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Phase transitions in the frustrated Ising ladder with stoquastic and nonstoquastic catalysts

Physical Review Research 2021年第4期3卷 043013-043013页

作者： Kabuki Takada Shigetoshi Sota Seiji Yunoki Bibek Pokharel Hidetoshi Nishimori Daniel A. Lidar Department of Physics Tokyo Institute of Technology Yokohama Kanagawa 226-8503 Japan Computational Materials Science Research Team RIKEN Center for Computational Science (R-CCS) Kobe Hyogo 650-0047 Japan Computational Condensed Matter Physics Laboratory RIKEN Cluster for Pioneering Research (CPR) Wako Saitama 351-0198 Japan Computational Quantum Matter Research Team RIKEN Center for Emergent Matter Science (CEMS) Wako Saitama 351-0198 Japan Department of Physics University of Southern California Los Angeles California 90089 USA Center for Quantum Information Science & Technology University of Southern California Los Angeles California 90089 USA Institute of Innovative Research Tokyo Institute of Technology Yokohama Kanagawa 226-8503 Japan Graduate School of Information Sciences Tohoku University Sendai Miyagi 980-8579 Japan RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS) Wako Saitama 351-0198 Japan Department of Electrical & Computer Engineering and Department of Chemistry University of Southern California Los Angeles California 90089 USA

The role of nonstoquasticity in the field of quantum annealing and adiabatic quantum computing is an actively debated topic. We study a strongly-frustrated quasi-one-dimensional quantum Ising model on a two-leg ladder to elucidate how a first-order phase transition with a topological origin is affected by interactions of the ±XX-type. Such interactions are sometimes known as stoquastic (negative sign) and nonstoquastic (positive sign) “catalysts”. Carrying out a symmetry-preserving real-space renormalization group analysis and extensive density-matrix renormalization group computations, we show that the phase diagrams obtained by these two methods are in qualitative agreement with each other and reveal that the first-order quantum phase transition of a topological nature remains stable against the introduction of both XX-type catalysts. This is the first study of the effects of nonstoquasticity on a first-order phase transition between topologically distinct phases. Our results indicate that nonstoquastic catalysts are generally insufficient for removing topological obstacles in quantum annealing and adiabatic quantum computing.

关键词： Adiabatic quantum optimization Phase transitions by order Quantum spin models Density matrix renormalization group Renormalization group

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Correction: Metabolic modulation to improve MSC expansion and therapeutic potential for articular cartilage repair

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Stem cell research & therapy 2024年第1期15卷 403页

作者： Ching Ann Tee Daniel Ninio Roxby Rashidah Othman Vinitha Denslin Kiesar Sideeq Bhat Zheng Yang Jongyoon Han Lisa Tucker-Kellogg Laurie A Boyer Critical Analytics for Manufacturing Personalised-medicine (CAMP) Interdisciplinary Research Group Singapore-MIT Alliance for Research and Technology (SMART) Centre 1 Create Way Enterprise Wing #04-13/14 Singapore 138602 Republic of Singapore. NUS Tissue Engineering Program Life Sciences Institute National University of Singapore 27 Medical Drive DSO (Kent Ridge) Building Level 4 Singapore 117510 Republic of Singapore. Department of Bioresources University of Kashmir Hazratbal Srinagar 190006 India. Department of Orthopaedic Surgery National University of Singapore 1E Kent Ridge Road NUHS Tower Block 11 Singapore 119288 Republic of Singapore. Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology 50 Vassar St Cambridge MA 02139 USA. Department of Biological Engineering Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA. Critical Analytics for Manufacturing Personalised-medicine (CAMP) Interdisciplinary Research Group Singapore-MIT Alliance for Research and Technology (SMART) Centre 1 Create Way Enterprise Wing #04-13/14 Singapore 138602 Republic of Singapore. tuckernus@***. Cancer and Stem Cell Biology and Centre for Computational Biology Duke-NUS Medical School 8 College Rd Singapore 169857 Republic of Singapore. tuckernus@***. Critical Analytics for Manufacturing Personalised-medicine (CAMP) Interdisciplinary Research Group Singapore-MIT Alliance for Research and Technology (SMART) Centre 1 Create Way Enterprise Wing #04-13/14 Singapore 138602 Republic of Singapore. lboyer@mit.edu. Department of Biological Engineering Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA. lboyer@mit.edu. Department of Biology Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA. lboyer@mit.edu.

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Author Correction: Predicting the efficiency of prime editing guide RNAs in human cells

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Nature biotechnology 2024年第3期42卷 529页

作者： Hui Kwon Kim Goosang Yu Jinman Park Seonwoo Min Sungtae Lee Sungroh Yoon Hyongbum Henry Kim Department of Pharmacology Yonsei University College of Medicine Seoul Republic of Korea. Brain Korea 21 Plus Project for Medical Sciences Yonsei University College of Medicine Seoul Republic of Korea. Center for Nanomedicine Institute for Basic Science (IBS) Seoul Republic of Korea. Graduate Program of Nano Biomedical Engineering (NanoBME) Advanced Science Institute Yonsei University Seoul Republic of Korea. Electrical and Computer Engineering Seoul National University Seoul Republic of Korea. Interdisciplinary Program in Bioinformatics Seoul National University Seoul Republic of Korea. Graduate School of Data Science Seoul National University Seoul Republic of Korea. Department of Pharmacology Yonsei University College of Medicine Seoul Republic of Korea. hkim1@yuhs.ac. Brain Korea 21 Plus Project for Medical Sciences Yonsei University College of Medicine Seoul Republic of Korea. hkim1@yuhs.ac. Center for Nanomedicine Institute for Basic Science (IBS) Seoul Republic of Korea. hkim1@yuhs.ac. Graduate Program of Nano Biomedical Engineering (NanoBME) Advanced Science Institute Yonsei University Seoul Republic of Korea. hkim1@yuhs.ac. Severance Biomedical Science Institute Yonsei University College of Medicine Seoul Republic of Korea. hkim1@yuhs.ac. Graduate Program of NanoScience and Technology Yonsei University Seoul Republic of Korea. hkim1@yuhs.ac.

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Pre-training of deep bidirectional protein sequence representations with structural information

arXiv

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arXiv 2019年

作者： Min, Seonwoo Park, Seunghyun Kim, Siwon Choi, Hyun-Soo Lee, Byunghan Yoon, Sungroh Department of Electrical and Computer engineering Seoul National University Seoul08826 Korea Republic of LG AI Research Seoul07796 Korea Republic of Clova AI Research NAVER Corp. Seongnam13561 Korea Republic of Department of Computer Science and Engineering Kangwon National University Chuncheon24341 Korea Republic of Department of Electronic and IT Media Engineering Seoul National University of Science and Technology Seoul01811 Korea Republic of Interdisciplinary Program in Artificial Intelligence ASRI INMC Institute of Engineering Research Seoul National University Seoul08826 Korea Republic of

Bridging the exponentially growing gap between the numbers of unlabeled and labeled protein sequences, several studies adopted semi-supervised learning for protein sequence modeling. In these studies, models were pre-trained with a substantial amount of unlabeled data, and the representations were transferred to various downstream tasks. Most pre-training methods solely rely on language modeling and often exhibit limited performance. In this paper, we introduce a novel pre-training scheme called PLUS, which stands for Protein sequence representations Learned Using Structural information. PLUS consists of masked language modeling and a complementary protein-specific pre-training task, namely same-family prediction. PLUS can be used to pre-train various model architectures. In this work, we use PLUS to pre-train a bidirectional recurrent neural network and refer to the resulting model as PLUS-RNN. Our experiment results demonstrate that PLUS-RNN outperforms other models of similar size solely pre-trained with the language modeling in six out of seven widely used protein biology tasks. Furthermore, we present the results from our qualitative interpretation analyses to illustrate the strengths of PLUS-RNN. PLUS provides a novel way to exploit evolutionary relationships among unlabeled proteins and is broadly applicable across a variety of protein biology tasks. We expect that the gap between the numbers of unlabeled and labeled proteins will continue to grow exponentially, and the proposed pre-training method will play a larger role. All the data and codes used in this study are available at https://***/mswzeus/PLUS. © 2019, CC BY-NC-ND.

关键词： Proteins

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On Stability of Event-Triggered Systems With Sliding Mode Control

On Stability of Event-Triggered Systems With Sliding Mode Co...

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International Workshop on Variable Structure Systems, VSS

作者： Abhisek K. Behera Bijnan Bandyopadhyay Department of Electrical and Computer Engineering Seoul National University Seoul South Korea Interdisciplinary Program in Systems and Control Engineering Indian Institute of Technology Bombay Mumbai India

In this paper, we investigate the stability of a controlled system in the event-triggering framework. By designing the triggering scheme, the control signals are updated when it is demanded subject to some satisfactory system performance. However, the stability of the system is not yet fully investigated with respect to the triggering conditions. So, the main purpose of the paper is to analyse the stability of the system with respect to the proposed triggering scheme. In this paper, sliding mode control (SMC) is used to design the event-triggered control. Our analysis proposes a new notion called bounded event property for the event which guarantees the triggering instants are generated in finite-time for all possible values of the triggering parameter. It is shown that the event-triggered SMC ensures possess the bounded event property and moreover the proposed triggering mechanism also guarantees the stability of the closed loop system stability.

关键词： Stability analysis Trajectory Closed loop systems Manifolds Steady-state Sliding mode control System performance

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The application of an extracellular vesicle-based biosensor in early diagnosis and prediction of chemoresponsiveness in ovarian cancer

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Cancer Letters 2024年 581卷 216533-216533页

作者： Tsang, Benjamin K. Asare-Werehene, Meshach Hunter, Rob Gerber, Emma Reunov, Arkadiy Brine, Isaiah Chang, Chia-Yu Chang, Chia-Ching Shieh, Dar-Bin Burger, Dylan Anis, Hanan Departments of Obstetrics & Gynecology and Cellular & Molecular Medicine Centre for Infection Immunity and Inflammation Interdisciplinary School of Health Sciences University of Ottawa Ottawa ON K1N 6N5 Canada Chronic Disease Program Ottawa Hospital Research Institute The Ottawa Hospital Ottawa ON K1Y 4E9 Canada Department of Biology St. Francis Xavier University 2320 Notre Dame Avenue Antigonish NS B2G 2W5 Canada School of Electrical Engineering and Computer Science Ottawa-Carleton Institute for Biomedical Engineering University of Ottawa Ottawa ON K1N 6N5 Canada Department of Biological Science and Department of Electrophysics Technology Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B) National Yang Ming Chiao Tung University Hsinchu 30068 Taiwan Institute of Basic Medical Science Institute of Oral Medicine and Department of Stomatology Advanced Optoelectronic Technology Center and Center for Micro/Nano Science and Technology National Cheng Kung University Hospital National Cheng Kung University Tainan 704 Taiwan Institute of Physics Academia Sinica Taipei 10529 Taiwan

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Neuroprosthetics: Durable and Fatigue-Resistant Soft Peripheral Neuroprosthetics for In Vivo Bidirectional Signaling (Adv. Mater. 20/2021)

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Advanced Materials 2021年第20期33卷

作者： Hyunseon Seo Sang Ihn Han Kang-Il Song Duhwan Seong Kyungwoo Lee Sun Hong Kim Taesung Park Ja Hoon Koo Mikyung Shin Hyoung Won Baac Ok Kyu Park Soong Ju Oh Hyung-Seop Han Hojeong Jeon Yu-Chan Kim Dae-Hyeong Kim Taeghwan Hyeon Donghee Son School of Medicine Sungkyunkwan University Suwon 16419 Republic of Korea Center for Biomaterials Biomedical Research Institute Korea Institute of Science and Technology Seoul 02792 Republic of Korea Center for Nanoparticle Research Institute of Basic Science (IBS) Seoul 08826 Republic of Korea School of Chemical and Biological Engineering Seoul National University Seoul 08826 Republic of Korea Medical Device Development Center Daegu-Gyeongbuk Medical Innovation Foundation Daegu 41061 Republic of Korea Department of Electrical and Computer Engineering Sungkyunkwan University Suwon 16419 Republic of Korea Department of Electrical and Computer Engineering Inter-University Semiconductor Research Center Seoul National University Seoul 08826 Republic of Korea Department of Materials Science and Engineering Korea University Seoul 02841 Republic of Korea Interdisciplinary Program for Bioengineering Seoul National University Seoul 08826 Republic of Korea Department of Biomedical Engineering SKKU Institute for Convergence Sungkyunkwan University Suwon 16419 Republic of Korea Center for Neuroscience Imaging Research Institute for Basic Science (IBS) Suwon 16419 Republic of Korea Department of Superintelligence Engineering Sungkyunkwan University Suwon 16419 Republic of Korea

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Probing the universality of topological defect formation in a quantum annealer: Kibble-Zurek mechanism and beyond

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Physical Review Research 2020年第3期2卷 033369-033369页

作者： Yuki Bando Yuki Susa Hiroki Oshiyama Naokazu Shibata Masayuki Ohzeki Fernando Javier Gómez-Ruiz Daniel A. Lidar Sei Suzuki Adolfo del Campo Hidetoshi Nishimori Institute of Innovative Research Tokyo Institute of Technology Nagatsuta-cho Midori-ku Yokohama 226-8503 Japan Institute of Innovative Research Tokyo Institute of Technology Oh-okayama Meguro-ku Tokyo 152-8550 Japan Department of Physics Tohoku University Sendai 980-8578 Japan Graduate School of Information Sciences Tohoku University Sendai 980-8579 Japan Sigma-i Co. Ltd. Konan Minato-ku Tokyo 108-0075 Japan Donostia International Physics Center E-20018 San Sebastián Spain Departments of Electrical and Computer Engineering Chemistry and Physics University of Southern California Los Angeles California 90089 USA Center for Quantum Information Science & Technology University of Southern California Los Angeles California 90089 USA Department of Liberal Arts Saitama Medical University Moroyama Saitama 350-0495 Japan IKERBASQUE Basque Foundation for Science E-48013 Bilbao Spain Department of Physics University of Massachusetts Boston 100 Morrissey Boulevard Boston Massachusetts 02125 USA RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS) Wako Saitama 351-0198 Japan

The number of topological defects created in a system driven through a quantum phase transition exhibits a power-law scaling with the driving time. This universal scaling law is the key prediction of the Kibble-Zurek mechanism (KZM), and testing it using a hardware-based quantum simulator is a coveted goal of quantum information science. Here we provide such a test using quantum annealing. Specifically, we report on extensive experimental tests of topological defect formation via the one-dimensional transverse-field Ising model on two different D-Wave quantum annealing devices. We find that the quantum simulator results can indeed be explained by the KZM for open-system quantum dynamics with phase-flip errors, with certain quantitative deviations from the theory likely caused by factors such as random control errors and transient effects. In addition, we probe physics beyond the KZM by identifying signatures of universality in the distribution and cumulants of the number of kinks and their decay, and again find agreement with the quantum simulator results. This implies that the theoretical predictions of the generalized KZM theory, which assumes isolation from the environment, applies beyond its original scope to an open system. We support this result by extensive numerical computations. To check whether an alternative, classical interpretation of these results is possible, we used the spin-vector Monte Carlo model, a candidate classical description of the D-Wave device. We find that the degree of agreement with the experimental data from the D-Wave annealing devices is better for the KZM, a quantum theory, than for the classical spin-vector Monte Carlo model, thus favoring a quantum description of the device. Our work provides an experimental test of quantum critical dynamics in an open quantum system, and paves the way to new directions in quantum simulation experiments.

关键词： Critical exponents Nonequilibrium statistical mechanics Open quantum systems Quantum computation Quantum master equation Quantum simulation Quantum statistical mechanics Quantum spin models

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A high-order log barrier-based mesh generation and warping method

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Procedia engineering 2017年 203卷 180-192页

作者： Mike Stees Suzanne M. Shontz Department of Electrical Engineering and Computer Science Information and Telecommunication Technology Center The University of Kansas Lawrence KS 66045 USA Department of Electrical Engineering and Computer Science Bioengineering Graduate Program Information and Telecommunication Technology Center The University of Kansas Lawrence KS 66045 USA

The ability to generate high-order meshes that conform to the boundary of curved geometries is a hurdle in the adoption of high-order computational methods for the numerical solution of partial differential equations. In this paper, we propose a method for generating and warping second-order Lagrange triangular and tetrahedral meshes based on a log barrier method. In the case of generation, the approach consists of modifying an initial linear mesh by first, adding nodes at the midpoint of each edge; second, displacing the newly added boundary midpoints to the curved boundary, and third, solving for the final positions of the interior nodes based on the boundary deformation. By allowing all of the boundary nodes to move, the approach can also be used to warp second-order triangular and tetrahedral meshes. We present several numerical examples in both two and three dimensions which demonstrate the capabilities of our method in generating and warping second-order curvilinear meshes.

关键词： high-order mesh generation curvilinear high-order mesh high-order mesh warping numerical optimization

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Author Correction: Battery-free, wireless soft sensors for continuous multi-site measurements of pressure and temperature from patients at risk for pressure injuries

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Nature communications 2021年第1期12卷 6827页

作者： Yong Suk Oh Jae-Hwan Kim Zhaoqian Xie Seokjoo Cho Hyeonseok Han Sung Woo Jeon Minsu Park Myeong Namkoong Raudel Avila Zhen Song Sung-Uk Lee Kabseok Ko Jungyup Lee Je-Sang Lee Weon Gi Min Byeong-Ju Lee Myungwoo Choi Ha Uk Chung Jongwon Kim Mengdi Han Jahyun Koo Yeon Sik Choi Sung Soo Kwak Sung Bong Kim Jeonghyun Kim Jungil Choi Chang-Mo Kang Jong Uk Kim Kyeongha Kwon Sang Min Won Janice Mihyun Baek Yujin Lee So Young Kim Wei Lu Abraham Vazquez-Guardado Hyoyoung Jeong Hanjun Ryu Geumbee Lee Kyuyoung Kim Seunghwan Kim Min Seong Kim Jungrak Choi Dong Yun Choi Quansan Yang Hangbo Zhao Wubin Bai Hokyung Jang Yongjoon Yu Jaeman Lim Xu Guo Bong Hoon Kim Seokwoo Jeon Charles Davies Anthony Banks Hyung Jin Sung Yonggang Huang Inkyu Park John A Rogers Center for Bio-Integrated Electronics Northwestern University Evanston IL USA. Department of Mechanical Engineering Korea Advanced Institute of Science and Technology Daejeon Republic of Korea. Department of Electrical and Computer Engineering University of Illinois at Urbana-Champaign Urbana IL USA. Department of Materials Science and Engineering University of Illinois at Urbana Champaign Urbana IL USA. Querrey Simpson Institute for Bioelectronics Northwestern University Evanston IL USA. State Key Laboratory of Structural Analysis for Industrial Equipment Department of Engineering Mechanics Dalian University of Technology Dalian People's Republic of China. Ningbo Institute of Dalian University of Technology Ningbo People's Republic of China. Department of Biomedical Engineering Texas A&M University College Station TX USA. Department of Mechanical Engineering Northwestern University Evanston IL USA. Advanced 3D Printing Technology Development Division Korea Atomic Energy Research Institute Daejeon Republic of Korea. Qualcomm Institute La Jolla CA USA. Sibel Health Inc Niles IL USA. Department of Rehabilitation Medicine Gimhae Hansol Rehabilitation & Convalescent Hospital Gimhae Republic of Korea. Department of Planning and Development Gimhae Hansol Rehabilitation & Convalescent Hospital Gimhae Republic of Korea. Department of Rehabilitation Medicine Pusan national university hospital Busan Republic of Korea. Department of Materials Science and Engineering KAIST Institute for The Nanocentury (KINC) Korea Advanced Institute of Science and Technology Daejeon Republic of Korea. Department of Materials Science and Engineering Northwestern University Evanston IL USA. Department of Mechanical Engineering Kyung Hee University Yongin Republic of Korea. Department of Biomedical Engineering College of Future Technology Peking University Beijing People's Republic of China. School of Biomedical Engineering Korea University Seoul Republic of Korea. Interdisci

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