Nanopype: A modular and scalable nanopore data processing pipeline

Long-read third-generation nanopore sequencing enables researchers to now address a range of questions that are difficult to tackle with short read approaches. The rapidly expanding user base and continuously increasing throughput have sparked the development of a growing number of specialized analysis tools. However, streamlined processing of nanopore datasets using reproducible and transparent workflows is still lacking. Here we present Nanopype, a nanopore data processing pipeline that integrates a diverse set of established bioinformatics software while maintaining consistent and standardized output formats. Seamless integration into compute cluster environments makes the framework suitable for high-throughput applications. As a result, Nanopype facilitates comparability of nanopore data analysis workflows and thereby should enhance the reproducibility of biological insights

Co-flow microfluidic synthesis of liquid crystalline actuating Janus particles

A microfluidic synthesis of stimuli-responsive actuating Janus particles composed of a liquid crystalline elastomer (LCE) and a polymeric hydrogel is reported. , In this article the microfluidic synthesis and characterization of micrometer sized actuating Janus particles containing a liquid crystalline elastomer (LCE) is presented. On one side these Janus particles consist of a hydrophobic liquid crystalline part, featuring strong shape changes during the thermotropic phase transition, whereas the other side contains a hydrophilic polyacrylamide network. The synthesis is based upon the dispersion of two immiscible monomer mixtures in a continuously flowing silicone oil, using two glass capillaries side by side to form Janus microdroplets of different morphologies. Furthermore, the systematic adjustment of the morphology of the Janus particles as well as the optimization of the actuation properties is conducted by precise control and variation of the microfluidic parameters. The actuation properties of the particles are studied by polarized optical microscopy (POM), in which relative length changes up to 52% are investigated for the elongation of LCEs during the phase transition in rod-like Janus particles. Further wide-angle X-ray scattering (WAXS) measurements verify the mesogen's orientation in a bipolar director field, which corresponds to the observed geometry of the Janus particle's shape changes

A posteriori error analysis and adaptive non-intrusive numerical schemes for systems of random conservation laws

In this article we consider one-dimensional random systems of hyperbolic conservation laws. We first establish existence and uniqueness of random entropy admissible solutions for initial value problems of conservation laws which involve random initial data and random flux functions. Based on these results we present an a posteriori error analysis for a numerical approximation of the random entropy admissible solution. For the stochastic discretization, we consider a non-intrusive approach, the Stochastic Collocation method. The spatio-temporal discretization relies on the Runge--Kutta Discontinuous Galerkin method. We derive the a posteriori estimator using continuous reconstructions of the discrete solution. Combined with the relative entropy stability framework this yields computable error bounds for the entire space-stochastic discretization error. The estimator admits a splitting into a stochastic and a deterministic (space-time) part, allowing for a novel residual-based space-stochastic adaptive mesh refinement algorithm. We conclude with various numerical examples investigating the scaling properties of the residuals and illustrating the efficiency of the proposed adaptive algorithm

Ordering of ferromagnetic nanoparticles in nematic liquid crystals

Dispersions of magnetic nanoparticles in a nematic liquid crystal were investigated as magnetic fields were applied in three different boundary condition geometries: (i) planar substrates and B ⊥ n, (ii) planar substrates and B / n, and (iii) homeotropic substrates and B ⊥ n. Particle chaining is observed when a magnetic field is applied, with a periodicity perpendicular to the chains. Furthermore, linear chains are observed for the magnetic field applied perpendicular to the director, while zigzag chains are formed when the magnetic field direction is parallel to the director field. This is attributed to a change from a dipolar defect configuration around dispersed nanoparticles, to a quadrupolar one, i.e. the change from satellite to Saturn-ring defects. This effect is largely independent of the sample thickness. The dynamic development of the chain length, as well as their two-dimensional order parameter was studied in all cases. Chain lengths increased rapidly until saturation at approximately l = 30 μm after a time of about t = 10 s. Similarly, the chain order parameters increased until saturation between S = 0.8-0.9, independent of sample geometry

Orientational order parameters of a de Vries–type ferroelectric liquid crystal obtained by polarized Raman spectroscopy and x-ray diffraction

The orientational order parameters 〈P2〉 and 〈P4〉 of the ferroelectric, de Vries–type liquid crystal 9HL have been determined in the SmA* and SmC* phases by means of polarized Raman spectroscopy, and in the SmA* phase using x-ray diffraction. Quantum density functional theory predicts Raman spectra for 9HL that are in good agreement with the observations and indicates that the strong Raman band probed in the experiment corresponds to the uniaxial, coupled vibration of the three phenyl rings along the molecular long axis. The magnitudes of the orientational order parameters obtained in the Raman and x-ray experiments differ dramatically from each other, a discrepancy that is resolved by considering that the two techniques probe the orientational distributions of different molecular axes. We have developed a systematic procedure in which we calculate the angle between these axes and rescale the orientational order parameters obtained from x-ray scattering with results that are then in good agreement with the Raman data. At least in the case of 9HL, the results obtained by both techniques support a “sugar loaf” orientational distribution in the SmA* phase with no qualitative difference to conventional smectics A. The role of individual molecular fragments in promoting de Vries–type behavior is considered

Field-Dependent Tilt and Birefringence of Electroclinic Liquid Crystals: Theory and Experiment

An unresolved issue in the theory of liquid crystals is the molecular basis of the electroclinic effect in the smectic-A phase. Recent x-ray scattering experiments suggest that, in a class of siloxane-containing liquid crystals, an electric field changes a state of disordered molecular tilt in random directions into a state of ordered tilt in one direction. To investigate this issue, we measure the optical tilt and birefringence of these liquid crystals as functions of field and temperature, and we develop a theory for the distribution of molecular orientations under a field. Comparison of theory and experiment confirms that these materials have a disordered distribution of molecular tilt directions that is aligned by an electric field, giving a large electroclinic effect. It also shows that the net dipole moment of a correlated volume of molecules, a key parameter in the theory, scales as a power law near the smectic-A--smectic-C transition.Comment: 18 pages, including 9 postscript figures, uses REVTeX 3.0 and epsf.st

Ferroelectric ordering in chiral smectic C^* liquid crystals determined by nonchiral intermolecular interactions

General microscopic mechanism of ferroelectric ordering in chiral smectic C* liquid crystals is considered. It is shown that if the mesogenic molecules have a sufficiently low symmetry, the spontaneous polarization is proportional to one of the biaxial vector order parameters of the smectic C phase. This order parameter may be determined by intermolecular interactions which are not sensitive to molecular chirality. At the same time, the polarization is also proportional to a pseudoscalar parameter which vanishes if the molecules are nonchiral. The general statistical theory of ferroelectric ordering is illustrated by two particular models. The first model is based on electrostatic quadrupole-quadrupole interactions, and it enables one to obtain explicit analytical expressions for the spontaneous polarization. In the second model, the molecular chirality and polarity are determined by a pair of off-center nonparallel dipoles. For this case, the spontaneous polarization is calculated numerically as a function of temperature. The theory provides a more general interpretation of the previous approaches including the classical Boulder model