Amortised resource analysis with separation logic

Type-based amortised resource analysis following Hofmann and Jost—where resources are associated with individual elements of data structures and doled out to the programmer under a linear typing discipline—have been successful in providing concrete resource bounds for functional programs, with good support for inference. In this work we translate the idea of amortised resource analysis to imperative languages by embedding a logic of resources, based on Bunched Implications, within Separation Logic. The Separation Logic component allows us to assert the presence and shape of mutable data structures on the heap, while the resource component allows us to state the resources associated with each member of the structure. We present the logic on a small imperative language with procedures and mutable heap, based on Java bytecode. We have formalised the logic within the Coq proof assistant and extracted a certified verification condition generator. We demonstrate the logic on some examples, including proving termination of in-place list reversal on lists with cyclic tails

Quantum-coherent dynamics in photosynthetic charge separation revealed by wavelet analysis

Experimental/theoretical evidence for sustained vibration-assisted electronic (vibronic) coherence in the Photosystem II Reaction Center (PSII RC) indicates that photosynthetic solar-energy conversion might be optimized through the interplay of electronic and vibrational quantum dynamics. This evidence has been obtained by investigating the primary charge separation process in the PSII RC by two-dimensional electronic spectroscopy (2DES) and Redfield modeling of the experimental data. However, while conventional Fourier transform analysis of the 2DES data allows oscillatory signatures of vibronic coherence to be identified in the frequency domain in the form of static 2D frequency maps, the real-time evolution of the coherences is lost. Here we apply for the first time wavelet analysis to the PSII RC 2DES data to obtain time-resolved 2D frequency maps. These maps allow us to demonstrate that i) coherence between the excitons initiating the two different charge separation pathways is active for more than 500 fs, and ii) coherence between exciton and charge-transfer states, the reactant and product of the charge separation reaction, respectively, is active for at least 1 ps. These findings imply that the PSII RC employs coherence i) to sample competing electron transfer pathways, and ii) to perform directed, ultrafast and efficient electron transfer.Comment: Scientific reports 201

On the construction of high-order force gradient algorithms for integration of motion in classical and quantum systems

A consequent approach is proposed to construct symplectic force-gradient algorithms of arbitrarily high orders in the time step for precise integration of motion in classical and quantum mechanics simulations. Within this approach the basic algorithms are first derived up to the eighth order by direct decompositions of exponential propagators and further collected using an advanced composition scheme to obtain the algorithms of higher orders. Contrary to the scheme by Chin and Kidwell [Phys. Rev. E 62, 8746 (2000)], where high-order algorithms are introduced by standard iterations of a force-gradient integrator of order four, the present method allows to reduce the total number of expensive force and its gradient evaluations to a minimum. At the same time, the precision of the integration increases significantly, especially with increasing the order of the generated schemes. The algorithms are tested in molecular dynamics and celestial mechanics simulations. It is shown, in particular, that the efficiency of the new fourth-order-based algorithms is better approximately in factors 5 to 1000 for orders 4 to 12, respectively. The results corresponding to sixth- and eighth-order-based composition schemes are also presented up to the sixteenth order. For orders 14 and 16, such highly precise schemes, at considerably smaller computational costs, allow to reduce unphysical deviations in the total energy up in 100 000 times with respect to those of the standard fourth-order-based iteration approach.Comment: 23 pages, 2 figures; submitted to Phys. Rev.

Quantum Perfect-Fluid Kaluza-Klein Cosmology

The perfect fluid cosmology in the 1+d+D dimensional Kaluza-Klein spacetimes for an arbitrary barotropic equation of state $p= n \rho$ is quantized by using the Schutz's variational formalism. We make efforts in the mathematics to solve the problems in two cases. For the first case of the stiff fluid $n=1$ we exactly solve the Wheeler-DeWitt equation when the $d$ space is flat. After the superposition of the solutions we analyze the Bohmian trajectories of the final-stage wave-packet functions and show that the flat $d$ spaces and the compact $D$ spaces will eventually evolve into finite scale functions. For the second case of $n \approx 1$, we use the approximated wavefunction in the Wheeler-DeWitt equation to find the analytic forms of the final-stage wave-packet functions. After analyzing the Bohmian trajectories we show that the flat $d$ spaces will be expanding forever while the scale function of the contracting $D$ spaces would not become zero within finite time. Our investigations indicate that the quantum effect in the quantum perfect-fluid cosmology could prevent the extra compact $D$ spaces in the Kaluza-Klein theory from collapsing into a singularity or that the "crack-of-doom" singularity of the extra compact dimensions is made to occur at $t=\infty$.Comment: Latex 18 pages, add section 2 to introduce the quantization of perfect flui

A new broken U(1)-symmetry in extreme type-II superconductors

A phase transition within the molten phase of the Abrikosov vortex system without disorder in extreme type-II superconductors is found via large-scale Monte-Carlo simulations. It involves breaking a U(1)-symmetry, and has a zero-field counterpart, unlike vortex lattice melting. Its hallmark is the loss of number-conservation of connected vortex paths threading the entire system {\it in any direction}, driving the vortex line tension to zero. This tension plays the role of a generalized ``stiffness'' of the vortex liquid, and serves as a probe of the loss of order at the transition, where a weak specific heat anomaly is found.Comment: 5 pages, 3 figure

High-Contrast Interference in a Thermal Cloud of Atoms

The coherence properties of a gas of bosonic atoms above the BEC transition temperature were studied. Bragg diffraction was used to create two spatially separated wave packets, which interfere during expansion. Given sufficient expansion time, high fringe contrast could be observed in a cloud of arbitrary temperature. Fringe visibility greater than 90% was observed, which decreased with increasing temperature, in agreement with a simple model. When the sample was "filtered" in momentum space using long, velocity-selective Bragg pulses, the contrast was significantly enhanced in contrast to predictions

A Forward-Design Approach to Increase the Production of Poly-3-Hydroxybutyrate in Genetically Engineered Escherichia coli

Biopolymers, such as poly-3-hydroxybutyrate (P(3HB)) are produced as a carbon store in an array of organisms and exhibit characteristics which are similar to oil-derived plastics, yet have the added advantages of biodegradability and biocompatibility. Despite these advantages, P(3HB) production is currently more expensive than the production of oil-derived plastics, and therefore, more efficient P(3HB) production processes would be desirable. In this study, we describe the model-guided design and experimental validation of several engineered P(3HB) producing operons. In particular, we describe the characterization of a hybrid phaCAB operon that consists of a dual promoter (native and J23104) and RBS (native and B0034) design. P(3HB) production at 24 h was around six-fold higher in hybrid phaCAB engineered Escherichia coli in comparison to E. coli engineered with the native phaCAB operon from Ralstonia eutropha H16. Additionally, we describe the utilization of non-recyclable waste as a low-cost carbon source for the production of P(3HB)

Unzipping of DNA with correlated base-sequence

We consider force-induced unzipping transition for a heterogeneous DNA model with a correlated base-sequence. Both finite-range and long-range correlated situations are considered. It is shown that finite-range correlations increase stability of DNA with respect to the external unzipping force. Due to long-range correlations the number of unzipped base-pairs displays two widely different scenarios depending on the details of the base-sequence: either there is no unzipping phase-transition at all, or the transition is realized via a sequence of jumps with magnitude comparable to the size of the system. Both scenarios are different from the behavior of the average number of unzipped base-pairs (non-self-averaging). The results can be relevant for explaining the biological purpose of correlated structures in DNA.Comment: 22 pages, revtex4, 14 eps figures; reprinted in the June 15, 2004 issue of Virtual Journal of Biological Physics Researc

On Automated Lemma Generation for Separation Logic with Inductive Definitions

Separation Logic with inductive definitions is a well-known approach for deductive verification of programs that manipulate dynamic data structures. Deciding verification conditions in this context is usually based on user-provided lemmas relating the inductive definitions. We propose a novel approach for generating these lemmas automatically which is based on simple syntactic criteria and deterministic strategies for applying them. Our approach focuses on iterative programs, although it can be applied to recursive programs as well, and specifications that describe not only the shape of the data structures, but also their content or their size. Empirically, we find that our approach is powerful enough to deal with sophisticated benchmarks, e.g., iterative procedures for searching, inserting, or deleting elements in sorted lists, binary search tress, red-black trees, and AVL trees, in a very efficient way