Limits and tradeoffs in the control of autocatalytic systems

Despite the complexity of biological networks, we find that certain common architectures govern network structures. These architectures impose fundamental constraints on system performance and create tradeoffs that the system must balance in the face of uncertainty in the environment. This means that while a system may be optimized for a specific function through evolution, the optimal achievable state must follow these constraints. One such constraining architecture is autocatalysis, as seen in many biological networks including glycolysis and ribosomal protein synthesis. Using a minimal model, we show that ATP autocatalysis in glycolysis imposes stability and performance constraints and that the experimentally well-studied glycolytic oscillations are in fact a consequence of a tradeoff between error minimization and stability. We also show that additional complexity in the network results in increased robustness. Ribosome synthesis is also autocatalytic where ribosomes must be used to make more ribosomal proteins. When ribosomes have higher protein content, the autocatalysis is increased. We show that this autocatalysis destabilizes the system, slows down response, and also constrains the system’s performance. On a larger scale, transcriptional regulation of whole organisms also follows architectural constraints and this can be seen in the differences between bacterial and yeast transcription networks. We show that the degree distributions of bacterial transcription network follow a power law distribution while the yeast network follows an exponential distribution. We then explored the evolutionary models that have previously been proposed and show that neither the preferential linking model nor the duplication-divergence model of network evolution generates the power-law, hierarchical structure found in bacteria. However, in real biological systems, the generation of new nodes occurs through both duplication and horizontal gene transfers, and we show that a biologically reasonable combination of the two mechanisms generates the desired network.

Baryon number violation beyond the standard model

This thesis describes simple extensions of the standard model with new sources of baryon number violation but no proton decay. The motivation for constructing such theories comes from the shortcomings of the standard model to explain the generation of baryon asymmetry in the universe, and from the absence of experimental evidence for proton decay. However, lack of any direct evidence for baryon number violation in general puts strong bounds on the naturalness of some of those models and favors theories with suppressed baryon number violation below the TeV scale. The initial part of the thesis concentrates on investigating models containing new scalars responsible for baryon number breaking. A model with new color sextet scalars is analyzed in more detail. Apart from generating cosmological baryon number, it gives nontrivial predictions for the neutron-antineutron oscillations, the electric dipole moment of the neutron, and neutral meson mixing. The second model discussed in the thesis contains a new scalar leptoquark. Although this model predicts mainly lepton flavor violation and a nonzero electric dipole moment of the electron, it includes, in its original form, baryon number violating nonrenormalizable dimension-five operators triggering proton decay. Imposing an appropriate discrete symmetry forbids such operators. Finally, a supersymmetric model with gauged baryon and lepton numbers is proposed. It provides a natural explanation for proton stability and predicts lepton number violating processes below the supersymmetry breaking scale, which can be tested at the Large Hadron Collider. The dark matter candidate in this model carries baryon number and can be searched for in direct detection experiments as well. The thesis is completed by constructing and briefly discussing a minimal extension of the standard model with gauged baryon, lepton, and flavor symmetries.

Baryon and lepton numbers in particle physics beyond the standard model

The works presented in this thesis explore a variety of extensions of the standard model of particle physics which are motivated by baryon number (B) and lepton number (L), or some combination thereof. In the standard model, both baryon number and lepton number are accidental global symmetries violated only by non-perturbative weak effects, though the combination B-L is exactly conserved. Although there is currently no evidence for considering these symmetries as fundamental, there are strong phenomenological bounds restricting the existence of new physics violating B or L. In particular, there are strict limits on the lifetime of the proton whose decay would violate baryon number by one unit and lepton number by an odd number of units.

The first paper included in this thesis explores some of the simplest possible extensions of the standard model in which baryon number is violated, but the proton does not decay as a result. The second paper extends this analysis to explore models in which baryon number is conserved, but lepton flavor violation is present. Special attention is given to the processes of μ to e conversion and μ → eγ which are bound by existing experimental limits and relevant to future experiments.

The final two papers explore extensions of the minimal supersymmetric standard model (MSSM) in which both baryon number and lepton number, or the combination B-L, are elevated to the status of being spontaneously broken local symmetries. These models have a rich phenomenology including new collider signatures, stable dark matter candidates, and alternatives to the discrete R-parity symmetry usually built into the MSSM in order to protect against baryon and lepton number violating processes.

A model for energy and morphology of crystalline grain boundaries with arbitrary geometric character

It has been well-established that interfaces in crystalline materials are key players in the mechanics of a variety of mesoscopic processes such as solidification, recrystallization, grain boundary migration, and severe plastic deformation. In particular, interfaces with complex morphologies have been observed to play a crucial role in many micromechanical phenomena such as grain boundary migration, stability, and twinning. Interfaces are a unique type of material defect in that they demonstrate a breadth of behavior and characteristics eluding simplified descriptions. Indeed, modeling the complex and diverse behavior of interfaces is still an active area of research, and to the author's knowledge there are as yet no predictive models for the energy and morphology of interfaces with arbitrary character. The aim of this thesis is to develop a novel model for interface energy and morphology that i) provides accurate results (especially regarding "energy cusp" locations) for interfaces with arbitrary character, ii) depends on a small set of material parameters, and iii) is fast enough to incorporate into large scale simulations.

In the first half of the work, a model for planar, immiscible grain boundary is formulated. By building on the assumption that anisotropic grain boundary energetics are dominated by geometry and crystallography, a construction on lattice density functions (referred to as "covariance") is introduced that provides a geometric measure of the order of an interface. Covariance forms the basis for a fully general model of the energy of a planar interface, and it is demonstrated by comparison with a wide selection of molecular dynamics energy data for FCC and BCC tilt and twist boundaries that the model accurately reproduces the energy landscape using only three material parameters. It is observed that the planar constraint on the model is, in some cases, over-restrictive; this motivates an extension of the model.

In the second half of the work, the theory of faceting in interfaces is developed and applied to the planar interface model for grain boundaries. Building on previous work in mathematics and materials science, an algorithm is formulated that returns the minimal possible energy attainable by relaxation and the corresponding relaxed morphology for a given planar energy model. It is shown that the relaxation significantly improves the energy results of the planar covariance model for FCC and BCC tilt and twist boundaries. The ability of the model to accurately predict faceting patterns is demonstrated by comparison to molecular dynamics energy data and experimental morphological observation for asymmetric tilt grain boundaries. It is also demonstrated that by varying the temperature in the planar covariance model, it is possible to reproduce a priori the experimentally observed effects of temperature on facet formation.

Finally, the range and scope of the covariance and relaxation models, having been demonstrated by means of extensive MD and experimental comparison, future applications and implementations of the model are explored.