Biochemistry, Biophysics, and Structural Biology Commons^™

Cultivating Collaboration In Biomolviz: Key Attributes For Building A Stem Educator Community Of Practice, Pamela S. Mertz, Charmita Burch, Roderico Acevedo, Josh T. Beckham, Didem Vardar-Ulu, Kristin M. Fox, Lauren A. Genova, Rachel M. Mitton-Fry, Swati Agrawal, Daniel R. Dries, Kristen Procko

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

BioMolViz is an educational community of practice (CoP) focused on creating resources to improve biomolecular visual literacy instruction and assessment. The community of life science instructors developed in three phases, beginning with a small Core Team that emerged from a conference session and established the domain of interest for the CoP. In-person workshops, supported by short-term funding, drove the initial expansion of the community and the development of shared activities in Phase 2. This CoP was sustained through intentional choices about how members interact, collaborate, and share work. As the community matured in Phase 3, it was supported by longer-term …

Waste Streams From Next Generation Molten Salt Reactors: The Challenge Of Creating An Insoluble Ceramic For Chloride Salt Waste, Alevtina A. Maksimova, Jake W. Amoroso, Matthew Page, Gregory Morrison, Hans Conrad Zur Loye

Faculty Publications

Molten salt reactors (MSRs) design development is of interest to many research groups and companies. Waste management for MSRs is one of the most important issues that needs to be resolved due to its impact on environmental safety, primarily via the dissolution of radionuclides in water. Furthermore, the waste treatment strategy will have a significant influence on the operating cost of MSRs, which is why a reliable process for the immobilization, transportation, storage and disposal of MSR waste must be addressed. This work presents a new approach for the immobilization of chloride salts from molten salt reactors in stable oxyhalide …

The Role Of External Factors In Shaping Carbohydrate Conformational Landscapes, Murat Yaman

Dissertations, Theses, and Capstone Projects

Carbohydrates (glycans) are among the most structurally diverse biomolecules and participate in a wide range of biological processes, including molecular recognition, cell adhesion, immune response, host-pathogen interactions, and cellular signaling. Their biological functions are governed by a complex interplay between sequence, stereochemistry, conformational flexibility, and environmental factors. However, the structural heterogeneity and dynamic nature of glycans present significant challenges for both experimental characterization and theoretical modeling. In particular, the relationships between glycan structure, conformational dynamics, and the resulting potential energy surfaces remain incomplete.

This dissertation investigates how external factors modulate the potential energy surfaces of carbohydrates through a combination of …

Development Of Ultrafast Protein Digestion And Standards Free Quantitation Methods For Mass Spectrometric Analysis, Praneeth Ivan Joel Fnu

Dissertations

A wide variety of biologically important molecules, such as enzymes, antibodies, hormones, transporters and receptors are proteins by composition and they play key roles in biological functions such as cellular regulation, communication, metabolism and physiological function. Protein dysfunctions and abnormalities are associated with numerous diseases, making proteins critical targets for understanding disease mechanisms and developing therapeutic interventions. Protein-based therapeutics such as monoclonal antibodies, hormones and vaccines gained popularity due to their high specificity, efficacy, and ability to treat complex diseases that are often difficult to address with small-molecule drugs.

Given the important role of proteins in a variety of biological …

Modeling Kinetics Of 5-Aminolevulinic Acid-Induced Protoporphyrin Ix Accumulation For Optimal Photodynamic Therapy, Priscilla Melebor

Graduate Masters Theses

Photodynamic therapy (PDT) is a minimally invasive treatment that uses light-activated photosensitizers to selectively destroy diseased tissue through the generation of reactive oxygen species. However, conventional in vitro models often fail to accurately reproduce the pharmacokinetics of photosensitizer accumulation and clearance observed in vivo. This study investigated protoporphyrin IX (PpIX) accumulation following 5-aminolevulinic acid (ALA) exposure under physiologically relevant conditions using two-dimensional (2D) monolayers and three-dimensional (3D) spheroids. By comparing continuous ALA exposure with transient exposure followed by ALA washout, this work provides a more biologically relevant framework for studying PpIX kinetics and optimizing photodynamic therapy.

Three-Dimensional Cell And Nuclear Geometries Inform Tissue Level Fluid Mechanics During Epithelial Remodeling, Liam Joseph Russell

Electronic Theses and Dissertations

During epithelial remodeling, mechanical and molecular programs must coordinate to drive the cell shape changes that enable new tissue topologies. Dynamic morphogenesis requires epithelia to preferentially exhibit solid- or fluidlike properties depending on developmental and biophysical constraints. Convergent extension in the Drosophila germband epithelium is one such remodeling event, during which the lateral ectoderm lengthens by two-fold along the primary body axis while concomitantly shortening orthogonally. This process is an incredibly dynamic and attractable system for studying tissue morphogenesis mechanics in vivo.

Germband extension is driven by oriented cell intercalation through T1 transitions, where cells directionally interdigitate with one another …

Synthesis, Utilization And Biological Evaluation Of Β-Hairpin Peptides As Inhibitors Of Immune Checkpoints, Sarah Naylon

Electronic Theses and Dissertations 2020 - Present

Peptide therapeutics have emerged as promising alternatives to monoclonal antibodies because of their smaller size, improved tissue penetration, and synthetic versatility. Yet their broader application is often limited by poor structural stability, rapid clearance, and reduced target residence times. This dissertation describes the design, synthesis, structural characterization, and biological evaluation of β-hairpin peptides as inhibitors of immune checkpoints and as peptide vaccine scaffolds while developing strategies to overcome these limitations. At first a series of antibody-derived β-hairpin peptides (mimics of complementary determining region heavy-chain 3: CDR-H3s) as covalent inhibitors of the PD-1/PD-L1 immune checkpoint were investigated. Electrophilic warheads were incorporated …

Crystal Structure Of New Polar Rare Earth Borates Na2.62Ln2.12(Bo3)3 (Ln = Pr, Nd, Sm) Containing Isolated Bo3 Groups, Alevtina A. Maksimova, Mark D. Smith, Hans Conrad Zur Loye

Faculty Publications

Three new rare earth borates, Na2.62Ln2.12(BO3)3 (Ln = Pr, Nd, Sm), were synthesized via a high-temperature solution reaction using a BaCO3–H3BO3–NaF flux and structurally characterized by single-crystal X-ray diffraction analysis. The compounds crystallize in the orthorhombic space group Amm2 with lattice parameters a = 5.0985(10) Å, b = 11.180(2) Å, c = 7.1483(14) Å, and a unit cell volume of 407.48(14) ų (Z = 2) for Na2.62Pr2.12(BO3)3, a = 5.0983(10) Å, b = 11.181(2) Å, c = 7.1491(14) Å, and a unit cell volume of 407.51(14) ų (Z = 2) for Na2.62Nd2.12(BO3)3, and a = 5.08630(10) Å, b …

Single Crystal Growth Of The Orthoborate Nabalu(Bo3)2 And Optical Investigation Of Eu3+ And Tb3+ Doped Nabalu(Bo3)2, Alevtina A. Maksimova, Mark D. Smith, Lakshani W. Masachchi, Hans Conrad Zur Loye

Faculty Publications

Sodium barium lutetium borate NaBaLu(BO₃)₂ crystals were synthesized using a high-temperature solution method. The crystal structure of this layered orthoborate is described and corresponds to that of an extensive orthoborates family, NaBaR(BO₃)₂ (R = Sc, Y, Yb, Tb – Lu). NaBaLu(BO₃)₂ was doped by Eu³⁺ and Tb³⁺ to explore its performance as a host material and to investigate the luminescent properties of the Eu³⁺ and Tb³⁺ doped materials. The emission spectra of the NaBaLu(BO₃)₂:Ln (Ln = Eu, Tb) crystals are presented. The most …

Expression Levels Of Heat Shock Protein 72 And Their Correlation With Biomarkers Of Renal Function Among Hispanic Construction Workers Exposed To Ambient Heat In El Paso, Texas, Maria Fuentes

Open Access Theses & Dissertations

Heat shock proteins (HSP) are intracellular molecular proteins that are upregulated in response to cellular stress, including heat exposure. Through their protective functions, HSP help maintain protein structure, prevent protein denaturation, and preserve cellular homeostasis during states of physiological stress. Because of their cytoprotective properties, HSP have emerged as potential biomarkers for detecting early signs of tissue injury and predicting clinical outcomes associated with heat related illnesses (HRI), including acute kidney injuries (AKI). AKI is a leading cause of hospitalizations due to heat stress exposure and heat stroke. In the absence of early detection and effective therapeutic interventions, AKI may …

Machine Learning Integrated Designing And Screening Of 8-Hydroxyquinoline Based Metallo-Beta-Lactamase Inhibitors, Anthony M. Baudino, Kari Stone

Chemistry Department Faculty Articles

The rapid emergence of metallo-b-lactamase-mediated antibiotic resistance has created an urgent need for new inhibitor discovery strategies. In this work, a machine-learning-guided workflow was developed to generate and prioritize potential inhibitors targeting NDM-1. A SMILES-based variational autoencoder was first pretrained on a broad molecular dataset to learn general chemical syntax and latent molecular representations. The model was then fine-tuned on an 8-hydroxyquinoline-enriched dataset to bias molecular generation toward zinc-binding chemical space relevant to metallo-β-lactamase inhibition. Generated compounds were processed through structural filtering and docking-based evaluation to create training data for downstream predictive modeling. Molecular fingerprints and physicochemical descriptors were then …

Bridging The Gap In Science Research: Preparing Students For College- Level Research In The Sciences, Victoria Helwig, Yaoguang Li

UConn Library Presentations

Many first-year students enter college unprepared to fully engage with scientific literature and academic library resources. Drawing on experiences from academic librarians working with STEM students, this session explores common gaps in science research skills, including navigating databases, identifying scholarly sources, and understanding the structure of scientific literature. Participants will be introduced to practical strategies and classroom-ready activities to better prepare students for college-level research. Discussion questions: What science research skills do students struggle with most when entering college? How can high school instruction better support these skills? Where can librarians and educators collaborate to support student success?

Ionophore-Based Plga Nanosensor For Selective Ion Detection And Imaging, Zhiyu Tang

Electronic Theses and Dissertations 2020 - Present

Accurate detection of electrolyte ions is essential for biological research, disease diagnosis, and the investigation of cellular function. In this study, we developed ionophore-based PLGA nanosensors for the optical detection of biologically important ions. The nanosensors were prepared by encapsulating ionophores, chromoionophore III, and ion exchangers within PLGA nanoparticles. The resulting nanosensors showed uniform morphology, good colloidal stability, and concentration-dependent optical responses toward Na⁺, K⁺, and Ca²⁺ over the range of 10⁻⁶ to 10⁻¹ M. Reversible fluorescence responses under repeated ion concentration changes confirmed the stability and robustness of the sensors. The nanosensors also demonstrated reliable analytical performance for K⁺ …

Selenoprotein P And Selenium As Potential Diagnostic Biomarkers For Breast Cancer Patients, Farah A. Rashid, Rawaa A. Ali, Hanaa A. Ali

Karbala International Journal of Modern Science

Breast cancer incidence increases in last decade. Oxidative stress increases during cancer development causes consuming of antioxidants. Selenium and its transporting protein, selenoprotein P have an important role in redox homeostasis. This study aims to investigate whether or not selenium and selenoprotein P could be diagnostic biomarkers for breast cancer patients. This study was included 30 individuals in control group who is age- and BMI-matched with 60 breast cancer patients. Selenium was measured by colorimetric assay kit and selenoprotein P was determined by Sandwich ELISA kits. The results indicate significant decrease (p < 0.0001) of serum selenium and selenoprotein P in breast cancer patients compared to control. A positive significant correlation (r = 0.6214, p < 0.0001) was found between selenium and selenoprotein P in breast cancer patients. Selenium has an excellent diagnostic accuracy with area under curve 0.9831, sensitivity 95% and specificity 100% at cut-off less than 3.54 mmol/L. Furthermore, selenoprotein P has also an excellent area under curve 0.9958 with sensitivity 96.77% and specificity 100% at cut-off less than 4.15 ng/ml. These exploratory findings appear that selenium and selenoprotein P could be potential diagnostic biomarkers for breast cancer patients. Further investigations in large-multicenter populations are needed to confirm results.

Out Of This World: An Exoplanetary Workshop, Monica Storss, Bart Kuipers

ELO (un)supervised 2026

The workshop investigates how scientific constraints can productively defamiliarize human experience and create new frameworks for creativity and expression. Participants will produce original work while considering broader questions about environment, perception, and cultural formation in speculative contexts, and how the arts, sciences, and technology inform each other in relational multiplicities. This generative workshop explores how astronomical data from confirmed exoplanets can generate new poetic forms and linguistic constraints. Participants will examine how exoplanetary conditions can shape language, metaphor, and narrative structure. We'll develop from writing exercises that respond to non-terrestrial physical parameters: alternative light spectra, gravitational variations, and atmospheric compositions. …

Fish Tissue Digestion And Microplastic Polymer Identification Protocol Using Open-Source Ftir Database, Shawn L. Kissinger, Vick-Ariel Privert, Jason Bystriansky, Kyle A. Grice

DePaul Discoveries

Microplastic (MP) contamination in aquatic ecosystems poses significant concerns for environmental and public health, as seafood represents a critical food source worldwide. Despite increasing evidence of MP presence in marine organisms, efficient and accessible detection methods remain essential for characterizing contamination patterns and informing regulatory frameworks. This study extracted MPs from brain, gill, intestine, liver, and muscle tissues of gilt-head bream (Sparus aurata) and European sea bass (Dicentrarchus labrax), two commercially important species from the Gulf of Cádiz, Spain, using a NaOH–HNO₃ chemical digestion protocol. Isolated particles were characterized by Fourier Transform Infrared (FTIR) spectroscopy, with …

Decoding The Allosteric Grammar Of Protein Kinases: A Dual-Stream Framework Integrating Protein Language Models And Energy Landscape Frustration Analysis, Will Gatlin, Max Ludwick, Lucas Turano, Brandon Foley, Kamila Riedlova, Vít Škrhák, Marian Novotný, David Hoksza, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The spatial and energetic encoding of allosteric regulatory sites remains a major challenge in structural biology, frequently representing a “blind spot” for sequence-based artificial intelligence (AI) models. We present a protein language model (PLM)-guided approach complemented by the energy landscape frustration analysis as a dual-stream framework to investigate the relationship between AI prediction of binding sites and biophysical organization of regulatory pockets across the human kinome. By probing a fine-tuned residue-level PLM classifier across 453 kinase structures, a clear performance gap is discovered between highly predictable orthosteric pockets (Types I, I.5, and II) and poorly resolved distal allosteric sites (Type …

Recent Advances In Phosphatidylinositol Phosphate Kinases (Pipks) And Their Inhibitors, Mengxia Sun, Jian Hu, Xuefei Huang

BAU Journal - Science and Technology

Phosphatidylinositol phosphate kinases (PIPKs) are an important class of enzymes in humans, which produce lipid signaling molecules playing central roles in pathogenesis of diseases such as cancer, neurodegenerative diseases, and viral infection. Consequently, they are attracting increasing attention as drug targets for disease treatment. This review summarizes the functions of the PIPK family enzymes and highlights recent efforts on designing novel inhibitors against PIPKs. These advances are extensively discussed to stimulate interest in this field and promote further development of highly potent and selective inhibitors for innovative therapeutic applications.

Main-Chain Ion-Pair Polybenzimidazole Membranes Enabling Reduced-Temperature Ht-Pemfc Operation (Down To 120°C), Brian C. Benicewicz, Huina Lin

Faculty Publications

Proton exchange membrane (PEM) fuel cells are promising for clean and efficient energy conversion across diverse applications. High-temperature PEM fuel cells (HT-PEMFCs) using phosphoric acid (PA)-doped polybenzimidazole (PBI) can operate up to 200°C, but at lower temperatures, water-induced PA loss often leads to performance degradation and reduced durability. In this work, we present a new class of main-chain ion-pair PBI membranes by integrating the imidazolium-biphosphate ion-pair units directly into the PBI backbone. This design results in membranes with high acid content, stronger acid-polymer interactions and stabilized acid retention. In single-cell tests, the Im+-PBI15-3 wt.% exhibits peak power densities of 0.79 …

Allosteric And Uncompetitive Inhibition Of Yeast Alcohol Dehydrogenase Identified By Enzyme Kinetics, Dylan Jeremy Harrison, Jenny A. Cappuccio

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

Enzyme kinetics is a powerful technique used to quantify the rate at which an enzyme converts a substrate into a product and to identify potential inhibitors. In this study, kinetic analysis was employed to assess the activity of yeast alcohol dehydrogenase (YADH) in the presence and absence of sweeteners commonly found in alcoholic beverages. YADH catalyzes the oxidation of ethanol to acetaldehyde using NAD⁺ as a cofactor; the reduction to NADH can be monitored spectrophotometrically at 340 nm. Based on structural similarities to the ribose moiety of NAD⁺, it was hypothesized that sucrose and sucralose could directly interact with the …

Synthesis And Characterization Of Organometallic Polymers And Their Cytotoxicity Towards Human Cancer Cell Lines, Paul Peter Slawek

Electronic Theses and Dissertations 2020 - Present

This research aimed to synthesize organometallic polymers from dialkyl (methyl, ethyl, butyl, cyclohexyl, and octyl) and diaryl (phenyl) tin dichlorides and three organic monomers, dipicolinic acid (DPA), chloramphenicol (CH), and isomannide (IS), using interfacial polymerization. Structure-activity relationships were investigated through physicochemical characterization (light-scattering photometry, proton NMR, and IR spectroscopy) and cytotoxicity was evaluated against six human cancer cell lines (AsPC-1, PANC-1, MCF-7, MDA-MB-231, HT-29, PC-3), with cisplatin serving as the reference standard.

Five DPA/tin polymers were synthesized, with IC₅₀ values in the range of 0.60–0.71 μg/mL. Their cytotoxicity was significantly lower than that of cisplatin (0.0023-0.044 μg/mL), suggesting that …

Synthesis And Characterization Of Synergistic Bioactive– Organometallic Condensation Polymers, Francesca Isabel Mosca

Electronic Theses and Dissertations 2020 - Present

This research focuses on the synthesis and structural characterization of polymers with anticipated anticancer and antiviral properties by combining metal-containing Lewis acids, organotin dichlorides (R2SnCl2), Group 4 metallocene dichlorides (Cp2TiCl2, Cp2ZrCl2 and Cp2HfCl2), and triphenyl Group 15 metal dichlorides (Ph3AsCl2, Ph3SbCl2 and Ph3BiCl2), with biologically active Lewis bases, lamivudine, a synthetic nucleoside, and camphoric acid, a dicarboxylic acid, to achieve synergistic effect.

Five classes of polymers were synthesized using interfacial polymerization: lamivudine and organotin dichlorides, lamivudine and Group 4 metallocene dichlorides, camphoric acid and triphenyl Group 15 metal dichlorides, camphoric acid and organotin dichlorides, and camphoric acid and Group 4 …

Developing A High-Resolution Off-Axis Common-Mode Digital Holographic Microscope, Lucy Cook

University Honors Theses

Off-axis digital holographic microscopy (DHM) is a powerful tool for 3D, non-invasive live-cell tracking without moving parts. However, traditional setups face an inherent dilemma: split-path interferometers offer high spatial resolution but poor temporal stability, while more stable common-mode configurations are historically limited to lower numerical aperture (NA) regimes. This thesis bridges that gap by scaling a common-mode DHM architecture into a high-resolution benchtop instrument featuring NA = 0.65 objectives, paired with a high-power 520 nm laser source to combat transmission losses and sustain imaging frame rates across an expanded optical footprint. We map the multi-variable design space required to satisfy …

Supramolecular Assembly In Short Peptide Systems For Selective Metabolite Recognition And Drug Nanoencapsulation, Maithreyi Ramakrishnan

Dissertations, Theses, and Capstone Projects

Short peptides can form adaptive supramolecular assemblies, and understanding how minimal sequences organize around neurometabolites or hydrophobic cancer drugs enables the rational design of functional materials. This thesis combines molecular dynamics with experimental validation to establish design rules linking peptide sequence to emergent structure and function. Chapter 1 outlines the molecular determinants governing peptide assembly. Chapter 2 reviews computational workflows that reveal sequence-dependent conformations and supramolecular organization. Chapter 3 applies these principles to Dynamic Peptide Libraries which identify tetrapeptides that selectively interact with neurometabolites. Chapter 4 extends the same interaction-driven framework to design tryptophan-rich pentapeptides that co-assemble with kinase inhibitors …

Computational Insights Into Nucleosome Dynamics In Epigenetics Using Molecular Dynamics Simulations, Rutika Patel

Dissertations, Theses, and Capstone Projects

Nucleosome core particles (NCP) are the building blocks that form a highly organized and compact chromatin structure. Nucleosomes package DNA in the nucleus of eukaryotic cells. The NCP consists of about 147 base pairs of DNA wrapped around the histone octamer, with 1.65 superhelical turns in a left-handed manner. The histone octamer is composed of two copies of H3, H4, H2A, and H2B. Together with histone H1 and linker DNA, they further assemble into a higher-order chromatin structure. The nucleosome complex is stabilized by electrostatic interactions between positively charged histone residues and the negatively charged DNA backbone. To effectively access …

Identifying Textual Predictors Of Early Termination In Clinical Trials In Medicine: An Explainable Machine-Learning Study, Rohan Ramnarain

Dissertations, Theses, and Capstone Projects

About one in five clinical trials in medicine ends early, wasting valuable resources and reducing the evidence available for developing life-saving medical treatments. This project uses a method called Trial2Vec, which is a self-supervised machine-learning method that converts clinical trial documents into dense numerical representations that capture their key design and clinical characteristics, to turn each proposed clinical trial’s written protocol into a compact numerical profile (a process referred to as embedding). These profiles are then paired with a predictive machine learning models to identify the words and phrases in the trial documents that can signal a higher risk of …

High-Throughput Robotic Ethanol Inhibition Assays For Engineered Thermophilic Biofuel Strains, Kevin He, Daniel Olson, Marybeth Maloney, Anthony Lanahan

Wetterhahn Science Symposium Posters

Ethanol stress assays are commonly used to evaluate microbial tolerance, metabolic adaptation, and fermentation performance. However, manual liquid handling introduces variability across replicate wells and small-volume pipetting steps, limiting reproducibility and throughput. This study developed an automated OT-2 robotic workflow to generate replicated ethanol concentration gradients for high-throughput inhibition assays in engineered thermophilic biofuel strains. Kinetic plate-reader measurements were used to quantify ethanol-dependent growth responses under anaerobic fermentation conditions. The reasearch question is: How do engineered thermophilic biofuel strains differ in ethanol-dependent growth inhibition under anaerobic fermentation conditions, and can automated robotic assays improve the reproducibility of these measurements? Can …

Somatic Prosthetics For Planetary Resonance, Disha Dharesh Kumar R

Masters Theses

This thesis investigates how industrial design can transcend extractive technological paradigms in favor of relational interfaces that foster planetary attunement. Framing the climate crisis as a 'crisis of imagination', the research challenges the Western bifurcation of nature and culture by drawing on Indic cosmologies- which recognize stones, plants, and ecosystems as conscious at different levels and participants in a shared cosmic field. By synthesizing research in Biosemiotics, Quantum Information Pansycishm, and Neuroscience, the project redefines intelligence as a distributed, more-than-human phenomenon.

The research materializes as a speculative design artifact: a device that functions as a somatic prosthetic for planetary resonance. …

Microtubules In Breast Cancer: Exploring The Α/Β-Tubulin Toggle Switch And Its Implications In Human Breast Cancer, Annemarie Ianos

Student Theses and Dissertations

Microtubules, composed of a/b-tubulin heterodimers, play a central role in breast cancer tumor growth by polymerizing, leading to metastasis and depolymerizing, contributing to proliferation. Human enzymes protein kinase Ca (PKC-a) and cyclin-dependent kinase 1 (Cdk-1) mediate phosphorylation at sites a:Ser165 and b:Ser172, respectively, influencing the growth of microtubules. It is possible that alternating phosphorylation at these sites contribute to an a/b-tubulin “toggle switch” that mediates microtubule instability and tumor growth.

The project investigates the influence of the toggle switch model on microtubule stability by determining the impact of mutants (a:S165D, a:S165N, a:S165S_P, b:S172S_P and a:S165S_P/b:S172S …

Computational Design Of Peptides And Proteins Through Machine Learning Approaches, Emily J. Hendrix

Chemistry and Chemical Biology ETDs

Advancements in machine learning have emerged as a pivotal tool in computational biochemistry, offering new advancements to address challenges in protein structure and function. However, current machine-learning approaches offer limited insight in understanding protein dynamics. The purpose of this work is to combine traditional physics-based computational tools, such as molecular dynamics and coarse-grained simulations, with recently developed AI-driven computational tools to bridge gaps and advance the understanding of proteins in both structural and dynamic aspects. I investigated several approaches such as (i) traditional physics-based methods to study protein conformation and ensembles; (ii) identifying a peptide inhibitor for the PICK1 PDZ …