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Projects
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Dynamical traps in Wang-Landau sampling of continuous systems
- Monte Carlo simulation using the Wang-Landau algorithm to explore density of states of peptide conformations
- Explored the causes for dynamical traps that lead to inefficient sampling
- Proposed inter-swapping multiple parallel Wang-Landau trajectories to avoid trapping
[Koh Y.W., Sim A.Y.L., Lee H.K., Dynamical traps in Wang-Landau sampling of continuous systems: Mechanism and solution, Phys. Rev. E, 92, 773 (2015)] -
Effect of hydrocarbon staple on peptide hydrophobicity
- Time series analysis of molecular simulation data to determine extent of molecular dewetting phenomena
- Visualization of high-dimensional simulation data
- Clustering of molecular simulation snapshots to distinguish extent of dewetting
- Explored the role of hydration on peptide binding kinetics
[Sim A.Y.L., Verma C.S., How does a hydrocarbon staple affect peptide hydrophobicity?, J. Comput. Chem., 36, 773 (2015)] -
Hierarchical Natural Moves Monte Carlo for modeling nucleic acid conformation effectively
- Developed a method to efficiently explore nucleic acid conformation space by reducing sampling degrees of freedom (DoFs) while preserving all-atom representation
- This reduction in DoFs was inspired by the (generally) hierarchical nature of RNA folding
- Method scales well with nucleic acid size, and can be adopted to study and design nucleic acid nanostructures
[Sim A.Y.L., Levitt M., Minary P., Modeling and design by hierarchical natural moves, Proc. Nat. Acad. Sci. USA, 109…- Developed a method to efficiently explore nucleic acid conformation space by reducing sampling degrees of freedom (DoFs) while preserving all-atom representation
- This reduction in DoFs was inspired by the (generally) hierarchical nature of RNA folding
- Method scales well with nucleic acid size, and can be adopted to study and design nucleic acid nanostructures
[Sim A.Y.L., Levitt M., Minary P., Modeling and design by hierarchical natural moves, Proc. Nat. Acad. Sci. USA, 109, 2890 (2012)] -
Nucleic acid electrostatics
- Computational and experimental probing of the effect of ionic conditions on nucleic acid conformation, flexibility, folding and ligand binding
- Computational methods include molecular dynamics, molecular modeling and electrostatics calculations (using non-linear Poisson-Boltzmann equation)
- Experimental methods include small-angle x-ray scattering and hydroxyl radical footprinting
[Anthony P.C., Sim A.Y.L., Chu V.B., Doniach S., Block S.M., Herschlag D., Electrostatics of nucleic…- Computational and experimental probing of the effect of ionic conditions on nucleic acid conformation, flexibility, folding and ligand binding
- Computational methods include molecular dynamics, molecular modeling and electrostatics calculations (using non-linear Poisson-Boltzmann equation)
- Experimental methods include small-angle x-ray scattering and hydroxyl radical footprinting
[Anthony P.C., Sim A.Y.L., Chu V.B., Doniach S., Block S.M., Herschlag D., Electrostatics of nucleic acid folding under conformational constraint, J. Am. Chem. Soc., 134, 4607 (2012); Lipfert J.*, Sim A.Y.L.*, Herschlag D., Doniach S., Dissecting electrostatics screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding, RNA, 16, 708 (2010)] -
RNA conformational clustering
- Developed a procedure to cluster RNA conformations constrained by secondary structure
- Density-based clustering leverages on the stochastic nature of k-means clustering
- Clustering feature engineering involved dimension reduction using internal coordinate projection
[Sim A.Y.L., Levitt M., Clustering to identify RNA conformations constrained by
secondary structure, Proc. Nat. Acad. Sci. USA, 108, 3590 (2011)] -
Towards autonomous assessment: insights into objective evaluation of student online class engagement
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- Studied patterns of student class participation based on gender and age
- Used various data mining techniques and statistical tests
- Developed a classifier based on pre-trained word vectors to assess quality of student participation
(Paper submitted)
Honors & Awards
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Best Mentor Award
A*STAR Graduate Academy
For mentoring a high school vacation internship student
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A*STAR Career Development Award
A*STAR Joint Council Office
Targeting riboswitches to combat drug-resistant bacteria
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National Science Scholarship (BS-PhD)
Agency of Science Technology and Research (A*STAR), Singapore
Fully funded undergraduate and graduate studies
Languages
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English
Native or bilingual proficiency
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Chinese (Mandarin)
Native or bilingual proficiency
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Japanese
Elementary proficiency
Websites
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