Shaper-assisted full-phase characterization of UV pulses without a spectrometer

A full-phase measurement of low-energy femtosecond UV pulses is presented. The method relies on phase retrieval of measured sonogram traces and is greatly simplified by a two-dimensional shaper-assisted cross correlation setup. As all required pulses are generated by the pulse shaper, the method is free of external references and additional tunable filter setups.     

An efficient and robust numerical algorithm for estimating parameters in Turing systems

We present a new algorithm for estimating parameters in reaction–diffusion systems that display pattern formation via the mechanism of diffusion-driven instability. A Modified Discrete Optimal Control Algorithm (MDOCA) is illustrated with the Schnakenberg and Gierer–Meinhardt reaction–diffusion systems using PDE constrained optimization techniques. The MDOCA algorithm is a modification of a standard variable step gradient algorithm that yields a huge saving in computational cost. The results of numerical experiments demonstrate that the algorithm accurately estimated key parameters associated with stationary target functions generated from the models themselves. Furthermore, the robustness of the algorithm was verified by performing experiments with target functions perturbed with various levels of additive noise. The MDOCA algorithm could have important applications in the mathematical modeling of realistic Turing systems when experimental data are available.     

Allylic rearrangement of trans-pinocarveol esters

The allylic rearrangement of trans-pinocarveol esters ( I ) to myrtenol esters ( II ), a reaction of interest in the chemistry of terpenes and cannabinoids, has been theoretically investigated. The intramolecular, cyclization-induced rearrangement results in equilibrium mixtures of the starting compounds and the products with the ratio of I vs. II in the equilibrium mixture being determined by their thermodynamic stabilities. The relative thermodynamic stabilities as reflected by calculated AM1 heats of formations (ΔHf) were determined for various I-II ester pairs. The study, in agreement with available experimental evidence, indicates that generally I , which contain an endocyclic double bond, are more stable and thus predominantly form following rearrangements. In two cases (acetate and pivalate) the stability is reversed. Calculations performed for similar structures, esters of 2-methylene cyclohexane-1-ol ( IV ) and 1-cyclohexene-1-methanol ( V ) gave similar results. Structural and electronic factors which might influence the stability of these compounds were examined. Interestingly, a correlation between thermodynamic stability and dipole moments was observed. © 1996 John Wiley & Sons, Inc.     

The NiII,HgII and CuII complexes of 12‐membered‐ring mixed‐donor macrocycles

The structures of di­aqua(1,7‐dioxa‐4‐thia‐10‐aza­cyclo­do­decane)­nickel dinitrate, [Ni(C₈H₁₇NO₂S)(H₂O)₂](NO₃)₂, (I), bis­(nitrato‐O,O′)(1,4,7‐trioxa‐10‐aza­cyclo­do­decane)­mercury, [Hg(NO₃)₂(C₈H₁₇NO₃)], (II), and aqua­(nitrato‐O)(1‐oxa‐4,7,10‐tri­aza­cyclo­do­decane)copper nitrate, [Cu(NO₃)(C₈H₁₉N₃O)(H₂O)]NO₃, (III), reveal each macrocycle binding in a tetradentate manner. The conformations of the ligands in (I) and (III) are the same and distinct from that identified for (II). These differences are in agreement with molecular‐mechanics predictions of ligand conformation as a function of metal‐ion size.     

Singlet versus triplet dynamics of β-carotene studied by quantum control spectroscopy

Biomolecules very often present complex energy deactivation networks with overlapping electronic absorption bands, making their study a difficult task. This can be especially true in transient absorption spectroscopy when signals from bleach, excited state absorption and stimulated emission contribute to the signal. However, quantum control spectroscopy can be used to discriminate specific electronic states of interest by applying specifically designed laser pulses. Recently, we have shown the control of energy flow in bacterial light-harvesting using shaped pump pulses in the visible and the selective population of pathways in carotenoids using an additional depletion pulse in the transient absorption technique. Here, we apply a closed-loop optimization approach to β-carotene using a spatial light modulator to decipher the energy flow network after a multiphoton excitation with a shaped ultrashort pulse in the near-IR. After excitation, two overlapping bands were detected and identified as the S₁ state and the first triplet state T₁. Using the transient absorption signal at a specific probe delay as feedback, the triplet signal could be optimized over the singlet contribution.     

Tuning Human Serum Albumin (HSA) Hydrogels through Albumin Glycation

The changes of technological properties of albumin-based hydrogels induced by increasing degrees of post-translational modification of the protein are reported. Maillard-type modification of amino acids arginine and lysine of albumin is achieved through glyoxal as an α-dicarbonyl compound. The degrees of modification are fine-tuned using different molar ratios of glyoxal. Hydrogels are thermally induced by heating highly concentrated precursor solutions above the protein's denaturation temperature. While the post-translational modifications are determined and quantified with mass spectrometry, continuous-wave (CW) electron paramagnetic resonance (EPR) spectroscopy shed light on the protein fatty acid binding capacity and changes thereof in solution and in the gel state. The viscoelastic behavior is characterized as a measure of the physical strength of the hydrogels. On the nanoscopic level, the modified albumins in low concentration solution reveal lower binding capacities with increasing degrees of modification. On the contrary, in the gel state, the binding capacity remains constant at all degrees of modifications. This indicates that the loss of fatty acid binding capacity for individual albumin molecules is partially compensated by new binding sites in the gel state, potentially formed by modified amino acids. Such, albumin glycation offers a fine-tuning method of technological and nanoscopic properties of these gels.     

Stoichiometric inhibition of amyloid beta-protein aggregation with peptides containing alternating alpha,alpha-disubstituted amino acids

We have prepared two peptides based on the hydrophobic core (Lys-Leu-Val-Phe-Phe) of amyloid beta-protein (Abeta) that contain alpha,alpha-disubstituted amino acids at alternating positions, but differ in the positioning of the oligolysine chain (AMY-1, C-terminus; AMY-2, N-terminus). We have studied the effects of AMY-1 and AMY-2 on the aggregation of Abeta and find that, at stoichiometric concentrations, both peptides completely stop Abeta fibril growth. Equimolar mixtures of AMY-1 and Abeta form only globular aggregates as imaged by scanning force microscopy and transmission electron microscopy. These samples show no signs of protofibrillar or fibrillar material even after prolonged periods of time (4.5 months). Also, 10 mol % of AMY-1 prevents Abeta self-assembly for long periods of time; aged samples (4.5 months) show only a few protofibrillar or fibrillar aggregates. Circular dichroism spectroscopy of equimolar mixtures of AMY-1 and Abeta show that the secondary structure of the mixture changes over time and progresses to a predominantly beta-sheet structure, which is consistent with the design of these inhibitors preferring a sheet-like conformation. Changing the position of the charged tail on the peptide, AMY-2 interacts with Abeta differently in that equimolar mixtures form large ( approximately 1 mum) globular aggregates which do not progress to fibrils, but precipitate out of solution. The differences in the aggregation mediated by the two peptides is discussed in terms of a model where the inhibitors act as cosurfactants that interfere with the native ability of Abeta to self-assemble by disrupting hydrophobic interactions either at the C-terminus or N-terminus of Abeta.     

Optimisation and robustness analysis of a hydrophobic interaction chromatography step

Process development, optimisation and robustness analysis for chromatography separations are often entirely based on experimental work and generic knowledge. The present study proposes a method of gaining process knowledge and assisting in the robustness analysis and optimisation of a hydrophobic interaction chromatography step using a model-based approach. Factorial experimental design is common practice in industry today for robustness analysis. The method presented in this study can be used to find the critical parameter variations and serve as a basis for reducing the experimental work. In addition, the calibrated model obtained with this approach is used to find the optimal operating conditions for the chromatography column. The methodology consists of three consecutive steps. Firstly, screening experiments are performed using a factorial design. Secondly, a kinetic-dispersive model is calibrated using gradient elution and column load experiments. Finally, the model is used to find optimal operating conditions and a robustness analysis is conducted at the optimal point. The process studied in this work is the separation of polyclonal IgG from BSA using hydrophobic interaction chromatography.     

Exploring the local conformational space of a membrane protein by site-directed spin labeling

Molecular modeling based on a hybrid evolutionary optimization and an information condensation algorithm, called GHOST, of spin label ESR spectra was applied to study the structure and dynamics of membrane proteins. The new method is capable of providing detailed molecular information about the conformational space of the spin-labeled segment of the protein in a membrane system. The method is applied to spin-labeled bacteriophage M13 major coat protein, which is used as a model membrane protein. Single cysteine mutants of the coat protein were labeled with nitroxide spin labels and incorporated in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers. The new computational method allows us to monitor distributions of local spatial constraints and molecular mobility, in addition to information about the location of the protein in a membrane. Furthermore, the results suggest that different local conformations may coexist in the membrane protein. The knowledge of different local conformations may help us to better understand the function-structure relationship of membrane proteins.