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At least 613 records · Page 34

Combinatorial transcription factor binding encodes cis -regulatory wiring of mouse forebrain GABAergic neurogenesis

Transcription factors (TFs) bind combinatorially to cis-regulatory elements, orchestrating transcriptional programs. Although studies of chromatin state and chromosomal interactions have demonstrated dynamic neurodevelopmental cis-regulatory landscapes, parallel understanding of TF interactions lags. To elucidate combinatorial TF binding driving mouse basal ganglia development, we integrated chromatin immunoprecipitation sequencing (ChIP-seq) for twelve TFs, H3K4me3-associated enhancer-promoter interactions, chromatin and gene expression data, and functional enhancer assays. We identified sets of putative regulatory elements with shared TF binding (TF-pRE modules) that orchestrate distinct processes of GABAergic neurogenesis and suppress other cell fates. The majority of pREs were bound by one or two TFs; however, a small proportion were extensively bound. These sequences had exceptional evolutionary conservation and motif density, complex chromosomal interactions, and activity as in vivo enhancers. Our results provide insights into the combinatorial TF-pRE interactions that activate and repress expression programs during telencephalon neurogenesis and demonstrate the value of TF binding toward modeling developmental transcriptional wiring.

59 BASIC BIOLOGICAL SCIENCES↗

Cropland abandonment between 1986 and 2018 across the United States: spatiotemporal patterns and current land uses

Knowing where and when croplands have been abandoned or otherwise removed from cultivation is fundamental to evaluating future uses of these areas, e.g. as sites for ecological restoration, recultivation, bioenergy production, or other uses. However, large uncertainties remain about the location and time of cropland abandonment and how this process and the availability of associated lands vary spatially and temporally across the United States. Here, we present a nationwide, 30 m resolution map of croplands abandoned throughout the period of 1986–2018 for the conterminous United States (CONUS). We mapped the location and time of abandonment from annual cropland layers we created in Google Earth Engine from 30 m resolution Landsat imagery using an automated classification method and training data from the U.S. Department of Agriculture Cropland Data Layer. Our abandonment map has overall accuracies of 0.91 and 0.65 for the location and time of abandonment, respectively. From 1986 to 2018, 12.3 (±2.87) million hectares (Mha) of croplands were abandoned across CONUS, with areas of greatest change over the Ogallala Aquifer, the southern Mississippi Alluvial Plain, the Atlantic Coast, North Dakota, northern Montana, and eastern Washington state. The average annual nationwide abandoned area across our study period was 0.51 Mha per year. Annual abandonment peaked between 1997 and 1999 at a rate of 0.63 Mha year –1 , followed by a continuous decrease to 0.41 Mha year –1 in 2009–2011. Among the abandoned croplands, 53% (6.5 Mha) changed to grassland and pasture, 18.6% (2.28 Mha) to shrubland and forest, 8.4% (1.03 Mha) to wetlands, and 4.6% (0.56 Mha) to non-vegetated lands. Of the areas that we mapped as abandoned, 19.6% (2.41 Mha) were enrolled in the Conservation Reserve Program as of 2020. Our new map highlights the long-term dynamic nature of agricultural land use and its relation to various competitive pressures and land use policies in the United States.

54 ENVIRONMENTAL SCIENCES↗

Bayesian analysis of (3 +1)⁢D relativistic nuclear dynamics with the RHIC beam energy scan data

This work presents a Bayesian inference study for relativistic heavy-ion collisions in the beam energy scan program at the BNL Relativistic Heavy-Ion Collider. The theoretical model simulates event-by-event (3+1)-dimensional [(3+1)⁢D] collision dynamics using hydrodynamics and hadronic transport theory. We analyze the model's 20-dimensional posterior distributions obtained using three model emulators with different accuracy and demonstrate the essential role of training an accurate model emulator in the Bayesian analysis. Our analysis provides robust constraints on the quark-gluon plasma's transport properties and various aspects of (3+1)⁢D relativistic nuclear dynamics. By running full model simulations with 100 parameter sets sampled from the posterior distribution, we make predictions for p T -differential observables and estimate their systematic theory uncertainty. Here, a sensitivity analysis is performed to elucidate how individual experimental observables respond to different model parameters, providing useful physics insights into the phenomenological model for heavy-ion collisions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Spectroscopic and Dynamical Studies of Highly Energized Small Polyatomic Molecules (End-of-Grant Report)

The aim of this research program has been to develop models for qualitative and quantitative understanding of complex processes in small molecules, such as vibronic coupling, predissociation, photodissociation, and isomerization. Simple models capture physical insights and lead to intuitive ideas that can enlighten a broad array of problems. Numerical fits can provide predictive power, but rarely impart insights into the underlying mechanisms responsible for the observed phenomena. This DOE supported program has prioritized a quantum mechanical understanding over a perfect numerical fit of spectra. Finding few-parameter models, when those parameters have physical meaning, allows the insights gained from one problem to be easily applied to related problems in other systems. The systems that have been under investigation include atmospherically relevant sulfur-containing compounds, various unimolecular dynamical processes of electronically excited acetylene, and the rovibrational dynamics of formaldehyde and SO 2 .

74 ATOMIC AND MOLECULAR PHYSICS↗

Delivery of Dynamic Thermal Energy Storage Models and Advanced Reactor Concept Models to the HYBRID Repository

This publication details newly created energy storage and reactor models developed within the HYBRID modeling repository as part of the Department of Energy Office of Nuclear Energy (DOE-NE) Integrated Energy Systems (IES) program, led by Idaho National Laboratory (INL). Model development to-date includes creation of dynamic systems-level models of a pebble bed high temperature gas reactor (HTGR), sodium fast reactor (SFR), compressed air energy storage (CAES), liquid air energy storage (LAES) and Modelica standard library based two-tank sensible heat storage (SHS) in the IES-based HYBRID repository. Models are developed using the latest publicly available data and incorporate the possibility of control strategy inclusion for use with the existing IES modeling, analysis, and optimization toolset. Simulations showcase the abilities of each technology to flexibly operate in ways consistent with IES operation expectations. When these models are available, they can be utilized within different integrated energy park concepts to understand optimal system operation, control, and dispatching. Moreover, given the generic nature of the models, industrial partner technologies can be quickly added to the repository using the existing models as a basis. Additional dynamic models for thermal energy storage concepts can be developed and added to the HYBRID repository as needed. Also detailed in this report are future development goals for the HYBRID repository including adding suites of steady-state models, economic costing information, and reduced-order models. By adding these models in addition to the physical transient models currently existing within HYBRID, HYBRID will be a fully integrable tool for FORCE users.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Assessment of NDE for Key Indicators of Aging Cables in Nuclear Power Plants – Interim Status

Degradation of the cable jacket, electrical insulation, and other cable components of installed cables within nuclear power plants (NPPs) is known to occur as a function of age, temperature, radiation, and other environmental factors. System tests verify cable function under normal loads; however, the concern is over cable performance under exceptional loads associated with design-basis events (DBEs). The cable’s ability to perform safely over the initial 40 year planned and licensed life has generally been demonstrated and there have been very few age-related cable failures. With greater than 1000 km of power, control, instrumentation, and other cables typically found in an NPP, replacing all the cables would be a severe cost burden. Justification for life extension to 60 and 80 years requires a cable aging management program to justify cable performance under normal operation as well as accident conditions. Currently the gold standard for determining cable insulation degradation is the elongation-at-break (EAB). This, however, is an ex-situ measurement and requires removal of a sample for laboratory investigation. A reliable nondestructive examination (NDE) in-situ approach is desirable to objectively determine the suitability of the cable for service. A variety of tests are available to assess various aspects of electrical and mechanical cable performance, but none of these tests are suitable for all cable configurations nor does any single test confirm all features of interest. Nevertheless, the complete collection of test possibilities offers a powerful range of tools to assure the integrity of critical cables. Licensees and regulators have settled on a practical program to justify continued operation based on condition monitoring of a lead sample set of cables where test data is tracked in a database and the required test data are continually adjusted based on plant and fleet-wide experience. As part of the Light Water Reactor Sustainability program sponsored by the U.S. Nuclear Regulatory Commission, the U.S. Department of Energy, and industry (represented by the Electric Power Research Institute), an assessment of cable NDE methods was commissioned. Technologies include both bulk electrical measurements (Tan d, time domain reflectometry, frequency domain reflectometry (FDR), partial discharge, and other techniques) and local insulation measurement (indenter, dynamic mechanical analysis interdigital capacitance, infrared spectral measurement, etc.). This aging cable NDE program update reviews the full range of techniques but focuses on the most interesting test approaches that have a chance to be deployed in-situ, particularly including Tan d, FDR, and ultrasound methods that have been reviewed most completely in this progress period.

cable aging inspection↗

Four-dimensional dose reconstruction through in vivo phase matching of cine images of electronic portal imaging device

Purpose: A method is proposed to reconstruct a four-dimensional (4D) dose distribution using phase matching of measured cine images to precalculated images of electronic portal imaging device (EPID). Methods: (1) A phantom, designed to simulate a tumor in lung (a polystyrene block with a 3 cm diameter embedded in cork), was placed on a sinusoidally moving platform with an amplitude of 1 cm and a period of 4 s. Ten-phase 4D computed tomography (CT) images of the phantom were acquired. A planning target volume (PTV) was created by adding a margin of 1 cm around the internal target volume of the tumor. (2) Three beams were designed, which included a static beam, a theoretical dynamic beam, and a planning-optimized dynamic beam (PODB). While the theoretical beam was made by manually programming a simplistic sliding leaf motion, the planning-optimized beam was obtained from treatment planning. From the three beams, three-dimensional (3D) doses on the phantom were calculated; 4D dose was calculated by means of the ten phase images (integrated over phases afterward); serving as “reference” images, phase-specific EPID dose images under the lung phantom were also calculated for each of the ten phases. (3) Cine EPID images were acquired while the beams were irradiated to the moving phantom. (4) Each cine image was phase-matched to a phase-specific CT image at which common irradiation occurred by intercomparing the cine image with the reference images. (5) Each cine image was used to reconstruct dose in the phase-matched CT image, and the reconstructed doses were summed over all phases. (6) The summation was compared with forwardly calculated 4D and 3D dose distributions. Accounting for realistic situations, intratreatment breathing irregularity was simulated by assuming an amplitude of 0.5 cm for the phantom during a portion of breathing trace in which the phase matching could not be performed. Intertreatment breathing irregularity between the time of treatment and the time of planning CT was considered by utilizing the same reduced amplitude when the phantom was irradiated. To examine the phase matching in a humanoid environment, the matching was also performed in a digital phantom (4D XCAT phantom). Results: For the static, the theoretical, and the planning-optimized dynamic beams, the 4D reconstructed doses showed agreement with the forwardly calculated 4D doses within the gamma pass rates of 92.7%, 100%, and 98.1%, respectively, at the isocenter plane given by 3%/3 mm criteria. Excellent agreement in dose volume histogram of PTV and lung-PTV was also found between the two 4D doses, while substantial differences were found between the 3D and the 4D doses. The significant breathing irregularities modeled in this study were found not to be noticeably affecting the reconstructed dose. The phase matching was performed equally well in a digital phantom. Conclusions: The method of retrospective phase determination of a moving object under irradiation provided successful 4D dose reconstruction. This method will provide accurate quality assurance and facilitate adaptive therapy when distinguishable objects such as well-defined tumors, diaphragm, and organs with markers (pancreas and liver) are covered by treatment beam apertures.

60 APPLIED LIFE SCIENCES↗

Quantum Electromagnetic Transients Program

This work devises a quantum electromagnetic transients program (QEMTP) which is the first attempt to tackle the computational challenges in solving EMTP through quantum computing. The main contributions lie in: (1) A quantum-enabled EMTP formulation with Dommel's model encoded in quantum states; 2) An Harrow-Hassidim-Lloyd (HHL)-based QEMTP to solve the discrete-time nodal equations; 3) An iteration-based HHL revision for mitigating temporal errors to achieve high accuracy of QEMTP with limited quantum resources. Case studies verify the correctness and efficacy of QEMTP in simulating both fast and slow dynamics.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Report on the Program “Fluid-mediated particle transport in geophysical flows” at the Kavli Institute for Theoretical Physics, UC Santa Barbara, September 23 to December 12, 2013

The Kavli Institute of Theoretical Physics (KITP) program held at UC Santa Barbara in the fall of 2013 addressed the dynamics of dispersed particulate flows in the environment. By focusing on the prototypes of aeolian transport and turbidity currents, it aimed to establish the current state of our understanding of such two-phase flows, to identify key open questions, and to develop collaborative research strategies for addressing these questions. Here, we provide a brief summary of the program outcome.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Transforming Cyber Education thru Open to All Accessible Pathways

Boise State University’s (BSU) Cyber Operations and Resilience CORe program was intentionally designed so that any student, especially non-traditional and non-technical students, with an interest in cybersecurity could have an education and training pathway to enter the cyber workforce. The CORe curriculum focuses on teaching students how to design, apply, and improve cybersecurity through the interaction of people, processes, and technology. CORe is a stackable curriculum with elective credit hours and options for various academic and industry certificates and certifications that enable students to customize their unique career pathway. The CORe program guides students to think about the system being managed, the risks presented, and the dynamic intersection of system elements when considering how to incorporate resilience frameworks in achieving a resilient system. By developing systems thinking, the students gain an understanding of the interdependencies interacting with the operational system. Further, the CORe program encourages students to integrate cybersecurity knowledge with models and frameworks found in other academic disciplines through a unifying systems approach. CORe is designed around the realities of today’s broad cyber landscape: that breaches will occur in any system over time and proactive design of resilience into systems to detect, respond, and recover in a timely and orderly manner is critical. Students are taught to think holistically about cybersecurity focusing on all system elements. CORe is not a traditional cybersecurity degree. CORe is distinguished by the non-traditional engineering, computer science approach to cybersecurity education with the singular focus on infusing resilience operations and transdisciplinary systems thinking principles throughout the curriculum.

99 GENERAL AND MISCELLANEOUS↗

A Privacy Preserving Model-Free Optimization and Control Framework for Demand Response from Residential Thermal Loads

We consider the problem of optimizing the cost of procuring electricity for a large collection of homes managed by a load serving entity, by pre-cooling or pre-heating the thermal inertial loads in the homes to avoid procuring power during periods of peak electricity pricing. We would like to accomplish this objective in a completely privacy-preserving and model-free manner, that is, without direct access to the state variables (temperatures or power consumption) or the dynamical models (thermal characteristics) of individual homes, while guaranteeing personal comfort constraints of the consumers. We propose a two-stage optimization and control framework to address this problem. In the first stage, we use a long short-term memory (LSTM) network to predict hourly electricity prices, based on historical pricing data and weather forecasts. Given the hourly price forecast and thermal models of the homes, the problem of designing an optimal power consumption trajectory that minimizes the total electricity procurement cost for the collection of thermal loads can be formulated as a large-scale integer program (with millions of variables) due to the on-off cyclical dynamics of such loads. We provide a simple heuristic relaxation to make this large-scale optimization problem model-free and computationally tractable. In the second stage, we translate the results of this optimization problem into distributed open-loop control laws that can be implemented at individual homes without measuring or estimating their state variables, while simultaneously ensuring consumer comfort constraints. We demonstrate the performance of this approach on a large-scale test case comprising of 500 homes in the Houston area and benchmark its performance against a direct model-based optimization and control solution.

Sivaranjani, S.↗

The linear and nonlinear response of infinite periodic systems to static and/or dynamic electric fields. Implementation in CRYSTAL code

An implementation of the vector potential approach (VPA) for treating the response of infinite periodic systems to static and dynamic electric fields has been initiated within the CRYSTAL code. The VPA method is based on the solution of a time-dependent Hartree-Fock or Kohn-Sham equation for the crystal orbitals wherein the usual scalar potential, that describes interaction with the field, is replaced by the vector potential. This equation may be solved either by perturbation theory or by finite field methods. With some modification all the computational procedures of molecular ab initio quantum chemistry can be adapted for periodic systems. Accessible properties include the linear and nonlinear responses of both the nuclei and the electrons. The programming of static field pure electronic (hyper)polarizabilities has been successfully tested. Dynamic electronic (hyper)polarizabilities, as well as infrared and Raman intensities, are in progress while the addition of finite fields for calculation of vibrational (hyper)polarizabilities, through nuclear relaxation procedures, will begin shortly.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Memory operation mechanism of fullerene-containing polymer memory

The memory operation mechanism in fullerene-containing nanocomposite gate insulators was investigated while varying the kind of fullerene in a polymer gate insulator. It was cleared what kind of traps and which positions in the nanocomposite the injected electrons or holes are stored in. The reason for the difference in the easiness of programming was clarified taking the role of the charging energy of an injected electron into account. The dependence of the carrier dynamics on the kind of fullerene molecule was investigated. A nonuniform distribution of injected carriers occurred after application of a large magnitude programming voltage due to the width distribution of the polystyrene barrier between adjacent fullerene molecules. Through the investigations, we demonstrated a nanocomposite gate with fullerene molecules having excellent retention characteristics and a programming capability. This will lead to the realization of practical organic memories with fullerene-containing polymer nanocomposites.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Artium mater in relativistic astrophysics : New perspectives for a European-Latin American PhD program

Following the successful scientific space missions by the European Space Agency (ESA) and the European Southern Observatory (ESO) in Chile, as well as the high-energy particle activities at CERN in Genve, we have created a Ph.D. program dedicated to the formation of scientists in the field of relativistic astrophysics. The students of such a program will lead the theoretical developments of one of the most active fields of research, based on the above observational and experimental facilities. This program needs expertise in the most advanced topics of mathematical and theoretical physics, and in relativistic field theories. It requires the ability to model the observational data received from the above facilities, as well as all the basic knowledge in astronomy, astrophysics and cosmology. This activity is necessarily international, no single university can cover the broad expertises. From this, the proposed program of the IRAP Ph.D., in one of the youngest and most dynamical French universities, pole of research and teaching in the Euro-Mediterranean region (PRES): the University of Nice. It benefits from the presence of the astrophysics research institute of Observatoire de la Cte d’Azur involved in relativistic and non-photonic astrophysics. The participation of the Freie Universitaet Berlin, Oldenburg and Bremen Universities and of the Einstein Institute in Potsdam offers the possibility of teaching in relativistic field theories at the highest level. The University of Savoy offers the link to the particle physics at CERN. The activities at the University of Rome, at Stockholm University and at ICRANet offer teaching programs in all the fields of relativistic astrophysics, including cosmology, the physics of gravitational collapse, gamma-ray bursts, and black hole physics. Finally, the University of Ferrara will be present with lectures and researches in the topics they have pioneered such as x-ray astrophysics and observational cosmology. Through ICRANet the extra-European connections with Brazil, China and India will be guaranteed: in China, with the Shanghai Observatory of the Chinese Academy of Science, studying the formation and evolution of large-scale structure and galaxies; in India, with the Indian Centre for Space Physics (ICSP), renowned for its research on compact objects as well as on solar physics and astrochemistry; in Brazil with ICRANet Brazil where a successful program of research and teaching in relativistic astrophysics has been established in recent years.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Energy-Efficient Maneuvering of Connected and Automated Vehicles (CAVs) with Situational Awareness at Intersections (Final Progress Report)

The increased development of Connected and Automated Vehicle (CAV) systems, currently used for safety and driver convenience, presents new opportunities to improve the energy efficiency of vehicles. Southwest Research Institute (SwRI) achieved a 20% energy consumption reduction in a 2017 Toyota Prius Prime plug-in hybrid by using connectivity (V2V, V2I, V2X) as part of the Next Generation Energy Technologies for Connected and Automated on-Road Vehicles (NEXTCAR) program. The energy consumption gains were achieved by a combination of vehicle dynamics and powertrain control algorithms with a focus on SAE L1 and L2 automated vehicles where a human is still responsible for safe operation. SwRI is now involved in NEXTCAR-II, focusing on energy-efficient control tech for SAE Level 4/5 automated vehicles, aiming for a 30% energy reduction compared to stock hybrids. The rise of Mobility as a Service (MaaS) is driving investments in L4 and L5 automated vehicles. A study by the University of Michigan shows these vehicles might increase energy use and emissions by 3-20%. Technology similar to NEXTCAR can enhance energy efficiency in highly automated vehicles, leveraging improved sensing and actuation capabilities. While the NEXTCAR programs targeted energy efficiency improvements for a single vehicle, this program adopts a more expansive approach. It places its focus on understanding and testing the cumulative effects within a region or corridor, aiming to assess how a subset of vehicles equipped with NEXTCAR-style technologies influence the overall energy consumption of all vehicles traveling within that area. Additionally, the program explores infrastructure-based mobility solutions to optimize efficiency, and seeks to understand and quantify public perception and likelihood of technology adoption.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Model of fracture of metal melts and the strength of melts under dynamic conditions

The development of a continuum model of deformation and fracture of melts is needed for the description of the behavior of metals in extreme states, in particular, under high-current electron and ultrashort laser irradiation. The model proposed includes the equations of mechanics of a two-phase continuum and the equations of the kinetics of phase transitions. The change (exchange) of the volumes of dispersed and carrier phases and of the number of dispersed particles is described, and the energy and mass exchange between the phases due to phase transitions is taken into account. Molecular dynamic (MD) calculations are carried out with the use of the LAMMPS program. The continuum model is verified by MD, computational, and experimental data. The strength of aluminum, copper, and nickel is determined at various temperatures and strain rates. It is shown that an increase in the strain rate leads to an increase in the strength of a liquid metal, while an increase in temperature leads to a decrease in its strength.

36 MATERIALS SCIENCE↗

Adaptive Runtime Features For Distributed Graph Algorithms

Performance of distributed graph algorithms can benefit greatly by forming rapport between algorithmic abstraction and the underlying runtime system that is responsible for scheduling work and exchanging messages. However, due to their dynamic and irregular nature of computation, distributed graph algorithms written in different programming models impose varying degree of workload pressure on the runtime. To cope with such vastly different workload characteristics, a runtime has to make several trade-offs. One such trade-off arises, for example, when the runtime scheduler has to choose among alternatives such as whether to execute algorithmic work, or progress the network by probing network buffers, or throttle sending messages (termed flow control). This tradeoff decides between optimizing the throughput of a runtime scheduler by increasing the rate of execution of algorithmic work, and reducing the latency of the network messages. Another trade-off exists when a decision has to be made about when to send aggregated messages in buffers (message coalescing). This decision chooses between trading off latency for network bandwidth and vice versa. At any instant, such trade-offs emphasize either on improving the quantity of work being executed (by maximizing the scheduler throughput) or on improving the quality of work (by prioritizing better work). However, encoding static policies for different runtime features (such as flow control, coalescing) can prevent graph algorithms from achieving their full potential, thus can undermine the actual performance of a distributed graph algorithm . In this paper, we investigate runtime support for distributed graph algorithms in the context of two paradigms: variants of wellknown Bulk-Synchronous Parallel model and asynchronous programming model. We explore generic runtime features such as message coalescing (aggregation) and flow control and show that execution policies of these features need to be adjusted over time to make a positive impact on the execution time of a distributed graph algorithm. Since synchronous and asynchronous graph algorithms have different workload characteristics, not all of such runtime features may be good candidates for adaptation. Each of these algorithmic paradigms may require different set of features to be adapted over time. We demonstrate which set of feature(s) can be useful in each case to achieve the right balance of work in the runtime layer. Existing implementation of different graph algorithms can benefit from adapting dynamic policies in the underlying runtime.

Firoz, Jesun S.↗