Dual Magnetic Separator for TRIμ\muP

The TRI$\mu$P facility, under construction at KVI, requires the production and separation of short-lived and rare isotopes. Direct reactions, fragmentation and fusion-evaporation reactions in normal and inverse kinematics are foreseen to produce nuclides of interest with a variety of heavy-ion beams from the superconducting cyclotron AGOR. For this purpose, we have designed, constructed and commissioned a versatile magnetic separator that allows efficient injection into an ion catcher, i.e., gas-filled stopper/cooler or thermal ionizer, from which a low energy radioactive beam will be extracted. The separator performance was tested with the production and clean separation of $^{21}$Na ions, where a beam purity of 99.5% could be achieved. For fusion-evaporation products, some of the features of its operation as a gas-filled recoil separator were tested.Comment: accepted by Nucl.Instr. Meth., final versio

Concerning the quark condensate

A continuum expression for the trace of the massive dressed-quark propagator is used to explicate a connection between the infrared limit of the QCD Dirac operator's spectrum and the quark condensate appearing in the operator product expansion, and the connection is verified via comparison with a lattice-QCD simulation. The pseudoscalar vacuum polarisation provides a good approximation to the condensate over a larger range of current-quark masses.Comment: 7 pages, LaTeX2e, revtex

Adaptive gene regulatory networks

Regulatory interactions between genes show a large amount of cross-species variability, even when the underlying functions are conserved: There are many ways to achieve the same function. Here we investigate the ability of regulatory networks to reproduce given expression levels within a simple model of gene regulation. We find an exponentially large space of regulatory networks compatible with a given set of expression levels, giving rise to an extensive entropy of networks. Typical realisations of regulatory networks are found to share a bias towards symmetric interactions, in line with empirical evidence.Comment: 5 pages RevTe

Alternative mechanism for bacteriophage adsorption to the motile bacterium Caulobacter crescentus

2D and 3D cryo-electron microscopy, together with adsorption kinetics assays of ϕCb13 and ϕCbK phage-infected Caulobacter crescentus, provides insight into the mechanisms of infection. ϕCb13 and ϕCbK actively interact with the flagellum and subsequently attach to receptors on the cell pole. We present evidence that the first interaction of the phage with the bacterial flagellum takes place through a filament on the phage head. This contact with the flagellum facilitates concentration of phage particles around the receptor (i.e., the pilus portals) on the bacterial cell surface, thereby increasing the likelihood of infection. Phage head filaments have not been well characterized and their function is described here. Phage head filaments may systematically underlie the initial interactions of phages with their hosts in other systems and possibly represent a widespread mechanism of efficient phage propagation

Confinement in the Deconfined Phase: A numerical study with a cluster algorithm

We have previously found analytically a very unusual and unexpected form of confinement in SU(3) Yang-Mills theory. This confinement occurs in the deconfined phase of the theory. The free energy of a single static test quark diverges, even though it is contained in deconfined bulk phase and there is no QCD string present. This phenomenon occurs in cylindrical volumes with a certain choice of spatial boundary conditions. We examine numerically an effective model for the Yang-Mills theory and, using a cluster algorithm, we observe this unusual confinement. We also find a new way to determine the interface tension of domain walls separating distinct bulk phases.Comment: LaTex, 14 pages, 4 figure

Pay What You Want as a Marketing Strategy in Monopolistic and Competitive Markets

Pay What You Want (PWYW) can be an attractive marketing strategy to price discriminate between fair-minded and selfish customers, to fully penetrate a market without giving away the product for free, and to undercut competitors that use posted prices. We report on laboratory experiments that identify causal factors determining the willingness of buyers to pay voluntarily under PWYW. Furthermore, to see how competition affects the viability of PWYW, we implement markets in which a PWYW seller competes with a traditional seller. Finally, we endogenize the market structure and let sellers choose their pricing strategy. The experimental results show that outcome-based social preferences and strategic considerations to keep the seller in the market can explain why and how much buyers pay voluntarily to a PWYW seller. We find that PWYW can be viable in isolation, but it is less successful as a competitive strategy because it does not drive traditional posted-price sellers out of the market. Instead, the existence of a posted-price competitor reduces buyers’ payments and prevents the PWYW seller from fully penetrating the market. If given the choice, the majority of sellers opt for setting a posted price rather than a PWYW pricing. We discuss the implications of these results for the use of PWYW as a marketing strategy

A priority paper for the societal and ethical aspects of synthetic biology

As synthetic biology develops into a promising science and engineering field, we need to have clear ideas and priorities regarding its safety, security, ethical and public dialogue implications. Based on an extensive literature search, interviews with scientists, social scientists, a 4 week long public e-forum, and consultation with several stakeholders from science, industry and civil society organisations, we compiled a list of priority topics regarding societal issues of synthetic biology for the years ahead. The points presented here are intended to encourage all stakeholders to engage in the prioritisation of these issues and to participate in a continuous dialogue, with the ultimate goal of providing a basis for a multi-stakeholder governance in synthetic biology. Here we show possible ways to solve the challenges to synthetic biology in the field of safety, security, ethics and the science–public interface

The land use change impact of biofuels consumed in the EU: Quantification of area and greenhouse gas impacts

Biofuels are promoted as an option to reduce climate emissions from the transport sector. As most biofuels are currently produced from land based crops, there is a concern that the increased consumption of biofuels requires agricultural expansion at a global scale, leading to additional carbon emissions. This effect is called Indirect Land Use Change, or ILUC. The EU Renewable Energy Directive (2009/28/EC) directed the European Commission to develop a methodology to account for the ILUC effect. The current study serves to provide new insights to the European Commission and other stakeholders about these indirect carbon and land impacts from biofuels consumed in the EU, with more details on production processes and representation of individual feedstocks than was done before. ILUC cannot be observed or measured in reality, because it is entangled with a large number of other changes in agricultural markets at both global and local levels. The effect can only be estimated through the use of models. The current study is part of a continuous effort to improve the understanding and representation of ILUC

Estimating Nuisance Parameters in Inverse Problems

Many inverse problems include nuisance parameters which, while not of direct interest, are required to recover primary parameters. Structure present in these problems allows efficient optimization strategies - a well known example is variable projection, where nonlinear least squares problems which are linear in some parameters can be very efficiently optimized. In this paper, we extend the idea of projecting out a subset over the variables to a broad class of maximum likelihood (ML) and maximum a posteriori likelihood (MAP) problems with nuisance parameters, such as variance or degrees of freedom. As a result, we are able to incorporate nuisance parameter estimation into large-scale constrained and unconstrained inverse problem formulations. We apply the approach to a variety of problems, including estimation of unknown variance parameters in the Gaussian model, degree of freedom (d.o.f.) parameter estimation in the context of robust inverse problems, automatic calibration, and optimal experimental design. Using numerical examples, we demonstrate improvement in recovery of primary parameters for several large- scale inverse problems. The proposed approach is compatible with a wide variety of algorithms and formulations, and its implementation requires only minor modifications to existing algorithms.Comment: 16 pages, 5 figure

A model of membrane contraction predicting initiation and completion of bacterial cell division

Bacterial cell division involves a complex and dynamic sequence of events whereby polymers of the protein FtsZ assemble at the division plane and rearrange to achieve the goal of contracting the cell membrane at the site of cell division, thus dividing the parent cell into two daughter cells. We present a mathematical model (which we refer to as CAM-FF: Critical Accumulation of Membrane-bound FtsZ Fibres) of the assembly of the contractile ring in terms of the accumulation of short linear polymers of FtsZ that associate and dissociate from the cell membrane. In prokaryotes, the biochemical function of FtsZ is thought to underpin the assembly and at least the initial kinetic force of ring contraction. Our model extends earlier work of Surovtsev et al. [PLoS Comput. Biol., 2008, 4, e1000102] by adding (i) the kinetics of FtsZ accumulation on cell membrane anchor proteins and (ii) the physical forces required to deform the cell against its surface tension. Moreover, we provide a more rigorous treatment of intracellular diffusion and we revise some of the model parameter values in light of the experimental evidence now available. We derive a critical contraction parameter which links the chemical population dynamics of membrane-bound FtsZ molecules to the force of contraction. Using this parameter as a tool to predict the ability of the cell to initiate division, we are able to predict the division outcome in cells depleted of key FtsZ-binding proteins