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Carlo Pierleoni

Publications and source records attributed to Carlo Pierleoni.

At least 37 records · Page 2Linked to original sources

Coupled Electron-Ion Monte Carlo simulation of hydrogen molecular crystals

We performed simulations for solid molecular hydrogen at high pressures (250GPa$\leq$P$\leq$500GPa) along two isotherms at T=200 K (phases III and VI) and at T=414 K (phase IV). At T=200K we considered likely candidates for phase III, the C2c and Cmca12 structures, while at T=414K in phase IV we studied the Pc48 structure. We employed both Coupled Electron-Ion Monte Carlo (CEIMC) and Path Integral Molecular Dynamics (PIMD) based on Density Functional Theory (DFT) using the vdW-DF approximation. The comparison between the two methods allows us to address the question of the accuracy of the xc approximation of DFT for thermal and quantum protons without recurring to perturbation theories. In general, we find that atomic and molecular fluctuations in PIMD are larger than in CEIMC which suggests that the potential energy surface from vdW-DF is less structured than the one from Quantum Monte Carlo. We find qualitatively different behaviors for systems prepared in the C2c structure for increasing pressure. Within PIMD the C2c structure is dynamically partially stable for P$\leq$250GPa only: it retains the symmetry of the molecular centers but not the molecular orientation; at intermediate pressures it develops layered structures like Pbcn or Ibam and transforms to the metallic Cmca-4 structure at P$\geq$450GPa. Instead, within CEIMC, the C2c structure is found to be dynamically stable at least up to 450GPa; at increasing pressure the molecular bond length increases and the nuclear correlation decreases. For the other two structures the two methods are in qualitative agreement although quantitative differences remain. We discuss various structural properties and the electrical conductivity. We find these structures become conducting around 350GPa but the metallic Drude-like behavior is reached only at around 500GPa, consistent with recent experimental claims.

cond-mat.mtrl-sci↗

On the force--velocity relationship of a bundle of rigid living filaments

In various cellular processes, biofilaments like F-actin and F-tubulin are able to exploit chemical energy associated to polymerization to perform mechanical work against an external load. The force-velocity relationship quantitatively summarizes the nature of this process. By a stochastic dynamical model, we give, together with the evolution of a staggered bundle of $N_f$ rigid living filaments facing a loaded wall, the corresponding force--velocity relationship. We compute systematically the simplified evolution of the model in supercritical conditions $ρ_1=U_0/W_0>1$ at $ε=d^2W_0/D=0$, where $d$ is the monomer size, $D$ is the obstacle diffusion coefficient, $U_0$ and $W_0$ are the polymerization and depolymerization rates. Moreover, we see that the solution at $ε=0$ is valid for a good range of small non-zero $ε$ values. We consider two classical protocols: the bundle is opposed either to a constant load or to an optical trap set-up, characterized by a harmonic restoring force. The constant force case leads, for each $F$ value, to a stationary velocity $V^{stat}(F;N_f,ρ_1)$ after a relaxation with characteristic time $τ_{micro}(F)$. When the bundle (initially taken as an assembly of filament seeds) is subjected to a harmonic restoring force (optical trap load), the bundle elongates and the load increases up to stalling (equilibrium) over a characteristic time $τ^{OT}$. Extracted from this single experiment, the force-velocity $V^{OT}(F;N_f,ρ_1)$ curve is found to coincide with $V^{stat}(F;N_f,ρ_1)$, except at low loads. We show that this result follows from the adiabatic separation between $τ_{micro}$ and $τ^{OT}$, i.e. $τ_{micro}\llτ^{OT}$.

cond-mat.stat-mech↗

On the Properties of a Bundle of Flexible Actin Filaments in an Optical Trap

We establish the Statistical Mechanics framework for a bundle of Nf living and uncrosslinked actin filaments in a supercritical solution of free monomers pressing against a mobile wall. The filaments are anchored normally to a fixed planar surface at one of their ends and, because of their limited flexibility, they grow almost parallel to each other. Their growing ends hit a moving obstacle, depicted as a second planar wall, parallel to the previous one and subjected to a harmonic compressive force. The force constant is denoted as trap strength while the distance between the two walls as trap length to make contact with the experimental optical trap apparatus. For an ideal solution of reactive filaments and free monomers at fixed free monomers chemical potential, we obtain the general expression for the grand potential from which we derive averages and distributions of relevant physical quantities, namely the obstacle position, the bundle polymerization force and the number of filaments in direct contact with the wall. The grafted living filaments are modeled as discrete Wormlike chains, with Factin persistence length, subject to discrete contour length variations to model single monomer (de)polymerization steps. Rigid filaments, either isolated or in bundles, all provide average values of the stalling force in agreement with Hill's predictions, independent of the average trap length. Flexible filaments instead, for values of the trap strength suitable to prevent their lateral escape, provide an average bundle force and an average trap length slightly larger than the corresponding rigid cases (few percents). Still the stalling force remains nearly independent on the average trap length, but results from the product of two strongly L dependent contributions: the fraction of touching filaments and the single filament buckling force.

physics.bio-ph↗

Theory of Finite Size Effects for Electronic Quantum Monte Carlo Calculations of Liquids and Solids

Concentrating on zero temperature Quantum Monte Carlo calculations of electronic systems, we give a general description of the theory of finite size extrapolations of energies to the thermodynamic limit based on one and two-body correlation functions. We introduce new effective procedures, such as using the potential and wavefunction split-up into long and short range functions to simplify the method and we discuss how to treat backflow wavefunctions. Then we explicitly test the accuracy of our method to correct finite size errors on example hydrogen and helium many-body systems and show that the finite size bias can be drastically reduced for even small systems.

physics.comp-ph↗

Phase diagram of mixtures of colloids and polymers in the thermal crossover from good to $θ$ solvent

We determine the phase diagram of mixtures of spherical colloids and neutral nonadsorbing polymers in the thermal crossover region between the $θ$ point and the good-solvent regime. We use the generalized free-volume theory (GFVT), which turns out to be quite accurate as long as $q = R_g/R_c\lesssim 1$ ($R_g$ is the radius of gyration of the polymer and $R_c$ is the colloid radius). Close to the $θ$ point the phase diagram is not very sensitive to solvent quality, while, close to the good-solvent region, changes of the solvent quality modify significantly the position of the critical point and of the binodals. We also analyze the phase behavior of aqueous solutions of charged colloids and polymers, using the extension of GFVT proposed by Fortini et al., J. Chem. Phys. 128, 024904 (2008).

cond-mat.soft↗

A semi-flexible model prediction for the polymerization force exerted by a living F-actin filament on a fixed wall

We consider a single living semi-flexible filament with persistence length l_p in chemical equilibrium with a solution of free monomers at fixed monomer chemical potential mu_1 and fixed temperature T. While one end of the filament is chemically active with single monomer (de)polymerization steps, the other end is grafted normally to a rigid wall to mimick a rigid network from which the filament under consideration emerges. A second rigid wall, parallel to the grafting wall, is fixed at distance L<<l_p from the filament seed. In supercritical conditions the filament tends to grow and impinges onto the second surface which, in suitable conditions (non-escaping filament regime) stops the filament growth. We first establish the grand-potential and derive some general properties, in particular the filament size distribution and the force exerted by the living filament on the obstacle wall. We apply this formalism to the semi-flexible, living, discrete Wormlike chain (d-WLC) model with step size d and persistence length l_p, hitting a hard wall. By original Monte-Carlo calculations we justify the use of the weak bending universal expressions of Gholami et al. (Phys.Rev.E. 74,(2006), 041803) over the whole non escaping filament regime. Employing this universal form for living filaments, we find that the average force exerted by a living filament on a wall at distance L is in practice L independent and very close to the value predicted by Hill, his expression being strictly valid in the rigid filament limit. The average filament force results from the product of the cumulative size fraction x, where the filament is in contact with the wall, times the buckling force on a filament of size L_c ~ L. We discuss several consequences of the L independence of the stalling force for our specific filament model.

physics.bio-ph↗

Integral-equation analysis of single-site coarse-grained models for polymer-colloid mixtures

We discuss the reliability of integral-equation methods based on several commonly used closure relations in determining the phase diagram of coarse-grained models of soft-matter systems characterized by mutually interacting soft and hard-core particles. Specifically, we consider a set of potentials appropriate to describe a system of hard-sphere colloids and linear homopolymers in good solvent, and investigate the behavior when the soft particles are smaller than the colloids, which is the regime of validity of the coarse-grained models. Using computer-simulation results as a benchmark, we find that the hypernetted-chain approximation provides accurate estimates of thermodynamics and structure in the colloid-gas phase in which the density of colloids is small. On the other hand, all closures considered appear to be unable to describe the behavior of the mixture in the colloid-liquid phase, as they cease to converge at polymer densities significantly smaller than those at the binodal. As a consequence, integral equations appear to be unable to predict a quantitatively correct phase diagram.

cond-mat.soft↗

Coarse-graining polymer solutions: a critical appraisal of single- and multi-site models

We critically discuss and review the general ideas behind single- and multi-site coarse-grained (CG) models as applied to macromolecular solutions in the dilute and semi-dilute regime. We first consider single-site models with zero-density and density-dependent pair potentials. We highlight advantages and limitations of each option in reproducing the thermodynamic behavior and the large-scale structure of the underlying reference model. As a case study we consider solutions of linear homopolymers in a solvent of variable quality. Secondly, we extend the discussion to multi-component systems presenting, as a test case, results for mixtures of colloids and polymers. Specifically, we found the CG model with zero-density potentials to be unable to predict fluid-fluid demixing in a reasonable range of densities for mixtures of colloids and polymers of equal size. For larger colloids, the polymer volume fractions at which phase separation occurs are largely overestimated. CG models with density-dependent potentials are somewhat less accurate than models with zero-density potentials in reproducing the thermodynamics of the system and, although they presents a phase separation, they significantly underestimate the polymer volume fractions along the binodal. Finally, we discuss a general multi-site strategy, which is thermodynamically consistent and fully transferable with the number of sites, and that allows us to overcome most of the limitations discussed for single-site models.

cond-mat.soft↗

Accurate coarse-grained models for mixtures of colloids and linear polymers under good-solvent conditions

A coarse-graining strategy, previously developed for polymer solutions, is extended here to mixtures of linear polymers and hard-sphere colloids. In this approach groups of monomers are mapped onto a single pseudoatom (a blob) and the effective blob-blob interactions are obtained by requiring the model to reproduce some large-scale structural properties in the zero-density limit. We show that an accurate parametrization of the polymer-colloid interactions is obtained by simply introducing pair potentials between blobs and colloids. For the coarse-grained model in which polymers are modelled as four-blob chains (tetramers), the pair potentials are determined by means of the iterative Boltzmann inversion scheme, taking full-monomer pair correlation functions at zero-density as targets. For a larger number $n$ of blobs, pair potentials are determined by using a simple transferability assumption based on the polymer self-similarity. We validate the model by comparing its predictions with full-monomer results for the interfacial properties of polymer solutions in the presence of a single colloid and for thermodynamic and structural properties in the homogeneous phase at finite polymer and colloid density. The tetramer model is quite accurate for $q\lesssim 1$ ($q=\hat{R}_g/R_c$, where $\hat{R}_g$ is the zero-density polymer radius of gyration and $R_c$ is the colloid radius) and reasonably good also for $q=2$. For $q=2$ an accurate coarse-grained description is obtained by using the $n=10$ blob model. We also compare our results with those obtained by using single-blob models with state-dependent potentials.

cond-mat.soft↗

Molecular-Atomic Transition in the Deuterium Hugoniot with Coupled Electron Ion Monte Carlo

We have performed accurate simulations of the Deuterium Hugoniot using Coupled Electron Ion Monte Carlo (CEIMC). Using highly accurate quantum Monte Carlo methods for the electrons, we study the region of maximum compression along the principal Hugoniot, where the system undergoes a continuous transition from a molecular fluid to a monatomic fluid. We include all relevant physical corrections so that a direct comparison to experiment can be made. Around 50 GPa we found a maximum compression of 4.85, roughly 10% larger than previous theoretical predictions and experimental data but still compatible with the latter because of their large uncertainty.

cond-mat.str-el↗

Depletion effects in colloid-polymer solutions

The surface tension, the adsorption, and the depletion thickness of polymers close to a single nonadsorbing colloidal sphere are computed by means of Monte Carlo simulations. We consider polymers under good-solvent conditions and in the thermal crossover region between good-solvent and $θ$ behavior. In the dilute regime we consider a wide range of values of $q$, from $q = 0$ (planar surface) up to $q\approx 30$-50, while in the semidilute regime, for $ρ_p/ρ_p^*\le 4$ ($ρ_p$ is the polymer concentration and $ρ_p^*$ is its value at overlap), we only consider $q = 0,0.5,1$ and 2. The results are compared with the available theoretical predictions, verifying the existing scaling arguments. Field-theoretical results, both in the dilute and in the semidilute regime, are in good agreement with the numerical estimates for polymers under good-solvent conditions.

cond-mat.soft↗

Benchmark of Exchange-Correlation Functionals for High Pressure Hydrogen using Quantum Monte Carlo

The ab-initio phase diagram of dense hydrogen is very sensitive to errors in the treatment of electronic correlation. Recently, it has been shown that the choice of the density functional has a large effect on the predicted location of both the liquid-liquid phase transition and the solid insulator-to-metal transition in dense hydrogen. To identify the most accurate functional for dense hydrogen applications, we systematically benchmark some of the most commonly used functionals using Quantum Monte Carlo. By considering several measures of functional accuracy, we conclude that the van der Waals and hybrid functionals significantly out perform LDA and PBE. We support these conclusions by analyzing the impact of functional choice on structural optimization in the molecular solid, and on the location of the liquid-liquid phase transition.

cond-mat.mtrl-sci↗

Predicting the thermodynamics by using state-dependent interactions

We reconsider the structure-based route to coarse graining in which the coarse-grained model is defined in such a way to reproduce some distributions functions of the original system as accurately as possible. We consider standard expressions for pressure and chemical potential applied to this family of coarse-grained models with density-dependent interactions and show that they only provide approximations to the pressure and chemical potential of the underlying original system. These approximations are then carefully compared in two cases: we consider a generic microscopic system in the low-density regime and polymer solutions under good-solvent conditions. Moreover, we show that the state-dependent potentials depend on the ensemble in which they have been derived. Therefore, care must be used in applying canonical state-dependent potentials to predict phase lines, which is typically performed in other ensembles.

cond-mat.stat-mech↗

Consistent coarse-graining strategy for polymer solutions in the thermal crossover from Good to Theta solvent

We extend our previously developed coarse-graining strategy for linear polymers with a tunable number n of effective atoms (blobs) per chain [D'Adamo et al., J. Chem. Phys. 137, 4901 (2012)] to polymer systems in thermal crossover between the good-solvent and the Theta regimes. We consider the thermal crossover in the region in which tricritical effects can be neglected, i.e. not too close to the Theta point, for a wide range of chain volume fractions Phi=c/c* (c* is the overlap concentration), up to Phi=30. Scaling crossover functions for global properties of the solution are obtained by Monte-Carlo simulations of the Domb-Joyce model. They provide the input data to develop a minimal coarse-grained model with four blobs per chain. As in the good-solvent case, the coarse-grained model potentials are derived at zero density, thus avoiding the inconsistencies related to the use of state-dependent potentials. We find that the coarse-grained model reproduces the properties of the underlying system up to some reduced density which increases when lowering the temperature towards the Theta state. Close to the lower-temperature crossover boundary, the tetramer model is accurate at least up to Phi<10, while near the good-solvent regime reasonably accurate results are obtained up to Phi<2. The density region in which the coarse-grained model is predictive can be enlarged by developing coarse-grained models with more blobs per chain. We extend the strategy used in the good-solvent case to the crossover regime. This requires a proper treatment of the length rescalings as before, but also a proper temperature redefinition as the number of blobs is increased. The case n=10 is investigated. Comparison with full-monomer results shows that the density region in which accurate predictions can be obtained is significantly wider than that corresponding to the n=4 case.

cond-mat.soft↗

Consistent and transferrable coarse-grained model for semidilute polymer solutions in good solvent

We present a coarse-grained model for linear polymers with a tunable number of effective atoms (blobs) per chain interacting by intra- and inter-molecular potentials obtained at zero density. We show how this model is able to accurately reproduce the universal properties of the underlying solution of athermal linear chains at various levels of coarse-graining and in a range of chain densities which can be widened by increasing the spatial resolution of the multiblob representation, i.e., the number of blobs per chain. The present model is unique in its ability to quantitatively predict thermodynamic and large scale structural properties of polymer solutions deep in the semidilute regime with a very limited computational effort, overcoming most of the problems related to the simulations of semidilute polymer solutions in good solvent conditions.

cond-mat.soft↗

Polymers as compressible soft spheres

We consider a coarse-grained model in which polymers under good-solvent conditions are represented by soft spheres whose radii, which should be identified with the polymer radii of gyrations, are allowed to fluctuate. The corresponding pair potential depends on the sphere radii. This model is a single-sphere version of the one proposed in Vettorel et al., Soft Matter 6, 2282 (2010), and it is sufficiently simple to allow us to determine all potentials accurately from full-monomer simulations of two isolated polymers (zero-density potentials). We find that in the dilute regime (which is the expected validity range of single-sphere coarse-grained models based on zero-density potentials) this model correctly reproduces the density dependence of the radius of gyration. However, for the thermodynamics and the intermolecular structure, the model is largely equivalent to the simpler one in which the sphere radii are fixed to the average value of the radius of gyration and radiiindependent potentials are used: for the thermodynamics there is no advantage in considering a fluctuating sphere size.

cond-mat.soft↗

Crystalline free energies of micelles of diblock copolymer solutions

We report a characterization of the relative stability and structural behavior of various micellar crystals of an athermal model of AB-diblock copolymers in solution. We adopt a previously devel- oped coarse-graining representation of the chains which maps each copolymer on a soft dumbbell. Thanks to this strong reduction of degrees of freedom, we are able to investigate large aggregated systems, and for a specific length ratio of the blocks f = MA/(MA + MB) = 0.6, to locate the order-disorder transition of the system of micelles. Above the transition, mechanical and thermal properties are found to depend on the number of particles per lattice site in the simulation box, and the application of a recent methodology for multiple occupancy crystals (B.M. Mladek et al., Phys. Rev. Lett. 99, 235702 (2007)) is necessary to correctly define the equilibrium state. Within this scheme we have performed free energy calculations at two reduced density ρ/ρ\ast = 4,5 and for several cubic structures as FCC,BCC,A15. At both densities, the BCC symmetry is found to correspond to the minimum of the unconstrained free energy, that is to the stable symmetry among the few considered, while the A15 structure is almost degenerate, indicating that the present sys- tem prefers to crystallize in less packed structures. At ρ/ρ\ast = 4 close to melting, the Lindemann ratio is fairly high (~ 0.29) and the concentration of vacancies is roughly 6%. At ρ/ρ\ast = 5 the mechanical stability of the stable BCC structure increases and the concentration of vacancies ac- cordingly decreases. The ratio of the corona layer thickness to the core radius is found to be in good agreement with experimental data for poly(styrene-b-isoprene)(22-12) in isoprene selective solvent which is also reported to crystallize in the BCC structure.

physics.comp-ph↗

Coarse-graining strategies in polymer solutions

We review a coarse-graining strategy (multiblob approach) for polymer solutions in which groups of monomers are mapped onto a single atom (a blob) and effective blob-blob interactions are obtained by requiring the coarse-grained model to reproduce some coarse-grained features of the zero-density isolated-chain structure. By tuning the level of coarse graining, i.e. the number of monomers to be mapped onto a single blob, the model should be adequate to explore the semidilute regime above the collapse transition, since in this case the monomer density is very small if chains are long enough. The implementation of these ideas has been previously based on a transferability hypothesis, which was not completely tested against full-monomer results (Pierleoni et al., J. Chem. Phys, 127, 171102 (2007)). We study different models proposed in the past and we compare their predictions to full-monomer results for the chain structure and the thermodynamics in the range of polymer volume fractions Φbetween 0 and 8. We find that the transferability assumption has a limited predictive power if a thermodynamically consistent model is required. We introduce a new tetramer model parametrized in such a way to reproduce not only zero-density intramolecular and intermolecular two-body probabilities, but also some intramolecular three-body and four-body distributions. We find that such a model correctly predicts three-chain effects, the structure and the thermodynamics up to Φ~ 2, a range considerably larger than that obtained with previous simpler models using zero-density potentials. Our results show the correctness of the ideas behind the multiblob approach but also that more work is needed to understand how to develop models with more effective monomers which would allow us to explore the semidilute regime at larger chain volume fractions.

cond-mat.soft↗