Engineering orthogonal dual transcription factors for multi-input synthetic promoters

Synthetic biology has seen an explosive growth in the capability of engineering artificial gene circuits from transcription factors (TFs), particularly in bacteria. However, most artificial networks still employ the same core set of TFs (for example LacI, TetR and cI). The TFs mostly function via repression and it is difficult to integrate multiple inputs in promoter logic. Here we present to our knowledge the first set of dual activator-repressor switches for orthogonal logic gates, based on bacteriophage λ cI variants and multi-input promoter architectures. Our toolkit contains 12 TFs, flexibly operating as activators, repressors, dual activator–repressors or dual repressor–repressors, on up to 270 synthetic promoters. To engineer non cross-reacting cI variants, we design a new M13 phagemid-based system for the directed evolution of biomolecules. Because cI is used in so many synthetic biology projects, the new set of variants will easily slot into the existing projects of other groups, greatly expanding current engineering capacities

Scaling-up quantum heat engines efficiently via shortcuts to adiabaticity

The finite-time operation of a quantum heat engine that uses a single particle as a working medium generally increases the output power at the expense of inducing friction that lowers the cycle efficiency. We propose to scale up a quantum heat engine utilizing a many-particle working medium in combination with the use of shortcuts to adiabaticity to boost the nonadiabatic performance by eliminating quantum friction and reducing the cycle time. To this end, we first analyze the finite-time thermodynamics of a quantum Otto cycle implemented with a quantum fluid confined in a time-dependent harmonic trap. We show that nonadiabatic effects can be controlled and tailored to match the adiabatic performance using a variety of shortcuts to adiabaticity. As a result, the nonadiabatic dynamics of the scaled-up many-particle quantum heat engine exhibits no friction and the cycle can be run at maximum efficiency with a tunable output power. We demonstrate our results with a working medium consisting of particles with inverse-square pairwise interactions, that includes noninteracting and hard-core bosons as limiting cases.Comment: 15 pages, 3 figures; typo in Eq. (51) fixed. Feature paper in the Special Issue "Quantum Thermodynamics" edited by Prof. Dr. Ronnie Koslof

Numerical simulation of random paths with a curvature dependent action

We study an ensemble of closed random paths, embedded in R^3, with a curvature dependent action. Previous analytical results indicate that there is no crumpling transition for any finite value of the curvature coupling. Nevertheless, in a high statistics numerical simulation, we observe two different regimes for the specific heat separated by a rather smooth structure. The analysis of this fact warns us about the difficulties in the interpretation of numerical results obtained in cases where theoretical results are absent and a high statistics simulation is unreachable. This may be the case of random surfaces.Comment: 9 pages, LaTeX, 4 eps figures. Final version to appear in Mod. Phys. Lett.

An introduction to local Black Hole horizons in the 3+1 approach to General Relativity

We present an introduction to dynamical trapping horizons as quasi-local models for black hole horizons, from the perspective of an Initial Value Problem approach to the construction of generic black hole spacetimes. We focus on the geometric and structural properties of these horizons aiming, as a main application, at the numerical evolution and analysis of black hole spacetimes in astrophysical scenarios. In this setting, we discuss their dual role as an "a priori" ingredient in certain formulations of Einstein equations and as an "a posteriori" tool for the diagnosis of dynamical black hole spacetimes. Complementary to the first-principles discussion of quasi-local horizon physics, we place an emphasis on the "rigidity" properties of these hypersurfaces and their role as privileged geometric probes into near-horizon strong-field spacetime dynamics.Comment: 37 pages, 5 figures. Notes prepared for the course at the 2011 Shanghai Asia-Pacific School and Workshop on Gravitation (Shanghai Normal University, February 10-14, 2011

Magnetism, structure, and charge correlation at a pressure-induced Mott-Hubbard insulator-metal transition

We use synchrotron x-ray diffraction and electrical transport under pressure to probe both the magnetism and the structure of single crystal NiS2 across its Mott-Hubbard transition. In the insulator, the low-temperature antiferromagnetic order results from superexchange among correlated electrons and couples to a (1/2, 1/2, 1/2) superlattice distortion. Applying pressure suppresses the insulating state, but enhances the magnetism as the superexchange increases with decreasing lattice constant. By comparing our results under pressure to previous studies of doped crystals we show that this dependence of the magnetism on the lattice constant is consistent for both band broadening and band filling. In the high pressure metallic phase the lattice symmetry is reduced from cubic to monoclinic, pointing to the primary influence of charge correlations at the transition. There exists a wide regime of phase separation that may be a general characteristic of correlated quantum matter.Comment: 5 pages, 3 figure

Extended diffeomorphism algebras in (quantum) gravitational physics

We construct an explicit representation of the algebra of local diffeomorphisms of a manifold with realistic dimensions. This is achieved in the setting of a general approach to the (quantum) dynamics of a physical system which is characterized by the fundamental role assigned to a basic underlying symmetry. The developed mathematical formalism makes contact with the relevant gravitational notions by means of the addition of some extra structure. The specific manners in which this is accomplished, together with their corresponding physical interpretation, lead to different gravitational models. Distinct strategies are in fact briefly outlined, showing the versatility of the present conceptual framework.Comment: 20 pages, LATEX, no figure

Mice and rats achieve similar levels of performance in an adaptive decision-making task

Two opposing constraints exist when choosing a model organism for studying the neural basis of adaptive decision-making: (1) experimental access and (2) behavioral complexity. Available molecular and genetic approaches for studying neural circuits in the mouse fulfill the first requirement. In contrast, it is still under debate if mice can perform cognitive tasks of sufficient complexity. Here we compare learning and performance of mice and rats, the preferred behavioral rodent model, during an acoustic flexible categorization two-alternative choice task. The task required animals to switch between two categorization definitions several times within a behavioral session. We found that both species achieved similarly high performance levels. On average, rats learned the task faster than mice, although some mice were as fast as the average rat. No major differences in subjective categorization boundaries or the speed of adaptation between the two species were found. Our results demonstrate that mice are an appropriate model for the study of the neural mechanisms underlying adaptive decision-making, and suggest they might be suitable for other cognitive tasks as well