1,021 research outputs found
Cooperative Chiral Order in Copolymers of Chiral and Achiral Units
Polyisocyanates can be synthesized with chiral and achiral pendant groups
distributed randomly along the chains. The overall chiral order, measured by
optical activity, is strongly cooperative and depends sensitively on the
concentration of chiral pendant groups. To explain this cooperative chiral
order theoretically, we map the random copolymer onto the one-dimensional
random-field Ising model. We show that the optical activity as a function of
composition is well-described by the predictions of this theory.Comment: 13 pages, including 3 postscript figures, uses REVTeX 3.0 and
epsf.st
Counterion-Mediated Weak and Strong Coupling Electrostatic Interaction between Like-Charged Cylindrical Dielectrics
We examine the effective counterion-mediated electrostatic interaction
between two like-charged dielectric cylinders immersed in a continuous
dielectric medium containing neutralizing mobile counterions. We focus on the
effects of image charges induced as a result of the dielectric mismatch between
the cylindrical cores and the surrounding dielectric medium and investigate the
counterion-mediated electrostatic interaction between the cylinders in both
limits of weak and strong electrostatic couplings (corresponding, e.g., to
systems with monovalent and multivalent counterions, respectively). The results
are compared with extensive Monte-Carlo simulations exhibiting good agreement
with the limiting weak and strong coupling results in their respective regime
of validity.Comment: 19 pages, 10 figure
Reconstruction of protein structures from a vectorial representation
We show that the contact map of the native structure of globular proteins can
be reconstructed starting from the sole knowledge of the contact map's
principal eigenvector, and present an exact algorithm for this purpose. Our
algorithm yields a unique contact map for all 221 globular structures of
PDBselect25 of length . We also show that the reconstructed contact
maps allow in turn for the accurate reconstruction of the three-dimensional
structure. These results indicate that the reduced vectorial representation
provided by the principal eigenvector of the contact map is equivalent to the
protein structure itself. This representation is expected to provide a useful
tool in bioinformatics algorithms for protein structure comparison and
alignment, as well as a promising intermediate step towards protein structure
prediction.Comment: 4 pages, 1 figur
Theory of Chiral Order in Random Copolymers
Recent experiments have found that polyisocyanates composed of a mixture of
opposite enantiomers follow a chiral ``majority rule:'' the chiral order of the
copolymer, measured by optical activity, is dominated by whichever enantiomer
is in the majority. We explain this majority rule theoretically by mapping the
random copolymer onto the random-field Ising model. Using this model, we
predict the chiral order as a function of enantiomer concentration, in
quantitative agreement with the experiments, and show how the sharpness of the
majority-rule curve can be controlled.Comment: 13 pages, including 4 postscript figures, uses REVTeX 3.0 and
epsf.st
Dynamical scaling of the DNA unzipping transition
We report studies of the equilibrium and the dynamics of a general set of
lattice models which capture the essence of the force-induced or mechanical DNA
unzipping transition. Besides yielding the whole equilibrium phase diagram in
the force vs temperature plane, which reveals the presence of an interesting
re-entrant unzipping transition for low T, these models enable us to
characterize the dynamics of the process starting from a non-equilibrium
initial condition. The thermal melting of the DNA strands displays a model
dependent time evolution. On the contrary, our results suggest that the
dynamical mechanism for the unzipping by force is very robust and the scaling
behaviour does not depend on the details of the description we adopt.Comment: 6 pages, 4 figures, A shorter version of this paper appeared in Phys.
Rev. Lett. 88, 028102 (2002
Statistical Properties of Contact Maps
A contact map is a simple representation of the structure of proteins and
other chain-like macromolecules. This representation is quite amenable to
numerical studies of folding. We show that the number of contact maps
corresponding to the possible configurations of a polypeptide chain of N amino
acids, represented by (N-1)-step self avoiding walks on a lattice, grows
exponentially with N for all dimensions D>1. We carry out exact enumerations in
D=2 on the square and triangular lattices for walks of up to 20 steps and
investigate various statistical properties of contact maps corresponding to
such walks. We also study the exact statistics of contact maps generated by
walks on a ladder.Comment: Latex file, 15 pages, 12 eps figures. To appear on Phys. Rev.
Lifelongα-tocopherol supplementation increases the median life span of C57BL/6 mice in the cold but has only minor effects on oxidative damage
The effects of dietary antioxidant supplementation on oxidative stress and life span are confused. We maintained C57BL/6 mice at 7 ± 2°C and supplemented their diet with α-tocopherol from 4 months of age. Supplementation significantly increased (p = 0.042) median life span by 15% (785 days, n = 44) relative to unsupplemented controls (682 days, n = 43) and also increased maximum life span (oldest 10%, p = 0.028). No sex or sex by treatment interaction effects were observed on life span, with treatment having no effect on resting or daily metabolic rate. Lymphocyte and hepatocyte oxidative DNA damage and hepatic lipid peroxidation were unaffected by supplementation, but hepatic oxidative DNA damage increased with age. Using a cDNA macroarray, genes associated with xenobiotic metabolism were significantly upregulated in the livers of female mice at 6 months of age (2 months supplementation). At 22 months of age (18 months supplementation) this response had largely abated, but various genes linked to the p21 signaling pathway were upregulated at this time. We suggest that α-tocopherol may initially be metabolized as a xenobiotic, potentially explaining why previous studies observe a life span extension generally when lifelong supplementation is initiated early in life. The absence of any significant effect on oxidative damage suggests that the life span extension observed was not mediated via any antioxidant properties of α-tocopherol. We propose that the life span extension observed following α-tocopherol supplementation may be mediated via upregulation of cytochrome p450 genes after 2 months of supplementation and/or upregulation of p21 signaling genes after 18 months of supplementation. However, these signaling pathways now require further investigation to establish their exact role in life span extension following α-tocopherol supplementation
Chiral molecule adsorption on helical polymers
We present a lattice model for helicity induction on an optically inactive
polymer due to the adsorption of exogenous chiral amine molecules. The system
is mapped onto a one-dimensional Ising model characterized by an on-site
polymer helicity variable and an amine occupancy one. The equilibrium
properties are analyzed at the limit of strong coupling between helicity
induction and amine adsorption and that of non-interacting adsorbant molecules.
We discuss our results in view of recent experimental results
Formation of helical states in wormlike polymer chains
We propose a potential for wormlike polymer chains which can be used to model
the low-temperature conformational structures. We successfully reproduced helix
ground states up to 6.5 helical loops, using the multicanonical Monte Carlo
simulation method. We demonstrate that the coil-helix transition involves four
distinct phases: coil(gaslike), collapsed globular(liquidlike), and two helical
phases I and II (both solidlike). The helix I phase is characterized by a
helical structure with dangling loose ends, and the helix II phase corresponds
to a near perfect helix ordering in the entire crystallized chain.Comment: 5 pages, 2 figures, Submitted to PR
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