拓扑物理学Topological Physics
A complete catalogue of high-quality topological materials
对高质量拓扑材料的完整分类
▲ 作者:M. G. Vergniory, L. Elcoro, Claudia Felser, Nicolas Regnault, et al
▲ 链接:
https://www.nature.com/articles/s41586-019-0954-4
▲ 摘要:
利用最近发展起来的一种叫做拓扑量子化学的形式体系,我们在无机晶体结构数据库中对“高质量”材料(其原子位置和结构已得到非常精确的测量)进行了高通量搜索,以识别新的拓扑相。
我们开发了代码来计算26938种化学计量材料的所有对称性的全部特征,并找到了3307种拓扑绝缘体、4078种拓扑半金属,但未发现脆弱相。对于这7385种材料,我们提供了电子带结构,包括一些电子性质(带隙和电子数)、对称性指标和其他拓扑信息。我们的结果表明,自然界中超过27%的物质具有拓扑性质。
▲ Abstract
Using a recently developed formalism called topological quantum chemistry, we perform a high-throughput search of ‘high-quality’ materials (for which the atomic positions and structure have been measured very accurately) in the Inorganic Crystal Structure Database in order to identify new topological phases. We develop codes to compute all characters of all symmetries of 26,938 stoichiometric materials, and find 3,307 topological insulators, 4,078 topological semimetals and no fragile phases. For these 7,385 materials we provide the electronic band structure, including some electronic properties (bandgap and number of electrons), symmetry indicators, and other topological information. Our results show that more than 27 per cent of all materials in nature are topological.
Comprehensive search for topological materials using symmetry indicators
利用对称性指标对拓扑材料进行全面搜索
▲ 作者:Feng Tang, Hoi Chun Po, Ashvin Vishwanath & Xiangang Wan
▲ 链接:
https://www.nature.com/articles/s41586-019-0937-5
▲ 摘要:
虽然理论上提出的一些拓扑材料已得到实验证实,但由于缺乏能使微小费米表面态的干扰最小化的拓扑材料,对拓扑性质的广泛实验探索以及在实际器件中的应用受到了限制。在这里,我们将对称性指标的方法应用于全部230个可能的空间基团中所有合适的非磁性化合物。
数据库搜索揭示了数千种候选拓扑材料,其中我们重点介绍了241种拓扑绝缘体和142种拓扑结晶绝缘体。这些绝缘体要么具有明显的全带隙,要么具有相当大的直接带隙,并带有微小的费米口袋。此外,我们列出了在费米能级附近拥有带交叉点的692种拓扑半金属材料。
▲ Abstract
Although several theoretically proposed topological materials have been experimentally confirmed, extensive experimental exploration of topological properties, as well as applications in realistic devices, has been restricted by the lack of topological materials in which interference from trivial Fermi surface states is minimized. Here we apply our method of symmetry indicators to all suitable nonmagnetic compounds in all 230 possible space groups. A database search reveals thousands of candidate topological materials, of which we highlight 241 topological insulators and 142 topological crystalline insulators that have either noticeable full bandgaps or a considerable direct gap together with small trivial Fermi pockets. Furthermore, we list 692 topological semimetals that have band crossing points located near the Fermi level.
Catalogue of topological electronic materials
对拓扑电子材料的分类
▲ 作者:Tiantian Zhang, Yi Jiang, Zhida Song, He Huang, Yuqing He, Zhong Fang, Hongming Weng & Chen Fang
▲ 链接:
https://www.nature.com/articles/s41586-019-0944-6
▲ 摘要:
硒化铋、砷化钽、铋钠等拓扑电子材料大多表现出非常规的线性响应,并且在边界处表现出异常的无间隙态。它们具有基础和应用价值,在高性能电子和量子计算领域具有应用潜力。
但迄今为止,由于计算拓扑不变性质(或拓扑节点)存在困难,对它们的搜寻受到阻碍,因为这既需要材料方面的经验,也需要使用先进理论工具的专业知识。在此,我们介绍了一种有效、高效和全自动的算法,用于诊断大量非磁性材料中的非平凡能带拓扑。我们的算法基于最近开发的已占用能带的对称表示和拓扑不变量之间的穷举映射。
我们浏览了晶体数据库中的39519种可用材料,发现其中多达8056种在拓扑结构上是非平凡的。所有结果都可以在具有交互式用户界面的数据库中获得和搜索。
▲ Abstract
Topological electronic materials such as bismuth selenide, tantalum arsenide and sodium bismuthide show unconventional linear response in the bulk, as well as anomalous gapless states at their boundaries. They are of both fundamental and applied interest, with the potential for use in high-performance electronics and quantum computing. But their detection has so far been hindered by the difficulty of calculating topological invariant properties (or topological nodes), which requires both experience with materials and expertise with advanced theoretical tools. Here we introduce an effective, efficient and fully automated algorithm that diagnoses the nontrivial band topology in a large fraction of nonmagnetic materials. Our algorithm is based on recently developed exhaustive mappings between the symmetry representations of occupied bands and topological invariants. We sweep through a total of 39,519 materials available in a crystal database, and find that as many as 8,056 of them are topologically nontrivial. All results are available and searchable in a database with an interactive user interface.
生物学Biology
The single-cell transcriptional landscape of mammalian organogenesis
哺乳动物器官形成的单细胞转录图谱
▲ 作者:Junyue Cao, Malte Spielmann, Xiaojie Qiu, Xingfan Huang
▲ 链接:
https://www.nature.com/articles/s41586-019-0969-x
▲ 摘要:
哺乳动物的器官形成是一个不寻常的过程。在很短的时间内,三个胚层的细胞转化成一个包括了大部分主要的内部和外部器官的胚胎。在这里,我们在单细胞分辨率的层面上研究了小鼠器官形成的转录动力学。
利用单细胞组合索引,我们在一项实验中分析了来自61个胚胎的约200万个细胞的转录组,这些胚胎在妊娠9.5~13.5天发育。由此产生的“小鼠器官形成细胞图谱”(MOCA)提供了这一关键时期发育过程的全局视图。我们使用Monocle 3识别了数百种细胞类型和56条轨迹,其中许多轨迹仅因为细胞覆盖的深度而被检测到,并共同定义了数千个相应的标记基因。
▲ Abstract
Mammalian organogenesis is a remarkable process. Within a short timeframe, the cells of the three germ layers transform into an embryo that includes most of the major internal and external organs. Here we investigate the transcriptional dynamics of mouse organogenesis at single-cell resolution. Using single-cell combinatorial indexing, we profiled the transcriptomes of around 2 million cells derived from 61 embryos staged between 9.5 and 13.5 days of gestation, in a single experiment. The resulting ‘mouse organogenesis cell atlas’ (MOCA) provides a global view of developmental processes during this critical window. We use Monocle 3 to identify hundreds of cell types and 56 trajectories, many of which are detected only because of the depth of cellular coverage, and collectively define thousands of corresponding marker genes.
A single-cell molecular map of mouse gastrulation and early organogenesis
小鼠原肠胚和早期器官形成的单细胞分子地图
▲ 作者:Blanca Pijuan-Sala, Jonathan A. Griffiths, Carolina Guibentif
▲ 链接:
https://www.nature.com/articles/s41586-019-0933-9
▲ 摘要:
在整个动物王国中,原肠胚形成代表了一次关键的发育事件。其间,胚胎多能细胞分化成能产生成年生物体的谱系特异性前体。
在此,我们报告了来自小鼠胚胎的116312个单细胞的转录图谱。这些细胞在受精后6.5~8.5天的9个连续时间点收集。我们构建了从多能性到所有主要胚胎谱系的细胞分化分子地图,并且探寻了涉及内脏和原始条纹衍生内胚层相结合的复杂事件。
此外,我们利用单细胞分析表明,Tal1−−/嵌合体胚胎在早期中胚层多样化中表现出缺陷,并且因此展示了如何结合时间和转录信息阐明基因功能。
▲ Abstract
Across the animal kingdom, gastrulation represents a key developmental event during which embryonic pluripotent cells diversify into lineage-specific precursors that will generate the adult organism. Here we report the transcriptional profiles of 116,312 single cells from mouse embryos collected at nine sequential time points ranging from 6.5 to 8.5 days post-fertilization. We construct a molecular map of cellular differentiation from pluripotency towards all major embryonic lineages, and explore the complex events involved in the convergence of visceral and primitive streak-derived endoderm. Furthermore, we use single-cell profiling to show that Tal1−/− chimeric embryos display defects in early mesoderm diversification, and we thus demonstrate how combining temporal and transcriptional information can illuminate gene function.
健康Health
Altered human oligodendrocyte heterogeneity in multiple sclerosis
多发性硬化症中被改变的人类少突胶质异质性
▲ 作者:Sarah Jäkel, Eneritz Agirre, Ana Mendanha Falcão, David van Bruggen, et al
▲ 链接:
https://www.nature.com/articles/s41586-019-0903-2
▲ 摘要:
在这里,我们对多发性硬化症(MS)患者和未受影响对照组的死后人脑白质区域进行了单核RNA测序。我们确定了控制人类白质的少突胶质亚群,其中一些与小鼠相似,并为这些细胞状态定义了新的标记。
值得注意的是,一些亚群在MS组织中代表性不足,而其他亚群更为普遍。这些成熟少突胶质细胞亚群内的差异可能表明MS病变中少突胶质细胞的功能状态不同。
我们在正常白质中也发现了类似的变化,表明多发性硬化症是一种比局部脱髓鞘更广泛的疾病。我们发现MS中少突胶质细胞异质性的改变,可能对了解该疾病恶化和开发治疗方法有重要意义。
▲ Abstract
Here we performed single-nucleus RNA sequencing from white matter areas of post-mortem human brain from patients with multiple sclerosis(MS) and from unaffected controls. We identified subclusters of oligodendroglia in control human white matter, some with similarities to mouse, and defined new markers for these cell states. Notably, some subclusters were underrepresented in MS tissue, whereas others were more prevalent. These differences in mature oligodendrocyte subclusters may indicate different functional states of oligodendrocytes in MS lesions. We found similar changes in normal-appearing white matter, showing that MS is a more diffuse disease than its focal demyelination suggests. Our findings of an altered oligodendroglial heterogeneity in MS may be important for understanding disease progression and developing therapeutic approaches.
Singlet molecular oxygen regulates vascular tone and blood pressure in inflammation
单线态分子氧调控炎症中的血管张力和血压
▲ 作者:Christopher P. Stanley, Ghassan J. Maghzal, Anita Ayer, et al
▲ 链接:
https://www.nature.com/articles/s41586-019-0947-3
▲ 摘要:
单线态分子氧(1O2)在光合植物、细菌和真菌中已经有了明确的作用,但在哺乳动物中没有。我们发现,动脉吲哚胺2,3—加双氧酶1通过1O2的形成调节血压。
我们观察到,在过氧化氢存在的情形下,这种酶产生1O2,而这与l -色氨酸通过之前未被识别的氧化激活加双氧酶活性,立体选择性氧化为三环过氧化氢有关。色氨酸来源的过氧化氢在体内作为信号分子,诱导动脉松弛和降低血压;这依赖于蛋白激酶G1αCys42。
我们的发现证明了1O2在哺乳动物中的病理生理作用,即通过形成一种氨基酸来源的过氧化氢,在炎症条件下调节血管张力和血压。
▲ Abstract
Singlet molecular oxygen (1O2) has well-established roles in photosynthetic plants, bacteria and fungi, but not in mammals. Here we show that arterial indoleamine 2,3-dioxygenase 1 regulates blood pressure via formation of 1O2. We observed that in the presence of hydrogen peroxide, the enzyme generates 1O2 and that this is associated with the stereoselective oxidation of L-tryptophan to a tricyclic hydroperoxide via a previously unrecognized oxidative activation of the dioxygenase activity. The tryptophan-derived hydroperoxide acts in vivo as a signalling molecule, inducing arterial relaxation and decreasing blood pressure; this activity is dependent on Cys42 of protein kinase G1α. Our findings demonstrate a pathophysiological role for 1O2 in mammals through formation of an amino acid-derived hydroperoxide that regulates vascular tone and blood pressure under inflammatory conditions.
拓扑物理学Topological Physics
A complete catalogue of high-quality topological materials
对高质量拓扑材料的完整分类
▲ 作者:M. G. Vergniory, L. Elcoro, Claudia Felser, Nicolas Regnault, et al
▲ 链接:
https://www.nature.com/articles/s41586-019-0954-4
▲ 摘要:
利用最近发展起来的一种叫做拓扑量子化学的形式体系,我们在无机晶体结构数据库中对“高质量”材料(其原子位置和结构已得到非常精确的测量)进行了高通量搜索,以识别新的拓扑相。
我们开发了代码来计算26938种化学计量材料的所有对称性的全部特征,并找到了3307种拓扑绝缘体、4078种拓扑半金属,但未发现脆弱相。对于这7385种材料,我们提供了电子带结构,包括一些电子性质(带隙和电子数)、对称性指标和其他拓扑信息。我们的结果表明,自然界中超过27%的物质具有拓扑性质。
▲ Abstract
Using a recently developed formalism called topological quantum chemistry, we perform a high-throughput search of ‘high-quality’ materials (for which the atomic positions and structure have been measured very accurately) in the Inorganic Crystal Structure Database in order to identify new topological phases. We develop codes to compute all characters of all symmetries of 26,938 stoichiometric materials, and find 3,307 topological insulators, 4,078 topological semimetals and no fragile phases. For these 7,385 materials we provide the electronic band structure, including some electronic properties (bandgap and number of electrons), symmetry indicators, and other topological information. Our results show that more than 27 per cent of all materials in nature are topological.
Comprehensive search for topological materials using symmetry indicators
利用对称性指标对拓扑材料进行全面搜索
▲ 作者:Feng Tang, Hoi Chun Po, Ashvin Vishwanath & Xiangang Wan
▲ 链接:
https://www.nature.com/articles/s41586-019-0937-5
▲ 摘要:
虽然理论上提出的一些拓扑材料已得到实验证实,但由于缺乏能使微小费米表面态的干扰最小化的拓扑材料,对拓扑性质的广泛实验探索以及在实际器件中的应用受到了限制。在这里,我们将对称性指标的方法应用于全部230个可能的空间基团中所有合适的非磁性化合物。
数据库搜索揭示了数千种候选拓扑材料,其中我们重点介绍了241种拓扑绝缘体和142种拓扑结晶绝缘体。这些绝缘体要么具有明显的全带隙,要么具有相当大的直接带隙,并带有微小的费米口袋。此外,我们列出了在费米能级附近拥有带交叉点的692种拓扑半金属材料。
▲ Abstract
Although several theoretically proposed topological materials have been experimentally confirmed, extensive experimental exploration of topological properties, as well as applications in realistic devices, has been restricted by the lack of topological materials in which interference from trivial Fermi surface states is minimized. Here we apply our method of symmetry indicators to all suitable nonmagnetic compounds in all 230 possible space groups. A database search reveals thousands of candidate topological materials, of which we highlight 241 topological insulators and 142 topological crystalline insulators that have either noticeable full bandgaps or a considerable direct gap together with small trivial Fermi pockets. Furthermore, we list 692 topological semimetals that have band crossing points located near the Fermi level.
Catalogue of topological electronic materials
对拓扑电子材料的分类
▲ 作者:Tiantian Zhang, Yi Jiang, Zhida Song, He Huang, Yuqing He, Zhong Fang, Hongming Weng & Chen Fang
▲ 链接:
https://www.nature.com/articles/s41586-019-0944-6
▲ 摘要:
硒化铋、砷化钽、铋钠等拓扑电子材料大多表现出非常规的线性响应,并且在边界处表现出异常的无间隙态。它们具有基础和应用价值,在高性能电子和量子计算领域具有应用潜力。
但迄今为止,由于计算拓扑不变性质(或拓扑节点)存在困难,对它们的搜寻受到阻碍,因为这既需要材料方面的经验,也需要使用先进理论工具的专业知识。在此,我们介绍了一种有效、高效和全自动的算法,用于诊断大量非磁性材料中的非平凡能带拓扑。我们的算法基于最近开发的已占用能带的对称表示和拓扑不变量之间的穷举映射。
我们浏览了晶体数据库中的39519种可用材料,发现其中多达8056种在拓扑结构上是非平凡的。所有结果都可以在具有交互式用户界面的数据库中获得和搜索。
▲ Abstract
Topological electronic materials such as bismuth selenide, tantalum arsenide and sodium bismuthide show unconventional linear response in the bulk, as well as anomalous gapless states at their boundaries. They are of both fundamental and applied interest, with the potential for use in high-performance electronics and quantum computing. But their detection has so far been hindered by the difficulty of calculating topological invariant properties (or topological nodes), which requires both experience with materials and expertise with advanced theoretical tools. Here we introduce an effective, efficient and fully automated algorithm that diagnoses the nontrivial band topology in a large fraction of nonmagnetic materials. Our algorithm is based on recently developed exhaustive mappings between the symmetry representations of occupied bands and topological invariants. We sweep through a total of 39,519 materials available in a crystal database, and find that as many as 8,056 of them are topologically nontrivial. All results are available and searchable in a database with an interactive user interface.
生物学Biology
The single-cell transcriptional landscape of mammalian organogenesis
哺乳动物器官形成的单细胞转录图谱
▲ 作者:Junyue Cao, Malte Spielmann, Xiaojie Qiu, Xingfan Huang
▲ 链接:
https://www.nature.com/articles/s41586-019-0969-x
▲ 摘要:
哺乳动物的器官形成是一个不寻常的过程。在很短的时间内,三个胚层的细胞转化成一个包括了大部分主要的内部和外部器官的胚胎。在这里,我们在单细胞分辨率的层面上研究了小鼠器官形成的转录动力学。
利用单细胞组合索引,我们在一项实验中分析了来自61个胚胎的约200万个细胞的转录组,这些胚胎在妊娠9.5~13.5天发育。由此产生的“小鼠器官形成细胞图谱”(MOCA)提供了这一关键时期发育过程的全局视图。我们使用Monocle 3识别了数百种细胞类型和56条轨迹,其中许多轨迹仅因为细胞覆盖的深度而被检测到,并共同定义了数千个相应的标记基因。
▲ Abstract
Mammalian organogenesis is a remarkable process. Within a short timeframe, the cells of the three germ layers transform into an embryo that includes most of the major internal and external organs. Here we investigate the transcriptional dynamics of mouse organogenesis at single-cell resolution. Using single-cell combinatorial indexing, we profiled the transcriptomes of around 2 million cells derived from 61 embryos staged between 9.5 and 13.5 days of gestation, in a single experiment. The resulting ‘mouse organogenesis cell atlas’ (MOCA) provides a global view of developmental processes during this critical window. We use Monocle 3 to identify hundreds of cell types and 56 trajectories, many of which are detected only because of the depth of cellular coverage, and collectively define thousands of corresponding marker genes.
A single-cell molecular map of mouse gastrulation and early organogenesis
小鼠原肠胚和早期器官形成的单细胞分子地图
▲ 作者:Blanca Pijuan-Sala, Jonathan A. Griffiths, Carolina Guibentif
▲ 链接:
https://www.nature.com/articles/s41586-019-0933-9
▲ 摘要:
在整个动物王国中,原肠胚形成代表了一次关键的发育事件。其间,胚胎多能细胞分化成能产生成年生物体的谱系特异性前体。
在此,我们报告了来自小鼠胚胎的116312个单细胞的转录图谱。这些细胞在受精后6.5~8.5天的9个连续时间点收集。我们构建了从多能性到所有主要胚胎谱系的细胞分化分子地图,并且探寻了涉及内脏和原始条纹衍生内胚层相结合的复杂事件。
此外,我们利用单细胞分析表明,Tal1−−/嵌合体胚胎在早期中胚层多样化中表现出缺陷,并且因此展示了如何结合时间和转录信息阐明基因功能。
▲ Abstract
Across the animal kingdom, gastrulation represents a key developmental event during which embryonic pluripotent cells diversify into lineage-specific precursors that will generate the adult organism. Here we report the transcriptional profiles of 116,312 single cells from mouse embryos collected at nine sequential time points ranging from 6.5 to 8.5 days post-fertilization. We construct a molecular map of cellular differentiation from pluripotency towards all major embryonic lineages, and explore the complex events involved in the convergence of visceral and primitive streak-derived endoderm. Furthermore, we use single-cell profiling to show that Tal1−/− chimeric embryos display defects in early mesoderm diversification, and we thus demonstrate how combining temporal and transcriptional information can illuminate gene function.
健康Health
Altered human oligodendrocyte heterogeneity in multiple sclerosis
多发性硬化症中被改变的人类少突胶质异质性
▲ 作者:Sarah Jäkel, Eneritz Agirre, Ana Mendanha Falcão, David van Bruggen, et al
▲ 链接:
https://www.nature.com/articles/s41586-019-0903-2
▲ 摘要:
在这里,我们对多发性硬化症(MS)患者和未受影响对照组的死后人脑白质区域进行了单核RNA测序。我们确定了控制人类白质的少突胶质亚群,其中一些与小鼠相似,并为这些细胞状态定义了新的标记。
值得注意的是,一些亚群在MS组织中代表性不足,而其他亚群更为普遍。这些成熟少突胶质细胞亚群内的差异可能表明MS病变中少突胶质细胞的功能状态不同。
我们在正常白质中也发现了类似的变化,表明多发性硬化症是一种比局部脱髓鞘更广泛的疾病。我们发现MS中少突胶质细胞异质性的改变,可能对了解该疾病恶化和开发治疗方法有重要意义。
▲ Abstract
Here we performed single-nucleus RNA sequencing from white matter areas of post-mortem human brain from patients with multiple sclerosis(MS) and from unaffected controls. We identified subclusters of oligodendroglia in control human white matter, some with similarities to mouse, and defined new markers for these cell states. Notably, some subclusters were underrepresented in MS tissue, whereas others were more prevalent. These differences in mature oligodendrocyte subclusters may indicate different functional states of oligodendrocytes in MS lesions. We found similar changes in normal-appearing white matter, showing that MS is a more diffuse disease than its focal demyelination suggests. Our findings of an altered oligodendroglial heterogeneity in MS may be important for understanding disease progression and developing therapeutic approaches.
Singlet molecular oxygen regulates vascular tone and blood pressure in inflammation
单线态分子氧调控炎症中的血管张力和血压
▲ 作者:Christopher P. Stanley, Ghassan J. Maghzal, Anita Ayer, et al
▲ 链接:
https://www.nature.com/articles/s41586-019-0947-3
▲ 摘要:
单线态分子氧(1O2)在光合植物、细菌和真菌中已经有了明确的作用,但在哺乳动物中没有。我们发现,动脉吲哚胺2,3—加双氧酶1通过1O2的形成调节血压。
我们观察到,在过氧化氢存在的情形下,这种酶产生1O2,而这与l -色氨酸通过之前未被识别的氧化激活加双氧酶活性,立体选择性氧化为三环过氧化氢有关。色氨酸来源的过氧化氢在体内作为信号分子,诱导动脉松弛和降低血压;这依赖于蛋白激酶G1αCys42。
我们的发现证明了1O2在哺乳动物中的病理生理作用,即通过形成一种氨基酸来源的过氧化氢,在炎症条件下调节血管张力和血压。
▲ Abstract
Singlet molecular oxygen (1O2) has well-established roles in photosynthetic plants, bacteria and fungi, but not in mammals. Here we show that arterial indoleamine 2,3-dioxygenase 1 regulates blood pressure via formation of 1O2. We observed that in the presence of hydrogen peroxide, the enzyme generates 1O2 and that this is associated with the stereoselective oxidation of L-tryptophan to a tricyclic hydroperoxide via a previously unrecognized oxidative activation of the dioxygenase activity. The tryptophan-derived hydroperoxide acts in vivo as a signalling molecule, inducing arterial relaxation and decreasing blood pressure; this activity is dependent on Cys42 of protein kinase G1α. Our findings demonstrate a pathophysiological role for 1O2 in mammals through formation of an amino acid-derived hydroperoxide that regulates vascular tone and blood pressure under inflammatory conditions.
(宗华)
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