抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

We study the time scales associated with diffusion processes that take place on multiplex networks, i.e., on a set of networks linked through interconnected layers. To this end, we propose the construction of a supra-Laplacian matrix, which consists of a dimensional lifting of the Laplacian matrix of each layer of the multiplex network. We use perturbative analysis to reveal analytically the structure of eigenvectors and eigenvalues of the complete network in terms of the spectral properties of the individual layers. The spectrum of the supra-Laplacian allows us to understand the physics of diffusionlike processes on top of multiplex networks.

/pdf/diffusion-dynamics-on-multiplex-networks-2ur1ufbtti.pdf

Diffusion dynamics on multiplex networks.

ALGEBRAIC VARIETIES By ALEXANDER GROTHENDIEGK It is less than four years since eohomologieal methods (i.e. methods of Homologieal Algebra) were introduced into Algebraic Geometry in Serre's fundamental paper, and it seems already certain that they are to overflow this part of mathematics in the coming years, from the foundations up to the most advanced parts. All we can do here is to sketch briefly some of the ideas and results. None of these have been published in their final form, but most of them originated in or were suggested by Serre's paper. Let us first give an outline of the main topics of eohomologieal investigation in Algebraic Geometry, as they appear at present. The need of a theory of cohomology for 'abstract' algebraic varieties was first emphasized by Weil, in order to be able to give a precise meaning to his celebrated conjectures in Diophantine Geometry. Therefore the initial aim was to find the 'Weil cohomology' of an algebraic variety, which should have as coefficients something 'at least as good as a field of characteristic 0, and have such formal properties (e.g. duality, Runneth formula) as to yield the analogue of Lefschetz's 'fixed-point formula '. Serre's general idea has been that the usual ' Zariski topology ' of a variety (in which the closed sets are the algebraic subsets) is a suitable one for applying methods of Algebraic Topology. His first approach was hoped to yield at least the right Betti numbers of a variety, it being evident from the start that it could not be considered as the Weil cohomology itself, as the coefficient field for cohomology was the ground field of the variety, and therefore not in general of characteristic 0. In fact, even the hope of getting the 'true ' Betti numbers has failed, and so have other attempts of Serre's to get Weil's cohomology by taking the cohomology of the variety with values, not in the sheaf of local rings themselves, but in the sheaves of Witt-vectors constructed on the latter. He gets in this way modules over the ring W{h) of infinite Witt vectors on the ground field h, and W{h) is a ring of characteristic 0 even if h is of characteristic p =t= 0. Unfortunately, modules thus obtained over W{h) may be infinitely generated, even when the variety V is an abelian variety. Although interesting relations must certainly exist between these cohomology groups and the 'true ones', it seems certain 104 ALEXANDER GROTHENDIECK now that the Weil cohomology has to be defined by a completely different approach. Such an approach was recently suggested to me by the connections between sheaf-theoretic cohomology and cohomology of Galois groups on the one hand, and the classification of unramified coverings of a variety on the other (as explained quite unsystematically in Serre's tentative Mexico paper), and by Serre's idea that a 'reasonable' algebraic principal fiber space with structure group G, defined on a variety V, if it is not locally trivial, should become locally trivial on some covering of V unramified over a given point of V. This has been the startingpoint of a definition of the Weil cohomology (involving both 'spatial' and Galois cohomology), which seems to be the right one, and which gives clear suggestions how Weil's conjectures may be attacked by the machinery of Homological Algebra. As I have not begun these investigations seriously as yet, and as moreover this theory has a quite distinct flavor from the one of the theory of algebraic coherent sheaves which we shall now be concerned with, we shall not dwell any longer on Weil's cohomology. Let us merely remark that the definition alluded to has already been the starting-point of a theory of eohomologieal dimension of fields, developed recently by Tate. The second main topic for eohomologieal methods is the cohomology theory of algebraic coherent sheaves, as initiated by Serre. Although inadequate for Weil's purposes, it is at present yielding a wealth of new methods and new notions, and gives the key even for results which were not commonly thought to be concerned with sheaves, still less with cohomology, such as Zariski's theorem on 'holomorphic functions' and his 'main theorem'—which can be stated now in a more satisfactory way, as we shall see, and proved by the same uniform elementary methods. The main parts of the theory, at present, can be fisted as follows: (a) General finiteness and asymptotic behaviour theorems. (6) Duality theorems, including (respectively identical with) a eohomologieal theory of residues. (c) Riemann-Roch theorem, including the theory of Chern classes for algebraic coherent sheaves. (cu) Some special results, concerning mainly abelian varieties. The third main topic consists in the application of the eohomologieal methods to local algebra. Initiated by Koszul and Cartan-Eilenberg in connection with Hubert's 'theorem of syzygies', the systematic use of COHOMOLOGY THEORY 105 these methods is mainly due again to Serre. The results are the characterization of regular local rings as those whose global eohomologieal dimension is finite, the clarification of Cohen-Macaulay's equidimensionality theorem by means of the notion of eohomologieal codimension\ and especially the possibility of giving (for the first time as it seems) a theory of intersections, really satisfactory by its algebraic simplicity and its generality. Serre's result just quoted, that regular local rings are the only ones of finite global eohomologieal dimension, accounts for the fact that only for such local rings does a satisfactory theory of intersections exist. I cannot give any details here on these subjects, nor on various results I have obtained by means of a local duality theory, which seems to be the tool which is to replace differential forms in the case of unequal characteristics, and gives, in the general context of commutative algebra, a clarification of the notion of residue, which as yet was not at all well understood. The motivation of this latter work has been the attempt to get a global theory of duality in cohomology for algebraic varieties admitting arbitrary singularities, in order to be able to develop intersection formulae for cycles with arbitrary singularities, in a nonsingular algebraic variety, formulas which contain also a 'Lefschetz formula mod.p'. In fact, once a proper local formalism is obtained, the global statements become almost trivial. As a general fact, it appears that, to a great extent, the 'local' results already contain a global one; more precisely, global results on varieties of dimension n can frequently be deduced from corresponding local ones for rings of Krull dimension n + l. We will therefore turn now to giving some main ideas in the second topic, that is, the cohomology theory of algebraic coherent sheaves. First, I would like, however, to emphasize one point common to all of the topics considered (except perhaps for {d)), and in fact to all of the standard techniques in Algebraic Geometry. Namely, that the natural range of the notions dealt with, and the methods used, are not really algebraic varieties. Thus, we know that an affine algebraic variety with ground field h is determined by its co-ordinate ring, which is an arbitrary finitely generated ^-algebra without nilpotent elements; therefore, any statement concerning affine algebraic varieties can be viewed also as a statement concerning rings A of the previous type. Now it appears that most of such statements make sense, and are true, if we assume only J. to be a commutative ring with unit, provided we sometimes submit it to some mild restriction, as being noetherian, for instance. In 106 ALEXANDER GROTHENDIECK the same way, most of the results proved for the local rings of algebraic geometry, make sense and are true for arbitrary noetherian local rings. Besides, frequently when it seemed at first sight that the statement only made sense when a ground field k was involved, as in questions in which differential forms are considered, further consideration of the matter showed that this impression was erroneous, and that a better understanding is obtained by replacing k by a ring B such that A is a finitely generated J5-algebra. Geometrically, this means that instead of a single affine algebraic variety V (as defined by A) we are considering a 'regular map' or 'morphism' of V into another affine variety W, and properties of the variety V then are generalized to properties of a morphism V -> W (the 'absolute' notion for V being obtained from the more general 'relative' notion by taking W reduced to a point). On the other hand, one should not prevent the rings having nilpotent elements, and by no means exclude them without serious reasons. Now just as arbitrary commutative rings can be thought of as a proper generalization of affine algebraic varieties, one can find a corresponding suitable generalization of arbitrary algebraic varieties (defined over an arbitrary field). This was done by Nagata in a particular case, yet following the definition of schemata given by Chevalley he had to stick to the irreducible case, and with no nilpotent elements involved. The principle of the right definition is again to be found in Serre's fundamental paper, and is as follows. If A is any commutative ring, then the set Spec {A) of all prime ideals of A can be turned into a topological space in a classical way, the closed subsets consisting of those prime ideals which contain a given subset of A. On the other hand, there is a sheaf of rings defined in a natural way on Spec {A), the fiber of this sheaf at the point p being the local ring Ap. More generally, every module M over A defines a sheaf of modules on Spec {A), the fiber of which at the point p is the localized moduleMp over Ap. Now we call pre-schema a topological space X with a sheaf of rings Gx on X, called its structure sheaf, such that every point of X has an open neighborhood isomorphic to some Spec {A). If X and Y are two pre-schemas, a morphism f fro

Proceedings of the International Congress of Mathematicians

What is discrete math? • The real numbers are continuous in the senses that: * between any two real numbers there is a real number • The integers do not share this property. In this sense the integers are lumpy, or " discrete " So discrete math is the study of mathematical objects that are discrete. " It's all the math that counts " Some discrete mathematical concepts: • Integers: Between two integers there is not another integer. • Propositions: Either true or false, there are no 1/2 truths (in math) • Sets: An item is either in a set or not in a set, never partly in and partly out. • Relations: A pair of items are related or not. • Networks (graphs): Between two terminals of a network connection there are no terminals. Propositional Logic Propositions are statements that are either true or false. Principles: Substituting an equivalent statement. Replacing a logic variable in a tautology. Defn algebraic proof

Discrete math = 離散数学

「Science」與「Nature」之科學計量分析

We study spectra of directed networks with inhibitory and excitatory couplings. We investigate in particular eigenvector localization properties of various model networks for different values of correlation among their entries. Spectra of random networks with completely uncorrelated entries show a circular distribution with delocalized eigenvectors, whereas networks with correlated entries have localized eigenvectors. In order to understand the origin of localization we track the spectra as a function of connection probability and directionality. As connections are made directed, eigenstates start occurring in complex-conjugate pairs and the eigenvalue distribution combined with the localization measure shows a rich pattern. Moreover, for a very well distinguished community structure, the whole spectrum is localized except few eigenstates at the boundary of the circular distribution. As the network deviates from the community structure there is a sudden change in the localization property for a very small value of deformation from the perfect community structure. We search for this effect for the whole range of correlation strengths and for different community configurations. Furthermore, we investigate spectral properties of a metabolic network of zebrafish and compare them with those of the model networks.

Spectral properties of directed random networks with modular structure.

We study the structural characteristics of complex networks using the representative eigenvectors of the adjacent matrix. The probability distribution function of the components of the representative eigenvectors are proposed to describe the localization on networks where the Euclidean distance is invalid. Several quantities are used to describe the localization properties of the representative states, such as the participation ratio, the structural entropy, and the probability distribution function of the nearest neighbor level spacings for spectra of complex networks. Whole-cell networks in the real world and the Watts-Strogatz small-world and Barabasi-Albert scale-free networks are considered. The networks have nontrivial localization properties due to the nontrivial topological structures. It is found that the ascending-order-ranked series of the occurrence probabilities at the nodes behave generally multifractally. This characteristic can be used as a structural measure of complex networks.

Localizations on complex networks.

In a complex network, different groups of nodes may have existed for different amounts of time. To detect the evolutionary history of a network is of great importance. We present a spectral-analysis based method to address this fundamental question in network science. In particular, we find that there are complex networks in the real-world for which there is a positive correlation between the eigenvalue magnitude and node age. In situations where the network topology is unknown but short time series measured from nodes are available, we suggest to uncover the network topology at the present (or any given time of interest) by using compressive sensing and then perform the spectral analysis. Knowledge of ages of various groups of nodes can provide significant insights into the evolutionary process underpinning the network. It should be noted, however, that at the present the applicability of our method is limited to the networks for which information about the node age has been encoded gradually in the eigen-properties through evolution.

/pdf/uncovering-evolutionary-ages-of-nodes-in-complex-networks-550miovmfa.pdf

Uncovering evolutionary ages of nodes in complex networks

The scaling properties of spectra of real world complex networks are studied by using the wavelet transform. It is found that the spectra of networks are multifractal. According to the values of the long-range correlation exponent, the Hust exponent H, the networks can be classified into three types, namely, H>0.5, H=0.5, and H<0.5. All real world networks considered belong to the class of H≥0.5, which may be explained by the hierarchical properties.

Self-affine fractals embedded in spectra of complex networks.

/pdf/magic-angle-in-thermal-conductivity-of-twisted-bilayer-2otxy5bh.pdf

Guimei Zhu

Papers

Spectral properties of directed random networks with modular structure.

Localizations on complex networks.

Uncovering evolutionary ages of nodes in complex networks

Self-affine fractals embedded in spectra of complex networks.

Magic angle in thermal conductivity of twisted bilayer graphene