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Concept# Sequence

Summary

In mathematics, a sequence is an enumerated collection of objects in which repetitions are allowed and order matters. Like a set, it contains members (also called elements, or terms). The number of elements (possibly infinite) is called the length of the sequence. Unlike a set, the same elements can appear multiple times at different positions in a sequence, and unlike a set, the order does matter. Formally, a sequence can be defined as a function from natural numbers (the positions of elements in the sequence) to the elements at each position. The notion of a sequence can be generalized to an indexed family, defined as a function from an arbitrary index set.
For example, (M, A, R, Y) is a sequence of letters with the letter 'M' first and 'Y' last. This sequence differs from (A, R, M, Y). Also, the sequence (1, 1, 2, 3, 5, 8), which contains the number 1 at two different positions, is a valid sequence. Sequences can be finite, as in these examples, or infinite, such as the sequence o

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Sequence dependent mechanics of DNA is believed to play a central role in the functioning of the cell through the expression of genetic information. Nucleosome positioning, gene regulation, DNA looping and packaging within the cell are only some of the processes that are believed to be at least partially governed by mechanical laws. Therefore it is important to understand how the sequence of DNA affects its mechanical properties. For exploring the mechanical properties of DNA, various discrete and continuum models have been, and continue to be, developed. A large family of these models, including the model considered in this work, assume that bases or base pairs of DNA are rigid bodies. The most standard are rigid base pair models, with parameters either obtained directly from experimental data or from Molecular Dynamics (MD) simulations. The drawback of current experimental data, such as crystal structures, is that only small ensembles of configurations are available for a small number of sequences. In contrast, MD simulations allow a much more detailed view of a larger number of DNA sequences. However, the drawback is that the results of these simulations depend on the choice of the simulation protocol and force field parameters. MD simulations also have sequence length limitations and are currently too intensive for (linear) molecules longer than a few tens of base pairs. The only way to simulate longer sequences is to construct a coarse-grain model. The goal of this work is to construct a small parameter set that can model a sequence- dependent equilibrium probability distribution for rigid base configurations of a DNA oligomer with any given sequence of any length. The model parameter sets previously available were for rigid base pair models ignoring all the couplings beyond nearest neighbour interactions. However it was shown in previous work, that this standard model of rigid base pair nearest neighbour interactions is inconsistent with a (then) large scale MD simulation of a single oligomer [36]. In contrast we here show that a rigid base nearest neighbour, dimer sequence dependent model is a quite good fit to many MD simulations of different duration and se- quence. In fact a hierarchy of rigid base models with different interaction range and length of sequence-dependence is discussed, and it is concluded that the nearest neighbour, dimer based model is a good compromise between accuracy and complexity of the model. A full parameter set for this model is estimated. An interesting feature is that despite the dimer dependence of the parameter set, due to the phenomenon of frustration, our model predicts non local changes in the oligomer shape as a function of local changes in the sequence, down to the level of a point mutation.

The goal of this work is to study Alexander-Whitney coalgebras (first defined in [HPST06]) from a topological point of view. An Alexander-Whitney coalgebra is a coassociative chain coalgebra over Z with an extra algebraic structure : the comultiplication must respect the coalgebra structure up to an infinite sequence of homotopies (this sequence is part of the data of the Alexander-Whitney coalgebra structure). Alexander-Whitney coalgebras are interesting for topologists because the normalized chain complex C(K) of a simplicial set K is endowed with an Alexander-Whitney coalgebra structure. This theorem is proved for the first time here (generalising a result proven in [HPST06]). This theorem gives the hope that the Alexander-Whitney coalgebra structure of C(K) contains interesting information that can be used to solve topological problems. This hope is strengthened by the success already obtained in the work of several topologists. Among others, [HPST06], [HL07], [Boy08], and [HR] use the Alexander-Whitney coalgebra structure of the normalized chains of a simplicial set in an essential way to solve topological problems. This thesis begins with some background material. In particular, the definition of a DCSH morphism between two coassociative chain coalgebras is recalled in complete detail. For example, signs are determined with great precision. Next we devote a chapter to the definition of Alexander-Whitney coalgebras and to their importance in topology. In the following chapter we begin the conceptual study of Alexander-Whitney coalgebras. A global study of these objects had not yet been carried out even if the Alexander-Whitney coalgebra structure has been studied and used in order to answer some specific questions. With the aim of studying Alexander-Whitney coalgebras in a nice setting, we develop an operadic description of these coalgebras in the following chapter. More precisely, we show that there is an explicit operad AW such that the coalgebras over this operad are exactly the Alexander-Whitney coalgebras. Furthermore, AW is shown to be a Hopf operad, so that the category formed by the Alexander-Whitney coalgebras is actually a monoidal category. These results are proven in a reasonably general framework. In fact, we associate an operad to each bimodule (over the associative operad) of a certain type, such that we get AW if this bimodule is well chosen. In particular, these results enable us to study Alexander-Whitney coalgebras from the standpoint of operads. This strategy is recognised to be successful in various mathematical situations, and especially in algebraic topology. Moreover, we develop a minimal model notion in the setting of right module over a chosen operad (which has to satisfy some reasonable conditions), with the aim of applying this result to the special case of the Alexander-Whitney coalgebras. This is possible because coalgebras over some fixed operad P can be seen as right modules over P. And the category of right modules over P has some nice features which do not appear to hold in the category of P-coalgebras. The inspiration for this part of our work comes from the notion of minimal model developed in the framework of rational homotopy theory. The two following facts show that it is reasonable to try to adapt some ideas of rational homotopy theory to the category of Alexander-Whitney coalgebras. A. There is a theorem that says that studying topological spaces up to rational equivalences is, essentially, equivalent to studying cocommutative chain coalgebras over the field of rational numbers. This is false if the ring of integers replaces the field of rational numbers, but Alexander-Whitney coalgebras are "almost" cocommutative in the sense which is explained in this thesis. B. It could be that the Alexander-Whitney coalgebra structure of the normalized chains of a simplicial set is weak enough to allow explicit computations. At least, it is clear that the Alexander-Whitney coalgebra structure on the normalized chains is far from being an E∞-structure (such a structure determines the homotopy type of the considered simplicial set, at least under some conditions). The chapter about minimal models in the framework of right modules over an operad includes an existence theorem and a discussion of the unicity of this model. In the second part of this chapter, we construct an explicit path-object in the model category of right modules over an operad. This path-object is then used to investigate the topologically relevant information that could stem from the minimal model in the case of the operad AW. Finally, we present and examine some interesting open questions about Alexander-Whitney coalgebras. These questions give a nice outlook on future research in this area.

The complex mechanisms involved in cellular processes have been increasingly understood this past century and the central role of the DNA molecule has been recognized. The base pair sequence along a DNA fragment is observed not only to encode the genomic information, but also to induce locally very specific physical properties, such as significantly bent or stiff regions. These variations in the molecule constitution are for instance believed to be involved in DNA-protein recognition and in nucleosomes positioning. Modelling the sequence dependent DNA mechanical properties is consequently an important step towards understanding many biological functions. However, in a cell, vastly different length scales are involved, ranging from a few base pairs to several thousands, which makes difficult the definition of \textit{one} appropriate model. A promising strategy seems then to be given by the multi-scale modeling of sequence dependent DNA mechanics. In this framework, the sequence dependent rigid base and rigid base pair models have been proposed. In these coarse grain models either each base pair or each base is described as a rigid body configuration, which leads to either a chain or a bichain representation of the DNA molecule. A sequence dependent configurational distribution has then been parametrized, either from experimental data or directly from atomistic molecular dynamic simulations, and provides an efficient and realistic description at the scale of hundreds of base pairs. Important questions that can be studied in these models are for instance the influence of the sequence on the probability of contact of two sites, which are distant along the molecule length, or on the expectation of the relative configuration of these two sites. In this thesis, we propose to approach these physical situations both from the discrete and the continuum modeling point of view, and then to discuss in which sense they actually constitute only one multi-scale point of view. In the first part, we discuss mechanical properties of heterogeneous rigid body chains and bichains, as well as continuum rod and birods, in classical statics and in equilibrium statistical physics. Equilibirum conditions, variational principles and configurational distributions are studied for single chains and rods, and then extended to bichains and birods. We have introduced in particular an original coordinate free Hamiltonian formulation in arc-length of the birod equilibrium conditions, and the notion of the persistence matrix for the configurational moment for chains and rods. We then present deterministic and stochastic exponential Cauchy-Born rules allowing to bridge the scales between the discrete and continuum representations. In the second part, we present applications of the proposed multi-scale mechanical theory for chains and rods to sequence dependent DNA modelling. We discuss the approximation using the birod model of most probable bichain configurations satisfying prescribed end conditions. Similarly, we then present the computation of the sequence dependent frame correlation matrix and the Flory persistence vector for chains using a continuum rod model. In addition, a homogenization method is proposed. These results are believed to constitute a substantial improvement in the multi-scale modeling of DNA mechanics.