3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy.

We use cryo-electron microscopy to compare 3D shapes of 158 bp long DNA minicircles that differ only in the sequence within an 18 bp block containing either a TATA box or a catabolite activator protein binding site. We present a sorting algorithm that correlates the reconstructed shapes and groups them into distinct categories. We conclude that the presence of the TATA box sequence, which is believed to be easily bent, does not significantly affect the observed shapes.

Bi-planar 2D-to-3D registration in Fourier domain for stereoscopic X-ray motion tracking

In this paper we present a new method to track bonemovements in stereoscopic X-ray image series of the kneejoint. The method is based on two different X-ray imagesets: a rotational series of acquisitions of the stillsubject knee that will allow the tomographicreconstruction of the three-dimensional volume (model),and a stereoscopic image series of orthogonal projectionsas the subject performs movements. Tracking the movementsof bones throughout the stereoscopic image series meansto determine, for each frame, the best pose of everymoving element (bone) previously identified in the 3Dreconstructed model. The quality of a pose is reflectedin the similarity between its simulated projections andthe actual radiographs. We use direct Fourierreconstruction to approximate the three-dimensionalvolume of the knee joint. Then, to avoid the expensivecomputation of digitally rendered radiographs (DRR) forpose recovery, we reformulate the tracking problem in theFourier domain. Under the hypothesis of parallel X-raybeams, we use the central-slice-projection theorem toreplace the heavy 2D-to-3D registration of projections inthe signal domain by efficient slice-to-volumeregistration in the Fourier domain. Focusing onrotational movements, the translation-relevant phaseinformation can be discarded and we only consider scalarFourier amplitudes. The core of our motion trackingalgorithm can be implemented as a classical frame-wiseslice-to-volume registration task. Preliminary results onboth synthetic and real images confirm the validity ofour approach.

Cosmic rays as probes of large extra dimensions and TeV gravity

If there are large extra dimensions and the fundamental Planck scale is at the TeV scale, then the question arises of whether ultrahigh energy cosmic rays might probe them. We study the neutrino-nucleon cross section in these models. The elastic forward scattering is analyzed in some detail, hoping to clarify earlier discussions. We also estimate the black hole production rate. We study energy loss from graviton mediated interactions and conclude that they cannot explain the cosmic ray events above the GZK energy limit. However, these interactions could start horizontal air showers with characteristic profile and at a rate higher than in the standard model.

Induced quantum metric fluctuations and the validity of semiclassical gravity

We propose a criterion for the validity of semiclassical gravity (SCG) which is based on the stability of the solutions of SCG with respect to quantum metric fluctuations. We pay special attention to the two-point quantum correlation functions for the metric perturbations, which contain both intrinsic and induced fluctuations. These fluctuations can be described by the Einstein-Langevin equation obtained in the framework of stochastic gravity. Specifically, the Einstein-Langevin equation yields stochastic correlation functions for the metric perturbations which agree, to leading order in the large N limit, with the quantum correlation functions of the theory of gravity interacting with N matter fields. The homogeneous solutions of the Einstein-Langevin equation are equivalent to the solutions of the perturbed semiclassical equation, which describe the evolution of the expectation value of the quantum metric perturbations. The information on the intrinsic fluctuations, which are connected to the initial fluctuations of the metric perturbations, can also be retrieved entirely from the homogeneous solutions. However, the induced metric fluctuations proportional to the noise kernel can only be obtained from the Einstein-Langevin equation (the inhomogeneous term). These equations exhibit runaway solutions with exponential instabilities. A detailed discussion about different methods to deal with these instabilities is given. We illustrate our criterion by showing explicitly that flat space is stable and a description based on SCG is a valid approximation in that case.

Cosmological perturbations from stochastic gravity

In inflationary cosmological models driven by an inflaton field the origin of the primordial inhomogeneities which are responsible for large-scale structure formation are the quantum fluctuations of the inflaton field. These are usually calculated using the standard theory of cosmological perturbations, where both the gravitational and the inflaton fields are linearly perturbed and quantized. The correlation functions for the primordial metric fluctuations and their power spectrum are then computed. Here we introduce an alternative procedure for calculating the metric correlations based on the Einstein-Langevin equation which emerges in the framework of stochastic semiclassical gravity. We show that the correlation functions for the metric perturbations that follow from the Einstein-Langevin formalism coincide with those obtained with the usual quantization procedures when the scalar field perturbations are linearized. This method is explicitly applied to a simple model of chaotic inflation consisting of a Robertson-Walker background, which undergoes a quasi-de Sitter expansion, minimally coupled to a free massive quantum scalar field. The technique based on the Einstein-Langevin equation can, however, deal naturally with the perturbations of the scalar field even beyond the linear approximation, as is actually required in inflationary models which are not driven by an inflaton field, such as Starobinsky¿s trace-anomaly driven inflation or when calculating corrections due to nonlinear quantum effects in the usual inflaton driven models.

Stability of de Sitter spacetime under isotropic perturbations in semiclassical gravity

A spatially flat Robertson-Walker spacetime driven by a cosmological constant is nonconformally coupled to a massless scalar field. The equations of semiclassical gravity are explicitly solved for this case, and a self-consistent de Sitter solution associated with the Bunch-Davies vacuum state is found (the effect of the quantum field is to shift slightly the effective cosmological constant). Furthermore, it is shown that the corrected de Sitter spacetime is stable under spatially isotropic perturbations of the metric and the quantum state. These results are independent of the free renormalization parameters.

Gravity in the Randall-Sundrum brane world

We discuss the weak gravitational field created by isolated matter sources in the Randall-Sundrum brane world. For the case of a single wall of positive tension, the field stays localized near the wall if the source is stationary. We calculate the leading Kaluza-Klein corrections to the linearized gravitational field of a nonrelativistic spherical object, which is different from the Schwarzschild solution at large distances. In the case of two branes of opposite tension, linearized Brans-Dicke (BD) gravity is recovered on either wall, with different BD parameters. On the wall with positive tension the BD parameter is larger than 3000 provided that the separation between walls is larger than 4 times the AdS radius. The gravitational field due to shadow matter is also considered.

Quantization of AdS3 black holes in external fields: semiclassical results from pure gravity

(2+1)-dimensional anti-de Sitter (AdS) gravity is quantized in the presence of an external scalar field. We find that the coupling between the scalar field and gravity is equivalently described by a perturbed conformal field theory at the boundary of AdS3. This allows us to perform a microscopic computation of the transition rates between black hole states due to absorption and induced emission of the scalar field. Detailed thermodynamic balance then yields Hawking radiation as spontaneous emission, and we find agreement with the semiclassical result, including greybody factors. This result also has application to four and five-dimensional black holes in supergravity.

Modelling the influence of change in fire regime on the local distribution of a Mediterranean pyrophytic plant species (Cistus salviifolius) at its northern range limit

Aims: To assess the potential distribution of an obligate seeder and active pyrophyte, Cistus salviifolius, a vulnerable species in the Swiss Red List; to derive scenarios by changing the fire return interval; and to discuss the results from a conservation perspective. A more general aim is to assess the impact of fire as a natural factor influencing the vegetation of the southern slopes of the Alps. Locations: Alps, southern Switzerland. Methods: Presence-absence data to fit the model were obtained from the most recent field mapping of C. salviifolius. The quantitative environmental predictors used in this study include topographic, climatic and disturbance (fire) predictors. Models were fitted by logistic regression and evaluated by jackknife and bootstrap approaches. Changes in fire regime were simulated by increasing the time-return interval of fire (simulating longer periods without fire). Two scenarios were considered: no fire in the past 15 years; or in the past 35 years. Results: Rock cover, slope, topographic position, potential evapotranspiration and time elapsed since the last fire were selected in the final model. The Nagelkerke R-2 of the model for C. salviifolius was 0.57 and the Jackknife area under the curve evaluation was 0.89. The bootstrap evaluation revealed model robustness. By increasing the return interval of fire by either up to 15 years, or 35 years, the modelled C. salviifolius population declined by 30-40%, respectively. Main conclusions: Although fire plays a significant role, topography and rock cover appear to be the most important predictors, suggesting that the distribution of C. salviifolius in the southern Swiss Alps is closely related to the availability of supposedly competition-free sites, such as emerging bedrock, ridge locations or steep slopes. Fire is more likely to play a secondary role in allowing C. salviifolius to extend its occurrence temporarily, by increasing germination rates and reducing the competition from surrounding vegetation. To maintain a viable dormant seed bank for C. salviifolius, conservation managers should consider carrying out vegetation clearing and managing wild fire propagation to reduce competition and ensure sufficient recruitment for this species.

Modelling diffusion of innovations in a social network

A simple model of diffusion of innovations in a social network with upgrading costs is introduced. Agents are characterized by a single real variable, their technological level. According to local information, agents decide whether to upgrade their level or not, balancing their possible benefit with the upgrading cost. A critical point where technological avalanches display a power-law behavior is also found. This critical point is characterized by a macroscopic observable that turns out to optimize technological growth in the stationary state. Analytical results supporting our findings are found for the globally coupled case.

Modelling the evolution and spread of HIV immune escape mutants.

During infection with human immunodeficiency virus (HIV), immune pressure from cytotoxic T-lymphocytes (CTLs) selects for viral mutants that confer escape from CTL recognition. These escape variants can be transmitted between individuals where, depending upon their cost to viral fitness and the CTL responses made by the recipient, they may revert. The rates of within-host evolution and their concordant impact upon the rate of spread of escape mutants at the population level are uncertain. Here we present a mathematical model of within-host evolution of escape mutants, transmission of these variants between hosts and subsequent reversion in new hosts. The model is an extension of the well-known SI model of disease transmission and includes three further parameters that describe host immunogenetic heterogeneity and rates of within host viral evolution. We use the model to explain why some escape mutants appear to have stable prevalence whilst others are spreading through the population. Further, we use it to compare diverse datasets on CTL escape, highlighting where different sources agree or disagree on within-host evolutionary rates. The several dozen CTL epitopes we survey from HIV-1 gag, RT and nef reveal a relatively sedate rate of evolution with average rates of escape measured in years and reversion in decades. For many epitopes in HIV, occasional rapid within-host evolution is not reflected in fast evolution at the population level.