Publications

Publications

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  1. 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
  2. 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. (accepted, 2024) preprint
  3. 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
  4. 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
  5. A. Pacheco-Pozo and D. Krapf, “Fractional Brownian motion with fluctuating diffusivities” Phys. Rev. E 110, 014105 (2024) pdf
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. C. Dieball, D. Krapf, M. Weiss, A. Godec, “Scattering fingerprints of two-state dynamics”, New. J. Phys.  24, 023004 (2022) pdf
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. M. Hedayati, M.J. Kipper, and D. Krapf, “Anomalous protein kinetics on low-fouling surfaces”, Phys. Chem. Chem. Phys. 22, 5264 (2020) preprint, SM
  30. 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
  31. D. Krapf and R. Metzler, “Strange interfacial molecular dynamics”, Physics Today 72, 9, 48 (2019) pdf
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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.
  37. D.S. Grebenkov and D. Krapf, “Steady-state reaction rate of diffusion-controlled reactions in sheets”, J. Chem. Phys. 149, 064117 (2018)  pdf
  38. G. Sikora, A. Wyłomańska, and D. Krapf, “Recurrence statistics for anomalous diffusion regime change detection”, Comput. Stat. Data Anal. 128, 380 (2018) pdf
  39. 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
  40. D. Krapf, “Compartmentalization of the plasma membrane”, Current Opinion in Cell Biology 53, 15 (2018) pdf
  41. 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
  42. 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
  43. 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
  44. 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.
  45. 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.
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  46. 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
  47. 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
  48. 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
  49. 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
  50. 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.
  51. 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
  52. D. Krapf, “Mechanisms underlying anomalous diffusion in the plasma membrane”, Current Topics in Membranes  75, 167 (2015) pdf
  53. 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
  54. 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
  55. 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
  56. 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
  57. D. Krapf, “Nonergodicity in nanoscale electrodes”, Phys. Chem. Chem. Phys. 15, 459 (2013) pdf
  58. 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
  59. 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
  60. 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.
  61. 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.
  62. 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
  63. T. Wojcik and D. Krapf, “Solid-state nanopore recognition and measurement using Shannon entropy”, IEEE Photonics J. 3, 337 (2011) pdf, MATLAB codes
  64. 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
  65. 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
  66. 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
  67. 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
  68. 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
  69. 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
  70. 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
  71. 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
  72. 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
  73. 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
  74. 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
  75. 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
  76. 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
  77. 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
  78. 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
  79. 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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