131 research outputs found
On the phase diagram of branched polymer collapse
The phase diagram of the collapse of a two-dimensional infinite branched
polymer interacting with the solvent and with itself through contact
interactions is studied from the limit of an extension of the
states Potts model. Exact solution on the Bethe lattice and Migdal-Kadanoff
renormalization group calculations show that there is a line of
transitions from the extended to a single compact phase. The line,
governed by three different fixed points, consists of two lines of
extended--compact transitions which are in different universality classes and
meet in a multicritical point.
On the other hand, directed branched polymers are shown to be completely
determined by the strongly embedded case and there is a single
transition which is in the directed percolation universality class.Comment: Latex 25 pages, 8 uucompressed figures, Phys. Rev. E, in pres
Simulations of deposition growth models in various dimensions. Are overhangs important?
We present simulation results of deposition growth of surfaces in 2, 3 and 4
dimensions for ballistic deposition where overhangs are present, and for
restricted solid on solid deposition where there are no overhangs. The values
of the scaling exponents for the two models are found to be different,
suggesting that they belong to different universality classes.Comment: figures available from author
Recurrent oligomers in proteins - an optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies
A novel scheme is introduced to capture the spatial correlations of
consecutive amino acids in naturally occurring proteins. This knowledge-based
strategy is able to carry out optimally automated subdivisions of protein
fragments into classes of similarity. The goal is to provide the minimal set of
protein oligomers (termed ``oligons'' for brevity) that is able to represent
any other fragment. At variance with previous studies where recurrent local
motifs were classified, our concern is to provide simplified protein
representations that have been optimised for use in automated folding and/or
design attempts. In such contexts it is paramount to limit the number of
degrees of freedom per amino acid without incurring in loss of accuracy of
structural representations. The suggested method finds, by construction, the
optimal compromise between these needs. Several possible oligon lengths are
considered. It is shown that meaningful classifications cannot be done for
lengths greater than 6 or smaller than 4. Different contexts are considered
were oligons of length 5 or 6 are recommendable. With only a few dozen of
oligons of such length, virtually any protein can be reproduced within typical
experimental uncertainties. Structural data for the oligons is made publicly
available.Comment: 19 pages, 13 postscript figure
Linking in domain-swapped protein dimers
The presence of knots has been observed in a small fraction of single-domain
proteins and related to their thermodynamic and kinetic properties. The
exchanging of identical structural elements, typical of domain-swapped
proteins, make such dimers suitable candidates to validate the possibility that
mutual entanglement between chains may play a similar role for protein
complexes. We suggest that such entanglement is captured by the linking number.
This represents, for two closed curves, the number of times that each curve
winds around the other. We show that closing the curves is not necessary, as a
novel parameter , termed Gaussian entanglement, is strongly correlated with
the linking number. Based on non redundant domain-swapped dimers, our
analysis evidences a high fraction of chains with a significant intertwining,
that is with . We report that Nature promotes configurations with
negative mutual entanglement and surprisingly, it seems to suppress
intertwining in long protein dimers. Supported by numerical simulations of
dimer dissociation, our results provide a novel topology-based classification
of protein-swapped dimers together with some preliminary evidence of its impact
on their physical and biological properties.Comment: v2: some new paragraphs and new abstrac
Exploring the correlation between the folding rates of proteins and the entanglement of their native states
The folding of a protein towards its native state is a rather complicated
process. However there are empirical evidences that the folding time correlates
with the contact order, a simple measure of the spatial organisation of the
native state of the protein. Contact order is related to the average length of
the main chain loops formed by amino acids which are in contact. Here we argue
that folding kinetics can be influenced also by the entanglement that loops may
undergo within the overall three dimensional protein structure. In order to
explore such possibility, we introduce a novel descriptor, which we call
"maximum intrachain contact entanglement". Specifically, we measure the maximum
Gaussian entanglement between any looped portion of a protein and any other
non-overlapping subchain of the same protein, which is easily computed by
discretized line integrals on the coordinates of the atoms. By
analyzing experimental data sets of two-state and multistate folders, we show
that also the new index is a good predictor of the folding rate. Moreover,
being only partially correlated with previous methods, it can be integrated
with them to yield more accurate predictions.Comment: 8 figures. v2: new titl
Melting behavior and different bound states in three-stranded DNA models
Thermal denaturation of DNA is often studied with coarse-grained models in
which native sequential base pairing is mimicked by the existence of attractive
interactions only between monomers at the same position along strands (Poland
and Scheraga models). Within this framework, the existence of a three strand
DNA bound state in conditions where a duplex DNA would be in the denaturated
state was recently predicted from a study of three directed polymer models on
simplified hierarchical lattices () and in dimensions. Such
phenomenon which is similar to the Efimov effect in nuclear physics was named
Efimov-DNA. In this paper we study the melting of the three-stranded DNA on a
Sierpinski gasket of dimensions by assigning extra weight factors to fork
openings and closings, to induce a two-strand DNA melting. In such a context we
can find again the existence of the Efimov-DNA-like state but quite
surprisingly we discover also the presence of a different phase, to be called a
mixed state, where the strands are pair-wise bound but without three chain
contacts. Whereas the Efimov DNA turns out to be a crossover near melting, the
mixed phase is a thermodynamic phase.Comment: corrected file uploade
Variational approach to protein design and extraction of interaction potentials
We present and discuss a novel approach to the direct and inverse protein
folding problem. The proposed strategy is based on a variational approach that
allows the simultaneous extraction of amino acid interactions and the
low-temperature free energy of sequences of amino acids. The knowledge-based
technique is simple and straightforward to implement even for realistic
off-lattice proteins because it does not entail threading-like procedures. Its
validity is assessed in the context of a lattice model by means of a variety of
stringent checks.Comment: 5 pages, 3 figure
Determination of Interaction Potentials of Amino Acids from Native Protein Structures: Test on Simple Lattice Models
We propose a novel method for the determination of the effective interaction
potential between the amino acids of a protein. The strategy is based on the
combination of a new optimization procedure and a geometrical argument, which
also uncovers the shortcomings of any optimization procedure. The strategy can
be applied on any data set of native structures such as those available from
the Protein Data Bank (PDB). In this work, however, we explain and test our
approach on simple lattice models, where the true interactions are known a
priori. Excellent agreement is obtained between the extracted and the true
potentials even for modest numbers of protein structures in the PDB.
Comparisons with other methods are also discussed.Comment: 24 pages, 4 figure
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