We 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. We 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 on the thermostat parameter also with regard to the dynamic properties.

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.

Graphene exhibits extraordinary electronic and mechanical properties, and extremely high thermal conductivity. Being a very stable atomically thick membrane that can be suspended between two leads, graphene provides a perfect test platform for studying thermal conductivity in two-dimensional systems, which is of primary importance for phonon transport in low-dimensional materials. Here we report experimental measurements and nonequilibrium molecular dynamics simulations of thermal conduction in suspended single-layer graphene as a function of both temperature and sample length. Interestingly and in contrast to bulk materials, at 300 K, thermal conductivity keeps increasing and remains logarithmically divergent with sample length even for sample lengths much larger than the average phonon mean free path. This result is a consequence of the two-dimensional nature of phonons in graphene, and provides fundamental understanding of thermal transport in two-dimensional materials.

Homogeneous ice nucleation from supercooled water was studied in the temperature range of 220-240 K through combining the forward flux sampling method (Allen et al., J. Chem. Phys., 2006, 124, 024102) with molecular dynamics simulations (FFS/MD), based on a recently developed coarse-grained water model (mW) (Molinero et al., J. Phys. Chem. B, 2009, 113, 4008). The calculated ice nucleation rates display a strong temperature dependence, ranging from 2.148 ± 0.635 × 10(25) m(-3) s(-1) at 220 K to 1.672 ± 0.970 × 10(-7) m(-3) s(-1) at 240 K. These rates can be fitted according to the classical nucleation theory, yielding an estimate of the effective ice-water interface energy γ(ls) of 31.01 ± 0.21 mJ m(-2) for the mW water model. Compared to experiments, our calculation underestimates the homogeneous ice nucleation rate by a few orders of magnitude. Possible reasons for the discrepancy are discussed. The nucleating ice embryo contains both cubic ice Ic and hexagonal ice Ih, with the fraction of each structure being roughly 50% when the critical size is reached. In particular, a novel defect structure containing nearly five-fold twin boundaries is identified in the ice clusters formed during nucleation. The way such defect structure is formed is found to be different from mechanisms proposed for the formation of the same defect in metallic nanoparticles and thin film. The quasi five-fold twin boundary structure found here is expected to occur in the crystallization of a wide range of materials with the diamond cubic structure, including ice.

Adaptive resolution schemes allow the simulation of a molecular fluid treating simultaneously different subregions of the system at different levels of resolution. In this work we present a new scheme formulated in terms of a global Hamiltonian. Within this approach equilibrium states corresponding to well defined statistical ensembles can be generated making use of all standard Molecular Dynamics or Monte Carlo methods. Models at different resolutions can thus be coupled, and thermodynamic equilibrium can be modulated keeping each region at desired pressure or density without disrupting the Hamiltonian framework.

We present a series of molecular dynamics, lattice dynamics, and Boltzmann transport equation calculations aimed at understanding heat transport in Silicon nanowires. In agreement with recent experiments, we find that the computed thermal conductivity strongly depends on the surface structure. It may be as high as that of bulk Si for crystalline wires, while wires with amorphous surfaces have the smallest thermal conductivity, about 100 times lower than the bulk. Two, combined effects are responsible for this dramatic difference: the presence, at disordered surfaces, of extended, nonpropagating modes analogous to heat carriers in amorphous Si, together with decreased lifetimes of propagating modes.

Using molecular dynamics, we investigate the crystal nucleation in a Lennard-Jones fluid as a function of the degree of supercooling. At moderate supercooling, a nucleation picture applies, while for deeper quenches, the phenomenon progressively acquires a spinodal character. We show that in the nucleation regime, the freezing is a two-step process. The formation of the critical nucleus is indeed preceded by the abrupt formation of a precritical crystallite from a density fluctuation in the fluid. In contrast, as the degree of supercooling is increased, crystallization proceeds in a more continuous and collective fashion and becomes more spatially diffuse, indicating that the liquid is unstable and crystallizes by a spinodal mechanism.

We derive expressions of interatomic force and heat current for many-body potentials such as the Tersoff, the Brenner, and the Stillinger-Weber potential used extensively in molecular dynamics simulations of covalently bonded materials. Although these potentials have a many-body nature, a pairwise force expression that follows Newton's third law can be found without referring to any partition of the potential. Based on this force formula, a stress applicable for periodic systems can be unambiguously defined. The force formula can then be used to derive the heat current formulas using a natural potential partitioning. Our heat current formulation is found to be equivalent to most of the seemingly different heat current formulas used in the literature, but to deviate from the stress-based formula derived from two-body potential. We validate our formulation numerically on various systems described by the Tersoff potential, namely three-dimensional silicon and diamond, two-dimensional graphene, and quasi-one-dimensional carbon nanotube. The effects of cell size and production time used in the simulation are examined.