Pharmacy and Pharmaceutical Sciences Commons^™

Exploring Red Palm Oil As A Sustainable Plasticizer For Carbon Black-Filled Ssbr/Br Tire Tread Compounds: A Comparative Evaluation Of Commercial Alternatives, Norma Arisanti Kinasih, Mohamad Irfan Fathurrohman, Santi Puspitasari, Dewi Kusuma Arti, Abdulhakim Masa

Journal of Materials Exploration and Findings

This study investigates the application of red palm oil (RPO) as an alternative vegetable oil resource to substitute petroleum-based plasticizers, which have environmental and health concerns, in carbon black (CB)-filled SSBR/BR tire tread compounds. The plasticizing effects of RPO were thoroughly evaluated by comparing them with a commercial bio-based plasticizer, Epoxidized Soybean Oil (ESBO), and two safer petroleum-based oils, Naphthenic Oil (NYNAS) and Treated Distillate Aromatic Extract (TDAE). The initial investigation shows that fatty acid composition is imposing regarding the plasticizing effect. The higher unsaturated fatty acid content in RPO than in ESBO improved tensile strength and degraded rolling resistance …

Metallurgical Investigation Of A Modified Eye Bolt Failure Caused By Improper Weld Extension, Specification Deviation, And Crevice Corrosion, Dimas Muhammad Fawwaz, Reza Miftahul Ulum, Johny Wahyuadi Soedarsono, Yudha Pratesa

Journal of Materials Exploration and Findings

A modified eye bolt from the David Arm Manhole Storage Tank underwent thorough metallurgical study due to the consequences of the bolt's malfunction during operation. Safety issues arose when the manhole door detached during operation. The mechanical testing and chemical composition analysis of the bolts indicated they were manufactured from an ASTM A193 Grade B7 material used for high-temperature bolting. This material did not conform to the engineering drawing, which mentioned SA 563A, which is about nuts, not bolts. This contradiction clearly shows that the eye bolt which was installed does not conform to the intended design. Welded connections of …

Rejection Of Fe (Iron) And Kmno4 (Organic Substance) Parameters In Peat Water Using Organic Membranes, Muhamad Rafli Sakti Mulia Gonera, Siti Umi Kalsum, Sarah Fiebrina Heraningsih

Journal of Materials Exploration and Findings

Peat water is a surface water source widely used by people in swampy and lowland areas, but it has poor quality characteristics such as high organic matter content, low pH, and dissolved metal levels such as iron that exceed the threshold. These conditions can cause health problems and reduce the quality of clean water so that effective treatment technology is needed. This study aims to analyze the effectiveness of ultrafiltration membranes made from chitosan from shrimp shell waste in rejecting iron (Fe) and organic substances in peat water, and to determine the effect of pressure on separation performance. This study …

Extracting Aromatic Compounds From Dehydrated Rose Buds, Lana Sheridan

Discovery Day - Daytona Beach

Eugenol (C10H12O2), methyl eugenol (C11H14O2), and 2-phenylethanol (C8H10O) are chemically aromatic, natural compounds commonly present in various botanical sources and essential oils. Structurally, eugenol is a methoxyphenol bearing an allyl side chain; its methyl ether derivative, methyl eugenol, shares a similar framework but features a methoxy group replacing the free phenolic hydroxyl group found in eugenol. 2-Phenylethanol is an aromatic alcohol comprised of a benzene ring linked to an ethanol moiety. The objective of this project was to isolate and characterize these compounds in dried rose buds using distillation followed by chromatographic and spectrometric analysis. For the experiment, a steam …

Steam Distillation Star Anise, Makayla Maso, Kiara Maso

Discovery Day - Daytona Beach

Star anise (Illicium verum) contains several volatile organic compounds responsible for its characteristic aroma, including trans-anethole, estragole, limonene, and linalool. These compounds differ in structure and chemical properties, which influence their behavior during isolation and analysis. Trans-anethole and estragole are classified as aromatic phenylpropene derivatives that contain benzene rings and ether functionalities. In contrast, limonene and linalool are non-aromatic terpenes, with linalool additionally possessing an alcohol functional group. These compounds are widely utilized as flavoring agents and fragrance components, while terpenes such as limonene and linalool are also commonly employed as solvents and in formulation chemistry due to their volatility …

Extraction Of Cedarwood Essential Oils Via Steam Distillation, Forrest Dohner

Discovery Day - Daytona Beach

Many natural materials, including pine and eucalyptus, produce distinct scents due to the presence of volatile organic compounds. In cedarwood, this aroma arises from a combination of aromatic molecules, which are organic compounds containing conjugated carbon ring systems that interact with olfactory receptors. Specifically, cedarwood contains three primary compounds responsible for its scent: cedrol, cedrene, and thujopene. The objective of this experiment was to extract these essential oils from cedarwood and identify their chemical composition. Steam distillation was used to isolate the volatile components by passing steam through the cedarwood, causing the essential oils to vaporize at temperatures below their …

Production And Analysis Of Lavender Essential Oil: Extraction, Composition, And Applications, Mary Zoeller

Discovery Day - Daytona Beach

Steam distillation was performed to extract essential oil from lavender and analyze its chemical composition. Lavender is known to contain several compounds such as linalool, terpinen-4-ol, and linalyl acetate, which contribute to its characteristic aroma and biological activity. The purpose of this experiment was to isolate these compounds without decomposition and identify them using gas chromatography–mass spectrometry (GC-MS). Approximately 14.851 g of lavender was heated with water to generate steam, which carried the volatile compounds into a condenser where the vapor was cooled and collected. The distillate was transferred to a separatory funnel to isolate the organic layer from the …

Steam Distillation Of Jasmine, Mikayla Hulvey, Meliah Martin

Discovery Day - Daytona Beach

This experiment aimed to isolate various components, including benzyl acetate, linalool, indole, and farnesene, from jasmine buds. The functional groups include an ester in benzyl acetate, an alcohol in linalool, an amine in indole, and alkenes in farnesene. Jasmine buds were combined with distilled water and steam distilled using a standard distillation apparatus. The distillate, containing hydrosol and trace amounts of essential oil, was then collected for extraction using methyl tert-butyl (MTBE) for a liquid-liquid extraction. The organic layer was then separated, washed using brine, dried over anhydrous sodium sulfate, and then transferred for later analysis. The essential oil obtained …

Investigation Of Warfarin–Human Serum Albumin Binding By Ultrafast Affinity Extraction Using Single- And Dual-Column Affinity Microcolumn Systems, Samiul Alim

Department of Chemistry: Dissertations, Theses, and Student Research

This dissertation examined the interaction of warfarin with human serum albumin (HSA) by using affinity chromatography, with particular emphasis on ultrafast affinity extraction (UAE) and affinity microcolumns. HSA affinity supports were prepared by immobilizing HSA onto diol-bonded silica via Schiff base chemistry and used to prepare affinity microcolumns for chromatographic studies under physiological-like conditions at pH 7.4 and 37.0 °C. UAE studies were performed to investigate the effects of residence time, flow rate, and column configuration on the measured apparent free fraction of warfarin and on the calculated apparent binding parameters. The results showed that the measured apparent free fraction …

Herbularyo (Folk Healer): An Herbal Medicine Card Game, Maryjane T. Magsino, Inah Marie Q. Rivera, Armando M. Guidote, Genejane M. Adarlo

Chemistry Faculty Publications

Herbularyo, a card game teaching about herbal plants (HPs), was created and evaluated as a viable educational card game based on Tuomisto and Aksela’s criteria. A quasi-experiment was performed on 81 Grade 8 students from a private high school and 50 Grade 11 from a public high school. Independent t-test revealed that the control group (CG) and experimental group (EG) (p=0.386), and EG1 (played ≤5) and EG2 (played >5) (p=0.681) are not comparable with each other. Paired t-test showed EG performed better (p=0.001) than CG (p=0.901) whereas ANCOVA showed that playing Herbularyo improved students’ information retention (p=0.006). EG1 and EG2 …

Techno-Enviro-Economic Analysis Of Precipitated Calcium Carbonate Production From Carbon Dioxide In Cement Industry Flue Gas And Calcium Hydroxide, Natalia Debora Panggabean, Widodo Wahyu Purwanto

Journal of Materials Exploration and Findings

CCUS is a technological solution to reduce emissions from the cement industry, which is the second largest CO2-intensive industry. This study aims to analyze technical, economic, and environmental performance of Precipitated Calcium Carbonate (PCC) synthesis in cement industry flue gas. The process simulation includes the CO2 capture system from cement plant, CO2 captured used as feedstock for PCC synthesis process through its reaction with calcium hydroxide. The simulation was carried out using ASPEN Plus software. Technical analysis was performed to determine the CO2 capture efficiency and PCC synthesis efficiency. Economic analysis was conducted to calculate CO2 capture cost and production …

Feasibility Analysis Of Thermal Oxidizer To Determine Remaining Life Using Fitness- For-Service Level 3 Method, Yudhi Yudistirawan, Donanta Dhaneswara, Wahyuaji Narottama Putra, Gama Widyaputra, Dewi Kurnia Suci, Agung Putra Mahardhika

Journal of Materials Exploration and Findings

An aged thermal oxidizer (TOX) in the oil and gas industry necessitates a comprehensive evaluation to ensure its continued safe operation. This study presents a Remaining Life Assessment (RLA) and a Fitness for Service (FFS) evaluation for the four main components of the TOX, in accordance with API 510, API 579/ASME FFS-1, and ASME BPVC Section VIII Div-1 standards. The investigation includes the determination of maximum stress and maximum temperature required to assess the operational viability of the reactor. The four components are radiant, convection, transition, and stack sections—were modeled using the finite element method (FEM). Following the geometric modeling, …

Folic Acid–Carbon Dot–Gemcitabine Nanoparticles For Targeted Cancer Drug Delivery, Irfan Huda, Hua Mei

SPARK Symposium Presentations

This project aims to develop a folic acid-attached carbon dot nanoparticle system (FA-CDs-GEM) for the targeted delivery of gemcitabine to cancer cells. While gemcitabine is widely used, its effectiveness is limited because a short in vivo half life and lack of selectivity, which lead to severe side effects. Carbon dots offer a simple and modifiable platform as the drug delivery and bioimaging agent. Conjugation of folic acid to the carbon dots enables selective targeting of cancer cells that overexpress folate receptors. In this study, we synthesized and characterized FA-CD-GEM nanoparticles and developed an HPLC calibration curve of GEM to accurately …

Absolute Quantification And Identification Of Rna From Rna-Lipid Nanoparticles Using High Resolution Mass Spectrometry, Jason C. Funderburk

Theses and Dissertations

RNA therapeutics are a rising drug category with potential use for a range of conditions encompassing infectious diseases to therapies for cancer, diseases, and genetic disorders. RNA-lipid nanoparticles (RNA-LNPs) are the prominent delivery method for these therapeutics approved products include mRNA vaccines and polyneuropathy treatments. The emergency use authorizations and orphan drug status of current RNA-LNP drugs has allowed approval without finalization of the regulatory analytical procedures for quality monitoring. The objective of the study was to develop an LC-MS assay to simultaneously measure identity and concentration of two therapeutically relevant intact RNA constructs extracted from RNA-LNPs to enhance quality …

Synthesis And Characterization Of Succinate Dehydrogenase Inhibitors H2/Z14 And C6/Z96 In Order To Combat Small Cell Lung Cancer, Lauren M. Graves

Honors Undergraduate Theses

The use of ubiquinone inhibitors to combat cancer is a recent development in medicinal science and procedures to efficiently synthesize these drugs remain limited. C6/Z96 and H2/Z14, two succinate dehydrogenase inhibitors, have been previously tested in vitro against NSCLC with positive results. Their similarity to ubiquinone is what makes them a strong candidate for a succinate dehydrogenase inhibitor at the ubiquinone binding site. The heterocyclic scaffolds and substituents are proposed to bind strongly through a combination of electronics, hydrogen-bonding, and fit, allowing them to bind well and prove to be more favorable than ubiquinone when competing for the Q-site. By …

Assessment Of Polymeric Chloroquine Formulations For Targeted Therapy Of Ulcerative Colitis And Metastatic Colorectal Cancer, Neha Kumari

Theses & Dissertations

Effective targeted drug delivery is a critical unmet need in the management of both ulcerative colitis and metastatic colorectal cancer, where conventional systemic therapies may be hindered by suboptimal efficacy and significant side effects. This thesis explores the development and preclinical assessment of polymeric chloroquine (PCQ)-based nanotherapeutics, leveraging stimuli-responsive designs for disease-specific delivery and action.

For ulcerative colitis, a reactive oxygen species (ROS)-responsive nanogel system was engineered to release PCQ, a macromolecular derivative of hydroxychloroquine, specifically in the inflamed areas within the colon. Nanogels with well-defined size and positive surface charge were synthesized via reversible fragmentation chain transfer (RAFT) polymerization …

Spilling The Tea: Effects Of Uv Disinfection On Bioactive Compounds In South African Rooibos Tea, Sora Ghanem, Leah Ankiah, Yusra Ahmed

Student Scholar Symposium

This study investigated the effects of ultraviolet (UV) light disinfection on key bioactive flavonoid compounds in rooibos tea (Aspalathus linearis). There is an interest in non-thermal food preservation technologies, and UV treatment offers potential advantages for beverage processing. However, concerns exist regarding possible degradation of health-promoting compounds during treatment. Rooibos tea samples were subjected to five UV exposure intensities (0, 25, 50, 75, and 100 mJ/cm²), and concentrations of four major flavonoids (aspalathin, orientin, vitexin, and rutin) were measured using high performance liquid chromatography (HPLC). Surprisingly, most flavonoids showed stability or slight concentration increases at higher UV doses. Aspalathin concentrations …

Assessment Of The Melt Quality Of A 30% Scrap Adc12 Aluminium Alloy Using The Inclusion And Fluidity Measurement Instrument (Ifmi) With Mullite Ceramic Filters, Gusti Ruri Ruri Lestari, Sandya Ananda Riswan, Muhammad Anis, Ahmad Ashari, Paramita Vidya Ayuningtyas, Bambang Suharno Prof, Donanta Dhaneswara

Journal of Materials Exploration and Findings

The increasing demand for sustainable practices in the metal casting industry has driven the use of recycled aluminum alloys such as ADC12. However, the addition of aluminum scrap tends to increase oxide inclusions, which reduce melt fluidity and compromise casting quality. This study utilizes the Inclusion and Fluidity Measurement Instrument (IFMI), equipped with mullite ceramic filters, to assess the melt quality of ADC12 aluminum alloy containing 30% scrap. Fluidity and inclusion characteristics were evaluated at five pouring temperatures (660°C, 680°C, 700°C, 720°C, and 740°C). The results show that fluidity increased with temperature, reaching a peak of 84.6 g·s⁻¹ at 740°C, …

Equipment Criticality Analysis To Determine Asset Integrity Management System Scheme In Supporting Production Optimization Scenarios In The Aeging Field, Donny Andryanto, Donanta Dhaneswara

Journal of Materials Exploration and Findings

This research investigates the production decline and cost increase in the X&Y oil and gas fields from 2022 to 2023. Production fell by 34%, while production costs per barrel rose by 79%. To address these issues, a series of optimization processes are proposed. These aim to restructure and enhance the production facilities to reduce current production costs. The optimizations include reducing pressure at the PPP Platform in 2024. Additional steps include shutting down CPP-ORF 14” pipelines and most processes at CPP 2 Platform by 2027 to convert it into an accommodation platform. Further, the plan involves optimizing the release of …

Morphological Test Of Areca Nut Fiber Ceramic Membrane Using Scanning Electron Microscopy Energy Dispersive X-Ray Mapping Spectroscopy, Amelia Marzain, Siti Umi Kalsum, Marhadi Marhadi, Ahmad Nabil Shahab

Journal of Materials Exploration and Findings

This study investigates the potential of ceramic membranes derived from areca nut fiber as a cost-effective and environmentally sustainable material for the removal of iron (Fe) and manganese (Mn) from groundwater. Two types of membranes were fabricated: one without activation and one chemically activated using 10% sodium hydroxide (NaOH). The morphological and elemental characteristics of both membranes were analyzed using Scanning Electron Microscopy (SEM) and Energy Dispersive X-ray (EDX) mapping. The concentrations of Fe and Mn before and after treatment were measured using Atomic Absorption Spectroscopy (AAS). The NaOH-activated membrane exhibited a more porous surface structure and higher oxygen content, …

Analysis Of Leakage In Nearshore Pipelines Using Fitness For Service Method To Ensure Mechanical Integrity Based On Api-579 Level 3, Elriandri Elriandri, Dedi Priadi

Journal of Materials Exploration and Findings

The Fitness for Service (FFS) analysis is performed as a quantitative assessment to evaluate the integrity condition of a pipeline. Essentially, FFS assessment helps determine whether equipment components can operate safely despite existing deficiencies. This evaluation is carried out using the Finite Element Method (FEM). In the case of an underwater pipeline that experiences leak due to anchor pull at the flange connection, it undergoes plastic deformation and is lifted approximately 1 meter. As a mitigation step, inspection and repairs have been carried out by the company. Subsequently, modeling is performed to reconstruct the deformation process of the pipeline. Then, …

Selenium Nanoparticles As Versatile Delivery Tools, Amir Nasrolahi Shirazi, Rajesh Vadlapatla, Ajoy Koomer, Kyle Yep, Keykavous Parang

Pharmacy Faculty Articles and Research

Selenium nanoparticles (SeNPs) have emerged as promising metal-based nanoparticles for drug delivery due to their unique physicochemical properties, intrinsic bioactivity, and biocompatibility. SeNPs offer a lower toxicity, higher bioavailability, and flexibility to be customized for surface chemistry compared to traditional selenium compounds. Advances in synthetic strategies, including chemical reduction, green biosynthesis, and surface functionalization with polymers, peptides, or ligands, have improved their stability, targeting capability, and circulation time. SeNP-based systems have demonstrated unique anticancer, antimicrobial, and anti-inflammatory activities, as they can function as drug carriers and active therapeutic agents. The surface of SeNPs has been functionalized with ligands such as …

Adipose Tissue Estrogen Receptor-Alpha Overexpression Ameliorates High-Fat Diet–Induced Adipose Tissue Inflammation, Marion C. Hope, Christian A. Unger, M. Chase Kettering, Cassidy E. Socia, Ahmed K. Aladhami, Barton C. Rice, Darya S. Niamira, Ben P. Wiznitzer, Diego Altomare Ph.D., William E. Cotham, Reilly T. Enos

Faculty Publications

Context

We created an innovative mouse model that enables inducible overexpression of estrogen receptor-alpha (ERα), specifically in adipose tissue (Adipo-ERα↑). Objective

We aimed to investigate how elevated Adipo-ERα↑ influences the development of high-fat diet (HFD)-induced obesity in both male and female mice. Methods

Male and female Adipo-ERα↑ mice and littermate controls were fed a low-fat diet (LFD) or HFD for 13 weeks. Adipo-ERα↑ was induced at the initiation of dietary treatment. Body morphology and composition, hepatic lipid accumulation, glucose tolerance, fasting insulin concentrations, and adipose tissue mRNA profiling were assessed. Liquid chromatography–mass spectrometry was used to determine circulating and adipose …

Techno-Enviro-Economic Approach For Electrification Of Rural And Shrimp Farming Regional Development Of An Isolated Island In Indonesia By Utilizing Hybrid Renewable Energy Systems, Fiqih Akbar Wijaya, Mohammad Akita Indianto

Journal of Materials Exploration and Findings

One of the challenges in developing and archipelagic countries such as Indonesia is maintaining energy demand in rural and isolated areas due to difficulties in electrical distribution. For instance, in areas like Bawean Island, no additional electricity capacity has been introduced in the past year, leading to an unmet potential customer demand. One of the possible options is by utilizing Hybrid Renewable Energy Systems (HRES) that are integrated with existing fossil fuel-based energy systems to support the growing energy demand in the remote island. A case study in Bawean Island is conducted with the projected energy demand covers the energy …

Remaining Life Assessment And Fitness For Service Evaluation Of Aging Chemical Reactors In Polyethylene Terephthalate Resin Industry, Aditya Pahlawan Munthe, Donanta Dhaneswara, Wahyuaji Narottama Putra, Gama Widyaputra

Journal of Materials Exploration and Findings

Aging chemical reactors in the polyethylene terephthalate (PET) resin industry require comprehensive evaluation to ensure safe continued operation. This study conducts a remaining life assessment (RLA) and fitness-for-service (FFS) evaluation on five 30-year-old reactors, based on API 510, API 579/ASME FFS-1, and ASME BPVC Section VIII Div. 1 standards. The analysis involves corrosion rate measurement, future corrosion allowance (FCA) projection, and minimum thickness verification. Among the reactors, R-120 was found to have the shortest remaining life less than 15 years. FFS assessments using three criteria Average Measured Thickness, MAWP from Point Thickness Readings, and Minimum Measured Thickness confirm that R-120 …

A Study Of Wear Measurement And Life Prediction Of Insert Chute Liner On Gold Ore Processing, Ferry Ardika Natanael, Nony Maulidya, Dedi Priadi

Journal of Materials Exploration and Findings

Chutes are critical materials handling assets to transport solid particles from one process step to another in mineral processing, coal mining and cement industries. The material transport, because of material characteristics, cause severe wear on internal lining of chutes or bins’ structure. The wear problem on internal lining of bins or chutes needs to be checked to keep production efficiency. Therefore, not checked wear rate causes liner replacement schedule becomes unpredictable. It leads to production loss and highly cost maintenance in industry. This study shows that condition-based maintenance through regular thickness measurement using Ultrasonic Transducer (UT) to predict life service …

Analysis Of Leak Testing Planning For Carbon Dioxide Piping Systems In The Development Of Carbon Capture, Utilization, And Storage Facilities In The Bintuni Basin, Devi Sentiani, Akhmad Herman Yuwono Professor

Journal of Materials Exploration and Findings

Carbon Capture, Utilization, and Storage (CCUS) technologies have become a key strategic response to global efforts to reduce CO₂ emissions. This study presents a leak testing strategy designed for a carbon dioxide (CO₂) piping system as part of a Carbon Capture, Utilization, and Storage (CCUS) project in the Bintuni Basin, West Papua, Indonesia. This study aims to ensure the system is properly prepared before commissioning by designing a leak test plan that is both practical and technical, based on ASME B31.3, ASME PCC-2, and API STD 520 Part 1. We conducted the process, which involves identifying the system boundaries, …

Synthesis Of Carboxymethyl Cellulose From Nypa Fruticans For Coating Metformin On Zn-Based Metal-Organic Framework Nanohybrid As A Bionanocomposite Drug Delivery System, Delviani Delviani, Viola Giary Rizkillah Maharani, Putri Nur Shadrina, Tri Warni, Regina Wan Azizah, Indra Lasmana Tarigan, Madyawati Latief

Makara Journal of Science

Diabetes is a common and rapidly spreading disease that affects 6.6% of the world’s population. Metformin hydrochloride (HCl) is an effective oral pharmacological treatment for type 2 diabetes mellitus (T2DM) patients because of its capability to reduce glucose levels and the risk of hypoglycaemia. However, gastrointestinal sensitivities to this drug can cause diarrhoea, nausea, vomiting and stomach ache. An alternative is controlled release technology by coating metformin with carboxymethyl cellulose (CMC) and zinc-metal-organic framework (Zn-MOF) through the encapsulation method. Therefore, this study aimed to coat metformin formulations using CMC in a Zn-MOF to control release into the body and minimise …

Molecular Insights Into The Role Of Estrogen Receptor Beta In Ecdysterone Mediated Anabolic Activity, Syeda Sumayya Tariq, Madiha Sardar, Muhammad Shafiq, Hendrick Heinz, Mohammad Nur-E-Alam, Aftab Ahmad, Zaheer Ul-Haq

Pharmacy Faculty Articles and Research

Ecdysterone, often dubbed a “natural steroid,” has garnered significant attention among athletes for its reputed growth-promoting and anabolic properties. Unlike synthetic anabolic steroids, which are classified as controlled substances, ecdysteroids remain largely unregulated in many countries and are widely marketed as dietary supplements. Notably, ecdysterone has been included in the World Anti-Doping Agency (WADA) monitoring program, highlighting its potential impact on athletic performance and raising questions about its regulation. Emerging evidence indicates that, unlike traditional anabolic steroids that act primarily via the Androgen Receptor (AR), ecdysterone’s anabolic effects may be mediated through Estrogen Receptors (ERs), particularly Estrogen Receptor beta (ERβ). …

Integrative Computational Modeling Of Distinct Binding Mechanisms For Broadly Neutralizing Antibodies Targeting Sars-Cov-2 Spike Omicron Variants: Balance Of Evolutionary And Dynamic Adaptability In Shaping Molecular Determinants Of Immune Escape, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

In this study, we conducted a comprehensive analysis of the interactions between the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein and four neutralizing antibodies—S309, S304, CYFN1006, and VIR-7229. Using integrative computational modeling that combined all-atom molecular dynamics (MD) simulations, mutational scanning, and MM-GBSA binding free energy calculations, we elucidated the structural, energetic, and dynamic determinants of antibody binding. Our findings reveal distinct dynamic binding mechanisms and evolutionary adaptation driving the broad neutralization effect of these antibodies. We show that S309 targets conserved residues near the ACE2 interface, leveraging synergistic van der Waals and electrostatic interactions, while S304 focuses on …