Séminaire Axe 3 présenté par Dr. Thijs Stuyver

Orateur : Dr. Thijs Stuyver (Chimie ParisTech, PSL)

Résumé :

Machine learning (ML) has had a significant impact on various subfields of science in recent years. Part of the reason for the success of ML is that it enables the generation of predictive models with only limited domain knowledge: usually, only minor modifications to a generic ML algorithm needs to be made to generate effective models for a specific application. That is of course under the condition that sufficient data is available, and then we usually mean hundreds of thousands or even millions of datapoints. In chemistry, there are several predictive tasks for which we have this abundancy of data, but for most specialized applications – particularly those related to chemical reactivity – we do not have this luxury.

              In principle, computational chemistry offers a way out when limited experimental data is available, since it enables data generation in a cheap and easy-to-automate manner. In the first part of my talk, I will explore this approach in a bit more detail and focus specifically on an ML accelerated computational workflow to screen for promising bioorthogonal click reactions that I recently developed.

              While quantum chemical simulations of reactivity tend to be relatively cheap compared to experimental characterizations, the cost of generating sufficient training data for a machine learning model still becomes prohibitive, fast. As such, in the second part of my talk I will discuss strategies to improve the data efficiency of ML-based computational workflows for reactivity prediction. Specifically, I will focus on models based on intermediate valence bond inspired representations, and demonstrate that these outperform conventional machine learning models by a wide margin for hydrogen atom transfer reactions in the low data regime.

References

  • Casetti, N.; Alfonso-Ramos, J. E.; Coley, C. W.*; Stuyver, T.*, Combining Molecular Modeling and Machine learning for accelerated reaction screening and discovery, Chem. Eur. J. 2023, e202301957.
  • Stuyver, T.*; Jorner, K.; Coley, C. W.*, Reaction profiles for quantum chemistry-computed [3+2] cycloaddition reactions, Sci. Data 2023, 10, 66.
  • Stuyver, T.*; Coley, C. W.*, Machine learning‐guided computational screening of new candidate reactions with high bioorthogonal click potential, Chem. Eur. J. 2023, e202300387.
  • Alfonso-Ramos, J.; Neeser, R.; Stuyver, T. Repurposing Quantum Chemical Descriptor Datasets for on-the-Fly Generation of Informative Reaction Representations: Application to Hydrogen Atom Transfer Reactions, ChemRxiv 2023, 10.26434/chemrxiv-2023-2n281.

Séminaire IPCMS présenté par Florence GAZEAU

Florence GAZEAU (MSC Med Lab and IVETh integrator , 45 rue des Saints Pères, 75006 Paris, France)

Résumé : The clinical use of extracellular vesicles (EVs) will progressively become a reality in view of the number of ongoing clinical trials worldwide harnessing EV potency for tissue healing, resolution of inflammation (notably in Covid 19 patients), vaccination, drug delivery or cancer therapies, among others. EVs, encompassing a variety of cell shed nanoscale membrane vesicles (exosomes, ectosomes, microvesicles, OMV from bacteria…), are released by all cell types, either spontaneously or after induction, and circulate in all body fluids playing an active role in many physio- and pathological processes. EVs contribute to intercellular communication and immunomodulation via delivering bio-molecules like nucleic acids, proteins, and lipids that modify the recipient cells. Numerous biological effects of cell therapy rely on the cells’ secretome and, in particular on biomolecules contained in EVs, which are now studied as potential therapeutic agents to recapitulate a substantial part of the parental cell’s benefits, especially for stem cell-derived EVs.  However the clinical translation of EV-based biotherapies face numerous challenges such as cost-effective large scale bioproduction compatible with a clinical use (GMP manufacturing), reproducibility from one batch to another and difficulties to isolate, characterize and identify the most potent nanosized subfractions from a complex and heterogeneous cell secretome. In addition, the technologies to engineer EVs in a pre-production or post-production step to convey specific proteins, nucleic acids, drugs and nanoparticles and improve or control their specific targeting and therapeutic activities are still in their infancy. In this presentation, we will present the breakthrough technologies for high throughput bioproduction, engineering and multimodal IA-assisted characterization of therapeutic stem cell-derived EVs, as well as EV delivery, that have been developed in our lab and led to the creation of two spin off. These technologies, based on multidisciplinary and physics-powered approaches (turbulence approach for high yield high throughput EV bioproduction and loading, EV delivery in a carrier gel, multimodal analysis tool box) are available for the industrial and academic partners on our innovation hub IVETh (https://iveth.u-paris.fr/) labelized as a national industrial integrator biotherapy-bioproduction in 2022

Séminaire AXE 1 “Sciences et Matériaux Quantiques” : présenté par Vikram Deshpande

Orateur : Vikram Deshpande, University of Utah, USA

Résumé : Topological materials have burgeoned of late due to their implications for the fields of electronics, spintronics and quantum computing, among others. While their electronic properties are important in their own right, they can also couple in fascinating ways to the lattice. We have developed techniques to deform materials controllably and study their resulting electronic properties in-situ, while complementarily sensing the electronic ground state through the mechanical degree of freedom. In this talk, by way of introduction, I will first present purely electrical measurements on the prototypical topological material, the three-dimensional (3D) topological insulator (TI), wherein we hybridize Dirac cones of 3D TI surfaces controllably to realize the quantum spin Hall effect in the ultrathin limit. Then I will present our recent results applying the above-mentioned mechanical techniques to two different topological materials, namely twisted bilayer graphene (TBG) and the intrinsic magnetic topological insulator (MTI) MnBi2Te4, respectively. We are able to tune the Hofstadter’s spectrum of non-magic angle TBG and induce magnetism in non-magnetic correlated insulating states of magic-angle TBG using isotropic strain, for example, and detect various magnetic states and measure magnetoelastic couplings in the case of MTIs. Our advances present unique routes to tuning and sensing the parameter space of these exciting materials.

Contact : Stéphane BERCIAUD (berciaud@unistra.fr)

Séminaire IPCMS présenté par Amélie JUHIN

Oratrice : Amélie JUHIN  (Institut de Minéralogie, Physique des Matériaux et Cosmochimie (IMPMC). CNRS-Sorbonne Université)

Résumé : X-ray spectroscopies performed at synchrotron light sources, such as X-ray Absorption Spectroscopy and Resonant Inelastic X-ray Scattering are powerful tools to study complex materials, due to their chemical selectivity that allows disentangling the respective contributions of different atomic species. In this talk, I will show how the use of incident polarized x-rays (either linear or circular) can allow a deeper understanding of the electronic structure and reveal emergent properties, with a focus on remarkable magnetic nanomaterials: Single Molecule Magnets, bimagnetic nanoparticles, ferrofluids, ultra-thin nanowires. Moreover, I will illustrate how the combination of these spectroscopies with x-ray microscopy can provide valuable information with nanoscale spatial resolution, exemplified by recent results obtained on magnetotactic organisms.

Séminaire AXE 1 “Sciences et Matériaux Quantiques” : présenté par Benjamin Besga

Orateur : Benjamin Besga, ILM Lyon

Résumé : The aim of stochastic thermodynamics is to study small non-equilibrium systems subject to thermal fluctuations. Some results from this field will be illustrated using experiments carried out on opto-mechanical systems, mainly colloidal particles in an optical trap. Using non-equilibrium statistical physics will see how we can accelerate the natural dynamics of a system, shorten the mean first passage time on a target, or measure the forces acting on a non-equilibrium probe. Finally, we’ll ask how we can interrogate the quantum limit of these results by looking at the opto-mechanical coupling of a self assembled supercrystal of quantum dots in an optical trap.

Séminaire DON , axes 1 et 4 présenté par Abdelghani Laraoui

Abdelghani Laraoui (Department of Mechanical & Materials Engineering, University of Nebraska-Lincoln)

Résumé :
Magnetic microscopy based on nitrogen vacancy (NV) centers in diamond has become a versatile tool to detect magnetic fields with an unprecedented combination of spatial resolution and magnetic sensitivity, opening up new frontiers in biological [1] and condensed physics matter research [2]. In this seminar, I will present two examples of using NV magnetic microscopy in both scanning probe microscopy (SPM) and wide-field microscopy (WFM) geometries to study nanoscale magnetic phenomena in different materials. First, I will discuss NV-SPM measurements of antiferromagnetic (AFM) domains switching in Cr2O3 and B-Cr2O3 thin films and device structures [3, 4]. Cr2O3 is an archetypical AFM oxide that permits voltage-control of the Néel vector. In addition, boron doping increases Néel temperature from 307 K to 400 K and allows realizing voltage controlled Néel vector at zero applied magnetic field, a promising finding to AFM spintronics. Then, I will discuss NV-WFM measurements on individual Fe(Htrz)2(trz)](BF4)] (Fe triazole) spin-crossover (SCO) nano-rods of size varying from 20 to 1000 nm [5]. Fe triazole SCO complexes exhibit thermal switching between low spin (LS) and high spin (HS) states which are applicable in thermal sensors and molecular switches. While the bulk magnetic properties of these molecules are widely studied by bulk magnetometry techniques their properties at the individual level are missing. The stray magnetic fields produced by individual Fe-triazole nano-rods are imaged by NV magnetic microscopy as a function of temperature (up to 150 0C) and applied magnetic field (up to 3500 G). We found that in most of the nanorods the LS state is slightly paramagnetic, possibly originating from the surface oxidation and/or the greater Fe(III) presence along the nanorods’ edges [5].

References: [1] I. Fescenko, A. Laraoui, et al., Phys. Rev. App. 11, 034029 (2019). [2] A. Laraoui and K.
Ambal, Appl. Phys. Lett. 121, 060502 (2022). [3] A. Erickson, A. Laraoui, et al., RSC Adv. 13, 178-185 (2023).
[4] A. Erickson, A. Laraoui, et al., to be submitted to Nat. Mat. (2023). [5] S. Lamichhane, A. Laraoui, et al.,
ACS Nano 17, 9, 8694–8704 (2023).

Contact : Valérie Halté (valerie.halte@ipcms.unistra.fr)