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A L Stella

Publications and source records attributed to A L Stella.

11 recordsLinked to original sources
PubMed2005

Scale-free network hidden in a collapsing polymer.

We show that the collapsed globular phase of a polymer accommodates a scale-free incompatibility graph of its contacts. The degree distribution of this network is found to decay with the exponent gamma=1/(2-c) up to a cutoff degree dc proportional to L(2-c), where is the loop exponent for dense polymers (c=11/8 in two dimensions) and is the length of the polymer. Our results exemplify how a scale-free network can emerge from standard criticality.

Journal Article↗
PubMed2005

Precise toppling balance, quenched disorder, and universality for sandpiles.

A single sandpile model with quenched random toppling matrices captures the crucial features of different models of self-organized criticality. With symmetric matrices avalanche statistics falls in the multiscaling Bak-Tang-Wiesenfeld universality class. In the asymmetric case the simple scaling of the Manna model is observed. The presence or absence of a precise toppling balance between the amount of sand released by a toppling site and the total quantity the same site receives when all its neighbors topple once determines the appropriate universality class.

Journal Article↗
PubMed2004

Pseudoknots in a homopolymer.

After a discussion of the definition and number of pseudoknots, we reconsider the self-attracting homopolymer paying particular attention to the scaling of the pseudoknot number (Npk) at different temperature regimes in two and three dimensions. We find that, although the total number of pseudoknots is extensive at all temperatures, the number of those forming between the two halves of the chain diverges logarithmically at (both dimensions) and below (two dimensions only) the theta temperature. We later introduce a simple model that emphasizes the role of pseudoknot formation during collapse. The resulting phase diagram involves swollen, branched, and collapsed homopolymer phases with transitions between each pair.

Journal Article↗
PubMed2003

RNA denaturation: excluded volume, pseudoknots, and transition scenarios.

A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous transition. Otherwise a smooth crossover occurs from the swollen linear polymer behavior to highly ramified, almost compact conformations with secondary structures. In the latter scenario, which is appropriate when these structures are much more stable than pseudoknot links, probability distributions for the lengths of both loops and main branches obey scaling with nonclassical exponents.

Models, Chemical↗
PubMed2003

Polymer theta-point as a knot delocalization transition.

We study numerically the tightness of prime flat knots in a model of self-attracting polymers with excluded volume. We find that these knots are localized in the high temperature swollen regime, but become delocalized in the low temperature globular phase. Precisely at the collapse transition, the knots are weakly localized. Some of our results can be interpreted in terms of the theory of polymer networks, which allows one to conjecture exact exponents for the knot length probability distributions.

Journal Article↗
PubMed2003

Interstrand distance distribution of DNA near melting.

The distance distribution between complementary base pairs of the two strands of a DNA molecule is studied near the melting transition. Scaling arguments are presented for a generalized Poland-Scheraga-type model that includes self-avoiding interactions. At the transition temperature and for a large distance r, the distribution decays as 1/r(kappa) with kappa=1+(c-2)/nu. Here nu is the self-avoiding walk correlation length exponent and c is the exponent associated with the entropy of an open loop in the chain. Results for the distribution function just below the melting point are also presented. Numerical simulations that fully take into account the self-avoiding interactions are in good agreement with the scaling approach.

Journal Article↗
PubMed2001

Directed polymers with tilted columnar disorder and Burgers-like turbulence.

The minimal energy variations of a directed polymer with tilted columnar disorder in two dimensions are shown numerically to obey multiscaling at short distances which crosses over to global simple scaling at large distances. The scenario is analogous to that of structure functions in bifractal Burgers turbulence. Some scaling properties are predicted from extreme value statistics. The multiscaling disappears for zero tilt.

Journal Article↗
PubMed2001

Peculiar scaling of self-avoiding walk contacts.

The nearest neighbor contacts between the two halves of an N-site lattice self-avoiding walk offer an unusual example of scaling random geometry: for N-->infinity they are strictly finite in number but their radius of gyration R(c) is power law distributed proportional to R(-tau)(c), where tau>1 is a novel exponent characterizing universal behavior. A continuum of diverging length scales is associated with the R(c) distribution. A possibly superuniversal tau = 2 is also expected for the contacts of a self-avoiding or random walk with a confining wall.

Journal Article↗
PubMed2001

Zipping and collapse of diblock copolymers.

Using exact enumeration methods and Monte Carlo simulations, we study the phase diagram relative to the conformational transitions of a diblock copolymer in two dimensions. The polymer is made of two homogeneous strands of monomers of different species which are joined to each other at one end. We find that, depending on the values of the energy parameters in the model, there is either a first order collapse from a swollen phase to a compact phase of spiral type, or a continuous transition to an intermediate zipped phase followed by a first order collapse at lower temperatures. Critical exponents of the zipping transition are computed, and their exact values are conjectured on the basis of a mapping onto percolation geometry, thanks to recent results on path-crossing probabilities.

Journal Article↗
PubMed1992

Point mutation of estrogen receptor (ER) in the ligand-binding domain changes the pharmacology of antiestrogens in ER-negative breast cancer cells stably expressing complementary DNAs for ER.

The antiestrogen tamoxifen is used in the treatment of hormone-responsive breast cancer. However, therapeutic failure has frequently been observed in both patients and animal models after long term treatment. We have studied the effect of a point mutation that leads to the substitution of Val for Gly at codon 400 in the ligand-binding domain of the estrogen receptor (ER) on estrogenic and antiestrogenic activities of 4-hydroxytamoxifen (4-OHT) and its derivatives. Stable ER transfectants derived from MDA-MB-231 CL10A, an ER-negative breast cancer cell line, have been used in these studies. 4-OHT and its fixed ring derivatives showed more estrogen-like activity in ER transfectants than in MCF-7, an ER-positive breast cancer cell line. In this study, 4-OHT was a partial agonist of cell growth in the transfectant S30 cells, which express the wild-type ER. However, it was a full agonist in the mutant ER transfectant ML alpha 2H, which expressed ER with Val at codon 400. The increased estrogenic activity of 4-OHT in ML alpha 2H cells was not due to the preferential isomerization of trans 4-OHT to cis 4-OHT, since the nonisomerizable fixed ring trans 4-OHT was a partial agonist for cell growth in S30 cells and was a full agonist in ML alpha 2H cells. Transient transfection using a reporter plasmid containing an estrogen response element demonstrated that fixed ring trans 4-OHT had estrogenic activity in ML alpha 2H cells.(ABSTRACT TRUNCATED AT 250 WORDS)

Breast Neoplasms↗