Ryan Melvin.
Public Presentation in Olin 107.
Mon. Mar. 19, 2018, at 2:00 PM.
Freddie R. Salsbury, Jr., Advisor.

The defense will follow.

ABSTRACT

Applying statistical and machine learning, I have addressed key issues in the field of computational biophysics. The guiding principle in this work has been removing bias and conveying uncertainty. To that end, I have contributed numerous methods for interpreting biopolymer ensemble data without the need for prior knowledge or setting of biasing parameters. Additionally, in all of these works, I have provided a careful discussion of the limits of these methods and how researchers might visually convey the inherent uncertainty, including displaying what are effectively error bars on biopolymer structures. I have worked to remove bias even in estimating the amount of sampling needed for any time-dependent multi-dimensional process. These contributions may move the field forward in its ability to remove bias and convey uncertainty in statistically rigorous ways.

After introducing these methods, I proceed with applications of them to the study of a chemotherapeutic nucleic acid called F10 – a 10mer of 5-fluoro-2′-deoxyuridine-5′-O-monophosphate. Here I uncover the mechanism for a previously observed interaction with zinc and magnesium, leading to a general investigation of F10’s interactions with metal ions. I conclude by proposing a stabilizing chemical perturbation to the polymer and discussing implications for drug delivery.

WFU Physics Colloquium

TITLE: “Electronic Stopping in Condensed Matter: Understanding Electronic Excitation Dynamics under Proton Irradiation”
SPEAKER: Professor Yosuke Kanai
University of North Carolina at Chapel Hill

TIME: Wed. Feb. 28, 2018, at 4:00 PM
PLACE: George P. Williams, Jr. Lecture Hall, (Olin 101)

There will be a reception with refreshments at 3:30 PM in the lounge. All interested persons are cordially invited to attend.

ABSTRACT

Transfer of the energy/momentum from highly-energetic ions to electrons in condensed matter is described by the so-called electronic stopping. The projectile ions bear highly localized electric field that is quite heterogeneous at the atomistic scale, and massive electronic excitations are produced in the electronic stopping process. Understanding this phenomenon in condensed matter systems under proton and other ion irradiation has implications in various modern technologies, ranging from nuclear fission/fusion reactors, to semiconductor devices for aerospace missions, to cancer therapy based on proton beam radiation. Electronic stopping has been long studied within linear response theory framework (e.g. Bethe theory), but recent advances in high-performance computers allow us to study the phenomena beyond such simplified treatment through the use of numerical simulations. In this talk, I will discuss how non-equilibrium dynamics simulations based on our recently-developed large-scale real-time time-dependent density functional theory enable us to study this electronic excitation process, using an important case of liquid water under proton irradiation as an example. In addition to determining the energy transfer rate (i.e. electronic stopping power), our work reveals several key features of the excitation dynamics at the mesoscopic and molecular levels for deciphering water radiolysis mechanism under proton irradiation.

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WFU Physics Colloquium

TITLE: “Why is Lettuce So Wrinkly?”
SPEAKER: Professor John Gemmer
Assistant Professor, Department of Mathematics and Statistics
Wake Forest University

TIME: Wed. Feb. 21, 2018, at 4:00 PM
PLACE: George P. Williams, Jr. Lecture Hall, (Olin 101)

There will be a reception with refreshments at 3:30 PM in the lounge. All interested persons are cordially invited to attend.

ABSTRACT

Many patterns in nature and industry arise from the system minimizing an appropriate energy. Examples range from the periodic rippling in hanging drapes to the six-fold symmetries observed in snowflakes. Torn plastic sheets and growing leaves provide striking examples of pattern forming systems which can transition from single wavelength geometries (hosta leaves) to complex fractal like shapes (lettuce). These fractal-like patterns seem to have many length scales – the same amount of extra detail can be seen when looking closer (“statistical self-similarity”). It is a mystery how such complex patterns could arise from energy minimization alone.

In this talk, I will address this puzzle by showing that such patterns naturally arise from the sheet adopting a hyperbolic non-Euclidean geometry. However, there are many different hyperbolic geometries that the growing leaf could select. I will show, using techniques from nonlinear elasticity, analysis, differential geometry and numerical optimization, that the fractal-like patterns are indeed the natural minimizers for the system.

WFU Physics Colloquium

TITLE: “Converting Agricultural Waste into Value-Added Products:  The Case of the Coconut”
SPEAKER: Professor Walter Bradley, PhD, PE
Emeritus Distinguished Professor of Mechanical Engineering, Baylor University
Emeritus Professor of Mechanical Engineering, Texas A&M University

TIME: Wed. Mar. 21, 2018, at 4:00 PM
PLACE: George P. Williams, Jr. Lecture Hall, (Olin 101)

There will be a reception with refreshments at 3:30 PM in the lounge. All interested persons are cordially invited to attend.

ABSTRACT

There is a growing interest in the use of renewable functional fillers in polymer composites and natural fibers in non-woven fabric composites to make more environmentally friendly products by reducing the use of petroleum.  This can be done using crops such as kenaf that are grown for this purpose. However, the use of agricultural waste has two advantages: the feedstock is essentially free and the volume of agricultural waste to be burned or buried is reduced.  This presentation will explore the possibilities of using coconut shell and coconut husks as feed stocks to make functional fillers for polymeric composite materials and non-woven fabric composites respectively.  The properties of the coconut shell and fiber from the coconut husk (called coir) will be presented.  Commercial applications that can take advantage of these families of physical properties will be used to illustrate a wider range of possibilities. The necessary materials science research that was performed to make possible their incorporation into commercial products will also be summarized.

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WFU Physics Colloquium

TITLE: “Computational Engineering of Thermoelectric Materials”
SPEAKER: Professor Kristian Berland
Centre for Materials Science and Nanotechnology,
University of Oslo
TIME:  Thursday, Feb. 8, 2018, at 4:00 PM
PLACE: George P. Williams, Jr. Lecture Hall, (Olin 101)

There will be a reception with refreshments at 3:30 PM in the lounge. All interested persons are cordially invited to attend.

ABSTRACT

By converting heat to electricity and vice versa without the need for moving parts, thermoelectric modules have found many niche applications, such as in space exploration and mini-coolers. If even more progress is made on improving their conversion efficacy, they could also help recover some of the immense waste heat generated in power plants, transportation, and industrial processes. Based on examples from my own research, I will discuss how atomistic material modeling can aid the development of new and better thermoelectric materials. I will also illustrate how new methodologies can enhance the reliability of computational predictions on thermoelectric materials.

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WFU Physics Colloquium

TITLE: “Energy Policy and the EPA”
SPEAKER: Professor Stan Meiburg
Director, Graduate Studies in Sustainability
Wake Forest University

TIME: Wed. Jan. 31, 2018, at 4:00 PM
PLACE: George P. Williams, Jr. Lecture Hall, (Olin 101)

There will be a reception with refreshments at 3:30 PM in the lounge. All interested persons are cordially invited to attend.

ABSTRACT

The mission of the U.S. Environmental Protection Agency has been inextricably bound up with the nation’s energy policy ever since the creation of the Agency in 1970. Controversies have flourished throughout this time, and while today’s debates have a different focus, EPA still finds itself in the middle of the action. Dr. Meiburg will review why this is so, give some examples of how past controversies resolved themselves, and suggest what to look for in the present debates.

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WFU Physics Colloquium

TITLE: “Effect of Crystal Packing on the Electronic Properties of Molecular Crystals”
SPEAKER: Professor Noa Marom
Department of Materials Science and Engineering,
Carnegie Mellon University,
Pittsburgh, PA

TIME: Wed. Dec. 6, 2017 at 4:00 PM
PLACE: George P. Williams, Jr. Lecture Hall, (Olin 101)

There will be a reception with refreshments at 3:30 PM in the lounge. All interested persons are cordially invited to attend.

ABSTRACT

Molecular crystals have applications in nonlinear optics, organic electronics, and particularly in pharmaceuticals, as most drugs are marketed in the form of crystals of the pharmaceutically active ingredient. Molecular crystals are bound by dispersion (van der Waals) interactions, whose weak nature generates potential energy landscapes with many local minima that may be extremely close in energy. This often results in polymorphism, the crystallization of the same molecule in several different structures. Crystal structure may profoundly influence the physical and chemical properties, including the electronic and optical properties relevant for device applications.

We perform large scale quantum mechanical simulations to predict the structure of molecular crystals and investigate the effect of crystal packing on their electronic and optical properties. The massively parallel genetic algorithm (GA) package, GAtor, relies on the evolutionary principle of survival of the fittest to find low-energy crystal structures of a given molecule. Dispersion-inclusive density functional theory (DFT) is used for structural relaxation and accurate energy evaluations. Evolutionary niching is performed by using machine learning to perform clustering on the fly. The structure generation package, Genarris, performs fast screening of randomly generated structures with a Harris approximation, whereby the molecular crystal density is constructed by replicating the single molecule density, which is calculated only once. Many-body perturbation theory, within the GW approximation and the Bethe-Salpeter equation (BSE), is then employed to describe properties derived from charged and neutral excitations.

An emerging application of molecular crystals is singlet fission (SF), the down-conversion of one photogenerated singlet exciton into two triplet excitons. SF has the potential to significantly increase the efficiency of organic photovoltaics beyond the Shockley-Queisser limit by harvesting two charge carriers from one photon. However, the realization of SF-based solar cells is hindered by the dearth of suitable materials. We aim to discover new SF materials and optimize the crystal packing of known materials to enhance SF efficiency. We predict that crystalline quaterrylene and a lesser known monoclinic crystal structure of rubrene may exhibit high singlet fission efficiency, possibly rivaling that of the quintessential SF material, pentacene. Quaterrylene has the additional advantages of high stability, a narrow band gap, and a triplet energy in the optimal range to maximize photoconversion efficiency.

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WFU Physics Colloquium

TITLE: “Kinetic Luminosity of Quasar Outflows and its Implications to Galaxy Formation”

SPEAKER:Professor Nahum Arav
Department of Physics
Virginia Tech
Blacksburg, VA

TIME: Wed. Nov. 29, 2017 at 4:00 PM

PLACE: George P. Williams, Jr. Lecture Hall, (Olin 101)

There will be a reception with refreshments at 3:30 PM in the lounge. All interested persons are cordially invited to attend.

ABSTRACT

Sub-relativistic mass-ejection outflows are seen as blue-shifted absorption troughs in the spectra of roughly one third of all quasars. I will describe recent results from observations with the Very Large
Telescope and the Hubble Space Telescope, that yield the mass flux and kinetic luminosity for the majority of these outflows. The derived values suggest that quasar absorption outflows have a profound effect on the formation of their host galaxy.

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WFU Physics Colloquium

TITLE: “What is fossilization? Casting new light (and electrons) on an old question”
SPEAKER: Professor Elizabeth Boatman
Department of Engineering,
Wake Forest University,
Winston-Salem, NC

TIME: Wed. Nov. 15, 2017 at 4:00 PM
PLACE: George P. Williams, Jr. Lecture Hall, (Olin 101)

There will be a reception with refreshments at 3:30 PM in the lounge. All interested persons are cordially invited to attend.

ABSTRACT

Our accepted understanding of the structure-property relationships in bone tissue, and in particular, its intrinsic damage tolerance behavior and repair mechanisms, falls short. Yet, if our understanding as materials engineers could be improved, the result would be significant advances in structural materials engineered based on the mimicry of biological structural tissues (i.e., biomimicry). For many reasons, extinct species (especially dinosaurs) are an important source of data for such pursuits, despite the obvious problem: the bodies of extinct species typically persist only as fossilized skeletal elements. As it turns out, the process of validating the persistence of those specimens using advanced synchrotron light- and electron-based techniques is inherently rewriting our definition of “fossilization”, in addition to informing our understanding of the structure-property relationships in bone.

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WFU Physics Colloquium

TITLE: “Materials and Measurements for Printed and Flexible Electronics”
SPEAKER: Dean M. DeLongchamp
Leader, Polymers Processing Group
National Institute of Standards and Technology
Gaithersburg, MD 20899

TIME: Wed. Nov. 8, 2017 at 4:00 PM
PLACE: George P. Williams, Jr. Lecture Hall, (Olin 101)

There will be a reception with refreshments at 3:30 PM in the lounge. All interested persons are cordially invited to attend.

ABSTRACT

Since the discovery of semiconducting organic molecules in the 70’s, they have enabled many new flexible electronics devices including transistors, solar cells, and displays. I will discuss the fundamentals of this technology and the important properties of materials that drive these exciting new applications. I will draw examples from the manufacturing of organic photovoltaics (OPV), a promising technology for low-cost solar cells. We have developed synchrotron-based X-ray scattering and a variety of benchtop spectroscopic methods to follow the structure evolution of these and other functional films as a printed ink dries. The measurements reveal the mechanisms by which the molecular design, formulation, and processing choices influence the nanoscale structure of the films.

The quest for structure-property relationships in OPV and other organic semiconductors has driven enormous advances in soft matter characterization over the past decade. Despite all the progress, surprisingly little consensus has been reached on what aspects of organic semiconductor film structure actually matter. Although order and orientation must matter, at what length scales are they relevant? I will discuss how a molecular-scale picture – the most difficult to obtain, particular in soft materials – may ultimately be required. We have recently made progress in developing new measurements that combine principles of spectroscopy, inelastic small-angle scattering, real-space imaging, and molecular simulation, which may at last provide a useful molecular scale structure measurement for soft materials and complex fluids.

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