Analytical description of finite size effects for RNA secondary structures

The ensemble of RNA secondary structures of uniform sequences is studied analytically. We calculate the partition function for very long sequences and discuss how the cross-over length, beyond which asymptotic scaling laws apply, depends on thermodynamic parameters. For realistic choices of parameters this length can be much longer than natural RNA molecules. This has to be taken into account when applying asymptotic theory to interpret experiments or numerical results.Comment: 10 pages, 13 figures, published in Phys. Rev.

Quantification of the differences between quenched and annealed averaging for RNA secondary structures

The analytical study of disordered system is usually difficult due to the necessity to perform a quenched average over the disorder. Thus, one may resort to the easier annealed ensemble as an approximation to the quenched system. In the study of RNA secondary structures, we explicitly quantify the deviation of this approximation from the quenched ensemble by looking at the correlations between neighboring bases. This quantified deviation then allows us to propose a constrained annealed ensemble which predicts physical quantities much closer to the results of the quenched ensemble without becoming technically intractable.Comment: 9 pages, 14 figures, submitted to Phys. Rev.

Localization-delocalization transition of disordered d-wave superconductors in class CI

A lattice model for disordered d-wave superconductors in class CI is reconsidered. Near the band-center, the lattice model can be described by Dirac fermions with several species, each of which yields WZW term for an effective action of the Goldstone mode. The WZW terms cancel out each other because of the four-fold symmetry of the model, which suggests that the quasiparticle states are localized. If the lattice model has, however, symmetry breaking terms which generate mass for any species of the Dirac fermions, remaining WZW term which avoids the cancellation can derive the system to a delocalized strong-coupling fixed point.Comment: 4 pages, revte

Weak localization of disordered quasiparticles in the mixed superconducting state

Starting from a random matrix model, we construct the low-energy effective field theory for the noninteracting gas of quasiparticles of a disordered superconductor in the mixed state. The theory is a nonlinear sigma model, with the order parameter field being a supermatrix whose form is determined solely on symmetry grounds. The weak localization correction to the field-axis thermal conductivity is computed for a dilute array of s-wave vortices near the lower critical field H_c1. We propose that weak localization effects, cut off at low temperatures by the Zeeman splitting, are responsible for the field dependence of the thermal conductivity seen in recent high-T_c experiments by Aubin et al.Comment: RevTex, 8 pages, 1 eps figure, typos correcte

RNA denaturation: excluded volume, pseudoknots and transition scenarios

A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous transition. Otherwise a smooth crossover occurs from the swollen linear polymer behavior to highly ramified, almost compact conformations with secondary structures. In the latter scenario, which is appropriate when these structures are much more stable than pseudoknot links, probability distributions for the lengths of both loops and main branches obey scaling with nonclassical exponents.Comment: 4 pages 3 figure

Partitioning spatial, environmental, and community drivers of ecosystem functioning

Context: Community composition, environmental variation, and spatial structuring can influence ecosystem functioning, and ecosystem service delivery. While the role of space in regulating ecosystem functioning is well recognised in theory, it is rarely considered explicitly in empirical studies. Objectives: We evaluated the role of spatial structuring within and between regions in explaining the functioning of 36 reference and human-impacted streams. Methods: We gathered information on regional and local environmental variables, communities (taxonomy and traits), and used variance partitioning analysis to explain seven indicators of ecosystem functioning. Results: Variation in functional indicators was explained not only by environmental variables and community composition, but also by geographic position, with sometimes high joint variation among the explanatory factors. This suggests spatial structuring in ecosystem functioning beyond that attributable to species sorting along environmental gradients. Spatial structuring at the within-region scale potentially arose from movements of species and materials among habitat patches. Spatial structuring at the between-region scale was more pervasive, occurring both in analyses of individual ecosystem processes and of the full functional matrix, and is likely to partly reflect phenotypic variation in the traits of functionally important species. Characterising communities by their traits rather than taxonomy did not increase the total variation explained, but did allow for a better discrimination of the role of space. Conclusions: These results demonstrate the value of accounting for the role of spatial structuring to increase explanatory power in studies of ecosystem processes, and underpin more robust management of the ecosystem services supported by those processes

RNA secondary structure formation: a solvable model of heteropolymer folding

The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the transition between the native and molten phase of the RNA as a function of temperature. The transition is driven by a competition between the energy gained from the polymer's overlap with the native structure and the entropic gain of forming random contacts. A simplified Go-like model is proposed and solved exactly. The predicted critical behavior is verified via exact numerical enumeration of a large ensemble of similarly designed sequences.Comment: 4 pages including 2 figure

Comparing effects of microplastic exposure, FPOM resource quality, and consumer density on the response of a freshwater particle feeder and associated ecosystem processes

Fine particulate organic matter (FPOM) is an important basal resource in stream ecosystems for deposit- and filter-feeding macroinvertebrates (collectively ‘particle feeders’). Microplastics (MP) share many characteristics with FPOM (e.g. size range, surface area to volume ratios) and are potentially consumed by particle feeders. Accordingly, MP contamination of natural FPOM pools might affect particle feeder growth and survival, particularly when background FPOM resource quality is low, or intraspecific competition is high. We conducted a microcosm experiment to evaluate how a realistic (1400 particles/kg sediment) polyethylene MP (ø = 45–53 µm) concentration interacts with FPOM (ø = 63–250 µm) resource quality (low versus high nutrient content) and consumer density (10 versus 20 individuals per microcosm) to affect growth and survival of larval Chironomus riparius (Diptera: Chironomidae), a model particle feeder. We additionally quantified community respiration, based on three hour measurements of oxygen consumption in the microcosms at the end of the experiment. MP exposure reduced larval body lengths by 26.7%, but only under the low consumer density treatment. MPs reduced community respiration by 26.2%, but only in the absence of chironomids, indicating an impact on microbial respiration. In comparison, low resource quality and high consumer density were associated with 53.5–70.2% reductions in community respiration, chironomid body length and/or body mass. These results suggest that effects of contamination of FPOM with MPs at environmentally realistic concentrations on the life histories of particle feeders such as C. riparius might be limited, especially relative to the effects of resource quality and consumer density. However, the reduction in microbial respiration when MPs were present highlights the need for further research addressing MP impacts on microbes, given their key roles in ecosystem functioning.publishedVersio

Responses of multiple structural and functional indicators along three contrasting disturbance gradients

Ecosystem functioning and community structure are recognized as key components of ecosystem integrity, but comprehensive, standardized studies of the responses of both structural and functional indicators to different types of anthropogenic pressures remain rare. Consequently, we lack an empirical basis for (i) identifying when monitoring ecosystem structure alone misses important changes in ecosystem functioning, (ii) recommending sets of structural and functional metrics best suited for detecting ecological change driven by different anthropogenic pressures, and (iii) understanding the cumulative effects of multiple, co-occurring stressors on structure and function. We investigated variation in community structure and ecosystem functioning of stream ecosystems along three gradients (10–16 independent stream sites each) of increasing impact arising from agriculture, forestry and river regulation for hydropower, respectively. For each stream, we quantified variation in (i) the abiotic environment, (ii) community composition of four organism groups and (iii) three basal ecosystem processes underpinning carbon and nutrient cycling in streams. We assessed the responsiveness of multiple biodiversity, community structure and ecosystem functioning indicators based on variance explained and effect size metrics. Along a gradient of increasing agricultural impact, diatoms and fish were the most responsive groups overall, but significant variation was detected in at least one aspect of community composition, abundance and/ or biodiversity of every organism group . In contrast, most of our functional metrics did not vary significantly along the agricultural gradient, possibly due to contrasting, antagonistic effects of increasing nutrient concentrations and turbidity on ecosystem process rates. The exception was detritivore-mediated litter decomposition which increased up to moderate levels of nutrient. Impacts of river regulation were most marked for diatoms, which were responsive to both increasingly frequent hydropeaking and to increasing seasonal river regulation. Among functional indicators, both litter decomposition and algal biomass accrual declined significantly with increasing hydropeaking. Few structural or functional metrics varied with forest management, with macroinvertebrate diversity increasing along the forestry gradient, as did algal and fungal biomass accrual. Together, these findings highlight the challenges of making inferences about the impacts of anthropogenic disturbances at the ecosystem level based on community data alone, and pinpoint the need to identify optimal sets of functional and structural indicators best suited for detecting ecological changes associated with different human activities

Statistical mechanics of secondary structures formed by random RNA sequences

The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical studies. First, a two-replica calculation is performed. By mapping the two-replica problem to the denaturation of a single homogeneous RNA in 6-dimensional embedding space, we show that sequence disorder is perturbatively irrelevant, i.e., an RNA molecule with weak sequence disorder is in a molten phase where many secondary structures with comparable total energy coexist. A numerical study of various models at high temperature reproduces behaviors characteristic of the molten phase. On the other hand, a scaling argument based on the extremal statistics of rare regions can be constructed to show that the low temperature phase is unstable to sequence disorder. We performed a detailed numerical study of the low temperature phase using the droplet theory as a guide, and characterized the statistics of large-scale, low-energy excitations of the secondary structures from the ground state structure. We find the excitation energy to grow very slowly (i.e., logarithmically) with the length scale of the excitation, suggesting the existence of a marginal glass phase. The transition between the low temperature glass phase and the high temperature molten phase is also characterized numerically. It is revealed by a change in the coefficient of the logarithmic excitation energy, from being disorder dominated to entropy dominated.Comment: 24 pages, 16 figure