Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars

Modeling molecules as undirected graphs and chemical reactions as graph rewriting operations is a natural and convenient approach tom odeling chemistry. Graph grammar rules are most naturally employed to model elementary reactions like merging, splitting, and isomerisation of molecules. It is often convenient, in particular in the analysis of larger systems, to summarize several subsequent reactions into a single composite chemical reaction. We use a generic approach for composing graph grammar rules to define a chemically useful rule compositions. We iteratively apply these rule compositions to elementary transformations in order to automatically infer complex transformation patterns. This is useful for instance to understand the net effect of complex catalytic cycles such as the Formose reaction. The automatically inferred graph grammar rule is a generic representative that also covers the overall reaction pattern of the Formose cycle, namely two carbonyl groups that can react with a bound glycolaldehyde to a second glycolaldehyde. Rule composition also can be used to study polymerization reactions as well as more complicated iterative reaction schemes. Terpenes and the polyketides, for instance, form two naturally occurring classes of compounds of utmost pharmaceutical interest that can be understood as "generalized polymers" consisting of five-carbon (isoprene) and two-carbon units, respectively

Observation of spatial quantum correlations induced by multiple scattering of non-classical light

We present the experimental realization of spatial quantum correlations of photons that are induced by multiple scattering of squeezed light. The quantum correlation relates photons propagating along two different light trajectories through the random medium and is infinite in range. Both positive and negative spatial quantum correlations are observed when varying the quantum state incident to the multiple scattering medium, and the magnitude of the correlations is controlled by the number of photons. The experimental results are in excellent agreement with recent theoretical proposals by implementing the full quantum model of multiple scattering

Hybrid quantum information processing

The development of quantum information processing has traditionally followed two separate and not immediately connected lines of study. The main line has focused on the implementation of quantum bit (qubit) based protocols whereas the other line has been devoted to implementations based on high-dimensional Gaussian states (such as coherent and squeezed states). The separation has been driven by the experimental difficulty in interconnecting the standard technologies of the two lines. However, in recent years, there has been a significant experimental progress in refining and connecting the technologies of the two fields which has resulted in the development and experimental realization of numerous new hybrid protocols. In this Review, we summarize these recent efforts on hybridizing the two types of schemes based on discrete and continuous variables.Comment: 13 pages, 6 figure

Raman-induced limits to efficient squeezing in optical fibers

We report new experiments on polarization squeezing using ultrashort photonic pulses in a single pass of a birefringent fiber. We measure what is to our knowledge a record squeezing of -6.8 +/- 0.3 dB in optical fibers which when corrected for linear losses is -10.4 +/- 0.8 dB. The measured polarization squeezing as a function of optical pulse energy, which spans a wide range from 3.5-178.8 pJ, shows a very good agreement with the quantum simulations and for the first time we see the experimental proof that Raman effects limit and reduce squeezing at high pulse energy.Comment: 3 pages, 3 figure

Self-energy and critical temperature of weakly interacting bosons

Using the exact renormalization group we calculate the momentum-dependent self-energy Sigma (k) at zero frequency of weakly interacting bosons at the critical temperature T_c of Bose-Einstein condensation in dimensions 3 <= D < 4. We obtain the complete crossover function interpolating between the critical regime k << k_c, where Sigma (k) propto k^{2 - eta}, and the short-wavelength regime k >> k_c, where Sigma (k) propto k^{2 (D-3)} in D> 3 and Sigma (k) \propto ln (k/k_c) in D=3. Our approach yields the crossover scale k_c on the same footing with a reasonable estimate for the critical exponent eta in D=3. From our Sigma (k) we find for the interaction-induced shift of T_c in three dimensions Delta T_c / T_c approx 1.23 a n^{1/3}, where a is the s-wave scattering length and n is the density.Comment: 4 pages,1 figur

Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete

Background: A classical problem in metabolic design is to maximize the production of desired compound in a given chemical reaction network by appropriately directing the mass flow through the network. Computationally, this problem is addressed as a linear optimization problem over the "flux cone". The prior construction of the flux cone is computationally expensive and no polynomial-time algorithms are known. Results: Here we show that the output maximization problem in chemical reaction networks is NP-complete. This statement remains true even if all reactions are monomolecular or bimolecular and if only a single molecular species is used as influx. As a corollary we show, furthermore, that the detection of autocatalytic species, i.e., types that can only be produced from the influx material when they are present in the initial reaction mixture, is an NP-complete computational problem. Conclusions: Hardness results on combinatorial problems and optimization problems are important to guide the development of computational tools for the analysis of metabolic networks in particular and chemical reaction networks in general. Our results indicate that efficient heuristics and approximate algorithms need to be employed for the analysis of large chemical networks since even conceptually simple flow problems are provably intractable