Introducing spatial information into predictive NF-kappa B modelling - an agent-based approach

Nature is governed by local interactions among lower-level sub-units, whether at the cell, organ, organism, or colony level. Adaptive system behaviour emerges via these interactions, which integrate the activity of the sub-units. To understand the system level it is necessary to understand the underlying local interactions. Successful models of local interactions at different levels of biological organisation, including epithelial tissue and ant colonies, have demonstrated the benefits of such 'agent-based' modelling [1-4]. Here we present an agent-based approach to modelling a crucial biological system the intracellular NF-kappa B signalling pathway. The pathway is vital to immune response regulation, and is fundamental to basic survival in a range of species [5-7]. Alterations in pathway regulation underlie a variety of diseases, including atherosclerosis and arthritis. Our modelling of individual molecules, receptors and genes provides a more comprehensive outline of regulatory network mechanisms than previously possible with equation-based approaches [8]. The method also permits consideration of structural parameters in pathway regulation; here we predict that inhibition of NF-kappa B is directly affected by actin filaments of the cytoskeleton sequestering excess inhibitors, therefore regulating steady-state and feedback behaviour

Trapping of Cold Excitons with Laser Light

Optical trapping and manipulation of neutral particles has led to a variety of experiments from stretching DNA-molecules to trapping and cooling of neutral atoms. An exciting recent outgrowth of the technique is an experimental implementation of atom Bose-Einstein condensation. In this paper, we propose and demonstrate laser induced trapping for a new system--a gas of excitons in quantum well structures. We report on the trapping of a highly degenerate Bose gas of excitons in laser induced traps.Comment: 9 pages, 3 figure

The Sendai Virus C Protein Binds the L Polymerase Protein to Inhibit Viral RNA Synthesis

AbstractThe Sendai virus nested set of C proteins which are expressed in an alternative open reading frame from the P mRNA has been shown to downregulate viral RNA synthesis. Utilizing a glutathioneS-transferase (gst) C fusion protein (gstC), we have shown that C protein forms a complex with the L, but not the P, subunit of the viral RNA polymerase. When P, L, and gstC are coexpressed, an oligomer of P, through its interaction with L, is also bound to beads. Since binding of C to L in the P-L complex does not disrupt P binding, the C and P binding sites appear to be different. GstC binding to L occurs only when the proteins are coexpressed in the same cell. The gstC, but not gst, protein inhibits viral transcriptionin vitro,showing that the fusion protein retains biological function. Pulse–chase experiments of the various complexes show that L protein synthesized alone has a half-life of 1.2 hr, which is increased 12.5-fold by binding P, but is not significantly increased by binding gstC. Analyses of complex formation with truncations of L protein show that the C-terminal 1333 amino acids of L are not required for binding C. The dose–response curves show that replication of the genomic DI-H RNA is more sensitive to inhibition by C protein than is the synthesis of DI leader RNA, suggesting that the downregulation of RNA synthesis may be more complex than just the inhibition of the initiation of RNA synthesis

Dissociation of Subjectively Reported and Behaviorally Indexed Mind Wandering by EEG Rhythmic Activity

Inattention to current activity is ubiquitous in everyday situations. Mind wandering is an example of such a state, and its related brain areas have been examined in the literature. However, there is no clear evidence regarding neural rhythmic activities linked to mind wandering. Using a vigilance task with thought sampling and electroencephalography recording, the current study simultaneously examined neural oscillatory activities related to subjectively reported and behaviorally indexed mind wandering. By implementing time-frequency analysis, we found that subjectively reported mind wandering, relative to behaviorally indexed, showed increased gamma band activity at bilateral frontal-central areas. By means of beamformer source imaging, we found subjectively reported mind wandering within the gamma band to be characterized by increased activation in bilateral frontal cortices, supplemental motor area, paracentral cortex and right inferior temporal cortex in comparison to behaviorally indexed mind wandering. These findings dissociate subjectively reported and behaviorally indexed mind wandering and suggest that a higher degree of executive control processes are engaged in subjectively reported mind wandering

Bound on Lorentz- and CPT-Violating Boost Effects for the Neutron

A search for an annual variation of a daily sidereal modulation of the frequency difference between co-located ${}^{129}$Xe and ${}^{3}$He Zeeman masers sets a stringent limit on boost-dependent Lorentz and CPT violation involving the neutron, consistent with no effect at the level of 150 nHz. In the framework of the general Standard-Model Extension, the present result provides the first clean test for the fermion sector of the symmetry of spacetime under boost transformations at a level of $10^{-27}$ GeV.Comment: 4 pages, 1 figur

Hidden Silicon-Vacancy Centers in Diamond

We characterize a high-density sample of negatively charged silicon-vacancy (SiV$^-$) centers in diamond using collinear optical multidimensional coherent spectroscopy. By comparing the results of complementary signal detection schemes, we identify a hidden population of \ce{SiV^-} centers that is not typically observed in photoluminescence, and which exhibits significant spectral inhomogeneity and extended electronic $T_2$ times. The phenomenon is likely caused by strain, indicating a potential mechanism for controlling electric coherence in color-center-based quantum devices

Stress Propagation through Frictionless Granular Material

We examine the network of forces to be expected in a static assembly of hard, frictionless spherical beads of random sizes, such as a colloidal glass. Such an assembly is minimally connected: the ratio of constraint equations to contact forces approaches unity for a large assembly. However, the bead positions in a finite subregion of the assembly are underdetermined. Thus to maintain equilibrium, half of the exterior contact forces are determined by the other half. We argue that the transmission of force may be regarded as unidirectional, in contrast to the transmission of force in an elastic material. Specializing to sequentially deposited beads, we show that forces on a given buried bead can be uniquely specified in terms of forces involving more recently added beads. We derive equations for the transmission of stress averaged over scales much larger than a single bead. This derivation requires the Ansatz that statistical fluctuations of the forces are independent of fluctuations of the contact geometry. Under this Ansatz, the $d(d+1)/2$-component stress field can be expressed in terms of a d-component vector field. The procedure may be generalized to non-sequential packings. In two dimensions, the stress propagates according to a wave equation, as postulated in recent work elsewhere. We demonstrate similar wave-like propagation in higher dimensions, assuming that the packing geometry has uniaxial symmetry. In macroscopic granular materials we argue that our approach may be useful even though grains have friction and are not packed sequentially.=17Comment: 15 pages, 4 figures, revised vertion for Phys. Rev.

Non-linear instability of Kerr-type Cauchy horizons

Using the general solution to the Einstein equations on intersecting null surfaces developed by Hayward, we investigate the non-linear instability of the Cauchy horizon inside a realistic black hole. Making a minimal assumption about the free gravitational data allows us to solve the field equations along a null surface crossing the Cauchy Horizon. As in the spherical case, the results indicate that a diverging influx of gravitational energy, in concert with an outflux across the CH, is responsible for the singularity. The spacetime is asymptotically Petrov type N, the same algebraic type as a gravitational shock wave. Implications for the continuation of spacetime through the singularity are briefly discussed.Comment: 11 pages RevTeX, two postscript figures included using epsf.st