Max Wang - July 11th, 2025

A method to compute and model small molecule binding with proteins in Wolfram is created along with a way to visualize residues and corresponding atom indices in a Molecule object. From the binding of the small-molecule lanraplenib to interleukin-8, lanraplenib was found to bind to the same binding site of interleukin-8 to its receptor, potentially acting as a interleukin-8 inhibitor.

Vikrant Chintanaboina - July 11th, 2025

This project develops functions to identify functional groups in a given molecule, aiming to improve understanding of molecular structure and reactivity.

Jasmine Zhao - July 11th, 2025

This project uses sickle cell anemia’s E6V mutation as a case study to visualize and quantify how amino acid substitutions alter protein structure, comparing wild-type and mutant hemoglobin through 3D modeling and atomic displacement analysis.

Sarah Park - July 11th, 2025

Chromatin tends to form knots within the nucleus, which, without proper resolution by topoisomerases, can lead to cell death and mutation. However, the mechanism of this knot formation is poorly understood. Using a mechanical model, this project aims to simulate different knots along randomly moving DNA segments, and analyze the knots’ motion and size. We found that chromatin knots in this model are prone to rightward movement, size decreases, and are heavily influenced by the ratio of knot to chain length. These results provide further insight into DNA knot dynamics and can be applied to future drug development and nanotechnology.

Sarim Mominkhawaja - July 11th, 2025

Cancer treatment and its interaction with the human body are not well understood, making improved comprehension essential for optimizing therapies. A series of mathematical models, from tumor-immune ODEs to delay differential systems with chemotherapy and drug resistance, is developed and analyzed through simulations, biomarker assessment, and optimization. Resistance emergence, immune-tumor dynamics, and the potential superiority of adaptive dosing protocols are demonstrated, highlighting the need for dynamic, patient-specific regimens.

Arnay Garhyan - July 11th, 2025

Having Type 1 diabetes can become a major inconvenience in day-to-day life. Both the classical insulin injection and a hybrid closed loop insulin dosing system require extensive user input into a program to avoid extremely high or low blood sugar levels. To evaluate the capability of a two-bolus dosing system independent of any user input apart from the time of meal, the insulin-glucose response in a virtual person with Type 1 diabetes was modeled, simulated, and utilized to optimize insulin dosing. In addition, the model was used to create an interactive and educational tool to visualize the glucose and insulin levels of an individual following a meal and insulin dose. The primary result was to determine the best dosing regimen for insulin through an interactive tool for a virtual patient.

Mariem El-Kady - July 11th, 2025

A cellular automaton rule is applied for optimized horizontal expansion in genomic modeling, including cases such as cells turning into infinity or similar-entropy twin rules. The rule’s behavior is examined to explore its potential for improving genome-related simulations.

Ian Asaf Muñoz Granados - July 11th, 2025

We use molecular dynamics simulation data of the CXCR7 protein. This protein is a G protein-coupled receptor (GPCRs), it scavenges chemokines and opioids, and recruit β-arrestins, so it is an atypical GPCR. For the protein helices, we extract the spatial coordinates of atoms of alpha carbon (“CA”) and monitor how their positions evolve over time using static and dynamic graphical analysis. In parallel, we compute pairwise contact distances between protein residues and analyze how these distances fluctuate throughout the simulation trajectory.

Júlia Campolim - July 11th, 2025

Due to computational irreducibility, predicting behaviour of cellular automata is a difficult, almost impossible task. However, can we induce the behaviour of a cellular automaton? More specifically, can we control its shape? In order to answer these questions, an experiment was conducted to evolve various cellular automata configurations to a specific shape, considering cellular automata boundary as its fitness function.

Erick Jesse Angeles Lopez - July 11th, 2025

In biology there are patterns of life that grow infinitely and uncontrollably (such as tumors), other that die out immediately under certain conditions and some other that persists for only a finite number of steps. Interestingly, some cellular automaton rules exhibit the similar behaviour. This work explore such rules within the context of one-dimensional totalistic cellular automata, focusing of those that generate finite life when starting from a single cell active.