arXiv subjects

H. Orland

Publications and source records attributed to H. Orland.

At least 37 records · Page 2Linked to original sources

arXiv2001

RNA Folding and Large N Matrix Theory

We formulate the RNA folding problem as an $N\times N$ matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is set up in such a way that the limit $N\to \infty$ yields the so-called secondary structure (Hartree theory). Tertiary structure and pseudo-knots are obtained by calculating the $1/N^2$ corrections to the partition function. We propose a generalization of the Hartree recursion relation to generate the tertiary structure.

cond-mat.stat-mech↗

arXiv2001

A simple model for DNA denaturation

Following Poland and Scheraga, we consider a simplified model for the denaturation transition of DNA. The two strands are modeled as interacting polymer chains. The attractive interactions, which mimic the pairing between the four bases, are reduced to a single short range binding term. Furthermore, base-pair misalignments are forbidden, implying that this binding term exists only for corresponding (same curvilinear abscissae) monomers of the two chains. We take into account the excluded volume repulsion between monomers of the two chains, but neglect intra-chain repulsion. We find that the excluded volume term generates an effective repulsive interaction between the chains, which decays as $1/r^{d-2}$. Due to this long-range repulsion between the chains, the denaturation transition is first order in any dimension, in agreement with previous studies.

cond-mat.soft↗

arXiv2000

Polyelectrolyte Titration: Theory and Experiment

Titration of methacrylic acid / ethyl-acrylate copolymers is studied experimentally and theoretically. At low salt concentrations, this polyacid exhibits a plateau in the titration curve below the neutralization point. The plateau has been often attributed to a first-order phase transition associated with polymer conformational changes. We argue that the specific shape of titration curves of hydrophobic polyelectrolytes is due to electrostatics and does not necessarily require a conformation change of the polyelectrolyte chains. We calculate the free energy at the mean-field level and its first-order (one loop) correction using a loop expansion. The latter is dominated by Debye-Huckel--like charge-charge correlations as well as by correlations between dissociation sites along the polymer chain. We show that the one-loop corrections to the free energy lead to titration curves that agree with experiments. In particular, the model explains the decrease of the pH at the plateau when the polymer concentration is increased or when salt is added to the solution.

cond-mat.soft↗

arXiv2000

Copolymer at a selective interface and two dimensional wetting: a grand canonical approach

We consider two different problems involving the localization of a single polymer chain: (i) a periodic $AB$ copolymer at a selective fluid-fluid interface, with the upper (resp. lower) fluid attracting $A$ (resp. $B$) monomers (ii) a homopolymer chain attracted to a hard wall (wetting). Self avoidance is neglected in both models, which enables us to study their localization transition in a grand canonical approach. We recover the results obtained in previous studies via transfer matrix methods. Moreover, we calculate in this way the loop length distribution functions in the localized phase. Some finite size effects are also determined and tested numerically.

cond-mat.soft↗

arXiv1999

Adsorption of Large Ions from an Electrolyte Solution: A Modified Poisson-Boltzmann Equation

The behavior of electrolyte solutions close to a charged surface is studied theoretically. A modified Poisson-Boltzmann equation which takes into account the volume excluded by the ions in addition to the electrostatic interactions is presented. In a formal lattice gas formalism the modified Poisson-Boltzmann equation can be obtained from a mean-field approximation of the partition function. In an alternative phenomenological approach, the same equation can be derived by including the entropy of the solvent molecules in the free energy. In order to visualize the effect of the steric repulsion, a simple case of a single, highly charged, flat surface is discussed. This situation resembles recent adsorption experiments of large ions onto a charged monolayer. A simple criterion for the importance of the steric effects is expressed in terms of the surface charge density and the size of the ions. It is shown that when these effects are important a saturated layer is formed near the surface. A modified Grahame equation relating the ion concentration at the surface to the surface charge density is obtained.

cond-mat.soft↗

arXiv1999

One and two-component hard core plasmas

A field theory is presented for particles which interact via Coulomb and hard-core potentials. We apply the method to the one-component plasma (OCP) with hard cores, consisting of identical particles of fixed charge and diameter in a neutralizing background, and the symmetric two-component plasma (TCP) with hard cores, consisting of equal numbers of positively and negatively charged particles of identical size. We obtain exactly the first few coefficients of a systematic low-density expansion of the free energy for both models. The OCP coefficients go over to the classical Abe result in the high-charge (or small hard-core diameter) limit. The TCP, on the other hand, exhibits diverging coefficients in the high-charge limit, which is due to the formation of strongly bound ion-pairs.

cond-mat.soft↗

arXiv1999

Phase diagram of magnetic polymers

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 $Θ$ 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 $Θ$-like. Monte Carlo simulations for the Ising case are in qualitative agreement with these results.

cond-mat.stat-mech↗

arXiv1998

Overlap properties and adsorption transition of two Hamiltonian paths

We consider a model of two (fully) compact polymer chains, coupled through an attractive interaction. These compact chains are represented by Hamiltonian paths (HP), and the coupling favors the existence of common bonds between the chains. Using a ($n=0$ component) spin representation for these paths, we show the existence of a phase transition for strong coupling (i.e. at low temperature) towards a ``frozen'' phase where one chain is completely adsorbed onto the other. By performing a Legendre transform, we obtain the probability distribution of overlaps. The fraction of common bonds between two HP, i.e. their overlap $q$, has both lower ($q_m$) and upper ($q_M$) bounds. This means in particuliar that two HP with overlap greater than $q_M$ coincide. These results may be of interest in (bio)polymers and in optimization problems.

cond-mat.stat-mech↗

arXiv1998

Random Polyelectrolytes and Polyampholytes in Solution

The behavior of polyelectrolytes and polyampholytes in semi-dilute solutions is investigated theoretically. Various statistical charge distributions along the polyelectrolyte chains are considered: smeared, annealed, permuted and quenched. Annealed polyampholytes are also considered. Path integral formulation was used to derive mean field free energies for the different models. Self-consistent field equation is obtained for the polymer order parameter and a Poisson-Boltzmann like equation for the electrostatic potential. The random phase approximation is used to calculate the monomer-monomer structure factor S(q) for the different statistical charge distribution models. We show that in the annealed model, fluctuations of the the monomer charges contribute to the electrostatic screening in addition to the free ions in the solution. The strength of this screening depends on the variance of the monomer charge distribution and is especially important for polyampholytes in bad solvent conditions where the mesophase separation is enhanced. The ratio between the variance and the net average charge determines whether polyampholytes behave as polyelectrolytes or as neutral chains.

cond-mat.soft↗

arXiv1998

The Effect of Polyelectrolyte Adsorption on Inter-Colloidal Forces

The behavior of polyelectrolytes between charged surfaces immersed in semi-dilute solutions is investigated theoretically. A continuum mean field approach is used for calculating numerically concentration profiles between two electrodes held at a constant potential. A generalized contact theorem relates the inter-surface forces to the concentration profiles. The numerical results show that over-compensation of the surface charges by adsorbing polyelectrolytes can lead to effective attraction between equally charged surfaces. Simple scaling arguments enable us to characterize qualitatively the inter-surface interactions as function of the fraction of charged monomers p and the salt concentration c_b. In the low salt regime we find strong repulsion at short distances, where the polymers are depleted from the inter-surface gap, followed by strong attraction when the two adsorbed layers overlap. The magnitude of this attraction scales as p^{1/2} and its dominant length scale is proportional to a/p^{1/2}, where a is the monomer size. At larger distances the two adsorbing surfaces interact via a weak electrostatic repulsion. For strong polyelectrolytes at high salt concentration the polymer contribution to attraction at short distances scales as p/c_b^{1/2} and the length scale is proportional to kappa*a^2/p, where kappa^{-1} is the Debye-Huckel screening length. For weak polyelectrolytes at high salt concentration the interaction is repulsive for all surface separations and decays exponentially with a decay length equal to kappa^{-1}. The effect of irreversible adsorption is discussed as well and it is shown that inter-surface attraction can be obtained in this case as well.

cond-mat.soft↗

arXiv1998

Protein Adsorption on Lipid Monolayers at their Coexistence Region

We investigate theoretically the behavior of proteins as well as other large macromolecules which are incorporated into amphiphilic monolayers at the air-water interface. We assume the monolayer to be in the coexistence region of the ``main'' transition, where domains of the liquid condensed phase coexist with the liquid expanded background. Using a simple mean-field free energy accounting for the interactions between proteins and amphiphilic molecules, we obtain the spatial protein distribution with the following characteristics. When the proteins preferentially interact with either the liquid condensed or liquid expanded domains, they will be dissolved in the respective phase. When the proteins are energetically rather indifferent to the density of the amphiphiles, they will be localized at the line boundary between the (two-dimensional) liquid expanded and condensed phases. In between these two limiting cases, a delocalization transition of the proteins takes place. This transition is accessible by changing the temperature or the amount of incorporated protein. These findings are in agreement with recent fluorescence microscopy experiments. Our results also apply to lipid multicomponent membranes showing coexistence of distinct fluid phases.

cond-mat.soft↗

arXiv1998

Steric Effects in Electrolytes: A Modified Poisson-Boltzmann Equation

The adsorption of large ions from solution to a charged surface is investigated theoretically. A generalized Poisson--Boltzmann equation, which takes into account the finite size of the ions is presented. We obtain analytical expressions for the electrostatic potential and ion concentrations at the surface, leading to a modified Grahame equation. At high surface charge densities the ionic concentration saturates to its maximum value. Our results are in agreement with recent experiments.

cond-mat.soft↗

arXiv1997

Gas of self-avoiding loops on the brickwork lattice

An exact calculation of the phase diagram for a loop gas model on the brickwork lattice is presented. The model includes a bending energy. In the dense limit, where all the lattice sites are occupied, a phase transition occuring at an asymmetric Lifshitz tricritical point is observed as the temperature associated with the bending energy is varied. Various critical exponents are calculated. At lower densities, two lines of transitions (in the Ising universality class) are observed, terminated by a tricritical point, where there is a change in the modulation of the correlation function. To each tricritical point an associated disorder line is found.

cond-mat.stat-mech↗

arXiv1997

Scaling Laws of Polyelectrolyte Adsorption

Adsorption of charged polymers (polyelectrolytes) from a semi-dilute solution to a charged surface is investigated theoretically. We obtain simple scaling laws for (i) the amount of polymer adsorbed to the surface, Gamma, and (ii) the width of the adsorbed layer D, as function of the fractional charge per monomer p and the salt concentration c_b. For strongly charged polyelectrolytes (p<1) in a low-salt solution, both Gamma and D scale as p^{-1/2}. In salt-rich solutions D~c_b^{1/2}/p whereas the scaling behavior of Gamma depends on the strength of the polymer charge. For weak polyelectrolytes (p<<1) we find that Gamma~p/c_b^{1/2} while for strong polyelectrolytes Gamma~c_b^{1/2}/p. Our results are in good agreement with adsorption experiments and with numerical solutions of mean-field equations.

cond-mat.soft↗

arXiv1997

Protein folding and heteropolymers

We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random heteropolymeric description of these non random biomolecules. Various kinds of randomness are investigated, and the connection with disordered systems is discussed. We conclude by a brief study of the dynamics of proteins.

cond-mat.dis-nn↗

arXiv1997

Protein folding, anisotropic collapse and blue phases

We study a homopolymer model of a protein chain, where each monomer carries a dipole moment. To mimic the geometry of the peptidic bond, these dipoles are constrained to be locally perpendicular to the chain. The tensorial character of the dipolar interaction leads naturally to a (tensorial) liquid crystal-like order parameter. For non chiral chains, a mean field study of this model shows that a classical $θ$ collapse transition occurs first; at lower temperature, nematic order sets in. For chiral chains, an anisotropic (tensorial) collapse transition may occur before the $θ$ temperature is reached: the ordered phase can be described as a ``compact phase of secondary structures'', and possesses great similarities with the liquid crystal blue phases.

cond-mat.soft↗

arXiv1996

Dynamics of the swelling or collapse of a homopolymer

We study the dynamics of a polymer when it is quenched from a $θ$ solvent into a good or bad solvent by means of a Langevin equation. The variation of the radius of gyration is studied as a function of time. For the first stage of collapse or swelling, the characteristic time-scale is found to be independent of the number of monomers. Other scaling laws are derived for the diffusion regime at larger times. Although the present model is solved only for homopolymers and doesn't include hydrodynamic interactions, these results may be a first step towards the understanding of the early stages of protein folding.

cond-mat.soft↗

arXiv1996

Directed polymers in a random medium: a variational approach

A disorder-dependent Gaussian variational approach is applied to the problem of a $d$ dimensional polymer chain in a random medium (or potential). Two classes of variational solutions are obtained. For $d<2$, these two classes may be interpreted as domain and domain wall. The critical exponent $ν$ describing the polymer width is $ν={1\over (4-d)}$ (domain solution) or $ν={3\over (d+4)}$ (domain wall solution). The domain wall solution is equivalent to the (full) replica symmetry breaking variational result. For $d>2$, we find $ν={1\over 2}$. No evidence of a phase transition is found for $2< d< 4$: one of the variational solutions suggests that the polymer chain breaks into Imry-Ma segments, whose probability distribution is calculated. For $d>4$, the other variational solution undergoes a phase transition, which has some similarity with B. Derrida's random energy models.

cond-mat↗