Calmodulin and myosin light chain kinase: how helices are bent
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NASA Discipline Exobiology↗
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Results for “Conformal models”
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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SN 2019yvq Does Not Conform to SN Ia Explosion Models
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M. A. Tucker↗
Supercooled phase transitions in conformal dark sectors explain NANOGrav data
According to recent lore, it is difficult to explain the evidence for a stochastic gravitational wave background obtained by pulsar timing arrays with supercooled first-order phase transitions (FOPTs). We demonstrate that supercooled FOPTs in dark U(1) models with a conformal dark sector easily explain the nHz signal at NANOGrav.
Conformal models↗
Collider phenomenology of a gluino continuum
Continuum supersymmetry is a class of models in which the supersymmetric partners together with part of the standard model come from a conformal sector, broken in the IR near the TeV scale. Such models not only open new doors for addressing the problems of the standard model, but also have unique signatures at hadron colliders, which might explain why we have not yet seen any superpartners at the LHC. Here we use gauge-gravity duality to model the conformal sector, generate collider simulations, and finally analyze continuum gluino signatures at the LHC. Due to the increase in the number of jets produced the bounds are weaker than for the minimal supersymmetric standard model with the same gluino mass threshold.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Integrating AlphaFold and deep learning for atomistic interpretation of cryo-EM maps
Abstract Interpretation of cryo-electron microscopy (cryo-EM) maps requires building and fitting 3D atomic models of biological molecules. AlphaFold-predicted models generate initial 3D coordinates; however, model inaccuracy and conformational heterogeneity often necessitate labor-intensive manual model building and fitting into cryo-EM maps. In this work, we designed a protein model-building workflow, which combines a deep-learning cryo-EM map feature enhancement tool, CryoFEM (Cryo-EM Feature Enhancement Model) and AlphaFold. A benchmark test using 36 cryo-EM maps shows that CryoFEM achieves state-of-the-art performance in optimizing the Fourier Shell Correlations between the maps and the ground truth models. Furthermore, in a subset of 17 datasets where the initial AlphaFold predictions are less accurate, the workflow significantly improves their model accuracy. Our work demonstrates that the integration of modern deep learning image enhancement and AlphaFold may lead to automated model building and fitting for the atomistic interpretation of cryo-EM maps.
59 BASIC BIOLOGICAL SCIENCES↗
Near conformal perturbation theory in SYK type models
We present a systematic procedure to extract the dynamics of the low energy soft mode in SYK type models with a single energy scale J and emergent reparametrization symmetry in the IR. This is given in the framework of the perturbative scheme of arXiv:1608.07567 based on a specific (off-shell) breaking of conformal invariance in the UV, adjusted to yield the exact large-N saddle point. While this breaking term formally vanishes on-shell, it has a non-trivial effect on correlation functions and the effective action. In particular, it leads to the Schwarzian action with a specific coupling to bi-local matter. The method is applied to the evaluation of O(1) corrections to the correlation function of bi-locals. As a byproduct we confirm precise agreement with the explicit, symmetry breaking procedure. We provide a verification in the large q limit (Liouville theory), where the correlators can be calculated exactly at all length scales. In this case, our scheme illuminates how the enhanced O(J) and the subleading O(1) contributions originate from the Schwarzian dynamics of the soft mode and its interaction with h = 2 (bi-local) matter.
1/N expansion↗
Testing Strategies for Model-Based Development
This report presents an approach for testing artifacts generated in a model-based development process. This approach divides the traditional testing process into two parts: requirements-based testing (validation testing) which determines whether the model implements the high-level requirements and model-based testing (conformance testing) which determines whether the code generated from a model is behaviorally equivalent to the model. The goals of the two processes differ significantly and this report explores suitable testing metrics and automation strategies for each. To support requirements-based testing, we define novel objective requirements coverage metrics similar to existing specification and code coverage metrics. For model-based testing, we briefly describe automation strategies and examine the fault-finding capability of different structural coverage metrics using tests automatically generated from the model.
Heimdahl, Mats P. E.↗
Machine Learning with Gradient-Based Optimization of Nuclear Waste Vitrification with Uncertainties and Constraints
Gekko is an optimization suite in Python that solves optimization problems involving mixed-integer, nonlinear, and differential equations. The purpose of this study is to integrate common Machine Learning (ML) algorithms such as Gaussian Process Regression (GPR), support vector regression (SVR), and artificial neural network (ANN) models into Gekko to solve data based optimization problems. Uncertainty quantification (UQ) is used alongside ML for better decision making. These methods include ensemble methods, model-specific methods, conformal predictions, and the delta method. An optimization problem involving nuclear waste vitrification is presented to demonstrate the benefit of ML in this field. ML models are compared against the current partial quadratic mixture (PQM) model in an optimization problem in Gekko. GPR with conformal uncertainty was chosen as the best substitute model as it had a lower mean squared error of 0.0025 compared to 0.018 and more confidently predicted a higher waste loading of 37.5 wt% compared to 34 wt%. The example problem shows that these tools can be used in similar industry settings where easier use and better performance is needed over classical approaches. Future works with these tools include expanding them with other regression models and UQ methods, and exploration into other optimization problems or dynamic control.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
A linear shock cell model for non-circular jets using conformal mapping with a pseudo-spectral hybrid scheme
The shock structure in non-circular supersonic jets is predicted using a linear model. This model includes the effects of the finite thickness of the mixing layer and the turbulence in the jet shear layer. A numerical solution is obtained using a conformal mapping grid generation scheme with a hybrid pseudo-spectral discretization method. The uniform pressure perturbation at the jet exit is approximated by a Fourier-Mathieu series. The pressure at downstream locations is obtained from an eigenfunction expansion that is matched to the pressure perturbation at the jet exit. Results are presented for a circular jet and for an elliptic jet of aspect ratio 2.0. Comparisons are made with experimental data.
Bhat, Thonse R. S.↗
Studying the Collective Functional Response of a Receptor in Alchemical Ligand Binding Free Energy Simulations with Accelerated Solvation Layer Dynamics
Ligand binding free energy simulations (LB-FES) that involve sampling of protein functional conformations have been longstanding challenges in research on molecular recognition. Particularly, modeling of the conformational transition pathway and design of the heuristic biasing mechanism are severe bottlenecks for the existing enhanced configurational sampling (ECS) methods. Inspired by the key role of hydration in regulating conformational dynamics of macromolecules, this report proposes a novel ECS approach that facilitates binding-associated structural dynamics by accelerated hydration transitions in combination with the lambda-exchange of free energy perturbation (FEP). Further, two challenging protein-ligand binding processes involving large configurational transitions of the receptor are studied, with hydration transitions at binding sites accelerated by Hamiltonian-simulated annealing of the hydration layer. Without the need for pathway analysis or ad hoc barrier flattening potential, LB-FES were performed with FEP/lambda-exchange molecular dynamics simulation at a minor overhead for annealing of the hydration layer. The LB-FES studies showed that the accelerated rehydration significantly enhances the collective conformational transitions of the receptor, and convergence of binding affinity calculations is obtained at a sweet-spot simulation time scale. Alchemical LB-FES with the proposed ECS strategy is free from the effort of trial and error for the setup and realizes efficient on-the-fly sampling for the collective functional response of the receptor and bound water and therefore presents a practical approach to high-throughput screening in drug discovery.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Enabling Assurance in the MBSE Environment
A number of specific benefits that fit within the hallmarks of effective development are realized with implementation of model-based approaches to systems and assurance. Model Based Systems Engineering (MBSE) enabled by standardized modeling languages (e.g., SysML®) is at the core. These benefits in the context of spaceflight system challenges can include [1]: • Improved management of complex development • Reduced risk in the development process • Improved cost management • Improved design decisions With appropriate modeling techniques the assurance community also can improve early oversight and insight into project development. NASA has shown the basic constructs of SysML in an MBSE environment offer several key advantages, within a Model Based Mission Assurance (MBMA) initiative [2, 3]. These include the following: • Model viewpoints that promote rapid and systematic assessment of requirements coverage, hazard tagging and risk management • Embedded safety assessments for launch vehicles • Deployment of model assisted development of reliability products - Failure Modes and Effects Analyses (FMEAs) and Fault Trees • Test Planning • Validation and Verification of complex functions • Support of Assurance Case development for complex systems In addition, while there are benefits to be harvested, there is a realization that these do not come without effort and cost. Enabling model-based approaches requires structure, not only in an organizational context, but in a modeling context as well. There can be a steep learning curve and costs associated to train skilled modelers. But, on the other hand, not all of the assurance community need to be modelers. Models themselves must conform to ontologies that enable assurance. This places constraints upon the models and modelers. Optimums have yet to be developed where resources and constraints on modeling must be traded off in the organization and modeling efforts for projects. A number of barriers need to be overcome, as well, which pose challenges to the developers of the software that supports MBSE/MBMA. Information and data must be made to flow seamlessly through the life cycle. Because there is a wide variety of tools used in the community, to avoid the problems of the past of silos, delays, and diverging interests, information should flow among these tools to support the “single source of truth” paradigm of MBSE. This will greatly facilitate MBMA and advancement of assurance functions.
Evans, John W.↗
Developing a model for the impact of non-conformal lithium contact on electro-chemo-mechanics and dendrite growth
Lithium dendrite growth hinders the use of lithium metal anodes in commercial batteries. We present a 3D model to study the mechanical and electrochemical mechanisms that drive microscale plating. With this model, we investigate electrochemical response across a lithium protrusion characteristic of rough anode surfaces, representing the separator as a porous polymer in non-conformal contact with a lithium anode. The impact of pressure on separator morphology and electrochemical response is of particular interest, as external pressure can improve cell performance. We explore the relationships between plating propensity, stack pressure, and material properties. External pressure suppresses lithium plating due to interfacial stress and separator pore closure, leading to inhomogeneous plating rates. For moderate pressures, dendrite growth is completely suppressed, as plating will occur in the electrolyte-filled gaps between anode and separator. In fast-charging conditions and systems with low electrolyte diffusivities, the benefits of pressure are overridden by ion transport limitations.
25 ENERGY STORAGE↗
Sphere and disk partition functions in Liouville and in matrix integrals
We compute the sphere and disk partition functions in semiclassical Liouville and analogous quantities in double-scaled matrix integrals. The quantity sphere/disk2 is unambiguous and we find a precise numerical match between the Liouville answer and the matrix integral answer. An application is to show that the sphere partition function in JT gravity is infinite.
2D Gravity↗
Using the conformal decomposition finite element method to model the Direct Ink Write process for sinusoidal extrusion patterns
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Kucala, Alec [Sandia National Laboratories (SNL-NM↗
Introduction to Information Visualization (InfoVis) Techniques for Model-Based Systems Engineering
This paper presents insights that conform to numerous system modeling languages/representation standards. The insights are drawn from best practices of Information Visualization as applied to aerospace-based applications.
MBSE↗
Arcjet Testing of Advanced Conformal Ablative TPS
A conformable TPS over a rigid aeroshell has the potential to solve a number of challenges faced by traditional rigid TPS materials (such as tiled Phenolic Impregnated Carbon Ablator (PICA) system on MSL. The compliant (high strain to failure) nature of the conformable ablative materials will allow integration of the TPS with the underlying aeroshell structure much easier and enable monolithic-like configuration and larger segments (or parts) to be used. In May of 2013 the CA250 project executed an arcjet test series in the Ames IHF facility to evaluate a phenolic-based conformal system (named Conformal-PICA) over a range of test conditions from 40-400Wcm2. The test series consisted of four runs in the 13-inch diameter nozzle. Test models were based on SPRITE configuration (a 55-deg sphere cone), as it was able to provide a combination of required heat flux, pressure and shear within a single entry. The preliminary in-depth TC data acquired during that test series allowed a mid-fidelity thermal response model for conformal-PICA to be created while testing of seam models began to address TPS attachment and joining of multiple segments for future fabrication of large-scale aeroshells. Discussed in this paper are the results.
Arcjet Testing↗
Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations
Abstract Motivation Techniques such as high-throughput chromosome conformation capture (Hi-C) have provided a wealth of information on nucleus organization and genome important for understanding gene expression regulation. Genome-Wide Association Studies have identified numerous loci associated with complex traits. Expression quantitative trait loci (eQTL) studies have further linked the genetic variants to alteration in expression levels of associated target genes across individuals. However, the functional roles of many eQTLs in noncoding regions remain unclear. Current joint analyses of Hi-C and eQTLs data lack advanced computational tools, limiting what can be learned from these data. Results We developed a computational method for simultaneous analysis of Hi-C and eQTL data, capable of identifying a small set of nonrandom interactions from all Hi-C interactions. Using these nonrandom interactions, we reconstructed large ensembles (×105) of high-resolution single-cell 3D chromatin conformations with thorough sampling, accurately replicating Hi-C measurements. Our results revealed many-body interactions in chromatin conformation at the single-cell level within eQTL loci, providing a detailed view of how 3D chromatin structures form the physical foundation for gene regulation, including how genetic variants of eQTLs affect the expression of associated eGenes. Furthermore, our method can deconvolve chromatin heterogeneity and investigate the spatial associations of eQTLs and eGenes at subpopulation level, revealing their regulatory impacts on gene expression. Together, ensemble modeling of thoroughly sampled single-cell chromatin conformations combined with eQTL data, helps decipher how 3D chromatin structures provide the physical basis for gene regulation, expression control, and aid in understanding the overall structure-function relationships of genome organization. Availability and implementation It is available at https://github.com/uic-liang-lab/3DChromFolding-eQTL-Loci.
Du, Lin (ORCID:0009000289869812)↗
Mechanosensitive Ion Channels in Bacteria: Functional Domains and Mechanisms of Gating
The past funding period was productive for the group. The progress in the mechanosensitive channel field was critically affected in the end of 1998 by the solution of the crystal structure of the mycobacterial homolog of MscL by our colleagues from Caltech. Having the structure of TbMscL in the closed state, we developed a detailed homology model of EcoMscL, and related the structural model with the wealth of functional phenomenology available for the E. coli version of the channel (EcoMscL). The biophysical properties of the open MscL helped to model the open conformation and infer the pathway for the entire gating transition. The following experiments provided strong support to the atomic model of the gating process, and allowed to make further predictions. The work has advanced our understanding of tension-driven conformational transitions in membrane-embedded mechanosensory proteins, determine major energetic contributions and set the stage for further exploration of the whole family of mechanosensitive channels. The results have been published in seven experimental and theoretical papers, with three other papers currently in press or in preparation.
Sukharev, Sergei↗