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At least 361 records · Page 20

The Zooplankton International Geospatial (ZIG) dataset: A global repository of spatiotemporal freshwater zooplankton community composition data to support ecological research

Zooplankton play critical roles in aquatic ecosystem function and food webs. Nevertheless, global syntheses of their abundance and community dynamics are challenging due to methodological differences across monitoring programs, taxonomic inconsistencies, and a lack of standardized metadata. To reconcile these challenges, we assembled, curated, validated, and harmonized the Zooplankton International Geospatial (ZIG) dataset, which includes co-located and contemporaneous zooplankton, water chemistry, and limnological data from 307 lakes and reservoirs. ZIG includes waterbodies from each major lake thermal region and range in size from 0.8-2,805,8600 hectares. Temporal coverage for individual waterbodies ranges between 1-60 years of data (median = 4 years) with sampling from once annually to weekly. ZIG is publicly available and can be used to understand freshwater biodiversity change and its drivers at unprecedented scales, and we consider it to be a cornerstone for future investigations of freshwater biology, chemistry, and ecology.

Figary, Stephanie [Cornell University, Ithaca, NY]↗

Feasibility of Hybrid Electro- and Acousto-Dynamical Systems for Quantum Optical Networks

We present results on an exploratory research program that aims to study the feasibility of novel, sustained, dense, and efficient quantum information generation, storage, retrieval, relay and distribution devices and systems towards future advanced quantum networking architectures. The pathfinder program is anchored on original ideas and device conceptual designs that turn the phononic-sourced challenges into an opportunity towards optimized transduction chains over a broad range of length and energy/temperature scales. The proposal involves conceptual design and feasibility towards integration, commissioning and benchmarking of challenging transduction devices in a scaled quantum network setup.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DeePMD-kit v2: A software package for deep potential models

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features, such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, DP-range correction, DP long range, graphics processing unit support for customized operators, model compression, non-von Neumann molecular dynamics, and improved usability, including documentation, compiled binary packages, graphical user interfaces, and application programming interfaces. This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, this article presents a comprehensive procedure for conducting molecular dynamics as a representative application, benchmarks the accuracy and efficiency of different models, and discusses ongoing developments.

97 MATHEMATICS AND COMPUTING↗

Oxygen vacancy dynamics in monoclinic metallic VO 2 domain structures

It was demonstrated recently that the nano-optical and nanoelectronic properties of VO 2 can be spatially programmed through the local injection of oxygen vacancies by atomic force microscope writing. In this work, we study the dynamic evolution of the patterned domain structures as a function of the oxygen vacancy concentration and the time. A threshold doping level is identified that is critical for both the metal–insulator transition and the defect stabilization. The diffusion of oxygen vacancies in the monoclinic phase is also characterized, which is directly responsible for the short lifetimes of sub-100 nm domain structures. This information is imperative for the development of oxide nanoelectronics through defect manipulations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Tri-Level Linear Programming Model for Automatic Load Shedding Using Spectral Clustering

Traditional load shedding schemes can be inadequate in grids with high renewable penetration, leading to unstable events and unnecessary grid islanding. Although for both manual and automatic operating modes load shedding areas have been predefined by grid operators, they have remained fixed, and may be sub-optimal due to dynamic operating conditions. In this work, a distributed tri-level linear programming model for automatic load shedding to avoid system islanding is presented. Preventing islanding is preferred because it reduces the need for additional load shedding besides the disconnection of transmission lines between islands. This is crucial as maintaining the local generation-demand balance is necessary to preserve frequency stability. Furthermore, uneven distribution of generation resources among islands can lead to increased load shedding, causing economic and reliability challenges. This issue is further compounded in modern power systems heavily dependent on non-dispatchable resources like wind and solar. The upper-level model uses complex power flow measurements to determine the system areas to shed load depending on actual operating conditions using a spectral clustering approach. The mid-level model estimates the area system state, while the lower-level model determines the locations and load values to be shed. The solution is practical and promising for real-world applications.

Baquedano-Aguilar, Mario D.↗

HYBRID Modeling of DETAIL Experimental Facility

Idaho National Laboratory continues to be at the forefront of advanced reactor systems and integrated energy systems research. Through the Thermal Energy Distribution System (TEDS) and Microreactor Agile Non-nuclear Test Bed (MAGNET) experiments in the Dynamic Energy Transport and Innovation Laboratory (DETAIL) within the Engineering Systems Laboratory, a mix of digital and physical testing systems can explore the operation of thermally and electrically integrated systems. Modeling of these systems has been done using the HYBRID modeling repository of the Integrated Energy Systems program. DETAIL also contains high temperature steam electrolysis (HTSE) units to produce hydrogen and generate the load imposed on MAGNET and TEDS. The dynamic modeling capabilities within the IES program describe the DETAIL components as-built and can be used to evaluate controls, process flows, and overall system conditions.

08 HYDROGEN↗

Implementing Ordinary Differential Equation Solvers in Rust Programming Language for Modeling Vehicle Powertrain Systems: Preprint

Efficient and accurate ordinary differential equation (ODE) solvers are necessary for powertrain and vehicle dynamics modeling. However, current commercial ODE solvers can be financially prohibitive, leading to a need for accessible, effective, open-source ODE solvers designed for powertrain modeling. Rust is a compiled programming language that has the potential to be used for fast and easy-to-use powertrain models, given its exceptional computational performance, robust package ecosystem, and short time required for modelers to become proficient. However, of the three commonly used (>3,000 downloads) packages in Rust with ODE solver capabilities, only one has more than four numerical methods implemented, and none are designed specifically for modeling physical systems. Therefore, the goal of the Differential Equation System Solver (DESS) was to implement accurate ODE solvers in Rust designed for the component-based problems often seen in powertrain modeling. DESS is a text-based software package that provides a flexible framework for building and solving systems of ODEs. This allows DESS to be included as a dependency for automotive powertrain models that require a variety of solvers and solver configurations. Seven explicit ODE solver methods have been implemented in DESS: Euler’s, Heun’s, midpoint, Ralston’s, classic Runge-Kutta, Bogacki-Shampine, and Cash-Karp. These represent five fixed-step methods and two adaptive-step methods. This paper shows that the solver implementations increase accuracy and computational efficiency compared to Euler's method when modeling a system of three thermal masses in Rust. DESS also includes features designed for modeling component-based physical systems. Users can define relationships between nodes in their system, which the package then translates into a system of equations, leading to simpler and more intuitive code. In the case of a three-thermal-mass system, the user can specify node thermal properties (e.g., thermal capacitance), how nodes are interconnected, and thermal conductance between nodes rather than providing a system of equations. The core contribution from this work is an open-source, text-based Rust package with ODE solvers for automotive powertrain modeling to support cost-free, fast, and accurate simulation.

ADVANCED PROPULSION SYSTEMS↗

Hoobas: A highly object-oriented builder for molecular dynamics

Polydispersity and random sequences are ubiquitous features of polymers, and molecular dynamics simulations can help elucidate the impact of disorder in polymer systems. However, currently available packages for building polymer topologies do not enable the user to include randomness in a straightforward fashion. Here, we introduce Hoobas, a molecular builder package that easily handles polydispersity using a prototype-builder design pattern. This enables fast and easy building of systems comprised of thousands of distinct objects. It is written in the Python programming language, which ensures compatibility with a wide range of molecular dynamics packages and tools, as well as easy integration into most workflows.

97 MATHEMATICS AND COMPUTING↗

E-PVT: enhanced position-velocity-time scheduler for computer-controlled optical finishing with comprehensive considerations of dynamics constraints, continuity and efficiency

Deterministic computer-controlled optical finishing is an essential approach for achieving high-quality optical surfaces. Its determinism and convergence rely heavily on precise and smooth motion control to guide the machine tool over an optical surface to correct residual errors. One widely supported and smooth motion control model is position-velocity-time (PVT), which employs piecewise cubic polynomials to describe positions. Our prior research introduced a PVT-based velocity scheduling method, demonstrating sub-nanometer level convergence in ion beam figuring (IBF) processes. However, three challenges remained. Firstly, this method relies on quadratic programming, resulting in computational intensiveness for dense tool paths. Secondly, the dynamics constraints and velocity and acceleration continuities are not comprehensively considered, limiting the full potential of PVT-based control. Thirdly, no compensation mechanism existed when dynamics constraints are exceeded. In this study, in response to these challenges, we proposed the Enhanced PVT (E-PVT) method, reducing the time complexity from O ( n 3 ) to O ( n ) while fully addressing dynamics constraints and continuities. A novel compensation method utilizing particle swarm optimization was proposed to address situations where dynamics constraints might be exceeded while maintaining the overall processing efficiency. Validation through simulation and experimentation confirmed the improved performance of E-PVT.

36 MATERIALS SCIENCE↗

Snowmass2021 Cosmic Frontier White Paper: Cosmological Simulations for Dark Matter Physics

Over the past several decades, unexpected astronomical discoveries have been fueling a new wave of particle model building and are inspiring the next generation of ever-more-sophisticated simulations to reveal the nature of Dark Matter (DM). This coincides with the advent of new observing facilities coming online, including JWST, the Rubin Observatory, the Nancy Grace Roman Space Telescope, and CMB-S4. The time is now to build a novel simulation program to interpret observations so that we can identify novel signatures of DM microphysics across a large dynamic range of length scales and cosmic time. This white paper identifies the key elements that are needed for such a simulation program. We identify areas of growth on both the particle theory side as well as the simulation algorithm and implementation side, so that we can robustly simulate the cosmic evolution of DM for well-motivated models. We recommend that simulations include a fully calibrated and well-tested treatment of baryonic physics, and that outputs should connect with observations in the space of observables. We identify the tools and methods currently available to make predictions and the path forward for building more of these tools. A strong cosmic DM simulation program is key to translating cosmological observations to robust constraints on DM fundamental physics, and provides a connection to lab-based probes of DM physics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Work Smarter, Not Harder: Improving Energy Efficiency and Safety through Smarter Ventilation: Preprint

Ventilation is a key component to maintaining healthy, safe indoor air quality. Especially important in laboratories, ventilation is the first line of defense against airborne hazards produced during research activities. Though a vital component, laboratory ventilation systems are often victim to ineffective operation, posing a risk to the most important asset - the researchers. Furthermore, system inefficiencies can lead to up to 50% wasted energy. To improve both energy efficiency and safety in laboratories, we present the Smart Labs Toolkit - a resource developed by the U.S. Department of Energy Federal Energy Management Program and the International Institute for Sustainable Laboratories that guides laboratory stakeholders through a straight-forward, holistic approach to achieve dynamic, high-performance laboratories. Smart Labs enable safe and efficient world class science to occur in laboratories through high-performance methods. A Smart Labs program employs a combination of physical, administrative, and management techniques to assess, optimize, and manage high performance laboratories. We will focus on a central component of the Smart Labs approach - the Laboratory Ventilation Risk Assessment, a systematic process for identifying risk due to airborne hazards to inform the operation of dynamic ventilation that optimizes safety and efficiency. Case studies of organizations who have successfully implemented Smart Labs ventilation management programs will also be shared. In learning ventilation strategies successful in critical laboratory environments, learn the tools and resources needed to successfully manage energy in any building through smarter, safer ventilation.

buildings↗

A compute-bound formulation of Galerkin model reduction for linear time-invariant dynamical systems

This work aims to advance computational methods for projection-based reduced-order models (ROMs) of linear time-invariant (LTI) dynamical systems. For such systems, current practice relies on ROM formulations expressing the state as a rank-1 tensor (i.e., a vector), leading to computational kernels that are memory bandwidth bound and, therefore, ill-suited for scalable performance on modern architectures. This weakness can be particularly limiting when tackling many-query studies, where one needs to run a large number of simulations. This work introduces a reformulation, called rank-2 Galerkin, of the Galerkin ROM for LTI dynamical systems which converts the nature of the ROM problem from memory bandwidth to compute bound. We present the details of the formulation and its implementation, and demonstrate its utility through numerical experiments using, as a test case, the simulation of elastic seismic shear waves in an axisymmetric domain. We quantify and analyze performance and scaling results for varying numbers of threads and problem sizes. In conclusion, we present an end-to-end demonstration of using the rank-2 Galerkin ROM for a Monte Carlo sampling study. We show that the rank-2 Galerkin ROM is one order of magnitude more efficient than the rank-1 Galerkin ROM (the current practice) and about 970 times more efficient than the full-order model, while maintaining accuracy in both the mean and statistics of the field.

97 MATHEMATICS AND COMPUTING↗

Numerical Model Development of a Variable-Geometry Attenuator Wave Energy Converter

Because the wave energy industry is still in its infancy, an optimal design for wave energy converters (WECs) has yet to be established; more work is needed to explore various cost-reduction pathways. The primary cost-reduction pathway considered for this work is the optimization of the geometric profile on an attenuator WEC to maximize power production while, at the same time, minimizing capital expenditures through the use of variable-geometry modules. In this investigation, the variable-geometry modules consist of inflatable bags placed on either side of a base central steel cylinder that would be inflated in low-moderate sea states to maximize power capture and then deflated in moderate-extreme sea states to minimize wave loading. The numerical model and simulation of the attenuator WEC were developed and completed using WEC-Sim, which is an open-source code that is appropriate for use in evaluating the dynamic response of the different WEC models in operational seas. The power production estimates were obtained from the Wave Energy Prize (WEP) sea states, which are representative of U. S. deployment sites, to calculate the average climate capture width that is used in the WEP ACE calculation. Preliminary capital expenditure costs were obtained assuming the base central steel cylinder mass was equal to the fluid displaced mass, minus the mass of the variable-geometry bags. The additional weight required to offset the additional buoyancy from the variable-geometry bags was assumed to come from the addition of seawater ballast. The variable-geometry attenuator model was found to have a similar power capture efficiency as a fixed-body model, but is expected to have a lower characteristic capital expenditure given its more streamlined profile, which demonstrates that variable-geometry modules may provide a realistic cost-reduction pathway to help design a more cost-competitive WEC.

50 EE - Wind and Water Power Program - Water (EE-4↗

Implementing Superresolution of Nonstationary Tides with Wavelets: An Introduction to CWT_Multi

Abstract Tides are often nonstationary due to nonastronomical influences. Investigating variable tidal properties implies a trade-off between separating adjacent frequencies (using long analysis windows) and resolving their time variations (short analysis windows). Previous continuous wavelet transform (CWT) tidal methods resolved tidal species. Here, we present CWT_Multi, a MATLAB code that 1) uses CWT linearity (via the “response coefficient method”) to implement superresolution, i.e., resolving tidal constituents beyond the Rayleigh criterion; 2) provides a Munk–Hasselmann constituent selection criterion appropriate for superresolution; and 3) introduces an objective, time-variable form of inference (“dynamic inference”) based on time-varying data properties. CWT_Multi resolves tidal species on time scales of days, and multiple constituents per species with fortnightly filters. It outputs astronomical phase lags and admittances, analyzes multiple records, and provides power spectra of the signal(s), residual(s), and reconstruction(s); confidence limits; and signal-to-noise ratios. Artificial data and water levels from the Lower Columbia River Estuary (LCRE) and San Francisco Bay Delta (SFBD) are used to test CWT_Multi and compare it to harmonic analysis programs NS_Tide and UTide. CWT_Multi provides superior reconstruction, detiding, dynamic analysis utility, and time resolution of constituents (but with broader confidence limits). Dynamic inference resolves closely spaced constituents (like K 1 , S 1 , and P 1 ) on fortnightly time scales, quantifying impacts of diel power peaking (with a 24-h period, like S 1 ) on water levels in the LCRE. CWT_Multi also helps quantify the impacts of high flows and a salt barrier closing on tidal properties in the SFBD. On the other hand, CWT_Multi does not excel at prediction, and results depend on analysis details, as for any method applied to nonstationary data. Significance Statement Ocean tides, especially in coastal and estuarine systems, are often nonstationary, in the sense that the mean and standard deviation of tidal properties vary over time, usually in response to some nontidal process. We introduce here a MATLAB code, CWT_Multi, that uses wavelet transforms to resolve both tidal species and constituents on time scales from a few days to months. Our code accommodates multiple scalar time series and has typical tidal analysis features like constituent selection and inference, plus two forms of uncertainty analyses. It is flexible, allowing the user to adapt analysis properties to diverse datasets. CWT_Multi is applicable to many problems involving time-variable tides, including sea level rise, compound flooding, sediment transport, and wetland habitat analyses. Application to vector data is a straightforward extension, but further development of our uncertainty analysis is merited. Because nonstationary tidal analysis is rapidly advancing, we also define the features of a “well-formed” analysis code.

Lobo, Matthew↗

MtrA modulates Mycobacterium tuberculosis cell division in host microenvironments to mediate intrinsic resistance and drug tolerance

The success of Mycobacterium tuberculosis (Mtb) is largely attributed to its ability to physiologically adapt and withstand diverse localized stresses within host microenvironments. Here, we present a data-driven model (EGRIN 2.0) that captures the dynamic interplay of environmental cues and genome-encoded regulatory programs in Mtb. Analysis of EGRIN 2.0 shows how modulation of the MtrAB two-component signaling system tunes Mtb growth in response to related host microenvironmental cues. Disruption of MtrAB by tunable CRISPR interference confirms that the signaling system regulates multiple peptidoglycan hydrolases, among other targets, that are important for cell division. Further, MtrA decreases the effectiveness of antibiotics by mechanisms of both intrinsic resistance and drug tolerance. Together, the model-enabled dissection of complex MtrA regulation highlights its importance as a drug target and illustrates how EGRIN 2.0 facilitates discovery and mechanistic characterization of Mtb adaptation to specific host microenvironments within the host.

59 BASIC BIOLOGICAL SCIENCES↗

Systems-Level Modeling for CRISPR-Based Metabolic Engineering

The CRISPR-Cas system has enabled the development of sophisticated, multigene metabolic engineering programs through the use of guide RNA-directed activation or repression of target genes. To optimize biosynthetic pathways in microbial systems, we need improved models to inform design and implementation of transcriptional programs. Recent progress has resulted in new modeling approaches for identifying gene targets and predicting the efficacy of guide RNA targeting. Genome-scale and flux balance models have successfully been applied to identify targets for improving biosynthetic production yields using combinatorial CRISPR-interference (CRISPRi) programs. Here, the advent of new approaches for tunable and dynamic CRISPR activation (CRISPRa) promises to further advance these engineering capabilities. Once appropriate targets are identified, guide RNA prediction models can lead to increased efficacy in gene targeting. Developing improved models and incorporating approaches from machine learning may be able to overcome current limitations and greatly expand the capabilities of CRISPR-Cas9 tools for metabolic engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Shape-Shifting Peptide Nanomaterials: Surface Asymmetry Enables pH-Dependent Formation and Interconversion of Collagen Tubes and Sheets

The fabrication of dynamic, transformable biomaterials that respond to environmental cues represents a significant step forward in the development of synthetic materials that rival their highly functional, natural counterparts. In this work, we describe the design and synthesis of crystalline supramolecular architectures from charge-complementary heteromeric pairs of collagen-mimetic peptides (CMPs). Under appropriate conditions, CMP pairs spontaneously assemble into either 1D ultraporous (pore diameter >100 nm) tubes or 2D bilayer nanosheets due to the structural asymmetry that arises from heteromeric self-association. Crystalline collagen tubes represent a heretofore unobserved morphology of this common biomaterial. In-depth structural characterization from a suite of biophysical methods, including TEM, AFM, high-resolution cryo-EM, and SAXS/WAXS measurements, reveals that the sheet and tube assemblies possess a similar underlying lattice structure. The experimental evidence suggests that the tubular structures are a consequence of the self-scrolling of incipient 2D layers of collagen triple helices and that the scrolling direction determines the formation of two distinct structural isoforms. Furthermore, we show that nanosheets and tubes can spontaneously interconvert through manipulation of the assembly pH and systematic adjustment of the CMP sequence. Altogether, we establish initial guidelines for the construction of dynamically responsive 1D and 2D assemblies that undergo a structurally programmed morphological transition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Coordinated Planning Strategy for Integrated Energy Systems in a District Energy Sector

With the ever-growing integration of diverse distributed energy resources, modern district energy sectors are transitioning into integrated energy systems (IESs), which generally consist of various energy carriers such as electric power, natural gas, and heat. Instead of modeling individual energy carriers, the emergence of IESs requires comprehensive consideration of all involved energy systems in both planning and operation phases. This paper proposes a comprehensive planning strategy for a district energy sector to address the challenges of IES planning considering the coupling of power, gas, and heat systems. The proposed planning model contains an operational module that develops a steady-state optimal multi-energy flow (OMEF) for the IES considered and a multi-stage expansion module that optimizes the investment decisions. To efficiently solve the proposed planning model, which is formulated as a mixed-integer nonlinear programming problem, an improved generalized Benders decomposition algorithm that utilizes dynamic dual multipliers to improve the convergence speed is employed. The effectiveness of the proposed planning model and the feasibility of the improved Benders decomposition algorithm are verified in case studies.

coordinated planning↗