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  • 1
    ISSN: 1520-4804
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of medicinal chemistry 32 (1989), S. 1398-1401 
    ISSN: 1520-4804
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1520-4804
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    The European physical journal 28 (2002), S. 467-473 
    ISSN: 1434-6036
    Keywords: PACS. 87.14.Gg DNA, RNA – 87.15.Aa Theory and modeling; computer simulation – 05.70.Jk Critical point phenomena
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract: The linking number (topological entanglement) and the writhe (geometrical entanglement) of a model of circular double stranded DNA undergoing a thermal denaturation transition are investigated by Monte Carlo simulations. By allowing the linking number to fluctuate freely in equilibrium we see that the linking probability undergoes an abrupt variation (first-order) at the denaturation transition, and stays close to 1 in the whole native phase. The average linking number is almost zero in the denatured phase and grows as the square root of the chain length, N, in the native phase. The writhe of the two strands grows as in both phases.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    The European physical journal 12 (1999), S. 261-268 
    ISSN: 1434-6036
    Keywords: PACS. 36.20.Ey Conformation (statistics and dynamics) - 64.70.-p Specific phase transitions - 75.50.-y Studies of specific magnetic materials
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract: We consider polymers made of magnetic monomers (Ising or Heisenberg-like) in a good solvent. These polymers are modeled as self-avoiding walks on a cubic lattice, and the ferromagnetic interaction between the spins carried by the monomers is short-ranged in space. At low temperature, these polymers undergo a magnetic induced first order collapse transition, that we study at the mean field level. Contrasting with an ordinary point, there is a strong jump in the polymer density, as well as in its magnetization. In the presence of a magnetic field, the collapse temperature increases, while the discontinuities decrease. Beyond a multicritical point, the transition becomes second order and -like. Monte Carlo simulations for the Ising case are in qualitative agreement with these results.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    The European physical journal 29 (2002), S. 129-134 
    ISSN: 1434-6036
    Keywords: PACS. 87.14.Gg DNA, RNA – 05.70.Jk Critical point phenomena – 05.70.Fh Phase transitions: general studies – 87.15.Aa Theory and modeling; computer simulation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract: Recently Garel, Monthus and Orland [Europhys. Lett. 55, 132 (2001)] considered a model of DNA denaturation in which excluded volume effects within each strand are neglected, while mutual avoidance is included. Using an approximate scheme they found a first order denaturation. We show that a first order transition for this model follows from exact results for the statistics of two mutually avoiding random walks, whose reunion exponent is c 〉 2, both in two and three dimensions. Analytical estimates of c due to the interactions with other denaturated loops, as well as numerical calculations, indicate that the transition is even sharper than in models where excluded volume effects are fully incorporated. The probability distribution of distances between homologous base pairs decays as a power law at the transition.
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    The European physical journal 6 (1998), S. 101-110 
    ISSN: 1434-6036
    Keywords: PACS. 61.41.+e Polymers, elastomers, and plastics[:AND:] 87.15.-v Molecular biophysics - 64.70.-p Specific phase transitions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract: We study a single self avoiding hydrophilic hydrophobic polymer chain, through Monte-Carlo lattice simulations. The affinity of monomer i for water is characterized by a (scalar) charge , and the monomer-water interaction is short-ranged. Assuming incompressibility yields an effective short ranged interaction between monomer pairs (i,j), proportional to . In this article, we take (resp. ( )) for hydrophilic (resp. hydrophobic) monomers and consider a chain with (i) an equal number of hydro-philic and -phobic monomers (ii) a periodic distribution of the along the chain, with periodicity 2p. The simulations are done for various chain lengths N, in d=2 (square lattice) and d=3 (cubic lattice). There is a critical value p c (d,N) of the periodicity, which distinguishes between different low temperature structures. For p 〉p c , the ground state corresponds to a macroscopic phase separation between a dense hydrophobic core and hydrophilic loops. For p 〈p c (but not too small), one gets a microscopic (finite scale) phase separation, and the ground state corresponds to a chain or network of hydrophobic droplets, coated by hydrophilic monomers. We restrict our study to two extreme cases, and to illustrate the physics of the various phase transitions. A tentative variational approach is also presented.
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Journal of statistical physics 66 (1992), S. 515-533 
    ISSN: 1572-9613
    Keywords: Mixing repellers ; Mellin transform ; potential and energy integrals ; corrections to scaling laws ; singularity spectrum and residues
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract The short-distance behavior of the measure of a sphere and of the correlation integral is determined, in the case of disconnected repellers, by scaling laws whose corrections are oscillating functions, periodic or aperiodic, depending on exact or approximate self-similarity of the measure. The Mellin transforms prove to be the correct analytic tool in order to investigate these corrections to scaling. It has been previously proved that they are meromorphic for linear Cantor sets and that the leading pole gives the correlation dimension in agreement with the results of the thermodynamic formalism. Here we show that the residues of these poles can also be computed to any desired accuracy with simple algorithms and that the knowledge of the singularity spectrum of the Mellin transforms provides the Fourier spectrum of the scaling correction for the self-similar measure and that it reproduces the damped oscillations in the generic case. The method applies to the nonlinear repellers such as the disconnected Julia sets by using an approximation theorem.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Journal of statistical physics 82 (1996), S. 155-181 
    ISSN: 1572-9613
    Keywords: Self-avoiding walks ; lattice models ; Markov chains ; Monte Carlo ; phase transitions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract We consider self-avoiding walks on the simple cubic lattice in which neighboring pairs of vertices of the walk (not connected by an edge) have an associated pair-wise additive energy. If the associated force is attractive, then the walk can collapse from a coil to a compact ball. We describe two Monte Carlo algorithms which we used to investigate this collapse process, and the properties of the walk as a function of the energy or temperature. We report results about the thermodynamic and configurational properties of the walks and estimate the location of the collapse transition.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Journal of statistical physics 82 (1996), S. 1159-1198 
    ISSN: 1572-9613
    Keywords: Ribbon ; lattice models ; Monte Carlo algorithm ; knotting and linking ; entanglements
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract A lattice ribbon is a connected sequence of plaquettes subject to certain selfavoidance conditions. The ribbon can be closed to form an object which is topologically either a cylinder or a Möbius band, depending on whether its surface is orientable or nonorientable. We describe a grand canonical Monte Carlo algorithm for generating a sample of these ribbons, prove that the associated Markov chain is ergodic, and present and discuss numerical results about the dimensions and entanglement complexity of the ribbons.
    Type of Medium: Electronic Resource
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