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Your search keyword '"Tao, Yutian"' showing total 15 results
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15 results on '"Tao, Yutian"'

1. A Symmetric Multigrid-Preconditioned Krylov Subspace Solver for Stokes Equations

Author

Tao, Yutian and Sifakis, Eftychios

Subjects
Mathematics - Numerical Analysis, Physics - Computational Physics
Abstract

Numerical solution of discrete PDEs corresponding to saddle point problems is highly relevant to physical systems such as Stokes flow. However, scaling up numerical solvers for such systems is often met with challenges in efficiency and convergence. Multigrid is an approach with excellent applicability to elliptic problems such as the Stokes equations, and can be a solution to such challenges of scalability and efficiency. The degree of success of such methods, however, is highly contingent on the design of key components of a multigrid scheme, including the hierarchy of discretizations, and the relaxation scheme used. Additionally, in many practical cases, it may be more effective to use a multigrid scheme as a preconditioner to an iterative Krylov subspace solver, as opposed to striving for maximum efficacy of the relaxation scheme in all foreseeable settings. In this paper, we propose an efficient symmetric multigrid preconditioner for the Stokes Equations on a staggered finite-difference discretization. Our contribution is focused on crafting a preconditioner that (a) is symmetric indefinite, matching the property of the Stokes system itself, (b) is appropriate for preconditioning the SQMR iterative scheme, and (c) has the requisite symmetry properties to be used in this context. In addition, our design is efficient in terms of computational cost and facilitates scaling to large domains.

Published
2023
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3. Optimized Processing of Localized Collisions in Projective Dynamics

Author

Wang, Qisi, Tao, Yutian, Brandt, Eric, Cutting, Court, and Sifakis, Eftychios

Subjects
Computer Science - Graphics
Abstract

We present a method for the efficient processing of contact and collision in volumetric elastic models simulated using the Projective Dynamics paradigm. Our approach enables interactive simulation of tetrahedral meshes with more than half a million elements, provided that the model satisfies two fundamental properties: the region of the model's surface that is susceptible to collision events needs to be known in advance, and the simulation degrees of freedom associated with that surface region should be limited to a small fraction (e.g. 5\%) of the total simulation nodes. Despite this conscious delineation of scope, our hypotheses hold true for common animation subjects, such as simulated models of the human face and parts of the body. In such scenarios, a partial Cholesky factorization can abstract away the behavior of the collision-safe subset of the face into the Schur Complement matrix with respect to the collision-prone region. We demonstrate how fast and accurate updates of penalty-based collision terms can be incorporated into this representation, and solved with high efficiency on the GPU. We also demonstrate the opportunity to iterate a partial update of the element rotations, akin to a selective application of the local step, specifically on the smaller collision-prone region without explicitly paying the cost associated with the rest of the simulation mesh. We demonstrate efficient and robust interactive simulation in detailed models from animation and medical applications.

Published
2020

4. MosaicBase: A Knowledgebase of Postzygotic Mosaic Variants in Noncancer Disease-related and Healthy Human Individuals

Author

Yang, Xiaoxu, Yang, Changhong, Zheng, Xianing, Xiong, Luoxing, Tao, Yutian, Wang, Meng, Ye, Adam Yongxin, Wu, Qixi, Dou, Yanmei, Luo, Junyu, Wei, Liping, and Huang, August Yue

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Rare Diseases, Aetiology, 2.1 Biological and endogenous factors, Databases, Genetic, Disease, Genome, Human, Health, Humans, Knowledge Bases, Mosaicism, Mutation, Phenotype, Software, User-Computer Interface, Zygote, Postzygotic, Noncancer, MosaicBase, Mathematical Sciences, Information and Computing Sciences, Bioinformatics, Biological sciences, Information and computing sciences, Mathematical sciences
Abstract

Mosaic variants resulting from postzygotic mutations are prevalent in the human genome and play important roles in human diseases. However, except for cancer-related variants, there is no collection of postzygotic mosaic variants in noncancer disease-related and healthy individuals. Here, we present MosaicBase, a comprehensive database that includes 6698 mosaic variants related to 266 noncancer diseases and 27,991 mosaic variants identified in 422 healthy individuals. Genomic and phenotypic information of each variant was manually extracted and curated from 383 publications. MosaicBase supports the query of variants with Online Mendelian Inheritance in Man (OMIM) entries, genomic coordinates, gene symbols, or Entrez IDs. We also provide an integrated genome browser for users to easily access mosaic variants and their related annotations for any genomic region. By analyzing the variants collected in MosaicBase, we find that mosaic variants that directly contribute to disease phenotype show features distinct from those of variants in individuals with mild or no phenotypes, in terms of their genomic distribution, mutation signatures, and fraction of mutant cells. MosaicBase will not only assist clinicians in genetic counseling and diagnosis but also provide a useful resource to understand the genomic baseline of postzygotic mutations in the general human population. MosaicBase is publicly available at http://mosaicbase.com/ or http://49.4.21.8:8000.

Published
2020

7. Genome-wide identification and analysis of anthocyanin synthesis-related R2R3-MYB genes in Fragaria pentaphylla.

Author

Xie, Liangmu, Wang, Yinuo, Tao, Yutian, Chen, Luxi, Lin, Hanyang, Qi, Zhechen, and Li, Junmin

Subjects
TRANSCRIPTION factors, CHROMOSOME duplication, GENE families, ANTHOCYANINS, BIOSYNTHESIS
Abstract

Background: MYB transcription factors regulate anthocyanin biosynthesis across numerous plant species. However, comprehensive genome-wide investigations regarding the R2R3-MYB gene family and its involvement in regulating anthocyanin biosynthesis in the red and white fruit color morphs of Fragaria pentaphylla remain scarce. Results: A total of 101 FpR2R3-MYB genes were identified from the F. pentaphylla genome and were divided into 34 subgroups based on phylogenetic analysis. Gene structure (exon/intron) and protein motifs were particularly conserved among the FpR2R3-MYB genes, especially members within the same subgroup. The FpR2R3-MYB genes were distributed over seven F. pentaphylla chromosomes. Analysis of gene duplication events revealed five pairs of tandem duplication genes and 16 pairs of segmental duplication genes, suggesting that segmental duplications are the major pattern for expansion of the FpR2R3-MYB gene family expansion in F. pentaphylla. Cis-regulatory elements of the FpR2R3-MYB promoters were involved in cellular development, phytohormones, environmental stress and photoresponse. Based on the analysis of the FpR2R3-MYB gene family and transcriptome sequencing (RNA-seq) data, FpMYB9 was identified as a key transcription factor involved in the regulation of anthocyanin synthesis in F. pentaphylla fruits. The expression of FpMYB9 increases significantly during the ripening stage of red fruits, as confirmed by reverse transcription quantitative real-time PCR. In addition, subcellular localization experiments further confirmed the nuclear presence of FpMYB9, supporting its role as a transcription factor involved in anthocyanin biosynthesis. Conclusion: Our results showed that the FpR2R3-MYB genes are highly conserved and play important roles in the anthocyanin biosynthesis in F. pentaphylla fruits. Our results also provide a compelling basis for further understanding of the regulatory mechanism underlying the role of FpMYB9 in anthocyanin formation in F. pentaphylla fruits. [ABSTRACT FROM AUTHOR]

Published
2024
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