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Toward understanding the role of genomic repeat elements in neurodegenerative diseases

Neural Regeneration Research 2025年第3期20卷 646-659页

作者： Zhengyu An Aidi Jiang Jingqi Chen institute of Science and Technology for Brain-Inspired Intelligence Fudan UniversityShanghaiChina MOE Frontiers Center for Brain Science Fudan UniversityShanghaiChina MOE Key Laboratory of computational Neuroscience and Brain-Inspired Intelligence Fudan UniversityShanghaiChina Zhangjiang Fudan International Innovation Center ShanghaiChina

Neurodegenerative diseases cause great medical and economic burdens for both patients and society;however, the complex molecular mechanisms thereof are not yet well understood. With the development of high-coverage sequencing technology, researchers have started to notice that genomic repeat regions, previously neglected in search of disease culprits, are active contributors to multiple neurodegenerative diseases. In this review, we describe the association between repeat element variants and multiple degenerative diseases through genome-wide association studies and targeted sequencing. We discuss the identification of disease-relevant repeat element variants, further powered by the advancement of long-read sequencing technologies and their related tools, and summarize recent findings in the molecular mechanisms of repeat element variants in brain degeneration, such as those causing transcriptional silencing or RNA-mediated gain of toxic function. Furthermore, we describe how in silico predictions using innovative computational models, such as deep learning language models, could enhance and accelerate our understanding of the functional impact of repeat element variants. Finally, we discuss future directions to advance current findings for a better understanding of neurodegenerative diseases and the clinical applications of genomic repeat elements.

关键词： Alzheimer's disease ataxia deep learning long-read sequencing neurodegeneration neurodegenerative diseases Parkinson's disease repeat element structural variant

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Small Alfvén number limit for incompressible magneto-hydrodynamics in a domain with boundaries

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Science China mathematics 2019年第11期62卷 2229-2248页

作者： Song Jiang Qiangchang Ju Xin Xu institute of Applied Physics and computational mathematics

For any fixed Alfvén number, the local well-posedness is proved for the equations of threedimensional ideal incompressible magneto-hydrodynamics in a domain with boundaries. Under appropriate conditions, a smooth solution is shown to exist in a time interval independent of the Alfvén number, and the solutions of the original system tend to the solutions of a two-dimensional Euler flow coupled with a linear transport equation as the Alfvén number goes to zero.

关键词： MHD equations vanishing Alfvén number limit small Mach number uniform estimates

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On two-dimensional large-scale primitive equations in oceanic dynamics (Ⅱ)

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Applied mathematics and Mechanics(English Edition) 2007年第5期28卷 581-592页

作者：黄代文郭柏灵 institute of Applied Physics and computational mathematics

The initial boundary value problem for the two-dimensional primitive equations of large scale oceanic motion in geophysics is considered. It is assumed that the depth of the ocean is a positive constant. Firstly, if the initial data are square integrable, then by Fadeo-Galerkin method, the existence of the global weak solutions for the problem is obtained. Secondly, if the initial data and their vertical derivatives are all square integrable, then by Faedo-Galerkin method and anisotropic inequalities, the existerce and uniqueness of the global weakly strong solution for the above initial boundary problem are obtained.

关键词： primitive equations of the ocean global weakly strong solution existence uniqueness

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Studying Validity of Single-Fluid Model in Inertial Confinement Fusion

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Communications in Theoretical Physics 2014年第3期61卷 370-376页

作者：谷建法范证锋戴振生叶文华裴文兵朱少平 institute of Applied Physics and computational mathematics

The validity of single-fluid model in inertial confinement fusion simulations is studied by comparing the results of the multi- and single-fluid models. The multi-fluid model includes the effects of collision and interpenetration between fluid species. By simulating the collision of fluid species, steady-state shock propagation into the thin DT gas and expansion of hohlraum Au wall heated by lasers, the results show that the validity of single-fluid model is strongly dependent on the ratio of the characteristic length of the simulated system to the particle mean free path. When the characteristic length L is one order larger than the mean free path A, the single-fluid model＇s results are found to be in good agreement with the multi-fluid model＇s simulations, and the modeling of single-fluid remains valid. If the value of L/A is lower than 10, the interpenetration between fluid species is significant, and the single-fluid simulations show some unphysical results; while the multi-fluid model can describe well the interpenetration and mix phenomena, and give more reasonable results.

关键词： multi-fluid model interpenetration mixing inertial confinement fusion

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Lagrangian cell-centered conservative scheme

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Applied mathematics and Mechanics(English Edition) 2012年第10期33卷 1329-1350页

作者：葛全文 institute of Applied Physics and computational mathematics

This paper presents a Lagrangian cell-centered conservative gas dynamics scheme. The piecewise constant pressures of cells arising from the current time sub-cell densities and the current time isentropic speed of sound are introduced. Multipling the initial cell density by the initial sub-cell volumes obtains the sub-cell Lagrangian masses, and dividing the masses by the current time sub-cell volumes gets the current time sub- cell densities. By the current time piecewise constant pressures of cells, a scheme that conserves the momentum and total energy is constructed. The vertex velocities and the numerical fluxes through the cell interfaces are computed in a consistent manner due to an original solver located at the nodes. The numerical tests are presented, which are representative for compressible flows and demonstrate the robustness and accuracy of the Lagrangian cell-centered conservative scheme.

关键词： sub-cell force Lagrange cell-centered scheme Lagrangian cell-centeredconservative gas dynamics scheme piecewise constant pressure of cell

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Optimization of the Doped Ablator Layers for the Plastic Ignition Capsule

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Communications in Theoretical Physics 2015年第2期63卷 236-242页

作者：谷建法戴振生李永升宋鹏叶文华邹士阳郑无敌朱少平 institute of Applied Physics and computational mathematics

The paper investigates theoretically the optimization of the doped ablator layers for the plastic ignition capsule. The high-resolved one-dimensional implosion simulations show that the inner pure CFI layer of the Si-doped design is excessively preheated by the hard x-ray, leading to the unstable ablator-fuel interface compared to the Ge-doped capsule. This is because that the Si K-shell absorption edge （1.8 keV） is higher than the Ge L-edge （1.3 keV）, and Si dopant makes more hard x-ray penetrate through the doped ablator layers to preheat the inner pure CH layer. So an optimization of the doped ablator layers （called ＂Si/Ge capsule＂） is performed： an Si-doped CH layer is placed next to the outer pure CH layer to keep the high implosion velocity; next to the Si-doped layer is a thin Ge-doped layer, in order to absorb the hard x-ray and protect the inner undoped CH-layer from excessively preheating. The simulations show that the Si/Ge capsule can effectively improve hydrodynamic stability at the ablator-fuel interface while keeping the high implosion velocity.

关键词： doped ablator tayer optimization ablator-fuel interface hydrodynamic instability ignition capsuleimplosion

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Zero dielectric constant limit to the non-isentropic compressible Euler-Maxwell system

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Science China mathematics 2015年第1期58卷 61-76页

作者： JIANG Song LI FuCai Laboratory of computational Physics Institute of Applied Physics and Computational Mathematics Department of mathematics Nanjing University

We investigate the zero dielectric constant limit to the non-isentropic compressible Euler-Maxwell *** justify this singular limit rigorously in the framework of smooth solutions and obtain the nonisentropic compressi... 详细信息

关键词： non-isentropic compressible Euler-Maxwell system non-isentropic compressible magnetohydro-dynamic equations zero dielectric constant limit

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High-order Lagrangian cell-centered conservative scheme on unstructured meshes

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Applied mathematics and Mechanics(English Edition) 2014年第9期35卷 1203-1222页

作者：葛全文 institute of Applied Physics and computational mathematics

A high-order Lagrangian cell-centered conservative gas dynamics scheme is presented on unstructured meshes. A high-order piecewise pressure of the cell is intro- duced. With the high-order piecewise pressure of the cell, the high-order spatial discretiza- tion fluxes are constructed. The time discretization of the spatial fluxes is performed by means of the Taylor expansions of the spatial discretization fluxes. The vertex velocities are evaluated in a consistent manner due to an original solver located at the nodes by means of momentum conservation. Many numerical tests are presented to demonstrate the robustness and the accuracy of the scheme.

关键词： high-order sub-cell force high-order Lagrangian cell-centered conservativescheme high-order piecewise pressure of cell unstructured mesh

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Local Discontinuous Galerkin Method for Parabolic Interface Problems

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Acta Mathematicae Applicatae Sinica 2015年第2期31卷 453-466页

作者： Zhi-juan ZHANG Xi-jun YU Department of mathematics Nanchang University Laboratory of computational Physics Institute of Applied Physics and Computational Mathematics

In this paper, the minimal dissipation local discontinuous Galerkin method is studied to solve the parabolic interface problems in two-dimensional convex polygonal domains. The interface may be arbitrary smooth curves. The proposed method is proved to be L2 stable and the order of error estimates in the given norm is O（h｜logh｜^1/2）. Numerical experiments show the efficiency and accuracy of the method.

关键词： parabolic interface problem minimal dissipation local discontinuous Galerkin method error estimates

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Macroscopic damping model for structural dynamics with random polycrystalline configurations

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Acta Mechanica Sinica 2018年第3期34卷 493-506页

作者： Yantao Yang Junzhi Cui Yifan Yu Meizhen Xiang Academy of mathematics and Systems Science Chinese Academy of Sciences Laboratory of computational Physics Institute of Applied Physics and Computational Mathematics

In this paper the macroscopic damping model for dynamical behavior of the structures with random polycrystalline configurations at micro-nano scales is established. First, the global motion equation of a crystal is decomposed into a set of motion equations with independent single degree of freedom （SDOF） along normal discrete modes, and then damping behavior is introduced into each SDOF motion. Through the interpolation of discrete modes, the continuous representation of damping effects for the crystal is obtained. Second, from energy conservation law the expression of the damping coefficient is derived, and the approximate formula of damping coefficient is given. Next, the continuous damping coefficient for polycrystalline cluster is expressed, the continuous dynamical equation with damping term is obtained, and then the concrete damping coefficients for a polycrystalline Cu sample are shown. Finally, by using statistical two-scale homogenization method, the macroscopic homogenized dynamical equation containing damping term for the structures with random polycrystalline configurations at micro-nano scales is set up.

关键词： Polycrystalline cluster Dynamical equation Damping coefficient Two-scale homogenization method Atomic-Continuum Coupled Model

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