Experience

Atomwise

• United States
• Biotechnology Research
• 1 - 100 Employee

• Associate Principal Scientist, CADD

  • Jul 2023 - Present

• Senior Scientist, CADD

  • Sep 2021 - Aug 2023

• Scientist and Project Manager

  • Oct 2020 - Sep 2021

• Scientist

  • Oct 2019 - Oct 2020



University of California, Berkeley

• United States
• Higher Education
• 700 & Above Employee

• Postdoctoral Scholar

  • Sep 2016 - Oct 2019

  California Institute for Quantitative Biosciences (QB3), Laboratory of Dr. Susan Marqusee ► Investigate the folding landscape, partially folded structures and their roles in amyloid fibril formation in a PDZ domain • Implemented an experimental and computational framework using a variety of techniques using such as molecular dynamics simulations, single-molecule force spectroscopy, fluorescence assays, etc. • Modeled protein structure and analyzed folding trajectories to identify… Show more California Institute for Quantitative Biosciences (QB3), Laboratory of Dr. Susan Marqusee ► Investigate the folding landscape, partially folded structures and their roles in amyloid fibril formation in a PDZ domain • Implemented an experimental and computational framework using a variety of techniques using such as molecular dynamics simulations, single-molecule force spectroscopy, fluorescence assays, etc. • Modeled protein structure and analyzed folding trajectories to identify flexible protein region and conformational changes • Designed experimental set-up based on computational predictions, performed single-molecule force-induced unfolding experiments, and confirmed the presence of an unfolding intermediate consistent with computational results • Conducted fluorescence assay to evaluate amyloid fibril formation kinetics of various protein variants • Presented findings at seven meetings in invited talks and poster sessions Show less California Institute for Quantitative Biosciences (QB3), Laboratory of Dr. Susan Marqusee ► Investigate the folding landscape, partially folded structures and their roles in amyloid fibril formation in a PDZ domain • Implemented an experimental and computational framework using a variety of techniques using such as molecular dynamics simulations, single-molecule force spectroscopy, fluorescence assays, etc. • Modeled protein structure and analyzed folding trajectories to identify… Show more California Institute for Quantitative Biosciences (QB3), Laboratory of Dr. Susan Marqusee ► Investigate the folding landscape, partially folded structures and their roles in amyloid fibril formation in a PDZ domain • Implemented an experimental and computational framework using a variety of techniques using such as molecular dynamics simulations, single-molecule force spectroscopy, fluorescence assays, etc. • Modeled protein structure and analyzed folding trajectories to identify flexible protein region and conformational changes • Designed experimental set-up based on computational predictions, performed single-molecule force-induced unfolding experiments, and confirmed the presence of an unfolding intermediate consistent with computational results • Conducted fluorescence assay to evaluate amyloid fibril formation kinetics of various protein variants • Presented findings at seven meetings in invited talks and poster sessions Show less



Rice University

• United States
• Higher Education
• 700 & Above Employee

• Postdoctoral Research Associate

  • Jun 2016 - Aug 2016

  Center for Theoretical Biological Physics (CTBP), Laboratory of Dr. Peter Wolynes ► Coarse-grained simulations to investigate the insertion of α-helical membrane proteins and to unfold of α-helical membrane protein under forces • Developed and improved the AWSEM-Membrane simulation code and applied it to various problems in protein physics and biology • Investigated the effect of membrane defect in various sizes on membrane protein folding • Implemented input files and computational… Show more Center for Theoretical Biological Physics (CTBP), Laboratory of Dr. Peter Wolynes ► Coarse-grained simulations to investigate the insertion of α-helical membrane proteins and to unfold of α-helical membrane protein under forces • Developed and improved the AWSEM-Membrane simulation code and applied it to various problems in protein physics and biology • Investigated the effect of membrane defect in various sizes on membrane protein folding • Implemented input files and computational set-up for studying membrane protein force-induced unfolding • Provided tutorials and technical supports to both internal and external researchers who wanted to integrate the AWSEM model to their own research • Project was continued by other Wolynes lab members and published in Nature Communications (2018)

• Graduate Research Assistant

  • Aug 2011 - May 2016

  Department of Chemistry and Center for Theoretical Biological Physics (CTBP), Laboratory of Dr. Peter Wolynes Dissertation Title: Exploring the Folding Energy Landscape: Designed, Simplified, and α-helical Membrane Proteins. ►Structure-based model with implicit membrane potential to investigate the folding and functional motion of an intramembrane protease, GlpG • Collaborated fruitfully with two laboratories of Dr. Daniel Otzen and Dr. Kresten Lindorff-Larsen in Denmark •… Show more Department of Chemistry and Center for Theoretical Biological Physics (CTBP), Laboratory of Dr. Peter Wolynes Dissertation Title: Exploring the Folding Energy Landscape: Designed, Simplified, and α-helical Membrane Proteins. ►Structure-based model with implicit membrane potential to investigate the folding and functional motion of an intramembrane protease, GlpG • Collaborated fruitfully with two laboratories of Dr. Daniel Otzen and Dr. Kresten Lindorff-Larsen in Denmark • Applied enhanced sampling techniques and Multistate Bennett Acceptance Ratio (MBAR) method to characterize the free energy landscape and folding mechanism • Provided a solution to a puzzling observation posed by a previous experimental study, and suggested that a more careful data interpretation and experimental set-up are needed to study membrane proteins experimentally • Characterized a conformational change that exposes GlpG’s active site, thereby allowing substrate access • Published findings in PNAS (2016) ► Predictive coarse-grained model to fold membrane protein assemblies • Predicted structures and binding interfaces of membrane protein oligomers using our novel coarse-grained model, AWSEM-membrane • Provided insights into the folding energy landscape of the oligomerization of membrane proteins • Demonstrated the essential roles of small molecules in both protein folding and activity • Published findings in J. Chem. Phys. (2015) ► Evaluate the folding landscapes of designed proteins and simplified sequences • Accurately performed structure prediction for naturally occurring proteins, designed proteins and five-letter code simplified sequences • Showed how topological frustration influences the complex folding kinetics of Top7 that were noted as puzzling in previous experiments by other researchers • Indicated that utilizing negative design and non-native interactions is crucial in the design of reliable and functional proteins • Published findings in J. Chem. Phys. (2013)

• Teaching Assistant

  • Jan 2012 - May 2013

  • Lectured weekly discussion sessions for General Chemistry Laboratory course of 20-30 students per session • Graded and provided feedback to students on their lab reports • Received an A+ in graded teaching performance review • Awarded the Harry B. Weiser Teaching Award



University of Oregon

• United States
• Higher Education
• 700 & Above Employee

• Undergraduate Research Assistant

  • Sep 2010 - Jun 2011

  Mentor: Dr. Marina Guenza • Ran molecular dynamics simulations using GROMACS • Studied the structures and dynamics of complex fluids

• Mathematics Tutor

  • Jan 2010 - Jun 2011

  • Provided public tutoring sessions in the Math Lab and private sessions to students on campus • Selected to run help session for group of students in Algebra, Calculus, Differential Equation, Linear Algebra and MultiVariable Calculus



Highline College

• United States
• Higher Education
• 700 & Above Employee

• International Leadership Student Council (ILSC)

  • Jun 2008 - Jun 2009

  • Held the position of Volunteer Bank Coordinator in ILSC, as a part of the International Student Programs. • Coordinated with organizations on and off campus to provide volunteering opportunities • Planed and engaged students to volunteering activities on and off campus • Represented as an international students mentor to provide helps to students in need and encourage students to be involved in activities • Worked with other members of ILSC in planning numerous of event throughout… Show more • Held the position of Volunteer Bank Coordinator in ILSC, as a part of the International Student Programs. • Coordinated with organizations on and off campus to provide volunteering opportunities • Planed and engaged students to volunteering activities on and off campus • Represented as an international students mentor to provide helps to students in need and encourage students to be involved in activities • Worked with other members of ILSC in planning numerous of event throughout the year including Halloween party in Fall, Dance party in Winter, and Global Fest in Spring • Scouted performers, planned rehearsals and directed performances for Global Fest, the biggest event of the year celebrating the diversity on campus

• Mathematics Tutor

  • Jan 2008 - Jun 2009

  • Provided helps for math classes up to Differential Equation and Linear Algebra • Helped tutees understand and develop an interest in studying Math by explaining and working on problems together • Created and organized activities and trainings in the Math Resource Center and Tutoring Center • Completed and earned certificates for tutor training level 1, 2, and 3