Salvatore Assenza - Soft Matter and Physics of Biopolymers

Home
Research
Publications
Tools
People
Teaching
Collaborators

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. Our current research is focused on the sequence-dependent mechanical properties of DNA, supported by a Junior Leader Fellowship from la Caixa Foundation and the Marie Skłodowoska-Curie COFUND action.

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

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!

16 December 2022
New preprint of the SMPB lab on the role of hydropathy on diffusion in lamellar mesophases, led by former MSc student Antonio Bosch!

10 October 2022
New cohort of undergraduate students at the SMPB lab: BSc students Diego Craviotto and Carlos Díaz, and MSc student Sebastián Jiménez. A big welcome!

13 September 2022
How do the elastic constants of nucleic acids change under mechanical stress? Have a look at the new preprint of the SMPB lab, great job led by Juan Luengo and our former BSc student Juan Zalvide!

04 September 2022
A first version of MADnaLAB is online, kudos to our strict collaborator Pablo Ibañez for enabling simulations with MADna on GPUs! Documentation and presenting article are in the oven!

01 August 2022
New paper on the forces at interfaces between ice and water stemming from Juan's Master Thesis. Congratulations to both Juan and his MSc tutor Luis MacDowell!

01 July 2022
A big welcome to Nerea Alcázar, who has joined the SMPB group as a Postdoctoral Researcher! Looking forward to a lot of interesting science!

21 June 2022
Juan and Salvatore presented the work of the group at the 8th Iberian Biophysics Congress. Congratulations to Juan for obtaining the prize for the best Poster presentation!

13 April 2022
Juan's paper accepted on J. Phys. Cond. Matter! Check out the theory on retardation effects in Van der Waals interactions between surfaces.

8 April 2022
Our paper on the development of MADna is finally out on JCTC! Check out the tools for its implementation in LAMMPS.

Contact & Links

Research Interests

DNA Mechanics

Other Research Interests

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.
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.

Lipidic Mesophases

Lipidic mesophases are interesting objects obtained by mixing water and lipids in suitable proportions. Depending on the specific details of the lipids employed as well as on lipid concentration and temperature, mesophases with different microscopic structures are obtained, including arrangements as hexagonal, lamellar and cubic phases. Lipidic mesophases are at the center of intense research due to many different applications, most of which are based on the molecular transport within these systems (see our recent review for more info). Our research on the topic is focused on understanding the interplay between structure and transport, with the goal of providing a reliable theoretical framework for devising related applications with tailored properties.
For example, in a paper we have provided the necessary theoretical framework to analyze the results of the so-called diffusion setup. Comparison of the theoretical predictions against experimental data from systems with known features shows an excellent quantitative agreement without any adjustable parameter, thus appointing our theory as a reliable tool for data analysis. In another work, by combining theory and experiments we showed that polymer diffusion within cubic mesophases can be regulated by as many as three different mechanisms, reminescent of Zimm, Rouse and reptation dynamics.
More recently, we have studied how the nanostructure of cubic phases affects diffusion by Brownian Dynamics simulations. Our results show that the effective diffusion coefficient is regulated by a subtle interplay between curvature and bottlenecks of the network of water channels. Moreover, comparison with experiments enables assessing the amount of immobilized water starting from the theoretical prediction. The results from this study can be used by experimental researchers to estimate the diffusion coefficient of a molecule diffusing within a cubic phase of interest. To ease such application, you can find here a tool that computes the effective diffusion coefficient starting from the structural parameters of the cubic phase.
Lipidic Cubic Phases also provide good environments for enzymatic reactions. For example, we have studied how the activity of the enzyme aldolase is enhanced when within a cubic phase and, based on the known structure of the enzyme and of mesophases, we suggested a microscopic picture of how such an enhancement can be achieved. The level of confinement as well as the nontrivial mobility features of water in nanochannels qualitatively and quantitatively affect the features of the enzymatic products (have a look at this article), providing useful tools for related applications, e.g. as biomarkers.
Lipid Phases further enable studying the mutual effect of water and lipids under nanoconfinement with biological relevance. Having disordered lipid phases can prevent water crystallization down to very low temperature , thus suggesting a possible mechanism of life survival at subzero temperatures.

Biomolecular Systems

Armed with the tools provided by polymer theory and soft matter, I am interested in providing physically-sound descriptions of biomolecular systems. Our research to date has been focused on two systems, namely amyloid fibrils and molecular chaperones.
Amyloid fibrils are proteinaceous aggregates first identified in neurodegenerative diseases such as Alzheimer's or Parkinson's, although they are now being investigated for biotechnological applications. In a work, we have studied their periodic properties at length scales of tens to hundreds of nanometers, which show universal features independently of the building blocks.
Molecular chaperones are proteins whose role in the cell is, loosely speaking, help out other proteins. Among them, the heat-shock protein Hsp70 is a versatile tool, as it has been shown to be involved in many cellular processes such as protein import into organelles, aid in folding out of ribosomes, prevention of misfolding or help in dissociating protein complexes. We are interested in giving a microscopic explanation and quantification to these tasks, based on coarse-grained molecular dynamics simulations. In a work, we have determined the effective thermodynamic force exerted by Hsp70 in protein import and outlined its essential role to achieve complete translocation in time windows compatible with the cell cycle. Combininig our coarse-grained simulations with a biochemical network model, we further studied the molecular details of the action of Hsp70 as unfoldase, a key role aimed at preventing protein misfolding and aggregation. Our numerical results were in quantitative agreement with experiments and provided a clear picture of this process, stressing the central role played by ATP consumption.

Polymers and Soft Matter Physics

Our research on polymer-based systems mostly deals with polymers at the single-molecule level, where we are interested in understanding the properties of polymers in dilute solutions or under the action of a pulling force, which is both of fundamental interest and important to quantify the action of biopolymers in vivo. For example, together with collaborators at EPFL we showed the existence of universal features in both the shape and orientation of stretched polymers, independently of the particular microscopic details. In another work with ETH and Delft University researchers, we have studied the effect of simultaneous application of a pulling force and nanoconfinement, using amyloid fibrils as a model system.
Amyloid fibrils can also be employed to study the physics of liquid crystals. For instance, we have employed these biopolymers to study the effect of nanoconfinement on cholesteric liquid crystals, finding as many as six different phases depending on the volume of the droplet under study.

Complex Networks

A very useful way to represent systems composed by many interacting units is by means of graphs, which is at the core of the complex networks field. This definition of the systems of interest is broad on purpose, as one can include disciplines as diverse as sociology, ecology, epidemiology, molecular biology, etc. Many such systems have been shown to share structural and dynamical features, thus attracting interest on fundamental research on networks as such. Our interest in the topic is related to the interplay between structure and dynamics, considering for example how topology can affect survival of cooperation in complex networks of gamers, or how features such as homophily and homeostasis can affect synchronization and topology in networks of oscillators (see also this paper).

Publications List

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)

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
bioRxiv (2023)

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)

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

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

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)

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)

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)

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 )

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 )

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) ( *Co-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)

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!

Structural info of mesophases

Diffusion Coefficient in Water Channels

Mechanically-accurate DNA (MADna)

IDP potential from this article

This tool computes the average lipid length within the bilayer and the radius of water channels for mesophases with Hexagonal, Pn3m, Im3m and Ia3d topologies, as well as lipid length and thickness of water lamellae in the case of Lamellar mesophases. The structural parameters are computed starting from the lattice parameter (as obtained by SAXS), the weight percentage of water used to produce the mesophase, and the density of the lipid used. For the cubic phases, the lipid length is computed following Turner et al., while the radius of water channels follows Briggs et al. For the hexagonal phase, the radius follows the derivation by Seddon, while for the lipid length two values are provided: the unfrustrated length L_unf (see Seddon or Mezzenga et al.), or the average length L_ave.

Relevant literature:
- Turner et al, J. Phys. II 2:2039 (1992)
- Briggs et al, J. Phys. II 6:723 (1996)
- Assenza and Mezzenga, J. Chem. Phys. 148:054902 (2018)
- Mezzenga et al, Langmuir, 21:3322 (2005)
- Seddon, Biochim. Biophys. Acta, 1031:1 (1990)

Inputs

Results

Radius Size (nm)

Lipid Length (nm)

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 (T_exp); 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 x_b (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

Results

x_b

D (10^-5cm²/s)

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

Nerea Alcázar Cano
Postdoc

Eva Zunzunegui Bru
PhD Student
(@ETH Zürich, co-advised with R. Mezzenga)

Juan Luengo Márquez
PhD Student

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 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.

Alumni

• Sebastián Jiménez Millán, MSc (2022-2023), Universidad Autónoma de Madrid, Spain
• Diego José Craviotto Villegas, BSc (2022-2023), Universidad Autónoma de Madrid, Spain
• Carlos Díaz Alcón, BSc (2022-2023), Universidad Autónoma de Madrid, Spain
• Julia Rubio Loscertales, BSc (2020-2021) and MSc (2021-2022), Universidad Autónoma de Madrid, Spain
• Antonio Miguel Bosch Fernández, MSc (2021-2022), Universidad Autónoma de Madrid, Spain
• Diego Alcón Vela, MSc (2021-2022), Universidad Autónoma de Madrid, Spain
• Juan Zalvide Pombo, BSc (2020-2021), Universidad Autónoma de Madrid, Spain
• Aarnau Martorell, MSc (2020-2021), Universidad Autónoma de Madrid, Spain
• Rodrigo Rosado del Castillo, BSc (2019-2020), Universidad Autónoma de Madrid, Spain
• Paride Azzari, MSc (2017-2018), ETH Zürich, Switzerland
• Luca Antognini, MSc (2016-2017), ETH Zürich & EPFL, Switzerland
• Alberto Sassi, MSc (2014-2015), EPFL, Switzerland

Teaching Notes

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

Physical Foundations for the Master in Physics of Condensed Matter and Biological Systems at Universidad Autónoma de Madrid, Spain (academic year 2021-2022)

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