Fluorescence-based strategies to investigate the structure and dynamics of aptamer-ligand complexes

This work was funded by the Scottish Universities Physics Alliance (SUPA), the University of St Andrews, the Engineering and Physical Sciences ResearchCouncil (EPSRC), the Canadian Institutes of Health Research (CIHR). Funding for open access charge: University of St Andrews.In addition to the helical nature of double-stranded DNA and RNA, single-stranded oligonucleotides can arrange themselves into tridimensional structures containing loops, bulges, internal hairpins and many other motifs. This ability has been used for more than two decades to generate oligonucleotide sequences, so-called aptamers, that can recognize certain metabolites with high affinity and specificity. More recently, this library of artificially-generated nucleic acid aptamers has been expanded by the discovery that naturally occurring RNA sequences control bacterial gene expression in response to cellular concentration of a given metabolite. The application of fluorescence methods has been pivotal to characterize in detail the structure and dynamics of these aptamer-ligand complexes in solution. This is mostly due to the intrinsic high sensitivity of fluorescence methods and also to significant improvements in solid-phase synthesis, post-synthetic labelling strategies and optical instrumentation that took place during the last decade. In this work, we provide an overview of the most widely employed fluorescence methods to investigate aptamer structure and function by describing the use of aptamers labelled with a single dye in fluorescence quenching and anisotropy assays. The use of 2-aminopurine as a fluorescent analog of adenine to monitor local changes in structure and fluorescence resonance energy transfer (FRET) to follow long-range conformational changes is also covered in detail. The last part of the review is dedicated to the application of fluorescence techniques based on single-molecule microscopy, a technique that has revolutionized our understanding of nucleic acid structure and dynamics. We finally describe the advantages of monitoring ligand-binding and conformational changes, one molecule at a time, to decipher the complexity of regulatory aptamers and summarize the emerging folding and ligand-binding models arising from the application of these single-molecule FRET microscopy techniques.Publisher PDFPeer reviewe

Towards conformant models of automated electric vehicles

Automated driving is one of the major tendencies in last decades, and it is presented as a reliable option to improve comfort during driving, including disable and elder in society and increasing persons safety in roads. This last topic produces the question how is it possible to verify planning and control algorithms for a reliable commercial use of this technology. The question can be answered from two perspective: experimental or formal methods, where the formal one is selected as the most robust between both. Hence, the current work presents a case study verification in automated driving for lane change and double lane change maneuvers, using as basis a trace conformance method presented in [1]. The verification method is performed in Dynacar as a precise multibody simulator tuned for a commercial Renault Twizy vehicle.H2020 UnCoVerCPS Project with grant number 643921

Validation of Slosh Model Parameters and Anti-Slosh Baffle Designs of Propellant Tanks by Using Lateral Slosh Testing

The slosh dynamics of propellant tanks can be represented by an equivalent mass-pendulum-dashpot mechanical model. The parameters of this equivalent model, identified as slosh mechanical model parameters, are slosh frequency, slosh mass, and pendulum hinge point location. They can be obtained by both analysis and testing for discrete fill levels. Anti-slosh baffles are usually needed in propellant tanks to control the movement of the fluid inside the tank. Lateral slosh testing, involving both random excitation testing and free-decay testing, are performed to validate the slosh mechanical model parameters and the damping added to the fluid by the anti-slosh baffles. Traditional modal analysis procedures were used to extract the parameters from the experimental data. Test setup of sub-scale tanks will be described. A comparison between experimental results and analysis will be presented

Entropy in the Classical and Quantum Polymer Black Hole Models

We investigate the entropy counting for black hole horizons in loop quantum gravity (LQG). We argue that the space of 3d closed polyhedra is the classical counterpart of the space of SU(2) intertwiners at the quantum level. Then computing the entropy for the boundary horizon amounts to calculating the density of polyhedra or the number of intertwiners at fixed total area. Following the previous work arXiv:1011.5628, we dub these the classical and quantum polymer models for isolated horizons in LQG. We provide exact micro-canonical calculations for both models and we show that the classical counting of polyhedra accounts for most of the features of the intertwiner counting (leading order entropy and log-correction), thus providing us with a simpler model to further investigate correlations and dynamics. To illustrate this, we also produce an exact formula for the dimension of the intertwiner space as a density of "almost-closed polyhedra".Comment: 24 page

The Quantum Transverse Field Ising Model on an Infinite Tree from Matrix Product States

We give a generalization to an infinite tree geometry of Vidal's infinite time-evolving block decimation (iTEBD) algorithm for simulating an infinite line of quantum spins. We numerically investigate the quantum Ising model in a transverse field on the Bethe lattice using the Matrix Product State ansatz. We observe a second order phase transition, with certain key differences from the transverse field Ising model on an infinite spin chain. We also investigate a transverse field Ising model with a specific longitudinal field. When the transverse field is turned off, this model has a highly degenerate ground state as opposed to the pure Ising model whose ground state is only doubly degenerate.Comment: 28 pages, 23 figures, PDFlate

A signature of quantum gravity at the source of the seeds of cosmic structure?

This article reviews a recent work by a couple of colleagues and myself about the shortcomings of the standard explanations of the quantum origin of cosmic structure in the inflationary scenario, and a proposal to address them. The point it that in the usual accounts the inhomogeneity and anisotropy of our universe seem to emerge from an exactly homogeneous and isotropic initial state through processes that do not break those symmetries. We argued that some novel aspect of physics must be called upon to able to address the problem in a fully satisfactory way. The proposed approach is inspired on Penrose's ideas regarding an quantum gravity induced, real and dynamical collapse of the wave function.Comment: LateX, (jpconference macros), Prepared for the proceedings the Third International Workshop DICE 2006, " Quantum Mechanics between decoherence and Determinism

Perspectives on Quantum Gravity Phenomenology

The idea that quantum gravity manifestations would be associated with a violation of Lorentz invariance is very strongly bounded and faces serious theoretical challenges. Other related ideas seem to be drowning in interpretational quagmires. This leads us to consider alternative lines of thought for such phenomenological search. We discuss the underlying viewpoints and briefly mention their possible connections with other current theoretical ideas.Comment: Latex, 23 page

The Seeds of Cosmic structure as a door to New Physics

There is something missing in our understanding of the origin of the seeds of Cosmic Structuture. The fact that the fluctuation spectrum can be extracted from the inflationary scenario through an analysis that involves quantum field theory in curved space-time, and that it coincides with the observational data has lead to a certain complacency in the community, which prevents the critical analysis of the obscure spots in the derivation. The point is that the inhomogeneity and anisotropy of our universe seem to emerge from an exactly homogeneous and isotropic initial state through processes that do not break those symmetries. This article gives a brief recount of the problems faced by the arguments based on established physics, which comprise the point of view held by a large majority of researchers in the field. The conclusion is that we need some new physics to be able to fully address the problem. The article then exposes one avenue that has been used to address the central issue and elaborates on the degree to which, the new approach makes different predictions from the standard analyses. The approach is inspired on Penrose's proposals that Quantum Gravity might lead to a real, dynamical collapse of the wave function, a process that we argue has the properties needed to extract us from the theoretical impasse described above.Comment: Prepared for the proceedings of the conference NEBXII " Recent Developments in Gravity", Napfio Grece June 2006. LateX, 15 page