GPUs are flexible parallel processors capable of accelerating real applications. To exploit them, programmers rewrite programs in new languages using intimate knowledge of the underlying hardware. This is a step backwards in abstraction and ease of use from sequential programming.…

Network-based modeling of complex systems with emergent behavior is increasingly being employed across different disciplines. Much of the focus in such efforts has been on detailed, "microscopic" modeling, in which the dynamics is described in terms of the individual nodes…

The body of research contained within this dissertation serves to shed light onto the influence hydrophyte communities exhibit on biogeochemical processes and subsequently on metal mobility within wetland systems. The focus of the first thesis is centered on the role…

Protein domain prediction is a key step in characterizing protein structure, function, and evolution. However, the genome of Plasmodium falciparum, the causative agent of malignant malaria, remains poorly-annotated using standard approaches to domain prediction. We identified several general problems with…

Human cells are protected by cell-intrinsic mechanisms that specifically detect microbial pathogens and elicit innate immune response. Such activities are essential in restricting viral infections. Despite the extensive knowledge about cytoplasmic sensing processes, little is understood about the nuclear counterpart.…

In this thesis we develop and test methods for numerically evolving hydrodynamics coupled to the Einstein field equations, and then apply them to several problems in gravitational physics and astrophysics. The hydrodynamics scheme utilizes high-resolution shock-capturing techniques with flux corrections…

Single-particle reconstruction of vitrified samples (cryogenic electron microscopy, or









cryo-EM) provides structural information for a large variety of biological molecules,









ranging from…

Machine learning is the science of discovering knowledge from data and making decisions based on this learnt structure. It has grown into a broad discipline that has established many statistical and computational learning principles. We are surrounded by the applications…

The aim of this thesis is to develop methods for variable selection and statistical prediction for high dimensional statistical problems. Along with proposing new and innovative procedures, this thesis also focuses on the theoretical properties of the proposed methods and…

Aquatic Microbial Oxygenic Phototrophs (AMOP's) capture carbon dioxide from the atmosphere and fix it into organic molecules used for growth and proliferation. However, the mechanisms that decide how photosynthetically fixed carbon is allocated between the major sinks (proteins, lipids, and…