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 …
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 …
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 …
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 …
Theoretical Study On Electrical Properties Of Molecular Junctions Of Viologen Derivatives,
2021
Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, China;
Theoretical Study On Electrical Properties Of Molecular Junctions Of Viologen Derivatives, Zhuan-Yun Cai, Jia Liu, Si-Yuan Guan, De-Yin Wu, Zhong-Qun Tian
Journal of Electrochemistry
In this paper, the electrical properties of molecular junctions formed N,N′-bis(4-thioalkyl)-4,4′-bipyridinium (viologen) moiety between two gold (Au) electrodes have been investigated by combining density functional theory and non-equilibrium Green’s functional approach. To modulate the viologen molecule to be a cation with one and two positive charges (V+ and V2+), we introduce one and two trifluoroacetic acid ions (TFA-) around the molecule, respectively. The valence states of V+ and V2+ are confirmed by checking Mulliken and NBO charges. Then the relationship between molecular conductance and electronic structures of the neutral state …
Computational Catalyst Discovery: Active Classification Through Myopic Multiscale Sampling,
2021
Carnegie Mellon University
Computational Catalyst Discovery: Active Classification Through Myopic Multiscale Sampling, Kevin Tran, Willie Neiswanger, Kirby Broderick, Eric Xing, Jeff Schneider, Zachary W. Ulissi
Machine Learning Faculty Publications
The recent boom in computational chemistry has enabled several projects aimed at discovering useful materials or catalysts. We acknowledge and address two recurring issues in the field of computational catalyst discovery. First, calculating macro-scale catalyst properties is not straightforward when using ensembles of atomic-scale calculations [e.g., density functional theory (DFT)]. We attempt to address this issue by creating a multi-scale model that estimates bulk catalyst activity using adsorption energy predictions from both DFT and machine learning models. The second issue is that many catalyst discovery efforts seek to optimize catalyst properties, but optimization is an inherently exploitative objective that is …
Application Of Graphene/Nickel Oxide Composite As A Humidity Sensor,
2021
Nanotechnology Research Centre (NTRC), The British University in Egypt (BUE), Suez Desert Road, El-Sherouk City, Cairo, 11837, Egypt
Application Of Graphene/Nickel Oxide Composite As A Humidity Sensor, Islam Gomaa, Medhat A. Ibrahim, Hanan Elhaes
Nanotechnology Research Centre
Molecular modeling analyses at Density functional theory DFT level was used to study the possible application of modified graphene (G) as gas sensor. A model molecules of graphene sheet was constructed then modified with nickel oxide NiO attached to graphene through covalent bonds forming G/NiO composite. DFT at B3LYP/6-31G(d,p) was utilized to investigate the physical properties of G; G/NiO; G/NiO/2H2O. Results show that interacting G/NiO composite with water molecules lowers the calculated energy of the formed structure reflecting the possibility of exposing G/NiO structure to humidity, since it forms more energetically stable composition that can be detected by a proper …
Numerical Simulations Of Current And Temperature Distribution Of Symmetrical Double-Cathode Solid Oxide Fuel Cell Stacks Based On The Theory Of Electric-Chemical-Thermal Coupling,
2020
1. Faculty of Civil Engineering and Mechanics, Jiangsu University, Zhenjiang 212013, China;2. Ningbo Institute of Material Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, China;
Numerical Simulations Of Current And Temperature Distribution Of Symmetrical Double-Cathode Solid Oxide Fuel Cell Stacks Based On The Theory Of Electric-Chemical-Thermal Coupling, Cheng-Rong Yu, Jian-Guo Zhu, Cong-Ying Jiang, Yu-Chen Gu, Ye-Xin Zhou, Zhuo-Bin Li, Rong-Min Wu, Zheng Zhong, Wan-Bing Guan
Journal of Electrochemistry
Solid oxide fuel cell (SOFC) is a high-efficient clean conversion device for future energy management. Because of the low antioxidant reduction ability and complex thermal stress, the structure of traditional asymmetrical thin anode-supported planar SOFC is easily to be broken under stack operating conditions. To overcome these defects, a new complete symmetrical SOFC based on double-sided cathodes was developed. To study the influences of gas flow direction and current collection mode on the cell performance inside stack, a numerical model was established by finite element method based on the theory of electro-thermo-chemo multiphysical coupling. By applying this model, the molar …
Fluorescence Spectroscopic And Molecular Modelling Studies On The Molecular Interaction Mechanism Of Bromodeoxyuridine With Human Serum Albumin,
2020
Universiti Malaya
Fluorescence Spectroscopic And Molecular Modelling Studies On The Molecular Interaction Mechanism Of Bromodeoxyuridine With Human Serum Albumin, Amira Adlin Roslan
Student Works (2020-2029)
The interaction of a nucleoside analogue, bromodeoxyuridine (BrdU) with human serum albumin (HSA) was studied to investigate the binding phenomenon and analyze the protein conformation upon BrdU binding. Multiple spectroscopic techniques, viz. intrinsic and three-dimensional (3-D) fluorescence, ultraviolet-visible (UV-Vis) absorption and circular dichroism (CD) spectroscopy along with molecular docking were used. A decrease in the Stern-Volmer constant (Ksv) with the increase in temperature suggested BrdU-induced quenching of protein fluorescence as static quenching and thus implied BrdU−HSA complex formation. This was also supported by UV-Vis absorption spectral results, showing hyperchromism in the absorption spectrum of HSA upon BrdU addition. Intermediate binding …
Identification Of Peptide Sequence To Block Dengue Virus Transmission Into Cells Via In Silico And In Vitro Assays,
2020
Universiti Malaya
Identification Of Peptide Sequence To Block Dengue Virus Transmission Into Cells Via In Silico And In Vitro Assays, Arumugam Aathe Cangaree
Student Works (2020-2029)
Dengue virus (DV) infection has become main public wellbeing concerns, affecting approximately 390 million people worldwide. This fact was reported by the World Health Organization. Yet, there is no commercial antiviral treatment for DV infection. Therefore, the development of potent and non-toxic anti-DV, as a complement for the existing treatment strategies, are urgently needed. Herein, we investigate a series of low molecular weight peptides inhibitors by aiming the cellular entry process as the promising approach to block DV infection. The peptides were designed based on previously reported peptide sequence, DN58opt (TWWCFYFCRRHHPFWFFYRHN), to identify minimal effective inhibitory sequence via molecular docking …
