Covariation of hot spring geochemistry with microbial genomic diversity, function, and evolution
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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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We introduce ToPolyAgent, a multi-agent AI framework for performing coarse-grained molecular dynamics (MD) simulations of topological polymers through natural language instructions. By integrating large language models (LLMs) with domain-specific computational tools, ToPolyAgent supports both interactive and autonomous simulation workflows across diverse polymer architectures, including linear, ring, brush, and star polymers, as well as dendrimers. The system consists of four LLM-powered agents: a Config Agent for generating initial polymer–solvent configurations, a Simulation Agent for executing LAMMPS-based MD simulations and conformational analyses, a Report Agent for compiling markdown reports, and a Workflow Agent for streamlined autonomous operations. Interactive mode incorporates user feedback loops for iterative refinements, while autonomous mode enables end-to-end task execution from detailed prompts. We demonstrate ToPolyAgent's versatility through case studies involving diverse polymer architectures under varying solvent conditions, thermostats, and simulation lengths. Furthermore, we highlight its potential as a research assistant by directing it to investigate the effect of interaction parameters on the linear polymer conformation, and the influence of grafting density on the persistence length of the brush polymer. By coupling natural language interfaces with rigorous simulation tools, ToPolyAgent lowers barriers to complex computational workflows and advances AI-driven materials discovery in polymer science. It lays the foundation for autonomous and extensible multi-agent scientific research ecosystems.
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The switching probability of magnetic elements for heat-assisted recording with pulsed laser heating was investigated. It was found that FePt elements with a diameter of 5 nm and a height of 10 nm show, at a field of 0.5 T, thermally written-in errors of 12%, which is significantly too large for bit-patterned magnetic recording. Thermally written-in errors can be decreased if larger-head fields are applied. However, larger fields lead to an increase in the fundamental thermal jitter. This leads to a dilemma between thermally written-in errors and fundamental thermal jitter. This dilemma can be partly relaxed by increasing the thickness of the FePt film up to 30 nm. For realistic head fields, it is found that the fundamental thermal jitter is in the same order of magnitude of the fundamental thermal jitter in conventional recording, which is about 0.5–0.8 nm. Composite structures consisting of high Curie top layer and FePt as a hard magnetic storage layer can reduce the thermally written-in errors to be smaller than 10{sup −4} if the damping constant is increased in the soft layer. Large damping may be realized by doping with rare earth elements. Similar to single FePt grains in composite structure, an increase of switching probability is sacrificed by an increase of thermal jitter. Structures utilizing first-order phase transitions breaking the thermal jitter and writability dilemma are discussed.
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Prescribed fire is used as a tool to achieve various ecological objectives in fire-adapted ecosystems (Ryan et al. 2013). These objectives often include targeted mortality of encroaching species to minimize the risk of catastrophic wildfire (Ryan et al. 2013). Achieving mortality of some species while protecting others requires a foundational understanding of how different species respond to different types of fire at different times of year.
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A wedge bilayer of epitaxial 4–8 nm La 0.7 Sr 0.3 CoO 3 (LSCO)/6-nm La 0.7 Sr 0.3 MnO 3 (LSMO), hard and soft ferromagnets (FM) respectively, was studied using soft x-ray magnetic spectroscopy to elucidate the interplay between the magnetic and electronic properties of the constituent layers. This system exhibits magnetic and electronic segregation within the LSCO layer characterized by soft FM Co 2+ ions at the interface (s-LSCO), which is biased by the underlying hard LSCO layer (h-LSCO), characterized by predominantly Co 3+ /Co 4+ FM ions. For a 5.1-nm layer, the interfacial Co 2+ ion concentration is maximized and the h-LSCO coercivity is minimized, while the opposite is true for a 7.8-nm LSCO layer. Furthermore these dual trends in Co 2+ ion concentration and h-LSCO coercivity within the LSCO serve to independently affect the exchange bias and coercivity of the soft FM layer, resulting in inverse trends between these properties that typically vary simultaneously.
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A draft genome of a new Thermofilum sp. strain was obtained from an enrichment culture metagenome. Like its relatives, Thermofilum sp. strain NZ13 is adapted to organic-rich thermal environments and has to depend on other organisms and the environment for some key amino acids, purines, and cofactors.
ABSTRACT Desulfurococcus amylolyticus Z-533 T , a hyperthermophilic crenarcheon, ferments peptide and starch, generating acetate, isobutyrate, isovalerate, CO 2 , and hydrogen. Unlike D. amylolyticus Z-1312, it cannot use cellulose and is inhibited by hydrogen. The reported draft genome sequence of D. amylolyticus Z-533 T will help to understand the molecular basis for these differences.
The genus Comamonas contains species isolated from various environments, such as termite guts, wetlands, activated sludge, soil, humans, and fresh water. Here, we report the draft genome sequence of Comamonas thiooxydans strain S23 T capable of oxidizing thiosulfate under mixotrophic growth conditions. Based upon draft genome sequencing, the genome is 5.3 Mb and encodes 4,767 proteins. The Comamonas thiooxydans whole-genome sequence will help understand the metabolic diversity in sulfur oxidation pathways.
ABSTRACT The draft genome of Thermocrinis jamiesonii GBS1 T is 1,315,625 bp in 10 contigs and encodes 1,463 predicted genes. The presence of sox genes and various glycoside hydrolases and the absence of uptake NiFe hydrogenases ( hyaB ) are consistent with a requirement for thiosulfate and suggest the ability to use carbohydrate polymers.