Elucidating the structure of chiral molecules by using amplified vibrational circular dichroism: from theory to experimental realization

Recent experimental observations of enhanced vibrational circular dichroism (VCD) in molecular systems with low-lying electronically excited states suggest interesting new applications of VCD spectroscopy. The theory describing VCD enhancement through vibronic coupling schemes was derived by Nafie in 1983, but only recently experimental evidence of VCD amplification has demonstrated the extent to which this effect can be exploited as a structure elucidation tool to probe local structure. In this Concept paper, we give an overview of the physics behind vibrational circular dichroism, in particular the equations governing the VCD amplification effect, and review the latest experimental developments with a prospective view on the application of amplified VCD to locally probe biomolecular structure.

Stereochemistry and thermal stability of tartaric acid on the intrinsically chiral Cu{531} surface

Intrinsically chiral metal surfaces provide enantiospecific reaction environments without the need of coadsorbed modifiers. Amongst the intrinsically chiral copper surfaces, Cu{531} has the smallest unit cell and the highest density of chiral sites. XPS, NEXAFS and TPD were employed to investigate the adsorption and decomposition behaviour of the two chiral enantiomers of tartaric acid on this surface. The results obtained from XPS and NEXAFS show that at saturation coverage both enantiomers of tartaric acid adsorb in a μ4 configuration through the two carboxylic groups,which are rotatedwith respect to each other by 90°±≈15°within the surface plane. At intermediate coverage the R,R enantiomer adopts a similar configuration, but the S,S enantiomer is different and shows a high degree of dissociation. Growth of multilayers is observed at high exposures when the sample is kept at below 370 K. TPD experiments show that multilayers desorb between 390 K and 470 K and decomposition of the chemisorbed layer occurs between 470 K and 600 K. The desorption spectra support a two-step decomposition mechanism with a O_C_C_O or HO–HC_CH–OH intermediate that leads to production of CO2 and CO. Enantiomeric differences are observed in the desorption features related to the decomposition of the chemisorbed layer.

The utility of convection-permitting ensembles for the prediction of stationary convective bands

This study examines convection-permitting numerical simulations of four cases of terrain-locked quasi-stationary convective bands over the UK. For each case, a 2.2-km grid-length 12-member ensemble and 1.5-km grid-length deterministic forecast are analyzed, each with two different initialization times. Object-based verification is applied to determine whether the simulations capture the structure, location, timing, intensity and duration of the observed precipitation. These verification diagnostics reveal that the forecast skill varies greatly between the four cases. Although the deterministic and ensemble simulations captured some aspects of the precipitation correctly in each case, they never simultaneously captured all of them satisfactorily. In general, the models predicted banded precipitation accumulations at approximately the correct time and location, but the precipitating structures were more cellular and less persistent than the coherent quasi-stationary bands that were observed. Ensemble simulations from the two different initialization times were not significantly different, which suggests a potential benefit of time-lagging subsequent ensembles to increase ensemble size. The predictive skill of the upstream larger-scale flow conditions and the simulated precipitation on the convection-permitting grids were strongly correlated, which suggests that more accurate forecasts from the parent ensemble should improve the performance of the convection-permitting ensemble nested within it.

A new adaptive multiple modelling approach for non-linear and non-stationary systems

This paper proposes a novel adaptive multiple modelling algorithm for non-linear and non-stationary systems. This simple modelling paradigm comprises K candidate sub-models which are all linear. With data available in an online fashion, the performance of all candidate sub-models are monitored based on the most recent data window, and M best sub-models are selected from the K candidates. The weight coefficients of the selected sub-model are adapted via the recursive least square (RLS) algorithm, while the coefficients of the remaining sub-models are unchanged. These M model predictions are then optimally combined to produce the multi-model output. We propose to minimise the mean square error based on a recent data window, and apply the sum to one constraint to the combination parameters, leading to a closed-form solution, so that maximal computational efficiency can be achieved. In addition, at each time step, the model prediction is chosen from either the resultant multiple model or the best sub-model, whichever is the best. Simulation results are given in comparison with some typical alternatives, including the linear RLS algorithm and a number of online non-linear approaches, in terms of modelling performance and time consumption.

Non-stationary frequency analysis of extreme daily rainfall in Sao Paulo, Brazil

This work is an assessment of frequency of extreme values (EVs) of daily rainfall in the city of Sao Paulo. Brazil, over the period 1933-2005, based on the peaks-over-threshold (POT) and Generalized Pareto Distribution (GPD) approach. Usually. a GPD model is fitted to a sample of POT Values Selected With a constant threshold. However. in this work we use time-dependent thresholds, composed of relatively large p quantities (for example p of 0.97) of daily rainfall amounts computed from all available data. Samples of POT values were extracted with several Values of p. Four different GPD models (GPD-1, GPD-2, GPD-3. and GDP-4) were fitted to each one of these samples by the maximum likelihood (ML) method. The shape parameter was assumed constant for the four models, but time-varying covariates were incorporated into scale parameter of GPD-2. GPD-3, and GPD-4, describing annual cycle in GPD-2. linear trend in GPD-3, and both annual cycle and linear trend in GPD-4. The GPD-1 with constant scale and shape parameters is the simplest model. For identification of the best model among the four models WC used rescaled Akaike Information Criterion (AIC) with second-order bias correction. This criterion isolates GPD-3 as the best model, i.e. the one with positive linear trend in the scale parameter. The slope of this trend is significant compared to the null hypothesis of no trend, for about 98% confidence level. The non-parametric Mann-Kendall test also showed presence of positive trend in the annual frequency of excess over high thresholds. with p-value being virtually zero. Therefore. there is strong evidence that high quantiles of daily rainfall in the city of Sao Paulo have been increasing in magnitude and frequency over time. For example. 0.99 quantiles of daily rainfall amount have increased by about 40 mm between 1933 and 2005. Copyright (C) 2008 Royal Meteorological Society

Life history, morphological variability and growth rates of the life phases of Gracilaria tenuistipitata (Rhodophyta: Gracilariales) in vitro

Gracilaria tenuistipitata, a species of commercial interest, is becoming a model organism for studies on red algal physiology and molecular biology as it can be grown easily in vitro under a broad range of conditions. Most of the experiments carried out around the world have been based on a tetrasporophytic clone isolated in our laboratory from a specimen collected in China. Here we describe the life history of this species, give anatomic details of the reproductive structures, illustrate the morphological variability of tetraspore progeny and compare the growth rate of gametophytic and sporophytic thalli. Tetrasporophytic branches showed higher growth rates than gametophytic branches.

CspC and CspD are essential for Caulobacter crescentus stationary phase survival

The cold shock response in bacteria involves the expression of low-molecular weight cold shock proteins (CSPs) containing a nucleic acid-binding cold shock domain (CSD), which are known to destabilize secondary structures on mRNAs, facilitating translation at low temperatures. Caulobacter crescentus cspA and cspB are induced upon cold shock, while cspC and cspD are induced during stationary phase. In this work, we determined a new coding sequence for the cspC gene, revealing that it encodes a protein containing two CSDs. The phenotypes of C. crescentus csp mutants were analyzed, and we found that cspC is important for cells to maintain viability during extended periods in stationary phase. Also, cspC and cspCD strains presented altered morphology, with frequent non-viable filamentous cells, and cspCD also showed a pronounced cell death at late stationary phase. In contrast, the cspAB mutant presented increased viability in this phase, which is accompanied by an altered expression of both cspC and cspD, but the triple cspABD mutant loses this characteristic. Taken together, our results suggest that there is a hierarchy of importance among the csp genes regarding stationary phase viability, which is probably achieved by a fine tune balance of the levels of these proteins.

SpdR, a Response Regulator Required for Stationary-Phase Induction of Caulobacter crescentus cspD

The cold shock protein (CSP) family includes small polypeptides that are induced upon temperature downshift and stationary phase. The genome of the alphaproteobacterium Caulobacter crescentus encodes four CSPs, with two being induced by cold shock and two at the onset of stationary phase. In order to identify the environmental signals and cell factors that are involved in cspD expression at stationary phase, we have analyzed cspD transcription during growth under several nutrient conditions. The results showed that expression of cspD was affected by the medium composition and was inversely proportional to the growth rate. The maximum levels of expression were decreased in a spoT mutant, indicating that ppGpp may be involved in the signalization for carbon starvation induction of cspD. A Tn5 mutant library was screened for mutants with reduced cspD expression, and 10 clones that showed at least a 50% reduction in expression were identified. Among these, a strain with a transposon insertion into a response regulator of a two-component system showed no induction of cspD at stationary phase. This protein (SpdR) was able to acquire a phosphate group from its cognate histidine kinase, and gel mobility shift assay and DNase I footprinting experiments showed that it binds to an inverted repeat sequence of the cspD regulatory region. A mutated SpdR with a substitution of the conserved aspartyl residue that is the probable phosphorylation site is unable to bind to the cspD regulatory region and to complement the spdR mutant phenotype.

Micelles forming biaxial lyotropic nematic phases

The paper by Yu and Saupe on the first biaxial nematic phase created excitement for a number of reasons. Some theories of biaxial phases already existed, but experimental observation was still lacking. The phase was discovered in a lyotropic system with three components, which in theory is difficult. Lyotropic liquid crystals are composed of supramolecular assemblies of amphiphilic molecules, which may change shape and size as a function of concentration and temperature. The experimental phase diagram of the lyotropic biaxial phase was rather complex, with the biaxial region inserted between nematic cylindrical and nematic discotic phases via second-order transitions. In addition, re-entrant behaviour was evident. Saupe investigated further systems experimentally, observing that the biaxial phase might be absent in cases where a direct transition between the cylindrical and discotic phases occurred. He provided a range of theoretical and experimental contributions on the properties of these lyotropics, but was very cautious regarding the detailed amphiphilic assemblies involved. The present paper reviews this area, focusing on proposals for the structure of the micellar assemblies. Emphasis is placed on recent papers which indicate a transformation of the two uniaxial shapes, in mixing conditions, both from the theoretical and the experimental point of view, and to questions still requiring further study.

Aging and stationary properties of non-equilibrium symmetrical three-state models

We consider a non-equilibrium three-state model whose dynamics is Markovian and displays the same symmetry as the three-state Potts model, i.e. the transition rates are invariant under the cyclic permutation of the states. Unlike the Potts model, detailed balance is, in general, not satisfied. The aging and the stationary properties of the model defined on a square lattice are obtained by means of large-scale Monte Carlo simulations. We show that the phase diagram presents a critical line, belonging to the three-state Potts universality class, that ends at a point whose universality class is that of the Voter model. Aging is considered on the critical line, at the Voter point and in the ferromagnetic phase.

Infrared chiral anomaly at finite temperature

We study the Schwinger model at finite temperature and show that a temperature dependent chiral anomaly may arise from the long distance behavior of the electric field. At high temperature this anomaly depends linearly on the temperature T and is present not only in the two point function, but also in all even point amplitudes. (C) 2011 Elsevier B.V. All rights reserved.

NUCLEAR INTERACTIONS: THE CHIRAL PICTURE

Chiral expansions of the two-pion exchange components of both two- and three-nucleon forces are reviewed and a discussion is made of the predicted pattern of hierarchies. The strength of the scalar-isoscalar central potential is found to be too large and to defy expectations from the symmetry. The causes of this effect can be understood by studying the nucleon scalar form factor.

Shared information in stationary states at criticality

We consider bipartitions of one-dimensional extended systems whose probability distribution functions describe stationary states of stochastic models. We define estimators of the information shared between the two subsystems. If the correlation length is finite, the estimators stay finite for large system sizes. If the correlation length diverges, so do the estimators. The definition of the estimators is inspired by information theory. We look at several models and compare the behaviors of the estimators in the finite-size scaling limit. Analytical and numerical methods as well as Monte Carlo simulations are used. We show how the finite-size scaling functions change for various phase transitions, including the case where one has conformal invariance.

Influence of interlayer tunneling on the quantized Hall phases in intentionally disordered multilayer structures

Stability of the quantized Hall phases is studied in weakly coupled multilayers as a function of the interlayer correlations controlled by the interlayer tunneling and by the random variation of the well thicknesses. A strong enough interlayer disorder destroys the symmetry responsible for the quantization of the Hall conductivity, resulting in the breakdown of the quantum Hall effect. A clear difference between the dimensionalities of the metallic and insulating quantum Hall phases is demonstrated. The sharpness of the quantized Hall steps obtained in the coupled multilayers with different degrees of randomization was found consistent with the calculated interlayer tunneling energies. The observed width of the transition between the quantized Hall states in random multilayers is explained in terms of the local fluctuations of the electron density.

A general treatment of geometric phases and dynamical invariants

Based only on the parallel-transport condition, we present a general method to compute Abelian or non-Abelian geometric phases acquired by the basis states of pure or mixed density operators, which also holds for nonadiabatic and noncyclic evolution. Two interesting features of the non-Abelian geometric phase obtained by our method stand out: i) it is a generalization of Wilczek and Zee`s non-Abelian holonomy, in that it describes nonadiabatic evolution where the basis states are parallelly transported between distinct degenerate subspaces, and ii) the non-Abelian character of our geometric phase relies on the transitional evolution of the basis states, even in the nondegenerate case. We apply our formalism to a two-level system evolving nonadiabatically under spontaneous decay to emphasize the non- Abelian nature of the geometric phase induced by the reservoir. We also show, through the generalized invariant theory, that our general approach encompasses previous results in the literature. Copyright (c) EPLA, 2008.