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1. Quantum-centric supercomputing for materials science: A perspective on challenges and future directions

Author

Alexeev, Yuri, Amsler, Maximilian, Barroca, Marco Antonio, Bassini, Sanzio, Battelle, Torey, Camps, Daan, Casanova, David, Choi, Young Jay, Chong, Frederic T, Chung, Charles, Codella, Christopher, Córcoles, Antonio D, Cruise, James, Di Meglio, Alberto, Duran, Ivan, Eckl, Thomas, Economou, Sophia, Eidenbenz, Stephan, Elmegreen, Bruce, Fare, Clyde, Faro, Ismael, Fernández, Cristina Sanz, Ferreira, Rodrigo Neumann Barros, Fuji, Keisuke, Fuller, Bryce, Gagliardi, Laura, Galli, Giulia, Glick, Jennifer R, Gobbi, Isacco, Gokhale, Pranav, de la Puente Gonzalez, Salvador, Greiner, Johannes, Gropp, Bill, Grossi, Michele, Gull, Emanuel, Healy, Burns, Hermes, Matthew R, Huang, Benchen, Humble, Travis S, Ito, Nobuyasu, Izmaylov, Artur F, Javadi-Abhari, Ali, Jennewein, Douglas, Jha, Shantenu, Jiang, Liang, Jones, Barbara, de Jong, Wibe Albert, Jurcevic, Petar, Kirby, William, Kister, Stefan, Kitagawa, Masahiro, Klassen, Joel, Klymko, Katherine, Koh, Kwangwon, Kondo, Masaaki, Kürkçüog̃lu, Dog̃a Murat, Kurowski, Krzysztof, Laino, Teodoro, Landfield, Ryan, Leininger, Matt, Leyton-Ortega, Vicente, Li, Ang, Lin, Meifeng, Liu, Junyu, Lorente, Nicolas, Luckow, Andre, Martiel, Simon, Martin-Fernandez, Francisco, Martonosi, Margaret, Marvinney, Claire, Medina, Arcesio Castaneda, Merten, Dirk, Mezzacapo, Antonio, Michielsen, Kristel, Mitra, Abhishek, Mittal, Tushar, Moon, Kyungsun, Moore, Joel, Mostame, Sarah, Motta, Mario, Na, Young-Hye, Nam, Yunseong, Narang, Prineha, Ohnishi, Yu-ya, Ottaviani, Daniele, Otten, Matthew, Pakin, Scott, Pascuzzi, Vincent R, Pednault, Edwin, Piontek, Tomasz, Pitera, Jed, Rall, Patrick, Ravi, Gokul Subramanian, Robertson, Niall, Rossi, Matteo AC, Rydlichowski, Piotr, Ryu, Hoon, Samsonidze, Georgy, Sato, Mitsuhisa, and Saurabh, Nishant

Subjects
Data Management and Data Science, Distributed Computing and Systems Software, Information and Computing Sciences, Information Systems, Networking and Information Technology R&D (NITRD), Quantum-centric supercomputing, Quantum computing, Materials science, High-performance computing, Computer Software, Distributed Computing, Data management and data science, Distributed computing and systems software, Information systems
Abstract

Computational models are an essential tool for the design, characterization, and discovery of novel materials. Computationally hard tasks in materials science stretch the limits of existing high-performance supercomputing centers, consuming much of their resources for simulation, analysis, and data processing. Quantum computing, on the other hand, is an emerging technology with the potential to accelerate many of the computational tasks needed for materials science. In order to do that, the quantum technology must interact with conventional high-performance computing in several ways: approximate results validation, identification of hard problems, and synergies in quantum-centric supercomputing. In this paper, we provide a perspective on how quantum-centric supercomputing can help address critical computational problems in materials science, the challenges to face in order to solve representative use cases, and new suggested directions.

Published
2024

2. Neurotoxic Microglial Activation via IFNγ‐Induced Nrf2 Reduction Exacerbating Alzheimer's Disease

Author

Kang, You Jung, Hyeon, Seung Jae, McQuade, Amanda, Lim, Jiwoon, Baek, Seung Hyun, Diep, Yen N, V., Khanh, Jeon, Yeji, Jo, Dong‐Gyu, Lee, C Justin, Blurton‐Jones, Mathew, Ryu, Hoon, and Cho, Hansang

Subjects
Biochemistry and Cell Biology, Biological Sciences, Acquired Cognitive Impairment, Aging, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Dementia, Alzheimer's Disease, Neurodegenerative, Brain Disorders, Neurosciences, Aetiology, 2.1 Biological and endogenous factors, Neurological, Alzheimer Disease, Animals, NF-E2-Related Factor 2, Microglia, Humans, Mice, Interferon-gamma, Disease Models, Animal, Oxidative Stress, Mice, Transgenic, Alzheimer's diseases, interferon-gamma, microglia, neurodegeneration, neuroinflammation, oxidative stress, interferon‐gamma
Abstract

Microglial neuroinflammation appears to be neuroprotective in the early pathological stage, yet neurotoxic, which often precedes neurodegeneration in Alzheimer's disease (AD). However, it remains unclear how the microglial activities transit to the neurotoxic state during AD progression, due to complex neuron-glia interactions. Here, the mechanism of detrimental microgliosis in AD by employing 3D human AD mini-brains, brain tissues of AD patients, and 5XFAD mice is explored. In the human and animal AD models, amyloid-beta (Aβ)-overexpressing neurons and reactive astrocytes produce interferon-gamma (IFNγ) and excessive oxidative stress. IFNγ results in the downregulation of mitogen-activated protein kinase (MAPK) and the upregulation of Kelch-like ECH-associated Protein 1 (Keap1) in microglia, which inactivate nuclear factor erythroid-2-related factor 2 (Nrf2) and sensitize microglia to the oxidative stress and induces a proinflammatory microglia via nuclear factor kappa B (NFκB)-axis. The proinflammatory microglia in turn produce neurotoxic nitric oxide and proinflammatory mediators exacerbating synaptic impairment, phosphorylated-tau accumulation, and discernable neuronal loss. Interestingly, recovering Nrf2 in the microglia prevents the activation of proinflammatory microglia and significantly blocks the tauopathy in AD minibrains. Taken together, it is envisioned that IFNγ-driven Nrf2 downregulation in microglia as a key target to ameliorate AD pathology.

Published
2024

3. Entanglement-based quantum information protocols designed with silicon quantum dot platform

Author

Ryu, Junghee and Ryu, Hoon

Subjects
Quantum Physics, Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

Electron spins in silicon quantum dot platform provide great potential for quantum information processing due to excellent physical properties and modern fabrication technologies. Spin-based quantum bit (qubit) operations are intensively studied to realize universal logic gates with a high fidelity, fast gating operations, and basic programmability. Although recent experimental achievements can be considered as remarkable results for utilizing quantum computation, more advanced quantum information protocols should be demonstrated with a large number of qubit system to enable programmability of silicon devices. Here, we computationally explore entanglement-based quantum information protocols in electrically defined five silicon quantum dot system. To this end, device simulations are employed to demonstrate $1$-qubit gate and $2$-qubit gate operations. Additionally, we discuss the implementations of three applications: the generation of magic states, entanglement swapping, and quantum teleportation in our silicon device. All the results will secure the scalability of quantum information processing with electron spin qubits in silicon quantum dot system.

Published
2024

4. Brain hypothyroidism silences the immune response of microglia in Alzheimers disease animal model.

Author

Kim, Dong, Choi, Hyunjung, Lee, Woochan, Choi, Hayoung, Hong, Seok, Jeong, June-Hyun, Han, Jihui, Han, Jong, Ryu, Hoon, Kim, Jong-Il, and Mook-Jung, Inhee

Subjects
Mice, Animals, Alzheimer Disease, Microglia, Amyloid beta-Peptides, Brain, Immunity, Innate, Hypothyroidism, Models, Animal, Disease Models, Animal
Abstract

Thyroid hormone (TH) imbalance is linked to the pathophysiology of reversible dementia and Alzheimers disease (AD). It is unclear whether tissue hypothyroidism occurs in the AD brain and how it affects on AD pathology. We find that decreased iodothyronine deiodinase 2 is correlated with hippocampal hypothyroidism in early AD model mice before TH alterations in the blood. TH deficiency leads to spontaneous activation of microglia in wild-type mice under nonstimulated conditions, resulting in lowered innate immune responses of microglia in response to inflammatory stimuli or amyloid-β. In AD model mice, TH deficiency aggravates AD pathology by reducing the disease-associated microglia population and microglial phagocytosis. We find that TH deficiency reduces microglial ecto-5-nucleotidase (CD73) and inhibition of CD73 leads to impaired innate immune responses in microglia. Our findings reveal that TH shapes microglial responses to inflammatory stimuli including amyloid-β, and brain hypothyroidism in early AD model mice aggravates AD pathology by microglial dysfunction.

Published
2024

5. Quantum-centric Supercomputing for Materials Science: A Perspective on Challenges and Future Directions

Author

Alexeev, Yuri, Amsler, Maximilian, Baity, Paul, Barroca, Marco Antonio, Bassini, Sanzio, Battelle, Torey, Camps, Daan, Casanova, David, Choi, Young jai, Chong, Frederic T., Chung, Charles, Codella, Chris, Corcoles, Antonio D., Cruise, James, Di Meglio, Alberto, Dubois, Jonathan, Duran, Ivan, Eckl, Thomas, Economou, Sophia, Eidenbenz, Stephan, Elmegreen, Bruce, Fare, Clyde, Faro, Ismael, Fernández, Cristina Sanz, Ferreira, Rodrigo Neumann Barros, Fuji, Keisuke, Fuller, Bryce, Gagliardi, Laura, Galli, Giulia, Glick, Jennifer R., Gobbi, Isacco, Gokhale, Pranav, Gonzalez, Salvador de la Puente, Greiner, Johannes, Gropp, Bill, Grossi, Michele, Gull, Emmanuel, Healy, Burns, Huang, Benchen, Humble, Travis S., Ito, Nobuyasu, Izmaylov, Artur F., Javadi-Abhari, Ali, Jennewein, Douglas, Jha, Shantenu, Jiang, Liang, Jones, Barbara, de Jong, Wibe Albert, Jurcevic, Petar, Kirby, William, Kister, Stefan, Kitagawa, Masahiro, Klassen, Joel, Klymko, Katherine, Koh, Kwangwon, Kondo, Masaaki, Kurkcuoglu, Doga Murat, Kurowski, Krzysztof, Laino, Teodoro, Landfield, Ryan, Leininger, Matt, Leyton-Ortega, Vicente, Li, Ang, Lin, Meifeng, Liu, Junyu, Lorente, Nicolas, Luckow, Andre, Martiel, Simon, Martin-Fernandez, Francisco, Martonosi, Margaret, Marvinney, Claire, Medina, Arcesio Castaneda, Merten, Dirk, Mezzacapo, Antonio, Michielsen, Kristel, Mitra, Abhishek, Mittal, Tushar, Moon, Kyungsun, Moore, Joel, Motta, Mario, Na, Young-Hye, Nam, Yunseong, Narang, Prineha, Ohnishi, Yu-ya, Ottaviani, Daniele, Otten, Matthew, Pakin, Scott, Pascuzzi, Vincent R., Penault, Ed, Piontek, Tomasz, Pitera, Jed, Rall, Patrick, Ravi, Gokul Subramanian, Robertson, Niall, Rossi, Matteo, Rydlichowski, Piotr, Ryu, Hoon, Samsonidze, Georgy, Sato, Mitsuhisa, Saurabh, Nishant, Sharma, Vidushi, Sharma, Kunal, Shin, Soyoung, Slessman, George, Steiner, Mathias, Sitdikov, Iskandar, Suh, In-Saeng, Switzer, Eric, Tang, Wei, Thompson, Joel, Todo, Synge, Tran, Minh, Trenev, Dimitar, Trott, Christian, Tseng, Huan-Hsin, Tureci, Esin, Valinas, David García, Vallecorsa, Sofia, Wever, Christopher, Wojciechowski, Konrad, Wu, Xiaodi, Yoo, Shinjae, Yoshioka, Nobuyuki, Yu, Victor Wen-zhe, Yunoki, Seiji, Zhuk, Sergiy, and Zubarev, Dmitry

Subjects
Quantum Physics, Condensed Matter - Materials Science
Abstract

Computational models are an essential tool for the design, characterization, and discovery of novel materials. Hard computational tasks in materials science stretch the limits of existing high-performance supercomputing centers, consuming much of their simulation, analysis, and data resources. Quantum computing, on the other hand, is an emerging technology with the potential to accelerate many of the computational tasks needed for materials science. In order to do that, the quantum technology must interact with conventional high-performance computing in several ways: approximate results validation, identification of hard problems, and synergies in quantum-centric supercomputing. In this paper, we provide a perspective on how quantum-centric supercomputing can help address critical computational problems in materials science, the challenges to face in order to solve representative use cases, and new suggested directions., Comment: 60 pages, 14 figures; comments welcome

Published
2023

8. Crif1 deficiency in dopamine neurons triggers early-onset parkinsonism

Author

Heo, Jun Young, Park, Ah Hyung, Lee, Min Joung, Ryu, Min Jeong, Kim, Yong Kyung, Jang, Yun Seon, Kim, Soo Jeong, Shin, So Yeon, Son, Hyo Jin, Stein, Thor D., Huh, Yang Hoon, Chung, Sookja K., Choi, Song Yi, Kim, Jin Man, Hwang, Onyou, Shong, Minho, Hyeon, Seung Jae, Lee, Junghee, Ryu, Hoon, Kim, Daesoo, and Kweon, Gi Ryang

Published
2023
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9. Exploring entanglement resource in Si quantum dot systems with operational quasiprobability approach

Author

Ryu, Junghee and Ryu, Hoon

Subjects
Quantum Physics, Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

We characterize the quantum entanglement of the realistic two-qubit signals that are sensitive to charge noises. Our working example is the time response generated from a silicon double quantum dot (DQD) platform, where a single-qubit rotation and a two-qubit controlled-NOT operation are conducted sequentially in time to generate arbitrary entangled states. In order to characterize the entanglement of two-qubit states, we employ the marginal operational quasiprobability (OQ) approach that allows negative values of the probability function if a given state is entangled. While the charge noise, which is omnipresent in semiconductor devices, severely affects logic operations implemented in the DQD platform, causing huge degradation in fidelity of unitary operations as well as resulting two-qubit states, the pattern in the OQ-driven entanglement strength turns out to be quite invariant, indicating that the resource of quantum entanglement is not significantly broken though the physical system is exposed to noise-driven fluctuations in exchange interaction between quantum dots., Comment: 11 pages, 5 figures

Published
2022
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10. Devitalizing noise-driven instability of entangling logic in silicon devices with bias controls

Author

Ryu, Hoon and Kang, Ji-Hoon

Subjects
Quantum Physics, Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

The quality of quantum bits (qubits) in silicon is highly vulnerable to charge noise that is omni-present in semiconductor devices and is in principle hard to be suppressed. For a realistically sized quantum dot system based on a silicon-germanium heterostructure whose confinement is manipulated with electrical biases imposed on top electrodes, we computationally explore the noise-robustness of 2-qubit entangling operations with a focus on the controlled-X (CNOT) logic that is essential for designs of gate-based universal quantum logic circuits. With device simulations based on the physics of bulk semiconductors augmented with electronic structure calculations, we not only quantify the degradation in fidelity of single-step CNOT operations with respect to the strength of charge noise, but also discuss a strategy of device engineering that can significantly enhance noise-robustness of CNOT operations with almost no sacrifice of speed compared to the single-step case. Details of device designs and controls that this work presents can establish a rare but practical guideline for potential efforts to secure silicon-based quantum processors using an electrode-driven quantum dot platform., Comment: 23 pages, 6 figures

Published
2022
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23. Astrocytic hemoglobin is an H2O2-decomposing peroxidase and therapeutic target for Alzheimer's disease

Author

Won, Woojin, primary, Lee, Elijah Hwejin, additional, Gotina, Lizaveta, additional, Chun, Heejung, additional, Park, Uiyeol, additional, Kim, Daeun, additional, Kim, Tai Young, additional, Choi, Jiwon, additional, Kim, Yoowon, additional, Park, Sun Jun, additional, Bhalla, Mridula, additional, Lim, Jiwoon, additional, Park, Jong-Hyun, additional, Oh, Soo-Jin, additional, Ryu, Hoon, additional, Pae, Ae Nim, additional, Park, Ki Duk, additional, and Lee, C. Justin, additional

Published
2024
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41. Visualizing Cancer-Originating Acetate Uptake Through MCT1 in Reactive Astrocytes in the Glioblastoma Tumor Microenvironment

Author

Kim, Dongwoo, primary, Ko, Hae Young, additional, Chung, Jee-In, additional, Park, Yongmin Mason, additional, Lee, Sangwon, additional, Kim, Seon Yoo, additional, Kim, Jisu, additional, Chun, Joong-Hyun, additional, Han, Kyung-Seok, additional, Lee, Misu, additional, Ju, Yeon Ha, additional, Park, Sun Jun, additional, Park, Ki Duk, additional, Nam, Min-Ho, additional, Kim, Se Hoon, additional, Shim, Jin-Kyoung, additional, Park, Youngjoo, additional, Lim, Hyunkeong, additional, Park, Jaekyung, additional, Kim, Hyunjin, additional, Kim, Suhyun, additional, Park, Uiyeol, additional, Ryu, Hoon, additional, Lee, So Yun, additional, Park, Sunghyouk, additional, Kang, Seok-Gu, additional, Chang, Jong Hee, additional, Lee, C Justin, additional, and Yun, Mijin, additional

Published
2023
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43. Numerical guidelines for setting up a general purpose k.p simulator with applications to quantum dot heterostructures and topological insulators

Author

Sengupta, Parijat, Ryu, Hoon, Lee, Sunhee, Tan, Yaohua, and Klimeck, Gerhard

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

The k.p perturbation method for determination of electronic structure first pioneered by Kohn and Luttinger continues to provide valuable insight to several band structure features. This method has been adopted to heterostructures confined up to three directions. In this paper, numerical details of setting up a k.p Hamiltonian using the finite difference approximation for such confined nanostructures is explicitly demonstrated. Nanostructures belonging to two symmetry classes namely cubic zincblende and rhombohedral crystals are considered. Rhombohedral crystals, of late, have gained prominence as candidates for the recently discovered topological insulator (TI) class of materials. Lastly the incorporation of strain field to the k.p Hamiltonian and matrix equations for computing the intrinsic and externally applied strain in heterostructures within a continuum approximation is shown. Two applications are considered 1)Computation of the eigen states of a multi-million zincblende InAs quantum dot with a stress-reducing InGaAs layer of varying Indium composition embedded in a GaAs matrix and 2)Dispersion of a rhombohedral topological insulator Bi$_{2}$Se$_{3}$ film., Comment: 10 pages, 4 figures

Published
2014

45. Atomistic and continuum modeling of a zincblende quantum dot heterostructure

Author

Sengupta, Parijat, Lee, Sunhee, Steiger, Sebastian, Ryu, Hoon, and Klimeck, Gerhard

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

A multiscale approach was adopted for the calculation of confined states in self-assembled semiconductor quantum dots (QDs). While results close to experimental data have been obtained with a combination of atomistic strain and tight-binding (TB) electronic structure description for the confined quantum states in the QD, the TB calculation requires substantial computational resources. To alleviate this problem an integrated approach was adopted to compute the energy states from a continuum 8-band k.p Hamiltonian under the influence of an atomistic strain field. Such multi-scale simulations yield a roughly six-fold faster simulation. Atomic-resolution strain is added to the k.p Hamiltonian through interpolation onto a coarser continuum grid. Sufficient numerical accuracy is obtained by the multi-scale approach. Optical transition wavelengths are within 7% of the corresponding TB results with a proper splitting of p-type sub-bands. The systematically lower emission wavelengths in k.p are attributable to an underestimation of the coupling between the conduction and valence bands., Comment: 4 pages,4 figures

Published
2014

46. Severe reactive astrocytes precipitate pathological hallmarks of Alzheimer’s disease via H2O2− production

Author

Chun, Heejung, Im, Hyeonjoo, Kang, You Jung, Kim, Yunha, Shin, Jin Hee, Won, Woojin, Lim, Jiwoon, Ju, Yeonha, Park, Yongmin Mason, Kim, Sunpil, Lee, Seung Eun, Lee, Jaekwang, Woo, Junsung, Hwang, Yujin, Cho, Hyesun, Jo, Seonmi, Park, Jong-Hyun, Kim, Daesoo, Kim, Doo Yeon, Seo, Jeong-Sun, Gwag, Byoung Joo, Kim, Young Soo, Park, Ki Duk, Kaang, Bong-Kiun, Cho, Hansang, Ryu, Hoon, and Lee, C. Justin

Published
2020
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50. A Development on the SaaS Cloud Scientific Computing Platform for Education and Research in Nanoscience

Author

Jeon, Inho, Ma, Jin, Seo, Jerry H., Lee, Jongsuk Ruth, Cho, Kumwon, Ryu, Hoon, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Ruediger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Hirche, Sandra, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Liang, Qilian, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Möller, Sebastian, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zhang, Junjie James, Series Editor, Park, James J., editor, Loia, Vincenzo, editor, Yi, Gangman, editor, and Sung, Yunsick, editor

Published
2018
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