Stability of Climax Prairie and Some Environmental Changes Resulting from Breaking

Continued study of the great midcontinental grasslands of North America throughout a period of years has impressed the writers with the high degree of stability of the climax prairie. This phenomenon has been carefully considered in a study of the types of prairie in the Missouri Valley over an area of several thousand square miles centering in eastern Nebraska but including five neighboring states. Present studies on the deterioration of the prairie under the impact of grazing, and changes in edaphic and atmospheric environment with the breaking and cropping of the land have further emphasized the stabilizing influence of a cover of grassland

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

Theoretical studies of the kinetics of mechanical unfolding of cross-linked polymer chains and their implications for single molecule pulling experiments

We have used kinetic Monte Carlo simulations to study the kinetics of unfolding of cross-linked polymer chains under mechanical loading. As the ends of a chain are pulled apart, the force transmitted by each crosslink increases until it ruptures. The stochastic crosslink rupture process is assumed to be governed by first order kinetics with a rate that depends exponentially on the transmitted force. We have performed random searches to identify optimal crosslink configurations whose unfolding requires a large applied force (measure of strength) and/or large dissipated energy (measure of toughness). We found that such optimal chains always involve cross-links arranged to form parallel strands. The location of those optimal strands generally depends on the loading rate. Optimal chains with a small number of cross-links were found to be almost as strong and tough as optimal chains with a large number of cross-links. Furthermore, optimality of chains with a small number of cross-links can be easily destroyed by adding cross-links at random. The present findings are relevant for the interpretation of single molecule force probe spectroscopy studies of the mechanical unfolding of load-bearing proteins, whose native topology often involves parallel strand arrangements similar to the optimal configurations identified in the study

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

Dynamics and Thermodynamics of the Glass Transition

The principal theme of this paper is that anomalously slow, super-Arrhenius relaxations in glassy materials may be activated processes involving chains of molecular displacements. As pointed out in a preceding paper with A. Lemaitre, the entropy of critically long excitation chains can enable them to grow without bound, thus activating stable thermal fluctuations in the local density or molecular coordination of the material. I argue here that the intrinsic molecular-scale disorder in a glass plays an essential role in determining the activation rate for such chains, and show that a simple disorder-related correction to the earlier theory recovers the Vogel-Fulcher law in three dimensions. A key feature of this theory is that the spatial extent of critically long excitation chains diverges at the Vogel-Fulcher temperature. I speculate that this diverging length scale implies that, as the temperature decreases, increasingly large regions of the system become frozen and do not contribute to the configurational entropy, and thus ergodicity is partially broken in the super-Arrhenius region above the Kauzmann temperature $T_K$. This partially broken ergodicity seems to explain the vanishing entropy at $T_K$ and other observed relations between dynamics and thermodynamics at the glass transition.Comment: 20 pages, no figures, some further revision

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

Bethe lattice solution of a model of SAW's with up to 3 monomers per site and no restriction

In the multiple monomers per site (MMS) model, polymeric chains are represented by walks on a lattice which may visit each site up to K times. We have solved the unrestricted version of this model, where immediate reversals of the walks are allowed (RA) for K = 3 on a Bethe lattice with arbitrary coordination number in the grand-canonical formalism. We found transitions between a non-polymerized and two polymerized phases, which may be continuous or discontinuous. In the canonical situation, the transitions between the extended and the collapsed polymeric phases are always continuous. The transition line is partly composed by tricritical points and partially by critical endpoints, both lines meeting at a multicritical point. In the subspace of the parameter space where the model is related to SASAW's (self-attracting self-avoiding walks), the collapse transition is tricritical. We discuss the relation of our results with simulations and previous Bethe and Husimi lattice calculations for the MMS model found in the literature.Comment: 25 pages, 9 figure

Elasticity near the vulcanization transition

Signatures of the vulcanization transition--amorphous solidification induced by the random crosslinking of macromolecules--include the random localization of a fraction of the particles and the emergence of a nonzero static shear modulus. A semi-microscopic statistical-mechanical theory is presented of the latter signature that accounts for both thermal fluctuations and quenched disorder. It is found (i) that the shear modulus grows continuously from zero at the transition, and does so with the classical exponent, i.e., with the third power of the excess cross-link density and, quite surprisingly, (ii) that near the transition the external stresses do not spoil the spherical symmetry of the localization clouds of the particles.Comment: REVTEX, 5 pages. Minor change

Leadership Statistics in Random Structures

The largest component (``the leader'') in evolving random structures often exhibits universal statistical properties. This phenomenon is demonstrated analytically for two ubiquitous structures: random trees and random graphs. In both cases, lead changes are rare as the average number of lead changes increases quadratically with logarithm of the system size. As a function of time, the number of lead changes is self-similar. Additionally, the probability that no lead change ever occurs decays exponentially with the average number of lead changes.Comment: 5 pages, 3 figure

Orientational correlations in confined DNA

We study how the orientational correlations of DNA confined to nanochannels depend on the channel diameter D by means of Monte Carlo simulations and a mean-field theory. This theory describes DNA conformations in the experimentally relevant regime where the Flory-de Gennes theory does not apply. We show how local correlations determine the dependence of the end-to-end distance of the DNA molecule upon D. Tapered nanochannels provide the necessary resolution in D to study experimentally how the extension of confined DNA molecules depends upon D. Our experimental and theoretical results are in qualitative agreement.Comment: Revised version including supplemental material, 7 pages, 8 figure