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The dynamics of (bio) chemical reaction networks have been studied by different methods. Among these methods, the chemical reaction network theory has been proven to successfully predicate important qualitative properties, such as the existence of the steady state and the asymptotic behavior of the steady state. However, a constructive approach to the steady state locus has not been presented. In this thesis, with the help of toric geometry, we propose a generic strategy towards this question. This theory is applied to (bio)nano particle configurations. We also investigate Hopf bifurcation surfaces of various dynamical systems.

This thesis constructs tilting bundles obtained from full strong exceptional collections of line bundles on all smooth toric Fano fourfolds. The tilting bundles lead to a large class of explicit Calabi-Yau-5 algebras, obtained as the corresponding rolled-up helix algebra. We provide two different methods to show that a collection of line bundles is full, whilst the strong exceptional condition is checked using the package QuiversToricVarieties for the computer algebra system Macaulay2, written by the author. A database of the full strong exceptional collections can also be found in this package.

What is the cohomology of a graph? Cohomology is a topological invariant and encodes such information as genus and euler characteristic. Graphs are combinatorial objects which may not a priori admit a natural and isomorphism invariant cohomology ring. In this project, given any finite graph G, we constructively define a cohomology ring H*(G) of G. Our method uses graph associahedra and toric varieties. Given a graph, there is a canonically associated convex polytope, called the graph associahedron, constructed from G. In turn, a convex polytope uniquely determines a toric variety. We synthesize these results, and describe the cohomology of the associated variety directly in terms of the graph G itself.

Le premier chapitre montre par des méthodes toriques ($G-$graphes) que pour tout entier positif $n$, le quotient de l'espace affine à $n$ dimensions par le groupe cyclique $G_n$ d'ordre $2^n-1$ admet le $G_n$-schema de Hilbert comme résolution lisse crepante. Le deuxième chapitre contient des résultats sur les champs algébriques (construction du champ algébrique lisse associé à une log-paire). Le troisième chapitre montre l'équivalence entre la catégorie dérivée bornée des faisceaux cohérents $G_n-$équivariants sur l'espace affine et celle des faisceaux cohérents sur la résolution $G_n-$Hilb. Chapitre 4 donne une réalisation géométrique de la conjecture de Broué via la correspondance de McKay. L'annexe contient des résultats sur les groupes trihédraux, y compris un programme magma.

We study projective completions of affine algebraic varieties (defined over an algebraically closed field K) which are given by filtrations, or equivalently, integer valued `degree like functions' on their rings of regular functions. For a polynomial map P := (P_1, ..., P_n): X -> K^n of affine varieties with generically finite fibers, we prove that there are completions of the source such that the intersection of completions of the hypersurfaces {P_j = a_j} for generic (a_1, ..., a_n) in K^n coincides with the respective fiber (in short, the completions `do not add points at infinity' for P). Moreover, we show that there are `finite type' completions with the latter property, i.e. determined by the maximum of a finite number of `semidegrees', by which we mean degree like functions that send products into sums. We characterize the latter type completions as the ones for which ideal I of the `hypersurface at infinity' is radical. Moreover, we establish a one-to-one correspondence between the collection of minimal associated primes of I and the unique minimal collection of semidegrees needed to define the corresponding degree like function. We also prove an `affine Bezout type' theorem for polynomial maps P with finite fibers that admit semidegrees corresponding to completions that do not add points at infinity for P. For a wide class of semidegrees of a `constructive nature' our Bezout-type bound is explicit and sharp.

We study projective completions of affine algebraic varieties (defined over an algebraically closed field K) which are given by filtrations, or equivalently, integer valued `degree like functions' on their rings of regular functions. For a polynomial map P := (P_1, ..., P_n): X -> K^n of affine varieties with generically finite fibers, we prove that there are completions of the source such that the intersection of completions of the hypersurfaces {P_j = a_j} for generic (a_1, ..., a_n) in K^n coincides with the respective fiber (in short, the completions `do not add points at infinity' for P). Moreover, we show that there are `finite type' completions with the latter property, i.e. determined by the maximum of a finite number of `semidegrees', by which we mean degree like functions that send products into sums. We characterize the latter type completions as the ones for which ideal I of the `hypersurface at infinity' is radical. Moreover, we establish a one-to-one correspondence between the collection of minimal associated primes of I and the unique minimal collection of semidegrees needed to define the corresponding degree like function. We also prove an `affine Bezout type' theorem for polynomial maps P with finite fibers that admit semidegrees corresponding to completions that do not add points at infinity for P. For a wide class of semidegrees of a `constructive nature' our Bezout-type bound is explicit and sharp.

Depuis les 50 dernières années, de nombreux progrès ont été faits dans la compréhension du comportement asymptotique du nombre de points rationnels de hauteur bornée sur les variétés algébriques. Des conjectures précises ont été avancées par Baryrev, Manin et Peyre quant à la formule asymptotique attendue pour une variété générale.En 1962, à l'aide d'arguments issus de la méthode du cercle de Hardy et Littlewood, B. Birch a donné une estimation précise du nombre de points à coordonnées entières bornées dans une hypersurface définie par une équation homogène. Ceci revient à démontrer la conjecture de Batyrev-Manin-Peyre pour les hypersurfaces de l'espace projectif. Plus récemment, V. Blomer et J. Brüdern ont élaboré des techniques leur permettant d'établir une formule pour le comportement asymptotique du nombre de points de hauteur bornée pour des hypersurfaces d'espaces multiprojectifs définies par des équations multihomogènes diagonales. Parallèlement, D. Schindler a démontré la conjecture pour des hypersurfaces générales d'espaces biprojectifs, à l'aide de développements de la méthode de Birch.L'objet de cette thèse a été d'utiliser et de généraliser les techniques de Schindler, Blomer et Brüdern afin de démontrer la validité de la conjecture de Batyrev-Manin-Peyre pour le cas d'hypersurfaces de variétés toriques plus générales.Ce travail est composé de trois parties. La première partie concerne le cas particulier des hypersurfaces de tridegré (1,1,1) d'un espace triprojectif. Ce cas particulier constitue une première extension des techniques de Schindler à des variétés toriques dont le rang du groupe de Picard est 3. La deuxième partie est consacrée à l'étude des hypersurfaces d'une famille de variétés toriques dont le rang du groupe de Picard est 2 et contenant la famille des espaces biprojectifs. Il s'agit en effet d'étendre la méthode de Schindler afin d'obtenir une formule asymptotique pour le nombre de points de hauteur bornée sur ces variétés. Enfin, dans la dernière partie, nous généralisons les méthodes développées dans les deux parties précédentes à des hypersurfaces des variétés toriques complètes lisses de rang de groupe dont le cône effectif est supposé simplicial, ce qui nous permet de démontrer la conjecture de Batyrev-Manin-Peyre pour ces variétés. / For the last 50 years, many progresses have been made in the understanding of the asymptotic behaviour of the number of rational points of bouded height on algebraic varieties. Some precise conjectures have been advanced by Batyrev, Manin, and Peyre for the expected asymptotic formula for a general variety.In 1962, using some arguments of the Hardy-Littlewood circle method, B. Birch gave a precise estimate for the number of integral points whose coordinates are bounded on an hypersurface defined by an homogeneous equation. This amounts to demonstrating the Batyrev-Manin-Peyre conjecture for hypersurfaces of projective spaces. More recently, V. Blomer and J. Brüdern developed some methods permitting to establish a formula for the asymptotic growth of the number of points of bounded height on hypersurfaces of multiprojective spaces defined by multihomogeneous diagonal equations. In the same time, D. Schindler proved the conjecture for general hypersurfaces of biprojective spaces by using some developements of the method of Birch.The aim of this thesis was to use and generalize the methods of Schindler, blomer, and Brüdern in order to prove the Batyrev-Manin-Peyre conjecture in the case of hypersurfaces of some general toric varieties.This work contain three parts. The first one deals with the particular case of hypersurfaces of tridegree (1,1,1) of triprojective spaces. This particular case is a first extension of the method of Schindler to some toric varieties whose rank of the Picard group is 3. The second part deals with the study of hypersurfaces of a class of toric varieties whose rank of the Picard group is 2 and containing biprojective spaces. We establish a generalization of the method of Schindler method in order to find an asymptotic formula for the number of points of bounded height on these vrieties. Finally, in the last part, we generalize the methods developed in the last two part to treat the case of hypersurfaces of complete non-singular toric vareties whose effective cone is simplicial. This permits to prove the conjecture of batyrev-Manin-Peyre for these varieties.

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In this thesis we study the relation between algebraic torus actions on complex projective varieties and the birational geometry of their geometric quotients. Given a C*-action on a normal projective variety X, there exist two unique connected components of the fixed point locus, called the sink Y− and the source Y+, containing the limit at ∞ and 0 of the general orbit. Let GX− (resp. GX+) be the variety parametrizing the orbits converging to the sink (resp. the source). Since there exists an open subset of points converging to Y±, we obtain a birational map ψ: GX->GX+. By choosing different linearizations of ample line bundles on X, we obtain a factorization of the birational map ψ among inner geometric quotient, parametrizing different open subsets of stable points. In this setting, we investigate the local analytic geometry of the birational map ψ. On one hand we link certain birational transformations, called rooftop flips, with varieties with two projective bundles structures. On the other we study when the birational map ψ can be locally described by a toric flip of Atiyah type. If on one side a C*-action naturally induces a birational map among geometric quotients, it is meaningful to study the opposite direction: more precisely, given a birational map φ: Z+->Z− among normal projective varieties, how can we construct a normal projective variety X, endowed with a C*-action, such that Z− is the sink, Z+ is the source, and the natural birational map ψ constructed above coincide with φ? Such an X is called a geometric realization of the birational map φ. We propose a construction of a geometric realization of φ, whose geometry reflects the factorization of the map as a composition of flips, blow-ups and blow-downs. We describe in particular the case in which φ is a small modification of dream type, namely a birational map which is an isomorphism in codimension 1 associated to a finitely generated multisection ring. Moreover, we show that the cone of divisors associated to such multisection rings admits a chamber decomposition where the models are the geometric quotients of the C*-action. If in addition Z± are assumed to be toric varieties, we construct a function in SageMath to compute the polytope of the associated toric geometric realization.