A First Exposure to Statistical Mechanics for Life Scientists

Statistical mechanics is one of the most powerful and elegant tools in the quantitative sciences. One key virtue of statistical mechanics is that it is designed to examine large systems with many interacting degrees of freedom, providing a clue that it might have some bearing on the analysis of the molecules of living matter. As a result of data on biological systems becoming increasingly quantitative, there is a concomitant demand that the models set forth to describe biological systems be themselves quantitative. We describe how statistical mechanics is part of the quantitative toolkit that is needed to respond to such data. The power of statistical mechanics is not limited to traditional physical and chemical problems and there are a host of interesting ways in which these ideas can be applied in biology. This article reports on our efforts to teach statistical mechanics to life science students and provides a framework for others interested in bringing these tools to a nontraditional audience in the life sciences.Comment: 27 pages, 16 figures. Submitted to American Journal of Physic

Thermal Equilibration of 176-Lu via K-Mixing

In astrophysical environments, the long-lived (\T_1/2 = 37.6 Gy) ground state of 176-Lu can communicate with a short-lived (T_1/2 = 3.664 h) isomeric level through thermal excitations. Thus, the lifetime of 176-Lu in an astrophysical environment can be quite different than in the laboratory. We examine the possibility that the rate of equilibration can be enhanced via K-mixing of two levels near E_x = 725 keV and estimate the relevant gamma-decay rates. We use this result to illustrate the effect of K-mixing on the effective stellar half-life. We also present a network calculation that includes the equilibrating transitions allowed by K-mixing. Even a small amount of K-mixing will ensure that 176-Lu reaches at least a quasi-equilibrium during an s-process triggered by the 22-Ne neutron source.Comment: 9 pages, 6 figure

Effects of high order deformation on superheavy high-KK isomers

Using, for the first time, configuration-constrained potential-energy-surface calculations with the inclusion of $\beta_6$ deformation, we find remarkable effects of the high order deformation on the high-$K$ isomers in $^{254}$No, the focus of recent spectroscopy experiments on superheavy nuclei. For shapes with multipolarity six, the isomers are more tightly bound and, microscopically, have enhanced deformed shell gaps at $N=152$ and $Z=100$. The inclusion of $\beta_6$ deformation significantly improves the description of the very heavy high-$K$ isomers.Comment: 5 pages, 4 figures, 1 table, the version to appear in Phys. Rev.

Operator Sequence Alters Gene Expression Independently of Transcription Factor Occupancy in Bacteria

A canonical quantitative view of transcriptional regulation holds that the only role of operator sequence is to set the probability of transcription factor binding, with operator occupancy determining the level of gene expression. In this work, we test this idea by characterizing repression in vivo and the binding of RNA polymerase in vitro in experiments where operators of various sequences were placed either upstream or downstream from the promoter in Escherichia coli. Surprisingly, we find that operators with a weaker binding affinity can yield higher repression levels than stronger operators. Repressor bound to upstream operators modulates promoter escape, and the magnitude of this modulation is not correlated with the repressor-operator binding affinity. This suggests that operator sequences may modulate transcription by altering the nature of the interaction of the bound transcription factor with the transcriptional machinery, implying a new layer of sequence dependence that must be confronted in the quantitative understanding of gene expression

Conformational Entropy of Compact Polymers

Exact results for the scaling properties of compact polymers on the square lattice are obtained from an effective field theory. The entropic exponent \gamma=117/112 is calculated, and a line of fixed points associated with interacting chains is identified; along this line \gamma varies continuously. Theoretical results are checked against detailed numerical transfer matrix calculations, which also yield a precise estimate for the connective constant \kappa=1.47280(1).Comment: 4 pages, 1 figur

Statistical Topography of Glassy Interfaces

Statistical topography of two-dimensional interfaces in the presence of quenched disorder is studied utilizing combinatorial optimization algorithms. Finite-size scaling is used to measure geometrical exponents associated with contour loops and fully packed loops. We find that contour-loop exponents depend on the type of disorder (periodic ``vs'' non-periodic) and they satisfy scaling relations characteristic of self-affine rough surfaces. Fully packed loops on the other hand are unaffected by disorder with geometrical exponents that take on their pure values.Comment: 4 pages, REVTEX, 4 figures included. Further information can be obtained from [email protected]

Stretching short biopolymers by fields and forces

We study the mechanical properties of semiflexible polymers when the contour length of the polymer is comparable to its persistence length. We compute the exact average end-to-end distance and shape of the polymer for different boundary conditions, and show that boundary effects can lead to significant deviations from the well-known long-polymer results. We also consider the case of stretching a uniformly charged biopolymer by an electric field, for which we compute the average extension and the average shape, which is shown to be trumpetlike. Our results also apply to long biopolymers when thermal fluctuations have been smoothed out by a large applied field or force.Comment: 10 pages, 7 figure

Correlated quantum percolation in the lowest Landau level

Our understanding of localization in the integer quantum Hall effect is informed by a combination of semi-classical models and percolation theory. Motivated by the effect of correlations on classical percolation we study numerically electron localization in the lowest Landau level in the presence of a power-law correlated disorder potential. Careful comparisons between classical and quantum dynamics suggest that the extended Harris criterion is applicable in the quantum case. This leads to a prediction of new localization quantum critical points in integer quantum Hall systems with power-law correlated disorder potentials. We demonstrate the stability of these critical points to addition of competing short-range disorder potentials, and discuss possible experimental realizations.Comment: 15 pages, 12 figure

Monte-Carlo study of scaling exponents of rough surfaces and correlated percolation

We calculate the scaling exponents of the two-dimensional correlated percolation cluster's hull and unscreened perimeter. Correlations are introduced through an underlying correlated random potential, which is used to define the state of bonds of a two-dimensional bond percolation model. Monte-Carlo simulations are run and the values of the scaling exponents are determined as functions of the Hurst exponent H in the range -0.75 <= H <= 1. The results confirm the conjectures of earlier studies