Charles Plate
Welcome to my corner of innovation!
I’m Charles, a computational chemical engineer passionate about turning complex challenges into cutting-edge solutions.
Charles Plate
About Me
I am Charles Plate, a chemical engineer with a passion for computational chemical engineering and biochemistry. With a Ph.D. from Virginia Tech and extensive international research experience, I specialize in complex projects involving drug design and molecular simulations. My goal is to deliver innovative solutions to scientific and engineering challenges.
Skills in Action
Resume
Education
2021 - Present
Blacksburg, VAVirginia Polytechnic Institute and State University
PhD. in Chemical Engineering, GPA: 3.7/4.0
**Advisor: Dr. Sanket Deshmukh
2015 - 2019
Hoboken, NJStevens Institute of Technology
B.E. in Chemical Engineering, Minor in Computer Science, GPA: 3.7/4.0
Publication
2023
Journal of Physical Chemistry Letters
Singh, S. K.; King, K.; Gannet, C.; Chuong, C.; Joshi, S. Y.; Plate, C. J.; Farzeen, P.; Webb, E.; Kumar K. L.; Weger-Lucarelli, J.; Lowell. A. N.; Brown A. M.; Deshmukh, S. A; “Data driven computational design and experimental validation of drugs for SARS-CoV-2”
Award
2023 - 2024
Jülich, GermanyNSF Fellowship - IRES : ASSURE
Forschungzentrum Jülich - Computational Biomedcine INM-9
Program : International Research Experience for graduate Students (IRES) Algorithms and Software for SUpercomputers with emerging aRchitEctures (ASSURE)
Research Team : Mercedes Alfonso-Prieto, Christoph Falkhe, Paolo Carloni
Project : Metadynamics simulations to investigate substrate release from the D-galactonate transporter
Proposal : Submitted computational hours proposal, awarded 8 million core-hours on FZJ Jureca (accepted April 2024, valid through April 2025)
Research Skills
MDAnalysis
Rdkit
GROMACS
Docking
Optimization Algorithms
Coding Skills
Python
Bio-Python
Shell
Java
C++
Computational Tools
- Rdkit
- MDAnalysis
- GROMACS
- PLUMED
- AlphaFold
- BioPython
- AutoDock Vina
- PLANTS
- LeDock
- rDock
- PyMOL
- VMD
Methods /Models
- Molecular Dynamics
- Metadynamics
- MM/GBSA
- Docking
- Optimization Algorithms
- MachineLearning (coursework only)
Biological Systems
- Hepatitis E Virus
- RNA Dependent RNA Polymerase
- Cystine Protease | Hepatitis C Virus - RNA Dependent RNA Polymerase
- Picornavirus - RNA Dependent RNA Polymerase
- COVID 19 - Main Protease | Dengue Virus - Main Protease
Experience & Projects
Early Experience
2020
Stony Brook, NYStony Brook University
Research Assistant - Department of Marine and Atmospheric Sciences
** Analyzed marsh peat and lake sediment for heavy metal contaminates
** Designed and executed an atomic absorption spectroscopy procedure
2018 - 2019
Upton, NYBrookhaven National Laboratory
Sustainable Energy Technologies Department Intern
** Investigated the flue gas contaminants of wood burning stoves and helped to develop cleaner, more efficient
wood stove systems
** Programmed a data acquisition system for the judging of 12 teams from 4 countries in the Alliance for Green
Heat’s 2018 Wood Stove Design Challenge
** Incorporated mass and energy balance equations into the program for the calculation of flue gas emissions, burn
rate, and efficiency
** Quantified, recorded, and displayed detailed flue-gas emissions data during uncharted transient regions of the
wood burning process
** Selected to deliver an oral presentation to the staff at Brookhaven regarding the research
Teaching Experience
2019 - 2021
Huntington, NYDave’s Pod Learning
High School Classroom Instructor : Physics, Chemistry, Math, and Computer Science
2019 - 2021
Commack, NYThe Tutoring Center
Head Instructor : K-12 Math
2015 - 2019
Hoboken, NJStevens Institute of Technology
Hosted review sessions in Organic Chemistry, Chemical Thermodynamics, Mass Transfer
2015 - 2019
Hoboken, NJMathnasium
K-12 Mathematics Tutor
Primary Projects
MD Knockout
A framework/codebase for accelerated molecular dynamics in high throughput virtual screening applications, deployed on Virginia Tech’s ARC
HEV Drug Design
High throughput virtual screening, MD Knockout, and metadynamics to discover/design antiviral compounds targeting highly conserved regions of the RNA-dependent RNA polymerase
D-galactonate Transporter
Metadynamics simulations to determine protonation states in the D-galactonate transport mechanism
Affiliated Projects
Hyper-Soluble Glycans
Genetic algorithm for designing hyper-soluble carbohydrate materials
GyloData Website
Web server for polysaccharide generation and preparation for molecular dynamics
Polymeric Lubricants
Genetic algorithm for designing polymeric lubricant materials
Peptide-mimetics
Genetic algorithm for designing peptide-mimetic polymers binding truncated green flourescent protein
Presentations
May 2024
ChEGSA Symposium, Virginia TechOral - Winner of Session
MD Knockout: A Smart Approach to Molecular Dynamics for High Throughput Virtual Screening in Drug Design
May 2024
PPP DA Symposium, Virginia TechPoster
Integrated Computational and Experimental Approach for Identifying Drugs Targeting Hepatitis E Virus
April 2024
American Chemical Society, New OrleansPoster
MetaDynamics to investigate the binding mechanism of non-nucleoside inhibitor of picornavirus 3Dpol in the RNA template channel
April 2024
ACS, New OrleansPoster
Improving high-throughput structure-based virtual screening with MM/GBSA free energy and MD knockout
April 2023
American Chemical Society, IndianapolisOral
Fully automated drug design pipeline for the development of small molecule protein inhibitors
March 2023
GlycoMIP Annual Conference, University of GeorgiaPoster
Fully automated drug design pipeline for the development of carbohydrate-based protein inhibitors
March 2022
Cancer Research Alliance Retreat, Virginia Tech Roanoke CampusPoster
A Two-Step Computational Drug Design Framework using a Hybrid Evolutionary Algorithm
March 2022
ChEGSA Annual Research Symposium, Virginia TechOral
A Two-Step Computational Drug Design Framework using a Hybrid Evolutionary Algorithm
April 2022
VTCDD Spring 2022 Poster Session, Virginia TechPoster
A Two-Step Computational Drug Design Framework using a Hybrid Evolutionary Algorithm
Coursework
CHE 5044
AEngineering Mathematics
CHE 5094
AAdvanced Chemical Engineering Kinetics
CHE 5125
BTransport Phenomena
CHE 5144
BAdvanced Thermodynamics
CHEM 5424
B+Advanced Polysaccharide Chemistry
Coursework
MSE 5394
AAdvanced Molecular Dynamics Simulation
CS 5824
A-Advanced Machine Learning
CHE 5414
AExplainable Artificial Intelligence Domain Insights
BIOL 5884
AMolecular Biology of the Cell
PHYS 3355
A-Intermediate Mechanics
