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TransMut: a program to predict HLA-I peptide binding and optimize mutated peptides for vaccine design by the Transformer-derived self-attention model

Research Square

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Research Square 2021年

作者： Chu, Yanyi Zhang, Yan Wang, Qiankun Zhang, Lingfeng Wang, Xuhong Wang, Yanjing Wang, Jianmin Jiang, Xue Salahub, Dennis Russell Xiong, Yi Wei, Dong-Qing State Key Laboratory of Microbial Metabolism Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances Joint International Research Laboratory of Metabolic & Developmental Sciences School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai200030 China Department of Chemistry CMS - Centre for Molecular Simulation IQST - Institute for Quantum Science and Technology University of Calgary 2500 University Drive NW CalgaryABT2N 1N4 Canada Department of Clinical Oncology The University of Hong Kong-Shenzhen Hospital Shenzhen China School of Electrical Engineering and Computer Science University of Ottawa 75 Laurier Ave. OttawaONK1N 6N5 Canada The Ministry of Education Key Laboratory of System control and information processing Department of Automation School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai200030 China Integrative Biotechnology & Translational Medicine Yonsei University Incheon21983 Korea Republic of Peng Cheng Laboratory Vanke Cloud City Phase I Building 8 Xili Street Nanshan District Guangdong Shenzhen518055 China

Computational prediction of the interaction between human leukocyte antigen (HLA) and peptide (pHLA) can speed up epitope screening and vaccine design. Here, we develop the TransMut framework composed of TransPHLA for pHLA binding prediction and AOMP for mutated peptide optimization, which can be generalized to any binding and mutation task of biomolecules. Firstly, TransPHLA is developed by using a Transformer-derived self-attention model to predict pHLA binding, which is significantly superior to 11 previous methods on pHLA binding prediction, neoantigen and human papilloma virus vaccine identification. For vaccine design, the AOMP program is then developed to automatically optimize mutated peptides to search for mutant peptides with higher affinity to the target HLA and with high homology to the source peptide. Among 3660 non-binding pHLAs, 3630 were successfully mutated. Of these, 94% were verified by the IEDB recommended method, and 88% have homology higher than 80% to the source peptide. © 2021, CC BY.

关键词： Peptides

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Industrial Recommendation of Modeling of Inverter-Based Generators for power system Dynamic Studies with Focus on Photovoltaic

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IEEE power and Energy Technology systems Journal 2018年第1期5卷 1-10页

作者： Yamashita, Koji Renner, Herwig Martinez Villanueva, Sergio Lammert, Gustav Aristidou, Petros Carvalho Martins, Jose Zhu, Lingzhi Ospina, Luis David Pabon Van Cutsem, Thierry Department of Power System System Engineering Laboratory Central Research Institute of Electric Power Industry Kanagawa248 Japan Department of Institute of Electrical Power Systems Graz University of Technology Graz8010 Austria Department of Power System Reliability Red Eléctrica de España Alcobendas28109 Spain Department of Energy Management and Power System Operation University of Kassel Kassel34125 Germany School of Electronic and Electrical Engineering University of Leeds LeedsLS2 9JT United Kingdom Department of Asset and Network Planning EDP Distribuição Lisbon1050-045 Portugal Renewable Energy Research Center China Electric Power Research Institute Nanjing210003 China Department of System Stability and Grid Integration Fraunhofer Institute for Energy Economics and Energy System Technology Kassel34119 Germany Department of Electrical Engineering and Computer Science Fund for Scientific Research University of Liège Liège4000 Belgium

Dynamic simulations have played an important role in assessing the power system dynamic studies. The appropriate numerical model is the key to obtain correct dynamic simulation results. In addition, the appropriate model including the selection of the individual model component (such as protections, controls, and capabilities) is different depending on the type of phenomena to be observed or examined. However, the proper selection of the model is not an easy task, especially for inverter-based generators (IBGs). Considerable industry experience concerning power system dynamic studies and the dynamics of the IBGs is required for the proper selection of the IBG model. The established CIGRE C4/C6.35/CIRED joint working group (JWG) has gathered a wide variety of experts, which fully cover the required industry experience. The JWG provides the guidance on the model selection for analyzing the phenomena, such as frequency deviation, large voltage deviation, and long-term voltage deviation, individually. This helps to reduce the computational burden, as well as it clarifies the required characteristics/functions that should be represented for the power system dynamic studies with the IBGs. © 2014 IEEE.

关键词： Electric inverters

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Insulation Simulation Analysis of Press-Pack IGBT

Insulation Simulation Analysis of Press-Pack IGBT

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China International electrical and Energy Conference (CIEEC)

作者： Yuzhe Liu Chaoqun Jiao Zhibin Zhao Chengzong Pang Yuanliang Fan School of Electrical Engineering Beijing Jiaotong University Beijing China State Key Laboratory of Alternate Electrical Power System with Renewable Energy Sources North China Electric Power University Beijing China Department of Electrical Engineering and Computer Science Wichita State University Wichita USA Fujian Provincial Enterprise Key Laboratory of High Reliable Electric Power Distribution Technology State Grid Fujian Electric Power Research Institute Fuzhou China

ISBN: (数字)9781728116754

ISBN: (纸本)9781728116761

In high voltage applications such as power grid and rail transportation, IGBT devices generally operate under very harsh conditions, which places high demands on device reliability. In this paper, the electric field distribution of silicon chip termination area and press-pack IGBT package structure under high voltage reverse bias experimental conditions is simulated by Fem software. The results indicate the potential electrical insulation failure areas in the package model and the corresponding optimization measures are proposed. To some extent, the problem of breakdown discharge of IGBT devices during operation is alleviated.

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Enhancing sensitivity to ambient refractive index with tunable few-layer graphene/hBN nanoribbons

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Photonics Research 2019年第7期7卷 130-137页

作者： Huan Jiang Sajid Choudhury Zhaxylyk A.Kudyshev Di Wang Ludmila J.Prokopeva Peng Xiao Yongyuan Jiang Alexander V.Kildishev Institute of Modern Optics Department of PhysicsHarbin Institute of TechnologyHarbin 150001China School of Electrical and Computer Engineering and Birck Nanotechnology Center Purdue UniversityWest Lafayette Indiana 47907USA School of Electrical Engineering and Automation Harbin Institute of TechnologyHarbin 150001China Collaborative Innovation Center of Extreme Optics Shanxi UniversityTaiyuan 030006China Key Laboratory of Micro-Optics and Photonic Technology of Heilongjiang Province Harbin 150001China Key Laboratory of Micro-Nano Optoelectronic Information System of Ministry of Industry and Information Technology Harbin 150001China

Refractive index (RI) sensing helps to identify biomolecules and chemicals in the mid-infrared range for drug discovery, bioengineering, and environmental monitoring. In this paper, we numerically demonstrate an electrically tunable RI sensor with ultrahigh sensitivity using a three-layer graphene nanoribbon array separated by hexagonal boron nitride (hBN). Unlike the weak resonance in single-layer graphene nanoribbons, a much stronger plasmon resonance featuring a higher-quality factor can be excited in the graphene/hBN few-layer ribbon array. Simultaneously, the high purity of graphene on hBN results in an outstanding charge mobility above 4 ×10^4 cm^2 · V^-1·s^-1 at 300 K, which allows a larger modulation depth. The interaction between the locally enhanced field around graphene ribbons and its surrounding analyte leads to ultrahigh sensitivity (4.207μm/RIU), with the figure of merit reaching approximately ***, this ultrasensitive detector could selectively work in different wavebands by controlling gate voltages applied to *** merits of ultrahigh sensitivity and electrical tunability are major advances compared to previous RI sensors, paving a way toward ultrasensitive detection using graphene/hBN few-layer devices.

关键词： Enhancing sensitivity refractive index nanoribbons

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Robust Semi-Global Leaderless Consensus and Containment Control of Identical Linear systems with Imperfect Actuators

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Journal of systems Science & Complexity 2018年第1期31卷 69-86页

作者： SHI Liangren ZHAO Zhiyun LIN Zongli Department of Automation Shanghai Jiao Tong University and Key Laboratory of System Control and Information Processing of Ministry of Education Shanghai 200240 China Key Laboratory of Advanced Control and Optimization for Chemical Processes (East China University of Science and Technology) Ministry of Education Shanghai 200237 China Charles L. Brown Department of Electrical and Computer Engineering University of Virginia P.O. Box 400743 Charlottesville VA 22904-4743 USA

This paper investigates both the robust semi-global leaderless consensus problem and the robust semi-global containment control problem for a group of identical linear systems with imperfect actuators. The imperfect actuators are characterized by nonlinearities such as saturation and dead zone and there input output relationships are not precisely known. The dynamics of follower agents are also affected by the input additive disturbances. Low-and-high gain feedback consensus protocols are constructed to solve these problems. More specifically, it is shown that robust semi-global leaderless consensus can be achieved over a connected undirected graph and robust semi-global containment control can be achieved when each follower agent has access to the information of at least one leader agent. Numerical simulation illustrates the theoretical results.

关键词： Consensus containment control dead zone leaderless consensus multi-agent systems saturation

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Erratum to: The formation mechanism of aqueous hydrogen peroxide in a plasma-liquid system with liquid as the anode

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The European Physical Journal D 2020年第7期74卷 1-2页

作者： Lin, Jiao He, Xinyi Chen, Qiang Xiong, Qing Li, Junshuai Wang, Xin Chen, Guolong Liu, Qing Huo Ostrikov, Kostya (Ken) Institute of Electromagnetics and Acoustics Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance Department of Electronic Science Xiamen University Xiamen P.R. China State Key Laboratory of Power Transmission Equipment & System Security and New Technology Chongqing University Chongqing P.R. China Key Laboratory of Special Function Materials & Structure Design of the Ministry of Education School of Physical Science & Technology Lanzhou University Lanzhou P.R. China Department of Electrical and Computer Engineering Duke University Durham USA Institute for Future Environments and School of Chemistry Physics and Mechanical Engineering Queensland University of Technology Brisbane Australia CSIRO-QUT Joint Sustainable Processes and Devices Laboratory Commonwealth Scientific and Industrial Research Organization Lindfield Australia

We find that we made a mistake in the estimation of the H2O2 concentration by the colorimetric method in our previous paper (J. Lin et al., Eur. Phys. J. D (2020) 74: 80) [1].

关键词： Atomic and Molecular Collisions

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Control of Nonlinear Constrained Ultra-Supercritical Boiler–Turbine Units Using Offset-Free Output-Feedback Stable MPC

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IFAC-PapersOnLine 2018年第28期51卷 155-160页

作者： Chen, Chen Pan, Lei Shen, Jiong Lee, Kwang Y. Zhang, Fan Sun, Li Wu, Xiao Zhang, Junli Xue, Wenchao Key Laboratory of Energy Thermal Conversion and Control of Ministry of Education Southeast University Nanjing210096 China Department of Electrical and Computer Engineering Baylor University One Bear Place #97356 WacoTX76798-7356 United States State Key Lab of Power System Department of Energy and Power Engineering Tsinghua University Beijing100084 China Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing China

It is extremely challenging to control ultra-supercritical boiler–turbine unit on account of its nonlinearity, coupling among multi-variables, hard input constraints, and unknown disturbances. An offset-free output-feedback stable model predictive control (MPC) (OFOF-SMPC) for nonlinear constrained ultra-supercritical boiler-turbine units is investigated. It is shown that the OFOF-SMPC is composed of a disturbance and state observer, a steady-state target calculator as well as a stable MPC, which can remove unknown disturbances from output channels and ensure the stability of the closed-loop system with input constraints. Simulation results demonstrate the effectiveness of the proposed algorithm. © 2018

关键词： Feedback

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Spatial sparse subspace clustering for compressive spectral imaging

arXiv

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arXiv 2019年

作者： Zhu, Jianchen Zhang, Tong Zhao, Shengjie Hinojosa, Carlos Liu, Zengli Arce, Gonzalo R. Key Laboratory of Embedded System and Service Computing Ministry of Education School of Software Engineering Tongji University Shanghai201804 China School of Electronic and Information Engineering Tongji University Shanghai201804 China Department of System Engineering and Informatics Universidad Industrial de Santander Bucaramanga680002 Colombia Institute of information engineering and automation Computer Center Kunming University of Science and Technology Kunming650500 China Department of Electrical and Computer Engineering University of Delaware NewarkDE19716 United States

This paper aims at developing a clustering approach with spectral images directly from CASSI compressive measurements. The proposed clustering method first assumes that compressed measurements lie in the union of multiple low-dimensional subspaces. Therefore, sparse subspace clustering (SSC) is an unsupervised method that assigns compressed measurements to their respective subspaces. In addition, a 3D spatial regularizer is added into the SSC problem, thus taking full advantages of the spatial information contained in spectral images. The performance of the proposed spectral image clustering approach is improved by taking optimal CASSI measurements obtained when optimal coded apertures are used in CASSI system. Simulation with one real dataset illustrates the accuracy of the proposed spectral image clustering approach. Copyright © 2019, The Authors. All rights reserved.

关键词： Spectroscopy

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Mitigate the obstructing effect of vehicles on the propagation of VANETs safety-related information

Mitigate the obstructing effect of vehicles on the propagati...

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作者： Huang, Rui Wu, Jing Long, Chengnian Zhu, Yanmin Li, Bo Lin, Yi-Bing Department of Automation Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai200240 China Department of Computer Science School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai200240 China Department of Computer Science and Engineering The Hong Kong University of Science and Technology Hong Kong China Department of Computer Science and Information Engineering National Chiao Tung University Taiwan

As physical obstacles, vehicles have significant impacts on the efficient propagations of safety-related information in vehicular ad hoc networks (VANETs) by frequently obstructing the LOS links between transmitters and receivers. Obstructing effect will diminish the effective coverage of safety-related information and incur severe impact on road safety. However, this impact has not been addressed effectively. In this paper, we first present the definition of broadcast efficiency as the metric for quantizing the obstructing effect. We investigate the optimization issue for mitigating the impact of obstructing effect on the propagation of safety-related information and propose a graph theory-based optimization algorithm. For a distributed implementation of this optimization in VANETs, we further propose the maximum broadcast efficiency relaying (MBER) algorithm. MBER maximizes the effective coverage of information, meanwhile, meets delay and reliability constraints by incorporating broadcast efficiency and propagation distance in relay contention. Simulation results demonstrate that MBER promotes the effective coverage of safety-related information in VANETs with varying vehicular distribution. © 1967-2012 IEEE.

关键词： Vehicular ad hoc networks

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Semi-global leader-following output consensus of discrete-time linear multi-agent systems with input saturation

Semi-global leader-following output consensus of discrete-ti...

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2018 IEEE International Conference on Real-Time Computing and Robotics, RCAR 2018

作者： Shi, Liangren Li, Yuanlong Lin, Zongli Brown, Charles L. Innovation Center Department of Automation Shanghai Jiao Tong University China Key Laboratory of System Control and Information Processing Ministry of Education Shanghai200240 China Department of Automation Shanghai Jiao Tong University China Department of Electrical and Computer Engineering University of Virginia P.O. Box 400743 CharlottesvilleVA22904-4743 United States

ISBN: (纸本)9781538668689

We consider the problem of semi-global leader-following output consensus for a group of agents, consisting of a leader agent and some follower agents, which are described by discrete-time linear systems and connected on a directed network. For each follower agent, a distributed observer is built that estimates the state of the leader. Based on the estimates of the leader state and the solution of a parameterized algebraic Riccati equation, we design low gain consensus protocols that are shown to solve the semi-global output consensus problem as long as the leader agent is reachable globally on the network. Numerical simulation shows the performance of the proposed consensus protocols. © 2018 IEEE.

关键词： Multi agent systems

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