Physics Commons^™

Extracting The Structure And Conformations Of Biological Entities From Large Datasets, Ali Dashti

Theses and Dissertations

In biology, structure determines function, which often proceeds via changes in conformation. Efficient means for determining structure exist, but mapping conformations continue to present a serious challenge. Single-particles approaches, such as cryogenic electron microscopy (cryo-EM) and emerging "diffract & destroy" X-ray techniques are, in principle, ideally positioned to overcome these challenges. But the algorithmic ability to extract information from large heterogeneous datasets consisting of "unsorted" snapshots - each emanating from an unknown orientation of an object in an unknown conformation - remains elusive.

It is the objective of this thesis to describe and validate a powerful suite of manifold-based algorithms …

Contributions To The Cuore Collaboration, Samuel Joseph Meijer

Physics

This paper describes work done between 2010 and 2013 to contribute to the CUORE collaboration, a physics collaboration searching for neutrinoless double-beta decay in tellurium. Measurement of this decay would indicate fundamental information about the nature of the neutrino. The implementation of a parylene-coated detector frame is described. Also, a temperature stabilization system for an automated gluing system was constructed. An image recognition algorithm is described for locating spots of glue and evaluating their acceptability.

Dynamics Of The Fitzhugh-Nagumo Neuron Model, Zechariah Thurman

Physics

In this paper, the dynamical behavior of the Fitzhugh-Nagumo model is examined. The relationship between neuron input current and the firing frequency of the neuron is characterized. Various coupling schemes are also examined, and their effects on the dynamics of the system is discussed. The phenomenon of stochastic resonance is studied for a single uncoupled Fitzhugh-Nagumo neuron.

Directed Percolation And The Abstract Tile Assembly Model, Tyler Garrett Moore

Graduate Theses and Dissertations

Self-assembly is a process by which simple components build complex structures through local interactions. Directed percolation is a statistical physical model for describing competitive spreading processes on lattices. The author describes an algorithm which can transform a tile assembly system in the abstract Tile Assembly Model into a directed percolation problem, and then shows simulations of the aTAM which support this algorithm. The author also investigates two new constructs designed for Erik Winfree's abstract Tile Assembly Model called the NULL tile and temperature 1.5. These constructs aid the translation between self-assembly and directed percolation and may assist self-assembly researchers in …

Upgrades To Nrlmol Code, Luis Basurto

Open Access Theses & Dissertations

This project consists of performing upgrades to the massively parallel NRLMOL electronic structure code in order to enhance its performance by increasing its flexibility by: a) Utilizing dynamically allocated arrays, b) Executing in a parallel environment sections of the program that were previously executed in a serial mode, c) Exploring simultaneous concurrent executions of the program through the use of an already existing MPI environment; thus enabling the simulation of larger systems than it is currently capable of performing. Also developed was a graphical user interface that will allow less experienced users to start performing electronic structure calculations by aiding …