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Overcoming the Time Limitation in Molecular Dynamics Simulation of Crystal Nucleation: A Persistent-Embryo Approach
The crystal nucleation from liquid in most cases is too rare to be accessed within the limited time scales of the conventional molecular dynamics (MD) simulation. Here, we developed a “persistent embryo” method to facilitate crystal nucleation in MD simulations by preventing small crystal embryos from melting using external spring forces. We applied this method to the pure Ni case for a moderate undercooling where no nucleation can be observed in the conventional MD simulation, and obtained nucleation rate in good agreement with the experimental data. Moreover, the method is applied to simulate an even more sluggish event: the nucleation of the B2 phase in a strong glass-forming Cu-Zr alloy. The nucleation rate was found to be 8 orders of magnitude smaller than Ni at the same undercooling, which well explains the good glass formability of the alloy. In conclusion, our work opens a new avenue to study solidification under realistic experimental conditions via atomistic computer simulation.
Observation of the χ b 1 ( 3 P ) and χ b 2 ( 3 P ) and Measurement of their Masses
The $\chi_\mathrm{b1}$(3P) and $\chi_\mathrm{b2}$(3P) states are observed through their $\Upsilon$(3S) $\gamma$ decays, using an event sample of proton-proton collisions collected by the CMS experiment at the CERN LHC. The data were collected at a center-of-mass energy of 13 TeV and correspond to an integrated luminosity of 80.0 fb$^{-1}$. The $\Upsilon$(3S) mesons are identified through their dimuon decay channel, while the low-energy photons are detected after converting to e$^+$e$^-$ pairs in the silicon tracker, leading to a $\chi_\mathrm{b}$(3P) mass resolution of 2.2 MeV. This is the first time that the $J =$ 1 and 2 states are well resolved and their masses individually measured: 10$\,$513.42 $\pm$ 0.41 (stat) $\pm$ 0.18 (syst) MeV and 10$\,$524.02 $\pm$ 0.57 (stat) $\pm$ 0.18 (syst) MeV; they are determined with respect to the world-average value of the $\Upsilon$(3S) mass, which has an uncertainty of 0.5 MeV. As a result, the mass splitting is measured to be 10.60 $\pm$ 0.64 (stat) $\pm$ 0.17 (syst) MeV.
Linear Complexions: Metastable Phase Formation and Coexistence at Dislocations
The unique three-phase coexistence of metastable B2–FeNi with stable L1 0 –FeNi and L1 2 –FeNi 3 is discovered near edge dislocations in body-centered cubic Fe-Ni alloys using atomistic simulations. Stable nanoscale precipitate arrays, formed along the compression side of dislocation lines and defined as linear complexions, were observed for a wide range of compositions and temperatures. Here, by analyzing the thermodynamics associated with these phase transitions, we are able to explain the metastable phase formation and coexistence, in the process defining new research avenues for theoretical and experimental investigations.
Observation of e + e – → ω χ b J ( 1 P ) and Search for X b → ω Υ ( 1 S ) at s near 10.75 GeV
We study the processes $e^{+}e^{–} → ωχ_{bJ}$(1P) (J=0, 1, or 2) using samples at center-of-mass energies $\sqrt{s}$ = 10.701, 10.745, and 10.805 GeV, corresponding to 1.6, 9.8, and 4.7 fb –1 of integrated luminosity, respectively. These data were collected with the Belle II detector during special operations of the SuperKEKB collider above the Υ(4S) resonance. We report the first observation of $ωχ_{bJ}$(1P) signals at $\sqrt{s}$ = 10.745 GeV. By combining Belle II data with Belle results at $\sqrt{s}$ = 10.867 GeV, we find energy dependencies of the Born cross sections for $e^{+}e^{–} → ωχ_{b1,b2}$(1P) to be consistent with the shape of the Υ(10753) state. These data indicate that the internal structures of the Υ(10753) and Υ(10860) states may differ. Including data at $\sqrt{s}$ = 10.653 GeV, we also search for the bottomonium equivalent of the X(3872) state decaying into ωΥ(1S). No significant signal is observed for masses between 10.45 and 10.65 GeV/c 2 .
Structural and chemical orders in N i 64.5 Z r 35.5 metallic glass by molecular dynamics simulation
The atomic structure of Ni 64.5 Zr 35.5 metallic glass has been investigated by molecular dynamics (MD) simulations. The calculated structure factors from the MD glassy sample at room temperature agree well with the X-ray diffraction (XRD) and neutron diffraction (ND) experimental data. Using the pairwise cluster alignment and clique analysis methods, we show that there are three types dominant short-range order (SRO) motifs around Ni atoms in the glass sample of Ni 64.5 Zr 35.5 , i.e., Mixed- Icosahedron(ICO)-Cube, Twined-Cube and icosahedron-like clusters. Furthermore, chemical order and medium-range order (MRO) analysis show that the Mixed-ICOCube and Twined-Cube clusters exhibit the characteristics of the crystalline B2 phase. In conclusion, our simulation results suggest that the weak glass-forming ability (GFA) of Ni 64.5 Zr 35.5 can be attributed to the competition between the glass forming ICO SRO and the crystalline Mixed-ICO-Cube and Twined-Cube motifs.
Effects of Al content and annealing on the phases formation, lattice parameters, and magnetization of A l x F e 2 B 2 ( x = 1.0 , 1.1 , 1.2 ) alloys
AlFe 2 B 2 is a ferromagnet with the Curie temperature around 300 K and has the potential to be an outstanding rare-earth free candidate for magnetocaloric applications. However, samples prepared from the melt contain additional phases which affect the functional response of the AlFe 2 B 2 phase. Here, we report on the effects of Al content in samples with the initial (nominal) composition of Al x Fe 2 B 2 where x=1.0, 1.1, and 1.2 prepared by arc-melting followed by suction casting and annealing. The as-cast Al x Fe 2 B 2 alloys contain AlFe 2 B 2 as well as additional phases including the primary solidifying FeB and Al 13 Fe 4 compounds which are ferromagnetic and paramagnetic, respectively, at 300 K. The presence of these phases makes it difficult to extract the intrinsic magnetic properties of AlFe 2 B 2 phase. Annealing of Al x Fe 2 B 2 alloys at 1040°C for 3 days allows for reaction of the FeB with Al 13 Fe 4 to form the AlFe 2 B 2 phase, significantly reduces the amount of additional phases, and results in nearly pure AlFe 2 B2 phase as confirmed with XRD, magnetization, scanning electron microscopy, and electronic transport. The values of the magnetization, effective magnetic moment per Fe atom, specific heat capacity, electrical resistivity and Seebeck coefficient for the AlFe 2 B 2 compound have been established.
Antiferromagnetic-ferromagnetic phase domain development in nanopatterned FeRh islands
The antiferromagnetic-to-ferromagnetic phase transition in B2-ordered FeRh is imaged in laterally confined nanopatterned islands using photoemission electron microscopy with x-ray magnetic circular dichroism contrast. The resulting magnetic images directly detail the progression in the shape and size of the FM phase domains during heating and cooling through the transition. In 5-μm-square islands this domain development during heating is shown to proceed in three distinct modes - nucleation, growth, and merging - each with subsequently greater energy costs. In 0.5-μm islands, which are smaller than the typical final domain size, the growth mode is stunted and the transition temperature is found to be reduced by 20 K. The modification to the transition temperature is found by high-resolution scanning transmission electron microscopy to be due to a 100-nm chemically disordered edge grain present as a result of ion implantation damage during the patterning. FeRh has unique possibilities for magnetic memory applications; the inevitable changes to its magnetic properties due to subtractive nanofabrication will need to be addressed in future work in order to progress from sheet films to suitable patterned devices.
Stacking faults and alternate crystal structures for the shape-memory alloy NiTi
Here, we use ab initio calculations to study the role of stacking faults in connecting the high-temperature B2 and the theoretically predicted low-temperature B33 NiTi phases. In contrast with prior work, we describe the B 2 → B 33 phase transformation in terms of alternate bilayer shifts by 1 2 [100] on the ( 011 ) B 2 plane, obtaining a viable pathway; the same mechanism could also work with the B19 parent phase. We then examine B33-like structures built from alternate stacking sequences of B19 bilayers, constructed to have monoclinic tilt angles close to the experimentally reported NiTi B19' martensite, and find four low-energy stacking-fault variants with energies 5.8–8.5 meV/atom above the calculated B19' martensite structure, suggesting that such structures might appear as a part of the NiTi martensite phase at low temperatures. Investigating further the occurrence of specific coordinated planar shifts in NiTi systems, we report a dynamically stable NiTi B27 phase and find that it is only 1.2 meV/atom above the calculated B33 ground-state structure, thus having a potential to also play a role in NiTi martensitic phase transformation.
Simulated structure and thermodynamics of decagonal Al-Co-Cu quasicrystals
Atomic structures of Al-Co-Cu decagonal quasicrystals (dQCs) are investigated using empirical oscillating pair potentials (EOPP) in molecular dynamic (MD) simulations that we enhance by Monte Carlo (MC) swapping of chemical species and replica exchange. Predicted structures exhibit planar decagonal tiling patterns and are periodic along the perpendicular direction. We then recalculate the energies of promising structures using first-principles density functional theory (DFT), along with energies of competing phases. We find that our τ -inflated sequence of QC approximants (QCAs) are energetically unstable at low temperature by at least 3 meV/atom. Extending our study to finite temperatures by calculating harmonic vibrational entropy, as well as anharmonic contributions that include chemical species swaps and tile flips, our results suggest that the quasicrystal phase is entropically stabilized at temperatures in the range 600-800 K and above. It decomposes into ordinary (though complex) crystal phases at low temperatures, including a partially disordered B2-type phase. We discuss the influence of density and composition on QC phase stability; we compare the structural differences between Co-rich and Cu-rich quasicrystals; and we analyze the role of entropy in stabilizing the quasicrystal, concluding with a discussion of the possible existence of “high entropy” quasicrystals. Published by the American Physical Society 2024
AutoReP: Automatic ReLU Replacement for Fast Private Network Inference
The proliferation of the Machine-Learning-As-A-Service (MLaaS) market has brought to light a number of clients’ data privacy and security concerns. One promising solution is private inference (PI) techniques using cryptographic primitives. These techniques often come with high computation and communication overhead associated with the non-linear operator such as ReLU. Several approaches have been developed in reducing the number of ReLU operations, however, they either require a heuristic threshold selection or introduce significant accuracy drop. This work presents AutoReP, a gradient-based framework for non-linear operators reduction that aims to mitigate these concerns from a systematic perspective. AutoReP automates the process of discrete selection of ReLU and polynomial functions on neurons to accelerate PI applications. We also introduce distribution-aware polynomial approximation (DaPa) to accurately approximate ReLUs under given distribution, preserving model expressivity. Our experimental results demonstrate significant accuracy improvements of 6.12% (94.31%, 12.9K ReLU budget, CIFAR-10), 8.39% (74.92%, 12.9K ReLU budget, CIFAR-100), and 9.45% (63.69%, 55K ReLU budget, Tiny-ImageNet) over current state-of-the-art methods, e.g., SNL. Morever, AutoReP is applied to EfficientNet-B2 on ImageNet dataset, and achieved 75.55% accuracy with 176.1 × ReLU budget reduction.
Genomic distribution of B-vitamin auxotrophy and uptake transporters in environmental bacteria from the Chloroflexi phylum
Bacteria from the Chloroflexi phylum are dominant members of phototrophic microbial mat communities in terrestrial thermal environments. Vitamins of B-group are key intermediates (precursors) in the biosynthesis of indispensable enzyme cofactors driving numerous metabolic processes in all forms of life. A genomics-based reconstruction and comparative analysis of respective biosynthetic and salvage pathways and riboswitch regulons in over 20 representative Chloroflexi genomes revealed a widespread auxotrophy for some of the vitamins. The most prominent predicted phenotypic signature, auxotrophy for vitamins B1 and B7 was experimentally confirmed for the best studied model organism Chloroflexus aurantiacus. These observations along with identified candidate genes for the respective uptake transporters pointed to B vitamin exchange as an important aspect of syntrophic metabolism in microbial communities. Inferred specificities of homologous substrate-binding components of ABC transporters for vitamins B1 (ThiY) and B2 (RibY) were verified by thermofluorescent shift approach. A functional activity of the thiamine-specific transporter ThiXYZ from C. aurantiacus was experimentally verified by genetic complementation in E. coli. Expanding the integrative approach, which was applied here for a comprehensive analysis of B-vitamin metabolism in Chloroflexi would allow reconstruction of metabolic interdependencies in microbial communities.
Utilization of lasso peptides for biodegradation of polycyclic aromatic hydrocarbons
Abstract Many microbial genes involved in degrading recalcitrant environmental contaminants such as polycyclic aromatic hydrocarbons (PAHs) have been identified and characterized. However, all molecular mechanisms required for PAH utilization have not yet been elucidated. In this work, we demonstrate the proposed involvement of lasso peptides in the utilization of the PAH phenanthrene in Sphingomonas BPH. Transpositional mutagenesis of Sphingomonas BPH with the miniTn5 transposon yielded 3 phenanthrene utilization deficient mutants, #257, #1778, and #1782. In mutant #1782, Tn5 had inserted into the large subunit of the naph/bph dioxygenase gene. In mutant #1778, Tn5 had inserted into the B2 protease gene of a lasso peptide cluster. This finding is the first report on the role of lasso peptides in PAH utilization. Our studies also demonstrate that interruption of the lasso peptide cluster resulted in a significant increase in the amount of biosurfactant produced in the presence of glucose when compared to the wild‐type strain. Collectively, these results suggest that the mechanisms Sphingomonas BPH utilizes to degrade phenanthrene are far more complex than previously understood and that the #1778 mutant may be a good candidate for bioremediation when glucose is applied as an amendment due to its higher biosurfactant production.
Enhanced Light-Harvesting Capacity by Micellar Assembly of Free Accessory Chromophores and LH1-like Antennas
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Narrow thermal hysteresis of NiTi shape memory alloy thin films with submicrometer thickness
NiTi shape memory alloy (SMA) thin films were fabricated using biased target ion beam deposition (BTIBD), which is a new technique for fabricating submicrometer-thick SMA thin films, and the capacity to exhibit shape memory behavior was investigated. The thermally induced shape memory effect (SME) was studied using the wafer curvature method to report the stress-temperature response. The films exhibited the SME in a temperature range above room temperature and a narrow thermal hysteresis with respect to previous reports. To confirm the underlying phase transformation, in situ x-ray diffraction was carried out in the corresponding phase transformation temperature range. The B2 to R-phase martensitic transformation occurs, and the R-phase transformation is stable with respect to the expected conversion to the B19′ martensite phase. The narrow hysteresis and stable R-phase are rationalized in terms of the unique properties of the BTIBD technique.
SU-E-T-386: Evaluation of EBT3 Film Response in Different Batches
Purpose: To investigate the uniformity of film response of EBT3 film of two different film batches. It has been reported that the response of the EBT film family is not homogenous between film batches. The later may have an impact in the dosimetry of small radiotherapy beams. Methods: A solid water phantom was used for dosimetric measurements. EBT3 film irradiation was performed with a 6 MV photon beam at 5 cm depth with a SAD of 100 cm. All irradiations were performed perpendicularly to the film plane covering the dose range 1 to 10 Gy. Three square field sizes were used to analyze the film response energy dependence: 10, 5 and 1 cm{sup 2}. Two batches of film EBT3 were used #A03181302 (B1) and #03031403 (B2). Film read out was carrying out with an Epson Perfection V750-Pro flatbed scanner in transmission mode with a spatial resolution of 72 dpi, with all post-processing and colour management options turned off, using 48 bits RGB colour depth. The scans were analyzed with the red channel. Results: The results shown that there were differences between the film response for each batch. The differences between batches for 1 Gy were 2%, 6% and 12% for 10, 5 and 1 cm2 square field sizes, respectively. The differences found for 10 Gy were 13%, 14% and 13% for 10, 5 and 1 cm{sup 2} square field sizes, respectively. It can be observed that the dependence with field size dismissed for higher doses. The later may be due to film response saturation at 10 Gy. Conclusion: The EBT3 film -as its predecessors-, it suffer for inter-batch variability in the film response. Further research is required to assess the possible impact in small beam dosimetry.
SU-F-J-213: Feasibility Study of Using a Dual-Energy Cone Beam CT (DECBCT) in Proton Therapy Treatment Planning
Purpose: The aim of this study is to evaluate the feasibility of using a dual-energy CBCT (DECBCT) in proton therapy treatment planning to allow for accurate electron density estimation. Methods: For direct comparison, two scenarios were selected: a dual-energy fan-beam CT (high: 140 kVp, low: 80 kVp) and a DECBCT (high: 125 kVp, low: 80 kVp). A Gammex 467 tissue characterization phantom was used, including the rods of air, water, bone (B2–30% mineral), cortical bone (SB3), lung (LN-300), brain, liver and adipose. For the CBCT, Hounsfield Unit (HU) numbers were first obtained from the reconstructed images after a calibration was made based on water (=0) and air materials (=−1000). For each tissue surrogate, region-of-interest (ROI) analyses were made to derive high-energy and low-energy HU values (HUhigh and HUlow), which were subsequently used to estimate electron density based on the algorithm as previously described by Hunemohr N., et al. Parameters k1 and k2 are energy dependent and can be derived from calibration materials. Results: While for the dual-energy FBCT, the electron density is found be within +/−3% error relative to the values provided by the phantom vendor: −1.8% (water), 0.03% (lung), 1.1% (brain), −2.82% (adipose), −0.49% (liver) and −1.89% (cortical bones). While for the DECBCT, the estimation of electron density exhibits a relatively larger variation: −1.76% (water), −36.7% (lung), −1.92% (brain), −3.43% (adipose), 8.1% (liver) and 9.5% (cortical bones). Conclusion: For DECBCT, the accuracy of electron density estimation is inferior to that of a FBCT, especially for materials of either low-density (lung) or high density (cortical bone) compared to water. Such limitation arises from inaccurate HU number derivation in a CBCT. Advanced scatter-correction and HU calibration routines, as well as the deployment of photon counting CT detectors need be investigated to minimize the difference between FBCT and CBCT.
SU-F-T-351: Establishing a Workflow for IMRT Pre-Treatment Reviews for NRG-GY006 Clinical Trial
Purpose: To establish a workflow for NRG-GY006 IMRT pre-treatment reviews, incorporating advanced radiotherapy technologies being evaluated as part of the clinical trial. Methods: Pre-Treatment reviews are required for every IMRT case as part of NRG-GY006 (a randomized phase II trial of radiation therapy and cisplatin alone or in combination with intravenous triapine in women with newly diagnosed bulky stage I B2, stage II, IIIB, or IVA cancer of the uterine cervix or stage II-IVA vaginal cancer. The pretreatment review process includes structures review and generating an active bone marrow(ABM)- to be used as an avoidance structure during IMRT optimization- and evaluating initial IMRT plan quality using knowledgeengineering based planning (KBP). Institutions will initially submit their simulation CT scan, structures file and PET/CT to IROC QA center for generating ABM. The ABM will be returned to the institution for use in planning. Institutions will then submit an initial IMRT plan for review and will receive information back following implementation of a KBP algorithm, for use in re-optimization, before submitting the final IMRT used for treatment. Results: ABM structure is generated using MIM vista software (Version 6.5, MIM corporation, Inc.). Here, the planning CT and the diagnostic PET/CT are fused and a sub threshold structure is auto segmented above the mean value of the SUV of the bone marrow. The generated ABM were compared with those generated with other software system (e.g. Velocity, Varian) and Dice coefficient (reflects the overlap of structures) ranged between 80 – 90% was achieved. A KBP model was built in Varian Eclipse TPS using the RapidPlan KBP software to perform plan quality assurance. Conclusion: The workflow for IMRT pretreatment reviews has been established. It represents a major improvement of NRG Oncology clinical trial quality assurance and incorporates the latest radiotherapy technologies as part of NCI clinical trials. This project was supported by grants U24CA180803 (IROC), UG1CA189867 (NCORP), U10CA180868 (NRG Oncology Operations), U10CA180822 (NRG Oncology SDMC) from the National Cancer Institute (NCI) and PA CURE grant.