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Mic-hackathon 2024: Hackathon on Machine Learning for Electron and Scanning Probe Microscopy
Authors:
Utkarsh Pratiush,
Austin Houston,
Kamyar Barakati,
Aditya Raghavan,
Dasol Yoon,
Harikrishnan KP,
Zhaslan Baraissov,
Desheng Ma,
Samuel S. Welborn,
Mikolaj Jakowski,
Shawn-Patrick Barhorst,
Alexander J. Pattison,
Panayotis Manganaris,
Sita Sirisha Madugula,
Sai Venkata Gayathri Ayyagari,
Vishal Kennedy,
Ralph Bulanadi,
Michelle Wang,
Kieran J. Pang,
Ian Addison-Smith,
Willy Menacho,
Horacio V. Guzman,
Alexander Kiefer,
Nicholas Furth,
Nikola L. Kolev
, et al. (48 additional authors not shown)
Abstract:
Microscopy is a primary source of information on materials structure and functionality at nanometer and atomic scales. The data generated is often well-structured, enriched with metadata and sample histories, though not always consistent in detail or format. The adoption of Data Management Plans (DMPs) by major funding agencies promotes preservation and access. However, deriving insights remains d…
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Microscopy is a primary source of information on materials structure and functionality at nanometer and atomic scales. The data generated is often well-structured, enriched with metadata and sample histories, though not always consistent in detail or format. The adoption of Data Management Plans (DMPs) by major funding agencies promotes preservation and access. However, deriving insights remains difficult due to the lack of standardized code ecosystems, benchmarks, and integration strategies. As a result, data usage is inefficient and analysis time is extensive. In addition to post-acquisition analysis, new APIs from major microscope manufacturers enable real-time, ML-based analytics for automated decision-making and ML-agent-controlled microscope operation. Yet, a gap remains between the ML and microscopy communities, limiting the impact of these methods on physics, materials discovery, and optimization. Hackathons help bridge this divide by fostering collaboration between ML researchers and microscopy experts. They encourage the development of novel solutions that apply ML to microscopy, while preparing a future workforce for instrumentation, materials science, and applied ML. This hackathon produced benchmark datasets and digital twins of microscopes to support community growth and standardized workflows. All related code is available at GitHub: https://github.com/KalininGroup/Mic-hackathon-2024-codes-publication/tree/1.0.0.1
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Submitted 27 June, 2025; v1 submitted 9 June, 2025;
originally announced June 2025.
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Assembly, testing, and installation of mPMT photosensor for the Water Cherenkov Test Experiment
Authors:
M. Gola,
M. Barbi,
V. Berardi,
A. Buchowicz,
N. Buril,
L. Cook,
S. Cuen-Rochin,
G. DeRosa,
P. de Perio,
K. Dygnarowicz,
B. Ferrazzi,
A. Fiorentini,
C. S. Garde,
G. Galiński,
K. Graham,
R. Gornea,
M. Hartz,
J. Holeczek,
S. Jagtap,
M. Kala,
D. Karlen,
S. Kothekar,
L. Koerich,
N. Kolev,
A. Konaka
, et al. (24 additional authors not shown)
Abstract:
The multi-Photomultiplier Tube (mPMT) photosensors will be used in the Water Cherenkov Test Experiment (WCTE) to efficiently detect the photons produced in the whole detector. One of the aims behind the development of WCTE is to test the technology and implement it in future water Cherenkov experiments such as the Hyper-Kamiokande experiment and its Intermediate Water Cherenkov Detector. Each mPMT…
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The multi-Photomultiplier Tube (mPMT) photosensors will be used in the Water Cherenkov Test Experiment (WCTE) to efficiently detect the photons produced in the whole detector. One of the aims behind the development of WCTE is to test the technology and implement it in future water Cherenkov experiments such as the Hyper-Kamiokande experiment and its Intermediate Water Cherenkov Detector. Each mPMT is built using nineteen 3-inch PMTs arranged on a semi-spherical support matrix. In this paper, we describe the design and manufacture of the mechanical components, the procedures for casting an optical gel between PMTs and acrylic cover, and the overall assembly procedure of the mPMTs. Details of the electronics used in the mPMT modules are not included in this paper and will be presented in a separate publication. We also report on the R&D performed on the selection of the optical gel ratio along with transmittance measurements and the reflectance measurements performed on the aluminium reflector. We also present the optical tests performed on the mPMT module using a 405 nm LED and the resulting increase in the effective photosensitive area by surrounding the PMTs with a reflector. A summary of the production and installation of the mPMTs for the WCTE is also presented in this paper.
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Submitted 2 July, 2025; v1 submitted 9 April, 2025;
originally announced April 2025.
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Detection Sensitivity Limit of Hundreds of Atoms with X-Ray Fluorescence Microscopy
Authors:
Mateus G. Masteghin,
Toussaint Gervais,
Steven K. Clowes,
David C. Cox,
Veronika Zelyk,
Ajith Pattammattel,
Yong S. Chu,
Nikola Kolev,
Taylor Z. Stock,
Neil Curson,
Paul G. Evans,
Michael Stuckelberger,
Benedict N. Murdin
Abstract:
We report X-ray fluorescence (XRF) imaging of nanoscale inclusions of impurities for quantum technology. A very bright diffraction-limited focus of the X-ray beam produces very high sensitivity and resolution. We investigated gallium (Ga) dopants in silicon (Si) produced by a focused ion beam (FIB). These dopants might provide 3/2-spin qubits or p-type electrical contacts and quantum dots. We find…
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We report X-ray fluorescence (XRF) imaging of nanoscale inclusions of impurities for quantum technology. A very bright diffraction-limited focus of the X-ray beam produces very high sensitivity and resolution. We investigated gallium (Ga) dopants in silicon (Si) produced by a focused ion beam (FIB). These dopants might provide 3/2-spin qubits or p-type electrical contacts and quantum dots. We find that the ion beam spot is somewhat larger than expected, and the technique provides a useful calibration for the resolution of FIBs. Enticingly, we demonstrate that with a single shot detection of 1 second integration time, the sensitivity of the XRF would be sufficient to find amongst background a single isolated inclusion of unknown location comprising only 3000 Ga impurities (a mass of just 350 zg) without any need for specialized nm-thickness lamellae, and down from >105 atoms in previous reports of similar work. With increased integration we were able to detect 650 impurities. The results show that planned facility upgrades might achieve single atom sensitivity with a generally applicable, non-destructive technique in the near future.
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Submitted 5 October, 2023;
originally announced October 2023.
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Time-Resolved Rubidium-Assisted Electron Capture by Barium (II) Cation
Authors:
Axel Molle,
Jan Philipp Drennhaus,
Viktoria Noel,
Nikola Kolev,
Annika Bande
Abstract:
Non-local energy transfer between bound electronic states close to the ionisation threshold is employed for efficient state preparation in dilute atom systems from technological foundations to quantum computing. The generalisation to electronic transitions into and out of the continuum is lacking quantum simulations necessary to motivate such potential experiments. Here, we present the first devel…
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Non-local energy transfer between bound electronic states close to the ionisation threshold is employed for efficient state preparation in dilute atom systems from technological foundations to quantum computing. The generalisation to electronic transitions into and out of the continuum is lacking quantum simulations necessary to motivate such potential experiments. Here, we present the first development of a electron-dynamical model simulating fully three-dimensional atomic systems for this purpose. We investigate the viability of this model for the prototypical case of recombination of ultracold barium(II) by environment-assisted electron capture thanks to a rubidium atom in its vicinity. Both atomic sites are modelled as effective one-electron systems using the Multi Configuration Time Dependent Hartree (MCTDH) algorithm and can transfer energy by dipole-dipole interaction. We find that the simulations are robust enough to realise assisted capture over a dilute interatomic distance which we are able to quantify by comparing to simulations without interatomic energy exchange. For our current parameters not yet optimised for reaction likelihood, an environment-ionising assisted capture has a probability of $1.9\times10^{-5}~\%$ over the first $15~\mathrm{fs}$ of the simulation. The environment-exciting assisted-capture path to $[\text{Ba}^{+*}\text{Rb}^{*}]$ appears as a stable long-lived intermediate state with a probability of $8.2\times10^{-4}~\%$ for at least $20~\mathrm{fs}$ after the capture has been completed. This model shows potential to predict optimised parameters as well as to accommodate the conditions present in experimental systems as closely as possible. We put the presented setup forward as a suitable first step to experimentally realise environment-assisted electron capture with current existing technologies.
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Submitted 2 May, 2024; v1 submitted 15 June, 2023;
originally announced June 2023.
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A measurement of proton-carbon forward scattering in a proof-of-principle test of the EMPHATIC spectrometer
Authors:
M. Pavin,
L. Aliaga-Soplin,
M. Barbi,
L. Bellantoni,
S. Bhadra,
B. Ferrazzi,
L. Fields,
A. Fiorentini,
T. Fukuda,
K. Gameil,
Y. Al Hakim,
M. Hartz,
B. Jamieson,
M. Kiburg,
N. Kolev,
H. Kawai,
A. Konaka,
P. Lebrun,
T. Lindner,
T. Mizuno,
N. Naganawa,
J. Paley,
R. Rivera,
G. Santucci,
O. Sato
, et al. (8 additional authors not shown)
Abstract:
The next generation of long-baseline neutrino experiments will be capable of precision measurements of neutrino oscillation parameters, precision neutrino-nucleus scattering, and unprecedented sensitivity to physics beyond the Standard Model. Reduced uncertainties in neutrino fluxes are necessary to achieve high precision and sensitivity in these future precise neutrino measurements. New measureme…
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The next generation of long-baseline neutrino experiments will be capable of precision measurements of neutrino oscillation parameters, precision neutrino-nucleus scattering, and unprecedented sensitivity to physics beyond the Standard Model. Reduced uncertainties in neutrino fluxes are necessary to achieve high precision and sensitivity in these future precise neutrino measurements. New measurements of hadron-nucleus interaction cross sections are needed to reduce uncertainties of neutrino fluxes. We report measurements of the differential cross-section as a function of scattering angle for proton-carbon interactions with a single charged particle in the final state at beam momenta of 20, 30, and 120 GeV/c. These measurements are the result of a beam test for EMPHATIC, a hadron-scattering and hadron-production experiment. The total, elastic and inelastic cross-sections are also extracted from the data and compared to previous measurements. These results can be used in current and future long-baseline neutrino experiments, and demonstrate the feasibility of future measurements by an upgraded EMPHATIC spectrometer.
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Submitted 29 June, 2021;
originally announced June 2021.
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Supernova Model Discrimination with Hyper-Kamiokande
Authors:
Hyper-Kamiokande Collaboration,
:,
K. Abe,
P. Adrich,
H. Aihara,
R. Akutsu,
I. Alekseev,
A. Ali,
F. Ameli,
I. Anghel,
L. H. V. Anthony,
M. Antonova,
A. Araya,
Y. Asaoka,
Y. Ashida,
V. Aushev,
F. Ballester,
I. Bandac,
M. Barbi,
G. J. Barker,
G. Barr,
M. Batkiewicz-Kwasniak,
M. Bellato,
V. Berardi,
M. Bergevin
, et al. (478 additional authors not shown)
Abstract:
Core-collapse supernovae are among the most magnificent events in the observable universe. They produce many of the chemical elements necessary for life to exist and their remnants -- neutron stars and black holes -- are interesting astrophysical objects in their own right. However, despite millennia of observations and almost a century of astrophysical study, the explosion mechanism of core-colla…
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Core-collapse supernovae are among the most magnificent events in the observable universe. They produce many of the chemical elements necessary for life to exist and their remnants -- neutron stars and black holes -- are interesting astrophysical objects in their own right. However, despite millennia of observations and almost a century of astrophysical study, the explosion mechanism of core-collapse supernovae is not yet well understood. Hyper-Kamiokande is a next-generation neutrino detector that will be able to observe the neutrino flux from the next galactic core-collapse supernova in unprecedented detail. We focus on the first 500 ms of the neutrino burst, corresponding to the accretion phase, and use a newly-developed, high-precision supernova event generator to simulate Hyper-Kamiokande's response to five different supernova models. We show that Hyper-Kamiokande will be able to distinguish between these models with high accuracy for a supernova at a distance of up to 100 kpc. Once the next galactic supernova happens, this ability will be a powerful tool for guiding simulations towards a precise reproduction of the explosion mechanism observed in nature.
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Submitted 20 July, 2021; v1 submitted 13 January, 2021;
originally announced January 2021.
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The Hyper-Kamiokande Experiment -- Snowmass LOI
Authors:
Hyper-Kamiokande Collaboration,
:,
K. Abe,
P. Adrich,
H. Aihara,
R. Akutsu,
I. Alekseev,
A. Ali,
F. Ameli,
L. H. V. Anthony,
A. Araya,
Y. Asaoka,
V. Aushev,
I. Bandac,
M. Barbi,
G. Barr,
M. Batkiewicz-Kwasniak,
M. Bellato,
V. Berardi,
L. Bernard,
E. Bernardini,
L. Berns,
S. Bhadra,
J. Bian,
A. Blanchet
, et al. (366 additional authors not shown)
Abstract:
Hyper-Kamiokande is the next generation underground water Cherenkov detector that builds on the highly successful Super-Kamiokande experiment. The detector which has an 8.4~times larger effective volume than its predecessor will be located along the T2K neutrino beamline and utilize an upgraded J-PARC beam with 2.6~times beam power. Hyper-K's low energy threshold combined with the very large fiduc…
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Hyper-Kamiokande is the next generation underground water Cherenkov detector that builds on the highly successful Super-Kamiokande experiment. The detector which has an 8.4~times larger effective volume than its predecessor will be located along the T2K neutrino beamline and utilize an upgraded J-PARC beam with 2.6~times beam power. Hyper-K's low energy threshold combined with the very large fiducial volume make the detector unique, that is expected to acquire an unprecedented exposure of 3.8~Mton$\cdot$year over a period of 20~years of operation. Hyper-Kamiokande combines an extremely diverse science program including nucleon decays, long-baseline neutrino oscillations, atmospheric neutrinos, and neutrinos from astrophysical origins. The scientific scope of this program is highly complementary to liquid-argon detectors for example in sensitivity to nucleon decay channels or supernova detection modes. Hyper-Kamiokande construction has started in early 2020 and the experiment is expected to start operations in 2027. The Hyper-Kamiokande collaboration is presently being formed amongst groups from 19 countries including the United States, whose community has a long history of making significant contributions to the neutrino physics program in Japan. US physicists have played leading roles in the Kamiokande, Super-Kamiokande, EGADS, K2K, and T2K programs.
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Submitted 1 September, 2020;
originally announced September 2020.
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EMPHATIC: A proposed experiment to measure hadron scattering and productioncross sections for improved neutrino flux predictions
Authors:
T. Akaishi,
L. Aliaga-Soplin,
H. Asano,
A. Aurisano,
M. Barbi,
L. Bellantoni,
S. Bhadra,
W-C. Chang,
L. Fields,
A. Fiorentini,
M. Friend,
T. Fukuda,
D. Harris,
M. Hartz,
R. Honda,
T. Ishikawa,
B. Jamieson,
E. Kearns,
N. Kolev,
M. Komatsu,
Y. Komatsu,
A. Konaka,
M. Kordosky,
K. Lang,
P. Lebrun
, et al. (25 additional authors not shown)
Abstract:
Hadron scattering and production uncertainties are a limiting systematic on accelerator and at-mospheric neutrino flux predictions. New hadron measurements are necessary for neutrino fluxpredictions with well-understood and reduced uncertainties. We propose a new compact experimentto measure hadron scattering and production cross sections at beam energies that are inaccessibleto currently operatin…
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Hadron scattering and production uncertainties are a limiting systematic on accelerator and at-mospheric neutrino flux predictions. New hadron measurements are necessary for neutrino fluxpredictions with well-understood and reduced uncertainties. We propose a new compact experimentto measure hadron scattering and production cross sections at beam energies that are inaccessibleto currently operating experiments. These measurements can reduce the current 10% neutrino fluxuncertainties by an approximate factor of two.
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Submitted 18 December, 2019;
originally announced December 2019.