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
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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#COVIDisAirborne
International Journal of High Performance Computing ApplicationsMorphodynamical cell state description via live-cell imaging trajectory embedding
Communications BiologyQuantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference
PLoS computational biologyWeighted ensemble
Journal of Chemical PhysicsContinuum dynamics and statistical correction of compositional heterogeneity in multivalent IDP oligomers resolved by single-particle EM
Journal of molecular biologyLigand-mediated Structural Dynamics of a Mammalian Pancreatic KATP Channel
Journal of molecular biologyWESTPA 2.0
Journal of Chemical Theory and ComputationA gentle introduction to the non-equilibrium physics of trajectories
American Journal of PhysicsConnexin 46 and connexin 50 gap junction channel properties are shaped by structural and dynamic features of their N-terminal domains
Journal of PhysiologyVascular KATP channel structural dynamics reveal regulatory mechanism by Mg-nucleotides
Proceedings of the National Academy of Sciences of the United States of AmericaWhat Markov State Models Can and Cannot Do
Journal of Chemical Theory and ComputationAccelerated Estimation of Long-Timescale Kinetics from Weighted Ensemble Simulation via Non-Markovian "microbin" Analysis
Journal of Chemical Theory and ComputationA kinetic mechanism for enhanced selectivity of membrane transport
PLoS computational biologyA systems-biology approach to molecular machines
PLoS computational biologyConnexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å
Nature communicationsEmrE reminds us to expect the unexpected in membrane transport
The Journal of general physiologyKey biology you should have learned in physics class
American Journal of PhysicsOptimizing weighted ensemble sampling of steady states
Multiscale Modeling and SimulationShould Virus Capsids Assemble Perfectly? Theory and Observation of Defects
Biophysical JournalComputational Estimation of Microsecond to Second Atomistic Folding Times
Journal of the American Chemical SocietyHigh-throughput single-particle tracking reveals 1 nested membrane domains that dictate krasg12d 2 diffusion and trafficking
eLifeMiddle-way flexible docking
PloS oneStatistical Uncertainty Analysis for Small-Sample, High Log-Variance Data
Journal of Chemical Theory and ComputationTransient probability currents provide upper and lower bounds on non-equilibrium steady-state currents in the Smoluchowski picture
Journal of Chemical PhysicsClinically Observed Estrogen Receptor Alpha Mutations within the Ligand-Binding Domain Confer Distinguishable Phenotypes
Oncology (Switzerland)Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways
Biophysical Journal