Competitive 15N kinetic isotope effects of nitrogenase-catalyzed dinitrogen reduction

Biological N2 fixation is achieved under ambient conditions by enzymatic catalysis. The enzyme nitrogenase has been studied extensively, but the N2 chemical reduction step is, by far, not rate limiting and hard to examine. A new method was developed that allows studying the reduction transition state within the enzyme's complex kinetic cascade by means of the 15N kinetic isotope effect on the reaction's second-order rate constant, V/K. A value of 1.7% +/- 0.2% was measured.     

Loss analysis of air-core photonic crystal fibers

By using a multipole moment approach, we analyze the loss of an air-core photonic crystal fiber and demonstrate that it is possible reduce the transmission loss that is due to photon radiation leakage through the photonic crystal cladding to a level below 0.01 dB/km, with eight rings of air holes. An analogy is drawn between air-core photonic crystal fiber modes and Bragg fiber modes. The influence of material absorption in the silica glass is discussed.     

Structure in the reaction π+p → Δ++ϱo AT 5 GeV/c

In a high statistics experiment a large dσ/dt′ slope of (23.7 ± 3.2) GeV^?2 is obtained in the forward direction. The natural parity exchange cross-section shows a dip at t′ ≈ 0.2 GeV² and peak at ≈ 0.6 GeV². The ?^o is separated from the S-wave background and we obtain ?₀₀^F ≈ 0.94, at t′ = 0.     

On the syntomic regulator for K 1 of a surface

We consider elements of K ₁(S), where S is a proper surface over a p-adic field with good reduction, which are given by a formal sum ??(Z _i , f _i ) with Z _i curves in S and f _i rational functions on the Z _i in such a way that the sum of the divisors of the f _i is 0 on S. Assuming compatibility of pushforwards in syntomic and motivic cohomologies, our result computes the syntomic regulator of such an element, interpreted as a functional on H _dR ² (S), when evaluated on the cup product ????[??] of a holomorphic form ?? by the first cohomology class of a form of the second kind ??. The result is ?? _i ??F _?? , log(f _i ); F _?? ??_gl,Z _i , where F _?? and F _?? are Coleman integrals of ?? and ??, respectively, and the symbol in brackets is the global triple index, as defined in our previous work.     

A Separated Cohomologically Complete Module is Complete

We prove two theorems on cohomologically complete complexes. These theorems are inspired by, and yield an alternative proof of, a recent theorem of P. Schenzel on complete modules.     

Effects of the donor-acceptor distance and dynamics on hydride tunneling in the dihydrofolate reductase catalyzed reaction

A significant contemporary question in enzymology involves the role of protein dynamics and hydrogen tunneling in enhancing enzyme catalyzed reactions. Here, we report a correlation between the donor-acceptor distance (DAD) distribution and intrinsic kinetic isotope effects (KIEs) for the dihydrofolate reductase (DHFR) catalyzed reaction. This study compares the nature of the hydride-transfer step for a series of active-site mutants, where the size of a side chain that modulates the DAD (I14 in E. coli DHFR) is systematically reduced (I14V, I14A, and I14G). The contributions of the DAD and its dynamics to the hydride-transfer step were examined by the temperature dependence of intrinsic KIEs, hydride-transfer rates, activation parameters, and classical molecular dynamics (MD) simulations. Results are interpreted within the framework of the Marcus-like model where the increase in the temperature dependence of KIEs arises as a direct consequence of the deviation of the DAD from its distribution in the wild type enzyme. Classical MD simulations suggest new populations with larger average DADs, as well as broader distributions, and a reduction in the population of the reactive conformers correlated with the decrease in the size of the hydrophobic residue. The more flexible active site in the mutants required more substantial thermally activated motions for effective H-tunneling, consistent with the hypothesis that the role of the hydrophobic side chain of I14 is to restrict the distribution and dynamics of the DAD and thus assist the hydride-transfer. These studies establish relationships between the distribution of DADs, the hydride-transfer rates, and the DAD's rearrangement toward tunneling-ready states. This structure-function correlation shall assist in the interpretation of the temperature dependence of KIEs caused by mutants far from the active site in this and other enzymes, and may apply generally to C-H→C transfer reactions.     

Distribution of Primary and Specialized Metabolites in <em>Nigella sativa</em> Seeds, a Spice with Vast Traditional and Historical Uses

Black cumin (Nigella sativa L., Ranunculaceae) is an annual herb commonly used in the Middle East, India and nowadays gaining worldwide acceptance. Historical and traditional uses are extensively documented in ancient texts and historical documents. Black cumin seeds and oil are commonly used as a traditional tonic and remedy for many ailments as well as in confectionery and bakery. Little is known however about the mechanisms that allow the accumulation and localization of its active components in the seed. Chemical and anatomical evidence indicates the presence of active compounds in seed coats. Seed volatiles consist largely of olefinic and oxygenated monoterpenes, mainly p-cymene, thymohydroquinone, thymoquinone, γ-terpinene and α-thujene, with lower levels of sesquiterpenes, mainly longifolene. Monoterpene composition changes during seed maturation. γ-Terpinene and α-thujene are the major monoterpenes accumulated in immature seeds, and the former is gradually replaced by p-cymene, carvacrol, thymo-hydroquinone and thymoquinone upon seed development. These compounds, as well as the indazole alkaloids nigellidine and nigellicine, are almost exclusively accumulated in the seed coat. In contrast, organic and amino acids are primarily accumulated in the inner seed tissues. Sugars and sugar alcohols, as well as the amino alkaloid dopamine and the saponin α-hederin accumulate both in the seed coats and the inner seed tissues at different ratios. Chemical analyses shed light to the ample traditional and historical uses of this plant.     

"Ideal" optical delay lines based on tailored-coupling and reflecting, coupled-resonator optical waveguides

We present a design of "ideal" optical delay lines (i.e., constant amplitude and constant group delay over the desired bandwidth). They are based on reflection from coupled-resonator optical waveguides (CROWs). The inter-resonator coupling coefficients are tailored and decrease monotonically with the distance from the input to realize all-pass Bessel filters. The tailored coupling coefficients result in a frequency-dependent propagating distance which compensates for the group velocity dispersion of CROWs. We present a simple formalism for deriving the time-domain coupling coefficients and convert these coefficients to field coupling coefficients of ring resonators. The reflecting CROWs possess a delay-bandwidth product of 0.5 per resonator, larger than that of any kind of transmitting CROW. In the presence of uniform gain, the gain enhanced by slow light propagation and the constant group delay result in efficient and dispersion-free amplifiers.     

Lossless Condensers,Unbalanced Expanders,And Extractors

Trevisan showed that many pseudorandom generator constructions give rise to constructions of explicit extractors. We show how to use such constructions to obtain explicit lossless condensers. A lossless condenser is a probabilistic map using only O(logn) additional random bits that maps n bits strings to poly(logK) bit strings, such that any source with support size K is mapped almost injectively to the smaller domain. Our construction remains the best lossless condenser to date. By composing our condenser with previous extractors, we obtain new, improved extractors. For small enough min-entropies our extractors can output all of the randomness with only O(logn) bits. We also obtain a new disperser that works for every entropy loss, uses an O(logn) bit seed, and has only O(logn) entropy loss. This is the best disperser construction to date, and yields other applications. Finally, our lossless condenser can be viewed as an unbalanced bipartite graph with strong expansion properties. * Much of this work was done while the author was in the Computer Science Division, University of California, Berkeley, and supported in part by a David and Lucile Packard Fellowship for Science and Engineering and NSF NYI Grant No. CCR-9457799. The work was also supported in part by an Alon fellowship and by the Israel Science Foundation. † Much of this work was done while the author was a graduate student in the Computer Science Division, University of California, Berkeley. Supported in part by NSF Grants CCR-9820897, CCF-0346991, and an Alfred P. Sloan Research Fellowship. ‡ Much of this work was done while the author was on leave at the Computer Science Division, University of California, Berkeley. Supported in part by a David and Lucile Packard Fellowship for Science and Engineering, NSF Grants CCR-9912428 and CCR-0310960, NSF NYI Grant CCR-9457799, and an Alfred P. Sloan Research Fellowship.