A collection of published articles from members of the Department of Chemistry and Biochemistry.

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Submissions from 2023

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Structure and dynamics of whole-sequence homology model of ORF3a protein of SARS-CoV-2: An insight from microsecond molecular dynamics simulations, Shaila Akter, Md Jahirul Islam, Md Ackas Ali, Md Zakaria Tashrif, Md Jaish Uddin, M. Obayed Ullah, and Mohammad A. Halim

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Elucidating the Structure, Dynamics, and Interaction of a Choline Chloride and Citric Acid Based Eutectic System by Spectroscopic and Molecular Modeling Investigations, Md Ackas Ali, Md Abdul Kaium, Sayed Nesar Uddin, Md Jaish Uddin, Oluseyi Olawuyi, Albert D. Campbell, Carl Jacky Saint-Louis, and Mohammad A. Halim

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A CsoR family transcriptional regulator, TTHA1953, controls the sulfur oxidation pathway in Thermus thermophilus HB8, John K. Barrows and Michael W. Van Dyke

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Using Restriction Endonuclease, Protection, Selection, and Amplification to Identify Preferred DNA-Binding Sequences of Microbial Transcription Factors, John K. Barrows and Michael W. Van Dyke

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Azomethine-Containing Pyrrolo[3,2-b]pyrrole Copolymers for Simple and Degradable Conjugated Polymers, Kimberley A. Bartlett, Ariane Charland-Martin, Jonathan Lawton, Aimée L. Tomlinson, and Graham S. Collier

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Structural dynamics and functional analysis of Saprolegnia parasitica chitin synthases 5 in a phospholipid bilayer, Sourav Biswas, Md Rubel Hossen, Shaila Akter, Md Ackas Ali, Mohammad A. Halim, and M. Obayed Ullah

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Organophosphorus Compound Formation Through the Oxidation of Reduced Oxidation State Phosphorus Compounds on the Hadean Earth, Maheen Gull, Tian Feng, Joe Bracegirdle, Heather Abbott-Lyon, and Matthew A. Pasek

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In silico peptide-based therapeutics against human colorectal cancer by the activation of TLR5 signaling pathways, Md Rubel Hossen, Sourav Biswas, Md Ackas Ali, Mohammad A. Halim, and M. Obayed Ullah

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Unraveling the impact of ORF3a Q57H mutation on SARS-CoV-2: insights from molecular dynamics, Md Jahirul Islam, Md Siddik Alom, Md Shahadat Hossain, Md Ackas Ali, Shaila Akter, Shafiqul Islam, M. Obayed Ullah, and Mohammad A. Halim

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Structural and functional effects of the L84S mutant in the SARS-COV-2 ORF8 dimer based on microsecond molecular dynamics study, Shafiqul Islam, Md Rimon Parves, Md Jahirul Islam, Md Ackas Ali, Faiyaz Md Efaz, Md Shahadat Hossain, M. Obayed Ullah, and Mohammad A. Halim

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A review on structural, non-structural, and accessory proteins of SARS-CoV-2: Highlighting drug target sites, Md Jahirul Islam, Nafisa Nawal Islam, Md Siddik Alom, Mahmuda Kabir, and Mohammad A. Halim

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Revisiting the N(N + 1)/2-site s-type Gaussian charge model for permutationally invariant polynomial fitting of global molecular tensor surfaces, Sophia A. Kudratov, Martina Kaledin, and Alexey L. Kaledin

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Potential antiviral peptides against the nucleoprotein of SARS-CoV-2, Iktedar Mahdi, Humyara Yeasmin, Imtiaz Hossain, Raina Masnoon Badhan, Md Ackas Ali, Md Abdul Kaium, Rajib Islam, Md Abu Sufian, and Mohammad A. Halim

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Promoting Meaningful Learning through Incorporation of Creative Exercises in Inorganic Chemistry, Janet L. Shaw

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Evolution of a self-renewing, participant-centered workshop series in BMB assessment, Ludmila Tyler, Peter J. Kennelly, Shelly Engelman, Kirsten F. Block, Jennifer C. Bobenko, Jaclyn Catalano, Jesica A. Jones, Margaret I. Kanipes-Spinks, Yang Mooi Lim, Jennifer Loertscher, Tejiri Olafimihan, Hailey Reiss, Territa L. Upchurch-Poole, Yufeng Wei, Kimberly J. Linenberger Cortes, Victoria Del Gaizo Moore, and Daniel R. Dries

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Large scale peptide screening against main protease of SARS CoV-2, Md Jaish Uddin, Hasina Akhter, Urmi Chowdhury, Jannatul Mawah, Sanzida Tul Karim, Mohammad Jomel, Md Sirajul Islam, Mohammad Raqibul Islam, Latifa Afrin Bhuiyan Onin, Md Ackas Ali, Faiyaz Md Efaz, and Mohammad A. Halim

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Probing Polaron Environment in a Doped Polymer via the Photoinduced Stark Effect, Abdul Rashid Umar, Austin L. Dorris, Naresh M. Kotadiya, Noel C. Giebink, Graham S. Collier, and Christopher Grieco

Submissions from 2022

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Impact of ethanol and NaCl on the acid yellow dye mediated self-aggregation of sodium dodecyl sulfate: A combined investigation by conductivity and molecular dynamics simulation, Md Ariful Haque, Md Khalid Bin Islam, Shamim Mahbub, and Mohammad A. Halim

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Hydrogen bonds and dispersion forces serving as molecular locks for tailored Group 11 bis(amidine) complexes, Janet Arras, Omar Ugarte Trejo, Nattamai Bhuvanesh, and Michael Stollenz

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Biolayer interferometry for DNA-protein interactions, John K. Barrows and Michael W. Van Dyke

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Intramolecular Proton Transfer in the Hydrogen Oxalate Anion and the Cooperativity Effects of the Low-Frequency Vibrations: A Driven Molecular Dynamics Study, Dalton Boutwell, Dominick Pierre-Jacques, Olivia Cochran, Jason Dyke, Dayana Salazar, Ciara Tyler, and Martina Kaledin

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Effects of supplementary nutrients (soil-nitrogen or foliar-iron) on switchgrass (Panicum virgatum L.) grown in Pb-contaminated soil, Sigurdur Greipsson, Thomas McElroy, and Marina Koether

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Foliar Application of Salicylic Acid and DA-6 on Swithgrass (Panicum virgatum L.) Grown in Pb-Contaminated Soil; Implications for Phytoextraction, Sigurdur Greipsson, Thomas McElroy, and Marina Koether

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Phytoextraction of lead (Pb) contaminated soil by switchgrass (Panicum virgatum L): Impact of BAP and NTA applications, Genna Hart, Austin Gilly, Marina Koether, Thomas McElroy, and Sigurdur Greipsson

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Energy Harvesting by Mesoporous Reduced Graphene Oxide Enhanced the Mediator-Free Glucose-Powered Enzymatic Biofuel Cell for Biomedical Applications, Md Humayun Kabir, Max Thompson, Altug S. Poyraz, and Huggins Z. Msimanga

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The microwave spectrum of the difluorocyanomethyl radical, ĊF2CN, Lu Kang, Ha Vinh Lam Nguyen, Christopher B. Falls, and Alexander B. Seys

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A student led computational screening of peptide inhibitors against main protease of SARS-CoV-2, Anika Tajrian Khan, Golam Mahmud Chowdhury, Juwairiyah Hafsah, and Mohammad A. Halim

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Classification of local diesel fuels and simultaneous prediction of their physicochemical parameters using FTIR-ATR data and chemometrics, Huggins Z. Msimanga, Christopher R. Dockery, and Deidre D. Vandenbos

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Permutationally invariant polynomial representation of polarizability tensor surfaces for linear regression analysis, Oluwaseun Omodemi, Martina Kaledin, and Alexey L. Kaledin

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On the Cartesian Representation of the Molecular Polarizability Tensor Surface by Polynomial Fitting to Data, Oluwaseun Omodemi, Sarah Sprouse, Destyni Herbert, Martina Kaledin, and Alexey L. Kaledin

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Probing the non-bonding interaction of small molecules with graphene oxide using DFT based vibrational circular dichroism, Muhammad Omor Faruk Patwary, M. Mahbubur Rahman, Md Khalid Bin Islam, and Mohammad A. Halim

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Exploring the molecular level interaction of Xenoestrogen phthalate plasticisers with oestrogen receptor alpha (ERα) Y537S mutant, Fahmida Khanam Raha, Jahid Hasan, Ackas Ali, and Mohammad A. Halim

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Evaluation of the experimental and computed properties of choline chloride-water formulated deep eutectic solvents, Md Sajjadur Rahman, Jennifer Kyeremateng, Mousumi Saha, and Mohammad A. Halim

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Acidic and basic amino acid-based novel deep eutectic solvents and their role in depolymerization of lignin, Md Sajjadur Rahman, Ranen Roy, Cynthia Montoya, and Mohammad A. Halim

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MAP kinases differentially bind and phosphorylate NOS3 via two unique NOS3 sites, Xzaviar K. Solone, Amber L. Caldara, Brady Wells, Hao Qiao, Lydia R. Wade, John C. Salerno, Katy A. Helms, Katherine E. Smith, Jonathan L. McMurry, and Carol A. Chrestensen

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Molecular dynamics investigation of ivermectin bound to importin alpha/beta heterodimer, Mossammad U.C. Sultana, Md Giash Uddin, Md Billal Hossain, and Mohammad A. Halim

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Insights into the leaves of Ceriscoides campanulata: Natural proanthocyanidins alleviate diabetes, inflammation, and esophageal squamous cell cancer via in vitro and in silico models, Md Josim Uddin, Immacolata Faraone, Md Anwarul Haque, and Mohammad A. Halim

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Bond Dissociation Energies of Carbene-Carbene and Carbene-Main Group Adducts, Monica Vasiliu, Kyle C. Edwards, Daniela Tapu, and Clarisa E. Castillo

Submissions from 2021

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Non-conventional hydrogen bonding and dispersion forces that support embedding mesitylgold into a tailored bis(amidine) framework, Janet Arras, Omar Ugarte Trejo, Nattamai Bhuvanesh, and Michael Stollenz

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Could Simultaneous Nasal and Oral Irrigation Be a Nontherapeutic Tool against SARS-CoV-2?, Bharat Baruah

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Polymer-capped gold nanoparticles and ZnO nanorods form binary photocatalyst on cotton fabrics: Catalytic breakdown of dye, Bharat Baruah, Christopher Kelley, Grace B. Djokoto, and Kelly M. Hartnett

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Effects of exogenous application of plant growth regulators (SNP and GA3) on phytoextraction by switchgrass (panicum virgatum L.) grown in lead (Pb) contaminated soil, Adrianne Beavers, Marina Koether, Thomas C. McElroy, and Sigurdur Greipsson

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Evolution of Ephemeral Phosphate Minerals on Planetary Environments, Tian Feng, Maheen Gull, Art Omran, Heather Abbott-Lyon, and Matthew Pasek

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Discharging Behavior of Hollandite α-MnO2 in a Hydrated Zinc-Ion Battery, Thanh Le, Nahian Sadique, Lisa M. Housel, Altug S. Poyraz, Esther S. Takeuchi, Kenneth J. Takeuchi, Amy C. Marschilok, and Ping Liu

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Identification of potent inhibitors against transmembrane serine protease 2 for developing therapeutics against SARS-CoV-2, Abdulla Al Mamun, Farjana Akter, Maksud Khan, Sayeda Samina Ahmed, Md Giash Uddin, Nabila Tabassum Tasfia, Faiyaz Md Efaz, Md Ackas Ali, Mossammad Umme Sultana, and Mohammad A. Halim

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A polarizability driven ab initio molecular dynamics approach to stimulating Raman activity: Application to C20, Dominick Pierre-Jacques, Ciara Tyler, Jason Dyke, Alexey L. Kaledin, and Martina Kaledin

A polarizability driven ab initio molecular dynamics approach to stimulating Raman activity: Application to C20, Dominick Pierre-Jacques, Ciara Tyler, Jason Dyke, Alexey L. Kaledin, and Martina Kaledin

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Low-Defect, High Molecular Weight Indacenodithiophene (IDT) Polymers Via a C-H Activation: Evaluation of a Simpler and Greener Approach to Organic Electronic Materials, James F. Ponder, Hu Chen, Alexander M.T. Luci, Stefania Moro, Marco Turano, Archie L. Hobson, Graham S. Collier, Luís M.A. Perdigão, Maximilian Moser, Weimin Zhang, Giovanni Costantini, John R. Reynolds, and Iain McCulloch

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Photo-Electroswitchable Arylaminoazobenzenes, Carl Jacky Saint-Louis, David J. Warner, Katie S. Keane, Melody D. Kelley, Connor M. Meyers, and Silas C. Blackstock

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Discovering the dna-binding consensus of the thermus thermophilus hb8 transcriptional regulator ttha1359, Josiah L. Teague, John K. Barrows, Cynthia A. Baafi, and Michael W. Van Dyke

Discovering the DNA-Binding Consensus of the HB8 Transcriptional Regulator TTHA1359, Josiah L. Teague, John K. Barrows, Cynthia A. Baafi, and Michael W. Van Dyke

Submissions from 2020

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Analysis of the Proton Transfer Bands in the Infrared Spectra of Linear N2H+···OC and N2D+···OC Complexes Using Electric Field-Driven Classical Trajectories, Dalton Boutwell, Onyinye Okere, Oluwaseun Omodemi, Alexander Toledo, Antonio Barrios, Monique Olocha, and Martina Kaledin

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Determination and dissection of dna-binding specificity for the thermus thermophilus hb8 transcriptional regulator tthb099, Kristi Moncja and Michael W. Van Dyke

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Tuning fullerene miscibility with porphyrin-terminated P3HTs in bulk heterojunction blends, Zach D. Seibers, Graham S. Collier, Benjamin W. Hopkins, Evan S. Boone, Thinh P. Le, Enrique D. Gomez, and S. Michael Kilbey

Submissions from 2019

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The LARP1 La-Module recognizes both ends of TOP mRNAs, Hiba A. Al-Ashtal, Courtney M. Rubottom, Thomas C. Leeper, and Andrea J. Berman

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Fabric-based composite materials containing ZnO-NRs and ZnO-NRs-AuNPs and their application in photocatalysis, Bharat Baruah, Latanya Downer, and David Agyeman

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Identification and Characterization of Preferred DNA-Binding Sites for the Thermus thermophilus HB8 Transcriptional Regulator TTHA0973, James Shell Cox, Kristi Moncja, Mykala Mckinnes, and Michael W. Van Dyke

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Two-to-three dimensional transition in neutral gold clusters: The crucial role of van der Waals interactions and temperature, Bryan R. Goldsmith, Jonathan T. Lyon, and Et al.

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Assignment of Infrared-Active Combination Bands in the Vibrational Spectra of Protonated Molecular Clusters Using Driven Classical Trajectories: Application to N4H+ and N4D+, Reagan Hooper, Dalton Boutwell, and Matrina Kaledin

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A stable Cerberus tris(maloNHC) and its coinage metal complexes, Reagan Hooper, Alexander Mason, Maleek Montgomery, and Braden Clinebell

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The Use of Visual Network Scales in Teacher Leader Development, Samuel J. Polizzi, Brandon Ofem, William Coyle, Keith Lundquist, and Gregory T. Rushton

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Improving the cycle life of cryptomelane type manganese dioxides in aqueous rechargeable zinc ion batteries: The effect of electrolyte concentration, Altug S. Poyraz, Josh Laughlin, and Zeljka Zec

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Evidence of the coexistence of multivalence cerium oxide nano-particles in a sodium borate glass, Kisa S. Ranasinghe, Rajnish Singh, Delbert E. Day, and Klaus Attenkofer

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Linear Copper Complex Arrays as Versatile Molecular Strings: Syntheses, Structures, Luminescence, and Magnetism, Michael Stollenz

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Correlated Multimodal Approach Reveals Key Details of Nerve-Agent Decomposition by Single-Site Zr-Based Polyoxometalates, Yiyao Tian, Anna M. Plonka, Amani M. Ebrahim, and Mark B. Mitchell

Submissions from 2018

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Archean Phosphorus Liberation Induced by Iron Redox Geochemistry, Barry Herschy, Sae Jung Chang, Ruth Blake, Aivo Lepland, Heather Abbott-Lyon, Jacqueline Sampson, Zachary Atlas, Terence P. Kee, and Matthew A. Pasek

Reduction of interferences in the analysis of Children's Dimetapp using ultraviolet spectroscopy data and target factor analysis, Huggins Z. Msimanga, Truong Thach Ho Lam, Nathaniel Latinwo, and Mihyang Kristy Song

Submissions from 2017

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Polyoxovanadate Fabricated Gold Nanoparticles: Application in SERS, Bharat Baruah and Toni-Ann Miller

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Hydrogen Peroxide Inhibition of Bicupin Oxalate Oxidase, John M. Goodwin, Hassan Rana, Joan Ndungu, Gaurab Chakrabarti, and Ellen W. Moomaw

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Identification and characterization of preferred DNA-binding sites for the Thermus thermophilus transcriptional regulator FadR, Minwoo Lee, Hyejin Um, and Michael W. Van Dyke

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A Versatile Cell-penetrating Peptide-adaptor System for Efficient Delivery of Molecular Cargos to Subcellular Destinations, Verra M. Ngwa, David S. Axford, Allison N. Healey, Scott J. Nowak, Carol A. Chrestensen, and Jonathan L. McMurry

Submissions from 2016

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Distinctive Coordination of CO vs N2 to Rhodium Cations: An Infrared and Computational Study, A. D. Brathwaite, H. L. Abbott-Lyon, and M. A. Duncan

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Characterization of Lead-Free Gunshot Residue Analogs, Lashaundra A. Fambro, Ethan T. Miller, Deidre D. Vandenbos, and Christopher R. Dockery

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Multimodal Vacuum-Assisted Plasma Ion (VaPI) Source with Transmission Mode and Laser Ablation Sampling Capabilities, Joel D. Keelor, Paul B. Farnsworth, Arthur L. Weber, and Heather Abbott-Lyon

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The Evolution of the Surface of the Mineral Schreibersite in Prebiotic Chemistry, Nikita L. La Cruz, Danna Qasim, Heather Abbott-Lyon, and Claire Pirim

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Antibacterial Activities of Wasabi Against Escherichia coli O157:H7 and Staphylococcus aureus, Zhongjing Lu, Christopher Dockery, Michael Crosby, Katherine Chavarria, Brett Patterson, and Matthew Giedd

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Isothermal Titration Calorimetry Uncovers Substrate Promiscuity of Bicupin Oxalate Oxidase from Ceriporiopsis Subvermispora, Hassan Rana, Patricia Moussatche, Lis Souza Rocha, and Ellen W. Moomaw

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Thermogravimetric Analysis of Target Inhibitors for the Spontaneous Self-Heating of Coal, Christopher J. Raymond, Justin Farmer, and Christopher R. Dockery

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Novel Cell Penetrating Peptide-adaptors Effect Intracellular Delivery and Endosomal Escape of Protein Cargos, John C. Salerno, Verra M. Ngwa, Scott J. Nowak, Carol A. Chrestensen, Allison N. Healey, and Jonathan L. McMurry

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Highly Luminescent Linear Complex Arrays of up to Eight Cuprous Centers, Michael Stollenz, Jeffery E. Raymond, Lisa M. Perez, Jessica Wiederkehr, and Nattami Bhuvanesh

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Identification of Preferred DNA-Binding Sites for the Thermus thermophilus Transcriptional Regulator SbtR by the Combinatorial Approach REPSA, Michael W. Van Dyke, Matthew D. Beyer, Emily Clay, and Jonathan L. McMurry

Submissions from 2014

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Biochemistry Students' Ideas abour Shape and Charge in Enzyme-Substrate Interactions, Kimberly J. Linenberger and Stacey Lowery Bretz

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Training the Foot Soldiers of Inquiry: Development and Evaluation of a Graduate Teaching Assistant Learning Community, Kimberly Linenberger, Michael C. Slade, Elizabeth A. Addis, and Emily R. Elliot

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Cyclodextrin Complexes of Reduced Bromonoscapine in Guar Gum Microspheres Enhance Colonic Drug Delivery, Jitender Madan, Sushma R. Gundala, Bharat Baruah, and Mulpuri Nagaraju

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Real-time Kinetic Studies of Bacillus Subtilis Oxalate Decarboxylase and Ceriporiopsis Subvermispora Oxalate Oxidase Using Luminescent Oxygen Sensor, Laura Molina, Thomas Goodall, Umar Twahir, and Ellen W. Moomaw

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Membrane Inlet Mass Spectrometry Reveals that Ceriporiopsis Subvermispora Bicupin Oxalate Oxidase is Inhibited by Nitric Oxide, Ellen W. Moomaw, Richard Uberto, and Tu Chingkuang

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Endothelial Nitric Oxide Synthase is Regulated by ERK Phosphorylation at Ser602, John C. Salerno, Dipak K. Ghosh, Raj Razdan, Katy A. Helms, Jonathan L. McMurry, Emily A. Rye, and Carol A. Chrestensen

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A dibenz[a,c]phenazine-Supported N-heterocyclic Carbene and Its Rhodium and Iridium Complexes, Daniela Tapu, Zachary McCarty, Lauren Hutchinson, Christopher Ghattas, Mahatab Chowdhury, John C. Salerno, and Donald VanDerveer

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A Stable Janus bis(maloNHC) and Its Zwitterionic Coinage Metal Complexes, Daniela Tapu, Zachary McCarty, and Colin McMillen

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Synthesis of a FTO Inhibitor with Anticonvulsant Activity, Guanqun Zheng, Thomas Cox, Leah Tribbey, and Gloria Z. Wang