Accurate biomolecular simulations account for electronic polarization

International audienceIn this perspective, we discuss where and how accounting for electronic many-body polarization affects the accuracy of classical molecular dynamics simulations of biomolecules.While the effects of electronic polarization are highly pronounced for molecules with an opposite total charge, they are also non-negligible for interactions with overall neutral molecules. For instance, neglecting these effects in important biomolecules like amino acids and phospholipids affects the structure of proteins and membranes having a large impact on interpreting experimental data as well as building coarse grained models. With the combined advances in theory, algorithms and computational power it is currently realistic to perform simulations with explicit polarizable dipoles on systems with relevant sizes and complexity. Alternatively, the effects of electronic polarization can also be included at zero additional computational cost compared to standard fixed-charge force fields using the electronic continuum correction, as was recently demonstrated for several classes of biomolecules

ReaxFF Simulations of Self-Assembled Monolayers On Silver Surfaces and Nanocrystals

The self-assembled monolayers of alkane thiolates on Ag (111) surfaces and nanoparticles are studied using molecular dynamics. Reactive force fields allow simulations of very large systems such as nanoparticles of 10 nm. Stable (sqrt(7) X sqrt(7))R19.1{\deg} assemblies are obtained as experimentally observed for these systems. Only nanoparticles smaller than 4 nm show a spontaneous restructuration of the metallic core. The preferred adsorption site is found to be in an on-top position, in good agreement with recent X-ray absorption near edge structure experiments. Moreover, similar distances between the sulfur headgroups are found on the facets and edges

Smooth Particle Mesh Ewald-integrated stochastic Lanczos Many-body Dispersion algorithm

We derive and implement an alternative formulation of the Stochastic Lanczos algorithm to be employed in connection with the Many-Body Dispersion model (MBD). Indeed, this formulation, which is only possible due to the Stochastic Lanczos' reliance on matrix-vector products, introduces generalized dipoles and fields. These key quantities allow for a state-of-the-art treatment of periodic boundary conditions via the O(Nlog(N)) Smooth Particle Mesh Ewald (SPME) approach which uses efficient fast Fourier transforms. This SPME-Lanczos algorithm drastically outperforms the standard replica method which is affected by a slow and conditionally convergence rate that limits an efficient and reliable inclusion of long-range periodic boundary conditions interactions in many-body dispersion modelling. The proposed algorithm inherits the embarrassingly parallelism of the original Stochastic Lanczos scheme, thus opening up for a fully converged and efficient periodic boundary condition treatment of MBD approaches

Electron Pair Localization Function (EPLF) for Density Functional Theory and ab Initio Wave Function-Based Methods: A New Tool for Chemical Interpretation

International audienceWe present a modified definition of the Electron Pair Localization Function (EPLF), initially defined within the framework of quantum Monte Carlo approaches [Scemama, A.; Caffarel, M.; Chaquin, P. J. Chem. Phys. 2004, 121, 1725] to be used in Density Functional Theories (DFT) and ab initio wave-function-based methods. This modified version of the EPLF--while keeping the same physical and chemical contents--is built to be analytically computable with standard wave functions or Kohn−Sham representations. It is illustrated that the EPLF defines a simple and powerful tool for chemical interpretation via selected applications including atomic and molecular closed-shell systems, σ and π bonds, radical and singlet open-shell systems, and molecules having a strong multiconfigurational character. Some applications of the EPLF are presented at various levels of theory and compared to Becke and Edgecombe's Electron Localization Function (ELF). Our open-source parallel software implementation of the EPLF opens the possibility of its use by a large community of chemists interested in the chemical interpretation of complex electronic structures

Open Source Variational Quantum Eigensolver Extension of the Quantum Learning Machine (QLM) for Quantum Chemistry

Quantum Chemistry (QC) is one of the most promising applications of Quantum Computing. However, present quantum processing units (QPUs) are still subject to large errors. Therefore, noisy intermediate-scale quantum (NISQ) hardware is limited in terms of qubits counts and circuit depths. Specific algorithms such as Variational Quantum Eigensolvers (VQEs) can potentially overcome such issues. We introduce here a novel open-source QC package, denoted Open-VQE, providing tools for using and developing chemically-inspired adaptive methods derived from Unitary Coupled Cluster (UCC). It facilitates the development and testing of VQE algorithms. It is able to use the Atos Quantum Learning Machine (QLM), a general quantum programming framework enabling to write, optimize and simulate quantum computing programs. Along with Open-VQE, we introduce myQLM-Fermion, a new open-source module (that includes the key QLM ressources that are important for QC developments (fermionic second quantization tools etc...). The Open-VQE package extends therefore QLM to QC providing: (i) the functions to generate the different types of excitations beyond the commonly used UCCSD ans{\"a}tz;(ii) a new implementation of the "adaptive derivative assembled pseudo-Trotter method" (ADAPT-VQE), written in simple class structure python codes. Interoperability with other major quantum programming frameworks is ensured thanks to myQLM, which allows users to easily build their own code and execute it on existing QPUs. The combined Open-VQE/myQLM-Fermion quantum simulator facilitates the implementation, tests and developments of variational quantum algorithms towards choosing the best compromise to run QC computations on present quantum computers while offering the possibility to test large molecules. We provide extensive benchmarks for several molecules associated to qubit counts ranging from 4 up to 24

Overlap-ADAPT-VQE: Practical Quantum Chemistry on Quantum Computers via Overlap-Guided Compact Ans\"atze

ADAPT-VQE is a robust algorithm for hybrid quantum-classical simulations of quantum chemical systems on near-term quantum computers. While its iterative process systematically reaches the ground state energy, ADAPT-VQE is sensitive to local energy minima, leading to over-parameterized ans\"atze. We introduce the Overlap-ADAPT-VQE to grow wave-functions by maximizing their overlap with any intermediate target wave-function that already captures some electronic correlation. By avoiding building the ansatz in the energy landscape strewn with local minima, the Overlap-ADAPT-VQE produces ultra-compact ans\"atze suitable for high-accuracy initializations of a new ADAPT procedure. Spectacular advantages over ADAPT-VQE are observed for strongly correlated systems including massive savings in circuit depth. Since this compression strategy can also be initialized with accurate Selected-Configuration Interaction (SCI) classical target wave-functions, it paves the way for chemically accurate simulations of larger systems, and strengthens the promise of decisively surpassing classical quantum chemistry through the power of quantum computing