Research Interests

Publications List

1. Conserved architecture of a functional lncRNA-protein interaction in the DNA damage response pathway
   S. Assenza, C. Blanco, C. Favard, J. Carnesecchi, M. Marcia and I. Chillón
   bioRxiv preprint (2025)
   


2. Hydrophilicity and topology interplay determines positioning of guest molecules in lipid cubic phases
   E. Zunzunegui-Bru, S. Assenza* and R. Mezzenga
   J. Coll. Interf. Sci. 702, 138802 (2026) ( *Co-corresponding Author )
   


3. Lipidic drug delivery systems are responsive to the human microbiome
   J. Caukwell, S. Assenza, K. A. Hassan, B. A. Neilan, A. J. Clulow, L. Salvati Manni and W.-K. Fong
   J. Coll. Interf. Sci. 677, 293 (2025)
   


4. Shape and size tunability of sheets of interlocked ring copolymers
   J. Luengo-Márquez*, S. Assenza and C. Micheletti
   Soft Matter 20, 6595 (2024) ( *Co-corresponding Author )
   


5. Universality in the Structure and Dynamics of Water under Lipidic Mesophase Soft Nanoconfinement
   E. Zunzunegui-Bru, S. R. Alfarano, P. Zueblin, H. Vondracek, F. Piccirilli, L. Vaccari, S. Assenza* and R. Mezzenga
   ACS Nano 18, 21376 (2024) ( *Co-corresponding Author )
   


6. Hierarchical Protofilament Intertwining Rules the Formation of Mixed-Curvature Amyloid Polymorphs
   J. Zhou, S. Assenza* , M. Tatli, J. Tian, I. M. Ilie, E. L. Starostin, A. Caflisch, T. P. J. Knowles, G. Dietler, F. S. Ruggeri, H. Stahlberg, S. K. Sekatskii and R. Mezzenga
   Adv. Sci. 11, 2402740 (2024) ( *Co-first Author )
   


7. 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 )
   


8. 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)
   


9. 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)
   


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


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


12. A 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)
    


13. 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)
    


14. 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)
    


15. 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 )
    


16. 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)
    


17. 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)
    


18. 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)
    


19. 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)
    


20. 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)
    


21. 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)
    


22. 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 )
    


23. 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
    Nature Nanotechnology 14, 609 (2019) ( *Co-first author )
    


24. 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)
    


25. 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)
    


26. 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)
    


27. Curvature and bottlenecks control molecular transport in inverse bicontinuous cubic phases
    S. Assenza and R. Mezzenga
    J. Chem. Phys. 148,054902 (2018)
    
28. Shape of a Stretched Polymer
    A. S. Sassi, S. Assenza* and P. De Los Rios
    Phys. Rev. Lett. 119, 037801 (2017) ( *Corresponding Author )
    
29. 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 )
    
30. 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)
    
31. 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 )
    
32. 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)
    
33. 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)
    
34. 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)
    
35. 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

Structural info of mesophases

Diffusion Coefficient in Water Channels

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!

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

Click on the pictures for further info

Salvatore Assenza

Principal Investigator

Módulo 5 (Office 501), Facultad de Ciencias, C/ Francisco Tomás y Valiente 7, 28049 Madrid (Spain)

I grew up in the cozy city of Modica, part of a UNESCO Heritage Site in the southmost part of Sicily (you may want to check it out for your next vacation, it will be a wonderful experience for both your eyes and your tummy!)

I carried out my undergraduate studies in Physics at the University of Catania, where I obtained my BSc (2008) and MSc Degrees (2010). In parallel, I attended Scuola Superiore di Catania, an excellence center within University of Catania where, after a competitive selection based on written and oral exams, 20 students selected within the whole University (independently of the discipline) receive a scholarship for the whole duration of their studies and attend additional courses aimed at boosting an early start of their research activity. This was the spark for my interest in a career as a researcher, as I had the possibility to interact with Prof. Latora and Prof. Gómez, with whom I pursued a prolific investigation vein on evolutionary dynamics and synchronization in Complex Networks.

This interest in complexity brought me to start a PhD in Physics (2011-2015) at EPF Lausanne supervised by Prof. De Los Rios and Dr. Barducci. There, I studied biomolecular systems under the lens provided by polymer physics, with focus on amyloid fibrils and molecular chaperones, and learned the foundations of soft matter and molecular simulations.

This background was extremely useful for my subsequent Postdoctoral experience (2015-2018) as a theorist in the group of experimentalists led by Prof. Mezzenga at ETH Zürich. There, I have reinforced my view that theory and experiment have a lot to earn, and learn, from a continuous interchange of views, as can be seen from my scientific production in this period. At ETH, I focused mainly on lipid-based mesophases, a class of materials apt for drug-delivery purposes. Such applications need a thorough understanding of the molecular diffusion within mesophases, which I have put on solid theoretical bases by providing both a theoretical framework to analyze experiments and simulation-based predictions in agreement with experiments, which enabled developing a tool to estimate the diffusion coefficient of a molecule within cubic phases from the knowledge of their structure. Apart from this main investigation line, I also worked actively in other soft-matter systems, such as amyloid-based cholesteric liquid crystals and cellulose nanofibrils.

Later, I was a Postdoc (2019-2020) in the group led by Prof. Pérez at Universidad Autónoma de Madrid and IFIMAC, where I worked on the microscopical origin of the mechanical properties of DNA, with focus on their sequence dependence.

Starting from the end of 2020, I am pursuing my own research line at IFIMAC focused on the theoretical study of several biophysical and biocellular phenomena. I have been first supported by a Junior Leader Fellowship from la Caixa Foundation jointly with the Marie Skłodowoska-Curie program (2020-2023). Since January 2024, I am counting on the support of the Spanish Agency for Research as a Ramón y Cajal Fellow.

Juan Luengo Márquez

PhD Student

Módulo 8 (Office 401-3), Facultad de Ciencias, C/ Francisco Tomás y Valiente 7, 28049 Madrid (Spain)

I studied a Bachelor's degree in Chemistry at the Complutense University of Madrid, where I specialized in Physical Chemistry. Afterwards, I studied the Master's degree in Condensed Matter Physics and Biological Systems at the Autónoma University of Madrid. During this period, my research interests channeled towards Statistical Physics, Thermodynamics, Computer Simulations, and Soft Matter Physics in general.

From 2018 to 2021, starting with my Bachelor's thesis, I carried out my research under the supervision of Prof. Luis G. MacDowell (Complutense U.), within the framework of the theoretical exploitation of the Lifshitz theory of the van der Waals forces.

From the beginning of 2021, I joined Dr. Salvatore Assenza's group, under whose supervision I develop my PhD thesis on the investigation of the mechanical properties of nucleic acids through Molecular Dynamics simulations and theoretical methods.

Currently, I am a member of the Instituto Nicolás Cabrera, and since early 2022, I earned a position as non-doctor assistant professor at the Department of Theoretical Condensed Matter Physics of the Autónoma University of Madrid.

Finally, my broadly neglected hobbies include classical literature, playing basketball, and blundering at chess.

Jorge García Inglés

PhD Student

Módulo 5 (Office 200-1), Facultad de Ciencias, C/ Francisco Tomás y Valiente 7, 28049 Madrid (Spain)

I hold a BSc in Physics and an MSc in Nanotechnology from Universidad Autónoma de Madrid, where I conducted research on electron transport in organic molecules and thermoelectric transport in inorganic semiconductors. Now, as a PhD student, my focus is on exploring electron transport in protein systems by combining molecular dynamics with electronic structure methods. Outside of work, you'll likely find me playing chess or doing anything sports-related.

Yago Casado Molinero

PhD Student

Módulo 5 (Office XXX), Facultad de Ciencias, C/ Francisco Tomás y Valiente 7, 28049 Madrid (Spain)

I studied a Bachelor's degree in Physics at the Complutense University of Madrid. During my final year, I was introduced to the world of molecular dynamics and, in particular, to active matter systems such as Active Brownian Particles (ABP) and Run-and-Tumble Particles (RTP). I found it fascinating how complex behaviors emerge from seemingly simple systems, and how simulations can provide deep insights into their dynamics. This was a completely new field for me, but one that immediately captured my interest due to its versatility and potential for future applications. Motivated by this discovery, I pursued a Master's degree in Condensed Matter Physics and Biological Systems, where I carried out my Master's thesis on the mechanical properties of the molecular chaperone Hsp70, an experience that allowed me to explore the physical principles underlying biological systems using quantitative and theoretical tools. Currently, I am doing my PhD focused on developing a theoretical framework to understand the behavior of metal-organic and covalent-organic frameworks (MOFs and COFs) and their potential applications in water purification, particularly in drug filtration; my research is part of a collaborative project with a large experimental group, where we will provide the theoretical support. In parallel, I continue to work on the mechanical properties of DNA.

Teaching Notes

These notes are licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License

Soft Matter and Physics of Biological Systems for the Master in Physics of Condensed Matter and Biological Systems at Universidad Autónoma de Madrid, Spain (2024-2025)

Thermodynamics
Statistical Mechanics
Simple applications of Statistical Mechanics
Van der Waals forces
Electrostatics in liquids
DLVO
Polymer Physics
Molecular transport
Law of mass action

Present and Past Collaborators