Histidine hydrogen bonding in MHC at pH 5 and pH 7 modeled by molecular docking and molecular dynamics simulations

Hydrogen bonds play important roles in maintaining the structure of proteins and in the formation of most biomolecular protein-ligand complexes. All amino acids can act as hydrogen bond donors and acceptors. Among amino acids, Histidine is unique, as it can exist in neutral or positively charged forms within the physiological pH range of 5.0 to 7.0. Histidine can thus interact with other aromatic residues as well as forming hydrogen bonds with polar and charged residues. The ability of His to exchange a proton lies at the heart of many important functional biomolecular interactions, including immunological ones. By using molecular docking and molecular dynamics simulation, we examine the influence of His protonation/deprotonation on peptide binding affinity to MHC class II proteins from locus HLA-DP. Peptide-MHC interaction underlies the adaptive cellular immune response, upon which the next generation of commercially-important vaccines will depend. Consistent with experiment, we find that peptides containing protonated His residues bind better to HLA-DP proteins than those with unprotonated His. Enhanced binding at pH 5.0 is due, in part, to additional hydrogen bonds formed between peptide His+ and DP proteins. In acidic endosomes, protein His79β is predominantly protonated. As a result, the peptide binding cleft narrows in the vicinity of His79β, which stabilizes the peptide - HLA-DP protein complex. © 2014 Bentham Science Publishers.

Influence of reaction atmosphere (H2O, N2, H2, CO2, CO) on fluidized-bed fast pyrolysis of biomass using detailed tar vapor chemistry in computational fluid dynamics

Secondary pyrolysis in fluidized bed fast pyrolysis of biomass is the focus of this work. A novel computational fluid dynamics (CFD) model coupled with a comprehensive chemistry scheme (134 species and 4169 reactions, in CHEMKIN format) has been developed to investigate this complex phenomenon. Previous results from a transient three-dimensional model of primary pyrolysis were used for the source terms of primary products in this model. A parametric study of reaction atmospheres (H2O, N2, H2, CO2, CO) has been performed. For the N2 and H2O atmosphere, results of the model compared favorably to experimentally obtained yields after the temperature was adjusted to a value higher than that used in experiments. One notable deviation versus experiments is pyrolytic water yield and yield of higher hydrocarbons. The model suggests a not overly strong impact of the reaction atmosphere. However, both chemical and physical effects were observed. Most notably, effects could be seen on the yield of various compounds, temperature profile throughout the reactor system, residence time, radical concentration, and turbulent intensity. At the investigated temperature (873 K), turbulent intensity appeared to have the strongest influence on liquid yield. With the aid of acceleration techniques, most importantly dimension reduction, chemistry agglomeration, and in-situ tabulation, a converged solution could be obtained within a reasonable time (∼30 h). As such, a new potentially useful method has been suggested for numerical analysis of fast pyrolysis.

Comprehensive secondary pyrolysis in fluidized-bed fast pyrolysis of biomass, a fluid dynamics based modelling effort

Homogenous secondary pyrolysis is category of reactions following the primary pyrolysis and presumed important for fast pyrolysis. For the comprehensive chemistry and fluid dynamics, a probability density functional (PDF) approach is used; with a kinetic scheme comprising 134 species and 4169 reactions being implemented. With aid of acceleration techniques, most importantly Dimension Reduction, Chemistry Agglomeration and In-situ Tabulation (ISAT), a solution within reasonable time was obtained. More work is required; however, a solution for levoglucosan (C6H10O5) being fed through the inlet with fluidizing gas at 500 °C, has been obtained. 88.6% of the levoglucosan remained non-decomposed, and 19 different decomposition product species were found above 0.01% by weight. A homogenous secondary pyrolysis scheme proposed can thus be implemented in a CFD environment and acceleration techniques can speed-up the calculation for application in engineering settings.

Real-time high-resolution heterodyne-based measurements of spectral dynamics in fibre lasers

Conventional tools for measurement of laser spectra (e.g. optical spectrum analysers) capture data averaged over a considerable time period. However, the generation spectrum of many laser types may involve spectral dynamics whose relatively fast time scale is determined by their cavity round trip period, calling for instrumentation featuring both high temporal and spectral resolution. Such real-time spectral characterisation becomes particularly challenging if the laser pulses are long, or they have continuous or quasi-continuous wave radiation components. Here we combine optical heterodyning with a technique of spatiooral intensity measurements that allows the characterisation of such complex sources. Fast, round-trip-resolved spectral dynamics of cavity-based systems in real-time are obtained, with temporal resolution of one cavity round trip and frequency resolution defined by its inverse (85 ns and 24 MHz respectively are demonstrated). We also show how under certain conditions for quasi-continuous wave sources, the spectral resolution could be further increased by a factor of 100 by direct extraction of phase information from the heterodyned dynamics or by using double time scales within the spectrogram approach.

Langevin dynamics, large deviations and instantons for the quasi-geostrophic model and two-dimensional Euler equations

We investigate a class of simple models for Langevin dynamics of turbulent flows, including the one-layer quasi-geostrophic equation and the two-dimensional Euler equations. Starting from a path integral representation of the transition probability, we compute the most probable fluctuation paths from one attractor to any state within its basin of attraction. We prove that such fluctuation paths are the time reversed trajectories of the relaxation paths for a corresponding dual dynamics, which are also within the framework of quasi-geostrophic Langevin dynamics. Cases with or without detailed balance are studied. We discuss a specific example for which the stationary measure displays either a second order (continuous) or a first order (discontinuous) phase transition and a tricritical point. In situations where a first order phase transition is observed, the dynamics are bistable. Then, the transition paths between two coexisting attractors are instantons (fluctuation paths from an attractor to a saddle), which are related to the relaxation paths of the corresponding dual dynamics. For this example, we show how one can analytically determine the instantons and compute the transition probabilities for rare transitions between two attractors.

Spatio-temporal intensity dynamics of passively mode-locked fiber laser

We present recent results on measurements of intensity spatio-temporal dynamics in passively mode-locked fibre laser. We experimentally uncover distinct, dynamic and stable spatio-temporal generation regimes of various stochasticity and periodicity properties in though-to-be unstable laser. We present a method to distinguish various types of generated coherent structures, including rogue and shock waves, within the radiation by means of introducing of intensity ACF evolution map. We also discuss how the spectral dynamics could be measured in fiber lasers generating irregular train of pulses of quasi-CW generation via combination of heterodyning and intensity spatio-temporal measurement concept.

Lattice approach to the dynamics of the DPSK-encoded soliton trains

We study the dynamical properties of the RZ-DPSK encoded sequences, focusing on the instabilities in the soliton train leading to the distortions of the information transmitted. The problem is reformulated within the framework of complex Toda chain model which allows one to carry out the simplified description of the optical soliton dynamics. We elucidate how the bit composition of the pattern affects the initial (linear) stage of the train dynamics and explain the general mechanisms of the appearance of unstable collective soliton modes. Then we discuss the nonlinear regime using asymptotic properties of the pulse stream at large propagation distances and analyze the dynamical behavior of the train classifying different scenarios for the pattern instabilities. Both approaches are based on the machinery of Hermitian and non-Hermitian lattice analysis. © 2010 IEEE.