Elastic energy of proteins and the stages of protein folding

We propose a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable parameters are fitted to data from the computer simulation of the folding of a set of proteins using the CSAW (conditioned self-avoiding walk) model. The elastic energy gives rise to scaling relations of the form $R_{g}\sim N^{\nu}$ in different regions. It shows three folding stages characterized by the progression with exponents $\nu = 3/5, 3/7, 2/5$, which we identify as the unfolded stage, pre-globule, and molten globule, respectively. The pre-globule goes over to the molten globule via a break in behavior akin to a first-order phase transition, which is initiated by a sudden acceleration of hydrogen bonding

Absorption/Expulsion of Oligomers and Linear Macromolecules in a Polymer Brush

The absorption of free linear chains in a polymer brush was studied with respect to chain size $L$ and compatibility $\chi$ with the brush by means of Monte Carlo (MC) simulations and Density Functional Theory (DFT) / Self-Consistent Field Theory (SCFT) at both moderate, $\sigma_g = 0.25$, and high, $\sigma_g = 1.00$, grafting densities using a bead-spring model. Different concentrations of the free chains $0.0625 \le \phi_o \le 0.375$ are examined. Contrary to the case of $\chi = 0$ when all species are almost completely ejected by the polymer brush irrespective of their length $L$, for $\chi < 0$ we find that the degree of absorption (absorbed amount) $\Gamma(L)$ undergoes a sharp crossover from weak to strong ($\approx 100$) absorption, discriminating between oligomers, $1\le L\le 8$, and longer chains. For a moderately dense brush, $\sigma_g = 0.25$, the longer species, $L > 8$, populate predominantly the deep inner part of the brush whereas in a dense brush $\sigma_g = 1.00$ they penetrate into the "fluffy" tail of the dense brush only. Gyration radius $R_g$ and end-to-end distance $R_e$ of absorbed chains thereby scale with length $L$ as free polymers in the bulk. Using both MC and DFT/SCFT methods for brushes of different chain length $32 \le N \le 256$, we demonstrate the existence of unique {\em critical} value of compatibility $\chi = \chi^{c}<0$. For $\chi^{c}(\phi_o)$ the energy of free chains attains the {\em same} value, irrespective of length $L$ whereas the entropy of free chain displays a pronounced minimum. At $\chi^{c}$ all density profiles of absorbing chains with different $L$ intersect at the same distance from the grafting plane. The penetration/expulsion kinetics of free chains into the polymer brush after an instantaneous change in their compatibility $\chi$ displays a rather rich behavior. We find three distinct regimes of penetration kinetics of free chains regarding the length $L$: I ($1\le L\le 8$), II ($8 \le L \le N$), and III ($L > N$), in which the time of absorption $\tau$ grows with $L$ at a different rate. During the initial stages of penetration into the brush one observes a power-law increase of $\Gamma \propto t^\alpha$ with power $\alpha \propto -\ln \phi_o$ whereby penetration of the free chains into the brush gets {\em slower} as their concentration rises

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.

Orthorhombic Phase of Crystalline Polyethylene: A Constant Pressure Path Integral Monte Carlo Study

In this paper we present a Path Integral Monte Carlo (PIMC) simulation of the orthorhombic phase of crystalline polyethylene, using an explicit atom force field with unconstrained bond lengths and angles. This work represents a quantum extension of our recent classical simulation (J. Chem. Phys. 106, 8918 (1997)). It is aimed both at exploring the applicability of the PIMC method on such polymer crystal systems, as well as on a detailed assessment of the importance of quantum effects on different quantities. We used the $NpT$ ensemble and simulated the system at zero pressure in the temperature range 25 - 300 K, using Trotter numbers between 12 and 144. In order to investigate finite-size effects, we used chains of two different lengths, C_12 and C_24, corresponding to the total number of atoms in the super-cell being 432 and 864, respectively. We show here the results for structural parameters, like the orthorhombic lattice constants a,b,c, and also fluctuations of internal parameters of the chains, such as bond lengths and bond and torsional angles. We have also determined the internal energy and diagonal elastic constants c_11, c_22 and c_33. We discuss the temperature dependence of the measured quantities and compare to that obtained from the classical simulation. For some quantities, we discuss the way they are related to the torsional angle fluctuation. In case of the lattice parameters we compare our results to those obtained from other theoretical approaches as well as to some available experimental data. In order to study isotope effects, we simulated also a deuterated polyethylene crystal at a low temperature. We also suggest possible ways of extending this study and present some general considerations concerning modeling of polymer crystals.Comment: 18 pages, RevTex, 18 figures, 3 tables, submitted to Phys. Rev.

Polymer-Chain Adsorption Transition at a Cylindrical Boundary

In a recent letter, a simple method was proposed to generate solvable models that predict the critical properties of statistical systems in hyperspherical geometries. To that end, it was shown how to reduce a random walk in $D$ dimensions to an anisotropic one-dimensional random walk on concentric hyperspheres. Here, I construct such a random walk to model the adsorption-desorption transition of polymer chains growing near an attractive cylindrical boundary such as that of a cell membrane. I find that the fraction of adsorbed monomers on the boundary vanishes exponentially when the adsorption energy decreases towards its critical value. When the adsorption energy rises beyond a certain value above the critical point whose scale is set by the radius of the cell, the adsorption fraction exhibits a crossover to a linear increase characteristic to polymers growing near planar boundaries.Comment: latex, 12 pages, 3 ps-figures, uuencode

Role of chemokines and cytokines in a reactivation model of arthritis in rats induced by injection with streptococcal cell walls

Intraarticular injection of streptococcal cell wall (SCW) antigen followed by intravenous challenge results in a T cellâ mediated monoarticular arthritis in female Lewis rats. Initial studies showed that this reactivation response to intravenous SCW antigen is dependent on the presence of interleukinâ 1 (ILâ 1) and tumor necrosis factor α (TNFâ α) and that the early phase of swelling is neutrophilâ dependent. Neutrophil depletion or passive immunization with antibodies to Pâ selectin or macrophage inflammatory proteinâ 2 reduced the intensity of ankle edema and the influx of neutrophils. After the first few days, however, the arthritic response is mediated primarily by mononuclear cells. Joint tissues showed upâ regulation of mRNA for monocyte chemotactic proteinâ 1 (MCPâ 1), which could be inhibited in part by antiâ ILâ 4; treatment of rats with antibodies to ILâ 4 or MCPâ 1 significantly suppressed development of ankle edema and histopathological evidence of inflammation. Antibodies to interferonâ γ or ILâ 10 had no effect. Treatment with antiâ MCPâ 1 also suppressed influx of 111Inâ labeled T cells into the ankle joint. These data suggest that the late, mononuclearâ dependent phase of SCWâ induced arthritis in female Lewis rats requires cytokines that upâ regulate MCPâ 1, which in turn may facilitate recruitment and extravasation of mononuclear cells into the joint. J. Leukoc. Biol. 63: 359â 363; 1998.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142294/1/jlb0359.pd

Effective interactions between star polymers and colloidal particles

Using monomer-resolved Molecular Dynamics simulations and theoretical arguments based on the radial dependence of the osmotic pressure in the interior of a star, we systematically investigate the effective interactions between hard, colloidal particles and star polymers in a good solvent. The relevant parameters are the size ratio q between the stars and the colloids, as well as the number of polymeric arms f (functionality) attached to the common center of the star. By covering a wide range of q's ranging from zero (star against a flat wall) up to about 0.75, we establish analytical forms for the star-colloid interaction which are in excellent agreement with simulation results. A modified expression for the star-star interaction for low functionalities, f < 10 is also introduced.Comment: 37 pages, 14 figures, preprint-versio

Critical Dynamics of Gelation

Shear relaxation and dynamic density fluctuations are studied within a Rouse model, generalized to include the effects of permanent random crosslinks. We derive an exact correspondence between the static shear viscosity and the resistance of a random resistor network. This relation allows us to compute the static shear viscosity exactly for uncorrelated crosslinks. For more general percolation models, which are amenable to a scaling description, it yields the scaling relation $k=\phi-\beta$ for the critical exponent of the shear viscosity. Here $\beta$ is the thermal exponent for the gel fraction and $\phi$ is the crossover exponent of the resistor network. The results on the shear viscosity are also used in deriving upper and lower bounds on the incoherent scattering function in the long-time limit, thereby corroborating previous results.Comment: 34 pages, 2 figures (revtex, amssymb); revised version (minor changes