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.
New preprint on the development of MADna, an accurate coarse-grained model for structure and elasticity of double-stranded DNA
Big welcome to the new MSc students: Julia Rubio, Juan Zalvide, Antonio Bosch and Diego Alcón
Congratulations to Julia and Juan for successfully defending their BSc projects!
Welcome to Juan Luengo as a new PhD student! Great projects lay ahead!
LaCaixa Junior Leader & Marie Skłodowska-Curie Fellow
Condensed Matter Physics Center (IFIMAC) & Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid
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 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.
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.
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)
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)
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)
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)
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)
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)
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 )
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 )
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)
- 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)
- 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)
Curvature and bottlenecks control molecular transport in inverse bicontinuous cubic phases
S. Assenza and R. Mezzenga
J. Chem. Phys. 148,054902 (2018)
Shape of a Stretched Polymer
A. S. Sassi, S. Assenza* and P. De Los Rios
Phys. Rev. Lett. 119, 037801 (2017) ( *Corresponding Author )
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 )
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)
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 )
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)
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)
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)
Enhancement of cooperation in highly clustered scale-free networks
S. Assenza, J. Gómez-Gardeñes and V. Latora
Phys. Rev. E 78,017101 (2008)
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!
- Assenza and Mezzenga, J. Chem. Phys. 148:054902 (2018)
- Antognini, Assenza, Speziale and Mezzenga, J. Chem. Phys. 145:084903 (2016)
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
• Juan Luengo Márquez, PhD candidate, Universidad Autónoma de Madrid, Spain (ongoing)
• Eva Zunzunegui Bru, PhD candidate, ETH Zürich, Switzerland (ongoing - external Advisor)
• Juan Zalvide Pombo, MSc, Universidad Autónoma de Madrid, Spain (ongoing)
• Julia Rubio Loscertales, MSc, Universidad Autónoma de Madrid, Spain (ongoing)
• Antonio Bosch Fernández, MSc, Universidad Autónoma de Madrid, Spain (ongoing)
• Diego Alcón, MSc, Universidad Autónoma de Madrid, Spain (ongoing)
• Juan Zalvide Pombo, BSc, Universidad Autónoma de Madrid, Spain (ongoing)
• Julia Rubio Loscertales, BSc, Universidad Autónoma de Madrid, Spain (ongoing)
• Aarnau Martorell, MSc, Universidad Autónoma de Madrid, Spain (ongoing)
• Rodrigo Rosado del Castillo, BSc, Universidad Autónoma de Madrid, Spain (2019-2020)
• Paride Azzari, MSc, ETH Zürich, Switzerland (2017-2018)
• Luca Antognini, MSc, ETH Zürich & EPFL, Switzerland (2016-2017)
• Alberto Sassi, MSc, EPFL, Switzerland (2014-2015)