ProfPPIdb: Pairs of physical protein-protein interactions predicted for entire proteomes

Motivation Protein-protein interactions (PPIs) play a key role in many cellular processes. Most annotations of PPIs mix experimental and computational data. The mix optimizes coverage, but obfuscates the annotation origin. Some resources excel at focusing on reliable experimental data. Here, we focused on new pairs of interacting proteins for several model organisms based solely on sequence-based prediction methods. Results We extracted reliable experimental data about which proteins interact (binary) for eight diverse model organisms from public databases, namely from Escherichia coli, Schizosaccharomyces pombe, Plasmodium falciparum, Drosophila melanogaster, Caenorhabditis elegans, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, and for the previously used Homo sapiens and Saccharomyces cerevisiae. Those data were the base to develop a PPI prediction method for each model organism. The method used evolutionary information through a profile-kernel Support Vector Machine (SVM). With the resulting eight models, we predicted all possible protein pairs in each organism and made the top predictions available through a web application. Almost all of the PPIs made available were predicted between proteins that have not been observed in any interaction, in particular for less well-studied organisms. Thus, our work complements existing resources and is particularly helpful for designing experiments because of its uniqueness. Experimental annotations and computational predictions are strongly influenced by the fact that some proteins have many partners and others few. To optimize machine learning, recent methods explicitly ignored such a network-structure and rely either on domain knowledge or sequence-only methods. Our approach is independent of domain-knowledge and leverages evolutionary information. The database interface representing our results is accessible from https://rostlab.org/services/ppipair/. The data can also be downloaded from https://figshare.com/collections/ProfPPI-DB/4141784

Kinetic modelling and molecular dynamics simulation of ultracold neutral plasmas including ionic correlations

A kinetic approach for the evolution of ultracold neutral plasmas including interionic correlations and the treatment of ionization/excitation and recombination/deexcitation by rate equations is described in detail. To assess the reliability of the approximations inherent in the kinetic model, we have developed a hybrid molecular dynamics method. Comparison of the results reveals that the kinetic model describes the atomic and ionic observables of the ultracold plasma surprisingly well, confirming our earlier findings concerning the role of ion-ion correlations [Phys. Rev. A {\bf 68}, 010703]. In addition, the molecular dynamics approach allows one to study the relaxation of the ionic plasma component towards thermodynamical equilibrium

Separation and identification of dominant mechanisms in double photoionization

Double photoionization by a single photon is often discussed in terms of two contributing mechanisms, {\it knock-out} (two-step-one) and {\it shake-off} with the latter being a pure quantum effect. It is shown that a quasi-classical description of knock-out and a simple quantum calculation of shake-off provides a clear separation of the mechanisms and facilitates their calculation considerably. The relevance of each mechanism at different photon energies is quantified for helium. Photoionization ratios, integral and singly differential cross sections obtained by us are in excellent agreement with benchmark experimental data and recent theoretical results.Comment: 4 pages, 5 figure

Ionization of clusters in strong X-ray laser pulses

The effect of intense X-ray laser interaction on argon clusters is studied theoretically with a mixed quantum/classical approach. In comparison to a single atom we find that ionization of the cluster is suppressed, which is in striking contrast to the observed behavior of rare-gas clusters in intense optical laser pulses. We have identified two effects responsible for this phenomenon: A high space charge of the cluster in combination with a small quiver amplitude and delocalization of electrons in the cluster. We elucidate their impact for different field strengths and cluster sizes.Comment: 4 pages, 4 figure

Threshold detachment of negative ions by electron impact

The description of threshold fragmentation under long range repulsive forces is presented. The dominant energy dependence near threshold is isolated by decomposing the cross section into a product of a back ground part and a barrier penetration probability resulting from the repulsive Coulomb interaction. This tunneling probability contains the dominant energy variation and it can be calculated analytically based on the same principles as Wannier's description for threshold ionization under attractive forces. Good agreement is found with the available experimental cross sections on detachment by electron impact from $D^{-}$, $O^{-}$ and $B^{-}$.Comment: 4 pages, 4 figures (EPS), to appear in Phys.Rev.Lett, Feb. 22nd, 199

Dynamical stabilization of classical multi electron targets against autoionization

We demonstrate that a recently published quasiclassical M\oller type approach [Geyer and Rost 2002, J. Phys. B 35 1479] can be used to overcome the problem of autoionization, which arises in classical trajectory calculations for many electron targets. In this method the target is stabilized dynamically by a backward--forward propagation scheme. We illustrate this refocusing and present total cross sections for single and double ionization of helium by electron impact.Comment: LaTeX, 6 pages, 2 figures; submitted to J. Phys.

Universal exit probabilities in the TASEP

We study the joint exit probabilities of particles in the totally asymmetric simple exclusion process (TASEP) from space-time sets of given form. We extend previous results on the space-time correlation functions of the TASEP, which correspond to exits from the sets bounded by straight vertical or horizontal lines. In particular, our approach allows us to remove ordering of time moments used in previous studies so that only a natural space-like ordering of particle coordinates remains. We consider sequences of general staircase-like boundaries going from the northeast to southwest in the space-time plane. The exit probabilities from the given sets are derived in the form of Fredholm determinant defined on the boundaries of the sets. In the scaling limit, the staircase-like boundaries are treated as approximations of continuous differentiable curves. The exit probabilities with respect to points of these curves belonging to arbitrary space-like path are shown to converge to the universal Airy$_2$ process.Comment: 46 pages, 7 figure

Crossover to the KPZ equation

We characterize the crossover regime to the KPZ equation for a class of one-dimensional weakly asymmetric exclusion processes. The crossover depends on the strength asymmetry $an^{2-\gamma}$ ($a,\gamma>0$) and it occurs at $\gamma=1/2$. We show that the density field is a solution of an Ornstein-Uhlenbeck equation if $\gamma\in(1/2,1]$, while for $\gamma=1/2$ it is an energy solution of the KPZ equation. The corresponding crossover for the current of particles is readily obtained.Comment: Published by Annales Henri Poincare Volume 13, Number 4 (2012), 813-82

Meristematic connectome: A cellular coordinator of plant responses to environmental signals?

Mechanical stress in tree roots induces the production of reaction wood (RW) and the formation of new branch roots, both functioning to avoid anchorage failure and limb damage. The vascular cambium (VC) is the factor responsible for the onset of these responses as shown by their occurrence when all primary tissues and the root tips are removed. The data presented confirm that the VC is able to evaluate both the direction and magnitude of the mechanical forces experienced before coordinating the most fitting responses along the root axis whenever and wherever these are necessary. The coordination of these responses requires intense crosstalk between meristematic cells of the VC which may be very distant from the place where the mechanical stress is first detected. Signaling could be facilitated through plasmodesmata between meristematic cells. The mechanism of RW production also seems to be well conserved in the stem and this fact suggests that the VC could behave as a single structure spread along the plant body axis as a means to control the relationship between the plant and its environment. The observation that there are numerous morphological and functional similarities between different meristems and that some important regulatory mechanisms of meristem activity, such as homeostasis, are common to several meristems, supports the hypothesis that not only the VC but all apical, primary and secondary meristems present in the plant body behave as a single interconnected structure. We propose to name this structure \u201cmeristematic connectome\u201d given the possibility that the sequence of meristems from root apex to shoot apex could represent a pluricellular network that facilitates long-distance signaling in the plant body. The possibility that the \u201cmeristematic connectome\u201d could act as a single structure active in adjusting the plant body to its surrounding environment throughout the life of a plant is now proposed