arXiv subjects

Isabella Daidone

Publications and source records attributed to Isabella Daidone.

5 recordsLinked to original sources

arXiv2026

Ion-Specific Anomalous Water Diffusion in Aqueous Electrolytes: A Machine-Learned Many-Body Force Field Study with MACE

The dynamics of water in electrolyte solutions exhibits a striking, ion-specific anomaly: the diffusion coefficient of water is enhanced relative to the neat liquid in chaotropic CsI solutions, yet suppressed in kosmotropic NaCl solutions. This phenomenon, long challenging for classical force-field-based molecular dynamics, is studied here using classical molecular dynamics simulations with a many-body machine-learned force field (MLFF) trained within the MACE equivariant graph neural network framework. The force field is trained on energies, forces, and stresses computed at the density functional theory level with the revPBE-D3 exchange--correlation functional, which provides a reliable balance between accuracy and computational efficiency for aqueous systems. Simulations of NaCl and CsI aqueous solutions at ambient conditions over a concentration range of 0.89--3.56 mol/kg reproduce the experimentally observed anomalous diffusion and show a quantitative improvement over previous results obtained with the DeePMD framework, trained on the same theory, particularly for NaCl solutions. This improvement is traced to a stronger Na$^{+}$--water interaction in the first hydration shell and the non-negligible retarding contribution of the second hydration shell of Na$^{+}$. For CsI solutions, the water acceleration is shown to be primarily driven by the anion I$^{-}$, whose diffuse and weakly structured hydration shell facilitates rapid water exchange with the bulk. These results are rationalised through a shell-decomposition analysis of time-dependent water diffusivities and ion--oxygen potentials of mean force providing a coherent microscopic picture of the acceleration--retardation mechanism in the studied aqueous electrolytes.

physics.chem-ph↗

arXiv2023

Plasmon-enhanced circular dichroism spectroscopy of chiral drug solutions

We investigate the potential of surface plasmon polaritons at noble metal interfaces for surface-enhanced chiroptical sensing of dilute chiral drug solutions. The high quality factor of surface plasmon resonances in both Otto and Kretschmann configurations enables the enhancement of circular dichroism differenatial absorption thanks to the large near-field intensity of such plasmonic excitations. Furthermore, the subwavelength confinement of surface plasmon polaritons is key to attain chiroptical sensitivity to small amounts of drug volumes placed around $\simeq 100$ nm by the metal surface. Our calculations focus on reparixin, a pharmaceutical molecule currently used in clinical studies for patients with community-acquired pneumonia, including COVID-19 and acute respiratory distress syndrome. Considering realistic dilute solutions of reparixin dissolved in water with concentration $\leq 5$ mg$/$ml, we find a circular-dichroism differential absorption enhancement factor of the order $\simeq 20$ and chirality-induced polarization distortion upon surface plasmon polariton excitation.

physics.optics↗

arXiv2022

Structural analysis of water networks

Liquid water, besides being fundamental for life on Earth, has long fascinated scientists due to several anomalies. Different hypotheses have been put forward to explain these peculiarities. The most accredited one foresees the presence in the supercooled region of two phases at different densities: the low-density liquid phase and the high-density liquid phase. In our previous work [Faccio et al., J. Mol. Liq. 355 (2022): 118922], we showed that it is possible to identify these two forms in water networks through a computational approach based on molecular dynamics simulation and on the calculation of the total communicability of the associated graph, in which the nodes correspond to water molecules and the edges represent the connections (interactions) between molecules. In this paper, we present a more in-depth investigation of the application of graph-theory based approaches to the analysis of the structure of water networks. In particular, we investigate different connectivity and centrality measures and we report on the use of a variety of global metrics aimed at giving a topological and geometrical characterization of liquid water.

math.NA↗

arXiv2021

Low, high and very-high density forms of liquid water revealed by a medium-range order descriptor

We present in this paper a computational approach based on molecular dynamics simulations and graph theory to characterize the structure of liquid water considering not only the local structural arrangement within the first (or second) hydration shell, but also the medium- to long-range order. In particular, a new order parameter borrowed from the graph-theory framework, i.e. the node total communicability (NTC ), is introduced to analyze the dynamic network of water molecules in the liquid phase. This order parameter is able not only to accurately report on the different high-density-liquid (HDL) and low-density-liquid (LDL) water phases postulated in the liquid-liquid phase transition hypothesis, but also to unveil the presence of very high density liquid (VHDL) clusters, both under pressure and at ambient conditions. To the best of our knowledge, VHDL water patches under moderate pressures were not observed before.

cond-mat.soft↗

arXiv2019

Tip-Enhanced Infrared Difference-Nanospectroscopy of the Proton Pump Activity of Bacteriorhodopsin in Single Purple Membrane Patches

Photosensitive proteins embedded in the cell membrane (about 5 nm thickness) act as photoactivated proton pumps, ion gates, enzymes, or more generally, as initiators of stimuli for the cell activity. They are composed of a protein backbone and a covalently bound cofactor (e.g. the retinal chromophore in bacteriorhodopsin (BR), channel rhodopsin, and other opsins). The light-induced conformational changes of both the cofactor and the protein are at the basis of the physiological functions of photosensitive proteins. Despite the dramatic development of microscopy techniques, investigating conformational changes of proteins at the membrane monolayer level is still a big challenge. Techniques based on atomic force microscopy (AFM) can detect electric currents through protein monolayers and even molecular binding forces in single-protein molecules but not the conformational changes. For the latter, Fourier-transform infrared spectroscopy (FTIR) using difference-spectroscopy mode is typically employed, but it is performed on macroscopic liquid suspensions or thick films containing large amounts of purified photosensitive proteins. In this work, we develop AFM-assisted, tip-enhanced infrared difference-nanospectroscopy to investigate light-induced conformational changes of the bacteriorhodopsin mutant D96N in single submicrometric native purple membrane patches. We obtain a significant improvement compared with the signal-to-noise ratio of standard IR nanospectroscopy techniques by exploiting the field enhancement in the plasmonic nanogap that forms between a gold-coated AFM probe tip and an ultraflat gold surface, as further supported by electromagnetic and thermal simulations. IR difference-spectra in the 1450-1800 cm^{-1} range are recorded from individual patches as thin as 10 nm, with a diameter of less than 500 nm, well beyond the diffraction limit for FTIR microspectroscopy...

physics.bio-ph↗