Polaron and Bipolaron Defects in a Charge Density Wave: a Model for Lightly Doped BaBiO3

BaBiO3 is a prototype ``charge ordering system'' forming interpenetrating sublattices with nominal valence Bi(3+) and Bi(5+). It can also be regarded as a three-dimensional version of a Peierls insulator, the insulating gap being a consequence of an ordered distortion of oxygen atoms. When holes are added to BaBiO3 by doping, it remains insulating until a very large hole concentration is reached, at which point it becomes superconducting. The mechanism for insulating behavior of more lightly-doped samples is formation of small polarons or bipolarons. These are self-organized point defects in the Peierls order parameter, which trap carriers in bound states inside the Peierls gap. We calculate properties of the polarons and bipolarons using the Rice-Sneddon model. Bipolarons are the stable defect; the missing pair of electrons come from an empty midgap state built from the lower Peierls band. Each bipolaron distortion also pulls down six localized states below the bottom of the unoccupied upper Peierls band. The activation energy for bipolaron hopping is estimated.Comment: 9 pages with 8 embedded figures. See also cond-mat/0108089, a paper of 5 pages on the related topic of self-trapped excitons in BaBiO

Focal adhesions as mechanosensors: the two-spring model

Adhesion-dependent cells actively sense the mechanical properties of their environment through mechanotransductory processes at focal adhesions, which are integrin-based contacts connecting the extracellular matrix to the cytoskeleton. Here we present first steps towards a quantitative understanding of focal adhesions as mechanosensors. It has been shown experimentally that high levels of force are related to growth of and signaling at focal adhesions. In particular, activation of the small GTPase Rho through focal adhesions leads to the formation of stress fibers. Here we discuss one way in which force might regulate the internal state of focal adhesions, namely by modulating the internal rupture dynamics of focal adhesions. A simple two-spring model shows that the stiffer the environment, the more efficient cellular force is built up at focal adhesions by molecular motors interacting with the actin filaments.Comment: Latex, 17 pages, 5 postscript figures include

Molecular and cellular factors control signal transduction via switchable allosteric modulator proteins (SAMPs)

Background: Rap proteins from Bacilli directly target response regulators of bacterial two-component systems and modulate their activity. Their effects are controlled by binding of signaling peptides to an allosteric site. Hence Raps exemplify a class of monomeric signaling receptors, which we call switchable allosteric modulator proteins (SAMPs). These proteins have potential applications in diverse biomedical and biotechnical settings, but a quantitative understanding of the impact of molecular and cellular factors on signal transduction is lacking. Here we introduce mathematical models that elucidate how signals are propagated though the network upon receptor stimulation and control the level of active response regulator. Results: Based on a systematic parameter analysis of the models, we show that key features of the dose-response behavior at steady state are controlled either by the molecular properties of the modulator or the signaling context. In particular, we find that the biochemical activity (i.e. non-enzymatic vs. enzymatic) and allosteric properties of the modulator control the response amplitude. The Hill coefficient and the EC50 are controlled in addition by the relative ligand affinities. By tuning receptor properties, either graded or more switch-like (memory-less) response functions can be fashioned. Furthermore, we show that other contextual factors (e.g. relative concentrations of network components and kinase activity) have a substantial impact on the response, and we predict that there exists a modulator concentration which is optimal for response amplitude. Conclusion: We discuss data on Rap-Phr systems in B. subtilis to show how our models can contribute to an integrated view of SAMP signaling by combining biochemical, structural and physiological insights. Our results also suggest that SAMPs could be evolved or engineered to implement diverse response behaviors. However—without additional regulatory controls—they can generate rather variable cellular outputs

Focal adhesions as mechanosensors: the two-spring model

Adhesion-dependent cells actively sense the mechanical properties of their environment through mechanotransductory processes at focal adhesions, which are integrin-based contacts connecting the extracellular matrix to the cytoskeleton. Here we present first steps towards a quantitative understanding of focal adhesions as mechanosensors. It has been shown experimentally that high levels of force are related to growth of and signaling at focal adhesions. In particular, activation of the small GTPase Rho through focal adhesions leads to the formation of stress fibers. Here we discuss one way in which force might regulate the internal state of focal adhesions, namely by modulating the internal rupture dynamics of focal adhesions. A simple two-spring model shows that the stiffer the environment, the more efficient cellular force is built up at focal adhesions by molecular motors interacting with the actin filaments.Comment: Latex, 17 pages, 5 postscript figures include

Effect of adhesion geometry and rigidity on cellular force distributions

The behaviour and fate of tissue cells is controlled by the rigidity and geometry of their adhesive environment, possibly through forces localized to sites of adhesion. We introduce a mechanical model that predicts cellular force distributions for cells adhering to adhesive patterns with different geometries and rigidities. For continuous adhesion along a closed contour, forces are predicted to be localized to the corners. For discrete sites of adhesion, the model predicts the forces to be mainly determined by the lateral pull of the cell contour. With increasing distance between two neighboring sites of adhesion, the adhesion force increases because cell shape results in steeper pulling directions. Softer substrates result in smaller forces. Our predictions agree well with experimental force patterns measured on pillar assays.Comment: 4 pages, Revtex with 4 figure

Self-Trapped Exciton Defects in a Charge Density Wave: Electronic Excitations of BaBiO3

In the previous paper, it was shown that holes doped into BaBiO3 self-trap as small polarons and bipolarons. These point defects are energetically favorable partly because they undo locally the strain in the charge-density-wave (Peierls insulator) ground state. In this paper the neutral excitations of the same model are discussed. The lowest electronic excitation is predicted to be a self-trapped exciton, consisting of an electron and a hole located on adjacent Bi atoms. This excitation has been seen experimentally (but not identified as such) via the Urbach tail in optical absorption, and the multi-phonon spectrum of the ``breathing mode'' seen in Raman scattering. These two phenomena occur because of the Franck-Condon effect associated with oxygen displacement in the excited state.Comment: 5 pages with 7 embedded figures. See also cond-mat/0108089 on polarons and bipolarons in BaBiO3 contains background informatio

Topological (Sliced) Doping of a 3D Peierls System: Predicted Structure of Doped BaBiO3

At hole concentrations below x=0.4, Ba_(1-x)K_xBiO_3 is non-metallic. At x=0, pure BaBiO3 is a Peierls insulator. Very dilute holes create bipolaronic point defects in the Peierls order parameter. Here we find that the Rice-Sneddon version of Peierls theory predicts that more concentrated holes should form stacking faults (two-dimensional topological defects, called slices) in the Peierls order parameter. However, the long-range Coulomb interaction, left out of the Rice-Sneddon model, destabilizes slices in favor of point bipolarons at low concentrations, leaving a window near 30% doping where the sliced state is marginally stable.Comment: 6 pages with 5 embedded postscript figure

Memory in Microbes: Quantifying History-Dependent Behavior in a Bacterium

Memory is usually associated with higher organisms rather than bacteria. However, evidence is mounting that many regulatory networks within bacteria are capable of complex dynamics and multi-stable behaviors that have been linked to memory in other systems. Moreover, it is recognized that bacteria that have experienced different environmental histories may respond differently to current conditions. These “memory” effects may be more than incidental to the regulatory mechanisms controlling acclimation or to the status of the metabolic stores. Rather, they may be regulated by the cell and confer fitness to the organism in the evolutionary game it participates in. Here, we propose that history-dependent behavior is a potentially important manifestation of memory, worth classifying and quantifying. To this end, we develop an information-theory based conceptual framework for measuring both the persistence of memory in microbes and the amount of information about the past encoded in history-dependent dynamics. This method produces a phenomenological measure of cellular memory without regard to the specific cellular mechanisms encoding it. We then apply this framework to a strain of Bacillus subtilis engineered to report on commitment to sporulation and degradative enzyme (AprE) synthesis and estimate the capacity of these systems and growth dynamics to ‘remember’ 10 distinct cell histories prior to application of a common stressor. The analysis suggests that B. subtilis remembers, both in short and long term, aspects of its cell history, and that this memory is distributed differently among the observables. While this study does not examine the mechanistic bases for memory, it presents a framework for quantifying memory in cellular behaviors and is thus a starting point for studying new questions about cellular regulation and evolutionary strategy