Proteins and polymers

Proteins, chain molecules of amino acids, behave in ways which are similar to each other yet quite distinct from standard compact polymers. We demonstrate that the Flory theorem, derived for polymer melts, holds for compact protein native state structures and is not incompatible with the existence of structured building blocks such as $\alpha$-helices and $\beta$-strands. We present a discussion on how the notion of the thickness of a polymer chain, besides being useful in describing a chain molecule in the continuum limit, plays a vital role in interpolating between conventional polymer physics and the phase of matter associated with protein structures.Comment: 7 pages, 6 figure

Universal Formulae for Percolation Thresholds

A power law is postulated for both site and bond percolation thresholds. The formula writes $p_c=p_0[(d-1)(q-1)]^{-a}d^{\ b}$, where $d$ is the space dimension and $q$ the coordination number. All thresholds up to $d\rightarrow \infty$ are found to belong to only three universality classes. For first two classes $b=0$ for site dilution while $b=a$ for bond dilution. The last one associated to high dimensions is characterized by $b=2a-1$ for both sites and bonds. Classes are defined by a set of value for $\{p_0; \ a\}$. Deviations from available numerical estimates at $d \leq 7$ are within $\pm 0.008$ and $\pm 0.0004$ for high dimensional hypercubic expansions at $d \geq 8$. The formula is found to be also valid for Ising critical temperatures.Comment: 11 pages, latex, 3 figures not include

Theoretical and numerical study of the phase diagram of patchy colloids: ordered and disordered patch arrangements

We report theoretical and numerical evaluations of the phase diagram for a model of patchy particles. Specifically we study hard-spheres whose surface is decorated by a small number f of identical sites ("sticky spots'') interacting via a short-range square-well attraction. We theoretically evaluate, solving the Wertheim theory, the location of the critical point and the gas-liquid coexistence line for several values of f and compare them to results of Gibbs and Grand Canonical Monte Carlo simulations. We study both ordered and disordered arrangements of the sites on the hard-sphere surface and confirm that patchiness has a strong effect on the phase diagram: the gas-liquid coexistence region in the temperature-density plane is significantly reduced as f decreases. We also theoretically evaluate the locus of specific heat maxima and the percolation line.Comment: preprint, 32 pages, 6 figures, 3 tables, J. Chem. Phys. in pres

What thermodynamic features characterize good and bad folders? Results from a simplified off-lattice protein model

The thermodynamics of the small SH3 protein domain is studied by means of a simplified model where each bead-like amino acid interacts with the others through a contact potential controlled by a 20x20 random matrix. Good folding sequences, characterized by a low native energy, display three main thermodynamical phases, namely a coil-like phase, an unfolded globule and a folded phase (plus other two phases, namely frozen and random coil, populated only at extremes temperatures). Interestingly, the unfolded globule has some regions already structured. Poorly designed sequences, on the other hand, display a wide transition from the random coil to a frozen state. The comparison with the analytic theory of heteropolymers is discussed

Grand canonical and canonical solution of self-avoiding walks with up to three monomers per site on the Bethe lattice

We solve a model of polymers represented by self-avoiding walks on a lattice which may visit the same site up to three times in the grand-canonical formalism on the Bethe lattice. This may be a model for the collapse transition of polymers where only interactions between monomers at the same site are considered. The phase diagram of the model is very rich, displaying coexistence and critical surfaces, critical, critical endpoint and tricritical lines, as well as a multicritical point. From the grand-canonical results, we present an argument to obtain the properties of the model in the canonical ensemble, and compare our results with simulations in the literature. We do actually find extended and collapsed phases, but the transition between them, composed by a line of critical endpoints and a line of tricritical points, separated by the multicritical point, is always continuous. This result is at variance with the simulations for the model, which suggest that part of the line should be a discontinuous transition. Finally, we discuss the connection of the present model with the standard model for the collapse of polymers (self-avoiding self-attracting walks), where the transition between the extended and collapsed phases is a tricritical point.Comment: 34 pages, including 10 figure

Clusterization, frustration and collectivity in random networks

We consider the random Erd{\H o}s--R\'enyi network with enhanced clusterization and Ising spins $s=\pm 1$ at the network nodes. Mutually linked spins interact with energy $J$. Magnetic properties of the system as dependent on the clustering coefficient $C$ are investigated with the Monte Carlo heat bath algorithm. For $J>0$ the Curie temperature $T_c$ increases from 3.9 to 5.5 when $C$ increases from almost zero to 0.18. These results deviate only slightly from the mean field theory. For $J<0$ the spin-glass phase appears below $T_{SG}$; this temperature decreases with $C$, on the contrary to the mean field calculations. The results are interpreted in terms of social systems.Comment: 10 pages, 6 figures; serious change of result

Density matrix renormalisation group study of the correlation function of the bilinear-biquadratic spin-1 chain

Using the recently developed density matrix renormalization group approach, we study the correlation function of the spin-1 chain with quadratic and biquadratic interactions. This allows us to define and calculate the periodicity of the ground state which differs markedly from that in the classical analogue. Combining our results with other studies, we predict three phases in the region where the quadratic and biquadratic terms are both positive.Comment: 13 pages, Standard Latex File + 5 PostScript figures in separate (New version with SUBSTANTIAL REVISIONS to appear in J Phys A

Diffusive transport of light in three-dimensional disordered Voronoi structures

The origin of diffusive transport of light in dry foams is still under debate. In this paper, we consider the random walks of photons as they are reflected or transmitted by liquid films according to the rules of ray optics. The foams are approximately modeled by three-dimensional Voronoi tessellations with varying degree of disorder. We study two cases: a constant intensity reflectance and the reflectance of thin films. Especially in the second case, we find that in the experimentally important regime for the film thicknesses, the transport-mean-free path does not significantly depend on the topological and geometrical disorder of the Voronoi foams including the periodic Kelvin foam. This may indicate that the detailed structure of foams is not crucial for understanding the diffusive transport of light. Furthermore, our theoretical values for transport-mean-free path fall in the same range as the experimental values observed in dry foams. One can therefore argue that liquid films contribute substantially to the diffusive transport of light in {dry} foams.Comment: 8 pages, 8 figure

Multifractal behavior of linear polymers in disordered media

The scaling behavior of linear polymers in disordered media modelled by self-avoiding random walks (SAWs) on the backbone of two- and three-dimensional percolation clusters at their critical concentrations p_c is studied. All possible SAW configurations of N steps on a single backbone configuration are enumerated exactly. We find that the moments of order q of the total number of SAWs obtained by averaging over many backbone configurations display multifractal behavior, i.e. different moments are dominated by different subsets of the backbone. This leads to generalized coordination numbers \mu_q and enhancement exponents \gamma_q, which depend on q. Our numerical results suggest that the relation \mu_1 = p_ c \mu between the first moment \mu_1 and its regular lattice counterpart \mu is valid.Comment: 11 pages, 12 postscript figures, to be published in Phys. Rev.

Stretching Semiflexible Polymer Chains: Evidence for the Importance of Excluded Volume Effects from Monte Carlo Simulation

Semiflexible macromolecules in dilute solution under very good solvent conditions are modeled by self-avoiding walks on the simple cubic lattice ($d=3$ dimensions) and square lattice ($d=2$ dimensions), varying chain stiffness by an energy penalty $\epsilon_b$ for chain bending. In the absence of excluded volume interactions, the persistence length $\ell_p$ of the polymers would then simply be $\ell_p=\ell_b(2d-2)^{-1}q_b^{-1}$ with $q_b= \exp(-\epsilon_b/k_BT)$, the bond length $\ell_b$ being the lattice spacing, and $k_BT$ is the thermal energy. Using Monte Carlo simulations applying the pruned-enriched Rosenbluth method (PERM), both $q_b$ and the chain length $N$ are varied over a wide range $(0.005 \leq q_b \leq 1, \; N \leq 50000$), and also a stretching force $f$ is applied to one chain end (fixing the other end at the origin). In the absence of this force, in $d=2$ a single crossover from rod-like behavior (for contour lengths less than $\ell_p$) to swollen coils occurs, invalidating the Kratky-Porod model, while in $d=3$ a double crossover occurs, from rods to Gaussian coils (as implied by the Kratky-Porod model) and then to coils that are swollen due to the excluded volume interaction. If the stretching force is applied, excluded volume interactions matter for the force versus extension relation irrespective of chain stiffness in $d=2$, while theories based on the Kratky-Porod model are found to work in $d=3$ for stiff chains in an intermediate regime of chain extensions. While for $q_b \ll 1$ in this model a persistence length can be estimated from the initial decay of bond-orientational correlations, it is argued that this is not possible for more complex wormlike chains (e.g. bottle-brush polymers). Consequences for the proper interpretation of experiments are briefly discussed.Comment: 23 pages, 17 figures, 2 tables, to be published in J. Chem. Phys. (2011