A modified nudged elastic band algorithm with adaptive spring lengths.

We present a modified version of the nudged elastic band (NEB) algorithm to find minimum energy paths connecting two known configurations. We show that replacing the harmonic band-energy term with a discretized version of the Onsager-Machlup action leads to a NEB algorithm with adaptive spring lengths that automatically increase the resolution of the minimum energy path around the saddle point of the potential energy surface. The method has the same computational cost per optimization step of the standard NEB algorithm and does not introduce additional parameters. We present applications to the isomerization of alanine dipeptide, the elimination of hydrogen from ethane, and the healing of a 5-77-5 defect in graphene.

Quantum Symmetry from Enhanced Sampling Methods.

We address the problem of the minus sign sampling for two-electron systems using the path integral approach. We show that this problem can be reexpressed as one of computing free energy differences and sampling the tails of statistical distributions. Using metadynamics, a realistic problem like that of two electrons confined in a quantum dot can be solved. We believe that this is a strategy that can possibly be extended to more complex systems.

Molecular dynamics simulations of solutions at constant chemical potential.

Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CµMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CµMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.

Enhanced sampling in the well-tempered ensemble.

We introduce the well-tempered ensemble (WTE) which is the biased ensemble sampled by well-tempered metadynamics when the energy is used as collective variable. WTE can be designed so as to have approximately the same average energy as the canonical ensemble but much larger fluctuations. These two properties lead to an extremely fast exploration of phase space. An even greater efficiency is obtained when WTE is combined with parallel tempering. Unbiased Boltzmann averages are computed on the fly by a recently developed reweighting method [M. Bonomi, J. Comput. Chem. 30, 1615 (2009)]. We apply WTE and its parallel tempering variant to the 2d Ising model and to a Go model of HIV protease, demonstrating in these two representative cases that convergence is accelerated by orders of magnitude.

Impacted post-traumatic maxillary central incisor: A multidisciplinary approach.

AIM: The aim of this paper is to provide clinicians useful information for the management of impacted central incisor due to early childhood trauma. CASE REPORT: It is reported the case of an impacted right maxillary central incisor in an 8-year-old male patient who had an intrusive luxation trauma of primary tooth at the age of 4. After clinical and radiographic evaluation, a multidisciplinary treatment plan was planned. Therapy involved a surgical and orthodontic approach in order to expose the tooth and move the incisor in the normal position with a self-ligating appliance system. RESULTS: Through a multidisciplinary approach it was possible to move the impacted incisor in the occlusal plane, preserving periodontal tissues and tooth vitality. CONCLUSION: When a permanent tooth is impacted, the multidisciplinary approach of surgery and orthodontic treatment is the best way to obtain a suitable outcome in terms of gingival contour, occlusal plane and aesthetics, when compared with other treatment options.

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics.

Metadynamics is a widely used and successful method for reconstructing the free-energy surface of complex systems as a function of a small number of suitably chosen collective variables. This is achieved by biasing the dynamics of the system. The bias acting on the collective variables distorts the probability distribution of the other variables. Here we present a simple reweighting algorithm for recovering the unbiased probability distribution of any variable from a well-tempered metadynamics simulation. We show the efficiency of the reweighting procedure by reconstructing the distribution of the four backbone dihedral angles of alanine dipeptide from two and even one dimensional metadynamics simulation.

Structural and electronic properties of la@c82.

The structural and electronic properties of the La@C(82) fullerene have been investigated by means of the Car-Parrinello method, which is based on the local density approximation of the density functional theory. The topological arrangement of the C(82) cage was assumed to be a C(3v) symmetry isomer. Three configurations were considered, one with the lanthanum atom at the center of the cluster, one with it along the threefold axis, and one with it at a low-symmetry, highly coordinated site. The structure was fully relaxed and it was found that the last of these configurations is energetically preferred. In this position, the lanthanum atom is nearly in a La(3+) state and the unpaired electron is somewhat delocalized on the cage, in agreement with available experimental data. This arrangement suggests that the chemical shifts of the 5s and 5p lanthanum states can be used as a structural probe and as a way of further validating this picture. It is argued that this conclusion is not affected by the assumed fullerene structure.

Ab initio calculation of the sound velocity of dense hydrogen: implications for models of Jupiter.

First-principles molecular dynamics simulations were used to calculate the sound velocity of dense hydrogen, and the results were compared with extrapolations of experimental data that currently conflict with either astrophysical models or data obtained from recent global oscillation measurements of Jupiter. Excellent agreement with the extrapolated experimental data was obtained. These results strongly support the notion that the existing models for the jovian interior need to be revised.

Melting of diamond at high pressure.

Melting of diamond at high pressure and the properties of liquid carbon at pressures greater than 1 megabar were investigated with a first-principles molecular dynamics technique. The results indicate an increase of the diamond melting temperature with pressure, which is opposite to the behavior of silicon and germanium. This is contrary to long-held assumptions, but agrees with recent experiments, and has important implications for geology and astrophysics. As is the case for the solid phase of carbon at low temperature, which changes greatly with pressure from graphite to diamond, the structural and bonding properties of liquid carbon vary strongly with pressure.

Autoionization in liquid water.

The dissociation of a water molecule in liquid water is the fundamental event in acid-base chemistry, determining the pH of water. Because of the short time scales and microscopic length scales involved, the dynamics of this autoionization have not been directly probed by experiment. Here, the autoionization mechanism is revealed by sampling and analyzing ab initio molecular dynamics trajectories. We identify the rare fluctuations in solvation energies that destabilize an oxygen-hydrogen bond. Through the transfer of protons along a hydrogen bond "wire," the nascent ions separate by three or more neighbors. If the hydrogen bond wire connecting the two ions is subsequently broken, a metastable charge-separated state is visited. The ions may then diffuse to large separations. If, however, the hydrogen bond wire remains unbroken, the ions recombine rapidly. Because of their concomitant large electric fields, the transient ionic species produced in this case may provide an experimentally detectable signal of the dynamics we report.

Superionic and metallic states of water and ammonia at giant planet conditions.

The phase diagrams of water and ammonia were determined by constant pressure ab initio molecular dynamic simulations at pressures (30 to 300 gigapascal) and temperatures (300 to 7000 kelvin) of relevance for the middle ice layers of the giant planets Neptune and Uranus. Along the planetary isentrope water and ammonia behave as fully dissociated ionic, electronically insulating fluid phases, which turn metallic at temperatures exceeding 7000 kelvin for water and 5500 kelvin for ammonia. At lower temperatures, the phase diagrams of water and ammonia exhibit a superionic solid phase between the solid and the ionic liquid. These simulations improve our understanding of the properties of the middle ice layers of Neptune and Uranus.

First-principles study of crystalline and amorphous Ge(2)Sb(2)Te(5) and the effects of stoichiometric defects.

Based on ab initio molecular dynamics simulations, we investigated the structural, electronic and vibrational properties of cubic and amorphous Ge(2)Sb(2)Te(5) (GST) phase change material, focusing in particular on the effects of defects in stoichiometry on the electronic properties. It turned out Ge/Sb deficiencies (excess) in the cubic phase induce a shift of the Fermi level inside the valence (conduction) bands. In contrast, the amorphous network is flexible enough to accommodate defects in stoichiometry, keeping the Fermi level pinned at the center of the bandgap (at zero temperature). Changes in the structural and electronic properties induced by the use of hybrid functionals (HSE03, PBE0) instead of gradient corrected functionals (PBE) are addressed as well. Analysis of vibrational spectra and Debye-Waller factors of cubic and amorphous GST is also presented.

Investigating the polymorphism in PR179: a combined crystal structure prediction and metadynamics study.

The polymorphism of an industrial important pigment (PR179) was studied with a combination of standard crystal structure prediction and metadynamics. The former provided a starting set of candidate polymorphs whose structural and thermal stability were then probed by metadynamics. Moreover, metadynamics allowed for exploring the free energy surface to look for other possible polymorphs that were not included in the original set. Our calculations indicate that two structures have a high structural stability and are therefore good candidates to be found in experiments. The lower energy phase of the two indeed corresponds to the known polymorph, and we suggest that the other might be a metastable polymorph not yet experimentally discovered.

HCl hydrates as model systems for protonated water.

Ab initio molecular dynamics simulations are presented of vibrational dynamics and spectra of crystal HCl hydrates. Depending on the composition, the hydrates include distinct protonated water forms, which in their equilibrium structures approximate either the Eigen ion H3O+(H2O)3 (in the hexahydrate) or the Zundel H2O...H+...OH2 ion (in the di- and trihydrate). Thus, the hydrates offer the opportunity to study spectra and dynamics of distinct species of protonated water trapped in a semirigid solvating environment. The experimentally measured spectra are reproduced quite well by BLYP/DZVP-level calculations employing Fourier transform of the system dipole. The large overall width (800-1000 cm-1) of structured proton bands reflects a broad range of solvating environments generated by crystal vibrations. The aqueous HCl solution was also examined in search of an objective criterion for separating the contributions of "Zundel-like" and "Eigen-like" protonated forms. It is suggested that no such criterion exists since distributions of proton-related structural properties appear continuous and unimodal. Dipole derivatives with respect to OH and O...H+ stretches in water and protonated water were also investigated to advance the understanding of the corresponding IR intensities. The effects of H bonding and solvation on the intensities were analyzed with the help of the Wannier centers' representation of electron density.

The microscopic switching mechanism of a [2]catenane.

We apply numerical simulations at an all-atom level to investigate the switching mechanism of a [2]catenane, a prototype of a molecular machine. This system is able to switch reversibly between two different stable states, upon external stimuli, with a time scale ranging from microseconds up to milliseconds, well over the typical domain of molecular dynamics (MD) computer simulations. However, combining a strategy recently developed for investigating rare events with ordinary MD, we are able to unravel the microscopic mechanism of the conformational rearrangements involved in the switching process, including dynamical effects. Along the path that connects the product and reactant state, we find several intermediate states characterized by pi-pi stacking interactions and hydrogen bonds. Moreover, counterions interact strongly with the system in a correlated way, in agreement with recent static calculations performed on [2]rotaxanes.

Ab initio molecular dynamics with a classical pressure reservoir: simulation of pressure-induced amorphization in a Si35H36 cluster

We present a new constant-pressure ab initio molecular dynamics method suitable for studying, e.g., pressure-induced structural transformations in finite nonperiodic systems such as clusters. We immerse an ab initio treated cluster into a model classical liquid, described by a soft-sphere potential, which acts as a pressure reservoir. The pressure is varied by tuning the parameter of the liquid potential. We apply the method to a Si35H36 cluster, which undergoes a pressure-induced amorphization at approximately 35 GPa, and remains in a disordered state even upon pressure release.

Ab initio simulation of phase transitions and dissociation of H2S at high pressure

By ab initio constant pressure molecular dynamics, we have identified the structure of phase V and phase VI of H2S at 35 and 65 GPa, respectively. The theoretical IR spectra of both phases are consistent with experimental findings and support our proposed structural models. We find that phase V is characterized by the presence of charged SH+3 and SH- species which are created and destroyed dynamically, whereas phase VI is no longer a molecular phase but consists of sheets of S with the majority of H intercalated between the layers. The stability of the two phases with respect to dissociation into elemental crystalline hydrogen and sulfur is discussed.

Two-membered silicon rings on the dehydroxylated surface of silica

We present extensive modeling of the amorphous silica surface, aimed at connecting its structural and chemical features. beta-cristobalite surfaces are initially studied to model the hydroxylated surfaces. A model reconstruction of the (111) surface is used to define a path leading to the formation of two-membered silicon rings upon dehydroxylation. Subsequently, a realistic model of the amorphous dehydroxylated (dry) surface is produced, by full ab initio annealing of an initial model generated by classical simulation. The presence of surface two-membered silicon rings emerges naturally. A calculation of IR activity yields an associated peak doublet in agreement with experimental data.

Density functional simulations of Sb-rich GeSbTe phase change alloys.

We generated models of the amorphous phase of Sb-rich GeSbTe phase change alloys by quenching from the melt within density functional molecular dynamics. We considered the two compositions Ge(1)Sb(1)Te(1) and Ge(2)Sb(4)Te(5). Comparison with previous results on the most studied Ge(2)Sb(2)Te(5) allowed us to draw some conclusions on the dependence of the structural properties of the amorphous phase on the alloy composition. Vibrational and electronic properties were also scrutinized. Phonons at high frequencies above 200 cm(-1) are localized in tetrahedra around Ge atoms in Sb-rich compounds as well as in Ge(2)Sb(2)Te(5). All compounds are semiconducting in the amorphous phase, with a band gap in the range 0.7-1.0 eV.