The Impacts Of The Molecular Education And Research Consortium In Undergraduate Computational Chemistry On The Careers Of Women In Computational Chemistry,
2022
Roanoke College
The Impacts Of The Molecular Education And Research Consortium In Undergraduate Computational Chemistry On The Careers Of Women In Computational Chemistry, Kelly Anderson, Sarah Arradondo, K Aurelia Ball, Chrystal D. Bruce, Maria A. Gomez, Kedan He, Heidi Hendrickson, Lindsey Madison, Ashley Ringer Mcdonald, Maria C. Nagan, Carol Parish, Caitlin E. Scott, Patricia Soto, Aime'e Tomlinson, Mychel Varner
2022 Faculty Bibliography
The Molecular Education and Research Consortium in Undergraduate Computational Chemistry (MERCURY) has supported a diverse group of faculty and students for over 20 years by providing computational resources as well as networking opportunities and professional support. The consortium comprises 38 faculty (42% women) at 34 different institutions, who have trained nearly 900 undergraduate students, more than two-thirds of whom identify as women and one-quarter identify as students of color. MERCURY provides a model for the support necessary for faculty to achieve professional advancement and career satisfaction. The range of experiences and expertise of the consortium members provides excellent networking opportunities …
Analyzing The Free Energy Of Ions Sampling A Voltage Gated Sodium Ion Channel,
2022
Colby College
Analyzing The Free Energy Of Ions Sampling A Voltage Gated Sodium Ion Channel, Isabel Varghese
Honors Theses
Voltage gated sodium ion channels are implicated in cardiac diseases, seizures, etc., and they play a role in maintaining ionic homeostasis in cells. Computational studies use prokaryotic model because they are simpler but function similarly to human voltage gated sodium ion channels. This study uses molecular dynamics (MD) to study three specific questions regarding voltage gated sodium ion channels of Magnetococcus marinus. The first question in this study is how the free energy of sodium diffusion compares to that of calcium ion diffusion. We were not able to find any physically significant information due to poor sampling and a lack …
Development Of Accurate And Efficient Computational Methodologies For Predicting Protein-Ligand And Protein-Protein Binding Free Energies,
2022
University of Kentucky
Development Of Accurate And Efficient Computational Methodologies For Predicting Protein-Ligand And Protein-Protein Binding Free Energies, Alexander Hamilton Williams
Theses and Dissertations--Pharmacy
Computational modeling is an invaluable tool in the drug discovery process either for small ligand or protein therapeutics. The widespread availability of protein X-Ray Crystal and Cryo-Electron Microscopy (Cryo-EM) structures has allowed for more accurate molecular dynamics (MD) simulations that are not reliant on methods such as homology modeling, which may produce structures that require significant computational time to demonstrate their stability. In this thesis we describe several novel methodologies for the computationally efficient modeling of protein/ligand and protein/protein complexes that may be employed within both large-scale virtual screenings and lead compound optimization. These methodologies may also be utilized in …
Theoretical Investigation On Optical Properties Of 2d Materials And Mechanical Properties Of Polymer Composites At Molecular Level,
2022
Michigan Technological University
Theoretical Investigation On Optical Properties Of 2d Materials And Mechanical Properties Of Polymer Composites At Molecular Level, Geeta Sachdeva
Dissertations, Master's Theses and Master's Reports
The field of two-dimensional (2D) layered materials provides a new platform for studying diverse physical phenomena that are scientifically interesting and relevant for technological applications. Theoretical predictions from atomically resolved computational simulations of 2D materials play a pivotal role in designing and advancing these developments. The focus of this thesis is 2D materials especially graphene and BN studied using density functional theory (DFT) and molecular dynamics (MD) simulations. In the first half of the thesis, the electronic structure and optical properties are discussed for graphene, antimonene, and borophene. It is found that the absorbance in (atomically flat) multilayer antimonene (group …
From Evaluating The Performance Of Approximations In Density Functional Theory To A Machine Learning Design,
2022
West Virginia University
From Evaluating The Performance Of Approximations In Density Functional Theory To A Machine Learning Design, Pedram Tavazohi
Graduate Theses, Dissertations, and Problem Reports (ETD)
Density-functional theory (DFT) has gained popularity because of its ability to predict the properties of a large group of materials a priori. Even though DFT is exact, there are inaccuracies introduced into the theory due to the approximations in the exchange-correlation (XC) functionals. Over the 50 years of its existence, scientists have tried to improve the design of the XC functionals. The errors introduced by these functionals are not consistent across all types of solid-state materials. In this project, a high throughput framework was utilized to compare the theoretical DFT predictions with the experimental results available in the Inorganic Crystal …
Nonhematopoietic Erythropoietin: A Study Of Signaling, Structure, And Behavior,
2022
University of South Dakota
Nonhematopoietic Erythropoietin: A Study Of Signaling, Structure, And Behavior, Nicholas John Pekas
Dissertations and Theses
Erythropoietin (EPO) is a cytokine hormone known for initiating red blood cell proliferation by binding to its homodimer receptor (EPOR)2 in the bone marrow. Recent progress in neurobiology has shown that EPO also exerts robust neurotrophic and neuroprotective activity in the CNS. It is widely thought that EPO’s neurotrophic activity is centrally involved in its antidepressant and cognitive enhancing effects. However, EPO’s potent erythropoietic effects prevent it from being used in the clinic to treat psychiatric disorders. A chemically engineered non-erythropoietic derivative of EPO, carbamoylated EPO (CEPO), produces psychoactive effects without activating hematopoiesis. However, CEPO is expensive to produce and …
Density Functional Theory Of Samarium(Ii) Reactivity In Thf And Water,
2022
University of South Dakota
Density Functional Theory Of Samarium(Ii) Reactivity In Thf And Water, Parisa Fasihianifard
Dissertations and Theses
Sm(II) diiodide is widely used in organic synthesis for the reduction of functional groups such as esters, anhydrides, amides, carbonyls, and arenes. Moreover, in aqueous systems and in mixtures of water and THF, the addition of Sm(II) diiodide can reduce water directly resulting in the formation of hydrogen gas. However, the mechanism of these reactions is not completely understood, making it difficult to improve experimental design. The reaction can proceed either through subsequent electron-transfer proton-transfer (ET-PT), subsequent proton transfer electron-transfer (PT-ET), or via proton coupled electron transfer (PCET). Density functional theory (DFT) calculations were performed to understand the speciation of …
Heterogeneous Oxidation Of Multi-Component Aqueous Organic Aerosols: The Effect Of Transport Phenomena And Reaction Compartment On Reaction Kinetics.,
2022
West Virginia University
Heterogeneous Oxidation Of Multi-Component Aqueous Organic Aerosols: The Effect Of Transport Phenomena And Reaction Compartment On Reaction Kinetics., Tadini Wenyika Masaya
Graduate Theses, Dissertations, and Problem Reports (ETD)
The surface-bulk partitioning of small organic molecules in aqueous droplets was investigated using molecular dynamics. The air-particle interface was modeled using a 80-Å cubic water box containing series of organic molecules and surrounded by gaseous OH radicals. The properties of the organic solutes within the interface and the water-bulk were examined at a molecular-level using density profiles and radial pair distribution functions. Molecules containing only polar functional groups such as urea and glucose are found predominantly in the water bulk, forming an exclusion layer near the water surface. Substitution of a single polar group by an alkyl group in sugars …
Multilevel Computational Investigation Into The Dynamics And Reaction Mechanisms Of Non-Heme Iron And 2-Oxoglutarate Dependent Enzymes,
2022
Michigan Technological University
Multilevel Computational Investigation Into The Dynamics And Reaction Mechanisms Of Non-Heme Iron And 2-Oxoglutarate Dependent Enzymes, Shobhit Sanjeev Chaturvedi
Dissertations, Master's Theses and Master's Reports
Computational chemistry methods have been extensively applied to investigate biological systems. This dissertation utilizes a multilevel computational approach to explore the dynamics and reaction mechanisms of two groups of enzymes belonging to non-heme Fe(II) and 2-oxoglutarate (2OG) dependent superfamily – histone lysine demethylases from class 7 and ethylene forming enzyme (EFE). Chapter 2 uncovers the role of conformational dynamics in the substrate selectivity of histone lysine demethylases 7A and 7B. The molecular dynamics (MD) simulations of the two enzymes revealed the importance of linker flexibility and dynamics in relative orientations of the reader (PHD) and the catalytic (JmjC) domains. Chapter …
Fluorescence Probes For Bioimaging: Synthesis, Photophysical Properties And Applications,
2021
New Jersey Institute of Technology
Fluorescence Probes For Bioimaging: Synthesis, Photophysical Properties And Applications, Mehrun Nahar Uddin
Dissertations
Fluorescent probes are a vital tool in the study of cell imaging. There are many types of fluorescent probes ranging from inorganic and organic nanoparticles to organic molecules. When used judiciously, they can help provide essential information on cellular structure and function. The introduction of two-photon microscopy has expanded the need for new probes, in particular near-infrared (NIR) absorbing and emitting fluorescent probes. The photochemical and photophysical properties of NIR probes play a crucial role in their effectiveness in cell imaging by both conventional and two-photon excitation (2PE) microscopy. In this research, the synthesis, photophysical properties, and two-photon absorption (2PA) …
Cyclic Voltammetric Simulations On Batteries With Porous Electrodes,
2021
Materials Genome Institute, Shanghai University, Shanghai 200444, China;
Cyclic Voltammetric Simulations On Batteries With Porous Electrodes, Xue-Fan Cai, Sheng Sun
Journal of Electrochemistry
Lithium-ion batteries (LIBs) are among the most widely used energy storage devices. Whole-cell modeling and simulations of LIBs can optimize the design of batteries with lower costs and higher speeds. The Pseudo-Two-Dimensional (P2D) electrochemical model is among the most famous whole-cell models and widely applied in LIB simulations. P2D model consists of a series of kinetic equations to model Li+/Li diffusion in working/counter electrodes and electrolytes, which are filled in the porous electrodes and separator, and reactions at the interface of electrolyte and active particles. The traditional applications of P2D model, however, are limited to the cases where …
Adsorption Of Helium On A Charged Propeller Molecule: Hexaphenylbenzene,
2021
University of Innsbruck
Adsorption Of Helium On A Charged Propeller Molecule: Hexaphenylbenzene, Siegfried Kollotzek, Florent Calvo, Serge Krasnokutski, Fabio Zappa, Paul Scheier, Olof E. Echt
Faculty Publications
Physisorption on planar or curved graphitic surfaces or aromatic rings has been investigated by various research groups, but in these studies the substrate was usually strictly rigid. Here we report a combined experimental and theoretical study of helium adsorption on cationic hexaphenylbenzene (HPB), a propeller-shaped molecule. The orientation of its propeller blades is known to be sensitive to the environment, with substantial differences between the molecule in the gas phase and in the crystalline solid. Mass spectra of HenHPB+, synthesized in helium nanodroplets, indicate enhanced stability for ions containing n = 2, 4, 14, 28, 42, …
Dft Study Of NiM@Pt1AuN-M-1 (N=19, 38, 55, 79; M = 1, 6, 13, 19) Core-Shell Orr Catalyst,
2021
1. State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, Liaoning, China;
Dft Study Of NiM@Pt1AuN-M-1 (N=19, 38, 55, 79; M = 1, 6, 13, 19) Core-Shell Orr Catalyst, Wen-Jie Li, Dong-Xu Tian, Hong Du, Xi-Qiang Yan
Journal of Electrochemistry
The slow kinetics of oxygen reduction reaction (ORR) limits the performance of low temperature fuel cells. Thus, it needs to design effective catalysts with low cost. Core-shell clusters (CSNCs) show promising activity because of their size-dependent geometric and electronic effects. The ORR activity trend of Nim@Pt1Aun-m-1(n = 19, 38, 55, 79; m = 1, 6, 13, 19) was studied using the GGA-PBE-PAW methods. The adsorption configurations of *O, *OH and *OOH were optimized and the reaction free energies of four proton electron (H+ + e-) transfer steps …
Computational Methodologies For The Simulation And Analysis Of Low-Frequency Vibrations In Molecular Crystals,
2021
Syracuse University
Computational Methodologies For The Simulation And Analysis Of Low-Frequency Vibrations In Molecular Crystals, Sara Jean Dampf
Dissertations - ALL
Quantum mechanical models are used to calculate a host of physical phenomena in molecular solids ranging from mechanical elasticity to the energetic stability ordering of polymorphs. However, with the many software packages and methodologies available, it can be difficult to select the most suitable model for the problem at hand without prior knowledge. A promising approach for evaluating the performance of solid-state models is the comparison of the simulations to experimentally measured low-frequency (sub-200 cm-1) vibrational spectra. As this region is dominated by weak intermolecular forces and shallow potential energy surfaces, even slight miscalculations in the solid-state packing arrangements can …
Molecular Simulation Of Rna Conformational Dynamics : An Example Of Micro-Rna Targeting Messenger Rna : Mir-34a-Msirt1,
2021
University at Albany, State University of New York
Molecular Simulation Of Rna Conformational Dynamics : An Example Of Micro-Rna Targeting Messenger Rna : Mir-34a-Msirt1, Parisa Ebrahimi
Legacy Theses & Dissertations (2009 - 2024)
MicroRNA (miRNA), as a distinct class of biological regulators and a ”guide” member of non-coding RNA-protein complexes (RNPs), regulates more than 60% of protein-coding genes expression through base-pairing with targeted messenger RNA (mRNA) in the RNA-Induced Silencing Complex (RISC). Most of miRNAs identified in human, are conserved in other animals, which have preferentially conserved interaction sites particularly in 3’ untranslated regions (3’UTRs) of many human messenger mRNAs.The capability of a single miRNA to target more than hundreds of mRNAs, suggests that miRNAs influence essentially all developmental process and diseases, which also makes them interesting candidates as therapeutics agents. The primary …
Structural, Dynamic, Elastic And Electronic Properties Of Anin (A = Li, Na, Mg, Ca): First-Principles Calculations,
2021
1. Department of Physics, Xiamen University, Xiaman 361005, Fujian, China;
Structural, Dynamic, Elastic And Electronic Properties Of Anin (A = Li, Na, Mg, Ca): First-Principles Calculations, Xia-Min Huang, Li-Hong Zhang, Shun-Qing Wu, Yong Yang, Zi-Zhong Zhu
Journal of Electrochemistry
Ternary transition metal nitrides ANiN (A = Li, Na, Mg, Ca) are potential electrode materials for rechargeable batteries. The physical properties, such as the thermodynamic stability, the electronic band gap as well as the elastic stability, are important for their battery applications. Here, comparative studies are performed for the structural, dynamic, elastic and electronic properties of ANiN by the first-principles method. The calculations on the cohesive energy versus unit-cell volume and phonon spectra are employed to determine the most stable structures of ANiN. The calculated elastic constants of the most stable structures indicate that the Born-Huang criterion for the elastic …
Complexes With Atomic Gold Ions: Efficient Bisligand Formation,
2021
University of Innsbruck
Complexes With Atomic Gold Ions: Efficient Bisligand Formation, Felix Duensing, Elisabeth Gruber, Paul Martini, Marcelo Goulart, Michael Gatchell, Bilal Rasul, Olof E. Echt, Fabio Zappa, Masoomeh Mahmoodi-Darian, Paul Scheier
Faculty Publications
Complexes of atomic gold with a variety of ligands have been formed by passing helium nanodroplets (HNDs) through two pickup cells containing gold vapor and the vapor of another dopant, namely a rare gas, diatomic molecule (H2, N2, O2, I2, P2), or various polyatomic molecules (H2O, CO2, SF6, C6H6, adamantane, imidazole, di-cyclopentadiene, and fullerene). The doped HNDs were irradiated by electrons; ensuing cations were identified in a high-resolution mass spectrometer. Anions were detected for benzene, di-cyclopentadiene, and fullerene. For most …
Computational Algorithms For Predicting Membrane Protein Assembly From Angstrom To Micron Scale,
2021
Syracuse University
Computational Algorithms For Predicting Membrane Protein Assembly From Angstrom To Micron Scale, Nandhini Rajagopal
Dissertations - ALL
Biological barriers in the human body are one of the most crucial interfaces perfected through evolution for diverse and unique functions. Of the wide range of barriers, the paracellular protein interfaces of epithelial and endothelial cells called tight junctions with high molecular specificities are vital for homeostasis and to maintain proper health. While the breakdown of these barriers is associated with serious pathological consequences, their intact presence also poses a challenge to effective delivery of therapeutic drugs. Complimenting a rigorous combination of in vitro and in vivo approaches to establishing the fundamental biological construct, in addition to elucidating pathological implications …
Sf6+: Stabilizing Transient Ions In Helium Nanodroplets,
2021
University of Innsbruck
Sf6+: Stabilizing Transient Ions In Helium Nanodroplets, Simon Albertini, Stefan Bergmeister, Felix Laimer, Paul Martini, Elisabeth Gruber, Fabio Zappa, Milan Ončák, Paul Scheier, Olof E. Echt
Faculty Publications
There are myriads of ions that are deemed too short-lived to be experimentally accessible. One of them is SF6+. It has never been observed, although not for lack of trying. We demonstrate that long-lived SF6+ can be formed by doping charged helium nanodroplets (HNDs) with sulfur hexafluoride; excess helium is then gently stripped from the doped HNDs by collisions with helium gas. The ion is identified by high-resolution mass spectrometry (resolution m/Dm = 15000), the close agreement between the expected and observed yield of ions that contain minor sulfur isotopes, and collision-induced dissociation …
Electronic Transitions In Rb2+ Dimers Solvated In Helium,
2021
University of Innsbruck
Electronic Transitions In Rb2+ Dimers Solvated In Helium, Simon Albertini, Paul Martini, Arne Schiller, Harald Schöbel, Elham Ghavidel, Milan Ončák, Olof E. Echt, Paul Scheier
Faculty Publications
We have measured depletion spectra of the heteronuclear (85Rb87Rb+) dimer cation complexed with up to 10 He atoms. Two absorption bands are observed between 920 and 250 nm. The transition into the repulsive 12Sigmau+ state of HeRb2+ gives rise to a broad feature at 790 nm (12650 cm–1); it exhibits a blueshift of 98 cm–1 per added He atom. The transition into the bound 1 2Piu state of HeRb2+ reveals vibrational structure with a band head at < 15522 cm–1, a harmonic …
