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Multistate genetic switches play a crucial role during embryonic development and tumorigenesis. An archetypical example is the three-way switch regulating epithelial-hybrid-mesenchymal transitions. We devise a special WKB-based approach to investigate white Gaussian and shot noise effects on three-way switches, and construct an effective landscape in good quantitative agreement with stochastic simulations. This approach allows efficient analytical or numerical calculation of the landscape contours, the optimal path, and the state relative stability for general multicomponent multistate switches.

Under sublethal antibiotics concentrations, the statistics of collectively swarming Bacillus subtilis transitions from normal to anomalous, with a heavy-tailed speed distribution and a two-step temporal correlation of velocities. The transition is due to changes in the properties of the bacterial motion and the formation of a motility-defective subpopulation that self-segregates into regions. As a result, both the colonial expansion and the growth rate are not affected by antibiotics. This phenomenon suggests a new strategy bacteria employ to fight antibiotic stress.

We propose a novel method for the detection and sorting of recorded neural spikes using wavelet packets. We employ the best basis via the Shannon's information cost function and local discriminant basis using mutual information. We demonstrate the efficiency of the method on data recorded in vitro from 2D neural networks. We show that our method is superior both in separation from noise and in identifying superimposed spikes.

A simple model with a novel type of dynamics is introduced in order to investigate the emergence of self-ordered motion in systems of particles with biologically motivated interaction. In our model particles are driven with a constant absolute velocity and at each time step assume the average direction of motion of the particles in their neighborhood with some random perturbation $(\ensuremath{\eta})$ added. We present numerical evidence that this model results in a kinetic phase transition from no transport (zero average velocity, $|{\mathbf{v}}_{a}|\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}0$) to finite net transport through spontaneous symmetry breaking of the rotational symmetry. The transition is continuous, since $|{\mathbf{v}}_{a}|$ is found to scale as $({\ensuremath{\eta}}_{c}\ensuremath{-}\ensuremath{\eta}{)}^{\ensuremath{\beta}}$ with $\ensuremath{\beta}\ensuremath{\simeq}0.45$.

The various human brain tasks are performed at different locations and time scales. Yet, we discovered the existence of time-invariant (above an essential time scale) partitioning of the brain activity into personal state-specific frequency bands. For that, we perform temporal and ensemble averaging of best wavelet packet bases from multi-electrode EEG recordings. These personal frequency-bands provide new templates for quantitative analyses of brain function, e.g., normal vs. epileptic activity., 4 pages, 4 figures (color), Phys. Rev. Lett. (in-press), minor English style changes

Utilization of a clustering algorithm on neuronal spatiotemporal correlation matrices recorded during a spontaneous activity of in vitro networks revealed the existence of hidden correlations: the sequence of synchronized bursting events (SBEs) is composed of statistically distinguishable subgroups each with its own distinct pattern of interneuron spatiotemporal correlations. These findings hint that each of the SBE subgroups can serve as a template for coding, storage, and retrieval of a specific information.

New quantified observables of complexity are identified and utilized to study sequences (time series) recorded during the spontaneous activity of different size cultured networks. The sequence is mapped into a tiled time-frequency domain that maximizes the information about local time-frequency resolutions. The sequence regularity is associated with the domain homogeneity and its complexity with its local and global variations. Shuffling the recorded sequence lowers its complexity down to artificially constructed ones. The new observables are utilized to identify self-regulation motifs in observed complex network activity.

Ordinarily, in vitro neurons self-organize into homogeneous networks of single neurons linked by dendrites and axons. We show that under special conditions they can also self-organize into neuronal clusters, which are linked by bundles of axons. Multielectrode array measurement reveals that the clusterized networks are also electrically active and exhibit synchronized bursting events similar to those observed in the homogeneous networks. From time-lapse recording, we deduced the features required for the neuronal clusterized versus homogeneous self-organization and developed a simple model for testing their validity.

We measured the long term spontaneous electrical activity of neuronal networks with different sizes, grown on lithographically prepared substrates and recorded with multi-electrode-array technology. The time sequences of synchronized bursting events were used to characterize network dynamics. All networks exhibit scale-invariant Levy distributions and long-range correlations. These observations suggest that different-size networks self-organize to adjust their activities over many time scales. As predictions of current models differ from our observations, this calls for revised models.

Bacterial colonies can develop chiral morphology in which the colony consists of twisted branches, all with the same handedness. Microscopic observations of the chiral growth are presented. We propose that the observed (macroscopic) chirality results from the microscopic chirality of the flagella (via handedness in tumbling) together with orientation interaction between the bacteria. The above assumptions are tested using a generalized version of the communicating walkers model.

The intermittent-type chaos occurring in rf- and dc-current-driven Josephson junctions is investigated. A simple physical model is proposed and is used for an analytic calculation of the power spectrum. The latter has a broadband part which decays algebraically at high frequencies. Comparison with numerical results shows good agreement. Further application and generalizations of this approach are outlined.

We impose anisotropy in modified Hele-Shaw experiments by engraving a grid on one of the plates. Without anisotropy, the dynamics is dominated by tip bifurcations leading to a branched ramified structure. With anisotropy, a dendritic pattern forms, in qualitative agreement with the prediction of recent studies of local growth models.

The current and voltage fluctuations in a normal tunnel junction are calculated from microscopic theory. The power spectrum can deviate from the familiar Johnson-Nyquist form when the self-capacitance of the junction is small, at low temperatures permitting experimental verification. The deviation reflects the discrete nature of the charge transfer across the junction and should be present in a wide class of similar systems.

It is shown that the dynamically selected velocity and tip radius of dendrites in the boundary-layer model of solidification have the special values which permit the existence of steady-state needle-crystal solutions. This result, in conjunction with considerations of stability, provides new insight concerning the validity of the marginal-stability hypothesis.

A phenomenological model of dendritic solidification incorporating interfacial kinetics, crystalline anisotropy, and a local approximation for the dynamics of the thermal diffusion field is proposed. The preliminary results are in qualitative agreement with natural dendritelike pattern formation.

We distinguish the roles of the Laplace and diffusion fields in electrochemical deposition during growth of the dense-branching morphology. The shape of the growth is controlled by the Laplace field; the microscopic morphology is characteristic of diffusion-field-controlled growth; and the branch size length scale is hypothesized to be the result of the interplay of the two fields. The branching rate varies with system parameters so as to select an apparently constant interfacial velocity.

We report an experiment in the Ohmically-limited electrochemical deposition of zinc which explicitly probes the link between microscopic structure and macroscopic morphology in the development of interfacial patterns far from equilibrium. We report a previously unrecognized transition region between diffusion-limited aggregation and dendritic growth; analysis of the microstructure suggests mechanisms for the macroscopic expression of crystalline anisotropy. We also report the discovery of a metastable crystalline form of zinc produced during electrodeposition.

We study ultrasmall Josephson junctions using the coherent picture to describe the pair dynamics and the semiclassical approach for the quasiparticles. We find that the dynamics depends crucially on the ratio of the superconducting gap energy \ensuremath{\Delta}(T) to the charging energy ${\mathrm{e}}^{2}$/2C. The pair ``Bloch oscillations'' can be practically observed when 2\ensuremath{\Delta}(T)g${\mathrm{e}}^{2}$/2C; for 2\ensuremath{\Delta}(T)${\mathrm{e}}^{2}$/2C the ${\mathrm{I}}_{\mathrm{dc}/\mathrm{e}}$ oscillations due to quasiparticle tunneling can be observed. We discuss under what conditions the I-V characteristic will be S-shaped, exhibiting both oscillations at different values of the current.

The I-V characteristics of two serially coupled small tunnel junctions (about ${10}^{\mathrm{\ensuremath{-}}18}$--${10}^{\mathrm{\ensuremath{-}}19}$ F capacitances) are measured at 4 K. The junctions are formed using a scanning-tunneling microscope to probe a metal droplet deposited on an oxidized metal substrate. Sharply defined Coulumb steps due to single-electron dynamics, oxide polarization, and nonlinear (voltage dependent) tunneling rates are observed. The results show very good quantitative agreement with theoretical calculations based on the semiclassical picture.

We present experimental evidence of a distinct dense branching morphology as a fundamental pattern for diffusion-controlled interfacial growth. The dense branching morphology is characterized by its circular envelope modulated by leading branch tips. The development of this pattern in two dimensions is studied in a Hele-Shaw cell and in amorphous annealing. We find agreement between the Hele-Shaw experiment and a linear stability analysis including a kinetic term.