Biological and Chemical Physics Commons^™

Clinical Impact Of Couch To P And Rails On Imrt And Arc Therapy, Kiley B. Pulliam

Dissertations and Theses (Open Access)

Purpose: To evaluate the clinical impact of the Varian Exact Couch on dose and volume coverage to targets and critical structures and tumor control probability (TCP) for 6-MV IMRT and Arc Therapy.

Methods: Five clinical prostate patients were planned with both, 6-MV 8-field IMRT and 6-MV 2-field RapidArc using the Eclipse treatment planning system (TPS). These plans neglected treatment couch attenuation, as is standard clinical practice. Dose distributions were then recalculated in Eclipse with the inclusion of the Varian Exact Couch (imaging couch top) and the rails in varying configurations. The changes in dose and coverage were evaluated using the …

The Development And Implementation Of An Anthropomorphic Head Phantom For The Assessment Of Proton Therapy Treatment Procedures, Paige A. Summers

Dissertations and Theses (Open Access)

Proton therapy has become an increasingly more common method of radiation therapy, with the dose sparing to distal tissue making it an appealing option, particularly for treatment of brain tumors. This study sought to develop a head phantom for the Radiological Physics Center (RPC), the first to be used for credentialing of institutions wishing to participate in clinical trials involving brain tumor treatment of proton therapy. It was hypothesized that a head phantom could be created for the evaluation of proton therapy treatment procedures (treatment simulation, planning, and delivery) to assure agreement between the measured dose and calculated dose within …

Relativistic Transformation Of Phase-Space Distributions, R A. Treumann, R Nakamura, W Baumjohann

Dartmouth Scholarship

We investigate the transformation of the distri- bution function in the relativistic case, a problem of interest in plasma when particles with high (relativistic) velocities come into play as for instance in radiation belt physics, in the electron-cyclotron maser radiation theory, in the vicin- ity of high-Mach number shocks where particles are acceler- ated to high speeds, and generally in solar and astrophysical plasmas. We show that the phase-space volume element is a Lorentz constant and construct the general particle distri- bution function from first principles. Application to thermal equilibrium lets us derive a modified version of the isotropic relativisticthermaldistribution,themodifiedJu …

Photodissociation Of N2O: Energy Partitioning, Johan A. Schmidt, M. S. Johnson, U. Lorenz, George C. Mcbane, Reinhard Schinke

Peer Reviewed Articles

The energy partitioning in the UV photodissociation of N₂O is investigated by means of quantum mechanical wave packet and classical trajectory calculations using recently calculated potential energy surfaces. Vibrational excitation of N₂ is weak at the onset of the absorption spectrum, but becomes stronger with increasing photon energy. Since the NNO equilibrium angles in the ground and the excited state differe by about 70°, the molecule experiences an extraordinarily large torque during fragmentation producing N₂in very high rotational states. The vibrational and rotational distributions obtained from the quantum mechanical and the classical calculations agree remarkably …

On The Role Of Electrostatics In Protein–Protein Interactions, Zhe Zhang, Shawn Witham, Emil Alexov

Publications

The role of electrostatics in protein–protein interactions and binding is reviewed in this paper. A brief outline of the computational modeling, in the framework of continuum electrostatics, is presented and the basic electrostatic effects occurring upon the formation of the complex are discussed. The effect of the salt concentration and pH of the water phase on protein–protein binding free energy is demonstrated which indicates that the increase of the salt concentration tends to weaken the binding, an observation that is attributed to the optimization of the charge–charge interactions across the interface. It is pointed out that the pH-optimum (pH of …

Communication: Bubbles, Crystals, And Laser-Induced Nucleation, Brandon C. Knott, Jerry L. Larue, Alec M. Wodtke, Michael F. Doherty, Baron Peters

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Short intense laser pulses of visible and infrared light can dramatically accelerate crystal nucleation from transparent solutions; previous studies invoke mechanisms that are only applicable for nucleation of ordered phases or high dielectric phases. However, we show that similar laser pulses induce CO₂bubblenucleation in carbonated water. Additionally, in water that is cosupersaturated with argon and glycine, argon bubbles escaping from the water can induce crystal nucleation without a laser. Our findings suggest a possible link between laser-induced nucleation of bubbles and crystals.

In Silico And In Vitro Investigations Of The Mutability Of Disease-Causing Missense Mutation Sites In Spermine Synthase, Zhe Zhang, Joy Norris, Charles Schwartz, Emil Alexov

Publications

Background

Spermine synthase (SMS) is a key enzyme controlling the concentration of spermidine and spermine in the cell. The importance of SMS is manifested by the fact that single missense mutations were found to cause Snyder-Robinson Syndrome (SRS). At the same time, currently there are no non-synonymous single nucleoside polymorphisms, nsSNPs (harmless mutations), found in SMS, which may imply that the SMS does not tolerate amino acid substitutions, i.e. is not mutable.

Methodology/Principal Findings

To investigate the mutability of the SMS, we carried out in silico analysis and in vitro experiments of the effects of amino acid substitutions at the …

The Economics Of The Atomic Bomb: Cost And Utilization, Jonathan M. Davis Mr.

Senior Honors Theses

Few moments in human history can be compared to the culmination of events that brought the atomic bomb into creation.  It is incredible to contemplate that while a nation was fighting a two front war that spanned from Europe into the Pacific, that the United States was able to utilize the time, energy, brains, materials, manpower, and capital to complete a project in four years. That under any other circumstances would have taken greater than half a century to complete.

First, this thesis will discuss breakthroughs in research that led scientists to believe that the atomic weapons could be built, …

Hipsec X-Ray Diffraction And Infrared Spectroscopy Studies On Energetic Materials Under Extreme Conditions, Mai Huong Bausch, Yu Liu

Festival of Communities: UG Symposium (Posters)

We conducted a series of experiments on the decompositions of the energetic materials NaBH4, NH3BH3, HMX, and RDX under different pressures using the x-ray diffraction (XRD) technique; we also studied the lesser known but high-performance explosive FOX-7’s behaviors under high pressures using the infrared spectroscopy (IR) technique. For the chemical decomposition of NaBH4 and NH3BH3 we discovered possible x-ray induced hydrogen gas generation; for the decomposition of HMX and RDX, we discovered that the decay rates of these two materials vary with pressure respectively; for the study of FOX-7’s high pressure behaviors we discovered potential phase changes and pressure induced …

Macular Pigment: Practical Implications For Optometric Practice In Preventative Health Care And Visual Performance Enhancement, Grainne Scanlon

Masters

The macula is a specialised part of the retina responsible for detailed central and colour vision. The carotenoids, lutein, zeaxanthin and meso-zeaxanthin are uniquely concentrated in the inner and central layers of the primate macula, where they are known as macular pigment (MP). It has been shown that MP is entirely of dietary origin and that lutein and zeaxanthin levels in serum, diet and retina correlate. Age-Related Macular Degeneration (AMD) is a disease of the macula and results in loss of central vision. MP, because of its optical filtration and antioxidant properties, may have an important role in the prevention …

Two-Photon-Excited Tryptophan Fluorescence Microscopy For Leukocytes And Cancer Cells Imaging, Jesus A. Valdez^, Chunqiang Li*

COURI Symposium Abstracts, Spring 2011

Cancer screening and early diagnosis is an important yet controversial issue due to the safety and practicality of methods used. Our objective is to study the efficiency of an in vivo two-photon microscope developed in our laboratories to monitor cell inflammation. First, leukocytes were separated by subpopulation.  The tryptophan fluorescence intensity level of each type of leukocyte was then quantified with two-photon microscopy, in their naïve and inflamed states, respectively. Finally the tryptophan fluorescence intensity of multiple myeloma cells was quantified and correlated to the resulting images. The cancerous tissue auto-fluorescence from NADH and FAD was also recorded as a …

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 …

Combating Biological Terrorism From Imported Food, Jeffrey S. Nelson

Theses and Dissertations

There is a threat that a terrorist or terrorist organization will use access to the US food supply to kill or sicken Americans by contaminating imported food products from Mexico. The food that Americans eat is coming more and more often from foreign countries such as Mexico. Foodborne diseases infect nearly fifty million people in the US each year, resulting in over three thousand deaths. There are many terrorist organizations that would like to deliberately contaminate American food. Drug cartels and terrorist organizations currently operate in Mexico, one of the leading food importers into the US. The purpose of this …

Modeling Of Bacillus Spores: Inactivation And Outgrowth, Alexis X. Hurst

Theses and Dissertations

This research models and analyzes the thermochemical damage produced in Bacillus spores by short, high-temperature exposures as well the repair process within damaged Bacillus spores. Thermochemical damage in spores is significantly due to reaction with water, hydrolysis reactions. Applying heat to the spore causes absorbed and chemically bound water molecules become mobile within the spore. These mobile water molecules react by hydrolysis reactions to degrade DNA and enzyme molecules in the spore. In order to survive the thermal inactivation, the spore must repair the damaged DNA during spore germination. The DNA repair process, as well as other germination functions, is …

Collisional Transfer Of Population And Orientation In Nak, Seth T. Ashman, C. M. Wolfe, J. Bai, B. Beser, E. H. Ahmed, A. M. Lyyra, J. Huennekens

Engineering & Physics Faculty Publications

Collisional satellite lines with |ΔJ| ≤ 58 have been identified in recent polarization spectroscopy V-type optical–optical double resonance (OODR) excitation spectra of the Rb₂ molecule [H. Salami et al., Phys. Rev.A80, 022515 (2009)]. Observation of these satellite lines clearly requires a transfer of population from the rotational level directly excited by the pump laser to a neighboring level in a collision of the molecule with an atomic perturber. However to be observed in polarization spectroscopy, the collision must also partially preserve the angular momentum orientation, which is at least somewhat surprising given the extremely large values of …

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 …

Ultrafast Rempi In Benzene And The Monohalobenzenes Without The Focal Volume Effect, Timothy D. Scarborough, James Strohaber, David B. Foote, Collin J. Mcacy, Cornelis J. Uiterwaal

C.J.G.J. Uiterwaal Publications

We report on the photoionization and photofragmentation of benzene (C₆H₆) and of the monohalobenzenes C₆H₅–X (X = F, Cl, Br, I) under intense-field, single-molecule conditions. We focus 50-fs, 804-nm pulses from a Ti:sapphire laser source, and record ion mass spectra as a function of intensity in the range ~10¹³ W/cm² to ~10¹⁵ W/cm². We count ions that were created in the central, most intense part of the focal area; ions from other regions are rejected. For all targets, stable parent ions (C₆H₅X+) are …

Comparative Imaging Study In Ultrasound, Mri, Ct And Dsa Using A Multi-Modality Renal Artery Phantom, Deirdre King, Andrew Fagan, Carmel Moran, Jacinta Browne

Articles

A range of anatomically realistic multimodality renal artery phantoms consisting of vessels with varying degrees of stenosis was developed and evaluated using four imaging techniques currently used to detect renal artery stenosis (RAS). The spatial resolution required to visualize vascular geometry and the velocity detection performance required to adequately characterize blood flow in patients suffering from RAS are currently ill-defined, with the result that no one imaging modality has emerged as a gold standard technique for screening for this disease.

Methods:

The phantoms, which contained a range of stenosis values (0%, 30%, 50%, 70%, and 85%), were designed for use …

In Silico Modeling Of Ph-Optimum Of Protein-Protein Binding, Rooplekha C. Mitra, Zhe Zhang, Emil Alexov

Publications

Protein-protein association is a pH-dependent process and thus the binding affinity depends on the local pH. In vivo the association occurs in a particular cellular compartment, where the individual monomers are supposed to meet and form a complex. Since the monomers and the complex exist in the same micro environment, it is plausible that they coevolved toward its properties, in particular, toward the characteristic subcellular pH. Here we show that the pH at which the monomers are most stable (pH-optimum) or the pH at which stability is almost pH-independent (pH-flat) of monomers are correlated with the pH-optimum of maximal affinity …

New To Ols For Monitoring Gamma Camera Uniformity, Brad K. Lofton

Dissertations and Theses (Open Access)

Detector uniformity is a fundamental performance characteristic of all modern gamma camera systems, and ensuring a stable, uniform detector response is critical for maintaining clinical images that are free of artifact. For these reasons, the assessment of detector uniformity is one of the most common activities associated with a successful clinical quality assurance program in gamma camera imaging. The evaluation of this parameter, however, is often unclear because it is highly dependent upon acquisition conditions, reviewer expertise, and the application of somewhat arbitrary limits that do not characterize the spatial location of the non-uniformities. Furthermore, as the goal of any …

Systematic Approach To Electrostatically Induced 2d Crystallization Of Nanoparticles At Liquid Interfaces, Sumit Kewalramani, Suntao Wang, Yuan Lin, Huong Giang Nguyen, Qian Wang, Masafumi Fukuto, Lin Yang

Faculty Publications

We report an experimental demonstration of a strategy for inducing two-dimensional (2D)crystallization of charged nanoparticles on oppositely charged fluid interfaces. This strategy aims to maximize the interfacial adsorption of nanoparticles, and hence their lateral packing density, by utilizing a combination of weakly charged particles and a high surface charge density on the planar interface. In order to test this approach, we investigated the assembly of cowpea mosaic virus (CPMV) on positively charged lipid monolayers at the aqueous solution surface, by means of in situX-ray scattering measurements at the liquid–vapor interface. Theassembly was studied as a function of the solution …

Simulations Of Energetic Neutral Hydrogen: Creation, Transport & Loss, Eric Zirnstein

Von Braun Symposium Student Posters

No abstract provided.

Mapping Water Collisions For Interstellar Space Conditions, C.-H. Yang, G. Sarma, J. J. Ter Meulen, D. H. Parker, George C. Mcbane, Laurent Wiesenfeld, A. Faure

Peer Reviewed Articles

We report a joint experimental and theoretical study that directly tests the quality of the potential energy surfaces used to calculate energy changing cross sections of water in collision with helium and molecular hydrogen, at conditions relevant for astrophysics. Fully state-to-state differential cross sections are measured for H₂O-He and H₂O-H₂ collisions at 429 and 575 cm^-1 collision energy, respectively. We compare these differential cross sections with theoretical ones for H₂O+H₂ derived from state-of-the-art potential energy surfaces [P. Valiron et al., J. Chem. Phys. 129, 134306 (2008)] and quantum scattering …

Jahn-Teller Coupling And Fragmentation After Core-Shell Excitation Ini Cf4 Investigated By Partial-Ion-Yield Spectroscopy, Renaud Guillemin, Wayne C. Stolte, Maria Novella Piancastelli, Dennis W. Lindle

Chemistry and Biochemistry Faculty Research

We investigate fragmentation processes induced by core-level photoexcitation in CF4 at both the carbon and fluorine K edges by means of partial-ion-yield spectroscopy. The molecule CF₄ is a textbook example of systems in which Jahn-Teller coupling strongly manifests itself in the photoabsorption spectrum. Spectral features related to Jahn-Teller and quasi-Jahn-Teller splitting are observed, and important differences in the fragmentation pathways are revealed depending on the symmetries of the core-excited states. We interpret these experimental observations on the grounds of symmetry lowering from the Td to the C3v point group as well as preferential orientation with respect …

Site-Specific Photocatalytic Splitting Of Methanol On Tio2(110), Chuanyao Zhou, Zefeng Ren, Shijing Tan, Zhibo Ma, Xinchun Mao, Dongxu Dai, Hongjun Fan, Xueming Yang, Jerry L. Larue, Russell Cooper, Alec M. Wodtke, Zhou Wang, Zhenyu Li, Bing Wang, Jinlong Yang, Jianguo Hou

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Clean hydrogen production is highly desirable for future energy needs, making the understanding of molecular-level phenomena underlying photocatalytic hydrogen production both fundamentally and practically important. Water splitting on pure TiO₂ is inefficient, however, adding sacrificial methanol could significantly enhance the photocatalyzed H₂ production. Therefore, understanding the photochemistry of methanol on TiO₂ at the molecular level could provide important insights to its photocatalytic activity. Here, we report the first clear evidence of photocatalyzed splitting of methanol on TiO₂ derived from time-dependent two-photon photoemission (TD-2PPE) results in combination with scanning tunneling microscopy (STM). STM tip induced molecular manipulation …

Computational Analysis Of Missense Mutations Causing Snyder-Robinson Syndrome, Zhe Zhang, Shaolei Teng, Liangjiang Wang, Charles E. Schwartz, Emil Alexov

Publications

The Snyder-Robinson syndrome is caused by missense mutations in the spermine sythase gene that encodes a protein (SMS) of 529 amino acids. Here we investigate, in silico, the molecular effect of three missense mutations, c.267G>A (p.G56S), c.496T>G (p.V132G), and c.550T>C (p.I150T) in SMS that were clinically identified to cause the disease. Single-point energy calculations, molecular dynamics simulations, and pKa calculations revealed the effects of these mutations on SMS's stability, flexibility, and interactions. It was predicted that the catalytic residue, Asp276, should be protonated prior binding the substrates. The pKa calculations indicated the p.I150T mutation causes pKa changes …

High Pressure Infrared Studies Of Hmx, Jennifer Wojno, Michael G. Pravica, Martin Galley

Undergraduate Research Opportunities Program (UROP)

We are studying the effects of pressure on HMX (Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine) using infrared spectroscopy. The sample is put under pressure using a diamond anvil cell at ambient temperature, data is collected at the National Synchrotron Light Source in Brookhaven National Laboratory. In analyzing this data, we hope to learn more about the molecular vibrations as the molecule bends and deforms under pressure. Such understanding could aid in determining new safety standards or more efficient ways of using HMX. In future studies, we intend to include the aspect of temperature variation in addition to pressure, with the goal of describing the molecule …

High Pressure Structural Studies On Eus Nano Particles Up To 52 Gpa, Kristie Canaday, Ravhi S. Kumar

Undergraduate Research Opportunities Program (UROP)

Crystal size reduction in bulk materials changes the structural and magnetic properties considerably [1]. More importantly the transition pressure is strongly influenced by temperature, pressure, and the crystallite size effect. Rare earth europium chalcogenides crystallize in the NaCl (rock salt) type structure. The interest in Eu nanomaterials is motivated by the possibility of their use in magnetic devices [2,3]. Recent studies suggest that europium chalcogenide nanocrystals exhibit significant changes in their structural and magnetic properties, compared to bulk chalcogenides, when the nanocrystal diameter decreases. The crystal structure and phase transition behavior of EuS nanoparticles have been investigated and compared as …

High Pressure Studies Of Titanium Hydride Up To 50 Gpa With Synchrotron X-Ray Diffraction, Greg Harding, Patricia Kalita, Stanislav Sinogeikin, Andrew Cornelius

Undergraduate Research Opportunities Program (UROP)

Titanium dihydride has the potential to play an important role in the efficiency of high density hydrogen storage. The structural instability of TiH2 at high pressures makes an accurate characterization of its structure a vital part of understanding its behavior. A sample of TiH2 was placed in a diamond anvil cell and studied from ambient pressure up to 53 GPa using in situ synchrotron x-ray diffraction at the Advanced Photon Source (APS) of Argonne National Laboratory (Sector 16, HPCAT). From data of the evolution of the structure with pressure, an equation of state was obtained to model the behavior of …

Structural And Magnetic Properties Of Iron Clusters, Andrew Mohrland, Eunja Kim

Undergraduate Research Opportunities Program (UROP)

Electronic, magnetic, and chemical properties of Fe nanoparticles are of particular interest for materials science, engineering, and metallurgical applications, including biomedical applications (e.g., medical imaging, cancer treatment, etc.). In this study, we search for the most stable geometries of the Fe clusters, Fen, up to n=8. Binding energies, magnetic moments, bond lengths, bond angles, and charge densities of clusters are computed and compared to the available experimental data. The various cluster isomers were examined energetically. We found that, in general, higher dimensional geometries are more stable than lower dimensions (i.e., 1-dimension or 2-dimension). Calculations for the Fe dimer yield a …