We investigate the effect of crowding on the short-time tracer diffusion of model proteins on the nanometer length and (sub-)nanosecond timescales both experimentally and with the aid of computer simulations [1]. Experimentally, we dissolve polyclonal immunoglobulin (Ig) antibody proteins of natural isotopic abundance as tracers in perdeuterated Escherichia coli cell lysate as crowder to mimic...
Finding harmless stabilizing compounds for proteins and nucleic acids is an important task in modern food and pharmaceutical industries. In this work sucrose and trehalose were investigated as stabilizing agents for myoglobin and the Aβ(1-42) peptide. Atomistic molecular dynamics (MD) simulations were carried out for several systems of myoglobin/Aβ(1-42) in both water and aqueous solutions of...
Structure and Dynamics of Huntingtin. A Segmental Labelling Approach
Xamuel L. Lund [1], Amin Sagar [1], Frank Gabel [2], Anne Martel [3], Pau Bernadó [1]
[1] Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 34090 Montpellier, France
[2] Université de Grenoble Alpes, CEA, CNRS, IBS, 38044 Grenoble, France
[3] Institut Laue-Langevin (ILL), 38044 Grenoble,...
Pentameric ligand-gated ion channels transform chemical signals into electrical ones, a process during which they undergo subtle conformational cycling resulting in rapid, reversible gating of an intrinsic transmembrane pore. The pH-gated bacterial channel GLIC has proved a valuable model system for this receptor family, in part due to its accessibility to X-ray crystallography - which has...
In the past two decades, advances in the organic chemistry of fullerenes has enabled chemists to synthesise fully closed fullerene cages with atoms/molecules trapped inside [1-4], allowing the study of interesting effects that arise due to the confinement. In this report, a methodology to determine the INS spectrum of a single atom trapped inside a nano-cavity in a near-spherical symmetry by...
Imogolite is an aluminosilicate clay mineral, composed of single-walled nanotubes with stoichiometry of 3(OH)Al2O3SiOH, and having a nanometric inner diameter. Thanks to their one-dimensional inner cavity, they are a model system for studying the dynamics of nanoconfined water. We will present, by means of molecular dynamics (MD) simulations, a study of the evolution of the structure and the...
Understanding the nanoscale dynamics of water molecules incorporated in layered and porous solids is key in designing next-generation materials for water filtration devices and fuel cells and requires the combination of experimental measurements and MD simulations. Cold neutrons, allowing investigations of molecular motions on a pico- to nano-seconds time regime, offer critical complementarity...
Water is an essential component in hydraulic binders, exerting control on the hydration reactions and on the long-term behavior of cementitious structures acting as a vector of ionic transportation. Here, a protocol based on water sorption isotherms, X-ray diffraction and thermogravimetric analysis was designed to obtain C-S-H with controlled distribution of interlayer, adsorbed and bulk pore...
Ionic liquids (ILs) have been described as molten salts with a melting point below 100 °C, consisting of a large asymmetric organic cations and organic or inorganic anions. Since the ionic liquids are essentially ionic conductors, their utilization as novel electrolytes for electrochemical devices, such as batteries, electric double layer separators, dye-sensitized solar cells and fuel cells...
In the recent years, software packages implementing the Density Functional Theory (DFT) formalism have made considerable advances. In particular, the advent of modern supercomputing techniques made possible routine quantum-mechanical simulations of systems that were difficult to treat only few years ago. This opens up possibilities of new interdisciplinary collaborations that can benefit from...
The interaction between proteins and hydration water stabilizes protein structure and promotes functional dynamics, with hydration water enabling protein flexibility. However, some engineered solvent-free protein-polymer hybrids have been shown to preserve protein structure, function and dynamics [1,2]. Here we have studied the dynamics of myoglobin conjugated with a polymer surfactant corona....
Neutron scattering represents a collection of powerful techniques useful for studying the microscopic sturcture and dynamics of materials at the atomic level. However, the interpretation of experimental data is not straightforward and usually requires the incorperation of computer simulations. LiquidLib (http://z-laboratory.github.io/LiquidLib/) is a post-processing package for analyzing the...
Poly(N-isopropylacrylamide), commonly known as PNIPAM, is a synthetic polymer mostly exploited for its thermo-responsive nature, but it is also of interest because of its affinity with proteins in terms of energy landscape and amphiphilic chemical composition. Depending on the specific synthesis protocol, different molecular architecture can be originated, such as linear chains or microgels,...
Complex metallic alloys (CMAs) are long range ordered materials, characterized by large cells, comprising several hundreds of atoms and cluster building blocks. A key property of CMAs is the low lattice thermal conductivity (1.3 W/m.K), which suggests a potential application for CMAs for thermoelectricity.
Engineering lattice thermal conductivity commonly implies controlling the heat flow...
Thermal expansion (positive or negative) is the result of phonon anharmonicity. These phonons can be probed using inelastic neutron scattering (INS). By measuring the generalized density of states (GDOS), a dynamical fingerprint of polycrystalline samples is created, which is often compared to DFT calculations. However, finite difference phonon calculations are based on the assumption of...
The group IV-VI chalcogenides have important thermoelectric applications. GeTe has emerged as a promising non-toxic candidate, especially when the high-temperature cubic phase is suppressed to room temperature. However, even the mechanism of phase transition is disputed, as is the presence of disorder. Here we apply ab-initio MD, synchrotron X-ray and dynamic neutron pair distribution function...
Persistent homology (PH) is a relatively new method from algebraic topology that can be used to find features in discrete datasets. The PH algorithms are distributed in a number of popular Python packages, making it easy to start with data analysis. We have shown that this method is useful in Monte Carlo simulations of Heisenberg spins and can reveal the phase diagram. The barcode (a concept...
