2,877 research outputs found
The thermodynamics of general anesthesia
It is known that the action of general anesthetics is proportional to their
partition coefficient in lipid membranes (Meyer-Overton rule). This solubility
is, however, directly related to the depression of the temperature of the
melting transition found close to body temperature in biomembranes. We propose
a thermodynamic extension of the Meyer-Overton rule which is based on free
energy changes in the system and thus automatically incorporates the effects of
melting point depression. This model provides a quantitative explanation of the
pressure reversal of anesthesia. Further, it explains why inflammation and the
addition of divalent cations reduce the effectiveness of anesthesia.Comment: 7 pages, 2 figure
The Effects of Stacking on the Configurations and Elasticity of Single Stranded Nucleic Acids
Stacking interactions in single stranded nucleic acids give rise to
configurations of an annealed rod-coil multiblock copolymer. Theoretical
analysis identifies the resulting signatures for long homopolynucleotides: A
non monotonous dependence of size on temperature, corresponding effects on
cyclization and a plateau in the extension force law. Explicit numerical
results for poly(dA) and poly(rU) are presented.Comment: 4 pages and 2 figures. Accepted in Phys. Rev. E Rapid Com
Membrane-protein interactions in mechanosensitive channels
In this paper, we examine the mechanical role of the lipid bilayer in ion
channel conformation and function with specific reference to the case of the
mechanosensitive channel of large conductance (MscL). In a recent paper
(Wiggins and Phillips, 2004), we argued that mechanotransduction very naturally
arises from lipid-protein interactions by invoking a simple analytic model of
the MscL channel and the surrounding lipid bilayer. In this paper, we focus on
improving and expanding this analytic framework for studying lipid-protein
interactions with special attention to MscL. Our goal is to generate simple
scaling relations which can be used to provide qualitative understanding of the
role of membrane mechanics in protein function and to quantitatively interpret
experimental results. For the MscL channel, we find that the free energies
induced by lipid-protein interaction are of the same order as the free energy
differences between conductance states measured by Sukharev et al. (1999). We
therefore conclude that the mechanics of the bilayer plays an essential role in
determining the conformation and function of the channel. Finally, we compare
the predictions of our model to experimental results from the recent
investigations of the MscL channel by Perozo et al. (2002), Powl et al. (2003),
Yoshimura et al. (2004), and others and suggest a suite of new experiments
Stretching Semiflexible Polymer Chains: Evidence for the Importance of Excluded Volume Effects from Monte Carlo Simulation
Semiflexible macromolecules in dilute solution under very good solvent
conditions are modeled by self-avoiding walks on the simple cubic lattice
( dimensions) and square lattice ( dimensions), varying chain
stiffness by an energy penalty for chain bending. In the absence
of excluded volume interactions, the persistence length of the
polymers would then simply be with , the bond length being the lattice spacing,
and is the thermal energy. Using Monte Carlo simulations applying the
pruned-enriched Rosenbluth method (PERM), both and the chain length
are varied over a wide range ), and
also a stretching force is applied to one chain end (fixing the other end
at the origin). In the absence of this force, in a single crossover from
rod-like behavior (for contour lengths less than ) to swollen coils
occurs, invalidating the Kratky-Porod model, while in a double crossover
occurs, from rods to Gaussian coils (as implied by the Kratky-Porod model) and
then to coils that are swollen due to the excluded volume interaction. If the
stretching force is applied, excluded volume interactions matter for the force
versus extension relation irrespective of chain stiffness in , while
theories based on the Kratky-Porod model are found to work in for stiff
chains in an intermediate regime of chain extensions. While for in
this model a persistence length can be estimated from the initial decay of
bond-orientational correlations, it is argued that this is not possible for
more complex wormlike chains (e.g. bottle-brush polymers). Consequences for the
proper interpretation of experiments are briefly discussed.Comment: 23 pages, 17 figures, 2 tables, to be published in J. Chem. Phys.
(2011
Cantor type functions in non-integer bases
Cantor's ternary function is generalized to arbitrary base-change functions
in non-integer bases. Some of them share the curious properties of Cantor's
function, while others behave quite differently
Effect of Lipid Characteristics on the Structure of Transmembrane Proteins
AbstractThe activity of embedded proteins is known to vary with lipid characteristics. Indeed, it has been shown that some cell-membrane proteins cannot function unless certain non-bilayer-forming lipids (i.e., nonzero spontaneous curvature) are present. In this paper we show that membranes exert a line tension on transmembrane proteins. The line tension, on the order of 1–100kT/protein, varies with the lipid properties and the protein configuration. Thus, membranes composed of different lipids favor different protein conformations. Model predictions are in excellent agreement with the data of Keller et al. (Biophys. J. 1993, 65:23–27) regarding the conductance of alamethicin channels
Statistical properties of extragalactic sources in the New Extragalactic WMAP Point Source (NEWPS) catalogue
We present results on spectral index distributions, number counts, redshift
distribution and other general statistical properties of extragalactic point
sources in the NEWPS5 sample L\'opez-Caniego et al. (2007). The flux
calibrations at all the WMAP channels have been reassessed both by comparison
with ground based observations and through estimates of the effective beam
areas. The two methods yield consistent statistical correction factors. A
search of the NED has yielded optical identifications for 89% of sources in the
complete sub-sample of 252 sources with S/N>5 and S>1.1 Jy at 23 GHz; 5 sources
turned out to be Galactic and were removed. The NED also yielded redshifts for
92% of the extragalactic sources at |b|>10deg. Their distribution was compared
with model predictions; the agreement is generally good but a possible
discrepancy is noted. Using the 5 GHz fluxes from the GB6 or PMN surveys, we
find that 76% of the 191 extragalactic sources with S_23GHz>1.3,Jy can be
classified as flat-spectrum sources between 5 and 23 GHz. A spectral steepening
is observed at higher frequencies: only 59% of our sources are still
flat-spectrum sources between 23 and 61 GHz and the average spectral indexes
steepen from = 0.01\pm 0.03 to = 0.37\pm 0.03. We
think, however, that the difference may be due to a selection effect. The
source number counts have a close to Euclidean slope and are in good agreement
with the predictions of the cosmological evolution model by De Zotti et al.
(2005). The observed spectral index distributions were exploited to get
model-independent extrapolations of counts to higher frequencies. The risks of
such operations are discussed and reasons of discrepancies with other recent
estimates are clarified.Comment: 8 pages, 4 figures. Accepted for publication in MNRA
Impact of Cholesterol on Voids in Phospholipid Membranes
Free volume pockets or voids are important to many biological processes in
cell membranes. Free volume fluctuations are a prerequisite for diffusion of
lipids and other macromolecules in lipid bilayers. Permeation of small solutes
across a membrane, as well as diffusion of solutes in the membrane interior are
further examples of phenomena where voids and their properties play a central
role. Cholesterol has been suggested to change the structure and function of
membranes by altering their free volume properties. We study the effect of
cholesterol on the properties of voids in dipalmitoylphosphatidylcholine (DPPC)
bilayers by means of atomistic molecular dynamics simulations. We find that an
increasing cholesterol concentration reduces the total amount of free volume in
a bilayer. The effect of cholesterol on individual voids is most prominent in
the region where the steroid ring structures of cholesterol molecules are
located. Here a growing cholesterol content reduces the number of voids,
completely removing voids of the size of a cholesterol molecule. The voids also
become more elongated. The broad orientational distribution of voids observed
in pure DPPC is, with a 30% molar concentration of cholesterol, replaced by a
distribution where orientation along the bilayer normal is favored. Our results
suggest that instead of being uniformly distributed to the whole bilayer, these
effects are localized to the close vicinity of cholesterol molecules
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Elements of fractal geometry in the 1H NMR spectrum of a copolymer intercalation-complex: Identification of the underlying Cantor set
Sequence-selective intercalation of pyrene into the chain-folds of a random, binary copolyimide under fast-exchange conditions results in the development of self-similar structure in the diimide region of the 1H NMR spectrum. The resulting spectrum can be described by the mathematics of fractals, an approach that is rationalised in terms of a dynamic summation of ring-current shielding effects produced by pyrene molecules intercalating into the chain at progressively greater distances from each "observed" diimide residue. The underlying set of all such summations is found to be a defined mathematical fractal namely the fourth-quarter Cantor set, within which the observed spectrum is embedded. The pattern of resonances predicted by a geometric construction of the fourth-quarter Cantor set agrees well with the observed spectrum
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