arXiv subjects

Francesco Sciortino

Publications and source records attributed to Francesco Sciortino.

At least 37 records · Page 2Linked to original sources

arXiv2023

Two-step nucleation in a binary mixture of Patchy Particles

Nucleation in systems with a metastable liquid-gas critical point is the prototypical example of a two-step nucleation process, in which the appearance of the critical nucleus is preceded by the formation of a liquid-like density fluctuation. So far, the majority of studies on colloidal and protein crystallization have focused on one-component systems, and we are lacking a clear description of two-step nucleation processes in multicomponent systems, where critical fluctuations involve coupled density and concentrations inhomogeneities. Here, we examine the nucleation process of a binary mixture of patchy particles designed to nucleate into a diamond lattice. By combining Gibbs-ensemble simulations and direct nucleation simulations over a wide range of thermodynamic conditions, we are able to pin down the role of the liquid-gas metastable phase diagram on the nucleation process. In particular, we show that the strongest enhancement of crystallization occurs at an azeotropic point with the same stoichiometric composition of the crystal.

cond-mat.soft↗

arXiv2023

A neural network potential with self-trained atomic fingerprints: a test with the mW water potential

We present a neural network (NN) potential based on a new set of atomic fingerprints built upon two- and three-body contributions that probe distances and local orientational order respectively. Compared to existing NN potentials, the atomic fingerprints depend on a small set of tuneable parameters which are trained together with the neural network weights. To tackle the simultaneous training of the atomic fingerprint parameters and neural network weights we adopt an annealing protocol that progressively cycles the learning rate, significantly improving the accuracy of the NN potential. We test the performance of the network potential against the mW model of water, which is a classical three-body potential that well captures the anomalies of the liquid phase. Trained on just three state points, the NN potential is able to reproduce the mW model in a very wide range of densities and temperatures, from negative pressures to several GPa, capturing the transition from an open random tetrahedral network to a dense interpenetrated network. The NN potential also reproduces very well properties for which it was not explicitly trained, such as dynamical properties and the structure of the stable crystalline phases of mW.

cond-mat.soft↗

arXiv2022

Designing enhanced entropy binding in single-chain nano particles

Single-chain nanoparticles (SCNP) are a new class of bio and soft-matter polymeric objects in which a fraction of the monomers are able to form equivalently intra- or inter-polymer bonds. Here we numerically show that a fully-entropic gas-liquid phase separation can take place in SCNP systems. Control over the discontinuous (first-order) change -- from a phase of independent diluted (fully-bonded) polymers to a phase in which polymers entropically bind to each other to form a (fully-bonded) polymer network -- can be achieved by a judicious design of the patterns of reactive monomers along the polymer chain. Such a sensitivity arises from a delicate balance between the distinct entropic contributions controlling the binding.

cond-mat.soft↗

arXiv2022

SAT-assembly: A new approach for designing self-assembling systems

We propose a general framework for solving inverse self-assembly problems, i.e. designing interactions between elementary units such that they assemble spontaneously into a predetermined structure. Our approach uses patchy particles as building blocks, where the different units bind at specific interaction sites (the patches), and we exploit the possibility of having mixtures with several components. The interaction rules between the patches is determined by transforming the combinatorial problem into a Boolean satisfiability problem (SAT) which searches for solutions where all bonds are formed in the target structure. Additional conditions, such as the non-satisfiability of competing structures (e.g. metastable states) can be imposed, allowing to effectively design the assembly path in order to avoid kinetic traps. We demonstrate this approach by designing and numerically simulating a cubic diamond structure from four particle species that assembles without competition from other polymorphs, including the hexagonal structure.

cond-mat.soft↗

arXiv2021

The physics of Empty Liquids: from Patchy particles to Water

Empty liquids represent a wide class of materials whose constituents arrange in a random network through reversible bonds. Many key insights on the physical properties of empty liquids have originated almost independently from the study of colloidal patchy particles on one side, and a large body of theoretical and experimental research on water on the other side. Patchy particles represent a family of coarse-grained potentials that allows for a precise control of both the geometric and the energetic aspects of bonding, while water has arguably the most complex phase diagram of any pure substance, and a puzzling amorphous phase behavior. It was only recently that the exchange of ideas from both fields has made it possible to solve long-standing problems and shed new light on the behavior of empty liquids. Here we highlight the connections between patchy particles and water, focusing on the modelling principles that make an empty liquid behave like water, including the factors that control the appearance of thermodynamic and dynamic anomalies, the possibility of liquid-liquid phase transitions, and the crystallization of open crystalline structures.

cond-mat.soft↗

arXiv2021

Structure of high-pressure supercooled and glassy water

We numerically investigate the metastable equilibrium structure of deep supercooled and glassy water under pressure, covering the range of densities corresponding to the experimentally produced high-density and very-high-density amorphous phases. At $T = 188$ K, a continuous increase in density is observed on varying pressure from $2.5$ to $13$ kbar, with no signs of first-order transitions. Exploiting a recently proposed approach to the analysis of the radial distribution function -- based on topological properties of the hydrogen-bond network -- we are able to identify well-defined local geometries that involve pair of molecules separated by multiple hydrogen bonds, specific of the high and very high density structures.

cond-mat.soft↗

arXiv2021

Structural and topological changes across the liquid-liquid transition in water

It has recently been shown that the TIP4P/Ice model of water can be studied numerically in metastable equilibrium at and below its liquid-liquid critical temperature. We report here simulations along a subcritical isotherm, for which two liquid states with the same pressure and temperature, but different density, can be equilibrated. This allows for a clear visualisation of the structural changes taking place across the transition. We specifically focus on how the topological properties of the H-bond network change across the liquid-liquid transition. Our results demonstrate that the structure of the high-density liquid, characterised by the existence of interstitial molecules and commonly explained in terms of the collapse of the second neighbour shell, actually originates from the folding back of long rings, bringing pairs of molecules separated by several hydrogen-bonds close by in space.

cond-mat.soft↗

arXiv2020

Gel Formation in Reversibly Cross-Linking Polymers

By means of Langevin dynamics simulations, we investigate the gel formation of randomly functionalized polymers in solution, with the ability to form both intra- and intermolecular reversible bonds. Under highly dilute conditions, these polymers form soft nano-objects (so-called single-chain nanoparticles, SCNPs), resulting from the purely intramolecular cross-linking of the reactive functional groups. Here we show that the competition between intra- and intermolecular bonds at finite concentration is governed by a delicate balance of various entropic contributions and leads to a density dependent effective valence. System-spanning networks are formed at relatively low monomer densities and their stability is mediated by just a small number of intermolecular connections per chain. The formation of intermolecular bonds furthermore can induce a non-monotonic dependence of the polymer size on the density for long bond lifetimes. Concomitantly, the polymers in the percolating cluster adopt an intramolecular structure characteristic for self-avoiding chains, which constitutes a strong contrast to the fractal globular behavior of irreversible SCNPs in crowded solutions with purely topological interactions (no intermolecular bonds). Finally, we study the dynamics of the system, which displays signatures expected for reversible gel-forming systems. An interesting behavior emerges in the reorganization dynamics of the percolating cluster. The relaxation is mostly mediated by the diffusion over long distances, through breaking and formation of bonds, of chains that do not leave the percolating cluster. Regarding the few chains that are transiently free, the time they spend until they reattach to the cluster is solely governed by the bond strength.

cond-mat.soft↗

arXiv2020

Hyperbranched DNA clusters

Taking advantage of the base-pairing specificity and tunability of DNA interactions, we investigate the spontaneous formation of hyperbranched clusters starting from purposely designed DNA tetravalent nanostar monomers, encoding in their four sticky-ends the desired binding rules. Specifically, we combine molecular dynamics simulations and Dynamic Light Scattering experiments to follow the aggregation process of the DNA nanostars at different concentrations and temperatures. At odd with the Flory-Stockmayer predictions, we find that, even when all possible bonds are formed, the system does not reach percolation due to the presence of intracluster bonds. We present an extension of the Flory-Stockmayer theory that properly describes the numerical and the experimental results.

cond-mat.soft↗

arXiv2020

The Dependence of the Impurity Transport on the Dominant Turbulent Regime in ELM-y H-mode Discharges

Laser blow-off injections of aluminum and tungsten have been performed on the DIII-D tokamak to investigate the variation of impurity transport in a set of dedicated ion and electron heating scans with a fixed value of the external torque. The particle transport is quantified via the Bayesian inference method, which, constrained by a combination of a charge exchange recombination spectroscopy, soft X-ray measurements, and VUV spectroscopy provides a detailed uncertainty quantification of the transport coefficients. Contrasting discharge phases with a dominant electron and ion heating reveal a factor of 30 increase in midradius impurity diffusion and a 3-fold drop in the impurity confinement time when additional electron heating is applied. Further, the calculated stationary aluminum density profiles reverse from peaked in electron heated to hollow in the ion heated case, following a similar trend as electron and carbon density profiles. Comparable values of a core diffusion have been observed for W and Al ions, while differences in the propagation dynamics of these impurities are attributed to pedestal and edge transport. Modeling of the core transport with non-linear gyrokinetics code CGYRO [J. Candy and E. Belly J. Comput. Phys. 324,73 (2016)], significantly underpredicts the magnitude of the variation in Al transport. The experiment demonstrates a 3-times steeper increase of impurity diffusion with additional electron heat flux and 10-times lower diffusion in ion heated case than predicted by the modeling. However, the CGYRO model correctly predicts that the Al diffusion dramatically increases below the linear threshold for the transition from the ion temperature gradient (ITG) to trapped electron mode (TEM).

physics.plasm-ph↗

arXiv2019

The stability-limit conjecture revisited

The stability-limit conjecture (SLC) proposes that the liquid spinodal of water returns to positive pressure in the supercooled region, and that the apparent divergence of water's thermodynamic response functions as temperature decreases are explained by the approach to this reentrant spinodal. Subsequently, it has been argued that the predictions of the SLC are inconsistent with general thermodynamic principles. Here we reconsider the thermodynamic viability of the SLC by examining a model equation of state for water first studied to clarify the relationship of the SLC to the proposed liquid-liquid phase transition in supercooled water. By demonstrating that a binodal may terminate on a spinodal at a point that is not a critical point, we show that the SLC is thermodynamically permissible in a system that has both a liquid-gas and a liquid-liquid phase transition. We also describe and clarify other unusual thermodynamic behavior that may arise in such a system, particularly that associated with the so-called "critical-point-free" scenario for a liquid-liquid phase transition, which may apply to the case of liquid Si.

cond-mat.stat-mech↗

arXiv2019

$q$-independent slow-dynamics in atomic and molecular systems

Investigating million-atom systems for very long simulation times, we demonstrate that the collective density-density correlation time ($τ_α$) in simulated supercooled water and silica becomes wavevector independent ($q^0$) when the probing wavelength is several times larger than the interparticle distance. The $q$-independence of the collective density-density correlation functions, a feature clearly observed in light-scattering studies of some soft-matter systems, is thus a genuine feature of many (but not all) slow-dynamics systems, either atomic, molecular or colloidal. Indeed, we show that when the dynamics of the density fluctuations is due to particle-type diffusion, as in the case of the Lennard Jones binary mixture model, the $q^0$ regime does not set in and the relaxation time continues to scale as $τ_α \sim q^{-2}$ even at small $q$.

cond-mat.stat-mech↗

arXiv2019

Glass Polymorphism in TIP4P/2005 Water: A Description Based on the Potential Energy Landscape Formalism

The potential energy landscape (PEL) formalism is a statistical mechanical approach to describe supercooled liquids and glasses. Here we use the PEL formalism to study the pressure-induced transformations between low-density amorphous ice (LDA) and high-density amorphous ice (HDA) using computer simulations of the TIP4P/2005 molecular model of water. We find that the properties of the PEL sampled by the system during the LDA-HDA transformation exhibit anomalous behavior. In particular, at conditions where the change in density during the LDA-HDA transformation is approximately discontinuous, reminiscent of a first-order phase transition, we find that (i) the inherent structure (IS) energy, $e_\text{IS}(V)$, is a concave function of the volume, and (ii) the IS pressure, $P_\text{IS}(V)$, exhibits a van der Waals-like loop. In addition, the curvature of the PEL at the IS is anomalous, a non-monotonic function of $V$. In agreement with previous studies, our work suggests that conditions (i) and (ii) are necessary (but not sufficient) signatures of the PEL for the LDA-HDA transformation to be reminiscent of a first-order phase transition. We also find that one can identify two different regions of the PEL, one associated to LDA and another to HDA. Our computer simulations are performed using a wide range of compression/decompression and cooling rates. In particular, our slowest cooling rate (0.01 K/ns) is within the experimental rates employed in hyperquenching experiments to produce LDA. Interestingly, the LDA-HDA transformation pressure that we obtain at $T=80$ K and at different rates extrapolates remarkably well to the corresponding experimental pressure.

cond-mat.stat-mech↗

arXiv2018

Size dependence of dynamic fluctuations in liquid and supercooled water

We study the evolution of dynamic fluctuations averaged over different space lengths and time scales to characterize spatially and temporally heterogeneous behavior of TIP4P/2005 water in liquid and supercooled states. Analysing a million particle simulated system we provide evidence of the existence, upon supercooling, of a significant enhancement of spatially localized dynamic fluctuations stemming from regions of correlated mobile molecules. We show that both the magnitude of the departure from the value expected for the system-size dependence of an uncorrelated system and the molecular size at which such trivial regime is finally recovered clearly increase upon supercooling. This provides a means to estimate an upper limit to the maximum length scale of influence of the regions of correlated mobile molecules. Notably, such upper limit grows two orders of magnitude on cooling, reaching a value corresponding to a few thousand molecules at the lowest investigated temperature.

cond-mat.soft↗

arXiv2018

Colloidomers: freely-jointed polymers made of droplets

An important goal of self-assembly is to achieve a preprogrammed structure with high fidelity. Here, we control the valence of DNA-functionalized emulsions to make linear and branched model polymers, or `colloidomers'. The distribution of cluster sizes is consistent with a polymerization process in which the droplets achieve their prescribed valence. Conformational dynamics reveals that the chains are freely-jointed, such that the end-to-end length scales with the number of bonds $N$ as $N^ν$, where $ν\approx3/4$, in agreement with the Flory theory in 2D. The chain diffusion coefficient $D$ approximately scales as $D\propto N^{-ν}$, as predicted by the Zimm model. Unlike molecular polymers, colloidomers can be repeatedly assembled and disassembled under temperature cycling, allowing for reconfigurable, responsive matter.

cond-mat.soft↗

arXiv2018

Dynamics of vitrimers: defects as a highway to stress relaxation

We propose a coarse-grained model to investigate stress relaxation in star-polymer networks induced by dynamic bond exchange processes. We show how the swapping mechanism, once activated, allows the network to reconfigure, exploring distinct topological configurations, all of them characterised by complete extent of reaction. Our results reveal the important role played by topological defects in mediating the exchange reaction and speeding up stress relaxation. The model provides a representation of the dynamics in vitrimers, a new class of polymers characterized by bond swap mechanisms which preserve the total number of bonds, as well as in other bond-exchange materials.

cond-mat.soft↗

arXiv2018

Evaluating the Laplace pressure of water nanodroplets from simulations

We calculate the components of the microscopic pressure tensor as a function of radial distance r from the centre of a spherical water droplet, modelled using the TIP4P/2005 potential. To do so, we modify a coarse-graining method for calculating the microscopic pressure [T. Ikeshoji, B. Hafskjold, and H. Furuholt, Mol. Simul. 29, 101 (2003)] in order to apply it to a rigid molecular model of water. As test cases, we study nanodroplets ranging in size from 776 to 2880 molecules at 220 K. Beneath a surface region comprising approximately two molecular layers, the pressure tensor becomes approximately isotropic and constant with r. We find that the dependence of the pressure on droplet radius is that expected from the Young-Laplace equation, despite the small size of the droplets.

cond-mat.soft↗

arXiv2018

Potential Energy Landscape of TIP4P/2005 water

We report an exhaustive numerical study of the statistical properties of the potential energy landscape of TIP4P/2005, one of the most accurate rigid water models. We show that, in the region where equilibrated configurations can be generated, a Gaussian landscape description is able to properly describe the model properties. We also find that the volume dependence of the landscape properties is consistent with the existence of a locus of density maxima in the phase diagram. The landscape-based equation of state accurately reproduces the TIP4P/2005 pressure-vs-volume curves, providing a sound extrapolation of the free-energy at low T. A positive-pressure liquid-liquid critical point is predicted by the resulting free-energy.

cond-mat.stat-mech↗