Proteins are essential parts in living organisms. They participate in most of the cellular processes such as gene expression, signal transmission, catalysis of chemical reactions, … Due to their large range of possible functions, the study of proteins interests other fields in addition to biology. Proteins are pharmaceutical targets and drugs, their catalytic properties are widely used in biotechnology, and they are used as components of nano-devises in the rising field of bionanotechnology. Although the properties of natural proteins can be directly exploited, new, designed proteins, with novel functions or improved activities, are of major interest in all these application areas. Protein design may involve the remodeling of a known protein scaffold in order to modify the protein function/activity, or, in the most general case, the complete (de novo) design of new protein structures to fulfill a particular function. The problem is extremely challenging since the number of possible combinations of amino acids to be tested is astronomically large. Experimentally testing all the possible sequences is practically impossible. Therefore, computational protein design methods have been developed for over a decade. In addition to the intrinsic combinatorial complexity of the protein design problem, computational methods have to face the natural flexibility of proteins (i.e. proteins are flexible molecules that fluctuate between nearly isoenergetic states). Indeed, the protein design problem is even more challenging if dynamical aspects (e.g. allosteric shifts, loop motions, ...) are considered in addition to static aspects (e.g. positional arrangement of catalytic residues for enzyme activity). Due to all these difficulties, and despite great advances in recent years, computational protein design remains a largely open problem. In particular, improvements in models and algorithms are essential to better explore the protein sequence combinatorial space while taking into account protein flexibility. Besides, accurate and computationally efficient energy functions, able to better account for interactions with solvent and entropy change, are necessary. The goal of this project is to yield advances in a general methodology for protein design, and to develop suitable computational design tools that will lead the development of new proteins for applications in biotechnology, biomolecular nanotechnology, molecular medicine and synthetic biology. The methodological breakthrough expected from this interdisciplinary project builds on the combination of cutting-edge methods in computational biology with efficient algorithms originating from robotics. Among all the possible applications of the methods developed in this project, special attention will be given to enzyme design for applications in biotechnology such as the production of high-valued molecules, the development of eco-friendly bioprocesses and the valorization of renewable carbon resources. Such applications are of high interest to the pre-industrial demonstrator Toulouse White Biotech (TWB), supporter of our project, and to the Competitive Cluster AgriMip. The achievement of the project relies on the complementary expertise of four partners: LAAS-CNRS for robotics and computer science, BIOS-Polytechnique and LISBP-INSA for computational biology & protein engineering, and Kineo CAM, a company specialized in software development for computer-aided design and manufacturing.

Biology is undergoing a historical revolution with the development of systems and synthetic approaches. Signaling pathways, transcriptional network and other cellular processes involve a large number of molecular actors with multiple interactions. While such processes are often well described mechanistically as lists of molecular reactions, not much is known on their quantitative and dynamical properties. Time-lapse fluorescent imaging of cells exposed to time-varying stimulus can be used to probe the dynamical behavior of gene circuits. Indeed, cells can be seen as complex machines, which response functions can be measured by time varying stimulations, as it is classically done in electrical and mechanical engineering. Several recent studies have used such methods to constrain the modeling of gene networks and signaling pathways. We are, however, far from being able to construct models of biological processes which are as predictive and robust as it is usually the case in physics and engineering. One of the main difficulties is the limited knowledge of the cell state that can be obtained simultaneously through fluorescence imaging and the existence of noise associated with gene transcription and translation. In turn, this strongly limits our ability to drive cellular processes, such as gene expression, over long time periods and with a quantitative accuracy. Recent developments in microfluidics, synthetic biology and optogenetics allow interrogating cellular processes in space and time at the single cell level. Having a mean to externally control, in real time, the expression level of a gene of interest, and use this to generate time-varying perturbations of the internal component of a regulatory network, would be a major step towards a quantitative understanding of how a cell functions. This would also have important consequences for applied biotechnology. As a matter of fact, a major challenge of synthetic biology is to engineer cells that can robustly perform a program in a broad range of environmental conditions and despite the stochastic nature of gene expression. However, given the complex, noisy nature of gene expression, an external control is usually needed to generate accurate time-varying perturbation of complex gene circuit for the interrogation of their behavior. The principle of controlling a dynamical system with a feedback-loop has been used extensively in engineering and is a key feature of most electromechanical devices of our everyday life. The basic idea is simple: monitor the readout and operate a change on the system to adjust it in real time so that it follows a given target profile. This permits to compensate for environmental fluctuations and un-modeled dynamics. We recently made a first step towards the construction of such a computer based control of gene expression in population of yeast cells. In this context, the CoGEx project aims at developing the experimental and theoretical tools for the computer-based remote-control of live cells and to use such a system to interrogate cellular processes at the single cell level. More specifically, our research project aims at (1) creating a versatile, open platform for the control of gene expression at the single cell level in yeast; (2) study the performance of real time control and (3) apply this method to find optimal conditions for the production of a biomolecule in an industrial fermentor. These research directions will be the basis for a larger, long term project that will aim at developing technologically and conceptually cell-machine interfaces based on genetics using advanced microfluidics, optogenetics, microscopy, control theory, modeling and synthetic biology.

IPM-4-Citrus aims to strengthen collaborations between academic and non-academic partners based in 3 European Member States (FR, GER, IT), 2 Associated Countries (Turkey and Tunisia) and 1 Third Country (Lebanon), in order to develop a new bio-pesticide active against citrus pests and scale it up from lab to market. The project’s research and innovation activities are based on a multidisciplinary approach, which aims at understanding and sensitising stakeholders about the health risk factors related to citrus pests and their treatment by chemical pesticides and developing an alternative Integrated Pest Management (IPM) approach based on biological control. Bacillus thuringiensis (Bt) based bio pesticides occupy almost 97% of the world’s bio pesticide market and their use was estimated to exceed 30,000 tons. Despite this widespread use, the originality of Citrus-IPM is to focus on 2 promising, newly identified strains (Bt kurstaki BLB1 and LIP), which were shown to be more efficient than the commercial (Bt kurstaki HD1). In conjunction with validation through field tests, the project will pave the way for future commercial exploitation of a new biopesticide product by drawing up a feasibility study for future spin-off activities and/or new production lines in partner SMEs. Staff secondments and inter-sector and international mobilities between complementary partners will represent a unique opportunity to optimise bioproduction processes and obtain high added-value bioproducts, while building up the partners’ skills and reinforcing the training of early-stage researchers through knowledge sharing and networking. Inter-sectors mobility will bring SMEs and researchers to work conjointly on conditioning procedures for field tests, impact evaluation and product maturation/exploitation. The project will also adopt a concrete RRI approach by favouring public engagement and informal education through the different outreach activities aimed at a variety of target groups.

The DensAr project concerns the synthesis and investigation of ultra-high density arrays of self-organized and single-crystalline 1D nanomagnets. We have recently discovered a process by which we can directly grow on a metallic surface, arrays of Co nanowires (NWs) of 5nm in diameter, separated by a 2nm layer of stabilizing organic ligands. These nanowires are ferromagnetic at room temperature and organized in a hexagonal arrangement over large scales (1×1cm²), with densities of more than 10×1012 NWs/in². The process is based on colloidal chemistry and consists in the reduction of a Co molecular precursor in solution and at low temperature (<150°C) in the presence of a single-crystalline Pt film. The Co NWs are single-crystalline and grow epitaxially on the film. Thanks to the common orientation of the magnetization easy axes of the NWs, the NW arrays exhibit a high magnetic anisotropy perpendicular to the film. Currently, there are no other systems possessing ultra-high densities of single-crystalline nanomagnets which combine shape and magnetocrystalline anisotropies in the same direction. Indeed, all precedent studies on interacting nanomagnets involve polycrystalline elements, and/or arrays with limited periodic arrangements and densities, and/or random easy axis orientations. In the context of future hard disk drives of ultra-high densities, several fabrication routes are planned but up to now, a method for producing arrays of nanomagnets with densities superior to 1 Tbits/in² did not exist. The objective of the DensAr project concerns the demonstration of the applicability of the material as a future ultra-high density magnetic recording medium. The project focuses on the synthesis and the study of the structural and magnetic properties of arrays of Co NWs. The proof of concept of the synthesis process has been shown and patented. The project is thus based on a detailed and extensive study of the fundamental mechanisms of the Co NW growth on substrates, i.e. the degrees of freedom of the synthesis (Co precursor/ligands concentration ratio, ligand nature, temperature, pressure, reaction time, substrate nature) that will modulate the system’s morphological characteristics thus allowing to reduce the different spatial distributions (diameter, length, aspect ratio, inter-NW distance). The structural properties (length, diameter, inter-NW distance, long range order, density, array roughness, epitaxy) will be investigated using state of the art techniques (X-ray diffraction, electron and atomic force microscopies and neutron scattering techniques) in order to fully describe the resulting system. A major effort will concern the study of the magnetic properties (anisotropy, coercivity, dipolar coupling, thermal stability, switching field distribution, magnetization reversal mechanisms, magnetic correlation lengths), both experimentally (magnetometry, neutron scattering techniques, ferromagnetic resonance), and theoretically (micromagnetic simulations). A special attention will be paid to the magnetic and structural features that fulfill the requirements for future ultra-high density magnetic media above the Tbit/in². The DensAr project is a “Jeune Chercheur” project and consequently involves a single partner, the LPCNO, the Laboratory of Physics and Chemistry of Nano-Objects, and particularly the NanoMagnétisme and Nanostructures et Chimie Organométallique groups. They have complementary skills in the synthesis, structural and magnetic analyses of nano-objects. The consortium thus combines a high expertise on colloidal chemistry in solution and on thin films, as well as on structural investigations of nanosystems and on nanomagnetism. The gathering of specialists in each field, that have already proven their ability to work efficiently together in a friendly atmosphere, will guarantee the success of this enterprising project, that aims at providing new advanced and highly relevant nanomagnet arrays for industrial purposes.

The choice of two-dimensional (2D) materials to engineer devices with atomically flat active regions is currently extending far beyond graphene to a wide range of new semiconductors, insulators, metals and superconductors. Taking advantage of each material’s properties, the stacking of diverse 2D layers to build van der Waals heterostructures, should open the way to a new class of devices with potential applications in optoelectronics, spintronics, flexible electronics or photovoltaics. Among the various families of 2D materials, semiconductor transition metal dichalcogenide (TMDC) materials (MoS2, WS2, MoSe2, WSe2 and MoTe2) exhibit especially exciting properties when thinned down to one monolayer. In contrast to graphene, TMDC monolayers have a direct band gap yielding interesting electronic and optical properties in the visible and near infrared regions of the optical spectrum. In particular, they exhibit a strong light-matter interaction governed by very robust excitons from cryogenic to room temperature (Coulomb bound electron-hole pairs with binding energy of several hundreds of meV). This strong light-matter interaction can be used for optoelectronics applications (photodetectors, LEDs, solar cells, non-linear optics). Secondly, the interplay between crystal inversion symmetry breaking and strong spin-orbit coupling provides a unique access to control simultaneously two degrees of freedom for data processing and storage: the spin (up or down) and the electron momentum in k-space (K+ or K- valleys at the corners of the Brillouin zone). Thus, in addition to rich spin-valley physics, TMDC materials open the way to the development of spintronics or valleytronics devices provided they can exhibit long spin-valley lifetimes and convenient manipulation of these degrees of freedom. The goal of this disruptive project is to develop precise tuning of the strong light matter interaction and spin-valley properties of TMDC monolayers by embedding them in innovative van der Waals heterostructures. Three tuning parameters that can easily be controlled in a functional device will be studied: the dielectric environment, the charge carrier density and the electric field. We will first improve the quality of our van der Waals heterostructures (mainly the stacking of TMDC monolayers, graphene and hexagonal boron-nitride) by fabricating them in strictly controlled environment. Then, we will evaluate the potential of dielectric environment engineering to tune the energy and the oscillator strength of the excitonic states and the electronic band gap. In parallel, we will study the spin-valley relaxation mechanisms in TMDC MLs. Most of the existing studies in the field have focused on the spin-valley properties of optically bright but short-lived excitons. We will deal with longer lived excitations which are more promising for long spin-valley lifetimes (dark excitons, spatially indirect excitons and resident carriers). The optical signatures of these species are more difficult to access than the well-studied bright excitons and will require the fabrication of complex structures (charge tunable devices, type II heterostructures, samples for edge excitation). Finally we will study the effects of external and internal electric fields on the excitonic and spin-valley properties of TMDC monolayers. In particular, we aim to demonstrate the Stark effect and the Bychkov-Rashba effect which may pave the way to the development of optoelectronics and spintronics devices based on TMDC materials. In particular, we aim to demonstrate a proof of concept of a spin-valley memory working at room temperature.