Physical Sciences and Mathematics Commons^™

Exploring Ancestral Enzymes Through Sequence Reconstruction And Stability Prediction, Jeyun Park, Masakatsu Watanabe

SACAD: Scholarly Activities

Proteins evolve through sequence changes that shape structure, stability,

and function. Ancestral sequence reconstruction (ASR) infers ancestral

proteins from modern homologs, but many studies focus on sequence

inference without evaluating structural or energetic feasibility.

β-lactamases provide an ideal model due to their evolutionary diversity and

clinical relevance in antibiotic resistance.

Here, we present an integrated ASR workflow combining phylogenetic

inference (IQ-TREE), ancestral reconstruction, and structural and stability

validation using AlphaFold and FoldX. By reanalyzing a curated β-

lactamase dataset and comparing with a recent study (Risso et al., 2013),

we provide a controlled comparison of ancestral sequences, predicted

structures, and …

David Berkowitz, Enzyme-Assisted Organic Synthesis & Nsf Officer, Mark A. Griep, David B. Berkowitz

Department of Chemistry: Faculty Interviews

Dr. Dave Berkowitz was born in Urbana, Illinois. He earned his bachelor's degree in chemistry from the University of Chicago, where he did undergraduate research. Next, he earned his doctorate from Harvard University. However, his advisor, Steve Benner, moved from Harvard to ETH Zurich, also called the Swiss Federal Institute of Technology. Dave accompanied him to Zurich, where he completed his dissertation work. When Dave returned to the U.S., he did a postdoc with the legendary Samuel Danishefsky at Yale University. In 1991, he joined UNL as an assistant professor of chemistry and quickly rose through the ranks. Dave is …

Desialylation And Sialidase Secretion From Monocytes And Macrophages Upon Lps Activation, Yu Zhao, Majdi Aljohani, Morgan Pychowycz, Xue-Long Sun

Chemistry Faculty Publications

Introduction The cell surface expresses a dense layer of glycans often terminated with sialic acids (Sias), known as sialylation, which represents different cellular statuses. Meanwhile, the removal of Sias from the glycans catalyzed by sialidase (desialylation) is also involved in many biological processes, such as inflammatory responses. Previous studies demonstrated that desialylation is involved in LPS/TLR4 signaling pathway and pro-inflammatory cytokine production. In this report, we systematically profiled desialylation and sialidase activity, expression and secretion from monocytes and macrophages upon LPS activation.Methods THP-1 monocytes and THP-1 macrophages were activated by LPS (100 ng/mL) for 24 hours. The cellular Sia changes …

Impact Of Collodion Thickness On Fission Track Generation Within Lexan Employed For Nuclear Forensic Analyses, Ryan K. Chapman, Zachary P. Meisel, Abigail A. Bickley

Faculty Publications

We report results from a computational study of fission track damage within a Lexan substrate caused by ²³⁵U suspended within a collodion film of varied thickness. MCNP6.3 was used to model energy deposition and displacements per atom within a Lexan film coated by a film of collodion, located within the air-filled 6 inch dry tube of a TRIGA reactor. The collodion layer was varied between 20 and 100 μm thickness, resulting in an 8.8% difference in energy deposition and 12% difference in displacements-per-atom within the Lexan substrate. These findings indicate that collodion adhesive thickness has a moderate impact on …

Understanding The Binding Of Nickel(Ii) Bromide To A Zirconium Metal-Organic Cage For Heterogeneous Catalysis, Luci Green

Caroliniana Undergraduate Research Journal

Heterogeneous catalysts offer inherent advantages in improving the sustainability of industrial chemical processes. Their high ease of separation and recyclability has the potential to reduce the cost, waste, and energy consumption of processes that currently rely on homogeneous catalysts. Metal–organic cages (MOCs) are an attractive material for heterogeneous catalysis due to their discrete and highly tunable structures, which can be functionalized by binding these complexes with catalytically active metals. The specific objective of this study is to provide preliminary insight into the binding of nickel(II) bromide (NiBr₂) to zirconium MOCs, which was done by studying the binding of …

Non-Markovian Quantum State Diffusion For Electron Transfer In The Biological Complexes, Muhammad Waqas Haseeb

Thesis/ Dissertation Defenses

The emerging field of quantum biology explores whether non-trivial quantum effects such as entanglement, tunnelling, and environmentally induced memory can contribute meaningfully to biological function alongside classical mechanisms. While such effects have been explored in photosynthesis, enzyme catalysis, and olfaction, their potential relevance to virology remains largely unexplored. Viruses, which straddle the boundary between living and non-living matter, provide a particularly compelling testbed for this inquiry. This thesis investigates a quantum-dynamical paradigm for viral entry, proposing that the earliest stage of SARS-CoV-2 infection may involve vibrationally assisted electron transfer (VA-ET) between the viral Spike protein and the host cell's angiotensin-converting …

Synthesis And Catalytic Activity Testing Of Coke-Resistant Nickel-Based Catalysts For Methane Reforming And Hydrogen Production, Abdulmuizz Adamson

Thesis/ Dissertation Defenses

Ni-based catalysts are widely used in methane reforming and hydrogen production, but their industrial application is limited by deactivation caused by carbon deposition (coking). This dissertation examines the role of iron as a dopant in improving catalytic performance and coking resistance, with emphasis on its incorporation method and impact on coke oxidation during different methane reforming reactions.

The results show that dispersing iron ions within the γ-Al₂O₃ support significantly enhances catalyst coking resistance and hence catalyst performance under partial oxidation and combined partial oxidation-dry reforming conditions. This improvement is attributed, mainly, to the redox function of Fe and the enhanced …

Organic Photocatalysts For Desulfurization Of Fuels, A K M Maksudul Hasan

Master's Theses (2009 -)

Desulfurization of fuels is a critical process for reducing sulfur contents in petroleum-based fuels to mitigate environmental pollution and meet the regulatory standards. Among various pollutants, Sulfur is the deadliest as inhaling leads to coughing, shortness of breath, sinus problem as well as the death of brain cells. Petroleum has a number of organosulfur derivatives, for example in crude oil (0.1 to 6wt% sulfur), which should be removed before using in combustion engines and other applications. High sulfur containing petroleum products used in engines and power plants would lead to the formation of sulfurdioxide (SO2) which would contribute to the …

Green Synthesis And Characterization Of Silver Nanoparticles Using Dadap Serep (Erythrina Lithosperma) Leaves Extract As A Bioreductor, Fairuz Hammad Albahi, Suyatno Sutoyo, Tukiran Tukiran

Chimica et Natura Acta

Silver nanoparticles (AgNPs) had been widely applied in various fields such as health, food, environment, catalysts, optics, and electronics. The synthesis of silver nanoparticles can be carried using a bottom-up method using by bioreductants derived from natural extracts (green synthesis). This study aims to describe the green synthesis of silver nanoparticles using a bioreductants from dadap serep (E. lithosperma) leaves extract and to determine its characteristics. The synthesis was carried out by varying the volume ratio of dadap serep leaves extract to silver nitrate solution at ratios of 1: 1, 1: 2, 1: 3, and 1: 4, followed by optimization …

Kinetic Analysis Of 2-Methylpentan-2-Ol*, Nicole Seheult

Campus Research Month

This experiment investigated the kinetics of 2-methylpentan-2-ol using UV-visible spectroscopy under strongly acidic conditions (96% sulfuric acid). The dehydration of the tert-amyl alcohol produced a carbocation intermediate whose absorbance at 300 nm was evaluated at various temperatures. An Arrhenius plot of ln(k) versus 1/T produced a linear relationship with a calculated activation energy of 90.0 kJ/mol. This value is consistent with literature expectations for tertiary carbocation formation and supports the acid-catalyzed dehydration mechanism predicted for this molecule.

Towards The Synthesis Of Soluble Benzophosphole Oxides Via Addition Of Amine Groups*, Nema Ogal

Campus Research Month

Benzophospholes possess unique properties that make them useful across a wide range of chemical applications, particularly in materials chemistry. Solubilizing benzophosphole oxides would be especially useful in advances in medicinal chemistry. This research is designed to improve the solubility of benzophosphole oxides by adding amino groups which could be protonated and turned to salt. Their synthesis is an ongoing process with many intricate steps, but ultimately very practical outcomes in the filed of organochemistry.

Calculating Potential Energy Curves Of Molecular Hydrogen And Its Ion Using Psi4 For Blinc Fusion Applications*, Angelina Castillo, Oscar Coral, Canaan Hercules, Blake Laing, Vola Andrianarijaona

Campus Research Month

Southern Adventist University’s Beamline for Ionic and Neutral Collisions (BLINC) is investigating the interactions between hydrogen molecules and fusion particles. To perform in-house theoretical calculations, the BLINC Theory and Analysis Group is testing Psi4 as a viable computational method for BLINC fusion research. Successful calculations of the potential energy curves and dissociation energies of H₂ and H₂⁺ have been completed and compared to known values. Preliminary results align with known values, demonstrating Psi4’s potential for BLINC research. Future work will focus on the vibrational energies, wavefunctions, and transition probabilities of H₂ and H₂⁺.

The Hartree-Fock Method: Quantum Theory To Python Code, Joshua Lohr

Campus Research Month

This poster presents a Restricted Hartree-Fock (RHF) program that solves the Roothaan-Hall equations within a finite basis set. Starting from an initial guess density, the Fock matrix is constructed via Coulomb and Exchange contributions. The resulting pseudo-eigenvalue problem is solved iteratively until self consistency. The electronic energy of water was calculated using the STO-3G basis set and validated against PySCF as a reference.

Elucidating The Structure And Binding Nature Of Thianaphthene Dimers Using Gas-Phase Infrared Spectroscopy, Gaia Zucali, Vincent J. Esposito, Sandra Brünken, Piero Ferrari

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Crucial for many biological systems, in astrochemistry, and for fundamental chemistry in general, the conformations adopted by weakly bound complexes of polycyclic aromatic hydrocarbons (PAHs) have been the focus of debate for decades. Still, there are great challenges in forming such complexes in the laboratory, measuring accurate spectroscopic information sensitive to structure, and computing molecular properties for systems subtly bound by dispersive interactions. Here, we employ a combination of gas-phase infrared spectroscopy with extensive density functional theory (DFT) calculations to unambiguously determine the preferred conformation adopted by dimers of neutral thianaphthene, a PAH composed of one six- and one five-membered …

Una To Put Names On 2 Buildings, Jennifer Edwards

Documents

the naming of the Academic Commons Building and the new Science and Technology Building at UNA

The Science And Technology Building University Of North Alabama, Barbie Hampel-University Advancement

Documents

Brochure and floor plans for the New Science and Technology Building at UNA

University Of North Alabama Science And Technology Building Grand Opening And Ribbon Cutting, University Of North Alabama

Documents

Invitation to the Grand Opening and Ribbon Cutting for the new Science and Technology Building at UNA

An Efficient Approximation To The Vibrational Coupled Cluster Method For Large Molecules, Nivedhitha P Ms

Theses and Dissertations

The Watson Hamiltonian is a widely used model for describing anharmonic vibrational motion in polyatomic molecules. It expresses the kinetic energy in separable dimensionless normal coordinates and represents the potential energy as a Taylor series expansion around the equilibrium geometry, usually up to the quartic approximation. Several computational methods have been developed to solve the corresponding vibrational Schrödinger equation for predicting infrared (IR), Raman, and vibrational circular dichroism (VCD) spectra. These include the Vibrational Self-Consistent Field (VSCF) method, Vibrational Configuration Interaction (VCI) and its approximations, and Vibrational Second-Order Perturbation Theory (VPT2), each providing different balances between computational cost and accuracy. …

Dna Barcoding Of Eight Freshwater Fish Species (Order Siluriformes) From The River Ravi, Pakistan, Hafiz Muhammad Ashraf, Hafiz Abdullah Shakir, Muhammad Irfan, Shaukat Ali, Chaman Ara, Noor Khan, Muhammad Khan, Abdul Qadir, Muhammad Zafar Saleem

Karbala International Journal of Modern Science

Pakistan's freshwater bodies host significant fish species, but molecular identification is still in its infancy, necessitating the use of morphological and molecular DNA barcoding techniques. The study confirmed the species of the order Siluriformes found in the River Ravi, Pakistan, using DNA extracted from muscle tissue, sequenced for the COI gene, and obtained accession and Barcode Index Numbers from GenBank and BOLD databases. In the BLAST search, identities ranged from 99.23–100% and 99.52–100% in the GenBank and BOLD databases, respectively. The study revealed that the Kimura 2-Parameter genetic distance increased from lower to higher taxonomic levels: within species (0.00%) < within genus (15.17%) < within family (19.77%). The study estimated average nucleotide differences (104.964) and nucleotide diversity (0.16099) but found Tajima's neutrality test to be statistically insignificant. The neighbor-joining tree displayed closely linked species under a node, whereas divergent species were grouped under distinct nodes. The COI gene-based DNA barcoding aids in Pakistan's fish resource inventory, monitoring, and management, providing valuable input for traditional methods.

Eco-Assisted Ultrasonic Synthesis, Characterization, And Electrical Conductivity Study Of Polyaniline/ Silica@Fe3o4 Q1 Nanocomposites, Ali Salim Shaway, Kholoud Dham Khamkheem, Jawad Kadhim Abaies, Athra G. Sager

Karbala International Journal of Modern Science

وفي هذه الدراسة الصوتية، أصبحت السيليكا المُنتجة بأكسيد الحديد (Fe₃O₄) ومركبات نانوية قائمة على البولي أنيلين مُطعّم بنسبة 5-15% من السيليكا المُعزز للحديد (Fe₃O₄). وأكملت نهائيا ماء أنيلين والمركبات العلمية المتنوعة الارتباط باستخدام تقنيات FT-IR وUV-Vis وXRD وSEM وTEM. وأحدثت نتائج XRD أن حجم جسيمات البولينج أنيلين الناي (PANI) يبلغ 55.5. مكثف هذا الحجم إلى 45.2 عند تطعيم بولي أنيلين بنسبة 15% وزناً من السيليكا المُغلفة بأكسيد الحديد (Fe₃O₄) مُحضّرة بطريقة جيدة بشكل جيد، مما يميل إلى التمدد بشكل ثابت في تشكيل المركب المتباين المنظم. ضاقت النطاق البصري من 3.2 إلى 2.5 إلكترون فولت مع زيادة نسبة المطعّم، مما يشير …

Monitoring Of Dissolved Calcium Levels In Creeks, Embayment, And Kentucky Lake Waters In Western Kentucky, Majeda Dalloul

Scholars Week

In order to reduce the economic and ecological impacts of aquatic alien species, studies are warranted across major taxonomic groups, geographic regions, and habitat types. This study addressed the dissolved calcium levels in Kentucky Lake and their implications for one of the top-ranked invasive species, the zebra mussel, and its colonization.  Zebra mussels (Dreissena polymorpha) are well known for their “biofouling” capabilities, costing billions of dollars (for northeastern and midwestern states) in their removal from industrial, public, and power plant water supply lines. Calcium is one of the essential elements that contribute to the growth and reproduction of zebra …

Synthesis And Hydrothermal Evaluation Of Poly(Styrene Phosphonate) For Conformance Control In Geothermal Reservoirs, Sara Mccauley

Miners Solving for Tomorrow Research Conference

As atmospheric carbon dioxide levels continue to rise, geothermal energy has emerged as a promising energy alternative to fossil fuels. A barrier to widespread implementation and energy production efficiency is macro-heterogeneity of the rock matrix. Cracks, void spaces, and flow conduits divert fluid flow away from unswept portions of the geothermal reservoir and can cause cooling of the reservoir. Flow heterogeneity has been treated in oil reservoirs by injecting hydrogel particles that travel preferentially to ultra-high permeability zones and selectively block fluid flow in these regions. We are applying polymer hydrogels that withstand hydrothermal conditions of 225 up to 275°C …

Transition Metal Chalcogenide As Multifunctional Biosenser To Detect Neurochemicals, Amitav Sen

Miners Solving for Tomorrow Research Conference

The development of highly sensitive real-time sensing platforms for selectively detecting dopamine (DA) and norepinephrine (NE) is of significant clinical importance since these are closely associated with several neurodegenerative disorders. Herein, we report copper telluride (Cu₂Te) nanostructure as a bifunctional electrocatalyst for the simultaneous detection of dopamine and norepinephrine. Cu₂Te exhibits excellent electrocatalytic activity toward both DA and NE oxidation, as demonstrated by detailed electrochemical measurements. High sensitivities of 24 and 40 µA cm⁻² µM⁻¹ for DA and NE, respectively, were obtained with a wide linear detection range of 10–200 nM and low limit of detection (LOD), 31 nM for …

Anti-Inflammatory And Insulin-Modulating Effects Of Tithonia-Curcuma-Moringa (Tcm) Formulation In Type 2 Diabetes: An Experimental Study In Mice, Rif’Atul Hawani Burhan, Nabila Shafa Yumna Salsabila, Devita Zulfa Pratama, La Tazkia Aulia Wibowo, Yulian Ervin Maulana, Moh Dliyauddin, Noviana Dwi Lestari, Agung Pramana Warih Marhendra, Aris Soewondo, Hideo Tsuboi, Muhaimin Rifa’I

Karbala International Journal of Modern Science

Type 2 diabetes is a chronic metabolic disorder characterized by hyperglycemia and chronic inflammation. This study investigated the anti-inflammatory and insulin-modulating effects of Tithonia-Curcuma-Moringa (TCM) formulation in type 2 diabetes model. Male BALB/c mice were divided into six groups: normal control, type 2 diabetes control, metformin treatment, and three TCM formulation treatment groups with three different dose combinations. Type 2 diabetes was induced using a high-fat diet combined with streptozotocin injection, supported by sucrose administration. After 21 days of treatment, the spleen and pancreas were isolated for flow cytometry analysis. The results showed that the expression levels of …

Literature Review Of Local Culture-Based Mathematics E-Module With Islamic Values In Probability, Maya Puspita Sari, Surya Sari Faradiba

Jurnal Pendidikan Sains

This study is grounded in the need to address the limitations of probability learning that is often procedural, decontextualized, and disconnected from students’ cultural and religious values. It aims to develop a comprehensive understanding of how local cultural contexts and Islamic values can be systematically integrated into mathematics e-modules, particularly for probability learning, and to formulate structured design principles and quality indicators for their development. This paper adopts a Systematic Literature Review (SLR) approach by analyzing empirical studies published between 2020 and 2025, using a structured selection process involving identification, screening, eligibility, and inclusion stages. A total of 11 high-quality …

The Effect Of Virtual Laboratories On Students Interest And Learning Outcomes In Spermatophyta At Sma Negeri 1 Sojol, Ismawati Ismawati, Sutrisnawati Sutrisnawati, Manap Trianto, Masrianih Masrianih, Abd Rauf, Musdalifah Nurdin

Jurnal Pendidikan Sains

Limited access to physical laboratory facilities and the abstract nature of Spermatophyta material reduce students’ learning interest and outcomes, necessitating the use of innovative digital learning media such as virtual laboratories. This study aims to analyze the effect of Virtual Laboratory (V-Lab) implementation on students’ learning interest and cognitive learning outcomes in Spermatophyta material at the senior high school level. A quantitative quasi-experimental design with a posttest-only control group was employed involving 66 eleventh-grade students divided into experimental and control classes; data were collected using a learning interest questionnaire and a multiple-choice test, and analyzed using independent samples t-test after …

Reading Literacy Research Trends In Science Learning (2015–2025), Siwi Handayani, Siswanto Siswanto, Rina Rahayu

Jurnal Pendidikan Sains

This study aims to analyze research trends in reading literacy within science learning from 2015 to 2025 through a Systematic Literature Review (SLR) following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) framework. The initial screening of 150 articles from the WoS Core Collection and SINTA databases yielded 29 articles that met the inclusion criteria. The analysis focused on publication dynamics, contributing countries, participant characteristics, research variables, and the science subjects investigated. The findings indicate that research on reading literacy in science learning remains limited and shows fluctuating development. Most publications originate from national journals indexed by SINTA, …

Florence State Prepares For Jet Age Needs With New, Expanded Facilities, Tommy Hill

Documents

News article from The Birmingham News about the expanded facilities at Florence State College

Scientist Floyd Retires At Florence State, Jack Bridges

Documents

Dr. Homer H. Floyd's retirement from Florence State College

Cytokinesis And Dbf2, Katharine Gray

Miners Solving for Tomorrow Research Conference

The Mitotic Exit Network (MEN) is a signaling pathway that allows a dividing cell to exit cytokinesis. Dbf2 is a MEN protein kinase in yeast, which provides a simplified model for studying this pathway. By altering Dbf2’s activity through phosphorylation mutants, its effect on cytokinesis can be studied. Transformed cells with a mutant and degron Dbf2 allele are prompted to destroy the degron Dbf2 protein, leaving only mutated Dbf2 behind. This allows for clear analysis of the effect of the phosphorylation mutant on division. Fluorescence microscopy can be used to visualise this degradation, and the impact on actin ring formation …