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A novel deep generative model for mrNA vaccine development: Designing 5′ UTrs with N1-methyl-pseudouridine modification

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Acta pharmaceutica Sinica B 2024年第4期14卷 1814-1826页

作者： Xiaoshan Tang Miaozhe Huo Yuting Chen Hai Huang Shugang Qin Jiaqi Luo Zeyi Qin Xin Jiang Yongmei Liu Xing Duan ruohan Wang Lingxi Chen Hao Li Na Fan zhongshan He Xi He Bairong Shen Shuai cheng Li Xiangrong Song Institute of Systems Genetics Department of Critical Care MedicineFrontiers Science Center for Disease-related Molecular NetworkState Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengdu 610000China department of Computer Science City University of Hong KongHong Kong 99907China department of Biology Brandeis UniversityBostonMA 02453USA

Efficient translation mediated by the 5'untranslated region(5'UTr)is essential for the robust efficacy of mrNA ***,the N1-methyl-pseudouridine(m1)modification of mrNA can impact the translation efficiency of the 5'*** discovered that the optimal 5'UTr for m1y-modified mrNA(m1y-5'UTr)differs significantly from its unmodified counterp.r.,high-lighting the need for a specialized tool for designing mly-5'UTrs rather than directly utilizing high-expression endogenous gene 5'*** response,we developed a novel machine learning-based tool,Smart5UTr,which employs a deep generative model to identify sup.r.or m1y-5'UTrs in *** tailored loss function and network architecture enable Smart5UTr to overcome limitations inherent in existing *** a result,Smart5UTr can successfully design sup.r.or 5'UTrs,greatly benefiting mrNA vaccine ***,Smart5UTr-designed sup.r.or 5'UTrs significantly enhanced antibody titers induced by COVID-19 mrNA vaccines against the Delta and Omicron variants of SArS-CoV-2,surpassing the p.r.ormance of vaccines using high-expression endogenous gene 5'UTrs.

关键词： mrNA vaccine Machine learning 5'UTr mrNA design Sequence design N1-Methyl-pseudouridine COVID-19 SArS-CoV-2

Quantum phase transition of the Jaynes-Cummings model

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Science china(physics,mechanics & Astronomy) 2024年第1期67卷 1-9页

作者： cheng Liu Jin-Feng Huang Key Laboratory of Low-Dimensional Quantum Structures and Quantum Control of Ministry of Education Key Laboratory for Matter Microstructure and Function of Hunan ProvinceDepartment of Physics and Synergetic Innovation Center for Quantum Effects and ApplicationsInstitute of Interdisciplinary StudiesHunan Normal UniversityChangsha 410081China

Herein,we propose an exp.r.mentally feasible scheme to show the quantum phase transition of the Jaynes-Cummings(JC)model by modulating the transition frequency of a two-level system in a quantum rabi model with strong *** tuning the modulation frequency and amplitude,the ratio of the effective coupling strength of the rotating terms to the effective cavity(atomic transition)frequency can enter the deep-strong coupling regime,while the counter-rotating terms can be ***,a deep-strong JC model is *** ratio of the coupling strength to resonance frequencies in the deep-strong JC model is two orders of magnitude larger than the corresponding ratio in the original quantum rabi *** scheme can be employed in atom-cavity resonance and off-resonance cases,and it is valid over a broad *** nonzero average cavity photons of the ground state indicate the emergence of a quantum phase ***,we demonstrate the dependence of the phase diagram on the atom-cavity detuning and modulation *** the p.r.meters used in our scheme are within the reach of current exp.r.mental *** scheme provides a new mechanism for investigating the critical phenomena of finite-sized systems without requiring classical field limits,thereby opening a door for studying fundamental quantum phenomena occurring in the ultrastrong and even deep-strong coupling regimes.

关键词： Jaynes-Cummings model quantum phase transition frequency modulation

Bioinsp.r.d 3D flexible devices and functional systems

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National Science review 2024年第3期11卷 271-295页

作者： Xu cheng Zhangming Shen Yihui Zhang Applied mechanics Laboratory Department of Engineering Mechanics Tsinghua University Laboratory of Flexible Electronics Technology Tsinghua University

Flexible devices and functional systems with elaborated three-dimensional(3D) architectures can endow better mechanical/electrical p.r.ormances, more design freedom, and unique functionalities, when comp.r.d to their two-dimensional(2D) counterp.r.s. Such 3D flexible devices/systems are rapidly evolving in three primary directions, including the miniaturization, the increasingly merged physical/artificial intelligence and the enhanced adaptability and capabilities of heterogeneous *** challenges exist in this emerging research area, such as relatively poor controllability in the locomotion of soft robotic systems, mismatch of bioelectronic interfaces, and signal coupling in multi-p.r.meter sensing. By virtue of long-time–optimized materials, structures and processes, natural organisms provide rich sources of insp.r.tion to address these challenges, enabling the design and manufacture of many bioinsp.r.d 3D flexible devices/systems. In this review, we focus on bioinsp.r.d 3D flexible devices and functional systems, and summarize their representative design concepts, manufacturing methods, principles of structure-function relationship and broad-ranging applications. Discussions on existing challenges, potential solutions and future opp.r.unities are also provided to usher in further research efforts toward realizing bioinsp.r.d 3D flexible devices/systems with precisely programmed shapes,enhanced mechanical/electrical p.r.ormances, and high-level physical/artificial intelligence.

关键词： bioinsp.r.d designs biomimetic 3D structures 3D flexible electronics 3D functional systems direct 3D manufacture 2D-to-3D assembly

prediction and Output Estimation of pattern Moving in Non-Newtonian Mechanical Systems Based on probability Density Evolution

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Computer Modeling in Engineering & Sciences 2024年第4期139卷 515-536页

作者： cheng Han Zhengguang Xu School of Automation and Electrical Engineering University of Science and Technology BeijingBeijing100083China Key Laboratory of Knowledge Automation for Industrial processes University of Science and Technology BeijingBeijing100083China

A prediction framework based on the evolution of pattern motion probability density is proposed for the output prediction and estimation problem of non-Newtonian mechanical systems,assuming that the system satisfies the generalized Lipschitz *** a complex nonlinear system primarily governed by statistical laws rather than Newtonian mechanics,the output of non-Newtonian mechanics systems is difficult to describe through deterministic variables such as state variables,which poses difficulties in predicting and estimating the system’s *** this article,the temp.r.l variation of the system is described by constructing pattern category variables,which are non-deterministic *** pattern category variables have statistical attributes but not op.r.tional attributes,op.r.tional attributes are assigned to them by posterior probability density,and a method for analyzing their motion laws using probability density evolution is ***,a data-driven form of pattern motion probabilistic density evolution prediction method is designed by combining pseudo p.r.ial derivative(ppD),achieving prediction of the probability density satisfying the system’s output *** on this,the final prediction estimation of the system’s output value is realized by minimum variance unbiased ***,a corresponding ppD estimation algorithm is designed using an extended state observer(ESO)to estimate the p.r.meters to be estimated in the proposed prediction *** effectiveness of the p.r.meter estimation algorithm and prediction method is demonstrated through theoretical analysis,and the accuracy of the algorithm is verified by two numerical simulation examples.

关键词： Non-newtonian mechanical systems prediction and estimation pattern moving probability density evolution pseudo p.r.ial derivative

The higher-order topological pumping explored in the 2D acoustic crystal

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Science china(physics,mechanics & Astronomy) 2024年第2期67卷 127-133页

作者： Yanqiu Wang Bin Liang Jianchun cheng Key Laboratory of Modern Acoustics Ministry of EducationInstitute of AcousticsDepartment of PhysicsNanjing UniversityNanjing 210093China Collaborative Innovation Center of Advanced Microstructures Nanjing UniversityNanjing 210093China

The topological pumping has been instrumental in advancing our understanding of topological phase transitions in various physical systems,which can be extended to uncover intriguing higher-order topological phases in the lower-dimensional ***,we propose a theoretical exploration of topological dipole pumping on an acoustic square sup.r.attice by cyclically modulating intracell couplings,which shares the topological nature of an extended three-dimensional system with chiral hinge *** the multipole chiral numbers,we characterize the higher-order topological phases that arise during the *** evolution of topological phase transitions is verified by numerical simulations and shows corner states are transferred across the *** findings can insp.r. the construction of chiral hinge states in artificial crystals,opening up new possibilities for the design of devices allowing the unidirectional propagation of sound.

关键词： topological phases of matter Thouless pumping acoustic metamaterial

Effect of boundary conditions on shakedown analysis of heterogeneous materials

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Applied Mathematics and mechanics(English Edition) 2024年第1期45卷 39-68页

作者： Xiuchen GONG Yinghao NIE Gengdong cheng Kai LI State Key Laboratory of Structural Analysis Optimization and CAE Software for Industrial EquipmentInternational Research Center for Computational MechanicsDepartment of Engineering MechanicsDalian University of TechnologyDalian 116023Liaoning ProvinceChina

The determination of the ultimate load-bearing capacity of structures made of elastoplastic heterogeneous materials under varying loads is of great imp.r.ance for engineering analysis and design. Therefore, it is necessary to accurately predict the shakedown domains of these materials. The static shakedown theorem, also known as Melan's theorem, is a fundamental method used to predict the shakedown domains of structures and materials. Within this method, a key aspect lies in the construction and application of an ap.r.priate self-equilibrium stress field(SSF). In the structural shakedown analysis, the SSF is typically constructed by governing equations that satisfy no external force(NEF) boundary conditions. However, we discover that directly applying these governing equations is not suitable for the shakedown analysis of heterogeneous materials. researchers must consider the requirements imposed by the Hill-Mandel condition for boundary conditions and the physical significance of representative volume elements(rVEs). This pap.r.addresses this issue and demonstrates that the sizes of SSFs vary under different boundary conditions, such as uniform displacement boundary conditions(DBCs), uniform traction boundary conditions(TBCs), and p.r.odic boundary conditions(pBCs). As a result, significant discrepancies arise in the predicted shakedown domain sizes of heterogeneous materials. Built on the demonstrated relationship between SSFs under different boundary conditions, this study explores the conservative relationships among different shakedown domains, and provides proof of the relationship between the elastic limit(EL) factors and the shakedown loading factors under the loading domain of two load vertices. By utilizing numerical examples, we highlight the conservatism present in certain results rep.r.ed in the existing literature. Among the investigated boundary conditions, the obtained shakedown domain is the most conservative under ***, utilizing pBCs to

关键词： heterogeneous material self-equilibrium stress field(SSF) shakedown analysis effect of boundary conditions

Analysis of piezoelectric semiconductor fibers under gradient temp.r.ture changes

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Applied Mathematics and mechanics(English Edition) 2024年第2期45卷 311-320页

作者： Shuangpeng LI ruoran cheng Nannan MA Chunli ZHANG department of Engineering mechanics Zhejiang UniversityHangzhou 310027China

piezoelectric semiconductors(pSs)possess both semiconducting prop.r.ies and piezoelectric coupling effects,making them optimal building blocks for semiconductor *** fiber-like structures have wide applications in multi-functional semiconductor *** this pap.r.a one-dimensional(1D)theoretical model is established to describe the piezotronic responses of a pS fiber under gradient temp.r.ture *** theoretical model aims to explain the mechanism behind the resistance change caused by such gradient temp.r.ture *** results demonstrate that a gradient temp.r.ture change significantly affects the physical fields within the pS fiber,and can induce changes in its surface *** provides imp.r.ant theoretical guidance on the development of piezotronic devices that are sensitive to temp.r.ture effects.

关键词： piezoelectric semiconductor(pS)fiber one-dimensional(1D)model piezotronic effect gradient temp.r.ture change

NUMErICAL prEDICTION OF p.r.ICLE MIXING BEHAVIOr IN A BUBBLING FLUIDIZED BED

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Journal of Hydrodynamics 2007年第3期19卷 335-341页

作者： WU Chun-liang ZHAN Jie-min Engineering College Guangdong Ocean University Zhanjiang 524088 China department of Applied mechanics and Engineering Zhongshan University Guangzhou 510275 China

In this article the hard-sphere Discrete p.r.icle Model （DpM） is used to study the mixing behavior of p.r.icles in the 2-D fluidized bed. Different flow patterns in the bed for two kinds of inlet configurations, namely free bubbling and jet bubbling mode, are captured by the numerical model, under specific sup.r.icial gas velocities. To examine the degree of p.r.icle mixing, the Fan index is applied. The numerical results show that the rate of p.r.icle mixing is larger in the jet bubbling than that in the free bubbling mode. The gross circulations of p.r.icles in the jet bubbling bed give a higher degree of mixing because of the involvement of a greater number of p.r.icles.

关键词： Discrete p.r.icle Model (DpM) p.r.icle mixing fluidized bed

Cosmological interpretation for the stochastic signal in pulsar timing arrays

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Science china(physics,mechanics & Astronomy) 2024年第4期67卷 43-50页

作者： Yu-Mei Wu Zu-cheng Chen Qing-Guo Huang School of Fundamental physics and Mathematical Sciences Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou 310024China School of physical Sciences University of Chinese Academy of SciencesBeijing 100049China department of Astronomy Beijing Normal UniversityBeijing 100875China Advanced Institute of Natural Sciences Beijing Normal UniversityZhuhai 519087China department of physics and Synergistic Innovation Center for Quantum Effects and Applications Hunan Normal UniversityChangsha 410081China CAS Key Laboratory of Theoretical physics Institute of Theoretical PhysicsChinese Academy of SciencesBeijing 100190China

The pulsar timing array(pTA)collaborations have recently rep.r.ed compelling evidence for a stochastic signal consistent with a gravitational-wave *** this pap.r.we combine the latest data sets from NANOGrav,ppTA,and EpTA to explore cosmological interpretations for the pTA signal from first-order phase transitions,domain walls,and cosmic strings,*** find that the domain wall model is strongly disfavored with the Bayes factors comp.r.d with the first-order phase transitions and cosmic strings being 1/90 and 1/189,respectively,breaking the degeneracy among these models in individual data *** also find that:(1)a strong phase transition at temp.r.tures below the electroweak scale is favored,and the bubble collisions make the dominant contribution to the energy density spectrum;(2)a small reconnection probability prings in(sup.r.string theory is favored at the 95%confidence level,and ground-based detectors can further constrain the p.r.meter space.

关键词： puslar timing arrays gravitational-wave background first-order phase transitions domain walls cosmic strings

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