The molecular to cellular universe

Published Research on Molecular Physiology, Computation, and Other Topics

Peer-Reviewed Publications

  1. S. Baral & M. Zwolak, Clustering atomistic DNA and RNA ensembles via secondary structure (submitted to Biophys. J., special issue on “Applications of Coarse-Grained and Multiscale Modeling”)
  2. G. Wójtowicz, S. Sarkar, B. Gardas, M. M. Rams, & M. Zwolak, Extended Reservoir Approaches to Quantum Transport: An Overview of Matrix Equations and Green’s Functions for Relaxation and Dephasing (invited article for “Festschrift for Abraham Nitzan” in J. Chem. Phys.)
  3. M. Lamontagne, S. M. Newell, I. Pazos, R. Tosh, J. Polf, M. Zwolak, & J. W. F. Robertson, Single-molecule biodosimetry, bioRxiv:2024.12.05.627019 (under review, PNAS)
  4. B. De, G. Wójtowicz, M. M. Rams, M. Zwolak, & J. Zakrzewski, Confluence of fractured resonances at points of dynamical many-body flare, Phys. Rev. B 107, 235148 (2024)
  5. B. De, G. Wójtowicz, J. Zakrzewski, M. Zwolak, M. M. Rams, Transport in a periodically driven tilted lattice via the extended reservoir approach: Stability criterion for recovering the continuum limit, Phys. Rev. B 107, 235148 (2023)
  6. G. Wójtowicz, A. Purkayastha, M. Zwolak, & M. M. Rams, Accumulative reservoir construction: Bridging continuously relaxed and periodically refreshed extended reservoirs, Phys. Rev. B 107, 035150 (2023)
  7. J. M. Majikes, M. Zwolak, & J. A. Liddle, Best practices for improved precision and accuracy: A critical reassessment of Van ‘t Hoff analysis of optical melt curves, Biophys. J. 121, 1986 (2022)
  8. M. Zwolak, Amplification, inference, and the manifestation of objective classical information, Entropy 24, 781 (2022)
  9. J. M. Majikes, P. N. Patrone, A. J. Kearsley, M. Zwolak, & J. A. Liddle, Failure mechanisms in DNA self-assembly: Barriers to single fold yield, ACS Nano 15, 3284 (2021)
  10. G. Wójtowicz, J. E. Elenewski, M. M. Rams, & M. Zwolak, Dual current anomalies and quantum transport within extended reservoir simulations, Phys. Rev. B 104, 165131 (2021)
  11. J. E. Elenewski, G. Wójtowicz, M. M. Rams, & M. Zwolak, Performance of reservoir discretizations in quantum transport simulations, J. Chem. Phys. 155, 124117 (2021)
  12. S. Sahu & M. Zwolak, Diffusion limitations and translocation barriers in atomically thin biomimetic pores, Special Issue on the Physics of Ionic Conduction in Narrow Biological and Artificial Channels, Entropy 22, 1326 (2020)
  13. M. Zwolak, Analytic expressions for the steady-state current with finite extended reservoirs, J. Chem. Phys. 153, 224107 (2020)
  14. J. M. Majikes, P. N. Patrone, D. Schiffels, M. Zwolak, A. J. Kearsley, S. P. Forry, & J. A. Liddle, Revealing Thermodynamics of DNA Origami Folding via Affine Transformations and Quantitative Fluorescence Reporting, Nucleic Acids Res. 48, 5268–5280 (2020)
  15. G. Wójtowicz, J. E. Elenewski, M. M. Rams, & M. Zwolak, Open System Tensor Networks and Kramers’ Crossover for Quantum Transport, Phys. Rev. A 101, 050301(Rapid) (2020)
  16. M. Rams & M. Zwolak, Breaking the entanglement barrier: Tensor network simulation of quantum transport, Phys. Rev. Lett. 124, 137701 (2020)
  17. C. Rohmann, M. A. Ochoa, & M. Zwolak, Communication: Metal adsorbate interactions and the convergence of density functional calculations, J. Chem. Phys. 152, 061102 (2020)
  18. M. A. Ochoa & M. Zwolak, Optimal in situ electromechanical sensing of molecular species, J. Chem. Phys. 152, 034109 (2020)
  19. J. E. Elenewski, K. A. Velizhanin, & M. Zwolak, Topology, Landscapes, and Biomolecular Energy Transport, Nat. Commun. 10, 4662 (2019)
  20. T. Unden, D. Louzon, M. Zwolak, W. Zurek & F. Jelezko, Revealing the emergence of classicality in nitrogen-vacancy centers, Phys. Rev. Lett. 123, 140402 (2019)
  21. S. Sahu, J. E. Elenewski, C. Rohmann, & M. Zwolak, Optimal transport and colossal ionic mechano-conductance in graphene crown ethers, Sci. Adv. 5, eaaw5478 (2019)
  22. S. Sahu & M. Zwolak, Colloquium: Ionic phenomena in nanoscale pores through 2D materials, Rev. Mod. Phys. 91, 021004 (2019)
  23. M. A. Ochoa & M. Zwolak, Communication: Generalized Voigt broadening due to thermal fluctuations of electromechanical nanosensors and molecular electronic junctions, J. Chem. Phys. 150, 141102 (2019)
  24. M. Zwolak, Communication: Gibbs phenomenon and the emergence of the steady-state in quantum transport » J. Chem. Phys. 149, 241102 (2018)
  25. D. Gruss, C.-C. Chien, J. T. Barreiro, M. Di Ventra & M. Zwolak, An energy-resolved atomic scanning probe » New J. Phys. 20, 115005 (2018)
  26. J. E. Elenewski, K. A. Velizhanin & M. Zwolak, A spin-1 representation for dual-funnel energy landscapes » J. Chem. Phys. 149, 035101 (2018)
  27. S. Sahu & M. Zwolak, The golden aspect ratio for ion transport » Phys. Rev. E 98, 012404 (2018)
  28. J. P. Zwolak, M. Zwolak & E. Brewe, Educational commitment and social networking: The power of informal networks » Phys. Rev. Phys. Educ. Res. 14, 010131 (2018).
  29. C.-C. Chien, K. A. Velizhanin, Y. Dubi, B. R. Ilic & M. Zwolak, Topological quantization of energy transport in micro- and nano-mechanical lattices » Phys. Rev. B 97, 125425 (2018)
  30. B. Gardas, J. Dziarmaga, W. H. Zurek, & M. Zwolak, Defects in quantum computers » Sci. Rep. 8, 4539 (2018)
  31. P. A. Lin, B. Natarajan, M. Zwolak & R. Sharma, Metastable morphological states of catalytic nanoparticles » Nanoscale 10, 4528 (2018)
  32. S. Sahu & M. Zwolak, Maxwell-Hall access resistance in graphene nanopores » Phys. Chem. Chem. Phys. 20, 4646 (2018)
  33. J. E. Elenewski, D. Gruss & M. Zwolak, Communication: Master Equations for Electron Transport: The Limits of the Markovian Limit » J. Chem. Phys. 147, 151101 (2017)
  34. D. Gruss, A. Smolyanitsky & M. Zwolak, Communication: Relaxation-limited electronic currents in extended reservoir simulations » J. Chem. Phys. 147, 141102 (2017)
  35. S. Sahu & M. Zwolak, Ionic selectivity and filtration from fragmented dehydration in multilayer graphene nanopores » Nanoscale 9, 11424 (2017)
  36. S. Sahu, M. Di Ventra & M. Zwolak, Dehydration as a Universal Mechanism for Ion Selectivity in Graphene and Other Atomically Thin Pores » Nano Lett. 17, 4719 (2017)
  37. H. Guo, E. Strelcov, A. Yulaev, J. Wang, N. Appathurai, S. Urquhart, J. Vinson, S. Sahu, M. Zwolak & A. Kolmakov, Enabling Photoemission Electron Microscopy in Liquids via Graphene-Capped Microchannel Arrays » Nano Lett. 17, 1034 (2017)
  38. M. Zwolak & W. H. Zurek, Redundancy of einselected information in quantum Darwinism: The irrelevance of irrelevant environment bits » Phys. Rev. A 95, 030101(R) (2017)
  39. C.-C. Chien, S. Kouachi, K. Velizhanin, Y. Dubi & M. Zwolak, Thermal transport in dimerized harmonic lattices: Exact solution, crossover behavior, and extended reservoirs » Phys. Rev. E 95, 012137 (2017)
  40. J. Kincaid, K. McLelland & M. Zwolak, Measurement-induced decoherence and information in double-slit interference, » Am. J. Phys. 84, 522 (2016) [an interactive Mathematica plot can be found here]
  41. D. Gruss, K. Velizhanin & M. Zwolak, Landauer’s formula with finite-time relaxation: Kramers’ crossover in electronic transport » Sci. Rep. 6, 24514 (2016)
  42. C. J. Riedel, W. H. Zurek & M. Zwolak, Objective past of a quantum universe: Redundant records of consistent histories » Phys. Rev. A 93, 032126 (2016)
  43. M. Zwolak, C. J. Riedel & W. H. Zurek, Amplification, Decoherence, and the Acquisition of Information by Spin Environments, » Sci. Rep. 6, 25277 (2016)
  44. K. Velizhanin, S. Sahu, C.-C. Chien, Y. Dubi & M. Zwolak, Crossover behavior of the thermal conductance and Kramers’ transition rate theory » Sci. Rep. 5, 17506 (2015)
  45. C.-C. Chien, M. Di Ventra & M. Zwolak, Landauer, Kubo, and microcanonical approaches to quantum transport and noise: A comparison and implications for cold-atom dynamics » Phys. Rev. A 90, 023624 (2014)
  46. M. Zwolak, C. J. Riedel & W. H. Zurek, Amplification, redundancy, and the Quantum Chernoff Information » Phys. Rev. Lett. 112, 140406 (2014)
  47. K. Doi, M. Tsutsui, T. Ohshiro, C.-C. Chien, M. Zwolak, M. Taniguchi, T. Kawai, S. Kawano & M. Di Ventra, Nonequilibrium Ionic Response of Biased Mechanically Controllable Break Junction (MCBJ) Electrodes » J. Phys. Chem. C 118, 3758–3765 (2014)
  48. C.-C. Chien, D. Gruss, M. Di Ventra & M. Zwolak, Interaction-induced conducting-nonconducting transition of ultra-cold atoms in 1D optical lattices » New J. Phys. 15, 063026 (2013)
  49. M. Zwolak & W. H. Zurek, Complementarity of quantum discord and classically accessible information » Sci. Rep. 3, 1729 (2013)
  50. R. Blume-Kohout, S. Croke & M. Zwolak, Quantum Data Gathering » Sci. Rep. 3, 1800 (2013)
  51. C.-C. Chien, K. Velizhanin, Y. Dubi & M. Zwolak, Tunable thermal switching via DNA-based nano devices » Nanotechnology 24, 095704 (2013)
  52. C. J. Riedel, W. H. Zurek & M. Zwolak, The rise and fall of redundancy in decoherence and quantum Darwinism » New J. Phys. 14, 083010 (2012)
  53. M. M. Rams, M. Zwolak & B. Damski, Quantum phase transition in a quantum external field: Superposing two magnetic phases » Sci. Rep. 2, 665 (2012)
  54. J. Dziarmaga, W. H. Zurek & M. Zwolak, Non-local quantum superpositions of topological defects » Nature Phys. 8, 49–53 (2012)
  55. M. Zwolak & M. Di Ventra, DNA Sequencing via Electron Tunneling » IEEE Int. Symp. Circ. S (2012)
  56. P. J. Coles, R. Colbeck, L. Yu & M. Zwolak, Uncertainty relations from simple entropic properties » Phys. Rev. Lett. 108, 210405 (2012)
  57. C.-C. Chien, M. Zwolak & M. Di Ventra, Bosonic and fermionic transport phenomena of ultracold atoms in one-dimensional optical lattices » Phys. Rev. A 85, 041601(R) (2012)
  58. K. Velizhanin, C.-C. Chien, Y. Dubi & M. Zwolak, Driving denaturation: Nanoscale heating as a probe of DNA melting » Phys. Rev. E 83, 050906(R) (2011)
  59. M. Zwolak, J. Wilson & M. Di Ventra, Dehydration and ionic conductance quantization in nanopores » J. Phys.: Condens. Matter 22, 454126 (2010)
  60. M. Zwolak, H. T. Quan & W. H. Zurek, Redundant imprinting of information in non-ideal environments: Objective reality via a noisy channel » Phys. Rev. A 81, 062110 (2010)
  61. M. Zwolak, H. T. Quan & W. H. Zurek, Quantum Darwinism in a hazy environment » Phys. Rev. Lett. 103, 110402 (2009)
  62. M. Zwolak, J. Lagerqvist & M. Di Ventra, Quantized ionic conductance in nanopores » Phys. Rev. Lett. 103, 128102 (2009)
  63. M. Krems, M. Zwolak, Y. V. Pershin & M. Di Ventra, Effect of noise on DNA sequencing via transverse electronic transport » Biophys. J. 97, 1990–1996 (2009)
  64. M. Zwolak, Finite representations of continuum environments » J. Chem. Phys. 129, 101101 (2008)
  65. M. Zwolak, Numerical ansatz for solving integro-differential equations with increasingly smooth memory kernels: spin-boson model and beyond » Comp. Sci. & Disc. 1, 015002 (2008)
  66. M. Zwolak & M. Di Ventra, Colloquium: Physical approaches to DNA sequencing and detection » Rev. Mod. Phys. 80, 141–165 (2008)
  67. J. Lagerqvist, M. Zwolak & M. Di Ventra, Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport » Biophys. J. 93, 2384 (2007)
  68. J. Lagerqvist, M. Zwolak & M. Di Ventra, Comment on ‘Characterization of the tunneling conductance across DNA bases’ » Phys. Rev. E 76, 013901 (2007)
  69. N. Sai, M. Zwolak, G. Vignale & M. Di Ventra, Reply to ‘Treatment of electron viscosity in quantum conductance’ » Phys. Rev. Lett. 98, 259702 (2007)
  70. J. Lagerqvist, M. Zwolak & M. Di Ventra, Fast DNA Sequencing via Transverse Electronic Transport » Nano Lett. 6, 779 (2006)
  71. E. Mullins, R. Oldland, Y. A. Liu, S. Wang, S. I. Sandler, C.-C. Chen, M. Zwolak & K. Seavey, Sigma-Profile Database for Using COSMO-Based Thermodynamic Methods » Ind. Eng. Chem. Res. 45, 4389 (2006)
  72. Y.-C. Chen, M. Zwolak & M. Di Ventra, Inelastic effects on the transport properties of alkanethiols » Nano Lett. 5, 621 (2005)
  73. M. Zwolak & M. Di Ventra, Electronic signature of DNA nucleotides via transverse transport » Nano Lett. 5, 421 (2005)
  74. N. Sai, M. Zwolak, G. Vignale & M. Di Ventra, Dynamical Corrections to the DFT-LDA Electron Conductance in Nanoscale Systems » Phys. Rev. Lett. 94, 186810 (2005)
  75. Z. Yang, M. Chshiev, M. Zwolak, Y.-C. Chen & M. Di Ventra, Role of heating and current-induced forces in the stability of atomic wires » Phys. Rev. B 71, 041402(R) (2005)
  76. M. Di Ventra & M. Zwolak, DNA Electronics » in Encyclopedia of Nanoscience and Nanotechnology edited by H. Singh-Nalwa, American Scientific Publishers, Stevenson Ranch, CA, Vol. 2, pp. 475 (2004)
  77. M. Zwolak & G. Vidal, Mixed-state dynamics in one-dimensional quantum lattice systems: A time-dependent superoperator renormalization algorithm » Phys. Rev. Lett. 93, 207205 (2004)
  78. Y.-C. Chen, M. Zwolak & M. Di Ventra, Inelastic current-voltage characteristics of atomic and molecular junctions » Nano Lett. 4, 1709 (2004)
  79. Y.-C. Chen, M. Zwolak & M. Di Ventra, Local heating in nanoscale conductors » Nano Lett. 3, 1691 (2003)
  80. M. Zwolak, D. Ferguson & M. Di Ventra, Chaotic transport in low-dimensional superlattices » Phys. Rev. B 67, 081303(R) (2003)
  81. M. Zwolak, R. Zallen & M. Di Ventra, Percolation study of defect tolerance in missing-crossbar networks » Solid State Commun. 124, 167 (2002)
  82. M. Zwolak & M. Di Ventra, DNA spintronics » Appl. Phys. Lett. 81, 925 (2002)