Probing the Mechanisms of Fibril Formation Using Lattice Models

Using exhaustive Monte Carlo simulations we study the kinetics and mechanism of fibril formation using lattice models as a function of temperature and the number of chains. While these models are, at best, caricatures of peptides, we show that a number of generic features thought to govern fibril assembly are present in the toy model. The monomer, which contains eight beads made from three letters (hydrophobic, polar, and charged), adopts a compact conformation in the native state. The kinetics of fibril assembly occurs in three distinct stages. In each stage there is a cascade of events that transforms the monomers and oligomers to ordered structures. In the first "burst" stage highly mobile oligomers of varying sizes form. The conversion to the aggregation-prone conformation occurs within the oligomers during the second stage. As time progresses, a dominant cluster emerges that contains a majority of the chains. In the final stage, the aggregation-prone conformation particles serve as a template onto which smaller oligomers or monomers can dock and undergo conversion to fibril structures. The overall time for growth in the latter stages is well described by the Lifshitz-Slyazov growth kinetics for crystallization from super-saturated solutions.Comment: 27 pages, 6 figure

Multiple Scales in the Fine Structure of the Isoscalar Giant Quadrupole Resonance in ^{208}Pb

The fine structure of the isoscalar giant quadrupole resonance in ^{208}Pb, observed in high-resolution (p,p') and (e,e') experiments, is studied using the entropy index method. In a novel way, it enables to determine the number of scales present in the spectra and their magnitude. We find intermediate scales of fluctuations around 1.1 MeV, 460 keV and 125 keV for an excitation energy region 0 - 12 MeV. A comparison with scales extracted from second RPA calculations, which are in good agreement with experiment, shows that they arise from the internal mixing of collective motion with two particle-two hole components of the nuclear wavefunction.Comment: 14 pages including 6 figures (to be published in Phys. Lett. B

Kaon Photoproduction and the Λ\Lambda Decay Parameter α−\alpha_-

The weak decay parameter $\alpha_-$ of the $\Lambda$ is an important quantity for the extraction of polarization observables in various experiments. Moreover, in combination with $\alpha_+$ from $\bar\Lambda$ decay it provides a measure for matter-antimatter asymmetry. The weak decay parameter also affects the decay parameters of the $\Xi$ and $\Omega$ baryons and, in general, any quantity in which the polarization of the $\Lambda$ is relevant. The recently reported value by the BESIII collaboration of $0.750(9)(4)$ is significantly larger than the previous PDG value of $0.642(13)$ that had been accepted and used for over 40 years. In this work we make an independent estimate of $\alpha_-$, using an extensive set of polarization data measured in kaon photoproduction in the baryon resonance region and constraints set by spin algebra. The obtained value is 0.721(6)(5). The result is corroborated by multiple statistical tests as well as a modern phenomenological model, showing that our new value yields the best description of the data in question. Our analysis supports the new BESIII finding that $\alpha_-$ is significantly larger than the previous PDG value. Any experimental quantity relying on the value of $\alpha_-$ should therefore be re-considered.Comment: 6 pages, 1 figure

Periodic force induced stabilization or destabilization of the denatured state of a protein

We have studied the effects of an external sinusoidal force in protein folding kinetics. The externally applied force field acts on the each amino acid residues of polypeptide chains. Our simulation results show that mean protein folding time first increases with driving frequency and then decreases passing through a maximum. With further increase of the driving frequency the mean folding time starts increasing as the noise-induced hoping event (from the denatured state to the native state) begins to experience many oscillations over the mean barrier crossing time period. Thus unlike one-dimensional barrier crossing problems, the external oscillating force field induces both \emph{stabilization or destabilization of the denatured state} of a protein. We have also studied the parametric dependence of the folding dynamics on temperature, viscosity, non-Markovian character of bath in presence of the external field

Earthquake source characteristics from dynamic rupture with constrained stochastic fault stress

One of the challenging tasks in predicting near-source ground motion for future earthquakes is to anticipate the spatiotemporal evolution of the rupture process. The final size of an event but also its temporal properties (propagation velocity, slip velocity) depend on the distribution of shear stress on the fault plane. Though these incipient stresses are not known for future earthquakes, they might be sufficiently well characterized in a stochastic sense. We examine the evolution of dynamic rupture in numerical models of a fault subjected to heterogeneous stress fields with varying statistical properties. By exploring the parameter space of the stochastic stress characterization for a large number of random realizations we relate generalized properties of the resulting events to the stochastic stress parameters. The nucleation zone of the simulated earthquake ruptures in general has a complex shape, but its average size is found to be independent of the stress field parameterization and is determined only by the material parameters and the friction law. Furthermore, we observe a sharp transition in event size from small to system-wide events, governed mainly by the standard deviation of the stress field. A simplified model based on fracture mechanics is able to explain this transition. Finally, we find that the macroscopic rupture parameters ( e. g., moment, moment rate, seismic energy) of our catalog of model quakes are generally consistent with observational data

Finite size effects on thermal denaturation of globular proteins

Finite size effects on the cooperative thermal denaturation of proteins are considered. A dimensionless measure of cooperativity, Omega, scales as N^zeta, where N is the number of amino acids. Surprisingly, we find that zeta is universal with zeta = 1 + gamma, where the exponent gamma characterizes the divergence of the susceptibility for a self-avoiding walk. Our lattice model simulations and experimental data are consistent with the theory. Our finding rationalizes the marginal stability of proteins and substantiates the earlier predictions that the efficient folding of two-state proteins requires the folding transition temperature to be close to the collapse temperature.Comment: 3 figures. Physical Review Letters (in press

Folding in two-dimenensional off-lattice models of proteins

Model off-lattice sequences in two dimensions are constructed so that their native states are close to an on-lattice target. The Hamiltonian involves the Lennard-Jones and harmonic interactions. The native states of these sequences are determined with a high degree of certainty through Monte Carlo processes. The sequences are characterized thermodynamically and kinetically. It is shown that the rank-ordering-based scheme of the assignment of contact energies typically fails in off-lattice models even though it generates high stability of on-lattice sequences. Similar to the on-lattice case, Go-like modeling, in which the interaction potentials are restricted to the native contacts in a target shape, gives rise to good folding properties. Involving other contacts deteriorates these properties.Comment: REVTeX, 9 pages, 8 EPS figure

"The dearest of our possessions": applying Floridi's information privacy concept in models of information behavior and information literacy

This conceptual paper argues for the value of an approach to privacy in the digital information environment informed by Luciano Floridi's philosophy of information and information ethics. This approach involves achieving informational privacy, through the features of anonymity and obscurity, through an optimal balance of ontological frictions. This approach may be used to modify models for information behavior and for information literacy, giving them a fuller and more effective coverage of privacy issues in the infosphere. For information behavior, the Information Seeking and Communication Model, and the Information Grounds conception, are most appropriate for this purpose. For information literacy, the metaliteracy model, using a modification a privacy literacy framework, is most suitable

Transient behavior in Single-File Systems

We have used Monte-Carlo methods and analytical techniques to investigate the influence of the characteristics, such as pipe length, diffusion, adsorption, desorption and reaction rates on the transient properties of Single-File Systems. The transient or the relaxation regime is the period in which the system is evolving to equilibrium. We have studied the system when all the sites are reactive and when only some of them are reactive. Comparisons between Mean-Field predictions, Cluster Approximation predictions, and Monte Carlo simulations for the relaxation time of the system are shown. We outline the cases where Mean-Field analysis gives good results compared to Dynamic Monte-Carlo results. For some specific cases we can analytically derive the relaxation time. Occupancy profiles for different distribution of the sites both for Mean-Field and simulations are compared. Different results for slow and fast reaction systems and different distribution of reactive sites are discussed.Comment: 18 pages, 19 figure