Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling.

Cryo-electron microscopy (cryo-EM) has become a mainstream technique for determining the structures of complex biological systems. However, accurate integrative structural modeling has been hampered by the challenges in objectively weighing cryo-EM data against other sources of information due to the presence of random and systematic errors, as well as correlations, in the data. To address these challenges, we introduce a Bayesian scoring function that efficiently and accurately ranks alternative structural models of a macromolecular system based on their consistency with a cryo-EM density map as well as other experimental and prior information. The accuracy of this approach is benchmarked using complexes of known structure and illustrated in three applications: the structural determination of the GroEL/GroES, RNA polymerase II, and exosome complexes. The approach is implemented in the open-source Integrative Modeling Platform (http://integrativemodeling.org), thus enabling integrative structure determination by combining cryo-EM data with other sources of information.

Water sub-diffusion in membranes for fuel cells.

We investigate the dynamics of water confined in soft ionic nano-assemblies, an issue critical for a general understanding of the multi-scale structure-function interplay in advanced materials. We focus in particular on hydrated perfluoro-sulfonic acid compounds employed as electrolytes in fuel cells. These materials form phase-separated morphologies that show outstanding proton-conducting properties, directly related to the state and dynamics of the absorbed water. We have quantified water motion and ion transport by combining Quasi Elastic Neutron Scattering, Pulsed Field Gradient Nuclear Magnetic Resonance, and Molecular Dynamics computer simulation. Effective water and ion diffusion coefficients have been determined together with their variation upon hydration at the relevant atomic, nanoscopic and macroscopic scales, providing a complete picture of transport. We demonstrate that confinement at the nanoscale and direct interaction with the charged interfaces produce anomalous sub-diffusion, due to a heterogeneous space-dependent dynamics within the ionic nanochannels. This is irrespective of the details of the chemistry of the hydrophobic confining matrix, confirming the statistical significance of our conclusions. Our findings turn out to indicate interesting connections and possibilities of cross-fertilization with other domains, including biophysics. They also establish fruitful correspondences with advanced topics in statistical mechanics, resulting in new possibilities for the analysis of Neutron scattering data.

Sub-diffusion and population dynamics of water confined in soft environments.

We have studied by using molecular dynamics computer simulations the dynamics of water confined in ionic surfactant phases, ranging from well ordered lamellar structures to micelles at low and high water loading, respectively. We have analysed in depth the main dynamical features in terms of mean-squared displacements and intermediate scattering functions, and found clear evidence of sub-diffusive behaviour. We have identified water molecules lying at the charged interface with the hydrophobic confining matrix as the main factor responsible for this unusual feature, and given a comprehensive picture of dynamics based on a very precise analysis of lifetimes at the interface. We conclude by providing, for the first time to our knowledge, a unique framework for rationalizing the existence of important dynamical heterogeneities in fluids adsorbed in soft confining environments.

Water confined in self-assembled ionic surfactant nano-structures.

We present a coarse-grained model for ionic surfactants in explicit aqueous solutions, and study by computer simulation both the impact of water content on the morphology of the system, and the consequent effect of the formed interfaces on the structural features of the absorbed fluid. On increasing the hydration level under ambient conditions, the model exhibits a series of three distinct phases: lamellar, cylindrical and micellar. We characterize the different structures in terms of diffraction patterns and neutron scattering static structure factors. We demonstrate that the rate of variation of the nano-metric sizes of the self-assembled water domains shows peculiar changes in the different phases. We also analyse in depth the structure of the water/confining matrix interfaces, the implications of their tunable degree of curvature, and the properties of water molecules in different restricted environments. Finally, we compare our results with experimental data and their impact on a wide range of important scientific and technological domains, where the behavior of water at the interface with soft materials is crucial.