Publications & code

Biological measurement, molecular simulation, and many-body computation

Selected work is grouped by scientific contribution rather than chronology. The complete list below is drawn from my current CV source and uses the first page or article number for compactness.

Google ScholarORCIDCV & resume

Selected publications

Biological measurement & data quality

  1. Single-Molecule Biodosimetry
    M. Lamontagne et al., including M. Zwolak, Anal. Chem. 97, 22004 (2025). Internal molecular standards and a mechanistic model convert variable nanopore signals into quantitative radiation-dose inference.
  2. Best practice for improved accuracy: A critical reassessment of van’t Hoff analysis of melt curves
    J. M. Majikes, M. Zwolak, & J. A. Liddle, Biophys. J. 121, 1986 (2022). Reassesses how model assumptions propagate into thermodynamic inference from experimental melt curves.
  3. Revealing thermodynamics of DNA origami folding via affine transformations
    J. M. Majikes et al., including M. Zwolak, Nucleic Acids Res. 48, 5268 (2020). Connects FRET measurements to folding yield and thermodynamic transitions.
  4. Topology, landscapes, and biomolecular energy transport
    J. E. Elenewski, K. A. Velizhanin, & M. Zwolak, Nat. Commun. 10, 4662 (2019). Extracts hidden transport pathways and landscape information from time-resolved data.

Biomolecular representations & simulation

  1. Clustering DNA and RNA molecular dynamics ensembles via secondary structure
    S. Baral & M. Zwolak, Biophys. J. 125, 515 (2026). Introduces an interpretable distance for clustering flexible nucleic-acid ensembles.
  2. Failure mechanisms in DNA self-assembly: Barriers to single-fold yield
    J. M. Majikes et al., including M. Zwolak, ACS Nano 15, 3284 (2021). Identifies design-dependent kinetic and thermodynamic obstacles to reliable self-assembly.
  3. Optimal transport and colossal ionic mechano-conductance in graphene crown ethers
    S. Sahu et al., including M. Zwolak, Sci. Adv. 5, eaaw5478 (2019). Reveals how atomic-scale geometry balances selectivity and transport.

Algorithms for many-body physical systems

  1. Golden aspect ratio for ion transport simulation in nanopores
    S. Sahu & M. Zwolak, Phys. Rev. E 98, 012404 (2018). Introduces a finite-size scaling construction that isolates access resistance in atomistic molecular dynamics.
  2. Breaking the entanglement barrier: Tensor network simulation of quantum transport
    M. M. Rams & M. Zwolak, Phys. Rev. Lett. 124, 137701 (2020). Introduces a representation that enables long-time interacting transport simulations.
  3. Open-system tensor networks and Kramers’ crossover for quantum transport
    G. Wójtowicz et al., including M. Zwolak, Phys. Rev. A 101, 050301 (2020). Connects open-system relaxation, tensor networks, and transport regimes.
  4. Performance of reservoir discretizations in quantum transport simulations
    J. E. Elenewski et al., including M. Zwolak, J. Chem. Phys. 155, 124117 (2021). Quantifies accuracy and efficiency across reservoir representations.

Current manuscript: Entanglement at the Fermi Edge and Tensor Networks for Transport is under review at Physical Review Letters. It identifies the information-theoretic structure controlling logarithmic entanglement growth and the efficiency of the transport representation.

Code & reproducibility

Clustering by secondary structure

All code used for secondary-structure-based clustering of DNA and RNA molecular-dynamics ensembles is publicly available with example datasets and scripts sufficient to reproduce the main analyses and figures.

Zenodo code & dataPublished article

Interpretable clustering of molecular ensembles

Complete record

Peer-reviewed publications and current manuscripts

Manuscripts are labeled by the status recorded in the current CV source. For citation counts and the most current indexing, use Google Scholar.

Open complete publication list

2026

  1. Clustering DNA and RNA molecular dynamics ensembles via secondary structure
    S. Baral & M. Zwolak, Biophys. J. 125, 515 (2026).

2025

  1. Complex cooperativity in DNA origami revealed via design dependent defectivity
    J. Majikes, A. Hasni, S. Haridas, J. Robertson, A. Pintar, M. Zwolak & J.A. Liddle, bioRxiv preprint (2025).
  2. Single-Molecule Biodosimetry
    M. Lamontagne, S.M. Newell, I.M. Pazos, R.E. Tosh, J.C. Polf, M. Zwolak & J.W.F. Robertson, Anal. Chem. 97, 22004 (2025).
  3. Approaching the scaling limit of transport through lattices with dephasing
    S. Sarkar, G. Wójtowicz, B. Gardas, M.M. Rams & M. Zwolak, J. Chem. Phys. 163, 114101 (2025).

2024

  1. Confluence of fractured resonances at points of dynamical many-body flare
    B. De, G. Wójtowicz, M.M. Rams, M. Zwolak & J. Zakrzewski, Phys. Rev. B 110, 155146 (2024).

2023

  1. Transport in a periodically driven tilted lattice via the extended reservoir approach: Stability criterion for recovering the continuum limit
    B. De, G. Wójtowicz, J. Zakrzewski, M. Zwolak & M.M. Rams, Phys. Rev. B 107, 235148 (2023).
  2. Accumulative reservoir construction: Bridging continuously relaxed and periodically refreshed extended reservoirs
    G. Wójtowicz, A. Purkayastha, M. Zwolak & M.M. Rams, Phys. Rev. B 107, 035150 (2023).

2022

  1. Best practice for improved accuracy: A critical reassessment of van’t Hoff analysis of melt curves
    J.M. Majikes, M. Zwolak & J.A. Liddle, Biophys. J. 121, 1986 (2022).
  2. Amplification, inference, and the manifestation of objective classical information
    M. Zwolak, Entropy 24, 781 (2022).

2021

  1. Dual current anomalies and quantum transport within extended reservoir simulations
    G. Wójtowicz, J.E. Elenewski, M.M. Rams & M. Zwolak, Phys. Rev. B 104, 165131 (2021).
  2. Performance of reservoir discretizations in quantum transport simulations
    J.E. Elenewski, G. Wójtowicz, M.M. Rams & M. Zwolak, J. Chem. Phys. 155, 124117 (2021).
  3. Failure mechanisms in DNA self-assembly: Barriers to single-fold yield
    J.M. Majikes, P.N. Patrone, A.J. Kearsley, M. Zwolak & J.A. Liddle, ACS Nano 15, 3284 (2021).

2020

  1. Analytic expressions for the steady-state current with finite extended reservoirs
    M. Zwolak, J. Chem. Phys. 153, 224107 (2020).
  2. Diffusion limitations and translocation barriers in atomically thin biomimetic pores
    S. Sahu & M. Zwolak, Entropy 22, 1326 (2020).
  3. Revealing thermodynamics of DNA origami folding via affine transformations
    J.M. Majikes, P.N. Patrone, D. Schiffels, M. Zwolak, A.J. Kearsley, S.P. Forry & J.A. Liddle, Nucleic Acids Res. 48, 5268 (2020).
  4. Open-system tensor networks and Kramers' crossover for quantum transport
    G. Wójtowicz, J.E. Elenewski, M.M. Rams & M. Zwolak, Phys. Rev. A 101, 050301 (2020).
  5. Breaking the entanglement barrier: Tensor network simulation of quantum transport
    M.M. Rams & M. Zwolak, Phys. Rev. Lett. 124, 137701 (2020).
  6. Metal adsorbate interactions and the convergence of density functional calculations
    C. Rohmann, M.A. Ochoa & M. Zwolak, J. Chem. Phys. 152, 061102 (2020).
  7. Optimal in situ electromechanical sensing of molecular species
    M.A. Ochoa & M. Zwolak, J. Chem. Phys. 152, 034109 (2020).

2019

  1. Topology, landscapes, and biomolecular energy transport
    J.E. Elenewski, K.A. Velizhanin & M. Zwolak, Nat. Commun. 10, 4662 (2019).
  2. Revealing the emergence of classicality using nitrogen-vacancy centers
    T.K. Unden, D. Louzon, M. Zwolak, W.H. Zurek & F. Jelezko, Phys. Rev. Lett. 123, 140402 (2019).
  3. Optimal transport and colossal ionic mechano-conductance in graphene crown ethers
    S. Sahu, J. Elenewski, C. Rohmann & M. Zwolak, Sci. Adv. 5, eaaw5478 (2019).
  4. Colloquium: Ionic phenomena in nanoscale pores through 2D materials
    S. Sahu & M. Zwolak, Rev. Mod. Phys. 91, 021004 (2019).
  5. Generalized Voigt broadening due to thermal fluctuations of electromechanical nanosensors and molecular electronic junctions
    M.A. Ochoa & M. Zwolak, J. Chem. Phys. 150, 141102 (2019).

2018

  1. Communication: Gibbs phenomenon and the emergence of the steady-state in quantum transport
    M. Zwolak, J. Chem. Phys. 149, 241102 (2018).
  2. A spin-1 representation for dual-funnel energy landscapes
    J.E. Elenewski, K.A. Velizhanin & M. Zwolak, J. Chem. Phys. 149, 035101 (2018).
  3. Golden aspect ratio for ion transport simulation in nanopores
    S. Sahu & M. Zwolak, Phys. Rev. E 98, 012404 (2018).
  4. Educational commitment and social networking: The power of informal networks
    J.P. Zwolak, M. Zwolak & E. Brewe, Phys. Rev. PER 14, 010131 (2018).
  5. Topological quantization of energy transport in micromechanical and nanomechanical lattices
    C.C. Chien, K.A. Velizhanin, Y. Dubi, B.R. Ilic & M. Zwolak, Phys. Rev. B 97, 125425 (2018).
  6. Defects in quantum computers
    B. Gardas, J. Dziarmaga, W.H. Zurek & M. Zwolak, Sci. Rep. 8, 4539 (2018).
  7. Metastable morphological states of catalytic nanoparticles
    P.A. Lin, B. Natarajan, M. Zwolak & R. Sharma, Nanoscale 10, 4528 (2018).
  8. Maxwell-Hall access resistance in graphene nanopores
    S. Sahu & M. Zwolak, Phys. Chem. Chem. Phys. 20, 4646 (2018).
  9. An energy-resolved atomic scanning probe
    D. Gruss, C.C. Chien, J.T. Barreiro, M.D. Ventra & M. Zwolak, New J. Phys. 20, 115005 (2018).

2017

  1. Communication: Master equations for electron transport: The limits of the Markovian limit
    J.E. Elenewski, D. Gruss & M. Zwolak, J. Chem. Phys. 147, 151101 (2017).
  2. Communication: Relaxation-limited electronic currents in extended reservoir simulations
    D. Gruss, A. Smolyanitsky & M. Zwolak, J. Chem. Phys. 147, 141102 (2017).
  3. Ionic selectivity and filtration from fragmented dehydration in multilayer graphene nanopores
    S. Sahu & M. Zwolak, Nanoscale 9, 11424 (2017).
  4. Dehydration as a universal mechanism for ion selectivity in graphene and other atomically thin pores
    S. Sahu, M. Di Ventra & M. Zwolak, Nano Lett. 17, 4719 (2017).
  5. Redundancy of einselected information in quantum Darwinism: The irrelevance of irrelevant environment bits
    M. Zwolak & W.H. Zurek, Phys. Rev. A 95, 030101 (2017).
  6. Enabling photoemission electron microscopy in liquids via graphene-capped microchannel arrays
    H. Guo, E. Strelcov, A. Yulaev, J. Wang, N. Appathurai, S. Urquhart, J. Vinson, S. Sahu, M. Zwolak & A. Kolmakov, Nano Lett. 17, 1034 (2017).
  7. Thermal transport in dimerized harmonic lattices: Exact solution, crossover behavior, and extended reservoirs
    C.C. Chien, S. Kouachi, K.A. Velizhanin, Y. Dubi & M. Zwolak, Phys. Rev. E 95, 012137 (2017).

2016

  1. Measurement-induced decoherence and information in double-slit interference
    M. Kincaid, K. McLelland & M. Zwolak, Am. J. Phys. 84, 522 (2016).
  2. Amplification, decoherence and the acquisition of information by spin environments
    M. Zwolak, C.J. Riedel & W.H. Zurek, Sci. Rep. 6, 25277 (2016).
  3. Landauer’s formula with finite-time relaxation: Kramers’ crossover in electronic transport
    D. Gruss, K.A. Velizhanin & M. Zwolak, Sci. Rep. 6, 24514 (2016).
  4. Objective past of a quantum universe: Redundant records of consistent histories
    C.J. Riedel, W.H. Zurek & M. Zwolak, Phys. Rev. A 93, 032126 (2016).

2015

  1. Crossover behavior of the thermal conductance and Kramers’ transition rate theory
    K.A. Velizhanin, S. Sahu, C.C. Chien, Y. Dubi & M. Zwolak, Sci. Rep. 5, 17506 (2015).

2014

  1. Landauer, Kubo, and microcanonical approaches to quantum transport and noise: A comparison and implications for cold-atom dynamics
    C.C. Chien, M. Di Ventra & M. Zwolak, Phys. Rev. A 90, 023624 (2014).
  2. Amplification, redundancy, and quantum Chernoff information
    M. Zwolak, C.J. Riedel & W.H. Zurek, Phys. Rev. Lett. 112, 140406 (2014).
  3. Nonequilibrium ionic response of biased mechanically controllable break junction (MCBJ) electrodes
    K. Doi, M. Tsutsui, T. Ohshiro, C.C. Chien, M. Zwolak, M. Taniguchi, T. Kawai, S. Kawano & M. Di Ventra, J. Phys. Chem. C 118, 3758 (2014).

2013

  1. Interaction-induced conducting-non-conducting transition of ultra-cold atoms in one-dimensional optical lattices
    C.C. Chien, D. Gruss, M.D. Ventra & M. Zwolak, New J. Phys. 15, 063026 (2013).
  2. Complementarity of quantum discord and classically accessible information
    M. Zwolak & W.H. Zurek, Sci. Rep. 3, 1729 (2013).
  3. Quantum data gathering
    R. Blume-Kohout, S. Croke & M. Zwolak, Sci. Rep. 3, 1800 (2013).
  4. Tunable thermal switching via DNA-based nano-devices
    C.C. Chien, K.A. Velizhanin, Y. Dubi & M. Zwolak, Nanotechnology 24, 095704 (2013).

2012

  1. A quantum phase transition in a quantum external field: Superposing two magnetic phases
    M.M. Rams, M. Zwolak & B. Damski, Sci. Rep. 2, 655 (2012).
  2. The rise and fall of redundancy in decoherence and quantum Darwinism
    C.J. Riedel, W.H. Zurek & M. Zwolak, New J. Phys. 14, 083010 (2012).
  3. Uncertainty relations from simple entropic properties
    P.J. Coles, R. Colbeck, L. Yu & M. Zwolak, Phys. Rev. Lett. 108, 210405 (2012).
  4. Bosonic and fermionic transport phenomena of ultracold atoms in one-dimensional optical lattices
    C.C. Chien, M. Zwolak & M. Di Ventra, Phys. Rev. A 85, 041601 (2012).
  5. Non-local quantum superpositions of topological defects
    J. Dziarmaga, W.H. Zurek & M. Zwolak, Nat. Phys. 8, 49 (2012).
  6. DNA sequencing via electron tunneling
    M. Zwolak & M. Di Ventra, IEEE Int. Sym. Cir. Sys., 2295 (2012).

2011

  1. Driving denaturation: Nanoscale thermal transport as a probe of DNA melting
    K.A. Velizhanin, C.C. Chien, Y. Dubi & M. Zwolak, Phys. Rev. E 83, 050906 (2011).

2010

  1. Redundant imprinting of information in nonideal environments: Objective reality via a noisy channel
    M. Zwolak, H.T. Quan & W.H. Zurek, Phys. Rev. A 81, 062110 (2010).
  2. Dehydration and ionic conductance quantization in nanopores
    M. Zwolak, J. Wilson & M.D. Ventra, J. Phys.: Condens. Matter 22, 454126 (2010).

2009

  1. Effect of noise on DNA sequencing via transverse electronic transport
    M. Krems, M. Zwolak, Y.V. Pershin & M.D. Ventra, Biophys. J. 97, 1990 (2009).
  2. Quantized ionic conductance in nanopores
    M. Zwolak, J. Lagerqvist & M. Di Ventra, Phys. Rev. Lett. 103, 128102 (2009).
  3. Quantum Darwinism in a mixed environment
    M. Zwolak, H.T. Quan & W.H. Zurek, Phys. Rev. Lett. 103, 110402 (2009).

2008

  1. Finite representations of continuum environments
    M. Zwolak, J. Chem. Phys. 129, 101101 (2008).
  2. Colloquium: Physical approaches to DNA sequencing and detection
    M. Zwolak & M. Di Ventra, Rev. Mod. Phys. 80, 141 (2008).
  3. Numerical ansatz for solving integro-differential equations with increasingly smooth memory kernels: spin-boson model and beyond
    M. Zwolak, Computational Science \& Discovery 1, 015002 (2008).

2007

  1. Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport
    J. Lagerqvist, M. Zwolak & M.D. Ventra, Biophys. J. 93, 2384 (2007).
  2. Comment on “Characterization of the tunneling conductance across DNA bases”
    J. Lagerqvist, M. Zwolak & M. Di Ventra, Phys. Rev. E 76, 013901 (2007).
  3. Comment on “Dynamical corrections to the DFT-LDA electron conductance in nanoscale systems”
    N. Sai, M. Zwolak, G. Vignale & M. Di Ventra, Phys. Rev. Lett. 98, 259702 (2007).

2006

  1. Sigma-profile database for using COSMO-based thermodynamic methods
    E. Mullins, R. Oldland, Y.A. Liu, S. Wang, S.I. Sandler, C.C. Chen, M. Zwolak & K.C. Seavey, Ind. Eng. Chem. Res. 45, 4389 (2006).
  2. Fast DNA sequencing via transverse electronic transport
    J. Lagerqvist, M. Zwolak & M. Di Ventra, Nano Lett. 6, 779 (2006).

2005

  1. Dynamical corrections to the DFT-LDA electron conductance in nanoscale systems
    N. Sai, M. Zwolak, G. Vignale & M. Di Ventra, Phys. Rev. Lett. 94, 186810 (2005).
  2. Inelastic effects on the transport properties of alkanethiols
    Y.C. Chen, M. Zwolak & M. Di Ventra, Nano Lett. 5, 621 (2005).
  3. Electronic signature of DNA nucleotides via transverse transport
    M. Zwolak & M. Di Ventra, Nano Lett. 5, 421 (2005).
  4. Role of heating and current-induced forces in the stability of atomic wires
    Z. Yang, M. Chshiev, M. Zwolak, Y.C. Chen & M. Di Ventra, Phys. Rev. B 71, 041402 (2005).

2004

  1. Mixed-state dynamics in one-dimensional quantum lattice systems: A time-dependent superoperator renormalization algorithm
    M. Zwolak & G. Vidal, Phys. Rev. Lett. 93, 207205 (2004).
  2. Inelastic current-voltage characteristics of atomic and molecular junctions
    Y.C. Chen, M. Zwolak & M. Di Ventra, Nano Lett. 4, 1709 (2004).
  3. DNA electronics
    M. Di Ventra & M. Zwolak, in Encyclopedia of Nanoscience and Nanotechnology (ed: Nalwa, H. S.) 2, 475 (2004).

2003

  1. Local heating in nanoscale conductors
    Y.C. Chen, M. Zwolak & M. Di Ventra, Nano Lett. 3, 1691 (2003).
  2. Chaotic transport in low-dimensional superlattices
    M. Zwolak, D. Ferguson & M. Di Ventra, Phys. Rev. B 67, 081303 (2003).

2002

  1. Percolation study of defect tolerance in missing-crossbar networks
    M. Zwolak, R. Zallen & M. Di Ventra, Solid State Commun. 124, 167 (2002).
  2. DNA spintronics
    M. Zwolak & M. Di Ventra, Appl. Phys. Lett. 81, 925 (2002).