Automated estimation of rare event probabilities in biochemical systems

In biochemical systems, the occurrence of a rare event can be accompanied by catastrophic consequences. Precise characterization of these events using Monte Carlo simulation methods is often intractable, as the number of realizations needed to witness even a single rare event can be very large. The weighted stochastic simulation algorithm (wSSA) [J. Chem. Phys. 129, 165101 (2008)] and its subsequent extension [J. Chem. Phys. 130, 174103 (2009)] alleviate this difficulty with importance sampling, which effectively biases the system toward the desired rare event. However, extensive computation coupled with substantial insight into a given system is required, as there is currently no automatic approach for choosing wSSA parameters. We present a novel modification of the wSSA--the doubly weighted SSA (dwSSA)--that makes possible a fully automated parameter selection method. Our approach uses the information-theoretic concept of cross entropy to identify parameter values yielding minimum variance rare event probability estimates. We apply the method to four examples: a pure birth process, a birth-death process, an enzymatic futile cycle, and a yeast polarization model. Our results demonstrate that the proposed method (1) enables probability estimation for a class of rare events that cannot be interrogated with the wSSA, and (2) for all examples tested, reduces the number of runs needed to achieve comparable accuracy by multiple orders of magnitude. For a particular rare event in the yeast polarization model, our method transforms a projected simulation time of 600 years to three hours. Furthermore, by incorporating information-theoretic principles, our approach provides a framework for the development of more sophisticated influencing schemes that should further improve estimation accuracy.     

Photocatalytic splitting of CS2 to S8 and a carbon-sulfur polymer catalyzed by a bimetallic ruthenium(II) compound with a tertiary amine binding site: toward photocatalytic splitting of CO2?

The catalytic photocleavage of CS(2) to S(8) and a (C(x)S(y))(n) polymer with visible light using a dinuclear ruthenium(II) compound with a bipyridine units for photoactivity and a vicinal tertiary amine binding site for CS(2) activation was studied. The catalyst was characterized by X-ray diffraction, (1)H NMR, and (13)C NMR, ESI-MS and elemental analysis. CS(2) photocleavage was significant (240 turnovers, 20 h) to yield isolable S(8) and a (C(x)S(y))(n) polymer. A mononuclear catalyst or one without an amine binding site showed significantly less activity. XPS of the (C(x)S(y))(n) polymer showed a carbon/sulfur ratio ～1.5-1.6 indicating that in part both C-S bonds of CS(2) had been cleaved. Catalyst was also included within the polymer. The absence of peaks in the (1)H NMR verified the (C(x)S(y))(n) nature of the polymer, while (13)C NMR and IR indicated that the polymer had multiple types of C-S and C-C bonds.     

A new tool to assess ceramide bioactivity: 6-bromo-7-hydroxycoumarinyl-caged ceramide

The bioactivity of natural, long-chain ceramides has until now been studied after its delivery to cells in organic solvent mixtures containing dodecane. We have synthesized ceramides conjugated to a (6-bromo-7-hydroxycoumarin-4-yl)methyl group. The photocaged ceramide is efficiently released with 350 nm light in aqueous solution at neutral pH, thus providing a promising new tool to study ceramide's properties.     

Hydrogenated amorphous silicon nanostructures: novel structure�Creactivity relationships for cyclization and ring opening in the gas phase

The effects of the reactive center connectivity and internal rotations on the reactivity of hydrogenated silicon nanostructures toward cyclization and ring opening pathways have been investigated. Rate coefficients for 25 cyclization and ring opening reactions for hydrides containing up to eight silicon atoms have been calculated using G3//B3LYP. The overall reactions exhibit two elementary steps. Overcoming the first barrier results in the formation of a hydrogen-bridged cyclic intermediate from a substituted silylene. Passing over the second barrier converts this intermediate into a cyclic silicon hydride. The rate-determining step varied according to the ring size formed and the temperature. Assuming a rate-determining step, values for the single-event Arrhenius pre-exponential factor, $ \tilde{A}$ , and the activation energy, E _a, were calculated from G3//B3LYP rate coefficients corrected for internal rotations, and a group additivity scheme was developed to predict $ \tilde{A}$ and E _a. The values predicted by group additivity are more accurate than structure?Creactivity relationships currently used in the literature, which rely on a representative $ \tilde{A}$ value for each reaction class and the Evans-Polanyi correlation to predict E _a. Internal rotation corrections played a prominent role in cyclization pathways, impacting $ \tilde{A}$ values for larger ring formation reactions more strongly than any variations in the connectivity of the reactive center.     

Optimized polymer-enzyme electrostatic interactions significantly improve penicillin G amidase efficiency in charged PEGA polymers

Hydrolytic yields as high as 80% were obtained by using penicillin G amidase (PGA) on substrates anchored on optimized positively charged PEGA polymers. By increasing the amount of permanent charges inside the polymer, electrostatic interactions between the positively charged PEGA⁺ and the negatively charged PGA (pI=5.2-5.4) were strengthened, thus favouring the accessibility of the bulky enzyme (MW=88 kDa) inside the pores. The effect of different amounts of charges on polymer swelling and protein retention inside the polymer was investigated and correlated to the enzyme efficiency demonstrating that electrostatic interactions predominate over swelling properties in determining enzyme accessibility.     

Singing power ratio: Quantitative evaluation of singing voice quality

This paper presents a parameter for objectively evaluating singing voice quality. Power spectrum of vowel sound / a / was analyzed by Fast Fourier Transform. The greatest harmonics peak between 2 and 4 kHz and the greatest harmonics peak between 0 and 2 kHz were identified. Power ratio of these peaks, termed singing power ratio (SPR), was calculated in 37 singers and 20 nonsingers. SPR of sung / a / in singers was significantly greater than in nonsingers. In singers, SPR of sung / a / was significantly greater than that of spoken / a /. By digital signal processing, power spectrum of sung / a / was varied, and the processed sounds were perceptually analyzed. SPR had a significant relationship with perceptual scores of “ringing” quality. SPR provides an important quantitative measurement for evaluating singing voice quality for all voice types, including soprano.     

Long-term trend in CHF2Cl (HCFC-22) from high spectral resolution infrared solar absorption measurements and comparison with in situ measurements

The average tropospheric volume mixing ratio of CHF₂Cl (HCFC-22) has been retrieved from a time series of high spectral resolution ground-based infrared solar absorption spectra recorded with the McMath Fourier transform spectrometer located at the U.S. National Solar Observatory facility on Kitt Peak in southern Arizona (31.9°N, 111.6°W, 2.09 km altitude) for the time period October 1987–November 2002. The retrievals are based on fits to the well-isolated, unresolved 2ν₆ Q branch at 829.05 cm⁻¹ and the SFIT2 retrieval algorithm. The measured daily averages show a near linear rise per year in the mean tropospheric volume mixing ratio as a function of time with a best fit yielding an average increase rate of (5.66±0.15) parts per trillion (10⁻¹²) by volume per year, corresponding to (6.47±0.17)%yr⁻¹, 1 sigma, at the beginning of the time series. The tropospheric mixing ratios retrieved from the solar spectra have been compared with monthly average surface flask sampling measurements from the Climate Monitoring and Diagnostic Laboratory (CMDL) station at Niwot Ridge, Colorado (40.0°N, 105.5°W, 3013 m altitude), archived measurement from the same location, and early CMDL northern hemisphere Pacific cruise measurements. The average ratio of the retrieved tropospheric mixing ratio relative to the CMDL surface mixing ratio is 1.053 for the overlapping 1987 to 2002 time period. The retrieved mean tropospheric mixing ratio is consistent with the surface measurements within the errors estimated for the remote sensing observations.     

Monitoring process for attributes with quality deterioration and diagnosis errors

The aim of this paper is to present an online economical quality-control procedure for attributes in a process subject to quality deterioration after random shift and misclassification errors during inspections. The process starts in control (State I) and, in a random time, it shifts to out of control (State II). Once at State II, the non-conforming fraction increases according to a non-decreasing function ψ(z), where z is the number of items produced after a shift. The monitoring procedure consists of inspecting a single item at every m produced items, which is examined r times independently to decide its condition. Once an inspected item is declared non-conforming, the process is stopped and adjusted. A direct search technique is used to find the optimum parameters which minimize the expected cost function. The proposed model is illustrated by a numerical example. Copyright © 2007 John Wiley & Sons, Ltd.     

Biotransformation of arsenate to arsenosugars by Chlorella vulgaris

Chlorella vulgaris was cultivated in a growth medium containing arsenate concentration of <0.01, 10, 100 and 1000 mg l^?1. Illumination was carried out in 12 h cycles for 5 days. The health status of the culture was monitored by continuous pH and dissolved oxygen (DO) readings. Destructive sampling was used for the determination of biomass, chlorophyll, total arsenic and arsenic species. The chlorophyll a content, the DO and pH cycles were not significantly different for the different arsenate concentrations in the culture. In contrast, biomass production was significantly (p < 0.05) increased for the arsenic(V) treatment at 1000 mg l^?1 compared with 100 mg l^?1. The arsenic concentration in the algae increased with the arsenate concentration in the culture. However, the bioconcentration factor decreased a hundred‐fold with increase of arsenate from the background level to 1000 mg l^?1. The arsenic species were identified by using strong anion‐exchange high‐performance liquid chromatography–inductively coupled plasma mass spectrometry analysis after methanol/water (1 : 1) extraction. The majority (87–100%) of the extractable arsenic was still arsenate; arsenite was found to be between 1 and 6% of total extractable arsenic in the algae. In addition to dimethylarsinic acid, one unknown arsenical (almost co‐eluting with methylarsonic acid) and three different arsenosugars have been identified for the first time in C. vulgaris growing in a culture containing a mixture of antibiotics and believed to be axenic. The transformation to arsenosugars in the algae is not dependent on the arsenate concentration in the culture and varies between 0.2 and 5% of total accumulated arsenic. Although no microbiological tests for bacterial contamination were made, this study supports the hypothesis that algae, and not associated bacteria, produce the arsenosugars. Copyright © 2003 John Wiley & Sons, Ltd.     

Practical aspects of suppressed ion chromatography for cations in human serum

In spite of the good accuracy and precision of ion chromatographic methods for the determination of mono- and divalent cations in human serum, the major drawback with these methods were problems with the membrane suppressor's performance. Here, we described experiments undertaken to solve these problems. We address in particular the use of histidine-sulfuric acid eluents, sample purification with OnGuard-A cartridges and chromatographic “front-cut” for divalent cations. The latter two adaptations, resulting in removal of the anionic species from the sample, were successful in solving the observed suppressor problems. The eluent substitution, moreover, allowed us to switch from the chemical to the electric suppression mode. We believe that these adaptations will allow secure and robust determination of cations in human serum samples with ion chromatography.