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While the microscopic structure of defected solid crystalline materials has significant impact on their physical properties, efficient and accurate determination of a given polycrystalline microstructure remains a challenge. In this paper we present a highly generalizable and reliable variational method to achieve this goal for two-dimensional crystalline and quasicrystalline materials. The method is benchmarked and optimized successfully using a variety of large-scale systems of defected solids, including periodic structures and quasicrystalline symmetries to quantify their microstructural characteristics, e.g., grain size and lattice misorientation distributions. We find that many microstructural properties show universal features independent of the underlying symmetries.

We conducted density functional theory (DFT) and molecular dynamics simulations to explore the mechanical/failure, thermal conductivity and stability, electronic and optical properties of three N-graphdiyne nanomembranes. Our DFT results of uniaxial tensile simulations reveal that these monolayers can yield remarkably high stretchability or tensile strength depending on the atomic structure and loading direction. Studied N-graphdiyne nanomembranes were found to exhibit semiconducting electronic character, with band-gap values ranging from 0.98 eV to 3.33 eV, based on the HSE06 estimations. The first absorption peak suggests that these 2D structures can absorb visible, IR and NIR light. Ab initio molecular dynamics results reveal that N-graphdiyne 2D structures can withstand at high temperatures, like 2000 K. Thermal conductivities of suspended single-layer N-graphdiyne sheets were predicted to be almost temperature independent and about three orders of magnitude smaller than that of the graphene. The comprehensive insight provided by this work highlights the outstanding physics of N-graphdiyne 2D nanomaterials, and suggest them as highly promising candidates for the design of novel stretchable nanodevices.

We compute the anisotropic in-plane thermal conductivity of suspended single-layer black phosphorous (SLBP) using three molecular dynamics (MD) based methods, including the equilibrium MD method, the nonequilibrium MD (NEMD) method, and the homogeneous nonequilibrium MD (HNEMD) method. Two existing parameterizations of the Stillinger-Weber (SW) potential for SLBP are used. Consistent results are obtained for all the three methods and conflicting results from previous MD simulations are critically assessed. Among the three methods, the HNEMD method is the most and the NEMD method the least efficient. The thermal conductivity values from our MD simulations are about an order of magnitude larger than the most recent predictions obtained using the Boltzmann transport equation approach considering long-range interactions in density functional theory calculations, suggesting that the short-range SW potential might be inadequate for describing the phonon anharmonicity in SLBP., Comment: 9 pages, 9 figures

Molecular dynamics simulations play an important role in studying heat transport in complex materials. The lattice thermal conductivity can be computed either using the Green-Kubo formula in equilibrium MD (EMD) simulations or using Fourier's law in nonequilibrium MD (NEMD) simulations. These two methods have not been systematically compared for materials with different dimensions and inconsistencies between them have been occasionally reported in the literature. Here we give an in-depth comparison of them in terms of heat transport in three allotropes of Si: three dimensional bulk silicon, two-dimensional silicene, and quasi-one-dimensional silicon nanowire. By multiplying the correlation time in the Green-Kubo formula with an appropriate effective group velocity, we can express the running thermal conductivity in the EMD method as a function of an effective length and directly compare it with the length-dependent thermal conductivity in the NEMD method. We find that the two methods quantitatively agree with each other for all the systems studied, firmly establishing their equivalence in computing thermal conductivity., Comment: 8 pages, 7 figures

The standard equilibrium Green-Kubo and nonequilibrium molecular dynamics (MD) methods for computing thermal transport coefficients in solids typically require relatively long simulation times and large system sizes. To this end, we revisit here the homogeneous nonequilibrium MD method by Evans [Phys. Lett. A \textbf{91}, 457 (1982)] and generalize it to many-body potentials that are required for more realistic materials modeling. We also propose a method for obtaining spectral conductivity and phonon mean free path from the simulation data. This spectral decomposition method does not require lattice dynamics calculations and can find important applications in spatially complex structures. We benchmark the method by calculating thermal conductivities of three-dimensional silicon, two-dimensional graphene, and a quasi-one-dimensional carbon nanotube and show that the method is about one to two orders of magnitude more efficient than the Green-Kubo method. We apply the spectral decomposition method to examine the long-standing dispute over thermal conductivity convergence vs divergence in carbon nanotubes., Comment: 10 pages, 7 figures

Van der Waals heterostructures have exhibited interesting physical properties. In this paper, heat transfer in hybrid coplanar bilayer/monolayer (BL-ML) graphene, as a model layered van der Waals heterostructure, was studied using non-equilibrium molecular dynamics (MD) simulations. Temperature profile and inter- and intra-layer heat fluxes of the BL-ML graphene indicated that, there is no fully developed thermal equilibrium between layers and the drop in average temperature profile at the step-like BL-ML interface is not attributable to the effect of Kapitza resistance. By increasing the length of the system up to 1 $\mu$m in the studied MD simulations, the thermally non-equilibrium region was reduced to a small area near the step-like interface. All MD results were compared to a continuum model and a good match was observed between the two approaches. Our results provide a useful understanding of heat transfer in nano- and micro-scale layered 2D materials and van der Waals heterostructures.

We study heat transport across individual grain boundaries in suspended monolayer graphene using extensive classical molecular dynamics (MD) simulations. We construct bicrystalline graphene samples containing grain boundaries with symmetric tilt angles using the two-dimensional phase field crystal method and then relax the samples with MD. The corresponding Kapitza resistances are then computed using nonequilibrium MD simulations. We find that the Kapitza resistance depends strongly on the tilt angle and shows a clear correlation with the average density of defects in a given grain boundary, but is not strongly correlated with the grain boundary line tension. We also show that quantum effects are significant in quantitative determination of the Kapitza resistance by applying the mode-by-mode quantum correction to the classical MD data. The corrected data are in good agreement with quantum mechanical Landauer-B\"utticker calculations., Comment: 8 pages, 7 figures

Grain boundaries in graphene are inherent in wafer-scale samples prepared by chemical vapor deposition. They can strongly influence the mechanical properties and electronic and heat transport in graphene. In this work, we employ extensive molecular dynamics simulations to study thermal transport in large suspended polycrystalline graphene samples. Samples of different controlled grain sizes are prepared by a recently developed efficient multiscale approach based on the phase field crystal model. In contrast to previous works, our results show that the scaling of the thermal conductivity with the grain size implies bimodal behaviour with two effective Kapitza lengths. The scaling is dominated by the out-of-plane (flexural) phonons with a Kapitza length that is an order of magnitude larger than that of the in-plane phonons. We also show that in order to get quantitative agreement with the most recent experiments, quantum corrections need to be applied to both the Kapitza conductance of grain boundaries and the thermal conductivity of pristine graphene and the corresponding Kapitza lengths must be renormalized accordingly., Comment: Accepted to Nano Lett.; Numerical samples and computer codes available

We present GPUQT, a quantum transport code fully implemented on graphics processing units. Using this code, one can obtain intrinsic electronic transport properties of large systems described by a real-space tight-binding Hamiltonian together with one or more types of disorder. The DC Kubo conductivity is represented as a time integral of the velocity auto-correlation or a time derivative of the mean square displacement. Linear scaling (with respect to the total number of orbitals in the system) computation time and memory usage are achieved by using various numerical techniques, including sparse matrix-vector multiplication, random phase approximation of trace, Chebyshev expansion of quantum evolution operator, and kernel polynomial method for quantum resolution operator. We describe the inputs and outputs of GPUQT and give two examples to demonstrate its usage, paying attention to the interpretations of the results., Comment: 22 pages, 2 figures, computer code available

For centuries, cutting and folding the papers with special patterns have been used to build beautiful, flexible and complex three-dimensional structures. Inspired by the old idea of kirigami (paper cutting), and the outstanding properties of graphene, recently graphene kirigami structures were fabricated to enhance the stretchability of graphene. However, the possibility of further tuning the electronic and thermal transport along the 2D kirigami structures have remained original to investigate. We therefore performed extensive atomistic simulations to explore the electronic, heat and load transfer along various graphene kirigami structures. The mechanical response and thermal transport were explored using classical molecular dynamics simulations. We then used a real-space Kubo-Greenwood formalism to investigate the charge transport characteristics in graphene kirigami. Our results reveal that graphene kirigami structures present highly anisotropic thermal and electrical transport. Interestingly, we show the possibility of tuning the thermal conductivity of graphene by four orders of magnitude. Moreover, we discuss the engineering of kirigami patterns to further enhance their stretchability by more than 10 times as compared with pristine graphene. Our study not only provides a general understanding concerning the engineering of electronic, thermal and mechanical response of graphene but more importantly can be useful to guide future studies with respect to the synthesis of other 2D material kirigami structures, to reach highly flexible and stretchable nanostructures with finely tunable electronic and thermal properties., Comment: 29 pages, 9 figures, 1 supplementary figure

Two-dimensional materials have unusual phonon structures 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 the 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 non-equilibrium 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., Comment: 12 pages, 9 figures

The dynamics of a two-dimensional superconductor under a constant electric field $E$ is studied by using the gauge/gravity correspondence. The pair breaking current induced by $E$ first increases to a peak value and then decreases to a constant value at late time, where the superconducting gap goes to zero, corresponding to a normal conducting phase. The peak value of the current is found to increase linearly with respect to the electric field. Moreover, the nonlinear conductivity, defined as an average of the conductivity in the superconducting phase, scales as $\sim E^{-2/3}$ for large $E$ when the system is close to the critical temperature, which agrees with predictions from solving the time dependent Ginzburg-Landau equation., Comment: v2, 11 pages,4 figures, referencs added

We study the spin relaxation of charge carriers in graphene in the presence of spin-polarized charged impurities by calculating the time evolution of initially polarized state. The spin relaxation time shows completely different energy behaviour for short-ranged and long-ranged spin scatterers and can be used to identify the dominant source of spin scattering. Our results agree well with recent experimental findings and indicate that their spin relaxation is likely caused by long-ranged scatterers., Comment: 5 pages, 4 figures

Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones. In the conventional force evaluation algorithm for many-body potentials, the force, virial stress, and heat current for a given atom are accumulated within different loops, which could result in write conflict between different threads in a CUDA kernel. In this work, we provide a new force evaluation algorithm, which is based on an explicit pairwise force expression for many-body potentials derived recently [Phys. Rev. B 92 (2015) 094301]. In our algorithm, the force, virial stress, and heat current for a given atom can be accumulated within a single thread and is free of write conflicts. We discuss the formulations and algorithms and evaluate their performance. A new open-source code, GPUMD, is developed based on the proposed formulations. For the Tersoff many-body potential, the double precision performance of GPUMD using a Tesla K40 card is equivalent to that of the LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) molecular dynamics code running with about 100 CPU cores (Intel Xeon CPU X5670 @ 2.93 GHz)., Comment: 8 pages, 4 figures

Experimentally produced graphene sheets exhibit a wide range of mobility values. Both extrinsic charged impurities and intrinsic ripples (corrugations) have been suggested to induce long-range disorder in graphene and could be a candidate for the dominant source of disorder. Here, using large-scale molecular dynamics and quantum transport simulations, we find that the hopping disorder and the gauge and scalar potentials induced by the ripples are short-ranged, in strong contrast with predictions by continuous models, and the transport fingerprints of the ripple disorder are very different from those of charged impurities. We conclude that charged impurities are the dominant source of disorder in most graphene samples, whereas scattering by ripples is mainly relevant in the high carrier density limit of ultraclean graphene samples (with a charged impurity concentration < 10 ppm) at room and higher temperatures.

We extend the phase field crystal (PFC) framework to quantitative modeling of polycrystalline graphene. PFC modeling is a powerful multiscale method for finding the ground state configurations of large realistic samples that can be further used to study their mechanical, thermal or electronic properties. By fitting to quantum-mechanical density functional theory (DFT) calculations, we show that the PFC approach is able to predict realistic formation energies and defect structures of grain boundaries. We provide an in-depth comparison of the formation energies between PFC, DFT and molecular dynamics (MD) calculations. The DFT and MD calculations are initialized using atomic configurations extracted from PFC ground states. Finally, we use the PFC approach to explicitly construct large realistic polycrystalline samples and characterize their properties using MD relaxation to demonstrate their quality., Comment: 18 pages, 15 figures

We theoretically study the atomic structure and energetics of silicon and silicon-nitrogen impurities in graphene. Using density-functional theory, we get insight into the atomic structures of the impurities, evaluate their formation energies and assess their abundance in realistic samples. We find that nitrogen, as well as oxygen and hydrogen, are trapped at silicon impurities, considerably altering the electronic properties of the system. Furthermore, we show that nitrogen doping can induce local magnetic moments resulting in spin-dependent transport properties, even though neither silicon nor nitrogen impurities are magnetic by themselves. To simulate large systems with many randomly distributed impurities, we derive tight-binding models that describe the effects of the impurities on graphene {\pi} electron structure. Then by using the linear-scaling real-space Kubo-Greenwood method, we evaluate the transport properties of large-scale systems with random distribution of impurities, and find the fingerprint-like scattering cross sections for each impurity type. The transport properties vary widely, and our results indicate that some of the impurities can even induce strong localization in realistic graphene samples., Comment: 17 pages, 9 figures

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 descried 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 time used in the simulation are examined., Comment: 14 pages, 6 figures

A graphene antidot lattice, created by a regular perforation of a graphene sheet, can exhibit a considerable band gap required by many electronics devices. However, deviations from perfect periodicity are always present in real experimental setups and can destroy the band gap. Our numerical simulations, using an efficient linear-scaling quantum transport simulation method implemented on graphics processing units, show that disorder that destroys the band gap can give rise to a transport gap caused by Anderson localization. The size of the defect induced transport gap is found to be proportional to the radius of the antidots and inversely proportional to the square of the lattice periodicity. Furthermore, randomness in the positions of the antidots is found to be more detrimental than randomness in the antidot radius. The charge carrier mobilities are found to be very small compared to values found in pristine graphene, in accordance with recent experiments., Comment: 8 pages, 8 figures, An unused figure from the previous version is removed

A quantum phase transition may occur in a system at zero temperature when a controlling parameter is tuned towards a critical point. An important question is whether such a critical point exists in a particular system and how stable it is. Here, we identify the critical point of a quantum phase transition as a singular point in the affine algebraic variety of the characteristic equation for the Hamiltonian describing the system, with an unstable critical point being associated with an isolated singular point which has a finite Tjurina number. The theory is illustrated by studying a model system of zero-dimensional (finite) Heisenberg spin chain with an impurity, which exhibits a nontrivial first-order quantum phase transition. Both analytical and numerical calculations show that the quantum phase transition always exists when the impurity has a $Z_2$ symmetry but only remains in systems with an even number of spin sites when the $Z_2$ symmetry is broken., Comment: 5 pages, 5 figures

We study Anderson localization in graphene with short-range disorder using the real-space Kubo-Greenwood method implemented on graphics processing units. Two models of short-range disorder, namely, the Anderson on-site disorder model and the vacancy defect model, are considered. For graphene with Anderson disorder, localization lengths of quasi-one-dimensional systems with various disorder strengths, edge symmetries, and boundary conditions are calculated using the real-space Kubo-Greenwood formalism, showing excellent agreement with independent transfer matrix calculations and superior computational efficiency. Using these data, we demonstrate the applicability of the one-parameter scaling theory of localization length and propose an analytical expression for the scaling function, which provides a reliable method of computing the two-dimensional localization length. This method is found to be consistent with another widely used method which relates the two-dimensional localization length to the elastic mean free path and the semiclassical conductivity. Abnormal behavior at the charge neutrality point is identified and interpreted to be caused by finite-size effects when the system width is comparable to or smaller than the elastic mean free path. We also demonstrate the finite-size effect when calculating the two-dimensional conductivity in the localized regime and show that a renormalization group beta function consistent with the one-parameter scaling theory can be extracted numerically. For graphene with vacancy disorder, we show that the proposed scaling function of localization length also applies. Lastly, we discuss some ambiguities in calculating the semiclassical conductivity around the charge neutrality point due to the presence of resonant states., Comment: 15 pages, 14 figures

We establish, through numerical calculations and comparisons with a recursive Green's function based implementation of the Landauer-B\"uttiker formalism, an efficient method for studying Anderson localization in quasi-one-dimensional and two-dimensional systems using the Kubo-Greenwood formalism. Although the recursive Green's function method can be used to obtain the localization length of a mesoscopic conductor, it is numerically very expensive for systems that contain a large number of atoms transverse to the transport direction. On the other hand, linear-scaling has been achieved with the Kubo-Greenwood method, enabling the study of effectively two-dimensional systems. While the propagating length of the charge carriers will eventually saturate to a finite value in the localized regime, the conductances given by the Kubo-Greenwood method and the recursive Green's function method agree before the saturation. The converged value of the propagating length is found to be directly proportional to the localization length obtained from the exponential decay of the conductance., Comment: 7 pages, 6 figures

We implement, optimize, and validate the linear-scaling Kubo-Greenwood quantum transport simulation on graphics processing units by examining resonant scattering in graphene. We consider two practical representations of the Kubo-Greenwood formula: a Green-Kubo formula based on the velocity auto-correlation and an Einstein formula based on the mean square displacement. The code is fully implemented on graphics processing units with a speedup factor of up to 16 (using double-precision) relative to our CPU implementation. We compare the kernel polynomial method and the Fourier transform method for the approximation of the Dirac delta function and conclude that the former is more efficient. In the ballistic regime, the Einstein formula can produce the correct quantized conductance of one-dimensional graphene nanoribbons except for an overshoot near the band edges. In the diffusive regime, the Green-Kubo and the Einstein formalisms are demonstrated to be equivalent. A comparison of the length-dependence of the conductance in the localization regime obtained by the Einstein formula with that obtained by the non-equilibrium Green's function method reveals the challenges in defining the length in the Kubo-Greenwood formalism at the strongly localized regime., Comment: 15 pages, 8 figures

In this paper, we investigate, by molecular dynamics simulations, the mechanical properties of a new carbon nanostructure, termed graphene nanochain, constructed by sewing up pristine or twisted graphene nanoribbons (GNRs) and interlocking the obtained nanorings. The obtained tensile strength of defect-free nanochain is a little lower than that of pristine GNRs and the fracture point is earlier than that of the GNRs. The effects of length, width and twist angle of the constituent GNRs on the mechanical performance are analyzed. Furthermore, defect effect is investigated and in some high defect coverage cases, an interesting mechanical strengthening-like behavior is observed. This structure supports the concept of long-cable manufacturing and advanced material design can be achieved by integration of nanochain with other nanocomposites. The technology used to construct the nanochain is experimentally feasible, inspired by the recent demonstrations of atomically precise fabrications of GNRs with complex structures [Phys. Rev. Lett,2009,\textbf{102},205501; Nano Lett., 2010, \textbf{10},4328; Nature,2010,\textbf{466},470], Comment: 26pages

In this paper, we develop a highly efficient molecular dynamics code fully implemented on graphics processing units for thermal conductivity calculations using the Green-Kubo formula. We compare two different schemes for force evaluation, a previously used thread-scheme where a single thread is used for one particle and each thread calculates the total force for the corresponding particle, and a new block-scheme where a whole block is used for one particle and each thread in the block calculates one or several pair forces between the particle associated with the given block and its neighbor particle(s) associated with the given thread. For both schemes, two different classical potentials, namely, the Lennard-Jones potential and the rigid-ion potential are implemented. While the thread-scheme performs a little better for relatively large systems, the block-scheme performs much better for relatively small systems. The relative performance of the block-scheme over the thread-scheme also increases with the increasing of the cutoff radius. We validate the implementation by calculating lattice thermal conductivities of solid argon and lead telluride.

Numerical optimization methods such as hillclimbing and simulated annealing have been applied to search for highly entangled multi-qubit states. Here the genetic algorithm is applied to this optimization problem -- to search not only for highly entangled states, but also for the corresponding quantum circuits creating these states. Simple quantum circuits for maximally (highly) entangled states are discovered for 3, 4, 5, and 6-qubit systems; and extension of the method to systems with more qubits is discussed. Among other results we have found explicit quantum circuits for maximally entangled 5 and 6-qubit circuits, with only 8 and 13 quantum gates respectively. One significant advantage of our method over previous ones is that it allows very simple construction of quantum circuits based on the quantum states found., Comment: 15 pages, 4 figures

We study various aspects of the topological quantum computation scheme based on the non-Abelian anyons corresponding to fractional quantum hall effect states at filling fraction 5/2 using the Temperley-Lieb recoupling theory. Unitary braiding matrices are obtained by a normalization of the degenerate ground states of a system of anyons, which is equivalent to a modification of the definition of the 3-vertices in the Temperley-Lieb recoupling theory as proposed by Kauffman and Lomonaco. With the braid matrices available, we discuss the problems of encoding of qubit states and construction of quantum gates from the elementary braiding operation matrices for the Ising anyons model. In the encoding scheme where 2 qubits are represented by 8 Ising anyons, we give an alternative proof of the no-entanglement theorem given by Bravyi and compare it to the case of Fibonacci anyons model. In the encoding scheme where 2 qubits are represented by 6 Ising anyons, we construct a set of quantum gates which is equivalent to the construction of Georgiev., Comment: 25 pages, 13 figures

We prove a no-ghost theorem for a bosonic string propagating in Nappi-Witten spacetime. This is achieved in two steps. We first demonstrate unitarity for a class of NW/U(1) modules: the norm of any state which is primary with respect to a chosen timelike U(1) is non-negative. We then show that physical states - states satisfying the Virasoro constraints - in a class of modules of an affinisation of the Nappi-Witten algebra are contained in the NW/U(1) modules. Similar to the case of strings on $AdS_3$, in order to saturate the spectrum obtained in light-cone quantization we are led to include modules with energy not bounded from below, which are related to modules with energy bounded from below by spectral flow automorphisms., Comment: 24 pages, 1 figure

It is known that a classical SU(2) Einstein-Yang-Mills theory in 3+1 dimensional anti-de Sitter spacetime can provide a holographic dual to a 2+1 dimensional time reversal symmetry breaking superconductor with a pseudogap. We study the properties of this holographic superconductor in the presence of an applied constant external magnetic field, neglecting backreaction on the geometry. The superconductor is immersed into a constant external magnetic field by adding a radially (the extra dimension) dependent magnetic field to the black hole. As for real superconductors, there is a critical magnetic field above which no superconductivity can appear. The continuity of the first derivative of the free energy difference between the superconducting phase and the normal phase at the critical temperature suggests that the superconducting phase transition with applied magnetic field is of second order., Comment: 12 pages, 3 figures, references added, typos corrected