Soft Matter and Physics of Biopolymers
Universidad Autónoma de Madrid & IFIMAC (Spain)
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
Very glad to welcome María López from EPFL as a visiting PhD student!
Miriam Moreno and Yago Casado join the SMPB group for their BSc and MSc projects. Welcome!
In collaboration with K. Fong and L. Salvati Manni, we publish a paper on JCIS quantifying the impact of the human microbiome(s) on the topology of cubosome, of relevance for their potential use as drug-delivery systems.
Paper alert! Led by Juan, we characterise curvature and metrics of polymer chainmails and their dependence on the network topology Check it out on Soft Matter!
New paper out led by Eva, showing unexpected universal features of water under soft nanoconfinement! Check it out on ACS Nano!
New paper out on the mesoscopic polymorphism of amyloid fibrils, published on Advanced Science !
Salvatore is the recipient of the "E. Pérez-Payá - SBE 40" prize from the Spanish Biophysical Society !
Our work on the systematic analysis of sequence-dependent elasticity throughout various atomistic force fields is out in JCTC!
Salvatore gives an invited talk at the CECAM workshop on "Modeling energy-consuming biomolecular processes" in the beautiful Lausanne!
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
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!
Congratulations to Juan for his well-deserved first prize “Chema Gómez” at the Young Investigators Meeting of Instituto Nicolás Cabrera! Ad Maiora!
Research Interests
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.
More recently, the role of RNA has also been shown to be more widespread than envisaged previously. For instance,
it has been demonstrated that long non-coding RNAs have key regulatory effects in the cell,
yet their molecular description is far from being clear. This is due to the single-stranded nature of the RNA
typically found in the cell and to the presence of many weak interactions, which confer to this molecule a rich
conformational heterogeneity.
Our current research line is focused on investigating the sequence-dependent molecular properties of DNA and RNA,
and their role in biocellular processes. For instance, via atomistic simulations
we have uncovered the change in
the elasticity response of double-stranded nucleic acids, finding that dsDNA becomes stiffer while dsRNA becomes
softer upon pulling. We have also shown that the stretching elasticity of dsDNA
is a universal function
of its local minimum-energy conformation.
We also look at larger molecules via coarse-grained approaches. For instance, we have developed
the coarse-grained model MADna,
which provides an accurate sequence-dependent description of the elasticity and conformation of
double-stranded DNA based on an extensive dataset of all-atom simulations. At even larger scales,
we have employed coars(er)-grained descriptions of topologically-bound membranes, inspired by the
kinetoplasts observed in certain parasytes, and
observed the emergence of
spontaneous Gaussian curvature induced by the linking chirality.
Publications List
-
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) -
Shape and size tunability of sheets of interlocked ring copolymers
J. Luengo-Márquez, S. Assenza and C. Micheletti
Soft Matter 20, 6595 (2024) -
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 ) -
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 ) -
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 ) -
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) -
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 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
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!
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
Click on the pictures for further info
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)
Teaching Notes
These notes are licensed under a
Creative Commons Attribution-NonCommercial 3.0 Unported License
Thermodynamics
Statistical Mechanics
Simple applications of Statistical Mechanics
Van der Waals forces
Electrostatics in liquids
DLVO
Polymer Physics
Molecular transport
Law of mass action