Shannon Entropy and Many-Electron Correlations: Theoretical Concepts, Numerical Results and Collins Conjecture

In this paper I will discuss the overlap between the concept of Shannon Entropy and the concept of electronic correlation. Quantum Monte Carlo numerical results for the uniform electron gas are also presented; these latter on the one hand enhance the hypothesis of a direct link between the two concepts but on the other hand leave a series of open questions which may be employed to trace a roadmap for the future research in the field.Comment: 27 pages with 3 figure

Grand-Canonical Adaptive Resolution Centroid Molecular Dynamics: Implementation and Application

We have implemented the Centroid Molecular Dynamics scheme (CMD) into the Grand Canonical-like version of the Adaptive Resolution Simulation Molecular Dynamics (GC-AdResS) method. We have tested the implementation on two different systems, liquid parahydrogen at extreme thermodynamic conditions and liquid water at ambient conditions; the reproduction of structural as well as dynamical results of reference systems are highly satisfactory. The capability of performing GC-AdResS CMD simulations allows for the treatment of a system characterized by some quantum features and open boundaries. This latter characteristic not only is of computational convenience, allowing for equivalent results of much larger and computationally more expensive systems, but also suggests a tool of analysis so far not explored, that is the unambiguous identification of the essential (quantum) degrees of freedom required for a given property

Solvation of positive ions in water: The dominant role of water-water interaction

Local polarization effects, induced by mono and divalent positive ions in water, influence (and in turn are influenced by) the large scale structural properties of the solvent. Experiments can only distinguish this process of interplay in a generic qualitative way. Instead, first principles quantum calculations can address the question at both electronic and atomistic scale, accounting for electronic polarization as well as geometrical conformations. For this reason we study the extension of the scales' interconnection by means of first principle Car-Parrinello molecular dynamics applied to systems of different size. In this way we identify the general aspects dominating the physics of the first solvation shell and their connection to the effects related to the formation of the outer shells and eventually the bulk. We show that while the influence of the ions is extended to the first shell only, the water-water interaction is instead playing a dominant role even within the first shell independently from the size or the charge of the ion.Comment: 4 pages 3 figures (color

Nanoscale domains in ionic liquids: A statistical mechanics definition for molecular dynamics studies

One of the many open questions concerning Ionic Liquids (ILs) is the existence of nanoscale supramolecular domains which characterize the bulk. The hypothesis of their existence does not meet a general consensus since their definition seems to be based on ad hoc arbitrary criteria rather than on general and solid first principles of physics. In this work, we propose a suitable definition of supramolecular domains based on first principles of statistical mechanics. Such principles can be realized through the application of a recently developed computational tool which employs adaptive molecular resolution. The method can identify the smallest region of a liquid for which the atomistic details are strictly required, while the exterior plays the role of a generic structureless thermodynamic reservoir. We consider four different imidazolium-based ILs and show that indeed one can quantitatively represent the liquid as a collection of atomistically self-contained nanodroplets embedded in a generic thermodynamic bath. Such nanodroplets express a characteristic length scale for heterogeneity in ILs.Comment: 9 page

Influence of pH and sequence in peptide aggregation via molecular simulation

We employ a recently developed coarse-grained model for peptides and proteins where the effect of pH is automatically included. We explore the effect of pH in the aggregation process of the amyloidogenic peptide KTVIIE and two related sequences, using three different pH environments. Simulations using large systems (24 peptides chains per box) allow us to correctly account for the formation of realistic peptide aggregates. We evaluate the thermodynamic and kinetic implications of changes in sequence and pH upon peptide aggregation, and we discuss how a minimalistic coarse-grained model can account for these details.Comment: 21 pages, 4 figure

Partitioning a macroscopic system into independent subsystems

We discuss the problem of partitioning a macroscopic system into a collection of independent subsystems. The partitioning of a system into replica-like subsystems is nowadays a subject of major interest in several field of theoretical and applied physics, and the thermodynamic approach currently favoured by practitioners is based on a phenomenological definition of an interface energy associated with the partition, due to a lack of easily computable expressions for a microscopic (i.e.~particle-based) interface energy. In this article, we outline a general approach to derive sharp and computable bounds for the interface free energy in terms of microscopic statistical quantities. We discuss potential applications in nanothermodynamics and outline possible future directions.Comment: This is an author-created, un-copyedited version of an article accepted for publication in JSTA

pH-dependent coarse-grained model of peptides

We propose the first, to our knowledge, coarse-grained modeling strategy for peptides where the effect of changes of the pH can be efficiently described. The idea is based on modeling the effects of the pH value on the main driving interactions. We use reference data from atomistic simulations and experimental databases and transfer its main physical features to the coarse-grained resolution according the principle of "consistency across the scales". The coarse-grained model is refined by finding a set of parameters that, when applied to peptides with different sequences and experimental properties, reproduces the experimental and atomistic data of reference. We use the such parameterized model for performing several numerical tests to check its transferability to other systems and to prove the universality of the related modeling strategy. We have tried systems with rather different response to pH variations, showing a highly satisfactory performance of the model.Comment: accepted for publication in Soft Matte

Autocatalytic and cooperatively-stabilized dissociation of water on a stepped platinum surface

Water-metal interfaces are ubiquitous and play a key role in many chemical processes, from catalysis to corrosion. Whereas water adlayers on atomically flat transition metal surfaces have been investigated in depth, little is known about the chemistry of water on stepped surfaces, commonly occurring in realistic situations. Using first-principles simulations we study the adsorption of water on a stepped platinum surface. We find that water adsorbs preferentially at the step edge, forming linear clusters or chains, stabilized by the cooperative effect of chemical bonds with the substrate and hydrogen bonds. In contrast with flat Pt, at steps water molecules dissociate forming mixed hydroxyl/water structures, through an autocatalytic mechanism promoted by hydrogen bonding. Nuclear quantum effects contribute to stabilize partially dissociated cluster and chains. Together with the recently demonstrated attitude of water chains adsorbed on stepped Pt surfaces to transfer protons via thermally activated hopping, these findings candidate these systems as viable proton wires.Comment: 19 pages, 4 figure