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Tissue dynamics and collective cell motion are crucial biological processes. Their biological machinery is mostly known, and simulation models such as the "active vertex model" (AVM) exist and yield reasonable agreement with experimental observations like tissue fluidization or fingering. However, a good and well-founded continuum description for tissues remains to be developed. In this work we derive a macroscopic description for a two-dimensional cell monolayer by coarse-graining the vertex model through the Poisson bracket approach. We obtain equations for cell density, velocity and the cellular shape tensor. We then study the homogeneous steady states, their stability (which coincides with thermodynamic stability), and especially their behavior under an externally applied shear. Our results contribute to elucidate the interplay between flow and cellular shape. The obtained macroscopic equations present a good starting point for adding cell motion, morphogenetic and other biologically relevant processes., Comment: 14 pages, 11 figures

Weakly coupled semiconductor superlattices under dc voltage bias are nonlinear systems with many degrees of freedom whose nonlinearity is due to sequential tunneling of electrons. They may exhibit spontaneous chaos at room temperature and act as fast physical random number generator devices. Here we present a general sequential transport model with different voltage drops at quantum wells and barriers that includes noise and fluctuations due to the superlattice epitaxial growth. Excitability and oscillations of the current in superlattices with identical periods are due to nucleation and motion of charge dipole waves that form at the emitter contact when the current drops below a critical value. Insertion of wider wells increases superlattice excitability by allowing wave nucleation at the modified wells and more complex dynamics. Then hyperchaos and different types of intermittent chaos are possible on extended dc voltage ranges. Intrinsic shot and thermal noises and external noises produce minor effects on chaotic attractors. However, random disorder due to growth fluctuations may suppress any regular or chaotic current oscillations. Numerical simulations show that more than 70\% of samples remain chaotic when the standard deviation of their fluctuations due to epitaxial growth is below 0.024 nm (10\% of a single monolayer) whereas for 0.015 nm disorder suppresses chaos., Comment: 25 pages, 11 figures

Collective cell migration plays a crucial role in many developmental processes that underlie morphogenesis, wound healing, or cancer progression. In such coordinated behaviours, cells are organised in coherent structures and actively migrate to serve different biological purposes. In some contexts, namely during epithelial wound healing, it is well known that a migrating free-edge monolayer develops finger-like instabilities, yet the onset is still under debate. Here, by means of theory and numerical simulations, we shed light on the main mechanisms driving the instability process, analysing the linear and nonlinear dynamics of a continuum compressible polar fluid. In particular, we assess the role of cell polarisation, substrate friction, and contractile stresses. Linear theory shows that it is crucial to analyse the perturbation transient dynamics, since we unravel a plethora of crossovers between different exponential growth rates during the linear regime. Numerical simulations suggest that cell-substrate friction could be the mechanism responsible for the formation of complex finger-like structures at the edge, since it triggers secondary fingering instabilities and tip-splitting phenomena. Finally, we obtain a critical contractile stress that depends on cell-substrate friction and the initial-to-nematic length ratio, characterising an active wetting-dewetting transition. In the dewetting scenario, the monolayer retracts and becomes stable without developing finger-like structures., Comment: 15 pages, 9 figures, 1 table, submitted to Soft Matter

Age-related macular degeneration (AMD) may cause severe loss of vision or blindness particularly in elderly people. Exudative AMD is characterized by angiogenesis of blood vessels growing from underneath the macula, crossing the blood-retina barrier (that comprise Bruch's membrane, BM, and the retinal pigmentation epithelium RPE), leaking blood and fluid into the retina and knocking off photoreceptors. Here, we simulate a computational model of angiogenesis from the choroid blood vessels via a cellular Potts model, as well as BM, RPE cells, drusen deposits and photoreceptors. Our results indicate that improving AMD may require fixing the impaired lateral adhesion between RPE cells and with BM, as well as diminishing Vessel Endothelial Growth Factor (VEGF) and Jagged proteins that affect the Notch signaling pathway. Our numerical simulations suggest that anti-VEGF and anti-Jagged therapies could temporarily halt exudative AMD while addressing impaired cellular adhesion could be more effective on a longer time span., Comment: 20 pages, 8 figures

The understanding of the dynamics of nonequilibrium cooling and heating processes at the nanoscale is still an open problem. These processes can follow surprising relaxation paths due to, e.g., memory effects, which significantly alter the expected equilibration routes. The Kovacs effect can take place when a thermalization process is suddenly interrupted by a change of the bath temperature, leading to a non-monotonic dependence of the energy of the system. Here, we demonstrate that the Kovacs effect can be observed in the thermalization of the center of mass motion of a levitated nanoparticle. The temperature is controlled during the experiment through an external source of white gaussian noise. We describe our experiments in terms of the dynamics of a Brownian particle in a harmonic trap without any fitting parameter, suggesting that the Kovacs effect canappear in a large variety of systems.

Collective electron transport causes a weakly coupled semiconductor superlattice under dc voltage bias to be an excitable system with $2N+2$ degrees of freedom: electron densities and fields at $N$ superlattice periods plus the total current and the field at the injector. External noise of sufficient amplitude induces regular current self-oscillations (coherence resonance) in states that are stationary in the absence of noise. Numerical simulations show that these oscillations are due to the repeated nucleation and motion of charge dipole waves that form at the emitter when the current falls below a critical value. At the critical current, the well-to-well tunneling current intersects the contact load line. We have determined the device-dependent critical current for the coherence resonance from experiments and numerical simulations. We have also described through numerical simulations how a coherence resonance triggers a stochastic resonance when its oscillation mode becomes locked to a weak ac external voltage signal. Our results agree with the experimental observations., Comment: 21 pages, 12 figures, preprint version including suppl. material

Noise-enhanced chaos in a doped, weakly coupled GaAs/Al_{0.45}Ga_{0.55}As superlattice has been observed at room temperature in experiments as well as in the results of the simulation of nonlinear transport based on a discrete tunneling model. When external noise is added, both the measured and simulated current-versus-time traces contain irregularly spaced spikes for particular applied voltages, which separate a regime of periodic current oscillations from a region of no current oscillations at all. In the voltage region without current oscillations, the electric field profile consist of a low-field domain near the emitter contact separated by a domain wall consisting of a charge accumulation layer from a high-field regime closer to the collector contact. With increasing noise amplitude, spontaneous chaotic current oscillations appear over a wider bias voltage range. For these bias voltages, the domain boundary between the two electric-field domains becomes unstable, and very small current or voltage fluctuations can trigger the domain boundary to move toward the collector and induce chaotic current spikes. The experimentally observed features are qualitatively very well reproduced by the simulations. Increased noise can consequently enhance chaotic current oscillations in semiconductor superlattices., Comment: Physical Review E 95, in press (2017)

We consider a simple spin-membrane model for rippling in graphene. The model exhibits transitions from a flat but rippled membrane to a buckled one. At high temperature the transition is second order but it is first order at low temperature for appropriate strength of the spin-spin coupling. Driving the system across the first order phase transition in nonequilibrium conditions that mimic interaction of the graphene membrane with a STM tip explains recent experiments. In particular, we observe a reversible behavior for small values of the STM current and an irreversible transition from flat rippled membrane to rigid buckled membrane when the current surpasses a critical value. This work opens the possibility to test mechanical properties of graphene under different temperature and electrostatic conditions., Comment: 20 pages, 8 figures

Previous theoretical and experimental work has put forward 50-period semiconductor superlattices as fast, true random number generators at room temperature. Their randomness stems from feedback between nonlinear electronic dynamics and stochastic processes that are intrinsic to quantum transitions. This work theoretically demonstrates that shorter superlattices with higher potential barriers contain fully chaotic dynamics over several intervals of the applied bias voltage compared to the 50-periods device which presented a much weaker chaotic behavior. The chaos arises from deterministic dynamics, hence it persists even in the absence of additional stochastic processes. Moreover, the frequency of the chaotic current oscillations is higher for shorter superlattices. These features should allow for faster and more robust generation of true random numbers., Comment: 12 pages, 4 figures

We investigate the in-plane oscillations of the relaxed shape graphene due to externally applied tensile edge stress along both the armchair and zigzag directions. We show that the total elastic energy density is enhanced with temperature for the case of applied tensile edge stress along the zigzag direction. Thermo-electromechanical effects are treated via pseudomorphic vector potentials to analyze the influence of these coupled effects on the bandstructures of bilayer graphene quantum dots (QDs). We report that the level crossing between ground and first excited states in the localized edge states can be achieved with the accessible values of temperature. In particular, the level crossing point extends to higher temperatures with decreasing values of externally applied tensile edge stress along the armchair direction. This kind of level crossings is absent in the states formed at the center of the graphene sheet due to the presence of three fold symmetry., Comment: 7 pages and 7 figures in press, Phys. Rev. B

The new contribution of this paper is to develop a cylindrical representation of an already known multiphysics model for embedded nanowire superlattices (NWSLs) of wurtzite structure that includes a coupled, strain dependent 8-band $\mathbf{k\cdot p}$ Hamiltonian in cylindrical coordinates and investigate the influence of coupled piezo-electromechanical effects on the barrier localization and critical radius in such NWSLs. The coupled piezo-electromechanical model for semiconductor materials takes into account the strain, piezoelectric effects and spontaneous polarization. Based on the developed 3D model, the band structures of electrons (holes) obtained from results of modeling in Cartesian coordinates are in good agreement with those values obtained from our earlier developed 2D model in cylindrical coordinates. Several parameters such as lattice mismatch, piezo-electric fields, valence and conduction band offsets at the heterojunction of $\mathrm{Al_xGa_{1-x}N/GaN}$ supperlattice can be varied as a function of the Al mole fraction. When the band offsets at the heterojunction of $\mathrm{Al_xGa_{1-x}N/GaN}$ are very small and the influence of the piezo-electromechanical effects can be minimized, then the barrier material can no longer be treated as an infinite potential well. In this situation, it is possible to visualize the penetration of the Bloch wave function into the barrier material that provides an estimation of critical radii of NWSLs. In this case, the NWSLs can act as inversion layers. Finally, we investigate the influence of symmetry of the square and cylindrical NWSLs on the band structures of electrons in the conduction band., Comment: 14 pages and 12 figures

We investigate the evolution of spin dynamics in graphene nanoribbon superlattices (GNSLs) with armchair and zigzag edges in the presence of a drift field. We determine the exact evolution operator and show that it exhibits spin echo phenomena due to rapid oscillations of the quantum states along the ribbon. The evolution of the spin polarization is accompanied by strong beating patterns. We also provide detailed analysis of the band structure of GNSLs with armchair and zigzag edges., Comment: 6 pages and 8 figures

In symmetric quantum dots (QDs), it is well known that the spin-hot spot (i.e., the cusp-like structure due to the presence of degeneracy near the level or anticrossing point) is present for the pure Rashba case but is absent for the pure Dresselhaus case [Phys. Rev. Lett. 95, 076805 (2005)]. Since the Dresselhaus spin-orbit coupling dominates over the Rashba spin-orbit coupling in GaAs and GaSb QDs, it is important to find the exact location of the spin-hot spot or the cusp-like structure even for the pure Dresselhaus case. In this paper, for the first time, we present analytical and numerical results that show that the spin-hot spot can also be seen for the pure Dresselhaus spin-orbit coupling case by inducing large anisotropy through external gates. At or nearby the spin-hot spot, the spin transition rate enhances and the decoherence time reduces by several orders of magnitude compared to the case with no spin-hot spot. Thus one should avoid such locations when designing QD spin based transistors for the possible implementation in quantum logic gates, solid state quantum computing and quantum information processing. It is also possible to extract the exact experimental data (Phys. Rev. Lett. 100, 046803 (2008)) for the phonon mediated spin-flip rates from our developed theoretical model., Comment: 9 pages, 7 figures

The interplay of dynamical nuclear polarization (DNP) and leakage current through a double quantum dot in the spin-blockade regime is analyzed. A finite DNP is built up due to a competition between hyperfine (HF) spin-flip transitions and another inelastic escape mechanism from the triplets, which block transport. We focus on the temperature dependence of the DNP for zero energy-detuning (i.e. equal electrostatic energy of one electron in each dot and a singlet in the right dot). Our main result is the existence of a transition temperature, below which the DNP is bistable, so a hysteretic leakage current versus external magnetic field B appears. This is studied in two cases: (i) Close to the crossing of the three triplet energy levels near B=0, where spin-blockade is lifted due to the inhomogeneity of the effective magnetic field from the nuclei. (ii) At higher B-fields, where the two spin-polarized triplets simultaneously cross two different singlet energy levels. We develop simplified models leading to different transition temperatures T_TT and T_ST for the crossing of the triplet levels and the singlet-triplet level crossings, respectively. We find T_TT analytically to be given solely by the HF couplings, whereas T_ST depends on various parameters and T_ST>T_TT. The key idea behind the existence of the transition temperatures at zero energy-detuning is the suppression of energy absorption compared to emission in the inelastic HF transitions. Finally, by comparing the rate equation results with Monte Carlo simulations, we discuss the importance of having both HF interaction and another escape mechanism from the triplets to induce a finite DNP., Comment: 26 pages, 17 figures

Berry phase in semiconductor quantum dots (QDs) can be induced by moving the dots adiabatically in a closed loop with the application of the distortion potential in the lateral direction. We show that the Berry phase is highly sensitive to the electric fields arising from the interplay between the Rashba and the Dresselhaus spin-orbit couplings. We report that the accumulated Berry phase can be induced from other available quantum state that are only differed by one quantum number of the same spin state. The sign change in the g-factor due to the penetration of the Bloch wavefunctions into the barrier material can be reflected in the Berry phase. We solve the time dependent Schr$\mathrm{\ddot{o}}$dinger equation and investigate the evolution of the spin dynamics during the adiabatic movement of the QDs in the 2D plane. Our results might open the possibilities of building a topological quantum dot quantum computer where the Berry phase can be engineered and can be manipulated with the application of the spin-orbit couplings through gate controlled electric fields., Comment: 10 pages, 11 figures

We investigate the role that noise plays in the hysteretic dynamics of a suspended nanotube or a graphene sheet subject to an oscillating force. We find that not only the size but also the position of the hysteresis region in these systems can be controlled by noise. We also find that nano-resonators act as noise rectifiers: by increasing the noise in the setup, the resonance width of the characteristic peak in these systems is reduced and, as a result, the quality factor is increased., Comment: 15 pages, 6 figures. Sent to PRB (in revision)

We investigate the influence of Rashba spin-orbit coupling in a parabolic nanowire modulated by longitudinal periodic potential. The modulation potential can be obtained from realistically grown supperlattices (SLs). Our study shows that the Rashba spin-orbit interaction induces the level crossing point in the parabolic nanowire SLs. We estimate large anticrossing width (approximately 117 $\mu eV$) between singlet-triplet states. We study the phonon and electromagnetic field mediated spin transition rates in the parabolic nanowire SLs. We report that the phonon mediated spin transition rate is several order of magnitude larger than the electromagnetic field mediated spin transition rate. Based on the Feynman disentangling technique, we find the exact spin transition probability. For the case wave vector $k=0$, we report that the transition probability can be tuned in the form of resonance at fixed time interval. For the general case ($k\neq 0$), we solve the Riccati equation and find that the arbitrary values of $k$ induces the damping in the transition probability. At large value of Rashba spin-orbit coupling coefficients for ($k\neq 0$), spin transition probability freezes., Comment: 7 pages, 4 figures

A semiclassical model of charge transport in a semiconductor superlattice is solved, using moments in the wavenumber direction and finite elements in the spatial direction (first order). The selection of numerical methods guarantees the conservation of current while allowing for high accuracy results. When a dc voltage bias is held between the ends of the sample, self-sustaining oscillations of the current through the superlattice are observed in a narrow range of voltages. the calculated solution displayed the expected accuracy: Spectral convergence in the number of moments used, and first-order convergence in the number of grid-cells. This result paves the way for higher-order methods (in the spatial direction) and the numerical solution of more complex models of charge transport including quantum models based on the Wigner function., Comment: 26 pages, 7 figures, to be submitted to JCP

In this paper, a detailed analysis of anisotropic effects on the phonon induced spin relaxation rate in III-V semiconductor quantum dots (QDs) is carried out. We show that the accidental degeneracy due to level crossing between the first and second excited states of opposite electron spin states in both isotropic and anisotropic QDs can be manipulated with the application of externally applied gate potentials. In particular, anisotropic gate potentials enhance the phonon mediated spin-flip rate and reduce the cusp-like structure to lower magnetic fields, in addition to the lower QDs radii in III-V semiconductor QDs. In InAs QDs, only the Rashba spin-orbit coupling contributes to the phonon induced spin relaxation rate. However, for GaAs QDs, the Rashba spin-orbit coupling has a contribution near the accidental degeneracy point and the Dresselhaus spin-orbit coupling has a contribution below and above the accidental degeneracy point in the manipulation of phonon induced spin relaxation rates in QDs., Comment: 7 pages, 5 figures

We study the anisotropic orbital effect in the electric field tunability of the phonon induced spin-flip rate in quantum dots (QDs). Our study shows that anisotropic gate potential enhances the spin-flip rate and reduces the level crossing point to a lower quantum dot radius due to the suppression of the Land$\acute{e}$ g-factor towards bulk crystal. In the range of $10^4-10^6$ V/cm, the electric field tunability of the phonon induced spin-flip rate can be manipulated through strong Dresselhaus spin-orbit coupling. These results might assist the development of a spin based solid state quantum computer by manipulating phonon induced spin-flip rate through spin-orbit coupling with the application of anisotropic gate potential in a regime where the g-factor changes its sign., Comment: 4 pages, 3 figures

We study the stability and evolution of various elastic defects in a flat graphene sheet and the electronic properties of the most stable configurations. Two types of dislocations are found to be stable: "glide" dislocations consisting of heptagon-pentagon pairs, and "shuffle" dislocations, an octagon with a dangling bond. Unlike the most studied case of carbon nanotubes, Stone Wales defects are unstable in the planar graphene sheet. Similar defects in which one of the pentagon-heptagon pairs is displaced vertically with respect to the other one are found to be dynamically stable. Shuffle dislocations will give rise to local magnetic moments that can provide an alternative route to magnetism in graphene.

Intriguing routes to chaos have been experimentally observed in semiconductor superlattices driven by an ac field. In this work, a theoretical model of time dependent transport in ac driven superlattices is numerically solved. In agreement with experiments, distorted Poincare maps in the quasiperiodic regime are found. They indicate the appearance of very complex attractors and routes to chaos as the amplitude of the AC signal increases. Distorted maps are caused by the discrete well-to-well jump motion of a domain wall during spiky high-frequency self-sustained oscillations of the current., Comment: 10 pages, 4 figures

Self-sustained current oscillations in weakly-coupled superlattices are studied by means of a self-consistent microscopic model of sequential tunneling including boundary conditions naturally. Well-to-well hopping and recycling of charge monopole domain walls produce current spikes (high frequency modulation) superimposed on the oscillation. For highly doped injecting contacts, the self-oscillations are due to dynamics of monopoles. As the contact doping decreases, a lower-frequency oscillatory mode due to recycling and motion of charge dipoles is predicted. For low contact doping, this mode dominates and monopole oscillations disappear. At intermediate doping, both oscillation modes coexist as stable solutions and hysteresis between them is possible., Comment: 4 pages, 4 figures

We propose a selfconsistent microscopic model of vertical sequential tunneling through a multi-quantum well.The model includes a detailed description of the contacts,uses the Transfer Hamiltonian for expressions of the current and it treats the Coulomb interaction within a mean field approximation. We analyze the current density through a double well and a superlattice and study the formation of electric field domains and multistability coming from the Coulomb interaction. Phase diagrams of parameter regions (bias, doping in the heterostructure and in the contacts,etc) where the different solutions exist are given., Comment: 4 pages, 8 Postscript Figures

The continuum limit of a recently-proposed model for charge transport in resonant-tunneling semiconductor superlattices is analyzed. It is described by a nonlinear hyperbolic integrodifferential equation on a one-dimensional spatial support, supplemented by shock and entropy conditions. For appropriate parameter values, a time-periodic solution is found in numerical simulations of the model. An asymptotic theory shows that the time-periodic solution is due to recycling and motion of shock waves representing domain walls connecting regions of the superlattice where the electric field is almost uniform., Comment: 24 pages, Latex. Figures on request. To appear in SIAM J. Appl. Math. 57(6) (1997)