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DOE OSTI2016

Evaluating OpenSHMEM Explicit Remote Memory Access Operations and Merged Requests

The OpenSHMEM Library Specification has evolved consid- erably since version 1.0. Recently, non-blocking implicit Remote Memory Access (RMA) operations were introduced in OpenSHMEM 1.3. These provide a way to achieve better overlap between communication and computation. However, the implicit non-blocking operations do not pro- vide a separate handle to track and complete the individual RMA opera- tions. They are guaranteed to be completed after either a shmem quiet(), shmem barrier() or a shmem barrier all() is called. These are global com- pletion and synchronization operations. Though this semantic is expected to achieve a higher message rate for the applications, the drawback is that it does not allow fine-grained control over the completion of RMA operations. In this paper, first, we introduce non-blocking RMA operations with requests, where each operation has an explicit request to track and com- plete the operation. Second, we introduce interfaces to merge multiple requests into a single request handle. The merged request tracks multiple user-selected RMA operations, which provides the flexibility of tracking related communication operations with one request handle. Lastly, we explore the implications in terms of performance, productivity, usability and the possibility of defining different patterns of communication via merging of requests. Our experimental results show that a well designed and implemented OpenSHMEM stack can hide the overhead of allocating and managing the requests. The latency of RMA operations with requests is similar to blocking and implicit non-blocking RMA operations. We test our implementation with the Scalable Synthetic Compact Applications (SSCA #1) benchmark and observe that using RMA operations with requests and merging of these requests outperform the implementation using blocking RMA operations and implicit non-blocking operations by 49% and 74% respectively.

Boehm, Swen↗

DOE OSTI2015

Wave induced density modification in RF sheaths and close to wave launchers

With the return to full metal walls - a necessary step towards viable fusion machines - and due to the high power densities of current-day ICRH (Ion Cyclotron Resonance Heating) or RF (radio frequency) antennas, there is ample renewed interest in exploring the reasons for wave-induced sputtering and formation of hot spots. Moreover, there is experimental evidence on various machines that RF waves influence the density profile close to the wave launchers so that waves indirectly influence their own coupling efficiency. The present study presents a return to first principles and describes the wave-particle interaction using a 2-time scale model involving the equation of motion, the continuity equation and the wave equation on each of the time scales. Through the changing density pattern, the fast time scale dynamics is affected by the slow time scale events. In turn, the slow time scale density and flows are modified by the presence of the RF waves through quasilinear terms. Although finite zero order flows are identified, the usual cold plasma dielectric tensor - ignoring such flows - is adopted as a first approximation to describe the wave response to the RF driver. The resulting set of equations is composed of linear and nonlinear equations and is tackled in 1D in the present paper. Whereas the former can be solved using standard numerical techniques, the latter require special handling. At the price of multiple iterations, a simple ’derivative switch-on’ procedure allows to reformulate the nonlinear problem as a sequence of linear problems. Analytical expressions allow a first crude assessment - revealing that the ponderomotive potential plays a role similar to that of the electrostatic potential arising from charge separation - but numerical implementation is required to get a feeling of the full dynamics. A few tentative examples are provided to illustrate the phenomena involved.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2015

FOREGROUND MODEL AND ANTENNA CALIBRATION ERRORS IN THE MEASUREMENT OF THE SKY-AVERAGED λ21 cm SIGNAL AT z∼ 20

The most promising near-term observable of the cosmic dark age prior to widespread reionization (z ∼ 15-200) is the sky-averaged λ21 cm background arising from hydrogen in the intergalactic medium. Though an individual antenna could in principle detect the line signature, data analysis must separate foregrounds that are orders of magnitude brighter than the λ21 cm background (but that are anticipated to vary monotonically and gradually with frequency, e.g., they are considered {sup s}pectrally smooth{sup )}. Using more physically motivated models for foregrounds than in previous studies, we show that the intrinsic spectral smoothness of the foregrounds is likely not a concern, and that data analysis for an ideal antenna should be able to detect the λ21 cm signal after subtracting a ∼fifth-order polynomial in log ν. However, we find that the foreground signal is corrupted by the angular and frequency-dependent response of a real antenna. The frequency dependence complicates modeling of foregrounds commonly based on the assumption of spectral smoothness. Our calculations focus on the Large-aperture Experiment to detect the Dark Age, which combines both radiometric and interferometric measurements. We show that statistical uncertainty remaining after fitting antenna gain patterns to interferometric measurements is not anticipated to compromise extraction of the λ21 cm signal for a range of cosmological models after fitting a seventh-order polynomial to radiometric data. Our results generalize to most efforts to measure the sky-averaged spectrum.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Are Marine Low Cloud Droplet Concentrations Buffered by Entrained Aitken‐Mode Aerosol (Final Technical Report)

During the summertime, the high-latitude oceans come to life with green phytoplankton, which gain their energy from sunlight and are food for sea creatures small and large. When the phytoplankton are eaten or die, sulfur-rich gases are released under the ocean surface and mix into the air. Observations suggest that, over the Southern Ocean, frequent storms lift this air high into the atmosphere while raining out particulates like salt. As a result, the sulfur-rich air then spawns high concentrations of small ‘Aitken-mode’ aerosol particles. We hypothesize that these particles work their way down into the marine boundary layer, where they can replenish the supply of cloud-condensation nuclei scavenged by frequent precipitation. Further, this process maintains high concentrations of liquid cloud droplets in austral summer, promoting more sunlight to be reflected to space. We call this ‘Aitken buffering’. The primary objective of this project has been to document and test what role Aitken-mode aerosols play in clouds over the Southern Ocean and elsewhere. This effort has included three main components: 1) developing a computer model that realistically simulates the aerosol processes and the small-scale turbulent air motions that move aerosols around and create the clouds, 2) using that model to interpret and extend these observations for process understanding, by allowing different factors that contribute to the aerosol budget, such as surface wind speed, precipitation, surface gas exchange, etc. to be separated, and 3) studying Aitken-mode aerosol and its variability with a focus over the Southern Ocean and Antarctica, using data from Atmospheric Radiation Measurement (ARM) sites and other available observations. Initial computer studies in more idealized conditions found that elevated concentrations of Aitken-mode aerosols above the clouds could help prevent the breakup of those clouds by acting as cloud-condensation nuclei after they were entrained into the cloudy boundary layer. Simulations of a day during the ACE-ENA field campaign showed that Aitken-mode aerosols could also prevent cloud breakup under more realistic conditions. A new method that extracts information about Aitken-mode aerosols from measurements of aerosols onto which cloud droplets can form finds that Aitken-mode aerosols do vary seasonally over the Southern Ocean, with a peak in summertime, as described above. Other work during this project has focused on understanding how patterns of water vapor, clouds and precipitation are coupled within low-lying clouds over the oceans, and also on how cloud droplets cluster within clouds and how the distribution of cloud droplet sizes change as dry air is mixed into clouds, with the latter studies also using observations from ACE-ENA.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2019

Aftershocks of the 2012 Off-Coast of Sumatra Earthquake Sequence

Aftershocks of the 2012 Off-Coast of Sumatra Earthquake Sequence exhibit a complex and diffuse spatial distribution. The first-order complexity in aftershock distribution is clear and well beyond the influence of typical earthquake location uncertainty. The sequence included rupture of multiple fault segments, spatially separated. We use surface-wave based relative centroid locations to examine whether, at the small scale, the distribution of the aftershocks was influenced by location errors. Surface-wave based relative location has delineated precise oceanic transform fault earthquake locations in multiple regions. However, the relocated aftershocks off the coast of Sumatra seldom align along simple linear trends that are compatible with the corresponding fault strikes as estimated for the GCMT catalog. The relocation of roughly 60 moderate-earthquake epicentroids suggests that the faulting involved in the 2012 earthquake aftershock sequence included strain release along many short fault segments. Statistical analysis and temporal variations of aftershocks show a typical decay of the aftershocks but a relatively low number of aftershocks, as is common for intraplate oceanic earthquakes. Coulomb stress calculations indicate that most of the moderate-magnitude aftershocks are compatible with stress changes predicted by the large-event slip models. Furthermore the patterns in the aftershocks suggest that the formation of the boundary and eventual localization of deformation between the Indian and Australian plate is a complicated process.

2012 Sumatra Earthquake↗

DOE OSTI2023

Porphene and porphite as porphyrin analogs of graphene and graphite

Two-dimensional materials have unusual properties and promise applications in nanoelectronics, spintronics, photonics, (electro)catalysis, separations, and elsewhere. Most are inorganic and their properties are difficult to tune. Here we report the preparation of Zn porphene, a member of the previously only hypothetical organic metalloporphene family. Similar to graphene, these also are fully conjugated two-dimensional polymers, but are composed of fused metalloporphyrin rings. Zn porphene is synthesized on water surface by two-dimensional oxidative polymerization of a Langmuir layer of Zn porphyrin with K 2 IrCl 6 , reminiscent of known one-dimensional polymerization of pyrroles. It is transferable to other substrates and bridges μm-sized pits. Contrary to previous theoretical predictions of metallic conductivity, it is a p-type semiconductor due to a predicted Peierls distortion of its unit cell from square to rectangular, analogous to the appearance of bond-length alternation in antiaromatic molecules. The observed reversible insertion of various metal ions, possibly carrying a fifth or sixth ligand, promises tunability and even patterning of circuits on an atomic canvas without removing any π centers from conjugation.

36 MATERIALS SCIENCE↗

DOE OSTI2018

Venous endothelium reactivity to Angiotensin II: A study in primary endothelial cultures of rat vena cava and portal vein

Highlights: • The venous endothelium is an unexplored site. • Cells from vena cava and portal vein can be isolated and cultured. • Cultures of venous endothelium present differences in growth pattern. • Resting cells from venous endothelium produce nitric oxide and prostanoids. • The venous endothelium is reactive to angiotensin II. The role of the vascular endothelium in modulating the arterial system has been widely investigated, but poorly explored at the venous site. In the present work, primary cultures of venous endothelium from rat Vena Cava (VC) and Portal Vein (PV) were established, characterized and analyzed according to their growth pattern and ability to produce nitric oxide (NO) and prostanoids (PGF{sub 2 α} and PGI{sub 2}), at basal state and after stimulation with Angiotensin II (Ang II, 1 μmol/L). Basal NO was detected in all examined cells in culture. Pre-incubation with Ang II increased NO production in cells from VC (but not in PV cultures), through activation of both AT{sub 1} and AT{sub 2} receptors. Both cultures exhibited detectable levels of PGF{sub 2 α} at resting conditions, which were similarly enhanced by Ang II. Basal PGI{sub 2} levels were higher in PV, but increased after Ang II treatment in VC, with no further effect on PV cells. We conclude that endothelial cells from VC and PV exhibit important properties and react to Ang II, probably influencing the whole circulatory system. This experimental cell model gives support to further studies concerning intracellular pathways of the venous endothelium, analyzed in separate from the vascular smooth muscle wall.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Reduction in total and major cause-specific mortality from tobacco smoking cessation: a pooled analysis of 16 population-based cohort studies in Asia

Little is known about the time course of mortality reduction following smoking cessation in Asians who have smoking behaviours distinct from their Western counterparts. We evaluated the level of reduction in all-cause, cardiovascular disease (CVD) and lung cancer mortality by years since quitting smoking, in Asia. Using Cox regression, we analysed individual participant data (n = 709 151) from 16 prospective cohorts conducted in China, Japan, Korea/Singapore, and India/Bangladesh, separately by cohorts. Cohort-specific hazard ratios (HRs) were combined using a random-effects meta-analysis. During a mean follow-up of 12.0 years, 108 287 deaths were ascertained—35 658 from CVD and 7546 from lung cancer. Among Asian men, a dose-response relationship of risk reduction in deaths from all causes, CVD and lung cancer was observed with an increase in years after smoking cessation. Compared with never smokers, however, all-cause and CVD mortality among former smokers remained elevated 10–14 years after quitting [multivariable-adjusted HR (95% confidence interval (CI) = 1.25 (1.13–1.37) and 1.20 (1.02–1.41), respectively]. Lung cancer mortality stayed almost 2-fold higher than among never smokers 15–19 years after smoking cessation [1.97 (1.41–2.73)], particularly among former heavy smokers [2.62 (1.71–4.00)]. Women who quitted for ≥5 years retained a significantly elevated mortality from all causes, CVD and lung cancer. Overall patterns of the cessation-mortality associations were similar across countries. Our findings suggest that adverse effects of tobacco smoking persist for an extended time period, even for more than two decades, which is beyond the time windows defined in current clinical guidelines for risk assessment of lung cancer and CVD.

Public, Environmental & Occupational Health↗

DOE OSTI2025

Multipartite entanglement structure of fibered link states

We study the patterns of multipartite entanglement in Chern-Simons theory with compact simple gauge group 𝐺 and level 𝑘 for states defined by the path integral on “link complements,” i.e., compact manifolds whose boundaries consist of 𝑛 topologically linked tori. We focus on link complements which can be described topologically as fibrations over a Seifert surface. We show that the entanglement structure of such fibered link complement states is controlled by a topological invariant, the monodromy of the fibration. Thus, the entanglement structure of a Chern-Simons link state is not simply a function of the link, but also of the background manifold in which the link is embedded. In particular, we show that any link possesses an embedding into some background that leads to Greenberger–Horne–Zeilinger state (GHZ)-like entanglement. Furthermore, we demonstrate that all fibered links with periodic monodromy have GHZ-like entanglement, i.e., a partial trace on any link component produces a separable state. These results generalize to any three dimensional topological field theory with a dual chiral rational conformal field theory.

conformal field theory↗

DOE OSTI2019

Consequences of Lattice Mismatch for Phase Equilibrium in Heterostructured Solids

Lattice mismatch - the difference in natural bond length between two species comprising a solid is a common occurrence in modern materials. Spatial patterns in certain nanocrystal heterostructures, for instance, are thought to be a result of elastic forces arising from lattice mismatch. However, the role of lattice mismatch in mediating the arrangement of atoms in such materials is incompletely understood. Here we consider a simple microscopic model for lattice mismatch, in which the difference in natural lengths between bonded atoms produces interactions mediated by elastic strain. Computer simulations reveal that the model exhibits rich phase behavior, including structures with periodic order and unusual coexistence scenarios. To explain this phase behavior, we derive an effective pairwise interaction potential between atoms, revealing preferred spatial arrangements of atoms driven by spatial variations in the interaction potential. We then develop a mean field theory based on this effective interaction which qualitatively captures observed transition to phases with modulated order. Finally, we explain the observed scenarios of coexistence between using a graphical construction, based on the realization that the free energy cost of phase separation in elastic systems grows with system size. Here, these results clarify the equilibrium effects of lattice mismatch in macroscopic solids and suggest a role for lattice mismatch in creating spatially heterogeneous compositions in nanoscale materials.

36 MATERIALS SCIENCE↗

DOE OSTI2017

From Ba{sub 3}Ta{sub 5}O{sub 14}N to LaBa{sub 2}Ta{sub 5}O{sub 13}N{sub 2}: Decreasing the optical band gap of a photocatalyst

Yellow LaBa{sub 2}Ta{sub 5}O{sub 13}N{sub 2} was successfully synthesized as phase-pure material crystallizing isostructurally to previously reported Ba{sub 3}Ta{sub 5}O{sub 14}N and mixed-valence Ba{sub 3}Ta{sup V}{sub 4}Ta{sup IV}O{sub 15}. The electronic structure of LaBa{sub 2}Ta{sub 5}O{sub 13}N{sub 2} was studied theoretically with the range-separated hybrid method HSE06. The most stable structure was obtained when lanthanum was placed on 2a and nitrogen on 4h sites confirming Pauling's second rule. By incorporating nitrogen, the measured band gap decreases from ∼3.8 eV for the oxide via 2.74 eV for Ba{sub 3}Ta{sub 5}O{sub 14}N to 2.63 eV for the new oxide nitride, giving rise to an absorption band well in the visible-light region. Calculated fundamental band gaps confirm the experimental trend. The atom-projected density of states has large contributions from N2p orbitals close to the valence band edge. These are responsible for the observed band gap reduction. Photocatalytic hydrogen formation was investigated and compared with that of Ba{sub 3}Ta{sub 5}O{sub 14}N revealing significantly higher activity for LaBa{sub 2}Ta{sub 5}O{sub 13}N{sub 2} under UV-light. - Graphical abstract: X-ray powder diffraction pattern of LaBa{sub 2}Ta{sub 5}O{sub 13}N{sub 2} with the results of the Rietveld refinements. Inset: Unit cell of LaBa{sub 2}Ta{sub 5}O{sub 13}N{sub 2} and polyhedral representation of the crystal structure. - Highlights: • Synthesis of a new oxide nitride LaBa{sub 2}Ta{sub 5}O{sub 13}N{sub 2}. • Refinement of the crystal structure. • Quantum chemical calculations provided band gap close to the measured value. • New phase shows a higher photocatalytic H{sub 2} evolution rate compared to prior tested Ba{sub 3}Ta{sub 5}O{sub 14}N.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

On the Formalization of Development and Assessment Process for Digital Twins in the Nearly Autonomous Management and Control System

In recent years, the autonomous control system has been encouraged in advanced reactors for restoring economic viability, simplifying the operation and maintenance, and enabling remote-site power generations [1]. Since the reactor is expected to be operated for a long period of time with a limited number of individuals onsite, it is recommended that the autonomous control system should have access to very realistic models of the state of processes in the whole lifecycle, together with these process behaviors in interaction with their environment in the real world. As a result, digital twin (DT) technology is suggested in autonomous control systems. DT is defined as a digital representation of a physical object or system, which contains a record for the histories of loads, operation and maintenance status, predictions for the near-term transient of important state variables, and decision-making process [2]. Since machine learning (ML) can recognize patterns within a complex system in real-time applications, it has been used to build DTs in the autonomous control systems for advanced reactors. Meanwhile, due to the rareness of operation data in accident scenarios, the development and assessment of DTs is expected to be mainly driven by simulations. Although the capability and feasibility of ML-based DTs are recognized in improving the safety and efficiency of reactor control, a major concern from the regulatory commission and the nuclear industry is whether the information from a DT is developed and assessed in accordance with expectation and requirements by the target decision. Such concerns not only affect the acceptance criteria for DTs, but also values that can be extracted from DTs and autonomous control system during operations. Inspired by the success of formal methods in improving the reliability and robustness of computer programming and software development, it is suggested that the development and assessment process (DAP) for both separate DTs and integral control system should be formalized in a transparent, consistent, and improvable manner. In this study, a digital-twin development and assessment process (DT-DAP) is proposed by adapting the evaluation model development and assessment process (EMDAP) [3] to requirements by the autonomous control system, ML algorithms, and DT technology. To demonstrate the framework, a baseline nearly autonomous management and control (NAMAC) system with ML-based DTs for diagnosis and prognosis is developed and assessed based on the framework. It is found that with selected testing methods and techniques, the DT-DAP can help identify errors in DTs and NAMAC which would otherwise be left unverified. Meanwhile, it is found that the DT-DAP can improve the DTs and NAMAC by continuously learning and iterating through different elements.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2021

Charge radii in covariant density functional theory: A global view

A systematic global investigation of differential charge radii has been performed within the CDFT framework for the first time. Theoretical results obtained with conventional covariant energy density functionals and the separable pairing interaction of Tian et al. [Phys. Lett. B 676, 44 (2009)] are compared with experimental differential charge radii in the regions of the nuclear chart in which available experimental data crosses the neutron shell closures at N=28,50,82, and 126. The analysis of absolute differential radii of different isotopic chains and their relative properties indicate clearly that such properties are reasonably well described in model calculations in the cases when the mean-field approximation is justified. However, while the observed clusterization of differential charge radii of different isotopic chains is well described above the N=50 and N=126 shell closures, it is more difficult to reproduce it above the N=28 and N=82 shell closures because of possible deficiencies in the underlying single-particle structure. The impact of the latter has been evaluated for spherical shapes and it was shown that the relative energies of the single-particle states and the patterns of their occupation with increasing neutron number have an appreciable impact on the evolution of the δ$\langle$r2$\rangle$N,N' values. These factors also limit the predictive power of model calculations in the regions of high densities of the single-particle states of different origin. It is shown that the kinks in the charge radii at neutron shell closures are due to the underlying single-particle structure and due to weakening or collapse of pairing at these closures. The regions of the nuclear chart in which the correlations beyond mean field are expected to have an impact on charge radii are indicated; the analysis shows that the assignment of a calculated excited prolate minimum to the experimental ground state allows us to understand the trends of the evolution of differential charge radii with neutron number in many cases of shape coexistence even at the mean-field level. It is usually assumed that pairing is a dominant contributor to odd-even staggering (OES) in charge radii. Our analysis paints a more complicated picture. It suggests a new mechanism in which the fragmentation of the single-particle content of the ground state in odd-mass nuclei due to particle-vibration coupling provides a significant contribution to OES in charge radii.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2016

Ordering pathway of block copolymers under dynamic thermal gradients studied by in situ GISAXS

Dynamic thermal gradient-based processes for directed self-assembly of block copolymer (BCP) thin films such as cold zone annealing (CZA) have demonstrated much potential for rapidly fabricating highly ordered patterns of BCP domains with facile orientation control. As a demonstration, hexagonally packed predominantly vertical cylindrical morphology, technologically relevant for applications such as membranes and lithography, was achieved in 1 μm thick cylinder-forming PS-b-PMMA (cBCP) films by applying sharp thermal gradients (CZA-Sharp) at optimum sample sweep rates. A thorough understanding of the molecular level mechanisms and pathways of the BCP ordering that occur during this CZA-S process is presented, useful to fully exploit the potential of CZA-S for large-scale BCP-based device fabrication. To that end, we developed a customized CZA-S assembly to probe the dynamic structure evolution and ordering of the PS-b-PMMA cBCP film in situ as it undergoes the CZA-S process using the grazing incidence small-angle X-ray scattering (GISAXS) technique. Four distinct regimes of BCP ordering were observed within the gradient that include microphase separation from an “as cast” unordered state (Regime I), evolution of vertical cylinders under a thermally imposed strain gradient (Regime II), reorientation of a fraction of cylinders due to preferential substrate interactions (Regime III), and finally grain-coarsening on the cooling edge (Regime IV). The ordering pathway in the different regimes is further described within the framework of an energy landscape. A novel aspect of this study is the identification of a grain-coarsening regime on the cooling edge of the gradient, previously obscure in zone annealing studies of BCPs. Furthermore, such insights into the development of highly ordered BCP nanostructures under template-free thermal gradient fields can potentially have important ramifications in the field of BCP-directed self-assembly and self-assembling polymer systems more broadly.

36 MATERIALS SCIENCE↗

DOE OSTI2026

High-precision phase control of an optical lattice with up to 50 dB noise suppression

An optical lattice is a periodic light crystal constructed from the standing-wave interference patterns of laser beams. It can be used to store and manipulate quantum degenerate atoms and is an ideal platform for the quantum simulation of many-body physics. A principal feature is that optical lattices are flexible and possess a variety of multidimensional geometries with modifiable band structure. An even richer landscape emerges when control functions can be applied to the lattice by modulation of the position or amplitude with Floquet driving. However, the desire of realizing high-modulation bandwidths while preserving extreme lattice stability has been difficult to achieve. In this paper, we demonstrate an effective solution that consists of overlapping two counterpropagating lattice beams and controlling the phase and intensity of each with independent acousto-optic modulators. Our phase controller mixes sampled light from both lattice beams with a common optical reference. This dual heterodyne locking method allows exquisite determination of the lattice position, while also removing parasitic phase noise accrued as the beams travel along separate paths. Here, we report up to 50 dB suppression in lattice phase noise in the 0.1–1 Hz band, along with significant suppression spanning more than 4 decades of frequency. The absolute phase diffusion of the lattice position is only 10 Å when integrated over 10 s. This method permits precise, high-bandwidth modulation (greater than 50 kHz) of the optical lattice intensity and phase. We demonstrate the efficacy of this approach by executing intricate time-varying phase profiles for atom interferometry.

Atom interferometry↗

DOE OSTI2026

Engineering and Application of a Thermostable MHETase for PET Depolymerization

Enzymatic hydrolysis of poly(ethylene terephthalate) (PET) releases mono(2-hydroxyethyl) terephthalate (MHET) as a major product, the accumulation of which can prolong reactor residence times and complicate downstream monomer separations. The use of a MHETase enzyme can enable MHET hydrolysis to the monomers, terephthalic acid and ethylene glycol, but industrial PETases typically operate at thermophilic temperatures and the well-known MHETase from Ideonella sakaiensis is a mesophilic enzyme, thus warranting the development of thermophilic MHETases. Here, we characterize thermostable MHET-active enzymes from a natural diversity screen by applying a hidden Markov model based on the previously reported, archaeal ferulic acid esterase, PET46. We identified enzymes with higher thermostability than PET46 and quantified their MHETase activity in reactions at 70 °C. The crystal structure of MHT077, the homologue with the highest MHETase activity and an apparent melting temperature (T m,app ) of 94.6 °C, informed site saturation mutagenesis in the active site and lid-domain interface. MHT077 exhibited a ∼100-fold slower unfolding rate at 65 °C than PET46, indicating substantially greater kinetic stability. In parallel, we applied evolution-informed design, a probabilistic model that leverages coevolutionary patterns in large multiple sequence alignments, to improve the activity and thermostability of five ferulic acid esterases. One design, EV-MHT043–5 was identified with a comparable thermostability (T m,app = 96.1 °C) and a 3-fold improvement in its MHETase activity relative to the wildtype enzyme, MHT043. Combination variants of beneficial mutations were screened and afforded a variant, MHT077 LFK , which reduced MHET accumulation in bioreactor experiments with postconsumer PET waste. Overall, this study expands the known MHET-hydrolyzing protein scaffolds available for enzymatic PET recycling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Coordinated Assembly of the Bacillus anthracis Coat and Exosporium during Bacterial Spore Outer Layer Formation

Bacterial spores produced by the Bacillales are composed of concentric shells, each of which contributes to spore function. Spores from all species possess a cortex and coat, but spores from many species possess additional outer layers. The outermost layer of Bacillus anthracis spores, the exosporium, is separated from the coat by a gap known as the interspace. Exosporium and interspace assembly remains largely mysterious. As a result, we have a poor understanding of the overarching mechanisms driving the assembly of one of the most ubiquitous cell types in nature. To elucidate the mechanisms directing exosporium assembly, we generated strains bearing mutations in candidate exosporium-controlling genes and analyzed the effect on exosporium formation. Biochemical and cell biological analyses argue that CotE directs the assembly of CotO into the spore and that CotO might be located at or close to the interior side of the cap. Taken together with data showing that CotE and CotO interact directly in vitro , we propose a model in which CotE and CotO are important components of a protein interaction network that connects the exosporium to the forespore during cap formation and exosporium elongation. Our data also suggest that the cap interferes with coat assembly at one pole of the spore, altering the pattern of coat deposition compared to the model organism Bacillus subtilis . We propose that the difference in coat assembly patterns between these two species is due to an inherent flexibility in coat assembly, which may facilitate the evolution of spore outer layer complexity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Comparison between target margins derived from 4DCT scans and real-time tumor motion tracking: Insights from lung tumor patients treated with robotic radiosurgery

Purpose: A unique capability of the CyberKnife system is dynamic target tracking. However, not all patients are eligible for this approach. Rather, their tumors are tracked statically using the vertebral column for alignment. When using static tracking, the internal target volume (ITV) is delineated on the four-dimensional (4D) CT scan and an additional margin is added to account for setup uncertainty [planning target volume (PTV)]. Treatment margins are difficult to estimate due to unpredictable variations in tumor motion and respiratory pattern during the course of treatment. The inability to track the target and detect changes in respiratory characteristics might result in geographic misses and local tumor recurrences. The purpose of this study is to develop a method to evaluate the adequacy of ITV-to-PTV margins for patients treated in this manner. Methods: Data from 24 patients with lesions in the upper lobe (n = 12), middle lobe (n = 3), and lower lobe (n = 9) were included in this study. Each patient was treated with dynamic tracking and underwent 4DCT scanning at the time of simulation. Data including the 3D coordinates of the target over the course of treatment were extracted from the treatment log files and used to determine actual target motion in the superior–inferior (S–I), anterior–posterior (A–P), and left–right (L–R) directions. Different approaches were used to calculate anisotropic and isotropic margins, assuming that the tumor moves as a rigid body. Anisotropic margins were calculated by separating target motion in the three anatomical directions, and a uniform margin was calculated by shifting the gross tumor volume contours in the 3D space and by computing the percentage of overlap with the PTV. The analysis was validated by means of a theoretical formulation. Results: The three methods provided consistent results. A uniform margin of 4.5 mm around the ITV was necessary to assure 95% target coverage for 95% of the fractions included in the analysis. In the case of anisotropic margins, the expansion required in the S–I direction was larger (8.1 mm) than those in the L–R (4.9 mm) and A–P (4.5 mm) directions. This margin accounts for variations of target position within the same treatment fraction. Conclusions: The use of bony alignment for CyberKnife lung stereotactic body radiation therapy requires careful considerations, in terms of the potential for increased toxicity or local miss. Our method could be used by other centers to determine the adequacy of ITV-to-PTV margins for their patients.

60 APPLIED LIFE SCIENCES↗