Solvent-aware Interfaces in Continuum Solvation

Continuum models to handle solvent and electrolyte effects in an effective way have a long tradition in quantum-chemistry simulations and are nowadays also being introduced in computational condensed-matter and materials simulations. A key ingredient of continuum models is the choice of the solute cavity, i.e. the definition of the sharp or smooth boundary between the regions of space occupied by the quantum-mechanical (QM) system and the continuum embedding environment. Although most of the solute-based approaches developed lead to models with comparable and high accuracy when applied to small organic molecules, they can introduce significant artifacts when complex systems are considered. As an example, condensed-matter simulations often deal with supports that present open structures. Similarly, unphysical pockets of continuum solvent may appear in systems featuring multiple molecular components. Here, we introduce a solvent-aware approach to eliminate the unphysical effects where regions of space smaller than the size of a single solvent molecule could still be filled with a continuum environment. We do this by defining a smoothly varying solute cavity that overcomes several of the limitations of straightforward solute-based definitions. This new approach applies to any smooth local definition of the continuum interface, being it based on the electronic density or the atomic positions of the QM system. It produces boundaries that are continuously differentiable with respect to the QM degrees of freedom, leading to accurate forces and/or Kohn-Sham potentials. Benchmarks on semiconductor substrates and on explicit water substrates confirm the flexibility and the accuracy of the approach and provide a general set of parameters for condensed-matter systems featuring open structures and/or explicit liquid components.

Coupling hydrophobic, dispersion, and electrostatic contributions in continuum solvent models

Recent studies of the hydration of micro- and nanoscale solutes have demonstrated a strong {it coupling} between hydrophobic, dispersion and electrostatic contributions, a fact not accounted for in current implicit solvent models. We present a theoretical formalism which accounts for coupling by minimizing the Gibbs free energy with respect to a solvent volume exclusion function. The solvent accessible surface is output of our theory. Our method is illustrated with the hydration of alkane-assembled solutes on different length scales, and captures the strong sensitivity to the particular form of the solute-solvent interactions in agreement with recent computer simulations.

Redox potential replica exchange molecular dynamics at constant pH in AMBER: Implementation and validation

Redox processes are important in chemistry, with applications in biomedicine, chemical analysis, among others. As many redox experiments are also performed at a fixed value of pH, having an efficient computational method to support experimental measures at both constant redox potential and pH is very important. Such computational techniques have the potential to validate experimental observations performed under these conditions and to provide additional information unachievable experimentally such as an atomic level description of macroscopic measures. We present the implementation of discrete redox and protonation states methods for constant redox potential Molecular Dynamics (CEMD), for coupled constant pH and constant redox potential MD (C(pH,E)MD), and for Replica Exchange MD along the redox potential dimension (E-REMD) on the AMBER software package. Validation results are presented for a small system that contains a single heme group: N-acetylmicroperoxidase-8 (NAcMP8) axially connected to a histidine peptide. The methods implemented allow one to make standard redox potential (Eo) predictions with the same easiness and accuracy as pKa predictions using the constant pH molecular dynamics and pH-REMD methods currently available on AMBER. In our simulations, we can correctly describe, in agreement also with theoretical predictions, the following behaviors: when a redox-active group is reduced, the pKa of a near pH-active group increases because it becomes easier for a proton to be attached; equivalently, when a pH-active group is protonated, the Eo of an adjacent redox-active group rises. Furthermore, our results also show that E-REMD is able to achieve faster statistical convergence than CEMD or C(pH,E)MD. Moreover, computational benchmarks using our methodologies show high-performance of GPU accelerated calculations in comparison to conventional CPU calculations.

A size-dependent ductile fracture model: Constitutive equations, Numerical implementation and Validation

Size effects have been predicted at the micro- or nano-scale for porous ductile materials from Molecular Dynamics, Discrete Dislocation Dynamics and Continuum Mechanics numerical simulations, as a consequence of Geometrically Necessary Dislocations or due to the presence of a void matrix interface. As voids size decreases, higher stresses are needed to deform the material, for a given porosity. However, the majority of the homogenized models for porous materials used in ductile fracture modeling are size-independent, even though micrometric or nanometric voids are commonly observed in structural materials. Based on yield criteria proposed in the literature for nanoporous materials, a size-dependent homogenized model for porous materials is proposed for axisymmetric loading conditions, including void growth and coalescence as well as void shape effects. Numerical implementation of the constitutive equations is detailed. The homogenized model is validated through comparisons to porous unit cells finite element simulations that consider interfacial stresses, consistently with the model used for the derivation of the yield criteria, aiming at modeling an additional hardening at the void matrix interface. Potential improvements of the model are finally discussed with respect to the theoretical derivation of refined yield criteria and evolution laws.

Implementation and validation of the LHC SUSY searches with MadAnalysis 5

Separate, validated implementations of the ATLAS and CMS new physics analyses are necessary to fully exploit the potential of these searches. To this end, we use MadAnalysis 5, a public framework for collider phenomenology. In this talk, we present recent developments of MadAnalysis 5, as well as a new public database of reimplemented LHC analyses. The validation of one ATLAS and one CMS search for supersymmetry, present in the database, is also summarized.