Control of light polarization by optically-induced-chirality in photosensitive nematic fluids.

Light polarization rotations, created by applied optical field, are examined experimentally and theoretically in a photosensitive chiral nematic fluid. The polarization rotation of the transmitted beam is initiated by illuminating the sample with uniform UV light. The operation is tunable and reversible, depending on the UV intensity. It was revealed that the rotations can be ascribed to the optical-field-induced chirality effect, where the helical structure in chiral nematics changes in accordance with the UV intensity. The evolution of the helical structure as well as its effect on the light polarization upon illumination by uniform UV light have been monitored experimentally and compared by calculations based on the continuum theory. Our results proved that a polarization field with specific characteristics can be achieved using the remote and precise optical control.

Computational Issues of Quantum Heat Engines with Non-Harmonic Working Medium.

In this work, we lay the foundations for computing the behavior of a quantum heat engine whose working medium consists of an ensemble of non-harmonic quantum oscillators. In order to enable this analysis, we develop a method based on the Schrödinger picture. We investigate different possible choices on the basis of expanding the density operator, as it is crucial to select a basis that will expedite the numerical integration of the time-evolution equation without compromising the accuracy of the computed results. For this purpose, we developed an estimation technique that allows us to quantify the error that is unavoidably introduced when time-evolving the density matrix expansion over a finite-dimensional basis. Using this and other ways of evaluating a specific choice of basis, we arrive at the conclusion that the basis of eigenstates of a harmonic Hamiltonian leads to the best computational performance. Additionally, we present a method to quantify and reduce the error that is introduced when extracting relevant physical information about the ensemble of oscillators. The techniques presented here are specific to quantum heat cycles; the coexistence within a cycle of time-dependent Hamiltonian and coupling with a thermal reservoir are particularly complex to handle for the non-harmonic case. The present investigation is paving the way for numerical analysis of non-harmonic quantum heat machines.

PRFect: a tool to predict programmed ribosomal frameshifts in prokaryotic and viral genomes.

BACKGROUND: One of the stranger phenomena that can occur during gene translation is where, as a ribosome reads along the mRNA, various cellular and molecular properties contribute to stalling the ribosome on a slippery sequence and shifting the ribosome into one of the other two alternate reading frames. The alternate frame has different codons, so different amino acids are added to the peptide chain. More importantly, the original stop codon is no longer in-frame, so the ribosome can bypass the stop codon and continue to translate the codons past it. This produces a longer version of the protein, a fusion of the original in-frame amino acids, followed by all the alternate frame amino acids. There is currently no automated software to predict the occurrence of these programmed ribosomal frameshifts (PRF), and they are currently only identified by manual curation. RESULTS: Here we present PRFect, an innovative machine-learning method for the detection and prediction of PRFs in coding genes of various types. PRFect combines advanced machine learning techniques with the integration of multiple complex cellular properties, such as secondary structure, codon usage, ribosomal binding site interference, direction, and slippery site motif. Calculating and incorporating these diverse properties posed significant challenges, but through extensive research and development, we have achieved a user-friendly approach. The code for PRFect is freely available, open-source, and can be easily installed via a single command in the terminal. Our comprehensive evaluations on diverse organisms, including bacteria, archaea, and phages, demonstrate PRFect's strong performance, achieving high sensitivity, specificity, and an accuracy exceeding 90%. The code for PRFect is freely available and installs with a single terminal command. CONCLUSION: PRFect represents a significant advancement in the field of PRF detection and prediction, offering a powerful tool for researchers and scientists to unravel the intricacies of programmed ribosomal frameshifting in coding genes.

Fluid Ferroelectric Filaments.

Freestanding slender fluid filaments of room-temperature ferroelectric nematic liquid crystals are described. They are stabilized either by internal electric fields of bound charges formed due to polarization splay or by external voltage applied between suspending wires. The phenomenon is similar to those observed in dielectric fluids, such as deionized water, except that in ferroelectric nematic materials the voltages required are three orders of magnitudes smaller and the aspect ratio is much higher. The observed ferroelectric fluid threads are not only unique and novel but also offer measurements of basic physical quantities, such as the ferroelectric polarization and viscosity. Ferroelectric nematic fluid threads may have practical applications in nano-fluidic micron-size logic devices, switches, and relays.

Undulations of Smectic A Layers in Achiral Liquid Crystals Manifested as Stripe Textures.

Self-assembly of organic molecules represents a fascinating playground to create various liquid crystalline nanostructures. In this Letter, we study layer undulations on micrometer scale in smectic A phases for achiral compounds, experimentally demonstrated as regular stripe patterns induced by thermal treatment. Undulations, including their anharmonic properties, are evaluated by means of polarimetric imaging and light diffraction experiments in cells with various thicknesses. The key role in stripe formation is played by high negative values of the thermal expansion coefficient.

The Telluride YAP/TAZ and TEAD Workshop: A Small Meeting with a Big Impact.

Funding the research needed to advance our understanding of rare cancers is very challenging [...].

PRFect: A tool to predict programmed ribosomal frameshifts in prokaryotic and viral genomes.

Background: One of the stranger phenomena that can occur during gene translation is where, as a ribosome reads along the mRNA, various cellular and molecular properties contribute to stalling the ribosome on a slippery sequence, shifting the ribosome into one of the other two alternate reading frames. The alternate frame has different codons, so different amino acids are added to the peptide chain, but more importantly, the original stop codon is no longer in-frame, so the ribosome can bypass the stop codon and continue to translate the codons past it. This produces a longer version of the protein, a fusion of the original in-frame amino acids, followed by all the alternate frame amino acids. There is currently no automated software to predict the occurrence of these programmed ribosomal frameshifts (PRF), and they are currently only identified by manual curation. Results: Here we present PRFect, an innovative machine-learning method for the detection and prediction of PRFs in coding genes of various types. PRFect combines advanced machine learning techniques with the integration of multiple complex cellular properties, such as secondary structure, codon usage, ribosomal binding site interference, direction, and slippery site motif. Calculating and incorporating these diverse properties posed significant challenges, but through extensive research and development, we have achieved a user-friendly approach. The code for PRFect is freely available, open-source, and can be easily installed via a single command in the terminal. Our comprehensive evaluations on diverse organisms, including bacteria, archaea, and phages, demonstrate PRFect's strong performance, achieving high sensitivity, specificity, and an accuracy exceeding 90%. Conclusion: PRFect represents a significant advancement in the field of PRF detection and prediction, offering a powerful tool for researchers and scientists to unravel the intricacies of programmed ribosomal frameshifting in coding genes.

Electric field-induced interfacial instability in a ferroelectric nematic liquid crystal.

Studies of sessile droplets and fluid bridges of a ferroelectric nematic liquid crystal in externally applied electric fields are presented. It is found that above a threshold, the interface of the fluid with air undergoes a fingering instability or ramification, resembling to Rayleigh-type instability observed in charged droplets in electric fields or circular drop-type instabilities observed in ferromagnetic liquids in magnetic field. The frequency dependence of the threshold voltage was determined in various geometries. The nematic director and ferroelectric polarization direction was found to point along the tip of the fingers that appear to repel each other, indicating that the ferroelectric polarization is essentially parallel to the director. The results are interpreted in connection to the Rayleigh and circular drop-type instabilities.

More Stages Decrease Dissipation in Irreversible Step Processes.

The dissipation in an irreversible step process is reduced when the number of steps is increased in any refinement of the steps in the process. This is a consequence of the ladder theorem, which states that, for any irreversible process proceeding by a sequence of relaxations, dividing any relaxation step into two will result in a new sequence that is more efficient than the original one. This results in a more-steps-the-better rule, even when the new sequence of steps is not reoptimized. This superiority of many steps is well established empirically in, e.g., insulation and separation applications. In particular, the fact that the division of any step into two steps improves the overall efficiency has interesting implications for biological evolution and emphasizes thermodynamic length as a central measure for dissipation.

Ferroelectric nematic liquid crystal thermomotor.

A thermal gradient-induced circular motion of particles placed on ferroelectric nematic liquid crystal sessile drops is demonstrated and explained. Unlike hurricanes and tornadoes that are the prime examples for thermal motors and where turbulent flows are apparent, here the texture without tracer particles appears completely steady indicating laminar flow. We provide a simple model showing that the tangential arrangement of the ferroelectric polarization combined with the vertical thermal gradient and the pyroelectricity of the fluid drives the rotation of the tracer particles that become electrically charged in the fluid. These observations provide a fascinating example of the unique nature of fluid ferroelectric liquid crystals.

Future Perspectives of Finite-Time Thermodynamics.

Finite-time thermodynamics was created 45 years ago as a slight modification of classical thermodynamics, by adding the constraint that the process in question goes to completion within a finite length of time [...].

Space-filling and benthic competition on coral reefs.

Reef-building corals are ecosystem engineers that compete with other benthic organisms for space and resources. Corals harvest energy through their surface by photosynthesis and heterotrophic feeding, and they divert part of this energy to defend their outer colony perimeter against competitors. Here, we hypothesized that corals with a larger space-filling surface and smaller perimeters increase energy gain while reducing the exposure to competitors. This predicted an association between these two geometric properties of corals and the competitive outcome against other benthic organisms. To test the prediction, fifty coral colonies from the Caribbean island of Curaçao were rendered using digital 3D and 2D reconstructions. The surface areas, perimeters, box-counting dimensions (as a proxy of surface and perimeter space-filling), and other geometric properties were extracted and analyzed with respect to the percentage of the perimeter losing or winning against competitors based on the coral tissue apparent growth or damage. The increase in surface space-filling dimension was the only significant single indicator of coral winning outcomes, but the combination of surface space-filling dimension with perimeter length increased the statistical prediction of coral competition outcomes. Corals with larger surface space-filling dimensions (Ds > 2) and smaller perimeters displayed more winning outcomes, confirming the initial hypothesis. We propose that the space-filling property of coral surfaces complemented with other proxies of coral competitiveness, such as life history traits, will provide a more accurate quantitative characterization of coral competition outcomes on coral reefs. This framework also applies to other organisms or ecological systems that rely on complex surfaces to obtain energy for competition.

Orientational self-assembly of nanoparticles in nematic droplets.

We demonstrate experimentally that the anchoring of a nematic liquid crystal on a solid substrate together with the anchoring of the liquid crystal on a nanoparticle surface induces orientational self-assembly of anisometric nanoparticles in liquid crystal droplets. The observed phenomenon opens a novel route for fabrication of thin colloidal films with tailored properties.

How It All Began.

The first paper published as Finite-Time Thermodynamics is from 1977 [...].

Quantum Finite-Time Thermodynamics: Insight from a Single Qubit Engine.

Incorporating time into thermodynamics allows for addressing the tradeoff between efficiency and power. A qubit engine serves as a toy model in order to study this tradeoff from first principles, based on the quantum theory of open systems. We study the quantum origin of irreversibility, originating from heat transport, quantum friction, and thermalization in the presence of external driving. We construct various finite-time engine cycles that are based on the Otto and Carnot templates. Our analysis highlights the role of coherence and the quantum origin of entropy production.

Power Law Behavior in Protein Desorption Kinetics Originating from Sequential Binding and Unbinding.

The study of protein adsorption at the single molecule level has recently revealed that the adsorption is reversible, but with a long-tailed residence time distribution which can be approximated with a sum of exponential functions putatively related to distinct adsorption sites. Here it is proposed that the shape of the residence time distribution results from an adsorption process with sequential and reversible steps that contribute to overall binding strength resembling "zippering". In this model, the survival function of the residence time distribution of single proteins varies from an exponential distribution for a single adsorption step to a power law distribution with exponent -1/2 for a large number of adsorption steps. The adsorption of fluorescently labeled fibrinogen to glass surfaces is experimentally studied with single molecule imaging. The experimental residence time distribution can be readily fit by the proposed model. This demonstrates that the observed long residence times can arise from stepwise adsorption rather than rare but strong binding sites and provides guidance for the control of protein adsorption to biomaterials.

PhANNs, a fast and accurate tool and web server to classify phage structural proteins.

For any given bacteriophage genome or phage-derived sequences in metagenomic data sets, we are unable to assign a function to 50-90% of genes, or more. Structural protein-encoding genes constitute a large fraction of the average phage genome and are among the most divergent and difficult-to-identify genes using homology-based methods. To understand the functions encoded by phages, their contributions to their environments, and to help gauge their utility as potential phage therapy agents, we have developed a new approach to classify phage ORFs into ten major classes of structural proteins or into an "other" category. The resulting tool is named PhANNs (Phage Artificial Neural Networks). We built a database of 538,213 manually curated phage protein sequences that we split into eleven subsets (10 for cross-validation, one for testing) using a novel clustering method that ensures there are no homologous proteins between sets yet maintains the maximum sequence diversity for training. An Artificial Neural Network ensemble trained on features extracted from those sets reached a test F1-score of 0.875 and test accuracy of 86.2%. PhANNs can rapidly classify proteins into one of the ten structural classes or, if not predicted to fall in one of the ten classes, as "other," providing a new approach for functional annotation of phage proteins. PhANNs is open source and can be run from our web server or installed locally.

A global streamflow reanalysis for 1980-2018.

Global and continental scale hydrological reanalysis datasets receive growing attention due to their increasing number of applications, ranging from water resources management, climate change studies, water related hazards and policy support. Until recently, their use was mostly limited to qualitative assessments, due to their coarse spatial and temporal resolution, large uncertainty and bias in the model output, and limited extent of the dataset in space and time. This research reports on the setup of a gridded hydrological model with quasi-global coverage, able to reproduce a seamless 39-year streamflow simulation in all world's medium to large river basins. The model was calibrated at 1226 river sections with a total drainage area of 51 million km2 within 66 countries, using ECMWF's latest atmospheric reanalysis ERA5. A performance assessment revealed large improvements in reproducing past discharge observations, in comparison to the calibration used in the current operational setup of the hydrological model as part of the Copernicus - Global Flood Awareness System (GloFAS, www.globalfloods.eu), with median scores of Kling-Gupta Efficiency KGE = 0.67 and correlation r = 0.8. The simulation bias was also dramatically reduced and narrowed around zero, with more than 60% of stations showing percent bias within ±20%. Pronounced regional differences in the simulation results remain, pointing out the need for detailed investigation of the hydrological processes in specific regions, including parts of Africa and South Asia. In addition, observed discharges with high data quality is key to achieving skillful model output. The new calibrated model will become part of the operational runs of GloFAS in the next system release foreseen for Spring 2020, together with a near real time extension of the streamflow reanalysis.

Range-dependent thresholds for global flood early warning.

Early warning systems (EWS) for river flooding are strategic tools for effective disaster risk management in many world regions. When driven by ensemble Numerical Weather Predictions (NWP), flood EWS can provide skillful streamflow forecasts beyond the monthly time scale in large river basins. Yet, effective flood detection is challenged by accurate estimation of warning thresholds that identify specific hazard levels along the entire river network and forecast horizon. This research describes a novel approach to estimate warning thresholds which retain statistical consistency with the operational forecasts at all lead times. The procedure is developed in the context of the Global Flood Awareness System (GloFAS). A 21-year forecast-consistent dataset is used to derive thresholds with global coverage and forecast range up to six weeks. These are compared with thresholds derived from ERA5, a state of the art atmospheric reanalysis used to run the baseline simulation for the years 1986-2017 and to give a best guess of the present hydrological states. Findings show that the use of constant thresholds for 30-day flood forecasting, as in the current operational GloFAS setup, is consistent throughout the entire forecast range in only 30% to 40% of the river network, depending on the flood return period. Findings show that range-dependent thresholds, of weekly duration, are a more suitable alternative to time-invariant thresholds, as they improve the model consistency as well as the skills in flood monitoring and early warning, particularly over longer forecasting range.

High-Contrast and Fast Photorheological Switching of a Twist-Bend Nematic Liquid Crystal.

Smart viscoelastic materials that respond to specific stimuli are one of the most attractive classes of materials important to future technologies, such as on-demand switchable adhesion technologies, actuators, molecular clutches, and nano-/microscopic mass transporters. Recently it was found that through a special solid-liquid transition, rheological properties can exhibit significant changes, thus providing suitable smart viscoelastic materials. However, designing materials with such a property is complex, and forward and backward switching times are usually long. Therefore, it is important to explore new working mechanisms to realize solid-liquid transitions, shorten the switching time, and enhance the contrast of rheological properties during switching. Here, a light-induced crystal-liquid phase transition is observed, which is characterized by means of polarizing light microscopy (POM), photorheometry, photo-differential scanning calorimetry (photo-DSC), and X-ray diffraction (XRD). The light-induced crystal-liquid phase transition presents key features such as (1) fast switching of crystal-liquid phases for both forward and backward reactions and (2) a high contrast ratio of viscoelasticity. In the characterization, POM is advantageous in offering information on the spatial distribution of LC molecule orientations, determining the type of liquid crystalline phases appearing in the material, and studying the orientation of LCs. Photorheometry allows measurement of a material's rheological properties under light stimuli and can reveal the photorheological switching properties of materials. Photo-DSC is a technique to investigate thermodynamic information of materials in darkness and under light irradiation. Lastly, XRD allows studying of microscopic structures of materials. The goal of this article is to clearly present how to prepare and measure the discussed properties of a photorheological material.