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Achille Giacometti

Publications and source records attributed to Achille Giacometti.

At least 55 records · Page 3Linked to original sources
arXiv2017

Cholesteric and screw-like nematic phases in systems of helical particles

Recent numerical simulations of hard helical particle systems unveiled the existence of a novel chiral nematic phase, termed screw-like, characterised by the helical organization of the particle C$_2$ symmetry axes round the nematic director with periodicity equal to the particle pitch. This phase forms at high density and can follow a less dense uniform nematic phase, with relative occurrence of the two phases depending on the helix morphology. Since these numerical simulations were conducted under three-dimensional periodic boundary conditions, two questions could remain open. Firstly, the real nature of the lower density nematic phase, expected to be cholesteric. Secondly, the influence that the latter, once allowed to form, may have on the existence and stability of the screw-like nematic phase. To address these questions, we have performed Monte Carlo and molecular dynamics numerical simulations of helical particle systems confined between two parallel repulsive walls. We have found that removal of the periodicity constraint along one direction allows a relatively-long-pitch cholesteric phase to form, in lieu of the uniform nematic phase, with helical axis perpendicular to the walls while the existence and stability of the screw-like nematic phase are not appreciably affected by this change of boundary conditions.

cond-mat.soft↗
arXiv2016

Phase diagram of heteronuclear Janus dumbbells

Using Aggregation-Volume-Bias Monte Carlo simulations along with Successive Umbrella Sampling and Histogram Re-weighting, we study the phase diagram of a system of dumbbells formed by two touching spheres having variable sizes, as well as different interaction properties. The first sphere ($h$) interacts with all other spheres belonging to different dumbbells with a hard-sphere potential. The second sphere ($s$) interacts via a square-well interaction with other $s$ spheres belonging to different dumbbells and with a hard-sphere potential with all remaining $h$ spheres. We focus on the region where the $s$ sphere is larger than the $h$ sphere, as measured by a parameter $1\le α\le 2 $ controlling the relative size of the two spheres. As $α\to 2$ a simple fluid of square-well spheres is recovered, whereas $α\to 1$ corresponds to the Janus dumbbell limit, where the $h$ and $s$ spheres have equal sizes. Many phase diagrams falling into three classes are observed, depending on the value of $α$. The $1.8 \le α\le 2$ is dominated by a gas-liquid phase separation very similar to that of a pure square-well fluid with varied critical temperature and density. When $1.3 \le α\le 1.8$ we find a progressive destabilization of the gas-liquid phase diagram by the onset of self-assembled structures, that eventually lead to a metastability of the gas-liquid transition below $α=1.2$.

cond-mat.soft↗
arXiv2016

Effective stiffness and formation of secondary structures in a protein-like model

We use Wang-Landau and replica exchange techniques to study the effect of an increasing stiffness on the formation of secondary structures in protein-like systems. Two possible models are considered. In both models, a polymer chain is formed by tethered beads where non-consecutive backbone beads attract each other via a square-well potential representing the tendency of the chain to fold. In addition, smaller hard spheres are attached to each non-terminal backbone bead along the direction normal to the chain to mimic the steric hindrance of side chains in real proteins. The two models, however, differ in the way bending rigidity is enforced. In the first model, partial overlap between consecutive beads is allowed. This reduces the possible bending angle between consecutive bonds thus producing an effective entropic stiffness that competes with a short-range attraction, and leads to a formation of secondary structures characteristic of proteins. We discuss the low-temperature phase diagram as a function of increasing interpenetration, and find a transition from a planar, beta-like structure, to helical shape. In the second model, an energetic stiffness is explicitly introduced by imposing an infinitely large energy penalty for bending above a critical angle between consecutive bonds, and no penalty below it. The low-temperature phase of this model does not show any sign of protein-like secondary structures. At intermediate temperatures, however, where the chain is still in the coil conformation but stiffness is significant, we find the two models to predict a quite similar dependence of the persistence length as a function of the stiffness. This behaviour is rationalized in terms of a simple geometrical mapping between the two models. Finally, we discuss the effect of shrinking side chains to zero, and find the above mapping to still hold true.

cond-mat.soft↗
arXiv2016

From polymers to proteins: effect of side chains and broken symmetry in the formation of secondary structures within a Wang-Landau approach

We study the equilibrium properties of a single flexible homopolymers where consecutive monomers are represented by impenetrable hard spherical beads tangential to each other, and non-consecutive monomers interact via a square-well potential. To this aim, we use both replica exchange canonical simulations and micro-canonical Wang-Landau techniques. We perform a close comparative analysis of the corresponding results, and find perfect agreement between the two methods as well as the past results. The model is then refined in two different directions. By allowing partial overlapping between consecutive beads, we break the spherical symmetry and thus provide a severe constraint on the possible conformations of the chain. This leads to a single helix or a double helix ground state, depending on the range of the interactions. Alternatively, we introduce additional spherical beads at specific positions to represent the steric hindrance of the side chains in real proteins. The ground state in this case is found to be again a globule, thus showing that contrary to some recent suggestions, side chains alone are not sufficient to insure a protein-like structure. Finally, we show that a combination of the above two effects increases the stability of the obtaining secondary structures, in agreement with previous results. The fundamental role played by the range of the square-well attraction is highlighted, and it is shown that they play a role similar to that found in simple liquids and polymers. Perspectives in terms of protein folding are finally discussed.

cond-mat.soft↗
arXiv2015

Phase diagram of the ground states of DNA condensates

Phase diagram of the ground states of DNA in a bad solvent is studied for a semi-flexible polymer model with a generalized local elastic bending potential characterized by a nonlinearity parameter $x$ and effective self-attraction promoting compaction. $x=1$ corresponds to the worm-like chain model. Surprisingly, the phase diagram as well as the transition lines between the ground states are found to be a function of $x$. The model provides a simple explanation for the results of prior experimental and computational studies and makes predictions for the specific geometries of the ground states. The results underscore the impact of the form of the microscopic bending energy at macroscopic observable scales.

q-bio.BM↗
arXiv2015

Chiral Self-Assembly of Helical Particles

The shape of the building blocks plays a crucial role in directing self-assembly towards desired architectures. Out of the many different shapes, helix has a unique position. Helical structures are ubiquitous in nature and a helical shape is exhibited by the most important biopolymers like polynucleotides, polypeptides and polysaccharides as well as by cellular organelles like flagella. Helical particles can self-assemble into chiral superstructures, which may have a variety of applications, e.g. as photonic (meta)materials. However,a clear and definite understanding of these structures has not been entirely achieved yet. We have recently undertaken an extensive investigation on the phase behaviour of hard helical particles, using numerical simulations and classical density functional theory. Here we present a detailed study of the phase diagram of hard helices as a function of their morphology. This includes a variety of liquid-crystal phases, with different degrees of orientational and positional ordering. We show how, by tuning the helix parameters, it is possible to control the organization of the system. Starting from slender helices, whose phase behaviour is similar to that of rodlike particles, the increase in curliness leads to the onset of azimuthal correlations between the particles and the formation of phases specific to helices. These phases feature a new kind of screw order, of which there is experimental evidence in colloidal suspensions of helical flagella.

cond-mat.soft↗
arXiv2015

Bridging and depletion mechanisms in colloid-colloid effective interactions: A reentrant phase diagram

A general class of nonadditive sticky-hard-sphere binary mixtures, where small and large spheres represent the solvent and the solute, respectively, is introduced. The solute-solute and solvent-solvent interactions are of hard-sphere type, while the solute-solvent interactions are of sticky-hard-sphere type with tunable degrees of size nonadditivity and stickiness. Two particular and complementary limits are studied using analytical and semi-analytical tools. The first case is characterized by zero nonadditivity, lending itself to a Percus-Yevick approximate solution from which the impact of stickiness on the spinodal curves and on the effective solute-solute potential is analyzed. In the opposite nonadditive case, the solvent-solvent diameter is zero and the model can then be reckoned as an extension of the well-known Asakura-Oosawa model with additional sticky solute-solvent interaction. This latter model has the property that its exact effective one-component problem involves only solute-solute pair potentials for size ratios such that a solvent particle fits inside the interstitial region of three touching solutes. In particular, we explicitly identify the three competing physical mechanisms (depletion, pulling, and bridging) giving rise to the effective interaction. Some remarks on the phase diagram of these two complementary models are also addressed through the use of the Noro-Frenkel criterion and a first-order perturbation analysis. Our findings suggest reentrance of the fluid-fluid instability as solvent density (in the first model) or adhesion (in the second model) is varied. Some perspectives in terms of the interpretation of recent experimental studies of microgels adsorbed onto large polystyrene particles are discussed.

cond-mat.soft↗
arXiv2015

Reference Interaction Site Model and Optimized Perturbation theories of colloidal dumbbells with increasing anisotropy

We investigate thermodynamic properties of anisotropic colloidal dumbbells in the frameworks provided by the Reference Interaction Site Model (RISM) theory and an Optimized Perturbation Theory (OPT), this latter based on a fourth-order high-temperature perturbative expansion of the free energy, recently generalized to molecular fluids. Our model is constituted by two identical tangent hard spheres surrounded by square-well attractions with same widths and progressively different depths. Gas-liquid coexistence curves are obtained by predicting pressures, free energies, and chemical potentials. In comparison with previous simulation results, RISM and OPT agree in reproducing the progressive reduction of the gas-liquid phase separation as the anisotropy of the interaction potential becomes more pronounced; in particular, the RISM theory provides reasonable predictions for all coexistence curves, bar the strong anisotropy regime, whereas OPT performs generally less well. Both theories predict a linear dependence of the critical temperature on the interaction strength, reproducing in this way the mean-field behavior observed in simulations; the critical density~--~that drastically drops as the anisotropy increases~--~turns to be less accurate. Our results appear as a robust benchmark for further theoretical studies, in support to the simulation approach, of self-assembly in model colloidal systems.

cond-mat.soft↗
arXiv2014

Cluster formation and phase separation in heteronuclear Janus dumbbells

We have recently investigated the phase behaviour of model colloidal dumbbells constituted by two identical tangent hard spheres, with the first one being surrounded by an attractive square-well interaction (Janus dumbbells, Munaò G et al 2014 Soft Matter 10 5269). Here we extend our previous analysis by introducing in the model the size asymmetry of the hard-core diameters, and study the enriched phase scenario thereby obtained. By employing standard Monte Carlo simulations we show that in such "heteronuclear Janus dumbbells" a larger hard-sphere site promotes the formation of clusters, whereas in the opposite condition a gas-liquid phase separation takes place, with a narrow interval of intermediate asymmetries wherein the two phase behaviours may compete. In addition, some peculiar geometrical arrangements, such as lamellae, are observed only around the perfectly symmetric case. A qualitative agreement is found with recent experimental results, where it is shown that the roughness of molecular surfaces in heterogeneous dimers leads to the formation of colloidal micelles.

cond-mat.soft↗
arXiv2014

Self-assembly of hard helices: a rich and unconventional polymorphism

Hard helices can be regarded as a paradigmatic elementary model for a number of natural and synthetic soft matter systems, all featuring the helix as their basic structural unit: from natural polynucleotides and polypeptides to synthetic helical polymers; from bacterial flagella to colloidal helices. Here we present an extensive investigation of the phase diagram of hard helices using a variety of methods. Isobaric Monte Carlo numerical simulations are used to trace the phase diagram: on going from the low-density isotropic to the high-density compact phases, a rich polymorphism is observed exhibiting a special chiral screw-like nematic phase and a number of chiral and/or polar smectic phases. We present a full characterization of the latter, showing that they have unconventional features, ascribable to the helical shape of the constituent particles. Equal area construction is used to locate the isotropic-to-nematic phase transition, and results are compared with those stemming from an Onsager-like theory. Density functional theory is also used to study the nematic-to-screw-nematic phase transition: within the simplifying assumption of perfectly parallel helices, we compare different levels of approximation, that is second- and third-virial expansions and Parsons-Lee correction.

cond-mat.soft↗
arXiv2014

Left or right cholesterics? A matter of helix handedness and curliness

We have investigated the relationship between the morphology of helical particles and the features of the cholesteric (N$^\ast $) phase that they form. Using an Onsager-like theory, applied to systems of hard helices, we show that the cholesteric handedness and pitch depend on both the pitch and the curliness of the particles. The theory leads to the definition of pseudoscalars that correlate the helical features of the phase to the chirality of the excluded volume of the constituent particles.

cond-mat.soft↗
arXiv2014

From rods to helices: evidence of a screw-like nematic phase

Evidence of a special chiral nematic phase is provided using numerical simulation and Onsager theory for systems of hard helical particles. This phase appears at the high density end of the nematic phase, when helices are well aligned, and is characterized by the C$_2$ symmetry axes of the helices spiraling around the nematic director with periodicity equal to the particle pitch. This coupling between translational and rotational degrees of freedom allows a more efficient packing and hence an increase of translational entropy. Suitable order parameters and correlation functions are introduced to identify this screw-like phase, whose main features are then studied as a function of radius and pitch of the helical particles. Our study highlights the physical mechanism underlying a similar ordering observed in colloidal helical flagella [E. Barry et al. \textit{Phys. Rev. Lett.} \textbf{96}, 018305 (2006)] and raises the question of whether it could be observed in other helical particle systems, such as DNA, at sufficiently high densities.

cond-mat.soft↗
arXiv2014

From square-well to Janus: Improved algorithm for integral equation theory and comparison with thermodynamic perturbation theory within the Kern-Frenkel model

Building upon past work on the phase diagram of Janus fluids [Sciortino et al., Phys. Rev. Lett. \textbf{103}, 237801 (2009)], we perform a detailed study of integral equation theory of the Kern-Frenkel potential with coverage that is tuned from the isotropic square-well fluid to the Janus limit. An improved algorithm for the reference hypernetted-chain (RHNC) equation for this problem is implemented that significantly extends the range of applicability of RHNC. Results for both structure and thermodynamics are presented and compared with numerical simulations. Unlike previous attempts, this algorithm is shown to be stable down to the Janus limit, thus paving the way for analyzing the frustration mechanism characteristic of the gas-liquid transition in the Janus system. The results are also compared with Barker-Henderson thermodynamic perturbation theory on the same model. We then discuss the pros and cons of both approaches within a unified treatment. On balance, RHNC integral equation theory, even with an isotropic hard-sphere reference system, is found to be a good compromise between accuracy of the results, computational effort, and uniform quality to tackle self-assembly processes in patchy colloids of complex nature. Further improvement in RHNC however clearly requires an \emph{anisotropic} reference bridge function.

cond-mat.soft↗
arXiv2014

From toroidal to rod-like condensates of semiflexible polymers

The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring molecules, using analytical theory supported by Monte Carlo simulations. Both conformations considered are characterized by a local nematic order with hexagonal packing symmetry of neighboring DNA molecules, but differ in global configuration of the chain and the distribution of its curvature as it wraps around to form a condensate. The long-range interactions driving the DNA condensation are assumed to be of the form pertaining to the attractive depletion potential as well as the attractive counterion induced soft potential. In the stiffness-length plane we find a transition between rod-like to toroid condensate for increasing stiffness at a fixed chain length $L$. Strikingly, the transition line is found to have a $L^{1/3}$ dependence irrespective of the details of the long-range interactions between neighboring molecules. When realistic DNA parameters are used, our description reproduces rather well some of the experimental features observed in DNA condensates.

cond-mat.soft↗
arXiv2014

A unified description of solvent effects in the helix-coil transition

We analyze the problem of the helix-coil transition in explicit solvents analytically by using spin-based models incorporating two different mechanisms of solvent action: explicit solvent action through the formation of solvent-polymer hydrogen bonds that can compete with the intrinsic intra-polymer hydrogen bonded configurations (competing interactions) and implicit solvent action, where the solvent-polymer interactions tune biopolymer configurations by changing the activity of the solvent (non-competing interactions). The overall spin Hamiltonian is comprised of three terms: the background \emph{in vacuo} Hamiltonian of the "Generalized Model of Polypeptide Chain" type and two additive terms that account for the two above mechanisms of solvent action. We show that on this level the solvent degrees of freedom can be {\sl explicitly} and {\sl exactly} traced over, the ensuing effective partition function combining all the solvent effects in a unified framework. In this way we are able to address helix-coil transitions for polypeptides, proteins, and DNA, with different buffers and different external constraints. Our spin-based effective Hamiltonian is applicable for treatment of such diverse phenomena as cold denaturation, effects of osmotic pressure on the cold and warm denaturation, complicated temperature dependence of the hydrophobic effect as well as providing a conceptual base for understanding the behavior of Intrinsically Disordered Proteins and their analogues.

q-bio.BM↗
arXiv2013

Flory theory for Polymers

We review various simple analytical theories for homopolymers within a unified framework. The common guideline of our approach is the Flory theory, and its various avatars, with the attempt of being reasonably self-contained. We expect this review to be useful as an introduction to the topic at the graduate students level.

cond-mat.stat-mech↗
arXiv2013

Phase diagrams of Janus fluids with up-down constrained orientations

A class of binary mixtures of Janus fluids formed by colloidal spheres with the hydrophobic hemispheres constrained to point either up or down are studied by means of Gibbs ensemble Monte Carlo simulations and simple analytical approximations. These fluids can be experimentally realized by the application of an external static electrical field. The gas-liquid and demixing phase transitions in five specific models with different patch-patch affinities are analyzed. It is found that a gas-liquid transition is present in all the models, even if only one of the four possible patch-patch interactions is attractive. Moreover, provided the attraction between like particles is stronger than between unlike particles, the system demixes into two subsystems with different composition at sufficiently low temperatures and high densities.

cond-mat.soft↗