<cellular biophysics- a study of the structure and function of living cells< progress report, period ending jul. 1, 1964
Cellular biophysics - ionizing radiation effect on genetics, cell mutation, and mutagenic nature of tritium decay
GENETICS↗
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Influence of cellular redox reactions on the structure and function of light harvesting and photosystems
Photosynthesis enables the conversion of one of the most abundant and free forms of energy, sunlight, into chemical bonds through the utilization of highly tailored protein complexes. These enzymes work in unison to absorb, convert, and transform light into high-energy electrons which are used for various functions important to metabolism and cellular protection. Over the last ∼50 years, photosynthetic organisms, such as cyanobacteria, have been adapted and engineered to produce valuable compounds like hydrogen and ethylene, among others. Often this is performed by removing native and/or adding in exogenous energy utilization pathways so that light energy is re-directed towards the synthesis of desired compounds. However, the interplay between primary light capture, conversion reactions, and the downstream electron utilization sinks is not fully understood. Further complicating these strategies are the plethora of compensatory mechanisms that facilitate steady electron flow and the maintenance of photosynthesis under dynamic conditions. This manifests as structural and functional plasticity of the photosynthetic machinery, often seen in modulations of oligomeric compositions or changes in protein-protein interactions and coupling with redox enzymes. Understanding these mechanisms is crucial to biotechnology applications because re-engineering electron utilization sinks has profoundly different effects on the light capture and conversion reactions of photosynthesis. Optimization requires a molecular-level understanding of the functional interrelationships between electron sinks and photosynthetic components that influence photosynthetic efficiencies to realize potential improvements in product yields. Here, we aim to highlight how perturbation of reductive reactions is revealing the functional plasticity in key components of the photosynthetic energy transduction pathway.
59 BASIC BIOLOGICAL SCIENCES↗
Is Water a Universal Solvent for Life?
There are strong reasons to believe that the laws, principles and constraints of physics and chemistry are universal. It is much less clear how this universality translates into our understanding of the origins of life. Conventionally, discussions of this topic focus on chemistry that must be sufficiently rich to seed life. Although this is clearly a prerequisite for the emergence of living systems, I propose to focus instead on self-organization of matter into functional structures capable of reproduction, evolution and responding to environmental changes. In biology, most essential functions are largely mediated by noncovalent interactions (interactions that do not involve making or breaking chemical bonds). Forming chemical bonds is only a small part of what living systems do. There are specific implications of this point of view for universality. I will concentrate on one of these implications. Strength of non-covalent interactions must be properly tuned. If they were too weak, the system would exhibit undesired, uncontrolled response to natural fluctuations of physical and chemical parameters. If they were too strong kinetics of biological processes would be slow and energetics costly. This balance, however, is not a natural property of complex chemical systems. Instead, it has to be achieved with the aid of an appropriate solvent for life. In particular, potential solvents for life must be characterized by a high dielectric constant to ensure solubility of polar species and sufficient flexibility of biological structures stabilized by electrostatic interactions. Among these solvents, water exhibits a remarkable trait that it also promotes solvophobic (hydrophobic) interactions between non-polar species, typically manifested by a tendency of these species to aggregate and minimize their contacts with the aqueous solvent. Hydrophobic interactions are responsible, at least in part, for many self-organization phenomena in biological systems, such as the formation of cellular boundary structures or protein folding. Strengths of electrostatic and hydrophobic interactions are similar and can be balanced over a wide range of temperatures, which considerably increases the repertoire of interactions that can be used to modulate biological functions. Some properties of water, e.g. its chemical activity against polymerization reactions, are considered as unfavorable to life. In actuality, this might be a favorable trait because life requires a balance between constructive and destructive processes. For example, molecules synthesized in response to specific conditions must be degraded once these conditions change. Otherwise regulation of biological processes would be virtually impossible. Water might not be the only liquid with favorable properties for supporting life. It has been proposed that formamide, which might be present elsewhere in the universe in sufficient quantities to warrant interest, could be a potential alternative to water for the origin of life. However, this will remain highly hypothetical until it is demonstrated in further studies on its physical, chemical and biological properties it is capable of mediating self-organization of matter and providing proper balance between different types of non-covalent interactions.
Pohorill, Andrew↗
In-situ radiation response of additively manufactured modified Inconel 718 alloys
Here in this study, a novel alloy of modified Inconel 718 produced by laser powder bed fusion is studied before and after in-situ Kr irradiation up to 3 dpa at 200 and 450 °C. Before irradiation, the microstructure consists of dislocation cells having a misorientation angle less than 5° and with an average size of ~500 nm. There are also second phase particles of MC type carbides, Laves phase and oxides such as Y-O, Y-(Ti)-Al-O. While the microstructure consists of stacking fault tetrahedra, faulted and perfect loops after irradiation at 200 °C, dislocation loops are the primary defects at 450 °C. With increasing dose, the size of the defects remains similar at 200 °C while it increases at 450 °C. This has been attributed to the existence of vacancy type defects at 200 °C and the different defect transport mechanisms at different temperatures. Moreover, matrix and second phase particle compositions seem to be similar after irradiation. The sink strengths of the structures have been calculated and superior radiation resistance of this alloy has been attributed to the existence of fine cell boundaries stabilized by the second phase particles produced by additive manufacturing.
36 MATERIALS SCIENCE↗
Multi-scale microstructural investigation of a laser 3D printed Ni-based superalloy
The heterogeneous microstructure of a laser 3D printed Ni-based superalloy was examined at multiple length scales. The sub-millimeter-sized columnar crystal grains are composed of micron-sized cellular colonies. The crystal grains grow in epitaxy with the substrate under the large temperature gradient and high cooling rate. The cell boundaries, decorated with γ/γ' eutectics, μ-phase precipitates and high density of dislocations, show enrichment of γ' forming elements and low-angle misorientations. Dislocations trapped in the intra-cellular regions are characterized as statistically stored dislocations with no detectable contribution to lattice curvature, and are the results of the interaction between dislocations and γ' precipitates.
36 MATERIALS SCIENCE↗
Uncovering grain and subgrain microstructure at the scale of additive manufacturing melt tracks with a scalable cellular automaton solidification model
Metal additive manufacturing, characterized by rapid solidification, yields refined grains with a distinctive cellular subgrain microstructure that plays a pivotal role in determining material properties. Due to the significant computational expense demanded to simulate the required physics with submicron spatial resolution, their numerical simulations have been limited to proof-of-concept studies to either 2D or small subregions of a melt pool. In this study, an open-source, scalable, solidification code, muMatScale, based on the cellular automaton method, has been developed to predict the grain and the underlying subgrain microstructure over an entire melt pool. The model incorporates flexible parallelization schemes, utilizing MPI and OpenMP GPU Offloading, in addition to appropriate multi-physics specific to non-equilibrium rapid solidification in AM. The impact of nucleation parameters on grain microstructures was investigated with a focus on grain size variations and morphology transitions. With selected nucleation parameters, the simulation predicted the grain size, subgrain morphology, crystallographic orientation, and microsegregation aligned with experimental measurements. The model demonstrates that epitaxial grain growth is a dominant factor at the melt pool boundary, influencing grain size variation under different grain sizes in the build plate while maintaining consistent primary dendrite arm spacing under identical thermal conditions. Here, the highly efficient numerical model enables large-scale simulations with a spatial resolution of 100 nm or less, unveiling unprecedented insights into thermal and solutal diffusion driven grain growth, and the subgrains with microsegregation within grains in 3D across scales. muMatScale will enable the linking of submicron length-scale microstructure to part-level material behavior by investigating fundamental solidification problems at the intercellular scale in many-track and many-layer builds.
36 MATERIALS SCIENCE↗
Influence of pore geometry and distribution on buckling under micro computed tomography
Not Available
36 MATERIALS SCIENCE↗
Preferential interactions of primary amine-terminated quantum dots with membrane domain boundaries and lipid rafts revealed with nanometer resolution
The initial interactions of engineered nanoparticles (NPs) with living cells are governed by physicochemical properties of the NP and the molecular composition and structure of the cell membrane. Eukaryotic cell membranes contain lipid rafts – liquid-ordered nanodomains involved in membrane trafficking and molecular signaling. However, the impact of these membrane structures on cellular interactions of NPs remains unclear. Here we investigate the role of membrane domains in the interactions of primary amine-terminated quantum dots (Qdots) with liquid-ordered domains or lipid rafts in model membranes and intact cells, respectively. Using correlative atomic force and fluorescence microscopy, we found that the Qdots preferentially localized to boundaries between liquid-ordered and liquid-disordered phases in supported bilayers. The Qdots also induced holes at these phase boundaries. Using super resolution fluorescence microscopy (STORM), we found that the Qdots preferentially co-localized with lipid rafts in the membrane of intact trout gill epithelial cells – a model cell type for environmental exposures. Our observations uncovered preferential interactions of amine-terminated Qdots with liquid-ordered domains and their boundaries, possibly due to membrane curvature at phase boundaries creating energetically favorable sites for NP interactions. The preferential interaction of the Qdots with lipid rafts supports their potential internalization via lipid raft-mediated endocytosis and interactions with raft-resident signaling molecules.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Cavitation model of the inflationary stage of Big Bang
In this study, we propose a model for the initial stage of the development of the universe analogous to cavitation in a liquid in a negative pressure field. It is assumed that at the stage of inflation, multiple breaks of the metric occur with the formation of areas of physical vacuum in which the generation of matter occurs. The proposed model explains the large-scale isotropy of the universe without ultrafast inflationary expansion and the emergence of a large-scale cellular (cluster) structure, as a result of the development of cavitation ruptures of a false vacuum. It is shown that the cavitation model can be considered on par with (or as an alternative to) the generally accepted inflationary multiverse model of the Big Bang.
79 ASTRONOMY AND ASTROPHYSICS↗
A MEMS dynamic mechanical analyzer for in situ viscoelastic characterization of 3D printed nanostructures
Cellular metamaterial structures with sub-micron features have shown the ability to become excellent energy absorbing materials for impact mitigation due to the enhanced mechanical properties of materials at the nanoscale. However, in order to optimize the design of these energy absorbing metamaterial structures we need to be able to measure the dynamic properties of the sub-micron features such as storage and loss moduli and the loss factor. Therefore, at scale testing is required to capture the scale, temperature, and strain rate dependent material properties of these nanoscale materials. This study presents the design, fabrication, and calibration of a MEMS-based dynamic mechanical analyzer (DMA) that can be directly integrated with the two photon lithography (TPL) process commonly used to fabricate metamaterial structures with nanoscale features. The MEMS-based DMA consists of a chevron style thermal actuator used to generate a tensile load on the structure and two differential capacitive sensors on each side of the structure used to measure load and displacement. This design demonstrated 1.5 ± 0.75 nm displacement resolution and 104 ± 52 nN load resolution, respectively. Dynamic mechanical analysis was successfully conducted on a single nanowire feature printed between the load and displacement stages of the MEMS device with testing frequencies ranging between 0.01–10 Hz and testing temperatures ranging between 22 °C–47 °C. These initial tests on an exemplar TPL part demonstrate that the printed nanowire behaves as a viscoelastic material wherein the transition from glassy to viscous behavior has already set in at the room temperature.
42 ENGINEERING↗
ssDNA is an allosteric regulator of the C. crescentus SOS-independent DNA damage response transcription activator, DriD
DNA damage repair systems are critical for genomic integrity. However, they must be coordinated with DNA replication and cell division to ensure accurate genomic transmission. In most bacteria, this coordination is mediated by the SOS response through LexA, which triggers a halt in cell division until repair is completed. Recently, an SOS-independent damage response system was revealed in Caulobacter crescentus. This pathway is controlled by the transcription activator, DriD, but how DriD senses and signals DNA damage is unknown. To address this question, we performed biochemical, cellular, and structural studies. We show that DriD binds a specific promoter DNA site via its N-terminal HTH domain to activate transcription of genes, including the cell division inhibitor didA. A structure of the C-terminal portion of DriD revealed a WYL motif domain linked to a WCX dimerization domain. Strikingly, we found that DriD binds ssDNA between the WYL and WCX domains. Comparison of apo and ssDNA-bound DriD structures reveals that ssDNA binding orders and orients the DriD domains, indicating a mechanism for ssDNA-mediated operator DNA binding activation. Biochemical and in vivo studies support the structural model. Our data thus reveal the molecular mechanism underpinning an SOS-independent DNA damage repair pathway.
59 BASIC BIOLOGICAL SCIENCES↗
Prediction of microstructure formation in laser powder bed fusion process.
The datasets are results analyzing the predicted microstructures in a single track during the laser powder bed fusion additive manufacturing process. They are the outputs by running the opensource code, muMatScale (The code can be cited at: Yuan, Lang, Fattebert, Jean-Luc, and Sabau, Adrian. (2023, August 03). muMatScale. [Computer software]. https://github.com/lang-yuan/muMatScale. https://doi.org/10.11578/dc.20240112.2.) For each set of data, it contains the time-dependent information of Temperature, Fraction Solid, Grain ID, Grain Angle ( crystallographic orientations by Euler angles), and solute Composition. The dataset can be visualized by Paraview (https://www.paraview.org/ ). The 6 datasets are: 1. Baseline_base1_n4e14_dt20: baseline case with bulk nucleation density of 4E+14/m^3, undercooling of 20K, substrate nucleation density of 1.5E+15/m^3 2. Nuc_n4e15_dt20: case with bulk nucleation density of 4E+15/m^3, undercooling of 20K, substrate nucleation density of 1.5E+15/m^3 3. Nuc_n4e15_dt50: case with bulk nucleation density of 4E+15/m^3, undercooling of 50K, substrate nucleation density of 1.5E+15/m^3 4. Nuc_n6e15_dt20: case with bulk nucleation density of 4E+16/m^3, undercooling of 20K, substrate nucleation density of 1.5E+15/m^3 5. Base4_n4e14_dt20: case with bulk nucleation density of 4E+14/m^3, undercooling of 20K, substrate nucleation density of 6.0E+15/m^3 6. Base16_n4e14_dt20: case with bulk nucleation density of 4E+14/m^3, undercooling of 20K, substrate nucleation density of 2.4E+16/m^3
36 MATERIALS SCIENCE↗
A goldilocks computational protocol for inhibitor discovery targeting DNA damage responses including replication-repair functions
While many researchers can design knockdown and knockout methodologies to remove a gene product, this is mainly untrue for new chemical inhibitor designs that empower multifunctional DNA Damage Response (DDR) networks. Here, we present a robust Goldilocks (GL) computational discovery protocol to efficiently innovate inhibitor tools and preclinical drug candidates for cellular and structural biologists without requiring extensive virtual screen (VS) and chemical synthesis expertise. By computationally targeting DDR replication and repair proteins, we exemplify the identification of DDR target sites and compounds to probe cancer biology. Our GL pipeline integrates experimental and predicted structures to efficiently discover leads, allowing early-structure and early-testing (ESET) experiments by many laboratories. By employing an efficient VS protocol to examine protein-protein interfaces (PPIs) and allosteric interactions, we identify ligand binding sites beyond active sites, leveraging in silico advances for molecular docking and modeling to screen PPIs and multiple targets. A diverse 3,174 compound ESET library combines Diamond Light Source DSI-poised, Protein Data Bank fragments, and FDA-approved drugs to span relevant chemotypes and facilitate downstream hit evaluation efficiency for academic laboratories. Two VS per library and multiple ranked ligand binding poses enable target testing for several DDR targets. This GL library and protocol can thus strategically probe multiple DDR network targets and identify readily available compounds for early structural and activity testing to overcome bottlenecks that can limit timely breakthrough drug discoveries. By testing accessible compounds to dissect multi-functional DDRs and suggesting inhibitor mechanisms from initial docking, the GL approach may enable more groups to help accelerate discovery, suggest new sites and compounds for challenging targets including emerging biothreats and advance cancer biology for future precision medicine clinical trials.
59 BASIC BIOLOGICAL SCIENCES↗
Analysis and Optimization of a Novel Hexagonal Waveguide Concentrator for Solar Thermal Applications
This paper analyzes a novel, cost-effective planar waveguide solar concentrator design that is inspired by cellular hexagonal structures in nature with the benefits of facile installation and low operation and maintenance cost. A coupled thermal and optical analysis of solar irradiation through an ideal hexagonal waveguide concentrator integrated with a linear receiver is presented, along with a cost analysis methodology, to establish the upper limit of performance. The techno-economic model, coupled with numerical optimization, is used to determine designs that maximized power density and minimized the cost of heat in the temperature range of 100–250 °C, which constitutes more than half of the industrial process heat demand. Depending on the incident solar irradiation and the application temperature, the cost of heat for the optimal design configuration ranged between 0.1–0.27 $/W and 0.075–0.18 $/W for waveguide made of ZK7 glass and polycarbonate, respectively. A techno-economic analysis showed the potential of the technology to achieve cost as low as 80 $/m2 and 61 $/m2 for waveguide made of ZK7 glass and polycarbonate material, respectively, which is less than half the cost of state-of-the-art parabolic trough concentrators. Overall, the hexagonal waveguide solar concentrator technology shows immense potential for decarbonizing the industrial process heat and thermal desalination sectors.
14 SOLAR ENERGY↗
Development of advanced material composites for use as internal insulation for LH2 tanks (gas layer concept)
A program is described that was conducted to develop an internal insulation system for potential application to the liquid hydrogen tanks of a reusable booster, where the tanks would be subjected to repeated high temperatures. The design of the internal insulation is based on a unique gas layer concept, in which capillary or surface tension effects are used to maintain a stable gas layer, within a cellular core structure, between the tank wall and the contained liquid hydrogen. Specific objectives were to select materials for insulation systems that would be compatible with wall temperatures of 350 F and 650 F during reentry into the earth's atmosphere, and to fabricate and test insulation systems under conditions simulating the operating environment. A materials test program was conducted to evaluate the properties of candidate materials at elevated temperatures and at the temperature of liquid hydrogen, and to determine the compatibility of the materials with a hydrogen atmosphere at the appropriate elevated temperature. The materials that were finally selected included Kapton polyimide films, silicone adhesives, fiber glass batting, and in the case of the 350 F system, Teflon film.
Gille, J. P.↗
Internal insulation system development
The development of an internal insulation system for cryogenic liquids is described. The insulation system is based on a gas layer concept in which capillary or surface tension effects are used to maintain a stable gas layer within a cellular core structure between the tank wall and the contained cryogen. In this work, a 1.8 meter diameter tank was insulated and tested with liquid hydrogen. Ability to withstand cycling of the aluminum tank wall to 450 K was a design and test condition.
Gille, J. P.↗
Regenerator matrix physical property data
Among several cellular ceramic structures manufactured by various suppliers for regenerator application in a gas turbine engine, three have the best potential for achieving durability and performance objectives for use in gas turbines, Stirling engines, and waste heat recovery systems: (1) an aluminum-silicate sinusoidal flow passage made from a corrugated wate paper process; (2) an extruded isosceles triangle flow passage; and (3) a second generation matrix incorporating a square flow passage formed by an embossing process. Key physical and thermal property data for these configurations presented include: heat transfer and pressure drop characteristics, compressive strength, tensile strength and elasticity, thermal expansion characteristics, chanical attack, and thermal stability.
Fucinari, C. A.↗
Dose rate and repair effects on cell damage in earth orbit
Radiobiology experiments performed in space will encounter continuous exposures to the cosmic rays and fractionated exposures to trapped protons which accumulate to several hundred dose fractions in a few weeks. Using models of track structure and cellular kinetics combined with models of the radiation environment and radiation transport, we consider calculations of damage rates for cell cultures. Analysis of the role of repair mechanisms for space exposures for the endpoints of survival and transformation is emphasized.
Cucinotta, F. A.↗