Molecules in Environments: Towards Systematic Quantum Embedding of Electrons and Drude Oscillators

We develop a quantum embedding method that enables accurate and efficient treatment of interactions between molecules and an environment, while explicitly including many-body correlations. The molecule is composed of classical nuclei and quantum electrons, whereas the environment is modeled via charged quantum harmonic oscillators. We construct a general Hamiltonian and introduce a variational ansatz for the correlated ground state of the fully interacting molecule/environment system. This wavefunction is optimized via variational Monte Carlo and the ground state energy is subsequently estimated through diffusion Monte Carlo. The proposed scheme allows an explicit many-body treatment of electrostatic, polarization, and dispersion interactions between the molecule and the environment. We study solvation energies and excitation energies of benzene derivatives, obtaining excellent agreement with explicit ab initio calculations and experiment

Cluster-Assembled Nanoporous Super-Hydrophilic Smart Surfaces for On-Target Capturing and Processing of Biological Samples for Multi-Dimensional MALDI-MS

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) on cluster-assembled super-hydrophilic nanoporous titania films deposited on hydrophobic conductive-polymer substrates feature a unique combination of surface properties that significantly improve the possibilities of capturing and processing biological samples before and during the MALDI-MS analysis without changing the selected sample target (multi-dimensional MALDI-MS). In contrast to pure hydrophobic surfaces, such films promote a remarkable biologically active film porosity at the nanoscale due to the soft assembling of ultrafine atomic clusters. This unique combination of nanoscale porosity and super-hydrophilicity provides room for effective sample capturing, while the hydrophilic-hydrophobic discontinuity at the border of the dot-patterned film acts as a wettability-driven containment for sample/reagent droplets. In the present work, we evaluate the performance of such advanced surface engineered reactive containments for their benefit in protein sample processing and characterization. We shortly discuss the advantages resulting from the introduction of the described chips in the MALDI-MS workflow in the healthcare/clinical context and in MALDI-MS bioimaging (MALDI-MSI)

Correlated Wave Functions for Electron–Positron Interactions in Atoms and Molecules

The positron, as the antiparticle of the electron, can form metastable states with atoms and molecules before its annihilation with an electron. Such metastable matter–positron complexes are stabilized by a variety of mechanisms, which can have both covalent and noncovalent character. Specifically, electron–positron binding often involves strong many-body correlation effects, posing a substantial challenge for quantum-chemical methods based on atomic orbitals. Here we propose an accurate, efficient, and transferable variational ansatz based on a combination of electron–positron geminal orbitals and a Jastrow factor that explicitly includes the electron–positron correlations in the field of the nuclei, which are optimized at the level of variational Monte Carlo (VMC). We apply this approach in combination with diffusion Monte Carlo (DMC) to calculate binding energies for a positron e+ and a positronium Ps (the pseudoatomic electron–positron pair), bound to a set of atomic systems (H–, Li+, Li, Li–, Be+, Be, B–, C–, O– and F–). For PsB, PsC, PsO, and PsF, our VMC and DMC total energies are lower than that from previous calculations; hence, we redefine the state of the art for these systems. To assess our approach for molecules, we study the potential-energy surfaces (PES) of two hydrogen anions H– mediated by a positron (e+H22–), for which we calculate accurate spectroscopic properties by using a dense interpolation of the PES. We demonstrate the reliability and transferability of our correlated wave functions for electron–positron interactions with respect to state-of-the-art calculations reported in the literature

miniaturized fish for screening of onco hematological malignancies

Fluorescence in situ hybridization (FISH) represents a major step in the analysis of chromosomal aberrations in cancer. It allows the precise detection of specific rearrangements, both for diagnost..

Angle-resolved photoemission spectroscopy from first-principles quantum Monte Carlo

Angle-resolved photoemission spectroscopy allows one to visualize in momentum space the probability weight maps of electrons subtracted from molecules deposited on a substrate. The interpretation of these maps usually relies on the plane wave approximation through the Fourier transform of single particle orbitals obtained from density functional theory. Here we propose a first-principle many-body approach based on quantum Monte Carlo (QMC) to directly calculate the quasi-particle wave functions (also known as Dyson orbitals) of molecules in momentum space. The comparison between these correlated QMC images and their single particle counterpart highlights features that arise from many-body effects. We test the QMC approach on the linear C2H2, CO2, and N2 molecules, for which only small amplitude remodulations are visible. Then, we consider the case of the pentacene molecule, focusing on the relationship between the momentum space features and the real space quasi-particle orbital. Eventually, we verify the correlation effects present in the metal CuCl42- planar complex

A new way for researchers to deposit files in HAL, the French Open Archive

Ce document constitue une nouvelle façon pour les chercheurs de déposer des fichiers dans HAL, les Archives ouvertes en français

MS26 Communications PoC between NAKALA and HAL

PoC: Working Communication between Nakala, the Huma-Num's research data repository, and the academic publications available on HAL.This document specifies the development of the proof of concept (POC) which will allow the linking of publications deposited in HAL (including its HAL-SHS portal), the French open archive (https://hal.archives-ouvertes.fr/) developed by the CCSD (https://www.ccsd.cnrs.fr/), and data or datasets deposited in Nakala (https://nakala.fr/) developed by Huma-num (https://www.huma- num.fr/), the French research data repository for SSH data. It describes the workflow to be set up between the two repositories, the creation of the bidirectional relationship between publications and data, prospection for the implementation of tools to visualize these links in the two repositories, and finally how to expose these relationships and publish them, so that they are available, findable and usable by research communities (and by all citizens)

Molecules in Environments: Toward Systematic Quantum Embedding of Electrons and Drude Oscillators

peer reviewe

Structure, stability and stress properties of amorphous and nanostructured carbon films

Structural and mechanical properties of amorphous and nanocomposite carbon are investigated using tight-binding molecular dynamics and Monte Carlo simulations. In the case of amorphous carbon, we show that the variation of sp^3 fraction as a function of density is linear over the whole range of possible densities, and that the bulk moduli follow closely the power-law variation suggested by Thorpe. We also review earlier work pertained to the intrinsic stress state of tetrahedral amorphous carbon. In the case of nanocomposites, we show that the diamond inclusions are stable only in dense amorphous tetrahedral matrices. Their hardness is considerably higher than that of pure amorphous carbon films. Fully relaxed diamond nanocomposites possess zero average intrinsic stress.Comment: 10 pages, 6 figure

Excitonic-insulator instability and Peierls distortion in one-dimensional semimetals

The charge density wave instability in one-dimensional semimetals is usually explained through a Peierls-like mechanism, where the coupling of electrons and phonons induces a periodic lattice distortion along certain modes of vibration, leading to a gap opening in the electronic band structure and to a lowering of the symmetry of the lattice. In this work, we study two prototypical Peierls systems: the one-dimensional carbon chain and the monatomic hydrogen chain with accurate ab initio calculations based on quantum Monte Carlo and hybrid density functional theory. We demonstrate that in one-dimensional semimetals at T=0, a purely electronic instability can exist independently of a lattice distortion. It is induced by spontaneous formation of low energy electron-hole pairs resulting in the electronic band gap opening, i.e., the destabilization of the semimetallic phase is due to an excitonic mechanism