Publications

Publications

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  1. A. Pacheco-Pozo and D. Krapf, “Effectively detecting anomalous diffusion via deep learning” Nat. Comput. Sci. (accepted)
  2. M. Balcerek, A. Pacheco-Pozo, A. Wyłomańska, K. Burnecki, and D. Krapf, “Two-dimensional Brownian motion with dependent components: turning angle analysis” arXiv [cond-mat]: 2407.06374 (2024) preprint
  3. A. Pacheco-Pozo, M. Balcerek, A. Wyłomańska, K. Burnecki, I.M. Sokolov, and D. Krapf, “Langevin equation in heterogeneous landscapes: how to choose the interpretation” Phys. Rev. Lett. 133, 067102 (2024) preprint
  4. M. Jabloñski, F.A. La Spina, L.J. Schiavi Ehrenhaus, C.I. Marín-Briggiler, M.D. Gómez-Elías, D. Krapf, P.E. Visconti, D. Krapf, G.M. Luque, and M.G. Buffone, “Dual role of Valosin-Containing Protein (VCP/p97) in mouse sperm during capacitation” Reproduction 168 (2), e240069 (2024) full text
  5. A.G. Novero, P. Torres Rodríguez, J.L. De la Vega Beltrán, L.J. Schiavi-Ehrenhaus, G.M. Luque, M. Carruba, C. Stival, I. Gentile, C. Ritagliati, C.M. Santi, T. Nishigaki, D. Krapf, M.G. Buffone, A. Darszon, C.L. Treviño, and D. Krapf, “The sodium-proton exchangers sNHE and NHE1 control plasma membrane hyperpolarization in mouse sperm” bioRxiv 10.1101/2024.03.04.583310 (2024) pdf
  6. A. Pacheco-Pozo and D. Krapf, “Fractional Brownian motion with fluctuating diffusivities” Phys. Rev. E 110, 014105 (2024) pdf
  7. M. Jabloñski, G.M. Luque, M. Gómez-Elías, C. Sanchez-Cardenas, X. Xu, J.L. de la Vega-Beltran, G. Corkidi, A. Linares, V.X. Abonza Amaro, D. Krapf, D. Krapf, A. Darszon, A. Guerrero, and M.G. Buffone, “Reorganization of the Flagellum Scaffolding Induces a Sperm Standstill Required for Fertilization”, eLife 13, RP93792 (2024) full text
  8. A.G. Novero, C. Curcio, T.J. Steeman, A. Binolfi, D. Krapf, M.G. Buffone, D. Krapf, and C. Stival, “A Versatile Kinase Mobility Shift Assay (KiMSA) for PKA Analysis and cyclic AMP detection in sperm physiology (and beyond)”,  Front. Cell Dev. Biol. 12, 1356566 (2024) pdf
  9. A.N. Leek, J.A. Quinn, D, Krapf, M. Tamkun, “GLT-1a glutamate transporter nanocluster localization is associated with astrocytic actin and neuronal Kv2 clusters at sites of neuron-astrocyte contact”,  Front. Cell Dev. Biol.  12, 1334861 (2024) pdf
  10. G. Muñoz, H. Bachimanchi, J. Pineda, B. Midtvedt, M. Lewenstein, R. Metzler, D. Krapf, G. Volpe, and C. Manzo, “Quantitative evaluation of methods to analyze motion changes in single-particle experiments [Registered Report Stage 1 Protocol]”, figshare. Journal contribution. https://doi.org/10.6084/m9.figshare.24771687.v1 (2023) pdf
  11. M.N Saxton, T. Morisaki, D. Krapf, H. Kimura, and T.J. Stasevich, “Live-cell imaging uncovers the relationship between histone acetylation, transcription initiation, and nucleosome mobility”,  Sci. Adv. 9, eadh4819 (2023) full text,  preprint
  12. M. Balcerek, A. Wyłomańska, K. Burnecki, R. Metzler, and D. Krapf, “Modelling intermittent anomalous diffusion with switching fractional Brownian motion” New J. Phys. 25, 103031 (2023) full text
  13. C. Agudo-Rios, A. Rogers, I. King, V. Bhagat, L.M. Nguyen, C. Córdova-Fletes, D. Krapf, J.F. Strauss III, L. Arévalo, G.E. Merges, H. Schorle, E.R.S. Roldan, M.E. Teves, “SPAG17 mediates nuclear translocation of protamines during spermiogenesis”, Front. Cell Dev. Biol. 11, 1125096 (2023) pdf
  14. V. Sposini, D. Krapf, E. Marinari, R. Sunyer, F. Ritort, F. Taheri, C. Selhuber-Unkel, R. Benelli, M. Weiss, R. Metzler, and G. Oshanin, “Towards a robust criterion of anomalous diffusion”, Commun. Phys. 5, 305 (2022) pdf
  15. E. Torres-García, R. Pinto-Cámara, A. Linares, D. Martínez, V. Abonza, E. Brito-Alarcón, C. Calcines-Cruz, G. Valdés-Galindo, D. Torres, M. Jabloñski, H.H. Torres-Martínez, J.L. Martínez, H.O. Hernández, J.P. Ocelotl-Oviedo, Y. Garcés, M. Barchi, R. D’Antuono, A. Bošković, J.G. Dubrovsky, A. Darszon, M.G. Buffone, R. Rodríguez Morales, J.M. Rendon-Mancha, C.D. Wood, A. Hernández-García, D. Krapf, A.H. Crevenna, and A. Guerrero, “Extending resolution within a single imaging frame”, Nat. Commun. 13, 7452 (2022) full text
  16. H. Vahabi, S. Vallabhuneni, M. Hedayati, W. Wang, D. Krapf, M.J. Kipper, N. Miljkovic, and A.K. Kota, “Designing non-textured, all-solid, slippery hydrophilic surfaces”, Matter  5, 4502 (2022) full text
  17. B. Ovryn, T.T. Bishop, and D. Krapf, “Physics of the Cell Membrane”, Physics of Molecular and Cellular Processes, Graduate Texts in Physics, K.B. Blagoev and H. Levine (eds.), Springer (2022) pdf
  18. D. Szarek, I. Jabłoński, D. Krapf, and A. Wyłomańska, “Multifractional Brownian motion characterization based on Hurst exponent estimation and statistical learning”, Chaos 32, 083148 (2022) full text
  19. O. Vilk, E. Aghion, T. Avgar, C. Beta, O. Nagel, A. Sabri, R. Sarfati, D.K. Schwartz, M. Weiss, D. Krapf, R. Nathan, R. Metzler, and M. Assaf, “Unravelling the origins of anomalous diffusion: From molecules to migrating storks”, Phys. Rev. Res. 4, 033055 (2022) pdf
  20. C. Dieball, D. Krapf, M. Weiss, A. Godec, “Scattering fingerprints of two-state dynamics”, New. J. Phys.  24, 023004 (2022) pdf
  21. 8. D. Szarek, K. Maraj- Zygmąt, G. Sikora, D. Krapf, and A. Wyłomańska, “Statistical test for anomalous diffusion based on empirical anomaly measure for Gaussian processes”, Comput. Stat. Data Anal. 168, 107401 (2022) pdf
  22. Z.R. Fox, E. Barkai, and D. Krapf, “Aging power spectrum of membrane protein transport and other subordinated random walks”, Nat. Commun. 12, 6162 (2021) full text, SM
  23. G.M. Luque, X. Xu, A. Romarowski, M.G. Gervasi, G. Orta, J.L. De la Vega-Beltrán, C. Stival, N. Gilio, T. Dalotto-Moreno, D. Krapf, P.E. Visconti, D. Krapf, A. Darszon, and M.G. Buffone, “Cdc42 localized in the CatSper signaling complex regulates cAMP-dependent pathways in mouse sperm”, FASEB J. 35, e21723 (2021) preprint
  24. G. Muñoz-Gil, G. Volpe, M.A. Garcia-March, E. Aghion, A. Argun, C.B. Hong, T. Bland, S. Bo, J.A. Conejero, N. Firbas, O. Garibo i Orts, A. Gentili, Z. Huang, J.-H. Jeon, H. Kabbech, Y. Kim, P. Kowalek, D. Krapf, H. Loch-Olszewska, M.A. Lomholt, J.-B. Masson, P.G. Meyer, S. Park, B. Requena, I. Smal, T. Song, J. Szwabiński, S. Thapa, H. Verdier, G. Volpe, A. Widera, M. Lewenstein, R. Metzler, and C. Manzo, “Objective comparison of methods to decode anomalous diffusion”, Nat. Commun. 12, 6253 (2021) pdf   ICFO press release
  25. J. Janczura, M. Balcerek, K. Burnecki, A. Sabri, M. Weiss, and D. Krapf, “Identifying heterogeneous diffusion states in the cytoplasm by a hidden Markov model”, New J. Phys. 23, 053018 (2021) pdf
  26. M. Hedayati, D. Krapf, and M. Kipper, “Dynamics of long-term protein aggregation on low-fouling surfaces”, J. Colloid Interface Sci. 589, 356 (2021) pdf
  27. S. Thapa, A. Wyłomańska, G. Sikora, C.E. Wagner, D. Krapf, H. Kantz, A. Chechkin, and R. Metzler, “Leveraging large-deviation statistics to decipher the stochastic properties of measured trajectories”, New J. Phys. 23, 013008 (2021) pdf
  28. A. Sabri, X. Xu, D. Krapf, and M. Weiss, “Elucidating the origin of heterogeneous anomalous diffusion in the cytoplasm of mammalian cells”, Phys. Rev. Lett.  125, 058101 (2020) preprint
  29. M.E. Teves, E.R.S. Roldan, D. Krapf, J.F. Strauss III, V. Bhagat, and P. Sapao, “Sperm Differentiation: The Role of Trafficking of Proteins”, Int. J. Mol. Sci. 21, 3702 (2020) pdf
  30. M. Hedayati, M.J. Kipper, and D. Krapf, “Anomalous protein kinetics on low-fouling surfaces”, Phys. Chem. Chem. Phys. 22, 5264 (2020) preprint, SM
  31. M. Hedayati, D.F. Marruecos, D. Krapf, J.L. Kaar, and M.J. Kipper, “Protein adsorption measurements on low fouling and ultralow fouling surfaces: A critical comparison of surface characterization techniques”, Acta Biomater. 102, 169 (2020) pdf
  32. D. Krapf and R. Metzler, “Strange interfacial molecular dynamics”, Physics Today 72, 9, 48 (2019) pdf
  33. D. Krapf, N. Lukat, E. Marinari, R. Metzler, G. Oshanin, C. Selhuber-Unkel, A. Squarcini, L. Stadler, M. Weiss, and X. Xu, “Spectral content of a single non-Brownian trajectory”, Phys. Rev. X 9, 011019 (2019) pdf, SM
  34. K. Burnecki, G. Sikora, A. Weron, M.M. Tamkun, and D. Krapf, “Identifying diffusive motions in single-particle trajectories on the plasma membrane via fractional time series models”, Phys. Rev. E 99, 012101 (2019) pdf, SM
  35. M.J. Metz, R.L. Pennock, D. Krapf, and S.T Hentges, “Temporal dependence of shifts in mu opioid receptor mobility at the cell surface after agonist binding observed by single-particle tracking”, Sci. Rep. 9, 7297 (2019) pdf
  36. A. Romarowski, A. Velasco Felix, P. Torres Gimenez, M.G. Gervasi, X. Xu, G.M. Luque, G. Contreras Gimenez, C. Sanchez Cardenas, H.V. Ramirez Gomez, D. Krapf, P.E. Visconti, D. Krapf, A.O. Guerrero, A. Darszon, and M.G. Buffone, “Super-resolution imaging of live sperm reveals dynamic changes of the actin cytoskeleton during acrosomal exocytosis” J. Cell Sci. 131, jcs218958 (2018) pdf, SI
  37. M. Hedayati, M.M. Reynolds, D. Krapf, and M.J. Kipper, “Nanostructured surfaces that mimic the vascular endothelial glycocalyx reduce blood protein adsorption and prevent fibrin network formation”, ACS Appl. Mater. Interfaces 10, 31892 (2018) pdf, Supp. Info.
  38. D.S. Grebenkov and D. Krapf, “Steady-state reaction rate of diffusion-controlled reactions in sheets”, J. Chem. Phys. 149, 064117 (2018)  pdf
  39. G. Sikora, A. Wyłomańska, and D. Krapf, “Recurrence statistics for anomalous diffusion regime change detection”, Comput. Stat. Data Anal. 128, 380 (2018) pdf
  40. C. Stival, C. Ritagliati, X. Xu, M.G. Gervasi, G. Luque, C. Baro Graf, J.L. Vega-Beltran, N. Torres, A. Darszon, D. Krapf, M.G. Buffone, P.E. Visconti, and D. Krapf, “Disruption of protein kinase A localization induces acrosomal exocytosis in capacitated mouse sperm”, J. Biol. Chem. 293, 9435 (2018) pdf, SI
  41. D. Krapf, “Compartmentalization of the plasma membrane”, Current Opinion in Cell Biology 53, 15 (2018) pdf
  42. D. Krapf, E. Marinari, R. Metzler, G. Oshanin, X. Xu, and A. Squarcini “Power spectral density of a single Brownian trajectory: what one can and cannot learn from it”, New J. Phys. 20, 023029 (2018) pdf
  43. M.G. Gervasi, X. Xu, B. Carbajal-Gonzalez, M.G. Buffone, P. Visconti, and D. Krapf, “The actin cytoskeleton of the mouse sperm flagellum is organized in a helical structure”, J. Cell Sci. 131, jcs215897 (2018), pdf
  44. G. Sikora, A. Wyłomańska, J. Gajda, L. Solé, E.J. Akin, M.M. Tamkun, and D. Krapf, “Elucidating distinct ion channel populations on the surface of hippocampal neurons via single-particle tracking recurrence analysis”, Phys. Rev. E 96, 062404 (2017)  pdf, SM
  45. A. Weron, K. Burnecki, E.J. Akin, L. Solé, M. Balcerek, M.M. Tamkun, and D. Krapf, “Ergodicity breaking on the neuronal surface emerges from random switching between diffusive states”, Sci. Rep. 7, 5404 (2017)  pdf, Suppl. Mat.
  46. S. Sadegh, J.L. Higgins, P.C. Mannion, M.M. Tamkun, and D. Krapf, “Plasma membrane is compartmentalized by a self-similar cortical actin meshwork”, Phys. Rev. X  7, 011031 (2017)  pdf, Suppl. Mat.
    Source story, Phys. Buzz story
  47. O. Wiggan, B. Schroder, D. Krapf, J.R. Bamburg, and J.G. DeLuca, “Cofilin regulates nuclear architecture through a myosin-II dependent mechanotransduction module”, Sci. Rep.  7, 40953 (2017)  pdf
  48. E.J. Akin, L. Solé, B. Johnson, M. el Beheiry, J.-B. Masson, D. Krapf, and M.M. Tamkun, “Single-molecule imaging of Nav1.6 on the surface of hippocampal neurons reveals somatic nanoclusters”, Biophys. J.  111, 1235 (2016)  pdf
  49. A. Alvau, M.A. Battistone, M.G. Gervasi, F.A. Navarrete, X. Xu, C. Sánchez-Cárdenas, J.L. De la Vega-Beltran, V.G. Da Ros, P. Greer, A. Darszon, D. Krapf, A.M. Salicioni, P. Cuasnicu, P.E. Visconti, “The tyrosine kinase FER is responsible for the capacitation-associated increase in tyrosine phosphorylation in murine sperm”, Development  143, 2325 (2016) pdf
  50. D. Krapf, G. Campagnola, K. Nepal, and O.B. Peersen, “Strange kinetics of bulk-mediated diffusion on lipid bilayers”, Phys. Chem. Chem. Phys. 18, 12633 (2016) pdf
  51. G. Campagnola, K. Nepal, B.W. Schroder, O.B. Peersen, and D. Krapf, “Superdiffusive motion of membrane-targeting C2 domains”, Sci. Rep. 5, 17721 (2015)  pdf,  Suppl. Mat.
  52. P.D. Fox, C.J. Haberkorn, E.J. Akin, P.J. Seel, D. Krapf, and M.M. Tamkun, “Induction of stable endoplasmic reticulum/plasma membrane junctions by Kv2.1 potassium channels”, J. Cell Sci. 128, 2096 (2015) pdf
  53. D. Krapf, “Mechanisms underlying anomalous diffusion in the plasma membrane”, Current Topics in Membranes  75, 167 (2015) pdf
  54. D. Krapf, “Dynamic fluctuations in single-molecule biophysics experiments – Comment on Extracting physics of life at the molecular level: A review of single-molecule data analyses”, Phys. Life Rev. 13, 148 (2015) pdf
  55. S. Sadegh, E. Barkai, and D. Krapf, “1/f noise for intermittent quantum dots exhibits non-stationarity and critical exponents“, New J. Phys.  16, 113054 (2014)  pdf,  Supporting Material
  56. A.V. Weigel, M.M. Tamkun, and D. Krapf, “Quantifying the dynamic interactions between a clathrin-coated pit and cargo molecules“, Proc. Natl. Acad. Sci. USA  110, E4591 (2013)  pdf,  Supporting Information
  57. P.D. Fox, C.J. Haberkorn, A.V. Weigel, J.L. Higgins, E.J. Akin, M.J. Kennedy, D. Krapf, and M.M. Tamkun, “Plasma membrane domains enriched in cortical endoplasmic reticulum function as membrane protein trafficking hubs”, Mol. Biol. Cell  24, 2703 (2013) pdf
  58. D. Krapf, “Nonergodicity in nanoscale electrodes”, Phys. Chem. Chem. Phys. 15, 459 (2013) pdf
  59. A. Mont, A.V. Wiegel, D. Krapf, and C.P. Calderon, “Uncertainty Quantification of Discrete Association Problems in Image Sequence-based Tracking”, arXiv:1304.5759 (2013), pdf
  60. A.V. Weigel, P.D. Fox, E.J. Akin, K.H. Ecklund, M.M. Tamkun, and D. Krapf, “Size of cell-surface Kv2.1 domains is governed by growth fluctuations”, Biophys. J.  103, 1727 (2012)  pdf,  Supporting Material
  61. E. Deutsch, A.V. Weigel, E.J. Akin, P. Fox, G. Hansen, C.J. Haberkorn, R. Loftus, D. Krapf, and M.M. Tamkun, “Kv2.1 cell surface clusters are insertion platforms for ion channel delivery to the plasma membrane”, Mol. Biol. Cell  23, 2917 (2012) pdf,  Suppl. Mat.
  62. A.V. Weigel, S. Ragi, M.L. Reid, E.K.P. Chong, M.M. Tamkun, and D. Krapf, “Obstructed diffusion propagator analysis for single-particle tracking”, Phys. Rev. E  85, 041924 (2012)  pdf,  Suppl. Mat.
  63. A.V. Weigel, B. Simon, M.M. Tamkun, and D. Krapf, “Ergodic and nonergodic processes coexist in the plasma membrane as observed by single molecule tracking”, Proc. Natl. Acad. Sci. USA 108, 6438 (2011) pdf,  Supporting Information
  64. T. Wojcik and D. Krapf, “Solid-state nanopore recognition and measurement using Shannon entropy”, IEEE Photonics J. 3, 337 (2011) pdf, MATLAB codes
  65. M.Y. Wu, R.M.M. Smeets, M. Zandbergen, U. Ziese, D. Krapf, P.E. Batson, N.H. Dekker, C. Dekker, and H.W. Zandbergen, “Control of Shape and Material Composition of Solid-State Nanopores”, Nano Lett. 9, 479 (2009) pdf
  66. M.A.G. Zevenbergen, D. Krapf, M.R. Zuiddam, and S.G. Lemay, “Mesoscopic concentration fluctuations in a fluidic nanocavity detected by redox cycling”, Nano Lett. 7, 384 (2007) pdf, cover page
  67. M.A.G. Zevenbergen, D. Krapf, M.R. Zuiddam, and S.G. Lemay, “Giant amplification of redox current in a nanofluidic channel”, Proceedings of the 10th Micro Total Analysis Systems Conference, 654-656 (2006) Tokyo, Japan. pdf
  68. D. Krapf, B.M. Quinn, M.Y. Wu, H. Zandbergen, C. Dekker and S.G. Lemay, “Experimental observation of nonlinear ionic transport at the nanometer scale”, Nano Lett. 6, 2531 (2006) pdf
  69. U.F. Keyser, B.N. Koeleman, S. van Dorp, D. Krapf, R.M.M. Smeets, S.G. Lemay, N.H. Dekker, and C. Dekker, “Direct force measurements on DNA in a solid-state nanopore”, Nature Physics 2, 473 (2006) pdf
  70. D. Krapf, M.Y. Wu, R.M.M. Smeets, H. Zandbergen, C. Dekker and S.G. Lemay, “Fabrication and characterization of nanopore-based electrodes with radii down to 2 nm”, Nano Lett. 6, 105 (2006) pdf
  71. R.M.M. Smeets, U.F. Keyser, D. Krapf, M.Y. Wu, N.H. Dekker y C. Dekker, “Salt-dependence of ion transport and DNA translocation through solid-state nanopores”, Nano Lett. 6, 89 (2006) pdf
  72. U.F. Keyser, D. Krapf, B.N. Koeleman, R.M.M. Smeets, N.H. Dekker, and C. Dekker, “Nanopore tomography of a laser focus”, Nano Lett. 5, 2253 (2005) pdf
  73. A. Sa’ar, Y. Reichman, M. Dovrat, D. Krapf, J. Jedrzejewski, I. Balberg, “Resonant coupling between surface vibrations and electronic states in silicon nanocrystals at the strong confinement regime”, Nano Lett. 5, 2443 (2005) pdf
  74. M.Y. Wu, D. Krapf, M. Zandbergen, H. Zandbergen, and P.E. Batson, “Formation of nanopores in a SiN/SiO2 membrane with an electron beam”, Appl. Phys. Lett. 87, 113106 (2005) pdf
  75. S.G. Lemay, D.M. van den Broek, A.J. Storm, D. Krapf, R.M.M. Smeets, H.A. Heering, C. Dekker, “Lithographically fabricated nanopore-based electrodes for electrochemistry”, Anal. Chem. 77, 1911 (2005) pdf
  76. D. Krapf, S.-H. Kan, U. Banin, O. Millo, and A. Sa’ar, “Intersublevel optical transitions in InAs nanocrystals probed by photoinduced absorption spectroscopy: The Role of Thermal Activation”, Phys. Rev. B 69, 073301 (2004) pdf
  77. D. Krapf, A. Davidi, J. Shappir, and A. Sa’ar, “Infrared photo-induced absorption spectroscopy of porous silicon”, Phys. St. Sol. A 197, 566 (2003) pdf
  78. D. Krapf, B. Adoram, K. L. Wang, J. Shappir and A. Sa’ar, “Infrared multispectral detection using Si/SixGe1-x quantum well infrared photodetectors”, Appl. Phys. Lett. 78, 495 (2001) pdf
  79. B. Adoram, D. Krapf, M. Levy, R. Besserman, K. L. Wang, J. Shappir, and A. Sa’ar, “Thermal relaxation processes in Si1-xGex/Si quantum wells studied by intersubband and inter-valence band optical spectroscopy”, Physica E 7, 255 (2000) pdf
  80. B. Adoram, D. Krapf, M. Levy, R. Besserman, S. Thomas, K. L. Wang, J. Shappir, and A. Sa’ar, “Thermal relaxation processes probed by intersubband and intervalence-band transitions in Si/Si1-xGex multiple quantum wells”, Appl. Phys. Lett. 75, 2232 (1999) pdf
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