158 research outputs found
Phase Transitions of Single Semi-stiff Polymer Chains
We study numerically a lattice model of semiflexible homopolymers with
nearest neighbor attraction and energetic preference for straight joints
between bonded monomers. For this we use a new algorithm, the "Pruned-Enriched
Rosenbluth Method" (PERM). It is very efficient both for relatively open
configurations at high temperatures and for compact and frozen-in low-T states.
This allows us to study in detail the phase diagram as a function of
nn-attraction epsilon and stiffness x. It shows a theta-collapse line with a
transition from open coils to molten compact globules (large epsilon) and a
freezing transition toward a state with orientational global order (large
stiffness x). Qualitatively this is similar to a recently studied mean field
theory (Doniach et al. (1996), J. Chem. Phys. 105, 1601), but there are
important differences. In contrast to the mean field theory, the
theta-temperature increases with stiffness x. The freezing temperature
increases even faster, and reaches the theta-line at a finite value of x. For
even stiffer chains, the freezing transition takes place directly without the
formation of an intermediate globule state. Although being in contrast with
mean filed theory, the latter has been conjectured already by Doniach et al. on
the basis of low statistics Monte Carlo simulations. Finally, we discuss the
relevance of the present model as a very crude model for protein folding.Comment: 11 pages, Latex, 8 figure
Topological effects in ring polymers: A computer simulation study
Unconcatenated, unknotted polymer rings in the melt are subject to strong
interactions with neighboring chains due to the presence of topological
constraints. We study this by computer simulation using the bond-fluctuation
algorithm for chains with up to N=512 statistical segments at a volume fraction
\Phi=0.5 and show that rings in the melt are more compact than gaussian chains.
A careful finite size analysis of the average ring size R \propto N^{\nu}
yields an exponent \nu \approx 0.39 \pm 0.03 in agreement with a Flory-like
argument for the topologica interactions. We show (using the same algorithm)
that the dynamics of molten rings is similar to that of linear chains of the
same mass, confirming recent experimental findings. The diffusion constant
varies effectively as D_{N} \propto N^{-1.22(3) and is slightly higher than
that of corresponding linear chains. For the ring sizes considered (up to 256
statistical segments) we find only one characteristic time scale \tau_{ee}
\propto N^{2.0(2); this is shown by the collapse of several mean-square
displacements and correlation functions onto corresponding master curves.
Because of the shrunken state of the chain, this scaling is not compatible with
simple Rouse motion. It applies for all sizes of ring studied and no sign of a
crossover to any entangled regime is found.Comment: 20 Pages,11 eps figures, Late
Simulating chemistry using quantum computers
The difficulty of simulating quantum systems, well-known to quantum chemists,
prompted the idea of quantum computation. One can avoid the steep scaling
associated with the exact simulation of increasingly large quantum systems on
conventional computers, by mapping the quantum system to another, more
controllable one. In this review, we discuss to what extent the ideas in
quantum computation, now a well-established field, have been applied to
chemical problems. We describe algorithms that achieve significant advantages
for the electronic-structure problem, the simulation of chemical dynamics,
protein folding, and other tasks. Although theory is still ahead of experiment,
we outline recent advances that have led to the first chemical calculations on
small quantum information processors.Comment: 27 pages. Submitted to Ann. Rev. Phys. Che
Deriving amino acid contact potentials from their frequencies of occurence in proteins: a lattice model study
The possibility of deriving the contact potentials between amino acids from
their frequencies of occurence in proteins is discussed in evolutionary terms.
This approach allows the use of traditional thermodynamics to describe such
frequencies and, consequently, to develop a strategy to include in the
calculations correlations due to the spatial proximity of the amino acids and
to their overall tendency of being conserved in proteins. Making use of a
lattice model to describe protein chains and defining a "true" potential, we
test these strategies by selecting a database of folding model sequences,
deriving the contact potentials from such sequences and comparing them with the
"true" potential. Taking into account correlations allows for a markedly better
prediction of the interaction potentials
The Origin of the Designability of Protein Structures
We examined what determines the designability of 2-letter codes (H and P)
lattice proteins from three points of view. First, whether the native structure
is searched within all possible structures or within maximally compact
structures. Second, whether the structure of the used lattice is bipartite or
not. Third, the effect of the length of the chain, namely, the number of
monomers on the chain. We found that the bipartiteness of the lattice structure
is not a main factor which determines the designability. Our results suggest
that highly designable structures will be found when the length of the chain is
sufficiently long to make the hydrophobic core consisting of enough number of
monomers.Comment: 17 pages, 2 figure
Energetic Components of Cooperative Protein Folding
A new lattice protein model with a four-helix bundle ground state is analyzed
by a parameter-space Monte Carlo histogram technique to evaluate the effects of
an extensive variety of model potentials on folding thermodynamics. Cooperative
helical formation and contact energies based on a 5-letter alphabet are found
to be insufficient to satisfy calorimetric and other experimental criteria for
two-state folding. Such proteinlike behaviors are predicted, however, by models
with polypeptide-like local conformational restrictions and
environment-dependent hydrogen bonding-like interactions.Comment: 11 pages, 4 postscripts figures, Phys. Rev. Lett. (in press
Protein structures and optimal folding emerging from a geometrical variational principle
Novel numerical techniques, validated by an analysis of barnase and
chymotrypsin inhibitor, are used to elucidate the paramount role played by the
geometry of the protein backbone in steering the folding to the correct native
state. It is found that, irrespective of the sequence, the native state of a
protein has exceedingly large number of conformations with a given amount of
structural overlap compared to other compact artificial backbones; moreover the
conformational entropies of unrelated proteins of the same length are nearly
equal at any given stage of folding. These results are suggestive of an
extremality principle underlying protein evolution, which, in turn, is shown to
be associated with the emergence of secondary structures.Comment: Revtex, 5 pages, 5 postscript figure
Wettability-independent bouncing on flat surfaces mediated by thin air films
The impingement of drops onto solid surfaces1, 2 plays a crucial role in a variety of processes, including inkjet printing, fog harvesting, anti-icing, dropwise condensation and spray coating3, 4, 5, 6. Recent efforts in understanding and controlling drop impact behaviour focused on superhydrophobic surfaces with specific surface structures enabling drop bouncing with reduced contact time7, 8. Here, we report a different universal bouncing mechanism that occurs on both wetting and non-wetting flat surfaces for both high and low surface tension liquids. Using high-speed multiple-wavelength interferometry9, we show that this bouncing mechanism is based on the continuous presence of an air film for moderate drop impact velocities. This submicrometre âair cushionâ slows down the incoming drop and reverses its momentum. Viscous forces in the air film play a key role in this process: they provide transient stability of the air cushion against squeeze-out, mediate momentum transfer, and contribute a substantial part of the energy dissipation during bouncing
Scale-free static and dynamical correlations in melts of monodisperse and Flory-distributed homopolymers: A review of recent bond-fluctuation model studies
It has been assumed until very recently that all long-range correlations are
screened in three-dimensional melts of linear homopolymers on distances beyond
the correlation length characterizing the decay of the density
fluctuations. Summarizing simulation results obtained by means of a variant of
the bond-fluctuation model with finite monomer excluded volume interactions and
topology violating local and global Monte Carlo moves, we show that due to an
interplay of the chain connectivity and the incompressibility constraint, both
static and dynamical correlations arise on distances . These
correlations are scale-free and, surprisingly, do not depend explicitly on the
compressibility of the solution. Both monodisperse and (essentially)
Flory-distributed equilibrium polymers are considered.Comment: 60 pages, 49 figure
A New Detached M Dwarf Eclipsing Binary
We describe a newly-discovered detached M-dwarf eclipsing binary system, the
fourth such system known. This system was first observed by the TrES network
during a long term photometry campaign of 54 nights. Analysis of the folded
light curve indicates two very similar components orbiting each other with a
period of 1.12079 +/- 0.00001 days. Spectroscopic observations with the
Hobby-Eberly Telescope show the system to consist of two M3e dwarfs in a
near-circular orbit. Double-line radial velocity amplitudes, combined with the
orbital inclination derived from light-curve fitting, yield Mass total = 0.983
+/- 0.007 solar masses, with component masses M(1) = 0.493 +/- 0.003 and M(2) =
0.489 +/- 0.003 solar masses. The light-curve fit yields component radii of
R(1) = 0.453 +/- 0.060 and R(2) = 0.452 +/- 0.050 solar radii. Though a precise
parallax is lacking, broadband VJHK colors and spectral typing suggest
component absolute magnitudes of M_V(1) = 11.18 +/- 0.30 and M_V(2) = 11.28 +/-
0.30.Comment: 15 pages, 3 figure, 3 tables, accepted by ApJL, additional reference
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