Biological and Chemical Physics Commons^™

Multiscale Network Modeling Of Native And Modified Photosynthetic Light-Harvesting Complexes, Zane E. Armijo

Chemical and Biological Engineering ETDs

Photosynthetic light-harvesting complexes harvest solar energy and direct electronic excitations toward reaction centers with exceptional efficiency. This dissertation models the Fenna--Matthews--Olson complex of green sulfur bacteria, coupled to the PscA1 reaction center, as a chromophoric network. Forster resonance energy transfer theory, validated against numerically exact hierarchical equations of motion, was implemented in kinetic Monte Carlo simulations to resolve fine-grained excitation-transport pathways. The predicted charge-transfer efficiency of 77\% agrees with experiment, with the FMO2 monomer and its gateway pigment governing interfacial transfer. Systematic single, multi, and symmetry-preserving site removals, interpreted through Mobius inversion, identify critical pigments and show that cooperative effects …

Low-Cost Cutaneous Protoporphyrin Ix (Ppix) Detection (Cpd) Device For Follow-Up Monitoring Of Patients After Photodynamic Therapy, Md Asaduzzaman Rasel

Graduate Masters Theses

Background: Photodynamic Therapy (PDT) utilizes specific wavelengths of light to activate photosensitizing chemical compounds, known as photosensitizers, which induce the generation of cytotoxic reactive oxygen species (ROS) for the targeted destruction of cancer cells. Among various photosensitizers for PDT, Protoporphyrin IX (PpIX) is widely employed in oncology and dermatology due to its natural in situ generation via the metabolic conversion of 5- aminolevulinic acid (ALA), a non-phototoxic prodrug. Systemic administration of ALA after 3-6 hr drug delay leads to peak PpIX accumulation in tissues, facilitating therapeutic and diagnostic applications. However, PpIX can persist in the skin for 24–48 hours post-treatment, …

Contributions Of Tunneling In 8Π-6Π Electrocyclic Cascade Reactions Of Bicyclo[4.2.0]Octa-2,4-Diene Moieties, Ishika Jain, Claire Castro, William L. Karney

Featured Student Work

Six-electron electrocyclic reactions usually require relatively high temperatures; however recent research has shown that such reactions can occur at significantly lower temperatures in biosynthetic and biomimetic pathways. Pathways resulting in bicyclo[4.2.0]octa-2,4-diene moieties arise from thermally allowed 8π-6π electrocyclization cascade reactions of 1,3,5,7-octatetraenes, as in the biosynthesis of endiandric acids, elysiapyrones, and numerous other natural products. We report multidimensional tunneling calculations to explore the possible contribution of heavy-atom tunneling (e.g. by carbon) to biosynthetic pathways and biomimetic syntheses, and thus to provide a more complete picture of biochemical kinetics. M06-2X/cc-pVDZ calculations on the 8π-6π cascade cyclizations of methylated octatetraene model systems …

An Ab Initio Computation Of The Potential Energy Surfaces Of The Dna Bases, Anjali F. Filinovich, Vola Andrianarijaona

Campus Research Month

The potential energy surfaces of atoms in DNA can be analyzed and compared to show how their bonds break. This DNA potential energy reference data is very useful to understanding how DNA damage occurs, however, a dataset of relevant potential energy surfaces is not available for scientific use. We obtain the potential energy surfaces of various atoms in the four DNA bases adenine, thymine, guanine, and cytosine, by moving an atom in these molecules in three orthogonal directions using ORCA, an ab initio quantum chemistry software. Density functional theory is
used to compute potential energies as an atom is moved, …

Modeling Excited State Processes In Molecular Aggregates By Constructing An Adaptive Basis For The Hierarchy Of Pure States, Leonel Varvelo

Chemistry Theses and Dissertations

Simulating excitation energy transfer (EET) in molecular materials is of crucial importance for the development of and understanding of materials such as organic photovoltaics and photosynthetic systems and further development of novel materials. The Hierarchy of Pure States (HOPS) is an exact framework for the time evolution of an open quantum system in which a hierarchy of stochastic wave functions are propagated in time. The adaptive HOPS (adHOPS) method achieves size-invariant scaling with the number of simulated molecules for sufficiently large aggregates by using an adaptive basis that moves with the excitation through the material. To demonstrate the power of …

Determination Of The Rydberg Constant From The Emission Spectra Of H And He+, Kyle D. Shaffer

Ramifications

Abstract

In this experiment, the Rydberg constants for the hydrogen atom and He⁺ were determined by analysis of the emission spectra of Hand He, respectively, in comparison to the principal quantum numbers of each transition. Using both a hydrogen and then a helium atomic lamp attached to a 0.5 m grating spectrometer and a photomultiplier detector (PMT), a change in voltage detected by the PMT can be paired with a corresponding wavelength passing through the spectrometer from each emission peak in the visible to ultraviolet range. The peaks acquired from this change in voltage were analyzed to find their …

Nuclear-Targeted Gold Nanoparticles Enhance The Effects Of Radiation Therapy With And Without Liposomal Delivery, Maureen Aliru

Dissertations and Theses (Open Access)

Less that 10% of pancreatic cancer patients are eligible for curative resection, and clinical trials evaluating chemoradiation in locally advanced patients with unresectable disease have been largely disappointing. New and creative therapeutic approaches are needed to address the unment need for treatment options. The objective of this thesis is to advance radiosensitization of treatment-resistant densely desmoplastic pancreatic cancer using nanoparticles to surmount biological barriers to effective particle distribution for DNA-targeting.

Clinical translation of radiosensitizing nanoparticles has stalled owing to technical challenges. Current strategies to use AuNPs for radiosensitization require large quantities of gold, kilovoltage x-rays, immediate irradiation after intravenous administration, …

Non-Adiabatic Quantum Dynamics Of The Ultracold Li+Lina→ Li2+Na Chemical Reaction, B. K. Kendrick, M. Li, H. Li, S. Kotochigova, J. F.E. Croft, Balakrishnan Naduvalath

Chemistry and Biochemistry Faculty Research

We report non-adiabatic dynamics of the Li+LiNa→Li2+Na chemical reaction at cold and ultracold temperatures employing accurate ab initio electronic potential energy surfaces in a quantum dynamics formulation employing a diabatic representation. Results are compared against those from a single adiabatic ground state potential energy surface and a universal model based on the long-range interaction potential. We discuss signatures of non-universal behavior in the total rate coefficients as well as strong non-adiabatic effects in the state-to-state rotationally resolved rate coefficients.

Topics In Three-Dimensional Imaging, Source Localization And Super-Resolution, Zhixian Yu

Physics & Astronomy ETDs

The realization that twisted light beams with helical phasefronts could carry orbital angular momentum (OAM) that is in excess of the photon's spin angular momentum (SAM) has spawned various important applications. One example is the design of novel imaging systems that achieve three-dimensional (3D) imaging in a single snapshot via the rotation of point spread function (PSF).

Based on a scalar-field analysis, a particular simple version of rotating PSF imagery, which was proposed by my advisor Dr. Prasad, furnishes a practical approach to perform 3D source localization using a spiral phase mask that generates a combination of Bessel vortex beams. …

Plasmonic Enhancement Of Photoluminescence And Photobrightening In Cdse Quantum Dots, David Alan French

Graduate Theses and Dissertations

Quantum dots are gaining recognition not just in the physics and chemistry community, but in the public eye as well. Quantum dot technologies are now being used in sensors, detectors, and even television displays. By exciting quantum dots with light or electricity, they can be made to emit light, and by altering the quantum dot characteristics the wavelength can be finely tuned. The light emitted can be also be made more intense by an increase in the excitation energy. The excitation light can be increased via plasmonic enhancement, leading to increased luminescence. Aside from the relatively steady-state response, quantum dots …

Achieving A Stable Magneto-Optical Trap, Chasen S. Himeda

Honors Thesis

The utilization of the Magneto-Optical Trap (MOT) as a method for cooling and confining atoms is a recent development in the field of modern optical physics. Producing an effective MOT relies on a constant magnetic field throughout the trapping region and successful laser cooling, a technique used to achieve optical molasses by slowing particles using a three-dimensional intersection of laser beams. A successful MOT occurs when the trapped atoms slow down to approximately 30 cm/s at a temperature in the microkelvin range and is observable when a small bright orb of atoms is located in the center of the chamber. …

Universality Of Quantum Information In Chaotic Cfts, Nima Lashkari, Anatoly Dymarsky, Hong Liu

Physics and Astronomy Faculty Publications

We study the Eigenstate Thermalization Hypothesis (ETH) in chaotic conformal field theories (CFTs) of arbitrary dimensions. Assuming local ETH, we compute the reduced density matrix of a ball-shaped subsystem of finite size in the infinite volume limit when the full system is an energy eigenstate. This reduced density matrix is close in trace distance to a density matrix, to which we refer as the ETH density matrix, that is independent of all the details of an eigenstate except its energy and charges under global symmetries. In two dimensions, the ETH density matrix is universal for all theories with the …

First-Principles Investigation Of The Interfacial Properties Of Boron Nitride, Kevin Waters

Dissertations, Master's Theses and Master's Reports

The interactions of nanomaterial surfaces with biological compounds, e.g. proteins, DNA, etc., unites the biological regime and nanomaterial world. Hybrid systems of boron-nitride nanotubes (BNNTs) and biological compounds are well-suited for a broad range of applications. First-principles methods are used to characterize the interface of these hybrid systems. Previous work has shown that the sensing capabilities of pristine BNNT are limited by long-ranged interactions. In this study the surfaces of pristine and functionalized BNNTs are investigated. The surfaces of the functionalized BNNTs give new properties to the tubes, which may enhance their sensing capabilities, while retaining their stability and chemical …

Wave Function For Harmonically Confined Electrons In Time-Dependent Electric And Magnetostatic Fields, Hong-Ming Zhu, Jin-Wang Chen, Xiao-Yin Pan, Viraht Sahni

Publications and Research

We derive via the interaction “representation” the many-body wave function for harmonically confined electrons in the presence of a magnetostatic field and perturbed by a spatially homogeneous time-dependent electric field—the Generalized Kohn Theorem (GKT) wave function. In the absence of the harmonic confinement – the uniform electron gas – the GKT wave function reduces to the Kohn Theorem wave function. Without the magnetostatic field, the GKTwave function is the Harmonic Potential Theorem wave function. We further prove the validity of the connection between the GKT wave function derived and the system in an accelerated frame of reference. Finally, we provide …

Quantumness And Coherence In Photosynthesis, Brian Doolittle

Honors Theses

Long-lived oscillations lasting up to 1800 fs have been observed in the Fenna--Mathews--Olsen (FMO) Pigment-Protein complex. It is unclear if the oscillations are quantum or classical in origin. Quantized intra-pigment normal modes are responsible for these long-lived oscillations. In this thesis we simulate a bacteriachlorophyll dimer in the FMO Complex at physiological conditions. Our model describes two electronically coupled pigments coupled to the vibrational protein environment. Our goal is to find system parameters that allow long-lived quantum coherences to exist in photosynthetic complexes. We calculate the time evolution of our system's density matrix using the numerically exact quantum adiabatic path …

Wave Function For Time-Dependent Harmonically Confined Electrons In A Time-Dependent Electric Field, Yu-Qi Li, Xiao-Yin Pan, Viraht Sahni

Publications and Research

The many-body wave function of a system of interacting particles confined by a time-dependent harmonic potential and perturbed by a time-dependent spatially homogeneous electric field is derived via the Feynman path-integral method. The wave function is comprised of a phase factor times the solution to the unperturbed time-dependent Schrödinger equation with the latter being translated by a time-dependent value that satisfies the classical driven equation of motion. The wave function reduces to that of the Harmonic Potential Theorem wave function for the case of the time-independent harmonic confining potential.

Novel Materials For Use In Homeland Security Research, Jason Osgood Ewen Young

Masters Theses & Specialist Projects

Organometallic pyridazines and compounds derived from them have been of interest in polymer research due to their atypical environmental stability (as compared to other non-aromatic organic semiconductors) as well as their conductivity. The off-metal synthesis and characterization of several pyridazyl thallium, manganese, and rhenium complexes, beginning with fulvenes 1,2- C5H3(COHR)(COR), are reported here. The diacyl fulvenes were treated with hydrazine hydrate to ring close to pyridazines. Next, the pyridazines were converted to their respective thallium salts through treatment with thallium (I) ethoxide. Lastly, the salts were transmetallated into the respective rhenium or manganese complexes through treatment with the respective metal …

Modeling Of Solvent Electrostatic Effects, Jose A. Rodriguez Lopez^, Luis Basurto, Tunna Baruah*

COURI Symposium Abstracts, Spring 2011

The photo-induced charge-transfer process is fundamental to light harvesting in organic donor-acceptor systems. The process is often enhanced when the system is in a polar solvent. The aim of this project is to create a simple, discrete model containing dipoles that can explain the solvent effects, where only dipole-dipole solvent interaction is considered. The goal is to reduce computational complexities and cost. We create a grid of solvents (water) which mimic the solvent’s density; and put one solute (a light-harvesting triad of β-carotene, porphyrin, and C60) at the grid’s center, keeping the grid points 1.5 times the Van der Waal …

Wave-Function Functionals For The Density, Marlina Slamet

Physics Faculty Publications

We extend the idea of the constrained-search variational method for the construction of wave-function functionals ψ[χ] of functions χ. The search is constrained to those functions χ such that ψ[χ] reproduces the density ρ(r) while simultaneously leading to an upper bound to the energy. The functionals are thereby normalized and automatically satisfy the electron-nucleus coalescence condition. The functionals ψ[χ] are also constructed to satisfy the electron-electron coalescence condition. The method is applied to the ground state of the helium atom to construct functionals ψ[χ] that reproduce the density as given by the Kinoshita correlated wave function. The expectation …