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Samuel Cho

Assistant Professor of Physics and Computer Science

Biography

With expertise in both biophysics and computer science, Samuel Cho has a unique perspective on biomolecular research of cellular processes: he understands how human cells work at the molecular level, and he can manipulate cutting-edge technology to create simulations that deepen that understanding for scientists everywhere. In his recent research into enzymes that aid tumor growth, Cho and his colleagues used computer simulations to understand how RNA functions. What he found –
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With expertise in both biophysics and computer science, Samuel Cho has a unique perspective on biomolecular research of cellular processes: he understands how human cells work at the molecular level, and he can manipulate cutting-edge technology to create simulations that deepen that understanding for scientists everywhere. In his recent research into enzymes that aid tumor growth, Cho and his colleagues used computer simulations to understand how RNA functions. What he found – new, in-depth views of how that RNA helps tumor cells grow – has opened a path for developing treatments that target cancerous tumors. Now, he’s working with students to use the graphic processing units in video gaming technology to make this work even quicker.

Areas of Expertise

Computational Biophysics
Molecular Dynamics Simulations
GPU-Based Programming
Protein and RNA Folding
Biomolecular Assembly
Molecular Machines
Protein Folding Kinetics
RNA Folding Mechanisms
Protein-RNA Machines: Ribosome Assembly
Protein-Nanoparticle Interactions
GPU-Based MD Simulations

Media

Education

University of California, San Diego: Ph.D., Physical Chemistry
University of Maryland Baltimore County: B.S., Biochemistry & Computer Science

Media Appearances

Video games take role in treating cancer at Wake Forest
WGHP
2/16/2012
Dr. Samuel Cho, an assistant professor of physics and computer science, uses graphics processing units (GPUs) -- the same technology that makes video ames look so realistic -- to simulate the inner-workings of human cells...

Articles

MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery
1/1/1970
While tRNA and aminoacyl-tRNA synthetases are classes of biomolecules that have been extensively studied for decades, the finer details of how they carry out their fundamental biological functions in protein synthesis remain a challenge. Recent molecular dynamics (MD) simulations are verifying experimental observations and providing new insight that cannot be addressed from experiments alone. Throughout the review, we briefly discuss important historical events to provide a context for how far the field has progressed over the past few decades. We then review the background of tRNA molecules, aminoacyl-tRNA synthetases, and current state of the art MD simulation techniques for those who may be unfamiliar with any of those fields. Recent MD simulations of tRNA dynamics and folding and of aminoacyl-tRNA synthetase dynamics and mechanistic characterizations are discussed. We highlight the recent successes and discuss how important questions can be addressed using current MD simulations techniques. We also outline several natural next steps for computational studies of AARS:tRNA complexes.
Coarse-Grained and Atomistic MD Simulations of RNA and DNA Folding
1/1/1970
Although the main features of the protein folding problem are coming into clearer focus, the microscopic viewpoint of nucleic acid folding mechanisms is only just beginning to be addressed. Experiments, theory, and simulations are pointing to complex thermodynamic and kinetic mechanisms. As is the case for proteins, molecular dynamics (MD) simulations continue to be indispensable tools for providing a molecular basis for nucleic acid folding mechanisms. In this review, we provide an overview of biomolecular folding mechanisms focusing on nucleic acids. We outline the important interactions that are likely to be the main determinants of nucleic acid folding energy landscapes. We discuss recent MD simulation studies of empirical force field and Go-type MD simulations of RNA and DNA folding mechanisms to outline recent successes and the theoretical and computational challenges that lie ahead.
Computational and Experimental Characterizations of Silver Nanoparticle–Apolipoprotein Biocorona
1/1/1970
With the advancement of nanotoxicology and nanomedicine, it has been realized that nanoparticles (NPs) interact readily with biomolecular species and other chemical and organic matter to result in biocorona formation. The field of the environmental health and safety of nanotechnology, or NanoEHS, is currently lacking significant molecular-resolution data, and we set out to characterize biocorona formation through electron microscopy imaging and circular dichroism spectroscopy that inspired a novel approach for molecular dynamics (MD) simulations of protein–NP interactions. In our present study, we developed a novel GPU-optimized coarse-grained MD simulation methodology for the study of biocorona formation, a first in the field. Specifically, we performed MD simulations of a spherical, negatively charged citrate-covered silver nanoparticle (AgNP) interacting with 15 apolipoproteins. At low ion concentrations, we observed the formation of an AgNP–apolipoprotein biocorona. Consistent with the circular dichroism (CD) spectra, we observed a decrease in α-helices coupled with an increase in β-sheets in apolipoprotein upon biocorona formation.
Origins of barriers and barrierless folding in BBL
1/1/1970
In contrast to classical chemical phenomenology, theory suggests that proteins may undergo downhill folding without an activation barrier under certain thermodynamic conditions. Recently, the BBL protein was proposed to fold by such a downhill scenario, but discrepancies between experimental results found in different groups argue against this...
P versus Q: Structural reaction coordinates capture protein folding on smooth landscapes
1/1/1970
Minding your p's and q's has become as important to protein-folding theorists as it is for those being instructed in the rules of etiquette. To assess the quality of structural reaction coordinates in predicting the transition-state ensemble (TSE) of protein folding, we benchmarked the accuracy of four structural reaction coordinates against the kinetic measure P fold, whose value of 0.50 defines the stochastic separatrix for a two-state folding mechanism...