nov. 2012

New paper: Understanding small biomolecule-biomaterial interactions: A review of fundamental theoretical and experimental approaches for biomolecule interactions with inorganic surfaces

Interactions between biomolecules and inorganic surfaces play an important role in natural environments and in industry, including a wide variety of conditions: marine environment, ship hulls (fouling), water treatment, heat exchange, membrane separation, soils, mineral particles at the earth's surface, hospitals (hygiene), art and buildings (degradation and biocorrosion), paper industry (fouling) and more. To better control the first steps leading to adsorption of a biomolecule on an inorganic surface, it is mandatory to understand the adsorption mechanisms of biomolecules of several sizes at the atomic scale, that is, the nature of the chemical interaction between the biomolecule and the surface and the resulting biomolecule conformations once adsorbed at the surface. This remains a challenging and unsolved problem. Here, we review the state of art in experimental and theoretical approaches. We focus on metallic biomaterial surfaces such as TiO(2) and stainless steel, mentioning some remarkable results on hydroxyapatite. Experimental techniques include atomic force microscopy, surface plasmon resonance, quartz crystal microbalance, X-ray photoelectron spectroscopy, fluorescence microscopy, polarization modulation infrared reflection absorption spectroscopy, sum frequency generation and time of flight secondary ion mass spectroscopy. Theoretical models range from detailed quantum mechanical representations to classical forcefield-based approaches.

Dominique Costa, Pierre-Alain Garrain, and Marc Baaden in J Biomed Mater Res A. ASAP (27 Sep 2012)

Postdoc or engineer position now open within the ExaViz project

We are seeking a highly motivated candidate to design and implement a next generation visualization platform for analysis of large-scale molecular simulations. In particular, we target two grand challenge applications: modeling a complete influenza virus and analyzing extensive simulations of the GLIC receptor that we recently published in Nature and PNAS, two leading journals. Project foundations were previously established, providing a well defined framework to get started (FvNano). Using visual analytics approaches and high performance interactive graphics, you will implement readily usable state-of-art tools scaling up to the next generation of simulations. This position is a unique training opportunity in a multi-disciplinary environment in collaboration with four leading teams in France and two international partners in the U.K. and in Germany.

PDF-page of this job offer and general background:

New paper: Modeling complex biological systems: From solution chemistry to membranes and channels

Complex biological systems are intimately linked to their environment, a very crowded and equally complex solution compartmentalized by fluid membranes. Modeling such systems remains challenging and requires a suitable representation of these solutions and their interfaces. Here, we focus on particle-based modeling at an atomistic level using molecular dynamics (MD) simulations. As an example, we discuss important steps in mod- eling the solution chemistry of an ion channel of the ligand-gated ion channel receptor fam- ily, a major target of many drugs including anesthetics and addiction treatments. The bacte- rial pentameric ligand-gated ion channel (pLGIC) called GLIC provides clues about the functional importance of solvation, in particular for mechanisms such as permeation and gat- ing. We present some current challenges along with promising novel modeling approaches.

Benoist Laurent, Samuel Murail, Franck Da Silva, Pierre-Jean Corringer, and Marc Baaden in Pure and Applied Chemistry ASAP