A thin film model for corotational Jeffreys fluids under strong slip

We derive a thin film model for viscoelastic liquids under strong slip which obey the stress tensor dynamics of corotational Jeffreys fluids.Comment: 3 pages, submitted to Eur. Phys. J.

A statistical procedure to adjust for time-interval mismatch in forensic voice comparison

The present paper describes a statistical modeling procedure that was developed to account for the fact that, in a forensic voice comparison analysis conducted for a particular case, there was a long time interval between when the questioned- and known-speaker recordings were made (six years), but in the sample of the relevant population used for training and testing the forensic voice comparison system there was a short interval (hours to days) between when each of multiple recordings of each speaker was made. The present paper also includes results of empirical validation of the procedure. Although based on a particular case, the procedure has potential for wider application given that relatively long time intervals between the recording of questioned and known speakers are not uncommon in casework

Compositionality, stochasticity and cooperativity in dynamic models of gene regulation

We present an approach for constructing dynamic models for the simulation of gene regulatory networks from simple computational elements. Each element is called a ``gene gate'' and defines an input/output-relationship corresponding to the binding and production of transcription factors. The proposed reaction kinetics of the gene gates can be mapped onto stochastic processes and the standard ode-description. While the ode-approach requires fixing the system's topology before its correct implementation, expressing them in stochastic pi-calculus leads to a fully compositional scheme: network elements become autonomous and only the input/output relationships fix their wiring. The modularity of our approach allows to pass easily from a basic first-level description to refined models which capture more details of the biological system. As an illustrative application we present the stochastic repressilator, an artificial cellular clock, which oscillates readily without any cooperative effects.Comment: 15 pages, 8 figures. Accepted by the HFSP journal (13/09/07

Slip vs viscoelasticity in dewetting thin films

Ultrathin polymer films on non-wettable substrates display dynamic features which have been attributed to either viscoelastic or slip effects. Here we show that in the weak and strong slip regime effects of viscoelastic relaxation are either absent or not distinguishable from slip effects. Strong-slip modifies the fastest unstable mode in a rupturing thin film, which questions the standard approach to reconstruct the effective interface potential from dewetting experiments.Comment: 4 pages, submitted to Eur. Phys. J.

Stability domains of actin genes and genomic evolution

In eukaryotic genes the protein coding sequence is split into several fragments, the exons, separated by non-coding DNA stretches, the introns. Prokaryotes do not have introns in their genome. We report the calculations of stability domains of actin genes for various organisms in the animal, plant and fungi kingdoms. Actin genes have been chosen because they have been highly conserved during evolution. In these genes all introns were removed so as to mimic ancient genes at the time of the early eukaryotic development, i.e. before introns insertion. Common stability boundaries are found in evolutionary distant organisms, which implies that these boundaries date from the early origin of eukaryotes. In general boundaries correspond with introns positions of vertebrates and other animals actins, but not much for plants and fungi. The sharpest boundary is found in a locus where fungi, algae and animals have introns in positions separated by one nucleotide only, which identifies a hot-spot for insertion. These results suggest that some introns may have been incorporated into the genomes through a thermodynamic driven mechanism, in agreement with previous observations on human genes. They also suggest a different mechanism for introns insertion in plants and animals.Comment: 9 Pages, 7 figures. Phys. Rev. E in pres

Exons, introns and DNA thermodynamics

The genes of eukaryotes are characterized by protein coding fragments, the exons, interrupted by introns, i.e. stretches of DNA which do not carry any useful information for the protein synthesis. We have analyzed the melting behavior of randomly selected human cDNA sequences obtained from the genomic DNA by removing all introns. A clear correspondence is observed between exons and melting domains. This finding may provide new insights in the physical mechanisms underlying the evolution of genes.Comment: 4 pages, 8 figures - Final version as published. See also Phys. Rev. Focus 15, story 1

Kinetic proofreading of gene activation by chromatin remodeling

Gene activation in eukaryotes involves the concerted action of histone tail modifiers, chromatin remodellers and transcription factors, whose precise coordination is currently unknown. We demonstrate that the experimentally observed interactions of the molecules are in accord with a kinetic proofreading scheme. Our finding could provide a basis for the development of quantitative models for gene regulation in eukaryotes based on the combinatorical interactions of chromatin modifiers.Comment: 8 pages, 2 Figures; application adde

Crackling Noise, Power Spectra and Disorder Induced Critical Scaling

Crackling noise is observed in many disordered non-equilibrium systems in response to slowly changing external conditions. Examples range from Barkhausen noise in magnets to acoustic emission in martensites to earthquakes. Using the non-equilibrium random field Ising model, we derive universal scaling predictions for the dependence of the associated power spectra on the disorder and field sweep rate, near an underlying disorder-induced non-equilibrium critical point. Our theory applies to certain systems in which the crackling noise results from avalanche-like response to a (slowly) increasing external driving force, and is characterized by a broad power law scaling regime of the power spectra. We compute the critical exponents and discuss the relevance of the results to experiments.Comment: 27 Latex Pages, 14 eps figure

When misconceptions impede best practices: evidence supports biological control of invasive Phragmites

Development of a biological control program for invasive Phagmites australis australis in North America required 20 years of careful research, and consideration of management alternatives. A recent paper by Kiviat et al. (Biol Invasions 21:2529–2541, 2019. https://doi.org/10.1007/s10530-019-02014-9) articulates opposition to this biocontrol program and questions the ethics and thoroughness of the researchers. Here we address inaccuracies and misleading statements presented in Kiviat et al. (2019), followed by a brief overview of why biological control targeting Phragmites in North America can be implemented safely with little risk to native species. Similar to our colleagues, we are very concerned about the risks invasive Phragmites represent to North American habitats. But to protect those habitats and the species, including P. australis americanus, we come to a different decision regarding biological control. Current management techniques have not been able to reverse the invasiveness of P. australis australis, threats to native rare and endangered species continue, and large-scale herbicide campaigns are not only costly, but also represent threats to non-target species. We see implementation of biocontrol as the best hope for managing one of the most problematic invasive plants in North America. After extensive review, our petition to release two host specific stem miners was approved by The Technical Advisory Group for the Release of Biological Control Agents in the US and Canadian federal authorities

Numerical evidence for relevance of disorder in a Poland-Scheraga DNA denaturation model with self-avoidance: Scaling behavior of average quantities

We study numerically the effect of sequence heterogeneity on the thermodynamic properties of a Poland-Scheraga model for DNA denaturation taking into account self-avoidance, i.e. with exponent c_p=2.15 for the loop length probability distribution. In complement to previous on-lattice Monte Carlo like studies, we consider here off-lattice numerical calculations for large sequence lengths, relying on efficient algorithmic methods. We investigate finite size effects with the definition of an appropriate intrinsic length scale x, depending on the parameters of the model. Based on the occurrence of large enough rare regions, for a given sequence length N, this study provides a qualitative picture for the finite size behavior, suggesting that the effect of disorder could be sensed only with sequence lengths diverging exponentially with x. We further look in detail at average quantities for the particular case x=1.3, ensuring through this parameter choice the correspondence between the off-lattice and the on-lattice studies. Taken together, the various results can be cast in a coherent picture with a crossover between a nearly pure system like behavior for small sizes N < 1000, as observed in the on-lattice simulations, and the apparent asymptotic behavior indicative of disorder relevance, with an (average) correlation length exponent \nu_r >= 2/d (=2).Comment: Latex, 33 pages with 15 postscript figure