Dickson Lab @ MSU

Education:
Hon. B. Sc. Chemical Physics, University of Toronto (2006)
M. Sc. Chemistry, University of Chicago (2007)
Ph. D. Chemistry, University of Chicago (2011)

Prof. Dickson has extensive experience developing new methods for the simulation of rare events, and is driven to apply these tools to the study of ligand binding processes that are relevant to human health. Alex is cross-appointed in the Department of Computational Mathematics, Science and Engineering, where he currently teaches graduate courses in computational modeling. He loves computational research, and still gets his hands dirty in the lab, assisting in the development of sampling tools and persuing his own research projects.

Before MSU, Alex was a Postdoctoral Researcher at the University of Michigan with Prof. Charles L. Brooks, III. Alex obtained his Ph.D. in Chemistry from the University of Chicago in 2011 in the group of Prof. Aaron Dinner.

ORCID: 0000-0002-9640-1380
Google Scholar: Alex Dickson
twitter: @DicksonLab
CV: link

Contact: bosesami [at] msu [dot] edu

Education:
B. Sc. Chemistry: St. Xavier’s College (Kolkata), India (2012) M. Sc. Chemistry: University of Hyderabad, India (2014) Ph. D. Chemical Science: Indian Association for the Cultivation of Science, Kolkata, India (2020)

Postdoctoral research: Michigan State University (advisor Dr. Alex Dickson) (2021-2024) Fixed Term Assistant Professor (2024-Present): Department of Computational Mathematics, Science and Engineering (CMSE), Michigan State University

Samik has been working in DicksonLab since February, 2021 with a goal of learning and developing state-of-the-art enhanced sampling methods to study long timescale, pharmacologically relevant bio-molecular phenomena. He has worked closely with various experimental collaborators within and outside MSU to gain kinetic and structural insights into complex processes such as ligand (un)binding in soluble epoxide hydrolase (sEH) protein and channel opening in metallopeptidase neurolysin (NLN). He has recently developed a method to combine two powerful enhanced sampling formalisms: Markov state modeling and Weighted Ensemble simulation. In the future, Samik aims to implement the WE resampling strategies within the framework of QM/MM, leveraging experience in this area from his PhD work. He is also enthusiastic about teaching and has taught a module in the graduate level course “Machine Learning for Molecular Dynamics” in BMB department of MSU. Currently, as a fixed-term assistant professor, he is the sole instructor of a 400-level course on ‘Computational Medicine’, offered by the CMSE department, MSU.

Education:
B. Sc. Chemical Engineering, Babol Noshirvani University of Technology, Iran (2015) M. Sc. Chemical Engineering, Iran University of Science and Technology, Iran (2018)

I am a graduate student in the Computational Mathematics, Science, and Engineering department at MSU. Currently I am working on Flexible Topology simulations for Bromodomain-ligand systems. Flexible Topology is a method currently being developed in the Dickson Lab that allows us to consider ligand-induced conformational changes in the virtual screening process. In Flexible Topology, we allow the chemical identities of ligand atoms to change over time in response to forces from surrounding protein and water molecules. The overall goal of this project is to, eventually, be able to determine the optimal ligand for a binding pocket and determine the correct pose for that ligand.

Education: B. Sc. Molecular Biology and Genetics, Yıldız Technical University, Turkey (2017) M. Sc. Molecular Biology-Genetics and Biotechnology, Istanbul Technical University, Turkey (2020)

I am a graduate student in the Biochemistry and Molecular Biology department at MSU. My research goal is the development and implementation of advanced computational techniques to discover the kinetics of biomolecular mechanisms. My current research focuses on the development of an automated machine learning framework using the Variational Approach for Markov Processes with neural networks (VAMPnets) to discover molecular recognition pathways. I am also working on developing machine learning-based predictors on the blood-brain barrier permeability of compounds.

Previously, I worked on the implementation of molecular dynamics simulations to understand protein dynamics. The projects I was involved with were investigating the activation mechanism of CHK2 protein and the dynamics of the RBD domain of SARS-CoV-2 Spike protein.

Education: B. Sc. Computer Engineering, Izmir Institute of Technology, Turkey (2021) M. Sc. Bioengineering, Izmir Institute of Technology, Turkey (2023)

I’m a graduate student at Michigan State University, specializing in Computational Mathematics, Science, and Engineering. My current research involves applying molecular dynamics simulations and advanced path sampling methods to understand the interactions between bacteriophages and bacterial LPS chains, using S. flexneri as a model. 

Previously, I have applied computational methods to study the interactions between HIV Capsid proteins and nanobodies, contributing to the understanding of viral mechanisms at the molecular level.

Shawn is pursuing a major in Biochemistry and Molecular Biology, as well as a minor in Computational Mathematics, Science, and Engineering. He is currently working with Dr. Samik Bose to analyze dynamics of the enzyme neurolysin using molecular dynamics simulations.

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