Digital Commons Network^™

Accurate Crystal Structure Prediction Of New 2d Hybrid Organic–Inorganic Perovskites, Nima Karimitari, William J. Baldwin, Evan W. Muller, Zachary J.L. Bare, W. Joshua Kennedy, Gábor Csányi, Christopher Sutton

Faculty Publications

Low-dimensional hybrid organic–inorganic perovskites (HOIPs) are promising electronically active materials for light absorption and emission. The design space of HOIPs is extremely large, as a variety of organic cations can be combined with different inorganic frameworks. This not only allows for tunable electronic and mechanical properties but also necessitates the development of new tools for in silico high throughput analysis of candidate materials. In this work, we present an accurate, efficient, and widely applicable machine learning interatomic potential (MLIP) trained on 86 diverse experimentally reported HOIP materials. This MLIP was tested on 73 experimentally reported perovskite compositions and achieves a …

Comparative Analysis In The Effectiveness Of Real Vs. Virtual Labs In Enhancing Students’ Conceptual Understanding Of Archimedes’ Principle, Judeanto Edy, Sutopo Sutopo, Edi Supriana

Jurnal Pendidikan Sains

This research aimed to investigate the effectiveness of virtual laboratories compared to real laboratories in improving students’ conceptual understanding of Archimedes’ principle. A quantitative approach was employed using a pretest-posttest design. The measurement instrument used in this study was a concept mastery test, consisting of 15 multiple-choice questions. Data were analyzed using an independent sample T-test. The research involved students from two XI IPA classes, each consisting of 33 students. The findings indicated that both virtual and real laboratories in the learning process could enhance students’ conceptual understanding. The study concluded that there was no significant difference between the virtual …

Exploration Of Students’ Scientific Argumentation Skills On Static Fluid Topics, Trio Junira Fernando, Parno Parno, Markus Diantoro

Jurnal Pendidikan Sains

The weakness in students’ scientific argumentation, particularly in providing evidence-based arguments, has become a significant concern in education. This study aims to assess students’ scientific argumentation skills specifically on the topic of static fluids. The survey was conducted with 78 twelfth-grade students from private high schools in East Java, Indonesia, who had previously studied this topic. A scientific argumentation test instrument, consisting of an essay format with five questions, was employed to collect data. The data were analyzed using descriptive statistics, followed by a classification based on static fluid subtopics and the level of scientific argumentation skill. The results indicated …

Quinoxaline 1,4-Di-N-Oxide Derivatives As New Antinocardial Agents, Isidro Palos, Alonzo Gonzalez-Gonzalez, Alma D. Paz-Gonzalez, José C. Espinoza-Hicks, Debasish Bandyopadhyay, Norma Paniagua-Castro, Marlene S. Galeana-Salazar, Jorge Ismael Castañeda-Sánchez, Julieta Luna-Herrera, Gildardo Rivera-Sanchez

School of Integrative Biological & Chemical Sciences Faculty Publications

Mycetoma is currently considered as a neglected tropical disease. The incidence of mycetoma is unknown but most of the worldwide cases are present in the “mycetoma belt” including countries like Mexico, India, Senegal, and others. The treatment of mycetoma depends on the etiological agent responsible for the case. Treatment success reaches 60 to 90%; however, common treatment has been reported to be ineffective in some cases, due in part to resistance to the prescribed antibiotics. Therefore, it is necessary to develop new therapeutic options. In the past two decades, quinoxaline derivatives have shown relevance as antibacterial agents. Therefore, in this …

Impact Of Problem-Based Learning Integrated With Blended Learning On Students’ Collaborative Skills, Angel Regina, Yustina Febblina Daryanes, Riki Apriyandi Putra

Jurnal Pendidikan Sains

This study investigates the impact of implementing a Problem-Based Learning (PBL) model integrated with Blended Learning on enhancing students’ collaborative abilities. Conducted in class XI of SMA Negeri Plus Riau Province during the 2021/2022 academic year, the research utilized a control group design to compare the collaborative skills of students in an experimental class, which employed the PBL model, with those in a control class. The study assessed four key indicators of collaborative ability: working productively, valuing opinions, compromising, and sharing responsibility. The findings revealed that students in the experimental class showed significant improvements in all four indicators compared to …

Influencing Factors Of Competency Achievement In Fiber Optic Installation Engineering: A Study On Vocational School Graduates In Indonesia, Pangadongan Elfin Pujianto, Djoko Kustono, Hakkun Elmunsyah

Jurnal Pendidikan Sains

This study investigates the factors influencing the achievement of competencies in the field of Fiber Optic Installation Engineering (TIFO) among vocational school graduates in Indonesia and their subsequent performance in the workforce. Utilizing a quantitative approach, the research examines the relationship between several key variables, including national examination scores, quality of infrastructure, teaching competence, and telecommunication systems subject scores. Path analysis structural equation modeling was employed to determine the direct and indirect effects of these variables on TIFO competency achievement and graduates’ performance. The findings reveal that the quality of infrastructure is the most significant contributor to competency achievement, accounting …

Development Of E-Modules Based On Pjbl-Steam And Virtual Simulation Media On Work And Energy Topic As An Effort To Improve Students’ Critical Thinking Skills, Farah Rafidah, Parno Parno, Nasikhudin Nasikhudin, Marlina Ali

Jurnal Pendidikan Sains

Work and energy are fundamental topics in physics. However, enhancing students’ critical thinking skills in these areas remains a challenge. This research aimed to develop and assess the validity and readability of e-modules designed with PjBL-STEAM and virtual simulation media to address this issue. The development process followed a 4D model, and the resulting e-modules were evaluated as strongly valid category. The validation tests yielded percentage scores of 91.6% for media, 89.3% for content, and 88.0% for lesson plans. Additionally, the readability test achieved a score of 84.6%, indicating a excellent level of comprehensibility. These findings suggest that the e-modules …

Integrating Data-Driven And Mechanism-Driven Modeling In Drug Discovery And Hepatotoxicity Evaluation, Xuelian Jia

Theses and Dissertations

The pharmacological activities and hepatotoxicity significantly influence the success or failure of new drugs during drug discovery and development. Traditional experimental methods, such as animal models, are costly and time-consuming for chemical testing. There is a great need to develop in vitro and computational modeling to help identify the pharmacological activities and hepatotoxicity potential in the early stage of drug discovery and safety evaluation. In this dissertation, new computational models and associated modeling frameworks were described for predicting the biological profile and hepatotoxicity of chemicals. Firstly, a novel data mining and Quantitative Structure-Activity Relationship (QSAR) workflow was developed to construct …

Preliminary Molecular Study Of Chloramphenicol Anchoring On Laccase Enzyme From Trametes Hirsuta, Hanzhola Gusman Riyanto, Afiten Rahmin Sanjaya

Makara Journal of Science

Antibiotics are one of emerging pollutants generally emitted from livestock production and the food industry to the environment. The presence of this pollutant could initiate the development of resistant bacteria that can be fatal to human health. The degradation of antibiotics using enzymes or microbe could be an alternative because the residue or intermediate product is less harmful than of the conventional method. This research aims to support a preliminary study of the degradation of antibiotics using enzyme through molecular docking via Molecular Operating Environment software and molecular dynamics (MD) study via CABSFLEX 2.0 and WebGro macromolecular simulations. The molecular …

Near-Infrared Ratiometric Hemicyanine Fluorescent Probes For Monitoring Mitochondrial Ph Dynamics In Live Cells During Oxidative Stress And Hypoxia, Sushil K. Dwivedi, Dilka Liyana Arachchige, Adenike Olowolagba, Mohamed Mahmoud, Subash Pandey, Tara Vohs, Haiying Liu, Rudy Luck

Michigan Tech Publications

Novel near-infrared ratiometric molecules (probes A and B) produced by linking formyl-functionalized xanthene and methoxybenzene moieties, respectively, onto a xanthene-hemicyanine framework are detailed. Probe A exhibited a primary absorption peak at 780 nm and a shoulder peak at 730 nm and exhibited fluorescence at 740 nm↓ (signifies a downward shift in intensity upon acidification) in a pH 9.3 buffer and 780 nm↑ at pH 2.8 under excitation at 700 nm. Probe B featured absorptions at 618 and 668 nm at pH 3.2 and at 717 nm at pH 8.6, and fluorescence at 693 nm↑ at pH 3.2 and at 739 …

Efforts Toward The Synthesis And Biological Evaluation Of Ym/Fr Analogs, Siyue Liu

Arts & Sciences Graduate Student Theses and Dissertations

Natural products FR900359 and YM254890, selective inhibitors of the Gq/11 protein signaling pathway, are crucial for therapeutic development, particularly in treating uveal melanoma. This dissertation focuses on efforts to understand the mechanisms behind this selective inhibition. A versatile synthetic approach to these natural product analogs and a potential method for evaluating their biological activity on the microelectrode array are presented. Chapter 1 provides an overview of Gq/11 proteins, detailing their roles in cellular signaling. Mutations lead to constitutively active oncogenic Gq/11 proteins, contributing to uveal melanoma. The building-block synthetic concept is introduced in the YM/FR synthesis, enabling relatively scalable and …

Efforts Toward The Synthesis And Biological Evaluation Of Ym/Fr Analogs, Siyue Liu

Arts & Sciences Graduate Student Theses and Dissertations

Natural products FR900359 and YM254890, selective inhibitors of the Gq/11 protein signaling pathway, are crucial for therapeutic development, particularly in treating uveal melanoma. This dissertation focuses on efforts to understand the mechanisms behind this selective inhibition. A versatile synthetic approach to these natural product analogs and a potential method for evaluating their biological activity on the microelectrode array are presented. Chapter 1 provides an overview of Gq/11 proteins, detailing their roles in cellular signaling. Mutations lead to constitutively active oncogenic Gq/11 proteins, contributing to uveal melanoma. The building-block synthetic concept is introduced in the YM/FR synthesis, enabling relatively scalable and …

Synthesis Of Zno: Zro2 Nanocomposites Using Green Method For Medical Applications, Mohammed J. Tuama, Maysoon F. Alias

Karbala International Journal of Modern Science

These days, nanocomposites are very popular, especially in medical applications. The spread of diseases in general, and those caused by microbes and cancerous diseases in particular, and the increased resistance of these diseases to antibiotics, have led to the need for the rapid, low-cost, and environmentally friendly production of nanocomposites. To create the chemical G-ZnO: ZrO2 and S-ZnO: ZrO2 (green technique), two different plant extracts were utilized: Z. officinal and S. aromaticum. The effective synthesis and acceptable properties features of the nanoparticles were confirmed using characterization techniques such as X-ray diffraction (XRD), Fourier transform infrared (FTIR) , diffuse reflectance spectroscopy …

A Preliminary Fuzzy Inference System For Predicting Atmospheric Ozone In An Intermountain Basin, John R. Lawson, Seth N. Lyman

Mathematics and Statistics Faculty Publications

High concentrations of ozone in the Uinta Basin, Utah, can occur after sufficient snowfall and a strong atmospheric anticyclone creates a persistent cold pool that traps emissions from oil and gas operations, where sustained photolysis of the precursors builds ozone to unhealthy concentrations. The basin's winter-ozone system is well understood by domain experts and supported by archives of atmospheric observations. Rules of the system can be formulated in natural language ("sufficient snowfall and high pressure leads to high ozone"), lending itself to analysis with a fuzzy-logic inference system. This method encodes human expertise as machine intelligence in a more prescribed …

Systematic Review On Isolation, Purification, Characterization, And Industrial Applications Of Thermophilic Microbial Α- Amylases, Rugaiyah A. Arfah, Sarlan Sarlan, Abdul Karim, Anita Anita, Ahyar Ahmad, Paulina Taba, Harningsih Karim, Siti Halimah Larekeng, Dorothea Agnes Rampisela, Rusdina Bte Ladju

Karbala International Journal of Modern Science

The α-amylase enzyme, sourced from diverse organisms, including plants, animals, and bacteria, plays a crucial role in multiple industries, notably food processing sectors like cakes, fruit juices, and starch syrup. Research identifies thermophilic organisms as prime sources of this enzyme thriving at temperatures ranging from 41°C to 122°C. The enzyme purification was carried out using liquid-liquid extraction, which involved the exchange of substances between two liquid phases that were immiscible or partially soluble. The optimal temperature for α-amylase was 45 to 90°C. The best pH for bacterial and fungal α-amylases ranged from 5.0 to 10.5 and 5.0 to 9.0. Based …

Table Of Contents

Journal of the South Carolina Academy of Science

No abstract provided.

The Effect Of Different Vegetable Oils (Macadamia Nut Oil And Walnut Oil) On The Coefficient Of Friction As A Finish For Oak Wood, Lee Dillon

Journal of the South Carolina Academy of Science

Slipping due to insufficient friction with flooring can cause fatal injuries in workplaces and homes. Oak wood flooring is commonly used in construction to build these environments. In the manufacturing process, wood finishing is conducted at the end of the process to strengthen the properties and longevity of the wood, although it could impact the coefficient of friction (COF) causing slip falls. Vegetable oils, such as macadamia nut and walnut oils, used as wood finishes have gained prominence due to their beneficial aspects to the environment. However, little is known about their effectiveness as a safe coating for wood floors. …

Cortisol And Alpha-Synuclein Stability In Saliva Under Varying Storage And Handling Conditions, Mo Zheng, Sujata Srikanth, Jeremiah Carpenter, Delphine Dean

Journal of the South Carolina Academy of Science

Parkinson’s disease (PD) is a progressive neurodegenerative disorder characterized by motor impairments and non-motor symptoms, significantly impacting patients' quality of life. Currently, cerebrospinal fluid (CSF) is the primary biofluid used for PD biomarker studies, notably α-synuclein, despite the invasive nature of lumbar puncture procedures. Recent work has shown that some of these PD biomarkers have been measured in saliva. As an alternative to CSF, saliva can be non-invasively self-collected by patients repeatedly over time to monitor biomarker levels. However, the stability of these biomarkers in saliva needs to be evaluated before saliva can be considered for patient self-collection studies. Therefore, …

Enhancing Cardiomyocyte Resilience To Ischemia-Reperfusion Injury: The Therapeutic Potential Of An Indole-Peptide-Tempo Conjugate (Iptc), Shanshan Hou, Xin Yan, Xiang Gao, Steffen Jockusch, K. Michael Gibson, Zhiying Shan, Lanrong Bi

Michigan Tech Publications

Ischemia/reperfusion (I/R) injury leads to apoptosis and extensive cellular and mitochondrial damage, triggered by the early generation and subsequent accumulation of mitochondrial reactive oxygen species (mtROS). This condition not only contributes to the pathology of I/R injury itself but is also implicated in a variety of other diseases, especially within the cardiovascular domain. Addressing mitochondrial oxidative stress thus emerges as a critical therapeutic target. In this context, our study introduces an indole-peptide-tempo conjugate (IPTC), a compound designed with dual functionalities: antioxidative properties and the ability to modulate autophagy. Our findings reveal that IPTC effectively shields H9C2 cardiomyocytes against hypoxia/reoxygenation (H/R) …

Alphafold2 Modeling And Molecular Dynamics Simulations Of The Conformational Ensembles For The Sars-Cov-2 Spike Omicron Jn.1, Kp.2 And Kp.3 Variants: Mutational Profiling Of Binding Energetics Reveals Epistatic Drivers Of The Ace2 Affinity And Escape Hotspots Of Antibody Resistance, Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

AlphaFold2-based atomistic predictions of structures and conformational ensembles of the SARS-CoV-2 spike complexes with the host receptor ACE2 for the most dominant Omicron variants JN.1, KP.1, KP.2 and KP.3 to examine the mechanisms underlying the role of convergent evolution hotspots in balancing ACE2 binding and antibody evasion. Using the ensemble-based mutational scanning of the spike protein residues and computations of binding affinities, we identified binding energy hotspots and characterized the molecular basis underlying epistatic couplings between convergent mutational hotspots. The results suggested the existence of epistatic interactions between convergent mutational sites at L455, F456, Q493 positions that protect and restore …

Breakthrough Conductivity Enhancement In Deep Eutectic Solvents Via Grotthuss-Type Proton Transport, Desiree Mae Prado, Clemens Burda, Anthony Jahng, Kayla Poling

Faculty Scholarship

There is an increasing demand for the development of ion-conducting electrolytes for energy storage systems. Much attention is directed toward deep eutectic solvents as potential candidates. In the search for highly conductive systems, the possibility of designing deep eutectic solvents with Grotthuss-type proton transport is widely overlooked. Herein, ethaline, a mixture of choline chloride and ethylene glycol is used in a 1:2 molar ratio, to induce a significant conductivity increase with the addition of water and sulfuric acid (H₂SO₄). The achieved breakthrough conductivity is analyzed experimentally and simulated with ab initio molecular dynamics (AIMD). At sufficient water content, an H-bonding …

Development And Benchmark Of Polarizable Models For Ions, Luke Landry

Dissertations

Metalloproteins are ubiquitous in biology, playing crucial roles in diverse processes. Meanwhile, molecular simulations have become an important tool in scientific research. To accurately simulate metalloprotein systems, accounting for polarization and charge transfer effects is required. The fluctuating charge (FQ) model can effectively simulate the charge transfer effect, but the existing models often lack specificity for metalloproteins. In our research, a tailored FQ model for zinc-containing metalloproteins, leveraging the extended charge equilibration (EQeq) scheme, was introduced. CM5 charges were used as the target in our model parameterization, which offers advantages over RESP/CHELPG charges. Most notably, CM5 charges hold independence over …

Improving Ligand Pharmacokinetics Via Bioisosteric Substitution Of Amides With 1, 2, 3-Triazoles While Maintaining Dopamine D4 Receptor Selectivity And Potency, Mohammad Alkhatib

Theses and Dissertations

Several neurophysiological functions, such as attention, cognition, and emotional regulation, are regulated by the binding of dopamine on G-Protein coupled receptors. D4Rs are mainly located in the prefrontal cortex and the hippocampus and are known to have a key role in decision-making, memory formation, cognition, and attention. Administration of D4Rs- selective ligands during the preclinical studies enhance the outcomes and the results in animal models suffering from neuropsychiatric disorders, including ADHD, substance use disorders (SUD), and Alzheimer's disease. Recently, we reported a group of D4R-selective ligands with different efficacies depending on their phenylpiperazine ring scaffold to illustrate D4R function during …

Potential Nec2/Nek1 Inhibitor And Inh1 Analog N-[4-(2,4-Dimethylphenyl)-2-Thiazolyl]-4-Pyridinecarboxamide Via Hantzsch Thiazol Condensation, Robert E. Lee Sr, Isabella G. Mcdonald, Paige E. Heiple, Lukas D. Shelton

Journal of the South Carolina Academy of Science

The potential active pharmaceutical ingredient (API), N-[4-(2,4-Dimethylphenyl)-2-thiazolyl]-4-pyridinecarboxamide (6) is a cancer cell metabolism mitosis inhibitor via the Nek2 and Hec1 enzymes. The three-step synthesis starts with the bromination of 1-(2,4-dimethylphenyl)ethan-1-one (1) using CuBr₂ to produce 2-bromo-1-(2,4-dimethylphenyl)ethan-1-one (2) with a yield of 90%.[i]^,[ii],[iii] Followed by Hantzsch thiazol ring synthesis as (2) reacts with thiourea (3) and, resulting in 4-(2,4-dimethylphenyl)thiazol-2-amine (4)[iv] in 80% yield. Finally, isonicotinoyl chloride hydrochloride (5) and (4) reacted to form the amide (6).[v]^{,[vi],[vii],[viii],[ix],[x]} Characterization of the final product was determined …

Examination Of Oncogenic Effects Of Environmental Pollutants, Andrew Ackerman, Matthew Behling, Brock Earley, Janay Vacharasin

Journal of the South Carolina Academy of Science

Chemical byproducts produced by surrounding industrial complexes have polluted the local estuaries of Georgetown, South Carolina for several decades¹. Previous studies completed by the EPA and SCDNR showed that the estuaries contained carcinogenic pollutants released from the local manufacturing plants¹. One of the mentioned pollutants was dioxins which are produced during the paper bleaching process². Dioxins are highly toxic compounds that have various carcinogenic effects on the organisms that inhabit the area. These previous studies were conducted over thirty years ago. Therefore, a current study to determine if chemical byproducts are contaminating local estuaries …

Striatal Beat Frequency Interval Timing Model With Microgravity Stressor, Jason Michael Fitzgerald, Sorinel Oprisan

Journal of the South Carolina Academy of Science

The Striatal Beat Frequency (SBF) model of interval timing uses frontal cortex (FC) neural oscillations to record the state of the brain at the reinforcement time Tc during fixed interval (FI) procedures in the long-term memory (LMEM). The state of the FC oscillators at any given time is stored in a short-term memory (SMEM) buffer. The SBF model uses the spiny neurons of the basal ganglia (BG) as coincidence detectors to produce beats between the content of the SMEM and LMEM. Across multiple species that can perform interval timing, there are two invariant properties: (a) the timing is precise, and …

Development And Validation Of A Chemistry Laboratory Safety Knowledge, Attitudes, Practices, And Mindset Questionnaire, Claudine Garcia, Genejane Adarlo, Anna Carissa San Esteban, Armando M. Guidote

Health Sciences Faculty Publications

Accidents in chemistry laboratories can be prevented by fostering a safety culture - the institution’s knowledge, attitudes, practices (KAP), and mindset regarding laboratory safety. To effectively promote a safety culture, robust tools are essential for evaluating safety KAP and mindset. Hence, this study developed and validated a questionnaire that can rapidly measure laboratory safety KAP and mindset to guide targeted interventions aimed at enhancing the safety culture in chemistry laboratories. The study was drawn from existing validated questionnaires in constructing a tool comprising 40 items that can measure the safety KAP and mindset in chemistry laboratories. Using a cross-sectional design, …

A Convenient Synthesis Of Short Α-/Β-Mixed Peptides As Potential Α-Amylase Inhibitors, Naeem Ahmed, Fakhira Razzaq, Muhammad Arfan, Mansour K. Gatasheh, Hammad Nasir, Joham Sarfraz Ali, Hamna Hafeez

Michigan Tech Publications

Over the last decades, the increased incidence of metabolic disorders, such as type two diabetes and obesity, has motivated researchers to investigate new enzyme inhibitors. Inhibition of the α-amylase enzyme is one therapeutic approach in lowering glucose levels in the blood to manage diabetes mellitus. The objective of this study was to synthesize short α-/β-mixed peptides in the solution phase. The Boc-protected α-L-leucine was converted to β-analogue by using Arndt–Eistert synthesis with the advantage of no racemization and retention of configuration. Three novel short peptides were successfully synthesized: N(Boc)-Gly-β-Leu–OCH3(14), N(Boc)-O(Bz)α-Ser-β-Leu–OCH3(16), and N(Boc)-O(Bz)-α-Tyr-α-Gly-β-Leu–OCH3(17), characterized by FTIR and 1H NMR analysis. The …

44ti/44sc Generator Development And Radiolabeling Optimization For Medical Applications, Christine E. Schmidt-Kennelty

Dissertations, Theses, and Capstone Projects

In recent years, there has been a growing interest in scandium-44 (⁴⁴Sc) for medical applications due to its favorable decay properties. With a relatively short half-life of 3.97 hours and high positron branching ratio of 94.3%, ⁴⁴Sc is an ideal candidate for positron emission tomography (PET) imaging. However, producing ⁴⁴Sc without an on-site cyclotron limits access, as its short half-life makes it impractical to ship to more remote locations.

To address this issue, ⁴⁴Ti/⁴⁴Sc generators have become a focal point of research, providing an onsite source of⁴⁴Sc. Despite their potential, current …

Incorporating Solvation Thermodynamic Mapping In Computer-Aided Drug Design, Yeonji Ji

Dissertations, Theses, and Capstone Projects

Advancements in computational techniques have revolutionized structure-based drug design, substantially improving the efficiency and effectiveness of the drug discovery process by reducing time, costs, and labor requirements. These advancements include various methods, such as investigating small molecule ligands binding to proteins, exploring alternative protein conformations, and solvation mapping on the protein surfaces. Among these methods, understanding the correlation between protein-ligand binding and the role of solvation is important.

A fundamental concept in protein-ligand binding is shape and electrostatic complementarity, which is complicated by the inherent flexibility of proteins. In the absence of small molecule ligands, proteins are complementary to surface …