Person: Bianco, Valentino
Universidad Complutense de Madrid
Faculty / Institute
Now showing 1 - 10 of 11
- PublicationIn silico evidence that protein unfolding is as a precursor of the protein aggregation(Wiley-VCH GmbH, Weinheim, 2019-11-13) Bianco, Valentino; Franzese, Giancarlo; Coluzza, IvanWe present a computational study on the folding and aggregation of proteins in an aqueous environment, as a function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding of the native conformation without the occurrence of aggregates. A further increment of the protein concentration results in the complete loss of the folded structures and induces the formation of protein aggregates. We discuss the effect of the protein interface on the water fluctuations in the protein hydration shell and their relevance in the protein-protein interaction.
- PublicationInterfacial Free Energy and Tolman Length of Curved Liquid-Solid Interfaces from Equilibrium Studies(American Chemical Society (ACS), 2020) Montero de Hijes, Pablo; Espinosa, Jorge R.; Bianco, Valentino; Sanz García, Eduardo; Vega de las Heras, CarlosIn this work, we study by means of simulations of hard spheres the equilibrium between a spherical solid cluster and the fluid. In the NVT ensemble we observe stable/metastable clusters of the solid phase in equilibrium with the fluid, representing configurations that are global/local minima of the Helmholtz free energy. Then, we run NpT simulations of the equilibrated system at the average pressure of the NVT run and observe that the clusters are critical because they grow/shrink with a probability of 1/2. Therefore, a crystal cluster equilibrated in the NVT ensemble corresponds to a Gibbs free energy máximum where the nucleus is in unstable equilibrium with the surrounding fluid, in accordance with what has been recently shown for vapor bubbles in equilibrium with the liquid. Then, within the Seeding framework, we use Classical Nucleation Theory to obtain both the interfacial free energy γ and the nucleation rate. The latter is in very good agreement with independent estimates using techniques that do not rely on Classical Nucleation Theory when the mislabeling criterion is used to identify the molecules of the solid cluster. We therefore argue that the radius obtained from the mislabeling criterion provides a good approximation for the radius of tension, R_s . We obtain an estimate of the Tolman length by extrapolating the difference between R e (the Gibbs dividing surface) and R s to infinite radius. We show that such definition of the Tolman length coincides with that obtained by fitting γ versus 1/R_s to a straight line as recently applied to hard spheres.
- PublicationAntifreeze proteins and homogeneous nucleation: On the physical determinants impeding ice crystal growth(American Institute of Physics (AIP), 2020) Bianco, Valentino; Espinosa, Jorge R.; Vega de las Heras, CarlosAntifreeze proteins (AFPs) are biopolymers capable of interfering with ice growth. Their antifreeze action is commonly understood considering that the AFPs, by pinning the ice surface, force the crystal–liquid interface to bend forming an ice meniscus, causing an increase in the surface free energy and resulting in a decrease in the freezing point ΔT max. Here, we present an extensive computational study for a model protein adsorbed on a TIP4P/Ice crystal, computing ΔT max as a function of the average distance d between AFPs, with simulations spanning over 1 μs. First, we show that the lower the d, the larger the ΔT max. Then, we find that the water–ice–protein contact angle along the line ΔT max(d) is always larger than 0○ , and we provide a theoretical interpretation. We compute the curvature radius of the stable solid–liquid interface at a given supercooling ΔT ≤ ΔT max, connecting it with the critical ice nucleus at ΔT. Finally, we discuss the antifreeze capability of AFPs in terms of the protein–water and protein–ice interactions. Our findings establish a unified description of the AFPs in the contest of homogeneous ice nucleation, elucidating key aspects of the antifreeze mechanisms and paving the way for the design of novel ice-controlling materials.
- PublicationSelf-Adaptation of Pseudomonas fluorescens Biofilms to Hydrodynamic Stress(Frontiers Media, 2021-01-12) Jara Pérez, Josué; Alarcón, Francisco; Monnappa, Ajay K.; Santos, José Ignacio; Bianco, Valentino; Nie, Pin; Ciamarra, Massimo Pica; Canales, Ángeles; Dinis Vizcaíno, Luis Ignacio; López-Montero, Iván; Valeriani, Chantal; Orgaz Martín, BelénIn some conditions, bacteria self-organize into biofilms, supracellular structures made of a self-produced embedding matrix, mainly composed of polysaccharides, DNA, proteins, and lipids. It is known that bacteria change their colony/matrix ratio in the presence of external stimuli such as hydrodynamic stress. However, little is still known about the molecular mechanisms driving this self-adaptation. In this work, we monitor structural features of Pseudomonas fluorescens biofilms grown with and without hydrodynamic stress. Our measurements show that the hydrodynamic stress concomitantly increases the cell density population and the matrix production. At short growth timescales, the matrix mediates a weak cell-cell attractive interaction due to the depletion forces originated by the polymer constituents. Using a population dynamics model, we conclude that hydrodynamic stress causes a faster diffusion of nutrients and a higher incorporation of planktonic bacteria to the already formed microcolonies. This results in the formation of more mechanically stable biofilms due to an increase of the number of crosslinks, as shown by computer simulations. The mechanical stability also relies on a change in the chemical compositions of the matrix, which becomes enriched in carbohydrates, known to display adhering properties. Overall, we demonstrate that bacteria are capable of self-adapting to hostile hydrodynamic stress by tailoring the biofilm chemical composition, thus affecting both the mesoscale structure of the matrix and its viscoelastic properties that ultimately regulate the bacteria-polymer interactions.
- PublicationHydrogen bond correlated percolation in a supercooled water monolayer as a hallmark of the critical region(Elsevier, 2019) Bianco, Valentino; Franzese, GiancarloNumerical simulations for a number of water models have supported the possibility of a metastable liquid-liquid critical point (LLCP) in the deep supercooled region. Here we consider a theoretical model for a supercooled liquid water monolayer and its mathematical mapping onto a percolation problem. The mapping allows us to identify the finite-size clusters at any state-point, and the infinite cluster at the critical point, with the regions of correlated hydrogen bonds (HBs). We show that the percolation line coincides with the first-order liquid-liquid phase transition ending at the LLCP. At pressures below the LLCP, the percolation line corresponds to the strong maxima of the thermodynamic response functions and to the locus of maximum correlation length (Widom line). At higher pressures, we find a percolation transition with a positive slope and we discuss its possible relation with the thermodynamics.
- PublicationRheology of Pseudomonas fluorescens biofilms: From experiments to predictive DPD mesoscopic modeling(American Institute of Physics, 2023-02-21) Martín Roca, José; Bianco, Valentino; Alarcón, Francisco; Monnappa, Ajay K.; Natale, Paolo; Monroy, Francisco; Orgaz, Belén; López Montero, Iván; Valeriani, ChantalBacterial biofilms mechanically behave as viscoelastic media consisting of micron-sized bacteria cross-linked to a self-produced network of extracellular polymeric substances (EPSs) embedded in water. Structural principles for numerical modeling aim at describing mesoscopic viscoelasticity without losing details on the underlying interactions existing in wide regimes of deformation under hydrodynamic stress. Here, we approach the computational challenge to model bacterial biofilms for predictive mechanics in silico under variable stress conditions. Up-to-date models are not entirely satisfactory due to the plethora of parameters required to make them functioning under the effects of stress. As guided by the structural depiction gained in a previous work with Pseudomonas fluorescens [Jara et al., Front. Microbiol. 11, 588884 (2021)], we propose a mechanical modeling by means of Dissipative Particle Dynamics (DPD), which captures the essentials of topological and compositional interactions between bacterial particles and cross-linked EPS-embedding under imposed shear. The P. fluorescens biofilms have been modeled under mechanical stress mimicking shear stresses as undergone in vitro. The predictive capacity for mechanical features in DPD-simulated biofilms has been investigated by varying the externally imposed field of shear strain at variable amplitude and frequency. The parametric map of essential biofilm ingredients has been explored by making the rheological responses to emerge among conservative mesoscopic interactions and frictional dissipation in the underlying microscale. The proposed coarse grained DPD simulation qualitatively catches the rheology of the P. fluorescens biofilm over several decades of dynamic scaling. Published under an exclusive license by AIP Publishing.
- PublicationRe-entrant limits of stability of the liquid phase and the Speedy scenario in colloidal model systems(AIP Publishing, 2017) Rovigatti, Lorenzo; Bianco, Valentino; Tavares, José María; Sciortino, FrancescoA re-entrant gas-liquid spinodal was proposed as a possible explanation of the apparent divergence of the compressibility and specific heat off supercooling water. Such a counter-intuitive possibility, e.g., a liquid that becomes unstable to gas-like fluctuations on cooling at positive pressure, has never been observed, neither in real substances nor in off-lattice simulations. More recently, such a reentrant scenario has been dismissed on the premise that the re-entrant spinodal would collide with the gas-liquid coexisting curve (binodal) in the pressure-temperature plane. Here we study, numerically and analytically, two previously introduced one-component patchy particle models that both show (i) a re-entrant limit of stability of the liquid phase and (ii) a re-entrant binodal, providing a neat in silico (and in charta) realization of such unconventional thermodynamic scenario.
- PublicationGlobulelike Conformation and Enhanced Diffusion of Active Polymers(American Physical Society, 2018-11) Bianco, Valentino; Locatelli, Emanuele; Malgaretti, PaoloWe study the dynamics and conformation of polymers composed by active monomers. By means of Brownian dynamics simulations we show that, when the direction of the self-propulsion of each monomer is aligned with the backbone, the polymer undergoes a coil-to-globulelike transition, highlighted by a marked change of the scaling exponent of the gyration radius. Concurrently, the diffusion coefficient of the center of mass of the polymer becomes essentially independent of the polymer size for sufficiently long polymers or large magnitudes of the self-propulsion. These effects are reduced when the self-propulsion of the monomers is not bound to be tangent to the backbone of the polymer. Our results, rationalized by a minimal stochastic model, open new routes for activity-controlled polymers and, possibly, for a new generation of polymer-based drug carriers.
- PublicationHow the stability of a folded protein depends on interfacial water properties and residue-residue interactions(Elsevier BV, 2017-11) Bianco, Valentino; Pagès-Gelabert, Neus; Coluzza, Ivan; Franzese, GiancarloProteins tend to adopt a single or a reduced ensemble of configurations at natural conditions , but changes in temperature T and pressure P induce their unfolding. Therefore for each protein there is a stability region (SR) in the T–P thermodynamic plane outside which the biomolecule is denaturated. It is known that the extension and shape of the SR depend on i) the specific protein residue-residue interactions in the native state of the amino acids sequence and ii) the water properties at the hydration interface. Here we analyze by Monte Carlo simulations the different coarse-grained protein models in explicit water how changes in i) and ii) affect the SR. We show that the solvent properties ii) are essential to rationalize the SR shape at low T and high P and that our findings are robust with respect to parameter changes and with respect to different protein models, representative of the ordered and disordered proteins. These results can help in developing new strategies for the design of novel synthetic biopolymers.
- PublicationSimulating Microswimmers Under Confinement With Dissipative Particle (Hydro) Dynamics(Frontiers Media S.A, 2022-07-22) Barriuso Gutiérrez, Carlos Miguel; Martín Roca, José; Bianco, Valentino; Pagonabarraga, Ignacio; Valeriani, ChantalIn this work we study microwimmers, whether colloids or polymers, embedded in bulk or in confinement. We explicitly consider hydrodynamic interactions and simulate the swimmers via an implementation inspired by the squirmer model. Concerning the surrounding fluid, we employ a Dissipative Particle Dynamics scheme. Differently from the Lattice-Boltzmann technique, on the one side this approach allows us to properly deal not only with hydrodynamics but also with thermal fluctuations. On the other side, this approach enables us to study microwimmers with complex shapes, ranging from spherical colloids to polymers. To start with, we study a simple spherical colloid. We analyze the features of the velocity fields of the surrounding solvent, when the colloid is a pusher, a puller or a neutral swimmer either in bulk or confined in a cylindrical channel. Next, we characterise its dynamical behaviour by computing the mean square displacement and the long time diffusion when the active colloid is in bulk or in a channel (varying its radius) and analyze the orientation autocorrelation function in the latter case. While the three studied squirmer types are characterised by the same bulk diffusion, the cylindrical confinement considerably modulates the diffusion and the orientation autocorrelation function. Finally, we focus our attention on a more complex shape: an active polymer. We first characterise the structural features computing its radius of gyration when in bulk or in cylindrical confinement, and compare to known results obtained without hydrodynamics. Next, we characterise the dynamical behaviour of the active polymer by computing its mean square displacement and the long time diffusion. On the one hand, both diffusion and radius of gyration decrease due to the hydrodynamic interaction when the system is in bulk. On the other hand, the effect of confinement is to decrease the radius of gyration, disturbing the motion of the polymer and thus reducing its diffusion.