Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Unfolding”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements

Residing in the 5' untranslated region of the mRNA, the 2'-deoxyguanosine (2'-dG) riboswitch mRNA element adopts an alternative structure upon binding of the 2'-dG molecule, which terminates transcription. RNA conformations are generally strongly affected by positively charged metal ions (especially Mg 2+ ). We have quantitatively explored the combined effect of ligand (2'-dG) and Mg 2+ binding on the energy landscape of the aptamer domain of the 2'-dG riboswitch with both explicit solvent all-atom molecular dynamics simulations (99 μsec aggregate sampling for the study) and selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) experiments. We show that both ligand and Mg 2+ are required for the stabilization of the aptamer domain; however, the two factors act with different modalities. The addition of Mg 2+ remodels the energy landscape and reduces its frustration by the formation of additional contacts. In contrast, the binding of 2'-dG eliminates the metastable states by nucleating a compact core for the aptamer domain. Mg 2+ ions and ligand binding are required to stabilize the least stable helix, P1 (which needs to unfold to activate the transcription platform), and the riboswitch core formed by the backbone of the P2 and P3 helices. Mg 2+ and ligand also facilitate a more compact structure in the three-way junction region.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Strengthening of enterococcal biofilms by Esp

Multidrug-resistant (MDR) Enterococcus faecalis are major causes of hospital-acquired infections. Numerous clinical strains of E . faecalis harbor a large pathogenicity island that encodes enterococcal surface protein (Esp), which is suggested to promote biofilm production and virulence, but this remains controversial. To resolve this issue, we characterized the Esp N-terminal region, the portion implicated in biofilm production. Small angle X-ray scattering indicated that the N-terminal region had a globular head, which consisted of two DEv-Ig domains as visualized by X-ray crystallography, followed by an extended tail. The N-terminal region was not required for biofilm production but instead significantly strengthened biofilms against mechanical or degradative disruption, greatly increasing retention of Enterococcus within biofilms. Biofilm strengthening required low pH, which resulted in Esp unfolding, aggregating, and forming amyloid-like structures. The pH threshold for biofilm strengthening depended on protein stability. A truncated fragment of the first DEv-Ig domain, plausibly generated by a host protease, was the least stable and sufficient to strengthen biofilms at pH ≤ 5.0, while the entire N-terminal region and intact Esp on the enterococcal surface was more stable and required a pH ≤ 4.3. These results suggested a virulence role of Esp in strengthening enterococcal biofilms in acidic abiotic or host environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

NOvA Inclusive Nue CC Cross Section Data Release

NOvA inclusive electron neutrino cross section results presented at Neutrino2020Exposure:8.09E20 protons-on-target, neutrino-enhanced beamData release contains 3 ROOT files containing the double-differential measurement with respect to electron angle (cos theta) and electron energy, a single-differential measurement with respect to squared four-momentum transfer (Q2), and the total cross section as a function of neutrino energy. The 1D cross-section measurements include the same kinematic phase space restrictions present in the double-differential analysis.The files, xsec_{dThdE/Enu/dQ2}.root, contain the extracted cross section and associated covariance matrices for the double-differential cross section with respect to the observed electron kinematics, dThdE, neutrino energy, Enu, and squared four-momentum transfer, Q^2.In each file there will be the following histograms:— TH2D/TH1D xsec: unfolded measured cross section— TH2D xsec_cov: cross section covariance matrix— TH2D stat_cov: statistical covariance matrixIncludes text files, xsec_{dThdE/Enu/dQ2}.txt show the corresponding histograms in plain text format.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Modeled estimates of permafrost hydrology and related fields for pan-Arctic region over the period 1980-2100

This dataset contains gridded estimates of total runoff (mm/day); subsurface runoff (mm/day); snow water equivalent (SWE, mm/day); vertical upward water flux of combined surface evaporation, evapotranspiration, and snow sublimation (mm/day); and soil temperature (C) across the pan-Arctic basin from simulations of the Permafrost Water Balance Model (PWBM v4). These data were generated to allow researchers to advance understanding of the changes unfolding in the Arctic's terrestrial water cycle under the influences of climate warming, hydrological cycle intensification, and permafrost thaw. The dataset will enable researchers to address important questions spanning multiple disciplines. For example, how will rising river flows exported to the coast impact critical zone ecosystems, near-shore ice dynamics, and ocean biogeochemical processes. Spatial resolution is 25x25 km with N=39926 grid cells spanning the domain. Three forcing datasets were used to drive simulations at an implicit daily time step over the period 1980-2100. Daily air temperature, precipitation, and wind speed data from the WATCH Forcing Data methodology applied to ERA5 reanalysis (W5E5) were used for meteorological forcings over the period 1980-2019. Simulations for the period 1980-2100 used meteorological data from two global climate models; IPSL-CM6A-LR and MPI-ESM1-2-HR. The PWBM hydrological outputs are organized by grid and month in gzipped ASCII text files within each archived tar file. Soil temperature is organized by grid cell and day of year from DOY 205 to DOY 260. No special software is required to work with these data. The package contains spatial domain and river basin information files. These data are most useful for analyses of the spatial and temporal variations in terrestrial hydrology and soil thermal dynamics. A manuscript describing the model simulations and associated analysis has been accepted for publication in The Cryosphere (Rawlins and Karmalkar, 2024).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

A microscopic realization of dS$_3$

We propose a precise duality between pure de Sitter quantum gravity in 2+1 2 + 1 dimensions and a double-scaled matrix integral. This duality unfolds in two distinct aspects. First, by carefully quantizing the gravitational phase space, we arrive at a novel proposal for the quantum state of the universe at future infinity. We compute cosmological correlators of massive particles in the universe specified by this wavefunction. Integrating these correlators over the metric at future infinity yields gauge-invariant observables, which are identified with the string amplitudes of the complex Liouville string [S. Collier et al., arXiv: 2409.17246]. This establishes a direct connection between integrated cosmological correlators and the resolvents of the matrix integral dual to the complex Liouville string, thereby demonstrating one aspect of the dS _3 3 /matrix integral duality. The second aspect concerns the cosmological horizon of the dS static patch and the Gibbons-Hawking entropy it is conjectured to encode. We show that this entropy can be reproduced exactly by counting the entries of the matrix.

Collier, Scott (ORCID:0000000286476653)↗
DOE OSTI2020

Climate Change Science Review 2018 and Associated Social and Economic Impacts

Climate change and its impacts on average temperature, water supply, agriculture, coastal flooding, biodiversity, social and economic stability, human migration, and overall global stability is one of the leading threats emerging for humanity, and is likely to increase as a threat for decades to come. This report represents a snapshot of climate change data, information, and understanding, as of 2018, and can serve as a kind of benchmark for changes going forward in time. This report covers temperature change and heat effects, atmospheric and ocean circulation, freshwater supply changes, sea level rise and flooding, extreme climate events, oceanic deoxygenation, land degredation, social and economic changes, migration, and food. Data and information on all these issues represent a compelling body of knowledge supporting the scientific hypothesis describing climate change, and an important mile marker in our effort to track the unfolding nature of the problem. A slide presentation that summarizes the content of this report is in Appendix A and can serve as an executive summary for the report.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2021

Thirty Minutes Before the Dawn

The Trinity test of July 16, 1945, marked the scientific apex of the Manhattan Project. Often recognized as the symbolic birth of the nuclear age, Trinity’s multifaceted legacy remains just as captivating and complex today as it did 75 years ago. This paper examines why the test was necessary from a technical standpoint, shows how Los Alamos scientists planned the event, and explores the physical and emotional aftermaths of Trinity. The author also uses rarely accessed original records to reconstruct the story of Trinity’s health hazards, as seen through the eyes of radiation technicians and medical doctors as events unfolded. Trinity was conducted as the Potsdam Conference began, weeks after the collapse of Nazi Germany. It was considered necessary to let President Harry S. Truman know whether the United States possessed a nuclear capability ahead of his negotiations with Joseph Stalin, the Soviet premier. The author examines the competing priorities that drove the timetable for the test: international politics, security, and safety. Three weeks after Trinity, a gun-assembled enriched-uranium bomb called Little Boy was used against the Japanese city of Hiroshima. Three days later, Fat Man, a weaponized version of the imploding Trinity device, was dropped on Nagasaki. The author briefly examines these strikes and what impact they may have had on the Japanese surrender. The paper concludes by examining the legacy of the Trinity test 75 years into the age it helped usher in.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2021

Autonomous reinforcement learning agents for improving predictions and observations of extreme climate events

Primary Focus Area: This proposal addresses focus area 2, “Predictive modeling through the use of AI techniques.” Science Challenge: Extreme climate events associated with severe weather, coastal and inland flooding, droughts, heat waves and wildfires are expected to increase in frequency and severity in the future. Due to the complexity and chaotic behavior of the climate system, accurately predicting and observing extreme climate events requires a tremendous amount of human intervention to run predictive climate simulations and deploy measurement systems. Extreme events often unfold very quickly, leaving little time to iterate on simulations or re-position instruments. Through reinforcement learning, autonomous AI agents can be designed to make real-time decisions to characterize extreme climate events more efficiently through adaptive models and targeted observations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

From the LHC and RHIC to the EIC: Probing QCD [Slides]

Outline: Understanding gluon PDFs using photon+jet cross section measurement from the CMS pp data; Heavy flavor “tagging”/classification using Machine Learning tools at PHENIX; Unfolding development for top quark pair spin correlation and polarization at the CMS; Other contributions to the CMS and PHENIX; and, the author's interests in the EIC physics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

COVID-19 Impact on Prison Population and Flow Dynamics

The goal of this project was to develop a unique, high-level, concept model that will (1) help examine the consequences COVID-19 has had on prison population and flow dynamics in Illinois and (2) explore (to the extent possible) how that will unfold in the short- and mid-term future. Argonne has unique expertise in dynamic systems modeling and highly specialized simulation capabilities, which will be helpful in developing such a model. The ultimate objective of this CRADA is to develop with the Illinois Public Sentencing Policy Advisory Council (SPAC) the capability to identify and understand factors and interactions associated with prison population and flow dynamics in Illinois. This understanding will then potentially lead to improvements in the allocation of various resources and services. This approach would also be useful to all other states.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Time-dependent density functional theory of charge, energy, and spin transport, and quantum continuum mechanics (Final Report)

The overarching goal of this project, which unfolded over a period of seventeen years, including two no-cost extensions in the last two years, was to extend and deepen our ability to use time-dependent density functional theory and related theoretical methods for the description of the transport of charge, spin, or energy in quantum electronic systems at the nanoscale. The output of our efforts is contained in 52 papers, listed below, which we have published since 2006. There have also been many presentations at international conferences, workshops, colloquia and seminars. This body of work has been carried out with the essential input of 8 postdoctoral students (who were supported by the grant) and several external senior collaborators and their postdocs.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

‘Spokesperson for everyone at the Laboratory who believed in Oppenheimer’ Los Alamos physicist Fred Ribe’s 1954 petition protested former Lab Director’s revoked clearance

In 1953, J. Robert Oppenheimer received an ultimatum. The Atomic Energy Commission (AEC) sent the "father of the atomic bomb" and former Los Alamos Director a letter outlining two options: give up his Q clearance and role as advisor or appear before a board to prove that he wasn’t a threat to national security. Oppenheimer chose the latter. The ensuing saga that unfolded throughout 1954 peaked with a four-week, closed-door hearing in April and May after which Oppenheimer’s security clearance was formally revoked. The long, complex affair consisted of national security concerns, a tangle of questionable charges, divided opinions, loyalties, egos, and vendettas. AEC Chairman Lewis L. Strauss and Oppenheimer were at the center of events, though an important part of the historical record is Fred L. Ribe and the 493 other Los Alamos scientists who risked harming their careers to protest Oppenheimer’s ordeal. Ribe wrote a one-page letter, signed by his colleagues, to President Dwight Eisenhower and the AEC commissioners “objecting the decision and the grounds for it” as Ribe later wrote. This petition – and Strauss’s written response – were donated by Ribe and are part of the unclassified historical collections in the National Security Research Center, which is the Lab’s classified library.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2022

Nuclear Weapons Theater Experience_V1

The theater experience is driven by the big message of nuclear deterrence through successful stockpile stewardship. This job enables other national and global security work with roots going back to the capabilities developed during the Manhattan Project and honed through the history of this successor scientific laboratory. The story that unfolds uses a narrative (traditional film-type approach), although the theater setup would offer immersion and decision-making (audience participation). The idea is to demonstrate how and why the Laboratory continues its mission in maintaining the nation’s stockpile while concurrently enabling the ever-evolving multi-disciplinary science and technology innovations developed for that purpose to take other scientists along vibrant paths.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2024

The 38 th Annual Interdisciplinary Plant Group Symposium: Enhancing the Resilience of Plant Systems to Climate Change (Meeting Summary)

The University of Missouri’s Interdisciplinary Plant Group held its 38th annual symposium on May 25–27. In short, it was a resounding success! The air was almost electric because of a confluence of events that were particular to this symposium. Not only was there great enthusiasm from students attending their first ever scientific meeting, but this was coupled with excitement and delight exuded by many of our senior invited speakers, who were attending their first in-person meeting since the Covid pandemic began. After a long planning period, and with the ongoing pandemic injecting uncertainty, it was gratifying to see the symposium unfold with such excitement and engagement among participants. The symposium was organized to address the grand challenge of “Enhancing the Resilience of Plant System to Climate Change”, by bringing together experts at the intersections of multiple disciplines to educate our community on the opportunities to develop innovative mitigation strategies and to adapt plants to climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Measurement of the top quark-antiquark pair charge asymmetry in events with highly boosted top quarks in proton-proton collisions at 13 TeV with the CMS detector

The top quark is the heaviest elementary particle, making it a unique tool to search for new physics. In this talk, I will present a new measurement of the top quark pair charge asymmetry for highly boosted top quarks decaying to a single lepton, missing transverse momentum and jets. The analysis is performed on 13TeV proton-proton collision data recorded by the CMS experiment during Run 2. We have defined a dedicated phase space that selects top quark-antiquark pairs with invariant mass greater than 750GeV in a semileptonic final state where the lepton is not necessarily isolated. This highly boosted sample is enhanced in valence quark production and thus expected to be more sensitive to deviations in the charge asymmetry caused by BSM processes. Dedicated tagging techniques are used to identify the decay products of hadronic top quarks and W bosons. An unfolding procedure is used to correct for detector resolution and acceptance, and inefficiencies in the event reconstruction. The result is presented in the full phase space at parton level and can be used as input to global EFT interpretations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Just Transition Principles: Prepared for the APEC Energy Working Group Workshop on Promoting a Just Energy Transition

A global energy transition from fossil energy to clean energy is unfolding. Just transition is an iterative, continuous process of moving from a fossil-fuel economy to a green economy that provides decent, productive, and ecologically sustainable livelihoods; nurtures social dialogue; and equitably distributes costs and benefits of the energy system. It is aimed at supporting affected workers and communities and affirms that the transition is towards a more equitable energy system. Though the Asia-Pacific Economic Cooperation (APEC) region as a whole is largely representative of global energy transition trends, APEC’s member economies – and communities within them – will have their own transition nuances. Approaches to just transition must therefore recognize both the global and the local transition dynamics. The report offers eight just transition principles that can help inform work that assures the current energy transition, and its future iterations, are fair and equitable.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2024

What are the Principles Controlling Biomimetic Heteropolymer Secondary Structure? (Final Technical Report)

The goal of the project was to develop improved theories to understand how nonbiological oligomers could be designed to cooperatively fold into 3D structures. These studies would lay the groundwork for materials made of such molecules, making it possible to create controlled and ordered materials for electron transport, efficient protein-like catalysts that work under extreme conditions, and sensors with highly-specific chemical responsiveness. Two different simulation thrusts were investigated, one focused on programs to identify stable low energy folded structures at a coarse-level of description of oligomers, and another to calculate thermodynamics of such oligomers. We used these theories to answer several specific questions about what properties of oligomers lead to cooperative transitions, and to identify how oligomer knots could serve as secondary structure elements. We also carried out significant collaborative investigation with Dr. Samuel Gellman (UW-Madison, National Academy of Sciences member) on stability for foldamers of interest to them. Only one of the experimentally tested foldamers stably folded, which was indicated by simulations as being the most likely to fold. Finally, we developed new theoretical descriptions of foldamers, showing how cooperativity was determined primarily by the entropy difference between the folded and unfolded state. The research did not answer all questions laid out in the original proposal but laid the groundwork for later efforts to design folded oligomers materials with high switchability.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Connected and Learning Based Optimal Freight Management for Efficiency

The management of the future heterogenous fleet is a complex decision-making problem. The heterogenous fleet is emerging as decarbonization technologies are deployed by fleets toward lowering the freight operation emissions in Medium and Heavy-duty vehicles. Traditionally, in fleets characterized by a homogeneous Diesel Internal Combustion Engine (ICE) powertrain, the process of fleet planning and operational optimization unfolds sequentially without the necessity to account for powertrain and vehicle-specific characteristics during dispatch decisions. Fleets with trucks less than 5 years old tend to maintain stable vehicle efficiency with minimal operational reliability risks for fleet managers. However, the landscape changes with the incorporation of emerging powertrain technologies, which lack extensive operational data and service experiences. This includes technologies like hybrid, Electric, Fuel Cell, or alternative fuel ICE. Operational decisions for fleets featuring heterogeneous powertrain technologies and facing limited access to alternative fueling and charging stations become intricate, requiring careful consideration and optimization at each dispatch. The difference in efficiency characteristics of emerging technologies, their range limitations, and the restricted availability of charging/alternative fueling infrastructure, coupled with sensitivity to driving conditions (e.g., EV range reduction in low temperatures) and their impact on component aging (such as batteries), become pivotal factors influencing the reliable and efficient freight transportation. To make the path toward low emission freight transportation efficient and reliable, an AI-assisted fleet management software is developed in this project to help fleet managers in optimizing both adoption of emerging powertrain decarbonization, connected and automated technologies and also operating the fleet after such technologies are deployed as schematically. Freight transportation requirements are different depending on the cargos to be shipped, customer requirements and regions of operations. This further highlights the need for software and digital solutions to tailor deployment and operation of emerging powertrain, connectivity, and automation technologies toward the specific fleet operation requirements. The fleet management optimizer was also integrated with a model of the fleet to simulate the operation of the fleet over 1 year of the baseline fleet operation (250,000+ shipments) indicating the significance of day-to-day variations on emissions and energy consumption of a freight transportation fleet. The results demonstrate ≥20% improvement in freight efficiency in terms of WTW CO2 per ton-mile of cargo shipments while all fleet operation constraints are enforced, and the cost (CapEx and OpEx) is minimized.

33 ADVANCED PROPULSION SYSTEMS↗