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

Generic Strategies for Chemical Space Exploration

Computational approaches to exploring "chemical universes", i.e., very large sets, potentially infinite sets of compounds that can be constructed by a prescribed collection of reaction mechanisms, in practice suffer from a combinatorial explosion. It quickly becomes impossible to test, for all pairs of compounds in a rapidly growing network, whether they can react with each other. More sophisticated and efficient strategies are therefore required to construct very large chemical reaction networks. Undirected labeled graphs and graph rewriting are natural models of chemical compounds and chemical reactions. Borrowing the idea of partial evaluation from functional programming, we introduce partial applications of rewrite rules. Binding substrate to rules increases the number of rules but drastically prunes the substrate sets to which it might match, resulting in dramatically reduced resource requirements. At the same time, exploration strategies can be guided, e.g. based on restrictions on the product molecules to avoid the explicit enumeration of very unlikely compounds. To this end we introduce here a generic framework for the specification of exploration strategies in graph-rewriting systems. Using key examples of complex chemical networks from sugar chemistry and the realm of metabolic networks we demonstrate the feasibility of a high-level strategy framework. The ideas presented here can not only be used for a strategy-based chemical space exploration that has close correspondence of experimental results, but are much more general. In particular, the framework can be used to emulate higher-level transformation models such as illustrated in a small puzzle game

Experimental demonstration of coherent state estimation with minimal disturbance

We investigate the optimal tradeoff between information gained about an unknown coherent state and the state disturbance caused by the measurement process. We propose several optical schemes that can enable this task, and we implement one of them, a scheme which relies on only linear optics and homodyne detection. Experimentally we reach near optimal performance, limited only by detection inefficiencies. In addition we show that such a scheme can be used to enhance the transmission fidelity of a class of noisy channels

Long-term high fat feeding of rats results in increased numbers of circulating microvesicles with pro-inflammatory effects on endothelial cells

Obesity and type 2 diabetes lead to dramatically increased risks of atherosclerosis and CHD. Multiple mechanisms converge to promote atherosclerosis by increasing endothelial oxidative stress and up-regulating expression of pro-inflammatory molecules. Microvesicles (MV) are small ( < 1 μm) circulating particles that transport proteins and genetic material, through which they are able to mediate cell–cell communication and influence gene expression. Since MV are increased in plasma of obese, insulin-resistant and diabetic individuals, who often exhibit chronic vascular inflammation, and long-term feeding of a high-fat diet (HFD) to rats is a well-described model of obesity and insulin resistance, we hypothesised that this may be a useful model to study the impact of MV on endothelial inflammation. The number and cellular origin of MV from HFD-fed obese rats were characterised by flow cytometry. Total MV were significantly increased after feeding HFD compared to feeding chow (P< 0·001), with significantly elevated numbers of MV derived from leucocyte, endothelial and platelet compartments (P< 0·01 for each cell type). MV were isolated from plasma and their ability to induce reactive oxygen species (ROS) formation and vascular cell adhesion molecule (VCAM)-1 expression was measured in primary rat cardiac endothelial cells in vitro. MV from HFD-fed rats induced significant ROS (P< 0·001) and VCAM-1 expression (P= 0·0275), indicative of a pro-inflammatory MV phenotype in this model of obesity. These findings confirm that this is a useful model to further study the mechanisms by which diet can influence MV release and subsequent effects on cardio-metabolic health

Improving information/disturbance and estimation/distortion trade-offs with non universal protocols

We analyze in details a conditional measurement scheme based on linear optical components, feed-forward loop and homodyne detection. The scheme may be used to achieve two different tasks. On the one hand it allows the extraction of information with minimum disturbance about a set of coherent states. On the other hand, it represents a nondemolitive measurement scheme for the annihilation operator, i.e. an indirect measurement of the Q-function. We investigate the information/disturbance trade-off for state inference and introduce the estimation/distortion trade-off to assess estimation of the Q-function. For coherent states chosen from a Gaussian set we evaluate both information/disturbance and estimation/distortion trade-offs and found that non universal protocols may be optimized in order to achieve better performances than universal ones. For Fock number states we prove that universal protocols do not exist and evaluate the estimation/distortion trade-off for a thermal distribution.Comment: 10 pages, 6 figures; published versio

Revivals of Coherence in Chaotic Atom-Optics Billiards

We investigate the coherence properties of thermal atoms confined in optical dipole traps where the underlying classical dynamics is chaotic. A perturbative expression derived for the coherence of the echo scheme of [Andersen et. al., Phys. Rev. Lett. 90, 023001 (2003)] shows it is a function of the survival probability or fidelity of eigenstates of the motion of the atoms in the trap. The echo coherence and the survival probability display "system specific" features, even when the underlying classical dynamics is chaotic. In particular, partial revivals in the echo signal and the survival probability are found for a small shift of the potential. Next, a "semi-classical" expression for the averaged echo signal is presented and used to calculate the echo signal for atoms in a light sheet wedge billiard. Revivals in the echo coherence are found in this system, indicating they may be a generic feature of dipole traps

The Electrostatic Ion Beam Trap : a mass spectrometer of infinite mass range

We study the ions dynamics inside an Electrostatic Ion Beam Trap (EIBT) and show that the stability of the trapping is ruled by a Hill's equation. This unexpectedly demonstrates that an EIBT, in the reference frame of the ions works very similar to a quadrupole trap. The parallelism between these two kinds of traps is illustrated by comparing experimental and theoretical stability diagrams of the EIBT. The main difference with quadrupole traps is that the stability depends only on the ratio of the acceleration and trapping electrostatic potentials, not on the mass nor the charge of the ions. All kinds of ions can be trapped simultaneously and since parametric resonances are proportional to the square root of the charge/mass ratio the EIBT can be used as a mass spectrometer of infinite mass range