Soft Matter and Physics of Biopolymers

Welcome to our webpage! We are interested in the theoretical and computational study of soft matter systems, with a special interest in biopolymers. Go to the "People" tab to meet us! You can find out what we are working on by clicking on the "Research" tab or peeking at the publication list.

News

28 February 2024
Our work on the systematic analysis of sequence-dependent elasticity throughout various atomistic force fields is out in JCTC!

22 January 2024
Salvatore gives an invited talk at the CECAM workshop on "Modeling energy-consuming biomolecular processes" in the beautiful Lausanne!

09 January 2024
If you happen to be in Madrid on February 6th, you will have the chance to hear Enrico Carlon on DNA topology at multiple scales! Lots of fun, not to be missed! See here for details

04 January 2024
Within the RSEF biennial conference (15-19 July 2024 in Donostia), Linda Zotti and Salvatore organize a symposium on single-molecule studies of biomolecules and charge transfers through biosystems, aiming at fostering the interaction between these two communities. Stay tuned for more info!

15 December 2023
Congratulations to Juan for his well-deserved first prize “Chema Gómez” at the Young Investigators Meeting of Instituto Nicolás Cabrera! Ad Maiora!

30 September 2023
Check out the book chapter on molecular properties of RNA, where Salvatore has contributed with a discussion on its elasticity

26 September 2023
New preprint on a systematic comparison between the bsc0, bsc1 and OL15 modifications in predicting elastic properties of double-stranded DNA

14 September 2023
Great news! Salvatore is the recipient of a Ramón y Cajal Fellowship!

29 June 2023
Do not miss Juan (talk+poster) and Nerea (poster) presenting their projects at the annual congress of the Spanish Biophysical society!

25 April 2023
Great talk by Nerea on her work on A-tracts at the ABC conference in Ascona (Switzerland)!

5 April 2023
The results from a collaboration on curious features of lipidic phase diagrams in ionic liquids have just been published on the Journal of Colloid and Interface Science!

16 March 2023
New article on the force-dependent elastic constants of nucleic acids out in Nanoscale! Congratulations to Juan Luengo and all the authors!

08 February 2023
Our work on hydropathy and diffusion within lamellar mesophase has been published! Congratulations Antonio!

02 February 2023
Nerea and Juan present their projects at the J2IFAM conference!

Contact & Links

Research Interests



DNA Mechanics

DNA Mechanics

DNA carries all the information needed for survival and reproduction of a cell. This information is physically encoded by forming chains of nucleotides (A,C,G,T) in a specific order, thus obtaining a four-letters encoding string. The well-known double helix in which these chains are geometrically organized is far from being homogeneous. Experimental evidence shows indeed that the actual geometry locally deviates from an ideal double-helix, according to the sequence of the fragment under inspection. Thus, the composition of the DNA molecule is also reflected into its specific conformational features, which in turn evidence the presence of sequence- dependent elastic properties. These features play a key role in promoting or inhibiting the interaction with the protein machinery of the cell, thus ultimately affecting the epigenetic regulation of DNA and the emergence of diseases should such regulation fail.
Our current research line is focused on investigating the sequence-dependent mechanical properties of DNA and their role in biocellular processes. This will be achieved mainly by means of our coarse-grained model MADna, which provides an accurate sequence-dependent description of the elasticity and conformation of double-stranded DNA based on a recent extensive dataset of all-atom simulations.

Publications List

  1. Lipidic drug delivery systems: is the microbiome a cause for concern?
    J. Caukwell, S. Assenza, K. Hassan, B. Neilan, L. Salvati Manni and W.-K. Fong
    ChemRxiv (2023)

  2. Systematic comparison of atomistic force fields for the mechanical properties of double-stranded DNA
    C. Roldán-Piñero, J. Luengo-Márquez , S. Assenza* and R. Pérez
    J. Chem. Theory Comput. 20, 2261 (2024) ( *Co-corresponding Author )

  3. RNA multiscale simulations as an interplay of electrostatic, mechanical properties, and structures inside viruses
    S. Cruz-León, S. Assenza, S. Poblete and H. V. Guzman
    Book chapter in Physical Virology. Springer Series in Biophysics, vol 24 - Editors M. Comas-García and S. Rosales-Mendoza (2023)

  4. Unusual phosphatidylcholine lipid phase behavior in the ionic liquid ethylammonium nitrate
    L. Salvati Manni, C. Davies, K. Wood, S. Assenza, R. Atkin and G. G. Warr
    J. Coll. Interf. Sci. 643, 276 (2023)

  5. Force-dependent elasticity of nucleic acids
    J. Luengo-Márquez, J. Zalvide-Pombo, R. Pérez and S. Assenza
    Nanoscale 15, 6738 (2023)

  6. Interplay of Hydropathy and Heterogeneous Diffusion in the Molecular Transport Within Lamellar Lipid Mesophases
    A. M. Bosch and S. Assenza
    Pharmaceutics 15, 573 (2023)

  7. A novel fluorescent multi-domain protein construct reveals the individual steps of the unfoldase action of Hsp70
    S. Tiwari, B. Fauvet, S. Assenza, P. De Los Rios and P. Goloubinoff
    Nature Chem. Biol. 19, 198 (2023)

  8. Intermolecular forces at ice and water interfaces: Premelting, surface freezing, and regelation
    J. Luengo-Márquez, F. Izquierdo-Ruiz and L. G. MacDowell
    J. Chem. Phys. 157, 044704 (2022)

  9. Accurate sequence-dependent coarse-grained model for conformational and elastic properties of double-stranded DNA
    S. Assenza and R. Pérez
    J. Chem. Theory Comput. 18, 3239 (2022)

  10. Analytical theory for the crossover from retarded to non-retarded interactions between metal plates
    J. Luengo-Márquez* and L. G. MacDowell
    J. Phys.: Condens. Matter. 34, 275701 (2022) ( *Co-corresponding Author )

  11. Lifshitz theory of wetting films at three phase coexistence: The case of ice nucleation on Silver Iodide (AgI)
    J. Luengo-Márquez* and L. G. MacDowell
    J. Coll. Interf. Sci. 590, 527 (2021) ( *Co-corresponding Author )

  12. Enzymatic hydrolysis of monoacylglycerols and their cyclopropanated derivatives: Molecular structure and nanostructure determine the rate of digestion
    L. Salvati Manni, M. Duss, S. Assenza, B. J. Boyd, E. M. Landau and W.-K. Fong
    J. Coll. Interf. Sci. 588, 767 (2021)

  13. Interplay between confinement and drag forces determine the fate of amyloid fibrils
    K. B. Smith, M. Wehrli, A. Japaridze, S. Assenza, C. Dekker and R. Mezzenga
    Phys. Rev. Lett. 124, 118102 (2020)

  14. Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones
    S. Assenza, A. S. Sassi, R. Kellner, B. Schuler, P. De Los Rios and A. Barducci
    eLife 8, e48491 (2019)

  15. Six-fold director field configuration in amyloid nematic and cholesteric phases
    M. Bagnani, P. Azzari, S. Assenza and R. Mezzenga
    Sci. Rep. 9, 12654 (2019)

  16. Soft condensed matter physics of foods and macronutrients
    S. Assenza and R. Mezzenga
    Nature Reviews Physics 1, 551 (2019)
    (Click here to access it for free)

  17. Spatiotemporal Control of Enzyme‐Induced Crystallization Under Lyotropic Liquid Crystal Nanoconfinement
    J. J. Vallooran, S. Assenza and R. Mezzenga
    Angew. Chem. Int. Ed. 58, 7289 (2019)

  18. Impact of Molecular Partitioning and Partial Equilibration on the Estimation of Diffusion Coefficients from Release Experiments
    R. Ghanbari, S. Assenza*, P. Zueblin and R. Mezzenga
    Langmuir 35, 5663 (2019) ( *Co-first author )

  19. Soft biomimetic nanoconfinement promotes amorphous water over ice
    L. Salvati Manni, S. Assenza*, M. Duss, J. J. Vallooran, F. Juranyi, S. Jurt, O. Zerbe, E. M. Landau and R. Mezzenga
    Nat. Nanotechnology 14, 609 (2019) ( *Co-first author )

  20. The interplay of channel geometry and molecular features determines diffusion in lipidic cubic phases
    R. Ghanbari, S. Assenza and R. Mezzenga
    J. Chem. Phys. 150, 094901 (2019)

  21. Confinement‐Induced Ordering and Self‐Folding of Cellulose Nanofibrils
    K. B. Smith, J.‐N. Tisserant, S. Assenza, M. Arcari, G. Nyström and R. Mezzenga
    Adv. Sci. 6, 1801540 (2019)

  22. Efficient Asymmetric Synthesis of Carbohydrates by Aldolase Nano-Confined in Lipidic Cubic Mesophases
    T. Zhou, J. J. Vallooran, S. Assenza, A. Szekrenyi, P. Clapés and R. Mezzenga
    ACS Catal. 8, 5810 (2018)

  23. Curvature and bottlenecks control molecular transport in inverse bicontinuous cubic phases
    S. Assenza and R. Mezzenga
    J. Chem. Phys. 148,054902 (2018)
  24. Shape of a Stretched Polymer
    A. S. Sassi, S. Assenza* and P. De Los Rios
    Phys. Rev. Lett. 119, 037801 (2017) ( *Corresponding Author )
  25. Diffusion of Polymers through Periodic Networks of Lipid-Based Nanochannels
    R. Ghanbari, S. Assenza*, A. Saha and R. Mezzenga
    Langmuir 33,3491 (2017) ( *Co-first author )
  26. Quantifying the transport properties of lipid mesophases by theoretical modelling of diffusion experiments
    L. M. Antognini, S. Assenza, C. Speziale and R. Mezzenga
    J. Chem. Phys. 145,084903 (2016)
  27. Quantifying the role of chaperones in protein translocation by computational modeling
    S. Assenza*, P. De Los Rios and A. Barducci
    Front. Mol. Biosci. 2,8 (2015) ( *Co-corresponding Author )
  28. Universal Behavior in the Mesoscale Properties of Amyloid Fibrils
    S. Assenza, J. Adamcik, R. Mezzenga and P. De Los Rios
    Phys. Rev. Lett. 113, 268103 (2014)
  29. Emerging Meso- and Macroscales from Synchronization of Adaptive Networks
    R. Gutiérrez, A. Amann, S. Assenza, J. Gómez-Gardeñes, V. Latora, and S. Boccaletti
    Phys. Rev. Lett. 107, 234103 (2011)
  30. Emergence of structural patterns out of synchronization in networks with competitive interactions
    S. Assenza, R. Gutiérrez, J. Gómez-Gardeñes, V. Latora, and S. Boccaletti
    Sci. Rep. 1,99 (2011)
  31. Enhancement of cooperation in highly clustered scale-free networks
    S. Assenza, J. Gómez-Gardeñes and V. Latora
    Phys. Rev. E 78,017101 (2008)

Software Tools

Here you can find some tools that we developed. Click on the image of the tool to use it (in some cases, you will be redirected to a GitHub page). The tools can be freely used, and relevant references are listed for each of them. Please cite the appropriate articles if you use the tools in your research!
Structure of lipid mesophases
Structural info of mesophases
Diffusion in mesophase
Diffusion Coefficient in Water Channels
DNA Mechanics
Mechanically-accurate DNA (MADna)

IDP potential
IDP potential from this article

Open Positions

We always welcome inquiries from prospective PhD students or postdocs interested in joining us to pursue nice research projects. Get in touch to discuss possible funding opportunities offered by national and international programs.

Current Members

Group Picture

Click on the pictures for further info

Salvatore Assenza
Salvatore Assenza
Principal Investigator
Eva Zunzunegui
Eva Zunzunegui Bru
PhD Student
(@ETH Zürich, co-advised with R. Mezzenga)
Juan Luengo
Juan Luengo Márquez
PhD Student

Alumni

• Nerea Alcázar Cano, Postdoc (2022-2023)
• Sebastián Jiménez Millán, MSc (2022-2023)
• Diego José Craviotto Villegas, BSc (2022-2023)
• Carlos Díaz Alcón, BSc (2022-2023)
• Julia Rubio Loscertales, BSc (2020-2021) and MSc (2021-2022)
• Antonio Miguel Bosch Fernández, MSc (2021-2022)
• Diego Alcón Vela, MSc (2021-2022)
• Juan Zalvide Pombo, BSc (2020-2021)
• Aarnau Martorell, MSc (2020-2021)
• Rodrigo Rosado del Castillo, BSc (2019-2020)
• Paride Azzari, MSc (2017-2018)
• Luca Antognini, MSc (2016-2017)
• Alberto Sassi, MSc (2014-2015)

Present and Past Collaborators

Fernando Moreno
Fernando Moreno Herrero
Centro Nacional de Biotecnología - CSIC (Spain)
Laura Arriaga
Laura R. Arriaga
IFIMAC & Universidad Autónoma de Madrid (Spain)
Juan Aragonés
Juan Aragonés
IFIMAC & Universidad Autónoma de Madrid (Spain)
Pablo Ibañez
Pablo Ibañez
Universidad Autónoma de Madrid (Spain)
Pierre Goloubinoff
Pierre Goloubinoff
University of Lausanne (Switzerland)
Livia Salvati Manni
Livia Salvati Manni
The University of Sydney (Australia)
Khay Fong
Wye-Khay Fong
Monash University (Australia)
Raffaele Mezzenga
Raffaele Mezzenga
ETH Zürich (Switzerland)
Paolo De Los Rios
Paolo De Los Rios
EPFL (Switzerland)
Rubén Pérez
Rubén Pérez
IFIMAC & Universidad Autónoma de Madrid (Spain)
Alessandro Barducci
Alessandro Barducci
Centre de Biochimie Structurale de Montpellier (France)
Vito Latora
Vito Latora
Queen Mary, University of London (United Kingdom)
Jesús Gómez Gardeñes
Jesús Gómez Gardeñes
Universidad de Zaragoza (Spain)