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This paper proposes a set of models to calculate contraction factor, which to maximum extent accounts for the kinetics of radical polymerization with transfer to polymer and recombination termination. The models are alternatives to the Zimm and Stockmayer's (1949) analytical expression of contraction factor for molecules with terminal branching. The results, being representative for polymers like as low-density Polyethylene (IdPE), show significantly stronger contraction than predicted by the model of Zimm and Stockmayer. In the case of termination by disproportionation only, molecular sizes turn out to be smaller by a factor of almost two. In presence of recombination termination molecules are less compact. It is shown that the interpretation of contraction factors as measured by the Size Exclusion Multi-Angle Light Scattering to find the branchedness of IdPE, with the new model would lead to a considerably lower estimate of branching than by using Zimm and Stockmayer's model. (C) 2015 Elsevier Ltd. All rights reserved.

We applied the single-replica multiple-state transition-interface sampling method to elucidate the equilibrium kinetic network of the 35-residue-fragment (HP-35) villin headpiece in implicit water at room temperature. Starting from the native Protein Data Bank structure, nine (meta)stable states of the system were identified, from which the kinetic network was built by sampling pathways between these states. Application of transition path theory allowed analysis of the (un)folding mechanism. The resulting (un)folding rates agree well with experiments. This work demonstrates that high (un)folding barriers can now be studied.

We consider the problem of detecting a percolating structure in an off-lattice model polymer system when periodic boundary conditions are used. Physically, with increasing polymer density, the point at which this first occurs is the gel point. A connected structure spans all space and the system becomes solid-like. This problem is similar to that of finding connected paths in lattice bond percolation and site percolation models. We show that algorithms that detect these structures in finite systems will not always yield the correct answer for a system that is periodically repeated in space (uses periodic boundary conditions). Here we describe an algorithm that detects clusters that connect to themselves over an arbitrary number of periodic replicas. Because of the periodic replication this means that they are connected over all space. For system sizes that are typically tractable in simulations we find a relatively minor proportion of configurations are mis-classified for a lattice model. However, the fraction that is mis-classified is significant for the polymer system. Mis-classified configurations when included in the calculation of ensemble averages will include configurations with spurious physical properties. Our algorithm allows this to be corrected for.

Various first-row transition metal cations (Cr3+, Mn2+, Fe3+, Co2+, Ni2+, Cu2+ and Zn2+) have been introduced to zeolite beta using ion exchange procedures. Both aluminum and transition metal sites were studied by UV–Vis spectroscopy, XPS and 27Al NMR. Generally, ion exchange favored the incorporation of Al defects into the zeolite framework. The effect of the divalent and trivalent cations on the final zeolite beta structure was found to be considerably different. While divalent cations were mainly exchanged for Bronsted acid sites after calcination, trivalent cations such as Fe3+ were mostly transformed into oxide-like species whilst Cr3+ species were oxidized to Cr6+ species. Their surface properties were quite distinct since only divalent cations generated strong Lewis acid sites, even though the Bronsted acidity decreased in all cases. Their catalytic performance was evaluated in the transformation of methanol to hydrocarbons. Various metal species, i.e., Cr6+, Mn2+, Fe3+ and Zn2+ were found to act as promoters of polymerization or aromatization reactions. In particular, Cr species were found to enhance the catalytic activity in the conversion of methanol and dimethyl ether into higher order hydrocarbons.

We investigate the molecular mechanism of monomer addition to a growing amyloid fibril composed of the main amyloidogenic region from the insulin peptide hormone, the LVEALYL heptapeptide. Applying transition path sampling in combination with reaction coordinate analysis reveals that the transition from a docked peptide to a locked, fully incorporated peptide can occur in two ways. Both routes involve the formation of backbone hydrogen bonds between the three central amino acids of the attaching peptide and the fibril, as well as a reorientation of the central Glu side chain of the locking peptide toward the interface between two β-sheets forming the fibril. The mechanisms differ in the sequence of events. We also conclude that proper docking is important for correct alignment of the peptide with the fibril, as alternative pathways result in misfolding.

The histone-like nucleoid structuring protein (H-NS) is a DNA-organizing protein in bacteria. It contains a DNA-binding domain and a dimerization domain, connected by a flexible linker region. Dimerization occurs through the formation of a helical bundle, including a coiled-coil interaction motif. Two conformations have been resolved, for different sequences of Escherichia coli H-NS, resulting in an antiparallel coiled-coil for the shorter wild-type sequence, and a parallel coiled-coil for the longer C21S mutant. Because H-NS functions as a thermo- and osmosensor, these conformations may both be functionally relevant. Molecular simulation can complement experiments by modeling the dynamical time evolution of biomolecular systems in atomistic detail. We performed a molecular-dynamics study of the H-NS dimerization domain, showing that the parallel complex is sensitive to changes in salt conditions: it is unstable in absence of NaCl, but stable at physiological salt concentrations. In contrast, the stability of the antiparallel complex is not salt-dependent. The stability of the parallel complex also appears to be affected by mutation of the critical but nonconserved cysteine residue at position 21, whereas the antiparallel complex is not. Together, our simulations suggest that osmoregulation could be mediated by changes in the ratio of parallel- and antiparallel-oriented H-NS dimers.

α-Synuclein (AS) is a intrinsically disordered protein involved in the pathogenesis of Parkinson's disease, which is known to form toxic aggregates as well as fibrils. From a computational point of view, it represents a challenging system, as the protein can be found in multiple conformers, separated by many high free energy barriers. To overcome these barriers, we conducted replica exchange molecular dynamics. Using the Amber force field in implicit solvent for the AS monomer, we find transitions between states with both alpha helix, beta sheet and disordered structure.

DNA duplexes predominantly contain Watson-Crick (WC) base pairs. Yet, a non-negligible number of base pairs converts to the Hoogsteen (HG) hydrogen bonding pattern, involving a 180° rotation of the purine base relative to Watson-Crick. These WC to HG conversions alter the conformation of DNA, and may play a role in several processes including recognition and replication. The transient nature of these processes hamper thorough experimental investigation. Molecular dynamics simulations can provide complementary insights to experiments at high spatial and temporal resolution. By using path sampling techniques, a framework that harvests molecular dynamics trajectories that undergo reactions of interest, we avoid long waiting times in stable states, thus focusing on the actual transition. Our results reveal that WC to HG conversion can proceed along different routes with a varying degree of exposure of the purine. Furthermore, we computed the rate constants for this transition using transition interface sampling.