Construction and calibration of an instrument for three-dimensional ion imaging

We describe a new instrument based on a delay-line detector for imaging the complete three-dimensional velocity distribution of photoionized products from photoinitiated reactions. Doppler-free [2+1] resonantly enhanced multiphoton ionization (REMPI) of H and D atoms formed upon photolysis of HBr and DBr in the range 203 nm < or = lambda photolysis < or = 243 nm yields radial speeds measured to be accurate within 1% of those calculated. The relative speed resolution is about 5% and limited by photoionization recoil broadening. A relative speed resolution of 3.4% is obtained for [3+1] REMPI, which minimizes the ionization recoil. We also determine the branching ratio between ground-state and spin-orbit-excited product channels and their associated anisotropies. We find that DBr photolysis dynamics differs slightly from its HBr counterpart.     

Subfactors of Index Less Than 5, Part 3: Quadruple Points

One major obstacle in extending the classification of small index subfactors beyond ${3 +\sqrt{3}}$ is the appearance of infinite families of candidate principal graphs with 4-valent vertices (in particular, the ??weeds?? ${\mathcal{Q}}$ and ${\mathcal{Q}'}$ from Part 1 (Morrison and Snyder in Commun. Math. Phys., doi:10.1007/s00220-012-1426-y, 2012). Thus instead of using triple point obstructions to eliminate candidate graphs, we need to develop new quadruple point obstructions. In this paper we prove two quadruple point obstructions. The first uses quadratic tangles techniques and eliminates the weed ${\mathcal{Q}'}$ immediately. The second uses connections, and when combined with an additional number theoretic argument it eliminates both weeds ${\mathcal{Q}}$ and ${\mathcal{Q}'}$ . Finally, we prove the uniqueness (up to taking duals) of the 3311 Goodman-de la Harpe-Jones subfactor using a combination of planar algebra techniques and connections.     

Robustness of Quantum Markov Chains

If the conditional information of a classical probability distribution of three random variables is zero, then it obeys a Markov chain condition. If the conditional information is close to zero, then it is known that the distance (minimum relative entropy) of the distribution to the nearest Markov chain distribution is precisely the conditional information. We prove here that this simple situation does not obtain for quantum conditional information. We show that for tri-partite quantum states the quantum conditional information is always a lower bound for the minimum relative entropy distance to a quantum Markov chain state, but the distance can be much greater; indeed the two quantities can be of different asymptotic order and may even differ by a dimensional factor.     

Development of continuous surfactin production from potato process effluent by Bacillus subtilis in an airlift reactor

The biosurfactant surfactin has the potential to aid in the recovery of subsurface organic contaminants (environmental remediation) or crude oils (oil recovery). However, high medium and purification costs limit its use in these high-volume applications. In previous work, we showed that surfactin can be produced from an inexpensive low-solids (LS) potato process effluent with minimal amendments or pretreatments. Previous research has also shown that 95% or more of the surfactin in Bacillus subtilis cultures can be recovered by foam fractionation. In this work, we present the results of research to integrate surfactin production with foam fractionation. Experiments were performed in an airlift reactor, with continuous collection of the foam through a tube at the top of the column. Preliminary results using both purified potato starch and unamended low-solids potato process effluent as substrates for surfactin production indicate that the process is oxygen limited and that recalcitrant indigenous bacteria in the potato process effluent may hamper continuous surfactin production.     

Orthogonal sampling in free‐energy calculations of residue mutations in a tripeptide: TI versus λ‐LEUS

In a recent article (Bieler et al., J. Chem. Theory Comput. 2014, 10, 3006), we introduced a combination of λ‐dynamics and local‐elevation umbrella‐sampling termed λ‐LEUS to calculate free‐energy changes associated with alchemical processes using molecular dynamics simulations. This method was suggested to be more efficient than thermodynamic integration (TI), because the dynamical variation of the alchemical variable λ opens up pathways to circumvent barriers in the orthogonal space (defined by the N – 1 degrees of freedom that are not subjected to the sampling enhancement), a feature λ‐LEUS shares with Hamiltonian replica‐exchange (HR) approaches. However, the mutation considered, hydroquinone to benzene in water, was no real challenge in terms of orthogonal‐space properties, which were restricted to solvent‐relaxation processes. In the present article, we revisit the comparison between TI and λ‐LEUS considering non‐trivial mutations of the central residue X of a KXK tripeptide in water (with X = G, E, K, S, F, or Y). Side‐chain interactions that may include salt bridges, hydrogen bonds or steric clashes lead to slow relaxation in the orthogonal space, mainly in the two‐dimensional subspace spanned by the central and ψ dihedral angles of the peptide. The efficiency enhancement afforded by λ‐LEUS is confirmed in this more complex test system and can be attributed explicitly to the improved sampling of the orthogonal space. The sensitivity of the results to the nontrivial choices of a mass parameter and of a thermostat coupling time for the alchemical variable is also investigated, resulting in recommended ranges of 50 to 100 u nm² and 0.2 to 0.5 ps, respectively. © 2015 Wiley Periodicals, Inc.     

Automatic discovery of photoisomerization mechanisms with nanosecond machine learning photodynamics simulations

Photochemical reactions are widely used by academic and industrial researchers to construct complex molecular architectures via mechanisms that often require harsh reaction conditions. Photodynamics simulations provide time-resolved snapshots of molecular excited-state structures required to understand and predict reactivities and chemoselectivities. Molecular excited-states are often nearly degenerate and require computationally intensive multiconfigurational quantum mechanical methods, especially at conical intersections. Non-adiabatic molecular dynamics require thousands of these computations per trajectory, which limits simulations to ∼1 picosecond for most organic photochemical reactions. Westermayr et al. recently introduced a neural-network-based method to accelerate the predictions of electronic properties and pushed the simulation limit to 1 ns for the model system, methylenimmonium cation (CH₂NH₂⁺). We have adapted this methodology to develop the Python-based, Python Rapid Artificial Intelligence Ab Initio Molecular Dynamics (PyRAI²MD) software for the cis–trans isomerization of trans-hexafluoro-2-butene and the 4π-electrocyclic ring-closing of a norbornyl hexacyclodiene. We performed a 10 ns simulation for trans-hexafluoro-2-butene in just 2 days. The same simulation would take approximately 58 years with traditional multiconfigurational photodynamics simulations. We generated training data by combining Wigner sampling, geometrical interpolations, and short-time quantum chemical trajectories to adaptively sample sparse data regions along reaction coordinates. The final data set of the cis–trans isomerization and the 4π-electrocyclic ring-closing model has 6207 and 6267 data points, respectively. The training errors in energy using feedforward neural networks achieved chemical accuracy (0.023–0.032 eV). The neural network photodynamics simulations of trans-hexafluoro-2-butene agree with the quantum chemical calculations showing the formation of the cis-product and reactive carbene intermediate. The neural network trajectories of the norbornyl cyclohexadiene corroborate the low-yielding syn-product, which was absent in the quantum chemical trajectories, and revealed subsequent thermal reactions in 1 ns.

Photochemical reactions are widely used by academia and industry to construct complex molecular architectures via mechanisms that are often inaccessible by other means.     

Bioactive Molecules of Mandarin Seed Oils Diminish Mycotoxin and the Existence of Fungi

Mandarin is a favorite fruit of the citrus family. Mandarin seeds are considered a source of nontraditional oil obtained from byproduct materials. This investigation aimed to assess the biomolecules of mandarin seeds and evaluated their antimycotic and antimycotoxigenic impact on fungi. Moreover, it evaluated the protective role of mandarin oil against aflatoxin toxicity in cell lines. The two types of extracted oil (fixed and volatile) were ecofriendly. The fatty acid composition, tocopherol, sterols, and carotenoids were determined in the fixed oil, whereas volatiles and phenolics were estimated in the essential oil. A mixture of the two oils was prepared and evaluated for its antimicrobial impact. The reduction effect of this mixture was also investigated to reduce mycotoxin secretion using a simulated experiment. The protective effect of the oil was evaluated using healthy strains of cell lines. Fixed oil was distinguished by the omega fatty acid content (76.24%), lutein was the major carotenoid (504.3 mg/100 g) and it had a high β-sitosterol content (294.6 mg/100 g). Essential oil contained limonene (66.05%), α-pinene (6.82%), β-pinene (4.32%), and γ-terpinene (12.31%) in significant amounts, while gallic acid and catechol were recorded as the dominant phenolics. Evaluation of the oil mix for antimicrobial potency reflected a considerable impact against pathogenic bacteria and toxigenic fungi. By its application to the fungal media, this oil mix possessed a capacity for reducing mycotoxin secretion. The oil mix was also shown to have a low cytotoxic effect against healthy strains of cell lines and had potency in reducing the mortality impact of aflatoxin B₁ applied to cell lines. These results recommend further study to involve this oil in food safety applications.     

A New Inequality for the von Neumann Entropy

Strong subadditivity of von Neumann entropy, proved in 1973 by Lieb and Ruskai, is a cornerstone of quantum coding theory. All other known inequalities for entropies of quantum systems may be derived from it. Here we prove a new inequality for the von Neumann entropy which we prove is independent of strong subadditivity: it is an inequality which is true for any four party quantum state, provided that it satisfies three linear relations (constraints) on the entropies of certain reduced states.