About

Deborah Fygenson is a professor in the Department of Physics at UC Santa Barbara. Her research focuses on the physics of soft and living matter, exploring the properties and behaviors of complex biological and soft materials. She is involved in developing and applying physical principles to understand biological systems, including their form, function, and dynamics. Her work contributes to the broader understanding of how soft materials and biological systems can be characterized and manipulated through physical methods, advancing knowledge in both fundamental physics and biological applications.

Research topics

• Chemistry
• Biology
• Materials science
• Chemical physics
• Biophysics
• Molecular physics
• Organic chemistry
• Nanotechnology
• Biochemistry

Selected publications

• Raw data for Nanostar-mediated nucleation and condensate-driven spatial organization of tiled DNA nanotubes

  Zenodo (CERN European Organization for Nuclear Research) · 2026-01-31

  otherOpen accessSenior author
  PublisherDOI

• Raw data for Nanostar-mediated nucleation and condensate-driven spatial organization of tiled DNA nanotubes

  Zenodo (CERN European Organization for Nuclear Research) · 2026-01-31

  otherOpen accessSenior author
  PublisherDOI

• Single-molecule capture, release, and dynamical manipulation via reversible electrokinetic confinement (RECON)

  Science Advances · 2025-09-17

  articleOpen access

  We present a nanofluidic device enabling single-molecule confinement through free-energy landscapes created by dynamic electrical gating of embedded nanoelectrodes. Unlike static geometric confinement, this system uses a parallel electrode configuration with nanoelectrodes placed in a dielectric layer. Localized electrokinetic fields at electrode wells form tunable attractive potential wells for bimolecular capture. By modulating the voltage bias waveform, the device allows precise control over confinement dynamics, enabling molecular capture, release, and exposure to periodic or stochastic confinement regimes. This flexibility facilitates the study of biomolecular behavior under dynamically adjustable conditions, including controlled confinement fluctuations. The device can manipulate diverse analytes such as double-stranded DNA, liposomes, and DNA nanotubes and facilitates introducing molecules into confined environments intact from bulk while providing enhanced tunability. With the ability to implement tailored confinement profiles, this platform represents a versatile tool for probing molecular confinement and behavior in complex, dynamically varying environments.

  PublisherDOI

• Patterning programmable spin arrays on DNA origami for quantum technologies

  ArXiv.org · 2025-09-13

  preprintOpen access

  The controlled assembly of solid-state spins with nanoscale spatial precision is an outstanding challenge for quantum technology. Here, we combine DNA-based patterning with nitrogen-vacancy (NV) ensemble quantum sensors in diamond to form and sense programmable 2D arrays of spins. We use DNA origami to control the spacing of chelated Gd$^{3+}$ spins, as verified by the observed linear relationship between proximal NVs' relaxation rate, $1/T_1$, and the engineered number of Gd$^{3+}$ spins per origami unit. We further show that DNA origami provides a robust way of functionalizing the diamond surface with spins as it preserves the charge state and spin coherence of proximal, shallow NV centers. Our work enables the formation and interrogation of ordered, strongly interacting spin networks with applications in quantum sensing and quantum simulation. We quantitatively discuss the prospects of entanglement-enhanced metrology and high-throughput proteomics.

  PublisherOA PDFDOI

• DNA Nanostructures Characterized via Dual Nanopore Resensing

  ACS Nano · 2025-10-03

  articleOpen accessCorresponding

  DNA nanotechnology uses predictable interactions of nucleic acids to precisely engineer complex nanostructures. Characterizing these self-assembled structures at the single-structure level is crucial for validating their design and functionality. Nanopore sensing is a promising technique for this purpose as it is label-free, solution-based, and high-throughput. Here, we present a device that incorporates dynamic feedback to control the translocation of DNA origami structures through and between two nanopores. We observe multiple translocations of the same structure through the two distinct nanopores as well as measure its time-of-flight between the pores. We use machine learning classification methods in tandem with classical analysis of dwell-time/blockade distributions to analyze the complex multitranslocation events generated by different nanostructures. With this approach, we demonstrate the ability to distinguish DNA nanostructures of different lengths and/or small structural differences, all of which are difficult to detect using conventional, single-nanopore sensing. In addition, we develop a finite element diffusion model of the time-of-flight process and estimate nanostructure size. This work establishes the dual nanopore device as a powerful tool for DNA nanostructure characterization.

  PublisherOA PDFDOI

• Electrokinetic nanofluidic sensing of DNA nanostar condensate

  Biosensors and Bioelectronics · 2025-06-12 · 2 citations

  articleSenior authorCorresponding
  PublisherDOI

• Electrokinetic nanofluidic sensing of DNA nanostar condensate

  arXiv (Cornell University) · 2024-12-11

  preprintOpen accessSenior author

  We demonstrate electronic sensing of DNA nanostar (NS) condensate. Specifically, we use electrokinetic nanofluidics to observe and interpret how temperature-induced NS condensation affects nanochannel current. The increase in current upon filling a nanochannel with NS condensate indicates that its electrophoretic mobility is about half that of a single NS and its effective ionic strength is $\sim35$% greater than that of 150mM NaCl in phosphate buffer. $ζ$-potential measurements before and after exposure to NS show that condensate binds the silica walls of a nanochannel more strongly than individual NS do under identical conditions. This binding increases electroosmotic flow, possibly enough to completely balance, or even exceed, the electrophoretic velocity of NS condensate. Although the current through a flat nanochannel is erratic in the presence of NS condensate, tilting the nanochannel to accumulate NS condensate at one entrance (and away from the other) results in a robust electronic signature of the NS phase transition at temperatures $T_c$ = $f$([NaCl]) that agree with those obtained by other methods. Electrokinetic nanofluidic detection and measurement of NS condensate thus provides a foundation for novel biosensing technologies based on liquid-liquid phase separation.

  PublisherOA PDFDOI

• Electrokinetic Nanofluidic Sensing of DNA Nanostar Condensate

  SSRN Electronic Journal · 2024-01-01

  preprintOpen accessSenior author
  PublisherDOI

• Towards rational design of power-law rheology via DNA nanostar networks

  arXiv (Cornell University) · 2023-08-28 · 3 citations

  preprintOpen accessSenior author

  We measure the rheology of transient hydrogels comprised of a single type of DNA nanostar that makes both strong and weak bonds. These gels exhibit power-law frequency-dependence of their storage and loss moduli, with scaling exponents that depend on the proportions of the two bonds. A diffusive stress-relaxation model, in which the strong-bond sub-network relieves stress by diffusing through an effective viscosity imposed by the weak bonds, explains the scaling of their moduli. The model has implications for the fractal dimensions of the strong-bond sub-network that are in good agreement with measurements and makes testable predictions for the viscoelasticity of other transient hydrogels. Overall, this work demonstrates the power of DNA nanotechnology to decipher, and potentially rationally design, power-law rheology.

  PublisherOA PDFDOI

• Emulsion imaging of a DNA nanostar condensate phase diagram reveals valence and electrostatic effects

  The Journal of Chemical Physics · 2022 · 30 citations

  • Chemical physics
  • Chemistry
  • Molecular physics

  Liquid-liquid phase separation (LLPS) in macromolecular solutions (e.g., coacervation) is relevant both to technology and to the process of mesoscale structure formation in cells. The LLPS process is characterized by a phase diagram, i.e., binodal lines in the temperature/concentration plane, which must be quantified to predict the system's behavior. Experimentally, this can be difficult due to complications in handling the dense macromolecular phase. Here, we develop a method for accurately quantifying the phase diagram without direct handling: We confine the sample within micron-scale, water-in-oil emulsion droplets and then use precision fluorescent imaging to measure the volume fraction of the condensate within the droplet. We find that this volume fraction grows linearly with macromolecule concentration; thus, by applying the lever rule, we can directly extract the dense and dilute binodal concentrations. We use this approach to study a model LLPS system of self-assembled, fixed-valence DNA particles termed nanostars (NSs). We find that temperature/concentration phase diagrams of NSs display, with certain exceptions, a larger co-existence regime upon increasing salt or valence, in line with expectations. Aspects of the measured phase behavior validate recent predictions that account for the role of valence in modulating the connectivity of the condensed phase. Generally, our results on NS phase diagrams give fundamental insight into limited-valence phase separation, while the method we have developed will likely be useful in the study of other LLPS systems.

  PublisherDOI

Recent grants

• CAREER: BioPolymer Physics-Understanding Protein Conformational Change

  NSF · $519k · 2000–2006

• DNA Patterned Pairs of Colloidal Quantum Dots: a scalabel approach to computing without wires

  NSF · $300k · 2006–2011

Frequent coauthors

• Patrick O’Neill

  19 shared

• Sumita Pennathur

  University of California, Santa Barbara

  15 shared

• Omar A. Saleh

  University of California, Santa Barbara

  14 shared

• Albert Libchaber

  Rockefeller University

  14 shared

• Lourdes Velazquez

  University of California, Santa Barbara

  13 shared

• Paul W. K. Rothemund

  California Institute of Technology

  12 shared

• Axel Ekani-Nkodo

  12 shared

• Daniel Schiffels

  National Institute of Standards and Technology

  12 shared

Labs

• Physics of Soft and Living MatterPI

Education

• Ph.D., Physics

  Princeton University

  1995

• B.Sc, Physics

  Massachusetts Institute of Technology

  1989