arXiv subjects

Cristiano De Michele

Publications and source records attributed to Cristiano De Michele.

At least 19 recordsLinked to original sources

arXiv2025

Relating thermodynamic quantities of convex-hard-body fluids to the body's shape

For a fluid of convex hard particles, characterized by a length scale $σ_\text{min}$ and an anisotropy parameter $ε$, we develop a formalism allowing one to relate thermodynamic quantities to the body's shape. In a first step its thermodynamics is reduced to that of spherical particles. The latter have a hard core of diameter $σ_\text{min }$ and a soft shell with a thickness $εσ_\text{min}/2$. Besides their hard core repulsion at $σ_\text{min }$ they interact by effective entropic forces which will be calculated. Based on this mapping, a second step provides a perturbative method for the systematic calculation of thermodynamic quantities with the shape anisotropy $ε$ as smallness parameter. In leading order in $ε$, the equation of state is derived as a functional of the particle's shape. To illustrate these findings, they are applied to a one- and two-dimensional fluid of ellipses and compared with results from different analytical approaches, and our computer simulations. The mapping to spherical particles also implies that any phase transition of spherical particles, e.g., the liquid-hexatic transition, also exists for the nonspherical ones, and shifts linearly with $ε$ for weak shape anisotropy. This is supported by our Monte-Carlo simulation.

cond-mat.stat-mech↗

arXiv2024

Fragile-to-strong glass transition in two-dimensional vortex liquids

The fragile-to-strong glass transition is a fascinating phenomenon that still presents many theoretical and experimental challenges. A major one is how to tune the fragility of a glass-forming liquid. Here, we study a two-dimensional (2D) system composed of vortices in a superconducting film, which effectively behaves as a 2D glass-forming liquid. We show that the kinetic fragility in this system can be experimentally varied by tuning a single parameter: the external magnetic field $H$ applied transversely to the film. This conclusion is supported by the direct comparison between the analysis of experimental measurements in an amorphous MoGe superconducting film and Monte Carlo simulations in a disordered XY model, that captures the universality class of the two-step melting transition. We show that by increasing disorder strength a fragile-to-strong transition is induced, in close similarity with the experimental findings in a magnetic field. Our numerical results shed light on the evolution of the dynamical heterogeneity from a fragile to strong glass, as due to the subtle interplay between caging effects arising from hexatic order and strong random pinning.

cond-mat.supr-con↗

arXiv2024

Polymeric Properties of Higher-Order G-Quadruplex Telomeric Structures: Effects of Chemically Inert Crowders

G-quadruplexes are non-canonical DNA structures rather ubiquitous in human genome, which are thought to play a crucial role in the development of 85-90 % of cancers. Here, we present a novel coarse-grained approach in modeling G-quadruplexes which accounts for their structural flexibility. We apply it to study the polymeric properties of G-quadruplex multimers, with and without crowder particles, to mimic in-vivo conditions. We find that, contrary to some suggestions found in the literature, long G-quadruplex multimers are rather flexible polymeric macromolecules, with a local persistence length comparable to monomer size, exhibiting chain stiffness variation profile consistent with a real polymer in good solvent. Moreover, in a crowded environment (up to 10% volume fraction), we report that G-quadruplex multimers exhibit an increased propensity for coiling, with a corresponding decrease in the measured chain stiffness. Accurately accounting for the polymeric properties of G4 multimers is crucial for understanding their interactions with anticancer G4-targeting drugs, thereby significantly enhancing the design and effectiveness of these drugs.

physics.comp-ph↗

arXiv2024

Dilute suspensions of Janus rods: the role of bond and shape anisotropy

Nanometer-sized clusters are often targeted due to their potential applications as nanoreactors or storage/delivery devices. One route to assemble and stabilize finite structures consists in imparting directional bonding patterns between the nanoparticles. When only a portion of the particle surface is able to form an inter-particle bond, finite-size aggregates such as micelles and vesicles may form. Building on this approach, we combine particle shape anisotropy with the directionality of the bonding patterns and investigate the combined effect of particle elongation and surface patchiness on the low density assembly scenario. To this aim, we study the assembly of tip-functionalised Janus hard spherocylinder by means of Monte Carlo simulations. By exploring the effects of changing the interaction strength and range at different packing fractions, we highlight the role played by shape and bond anisotropy on the emerging aggregates (micelles, vesicles, elongated micelles and lamellae). We observe that shape anisotropy plays a crucial role in suppressing phases that are typical to spherical Janus nanoparticles and that a careful tuning of the interaction parameters allows to promote the formation of spherical micelles. These finite-size spherical clusters composed of elongated particles might offer more interstitials and larger surface areas than those offered by micelles of spherical or almost-spherical units, thus enhancing their storage and catalytic properties.

cond-mat.soft↗

arXiv2024

Giant splitting of the hydrogen rotational eigenenergies in the C$_2$ filled ice

Hydrogen hydrates present a rich phase diagram influenced by both pressure and temperature, with the so-called C$_2$ phase emerging prominently above 2.5 GPa. In this phase, hydrogen molecules are densely packed within a cubic ice-like lattice and the interaction with the surrounding water molecules profoundly affects their quantum rotational dynamics. Herein, we delve into this intricate interplay by directly solving the Schrödinger's equation for a quantum H$_2$ rotor in the C$_2$ crystal field at finite temperature, generated through Density Functional Theory. Our calculations reveal a giant energy splitting relative to the magnetic quantum number of $\pm$3.2 meV for $l=1$. Employing inelastic neutron scattering, we experimentally measure the energy levels of H$_2$ within the C$_2$ phase at 6.0 and 3.4 GPa and low temperatures, finding remarkable agreement with our theoretical predictions. These findings underscore the pivotal role of hydrogen--water interactions in dictating the rotational behavior of the hydrogen molecules within the C$_2$ phase and indicate heightened induced-dipole interactions compared to other hydrogen hydrates.

cond-mat.soft↗

arXiv2022

Connecting Structure, Conformation and Energetics of Human Telomere G-quadruplex Multimers

G-quadruplexes (G4s) are helical four-stranded structures forming from guanine-rich nucleic acid sequences, which are thought to play a role in cancer development and malignant transformation. Most current studies focus on G4 monomers, yet under suitable and biologically relevant conditions G4s undergo multimerization. Here, we address the structural, conformational and energetic features of G4 multimers formed in solutions by the human telomere sequence. A novel multi-technique approach is used combining Small Angle X-ray Scattering (SAXS) and circular dichroism experiments with coarse-grained simulations, to provide quantitative information about large-scale structural features and the stability of G4 multimers. The latter show a significant polydispersity with an exponential distribution of contour lengths, suggesting a step-growth polymerization. On increasing DNA concentration, the strength of G4 stacking interaction increases, as well as the number of the units in the aggregates, with dimers and trimers as the most probable forms. At the same time, a variation of G4 conformation is observed. Our findings provide a quantitative picture of human telomere G4 multimers, which must be accounted for to achieve a rational design of anticancer drugs targeting DNA structures.

physics.bio-ph↗

arXiv2021

Transport signatures of fragile-glass dynamics in the melting of the two-dimensional vortex lattice

In two-dimensional (2D) systems, the melting from a solid to an isotropic liquid can occur via an intermediate phase that retains orientational order. However, in 2D superconducting vortex lattices, the effect of orientational correlations on transport, and their interplay with disorder remain open questions. Here we study a 2D weakly pinned vortex system in amorphous MoGe films over an extensive range of temperatures ($\bm{T}$) and perpendicular magnetic fields ($\bm{H}$) using linear and nonlinear transport measurements. We find that, at low fields, the resistivity obeys the Vogel-Fulcher-Tamman (VFT) form, $\bm{ρ(T)\propto\exp[-{W}(H)/(T-T_0(H))]}$, characteristic of fragile glasses. As $\bm{H}$ increases, $\bm{T_0(H)}$ is suppressed to zero, and a standard vortex liquid behavior consistent with a $\bm{T=0}$ superconducting transition is observed. Our findings, supported also by simulations, suggest that the presence of orientational correlations gives rise to a heterogeneous dynamics responsible for the VFT behavior. The effects of quenched disorder become dominant at high $\bm{H}$, where a crossover to a strong-glass behavior is observed. This is a new insight into the dynamics of melting in 2D systems with competing orders.

cond-mat.supr-con↗

arXiv2016

Anomalous dynamics of intruders in a crowded environment of mobile obstacles

Many natural and industrial processes rely on constrained transport, such as proteins moving through cells, particles confined in nanocomposite materials or gels, individuals in highly dense collec- tives and vehicular traffic conditions. These are examples of motion through crowded environments, in which the host matrix may retain some glass-like dynamics. Here we investigate constrained transport in a colloidal model system, in which dilute small spheres move in a slowly rearranging, glassy matrix of large spheres. Using confocal differential dynamic microscopy and simulations, we discover a critical size asymmetry at which anomalous collective transport of the small particles appears, manifested as a logarithmic decay of the density autocorrelation functions. We demonstrate that the matrix mobility is central for the observed anomalous behaviour. These results, crucially depending on size-induced dynamic asymmetry, are of relevance for a wide range of phenomena ranging from glassy systems to cell biology.

cond-mat.soft↗

arXiv2015

Non-universal Voronoi cell shapes in amorphous ellipsoid packings

In particulate systems with short-range interactions, such as granular matter or simple fluids, local structure plays a pivotal role in determining the macroscopic physical properties. Here, we analyse local structure metrics derived from the Voronoi diagram of configurations of oblate ellipsoids, for various aspect ratios $α$ and global volume fractions $ϕ_g$. We focus on jammed static configurations of frictional ellipsoids, obtained by tomographic imaging and by discrete element method simulations. In particular, we consider the local packing fraction $ϕ_l$, defined as the particle's volume divided by its Voronoi cell volume. We find that the probability $P(ϕ_l)$ for a Voronoi cell to have a given local packing fraction shows the same scaling behaviour as function of $ϕ_g$ as observed for random sphere packs. Surprisingly, this scaling behaviour is further found to be independent of the particle aspect ratio. By contrast, the typical Voronoi cell shape, quantified by the Minkowski tensor anisotropy index $β=β_0^{2,0}$, points towards a significant difference between random packings of spheres and those of oblate ellipsoids. While the average cell shape $β$ of all cells with a given value of $ϕ_l$ is very similar in dense and loose jammed sphere packings, the structure of dense and loose ellipsoid packings differs substantially such that this does not hold true. This non-universality has implications for our understanding of jamming of aspherical particles.

cond-mat.soft↗

arXiv2012

Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link

Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semi-flexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical concentration, which depends on temperature and duplex length, such chains order into liquid crystal phases. Here, we investigate the self-assembly of such double-helical duplexes with a combined numerical and theoretical approach. We simulate the bulk system employing the coarse-grained DNA model recently proposed by Ouldridge et al. [ J. Chem. Phys. 134, 08501 (2011) ]. Then we evaluate the input quantities for the theoretical framework directly from the DNA model. The resulting parameter-free theoretical predictions provide an accurate description of the simulation results in the isotropic phase. In addition, the theoretical isotropic-nematic phase boundaries are in line with experimental findings, providing a route to estimate the stacking free energy.

cond-mat.soft↗

arXiv2011

Self-assembly of bi-functional patchy particles with anisotropic shape into polymers chains: theory and simulations

Concentrated solutions of short blunt-ended DNA duplexes, down to 6 base pairs, are known to order into the nematic liquid crystal phase. This self-assembly is due to the stacking interactions between the duplex terminals that promotes their aggregation into poly-disperse chains with a significant persistence length. Experiments show that liquid crystals phases form above a critical volume fraction depending on the duplex length. We introduce and investigate via numerical simulations, a coarse-grained model of DNA double-helical duplexes. Each duplex is represented as an hard quasi-cylinder whose bases are decorated with two identical reactive sites. The stacking interaction between terminal sites is modeled via a short-range square-well potential. We compare the numerical results with predictions based on a free energy functional and find satisfactory quantitative matching of the isotropic-nematic phase boundary and of the system structure. Comparison of numerical and theoretical results with experimental findings confirm that the DNA duplexes self-assembly can be properly modeled via equilibrium polymerization of cylindrical particles and enables us to estimate the stacking energy.

cond-mat.soft↗

arXiv2010

Scaling between Structural Relaxation and Particle Caging in a Model Colloidal Gel

In polymers melts and supercooled liquids, the glassy dynamics is characterized by the rattling of monomers or particles in the cage formed by their neighbors. Recently, a direct correlation in such systems, described by a universal scaling form, has been established between the rattling amplitude and the structural relaxation time. In this paper we analyze the glassy dynamics emerging from the formation of a persistent network in a model colloidal gel at very low density. The structural relaxation time of the gel network is compared with the mean squared displacement at short times, corresponding to the localization length associated to the presence of energetic bonds. Interestingly, we find that the same type of scaling as for the dense glassy systems holds. Our findings well elucidate the strong coupling between the cooperative rearrangements of the gel network and the single particle localization in the structure. Our results further indicate that the scaling captures indeed fundamental physical elements of glassy dynamics.

cond-mat.soft↗

arXiv2010

Optimizing Event-Driven Simulations

Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model has been indeed widely used both for computational and theoretical description of physical systems. Recently further developments of computational techniques allow simulations of hard rigid objects of generic shape. In present paper we will present some optimizations for event-driven simulations that offered significant speedup over previous methods. In particular we will describe a generalization of well known linked list method and an improvement on nearest neighbor lists method recently proposed by us.

physics.comp-ph↗

arXiv2009

Simulating Hard Rigid Bodies

Several physical systems in condensed matter have been modeled approximating their constituent particles as hard objects. The hard spheres model has been indeed one of the cornerstones of the computational and theoretical description in condensed matter. The next level of description is to consider particles as rigid objects of generic shape, which would enrich the possible phenomenology enormously. This kind of modeling will prove to be interesting in all those situations in which steric effects play a relevant role. These include biology, soft matter, granular materials and molecular systems. With a view to developing a general recipe for event-driven Molecular Dynamics simulations of hard rigid bodies, two algorithms for calculating the distance between two convex hard rigid bodies and the contact time of two colliding hard rigid bodies solving a non-linear set of equations will be described. Building on these two methods, an event-driven molecular dynamics algorithm for simulating systems of convex hard rigid bodies will be developed and illustrated in details. In order to optimize the collision detection between very elongated hard rigid bodies, a novel nearest-neighbor list method based on an oriented bounding box will be introduced and fully explained. Efficiency and performance of the new algorithm proposed will be extensively tested for uniaxial hard ellipsoids and superquadrics. Finally applications in various scientific fields will be reported and discussed.

physics.comp-ph↗

arXiv2009

Connecting Irreversible to Reversible Aggregation: Time and Temperature

We report molecular dynamics simulations of a gel-forming mixture of ellipsoidal patchy particles with different functionality. We show that in this model, which disfavors the formation of bond-loops, elapsed time during irreversible aggregation -- leading to the formation of an extended network -- can be formally correlated with equilibrium temperature in reversible aggregation. We also show that it is possible to develop a parameter-free description of the self-assembly kinetics, bringing reversible and irreversible aggregation of loopless branched systems to the same level of understanding as equilibrium polymerization.

cond-mat.dis-nn↗

arXiv2008

A molecular dynamics study of chemical gelation in a patchy particle model

We report event-driven molecular dynamics simulations of the irreversible gelation of hard ellipsoids of revolution containing several associating groups, characterizing how the cluster size distribution evolves as a function of the extent of reaction, both below and above the gel point. We find that in a very large interval of values of the extent of reaction, parameter-free mean-field predictions are extremely accurate, providing evidence that in this model the Ginzburg zone near the gel point, where non-mean field effects are important, is very limited. We also find that the Flory's hypothesis for the post-gelation regime properly describes the connectivity of the clusters even if the long-time limit of the extent of reaction does not reach the fully reacted state. This study shows that irreversibly aggregating asymmetric hard-core patchy particles may provide a close realization of the mean-field model, for which available theoretical predictions may help control the structure and the connectivity of the gel state. Besides chemical gels, the model is relevant to network-forming soft materials like systems with bioselective interactions, functionalized molecules and patchy colloids.

cond-mat.soft↗

arXiv2007

Event-Driven Simulation of the Dynamics of Hard Ellipsoids

We introduce a novel algorithm to perform event-driven simulations of hard rigid bodies of arbitrary shape, that relies on the evaluation of the geometric distance. In the case of a monodisperse system of uniaxial hard ellipsoids,we perform molecular dynamics simulations varying the aspect-ratio X0 and the packing fraction phi. We evaluate the translational Dtrans and the rotational Drot diffusion coefficient and the associated isodiffusivity lines in the phi-X0 plane. We observe a decoupling of the translational and rotational dynamics which generates an almost perpendicular crossing of the Dtrans and Drot isodiffusivity lines. While the self intermediate scattering function exhibits stretched relaxation, i.e. glassy dynamics, only for large phi and X0 about equals to 1, the second order orientational correlator C2(t) shows stretching only for large and small X0 values. We discuss these findings in the context of a possible pre-nematic order driven glass transition.

cond-mat.soft↗

arXiv2007

Viscoelasticity and Stokes-Einstein relation in repulsive and attractive colloidal glasses

We report a numerical investigation of the visco-elastic behavior in models for steric repulsive and short-range attractive colloidal suspensions, along different paths in the attraction-strength vs packing fraction plane. More specifically, we study the behavior of the viscosity (and its frequency dependence) on approaching the repulsive glass, the attractive glass and in the re-entrant region where viscosity shows a non monotonic behavior on increasing attraction strength. On approaching the glass lines, the increase of the viscosity is consistent with a power-law divergence with the same exponent and critical packing fraction previously obtained for the divergence of the density fluctuations. Based on mode-coupling calculations, we associate the increase of the viscosity with specific contributions from different length scales. We also show that the results are independent on the microscopic dynamics by comparing newtonian and brownian simulations for the same model. Finally we evaluate the Stokes-Einstein relation approaching both glass transitions, finding a clear breakdown which is particularly strong for the case of the attractive glass.

cond-mat.soft↗