Million-atom molecular dynamics simulation by order-N electronic structure theory and parallel computation

Parallelism of tight-binding molecular dynamics simulations is presented by means of the order-N electronic structure theory with the Wannier states, recently developed (J. Phys. Soc. Jpn. 69,3773 (2000)). An application is tested for silicon nanocrystals of more than millions atoms with the transferable tight-binding Hamiltonian. The efficiency of parallelism is perfect, 98.8 %, and the method is the most suitable to parallel computation. The elapse time for a system of $2\times 10^6$ atoms is 3.0 minutes by a computer system of 64 processors of SGI Origin 3800. The calculated results are in good agreement with the results of the exact diagonalization, with an error of 2 % for the lattice constant and errors less than 10 % for elastic constants.Comment: 5 pages, 3 figure

Highly efficient and genotype-independent barley gene-editing based on anther culture

Recalcitrance to tissue culture and genetic transformation is the major bottleneck for gene manipulation in crops. In barley, immature embryos of Golden Promise have been mainly used as explants for transformation. However, the genotype-dependent approach limits the genetic modification in commercial varieties. Here, we develop an anther culture-based system that effectively creates transgenic and gene-edited plants from commercial barley varieties. The protocol was tested in four Australian varieties and Golden Promise with different phenology, callus induction and green plant regeneration responses. Agrobacterium-mediated transformation was performed on microspore-derived callus when targeting the HvPDS gene, and T0 albinos with targeted mutations were successfully obtained from commercial varieties. Further editing of three targets was achieved with an average mutation rate of 53% in the five varieties. In the 51 analysed T0 individuals, Cas9 induced about 69% of single-base insertion/deletions and two-base deletions in targeting sites, with variable mutation rates among targets and varieties. Both on-target and off-target activities were detected in T1 progenies. Compared with immature embryo protocols, this genotype-independent platform can deliver a high editing efficiency and more regenerants within a similar time frame. It is promising for functional genomics and application of CRISPR technologies for precise improvement in commercial varieties

An Empirical Charge Transfer Potential with Correct Dissociation Limits

The empirical valence bond (EVB) method [J. Chem. Phys. 52, 1262 (1970)] has always embodied charge transfer processes. The mechanism of that behavior is examined here and recast for use as a new empirical potential energy surface for large-scale simulations. A two-state model is explored. The main features of the model are: (1) Explicit decomposition of the total system electron density is invoked; (2) The charge is defined through the density decomposition into constituent contributions; (3) The charge transfer behavior is controlled through the resonance energy matrix elements which cannot be ignored; and (4) A reference-state approach, similar in spirit to the EVB method, is used to define the resonance state energy contributions in terms of "knowable" quantities. With equal validity, the new potential energy can be expressed as a nonthermal ensemble average with a nonlinear but analytical charge dependence in the occupation number. Dissociation to neutral species for a gas-phase process is preserved. A variant of constrained search density functional theory is advocated as the preferred way to define an energy for a given charge.Comment: Submitted to J. Chem. Phys. 11/12/03. 14 pages, 8 figure

Adjusting the melting point of a model system via Gibbs-Duhem integration: application to a model of Aluminum

Model interaction potentials for real materials are generally optimized with respect to only those experimental properties that are easily evaluated as mechanical averages (e.g., elastic constants (at T=0 K), static lattice energies and liquid structure). For such potentials, agreement with experiment for the non-mechanical properties, such as the melting point, is not guaranteed and such values can deviate significantly from experiment. We present a method for re-parameterizing any model interaction potential of a real material to adjust its melting temperature to a value that is closer to its experimental melting temperature. This is done without significantly affecting the mechanical properties for which the potential was modeled. This method is an application of Gibbs-Duhem integration [D. Kofke, Mol. Phys.78, 1331 (1993)]. As a test we apply the method to an embedded atom model of aluminum [J. Mei and J.W. Davenport, Phys. Rev. B 46, 21 (1992)] for which the melting temperature for the thermodynamic limit is 826.4 +/- 1.3K - somewhat below the experimental value of 933K. After re-parameterization, the melting temperature of the modified potential is found to be 931.5K +/- 1.5K.Comment: 9 pages, 5 figures, 4 table

Van der Waals loops and the melting transition in two dimensions

Evidence for the existence of van der Waals loops in pressure p versus volume v plots has for some time supported the belief that melting in two dimensions is a first order phase transition. We report rather accurate equilibrium p(v) curves for systems of hard disks obtained from long Monte Carlo simulations. These curves, obtained in the constant volume ensemble, using periodic boundary conditions, exhibit well defined van der Waals loops. We illustrate their existence for finite systems that are known to undergo a continuous transition in the thermodynamic limit. To this end, we obtain magnetization m versus applied field curves from Monte Carlo simulations of the 2D Ising model, in the constant m ensemble, at the critical point. Whether van der Waals loops for disk systems behave in the thermodynamic limit as they do for the 2D Ising model at the critical point cannot be ruled out. Thus, the often made claim that melting in 2D is a first order phase transition, based on the evidence that van der Waals loops exist, is not sound.Comment: 10 pages, 6 Postscript figures (submitted to Phys.Rev.E). For related work, see http://pipe.unizar.es/~jf

Absence of a Finite-Temperature Melting Transition in the Classical Two-Dimensional One-Component Plasma

Vortices in thin-film superconductors are often modelled as a system of particles interacting via a repulsive logarithmic potential. Arguments are presented to show that the hypothetical (Abrikosov) crystalline state for such particles is unstable at any finite temperature against proliferation of screened disclinations. The correlation length of crystalline order is predicted to grow as $\sqrt{1/T}$ as the temperature $T$ is reduced to zero, in excellent agreement with our simulations of this two-dimensional system.Comment: 3 figure

Anharmonic Decay of Vibrational States in Amorphous Silicon

Anharmonic decay rates are calculated for a realistic atomic model of amorphous silicon. The results show that the vibrational states decay on picosecond timescales and follow the two-mode density of states, similar to crystalline silicon, but somewhat faster. Surprisingly little change occurs for localized states. These results disagree with a recent experiment.Comment: 10 pages, 4 Postscript figure

Simulations of Two-Dimensional Melting on the Surface of a Sphere

We have simulated a system of classical particles confined on the surface of a sphere interacting with a repulsive $r^{-12}$ potential. The same system simulated on a plane with periodic boundary conditions has van der Waals loops in pressure-density plots which are usually interpreted as evidence for a first order melting transition, but on the sphere such loops are absent. We also investigated the structure factor and from the width of the first peak as a function of density we can show that the growth of the correlation length is consistent with KTHNY theory. This suggests that simulations of two dimensional melting phenomena are best performed on the surface of a sphere.Comment: 4 eps figure

Measuring kinetic coefficients by molecular dynamics simulation of zone melting

Molecular dynamics simulations are performed to measure the kinetic coefficient at the solid-liquid interface in pure gold. Results are obtained for the (111), (100) and (110) orientations. Both Au(100) and Au(110) are in reasonable agreement with the law proposed for collision-limited growth. For Au(111), stacking fault domains form, as first reported by Burke, Broughton and Gilmer [J. Chem. Phys. {\bf 89}, 1030 (1988)]. The consequence on the kinetics of this interface is dramatic: the measured kinetic coefficient is three times smaller than that predicted by collision-limited growth. Finally, crystallization and melting are found to be always asymmetrical but here again the effect is much more pronounced for the (111) orientation.Comment: 8 pages, 9 figures (for fig. 8 : [email protected]). Accepted for publication in Phys. Rev.