Soft Condensed Matter and Biophysics

Soft Matter and BiophysicsSoft condensed matter includes liquids, colloids, polymers, liquid crystals, gels, membranes, foams, etc. Each of these dense phases appears as the result of a finely tuned balance between the thermal fluctuations and the molecular attractions. The qualitatively different aspects and properties of soft condensed matter are very difficult to predict because it self organizes into mesoscopic physical structures that are much larger than the molecular scale, but yet are much smaller than the macroscopic scale of the material. Understanding the link between these scales, and the emergence of qualitatively new properties from the interactions of the molecular elements sets a fundamental problem in condensed matter physics.

The amazing complexity of biological systems is built on that variety of soft condensed matter mesoscale structures, and it sets the most outstanding challenge in our goal to understand the spontaneous self-assembly of matter. The connection between soft condensed matter physics and the study of biological systems opens a broad and fructiferous route to the interdisciplinary field of biophysics, in which researchers with very different backgrounds, from molecular biology to theoretical physics and mathematics, are contributing to a fully new perspective of that active field of research.

Soft condensed matter and biophysics are very active areas of activity at IFIMAC. The theory and simulations of liquids and their interfaces has already a long tradition among some of the members of the institute, with the younger researchers bringing new ideas and perspectives to cover more complex systems. Special simulation methods have been developed for the study to these systems out of equilibrium. Experimental and theoretical work on glasses has also been carried out for a long time, and it has recently being extended to the study of fossil amber samples and other ultra-stabilized glasses.

Among the multiple routes to biophysical systems, the experience of IFIMAC members in theoretical soft matter physics is being successfully used in different approaches to biological systems. First-principle simulations for the electronic structure of bio-molecules are being used to describe their chemical reactions. In a complementary top-down approach, the experience in the statistical physics of soft condensed matter system is been used to study bi-layer membranes and protein filaments, in close connection with experimental works. Younger members of the institute have incorporated new lines of biophysical research at IFIMAC, from genetic to neuronal networks, that open a fresh perspective based on the application of non-linear dynamics, the theory of stochastic processes and information theory.

Physical Virology

Direct measurement of phage phi29 stiffness provides evidence of internal pressureThe basic architecture of a virus consists of the capsid, a shell made up of repeating protein subunits, packing within the viral genome. Far or being static structures, viruses are highly dynamic nucleoprotein complexes that transport and deliver their genome from host to host in a fully automatic process.  Viral particles are endorsed with specific physicochemical properties which confer to their structures certain meta-stability whose modulation permits fulfilling each task of the viral cycle at the right time.

Revista Española de FísicaThese natural designed capabilities have impelled using viral capsids as protein containers of artificial cargoes (drugs, polymers, enzymes, minerals) with applications in biomedical and materials sciences. Both natural and artificial protein cages have to protect their cargo against a variety of physicochemical aggressive environments, including molecular impacts of highly crowded media, thermal and chemical stresses, and osmotic shocks.

Viral cages stability under these ambiences depend not only on the ultimate structure of the external capsid, which rely on the interactions between protein subunits, but also on the nature of the cargo. Thus, it is important to find methodologies that directly supply univocal information about protein cages stability not only under different environments, but also its evolution upon structural changes.

Key References

  1. Calcium Ions Modulate the Mechanics of Tomato Bushy Stunt Virus
    Llauró A, Coppari E, Imperatori F, Bizzarri AR, Castón JR, Santi L, Cannistraro S, de Pablo PJ.
    Biophys J. 109(2):390-7. doi: 10.1016/j.bpj.2015.05.039, (2015). [URL]
  2. Structural insights into magnetic clusters grown inside virus capsids
    Jaafar M, Aljabali AA, Berlanga I, Mas-Ballesté R, Saxena P, Warren S, Lomonossoff GP, Evans DJ, de Pablo PJ.
    ACS Appl Mater Interfaces. 6(23):20936-42. doi: 10.1021/am505682x. (2014). [URL]
  3. Mechanical Stability and Reversible Fracture of Vault Particles
    Llauró A, Guerra P, Irigoyen N, Rodríguez José F, Verdaguer N, de Pablo P J
    Biophysical journal 106(3): 687-695, (2014). [URL]
  4. The interplay between mechanics and stability of viral cages
    Hernando-Perez M, Pascual E, Aznar M, Ionel A, Caston JR, Luque A, Carrascosa JL, Reguera D, de Pablo PJ
    Nanoscale 6(5): 2702-2709, (2014). [URL]
  5. Interplay between the mechanics of bacteriophage fibers and the strength of virus-host links
    Ares P, Garcia-Doval C, Llauro A, Gomez-Herrero J, van Raaij MJ, de Pablo PJ
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics) 89(5): 052710 (052717 pp.)-052710 (052717 pp.). (2014). [URL]
  6. Cementing proteins provide extra mechanical stabilization to viral cages
    M. Hernando-Pérez, S. Lambert, E. Nakatani-Webster, C.E. Catalano & P.J. de Pablo
    Nature Communications 5, 4520 (2014). [URL]
  7. Communication: From rods to helices: Evidence of a screw-like nematic phase
    Hima Bindu Kolli, Elisa Frezza, Giorgio Cinacchi, Alberta Ferrarini, Achille Giacometti and Toby S. Hudson
    The Journal of Chemical Physics 140, 081101 (2014). [URL]
  8. Monte Carlo Adaptive Resolution Simulation of Multicomponent Molecular Liquids
    Raffaello Potestio, Pep Español, Rafael Delgado-Buscalioni, Ralf Everaers, Kurt Kremer and Davide Donadio
    Physical Review Letters 111, 060601 (2013). [URL]
  9. Monitoring dynamics of human adenovirus disassembly induced by mechanical fatigue
    Ortega-Esteban A, Perez-Berna AJ, Menendez-Conejero R, Flint SJ, Martin CS, de Pablo PJ
    Scientific Reports 3, 1434, (2013). [URL]
  10. Mapping in vitro local material properties of intact and disrupted virions at high resolution using multi-harmonic atomic force microscopy
    Cartagena A, Hernando-Perez M, Carrascosa JL, de Pablo PJ, Raman A
    Nanoscale 5(11): 4729-4736, (2013). [URL]
  11. Hamiltonian Adaptive Resolution Simulation for Molecular Liquids
    Raffaello Potestio, Sebastian Fritsch, Pep Español, Rafael Delgado-Buscalioni, Kurt Kremer, Ralf Everaers and Davide Donadio
    Physical Review Letters 110, 108301 (2013). [URL]
  12. Low-temperature thermal properties of a hyperaged geological glass
    Tomás Pérez-Castañeda, Rafael J. Jimenez Riobóo and Miguel A. Ramos
    Journal of Physics: Condensed Matter 25, 295402 (2013). [URL]
  13. A Mathematical Model for the Rational Design of Chimeric Ligands in Selective Drug Therapies
    V. Doldán-Martelli, R. Guantes and D.G. Míguez
    Pharmacometrics and Systems Pharmacology 2, e26 (2013). [URL]
  14. Thermal fluctuations and bending rigidity of bilayer membranes
    Pedro Tarazona, Enrique Chacón and Fernando Bresme
    The Journal of Chemical Physics 139, 094902 (2013). [URL]
  15. Intrinsic Fluid Interfaces and Nonlocality
    Eva M. Fernández, Enrique Chacón, Pedro Tarazona, Andrew O. Parry and Carlos Rascón
    Physical Review Letters 111, 096104 (2013). [URL]
  16. FtsZ protein on bilayer membranes: effects of specific lateral bonds
    Pablo González de Prado Salas, Mario Encinar, Marisela Vélez and Pedro Tarazona
    Soft Matter 9, 6072 (2013). [URL]
  17. Depolymerization dynamics of individual filaments of bacterial cytoskeletal protein FtsZ
    Pablo Mateos-Gil, Alfonso Paez, Ines Hörger, Germán Rivas, Miguel Vicente, Pedro Tarazona and Marisela Vélez
    PNAS 109, 21 (2012). [URL]
  18. The Role of Capsid Maturation on Adenovirus Priming for Sequential Uncoating
    Perez-Berna AJ, Ortega-Esteban A, Menendez-Conejero R, Winkler DC, Menendez M, Steven AC, Flint SJ, de Pablo PJ, San Martin C
    Journal of Biological Chemistry 287(37): 31582-31595, (2012). [URL]
  19. Minimizing tip-sample forces in jumping mode atomic force microscopy in liquid
    Ortega-Esteban A, Horcas I, Hernando-Perez M, Ares P, Perez-Berna AJ, San Martin C, Carrascosa JL, de Pablo PJ, Gomez-Herrero J
    Ultramicroscopy 11456-61, (2012). [URL]
  20. High Surface Water Interaction in Superhydrophobic Nanostructured Silicon Surfaces: Convergence between Nanoscopic and Macroscopic Scale Phenomena.
    Munoz-Noval A, Hernando Perez M, Torres Costa V, Martin Palma RJ, de Pablo PJ, Manso Silvan M
    Langmuir 28(3): 1909-1913, (2012). [URL]
  21. Resolving Structure and Mechanical Properties at the Nanoscale of Viruses with Frequency Modulation Atomic Force Microscopy
    Martinez-Martin D, Carrasco C, Hernando-Perez M, de Pablo PJ, Gomez-Herrero J, Perez R, Mateu MG, Carrascosa JL, Kiracofe D, Melcher J, Raman A
    Plos One 7(1), (2012). [URL]
  22. Direct Measurement of Phage phi29 Stiffness Provides Evidence of Internal Pressure
    Hernando-Perez M, Miranda R, Aznar M, Carrascosa JL, Schaap IAT, Reguera D, de Pablo PJ
    Small 8(15): 2366-2370, (2012). [URL]
  23. Mechanical Disassembly of Single Virus Particles Reveals Kinetic Intermediates Predicted by Theory
    Castellanos M, Perez R, Carrillo PJP, de Pablo PJ, Mateu MG
    Biophysical Journal 102(11): 2615-2624, (2012). [URL]
  24. Mechanical elasticity as a physical signature of conformational dynamics in a virus particle
    Castellanos M, Perez R, Carrasco C, Hernando-Perez M, Gomez-Herrero J, de Pablo PJ, Mateu MG
    Proceedings of the National Academy of Sciences of the United States of America 109(30): 12028-12033, (2012). [URL]
  25. Kinesin Walks the Line: Single Motors Observed by Atomic Force Microscopy
    Schaap IAT, Carrasco C, de Pablo PJ, Schmidt CF
    Biophysical Journal 100(10): 2450-2456, (2011). [URL]
  26. Built-In Mechanical Stress in Viral Shells
    Carrasco C, Luque A, Hernando-Perez M, Miranda R, Carrascosa JL, Serena PA, de Ridder M, Raman A, Gomez-Herrero J, Schaap IAT, Reguera D, de Pablo PJ
    Biophysical Journal 100(4): 1100-1108, (2011). [URL]
  27. MC simulations of water meniscus in nanocontainers: explaining the collapse of viral particles due to capillary forces
    Serena PA, Douas M, Marques MI, Carrasco C, de Pablo PJ, Miranda R, Carrascosa JL, Castellanos M, Mateu MG
    Physica Status Solidi C – Current Topics in Solid State Physics, Vol 6, No 10, eds. Correia A, Saenz JJ, & Ordejon P, pp. 2128-2132, (2009). [URL]
  28. Origins of phase contrast in the atomic force microscope in liquids
    Melcher J, Carrasco C, Xu X, Carrascosa JL, Gomez-Herrero J, Jose de Pablo P, Raman A
    Proceedings of the National Academy of Sciences of the United States of America 106(33): 13655-13660, (2009). [URL]
  29. The capillarity of nanometric water menisci confined inside closed-geometry viral cages
    Carrasco C, Douas M, Miranda R, Castellanos M, Serena PA, Carrascosa JL, Mateu MG, Marques MI, de Pablo PJ
    Proceedings of the National Academy of Sciences of the United States of America 106(14): 5475-5480, (2009). [URL]
  30. Pair Potential of Charged Colloidal Stars
    F. Huang, K. Addas, A. Ward, N.T. Flynn, E. Velasco, M.F. Hagan, Z. Dogic and S. Fraden
    Physical Review Letters 102, 108302 (2009). [URL]
  31. Unmasking imaging forces on soft biological samples in liquids when using dynamic atomic force microscopy: A case study on viral capsids
    Xu X, Carrasco C, Jose de Pablo P, Gomez-Herrero J, Raman A
    Biophysical Journal 95(5): 2520-2528, (2008). [URL]
  32. Manipulation of the mechanical properties of a virus by protein engineering
    Carrasco C, Castellanos M, de Pablo PJ, Mateu MG
    Proceedings of the National Academy of Sciences of the United States of America 105(11): 4150-4155, (2008). [URL]
  33. Intrinsic Structure of Hydrophobic Surfaces: The Oil-Water Interface
    Fernando Bresme, Enrique Chacón, Pedro Tarazona and Kafui Tay
    Physical Review Letters 101, 056102 (2008). [URL]
  34. Hydrodynamics of Nanoscopic Capillary Waves
    R. Delgado-Buscalioni, E. Chacón and P. Tarazona
    Physical Review Letters 101, 106102 (2008). [URL]
  35. Sodium pumps adapt spike bursting to stimulus statistics
    Sara Arganda, Raúl Guantes and Gonzalo G. de Polavieja
    Nature Neuroscience 10(11), 1467-73 (2007).  [URL]
  36. Elastic response, buckling, and instability of microtubules under radial indentation
    Schaap IAT, Carrasco C, de Pablo PJ, MacKintosh FC, Schmidt CF
    Biophysical Journal 91(4): 1521-1531, (2006). [URL]
  37. DNA-mediated anisotropic mechanical reinforcement of a virus
    Carrasco C, Carreira A, Schaap IAT, Serena PA, Gomez-Herrero J, Mateu MG, de Pablo PJ
    Proceedings of the National Academy of Sciences of the United States of America 103(37): 13706-13711, (2006). [URL]
  38. Resolving the molecular structure of microtubules under physiological conditions with scanning force microscopy
    Schaap IAT, de Pablo PJ, Schmidt CF
    European Biophysics Journal with Biophysics Letters 33(5): 462-467, (2004). [URL]
  39. Bacteriophage capsids: Tough nanoshells with complex elastic properties
    Ivanovska IL, de Pablo PJ, Ibarra B, Sgalari G, MacKintosh FC, Carrascosa JL, Schmidt CF, Wuite GJL
    Proceedings of the National Academy of Sciences of the United States of America 101(20): 7600-7605, (2004). [URL]
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