Helix Formation and Folding in an Artificial Peptide

We study the relation between $\alpha$-helix formation and folding for a simple artificial peptide, Ala$_{10}$-Gly$_5$-Ala$_{10}$. Our data rely on multicanonical Monte Carlo simulations where the interactions among all atoms are taken into account. The free-energy landscape of the peptide is evaluated for various temperatures. Our data indicate that folding of this peptide is a two-step process: in a first step two $\alpha$-helices are formed which afterwards re-arrange themselves into a U-like structure.Comment: 15 pages, with 9 eps figure

Helix vs. Sheet Formation in a Small Peptide

Segments with the amino acid sequence EKAYLRT appear in natural occurring proteins both in $\alpha$-helices and $\beta$-sheets. For this reason, we have use this peptide to study how secondary structure formation in proteins depends on the local environment. Our data rely on multicanonical Monte Carlo simulations where the interactions among all atoms are taken into account. Results in gas phase are compared with that in an implicit solvent. We find that both in gas phase and solvated EKAYLRT forms an $\alpha$-helix when not interacting with other molecules. However, in the vicinity of a $\beta$-strand, the peptide forms a $\beta$-strand. Because of this change in secondary structure our peptide may provide a simple model for the $\alpha \to \beta$ transition that is supposedly related to the outbreak of Prion diseases and similar illnesses.Comment: to appear in Physical Review

Bands, resonances, edge singularities and excitons in core level spectroscopy investigated within the dynamical mean field theory

Using a recently developed impurity solver we exemplify how dynamical mean field theory captures band excitations, resonances, edge singularities and excitons in core level x-ray absorption (XAS) and core level photo electron spectroscopy (cPES) on metals, correlated metals and Mott insulators. Comparing XAS at different values of the core-valence interaction shows how the quasiparticle peak in the absence of core-valence interactions evolves into a resonance of similar shape, but different origin. Whereas XAS is rather insensitive to the metal insulator transition, cPES can be used, due to nonlocal screening, to measure the amount of local charge fluctuation

The Development of Alcoholic Fermented Beverages Utilizing Plums with the Application of Innovative Beverage Fermentation Technology

The adaptation of existing technologies toward producing a white wine style alcoholic fermented plum beverage was undertaken. The Independent Variables (ID) were yeast strains (Saccharomyces cerevisiae VIN13 and Saccharomyces bayanus N96), with formulations containing various percentage pulp concentrations at (40%, 50% and 60%). The Dependent Variables (DV) constituted key quality parameters for white wines, namely %methanol, %ethanol, titratable acidity (TA), objective colour, total soluble solids (TDS), pH and sensory profile were measured. %Methanol was not detected in the samples, %ethanol, TA, colour, TDS and pH were within the range typical for white wine. The overall sensorial profile of the beverage samples, fruity aroma and sweet associated aroma were rated significantly higher as the pulp concentration increased from 40% to 50% (p < 0.05). Exhibiting comparable sensory attributes namely fruity aroma, sweet-associated aroma, yeasty aroma, sweet taste, sour taste, bitter taste, astringency and fruity flavour, that was typically associated with white wines (Sokolowsky et al., 2015). The results showed that existing technology can be adapted to produce an alcoholic fermented plum beverage of which the key quality parameters and attributes are comparable to white wines

Stochastic model for the CheY-P molarity in the neighbourhood of E. coli flagella motors

E.coli serves as prototype for the study of peritrichous enteric bacteria that perform runs and tumbles alternately. Bacteria run forward as a result of the counterclockwise (CCW) rotation of their flagella bundle and perform tumbles when at least one of their flagella rotates clockwise (CW), moving away from the bundle. The flagella are hooked to molecular rotary motors of nanometric diameter able to make transitions between CCW and CW rotations that last up to one hundredth of a second. At the same time, flagella move or rotate the bacteria's body microscopically during lapses that range between a tenth and ten seconds. We assume that the transitions between CCW and CW rotations occur solely by fluctuations of CheY-P molarity in the presence of two threshold values, and that a veto rule selects the run or tumble motions. We present Langevin eqs for the CheY-P molarity in the vicinity of each molecular motor. This model allows to obtain the run- or tumble-time distribution as a linear combination of decreasing exponentials that is a function of the steady molarity of CheY-P in the neighbourhood of the molecular motor, which fits experimental data. In turn, if the internal signaling system is unstimulated, we show that the runtime distributions reach power-law behaviour, a characteristic of self-organized systems, in some time range and, afterwards, exponential cutoff. In addition, our model explains without any fitting parameters the ultrasensitivity of the flagella motors as a function of the steady state of CheY-P molarity. In addition, we show that the tumble bias for peritrichous bacterium has a similar sigmoid-shape to the CW bias, although shifted to lower concentrations when the flagella number increases. Thus, the increment in the flagella number allows lower operational values for each motor increasing amplification and robustness of the chemotatic pathway.Comment: 13 pages, 7 figure

Global Optimization by Energy Landscape Paving

We introduce a novel heuristic global optimization method, energy landscape paving (ELP), which combines core ideas from energy surface deformation and tabu search. In appropriate limits, ELP reduces to existing techniques. The approach is very general and flexible and is illustrated here on two protein folding problems. For these examples, the technique gives faster convergence to the global minimum than previous approaches.Comment: to appear in Phys. Rev. Lett. (2002