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At least 847 records · Page 47

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),↗

Machine-learned closure of URANS for stably stratified turbulence: connecting physical timescales & data hyperparameters of deep time-series models

Stably stratified turbulence (SST), a model that is representative of the turbulence found in the oceans and atmosphere, is strongly affected by fine balances between forces and becomes more anisotropic in time for decaying scenarios. Moreover, there is a limited understanding of the physical phenomena described by some of the terms in the Unsteady Reynolds-Averaged Navier–Stokes (URANS) equations—used to numerically simulate approximate solutions for such turbulent flows. Rather than attempting to model each term in URANS separately, it is attractive to explore the capability of machine learning (ML) to model groups of terms, i.e. to directly model the force balances. We develop deep time-series ML for closure modeling of the URANS equations applied to SST. We consider decaying SST which are homogeneous and stably stratified by a uniform density gradient, enabling dimensionality reduction. We consider two time-series ML models: long short-term memory and neural ordinary differential equation. Both models perform accurately and are numerically stable in a posteriori (online) tests. Furthermore, we explore the data requirements of the time-series ML models by extracting physically relevant timescales of the complex system. We find that the ratio of the timescales of the minimum information required by the ML models to accurately capture the dynamics of the SST corresponds to the Reynolds number of the flow. The current framework provides the backbone to explore the capability of such models to capture the dynamics of high-dimensional complex dynamical system like SST flows.

97 MATHEMATICS AND COMPUTING↗

Towards a self-driving trigger at the LHC: adaptive response in real time

Real-time data filtering and selection—or trigger—systems at high-throughput scientific facilities such as the experiments at the Large Hadron Collider must process extremely high-rate data streams under stringent bandwidth, latency, and storage constraints. Yet these systems are typically designed as static, hand-tuned menus of selection criteria grounded in prior knowledge and simulation. In this work, we further explore the concept of a self-driving trigger, an autonomous data-filtering framework that reallocates resources and adjusts thresholds dynamically in real-time to optimize signal efficiency, rate stability, and computational cost as instrumentation and environmental conditions evolve. We introduce a benchmark ecosystem to emulate realistic collider scenarios and demonstrate real-time optimization of a menu including canonical energy sum triggers as well as modern anomaly-detection algorithms that target non-standard event topologies using machine learning. Using simulated data streams and publicly available collision data from the Compact Muon Solenoid experiment, we demonstrate the capability to dynamically and automatically optimize trigger performance under specific cost objectives without manual retuning. Our adaptive strategy shifts trigger design from static menus with heuristic tuning to intelligent, automated, data-driven control, unlocking greater flexibility and discovery potential in future high-energy physics analyses.

Emami, Shaghayegh [Michigan U.] (ORCID:00090007589↗

Environment-imposed selection rules for nuclear-spin conversion of H 2 in molecular crystals

Nuclear-spin conversion in molecular hydrogen is governed by strict symmetry rules that typically require magnetic fields or catalytic surfaces to break. Here we demonstrate that the intrinsic tensor composition of a non-magnetic molecular crystal field can impose and relax these rules without external fields. High-resolution infrared spectra of H 2 in crystalline CO 2 reveal large rank-2 (quadrupolar) crystal-field splittings of the 𝑚 sublevels, while nuclear-spin conversion occurs only through 𝛥𝑚 = 0 channels. Replacing CO 2 with polar N 2 O introduces rank-1 (dipole) components that partially open 𝛥⁢𝑚 ≠ 0 pathways, while incorporation of paramagnetic NO 2 fully lifts the restriction. Furthermore, these results establish a direct correspondence between crystal-field tensor rank and nuclear-spin dynamics, introducing a general symmetry-based framework for designing and controlling spin-isomer populations and quantum-state connectivity in molecular solids.

McLane, Nathan [University of Maryland, College Pa↗

Steps toward quantum simulations of hadronization and energy loss in dense matter

A framework for simulating the real-time dynamics of composite particles in a simple model of dense matter that is amenable to quantum computers is developed. As a demonstration, we perform classical simulations of heavy-hadrons propagating through a dense medium in the Schwinger model. Measurements of the time-dependent energy and charge density are used to identify mechanisms responsible for energy loss and hadron production (hadronization). A study of entanglement dynamics highlights the importance of quantum coherence between the particles that make up the dense medium. Throughout this work, care is taken to isolate, and remove, phenomena that arise solely from a finite lattice spacing. It is found that signatures of entanglement are more sensitive to lattice artifacts than other observables. Toward quantum simulations, we present an efficient method and the corresponding quantum circuits for preparing ground states in the presence of heavy mesons. Finally, these circuits are used to estimate the resources required to simulate in-medium energy loss and hadronization in the Schwinger model using quantum computers.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

First constraints on a pixelated universe in light of DESI observations

Pixelated dark energy is a string theory scenario with a quantum mechanically stable cosmological constant. The number of pixels that make up the universe slowly increases, manifesting as a time-dependent source of dark energy. DESI has recently reported evidence for dynamical dark energy that fits within this framework. In light of this, we perform the first cosmological analysis of the pixelated model. We find that the simplest model where the pixel growth rate is constant is able to accommodate the data, providing a marginally better fit than Λ⁢ CDM; and we show that models where the pixel growth rate is increasing and of order the Hubble constant today could provide better fits. Our analysis helps to clarify the features of UV constructions of dark energy necessary to accommodate the data.

dark energy↗

Decentralized Collaborative Learning with Probabilistic Data Protection

We discuss future directions of Blockchain as a collaborative value co-creation platform, in which network participants can gain extra insights that cannot be accessed when disconnected from the others. As such, we propose a decentralized machine learning framework that is carefully designed to respect the values of democracy, diversity, and privacy. Specifically, we propose a federated multi-task learning framework that integrates a privacy-preserving dynamic consensus algorithm. We show that a specific network topology called the expander graph dramatically improves the scalability of global consensus building. We conclude the paper by making some remarks on open problems.

Ide, Tsuyoshi↗

Leaf angle as a leaf and canopy trait: Rejuvenating its role in ecology with new technology

Abstract Life on Earth depends on the conversion of solar energy to chemical energy by plants through photosynthesis. A fundamental challenge in optimizing photosynthesis is to adjust leaf angles to efficiently use the intercepted sunlight under the constraints of heat stress, water loss and competition. Despite the importance of leaf angle, until recently, we have lacked data and frameworks to describe and predict leaf angle dynamics and their impacts on leaves to the globe. We review the role of leaf angle in studies of ecophysiology, ecosystem ecology and earth system science, and highlight the essential yet understudied role of leaf angle as an ecological strategy to regulate plant carbon–water–energy nexus and to bridge leaf, canopy and earth system processes. Using two models, we show that leaf angle variations have significant impacts on not only canopy‐scale photosynthesis, energy balance and water use efficiency but also light competition within the forest canopy. New techniques to measure leaf angles are emerging, opening opportunities to understand the rarely‐measured intraspecific, interspecific, seasonal and interannual variations of leaf angles and their implications to plant biology and earth system science. We conclude by proposing three directions for future research.

Yang, Xi↗

Dynamic Bayesian Networks for Fault Prognosis

A dynamic Bayesian Network (DBN)-based fault prognosis framework is proposed in this study to predict the future fault probabilities of gradual faults. The proposed framework utilizes the trend in prediction error generated from data driven forecasting models to estimate the future fault beliefs. The accuracy and scalability of the proposed method is evaluated using the data from a Modelica-based virtual testbed. Overall, the developed framework demonstrates good potential in estimating future fault probabilities of gradual faults.

Pradhan, Ojas↗

Data-Driven Learning of Non-Autonomous Systems

We present a numerical framework for recovering unknown non-autonomous dynamical systems with time-dependent inputs. To circumvent the difficulty presented by the non-autonomous nature of the system, our method transforms the solution state into piecewise integration of the system over a discrete set of time instances. The time-dependent inputs are then locally parameterized by using a proper model, for example, polynomial regression, in the pieces determined by the time instances. This transforms the original system into a piecewise parametric system that is locally time invariant. We then design a deep neural network structure to learn the local models. Once the network model is constructed, it can be iteratively used over time to conduct global system prediction. We provide theoretical analysis of our algorithm and present a number of numerical examples to demonstrate the effectiveness of the method.

97 MATHEMATICS AND COMPUTING↗

Consequences of Altered Root Nutrient Uptake for Soil Carbon Stabilization (Final Report)

Objectives: The primary objectives of this project are to improve our understanding of tropical forest belowground processes, and to increase representation of this biome in ecosystem-scale and global C cycle models. Belowground dynamics present a major source of uncertainty inhibiting our ability to predict C cycle responses to climate change. Representation of tropical forests in these models is particularly lacking, even though these ecosystems hold >25% of terrestrial C stocks. While the majority of humid tropical forests exist on relatively infertile soils (i.e. poor in rock-derived nutrients), enormous gradients in soil nutrient availability exist at landscape-scales due to shifts in geology and soil order. Soil fertility is likely to greatly influence how tropical soil C storage will respond to the declines in precipitation predicted for the tropics. In particular, root dynamics vary across soil fertility gradients, with roots representing the major input of C to subsurface soils. Root characteristics related to soil fertility include biomass, turnover, C exudates, tissue chemistry, and nutrient uptake rates, with each of these likely sensitive to changes in moisture. The proposed project will fully integrate field research with an existing ecosystem model to assess potential effects of drying on belowground tropical C dynamics across a range of soil fertilities. Project Description:. This project will identify key linkages among soil fertility, root nutrient uptake, root dynamics, and soil C storage. The hypothesized framework for understanding these linkages is: Tropical rainforest roots in relatively fertile soils have lesser root biomass, faster turnover, fewer exudates, and improved root tissue quality relative to infertile sites, all resulting from increased root nutrient uptake. Ultimately, these root characteristics in fertile soils promote proportionally greater long-term soil C storage in organo-mineral associations. Specifically, lower root exudates and improved root tissue quality in fertile soils reduce microbial respiration of extant soil C (i.e. “priming) and increase microbial C use efficiency, leading to sorption of protein-rich microbial and plant organic matter on soil mineral surfaces. However, the larger pools of mineral-associated C in fertile tropical soils are more vulnerable to decreased rainfall than smaller C pools in infertile soils, in part because of the lesser root biomass, faster turnover, and softer, more labile root tissues. Also, the shallower lateral rooting structures typical in fertile soils experience greater desiccation and death than deeper roots in infertile sites, with little short-term adaptation to drying.

54 ENVIRONMENTAL SCIENCES↗

FY24 Advanced Computing HPC Annual Report for allocation "vtocei"

This project aims to elucidate the mechanisms underlying the formation of the cathodeelectrolyte interphase (CEI) and its impact on the performance of Li-ion batteries during electrochemical cycling. Our approach integrates advanced multiscale modeling with multimodal characterization to offer a comprehensive understanding of CEI dynamics. We employ a validated multiscale modeling framework to analyze microstructure-dependent transport properties, alongside joint theory-experiment protocols for detailed resolution of interfacial chemistry via spectroscopy.

36 MATERIALS SCIENCE↗

String Theory, the Dark Sector, and the Hierarchy Problem

We discuss dark energy, dark matter and the hierarchy problem in the context of a general non-commutative formulation of string theory. In this framework dark energy is generated by the dynamical geometry of the dual spacetime while dark matter, on the other hand, comes from the degrees of freedom dual to the visible matter. This formulation of string theory is sensitive both to the IR and UV scales and the Higgs scale is radiatively stable by being a geometric mean of radiatively stable UV and IR scales. We also comment on various phenomenological signatures of this novel approach to dark energy, dark matter and the hierarchy problem. We find that this new view on the hierarchy problem is realized in a toy model based on a non-holomorphic deformation of the stringy cosmic string. Finally, we discuss a proposal for a new non-perturbative formulation of string theory, which sheds light on M theory and F theory, as well as on supersymmetry and holography.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Quantum Foundations of Classical Reversible Computing

The reversible computation paradigm aims to provide a new foundation for general classical digital computing that is capable of circumventing the thermodynamic limits to the energy efficiency of the conventional, non-reversible digital paradigm. However, to date, the essential rationale for, and analysis of, classical reversible computing (RC) has not yet been expressed in terms that leverage the modern formal methods of non-equilibrium quantum thermodynamics (NEQT). In this paper, we begin developing an NEQT-based foundation for the physics of reversible computing. We use the framework of Gorini-Kossakowski-Sudarshan-Lindblad dynamics (a.k.a. Lindbladians) with multiple asymptotic states, incorporating recent results from resource theory, full counting statistics and stochastic thermodynamics. Important conclusions include that, as expected: (1) Landauer’s Principle indeed sets a strict lower bound on entropy generation in traditional non-reversible architectures for deterministic computing machines when we account for the loss of correlations; and (2) implementations of the alternative reversible computation paradigm can potentially avoid such losses, and thereby circumvent the Landauer limit, potentially allowing the efficiency of future digital computing technologies to continue improving indefinitely. We also outline a research plan for identifying the fundamental minimum energy dissipation of reversible computing machines as a function of speed.

97 MATHEMATICS AND COMPUTING↗

Revisiting the guidelines for ending isolation for COVID-19 patients

Since the start of the COVID-19 pandemic, two mainstream guidelines for defining when to end the isolation of SARS-CoV-2-infected individuals have been in use: the one-size-fits-all approach (i.e. patients are isolated for a fixed number of days) and the personalized approach (i.e. based on repeated testing of isolated patients). We use a mathematical framework to model within-host viral dynamics and test different criteria for ending isolation. By considering a fixed time of 10 days since symptom onset as the criterion for ending isolation, we estimated that the risk of releasing an individual who is still infectious is low (0–6.6%). However, this policy entails lengthy unnecessary isolations (4.8–8.3 days). In contrast, by using a personalized strategy, similar low risks can be reached with shorter prolonged isolations. The obtained findings provide a scientific rationale for policies on ending the isolation of SARS-CoV-2-infected individuals.

Jeong, Yong Dam↗

Stability of large horizontal-axis axisymmetric wind turbines

The stability of large horizontal-axis, axisymmetric, power producing wind turbines is examined within the framework of an analytical model which includes dynamic coupling of the rotor, tower, and power generating system. The aerodynamic loading is derived from blade element theory. Stability is determined by the eigenvalues of a set of linearized constant-coefficient differential equations. All results presented are based on a 3-bladed, 300-ft diameter, 2.0-MW wind turbine. It is shown that unstable or weakly stable behavior can be caused by aerodynamic forces due to motion of the rotor blades and tower in the plane of rotation or by mechanical coupling between the rotor system and the tower.

Hirschbein, M. S.↗

Dynamic modeling of vegetation change in arid lands

A general framework for a digital desertification monitoring system (DDMS) for assessing the worldwide desertification growth rate is presented. The system relies on the development of Landsat derived indicators to identify local processes signalling the growth of arid regions. A study area consisting of the eastern edge of the Niger River delta in Mali was used to characterize three indicators in terms of the covariance of the multispectral scanner (MSS) bands 2 and 4, the correlation of the two bands, and the percent variance expressed by the first eigenvalue. The scenes are imaged multitemporallly in a 400 x 400 pixel array to detect vegetation cover changes. Criteria were defined which characterized the decrease or increase of vegetation. It was determined that the correlation coefficients are the best indicators, and are easily computed.

Robinson, V. B.↗

The use of remotely sensed soil moisture data in large-scale models of the hydrological cycle

Manabe (1982) has reviewed numerical simulations of the atmosphere which provided a framework within which an examination of the dynamics of the hydrological cycle could be conducted. It was found that the climate is sensitive to soil moisture variability in space and time. The challenge arises now to improve the observations of soil moisture so as to provide up-dated boundary condition inputs to large scale models including the hydrological cycle. Attention is given to details regarding the significance of understanding soil moisture variations, soil moisture estimation using remote sensing, and energy and moisture balance modeling.

Salomonson, V. V.↗