Soft Matter and Physics of Biopolymers

Welcome to my personal webpage! I am interested in the theoretical and computational study of soft matter systems, with a special interest in biopolymers. My current research is focused on the sequence-dependent mechanical properties of DNA, which I will study as a Junior Leader Fellow supported by a fellowship from la Caixa Foundation (ID 100010434) and from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowoska-Curie grant agreement No 874648.

You can find out what I am working on by clicking on the "Research" tab or peeking at my publication list.

News

09 July 2020
Happy to share that by the end of the year I will join IFIMAC as a Junior Leader Fellow funded by la Caixa Foundation and the Marie Curie program!

20 March 2020
New article on the simultaneous action of force and confinement on amyloid fibrils is out on Physical Review Letters!

04 February 2020
The final version of our article on simulating the action of Hsp70 as unfoldase is finally out on eLife.

02 September 2019
New article on cholesteric liquid crystals under confinement just published on Scientific Reports!

24 July 2019
Our Review on the soft matter foundations of food macrocomponents is finally out in Nature Reviews Physics! You can access it for free clicking here


Contact & Links

Salvatore

Salvatore Assenza

Postdoctoral Researcher

Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid
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 have worked as a Postdoc (2019-2020) in the group led by Prof. Pérez at Universidad Autónoma de Madrid and IFIMAC. My project has been focused on the development of a coarse-grained model of double-stranded DNA which captures its mechanical properties and their dependence on sequence with precision comparable to atomistic simulations, but with the advantage of a significant speed-up in the simulation time.

Starting from the end of 2020, I will start my own research line at IFIMAC by pursuing the theoretical study of several biophysical and biocellular phenomena based on the sequence-dependent mechanical properties of DNA, supported by a Junior Leader Fellowship from la Caixa Foundation (ID 100010434) and from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowoska-Curie grant agreement No 874648.

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.
My current research line is focused on investigating the sequence-dependent mechanical properties of DNA and their role in biocellular processes. This will be achieved by developing a novel coarse-grained setup focused on such features and based on a recent extensive dataset of all-atom simulations.
This project will receive the support of a fellowship from la Caixa Foundation (ID 100010434) and from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowoska-Curie grant agreement No 874648.

Publication List

  1. 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)

  2. 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)

  3. 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)

  4. 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)

  5. 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)

  6. 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 )

  7. 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 )

  8. 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)

  9. 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)

  10. 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)

  11. Curvature and bottlenecks control molecular transport in inverse bicontinuous cubic phases
    S. Assenza and R. Mezzenga
    J. Chem. Phys. 148,054902 (2018)
  12. Shape of a Stretched Polymer
    A. S. Sassi, S. Assenza* and P. De Los Rios
    Phys. Rev. Lett. 119, 037801 (2017) ( *Corresponding Author )
  13. 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 )
  14. 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)
  15. 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) ( *Corresponding Author )
  16. 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)
  17. 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)
  18. 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)
  19. 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 I developed to facilitate analysis of experimental results on cubic phases. Click on the title of the tool to use it. 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!


This tool estimates the effective diffusion coefficient of a hydrophilic molecule within a cubic phase with known structural features, by following the analysis reported in Assenza et al. The basic assumption is that the diffusing particle is prevented to access the lipid bilayer by short-range hard repulsion. Moreover, a layer of water in proximity of the lipid heads is assumed to be tightly bound to the latter, thus significantly slowing down diffusion in this region. The needed input parameters are: the size of the lattice parameter, as measured by SAXS; the weight percentage of water used to produce the cubic phase; the density of the lipid; a reference value of the diffusion coefficient of the molecule in pure water (D0) at a given temperature (T0, it can be different than the temperature used in the experiment with the cubic phase); the working temperature of the experiment (Texp); the thickness of the layer of "bound water" in proximity of the lipid heads (good values usually lie between 0.6 nm and 1.2 nm, corresponding to a layer thickness equal to roughly two and four water molecules respectively). The outputs of the tool are the total fraction of bound water xb (i.e. # of bound water molecules divided by total # of water molecules) and the effective diffusion coefficient D. The default input values correspond to glucose diffusion in a Pn3m cubic phase based on monolinolein at 37 oC (Antognini et al.)

Relevant Literature:
- Assenza and Mezzenga, J. Chem. Phys. 148:054902 (2018)
- Antognini, Assenza, Speziale and Mezzenga, J. Chem. Phys. 145:084903 (2016)


Inputs
Lattice Parameter (nm):
Water (% weight):
Lipid Density (g/cm3):
D0 (10-5cm2/s):
T0 (oC):
Texp (oC):
w (nm):



Results
xb
?

D (10-5cm2/s)
?

Open positions

I always welcome inquiries from prospective PhD students or postdocs interested in joining me to pursue nice research projects. I will be happy to discuss possible funding opportunities offered by national and international programs.

Present and Past Collaborators

Rubén Pérez
Rubén Pérez
IFIMAC & Universidad Autónoma de Madrid (Spain)
Livia Salvati Manni
Livia Salvati Manni
The University of Sydney (Australia)
Khay Fong
Khay Fong
The University of Newcastle (Australia)
Giovanni Dietler
Giovanni Dietler
EPFL (Switzerland)
Raffaele Mezzenga
Raffaele Mezzenga
ETH Zürich (Switzerland)
Paolo De Los Rios
Paolo De Los Rios
EPFL (Switzerland)
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)
Chiara Speziale
Chiara Speziale
ETH Zürich (Switzerland)



Supervised and Co-supervised Students

• Alberto Sassi, MSc, EPFL (Switzerland)
• Luca Antognini, MSc, ETH Zürich & EPFL (Switzerland)
• Paride Azzari, MSc, ETH Zürich (Switzerland)
• Rodrigo Rosado del Castillo, BSc, Universidad Autónoma de Madrid (Spain)