Structural dynamics of aqueous solutions (SDAQS)

Publications list

2023

Coherent X-ray Scattering Reveals Nanoscale Fluctuations in Hydrated Proteins
M. Bin, M. Reiser, M. Filianina, S. Berkowicz, S. Das, S. Timmermann, W. Roseker, R. Bauer, J. Öström, A. Karina, K. Amann-Winkel, M. Ladd-Parada, F. Westermeier, M. Sprung, J. Möller, F. Lehmkühler, C. Gutt, F. Perakis
arXiv:2301.11043 [cond-mat.soft] (2023)

Melting Domain Size and Recrystallization Dynamics of Ice Revealed by Time-Resolved X-ray Scattering
Ch. Yang, M. Ladd-Parada, K. Nam, S. Jeong, S. You, A. Späh, H. Pathak, T. Eklund, T. J. Lane, J. H. Lee, I. Eom, M. Kim, K. Amann-Winkel, F. Perakis, A. Nilsson, and K. H. Kim
arXiv:2302.03368 [physics.chem-ph] (2023)

Liquid-liquid phase separation in supercooled water from ultrafast heating of low-density amorphous ice
K. Amann-Winkel, K. H. Kim, N. Giovambattista, M. Ladd-Parada, A. Späh, F. Perakis, H. Pathak, C. Yang, T. Eklund, T. J. Lane, S. You, S. Jeong, J. Hyuk Lee, I. Eom, M. Kim, J. Park, S. Hwan Chun, P. H. Poole, and A. Nilsson
Nature Commun. 14, 442 (2023)

2022

Nanofocused x-ray photon correlation spectroscopy
S. Berkowicz, S. Das, M. Reiser, M. Filianina, M. Bin, G. Crevatin, F. Hennies, C. Weninger, A. Björling, P. Bell, and F. Perakis,
Phys. Rev. Res., 4, L032012 (2022)

Resolving molecular diffusion and aggregation of antibody proteins with megahertz X-ray free-electron laser pulses
M. Reiser*, A. Girelli, A. Ragulskaya, S. Das, S. Berkowicz, M. Bin, M. Ladd-Parada, M. Filianina, H.-F. Poggemann, N. Begam, M. S. Akhundzadeh, S. Timmermann, L. Randolph, Y. Chushkin, T. Seydel, U. Boesenberg, J. Hallmann, J. Möller, A. Rodriguez-Fernandez, R. Rosca, R. Schaffer, M. Scholz, R. Shayduk, A. Zozulya, A. Madsen, F. Schreiber, F. Zhang, F. Perakis* and C. Gutt* [*corresponding authors]
Nature Commun. 13, 5528 (2022)

Atom-Specific Probing of Electron Dynamics in an Atomic Adsorbate by Time-Resolved X-ray Spectroscopy
S. Schreck, E. Diesen, M. Dell'Angela, C. Liu, M. Weston, F. Capotondi, H. Ogasawara, J. LaRue, R. Costantini, M. Beye, P. S. Miedema, J. H. Stenlid, J. Gladh, B. Liu, H. Wang, F. Perakis, F. Cavalca, S. Koroidov, P. Amann, E. Pedersoli, D. Naumenko, I. Nikolov, L. Raimondi, F. Abild-Pedersen, T. F. Heinz, J. Voss, A. C. Luntz, A. Nilsson
Phys. Rev. Lett. 129, 276001 (2022)

Symmetry-resolved CO desorption and oxidation dynamics on O/Ru(0001) probed at the C K-edge by ultrafast X-ray spectroscopy
J. LaRue, B. Liu, G. L. S. Rodrigues, C. Liu, J. A. Garrido Torres, S. Schreck, E. Diesen, M. Weston, H. Ogasawara, F. Perakis, M. Dell'Angela, F. Capotondi, D. Ball, C. Carnahan, G. Zeri, L. Giannessi, E. Pedersoli, D. Naumenko, P. Amann, I. Nikolov, L. Raimondi, C. Spezzani, M. Beye, J. Voss, H. Y. Wang, F. Cavalca, J. Gladh, S. Koroidov, F. Abild-Pedersen, M. Kolb, P. S Miedema, R. Costantini, T. Heinz, A. Luntz, L. G.M. Pettersson, and A. Nilsson
J. Chem. Phys. 157, 164705 (2022)

Using Coherent X-rays to Follow Dynamics in Amorphous Ices
M. Ladd-Parada, H. Li, A. Karina, K. H.n Kim, F. Perakis, M. Reiser, F. Dallari, N. Striker, M. Sprung, F. Westermeier, G. Grübel, A. Nilsson, F. Lehmkühler, K. Amann-Winkel
Environ. sci. Atmos. 2, 1314-1323 (2022)

Following the Crystallization of Amorphous Ice after Ultrafast Laser Heating
M. Ladd-Parada, K. Amann-Winkel, K. H. Kim, A. Späh, F. Perakis, H. Pathak, C. Yang, D. Mariedahl, T. Eklund, T. J. Lane, S. You, S. Jeong, M. Weston, J. H. Lee, I. Eom, M. Kim, J. Park, S. H. Chun, and A. Nilsson
J. Phys. Chem. B, 126, 11 (2022)

2021

Exploring the validity of the Stokes-Einstein relation in supercooled water at nanometer length scales using nanomolecular probes
S. Berkowicz and F. Perakis
Phys. Chem. Chem. Phys., 23, 25490 (2021)

Wide-angle X-ray scattering and molecular dynamics simulations of supercooled protein hydration water
M. Bin, R. Yousif, S. Berkowicz, S. Das, D. Schlesinger, and F. Perakis
Phys. Chem. Chem. Phys. 23, 18308-18313 (2021)

Analysis Strategies for MHz XPCS at the European XFEL
F. Dallari, M. Reiser, I. Lockteva, A. Jain, J. Möller, M. Scholz, A. Madsen, G. Grübel, F. Perakis, F. Lehmkühler
Appl. Sci., 11, 8037 (2021)

Anomalous temperature dependence of the experimental x-ray structure factor of supercooled water
N. Esmaeildoost, H. Pathak, A.Späh, T. J. Lane, K. H. Kim, C. Yang, K. Amann-Winkel, M. Ladd-Parada, F. Perakis, J. Koliyadu, A. R. Oggenfuss, P. J. M. Johnson, Y.Deng, S. Zerdane, R. Mankowsky, P. Beaud, H. T. Lemke, A. Nilsson and J. A. Sellberg
J. Chem. Phys. 155, 214501 (2021)

Long-Range Structures of Amorphous Solid Water
H. Li, A. Karina, M. Ladd-Parada, A. Späh, F. Perakis, C. Benmore, and K. Amann-Winkel
J. Phys. Chem. B 125, 13320–13328 (2021)

Ultrafast adsorbate excitation probed with sub-ps resolution x-ray absorption spectroscopy
E. Diesen, H. Wang, S. Schreck, M. Weston, H. Ogasawara, J. LaRue, F. Perakis, M. Dell’Angela, F. Capotondi, L. Giannessi, E. Pedersoli, D. Naumenko, I. Nikolov, L. Raimondi, C. Spezzani, M. Beye, F. Cavalca, B. Liu, J. Gladh, S. Koroidov, P. S. Miedema, R. Costantini, T. F. Heinz, F. Abild-Pedersen, J. Voss, A. C. Luntz, A. Nilsson
Phys. Rev. Lett. 127, 016802 (2021)

Enhancement and maximum in the isobaric specific-heat capacity measurements of deeply supercooled water using ultrafast calorimetry
H. Pathak, A. Späh, N. Esmaeildoost, J. A. Sellberg, K. H. Kim, F. Perakis, K. Amann-Winkel, M. Ladd-Parada, J. Koliyadu, T. J. Lane, C. Yang, H. T. Lemke, A. R. Oggenfuss, J. M. Johnson, Y. Deng, S. Zerdane, R. Mankowsky, P. Beaud, A. Nilsson
Proc. Natl. Acad. Sci., 118, e2018379118 (2021)

2020

Experimental observation of the liquid-liquid transition in bulk supercooled water under pressure
K. H. Kim, K. Amann-Winkel, N. Giovambattista, A. Späh, F. Perakis, H. Pathak, M. Ladd Parada, C. Yang, D. Mariedahl, T. Eklund, T. J. Lane, S. You, S. Jeong, M. Weston, J. H. Lee, I. Eom, M. Kim, J. Park, S. Hwan Chun, P. H. Poole and A. Nilsson
Science, 270, 978-982 (2020)

Towards molecular movies with X-ray Photon Correlation Spectroscopy
F. Perakis and C. Gutt
Phys. Chem. Chem. Phys., 22, 19443-19453 (2020)

Anisotropic X-ray Scattering of Transiently Oriented Water
K. H. Kim, A. Späh, H. Pathak, C. Yang, S. Bonetti, K. Amann-Winkel, D. Mariedahl, D. Schlesinger, J. A. Sellberg, D. Mendez, G. van der Schot, H. Y. Hwang, J. Clark, O. Shigeki, T. Tadashi, Y. Harada, H. Ogasawara, T. Katayama, A. Nilsson, and F. Perakis
Phys. Rev. Lett. 125, 076002 (2020)

Brine rejection and crystallite formation upon freezing NaCl aqueous solutions
I. Tsironi, D. Schlesinger, A. Späh, L. Erikssonr M. Segad, F. Perakis
Phys. Chem. Chem. Phys. 22, 7625-7632 (2020)

Time-Resolved Observation of Transient Precursor State of CO on Ru(0001) Using Carbon K-edge spectroscopy
H. Wang, S. Schreck, M. Weston, C. Liu, H. Ogasawara, J. LaRue,F. Perakis, M. Dell’Angela, F.Capotondi, L.Giannessi, E.Pedersoli, N.Naumenko, I.P. Nikolov, L.Raimondi, C.Spezzani, M.Beye, F. Cavalca, B.Liu, J.Gladh, S.Koroidov, P.Miedema, R.Costantini, L.G.M. Pettersson and A. Nilsson
Phys. Chem. Chem. Phys., 22, 2677-2684 (2020)

2019

Temperature Dependent Anomalous Fluctuations in Water: Shift of 1 kbar Between Experiment and Classical Force Field Simulations
H. Pathak, A. Späh, K. Amann-Winkel, F. Perakis, K. H. Kimand A. Nilsson
Molecular Physics, 117, 3232-3240 (2019)

X-ray Studies of the Transformation from High-to Low-density Amorphous Water
D. Mariedahl, F. Perakis, A. Späh, H. Pathak, K. Hwan Kim, C. Benmore, A. Nilsson, K. Amann-Winkel
Philos. Trans. Royal Soc. A, 377, 20180164 (2019)

Apparent Power-law behavior of water’s isothermal compressibility and correlation length upon supercooling
A. Späh, H. Pathak, K. H.Kim, F. Perakis, D.Mariedahl, K. Amann-Winkel, J. A. Sellberg, J. H. Lee, S.Kim, J. Park, K. H. Nam, T.Katayama, and A. Nilsson
Phys. Chem. Chem. Phys, 21, 26-31 (2019)

2018

Coherent X-rays reveal the influence of cage effects on ultrafast water dynamics
F. Perakis, G. Camisasca, T. J. Lane, A. Späh, K. T.Wikfeldt, J. A. Sellberg, F. Lehmkühler, H. Pathak, K. H. Kim, K. Amann-Winkel, S. Schreck, S. Song, T. Sato, M. Sikorski, A. Eilert, T. McQueen, H. Ogasawara, D. Nordlund, W. Roseker, J. Koralek, S. Nelson, P. Hart, R. Alonso-Mori, Y. Feng, D. Zhu, A. Robert, G. Grübel, L. G. M. Pettersson, and A. Nilsson
Nature Comm., 9, 1917 (2018)

X-ray scattering and O-O pair correlation function of amorphous ices
D. Mariedahl, F. Perakis, A. Späh, H. Pathak, K. Hwan Kim, G. Camisasca, D. Schlesinger, C.Benmore, L.Pettersson, A. Nilsson, and K. Amann-Winkel
J. Phys. Chem. B, 122, 7616–7624 (2018)

Atom-Specific activation in CO Oxidation
S. Schreck, E. Diesen, J. LaRue, H. Ogasawara, K. Marks, D. Nordlund, M. Weston, M.Beye, F. Cavalca, F. Perakis, J. Sellberg, A. Eilert, K. H. Kim, G. Coslovich, R. Coffee, J. Krzywinski, A. Reid, S. Moeller, A. Lutman, H. Öström, L. G. M. Pettersson, and A. Nilsson
J. Chem. Phys. 149, 234707 (2018)

Response to Comment: Maxima in the Thermodynamic Response and Correlation Functions of Deeply Supercooled Water
K.H. Kim, A. Späh, H. Pathak, F. Perakis, D.Mariedahl, K. Amann-Winkel, J. A. Sellberg, J. H. Lee, S.Kim, J.Park, K. H. Nam, T. Katayama, and A. Nilsson
Science, 360, eaat1729 (2018)

2017

Diffusive dynamics during the high-to-low density transition in amorphous ice
F. Perakis, K. Amann-Winkel, F. Lehmkühler, M. Sprung, D. Mariedahl, J. A. Sellberg, H. Pathak, A. Späh, F. Cavalca, D. Schlesinger, A. Ricci, A. Jain, B. Massani, F. Aubree, C. J. Benmore, T. Loerting, G. Grübel, L. G. M. Pettersson and A. Nilsson
Proc. Natl. Acad. Sci., 114, 8193 (2017)

Maxima in the Thermodynamic Response and Correlation Functions of Deeply Supercooled Water
K.H. Kim, A. Späh, H. Pathak, F. Perakis, D.Mariedahl, K. Amann-Winkel, J. A. Sellberg, J. H. Lee, S.Kim, J.Park, K. H. Nam, T. Katayama, and A. Nilsson
Science, 358, 1589 (2017)

Temperature-Independent Nuclear Quantum Effects on the Structure of Water
K. H.Kim, H. Pathak, A. Späh, F. Perakis, D. Mariedahl, J. A. Sellberg, T. Katayama, Y. Harada, H. Ogasawara, L.G.M. Pettersson, and A. Nilsson
Phys. Rev. Lett., 119, 075502 (2017)

2016 and earlier

Vibrational Spectroscopy and Dynamics of Water
F. Perakis, L.D. Marco, A. Shalit, F. Tang, Z.R. Kann, T.D. Kühne, R. Torre, M. Bonn, and Y. Nagata
Chemical Reviews, 116, 7590 (2016)

Probing water with X-ray lasers
A.Nilsson, S. Schreck, F. Perakis, L.G.M Pettersson
Advances in Physics: X, 1, 226 (2016)

Small-world networks of optical fiber lattices
F. Perakis, M. Mattheakis and G.P. Tsironis
J. Optics, 16, 102003 (2014)

Testing for memory-free spectroscopic coordinates by 3D IR exchange spectroscopy
J. Borek, F. Perakis and P. Hamm
Proc. Natl. Acad. Sci., 111, 10462 (2014)

Disorder-suppressed vibrational relaxation in vapor-deposited high-density amorphous ice
A. Shalit, F. Perakis and P. Hamm
J. Chem. Phys., 140, 151102 (2014)

Three-dimensional infrared spectroscopy of isotope-diluted ice Ih
F. Perakis, J. Borek and P. Hamm
J. Chem. Phys., 136, 014501 (2013)

Two-dimensional infrared spectroscopy of isotope-diluted low density amorphous ice
A. Shalit, F. Perakis and P. Hamm
J. Phys. Chem. B, 117, 15512 (2013)

Erratum: “Azide–water intermolecular coupling measured by two-color two-dimensional infrared spectroscopy” [J. Chem. Phys. 136, 224503 (2012)]
J. Borek, F. Perakis,F. Kläsi, S. Garrett-Roe, P. Hamm
J. Chem. Phys., 137, 069902 (2012)

Azide-water intermolecular coupling measured by 2-color 2D-IR spectroscopy
J. Borek, F. Perakis, F. Klasi, S. Garrett-Roe and P. Hamm
J. Chem. Phys., 136, 224503 (2012)

Ultrafast Dynamics of liquid water and ice (Invited Contribution)
F. Perakis and P. Hamm
Chimia, 66, 244 (2012)

Two-dimensional infrared spectroscopy of neat ice Ih
F. Perakis and P. Hamm
Phys. Chem. Chem. Phys., 14, 6243 (2012)

Two-dimensional infrared spectroscopy of isotope-diluted ice Ih
F. Perakis, S. Widmer and P. Hamm
J. Chem. Phys., 134, 204505 (2011)

Two-Dimensional Infrared Spectroscopy of Supercooled Water
F. Perakis and P. Hamm
J. Phys. Chem. B, 115, 5289175293 (2011)

Three-Dimensional Infrared Spectroscopy of Isotope-Substituted Liquid Water Reveals Heterogeneous Dynamics
S. Garrett-Roe, F. Perakis, F. Rao and P. Hamm
J. Phys. Chem. B, 115, 6976176984 (2011)

Discrete Nonlinear Schrödinger equation in complex networks
F. Perakis and G.P. Tsironis
Phys. Lett. A, 375, 676 (2011)

Theses

The Role of Molecular Heterogeneity in the Structural Dynamics of Aqueous Solutions
Sharon Berkowicz Licentiate thesis, Stockholm University (2022)

Exploring the dynamic properties of apoferritin in aqueous solutions under crowded conditions
Huiting Huang Bachelor thesis, Stockholm University (2022)

Unveiling structural heterogeneities in aqueous solutions using dynamic light scattering
Oskar Eklund, Bachelor thesis, Stockholm University (2021)

Investigation on liquid-liquid phase separation of lysozyme by dynamic light scattering
H.-F. Poggemann, Master thesis, Stockholm University (2021)

Investigating the role of water in the protein dynamic transition
M. Bin, Master thesis, Stockholm University (2020)

Investigating the influence of water in lysozyme structure and dynamics using FT-IR and XRD
R. Yousif, Bachelor thesis, Stockholm University (2019)

Hydrogen Bond Dynamics of Water Below Freezing Point
F. Perakis, Ph.D. thesis, University of Zurich (2014)

Book chapters

X-ray Studies of Water
A. Nilsson and F. Perakis
Synchrotron Light Sources and Free-Electron Lasers, 1935-1988
Springer, ISBN 978-3-030-23201-6 (2019)

Chemical Dynamics in Liquid Water and at Catalytic Surfaces
H. Ogasawara, F. Perakis and A. Nilsson
X-Ray Free Electron Lasers Applications in Materials, Chemistry and Biology, 187-200
Edited by Uwe Bergmann, Vittal Yachandra and Junko Yano, ISBN 9781849731003 (2017)