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.
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.
New article on the force-dependent elastic constants of nucleic acids out in Nanoscale! Congratulations to Juan Luengo and all the authors!
Our work on hydropathy and diffusion within lamellar mesophase has been published! Congratulations Antonio!
Nerea and Juan present their projects at the J2IFAM conference!
New preprint of the SMPB lab on the role of hydropathy on diffusion in lamellar mesophases, led by former MSc student Antonio Bosch!
New cohort of undergraduate students at the SMPB lab: BSc students Diego Craviotto and Carlos Díaz, and MSc student Sebastián Jiménez. A big welcome!
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!
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!
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!
A big welcome to Nerea Alcázar, who has joined the SMPB group as a Postdoctoral Researcher! Looking forward to a lot of interesting science!
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!
Juan's paper accepted on J. Phys. Cond. Matter! Check out the theory on retardation effects in Van der Waals interactions between surfaces.
Our paper on the development of MADna is finally out on JCTC! Check out the tools for its implementation in LAMMPS.
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.
Force-dependent elasticity of nucleic acids
J. Luengo-Márquez, J. Zalvide-Pombo, R. Pérez and S. Assenza
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)
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
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 MembersClick on the pictures for further info
• Julia Rubio Loscertales, BSc (2020-2021) and MSc (2021-2022), Universidad Autónoma de Madrid, Spain
• Antonio Miguel Bosch Fernández, MSc (2020-2021), Universidad Autónoma de Madrid, Spain
• Diego Alcón Vela, MSc (2020-2021), 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
These notes are licensed under a
Creative Commons Attribution-NonCommercial 3.0 Unported License
Simple applications of Statistical Mechanics
Van der Waals forces
Electrostatics in liquids
Law of mass action