Crawling motility through the analysis of model locomotors: Two case studies

We study model locomotors on a substrate, which derive their propulsive capabilities from the tangential (viscous or frictional) resistance offered by the substrate. Our aim is to develop new tools and insight for future studies of cellular motility by crawling and of collective bacterial motion. The purely viscous case (worm) is relevant for cellular motility by crawling of individual cells. We re-examine some recent results on snail locomotion in order to assess the role of finely regulated adhesion mechanisms in crawling motility. Our main conclusion is that such regulation, although well documented in several biological systems, is not indispensable to accomplish locomotion driven by internal deformations, provided that the crawler may execute sufficiently large body deformations. Thus, there is no snail theorem. Namely, the crawling analog of the scallop theorem of low Reynolds number hydrodynamics does not hold for snail-like crawlers. The frictional case is obtained by assuming that the viscous coefficient governing tangential resistance forces, which act parallel and in the direction opposite to the velocity of the point to which they are applied, depends on the normal force acting at that point. We combine these surface interactions with inertial effects in order to investigate the mechanisms governing the motility of a bristle-robot. This model locomotor is easily manufactured and has been proposed as an effective tool to replicate and study collective bacterial motility.     

The study of banded spherulite patterns by coupled logistic map lattice model

Banded spherulite patterns are simulated in two dimensions by means of a coupled logistic map lattice model. Both target pattern and spiral pattern which have been proved to be existent experimentally in banded spherulite are obtained by choosing suitable parameters in the model. The simulation results also indicate that the band spacing is decreased with the increase of parameter μ in the logistic map and increased with the increase of the coupling parameter ε, which is quite similar to the results in some experiments. Moreover, the relationship between the parameters and the corresponding patterns is obtained, and the target patterns and spiral patterns are distinguished for a given group of initial values, which may guide the study of banded spherulite.     

Bulk matter physics and its future at the Large Hadron Collider

Measurements at low transverse momentum will be performed at the LHC for studying particle production mechanisms in pp and heavy-ion collisions. Some of the experimental capabilities for bulk matter physics are presented, focusing on tracking elements and particle identification. In order to anticipate the study of baryon production for both colliding systems at multi-TeV energies, measurements for identified species and recent model extrapolations are discussed. Several mechanisms are expected to compete for hadro-production in the low momentum region. For this reason, experimental observables that could be used for investigating multi-parton interactions and help understanding the “underlying event” content in the first pp collisions at the LHC are also mentioned.     

Multi-species simple exclusion processes

A motility mechanism based on a simple exclusion process, where the movement of discrete agents on a lattice is either unbiased (symmetric) or biased (asymmetric) is considered. Estimates of diffusivities from tracking data do not describe the population-level response of the system. This mismatch between the individual-level and population-level behaviour can be resolved by averaging the individual-level mechanism in terms of an expected site occupancy. New insight into simple exclusion processes is obtained by representing the system as a series of interacting subpopulations. This formalism leads to a system of nonlinear advection-diffusion equations which can be interpreted in terms of the agent fluxes. These interactions have consequences for both agent-based modelling and continuum modelling in cell biology, such as tracking subpopulations of cells within a total cell population.     

Polymer confinement and bacterial gliding motility

Cyanobacteria and myxobacteria use slime secretion for gliding motility over surfaces. The slime is produced by the nozzle-like pores located on the bacteria surface. To understand the mechanism of gliding motion and its relation to slime polymerization, we have performed molecular dynamics simulations of a molecular nozzle with growing inside polymer chains. These simulations show that the compression of polymer chains inside the nozzle is a driving force for propulsion. There is a linear relationship between the average nozzle velocity and the chain polymerization rate with a proportionality coefficient dependent on the geometric characteristics of the nozzle such as its length and friction coefficient. This minimal model of the molecular engine was used to explain the gliding motion of bacteria over surfaces.     

Angle-dependent THz tomography – characterization of thin ceramic oxide films for fuel cell applications

A time-resolved THz tomography system for the incidence-angle-dependent three-dimensional characterization of layered structures is presented. The capabilities of the developed system are demonstrated on multi-layer ceramic samples used for solid oxide fuel cells (SOFC). Appropriate methods for determining unknown refractive indices are discussed. It is shown how the angle of incidence of a THz imaging system has a significant influence on measured signals. This fact can be exploited especially in Brewster-angle configurations to enhance the capabilities of any THz tomography system. Data evaluation algorithms are presented. Received: 8 June 2000 / Revised version: 13 September 2000 / Published online: 10 January 2001     

Experimental study of vapor-cell magneto-optical traps for efficient trapping of radioactive atoms

We have studied magneto-optical traps (MOTs) for efficient on-line trapping of radioactive atoms. After discussing a model of the trapping process in a vapor cell and its efficiency, we present the results of detailed experimental studies on Rb MOTs. Three spherical cells of different sizes were used. These cells can be easily replaced, while keeping the rest of the apparatus unchanged: atomic sources, vacuum conditions, magnetic field gradients, sizes and power of the laser beams, detection system. By direct comparison, we find that the trapping efficiency only weakly depends on the MOT cell size. It is also found that the trapping efficiency of the MOT with the smallest cell, whose diameter is equal to the diameter of the trapping beams, is about 40% smaller than the efficiency of larger cells. Furthermore, we also demonstrate the importance of two factors: a long coated tube at the entrance of the MOT cell, used instead of a diaphragm; and the passivation with an alkali vapor of the coating on the cell walls, in order to minimize the losses of trappable atoms. These results guided us in the construction of an efficient large-diameter cell, which has been successfully employed for on-line trapping of Fr isotopes at INFN’s national laboratories in Legnaro, Italy.     

Excitable scale free networks

When a simple excitable system is continuously stimulated by a Poissonian external source, the response function (mean activity versus stimulus rate) generally shows a linear saturating shape. This is experimentally verified in some classes of sensory neurons, which accordingly present a small dynamic range (defined as the interval of stimulus intensity which can be appropriately coded by the mean activity of the excitable element), usually about one or two decades only. The brain, on the other hand, can handle a significantly broader range of stimulus intensity, and a collective phenomenon involving the interaction among excitable neurons has been suggested to account for the enhancement of the dynamic range. Since the role of the pattern of such interactions is still unclear, here we investigate the performance of a scale-free (SF) network topology in this dynamic range problem. Specifically, we study the transfer function of disordered SF networks of excitable Greenberg-Hastings cellular automata. We observe that the dynamic range is maximum when the coupling among the elements is critical, corroborating a general reasoning recently proposed. Although the maximum dynamic range yielded by general SF networks is slightly worse than that of random networks, for special SF networks which lack loops the enhancement of the dynamic range can be dramatic, reaching nearly five decades. In order to understand the role of loops on the transfer function we propose a simple model in which the density of loops in the network can be gradually increased, and show that this is accompanied by a gradual decrease of dynamic range.     

Investigation of transmit and receive performance at the fundamental and third harmonic resonance frequency of a medical ultrasound transducer

In this study, the phenomenon of higher harmonic thickness resonance of a piezoelectric transducer was used to investigate potentially additional sensitivity at the third harmonic frequency for conventional medical transducers. The motivation for this research is that some applications in medical ultrasound (e.g. third harmonic transmit phasing and contrast imaging) need probes which are sensitive around both the fundamental and third harmonic frequencies, and that these higher harmonic thickness modes, although often considered as undesired, might be used beneficially. The novelty aspect in this study is the presented transmit and receive potential at both the fundamental and third harmonic of a conventional cardiac probe with modified electrical tuning. Elements of an experimental PZT-based phased-array probe (f_c = 3 MHz, 64 elements, element width = 0.3 mm, elevation aperture = 13 mm) were electrically retuned with series inductors around the third harmonic resonance frequency at 10 MHz. Hydrophone measurements with 10-MHz-tuned elements showed that, as compared to a conventionally tuned element, the transmit transfer function at the third harmonic increased more than 23 dB, while the sensitivity at the fundamental frequency was only 6 dB lower. Pulse-echo measurements showed that the two-way transfer function of a 10-MHz-tuned element resulted in 20 dB increased sensitivity around the third harmonic as compared to an untuned element. Simulated transfer functions, from both a 1D KLM and 2D finite element model of an element of the experimental array transducer, confirmed the measured sensitivity peaks at the fundamental and third harmonic. In conclusion, this study demonstrated the effect of changing the electrical tuning on a conventional array transducer which increased the sensitivity around the third harmonic resonance frequency, while maintaining good sensitivity at the fundamental frequency.     

Nematic liquid crystals formed by living amoeboid cells

Interacting cells have the ability to form liquid crystal phases: (i) A cluster of a polar nematic liquid crystal is formed by cells which emit molecules for attracting other cells and (ii) an apolar nematic liquid crystal is formed by elongated cells which have an anisotropic steric repulsion. The angle distribution function is predicted by using the characteristics of an automatic controller where the extracellular guiding field is approximated by two-dimensional mean-field. The nematic liquid crystal state is quite well described by the model. Received 7 September 1998 and Received in final form 4 March 1999     

Motility States of Molecular Motors Engaged in a Stochastic Tug-of-War

Intracellular transport is mediated by molecular motors that pull cargos along cytoskeletal filaments. Many cargos move bidirectionally and are transported by two teams of motors which move into opposite directions along the filament. We have recently introduced a stochastic tug-of-war model for this situation. This model describes the motion of the cargo as a Markov process on a two-dimensional state space defined by the numbers of active plus and active minus motors. In spite of its simplicity, this tug-of-war model leads to a complex dependence of the cargo motility on the motor parameters. We present new numerical results for the dependence on the number of involved motors. In addition, we derive a simple and intuitive sharp maxima approximation, from which one obtains the cargo motility state from only four simple inequalities. This approach provides a fast and reliable method to determine the cargo motility.     

On the dynamics of a novel ocean wave energy converter

Buoy-type ocean wave energy converters are designed to exhibit resonant responses when subject to excitation by ocean waves. A novel excitation scheme is proposed which has the potential to improve the energy harvesting capabilities of these converters. The scheme uses the incident waves to modulate the mass of the device in a manner which amplifies its resonant response. To illustrate the novel excitation scheme, a simple one-degree of freedom model is developed for the wave energy converter. This model has the form of a switched linear system. After the stability regime of this system has been established, the model is then used to show that the excitation scheme improves the power harvesting capabilities by 25-65 percent even when amplitude restrictions are present. It is also demonstrated that the sensitivity of the device's power harvesting capabilities to changes in damping becomes much smaller when the novel excitation scheme is used.     

Pressure amorphization through displacive disorder

After classifying amorphous materials according to their topology, we review a recently proposed theory of pressure amorphization (PA) that arises from some degree of displacive disorder while retaining a crystalline topology. That theory is based on the notion that one or more branches of the phonon spectrum become soft and flat with increasing pressure and is illustrated by a simple model that possesses the range of features displayed by many of the materials which undergo PA with displacive disorder. We report the results of Langevin simulations of the simple model which show how the probability of amorphization increases with the number of unit cells in the system and support our theory. We comment on how to generalize the model for the study of real systems. Received 29 march 2002     

Modeling subspecies and the tumor-immune system interaction: Steps toward understanding therapy

A mesoscopic nutrient competition model for cancer growth is generalized to describe the growth of a heterogeneous tumor and the interactions between the tumor and the immune system. Our simulations show that the success of a mutation depends not only on its intrinsic competitive advantages, but also on its location in the tumor mass. It is also shown that the simple killing of tumor cells by immune cells, even when their activity is increased by therapy, is not sufficient to stem tumor growth, but another mechanism (such as pinning) is needed for a successful therapy.     

Vector bosons in heavy-ion collisions at the LHC

Vector bosons become accessible experimental probes in heavy-ion collisions at the LHC. The capabilities of the LHC experiments to perform their measurement are outlined. The focus is given to their utility to study the possible formation and properties of the Quark Gluon Plasma (QGP) in the most central heavy-ion collisions. Their own sensitivity (if any) to the QGP is discussed. Their interest as references to observe multiple QGP sensitive probes is justified.     

Social behavior of bacteria: from physics to complex organization

I describe how bacteria develop complex colonial patterns by utilizing intricate communication capabilities, such as quorum sensing, chemotactic signaling and exchange of genetic information (plasmids) Bacteria do not store genetically all the information required for generating the patterns for all possible environments. Instead, additional information is cooperatively generated as required for the colonial organization to proceed. Each bacterium is, by itself, a biotic autonomous system with its own internal cellular informatics capabilities (storage, processing and assessments of information). These afford the cell certain plasticity to select its response to biochemical messages it receives, including self-alteration and broadcasting messages to initiate alterations in other bacteria. Hence, new features can collectively emerge during self-organization from the intra-cellular level to the whole colony. Collectively bacteria store information, perform decision make decisions (e.g. to sporulate) and even learn from past experience (e.g. exposure to antibiotics)-features we begin to associate with bacterial social behavior and even rudimentary intelligence. I also take Schrdinger’s’ “feeding on negative entropy” criteria further and propose that, in addition organisms have to extract latent information embedded in the environment. By latent information we refer to the non-arbitrary spatio-temporal patterns of regularities and variations that characterize the environmental dynamics. In other words, bacteria must be able to sense the environment and perform internal information processing for thriving on latent information embedded in the complexity of their environment. I then propose that by acting together, bacteria can perform this most elementary cognitive function more efficiently as can be illustrated by their cooperative behavior.     

Non-trivial effect of the in-plane shear elasticity on the phase transitions of fixed-connectivity meshwork models

We numerically study the phase structure of two types of triangulated spherical surface models, which includes an in-plane shear energy in the Hamiltonian, and we found that the phase structure of the models is considerably influenced by the presence of the in-plane shear elasticity. The models undergo a first-order collapsing transition and a first-order (or second-order) transition of surface fluctuations; the latter transition was reported to be of second-order in the first model without the in-plane shear energy. This leads us to conclude that the in-plane elasticity strengthens the transition of surface fluctuations. We also found that the in-plane elasticity decreases the variety of phases in the second model without the in-plane energy. The Hamiltonian of the first model is given by a linear combination of the Gaussian bond potential, a one-dimensional bending energy, and the in-plane shear energy. The second model is obtained from the first model by replacing the Gaussian bond potential with the Nambu-Goto potential, which is defined by the summation over the area of triangles.     

Regime independent coupled-wave equations in anisotropic photorefractive media

An extension to coupled wave theory suitable for all regimes of diffraction is presented. The model assumes that the refractive index grating has an arbitrary profile in one direction and is periodic (but not necessarily sinusoidal) in the other. Higher order diffracted terms are considered and appropriate mismatch terms dealt with. It is shown that this model is analytically equivalent to both the Bragg and Raman–Nath regime coupling models under an appropriate set of assumptions. This model is applied to cases such as optical coupling in liquid crystal cells with photoconductive layers. Its predictions are successfully compared to finite element simulations of the full Maxwell’s equations.     

Nose-cone calorimeter: PHENIX forward upgrade

PHENIX is a high rate experiment efficient at measuring rare processes, but has limited acceptance in azimuth and pseudorapidity (η). The Nose Cone Calorimeter (NCC), a W–Si sampling calorimeter in the region of 0.9<η<3, is one of the upgrades which will significantly increase coverage in both azimuth and pseudorapidity. The NCC will expand PHENIX’s precision measurements of electromagnetic probes in η, reconstruct jets, perform a wide scope of correlation measurements, and enhance triggering capabilities. The detector will significantly contribute to measurements of γ-jet correlations, quarkonia production, and low-x nuclear structure functions. This report discusses details of the detector design and its performance concerning a sample of the physics topics which will benefit from the NCC. In view of recent funding difficulties, outlook of the activities is discussed.