Davide Donadio

Canonical sampling through velocity rescaling

The authors present a new molecular dynamics algorithm for sampling the canonical distribution. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. The algorithm is formally justified and it is shown that, in spite of its stochastic nature, a quantity can still be defined that remains constant during the evolution. In numerical applications this quantity can be used to measure the accuracy of the sampling. The authors illustrate the properties of this new method on Lennard-Jones and TIP4P water models in the solid and liquid phases. Its performance is excellent and largely independent of the thermostat parameter also with regard to the dynamic properties.

PLUMED: a portable plugin for free-energy calculations with molecular dynamics

Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure. This leaves the possibility for the user to exploit many different MD engines depending on the system simulated and on the computational resources available. Free-energy calculations can be performed as a function of many collective variables, with a particular focus on biological problems, and using state-of-the-art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The present software, written in ANSI-C language, can be easily interfaced with both Fortran and C/C++ codes.

Surface-induced crystallization in supercooled tetrahedral liquids

Surfaces have long been known to have an intricate role in solid-liquid phase transformations. Whereas melting is often observed to originate at surfaces, freezing usually starts in the bulk, and only a few systems have been reported to exhibit signatures of surface-induced crystallization. These include assembly of chain-like molecules, some liquid metals and alloys and silicate glasses. Here, we report direct computational evidence of surface-induced nucleation in supercooled liquid silicon and germanium, and we illustrate the crucial role of free surfaces in the freezing process of tetrahedral liquids exhibiting a negative slope of their melting lines (dT/dP|coexist<0). Our molecular dynamics simulations show that the presence of free surfaces may enhance the nucleation rates by several orders of magnitude with respect to those found in the bulk. Our findings provide insight, at the atomistic level, into the nucleation mechanism of widely used semiconductors, and support the hypothesis of surface-induced crystallization in other tetrahedrally coordinated systems, in particular water in the atmosphere.

Polyamorphism of ice at low temperatures from constant-pressure simulations.

We report results of molecular dynamics simulations of amorphous ice in the pressure range 0-22.5 kbar. The high-density amorphous (HDA) ice prepared by compression of Ih ice at T=80 K is annealed to T=170 K at intermediate pressures in order to generate relaxed states. We confirm the existence of recently observed phenomena, the very high-density amorphous ice, and a continuum of HDA forms. We suggest that both phenomena have their origin in the evolution of the network topology of the annealed HDA phase with decreasing volume, resulting at low temperatures in the metastability of a range of densities.

Evolution of the structure of amorphous ice: from low-density amorphous through high-density amorphous to very high-density amorphous ice.

We report results of molecular dynamics simulations of amorphous ice for pressures up to 22.5 kbar. The high-density amorphous ice (HDA) as prepared by pressure-induced amorphization of I(h) ice at T=80 K is annealed to T=170 K at various pressures to allow for relaxation. Upon increase of pressure, relaxed amorphous ice undergoes a pronounced change of structure, ranging from the low-density amorphous ice at p=0, through a continuum of HDA states to the limiting very high-density amorphous ice (VHDA) regime above 10 kbar. The main part of the overall structural change takes place within the HDA megabasin, which includes a variety of structures with quite different local and medium-range order as well as network topology and spans a broad range of densities. The VHDA represents the limit to densification by adapting the hydrogen-bonded network topology, without creating interpenetrating networks. The connection between structure and metastability of various forms upon decompression and heating is studied and discussed. We also discuss the analogy with amorphous and crystalline silica. Finally, some conclusions concerning the relation between amorphous ice and supercooled water are drawn.

Experimental and theoretical evidence for bilayer-by-bilayer surface melting of crystalline ice

Significance Over 150 years ago, Faraday discovered the presence of a water layer on ice below the bulk melting temperature. This layer is important for surface chemistry and glacier sliding close to subfreezing conditions. The nature and thickness of this quasi-liquid layer has remained controversial. By combining experimental and simulated surface-specific vibrational spectroscopy, the thickness of this quasi-liquid layer is shown to change in a noncontinuous, stepwise fashion around 257 K. Below this temperature, the first bilayer is already molten; the second bilayer melts at this transition temperature. The blue shift in the vibrational response of the outermost water molecules accompanying the transition reveals a weakening of the hydrogen bond network upon an increase of the water layer thickness. On the surface of water ice, a quasi-liquid layer (QLL) has been extensively reported at temperatures below its bulk melting point at 273 K. Approaching the bulk melting temperature from below, the thickness of the QLL is known to increase. To elucidate the precise temperature variation of the QLL, and its nature, we investigate the surface melting of hexagonal ice by combining noncontact, surface-specific vibrational sum frequency generation (SFG) spectroscopy and spectra calculated from molecular dynamics simulations. Using SFG, we probe the outermost water layers of distinct single crystalline ice faces at different temperatures. For the basal face, a stepwise, sudden weakening of the hydrogen-bonded structure of the outermost water layers occurs at 257 K. The spectral calculations from the molecular dynamics simulations reproduce the experimental findings; this allows us to interpret our experimental findings in terms of a stepwise change from one to two molten bilayers at the transition temperature.

Nucleation of tetrahedral solids: A molecular dynamics study of supercooled liquid silicon

The early stages of crystallization of tetrahedral systems remain largely unknown, due to experimental limitations in spatial and temporal resolutions. Computer simulations, when combined with advanced sampling techniques, can provide valuable details about nucleation at the atomistic level. Here we describe a computational approach that combines the forward flux sampling method with molecular dynamics, and we apply it to the study of nucleation in supercooled liquid silicon. We investigated different supercooling temperatures, namely, 0.79, 0.86, and 0.95 of the equilibrium melting point T(m). Our results show the calculated nucleation rates decrease from 5.52+/-1.75x10(28) to 4.77+/-3.26x10(11) m(-3) s(-1) at 0.79 and 0.86 T(m), respectively. A comparison between simulation results and those of classical nucleation theory shows that the free energy of the liquid solid interface gamma(ls) inferred from our computations differ by about 28% from that obtained for bulk liquid solid interfaces. However the computed values of gamma(ls) appear to be rather insensitive to supercooling temperature variations. Our simulations also yield atomistic details of the nucleation process, including the atomic structure of critical nuclei and lifetime distributions of subcritical nuclei.

Thermal conductivity decomposition in two-dimensional materials: Application to graphene

Two-dimensional materials have unusual phonon spectra due to the presence of flexural (out-of-plane) modes. Although molecular dynamics simulations have been extensively used to study heat transport in such materials, conventional formalisms treat the phonon dynamics isotropically. Here, we decompose the microscopic heat current in atomistic simulations into in-plane and out-of-plane components, corresponding to in-plane and out-of-plane phonon dynamics, respectively. This decomposition allows for direct computation of the corresponding thermal conductivity components in two-dimensional materials. We apply this decomposition to study heat transport in suspended graphene, using both equilibrium and nonequilibrium molecular dynamics simulations. We show that the flexural component is responsible for about two-thirds of the total thermal conductivity in unstrained graphene, and the acoustic flexural component is responsible for the logarithmic divergence of the conductivity when a sufficiently large tensile strain is applied.

Microscopic Mechanism and Kinetics of Ice Formation at Complex Interfaces: Zooming in on Kaolinite

Most ice in nature forms because of impurities which boost the exceedingly low nucleation rate of pure supercooled water. However, the microscopic details of ice nucleation on these substances remain largely unknown. Here, we have unraveled the molecular mechanism and the kinetics of ice formation on kaolinite, a clay mineral playing a key role in climate science. We find that the formation of ice at strong supercooling in the presence of this clay is about 20 orders of magnitude faster than homogeneous freezing. The critical nucleus is substantially smaller than that found for homogeneous nucleation and, in contrast to the predictions of classical nucleation theory (CNT), it has a strong two-dimensional character. Nonetheless, we show that CNT describes correctly the formation of ice at this complex interface. Kaolinite also promotes the exclusive nucleation of hexagonal ice, as opposed to homogeneous freezing where a mixture of cubic and hexagonal polytypes is observed.

Theoretical investigation of methane under pressure

We present computer simulations of liquid and solid phases of condensed methane at pressures below 25 GPa, between 150 and 300 K, where no appreciable molecular dissociation occurs. We used molecular dynamics (MD) and metadynamics techniques and empirical potentials in the rigid molecule approximation, whose validity was confirmed a posteriori by carrying out ab initio MD simulations for selected pressure and temperature conditions. Our results for the melting line are in satisfactory agreement with existing measurements. We find that the fcc crystal transforms into a hcp structure with four molecules per unit cell (B phase) at about 10 GPa and 150 K, and that the B phase transforms into a monoclinic high pressure phase above 20 GPa. Our results for solid/solid phase transitions are consistent with those of Raman studies but the phase boundaries estimated in our calculations are at higher pressure than those inferred from spectroscopic data.