Intermolecular Pauli repulsion: a QMC study of molecules in ground and excited state in free space and in solution

In this work we present a method to compute the Pauli repulsion interaction energy between two molecules and for a molecule solvated by a discrete medium. The method of Amovilli and Mennucci, that has been developed within a continuum solvent model approach, is here revised in order to treat the solvation environment with a discrete number of solvent molecules. In our model, one of the two interacting systems, and the solvent in the case of solvation, acts as ‘probe’. A probe has a volume domain defined by the atomic spheres centred on the nuclei of the relevant molecule. The probe measures the fraction of electrons of the solute molecule falling in its domain leading to the evaluation of Pauli repulsion energy. To this end, Quantum Monte Carlo calculations are used to sample the electronic configurations of the solute. The method has been designed to be applied also to excited states. We show results for test systems in the ground state and for the ground and the (Formula presented.) excited states of acetone in a cluster with 14 water molecules

Detecting vapour bubbles in simulations of metastable water

International audienceThe investigation of cavitation in metastable liquids with molecular simulations requires an appropriate definition of the volume of the vapour bubble forming within the metastable liquid phase. Commonly used approaches for bubble detection exhibit two significant flaws: first, when applied to water they often identify the voids within the hydrogen bond network as bubbles thus masking the signature of emerging bubbles and, second, they lack thermodynamic consistency. Here, we present two grid-based methods, the M-method and the V-method, to detect bubbles in metastable water specifically designed to address these shortcomings. The M-method incorporates information about neighbouring grid cells to distinguish between liquid- and vapour-like cells, which allows for a very sensitive detection of small bubbles and high spatial resolution of the detected bubbles. The V-method is calibrated such that its estimates for the bubble volume correspond to the average change in system volume and are thus thermodynamically consistent. Both methods are computationally inexpensive such that they can be used in molecular dynamics and Monte Carlo simulations of cavitation. We illustrate them by computing the free energy barrier and the size of the critical bubble for cavitation in water at negative pressure

The generalized identification of truly interfacial molecules (ITIM) algorithm for nonplanar interfaces

We present a generalized version of the ITIM algorithm for the identification of interfacial molecules, which is able to treat arbitrarily shaped interfaces. The algorithm exploits the similarities between the concept of probe sphere used in ITIM and the circumsphere criterion used in the α-shapes approach, and can be regarded either as a reference-frame independent version of the former, or as an extended version of the latter that includes the atomic excluded volume. The new algorithm is applied to compute the intrinsic orientational order parameters of water around a dodecylphosphocholine and a cholic acid micelle in aqueous environment, and to the identification of solvent-reachable sites in four model structures for soot. The additional algorithm introduced for the calculation of intrinsic density profiles in arbitrary geometries proved to be extremely useful also for planar interfaces, as it allows to solve the paradox of smeared intrinsic profiles far from the interface. © 2013 American Institute of Physics

Real-Time analysis and visualization for single-molecule based super-resolution microscopy

Accurate multidimensional localization of isolated fluorescent emitters is a time consuming process in single-molecule based super-resolution microscopy. We demonstrate a functional method for real-time reconstruction with automatic feedback control, without compromising the localization accuracy. Compatible with high frame rates of EM-CCD cameras, it relies on a wavelet segmentation algorithm, together with a mix of CPU/GPU implementation. A combination with Gaussian fitting allows direct access to 3D localization. Automatic feedback control ensures optimal molecule density throughout the acquisition process. With this method, we significantly improve the efficiency and feasibility of localization-based super-resolution microscopy

Systematically convergent method for accurate total energy calculations with localized atomic orbitals

We introduce a method for solving a self consistent electronic calculation within localized atomic orbitals, that allows us to converge to the complete basis set (CBS) limit in a stable, controlled, and systematic way. We compare our results with the ones obtained with a standard quantum chemistry package for the simple benzene molecule. We find perfect agreement for small basis set and show that, within our scheme, it is possible to work with a very large basis in an efficient and stable way. Therefore we can avoid to introduce any extrapolation to reach the CBS limit. In our study we have also carried out variational Monte Carlo (VMC) and lattice regularized diffusion Monte Carlo (LRDMC) with a standard many-body wave function (WF) defined by the product of a Slater determinant and a Jastrow factor. Once the Jastrow factor is optimized by keeping fixed the Slater determinant provided by our new scheme, we obtain a very good description of the atomization energy of the benzene molecule only when the basis of atomic orbitals is large enough and close to the CBS limit, yielding the lowest variational energies.Comment: 22 pages, 6 figures, accepted in Physical Review