Solvation in atomic liquids: connection between Gaussian field theory and density functional theory

For the problem of molecular solvation, formulated as a liquid submitted to the external potential field created by a molecular solute of arbitrary shape dissolved in that solvent, we draw a connection between the Gaussian field theory derived by David Chandler [Phys. Rev. E, 1993, 48, 2898] and classical density functional theory. We show that Chandler's results concerning the solvation of a hard core of arbitrary shape can be recovered by either minimising a linearised HNC functional using an auxiliary Lagrange multiplier field to impose a vanishing density inside the core, or by minimising this functional directly outside the core --- indeed a simpler procedure. Those equivalent approaches are compared to two other variants of DFT, either in the HNC, or partially linearised HNC approximation, for the solvation of a Lennard-Jones solute of increasing size in a Lennard-Jones solvent. Compared to Monte-Carlo simulations, all those theories give acceptable results for the inhomogeneous solvent structure, but are completely out-of-range for the solvation free-energies. This can be fixed in DFT by adding a hard-sphere bridge correction to the HNC functional.Comment: 14 pages, 4 figure

Polarization control at the microscopic and electronic structure observatory

The new Microscopic and Electronic Structure Observatory (MAESTRO) at the Advanced Light Source (ALS) in Berkeley provides X-rays of variable polarization, produced by an elliptically polarized undulator (EPU), for angle resolved photoemission (ARPES) and photoemission electron microscopy (PEEM) experiments. The interpretation of photoemission data, in particular of dichroism effects in ARPES, requires the precise knowledge of the exact polarization state. Numerical simulations show that the first harmonics of the EPU at MAESTRO provides soft X-rays of almost 100% on axis polarization. However, the higher harmonics as well as the downstream optical elements of the beamline, have a considerable impact on the polarization of the light delivered to the experimental end-station. Employing a simple reflective polarimeter, the polarization is characterized for variable EPU and beamline settings and the overall degree of polarization in the MAESTRO end-stations is estimated to be on the order of 83%

Jean-Pierre Hansen - a stimulating history of simulating fluids

International audienc

Diffusion coefficient and shear viscosity of rigid water models

We report the diffusion coefficient and viscosity of popular rigid water models: Two non polarizable ones (SPC/E with 3 sites, and TIP4P/2005 with 4 sites) and a polarizable one (Dang-Chang, 4 sites). We exploit the dependence of the diffusion coefficient on the system size [Yeh and Hummer, J. Phys. Chem. B 108, 15873 (2004)] to obtain the size-independent value. This also provides an estimate of the viscosity of all water models, which we compare to the Green-Kubo result. In all cases, a good agreement is found. The TIP4P/2005 model is in better agreement with the experimental data for both diffusion and viscosity. The SPC/E and Dang-Chang water overestimate the diffusion coefficient and underestimate the viscosity.Comment: 10 pages, 2 figures. To be published in J. Phys.: Condens. Matte

Quasiparticle Transformation During a Metal-Insulator Transition in Graphene

Here we show, with simultaneous transport and photoemission measurements, that the graphene terminated SiC(0001) surface undergoes a metal-insulator transition (MIT) upon dosingwith small amounts of atomic hydrogen. We find the room temperature resistance increases by about 4 orders of magnitude, a transition accompanied by anomalies in the momentum-resolved spectral function including a non-Fermi Liquid behaviour and a breakdown of the quasiparticle picture. These effects are discussed in terms of a possible transition to a strongly (Anderson) localized ground state.Comment: 11 pages, 4 figure

Molecular hydrodynamics from memory kernels

The memory kernel for a tagged particle in a fluid, computed from molecular dynamics simulations, decays algebraically as t−3/2. We show how the hydrodynamic Basset-Boussinesq force naturally emerges from this long-time tail and generalize the concept of hydrodynamic added mass. This mass term is negative in the present case of a molecular solute, which is at odds with incompressible hydrodynamics predictions. Lastly, we discuss the various contributions to the friction, the associated time scales, and the crossover between the molecular and hydrodynamic regimes upon increasing the solute radius

String attractors : Verification and optimization

String attractors [STOC 2018] are combinatorial objects recently introduced to unify all known dictionary compression techniques in a single theory. A set γ ⊆ [1.n] is a k-attractor for a string S ∈ Σn if and only if every distinct substring of S of length at most k has an occurrence crossing at least one of the positions in γ. Finding the smallest k-attractor is NP-hard for k ≥ 3, but polylogarithmic approximations can be found using reductions from dictionary compressors. It is easy to reduce the k-attractor problem to a set-cover instance where the string's positions are interpreted as sets of substrings. The main result of this paper is a much more powerful reduction based on the truncated suffix tree. Our new characterization of the problem leads to more efficient algorithms for string attractors: we show how to check the validity and minimality of a k-attractor in near-optimal time and how to quickly compute exact solutions. For example, we prove that a minimum 3-attractor can be found in O(n) time when |Σ| ∈ O(3+ϵ√log n) for some constant ϵ > 0, despite the problem being NP-hard for large Σ. © Dominik Kempa, Alberto Policriti, Nicola Prezza, and Eva Rotenberg.Peer reviewe

Reduced variance analysis of molecular dynamics simulations by linear combination of estimators

International audienceBuilding upon recent developments of force-based estimators with a reduced variance for the computation of densities, radial distribution functions or local transport properties from molecular simulations, we show that the variance can be further reduced by considering optimal linear combinations of such estimators. This control variates approach, well known in Statistics and already used in other branches of computational Physics, has been comparatively much less exploited in molecular simulations. We illustrate this idea on the radial distribution function and the one-dimensional density of a bulk and confined Lennard-Jones fluid, where the optimal combination of estimators is determined for each distance or position, respectively. In addition to reducing the variance everywhere at virtually no additional cost, this approach cures an artefact of the initial force-based estimators, namely small but non-zero values of the quantities in regions where they should vanish. Beyond the examples considered here, the present work highlights more generally the underexplored potential of control variates to estimate observables from molecular simulations

Cluster sum rules for three-body systems with angular-momentum dependent interactions

We derive general expressions for non-energy weighted and energy-weighted cluster sum rules for systems of three charged particles. The interferences between pairs of particles are found to play a substantial role. The energy-weighted sum rule is usually determined by the kinetic energy operator, but we demonstrate that it has similar additional contributions from the angular momentum and parity dependence of two- and three-body potentials frequently used in three-body calculations. The importance of the different contributions is illustrated with the dipole excitations in $^6$He. The results are compared with the available experimental data.Comment: 11 pages, 3 figures, 2 table