Projects

Our program for high-schools

Our research laboratory is hosting an annual program dedicated to high school teachers and students, aimed at teaching the foundations of computational chemistry and biology. We will provide a first hands-on experience in our computational laboratory and the opportunity to pursue a computational research project on the most recent breakthroughs in biology and chemistry.

Our program takes shape in two phases of 10-weeks (i.e., the spring and summer quarters of the UC academic year), and is dedicated to 9th to 12th grade classes of Chemistry and Biology, offering lectures and hands-on research training. During the spring quarter, the teachers will be trained on the foundations of molecular simulations and their applications covered in our technical elective undergraduate class (BIEN165). This will provide them advanced knowledge that will be important to guide their students. During the summer, the teachers and their students will join the lab to pursue a computational research project. They will learn scripting and coding on the Linux operating system, software and programming tools for biomolecular simulations. The project will be chosen in light of the most recent breakthroughs in Biology and Chemistry.

2021 – Understanding genome editing molecules

CRISPR-Cas is a revolutionary system that is transforming biology providing the ability to manipulate nucleic acid and perform genome editing. In 2012, researchers demonstrated that RNAs could be used to guide a Cas nuclease (Cas9 was the first) to bind and cleave any desired DNA sequence.

Our project focuses on an emerging CRISPR-Cas protein – namely Cas12a – used to not only perform easy genome editing, but also to detect nucleic acids, which is enabling rapid and precise detection of viruses, such as the SARS-CoV2 coronavirus. The goal of this project is to understand the biophysical function of the Cas12a protein bound to DNA and RNA through molecular simulations. Our team first introduced the significance of Cas12a and described the basics of molecular simulations to the participants. Since we are working from home, we granted virtual access to our computational facilities and we assisted the participants through Zoom to perform simulations. This research project has been development taking inspiration from the PhD thesis of Aakash Saha, graduate student in the lab. A first paper was also published in J. Chem. Inf. Model.

Participants: Alexandra Lowe, Sara Young & Abhinav Reddy

Led by: Rohaine V. Hsu, Aakash Saha & Pablo R. Arantes

Outcomes: participants are taking home the ability to visualize proteins using computers, perform simulations, analyze data & learn about gene editing.

2020 – Visualizing the SARS-CoV-2 coronavirus in action

We introduced undergraduate to molecular dynamics simulations through a small research project on the SARS-CoV2 main protease MPro. The project involved a brief literature introduction, explaining the mechanism of action of the SARS-CoV2 coronavirus and the role of the protease MPro. This protein is sufficiently small to enable an introductory tutorial on MD simulations.
The project has been carried out by our undergraduate students Emelda Fonki, from the African American community, joining our lab thanks to the Research in Science and Engineering (RISE) summer program, Marco Medrano, Hispanic, and Yisi He, joining our lab from the Women Scripps Community College in Claremont thanks to the Summer Bridge Research Program, supported by the Navy Engagement (TUNE) Grant from the Office of Naval Research.

The students have expressed a great interest and passion toward the understanding of the SARS-CoV2 mechanism of action. They have independently pursued a research in the literature collecting he most relevant papers using Molecular Dynamics on this topic. They dowloaded the Molecular Dynamics trajectories of the glycolsilated Spike protein from the Amaro Lab, reporting to our group members the current hypotheses on the role of Spike in SARS-CoV2 function. Undergraduate students have been assisted by Aakash Saha and Pablo Arantes, who also published a First Reaction Article on the Amaro Lab work on ACS Central Science.

Participants: Emelda Fonki, Marco Medrano, Yisi He

Led by: Brandon P. Mitchell, Aakash Saha, Pablo R. Arantes

Outcomes: participants learned the mechanism of action of the SARS-CoV2 coronavirus, visualizing its components and performing molecular simulations.

Computations and analysis have been performed on the supercomputers awarded by the COVID19 HPC consortium, which is a unique private-public effort to bring together government, industry, and academic leaders who are volunteering free compute time and resources in support of COVID-19 research.