Larry's Blog

A blog documenting the journey of a computational biophysicist at the intersection of molecular simulation, artificial intelligence, chemistry, gene editing, and beyond.

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Cal State LA: Annenberg Science Complex

Picture: My flash talk presentation at the minority opportunities in research (MORE) programs UCLA Lake Arrowhead Retreat.

Some Background on Me:

I am a graduate student in Bioengineering at the University of California, Riverside under the adisement Dr. Giulia Palermo (We are soon moving to UCLA!). I studied Biology and biochemistry as my undergraduate major at Cal State LA and graduated with my masters in chemistry in 2024 under the advisement of Dr. Olseni Sode. My long term career plan is become a research scientist exploring the molecular basis of biological reactions, exploring electronic, and vibrational structures in the subfield of theoretical chemistry utilizing quantum computational methods, quantum molecular dynamics, classical and enhanced samplied molecular dynamics with additional explorations in using machine learning and neural networks to accelerate these calculations and simulations to speed the drug and molecular discovery process. I find that exploring the fundamental theory of the chemical reactions of biomolecualar systems is a rewarding experience with vast consequences for the scientific community. This website serves as my personal accountability tracker, where I plan to document a wealth of information about my career experiences. Additionally, it will function as a repository for the knowledge and research that I come across.

My Research Experience:

My first break in research was via the lab of Dr. Yong Ba in 2016 where I explored the synthesis and characterization of beta-cyclodextrin dimers for the inclusion of anti-cancer drugs like sorafenib. Later, I concurrently joined the laboratory of Dr. Micheal Hayes where I investigated the VAC1 knockout of pentatricopeptide repeats in S. lycopersicum and the establishment of CRISPR Cas9 methods/protocols in glyphosate resistance so that the laboratory could have a pipeline protocol for future CRISPR explorations. I was inspired to join his lab based on casual hallway conversations that I would have with him while I worked as an assistant at the university’s office of Environmental Health and Safety.

I joined Dr. Sode’s lab in Fall 2020 and I graduated with my BS in 2021. Thanks to Dr. Sode’s mentorship, I learned the basics of quantum mechanics (enrolling also in this class), and computational chemistry. This kindled a great passion and curiosity in computational science, which enriched my hobbies of creating and scripting 3D-printed robots.

In Dr. Sode’s lab I undertook constructing a set of potential energy surfaces for four van der Waals rare-gas CO2 complexes (Rg-CO2; Rg = He, Ne, Kr, Xe). We used permutationally invariant polynomials to construct a potential energy function for each complex and fit these against a set of 44,000 Rg-CO2 configuration potentials calculated at the CCSD[t] level of theory using Tikhonov regularization. A paper on this is in preparation to be submitted to the Journal of Physical Chemistry A in early 2024.

Recently, I joined Dr. Giulia Palermo’s lab at UCR in Fall 2024 as a doctoral student in biogineering where I am currently exploring the molecular mechanisms of CRISPR-Cas9 systems using a combination of quantum mechanics/molecular mechanics (QM/MM) simulations, classical molecular dynamics (MD) simulations, and machine learning CV generation for enhanced sampling methods.

For more information on my research, please visit my research page