Nonlinear breathing modes at a defect

Recent molecular dynamics (MD) simulations of Cubero et al (1999) of a DNA duplex containing the 'rogue' base difluorotoluene (F) in place of a thymine (T) base show that breathing events can occur on the nanosecond timescale, whereas breathing events in a normal DNA duplex take place on the microsecond timescale. The main aim of this paper is to analyse a nonlinear Klein-Gordon lattice model of the DNA duplex including both nonlinear interactions between opposing bases and a defect in the interaction at one lattice site; each of which can cause localisation of energy. Solutions for a breather mode either side of the defect are derived using multiple-scales asymptotics and are pieced together across the defect to form a solution which includes the effects of the nonlinearity and the defect. We consider defects in the inter-chain interactions and in the along chain interactions. In most cases we find in-phase breather modes and/or out-of-phase breather modes, with one case displaying a shifted mode.

Manipulating the structural and electronic properties of epitaxial NaNbO3 films via strain and stoichiometry

Due to their intriguing dielectric, pyroelectric, elasto-electric, or opto-electric properties, oxide ferroelectrics are vital candidates for the fabrication of most electronics. However, these extraordinary properties exist mainly in the temperature regime around the ferroelectric phase transition, which is usually several hundreds of K away from room temperature. Therefore, the manipulation of oxide ferroelectrics, especially moving the ferroelectric transition towards room temperature, is of great interest for application and also basic research. In this thesis, we demonstrate this using examples of NaNbO3 films. We show that the transition temperature of these films can be modified via plastic strain caused by epitaxial film growth on a structurally mismatched substrate, and this strain can be fixed by controlling the stoichiometry. The structural and electronic properties of Na1+xNbO3+δ thin films are carefully examined by among others XRD (e.g. RSM) and TEM and cryoelectronic measurements. Especially the electronic features are carefully analyzed via specially developed interdigitated electrodes in combination with integrated temperature sensor and heater. The electronic data are interpreted using existing as well as novel theories and models, they are proved to be closely correlated to the structural characteristics. The major results are: -Na1+xNbO3+δ thin films can be grown epitaxially on (110)NdGaO3 with a thickness up to 140 nm (thicker films have not been studied). Plastic relaxation of the compressive strain sets in when the thickness of the film exceeds approximately 10 – 15 nm. Films with excess Na are mainly composed of NaNbO3 with minor contribution of Na3NbO4. The latter phase seems to form nanoprecipitates that are homogeneously distributed in the NaNbO3 film which helps to stabilize the film and reduce the relaxation of the strain. -For the nominally stoichiometric films, the compressive strain leads to a broad and frequency-dispersive phase transition at lower temperature (125 – 147 K). This could be either a new transition or a shift in temperature of a known transition. Considering the broadness and frequency dispersion of the transition, this is actually a transition from the dielectric state at high temperature to a relaxor-type ferroelectric state at low temperature. The latter is based on the formation of polar nano-regions (PNRs). Using the electric field dependence of the freezing temperature, allows a direct estimation of the volume (70 to 270 nm3) and diameter (5.2 to 8 nm, spherical approximation) of the PNRs. The values confirm with literature values which were measured by other technologies. -In case of the off-stoichiometric samples, we observe again the classical ferroelectric behavior. However, the thermally hysteretic phase transition which is observed around 620 – 660 K for unstrained material is shifted to room temperature due to the compressive strain. Beside to the temperature shift, the temperature dependence of the permittivity is nearly identical for strained and unstrained materials. -The last but not least, in all cases, a significant anisotropy in the electronic and structural properties is observed which arises automatically from the anisotropic strain caused by the orthorhombic structure of the substrate. However, this anisotropy cannot be explained by the classical model which tries to fit an orthorhombic film onto an orthorhombic substrate. A novel “square lattice” model in which the films adapt a “square” shaped lattice in the plane of the film during the epitaxial growth at elevated temperature (~1000 K) nicely explains the experimental results. In this thesis we sketch a way to manipulate the ferroelectricity of NaNbO3 films via strain and stoichiometry. The results indicate that compressive strain which is generated by the epitaxial growth of the film on mismatched substrate is able to reduce the ferroelectric transition temperature or induce a phase transition at low temperature. Moreover, by adding Na in the NaNbO3 film a secondary phase Na3NbO4 is formed which seems to stabilize the main phase NaNbO3 and the strain and, thus, is able to engineer the ferroelectric behavior from the expected classical ferroelectric for perfect stoichiometry to relaxor-type ferroelectric for slightly off-stoichiometry, back to classical ferroelectric for larger off-stoichiometry. Both strain and stoichiometry are proven as perfect methods to optimize the ferroelectric properties of oxide films.

Numerical study on viscoelastic behavior of polypropylene fiber reinforced concrete subjected to temperature variations using LDPM theory

This thesis is focused on the viscoelastic behavior of macro-synthetic fiber-reinforced concrete (MSFRC) with polypropylene studied numerically when subjected to temperature variations (-30 oC to +60 oC). LDPM (lattice discrete particle model), a meso-scale model for heterogeneous composites, is used. To reproduce the MSFRC structural behavior, an extended version of LDPM that includes fiber effects through fiber-concrete interface micromechanics, called LDPM-F, is applied. Model calibration is performed based on three-point bending, cube, and cylinder test for plain concrete and MSFRC. This is followed by a comprehensive literature study on the variation of mechanical properties with temperature for individual fibers and plain concrete. This literature study and past experimental test results constitute inputs for final numerical simulations. The numerical response of MSFRC three-point bending test is replicated and compared with the previously conducted experimental test results; finally, the conclusions were drawn. LDPM numerical model is successfully calibrated using experimental responses on plain concrete. Fiber-concrete interface micro-mechanical parameters are subsequently fixed and LDPM-F models are calibrated based on MSFRC three-point bending test at room temperature. Number of fibers contributing crack bridging mechanism is computed and found to be in good agreement with experimental counts. Temperature variations model for individual constituents of MSFRC, fibers and plain concrete, are implemented in LDPM-F. The model is validated for MSFRC three-point bending stress-CMOD (crack mouth opening) response reproduced at -30 oC, -15 oC, 0 oC, +20 oC, +40 oC and +60 oC. It is found that the model can well describe the temperature variation behavior of MSFRC. At positive temperatures, simulated responses are in good agreement. Slight disagreement in negative regimes suggests an in-depth study on fiber-matrix interface bond behavior with varying temperatures.

Phase diagram of a model for a binary mixture of nematic molecules on a Bethe lattice

We investigate the phase diagram of a discrete version of the Maier-Saupe model with the inclusion of additional degrees of freedom to mimic a distribution of rodlike and disklike molecules. Solutions of this problem on a Bethe lattice come from the analysis of the fixed points of a set of nonlinear recursion relations. Besides the fixed points associated with isotropic and uniaxial nematic structures, there is also a fixed point associated with a biaxial nematic structure. Due to the existence of large overlaps of the stability regions, we resorted to a scheme to calculate the free energy of these structures deep in the interior of a large Cayley tree. Both thermodynamic and dynamic-stability analyses rule out the presence of a biaxial phase, in qualitative agreement with previous mean-field results.

Critical behavior of the susceptible-infected-recovered model on a square lattice

By means of numerical simulations and epidemic analysis, the transition point of the stochastic asynchronous susceptible-infected-recovered model on a square lattice is found to be c(0)=0.176 500 5(10), where c is the probability a chosen infected site spontaneously recovers rather than tries to infect one neighbor. This point corresponds to an infection/recovery rate of lambda(c)=(1-c(0))/c(0)=4.665 71(3) and a net transmissibility of (1-c(0))/(1+3c(0))=0.538 410(2), which falls between the rigorous bounds of the site and bond thresholds. The critical behavior of the model is consistent with the two-dimensional percolation universality class, but local growth probabilities differ from those of dynamic percolation cluster growth, as is demonstrated explicitly.

Dynamic transitions in a three dimensional associating lattice gas model

The aggregation of interacting Brownian particles in sheared concentrated suspensions is an important issue in colloid and soft matter science per se. Also, it serves as a model to understand biochemical reactions occurring in vivo where both crowding and shear play an important role. We present an effective medium approach within the Smoluchowski equation with shear which allows one to calculate the encounter kinetics through a potential barrier under shear at arbitrary colloid concentrations. Experiments on a model colloidal system in simple shear flow support the validity of the model in the concentration range considered. By generalizing Kramers' rate theory to the presence of shear and collective hydrodynamics, our model explains the significant increase in the shear-induced reaction-limited aggregation kinetics upon increasing the colloid concentration.

Dynamic transitions in a two dimensional associating lattice gas model

Using Monte Carlo simulations we investigate some new aspects of the phase diagram and the behavior of the diffusion coefficient in an associating lattice gas (ALG) model on different regions of the phase diagram. The ALG model combines a two dimensional lattice gas where particles interact through a soft core potential and orientational degrees of freedom. The competition between soft core potential and directional attractive forces results in a high density liquid phase, a low density liquid phase, and a gas phase. Besides anomalies in the behavior of the density with the temperature at constant pressure and of the diffusion coefficient with density at constant temperature are also found. The two liquid phases are separated by a coexistence line that ends in a bicritical point. The low density liquid phase is separated from the gas phase by a coexistence line that ends in tricritical point. The bicritical and tricritical points are linked by a critical lambda-line. The high density liquid phase and the fluid phases are separated by a second critical tau-line. We then investigate how the diffusion coefficient behaves on different regions of the chemical potential-temperature phase diagram. We find that diffusivity undergoes two types of dynamic transitions: a fragile-to-strong transition when the critical lambda-line is crossed by decreasing the temperature at a constant chemical potential; and a strong-to-strong transition when the critical tau-line is crossed by decreasing the temperature at a constant chemical potential.

Statistics of opinion domains of the majority-vote model on a square lattice

The existence of juxtaposed regions of distinct cultures in spite of the fact that people's beliefs have a tendency to become more similar to each other's as the individuals interact repeatedly is a puzzling phenomenon in the social sciences. Here we study an extreme version of the frequency-dependent bias model of social influence in which an individual adopts the opinion shared by the majority of the members of its extended neighborhood, which includes the individual itself. This is a variant of the majority-vote model in which the individual retains its opinion in case there is a tie among the neighbors' opinions. We assume that the individuals are fixed in the sites of a square lattice of linear size L and that they interact with their nearest neighbors only. Within a mean-field framework, we derive the equations of motion for the density of individuals adopting a particular opinion in the single-site and pair approximations. Although the single-site approximation predicts a single opinion domain that takes over the entire lattice, the pair approximation yields a qualitatively correct picture with the coexistence of different opinion domains and a strong dependence on the initial conditions. Extensive Monte Carlo simulations indicate the existence of a rich distribution of opinion domains or clusters, the number of which grows with L(2) whereas the size of the largest cluster grows with ln L(2). The analysis of the sizes of the opinion domains shows that they obey a power-law distribution for not too large sizes but that they are exponentially distributed in the limit of very large clusters. In addition, similarly to other well-known social influence model-Axelrod's model-we found that these opinion domains are unstable to the effect of a thermal-like noise.

Ferromagnetism, paramagnetism, and a Curie-Weiss metal in an electron-doped Hubbard model on a triangular lattice

Motivated by the unconventional properties and rich phase diagram of NaxCoO2 we consider the electronic and magnetic properties of a two-dimensional Hubbard model on an isotropic triangular lattice doped with electrons away from half-filling. Dynamical mean-field theory (DMFT) calculations predict that for negative intersite hopping amplitudes (t < 0) and an on-site Coulomb repulsion, U, comparable to the bandwidth, the system displays properties typical of a weakly correlated metal. In contrast, for t > 0 a large enhancement of the effective mass, itinerant ferromagnetism, and a metallic phase with a Curie-Weiss magnetic susceptibility are found in a broad electron doping range. The different behavior encountered is a consequence of the larger noninteracting density of states (DOS) at the Fermi level for t > 0 than for t < 0, which effectively enhances the mass and the scattering amplitude of the quasiparticles. The shape of the DOS is crucial for the occurrence of ferromagnetism as for t > 0 the energy cost of polarizing the system is much smaller than for t < 0. Our observation of Nagaoka ferromagnetism is consistent with the A-type antiferromagnetism (i.e., ferromagnetic layers stacked antiferromagnetically) observed in neutron scattering experiments on NaxCoO2. The transport and magnetic properties measured in NaxCoO2 are consistent with DMFT predictions of a metal close to the Mott insulator and we discuss the role of Na ordering in driving the system towards the Mott transition. We propose that the Curie-Weiss metal phase observed in NaxCoO2 is a consequence of the crossover from a bad metal with incoherent quasiparticles at temperatures T > T-* and Fermi liquid behavior with enhanced parameters below T-*, where T-* is a low energy coherence scale induced by strong local Coulomb electron correlations. Our analysis also shows that the one band Hubbard model on a triangular lattice is not enough to describe the unusual properties of NaxCoO2 and is used to identify the simplest relevant model that captures the essential physics in NaxCoO2. We propose a model which allows for the Na ordering phenomena observed in the system which, we propose, drives the system close to the Mott insulating phase even at large dopings.

Simulation of the load-unload response ratio and critical sensitivity in the lattice solid model

The Load-Unload Response Ratio (LURR) method is an intermediate-term earthquake prediction approach that has shown considerable promise. It involves calculating the ratio of a specified energy release measure during loading and unloading where loading and unloading periods are determined from the earth tide induced perturbations in the Coulomb Failure Stress on optimally oriented faults. In the lead-up to large earthquakes, high LURR values are frequently observed a few months or years prior to the event. These signals may have a similar origin to the observed accelerating seismic moment release (AMR) prior to many large earthquakes or may be due to critical sensitivity of the crust when a large earthquake is imminent. As a first step towards studying the underlying physical mechanism for the LURR observations, numerical studies are conducted using the particle based lattice solid model (LSM) to determine whether LURR observations can be reproduced. The model is initialized as a heterogeneous 2-D block made up of random-sized particles bonded by elastic-brittle links. The system is subjected to uniaxial compression from rigid driving plates on the upper and lower edges of the model. Experiments are conducted using both strain and stress control to load the plates. A sinusoidal stress perturbation is added to the gradual compressional loading to simulate loading and unloading cycles and LURR is calculated. The results reproduce signals similar to those observed in earthquake prediction practice with a high LURR value followed by a sudden drop prior to macroscopic failure of the sample. The results suggest that LURR provides a good predictor for catastrophic failure in elastic-brittle systems and motivate further research to study the underlying physical mechanisms and statistical properties of high LURR values. The results provide encouragement for earthquake prediction research and the use of advanced simulation models to probe the physics of earthquakes.

Simulation of the influence of rate- and state-dependent friction on the macroscopic behavior of complex fault zones with the lattice solid model

In order to understand the earthquake nucleation process, we need to understand the effective frictional behavior of faults with complex geometry and fault gouge zones. One important aspect of this is the interaction between the friction law governing the behavior of the fault on the microscopic level and the resulting macroscopic behavior of the fault zone. Numerical simulations offer a possibility to investigate the behavior of faults on many different scales and thus provide a means to gain insight into fault zone dynamics on scales which are not accessible to laboratory experiments. Numerical experiments have been performed to investigate the influence of the geometric configuration of faults with a rate- and state-dependent friction at the particle contacts on the effective frictional behavior of these faults. The numerical experiments are designed to be similar to laboratory experiments by DIETERICH and KILGORE (1994) in which a slide-hold-slide cycle was performed between two blocks of material and the resulting peak friction was plotted vs. holding time. Simulations with a flat fault without a fault gouge have been performed to verify the implementation. These have shown close agreement with comparable laboratory experiments. The simulations performed with a fault containing fault gouge have demonstrated a strong dependence of the critical slip distance D-c on the roughness of the fault surfaces and are in qualitative agreement with laboratory experiments.

Lattice-gas model of particles with orientational and positional degrees of freedom: Mean-field treatment

We consider a lattice-gas model of particles with internal orientational degrees of freedom. In addition to antiferromagnetic nearest-neighbor (NN) and next-nearest-neighbor (NNN) positional interactions we also consider NN and NNN interactions arising from the internal state of the particles. The system then shows positional and orientational ordering modes with associated phase transitions at Tp and To temperatures at which long-range positional and orientational ordering are, respectively, lost. We use mean-field techniques to obtain a general approach to the study of these systems. By considering particular forms of the orientational interaction function we study coupling effects between both phase transitions arising from the interplay between orientational and positional degrees of freedom. In mean-field approximation coupling effects appear only for the phase transition taking place at lower temperatures. The strength of the coupling depends on the value of the long-range order parameter that remains finite at that temperature.