Selection to minimise noise in living systems and its implications for the evolution of gene expression

Gene expression, like many biological processes, is subject to noise. This noise has been measured on a global scale, but its general importance to the fitness of an organism is unclear. Here, I show that noise in gene expression in yeast has evolved to prevent harmful stochastic variation in the levels of genes that reduce fitness when their expression levels change. Therefore, there has probably been widespread selection to minimise noise in gene expression. Selection to minimise noise, because it results in gene expression that is stable to stochastic variation in cellular components, may also constrain the ability of gene expression to respond to non-stochastic variation. I present evidence that this has indeed been the case in yeast. I therefore conclude that gene expression noise is an important biological trait, and one that probably limits the evolvability of complex living systems

Review of Linac-Ring Type Collider Proposals

There are three possibly types of particle colliders schemes: familiar (well known) ring-ring colliders, less familiar however sufficiently advanced linear colliders and less familiar and less advanced linac-ring type colliders. The aim of this paper is two-fold: to present possibly complete list of papers on linac-ring type collider proposals and to emphasize the role of linac-ring type machines for future HEP research.Comment: quality of figures is improved, some misprints are correcte

Ergodicity and Slowing Down in Glass-Forming Systems with Soft Potentials: No Finite-Temperature Singularities

The aim of this paper is to discuss some basic notions regarding generic glass forming systems composed of particles interacting via soft potentials. Excluding explicitly hard-core interaction we discuss the so called `glass transition' in which super-cooled amorphous state is formed, accompanied with a spectacular slowing down of relaxation to equilibrium, when the temperature is changed over a relatively small interval. Using the classical example of a 50-50 binary liquid of N particles with different interaction length-scales we show that (i) the system remains ergodic at all temperatures. (ii) the number of topologically distinct configurations can be computed, is temperature independent, and is exponential in N. (iii) Any two configurations in phase space can be connected using elementary moves whose number is polynomially bounded in N, showing that the graph of configurations has the `small world' property. (iv) The entropy of the system can be estimated at any temperature (or energy), and there is no Kauzmann crisis at any positive temperature. (v) The mechanism for the super-Arrhenius temperature dependence of the relaxation time is explained, connecting it to an entropic squeeze at the glass transition. (vi) There is no Vogel-Fulcher crisis at any finite temperature T>0Comment: 10 pages, 9 figures, submitted to PR

Ion size effects at ionic exclusion from dielectric interfaces and slit nanopores

A previously developed field-theoretic model [R.D. Coalson et al., J. Chem. Phys. 102, 4584 (1995)] that treats core collisions and Coulomb interactions on the same footing is investigated in order to understand ion size effects on the partition of neutral and charged particles at planar interfaces and the ionic selectivity of slit nanopores. We introduce a variational scheme that can go beyond the mean-field (MF) regime and couple in a consistent way pore modified core interactions, steric effects, electrostatic solvation and image-charge forces, and surface charge induced electrostatic potential. We show that in the dilute limit, the MF and the variational theories agree well with MC simulation results, in contrast to a recent RPA method. The partition of charged Yukawa particles at a neutral dielectric interface (e.g air-water or protein-water interface) is investigated. It is shown that as a result of the competition between core collisions that push the ions towards the surface, and repulsive solvation and image forces that exclude them from the interface, a concentration peak of finite size ions sets in close to the dielectric interface. We also characterize the role played by the ion size on the ionic selectivity of neutral slit nanopores. We show that the complex interplay between electrostatic forces, excluded volume effects induced by core collisions and steric effects leads to an unexpected reversal in the ionic selectivity of the pore with varying pore size: while large pores exhibits a higher conductivity for large ions, narrow pores exclude large ions more efficiently than small ones

Experimental triplet and quadruplet fluctuation densities and spatial distribution function integrals for pure liquids

Citation: Ploetz, E. A., Karunaweera, S., & Smith, P. E. (2015). Experimental triplet and quadruplet fluctuation densities and spatial distribution function integrals for pure liquids. Journal of Chemical Physics, 142(4), 14. doi:10.1063/1.4905562Fluctuation solution theory has provided an alternative view of many liquid mixture properties in terms of particle number fluctuations. The particle number fluctuations can also be related to integrals of the corresponding two body distribution functions between molecular pairs in order to provide a more physical picture of solution behavior and molecule affinities. Here, we extend this type of approach to provide expressions for higher order triplet and quadruplet fluctuations, and thereby integrals over the corresponding distribution functions, all of which can be obtained from available experimental thermodynamic data. The fluctuations and integrals are then determined using the International Association for the Properties of Water and Steam Formulation 1995 (IAPWS-95) equation of state for the liquid phase of pure water. The results indicate small, but significant, deviations from a Gaussian distribution for the molecules in this system. The pressure and temperature dependence of the fluctuations and integrals, as well as the limiting behavior as one approaches both the triple point and the critical point, are also examined. (C) 2015 AIP Publishing LLC