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At least 829 records · Page 46

ToPolyAgent: AI agents for coarse-grained bead-spring topological polymer simulations

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.

Ding, Lijie [Oak Ridge National Laboratory (ORNL),↗

Fundamental limits in heat-assisted magnetic recording and methods to overcome it with exchange spring structures

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.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Tree mortality after a spring fire: the role of reduced live leaf area in depletion of early growing season bole NSC

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.

59 BASIC BIOLOGICAL SCIENCES↗

Decoupling exchange bias and coercivity enhancement in a perovskite oxide exchange spring bilayer

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.

36 MATERIALS SCIENCE↗

Permanent Draft Genome Sequence of Desulfurococcus amylolyticus Strain Z-533 T , a Peptide and Starch Degrader Isolated from Thermal Springs in the Kamchatka Peninsula and Kunashir Island, Russia

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.

59 BASIC BIOLOGICAL SCIENCES↗

Draft Genome Sequence of Comamonas thiooxydans Strain S23 T (DSM 17888 T ), a Thiosulfate-Oxidizing Bacterium Isolated from a Sulfur Spring in India

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.

54 ENVIRONMENTAL SCIENCES↗