arXiv subjects

Pablo M. Piaggi

Publications and source records attributed to Pablo M. Piaggi.

27 records · Page 2Linked to original sources

arXiv2019

Simulations of Crystal Nucleation from Solution at Constant Chemical Potential

A widely spread method of crystal preparation is to precipitate it from a supersaturated solution. In such a process, control of solution concentration is of paramount importance. Nucleation process, polymorph selection, and crystal habits depend crucially on this thermodynamic parameter. When performing simulations in the canonical ensemble as the crystalline phase is deposited the solution is depleted of solutes. This unavoidable modification of the thermodynamic conditions leads to significant artifact. Here we adopt the idea of the constant chemical potential molecular dynamics approach of Perego et al. [J. Chem. Phys. 2015, 142, 144113] to the study of nucleation. Our method allows determining the crystal nucleus size and nucleation rates at constant supersaturation. As an example we study the homogeneous nucleation of sodium chloride from its supersaturated aqueous solution.

cond-mat.soft↗

arXiv2019

Calculation of phase diagrams in the multithermal-multibaric ensemble

From the Ising model and the Lennard-Jones fluid, to water and the iron-carbon system, phase diagrams are an indispensable tool to understand phase equilibria. In spite of the effort of the simulation community the calculation of a large portion of a phase diagram using computer simulation is still today a significant challenge. Here we propose a method to calculate phase diagrams involving liquid and solid phases by the reversible transformation of the liquid and the solid. To this end we introduce an order parameter that breaks the rotational symmetry and we leverage our recently introduced method to sample the multithermal-multibaric ensemble. In this way in a single molecular dynamics simulation we are able to compute the liquid-solid coexistence line for entire regions of the temperature and pressure phase diagram. We apply our approach to the bcc-liquid phase diagram of sodium and the fcc-bcc-liquid phase diagram of aluminum.

cond-mat.stat-mech↗

arXiv2019

A local fingerprint for hydrophobicity and hydrophilicity: from methane to peptides

An important characteristic that determines the behavior of a solute in water is whether it is hydrophobic or hydrophilic. The traditional classification is based on chemical experience and heuristics. However, this does not reveal how the local environment modulates this important property. We present a local fingerprint for hydrophobicity and hydrophilicity inspired by the two body contribution to the entropy. This fingerprint is an inexpensive, quantitative and physically meaningful way of studying hydrophilicity and hydrophobicity that only requires as input the water-solute radial distribution functions. We apply our fingerprint to octanol, benzene and the 20 proteinogenic amino acids. Our measure of hydrophilicity is coherent with chemical experience and, moreover, it also shows how the character of an atom can change as its environment is changed. Lastly, we use the fingerprint as collective variable in a funnel metadynamics simulation of a host-guest system. The fingerprint serves as a desolvation collective variable that enhances transitions between the bound and unbound states.

physics.chem-ph↗

arXiv2019

Naphthalene crystal shape prediction from molecular dynamics simulations

We used molecular dynamics simulations to predict the steady state crystal shape of naphthalene grown from ethanol solution. The simulations were performed at constant supersaturation by utilizing a recently proposed algorithm [Perego et al., J. Chem. Phys., 142, 2015, 144113]. To bring the crystal growth within the timescale of a molecular dynamics simulation we applied Well-Tempered Metadynamics with a spatially constrained collective variable, which focuses the sampling on the growing layer. We estimated that the resulting steady state crystal shape corresponds to a rhombic prism, which is in line with experiments. Further, we observed that at the investigated supersaturations, the $\{00\bar{1}\}$ face grows in a two step two dimensional nucleation mechanism while the considerably faster growing faces $\{1\bar{1}0\}$ and $\{20\bar{1}\}$ grow new layers with a one step two dimensional nucleation mechanism.

physics.chem-ph↗

arXiv2019

Multithermal-multibaric molecular simulations from a variational principle

We present a method for performing multithermal-multibaric molecular dynamics simulations that sample entire regions of the temperature-pressure (TP) phase diagram. The method uses a variational principle [Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] in order to construct a bias that leads to a uniform sampling in energy and volume. The intervals of temperature and pressure are taken as inputs and the relevant energy and volume regions are determined on the fly. In this way the method guarantees adequate statistics for the chosen TP region. We show that our multithermal-multibaric simulations can be used to calculate all static physical quantities for all temperatures and pressures in the targeted region of the TP plane. We illustrate our approach by studying the density anomaly of TIP4P/Ice water.

cond-mat.stat-mech↗

arXiv2018

A variational approach to nucleation simulation

We study by computer simulation the nucleation of a supersaturated Lennard-Jones vapor into the liquid phase. The large free energy barriers to transition make the time scale of this process impossible to study by ordinary molecular dynamics simulations.Therefore we use a recently developed enhanced sampling method [Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] based on the variational determination of a bias potential. We differ from previous applications of this method in that the bias is constructed on the basis of the physical model provided by the classical theory of nucleation. We examine the technical problems associated with this approach. Our results are very satisfactory and will pave the way for calculating the nucleation rates in many systems.

cond-mat.stat-mech↗

arXiv2018

Predicting polymorphism in molecular crystals using orientational entropy

We introduce a computational method to discover polymorphs in molecular crystals at finite temperature. The method is based on reproducing the crystallization process starting from the liquid and letting the system discover the relevant polymorphs. This idea, however, conflicts with the fact that crystallization has a time scale much longer than that of molecular simulations. In order to bring the process within affordable simulation time, we enhance the fluctuations of a collective variable by constructing a bias potential with well tempered metadynamics. We use as collective variable an entropy surrogate based on an extended pair correlation function that includes the correlation between the orientation of pairs of molecules. We also propose a similarity metric between configurations based on the extended pair correlation function and a generalized Kullback-Leibler divergence. In this way, we automatically classify the configurations as belonging to a given polymorph using our metric and a hierarchical clustering algorithm. We find all relevant polymorphs for both substances and we predict new polymorphs. One of them is stabilized at finite temperature by entropic effects.

physics.chem-ph↗

arXiv2017

Entropy based fingerprint for local crystalline order

We introduce a new fingerprint that allows distinguishing between liquid-like and solid-like atomic environments. This fingerprint is based on an approximate expression for the entropy projected on individual atoms. When combined with a local enthalpy, this fingerprint acquires an even finer resolution and it is capable of discriminating between different crystal structures.

cond-mat.mtrl-sci↗

arXiv2017

Enhancing entropy and enthalpy fluctuations to drive crystallization in atomistic simulations

Crystallization is a process of great practical relevance in which rare but crucial fluctuations lead to the formation of a solid phase starting from the liquid. Like in all first order first transitions there is an interplay between enthalpy and entropy. Based on this idea, to drive crystallization in molecular simulations, we introduce two collective variables, one enthalpic and the other entropic. Defined in this way, these collective variables do not prejudge the structure the system is going to crystallize into. We show the usefulness of this approach by studying the case of sodium and aluminum that crystallize in the bcc and fcc crystalline structure, respectively. Using these two generic collective variables, we perform variationally enhanced sampling and well tempered metadynamics simulations, and find that the systems transform spontaneously and reversibly between the liquid and the solid phases.

cond-mat.stat-mech↗