Daniel Zuckerman, Ph.D.

  • Professor of Biomedical Engineering, School of Medicine
  • Biomedical Engineering Graduate Program, School of Medicine
  • Program in Molecular and Cellular Biosciences, School of Medicine

Biography

I’m a biophysicist working in systems biology who develops and applies computational methods to study single molecules, molecular machines and cellular behavior. At the molecular scale, my group extends the timescales observable in simulations, as well as to characterize mechanistic information that emerges from biophysical experiments. At the cellular scale, we quantify cell shape and motions observed in live-cell microscopy and connect these to RNA and protein behavior.   

In addition to research, I’m involved with initiatives to strengthen the role of quantitative biology at OHSU. I direct the Quantitative and Systems Biology Program, which brings together computational and systems biologists from across disciplines throughout the university.  I co-direct the Integrated Training in Quantitative and Experimental Cancer Systems Biology fellowship program which provides training and financial support to both postdocs and graduate students. 

I channel my passion for teaching and mentoring into writing textbooks, a blog and pedagogical articles. My goal is to help non-experts gain a rigorous grounding in the physics of biological systems. I also helped to start Living Journal of Computational Molecular Science devoted to pedagogically oriented articles. I’m proud that my trainees have gone on to successful careers in both academia and industry. I believe that trainees deserve respect, rigorous training, inspiration and a warm, welcoming environment. 

The Pacific Northwest is wonderful for exploring nature, and I love to be outside in any way possible. 
 

Education and training

  • Degrees

    • A.B., 1989, Harvard University
    • M.S., 1995, University of California
    • Ph.D., 1998, University of Maryland

Publications

Publications

  • From Average Transient Transporter Currents to Microscopic Mechanism─A Bayesian Analysis

    Journal of Physical Chemistry B
    1. August George
    2. Daniel M. Zuckerman
  • #COVIDisAirborne

    International Journal of High Performance Computing Applications
    1. Abigail Dommer
    2. Lorenzo Casalino
    3. Fiona Kearns
    4. Mia Rosenfeld
    5. Nicholas Wauer
    6. Surl Hee Ahn
    7. John Russo
    8. Sofia Oliveira
    9. Clare Morris
    10. Anthony Bogetti
    11. Anda Trifan
    12. Alexander Brace
    13. Terra Sztain
    14. Austin Clyde
    15. Heng Ma
    16. Chakra Chennubhotla
    17. Hyungro Lee
    18. Matteo Turilli
    19. Syma Khalid
    20. Teresa Tamayo-Mendoza
    21. Matthew Welborn
    22. Anders Christensen
    23. Daniel G.A. Smith
    24. Zhuoran Qiao
    25. Sai K. Sirumalla
    26. Michael O’Connor
    27. Frederick Manby
    28. Anima Anandkumar
    29. David Hardy
    30. James Phillips
    31. Abraham Stern
    32. Josh Romero
    33. David Clark
    34. Mitchell Dorrell
    35. Tom Maiden
    36. Lei Huang
    37. John McCalpin
    38. Christopher Woods
    39. Alan Gray
    40. Matt Williams
    41. Bryan Barker
    42. Harinda Rajapaksha
    43. Richard Pitts
    44. Tom Gibbs
    45. John Stone
    46. Daniel M. Zuckerman
    47. Adrian J. Mulholland
    48. Thomas Miller
    49. Shantenu Jha
    50. Arvind Ramanathan
    51. Lillian Chong
    52. Rommie E. Amaro
  • Morphodynamical cell state description via live-cell imaging trajectory embedding

    Communications Biology
    1. Jeremy Copperman
    2. Sean M. Gross
    3. Young Hwan Chang
    4. Laura M. Heiser
    5. Daniel M. Zuckerman
  • Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference

    PLoS computational biology
    1. Aidan B. Estelle
    2. August George
    3. Elisar J. Barbar
    4. Daniel M. Zuckerman
  • Weighted ensemble

    Journal of Chemical Physics
    1. D. Aristoff
    2. J. Copperman
    3. G. Simpson
    4. R. J. Webber
    5. D. M. Zuckerman
  • Continuum dynamics and statistical correction of compositional heterogeneity in multivalent IDP oligomers resolved by single-particle EM

    Journal of molecular biology
    1. Barmak Mostofian
    2. Russell McFarland
    3. Aidan Estelle
    4. Jesse Howe
    5. Elisar Barbar
    6. Steve L. Reichow
    7. Daniel M. Zuckerman
  • Ligand-mediated Structural Dynamics of a Mammalian Pancreatic KATP Channel

    Journal of molecular biology
    1. Min Woo Sung
    2. Camden M. Driggers
    3. Barmak Mostofian
    4. John D. Russo
    5. Bruce L. Patton
    6. Daniel M. Zuckerman
    7. Show Ling Shyng
  • WESTPA 2.0

    Journal of Chemical Theory and Computation
    1. John D. Russo
    2. She Zhang
    3. Jeremy M.G. Leung
    4. Anthony T. Bogetti
    5. Jeff P. Thompson
    6. Alex J. Degrave
    7. Paul A. Torrillo
    8. A. J. Pratt
    9. Kim F. Wong
    10. Junchao Xia
    11. Jeremy Copperman
    12. Joshua L. Adelman
    13. Matthew C. Zwier
    14. David N. Lebard
    15. Daniel M. Zuckerman
    16. Lillian T. Chong
  • A gentle introduction to the non-equilibrium physics of trajectories

    American Journal of Physics
    1. Daniel M. Zuckerman
    2. John D. Russo
  • Connexin 46 and connexin 50 gap junction channel properties are shaped by structural and dynamic features of their N-terminal domains

    Journal of Physiology
    1. Benny Yue
    2. Bassam G. Haddad
    3. Umair Khan
    4. Honghong Chen
    5. Mena Atalla
    6. Ze Zhang
    7. Daniel M. Zuckerman
    8. Steve L. Reichow
    9. Donglin Bai
  • Vascular KATP channel structural dynamics reveal regulatory mechanism by Mg-nucleotides

    Proceedings of the National Academy of Sciences of the United States of America
    1. Min Woo Sung
    2. Zhongying Yang
    3. Camden M. Driggers
    4. Bruce L. Patton
    5. Barmak Mostofian
    6. John D. Russo
    7. Daniel M. Zuckerman
    8. Show Ling Shyng
  • What Markov State Models Can and Cannot Do

    Journal of Chemical Theory and Computation
    1. Ernesto Suárez
    2. Rafal P. Wiewiora
    3. Chris Wehmeyer
    4. Frank Noé
    5. John D. Chodera
    6. Daniel M. Zuckerman
  • Accelerated Estimation of Long-Timescale Kinetics from Weighted Ensemble Simulation via Non-Markovian "microbin" Analysis

    Journal of Chemical Theory and Computation
    1. Jeremy Copperman
    2. Daniel M. Zuckerman
  • A kinetic mechanism for enhanced selectivity of membrane transport

    PLoS computational biology
    1. Paola Bisignano
    2. Michael A. Lee
    3. August George
    4. Daniel M. Zuckerman
    5. Michael Grabe
    6. John M. Rosenberg
  • A systems-biology approach to molecular machines

    PLoS computational biology
    1. August George
    2. Paola Bisignano
    3. John M. Rosenberg
    4. Michael Grabe
    5. Daniel M. Zuckerman
  • Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å

    Nature communications
    1. Jonathan A. Flores
    2. Bassam G. Haddad
    3. Kimberly A. Dolan
    4. Janette B. Myers
    5. Craig C. Yoshioka
    6. Jeremy Copperman
    7. Daniel M. Zuckerman
    8. Steve L. Reichow
  • EmrE reminds us to expect the unexpected in membrane transport

    The Journal of general physiology
    1. Michael Grabe
    2. Daniel M. Zuckerman
    3. John M. Rosenberg
  • Key biology you should have learned in physics class

    American Journal of Physics
    1. Daniel M. Zuckerman
  • Optimizing weighted ensemble sampling of steady states

    Multiscale Modeling and Simulation
    1. David Aristoff
    2. Daniel M. Zuckerman
  • Should Virus Capsids Assemble Perfectly? Theory and Observation of Defects

    Biophysical Journal
    1. Justin Spiriti
    2. James F. Conway
    3. Daniel M. Zuckerman
  • Computational Estimation of Microsecond to Second Atomistic Folding Times

    Journal of the American Chemical Society
    1. Upendra Adhikari
    2. Barmak Mostofian
    3. Jeremy Copperman
    4. Sundar Raman Subramanian
    5. Andrew A. Petersen
    6. Daniel M. Zuckerman
  • High-throughput single-particle tracking reveals 1 nested membrane domains that dictate krasg12d 2 diffusion and trafficking

    eLife
    1. Yerim Lee
    2. Carey Phelps
    3. Tao Huang
    4. Barmak Mostofian
    5. Lei Wu
    6. Ying Zhang
    7. Kai Tao
    8. Young Hwan Chang
    9. Philip J.S. Stork
    10. Joe W. Gray
    11. Daniel M. Zuckerman
    12. Xiaolin Nan
  • Middle-way flexible docking

    PloS one
    1. Justin Spiriti
    2. Sundar Raman Subramanian
    3. Rohith Palli
    4. Maria Wu
    5. Daniel M. Zuckerman
  • Statistical Uncertainty Analysis for Small-Sample, High Log-Variance Data

    Journal of Chemical Theory and Computation
    1. Barmak Mostofian
    2. Daniel M. Zuckerman
  • Transient probability currents provide upper and lower bounds on non-equilibrium steady-state currents in the Smoluchowski picture

    Journal of Chemical Physics
    1. Jeremy Copperman
    2. David Aristoff
    3. Dmitrii E. Makarov
    4. Gideon Simpson
    5. Daniel M. Zuckerman
  • Clinically Observed Estrogen Receptor Alpha Mutations within the Ligand-Binding Domain Confer Distinguishable Phenotypes

    Oncology (Switzerland)
    1. Shanhang Jia
    2. Mark T. Miedel
    3. Marilyn Ngo
    4. Ryan Hessenius
    5. Ning Chen
    6. Peilu Wang
    7. Amir Bahreini
    8. Zheqi Li
    9. Zhijie Ding
    10. Tong Ying Shun
    11. Daniel M. Zuckerman
    12. D. Lansing Taylor
    13. Shannon L. Puhalla
    14. Adrian V. Lee
    15. Steffi Oesterreich
    16. Andrew M. Stern
  • Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways

    Biophysical Journal
    1. Ariane Nunes-Alves
    2. Daniel M. Zuckerman
    3. Guilherme Menegon Arantes