other scales J. Schuemann, NCI/NIH grantsS. McMahon, Funding: European Commission FP7 (grant EC FP7 MC-IOF-623630)

60 APPLIED LIFE SCIENCES↗

NASA NTRS2019

Uncertainties in the Geostationary Ocean Color Imager (GOCI) Remote Sensing Reflectance for Assessing Diurnal Variability of Biogeochemical Processes

Short-term (sub-diurnal) biological and biogeochemical processes cannot be fully captured by the current suite of polar-orbiting satellite ocean color sensors, as their temporal resolution is limited to potentially one clear image per day. Geostationary sensors, such as the Geostationary Ocean Color Imager (GOCI) from the Republic of Korea, allow the study of these short-term processes because their orbit permit the collection of multiple images throughout each day for any area within the sensor’s field of regard. Assessing the capability to detect sub-diurnal changes in in-water properties caused by physical and biogeochemical processes characteristic of open ocean and coastal ocean ecosystems, however, requires an understanding of the uncertainties introduced by the instrument and/or geophysical retrieval algorithms. This work presents a study of the uncertainties during the daytime period for an ocean region with characteristically low-productivity with the assumption that only small and undetectable changes occur in the in-water properties due to biogeochemical processes during the daytime period. The complete GOCI mission data were processed using NASA’s SeaDAS/l2gen package. The assumption of homogeneity of the study region was tested using three-day sequences and diurnal statistics. This assumption was found to hold based on the minimal diurnal and day-to-day variability in GOCI data products. Relative differences with respect to the midday value were calculated for each hourly observation of the day in order to investigate what time of the day the variability is greater. Also, the influence of the solar zenith angle in the retrieval of remote sensing reflectances and derived products was examined. Finally, we determined that the uncertainties in water-leaving “remote-sensing” reflectance (Rrs) for the 412, 443, 490, 555, 660 and 680 nm bands on GOCI are 8.05 × 10−4, 5.49 × 10−4, 4.48 × 10−4, 2.51 × 10−4, 8.83 × 10−5, and 1.36 × 10−4 sr−1, respectively, and 1.09 × 10−2 mg m−3 for the chlorophyll-a concentration (Chl-a), 2.09 × 10−3 m−1 for the absorption coefficient of chromophoric dissolved organic matter at 412 nm (ag (412)), and 3.7 mg m−3 for particulate organic carbon (POC). These Rrs values can be considered the threshold values for detectable changes of the in-water properties due to biological, physical or biogeochemical processes from GOCI.

Geostationary Ocean Color Imager (GOCI)↗

NASA NTRS2019

Uncertainties in the Geostationary Ocean Color Imager (GOCI) Remote Sensing Reflectance for Assessing Diurnal Variability of Biogeochemical Processes

Short-term (sub-diurnal) biological and biogeochemical processes cannot be fully captured by the current suite of polar-orbiting satellite ocean color sensors, as their temporal resolution is limited to potentially one clear image per day. Geostationary sensors, such as the Geostationary Ocean Color Imager (GOCI) from the Republic of Korea, allow the study of these short-term processes because their orbit permit the collection of multiple images throughout each day for any area within the sensor’s field of regard. Assessing the capability to detect sub-diurnal changes in in-water properties caused by physical and biogeochemical processes characteristic of open ocean and coastal ocean ecosystems, however, requires an understanding of the uncertainties introduced by the instrument and/or geophysical retrieval algorithms. This work presents a study of the uncertainties during the daytime period for an ocean region with characteristically low-productivity with the assumption that only small and undetectable changes occur in the in-water properties due to biogeochemical processes during the daytime period. The complete GOCI mission data were processed using NASA’s SeaDAS/l2gen package. The assumption of homogeneity of the study region was tested using three-day sequences and diurnal statistics. This assumption was found to hold based on the minimal diurnal and day-to-day variability in GOCI data products. Relative differences with respect to the midday value were calculated for each hourly observation of the day in order to investigate what time of the day the variability is greater. Also, the influence of the solar zenith angle in the retrieval of remote sensing reflectances and derived products was examined. Finally, we determined that the uncertainties in water-leaving “remote-sensing” reflectance (Rrs) for the 412,443, 490, 555, 660 and 680 nm bands on GOCI are 8.05 x 10(exp -4), 5.49 x 10(exp -4), 4.48 x 10(exp -4), 2.51 x 10(exp -4), 8.83 x 10(exp -5), and 1.36 x 10(exp -4)/sr, respectively, and 1.09 x 10(exp -2)/cu.mgm for the chlorophyll-a concentration (Chl-a), 2.09 x 10(exp -3)/m for the absorption coefficient of chromophoric dissolved organic matter at 412 nm (a(sub g) (412)), and 3.7 mg/cu.m for particulate organic carbon (POC). These R(sub rs) values can be considered the threshold values for detectable changes of the in-water properties due to biological, physical or biogeochemical processes from GOCI.

Concha, Javier↗

DOE OSTI2018

Correction of Fluorescent Images of Biological Tissues for the Effects of Light Absorption and Scattering

A method for correcting the influence of light attenuation processes in biological tissues on their fluorescent images is proposed. The transfer function that takes into account the radiation losses in the medium at the wavelengths of excitation and emission of fluorescence is calculated analytically, depending on the transport scattering index and the hemoglobin tissue index. The latter is determined on the basis of a color image of the tissue in reflected visible light. Verification of the developed method was carried out on the basis of computer simulation of fluorescent images of biological tissue by the Monte Carlo method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2018

Biochemical Mechanisms and Associated Biomolecular Signatures Underlying Energy Strategies of Geobacter Sulfurreducens

To provide the scientific understanding required to allow DOE sites to incorporate relevant biological, chemical, and physical processes into decisions concerning environmental remediation, a fundamental understanding of the controls on micro-organism growth in the subsurface is necessary. Specifically, mobility of metals in the environment, including chromium, technetium and uranium, is greatly affected by the process of dissimilatory metal reduction (DMR). DMR has been shown to be an important biological activity controlling contaminant mobility in the subsurface at many DOE sites. Long-term maintenance of DMR at constant rates must rely upon steady fluxes of electron donors to provide the maintenance energy needed by organisms such as Geobacter sulfurreducens to maintain steady state populations in the subsurface. At present, much effort has been put forth to develop biomolecular signatures which inform on the relevant biological processes at DOE field sites. These signatures are also being developed in defined laboratory conditions to which the field data can be compared to. These signatures include metagenomic, metatranscriptomic and proteomic characterization. While the relevant processes involve reduction of metal contaminants, we suggest that the predominant biochemistry that impacts the biomolecular signature is nutrient availability/limitation. As such, the present proposal aims at characterizing the survival strategy of Geobacter and obtaining biomolecular signatures that would reflect on its energy flux status. In addition, we lack the fundamental knowledge needed to answer fundamental questions such as these: What influxes of electron donors are required to maintain a growing versus a non-growing population of Geobacter? How do changes in nutrient availability or other environmental conditions such as pH and ionic strength affect such required electron-donor influxes? How are these electron-donor influxes controlled by availability and nature of electron acceptors? Under survival conditions, where availability of electron acceptors and nutrients are extremely low, what physiological and genetic modifications occur in Geobacter to enable long-term survival? How do these changes affect the required electron-donor influxes? Is it possible to relate the metabolic activities of Geobacter living under survival mode to the required fluxes of electron donors? What conceptual models can be used to predict maintenance energies of Geobacter under different phases of growth when measured under different environmental conditions? How can these models help the DOE predict the long-term evolution of contaminated sites? We outline a strategy to tackle these questions and lay the framework for DOE to make long-term predictions concerning DMR in the subsurface. We will test the following hypothesis: Geobacter requires different fluxes of substrate for metabolism when existing under growth, stationary, or survival modes, and these substrate fluxes can be related to specific metabolic activities utilized under different geochemical conditions. Our project has two specific objectives: i) Determine the survival characteristics of Geobacter under long-term stationary phase by characterize the physiological response of Geobacter in growth, stationary, and survival phases using genomic sequencing, DNA microarray chips and iTRAQ (proteomics) and relate these responses to the measured substrate fluxes; ii) Determination of growth yield and maintenance energy. While site-specific studies are necessary for site-specific remediation, our work will provide the fundamental knowledge necessary for long-term stewardship of all DOE sites where contaminant mobility is affected by dissimilatory metal reduction.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1990

Optical constraints of kerogen from 0.15 to 40 microns: Comparison with meteoritic organics

Kerogens are dark, complex organic materials produced on the Earth primarily by geologic processing of biologic materials, but kerogens have chemical and spectral similarities to some classes of highly processed extraterrestrial organic materials. Kerogen-like solids were proposed as constitutents of the very dark reddish surfaces of some asteroids and are also spectrally similar to some carbonaceous organic residues and the Iapetus dark material. Kerogen can thus serve as a useful laboratory analog to very dark, spectrally red extraterrestrial materials; its optical constants can be used to investigate the effects of particle size, void space and mixing of bright and dark components in models of scattering by dark asteroidal, cometary, and satellite surfaces. Measurements of the optical constants of both Type 2 kerogen and of macromolecular organic residue from the Murchison carbonaceous chondrite via transmission and reflection measurements on thin films are reported. The real part of the refractive index, n, is determined by variable incidence-angle reflectance to be 1.60 + or - 0.05 from 0.4 to 2.0 micrometers wavelength. Work extending the measurement of n to longer wavelengths is in progress. The imaginary part of the refractive index, k, shows substantial structure from 0.15 to 40 micrometers. The values are accurate to + or - 20 percent in the UV and IR regions and to + or - 30 percent in the visible. The k values of organic residues were also measured from the Murchison meteorite. Comparison of the kerogen and Murchison data reveals that between 0.15 and 40 microns, Murchison has a similar structure but no bands as sharp as in kerogen, and that the k values for Murchison are significantly higher than those of kerogen.

Khare, Bishun N.↗

NASA NTRS2000

Genetic Network Inference: From Co-Expression Clustering to Reverse Engineering

Advances in molecular biological, analytical, and computational technologies are enabling us to systematically investigate the complex molecular processes underlying biological systems. In particular, using high-throughput gene expression assays, we are able to measure the output of the gene regulatory network. We aim here to review datamining and modeling approaches for conceptualizing and unraveling the functional relationships implicit in these datasets. Clustering of co-expression profiles allows us to infer shared regulatory inputs and functional pathways. We discuss various aspects of clustering, ranging from distance measures to clustering algorithms and multiple-duster memberships. More advanced analysis aims to infer causal connections between genes directly, i.e., who is regulating whom and how. We discuss several approaches to the problem of reverse engineering of genetic networks, from discrete Boolean networks, to continuous linear and non-linear models. We conclude that the combination of predictive modeling with systematic experimental verification will be required to gain a deeper insight into living organisms, therapeutic targeting, and bioengineering.

Dhaeseleer, Patrik↗

DOE OSTI2021

The Role of Quantum Science Concepts in Enhancing Sensing and Imaging Technologies: Applications for Biology: Proceedings of a Workshop

Quantum concepts hold the potential to enable significant advances in sensing and imaging technologies that could be vital to the study of biological systems. The workshop Quantum Science Concepts in Enhancing Sensing and Imaging Technologies: Applications for Biology, held online March 8–10, 2021, was organized to examine the research and development needs to advance biological applications of quantum technology. Hosted by the National Academies of Sciences, Engineering, and Medicine, the event brought together experts working on state-of-the-art, quantum-enabled technologies and scientists who are interested in applying these technologies to biological systems. Through talks, panels, and discussions, the workshop facilitated a better understanding of the current and future biological applications of quantum-enabled technologies in fields such as microbiology, molecular biology, cell biology, plant science, mycology, and many others. The workshop was organized around three main themes. The first, quantum in biology, examined quantum concepts that are hypothesized to be important for life processes and that researchers are working to observe through biological imaging and sensing. The second, quantum for biology, addressed ways to use quantum concepts to enhance technologies for biological imaging and sensing. The third, biology for quantum, offered a wider discussion of how the frontiers of biological imaging and sensing could enable future study using quantum concepts, tools, or technologies. Throughout the workshop, participants identified a wide range of emerging approaches and opportunities at the intersection of quantum physics and biological sensing and imaging. During the workshop, there were some differences in how each speaker defined the term quantum. During one of the panels, Prem Kumar offered thoughts on what phenomena are classical versus quantum, explaining that techniques get progressively more quantum as you move from just having superposition to having superposition with measurement and entanglement. Another explanation from Clarice Aiello delineates the definition into several levels. This includes a base level of “quantum-ness,” which reflects that all matter is made of atoms, and when these particles are isolated they behave based on quantum mechanical principles. A second level is related to quantum coherence, where a single quantum object might be found in a coherent superposition state. A final level, which she described as the quantum-entangled level, involves multiple quantum systems which are entangled among themselves. Overall, the workshop touched on concepts such as superposition, entanglement, and squeezing and their potential implications for communication, computing, and simulation, in addition to the workshop’s main focal area, biological sensing and imaging. At the opening of the workshop, Thorsten Ritz of the University of California, Irvine, identified two questions at the heart of quantum biology: Is the machinery of life quantum mechanical, and can quantum mechanics be used to study the machinery of life in new ways? Participants highlighted systems in which researchers have explored these questions, from the vast array of molecular interactions involved in biological processes such as photosynthesis, to the mechanics involved in cellular functions such as differentiation and aggregation, to the role of oscillating magnetic fields in flight orientation among birds. Sensing and imaging technologies are crucial to biological research; these technologies could both enhance the study of quantum effects and be enhanced by quantum concepts. A critical challenge in biological research is to develop imaging and sensing tools that do not damage or interfere with the often fragile and fleeting systems being studied. Attendees discussed a variety of established and emerging technologies that could enhance noninvasive biological imaging, including single- and two-photon spectroscopy, single-molecule spectroscopy, quantum illumination, ghost imaging, and cryo-electron microscopy. One example came from Marlan Scully who gave a keynote address on the first day of the workshop. Scully emphasized the use of different laser technologies, which exhibit coherence and other quantum properties, in moving toward real-world biological applications, such as the detection of SARS-CoV-2. Both tools and theory will play an important role in advancing quantum biology research and applications. Several participants suggested theorists and experimentalists should work in tandem to understand and model biological processes. While physics often reduces systems to their simplest forms for fundamental insights, participants also noted the value of observing and understanding biological systems in all their “messiness,” capturing both the inner workings of biological systems and the complex interactions that occur within and between organisms. In discussions among participants, several attendees stressed the need to match emerging tools with the right scientific questions. Rather than developing quantum technologies as “a hammer looking for a nail,” participants emphasized a focus on exploring the problems these technologies are best suited to address. For example, it is important to consider the size of the phenomenon being studied, the timescales that are important in answering the scientific question, and other relevant considerations. Every tool along the spectrum from classical to quantum involves its own set of trade-offs. For example, Ted Laurence of the Lawrence Livermore National Laboratory said that quantum measurements, such as single photon counting, fluorescence transitions, and lasers, can take longer to produce the same results as classical measurements. These quantum measurements, however, do not require calibration and can enable new research questions to be answered. Prem Kumar, Northwestern University, noted that, despite their promise, quantum approaches should not be used simply for the sake of using quantum, especially in situations where classical approaches better meet the needs of the researcher. Understanding and applying quantum concepts could enable advances in a wide range of application areas including energy, synthetic biology, medicine, and sustainability. For example, Michelle O’Malley, University of California, Santa Barbara, described how improved noninvasive imaging approaches could help capture the complex interactions and functions involved in the breakdown of organic matter by microbial communities and lead to new technologies for capturing valuable products from plant waste. Several other participants discussed needs in tracking the movement of metabolites and molecules in microbial communities for insights into nutrient cycling in environments such as soil. Margaret Ahmad, Sorbonne University, discussed potential opportunities to leverage the magnetic properties of cryptochromes to advance new treatment approaches for diseases such as COVID-19 and cancer. Looking toward the future development of the field, participants discussed challenges to advancing quantum biology that arise from disciplinary disconnects between physicists and biologists. The siloing of academic research disciplines represents a significant barrier to progress. Disconnects in terminology, motivations and priorities, and structural barriers to collaborative work underscore the need for concerted efforts to bridge these divides. Attendees and speakers offered suggestions for resolving these divergences, establishing a shared language, moving the field forward, and fostering meaningful feedback between disciplines. Overall, participants stressed a need for balance, open communication, collaboration, unity, and clear dialogue on trade-offs between quantum and classical approaches. Keiko Torii, The University of Texas at Austin, said that the best collaborations happen when the project provides mutual advantages that can show off everyone’s talents, each team finds the work interesting, and partners develop a camaraderie to pursue new knowledge. To enable near- and long-term opportunities in this space, participants suggested that exploratory, high-risk funding could improve existing instrumentation to explore quantum enhancement collaboratively. They also emphasized the need for collaboration between quantum physicists and sensing/imaging scientists, which could be advanced through a dedicated quantum biology investigator program. People, even more than technology, will be crucial to the future of quantum biology. Participants explored training, education, and workforce needs to further develop this burgeoning field and cultivate the next generation of scientists. While many programs are still in their nascent stages, participants highlighted examples of approaches and programs being developed at various types of institutions to engage students and professional scientists in quantum biology research. Several participants stressed the need for an inclusive approach, spanning disciplines as well as communities to foster a diverse field fueled by the intellectual contributions of a wide range of people, including historically under-resourced schools and students. To increase awareness and excitement about quantum physics and related areas of biology, attendees suggested capitalizing on the “buzz” around quantum. Several participants emphasized the need to start early, introducing students to quantum concepts and their appealing “weirdness” in K–12 education. Engaging students early—before they become entrenched in traditional disciplinary siloes as typically happens in graduate school—could help to galvanize interest in the area and foster a generation of scientists with the interdisciplinary mindset and skills needed to advance this interdisciplinary field. While these efforts could be advanced at many levels and across multiple sectors, several participants suggested a national quantum biology center could be a valuable hub to coordinate and support quantum biology education and workforce development across academia, industry, and government.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Quantum information in the Posner model of quantum cognition

Matthew Fisher recently postulated a mechanism by which quantum phenomena could influence cognition: Phosphorus nuclear spins may resist decoherence for long times. The spins would serve as biological qubits. The qubits may resist decoherence longer when in Posner molecules. We imagine that Fisher postulates correctly. How adroitly could biological systems process quantum information (QI)? We establish a framework for answering. Additionally, we construct applications of biological qubits to quantum error correction, quantum communication, and quantum computation. First, we posit how the QI encoded by the spins transforms as Posner molecules form. The transformation points to a natural computational basis for qubits in Posner molecules. From the basis, we construct a quantum code that detects arbitrary single-qubit errors. Each molecule encodes one qutrit. Shifting from information storage to computation, we define the model of Posner quantum computation. To illustrate the model’s quantum-communication ability, we show how it can teleport information incoherently: A state’s weights are teleported. Dephasing results from the entangling operation’s simulation of a coarse-grained Bell measurement. Whether Posner quantum computation is universal remains an open question. However, the model’s operations can efficiently prepare a Posner state usable as a resource in universal measurement-based quantum computation. The state results from deforming the Affleck–Kennedy–Lieb–Tasaki (AKLT) state and is a projected entangled-pair state (PEPS). Finally, we show that entanglement can affect molecular-binding rates, boosting a binding probability from 33.6% to 100% in an example. This work opens the door for the QI-theoretic analysis of biological qubits and Posner molecules.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Determination of Total, Organic, and Inorganic Carbon and Total Nitrogen in Biological Cultures and Liquid Fraction Process Samples: Laboratory Analytical Procedure (LAP)

This Laboratory Analytical Procedure (LAP) describes the quantitative determination of total organic carbon, inorganic carbon in whole suspended biological samples and in the cell-free supernatant, by combustion and CO 2 detection with a non-dispersive infrared (NDIR) detector. This allows for distinct reporting of soluble and insoluble organic and inorganic carbon. In addition, this procedure covers the quantitative determination of soluble nitrogen in the cell-free supernatant.

09 BIOMASS FUELS↗

NASA NTRS1976

Apollo-Soyuz Test Project: Preliminary Science Report

This document summarizes the experimental concepts and preliminary analyses (as of December 1975) for each of the 28 scientific experiments conducted during the Apollo-Soyuz Test Project from July 15 to 24, 1975. The scientific topics are X- ray and extreme ultraviolet astronomy, solar astronomy, gamma- ray detectors, Earth studies (including the upper atmosphere, meteorological phenomena, hydrology, oceanography, geology, desert studies, and gravity field studies), microbiology, heavy cosmic particle interaction with live cells, vestibular system studies, and materials processing (including high-temperature and ambient-temperature processing of industrial materials and electrophoretic processing of biological materials) .

Orbital science↗

DOE OSTI2020

One Electron Multiple Proton Transfer in Model Organic Donor–Acceptor Systems: Implications for High-Frequency EPR

EPR spectroscopy is an important spectroscopic method for identification and characterization of radical species involved in many biological reactions. The tyrosyl radical is one of the most studied amino acid radical intermediates in biology. Often in conjunction with histidine residues, it is involved in many fundamental biological electron and proton transfer processes, such as in the water oxidation in photosystem II. As biological processes are typically extremely complicated and hard to control, molecular bio-mimetic model complexes are often used to clarify the mechanisms of the biological reactions. In this work, we present theoretical calculations to investigate the sensitivity of magnetic resonance parameters to proton-coupled electron transfer events, as well as conformational substates of the molecular constructs which mimic the tyrosine-histidine (Tyr-His) pairs found in a large variety of proteins. Upon oxidation of the phenol, the Tyr analog, these complexes can perform not only one-electron one-proton transfer (EPT), but also one-electron two-proton transfers (E2PT). It is shown that in aprotic environment the g X -components of the electronicg-tensor are extremely sensitive to the first proton transfer from the phenoxyl oxygen to the imidazole nitrogen (EPT product), leading to a significant increase of the g X -value of up to 0.003, but are not sensitive to the second proton transfer (E2PT). In the latter case, the change of the g X -value is much smaller (ca. 0.0001), which is too small to be distinguished even by high-frequency EPR. The 14 N hyperfine values are also too similar to allow differentiation between the different protonation states in EPT and E2PT. The magnetic resonance parameters were also calculated as a function of the rotation angles around single bonds. It was demonstrated that rotation of the phenoxyl group results in large positive changes (> 0.001) in the g X -values. Analysis of the data reveals that the main source of these changes is related to the strength of the H-bond between phenoxyl oxygen and the proton(s) on N 1 and N 2 positions of the imidazole.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

PetaVision version 2.0

PetaVision is an open source, object oriented neural simulation toolbox optimized for high-performance multi-core, multi-node computer architectures. PetaVision is intended for computational neuroscientists who seek to apply neuromorphic models to hard signal processing problems; both to improve on the performance of existing algorithms and/or to gain insight into the computational mechanisms underlying biological neural processing. Please note that this assertion and ESTSC deposit are only for the portions of PetaVision which have been funded and written by LANL developers.

Lundquist, Sheng↗