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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 employs a parallel electrode configuration with nanoelectrodes in a dielectric layer. Localized electrokinetic fields at electrode wells form tunable attractive potential wells, which can capture biomolecules. 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 fluctuations. The device manipulates diverse samples such as dsDNA, liposomes, and DNA nanotubes, overcoming challenges like intact molecular confinement from bulk, and limited in-situ 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. Some findings of this work are summarized below.
a) Device construction. (a) The device is formed from two parallel conductive plates. The bottom plate is covered by a dielectric layer locally etched to form wells with embedded electrodes (wells are in the shape of circular pads or grooves). (b) Molecules are initially in bulk solution (far from surface). (c). When the field is applied, molecules are captured and confined. (d) Fluorescence image of lambda-DNA confined in an array of circular wells. (e) Tracked center position of confined lambda-DNA molecule; when field is turned off (at t=12s), molecules are released. (f) Dependence of molecule confinement in well (Mean Square Displacement, MSD) on frequency of applied bias. At higher frequency, molecules are more strongly trapped. (g, h) Reversible confinement of lambda-DNA and T4-DNA in nano/micro cavities. (i) Periodic modulation of the applied voltage. (j,h) Reversible confinement of liposomes in microcavities and DNA nanotubes in nanogrooves.
GIF: When we apply a waveform that mimics Gaussian distributed noise, we observe transitions between different cavities. An interesting way to study stochastic behavior of DNA which executes Brownian motion.
2025
M.A.S. Pessôa, P. Jakuc, C. Martins e Queiroz, N. Duggan, R. Liu, S. Kautz, et al. “Single-molecule capture, release, and dynamical manipulation via reversible electrokinetic confinement (RECON).” Science Advances, 11(38), eadv8863.
Z. Liu, W. Dong, T. St-Denis, M.A.S. Pessôa, S. Shiekh, P. Ravikumar, et al. “DNA Dynamics in Dual Nanopore Tug-of-War.” arXiv preprint arXiv:2508.21144.
2024
M.A.S. Pessôa, R. Brosseau, B.J. Dringoli, A. Yazdani, J. Sankey, T. Brunner, et al. “Assessing Students' Understanding of Uncertainty in Undergraduate Physics Laboratory Courses at a Major Canadian University.” arXiv preprint arXiv:2412.15382.
R.A. Monsalve, C. Altamirano, V. Bidula, R. Bustos, C.H. Bye, H.C. Chiang, M.A.S. Pessôa, et al. “Mapper of the IGM Spin Temperature: Instrument Overview.” Monthly Notices of the Royal Astronomical Society, 530(4), 4125–4147.
M.A.S. Pessôa, J. Kljunak, E. Zhivaljevikj, M. Smilevska. “Experimental Validation of the Brachistochrone Curve.” Physics Education, 59(3), 035008.
I.I. Hosseini, S.V. Hamidi, X. Capaldi, Z. Liu, M.A.S. Pessôa, S. Mahshid, et al. “Tunable Nanofluidic Device for Digital Nucleic Acid Analysis.” Nanoscale, 16(19), 9583–9592.
2022
M.A.S. Pessôa, A.A.R. Neves. “3-D Acoustic Trapping with Standing Waves.” arXiv preprint arXiv:2204.08093.
2021
M.A.S. Pessôa, F.M. Silva, M.P. Lima Jr, G. Galhardo, P.H.M. Olyntho, et al. “The Physics of a Disinfector With UV–C Radiation.” Revista Brasileira de Ensino de Física, 43, e20210217.
2020
M.A.S. Pessôa, A.A.R. Neves. “Acoustic Scattering and Forces on an Arbitrarily Sized Fluid Sphere by a General Acoustic Field.” Journal of Sound and Vibration, 479, 115373.
2019
H. Ferreira, M. Pessôa, R.R. Gitti, A.J. Ferreira-Martins, G. de Souza, et al. “The Screaming Balloon: Predicting the Sound Produced by a Hex Nut Inside a Balloon.” Emergent Scientist, 3, 7.
2018
H. Ferreira, R.R. Gitti, A.J. Ferreira-Martins, M. Pessôa, P.R. Sardelich, et al. “Method to Mix Tea With Honey and Use of Transient Light Attenuation as an Indicator of Homogeneity.” Emergent Scientist, 2(2).
Theses
Masters - "Development and testing of antenna and subsystems for MIST, a 21-cm global signal experiment to study the Cosmic Dawn epoch of the Universe". Supervisor: Hsin Cynthia Chiang, Raul Monsalve. Complete thesis available here.
Undergraduate - "Acoustic scattering and forces on an arbitrarily sized fluid sphere by a general acoustic field". Supervisor: Antonio Alvaro Ranha Neves. Complete thesis available here.
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