Intracellular detection of singlet oxygen using fluorescent nanosensors.

Detection of singlet oxygen is of great importance for a range of therapeutic applications, particularly photodynamic therapy, plasma therapy and also during photo-endosomolytic activity. Here we present a novel method of intracellular detection of singlet oxygen using biocompatible polymeric nanosensors, encapsulating the organic fluorescent dye, Singlet Oxygen Sensor Green (SOSG) within its hydrophobic core. The singlet oxygen detection efficiency of the nanosensors was quantified experimentally by treating them with a plasma source and these results were further validated by using Monte Carlo simulations. The change in fluorescence intensity of the nanosensors serves as a metric to detect singlet oxygen in the local micro-environment inside mammalian cancer cells. We used these nanosensors for monitoring singlet oxygen inside endosomes and lysosomes of cancer cells, during cold plasma therapy, using a room-temperature Helium plasma jet.

Kinetically driven island morphology in growth on strained Cu(100).

We study the effects of strain on the monomer and dimer diffusion mechanisms and island morphology during the growth of Cu on a biaxially strained Cu(100) substrate. We find an approximately linear dependence of the activation barriers on strain. In particular, while hopping is favored for compressive and/or small (<2%) tensile strain, for greater than 2% tensile strain, the exchange mechanism is favored. We then present the results of temperature-accelerated dynamics simulations of submonolayer growth at 200 K. For the case of 2% compressive strain we find that, as in previous kinetic Monte Carlo simulations of Cu/Ni(100) growth, the competition between island growth and multi-atom relaxation ("pop-out") events leads to an island morphology with a mixture of open and closed steps. At slightly higher coverage, island coalescence then leads to elongated islands. However, annealing leads to a significant decrease in the number of open steps. In contrast, for the case of 8% tensile strain, only one large strongly anisotropic island is formed. Surprisingly, we find that despite the large strain, the island anisotropy is not due to energetics but is instead due to anisotropic attachment barriers that favor the exchange-mediated attachment of monomers to corners over close-packed step-edges. An explanation for the asymmetry in attachment barriers is provided. Our results provide a new general kinetic mechanism for the formation of anisotropic islands in the presence of isotropic diffusion and tensile strain.

Island nucleation and growth with anomalous diffusion in one-dimension.

Recently a general rate-equation (RE) theory of submonolayer island nucleation and growth was developed [J. G. Amar and M. Semaan, Phys. Rev. E 93, 062805 (2016)] which takes into account the critical island-size i, island fractal dimension df, substrate dimension d, and diffusion exponent µ, and good agreement with simulations was found for the case of irreversible growth corresponding to a critical island-size i=1 with d = 2. Here we present the results of simulations carried out in 1D (corresponding to d = 1) of island nucleation and growth with anomalous diffusion which were carried out for both the case of superdiffusion (µ>1) and subdiffusion (µ<1). Excellent agreement is found with the general RE theory for both irreversible growth (i=1) and reversible growth with i=2 for all 0≤µ≤2.

Improved scaling of temperature-accelerated dynamics using localization.

While temperature-accelerated dynamics (TAD) is a powerful method for carrying out non-equilibrium simulations of systems over extended time scales, the computational cost of serial TAD increases approximately as N(3) where N is the number of atoms. In addition, although a parallel TAD method based on domain decomposition [Y. Shim et al., Phys. Rev. B 76, 205439 (2007)] has been shown to provide significantly improved scaling, the dynamics in such an approach is only approximate while the size of activated events is limited by the spatial decomposition size. Accordingly, it is of interest to develop methods to improve the scaling of serial TAD. As a first step in understanding the factors which determine the scaling behavior, we first present results for the overall scaling of serial TAD and its components, which were obtained from simulations of Ag/Ag(100) growth and Ag/Ag(100) annealing, and compare with theoretical predictions. We then discuss two methods based on localization which may be used to address two of the primary "bottlenecks" to the scaling of serial TAD with system size. By implementing both of these methods, we find that for intermediate system-sizes, the scaling is improved by almost a factor of N(1/2). Some additional possible methods to improve the scaling of TAD are also discussed.

Critical island-size, stability, and morphology of 2D colloidal Au nanoparticle islands.

The critical island-size, stability, and morphology of 2D colloidal Au nanoparticle islands formed during drop-drying are studied using an empirical potential which takes into account core-core, ligand-ligand, and ligand-solvent interactions. Good agreement with experiment is obtained for the dependence of the critical island-size on nanoparticle diameter. Our results for the critical length-scale for smoothing via edge-diffusion are also consistent with the limited facet size and island-relaxation observed in experiments. In addition, the relatively high rate of monomer diffusion on an island as well as the low barrier for interlayer diffusion are consistent with experimental observations that second-layer growth does not occur until after the first layer is complete.

Adsorption and diffusion of colloidal Au nanoparticles at a liquid-vapor interface.

Motivated by recent drop-drying experiments of Au nanoparticle (NP) island self-assembly, we investigate the structure, diffusion, and binding of dodecanethiol-coated Au NPs adsorbed at the toluene-vapor interface using molecular dynamics (MD) simulations as well as analytical calculations. For a 6 nm core diameter NP our results indicate the existence of significant intermixing between the ligands and the solvent. As a result, the NP lies primarily below the interface with only a portion of the ligands sticking out, while the toluene-vapor interface is significantly higher in the region above the NP core than away from the NP. These results are consistent with a competition between the negative free energy of mixing of toluene and the dodecanethiol ligands, which tends to keep the NP below the interface, and the effects of surface tension which keeps the NP near the interface. Consistent with this result, we find that the coefficient for nanoparticle diffusion along the interface is close to the Stokes-Einstein prediction for three-dimensional bulk diffusion. An analysis of the ligand arrangement surrounding the NP also indicates that there is relatively little asymmetry in the ligand-coating. We then consider the effects of van der Waals interactions on the adsorption energy. In particular, we derive an analytical expression for the van der Waals interaction energy between a coated nanoparticle and the surrounding solvent along with a closed-form expression for the van der Waals corrections to the binding energy at the interface due to the long-range core-solvent interaction. Using these results along with the results of our MD simulations, we then estimate the van der Waals corrections to the adsorption energy for dodecanethiol-coated Au nanoparticles at the toluene-vapor interface as well as for decanethiol-coated nanoparticles at the water-vapor interface. In both cases, we find that the long-range core-solvent interaction may significantly reduce the binding energy. Based on these results, we conclude that in many cases, the core-solvent van der Waals interaction is likely to have a significant effect on the binding energy and interface position of Au NPs. Our results also indicate that the competition between the van der Waals interaction and the short-range attraction to the interface leads to the existence of well-defined activation barriers for nanoparticle adsorption from the solvent as well as for interfacial desorption.

Strain-dependence of Te interstitial diffusion in CdTe.

While the dominant defects which control non-radiative recombination and long-range interstitial diffusion in CdTe correspond to Cd vacancies and Te anti-sites, the short-range diffusion of Te and Se interstitials between these defects is also of interest, since they both play a role in defect passivation. In addition, since CdTe thin films are typically polycrystalline and may also involve interfaces with materials with different lattice constants, the effects of strain are also of interest. Here we present the results of molecular dynamics (MD) simulations of Te interstitial diffusion in zincblende CdTe for values of the triaxial strain ranging from -2% (compressive) strain to +2.8% (tensile) strain. By carrying out MD simulations of Te interstitial diffusion over a range of temperatures, and then carrying out Arrhenius fits, we have determined the effective activation barrierEaand prefactorD0for each value of the global strain. We find that bothEaandD0exhibit non-monotonic behavior, increasing with both compressive and tensile strain. We also present an analysis of the key diffusion pathways for 3 different values of the strain which explains the non-monotonic strain dependence obtained in our simulations. Our results also indicate that in each case, the diffusion of interstitial Te involves a variety of concerted events with a wide range of activation barriers.

Island density scaling in reversible submonolayer growth with attachment barriers.

Island nucleation and growth play an important role in thin-film growth. One quantity of particular interest is the exponent χ, which describes the dependence of the saturation island density N_{sat}∼(D_{h}/F)^{-χ} on the ratio D_{h}/F of the monomer hopping rate D_{h} to the deposition rate F. While standard rate equation (RE) theory predicts that χ=i/(i+2) (where i is the critical island size), more recently it has been predicted that in the presence of a strong barrier to the attachment of monomers to islands, a significantly larger value χ=2i/(i+3) may be observed. While this prediction has recently been tested using kinetic Monte Carlo simulations for the case of irreversible growth corresponding to i=1, it has not been tested for the case of reversible island growth corresponding to i>1. Here we present a mean-field self-consistent RE method which we have used to study the dependence of the effective value of χ on D_{h}/F and barrier-strength for i=1,2,3, and 6. Both the no-nucleation-barrier case in which there exists a barrier for monomers to attach to islands larger than the critical island size (but not to smaller islands) and the nucleation-barrier case in which there is a barrier for monomers to attach to islands of all sizes are studied. In all cases, we find that the existence of attachment barriers significantly increases the effective value of χ for a given barrier strength. In addition, for i=1 we find good agreement between our extrapolated asymptotic value of χ and the theoretical strong-barrier prediction both with and without a nucleation barrier. In contrast, for i>1 the value of χ is significantly larger in the presence of a nucleation barrier than in its absence. In particular, while an asymptotic analysis of our results for i>1 also leads to excellent agreement with the strong barrier prediction in the presence of a nucleation barrier, in the absence of a nucleation barrier the asymptotic values are significantly lower.

Localized saddle-point search and application to temperature-accelerated dynamics.

We present a method for speeding up temperature-accelerated dynamics (TAD) simulations by carrying out a localized saddle-point (LSAD) search. In this method, instead of using the entire system to determine the energy barriers of activated processes, the calculation is localized by only including a small chunk of atoms around the atoms directly involved in the transition. Using this method, we have obtained N-independent scaling for the computational cost of the saddle-point search as a function of system size N. The error arising from localization is analyzed using a variety of model systems, including a variety of activated processes on Ag(100) and Cu(100) surfaces, as well as multiatom moves in Cu radiation damage and metal heteroepitaxial growth. Our results show significantly improved performance of TAD with the LSAD method, for the case of Ag/Ag(100) annealing and Cu/Cu(100) growth, while maintaining a negligibly small error in energy barriers.

Shape transitions in strained Cu islands on Ni(100): kinetics versus energetics.

We examine the ramified islands observed in submonolayer Cu/Ni(100) growth. Our results indicate that the strain-energy contribution to the dependence of island energy on shape is surprisingly weak. In contrast, our accelerated dynamics simulations indicate that unexpected concerted popout processes occurring at step edges may be responsible. Kinetic Monte Carlo (KMC) simulations which include these processes produce island shapes which are very similar to those observed in experiment. These results suggest that the shape transition is of kinetic origin but is strongly mediated by strain.

Adaptive temperature-accelerated dynamics.

We present three adaptive methods for optimizing the high temperature T(high) on-the-fly in temperature-accelerated dynamics (TAD) simulations. In all three methods, the high temperature is adjusted periodically in order to maximize the performance. While in the first two methods the adjustment depends on the number of observed events, the third method depends on the minimum activation barrier observed so far and requires an a priori knowledge of the optimal high temperature T(high)(opt)(E(a)) as a function of the activation barrier E(a) for each accepted event. In order to determine the functional form of T(high)(opt)(E(a)), we have carried out extensive simulations of submonolayer annealing on the (100) surface for a variety of metals (Ag, Cu, Ni, Pd, and Au). While the results for all five metals are different, when they are scaled with the melting temperature T(m), we find that they all lie on a single scaling curve. Similar results have also been obtained for (111) surfaces although in this case the scaling function is slightly different. In order to test the performance of all three methods, we have also carried out adaptive TAD simulations of Ag/Ag(100) annealing and growth at T = 80 K and compared with fixed high-temperature TAD simulations for different values of T(high). We find that the performance of all three adaptive methods is typically as good as or better than that obtained in fixed high-temperature TAD simulations carried out using the effective optimal fixed high temperature. In addition, we find that the final high temperatures obtained in our adaptive TAD simulations are very close to our results for T(high)(opt)(E(a)). The applicability of the adaptive methods to a variety of TAD simulations is also briefly discussed.

Capture-zone areas in submonolayer nucleation: effects of dimensionality and short-range interactions.

Simulation results for the asymptotic scaled capture-zone distribution (CZD) for the case of irreversible nucleation and growth of point islands are presented for substrate dimension d=1 , 2, 3, and 4 and compared with a recent conjecture based on the Wigner distribution. Poor agreement is found between the predicted Wigner distributions and the asymptotic CZD in the limit of infinite DF (corresponding to the ratio of monomer hopping rate D to deposition rate F ). Our results also indicate that for d=2 and 3 the asymptotic CZD for point islands is independent of model details and dimension. However, for d=1 and d=4 the resulting distribution is significantly more sharply peaked. We also find that in contrast to the island-size distribution, for which mean-field-like behavior is observed in d=3 and above, the asymptotic CZD is significantly broadened by fluctuations even in d=4 .

Effects of substrate rotation in oblique-incidence metal(100) epitaxial growth.

The effects of substrate rotation on the surface morphology in oblique-incidence metal(100) epitaxial growth are studied via kinetic Monte Carlo simulations of a simplified model, and compared with previous results obtained without rotation. In general, we find that substrate rotation leads to two main effects. At high deposition angles with respect to the substrate normal, rotation leads to a significant change in the surface morphology. In particular, it leads to isotropic mounds and pyramids with (111) facets rather than the anisotropic ripples and rods observed in the absence of rotation. Due to the existence of rapid transport on these facets, the lateral feature size increases approximately linearly with film thickness. Due to the fact that substrate rotation tends to reduce the effects of shadowing, the surface roughness is also decreased compared to the roughness in the absence of rotation. While this leads to a moderate reduction in the roughness for the case of ballistic deposition, the effect is significantly larger in the case of deposition with attraction. In the case of ballistic deposition, we also find that the surface roughness increases with rotation rate Omega for Omega<1 rev/monolayer (ML) before saturating at larger rotation rates ( Omega>1 rev/ML). In contrast, for the case of attraction the surface roughness exhibits a negligible dependence on rotation rate for finite rotation rate.

Parallel kinetic Monte Carlo simulations of Ag(111) island coarsening using a large database.

The results of parallel kinetic Monte Carlo (KMC) simulations of the room-temperature coarsening of Ag(111) islands carried out using a very large database obtained via self-learning KMC simulations are presented. Our results indicate that, while cluster diffusion and coalescence play an important role for small clusters and at very early times, at late time the coarsening proceeds via Ostwald ripening, i.e. large clusters grow while small clusters evaporate. In addition, an asymptotic analysis of our results for the average island size S(t) as a function of time t leads to a coarsening exponent n = 1/3 (where S(t)∼t(2n)), in good agreement with theoretical predictions. However, by comparing with simulations without concerted (multi-atom) moves, we also find that the inclusion of such moves significantly increases the average island size. Somewhat surprisingly we also find that, while the average island size increases during coarsening, the scaled island-size distribution does not change significantly. Our simulations were carried out both as a test of, and as an application of, a variety of different algorithms for parallel kinetic Monte Carlo including the recently developed optimistic synchronous relaxation (OSR) algorithm as well as the semi-rigorous synchronous sublattice (SL) algorithm. A variation of the OSR algorithm corresponding to optimistic synchronous relaxation with pseudo-rollback (OSRPR) is also proposed along with a method for improving the parallel efficiency and reducing the number of boundary events via dynamic boundary allocation (DBA). A variety of other methods for enhancing the efficiency of our simulations are also discussed. We note that, because of the relatively high temperature of our simulations, as well as the large range of energy barriers (ranging from 0.05 to 0.8 eV), developing an efficient algorithm for parallel KMC and/or SLKMC simulations is particularly challenging. However, by using DBA to minimize the number of boundary events, we have achieved significantly improved parallel efficiencies for the OSRPR and SL algorithms. Finally, we note that, among the three parallel algorithms which we have tested here, the semi-rigorous SL algorithm with DBA led to the highest parallel efficiencies. As a result, we have obtained reasonable parallel efficiencies in our simulations of room-temperature Ag(111) island coarsening for a small number of processors (e.g. N(p) = 2 and 4). Since the SL algorithm scales with system size for fixed processor size, we expect that comparable and/or even larger parallel efficiencies should be possible for parallel KMC and/or SLKMC simulations of larger systems with larger numbers of processors.

Parallel kinetic Monte Carlo simulations of two-dimensional island coarsening.

The results of parallel kinetic Monte Carlo (KMC) simulations of island coarsening based on a bond-counting model are presented. Our simulations were carried out both as a test of and as an application of the recently developed semirigorous synchronous sublattice (SL) algorithm. By carrying out simulations over long times and for large system sizes the asymptotic coarsening behavior and scaled island-size distribution (ISD) were determined. Our results indicate that while cluster diffusion and coalescence play a role at early and intermediate times, at late times the coarsening proceeds via Ostwald ripening. In addition, we find that the asymptotic scaled ISD is significantly narrower and more sharply peaked than the mean-field theory prediction. The dependence of the scaled ISD on coverage is also studied. Our results demonstrate that parallel KMC simulations can be used to effectively extend the time scale over which realistic coarsening simulations can be carried out. In particular, for simulations of the late stages of coarsening with system size L=1600 and eight processors, a parallel efficiency larger than 80% was obtained. These results suggest that the SL algorithm is likely to be useful in the future in parallel KMC simulations of more complicated models of coarsening.

Upper critical dimension for irreversible cluster nucleation and growth in the point-island regime.

We compare the results of kinetic Monte Carlo (KMC) simulations of a point-island model of irreversible nucleation and growth in four dimensions (4D) with the corresponding mean-field (MF) rate-equation predictions for the monomer density, island density, island-size distribution (ISD), capture-number distribution (CND), and capture-zone distribution (CZD), in order to determine the critical dimension d(c) for mean-field behavior. The asymptotic behavior is studied as a function of the fraction of occupied sites (coverage) and the ratio DF of the monomer hopping rate D to the (per site) monomer creation rate F. Excellent agreement is found between our KMC simulation results and the MF rate equation results for the average island and monomer densities. For large D/F, the scaled CND and CZD do not depend on island size, in good agreement with the MF prediction, while the scaled ISD also agrees well with the MF prediction except for a slight difference at the peak values. Coupled with previous results obtained in d = 3 , these results indicate that for growth in the point-island regime, the upper critical dimension for irreversible cluster nucleation and growth is equal to 4.

Island nucleation and growth with anomalous diffusion.

While most studies of submonolayer island nucleation and growth have been based on the assumption of ordinary monomer diffusion corresponding to diffusion exponent µ=1, in some cases either subdiffusive (µ<1) or superdiffusive (µ>1) behavior may occur. Here we present general expressions for the exponents describing the flux dependence of the island and monomer densities as a function of the critical island size i, substrate dimension d, island fractal dimension d_{f}, and diffusion exponent µ, where 0≤µ≤2. Our results are compared with kinetic Monte Carlo simulations for the case of irreversible island growth (i=1) with 0≤µ≤2 and d=2 as well as simulation results for d=1, 3, and 4, and excellent agreement is found.

Dynamical scaling behavior in two-dimensional ballistic deposition with shadowing.

The dynamical scaling behavior in two-dimensional ballistic deposition with shadowing is studied as a function of the angular distribution of incoming particles and of the underlying lattice structure. Using a dynamical scaling form for the surface box number, results for the scaling of the surface fractal dimension are also presented. Our results indicate that, in addition to the usual self-affine universality class corresponding to vertical deposition, there exist at least two additional universality classes characterized by distinct values of the coarsening and roughening exponents p and beta describing the evolution of the lateral feature size and surface roughness with film thickness, as well as the surface fractal dimension D(f). For the case of a uniform angular distribution corresponding to an anisotropic flux, we find p=beta=1 and D(f) approximately 1.7. However, for ballistic deposition with an isotropic flux (corresponding to a "cosine" angular distribution), we find p approximately 2/3 and D(f) approximately 1.5 while the effective roughening exponent beta approximately 0.52-0.64 was found to be slightly lattice dependent. In both cases, anomalous scaling of the height-height correlation function is also observed. In contrast, vertical deposition leads to a self-affine surface with p=2/3, beta=1/3, and D(f)=1. The asymptotic scaling behavior appears to depend on the behavior of the angular distribution at large angles but does not depend on other details. An analysis that clarifies the relationship between the launch angle distribution used in the simulations and the flux distribution is also presented.

Scaling behavior of the surface in ballistic deposition.

Using a dynamical scaling form for the surface fractal dimension as well as efficient algorithms for the simulation and analysis of the surface in three-dimensional ballistic deposition, we show that while the top of the surface is self-affine, the complete surface including overhangs has fractal dimension D(f) approximately 3. The existence of such a fractal surface is a consequence of the difficulty of closing off voids in three and higher dimensions. By studying a modified ballistic deposition model in which sticking is allowed with a given probability p, we show that the surface undergoes a phase transition from fractal to compact at a finite value of p. Our results also have implications for understanding the surface morphology in sedimentary rocks and low-temperature thin films.

Critical island size, scaling, and ordering in colloidal nanoparticle self-assembly.

In order to obtain a better understanding of short-range (SR) and long-range (LR) nanoparticle (NP) interactions during the self-assembly of dodecanethiol-coated Au NPs in toluene via drop drying, we have investigated the dependence of the island density, scaled island-size distribution (ISD), and scaled capture-zone distribution (CZD) on coverage, deposition flux, and NP size. Our results indicate that, while the critical island size is larger than 1 for all NP sizes studied, due to the increase in the strength of the SR attraction between NPs with increasing NP size, both the exponent describing the dependence of the island density on deposition flux and the critical island-size decrease with increasing NP size. We also find that, despite the existence of significant cluster diffusion and coalescence, the ISD is sharply peaked as in epitaxial growth. In particular, for large NP size, we find good agreement between the scaled ISD and epitaxial growth models as well as good agreement between the scaled CZD and scaled ISD. However, for smaller NPs the scaled ISD is less sharply peaked despite the fact that the critical island size is larger. This latter result suggests that in this case additional effects such as enhanced island coalescence or NP detachment from large islands may play an important role. Results for the ordering of NP islands are also presented which indicate the existence of LR repulsive interactions. One possible mechanism for such an interaction is the existence of a small dipole moment on each NP which arises as a result of an asymmetry, driven by surface tension, in the thiol distribution for NPs adsorbed at the toluene-air interface. Consistent with this mechanism, we find good agreement between experimental results for the nearest-neighbor island-distance distribution and simulations which include dipole repulsion.