Comparative analysis of protein-coding and long non-coding transcripts based on RNA sequence features.

RNA plays an important role in the intracellular cell life and in the organism in general. Besides the well-established protein coding RNAs (messenger RNAs, mRNAs), long non-coding RNAs (lncRNAs) have gained the attention of recent researchers. Although lncRNAs have been classified as non-coding, some authors reported the presence of corresponding sequences in ribosome profiling data (Ribo-seq).

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis.

We present a major update of the HOCOMOCO collection that consists of patterns describing DNA binding specificities for human and mouse transcription factors. In this release, we profited from a nearly doubled volume of published in vivo experiments on transcription factor (TF) binding to expand the repertoire of binding models, replace low-quality models previously based on in vitro data only and cover more than a hundred TFs with previously unknown binding specificities. This was achieved by systematic motif discovery from more than five thousand ChIP-Seq experiments uniformly processed within the BioUML framework with several ChIP-Seq peak calling tools and aggregated in the GTRD database.

[Protein-Protein Interactions of Huntingtin in the Hippocampus].

Huntingtin (HTT) occurs in the neuronal cytoplasm and can interact with structural elements of synapses. Huntington's disease (HD) results from pathological expansion of a polyglutamine stretch in the HTT molecule, being probably associated with aberrant protein-protein interactions. The pathogenetic mechanism is still incompletely understood.

Spectral comb of highly chirped pulses generated via cascaded FWM of two frequency-shifted dissipative solitons.

Dissipative solitons generated in normal-dispersion mode-locked lasers are stable localized coherent structures with a mostly linear frequency modulation (chirp). The soliton energy in fiber lasers is limited by the Raman effect, but implementation of the intracavity feedback at the Stokes-shifted wavelength enables synchronous generation of a coherent Raman dissipative soliton. Here we demonstrate a new approach for generating chirped pulses at new wavelengths by mixing in a highly-nonlinear fiber of these two frequency-shifted dissipative solitons, as well as cascaded generation of their clones forming in the spectral domain a comb of highly chirped pulses.

Double-Wall Carbon Nanotube Hybrid Mode-Locker in Tm-doped Fibre Laser: A Novel Mechanism for Robust Bound-State Solitons Generation.

The complex nonlinear dynamics of mode-locked fibre lasers, including a broad variety of dissipative structures and self-organization effects, have drawn significant research interest. Around the 2 μm band, conventional saturable absorbers (SAs) possess small modulation depth and slow relaxation time and, therefore, are incapable of ensuring complex inter-pulse dynamics and bound-state soliton generation. We present observation of multi-soliton complex generation in mode-locked thulium (Tm)-doped fibre laser, using double-wall carbon nanotubes (DWNT-SA) and nonlinear polarisation evolution (NPE).

Mechanical Behavior of Cells within a Cell-Based Model of Wheat Leaf Growth.

Understanding the principles and mechanisms of cell growth coordination in plant tissue remains an outstanding challenge for modern developmental biology. Cell-based modeling is a widely used technique for studying the geometric and topological features of plant tissue morphology during growth. We developed a quasi-one-dimensional model of unidirectional growth of a tissue layer in a linear leaf blade that takes cell autonomous growth mode into account.

GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments.

GTRD-Gene Transcription Regulation Database (http://gtrd.biouml.org)-is a database of transcription factor binding sites (TFBSs) identified by ChIP-seq experiments for human and mouse.

Mode-locking via dissipative Faraday instability.

Emergence of coherent structures and patterns at the nonlinear stage of modulation instability of a uniform state is an inherent feature of many biological, physical and engineering systems. There are several well-studied classical modulation instabilities, such as Benjamin-Feir, Turing and Faraday instability, which play a critical role in the self-organization of energy and matter in non-equilibrium physical, chemical and biological systems. Here we experimentally demonstrate the dissipative Faraday instability induced by spatially periodic zig-zag modulation of a dissipative parameter of the system-spectrally dependent losses-achieving generation of temporal patterns and high-harmonic mode-locking in a fibre laser.

Light self-focusing in the atmosphere: thin window model.

Ultra-high power (exceeding the self-focusing threshold by more than three orders of magnitude) light beams from ground-based laser systems may find applications in space-debris cleaning. The propagation of such powerful laser beams through the atmosphere reveals many novel interesting features compared to traditional light self-focusing. It is demonstrated here that for the relevant laser parameters, when the thickness of the atmosphere is much shorter than the focusing length (that is, of the orbit scale), the beam transit through the atmosphere in lowest order produces phase distortion only.

Laminar-Turbulent Transition in Raman Fiber Lasers: A First Passage Statistics Based Analysis.

Loss of coherence with increasing excitation amplitudes and spatial size modulation is a fundamental problem in designing Raman fiber lasers. While it is known that ramping up laser pump power increases the amplitude of stochastic excitations, such higher energy inputs can also lead to a transition from a linearly stable coherent laminar regime to a non-desirable disordered turbulent state. This report presents a new statistical methodology, based on first passage statistics, that classifies lasing regimes in Raman fiber lasers, thereby leading to a fast and highly accurate identification of a strong instability leading to a laminar-turbulent phase transition through a self-consistently defined order parameter.

Pattern Generation by Dissipative Parametric Instability.

Nonlinear instabilities are responsible for spontaneous pattern formation in a vast number of natural and engineered systems, ranging from biology to galaxy buildup. We propose a new instability mechanism leading to pattern formation in spatially extended nonlinear systems, which is based on a periodic antiphase modulation of spectrally dependent losses arranged in a zigzag way: an effective filtering is imposed at symmetrically located wave numbers k and -k in alternating order. The properties of the dissipative parametric instability differ from the features of both key classical concepts of modulation instabilities, i.

Inverse four-wave-mixing and self-parametric amplification effect in optical fibre.

An important group of nonlinear processes in optical fibre involves the mixing of four waves due to the intensity dependence of the refractive index. It is customary to distinguish between nonlinear effects that require external/pumping waves (cross-phase modulation and parametric processes such as four-wave mixing) and self-action of the propagating optical field (self-phase modulation and modulation instability). Here, we present a new nonlinear self-action effect, self-parametric amplification (SPA), which manifests itself as optical spectrum narrowing in normal dispersion fibre, leading to very stable propagation with a distinctive spectral distribution.

Stochasticity, periodicity and localized light structures in partially mode-locked fibre lasers.

Physical systems with co-existence and interplay of processes featuring distinct spatio-temporal scales are found in various research areas ranging from studies of brain activity to astrophysics. The complexity of such systems makes their theoretical and experimental analysis technically and conceptually challenging. Here, we discovered that while radiation of partially mode-locked fibre lasers is stochastic and intermittent on a short time scale, it exhibits non-trivial periodicity and long-scale correlations over slow evolution from one round-trip to another.

Adiabatic soliton laser.

The key to generating stable optical pulses is mastery of nonlinear light dynamics in laser resonators. Modern techniques to control the buildup of laser pulses are based on nonlinear science and include classical solitons, dissipative solitons, parabolic pulses (similaritons) and various modifications and blending of these methods. Fiber lasers offer remarkable opportunities to apply one-dimensional nonlinear science models for the design and optimization of very practical laser systems.

Multicolour nonlinearly bound chirped dissipative solitons.

The dissipative soliton regime is one of the most advanced ways to generate high-energy femtosecond pulses in mode-locked lasers. On the other hand, the stimulated Raman scattering in a fibre laser may convert the excess energy out of the coherent dissipative soliton to a noisy Raman pulse, thus limiting its energy. Here we demonstrate that intracavity feedback provided by re-injection of a Raman pulse into the laser cavity leads to formation of a coherent Raman dissipative soliton.

Numerical modeling of fiber lasers with long and ultra-long ring cavity.

We highlight two important aspects related to a mathematical modeling of pulsed fiber lasers with long and ultra-long ring cavity -impact of an initial noise and a cavity length on generation of single optical pulses. Using as an example a simple scalar model of a ring fiber laser that describes the radiation build-up from noise and the following intra-cavity pulse dynamics during a round trip we study dependence of generated pulse characteristics on the resonator length in the range from 30 m up to 2 km.

Generation dynamics of the narrowband Yb-doped fiber laser.

We present direct real-time experimental measurements and numerical modeling of temporal and statistical properties for the Ytterbium-doped fiber laser with spectral bandwidth of ~2 GHz. The obtained results demonstrate nearly exponential probability density function for intensity fluctuations. A significant decrease below the Gaussian probability has been experimentally observed for intensity fluctuations having value more than 2.

Plasma-formation dynamics in intense laser-droplet interaction.

We study the ionization dynamics in intense laser-droplet interaction using three-dimensional, relativistic particle-in-cell simulations. Of particular interest is the laser intensity and frequency regime for which initially transparent, wavelength-sized targets are not homogeneously ionized. Instead, the charge distribution changes both in space and in time on a subcycle scale.

Autosolitons in dispersion-managed systems with in-line saturable absorbers.

We study the formation of stable solitonlike pulses in dispersion-managed fiber transmission systems using an in-line fast saturable absorber. Operational regimes suitable for 40-Gbit/s channel rate transmission are demonstrated.

Electron acceleration by few-cycle laser pulses with single-wavelength spot size.

Generation of relativistic electrons from the interaction of a laser pulse with a high density plasma foil, accompanied by an underdense preplasma in front of it, has been studied with two-dimensional particle-in-cell (PIC) simulations for pulse durations comparable to a single cycle and for single-wavelength spot size. The electrons are accelerated predominantly in forward direction for a preplasma longer than the pulse length. Otherwise, both forward and backward electron accelerations occur.

Path-averaged optical soliton in double-periodic dispersion-managed systems.

A path-averaged Gabitov-Turitsyn model governing optical signal propagation down the dispersion-managed (DM) transmission line is studied numerically. A different numerical algorithm to find a soliton solution for an arbitrary periodic DM system is proposed. Applying developed technique we analyze soliton solutions for few important practical systems.