Dynamic_Syringe_Pump_Controller
A LabVIEW based programmable user interface for operating ISCO D-series and SyriXus-series syringe pumps that enables advanced user operations and integration with auxiliary data sources.
Frash, Luke↗
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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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Editorial: Advanced in situ characterization of biological interfaces and materials
Rapid changes are occurring on this dynamic planet–in 2020 anthropogenic mass was reported to not only match but exceed the mass of natural origins (Elhacham et al., 2020). These indications do not bold well for humanity in the coming generations, as we face 2 degree overall temperature increases over the next 5 years, CO 2 is spewing into the atmosphere at the Gigatonne (Gt) rate per year without any signs of mitigation in the foreseeable future, ocean water levels are rising to incredible levels, drinking water availability is disappearing, humanity is heavily reliant on the “drill-and-fill” culture, and two wars are currently being fought in Gaza and Ukraine (Carr et al., 2024). And even with these pressures, humanity continues to eke out impressive scientific and technological achievements in the recent past including mRNA vaccines to counter a global pandemic (Hogan and Pardi, 2022) and the development of CRISPR-Cas9 drugs (Parums, 2024). All these developments are only possible from the incremental methodological improvements taking place presently.
36 MATERIALS SCIENCE↗
High-fidelity, hyper-accurate, and evolved mutants rewire atomic-level communication in CRISPR-Cas9
The high-fidelity (HF1), hyper-accurate (Hypa), and evolved (Evo) variants of the CRISPR-associated protein 9 (Cas9) endonuclease are critical tools to mitigate off-target effects in the application of CRISPR-Cas9 technology. The mechanisms by which mutations in recognition subdomain 3 (Rec3) mediate specificity in these variants are poorly understood. Here, solution nuclear magnetic resonance and molecular dynamics simulations establish the structural and dynamic effects of high-specificity mutations in Rec3, and how they propagate the allosteric signal of Cas9. We reveal conserved structural changes and dynamic differences at regions of Rec3 that interface with the RNA:DNA hybrid, transducing chemical signals from Rec3 to the catalytic His-Asn-His (HNH) domain. The variants remodel the communication sourcing from the Rec3 α helix 37, previously shown to sense target DNA complementarity, either directly or allosterically. This mechanism increases communication between the DNA mismatch recognition helix and the HNH active site, shedding light on the structure and dynamics underlying Cas9 specificity and providing insight for future engineering principles.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Solidification Furnace for In Situ Observation of Bulk Transparent Systems and Image Analysis Methods
This paper aims to describe the experimental framework of the Directional Solidification Insert (DSI), installed onboard the International Space Station (ISS), dedicated to the in situ and real-time characterization of the dynamic selection of the solid-liquid interface morphology in bulk samples of transparent materials under diffusive growth conditions. The in situ observation of the solid-liquid interface is an invaluable tool for gaining knowledge on the time-evolution of the interface pattern because the initial morphological instability evolves nonlinearly and undergoes a reorganization process. The result of each experiment, characterized by the sample concentration, a thermal gradient and a pulling rate, is a large number of images. Interpretation of these images necessitates a robust identification of each cell/dendrite position and size during the entire solidification. Several image analysis methods have been developed to achieve this goal reliably despite varying contrast and noise levels, and are described in details. Typical solidification experiments are presented and the dynamics of the pattern formation are analyzed to illustrate the application of the image analysis methods.
Programming languages↗
Hydrodynamics of liquid surfaces
Hydrodynamics of liquids and gases, surface tension forces, and liquid-vapor interfaces for coasting space vehicles
GAS DYNAMICS↗
Real-Sim Interface: Enabling Multi-resolution Simulation and X-in-the-Loop Development for Connected and Automated Vehicles
We report connected and automated vehicles (CAVs) can bring safety, mobility, and energy benefits to transportation systems. Ideally, CAV applications would be fully evaluated and validated prior to real-world implementation. However, many technical challenges in both software and hardware hinder the process. To comprehensively evaluate all aspects of CAV applications, an integrated evaluation environment is needed with various simulation tools from different domains. In the current literature, there lacks a well-developed interface to enable multi-resolution simulation of vehicle, traffic, virtual environment, and hardware-in-the-loop (HIL) simulation. In this work, a modular and flexible interface is developed to enable multi-resolution vehicle and traffic co-simulation for CAV applications. This interface is built upon Oak Ridge National Laboratory’s (ORNL’s) Real-Sim approach, can support various simulation tools and real-time X-in-the-loop (XIL) simulations, and is based on network communication protocols. The network communication delays are analyzed for simultaneous connection of up to 20 simulators. Then, two example applications are studied to demonstrate the potential usage of the Real-Sim interface: (1) a centralized merging scenario where the dynamics of two ego vehicles are emulated with detailed vehicle and powertrain dynamics models and (2) a signal-controller-in-the-loop (SCIL) evaluation where one intersection of the simulated traffic scenario is controlled by a physical signal controller. This Real-Sim interface is a tool that allows researchers to bring real, tangible hardware and software into simulated environments to comprehensively evaluate and support a wide variety of CAV applications.
33 ADVANCED PROPULSION SYSTEMS↗
Probing and Tuning Spatiotemporal pH Evolution in Aqueous Zinc Ion Batteries
Aqueous zinc-ion batteries (AZIBs) offer a combination of safety and low cost, but they suffer from dynamic pH fluctuations that drive parasitic reactions and capacity fading. In this review, we report the current mechanistic understanding of the dynamic pH evolution across the electrolyte-electrode interface and its role in triggering interphase instability. We summarize advanced strategies to regulate pH, including electrolyte engineering, electrode surface modification, and interphase construction. We further discuss current methods for probing pH dynamics and outline potential future approaches for gaining deeper mechanistic and design insights.
Zheng, Xueli [SLAC]↗
Recognition of a Key Anchor Residue by a Conserved Hydrophobic Pocket Ensures Subunit Interface Integrity in DNA Clamps
Sliding clamp proteins encircle duplex DNA and are involved in processive DNA replication and the DNA damage response. Clamp proteins are ring-shaped oligomers (dimers or trimers) and are loaded onto DNA by an ATP-dependent clamp loader complex that ruptures the interface between two adjacent subunits. Here we measured the solution dynamics of the human clamp protein, proliferating cell nuclear antigen, by monitoring the change in the fluorescence of a site-specifically labeled. To unravel the origins of clamp subunit interface stability, we carried out comprehensive comparative analysis of the interfaces of seven sliding clamps. Here, we used computational modeling (molecular dynamic simulations and MM/GBSA binding energy decomposition analyses) to identify conserved networks of hydrophobic residues critical for clamp stability and ring-opening dynamics. The hydrophobic network is shared among clamp proteins and exhibits a “key in a keyhole” pattern where a bulky aromatic residue from one clamp subunit is anchored into a hydrophobic pocket of the opposing subunit. Bioinformatics and dynamic network analyses showed that this oligomeric latch is conserved across DNA sliding clamps from all domains of life and dictates the dynamics of clamp opening and closing.
59 BASIC BIOLOGICAL SCIENCES↗
Ion Dissociation Dynamics in an Aqueous Premelting Layer
Using molecular dynamics simulations and methods of importance sampling, we study the thermodynamics and dynamics of sodium chloride in the aqueous premelting layer formed spontaneously at the interface between ice and its vapor. We uncover a hierarchy of time scales that characterize the relaxation dynamics of this system, spanning the picoseconds of ionic motion to the tens or hundreds of nanoseconds associated with fluctuations of the liquid-crystal interface in their presence. We find that ions distort both local interfaces, incurring restoring forces that result in the ions preferentially residing in the middle of the layer. While ion pair dissociation is thermodynamically favorable, these structural and dynamic effects cause its rate to vary by over an order of magnitude through the layer, with a maximum rate significantly depressed from the corresponding bulk value. The solvation environment of ions in the premelting layer is distinct from that in a bulk liquid, being dominated by slow reorganization of water molecules and a water structure intermediate between ice and its melt.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Clippy
Clippy (CLI + PYthon) is a Python language interface to HPC resources. Precompiled binaries that execute on HPC systems are exposed as methods to a dynamically-created Clippy Python object, where they present a familiar interface to researchers, data scientists, and others. Clippy allows these users to interact with HPC resources in an easy, straightforward environment - at the REPL, for example, or within a notebook - without the need to learn complex HPC behavior and arcane job submission commands.
Bromberger, SethA.↗
On the importance of species immiscibility in mixing-layer dynamics at supercritical pressures
The mixing dynamics of injected propellants is a key factor in determining the ignition performance and combustion-instability response of rocket engines, internal combustion engines, and gas turbines. A key source of uncertainty in the prediction of phase-exchange dynamics is the immiscibility of the injected propellants at supercritical pressure conditions, which induces liquid/vapor phase separation and surface-tension dynamics. While experimental observations indicate the presence of liquid/vapor interfacial structures, this interfacial dynamics is typically neglected in numerical analyses. To address this issue, the objective of the present study is to systematically evaluate the importance of species immiscibility on the phase-exchange dynamics of cryogenic LOX/GH2 mixing layers at typical rocket engine injection conditions. This is accomplished by comparing simulations of (i) a recently developed interface-capturing Regularized-Interface Method (RIM) formulation, and (ii) the commonly employed Diffuse-Interface Method (DIM) formulation. Analysis shows that the interfacial dynamics significantly impact the atomization and mixing of the propellants in the near-injector region, which is not captured by the DIM formulation. The findings of this study extend to other immiscible injection systems, such as LOX/kerosene and hydrocarbon-fuel/air, thereby highlighting the importance of resolving species immiscibility in simulating high-pressure combustion engines.
diffused-interface method↗
WHONDRS-GUI: a web application for global survey of surface water metabolites
Background The Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) is a consortium that aims to understand complex hydrologic, biogeochemical, and microbial connections within river corridors experiencing perturbations such as dam operations, floods, and droughts. For one ongoing WHONDRS sampling campaign, surface water metabolite and microbiome samples are collected through a global survey to generate knowledge across diverse river corridors. Metabolomics analysis and a suite of geochemical analyses have been performed for collected samples through the Environmental Molecular Sciences Laboratory (EMSL). The obtained knowledge and data package inform mechanistic and data-driven models to enhance predictions of outcomes of hydrologic perturbations and watershed function, one of the most critical components in model-data integration. To support efforts of the multi-domain integration and make the ever-growing data package more accessible for researchers across the world, a Shiny/R Graphical User Interface (GUI) called WHONDRS-GUI was created. Results The web application can be run on any modern web browser without any programming or operational system requirements, thus providing an open, well-structured, discoverable dataset for WHONDRS. Together with a context-aware dynamic user interface, the WHONDRS-GUI has functionality for searching, compiling, integrating, visualizing and exporting different data types that can easily be used by the community. The web application and data package are available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1484811 , which enables users to simultaneously obtain access to the data and code and to subsequently run the web app locally. The WHONDRS-GUI is also available for online use at Shiny Server ( https://xmlin.shinyapps.io/whondrs/ ).
59 BASIC BIOLOGICAL SCIENCES↗
Evidence of topological charge polarization at active-passive interfaces in acoustically powered active liquid crystals
Theoretical and computational studies predict topological charge separation at active-passive interfaces in active nematics, but reliable experimental validation has been lacking. We utilize a synthetic acoustically energized liquid crystal to experimentally investigate the dynamics of topological defects across an active-passive interface. The interference pattern induced by the acoustic wave inside the experimental cell creates a spatial distribution of activity, resulting in the formation of active-passive interfaces with the liquid-crystalline director field aligned parallel to those interfaces. The activity gradient drives the reorientation of positively charged topological defects along its direction, causing them to migrate into the passive zone and form a layer with net topological charge. That layer “discharges” upon cessation of activity through annihilation of positive and negative topological charges, resembling the discharge of a capacitor.
Active defects↗
Dynamic Wetting of High-Al Steel by CaO-SiO{sub 2}- and CaO-Al{sub 2}O{sub 3}-Based Mold Fluxes
Wetting of steel by mold fluxes affects the surface quality of steel products. Reaction between [Al] and mold fluxes in the continuous casting of high-Al steel leads to a dynamic interfacial phenomenon. This work investigated the wetting of the high-Al steel substrate by CaO-SiO{sub 2}-based and CaO-Al{sub 2}O{sub 3}-based mold fluxes. The interfacial tensions were estimated and related to their high-temperature structures. The interface morphology revealed that CaO-SiO{sub 2}-based mold flux and CaO-Al{sub 2}O{sub 3}-based mold flux with CaO/Al{sub 2}O{sub 3} = 1 exhibited deep reaction zones in the steel substrates and irregular flux/steel interfaces, while CaO-Al{sub 2}O{sub 3}-based mold fluxes with CaO/Al{sub 2}O{sub 3} = 2 and 3 showed smooth interfaces and superficial reaction zones. The sedation of dynamic wetting behavior in Samples 3 and 4 was related to the high viscosity in the flux droplet after the initial composition change, which led to the stabilization of the interface.
36 MATERIALS SCIENCE↗
Surface Instability of Liquid Propellant under Vertical Oscillatory Forcing
Fluid motion in a fuel tank produced during thrust oscillations can circulate sub-cooled hydrogen near the liquid-vapor interface resulting in increased condensation and ullage pressure collapse. The first objective of this study is to validate the capabilities of a Computational Fluid Dynamics (CFD) tool, CFD-ACE+, in modeling the fundamental interface transition physics occurring at the propellant surface. The second objective is to use the tool to assess the effects of thrust oscillations on surface dynamics. Our technical approach is to first verify the CFD code against known theoretical solutions, and then validate against existing experiments for small scale tanks and a range of transition regimes. A 2D axisymmetric, multi-phase model of gases, liquids, and solids is used to verify that CFD-ACE+ is capable of modeling fluid-structure interaction and system resonance in a typical thrust oscillation environment. Then, the 3D mode is studied with an assumed oscillatory body force to simulate the thrust oscillating effect. The study showed that CFD modeling can capture all of the transition physics from solid body motion to standing surface wave and to droplet ejection from liquid-gas interface. Unlike the analytical solutions established during the 1960 s, CFD modeling is not limited to the small amplitude regime. It can extend solutions to the nonlinear regime to determine the amplitude of surface waves after the onset of instability. The present simulation also demonstrated consistent trends from numerical experiments through variation of physical properties from low viscous fluid to high viscous fluids, and through variation of geometry and input forcing functions. A comparison of surface wave patterns under various forcing frequencies and amplitudes showed good agreement with experimental observations. It is concluded that thrust oscillations can cause droplet formation at the interface, which results in increased surface area and enhanced heat transfer between the liquid and gas phases as the ejected droplets travel well into the warmer gas region.
Yang, H. Q.↗
Novel Superionic Na Conductors for Solid‐State Na batteries: Materials and Interface
This project aims to advance the fundamental understanding on how the cation or anion doping influence on the crystal structure, phase stability and ion transport of novel Na superionic conductors. Specifically, we focus on the Na 3-x A x SbS 4-y X y family solid electrolytes (A: cation dopant, X: anion dopant), a class of promising materials for all-solid-state sodium batteries owing to their high ionic conductivity and compositional tunability. By integrating materials synthesis, neutron scattering, and electrochemical characterization and theoretical simulations, this project sees to elucidate 1) how does the synthesis approaches (solid-state reaction, low-temperature reaction) on the phase purity and doping process; 2) how chemical doping (A: cation dopants such as Sn; X: anion dopants such as Se, F) modulate lattice dynamics and Na+ migration as well as interface stability toward Na metal. Specifically, this project’s proposed technology involves three objectives: (1) synthesize novel Na-ion conductors (anion or cation doped Na 3 SbS 4 ) with high phase purity and examine their structural features (e.g., phase stability); (2) understand Na-ion conductive properties of new Na-ion conductors through a combination of experimental characterizations and theoretical simulations; (3) investigate the interface stability of novel Na superionic conductors with electrode materials in solid-state Na batteries. These objectives will be achieved through combined experimental synthesis/characterizations and computational approaches. The obtained knowledge will provide a comprehensive synthesis-structure-property correlation, enabling the rational design of novel solid-state conductors with excellent conductivity and stability.
25 ENERGY STORAGE↗
Large Language Model for Validation, Optical Calibration, and Learning (VOCAL) Distributed Temperature Sensing Interface
Distributed temperature sensing (DTS) using fiber optic sensors (FOS) offers a promising method for temperature measurements in advanced reactors, such as sodium fast reactors and molten salt cooled reactors. To support the calibration and validation of DTS measurements, Argonne National Laboratory developed the Validation, Optical Calibration, and Learning (VOCAL) software package. This report describes the integration of a local large language model (LLM) with a retrieval-augmented generation (RAG) system into the VOCAL interface to serve as an interactive user assistant. The LLM framework enhances the VOCAL platform’s accessibility to users by explaining interface components, clarifying inputs and outputs, and answering user queries dynamically in real-time. The accuracy of the LLM assistant performance was evaluated with 20 queries regarding the interface and its parameters using experimental data from the Thermal Hydraulic Experimental Test Article (THETA) facility. Results demonstrate that the LLM achieved a 95% accuracy rate, with a BERTScore of 0.8816 and SBERT value of 0.7417. Furthermore, validation of the RAG system within the LLM framework showed optimal accuracy with k-values between 1 and 2 using the k-refinement convergence test. The prompt perturbation analysis demonstrated good initial consistency for the RAG system, exhibiting the highest accuracy under punctuation variations and the greatest sensitivity under query reordering. Notably, the model’s errors were limited to data retrieval failures rather than factual hallucinations, reinforcing its baseline reliability. The integration of LLM provides a highly accurate, userfriendly enhancement to the VOCAL platform without disrupting its core computational capabilities for FOS calibration and validation.
Hong, Evan↗
Synthesis and Control of Flexible Systems with Component-Level Uncertainties
An efficient and computationally robust method for synthesis of component dynamics is developed. The method defines the interface forces/moments as feasible vectors in transformed coordinates to ensure that connectivity requirements of the combined structure are met. The synthesized system is then defined in a transformed set of feasible coordinates. The simplicity of form is exploited to effectively deal with modeling parametric and non-parametric uncertainties at the substructure level. Uncertainty models of reasonable size and complexity are synthesized for the combined structure from those in the substructure models. In particular, we address frequency and damping uncertainties at the component level. The approach first considers the robustness of synthesized flexible systems. It is then extended to deal with non-synthesized dynamic models with component-level uncertainties by projecting uncertainties to the system level. A numerical example is given to demonstrate the feasibility of the proposed approach.
Maghami, Peiman G.↗