Discreteness-Induced Oscillatory Instabilities of Dark Solitons

We reveal that even weak inherent discreteness of a nonlinear model can lead to instabilities of the localized modes it supports. We present the first example of an oscillatory instability of dark solitons, and analyse how it may occur for dark solitons of the discrete nonlinear Schrodinger and generalized Ablowitz-Ladik equations.Comment: 11 pages, 4 figures, to be published in Physical Review Letter

Hamiltonian Hopf bifurcations in the discrete nonlinear Schr\"odinger trimer: oscillatory instabilities, quasiperiodic solutions and a 'new' type of self-trapping transition

Oscillatory instabilities in Hamiltonian anharmonic lattices are known to appear through Hamiltonian Hopf bifurcations of certain time-periodic solutions of multibreather type. Here, we analyze the basic mechanisms for this scenario by considering the simplest possible model system of this kind where they appear: the three-site discrete nonlinear Schr\"odinger model with periodic boundary conditions. The stationary solution having equal amplitude and opposite phases on two sites and zero amplitude on the third is known to be unstable for an interval of intermediate amplitudes. We numerically analyze the nature of the two bifurcations leading to this instability and find them to be of two different types. Close to the lower-amplitude threshold stable two-frequency quasiperiodic solutions exist surrounding the unstable stationary solution, and the dynamics remains trapped around the latter so that in particular the amplitude of the originally unexcited site remains small. By contrast, close to the higher-amplitude threshold all two-frequency quasiperiodic solutions are detached from the unstable stationary solution, and the resulting dynamics is of 'population-inversion' type involving also the originally unexcited site.Comment: 25 pages, 11 figures, to be published in J. Phys. A: Math. Gen. Revised and shortened version with few clarifying remarks adde

ac Josephson effect in superconducting d-wave junctions

We study theoretically the ac Josephson effect in superconducting planar d-wave junctions. The insulating barrier assumed to be present between the two superconductors may have arbitrary strength. Many properties of this system depend on the orientation of the d-wave superconductor: we calculate the ac components of the Josephson current. In some arrangements there is substantial negative differential conductance due to the presence of mid-gap states. We study how robust these features are to finite temperature and also comment on how the calculated current-voltage curves compare with experiments. For some other configurations (for small barrier strength) we find zero-bias conductance peaks due to multiple Andreev reflections through midgap states. Moreover, the odd ac components are strongly suppressed and even absent in some arrangements. This absence will lead to a doubling of the Josephson frequency. All these features are due to the d-wave order parameter changing sign when rotated $90^{\circ}$. Recently, there have been several theoretical reports on parallel current in the d-wave case for both the stationary Josephson junction and for the normal metal-superconductor junction. Also in our case there may appear current density parallel to the junction, and we present a few examples when this takes place. Finally, we give a fairly complete account of the method used and also discuss how numerical calculations should be performed in order to produce current-voltage curves

Middleborns disadvantaged? testing birth-order effects on fitness in pre-industrial finns

Parental investment is a limited resource for which offspring compete in order to increase their own survival and reproductive success. However, parents might be selected to influence the outcome of sibling competition through differential investment. While evidence for this is widespread in egg-laying species, whether or not this may also be the case in viviparous species is more difficult to determine. We use pre-industrial Finns as our model system and an equal investment model as our null hypothesis, which predicts that (all else being equal) middleborns should be disadvantaged through competition. We found no overall evidence to suggest that middleborns in a family are disadvantaged in terms of their survival, age at first reproduction or lifetime reproductive success. However, when considering birth-order only among same-sexed siblings, first-, middle-and lastborn sons significantly differed in the number of offspring they were able to rear to adulthood, although there was no similar effect among females. Middleborn sons appeared to produce significantly less offspring than first-or lastborn sons, but they did not significantly differ from lastborn sons in the number of offspring reared to adulthood. Our results thus show that taking sex differences into account is important when modelling birth-order effects. We found clear evidence of firstborn sons being advantaged over other sons in the family, and over firstborn daughters. Therefore, our results suggest that parents invest differentially in their offspring in order to both preferentially favour particular offspring or reduce offspring inequalities arising from sibling competition

Determining Peptide Partitioning Properties via Computer Simulation

The transfer of polypeptide segments into lipid bilayers to form transmembrane helices represents the crucial first step in cellular membrane protein folding and assembly. This process is driven by complex and poorly understood atomic interactions of peptides with the lipid bilayer environment. The lack of suitable experimental techniques that can resolve these processes both at atomic resolution and nanosecond timescales has spurred the development of computational techniques. In this review, we summarize the significant progress achieved in the last few years in elucidating the partitioning of peptides into lipid bilayer membranes using atomic detail molecular dynamics simulations. Indeed, partitioning simulations can now provide a wealth of structural and dynamic information. Furthermore, we show that peptide-induced bilayer distortions, insertion pathways, transfer free energies, and kinetic insertion barriers are now accurate enough to complement experiments. Further advances in simulation methods and force field parameter accuracy promise to turn molecular dynamics simulations into a powerful tool for investigating a wide range of membrane active peptide phenomena

Predicting Cell Cycle Regulated Genes by Causal Interactions

The fundamental difference between classic and modern biology is that technological innovations allow to generate high-throughput data to get insights into molecular interactions on a genomic scale. These high-throughput data can be used to infer gene networks, e.g., the transcriptional regulatory or signaling network, representing a blue print of the current dynamical state of the cellular system. However, gene networks do not provide direct answers to biological questions, instead, they need to be analyzed to reveal functional information of molecular working mechanisms. In this paper we propose a new approach to analyze the transcriptional regulatory network of yeast to predict cell cycle regulated genes. The novelty of our approach is that, in contrast to all other approaches aiming to predict cell cycle regulated genes, we do not use time series data but base our analysis on the prior information of causal interactions among genes. The major purpose of the present paper is to predict cell cycle regulated genes in S. cerevisiae. Our analysis is based on the transcriptional regulatory network, representing causal interactions between genes, and a list of known periodic genes. No further data are used. Our approach utilizes the causal membership of genes and the hierarchical organization of the transcriptional regulatory network leading to two groups of periodic genes with a well defined direction of information flow. We predict genes as periodic if they appear on unique shortest paths connecting two periodic genes from different hierarchy levels. Our results demonstrate that a classical problem as the prediction of cell cycle regulated genes can be seen in a new light if the concept of a causal membership of a gene is applied consequently. This also shows that there is a wealth of information buried in the transcriptional regulatory network whose unraveling may require more elaborate concepts than it might seem at first

Tailored vs. Standardized Internet-Based Cognitive Behavior Therapy for Depression and Comorbid Symptoms: A Randomized Controlled Trial

Background and Aims:Major depression can be treated by means of cognitive behavior therapy, delivered via the Internet as guided self-help. Individually tailored guided self-help treatments have shown promising results in the treatment of anxiety disorders. This randomized controlled trial tested the efficacy of an Internet-based individually tailored guided selfhelp treatment which specifically targeted depression with comorbid symptoms. The treatment was compared both to standardized (non-tailored) Internet-based treatment and to an active control group in the form of a monitored online discussion group. Both guided self-help treatments were based on cognitive behavior therapy and lasted for 10 weeks. The discussion group consisted of weekly discussion themes related to depression and the treatment of depression. Methods:A total of 121 participants with diagnosed major depressive disorder and with a range of comorbid symptoms were randomized to three groups. The tailored treatment consisted of a prescribed set of modules targeting depression as well as comorbid problems. The standardized treatment was a previously tested guided self-help program for depression. Results:From pre-treatment to post-treatment, both treatment groups improved on measures of depression, anxiety and quality of life. The results were maintained at a 6-month follow-up. Subgroup analyses showed that the tailored treatment was more effective than the standardized treatment among participants with higher levels of depression at baseline and more comorbidity, both in terms of reduction of depressive symptoms and on recovery rates. In the subgroup with lower baseline scores of depression, few differences were seen between treatments and the discussion group. Conclusions:This study shows that tailored Internet-based treatment for depression is effective and that addressing comorbidity by tailoring may be one way of making guided self-help treatments more effective than standardized approaches in the treatment of more severe depression