An extended dead-end elimination algorithm to determine gap-free lists of low energy states

Proteins are flexible systems and commonly populate several functionally important states. To understand protein function, these states and their energies have to be identified. We introduce an algorithm that allows the determination of a gap-free list of the low energy states. This algorithm is based on the dead-end elimination (DEE) theorem and is termed X-DEE (extended DEE). X-DEE is applicable to discrete systems whose state energy can be formulated as pairwise interaction between sites and their intrinsic energies. In this article, the computational performance of X-DEE is analyzed and discussed. X-DEE is implemented to determine the lowest energy protonation states of proteins, a problem to which DEE has not been applied so far. We use X-DEE to calculate a list of low energy protonation states for two bacteriorhodopsin structures that represent the first proton transfer step of the bacteriorhodopsin photocycle.     

Photodissociation of alkyl iodides in helium nanodroplets. III. Recombination

The recombination of fragments resulting from the photodissociation of (fluorinated) alkyl iodides in helium nanodroplets at a wavelength of 266 nm has been investigated by means of ion imaging techniques. It is found that in the case of CH3I an appreciable fraction of the fragments recombine in the aftermath of the photolysis. The proposed mechanism involves a complete translational relaxation of both photofragments inside the nanodroplets followed by geminate recombination of the fragments. In contrast with CH3I, no recombination is observed for CF3I. This is attributed to the larger masses and the different initial kinetic energies of the fragments produced by the photolysis of CF3I, which strongly diminishes the fragment thermalization efficiency.     

Effects of cocaine on blood flow and oxygen metabolism in the rat brain: implications for phMRI

The effects of cocaine on cerebral blood flow and tissue oxygen levels in the rat brain were investigated with concurrent laser Doppler flowmetry and fluorescence quenching spectroscopy. Responses elicited by mild hypercapnia were used as calibration to assess the effects of cocaine on oxidative metabolism. Intravenous cocaine challenge of 0.5 mg/kg induced significant increases in tissular oxygenation and perfusion in all regions investigated (primary motor cortex, medial prefrontal cortex and dorsal striatum). Mild hypercapnia, a challenge that affects haemodynamics but not metabolism, elicited comparable changes in blood flow but substantially larger changes in tissue oxygen levels. These differences in tissue oxygen build-up suggest that increased oxidative metabolism is a significant component of the cerebral metabolic response to acute cocaine challenge. The implications for the interpretation of pharmacological MRI data are discussed.     

Glassy arrest in colloidal fluids with size polydispersity

Short-range attraction between colloidal particles such as proteins can drive a glass-like structural arrest. For monodisperse systems, mode-coupling theory affords a simple asymptotic prediction of the transition. Here, using a depletion mapping framework, we extend this result to incorporate size polydispersity. For comparison, we also give an energy landscape formulation of the transition. We comment on the relevance to subcellular crowding, recombinant protein expression, and osmotic stress in microbial organisms.     

Determination of volatile organic hydrocarbons in water samples by solid-phase dynamic extraction

In the present study a headspace solid-phase dynamic extraction method coupled to gas chromatography–mass spectrometry (HS-SPDE-GC/MS) for the trace determination of volatile halogenated hydrocarbons and benzene from groundwater samples was developed and evaluated. As target compounds, benzene as well as 11 chlorinated and brominated hydrocarbons (vinyl chloride, dichloromethane, cis-1,2-dichloroethylene, trans-1,2-dichloroethylene, carbon tetrachloride, chloroform, trichloroethylene, tetrachloroethylene, bromoform) of environmental and toxicological concern were included in this study. The analytes were extracted using a SPDE needle device, coated with a poly(dimethylsiloxane) with 10% embedded activated carbon phase (50-μm film thickness and 56-mm film length) and were analyzed by GC/MS in full-scan mode. Parameters that affect the extraction yield such as extraction and desorption temperature, salting-out, extraction and desorption flow rate, extraction volume and desorption volume, the number of extraction cycles, and the pre-desorption time have been evaluated and optimized. The linearity of the HS-SPDE-GC/MS method was established over several orders of magnitude. Method detection limits (MDLs) for the compounds investigated ranged between 12 ng/L for cis-dichloroethylene and trans-dichloroethylene and 870 ng/L for vinyl chloride. The method was thoroughly validated, and the precision at two concentration levels (0.1 mg/L and a concentration 5 times above the MDL) was between 3.1 and 16% for the analytes investigated. SPDE provides high sensitivity, short sample preparation and extraction times and a high sample throughput because of full automation. Finally, the applicability to real environmental samples is shown exemplarily for various groundwater samples from a former waste-oil recycling facility. Groundwater from the site showed a complex contamination with chlorinated volatile organic compounds and aromatic hydrocarbons. Figure SPDE Principle     

Hereditary and maximal crossed product orders

We first deal with classical crossed products , where is a finite group acting on a Dedekind domain and (the -invariant elements in ) a DVR, admitting a separable residue fields extension. Here is a 2-cocycle. We prove that is hereditary if and only if is semi-simple. In particular, the heredity property may hold even when is not tamely ramified (contradicting standard textbook references). For an arbitrary Krull domain , we use the above to prove that under the same separability assumption, is a maximal order if and only if its height one prime ideals are extended from . We generalize these results by dropping the residual separability assumptions. An application to non-commutative unique factorization rings is also presented.

     

Multiscale spectroscopy using a monolithic liquid core waveguide with laterally attached fiber ports

In conventional absorption spectrometers, the range of accessible concentrations of analytes in aqueous solution is significantly limited by the dynamic range of the measurement system. Here we introduce the concept of multiscale spectroscopy allowing extending that range by orders of magnitude within one single device. The concept relies on using multiple light-sample interaction lengths, boosting the accessible concentration range by a particular extension factor. We experimentally implement our concept by a liquid core waveguide having multiple fiber ports side-wise attached to the waveguide, thus probing the light propagating inside the core at predefined distances from the input. This configuration provides three orders of magnitude of interaction length in one device. To verify the concept we exemplarily determine the concentrations of nitrate and of Rhodamine 6G in water, showing one hundred times improved measurement capabilities. The multiscale spectrometer uses the entire sample volume and allows the simultaneous measurement of fluorescence and attenuance. Due to its integrated design and the extended measurements capabilities, we anticipate application of our device in many application-relevant areas such as water quality analysis or environmental science.