Undergraduate Students

Andrew Jumanca

B.S. Applied and Computational Mathematical Sciences (ACMS) | University of Washington, Seattle, WA

Research: Applying electron interaction potentials in Amino-Acids as a sequence encoder in Convolutional Neural Networks to predict peptide binding affinity to proteins and inorganic substrates towards vaccines, therapeutics and solid-binding-peptide design

Andy Luong

B.S. | University of Washington, Seattle

designing and optimizing a lozenge with the aid of peptides that will remineralize loss tooth material

Antonio Crowe

B.S. Materials Science and Engineering | University of Washington, Seattle, WA

Research: Finite element simulations of peptide/surface nanomechanical interactions with a linear spring model, towards understanding the choice of chiral angles and repeating units for spontaneous coherent self-assembly of peptides on single-layer materials.

Chandler King

B.S. Informatics (Intended) | University of Washington, Seattle, WA

Research:  I am currently on the Molecular Graph Convolution Network that uses multiple datasets from different disciplines in order to predict and target functionality for peptide/nanomaterial systems. My work specifically has consisted of creating API for some of these datasets and running variable data size experiments.

LinkedIn: https://www.linkedin.com/in/chandler-king-173567cjk?lipi=urn%3Ali%3Apage%3Ad_flagship3_profile_view_base_contact_details%3BCq0tVjJXS1K3Zb0KGVFuZQ%3D%3D

Christian Frech

B.S. Physics (Major) & Math (Minor) | Carnegie Mellon University, Pittsburgh, PA

Research: Random Matrix Theory on graph-structured Hamiltonians to model electron energetics and wavefunction dynamics in biomolecular and bio/inorganic hybrid systems.

Conan Brkanac

B.S. Pre-Engineering | University of Washington, Seattle, WA

Research:  Multiresolution Dynamic Mode Decomposition

David Corbo

B.S. Computer Science & Engineering | University of Washington, Seattle, WA

Research: Continuous entropy-based learning rules for molecularly inspired Graph-Structured Symmetric Hermitian Matrices towards predicting peptide folding dynamics.

Dylan Hylander

B.S Electrical and Computer Engineering | University of Washington, Seattle, WA

Research: The Pairwise Similarity Score is a proven predictor of relative binding affinity and has been used to predict GEPIs specific for quartz, gold, hydroxyapatite, and MoS2. In previous work, a similarity matrix was updated based on whether a peptide (Strong or Weak binding) had higher similarity to strong peptides and less similarity with weak peptides.

Dylan is instead developing a method using stochastic gradient descent to obtain the most ideal similarity matrix to best predict the relative binding affinities.

LinkedIn: https://www.linkedin.com/in/dylan-hylander-805289172/

This would compound work done by the high throughput screening, confirming count numbers observed during phage display are correlated with their actual binding affinity, while using a novel large dataset to test known successful predictive models. All in all, the work carried out in this project accelerates the development pace of bio-nano-devices of the future.

Eileen Chang

B.S. computer Science and Engineering | University of Washington, Seattle, WA

Research: Molecular Graph Convolution

Evan Yip

B.S Bioengineering and Biomedical Engineering| University of Washington, Seattle, WA

Research: I am looking to map the conformation space of peptide sequences using advanced molecular dynamics and Python.

LinkedIn: https://www.linkedin.com/in/evan-yip-990518171/

Hannah Gunderman

B.S. Molecular Biology & Bioengineering | University of Washington

Using molecular biomimetics, optimizing a candy-like lozenge that remineralizes lost tooth enamel

Jackson Frank

B.S Informatics (Intended)| University of Washington, Seattle, WA

Research: Metadata standards and API development

LinkedIn: https://www.linkedin.com/in/jackson-frank-88a534171/

Jeffrey Hanlon

B.S. Mechanical Engineering| University of Washington, Seattle, WA

Research: Sparse Identification of Non Linear Dynamics (SINDy) analysis of molecular dynamics trajectories of peptide adsorption to solid surfaces

Jonathan Francis-Landau

B.A Mathematics| University of Washington, Seattle, WA

LinkedIn: https://www.linkedin.com/in/jonathan-francis-landau-70bb49135/

Julia Wang

B.S. Computer Science & Engineering | University of Washington, Seattle, WA

Research: Database management of metadata standards and front-end API development
LinkedIn: https://www.linkedin.com/in/julia-l-wang/

Justin Shaw

B.S. Computer Science and Engineering| University of Washington, Seattle, WA

Research: Hilbert Space-Filling Curves and Dynamic Mode Decomposition to characterize and discover underlying physics of peptide adsorption dynamics on single-layer materials

Kaushal Bommena

| University of Washington, Seattle, WA

Research: Molecular Graph Convolution

Kimmy Zhao

B.S. Physics | University of Washington, Seattle

Research: Simulated Scanning Electron Microscopy of self-assembled peptides on Single-layer atomic materials

Kyle Jonson

B.S. Computer Science and Engineering | University of Washington, Seattle, WA

Research: Molecular Graph Convolution

Michael Collins

B.S. Mathematics (Intended)| University of Washington, Seattle, WA

Research: Random Matrix Theory application on Graph structured matrices to obtain trends in continuous entropy with changing graph structure, towards addressing peptide folding problems.

Michael Malone

B.S Mechanical Engineering| University of Washington, Seattle, WA

Research: Asynchronous Markov Models to model particulate active-matter (peptides) adsorption, diffusion, and phase changes, including self-assembly on a triangular or hexagonal lattice (e.g., Graphene)

Michael Yusov

B.S Chemical Engineering and Mathematics| University of Washington, Seattle, WA

Nathan Isler

B.S Material Science and Engineering| University of Washington, Seattle, WA

Research: I have been working with Deniz on the dissolution tests for the lozenges. I’ve been apart of the whole process, including the making of the lozenges and the Calcium Assay, but my main focus has been on the dissolving of the lozenges and collecting samples.

LinkedIn: https://www.linkedin.com/in/nathan-isler-9a6310193/

Nina Ulbrich

B.S. Mathematics| University of Washington, Seattle, WA

Research: Principal Component Analysis method (PCA) is used to identify patterns in complex datasets as well as which variables play the most important role. PCA uses eigen-decomposition to reduce a matrix to its eigenvectors and eigenvalues in order to work with a simpler lower-dimensional matrix.

In order to understand the data more, we can use PCA to see clusters in the data. Currently, the dataset contains 2 million peptides (each 12 amino acids long), results from 3 washes and 1 elution, and the binding affinities in terms of their survival rates. Using PCA, the data can be condensed from 16 dimensions to 3 dimensions, allowing us to visualize clusters in the data.

LinkedIn: https://www.linkedin.com/in/nina-tantalean-ulbrich-54a418137/

Nitya Krishna Kumar

B.S. Informatics, Computational Neuroscience Training Program | University of Washington, Seattle, WA

Research: GrBP5 is a peptide that is important to understanding how biological polymers can be assembled to be used in technological devices. Previous research at GEMSEC revealed that GrBP5 self assembled when placed on graphene. Using different assemblies of this peptide we can store different types of information by creating a bioelectric interface.

Under the mentorship of Siddharth Rath and Prof. Mehmet Sarikaya, two other undergraduate students and I are working to computationally simulate and predict different assembly (or conformation) structures of nine different mutations of GrBP5 under varying conditions of temperature and pH. I specifically work on running molecular dynamics simulations on three of the nine mutations.

LinkedIn: https://www.linkedin.com/in/nityakrishnakumar/

Owen Brodie

B.S. Industrial Engineering| University of Washington, Seattle, WA

Research: I work on analyzing the electronic properties of amino acids and their effects on signal transduction between peptides/proteins and the substrates they interact with.

Padma Gundapaneni

B.S. Informatics| University of Washington, Seattle, WA

Pedro Fischer Marques

B.S Chemical Engineering| University of Washington, Seattle, WA

Research: Molecular Dynamics simulations for the predicted structures of peptides (variants of designated Wild Type peptide) under various conditions of pH and temperature.

Results will be used for the furthering of connections between experimental and simulation data, especially through the usage of a neural network to determine future peptide conformations without running extensive simulations or experiments.

These results will also be used to determine how different experimental conditions affect the conformations of the peptides, which can be used to predict under which conditions a peptide may have a larger or smaller binding or assembly affinity.

Ravi Sangani

| University of Washington, Seattle, WA

Research: Molecular Graph Convolution

Reva Kane

B.S. Computer Science and Engineering | University of Washington, Seattle, WA

Research: Molecular Graph Convolution

Shalabh Shukla

B.S. Biochemistry| University of Washington, Seattle, WA

Research: Molecular Graph Convolution and predicting binding pockets of MHC proteins with antigen epitopes.

Sedona Sarobon

B.S. Biochemistry & Materials Science and Engineering | University of Washington

Research and development of a lozenge that remineralizes lost tooth enamel via molecular biomimetics

Tatum G Hennig

B.S. Atmospheric Chemistry. Minors: Chemistry and Applied Mathematics| University of Washington, Seattle, WA

Research: Molecular dynamics simulations and trajectory analysis; Dimension reduction and clustering; Markov State analysis.

Tosh Brown-Moore

B.S. Physics and Materials Science & Engineering| University of Washington, Seattle, WA

Research: Geometric Entropy maximization for obtaining stable conformations of peptides and proteins on solid surfaces.

Valerie Yuryk

B.S. Environment, Ecology and Conservation Biology with minor in Chemistry| University of Washington, Seattle, WA

Research: Oral diseases are the one of the most prevalent health problems that affects the quality of life and well-being of the society. 

Adapting biology’s ways to repair dental hard tissues (enamel, dentin, cementum and alveolar bone), the GEMSEC team uses molecular biomimetic approaches that combine material science, genetic engineering, and clinical dental methods to implement natural biomineralization that cures defective hard tissues at the tissue interface by using ADPs (amelogenin-derived peptides) that remineralize the lost tissue towards forming practical formulations and therapies.

Working in a group alongside Andrea Dao and Laura Lyu, our team focuses on the synthesis and purification of peptides that are used as the base of GEMSEC projects and research. Under the mentorship of Deniz Yucesoy, I have been learning laboratory techniques, have repeatedly performed peptide purification, and am working toward a masterful understanding of peptide synthesis and mass spectroscopy.

LinkedIn: https://www.linkedin.com/in/vyuryk/

Warren Register

B.S Computer Science and Engineering| University of Washington, Seattle, WA

Yifei(Laura) Lyu

B.S. Pre-Engineering (Intended Bioengineering)| University of Washington, Seattle, WA

Zoey Surma

B.S. Chemistry| University of Washington, Seattle, WA

Research: I work on applying Molecular Modeling through molecular dynamics and metadynamics to characterize peptide conformation dynamics and energetics during adsorption to solid surfaces.

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