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At least 181 records · Page 10

Molecular Dynamical and Quantum Mechanical Exploration of the Site-Specific Dynamics of Cy3 Dimers Internally Linked to dsDNA

Performing spectroscopic measurements on biomolecules labeled with fluorescent probes is a powerful approach to locating the molecular behavior and dynamics of large systems at specific sites within their local environments. The indocarbocyanine dye Cy3 has emerged as one of the most commonly used chromophores. The incorporation of Cy3 dimers into DNA enhances experimental resolution owing to the spectral characteristics influenced by the geometric orientation of excitonically coupled monomeric units. Various theoretical models and simulations have been utilized to aid in the interpretation of the experimental spectra. In this study, we employ all-atom molecular dynamics simulations to study the structural dynamics of Cy3 dimers internally linked to the dsDNA backbone. We used quantum mechanical calculations to derive insights from both the linear absorption spectra and the circular dichroism data. Furthermore, we explore potential limitations within a commonly used force field for cyanine dyes. The molecular dynamics simulations suggest the presence of four possible Cy3 dimeric populations. The spectral simulations on the four populations show one of them to agree better with the experimental signatures, suggesting it to be the dominant population. Furthermore, the relative orientation of Cy3 in this population compares very well with previous predictions from the Holstein–Frenkel Hamiltonian model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Selection of Sampling and Surrogate Modeling Methods for State-Point Evaluations of an AGN-201M Reactor

Nuclear reactor digital twins (DTs) have been proposed for use as a safeguards technology to efficiently monitor new and novel reactors as they come online. A safeguards DT needs to be capable of detecting misuse and diversion as they occur, requiring physics models to be accurate and efficient. Mathematical surrogate models are capable of achieving the necessary efficiency and can largely maintain the accuracy of higher-order models given a quality training sample. The Multiphysics Object-Oriented Simulation Environment (MOOSE) code framework is specifically equipped to generate training samples and create surrogate models using full-order reactor physics models. Utilizing an operational AGN-201M reactor’s specifications, two surrogate types were trained on samples of variable size, and using Cartesian products, Latin hypercube sampling, and quadrature sampling, each was compared and evaluated on accuracy when compared to a full-order Monte Carlo model. Both surrogate types were able to capture reactivity changes within 0.05 $ of the Monte Carlo model while reducing the computation costs by eight orders of magnitude.

MOOSE↗

Multi-Neutrino Entanglement and Correlations in Dense Neutrino Systems

The time-evolution of multi-neutrino entanglement and correlations are studied in two-flavor collective neutrino oscillations, relevant for dense neutrino environments, building upon previous works. Specifically, simulations performed of systems with up to 12 neutrinos using Quantinuum’s H1-1 20 qubit trapped-ion quantum computer are used to compute n-tangles, and two- and three- body correlations, probing beyond mean-field descriptions. n-tangle re-scalings are found to converge for large system sizes, signaling the presence of genuine multi-neutrino entanglement.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

pnnl-predictive-phenomics/csc052-gem

Genome-Scale Metabolic Model Continuous Validation with Memote for CarbStor Community Member Bacillus These repositories contain the continuous validation environment for an organism-specific genome-scale metabolic model (GEM) using Memote. Memote is a software tool that provides a suite of tests to ensure the quality and consistency of metabolic models. By integrating Memote into a continuous integration (CI) workflow, we can automatically validate updates to the GEM, ensuring that model modifications improve or maintain the model's integrity.

Torres, Victor E.↗

pnnl-predictive-phenomics/csc031-gem

Genome-Scale Metabolic Model of CarbStor Community member Microbacterium (csc031) Continuous Validation with Memote These repositories contain the continuous validation environment for an organism-specific genome-scale metabolic model (GEM) using Memote. Memote is a software tool that provides a suite of tests to ensure the quality and consistency of metabolic models. By integrating Memote into a continuous integration (CI) workflow, we can automatically validate updates to the GEM, ensuring that model modifications improve or maintain the model's integrity

McNaughton, Andrew [@PNNL]↗

pnnl-predictive-phenomics/csc009-gem

Genome-Scale Metabolic Model of CarbStore Community member Curtobacterium (csc009) Continuous Validation with Memote These repositories contain the continuous validation environment for an organism-specific genome-scale metabolic model (GEM) using Memote. Memote is a software tool that provides a suite of tests to ensure the quality and consistency of metabolic models. By integrating Memote into a continuous integration (CI) workflow, we can automatically validate updates to the GEM, ensuring that model modifications improve or maintain the model's integrity

Lin, Tesia↗

pnnl-predictive-phenomics/csc040-gem

Genome-Scale Metabolic Model Continuous Validation with Memote for CarbStor Community Member Rhodococcus These repositories contain the continuous validation environment for an organism-specific genome-scale metabolic model (GEM) using Memote. Memote is a software tool that provides a suite of tests to ensure the quality and consistency of metabolic models. By integrating Memote into a continuous integration (CI) workflow, we can automatically validate updates to the GEM, ensuring that model modifications improve or maintain the model's integrity.

McNaughton, Andrew [@PNNL]↗

pnnl-predictive-phenomics/csc043-gem

Genome-Scale Metabolic Model Continuous Validation with Memote for CarbStor Community Member Paenibacillus These repositories contain the continuous validation environment for an organism-specific genome-scale metabolic model (GEM) using Memote. Memote is a software tool that provides a suite of tests to ensure the quality and consistency of metabolic models. By integrating Memote into a continuous integration (CI) workflow, we can automatically validate updates to the GEM, ensuring that model modifications improve or maintain the model's integrity.

Zucker, Jeremy [Pacific Northwest National Laborat↗

Fresnel zone plate development for x-ray radiography of hydrodynamic instabilities at the National Ignition Facility

The study of Rayleigh–Taylor (RT) and Richtmyer–Meshkov (RM) instabilities in a planar geometry at high energy densities at the National Ignition Facility (NIF) requires high spatial resolution imaging. We demonstrate the potential of Fresnel zone plates (FZPs) to achieve resolution that would unlock such studies. FZPs are circular aperiodic gratings that use diffraction to focus x rays and produce an image with high spatial resolution. Taking into account the NIF’s challenging environment, we have designed a specific array of five FZPs for a zinc backlighter to take a radiograph of a target with 9 keV x rays. We measured a mean resolution for the FZP of 1.9µm±0.5µm and a ±1mm depth of focus at an x-ray calibration facility as well as a 2.3µm±0.4µm resolution on a resolution wire mesh shot on the NIF. We also performed an in-depth analysis of the image quality to assess the capability to resolve the small features present in RT and RM instabilities.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Optimization of Conditions for Photoluminescence-Based Sensing of Critical Minerals: Strategies and Outlook

Economically critical minerals and metals are vital to America’s security, with application areas in energy, advanced technologies, and defense systems. The growing implementation of renewable energy sources such as electric vehicles is expected to significantly increase demand for these minerals, while the global supply is monopolistic, with most of the production occurring in a few countries outside of the US. To mitigate potential supply chain vulnerabilities, the domestic production of economically critical metals has become a bipartisan priority of the US government, and unconventional sources such as coal and its utilization byproducts such as fly ash and acid mine drainage are being actively explored as an alternative method for meeting domestic demand. Slow and expensive characterization methods for critical metals present a significant pain point for domestic production, which has led to the exploration of alternative low-cost, portable platforms capable of detecting target metals during resource prospecting and downstream process monitoring. The National Energy Technology Laboratory has developed a portable fiber optic-based luminescence spectrometer that utilizes a metal-organic framework (MOF) material to detect and distinguish parts-per-billion levels of the visible-emitting rare earth elements terbium, dysprosium, samarium, and europium, which are all economically critical metals. Although preliminary results with this system are promising, a crucial barrier to practical deployment is the ability to operate in low pH, high ionic strength environments, as acidic conditions and the presence of other metal ions can significantly reduce luminescence signal. Here, current strategies related to sample treatment, material design, and sensor configuration are discussed in the context of improving sensor performance in application-relevant conditions. Additionally, future opportunities, such as the optimization of the sensing binding environment through computational methods and specific metals to be removed for treatment will be discussed, presenting a forward-looking view for innovation in luminescent sensing of critical metals.

36 MATERIALS SCIENCE↗

Surveillance & Detection (CRADA 567 Final Report)

This Cooperative Research and Development Agreement (CRADA) Final Report covers the work achieved by PNNL and it's commercial partner (Consolidated Resource Imaging, LLC) on video analytics for the DHS S&T Surveillance & Detection project. This project has been focused on development of the next-generation camera system (Guardian iiS) with extremely high resolution and video analytics specifically designed for crowded urban environments and congested transportation hubs.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Overcoming Challenges to Nuclear-Maritime Applications

This report is the fifth deliverable in a series of reports set forth by the Department of Energy (DOE), led by the American Bureau of Shipping (ABS), for the research award titled “Accelerating Commercial Maritime Demonstration Projects for Advanced Nuclear Reactor Technologies.” The report highlights guidance to bridge the gaps between innovative nuclear technologies and their practical implementation in maritime environments. The previous reports discussed specific technical, economic and regulatory challenges that may be expected when developing and establishing advanced nuclear technologies for commercial maritime applications. This report supports the mission of the U.S. National Reactor Innovation Center (NRIC) to demonstrate projects with industry and acts as a resource for the various stakeholders associated with the development of novel applications for advanced reactors. The previous reports discuss the interest in nuclear technology applications for decarbonized energy and identify the potential demands in nuclear energy supply and price. The work in these reports supports the recently issued nuclear Executive Orders (EOs). Specifically, EO 14299, “Deploying Advanced Nuclear Reactor Technologies for National Security”, and EO 14300, “Ordering the Reform of the Nuclear Regulatory Commission,” by ensuring the rapid development, deployment, and use of advanced nuclear technologies; and increasing the deployment of new nuclear reactor technologies, such as Generation III+ and IV reactors, modular reactors, and microreactors to support America leading the commercialization of affordable and abundant nuclear energy.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

Heating and cooling devices, systems and related method

Embodiments disclosed herein relate to devices, systems, and methods for cooling and/or heating a medium as well as cooling and/or heating an environment containing the medium. More specifically, at least one embodiment includes a heat pump that may heat and/or cool a medium and, in some instances, may transfer heat from one location to another location.

Kariya, Harumichi Arthur↗

Coordinated Thermal Safety Attack and Defense on EV Battery Management Systems

Battery temperature sensor and battery current sensor data which are key sensing inputs to the Battery Management Controllers in electric vehicles, are vulnerable to possible cyber/ physical manipulation due to known vulnerabilities inherited from CAN bus technology that is used for in-vehicle communications between electronic control units that transfer sensing and control data. In this paper, we first create a simulation that enables us to evaluate impact of cyber physical attacks on electric vehicle battery management system in a controlled environment that violates thermal safety. Specifically, we emulate a Level 3 - DC fast charging system with SAE J1772/CCS, integrated with standard charging controls and thermal safety controls on EVs, and various sensing data flows. Second, we propose a coordinated current and battery temperature attack that has crippling economic, and safety impacts. Third, we quantify the usability, economic and safety impacts of such attacks as a function of the extent of data manipulation. Finally, we propose a physics model driven detection technique to detect presence of such attacks.

25 ENERGY STORAGE↗

Updraft Width Implications for Cumulonimbus Growth in a Moist Marine Environment

Abstract An idealized large-eddy simulation of a tropical marine cloud population was performed. At any time, it contained hundreds of clouds, and updraft width in shallow convection emerging from a subcloud layer appeared to be an important indicator of whether specific convective elements deepened. In an environment with 80%–90% relative humidity below the 0°C level, updrafts that penetrated the 0°C level were larger at and above cloud base, which occurred at the lifting condensation level near 600 m. Parcels rising in these updrafts appeared to emerge from boundary layer eddies that averaged ∼200 m wider than those in clouds that only reached 1.5–3 km height. The deeply ascending parcels (growers) possessed statistically similar values of effective buoyancy below the level of free convection (LFC) as parcels that began to ascend in a cloud but stopped before reaching 3000 m (nongrowers). The growers also experienced less dilution above the LFC. Nongrowers were characterized by negative effective buoyancy and rapid deceleration above the LFC, while growers continued to accelerate well above the LFC. Growers occurred in areas with a greater magnitude of background convergence (or weaker divergence) in the subcloud layer, especially between 300 m and cloud base, but whether the convergence actually led to eddy widening is unclear. Significance Statement Cumulonimbus clouds are responsible for many extreme weather phenomena and are important contributors to Earth’s energy balance. However, the processes leading to the growth of individual clouds are not completely understood nor well-represented in weather prediction models. We find that the clouds containing updrafts that start out wider at early stages of their life cycles grow taller, possibly because they are protected more from drier air outside the cloud than narrow clouds. In addition, this work shows how the initial width of clouds might be related to convergence in the lowest part of the atmosphere, at heights where clouds initially develop. However, meteorologists must be careful not to overinterpret these results because numerical simulations inherently include assumptions that may not reflect reality. This reinforces the need to also observe processes occurring at the scales of individual clouds.

54 ENVIRONMENTAL SCIENCES↗

Policy and Regulatory Environment for Utility-Scale Energy Storage: Nepal

This report—Policy and Regulatory Environment for Utility-Scale Energy Storage: Nepal—is part of a series investigating the potential for utility-scale energy storage in South Asia. This report is the second in a series of country-specific evaluations of policy and regulatory environments for energy storage in the region. These evaluations apply the previously developed Energy Storage Readiness Assessment to evaluate the policy and regulatory environment for energy storage in Nepal. A similar assessment is already complete for India and a forthcoming report will expand this analysis to Bangladesh. These evaluations are designed to provide insights on the opportunities and barriers for energy storage growth and deployment in each country.

25 ENERGY STORAGE↗

Living-off-the-land Techniques Unlikely to Supplant Energy Sector-Focused OT-Specific Malware

Despite increased reports of energy sector-focused threat actors using living-off-the-land (LOTL) techniques, it is unlikely LOTL techniques will wholly supplant malware in energy sector operational technology (OT)-focused cyber operations. Threat actors leverage LOTL techniques to access energy sector networks, abstracting process information and maintaining persistence. Although threat actors using LOTL techniques have successfully interrupted energy sector industrial control environments, designed features of OT-specific malware likely increase the cyber-physical impact of an attack and delay recovery of critical functions and services. Malicious actors will very likely continue to use LOTL techniques for stealth, while designing malware to bolster final impacts on cyber-physical systems in energy sector OT environments.

99 GENERAL AND MISCELLANEOUS↗

From occupants to occupants: A review of the occupant information understanding for building HVAC occupant-centric control

Occupants are the core of the built environment. Traditional Heating, Ventilation, and Air-Conditioning (HVAC) systems operate with predefined schedules and maximum occupancy assumptions with no consideration of specific occupant information. These generalized assumptions usually do not align with the actual demand and result in over-conditioning and occupant discomfort. In recent years, with the aid of Information & Communication Technology (ICT) and Computer Science (CS), it is possible to acquire real-time and accurate occupant information to satisfy the exact thermal requirement through specific HVAC control in one particular built environment. This mechanism is called HVAC “Occupant-centric Control (OCC).” HVAC OCC strategy starts with collecting the occupant’s information (e.g., presence/absence) and then applies it to meet the occupant’s requirement (e.g., thermal comfort). However, even though some research studies and field pilot demonstrations have been devoted to the field of OCC, there is a lack of systematic knowledge about occupant data, which is the principal component of OCC for HVAC researchers and practitioners. To fill this gap, this review paper discusses OCC with a particular emphasis on occupant information and investigates how this information can assist HVAC operation in providing an acceptable built environment in required spaces during the required time. Finally, we provide a fine-grained, comprehensive picture of occupant information, discuss its features, the modalities of information feed-in into the HVAC control, and the application of commonly utilized occupant information for OCC.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗