Shankar Dutt · Research Fellow, ANU
I build solid-state nanopore instruments that read single molecules, and teach machines to interpret them. The measurements connect nanoscale physics with questions in biology and diagnostics.
Research School of Physics, Australian National University, Canberra. Curriculum vitae (PDF)
Illustrative schematic · not experimental data · not to scale
The depth of the blockade (ΔI) and its duration (Δt) are the measurement. Their distribution over many events is what distinguishes one kind of molecule from another.
02Selected discoveries
01Published result
Can a nanopore distinguish proteins of similar size without any labels?
Each protein that crosses the pore leaves a brief current blockade. We trained machine-learning models on features of thousands of such events to identify which protein produced each one.
Label-free identification of similarly sized proteins reached F-values up to 88.7%, with specificity of 96.4%.
First author. Small Methods 7(11), 2300676 (2023).
02Published result
Does a disease-linked mutation change how a transfer RNA folds?
Transfer RNAs must fold correctly to work. We used solid-state nanopores to read individual tRNA molecules in real time and follow the conformations that a single mutation produces.
Single-molecule detection of metastable conformers of a neuron-specific tRNA, whose mutation causes neurodegeneration in mice; these states are invisible to ensemble methods.
First author. The first solid-state nanopore study of RNA conformational dynamics. Nucleic Acids Research 54(2), gkaf1411 (2026).
03Published result
Can a solid-state pore stay stable long enough to collect the data machine learning needs?
Classifiers need very large numbers of events from the same pore. We developed a scalable way to make ultra-thin silicon nitride membranes that stay stable for long recordings.
Membranes with an effective thickness of about 3 nm supported more than 500,000 DNA and 1.8 million protein translocations through a single pore.
First author; featured on the cover of Analytical Chemistry. Analytical Chemistry 95(13), 5754–5763 (2023).
03Inside the research
I trained as a physicist, and I still think like one: build the instrument carefully, then trust what it measures.
My PhD at ANU was on making solid-state nanopore membranes, using ion-track etching, controlled breakdown and thin-film deposition, and measuring pore shapes with small-angle X-ray scattering at the Australian Synchrotron. Since 2023 I have led the lab's work on using those pores as sensors: recording single proteins and RNAs, and writing the software and models that turn millions of current blockades into answers.
I co-manage the biosensing, solid-state nanopore and thin-film laboratories, supervise research students at every level, and run the first-year physics laboratories.
04Selected papers
Three further papers from a list of twenty-two. The three studies above are cited with their stories.
S. Dutt, P. Apel, N. Lizunov, C. Notthoff, Q. Wen, C. Trautmann, P. Mota-Santiago, N. Kirby, P. Kluth
Journal of Membrane Science 638, 119681 (2021)
First quantitative characterisation of nanopore shape in track-etched polycarbonate membranes, a question that had been open for about 40 years.
Y. M. Bandara, S. Dutt, B. Karawdeniya, J. Saharia, P. Kluth, A. Tricoli
Small Methods 8(12), 2400045 (2024)
A parallel, multi-core event-extraction framework for large nanopore datasets, up to 1120× faster than existing tools under the benchmark conditions reported.
A. Kiy, S. Dutt, C. Notthoff, M. E. Toimil-Molares, N. Kirby, P. Kluth
ACS Applied Nano Materials 6(10), 8564–8573 (2023)
Conical nanopores in amorphous SiO2 with finely tunable surface charge and strong ionic rectification, made by a scalable method.
05Recognition and recent work
100+ News stories on the 2023 protein-identification study, including ABC and 2GB radio and outlets in the US, UK and China.
ABC Radio2GBANU ReporterANU ScienceANU Physics
All coverage“We can directly detect and measure shapes in real time, and see how they change their shape from one form to another, at scale.”