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 bound to five carbonyl groups and one bromide (MnCO5Br, ReCO5Br). Our research focused on the synthesis of a variety of 5,6-fused ring pyridazines that will act as a model for homeland security research in polymer studies and medicinal research. Synthesis and characterization of several aryl-substituted 5,6-fused ring pyridazines have been completed. The fulvenes, pyridazines, and thallium salts are important compounds for research due to their reactivity and stability in moisture and air. The complexes synthesized were confirmed using mass spectrometry, infrared spectroscopy, nuclear magnetic resonance spectroscopy, and elemental analysis. Single crystal X-ray diffraction confirmed the structure of x compound 1A. As evidenced by related previous papers published by the research group, the synthesized complexes displayed stability to air, moisture, and temperature.18, 19, 23, 25

Telechelic associating polymer networks consist of polymer chains terminated by endgroups that have a different chemical composition than the polymer backbone. When dissolved in a solution, the endgroups cluster together to form aggregates. At low temperature, a strongly connected reversible network is formed and the system behaves like a gel. Telechelic networks are of interest since they are representative for biopolymer networks (e.g. F-actin) and are widely used in medical applications (e.g. hydrogels for tissue engineering, wound dressings) and consumer products (e.g. contact lenses, paint thickeners). In this thesis such systems are studied by means of a molecular dynamics/Monte Carlo simulation. At first, the system in rest is studied by means of graph theory. The changes in network topology upon cooling to the gel state, are characterized. Hereto an extensive study of the eigenvalue spectrum of the gel network is performed. As a result, an in-depth investigation of the eigenvalue spectra for spatial ER, scale-free, and small-world networks is carried out. Next, the gel under the application of a constant shear is studied, with a focus on shear banding and the changes in topology under shear. Finally, the relation between the gel transition and percolation is discussed.

Multifunctional proteins that undergo major structural changes to perform different functions are known as “Transformer Proteins”, which is a recently identified class of proteins. One such protein that shows a remarkable structural plasticity and has two distinct functions is the transcription antiterminator, RfaH. Depending on the interactions between its N-terminal domain and its C-terminal domain, the RfaH CTD exists as either an all-α-helix bundle or all-β-barrel structure. Another example of a transformer protein is the Ebola virus protein VP40 (eVP40), which exists in different conformations and oligomeric states (dimer, hexamer, and octamer), depending on the required function.I performed Molecular Dynamics (MD) computations to investigate the structural conversion of RfaH-CTD from its all-a to all-b form. I used various structural and statistical mechanics tools to identify important residues involved in controlling the conformational changes. In the full-length RfaH, the interdomain interactions were found to present the major barrier in the structural conversion of RfaH-CTD from all-a to all-b form. I mapped the energy landscape for the conformational changes by calculating the potential of mean force using the Adaptive Biasing Force and Jarzynski Equality methods. Similarly, the interdomain salt-bridges in the eVP40 protomer were found to play a critical role in domain association and plasma membrane (PM) assembly. This molecular dynamic simulation study is supported by virus like particle budding assays investigated by using live cell imaging that highlighted the important role of these saltbridges. I also investigated the plasma membrane association of the eVP40 dimer in various PM compositions and found that the eVP40 dimer readily associates with the PM containing POPS and PIP2 lipids. Also, the CTD helices were observed to be important in stabilizing the dimer-membrane complex. Coarse-grained MD simulations of the eVP40 hexamer and PM system revealed that the hexamer enhances the PIP2 lipid clustering at the lower leaflet of the PM. These results provide insight on the critical steps in the Ebola virus life cycle.

Fluorescent proteins are valuable tools as biochemical markers for studying cellular processes. Red fluorescent proteins (RFPs) are highly desirable for in vivo applications because they absorb and emit light in the red region of the spectrum where cellular autofluorescence is low. The naturally occurring fluorescent proteins with emission peaks in this region of the spectrum occur in dimeric or tetrameric forms. The development of mutant monomeric variants of RFPs has resulted in several novel FPs known as mFruits. Though oxygen is required for maturation of the chromophore, it is known that photobleaching of FPs is oxygen sensitive, and oxygen-free conditions result in improved photostabilities. Therefore, understanding oxygen diffusion pathways in FPs is important for both photostabilites and maturation of the chromophores. We used molecular dynamics calculations to investigate the protein barrel fluctuations in mCherry, which is one of the most useful monomeric mFruit variants, and its GFP homolog citrine. We employed implicit ligand sampling and locally enhanced sampling to determine oxygen pathways from the bulk solvent into the mCherry chromophore in the interior of the protein. The pathway contains several oxygen hosting pockets, which were identified by the amino acid residues that form the pocket. We calculated the free-energy of an oxygen molecule at points along the path. We also investigated an RFP variant known to be significantly less photostable than mCherry and find much easier oxygen access in this variant. We showed that oxygen pathways can be blocked or altered, and barrel fluctuations can be reduced by strategic amino acid substitutions. The results provide a better understanding of the mechanism of molecular oxygen access into the fully folded mCherry protein barrel and provide insight into the photobleaching process in these proteins.

The purpose of this research project was to study the αᵧ phase in Alnico 6. Other phases were studies for comparison. Also the effect of an applied magnetic field on the formation of the αᵧ phase was investigated. Three single crystals of Alnico 6 were heat treated for one hour—one at 1250°C, one at 1000°C, and one at 800°C—and water-quenched. The microstructure of each sample was observed with the optical microscope, and X-ray diffraction patterns were taken to determine the crystal structure of the phases present. Several single crystal samples of Alnico 6 were heat treated at 1000°C and furnace-cooled. Some of the samples were heat treated and furnace-cooled in the presence of an applied magnetic field of about 5000Oe, and the others were heat treated and furnace-cooled without an applied magnetic field. Each set of samples were electrothinned, and the microstructure of the αᵧ and α₁ ₊ α₂ phases was studied using the electron microscope. Electron diffraction patterns and electron micrographs were taken from αᵧ regions and α₁ ₊ α₂ regions of each sample. By a combination of X-ray and electron diffraction, it was determined that the crystal structure of the α, α₁, α₂ and αᵧ phases is body-centered cubic, with a lattice parameter of 2.87 Å. Electron diffraction showed that the crystal structure of the combined α₁ ₊ α₂ phases is ordered body-centered cubic, and that the lattices of these two phases are coherent. Other investigators have found that only the α₁ phase is ordered in Alnico 5 and Alnico 8 and thus is believed be the case in Alnico 6 also. Electron diffraction showed the αᵧ phase to be ordered, with the degree of ordering less than that in the α₁ phase. Some difference was noted between the αᵧ phase formed with a magnetic field and that formed without a magnetic field. The αᵧ formed with a magnetic field showed twinning and some small lattice rotations, while stat formed without a field did not. The reason for this is not known.

In this thesis, we have employed two computational methods, molecular dynamics (MD) and hybrid quantum mechanics/molecular mechanics (QM/MM) MD simulations with umbrella sampling (US), to gain insights into the molecular mechanism governing the molecular recognition and reactivity in several protein-ligand complexes. Three systems involving protein-ligand interactions are examined in this dissertation utilizing well-established computational methodologies and mathematical modeling. The three proteins studied here are acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1). These enzymes are known to interact with a variety of ligands. AChE dysfunction caused by organophosphorus (OP) chemicals is a severe hazard since AChE is a critical enzyme in neurotransmission. Oximes are chemical compounds that can reactivate inhibited AChE; hence in the development of better oximes, it is critical to understand the mechanism through which OPs block AChE. We have described the covalent inhibition mechanism between AChE and the OP insecticide phorate oxon and its more potent metabolites and established their free energy profiles using QM/MM MD-US for the first time. Our results suggest a concerted mechanism and provide insights into the challenges in reactivating phorate oxon inhibited AChE. Reactivating BChE is another therapeutic approach to detoxifying circulating OP molecules before reaching the target AChE. We explored the covalent modification of BChE with phorate oxon and its metabolites using hybrid quantum mechanics/molecular mechanics (QM/MM) umbrella sampling simulations (PM6/ff14SB) for the inhibition process. Our results reveal that the mechanism is distinct between the inhibitors. The PM6 methodology is a good predictor of these compounds' potency, which may efficiently help study OPs like phorate oxon with larger leaving groups. Finally, we investigated the interactions between Peptidyl-prolyl isomerase (PPIase), which consists of a peptidyl isomerase (PPIase) domain flexibly tethered to a smaller Trp-Trp (WW) protein-binding domain, and chimeric peptides based on the human histone H1.4 sequence (KATGAApTPKKSAKW), as well as the effects on inter-domain dynamics. Using explicit solvent MD simulations, simulated annealing, and native contact analysis, our modeling sugget that the residues in the N-terminal immediate to the pSer/Thr Pro site connect the PPIase and WW domains via a series of hydrogen bonds and native contacts.

The goal of this thesis has been to find a means of i) designing an active square particle, and ii) continuously varying its degree of activity with the objective of understanding the effects of activity on the various phases of granular matter. The motivations, results and limitations of our methods of creating active particles are discussed in this thesis. The applicability of a stochastic model based on the Langevin equation in 2D as well as implications for future experiments are also discussed.

Examples of superhydrophobic surfaces found in nature such as self-cleaning property of lotus leaf and walking on water ability of water strider have led to an extensive investigation in this area over the past few decades. When a water droplet rests on a textured surface, it may either form a liquid-solid-vapor composite interface by which the liquid droplet partially sits on air pockets or it may wet the surface in which the water replaces the trapped air depending on the surface roughness and the surface chemistry. Super water repellent surfaces have numerous applications in our daily life such as drag reduction, anti-icing, anti-fogging, energy conservation, noise reduction, and self-cleaning. In fact, the same concept could be applied in designing and producing surfaces that repel organic contaminations (e.g. low surface tension liquids). However, superoleophobic surfaces are more challenging to fabricate than superhydrophobic surfaces since the combination of multiscale roughness with re-entrant or overhang structure and surface chemistry must be provided. In this study, simple, cost-effective and potentially scalable techniques, i.e., airbrush and electrospray, were employed for the sake of making superhydrophobic and superoleophobic coatings with random and patterned multiscale surface roughness. Different types of silicon dioxide were utilized in this work to in order to study and to characterize the effect of surface morphology and surface roughness on surface wettability. The experimental findings indicated that super liquid repellent surfaces with high apparent contact angles and extremely low sliding angles were successfully fabricated by combining re-entrant structure, multiscale surface roughness, and low surface energy obtained from chemically treating the fabricated surfaces. In addition to that, the experimental observations regarding producing textured surfaces in mask-assisted electrospray were further validated by simulating the actual working conditions and geometries using COMSOL Multiphysics.

Ligands of the human monoamine transporters encompass a wide range of both illicit and therapeutic drugs that act upon neural circuitry related to reward, motivation, and the processing of salient stimuli. The present study utilizes two methods for analyzing transporter substrates and inhibitors in order to characterize activity and assess potency. The first measures transient changes in intracellular calcium as a surrogate for transporter activity by harnessing the electrical coupling of monoamine transporters and L-type calcium channels. This is used to analyze novel chimera of the strong hDAT inhibitors methylphenidate and 𝛼-PPP in order to assess the contribution of specific moieties to potency. The observed reduction in potency suggests that methylphenidate may bind to the transporter in a manner distinct from 𝛼-PPP, as chimera would otherwise be expected to show similar activity to parent compounds. These results highlight the importance of 𝛼-carbon substituents and the relatively small contribution of beta-carbon groups to inhibitor potency at hDAT, while the lack of activity at hSERT suggests potency is not strongly influenced by beta-carbon or N-alkyl substituents. In order to further characterize drug-transporter interaction, a method was developed to analyze the kinetics of binding and unbinding using both known and novel hNET ligands, including a series of N-alkyl derivatives of 4-methylamphetamine. The study emphasizes the importance of both association and dissociation kinetics to affinity and sets up a methodological framework with two ways for determining Kd, with notable advantages over current models. The results indicate that lengthening the N-alkyl chain of 4-methylamphetamine leads to a decrease in potency and a shift in activity from substrate to blocker, with the results of N-propyl 4-methylamphetamine in particular indicating the potential existence of multiple low-affinity binding sites, each with distinct on and off kinetics. The implications of these results help elucidate the mechanism of action of transporter ligands and set up a framework for future studies that can more specifically classify the interaction between transporters and inhibitors or releasing agents.

The capability to resolve the contributions from spectroscopically overlapping fluorophores has enabled significant breakthroughs in cellular imaging. However, commercial microscopes for this purpose use analog light detection with least squares curve-fitting analysis and improvements in sensitivity are needed. To this end, a microscope has been constructed with high throughput and single-photon detection capability. The fluorescence is separated through use of a prism spectrometer or a series of dichroic mirrors into four spectral bands and detected using four single-photon avalanche diode (SPAD) detectors, which provide high-quantum efficiency in the red spectral region. The detectors are connected to a time-correlated single photon counting module to provide sub-nanosecond temporal resolution for distinguishing fluorophores with different fluorescence lifetimes. Maximum-likelihood (ML) methods have been developed for analyzing the temporally and spectrally resolved photon count data from the SPADs to find the contributions from different fluorescent species and from background. Commercially available SPADs exhibit a count-rate dependent time shift in the impulse response function, and hence the instrument incorporates custom modified SPADs with improved timing stability. Nevertheless, there is still some time shift, and hence the ML-analysis has been extended to include this as an adjustable parameter for each individual SPAD. Monte Carlo simulations have also been developed to enable studies of the number of photons needed to resolve specific fluorophores.