Engineering Commons^™

Magnetized Inulin By Fe3o4 As A Bio-Nano Adsorbent For Treating Water Contaminated With Methyl Orange And Crystal Violet Dyes, Kamran Valizadeh, Amir Bateni, Nazanin Sojoodi, Maryam Rostami Ataabadi, Amir Hossein Behroozi, Ali Maleki, Zhenjiang You

Research outputs 2022 to 2026

Current work focuses on fabricating a new bio-nano adsorbent of Fe₃O₄@inulin nanocomposite via an in-situ co-precipitation procedure to adsorb methyl orange (MO) and crystal violet (CV) dyes from aqueous solutions. Different physical characterization analyses verified the successful fabrication of the magnetic nanocomposite. The adsorbent performance in dye removal was evaluated by varying initial dye concentration, adsorbent dosage, pH and temperature in 5110 mg/L, 0.10.8 g/L, 111 and 283 – 338 K, respectively. Due to the pH of zero point of charge and intrinsic properties of dyes, the optimum pHs were 5 and 7 for MO and …

Tunable Electronic Structure Via Dna-Templated Heteroaggregates Of Two Distinct Cyanine Dyes, Jonathan S. Huff, Matthew S. Barclay, Azhad U. Chowdhury, Lance K. Patten, Simon K. Roy, Aaron Sup, Austin Biaggne, Lan Li, Jeunghoon Lee, Paul H. Davis, Bernard Yurke, William B. Knowlton, Daniel B. Turner, Ryan D. Pensack

Materials Science and Engineering Faculty Publications and Presentations

Molecular excitons are useful for applications in light harvesting, organic optoelectronics, and nanoscale computing. Electronic energy transfer (EET) is a process central to the function of devices based on molecular excitons. Achieving EET with a high quantum efficiency is a common obstacle to excitonic devices, often owing to the lack of donor and acceptor molecules that exhibit favorable spectral overlap. EET quantum efficiencies may be substantially improved through the use of heteroaggregates─aggregates of chemically distinct dyes─rather than individual dyes as energy relay units. However, controlling the assembly of heteroaggregates remains a significant challenge. Here, we use DNA Holliday junctions to …

Molecular Dynamics Simulations Of Cyanine Dimers Attached To Dna Holliday Junctions, Austin Biaggne, Young C. Kim, Joseph S. Melinger, William B. Knowlton, Bernard Yurke, Lan Li

Materials Science and Engineering Faculty Publications and Presentations

Dye aggregates and their excitonic properties are of interest for their applications to organic photovoltaics, non-linear optics, and quantum information systems. DNA scaffolding has been shown to be effective at promoting the aggregation of dyes in a controllable manner. Specifically, isolated DNA Holliday junctions have been used to achieve strongly coupled cyanine dye dimers. However, the structural properties of the dimers and the DNA, as well as the role of Holliday junction isomerization are not fully understood. To study the dynamics of cyanine dimers in DNA, molecular dynamics simulations were carried out for adjacent and transverse dimers attached to Holliday …

Oblique Packing And Tunable Excitonic Coupling In Dna-Templated Squaraine Rotaxane Dimer Aggregates, Matthew S. Barclay, Christopher K. Wilson, Simon K. Roy, Olga A. Mass, Azhad U. Chowdhury, Jonathan S. Huff, Daniel B. Turner, Paul H. Davis, Bernard Yurke, William B. Knowlton, Jeunghoon Lee, Ryan D. Pensack

Materials Science and Engineering Faculty Publications and Presentations

When molecules are aggregated such that their excited states form delocalized excitons, their spatial arrangement, or packing, can be coarsely controlled by templating and finely controlled by chemical substitution; however, challenges remain in controlling their packing on intermediate length scales. Here, we use an approach based on mechanically interlocked molecules to promote an elusive oblique packing arrangement in a series of three squaraine rotaxane dimers. We template the squaraine rotaxane dimers using DNA and observe two excitonically split bands of near-equal intensity in their absorption spectra – a distinct signature of oblique packing, validated by theoretical modeling of the experimental …

Strategies For Controlling The Spatial Orientation Of Single Molecules Tethered On Dna Origami Templates Physisorbed On Glass Substrates: Intercalation And Stretching, Keitel Cervantes-Salguero, Austin Biaggne, John M. Youngsman, Brett M. Ward, Young C. Kim, Lan Li, John A. Hall, William B. Knowlton, Elton Graugnard, Wan Kuang

Electrical and Computer Engineering Faculty Publications and Presentations

Nanoarchitectural control of matter is crucial for next-generation technologies. DNA origami templates are harnessed to accurately position single molecules; however, direct single molecule evidence is lacking regarding how well DNA origami can control the orientation of such molecules in three-dimensional space, as well as the factors affecting control. Here, we present two strategies for controlling the polar (θ) and in-plane azimuthal (ϕ) angular orientations of cyanine Cy5 single molecules tethered on rationally-designed DNA origami templates that are physically adsorbed (physisorbed) on glass substrates. By using dipolar imaging to evaluate Cy5′s orientation and super-resolution microscopy, the absolute …

Characterizing Mode Anharmonicity And Huang–Rhys Factors Using Models Of Femtosecond Coherence Spectra, Matthew S. Barclay, Jonathan S. Huff, Ryan D. Pensack, Paul H. Davis, William B. Knowlton, Bernard Yurke, Jacob C. Dean, Paul C. Arpin, Daniel B. Turner

Materials Science and Engineering Faculty Publications and Presentations

Femtosecond laser pulses readily produce coherent quantum beats in transient–absorption spectra. These oscillatory signals often arise from molecular vibrations and therefore may contain information about the excited-state potential energy surface near the Franck–Condon region. Here, by fitting the measured spectra of two laser dyes to microscopic models of femtosecond coherence spectra (FCS) arising from molecular vibrations, we classify coherent quantum-beat signals as fundamentals or overtones and quantify their Huang–Rhys factors and anharmonicity values. We discuss the extracted Huang–Rhys factors in the context of quantum-chemical computations. This work solidifies the use of FCS for analysis of coherent quantum beats arising from …

Data-Driven And Multiscale Modeling Of Dna-Templated Dye Aggregates, Austin Biaggne, Lawrence Spear, German Barcenas, Maia Ketteridge, William B. Knowlton, Bernard Yurke, Lan Li

Materials Science and Engineering Faculty Publications and Presentations

Dye aggregates are of interest for excitonic applications, including biomedical imaging, organic photovoltaics, and quantum information systems. Dyes with large transition dipole moments (μ) are necessary to optimize coupling within dye aggregates. Extinction coefficients (ε) can be used to determine the μ of dyes, and so dyes with a large ε (>150,000 M⁻¹) should be engineered or identified. However, dye properties leading to a large ε are not fully understood, and low-throughput methods of dye screening, such as experimental measurements or density functional theory (DFT) calculations, can be time-consuming. In order to screen large datasets of molecules …

Chemistry And Functionality Of Plant Waxes: Applications Toward Postharvest Coatings, Francisco Miguel Angel Leyva Gutierrez

Doctoral Dissertations

The cuticle of all higher-plants is covered in lipidic layers of amorphous and crystalline waxes. The chemical composition and structure of cuticular waxes impart numerous functional properties to the surfaces of plants. Moreover, plant waxes are valuable industrial products with myriad applications; the postharvest coating of agricultural commodities for preservation serves as a salient example. There is an unfulfilled need in the agricultural sector for alternative wax materials to reduce reliance on imported waxes of botanical origin. Plant waxes are inherently complex mixtures composed of n-alkanes, as well as aliphatic alcohols, aldehydes, fatty acids, ketones, esters, and derivatives thereof. …

Metal Complexes Of Redox Active Ligands, Alexandra Chaparro, Parker Keller

Chemistry & Biochemistry Student Scholarship

Alexandra Chaparro ’22, Major: Biochemistry

Parker Keller ’24, Major: Chemistry

Mentor: Dr. Maria Carroll, Chemistry and Biochemistry

Our research focuses on synthesizing and studying the properties of metal complexes that contain redox active ligands. Ligands are molecules or ions that can bind to a metal ion, and this particular class of ligands is interesting because they can either accept or lose electrons. We synthesized zinc complexes, in order to measure the reduction potentials of the ligands, which provide information about the ease with which they accept electrons. We then synthesized iron complexes and determined their structures. These complexes are potentially …

A Preliminary Comparative Study Of Molecular Visualization Software For Education, Ruoming Shen

Modeling, Simulation and Visualization Student Capstone Conference

Chemistry and biology are sciences vital for understanding metabolic processes, developing disease treatments, and improving environmental conditions. With extensive knowledge of biochemistry, we can take advantage of a material’s unique chemical composition and properties in various applications. Visualization software is essential for analyzing complex chemical and biological structures and predicting their interactions with each other. This paper presents a preliminary study of three open source molecular visualization software tools - Visual Molecular Dynamics (VMD), Jmol, and Mol*, and evaluates their strengths and deficiencies. This paper utilizes the March Molecule of the Month, Vascular Endothelial Growth Factor (VEGF), from the Protein …

Tuning Between Quenching And Energy Transfer In Dna-Templated Heterodimer Aggregates, Azhad U. Chowdhury, Jonathan S. Huff, Matthew S. Barclay, Lance K. Patten, Aaron Sup, Natalya Hallstrom, Jeunghoon Lee, Paul H. Davis, Daniel B. Turner, Bernard Yurke, William B. Knowlton, Ryan D. Pensack

Materials Science and Engineering Faculty Publications and Presentations

Molecular excitons, which propagate spatially via electronic energy transfer, are central to numerous applications including light harvesting, organic optoelectronics, and nanoscale computing; they may also benefit applications such as photothermal therapy and photoacoustic imaging through the local generation of heat via rapid excited-state quenching. Here we show how to tune between energy transfer and quenching for heterodimers of the same pair of cyanine dyes by altering their spatial configuration on a DNA template. We assemble “transverse” and “adjacent” heterodimers of Cy5 and Cy5.5 using DNA Holliday junctions. We find that the transverse heterodimers exhibit optical properties consistent with excitonically interacting …

Influence Of Hydrophobicity On Excitonic Coupling In Dna-Templated Indolenine Squaraine Dye Aggregates, Olga A. Mass, Christopher K. Wilson, German Barcenas, Lan Li, Bernard Yurke, William B. Knowlton, Ryan D. Pensack, Jeunghoon Lee

Materials Science and Engineering Faculty Publications and Presentations

Control over the strength of excitonic coupling in molecular dye aggregates is a substantial factor for the development of technologies such as light harvesting, optoelectronics, and quantum computing. According to the molecular exciton model, the strength of excitonic coupling is inversely proportional to the distance between dyes. Covalent DNA templating was proved to be a versatile tool to control dye spacing on a subnanometer scale. To further expand our ability to control photophysical properties of excitons, here, we investigated the influence of dye hydrophobicity on the strength of excitonic coupling in squaraine aggregates covalently templated by DNA Holliday Junction (DNA …

Uio-Type Metal-Organic Framework Derivatives As Sorbents For The Detection Of Gas-Phase Explosives, Matthew Ryan Sherrill

Legacy Theses & Dissertations (2009 - 2024)

The detection of energetic compounds – better known to the public as explosives – has is an important cornerstone of counterterrorism and homeland security . While significant advances have been achieved for the detection of trace explosives in various matrices such as soil, wastewater, and clothing, the detection of explosives in the gas phase remains challenging due to their infamously low vapor pressures. In this thesis, we leverage the high sensitivity of direct analysis in real-time mass spectrometry (DART-MS) and the microporosity of metal-organic frameworks (MOFs) to adsorb and therefore concentrate explosives from the vapor phase and subsequently detect them …