The High Performance Computing Club sponsors a mentorship program for undergraduate students interested in high performance and/or distributed computing methods. Our mentors come from diverse fields in physical, life, and social sciences.

The application session for Fall Quarter 2017 has closed. For those interested, please be on the lookout for our Winter Quarter Application in mid-November.

**Available Mentors & Projects**

**Sarah Alamdari – Chemical Engineering**

**Research Topic: ** Molecular dynamic simulations on enzymatic reactions

**Research Interest(s): ** Data science

**Project Description: ** Molecular Dynamics (MD) simulations are a computational method used to study system dynamics on the atomic scale by iteratively solving Newton’s equations of motion. Many important processes, like chemical reactions, can be characterized by different metastable states (i.e. reactants, products, and transition states). We are interested in understanding the underlying minimum energy reaction pathways that connect these states. These metastable states converge very slowly on the time scales accessible by computers, however enhanced sampling techniques can be applied to overcome these problems. You will apply enhanced sampling techniques to MD simulations to explore the reaction coordinate of a sample reaction system.

**Project Requirements: ** Mentee must have taken a Chemistry course

**Aakash Sur – Bioinformatics/Genomics**

**Research Topic: ** Genome assembly and structure

**Research Interest(s): ** Web development for scientific data visualization, signal processing, statistical analysis

**Project Description: ** One of several 1) Run and analyze a GPU based genome assembler in the cloud. 2) Integrate web visualization tools to explore and understand high dimensional genomics data 3) Explore/Implement/Develop peak detection algorithms for genomics data (signal processing)

**Arushi Prakash – Chemical Engineering**

**Research Topic: ** Understanding the assembly of proteins on surfaces

**Research Interest(s): ** Computational Chemistry, Molecular Simulations, Unsupervised Machine Learning (Clustering Methods)

**Project Description: ** In order to understand the structure of proteins, the mentee would have to cluster the structure from data(already generated). The mentee would be required to use existing clustering tools and write their own clustering scripts in Python.

**Project Requirements: ** Python proficiency (preferred), comfortable with bash

**Andrew Wildman – Chemistry**

**Research Topic: ** Electronic Structure Theory (Quantum Chemistry)

**Research Interest(s): ** Data Science

**Programming Langauges: ** Python, C++, FORTRAN

**Frameworks: ** Gaussian, MatLab

**Joe Kasper – Chemistry**

**Research Topic: ** Spectroscopy and Relativistic Quantum Chemistry

**Research Interest(s): ** Mathematics, Machine Learning, Physics

**Programming Langauges: ** Python, C

**Frameworks: ** Gaussian, MatLab, Mathematica

**Sharon Solis – Applied Math**

**Research Interest(s): ** PDEs, Dynamical Systems, Predator-Prey models, Machine learning

**Programming Langauges: ** R, Python, SQL, C++

**Frameworks: ** MatLab, Mathematica

**John Schaefer – Chemistry and Applied Mathematics**

**Research Topic: ** Excited State Chemistry / Numerical LA

**Research Interest(s): ** Games Theory, Epidemiological Modeling

**Programming Langauges: ** Python, Java, C

**Frameworks: ** Gaussian, MatLab, Mathematica

**Alicia Clark – Mechanical Engineering**

**Research Topic: ** Mechanical/Biomedical Engineering

**Research Interest(s): ** HPC projects related to Python/MatLab

**Programming Langauges: ** Python

**Frameworks: ** MatLab

**Will Kearns – Biomedical and Health Informatics**

**Research Topic: ** Conversational Agents for Consumer Health Question Answering

**Research Interest(s): ** Bayesian Networks, Disease Modeling, Genetics

**Programming Langauges: ** Python, C, Javascript

**Frameworks: ** Spark, Pytorch, Tensorflow, Keras

**Torin Stetina – Computational Chemistry**

**Research Topic: ** Quantum chemical simulations of light-matter interactions

**Research Interest(s): ** Physics, General Data Science

**Programming Langauges: ** Python, C

**Frameworks: ** Gaussian, MatLab, Mathematica

**Sarah Stansfield – Anthropology/Epidemiology**

**Research Topic: ** HIV evolution and spread with network models

**Research Interest(s): ** Network Modeling, Infectious Diseases

**Programming Langauges: ** R

**Frameworks: **

**Arshiya Hoseyni Chime – Mechanical Engineering**

**Research Topic: ** Combustion of alternative and pure fuels

**Research Interest(s): ** CFD, Combustion, Renewable Energy, HPC

**Project Description: ** The mentee will be running CFD simulation of a combustion chamber to compare against experimental data.

**Frameworks: ** STAR-CCM+

**Christopher Fu – Chemical Engineering**

**Research Topic: ** Developing methods for studying complex reactions through molecular dynamics simulations

**Research Interest(s): ** Molecular Dynamics Simulations, Complex Reacting Systems, Data Science

**Programming Langauges: ** Python

**Frameworks: ** Gaussian, MatLab, Mathematica, GROMACS, AMBER, PLUMED, CP2K