Headshot of Daniel Zuckerman

Daniel M. Zuckerman, Ph.D.
Professor and Principal Investigator
OHSU Biography

Sagar Kania Portrait 100px

Sagar Kania, Ph. D., postdoctoral scholar

As a solution-oriented researcher deeply engaged in computational statistical physics and biology, I am committed to enhancing the practicality and accuracy of biomolecular simulations. I am developing a method to predict steady-state distributions of molecular systems from significantly unconverged simulation data. This method aims to radically reduce the computational overhead required to obtain unbiased estimates of observables, potentially accelerating discoveries in molecular dynamics across complex systems. Concurrently, I am devising algorithms to optimize Bayesian analysis of diverse experimental datasets, thus enhancing the balance between computational cost and analytical precision.  Outside of work, I love Portland's dynamic vibe, from city biking to hiking through the nearby beautiful national forests. 

Lisa Otten

Lisa Otten, Ph. D., postdoctoral scholar

My research uses Bayesian inference and Markov chain Monte Carlo sampling to estimate the kinetic parameters governing the behavior of secondary active transporters, based on experimental data. My background is in theoretical quantum physics. As a newcomer to the Pacific Northwest, I am looking forward to exploring the area on hiking and camping adventures. 

Harry (Won Hee) Ryu

Harry (Won Hee) Ryu, Ph.D., postdoctoral scholar

I work on optimizing the weighted ensemble (WE) enhanced sampling method by minimizing the variance in rate constants computed in WE simulations. I study the free energy surfaces of kinetically controlled protein systems using molecular dynamics and weighted ensemble simulations.  I received a B.A. (chemistry and mathematics) from Oberlin College in 2016 and Ph.D. (theoretical and computational chemistry) from University of Chicago in 2021. When not thinking about proteins wiggling, I enjoy reading and exploring Portland. 

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Shelby Santos, Ph.D student, biomedical engineering

My focus is on modeling the interactions between the LC8 molecular hub protein and intrinsically disordered proteins using molecular dynamics simulations. My work, in collaboration with the Elisar Barbar group at Oregon State University, explores the intricate binding dynamics of LC8 with various partners, contributing to a deeper understanding of protein cooperativity in cellular processes. As an undergraduate, I studied biochemistry, molecular biology, biotechnology and computational mathematics. Outside of work, I enjoy going on hikes on the Oregon coast, skiing at Mt. Hood and going to readings at Powell’s Books. 

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Jalim Singh, Ph. D., postdoctoral scholar

My project, which has implications for breast cancer, investigates the crucial epithelial-mesenchymal transition affecting a cell’s ability to migrate actively. Utilizing the MCF10A cell line in collaboration with the Heiser Lab, my work integrates bulk RNA sequencing with live-cell microscopy to map connections between gene expression levels and cellular morphodynamics. This work aims to create predictive models linking gene expression to cell behavior, potentially opening new avenues for cancer diagnostics and treatment. I love hiking and the Portland area has great trails, for example, around the Columbia Gorge, Mount Hood and Mount Saint Helens. 


  • Jeremy Copperman, Postdoctoral Scholar 2018-2023; currently Associate Scientist,  Cancer Early Detection Advanced Research Center, Oregon Health and Science University.
  • John Russo, Graduate Student 2019-2023; currently Data Engineer, Treeline Biosciences.
  • August George, Graduate student 2018-2023; currently Postdoctoral Scholar, Pacific Northwest National Laboratory.
  • Barmak Mostofian, Ph.D. Postdoctoral Scholar 2017-2021; currently Senior Investigator, Roivant Sciences.
  • Upendra Adhikari, Ph.D. Postdoctoral Scholar 2017-18; currently assistant professor, Missouri Valley College.
  • Svetlana Aroutiounian, Ph.D. Postdoctoral Scholar 2006-07.
  • Divesh Bhatt, Ph.D. Postdoctoral Scholar 2007-10; currently lead scientist, Kimberly-Clark Corporation.
  • Derek Cashman, Ph.D. Postdoctoral Scholar 2007-10; currently lecturer, Tennessee Technological University.
  • Ying Ding, Ph.D. Graduate Student 2007-11; currently senior scientist, Pfizer.
  • Rory Donovan, Ph.D. Graduate Student 2012-16; currently Scientist, Allen Institute for Cell Science.
  • Steven Lettieri, Ph.D. Postdoctoral Scholar 2009-12; currently data scientist, Highmark.
  • Edward Lyman, Ph.D. Postdoctoral Scholar 2004-07; currently associate professor of physics, U. Delaware.
  • Artem Mamonov, Ph.D. Postdoctoral Scholar 2006-10; currently scientific programmer, Massachusetts General Hospital.
  • Rohith Palli. Undergraduate Researcher 2011-14; currently M.D./Ph.D. student, University of Rochester.
  • Andrew Petersen, Ph.D. Postdoctoral Scholar 2008-10; data sciences research specialist, N. Carolina State University.
  • Justin Spiriti, Ph.D.  Postdoctoral Scholar (2013 – 2019); currently postdoctoral fellow, University of Missouri, St. Louis.
  • Carsen Stringer. Undergraduate Researcher 2011; Postdoc, HHMI Janelia Research Campus.
  • Ernesto Suarez, Ph.D. Postdoctoral Scholar 2012-17; Senior Scientist, National Cancer Institute.
  • Marty Ytreberg, Ph.D. Postdoctoral Scholar 2003-06; currently professor of physics, U. Idaho.
  • Bin Zhang, Ph.D. Graduate Student 2004-08; currently associate research professor, Temple University.
  • Xin Zhang, Ph.D. Graduate Student 2006-10; currently Software Engineer, Amazon.
  • Zining Zhang. Undergraduate Researcher 2014-15; currently graduate student in statistics, Columbia University.