719 research outputs found
Local isotropy and refractive index fluctuations in the surface layer of the atmosphere
Theoretical and experimental evidence for the existence of local isotropy is briefly examined and conflicting results are found. Recent measurements of temperature spectra support earlier hot wire anemometer and optical scintillation measurements that show little evidence of local isotropy at 1 to 1.5 meters over an extensive uniform and level grass covered field
Microscopic Theory of Protein Folding Rates.I: Fine Structure of the Free Energy Profile and Folding Routes from a Variational Approach
A microscopic theory of the free energy barriers and folding routes for
minimally frustrated proteins is presented, greatly expanding on the
presentation of the variational approach outlined previously [J. J. Portman, S.
Takada, P. G. Wolynes, Phys. Rev. Lett. {\bf 81}, 5237 (1998)]. We choose the
-repressor protein as an illustrative example and focus on how the
polymer chain statistics influence free energy profiles and partially ordered
ensembles of structures. In particular, we investigate the role of chain
stiffness on the free energy profile and folding routes. We evaluate the
applicability of simpler approximations in which the conformations of the
protein molecule along the folding route are restricted to have residues that
are either entirely folded or unfolded in contiguous stretches. We find that
the folding routes obtained from only one contiguous folded region corresponds
to a chain with a much greater persistence length than appropriate for natural
protein chains, while the folding route obtained from two contiguous folded
regions is able to capture the relatively folded regions calculated within the
variational approach. The free energy profiles obtained from the contiguous
sequence approximations have larger barriers than the more microscopic
variational theory which is understood as a consequence of partial ordering.Comment: 16 pages, 11 figure
Non-Gaussian dynamics from a simulation of a short peptide: Loop closure rates and effective diffusion coefficients
Intrachain contact formation rates, fundamental to the dynamics of biopolymer
self-organization such as protein folding, can be monitored in the laboratory
through fluorescence quenching measurements. The common approximations for the
intrachain contact rate given by the theory of Szabo, Schulten, and Schulten
(SSS) [J. Chem. Phys. {\bf 72}, 4350 (1980)] and Wilemski--Fixman (WF) [J.\
Chem. Phys. {\bf 60},878 (1973)] are shown to be complementary variational
bounds: the SSS and WF approximations are lower and upper bounds, respectively,
on the mean first contact times. As reported in the literature, the SSS
approximation requires an effective diffusion coefficient 10 to 100 times
smaller than expected to fit experimentally measured quenching rates. An all
atom molecular dynamics simulation of an eleven residue peptide sequence in
explicit water is analyzed to investigate the source of this surprising
parameter value. In analytical work, the polymer is typically modeled by a
Gaussian chain of effective monomers. Compared to Gaussian dynamics, the
simulated end-to-end distance autocorrelation has a much slower relaxation. The
long time behavior of the distance autocorrelation function can be approximated
by a Gaussian model in which the monomer diffusion coefficient D_0 is reduced
to D_0/6. This value of the diffusion coefficient brings the mean end-to-end
contact time from analytical approximations and simulation into agreement in
the sense that the SSS and WF approximations bracket the simulated mean first
contact time.Comment: 12 pages, 7 eps figures, to appear in J. Chem. Phy
Microscopic Theory of Protein Folding Rates.II: Local Reaction Coordinates and Chain Dynamics
The motion involved in barrier crossing for protein folding are investigated
in terms of the chain dynamics of the polymer backbone, completing the
microscopic description of protein folding presented in the previous paper.
Local reaction coordinates are identified as collective growth modes of the
unstable fluctuations about the saddle-points in the free energy surface. The
description of the chain dynamics incorporates internal friction (independent
of the solvent viscosity) arising from the elementary isomerizations of the
backbone dihedral angles. We find that the folding rate depends linearly on the
solvent friction for high viscosity, but saturates at low viscosity because of
internal friction. For -repressor, the calculated folding rate
prefactor, along with the free energy barrier from the variational theory,
gives a folding rate that agrees well with the experimentally determined rate
under highly stabilizing conditions, but the theory predicts too large a
folding rate at the transition midpoint. This discrepancy obtained using a
fairly complete quantitative theory inspires a new set of questions about chain
dynamics, specifically detailed motions in individual contact formation.Comment: 18 pages, 8 figure
First Records of the Adventive Pseudoanthidium nanum (Mocsáry) (Hymenoptera: Megachilidae) in Illinois and Minnesota, with Notes on its Identification and Taxonomy
We report the first records of Pseudoanthidium nanum (Mocsáry) in Illinois and Minnesota in 2016 and 2018, respectively. This represents a relatively rapid expansion since P. nanum was first detected in New Jersey in 2008. In order to help monitor the spread of this bee, we provide information on how to identify P. nanum and provide images of the general habitus, diagnostic features, and male genitalia. Finally, we confirm the taxonomic identity of P. nanum in the United States and highlight potential impacts on native anthidiines
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