Standard Molecular Dynamics Methods Research Articles

Grotthuss Molecular Dynamics Simulations for Modeling Proton Hopping in Electrosprayed Water Droplets.

Excess protons in water exhibit unique transport properties because they can rapidly hop along H-bonded water wires. Considerable progress has been made in unraveling this Grotthuss diffusion mechanism using quantum mechanical-based computational techniques. Unfortunately, high computational cost tends to restrict those techniques to small systems and short times. Molecular dynamics (MD) simulations can be applied to much larger systems and longer time windows. However, standard MD methods do not permit the dissociation/formation of covalent bonds, such that Grotthuss diffusion cannot be captured. Here, we bridge this gap by combining atomistic MD simulations (using Gromacs and TIP4P/2005 water) with proton hopping. Excess protons are modeled as hydronium ions that undergo H3O+ + H2O → H2O + H3O+ transitions. In accordance with ab initio MD data, these Grotthuss hopping events are executed in "bursts" with quasi-instantaneous hopping across one or more waters. The bursts are separated by regular MD periods during which H3O+ ions undergo Brownian diffusion. The resulting proton diffusion coefficient agrees with the literature value. We apply this Grotthuss MD technique to highly charged water droplets that are in a size regime encountered during electrospray ionization (5 nm radius, ∼17,000 H2O). The droplets undergo rapid solvent evaporation and occasional H3O+ ejection, keeping them at ca. 81% of the Rayleigh limit. The simulated behavior is consistent with phase Doppler anemometry data. The Grotthuss MD technique developed here should be useful for modeling the behavior of various proton-containing systems that are too large for high-level computational approaches. In particular, we envision future applications related to electrospray processes, where earlier simulations used metal cations while in reality excess protons dominate.

Reliability assessment for large-scale molecular dynamics approximations.

Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems, however, create the need for approximations to the standard MD methods and for uncertainty quantification and reliability assessment of those approximations. In this paper, we exploit the intrinsic two-scale nature of MD to construct a class of large-scale dynamics approximations. The reliability of these methods is evaluated here by measuring the differences between full, classical MD simulations and those based on these large-scale approximations. Molecular dynamics evolutions are non-linear and chaotic, so the complete details of molecular evolutions cannot be accurately predicted even using full, classical MD simulations. This paper provides numerical results that demonstrate the existence of computationally efficient large-scale MD approximations which accurately model certain large-scale properties of the molecules: the energy, the linear and angular momenta, and other macroscopic features of molecular motions.

Discontinuous molecular dynamics for rigid bodies: Applications

Event-driven molecular dynamics simulations are carried out on two rigid-body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous potentials are compared with simulations in which the molecules interact through standard continuous Lennard-Jones potentials. It is shown that under similar conditions of temperature and pressure, the rigid discontinuous molecular dynamics method reproduces the essential dynamical and structural features found in continuous-potential simulations at both gas and liquid densities. Moreover, the discontinuous molecular dynamics approach is demonstrated to be between 3 and 100 times more efficient than the standard molecular dynamics method depending on the specific conditions of the simulation. The rigid discontinuous molecular dynamics method is also applied to a discontinuous-potential model of a liquid composed of rigid benzene molecules, and equilibrium and dynamical properties are shown to be in qualitative agreement with more detailed continuous-potential models of benzene. The few qualitative differences in the angular dynamics of the two models are related to the relatively crude treatment of variations in the discontinuous repulsive interactions as one benzene molecule rotates by another.

Semimicroscopic Modeling of Permeation Energetics in Ion Channels

The semimicroscopic (SMC) approach to modeling the energetics of ion permeation through biological channels provides an alternative perspective to standard molecular dynamics methods. It exploits the timescale separation between electronic and structural contributions to dielectric stabilization and accounts for electronic polarization by embedding the channel in a milieu that, on average, describes this polarization. Ions, water, and selected peptide moieties are mobile and comprise the reorganizational contribution to dielectric stabilization. The conceptual advantages and limitations of the technique are described. Methodological details are outlined, stressing three convenient electrical geometries. Practical aspects of the SMC procedure are explained, highlighting the areas ripe for further development. Finally, some specific applications are considered.

超純水のみによる電気化学的加工法の研究―陰極Ａｌ（００１）表面における除去加工現象の第一原理分子動力学シミュレーション―

In order to reveal the mechanism of the electrochemical processes of cathode surfaces in ultrapure water, first-principles molecular-dynamics simulations of chemical reaction on the Al(001) surfaces interacting with H atoms, H2O molecules and OH molecule were carried out on the basis of the Kohn-Sham local-density-functional formalism. A plane-wave basis set was used, and the cut-off energy is 594eV(64Ry). A norm-conserving pseudopotential was also used. We adopt the standard molecular-dynamics method for the optimization of the ionic system and the preconditioned conjugate-gradient (CG) method for the quenching procedure of the electronic degrees of freedom. We determined the optimized atomic configurations and electronic distributions for H atom and H2O or OH molecule chemisorbed Al(001) surfaces. It was confirmed that an H atom reacts with H2O molecules on the Al(001) surface to produce an OH molecule. Chemisorption of an OH molecules and H atoms to the Al(001) surface atom breaks the back-bonds and side-bonds, and the Al(001) surface atom is etched as an AIH2OH molecule. From these simulated results, we concluded that the electrochemical etching of Al(001) cathode surface in ultrapure water is induced by H atoms and OH molecules.

Finite-size effects in molecular dynamics simulations: intermediate scattering function and velocity of sound. III. Theory and application to a model krypton fluid.

We describe a method for obtaining the intermediate scattering function I(Q,t) from a computer simulation: it is an extension of our earlier calculation [Salacuse, Denton, and Egelstaff, Phys. Rev. E 53, 2382 (1996)] for the t-->0 limit. We use this approach to obtain I(Q,t) for low Q and t from molecular dynamics (MD) simulations of a model krypton fluid whose atoms interact via a truncated Aziz pair potential, and the results are compared over their range of validity to I(Q,t) determined by the standard MD method and also by a time expansion approach. In its range of validity our approach is much more efficient than the standard MD method; however, it covers a restricted range of t due to the movement of density fluctuations (sound waves) through the simulated fluid which produces an anomaly in the time behavior of I(Q,t). By analyzing I(Q=0,t) the velocity of sound in the simulation is determined, and the results compare favorably with published experimental results for the sound velocity of liquid krypton.

超純水のみによる電気化学的加工法の研究 陽極Ｓｉ（００１）表面の反応素過程

In order to reveal the mechanism of the electrochemical machining process in ultrapure water, first-principles molecular-dynamics simulations of Si(001) surfaces interacting with OH molecules were carried out on the basis of the Kohn-Sham local-density-functional formalism. A plane-wave basis set was used, and the cut-off energy is 327eV(24Ry). A norm-conserving pseudopotential was also used. We adopt the standard molecular-dynamics method for the optimization of the ionic system and the preconditioned conjugate-gradient (CG) method for the quenching procedure of the electronic degrees of freedom. We determined the optimized ionic configurations and electronic distributions for OH chemisorbed Si(001) surfaces and clarify the elemental process of the chemical reactions. It was confirmed that the Si surface atom cannot bond with four OH molecules, so it cannot be etched as an Si(OH)4 molecule. In this simulation, it was also confirmed that two OH molecules react with each other producing an H2O molecule and an oxygen atom. The oxygen atom bonds with two Si surface atoms at the surface bridge site or back-bond. We concluded that the Si surface atom cannot be etched with Si(OH)4 molecule but oxidized by oxygen atom produced by two OH molecules. These results agree with the experimental results of anodic oxidation of Si surface.

超純水のみによる電気化学的加工法の研究 Ｓｉ（００１）水素終端化表面のＯＨ｀−´イオンによる加工現象の第一原理分子動力学シミュレーション

In order to reveal the mechanism of the electrochemical etching process in ultrapure water, first-principles molecular -dynamics simulations for etching process of the hydrogen-terminated Si(001) surfaces by hydroxyl ion in ultrapure water were carried out on the basis of the Kohn-Sham local-density-functional formalism. A plane-wave basis set and a norm-conserving pseudopotential were used. The standard molecular-dynamics method for the optimization of the ionic system and the steepest-descents (SD) method for the quenching procedure of the electronic degrees of freedom were adopted. It was confirmed that the chemisorbed four hydroxyl ions on the hydrogen-terminated Si(001) step edge decrease the covalent bond strength of Si-Si back-bond and initiate the etching process.

超純水のみによる電気化学的加工法の研究 水素終端化されていないＳｉ（００１）表面原子とＯＨとの反応素過程

In order to reveal the mechanism of the electrochemical etching process in ultrapure water, first-principles molecular-dynamics simulations of Si(001) surfaces interacting with OH molecules were carried out on the basis of the Kohn-Sham local-density-functional formalism. A plane-wave basis set was used, and the cut-off energy is 327eV(24Ry). A norm-conserving pseudopotential was also used. We adopt the standard molecular-dynamics method for the optimization of the ionic system and the preconditioned conjugate-gradient (CG) method for the quenching procedure of the electronic degrees of freedom. We determined the optimized ionic configurations and electronic distributions for OH chemisorbed Si(001) surfaces and clarify the etching mechanism. It was confirmed that three OH molecules can chemisorb on the Si surface atom but it cannot be etched and four OH molecules cannot chemisorb on. We concluded that the Si surface atom cannot be etched as Si(OH)4 molecule and hydrogen-termination is necessary to etch the Si surface atom.

超純水のみによる電気化学的加工法の研究 陰極Ｓｉ（００１）表面における除去加工現象の第一原理分子動力学シミュレーション

In order to reveal the mechanism of the electrochemical processes of cathode surface in ultrapure water, first-principles molecular-dynamics simulations of hydrogen-terminated Si(001) surfaces interacting with H atoms and H20 molecules were carried out on the basis of the Kohn-Sham local-density-functional formalism. A plane-wave basis set was used, and the cut-off energy is 327eV(24Ry). A norm-conserving pseudopotential was also used. We adopt the standard molecular-dynamics method for the optimization of the ionic system and the preconditioned conjugate-gradient (CG) method for the quenching procedure of the electronic degrees of freedom. We determined the optimized atomic configurations and electronic distributions for H and H2O chemisorbed hydrogen-terminated Si(001) surfaces. It was confirmed that an H atom reacts with H20 molecules on the hydrogen-terminated Si(001) surface to produce an OH molecule, and chemisorption of two OH molecules to the hydrogen-terminated Si(001) surface atom breaks the back-bonds and the Si surface atom is etched with forming an SiH2(OH)2 molecule. From these simulation results, we deduced that the electrochemical machining of Si(001) cathode surface in ultrapure water is possible.

超純水のみによる電気化学的加工法の研究 Ｓｉ（００１）水素終端化表面原子のＯＨによる加工現象の反応素過程

In order to reveal the mechanism of the electrochemical etching process in ultrapure water, first-principles molecular-dynamics simulations for the etching process of hydrogen-terminated Si(001) surfaces interacting with OH molecules were carried out on the basis of the Kohn-Sham local-density-functional formalism. A plane-wave basis set was used, and the cut-off energy is 327eV(24Ry). A norm-conserving pseudopotential was also used. The standard molecular-dynamics method for the optimization of the ionic system and the preconditioned conjugate-gradient (CG) method for the quenching procedure of the electronic degrees of freedom were adopted. The optimized ionic configurations, local density of states, and atomic and bond populations for OH chemisorbed Si(001) surfaces were determined and the electronic structures relevant to the etching mechanism were clarified. It was confirmed that the interaction between two OH molecules and the hydrogen-terminated surface silicon atom on the step edge breaks the Si-Si back-bond and initiates the etching process forming a SiH2(OH)2 molecule.

Formation of quasiperiodic patterns within a simple two-dimensional model system

We present a simple two-dimensional model system which tends to organize itself in the form of a quasiperiodic state. The system is composed of one sort of particles only, with mutual interactions that strongly deviate from the standard Lennard-Jones-type of potentials at intermediate distances. The dynamics of this system are simulated by using standard molecular dynamics methods for classical systems.

Two-dimensional orientational motion as a multichannel reaction by computer simulation

The orientational diffusion of a nitrogen molecule N2 in a three-dimensional crystal of argon atoms is studied by using the reaction coordinate formalism and the Bennett–Chandler approach. To study the two-dimensional orientational diffusion the reaction coordinate formalism has to be generalized to multichannel reactions. The rate coefficient for the motion between the six stable orientational states is determined from correlation function expressions, which include corrections to transition-state theory due to recrossings of free energy barriers. At high temperatures the simulation results are compared with results obtained by standard molecular dynamics methods. At low temperatures the transmission coefficient is computed and the dependence of the plateau value upon the density of the surrounding argon matrix and upon the isotopes, chosen to form the N2 molecule, is investigated.

Low-temperature growth and ion-assisted deposition.

Using standard molecular-dynamics methods, we have simulated silicon molecular-beam epitaxy on a (100) substrate, subject to a second beam of low-energy argon atoms. We find that the presence of the ion beam has an important effect on the structure of the deposits formed: good crystalline material forms at significantly lower temperatures, where otherwise a thermal beam yields an amorphous deposit. This is because the ion beam provides local excitations, which allow the deposited atoms to find their proper crystal lattice sites.

Epitaxy on surfaces vicinal to Si(001). II. Growth properties of Si(001) steps.

There is considerable interest in understanding the factors important for epitaxial growth. In particular, one would like to know how aspects of the growth kinetics affect the structures produced. To study epitaxial growth on the Si(001) surface, we have mapped out the potential-energy surfaces seen by a single silicon adatom, as it moves over the Si(001) steps. Standard molecular-dynamics methods were used. The energy surfaces identify the binding sites and give the activation energy for diffusion hops, so that likely pathways for adatom motion can be identified. We find that generally the binding at the step edges is about one-tenth of an eV more than that on the flat surface, so that at low adatom coverage, these steps are relatively weak sinks. Growth, however, does take place more readily at the step edges, because the steps act as heterogeneous nucleation sites for dimers. We have developed simple rate equations to estimate nucleation rates, accommodation coefficients, and step velocities, using the microscopic information given by the energy surfaces as input. The variation of these quantities with temperature and external driving force is explored. In agreement with experimental results, we find that growth takes place most readily at the ends of dimer rows. Furthermore, the predicted anisotropy in the growth properties of the ${\mathit{S}}_{\mathit{A}}$ and ${\mathit{S}}_{\mathit{B}}$ steps is large enough to account for the formation of dimer strings on the flat terraces. We also report on direct simulations of the impingement of atoms from an atomic beam onto the vicinal Si(001) surfaces. These simulations show the formation of kink sites at step edges and the formation of dimer strings on the terraces.

Combining Molecular Dynamics and Monte Carlo Simulations to Model Chemical Vapor Deposition: Application to Diamond

AbstractGas-surface reactions of the type that contribute to growth during the chemical vapor deposition (CVD) of diamond films are generally completed in picoseconds, well within timescales accessible by molecular dynamics (MD) simulations. For low-pressure deposition, however, the time between collisions for a surface site can be microseconds, which makes direct modeling of CVD crystal growth impossible using standard MD methods. To effectively bridge this discrepancy in timescales, the gas-surface reactions can be modeled using MD trajectories, and then this data can be used to define probabilities in a Monte Carlo algorithm where each step represents a gas-surface collision. We illustrate this approach using the reaction of atomic hydrogen with a diamond (111) surface as an example, where we use abstraction and sticking probabilities generated using classical trajectories in a simple Monte Carlo algorithm to determine the number of open sites as a function of temperature. We also include models for the thermal desorption of hydrogen that predict that growth temperatures are not restricted by the thermal loss of chemisorbed hydrogen.

Maximally discretized molecular dynamics.

It is shown that the coarsest discretization of positions and velocities in molecular dynamics leads to qualitatively correct transport coefficients and quantitatively predictable long-time tails in the velocity autocorrelation function, but requires orders of magnitude less computer time than standard molecular-dynamics methods.