Georgia Institute of Technology College of Sciences

Further discussion of alternative metrics on RNA secondary structures.

This dissertation has two principal components: the dimension of posets with planar cover graphs, and the cartesian product of posets whose cover graphs have hamiltonian cycles that parse into symmetric chains. Posets of height two can have arbitrarily large dimension. In 1981, Kelly provided an infinite sequence of planar posets that shows that the dimension of planar posets can also be arbitrarily large. However, the height of the posets in this sequence increases with the dimension. In 2009, Felsner, Li, and Trotter conjectured that for each integer h \geq 2, there exists a least positive integer c_h so that if P is a poset having a planar cover graph (hence P is a planar poset as well) and the height of P is h, then the dimension of P is at most c_h. In the first principal component of this dissertation we prove this conjecture. We also give the best known lower bound for c_h, noting that this lower bound is far from the upper bound. In the second principal component, we consider posets with the Hamiltonian Cycle--Symmetric Chain Partition (HC-SCP) property. A poset of width w has this property if its cover graph has a Hamiltonian cycle which parses into w symmetric chains. This definition is motivated by a proof of Sperner's Theorem that uses symmetric chains, and was intended as a possible method of attack on the Middle Two Levels Conjecture. We show that the subset lattices have the HC-SCP property by showing that the class of posets with the strong HC-SCP property, a slight strengthening of the HC-SCP property, is closed under cartesian product with a two-element chain. Furthermore, we show that the cartesian product of any two posets from this class has the HC-SCP property.

In 1988, Owen introduced empirical likelihood as a nonparametric method for constructing confidence intervals and regions. It is well known that empirical likelihood has several attractive advantages comparing to its competitors such as bootstrap: determining the shape of confidence regions automatically; straightforwardly incorporating side information expressed through constraints; being Bartlett correctable. In this talk, I will discuss some extensions of the empirical likelihood method to several interesting and important statistical inference situations including: the smoothed jackknife empirical likelihood method for the receiver operating characteristic (ROC) curve, the smoothed empirical likelihood method for the conditional Value-at-Risk with the volatility model being an ARCH/GARCH model and a nonparametric regression respectively. Then, I will propose a method for testing nested stochastic models with discrete and dependent observations.

The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) system is a recently discovered immune defense in bacteria and archaea (hosts) that functions via directed incorporation of viral DNA intohost genomes. Here, we introduce a multi-scale model of dynamic coevolution between hosts and viruses in an ecological context that incorporates CRISPR immunity principles. We analyze the model to test whether and how CRISPR immunity induces host and viral diversification and maintenance of coexisting strains. We show that hosts and viruses coevolve to form highly diverse communities through punctuated replacement of extant strains. The populations have very low similarity over long time scales. However overshort time scales, we observe evolutionary dynamics consistent with incomplete selective sweeps of novel strains, recurrence of previously rare strains, and sweeps of coalitions of dominant host strains with identical phenotypes but different genotypes. Our explicit eco-evolutionary model of CRISPR immunity can help guide efforts to understand the drivers of diversity seen in microbial communities where CRISPR systems are active.