Analyzing phase transitions using the inherent geometrical attributes of a system has garnered enormous interest over the past few decades. The usual candidate often used for investigation is graphene- the most celebrated material among the family of tri co-ordinated graphed lattices. We show in this report that other inhabitants of the family demonstrate equally admirable structural and functional properties that at its core are controlled by their topology. Two interesting members of the family are Cylooctatrene(COT) and COT-based polymer: poly-bi--annulenylene both in one and two dimensions that have been investigated by polymer chemists over a period of 50 years for its possible application in batteries exploiting its conducting properties. A single COT unit is demonstrated herein to exhibit topological solitons at sites of a broken bond similar to an open one-dimensional Su-Schrieffer-Heeger (SSH) chain. We observe that Poly-bi--annulenylene in 1D mimics two coupled SSH chains in the weak coupling limit thereby showing the presence of topological edge modes. In the strong coupling limit, we investigate the different parameter values of our system for which we observe zero energy modes. Further, the application of an external magnetic field and its effects on the band-flattening of the energy bands has also been studied. In 2D, poly-bi--annulenylene forms a square-octagon lattice which upon breaking time-reversal symmetry goes into a topological phase forming noise-resilient edge modes. We hope our analysis would pave the way for synthesizing such topological materials and exploiting their properties for promising applications in optoelectronics, photovoltaics, and renewable energy sources.
The two-dimensional paraxial equation of optics and the twodimensional time-dependent Schr odinger equation, derived as approximations of the three-dimensional Helmholtz equation and the three-dimensional time-independent Schr odinger equation respectively, are identical. Here the free propagation in space and time of Hermite-Gauss wavepackets (optics) or Harmonic Oscillator eigenfunctions (quantum mechanics) is examined in detail. The Gouy phase is shown to be a dynamic phase, appearing as the integral of the adiabatic eigenfrequency or eigenenergy. The wave packets propagate adiabatically in that at each space or time point they are solutions of the instantaneous harmonic problem. In both cases, it is shown that the form of the wave function is unchanged along the loci of the normals to wave fronts. This invariance along such trajectories is connected to the propagation of the invariant amplitude of the corresponding free wave number (optics) or momentum (quantum mechanics) wavepackets. It is shown that the van Vleck classical density of trajectories function appears in the wave function amplitude over the complete trajectory. A transformation to the co-moving frame along a trajectory gives a constant wave function multiplied by a simple energy or frequency phase factor. The Gouy phase becomes the proper time in this frame.
Three-dimensional (3D) imaging, such as micro-computed tomography (micro-CT), is increasingly being used by organismal biologists for precise and comprehensive anatomical characterization. However, the segmentation of anatomical structures remains a bottleneck in research, often requiring tedious manual work. Here, we propose a pipeline for the fully-automated segmentation of anatomical structures in micro-CT images utilizing state-of-the-art deep learning methods, selecting the ant brain as a test case. We implemented the U-Net architecture for 2D image segmentation for our convolutional neural network (CNN), combined with pixel-island detection. For training and validation of the network, we assembled a dataset of semi-manually segmented brain images of 76 ant species. The trained network predicted the brain area in ant images fast and accurately; its performance tested on validation sets showed good agreement between the prediction and the target, scoring 80% Intersection over Union (IoU) and 90% Dice Coefficient (F1) accuracy. While manual segmentation usually takes many hours for each brain, the trained network takes only a few minutes. Furthermore, our network is generalizable for segmenting the whole neural system in full-body scans, and works in tests on distantly related and morphologically divergent insects (e.g., fruit flies). The latter suggests that methods like the one presented here generally apply across diverse taxa. Our method makes the construction of segmented maps and the morphological quantification of different species more efficient and scalable to large datasets, a step toward a big data approach to organismal anatomy.
SARS-CoV-2 and its ever-emerging variants, are spread from host-to-host via expelled respiratory aerosols and saliva droplets. Knowing the number of virions which are exhaled by a person requires precise measurements of the size, count, velocity and trajectory of the virus-laden particles that are ejected directly from the mouth. These measurements are achieved in 3D, at 15000 images/second, and are applied when speaking, yelling, and coughing. In this study 33 events have been analysed by post-processing ~500000 images. Using these data, the flow rate of SARS-CoV-2 virions have been evaluated. At high concentrations, 10^7 virions/mL, it is found that 136 to 231 virions are ejected during a single cough, where the virion flow rate peak is capable of reaching 32 virions within a millisecond. This peak can reach tens of virions/ms when yelling, but reduced to only a few virions/ms when speaking. At medium concentrations, ~10^5 virions/mL, those results are hundreds of times lower. The total number of virions that are ejected when yelling at 110db, instead of speaking at 85db, increases by two to three fold. From the measured data analysed in this article, the flow rate of other diseases such as influenza, tuberculosis or measles, can also be estimated. As these data are openly accessible, they can be used by modellers for the simulation of saliva droplet transport and evaporation, allowing to further advance our understanding of airborne pathogen transmission.
When a chemical reaction occurs via tunnelling, a simple mass-dependence is expected, where substitution of atoms by heavier isotopes leads to a reduced reaction rate. However, as shown in a recent study of CO orientational isomerization at the NaCl(100) interface [Choudhury et al., Nature 612, 691 (2022)], the lightest isotopologue need not exhibit the fastest tunnelling; for the CO/NaCl system, the non-monotonic mass-dependence is understood through a new picture of condensed phase tunnelling where the overall rate is dominated by a few pairs of reactant/product states. These state-pairs – termed quantum gateways – gain dynamical importance through accidentally-enhanced tunnelling probabilities, facilitated by a confluence of the energetic landscape underlying the reaction as well as the phonon bath of the surrounding medium. Here, we explore gateway tunnelling through measurements of the kinetic isotope effect (KIE) for CO isomerization in a monolayer buried by many layers of either CO or N2. With an N2 overlayer, tunnelling rates are accelerated for all four isotopologues (12C16O, 13C16O, 12C18O, and 13C18O), but the degree of acceleration is isotopologue-specific and non-intuitively mass dependent. A one-dimensional tunnelling model involving an Eckart barrier cannot capture this behaviour. This reflects how a change to the potential energy surface moves states in and out of resonance, changing which tunnelling gateways can be accessed in the isomerization reaction.
: Proteins are useful chiral selectors. In order to understand the recognition mechanism and the chiral discrimination, binding of the (R)- and (S)-enantiomers of a series of designed amino alcohol inhibitors based on propranolol to cellobiohydrolase Cel7A (Trichoderma reesei) has been studied more closely. X-ray crystal structures were determined of the protein complex with the (R)- and (S)-enantiomers of the strongest binding propranolol analog. The combination of the structural data, thermodynamic data from capillary electrophoresis and microcalorimetry experiments and computational modeling give a clearer insight into the origin of the enantioselectivity and its opposite thermodynamic signature. The new crystal structures were used in computational molecular flexible dockings of the propranolol analogues using the program Glide. The results indicated that several water molecules in the active site were essential for the docking of the (R)-enantiomers, but not for the (S)-enantiomers. The results are discussed in relation to the enantiomeric discrimination of the enzyme. Both dissociation constants (Kd-values) and thermodynamical data are included to show the effects of the structural modifications in the ligand on enthalpy and entropy in relation to the enantioselectivity.
Spearing mantis shrimps are aggressive crustaceans using specialized appendages with sharp spikes to capture fishes with a fast movement. Each spike is a biological tool that have to combine high toughness, as required by the initial impact with the victim, with high stiffness and strength, to ensure sufficient penetration while avoid breaking. We performed a multimodal analysis to uncover the design strategies of this harpoon based on chitin. We found that the spike is a slightly hooked hollow beam with the outer surface decorated by serrations and grooves to enhance cutting and interlocking. The cuticle of the spike resembles a multilayer composite: an outer heavily mineralized, stiff and hard region (with average indentation modulus and hardness of 68 and 3 GPa), providing high resistance to contact stresses, is combined with a less mineralized region, which occupies a large fraction of the cuticle (up to 50%) and features parallel fibers oriented longitudinally, enhancing stiffness and strength. A central finding of our work is the presence of a tiny interphase (less than 10 μm in width) based on helical fibers and showing a spatial modulation in mechanical properties, which has the critical task to integrate the stiff but brittle outer layer with the more compliant highly anisotropic parallel fiber region. We highlighted the remarkable ability of this helicoidal region to stop nanoindentation-induced cracks. Using three-dimensional multimaterial printing to prototype spike-inspired composites, we showed how the observed construction principles can not only hamper damage propagation between highly dissimilar layers (resulting in composites with the helical interphase absorbing 50% more energy than without it) but can also enhance resistance to puncture (25% increase in the force required to penetrate the composites with a blunt tool). Such findings may provide guidelines to design lightweight harpoons relying on environmentally friendly and recyclable building blocks.
We recount the life, work, and legacy of the theoretical physicist Roy Glauber (1925-2018). Admitted to Harvard at age sixteen, called upon to participate in the Manhattan Project at age eighteen, and appointed to the Harvard Physics faculty at age twenty-nine, Glauber is credited with seminal contributions to three separate fields of physics: nuclear scattering, statistical physics, and foundational work in quantum optics, which earned him the 2005 Nobel Prize in Physics. Over decades, Glauber was also a dedicated teacher of high-school, college, and graduate students. His pedagogical gifts are reflected in his lucid papers that read as if they were written yesterday.
The mid-infrared (mid-IR) anisotropic optical response of a material probes vibrational fingerprints and absorption bands sensitive to order, structure and direction dependent stimuli. Such anisotropic properties play a fundamental role in catalysis, optoelectronic, photonic, polymer and biomedical research and applications. Infrared dual-comb polarimetry (IR-DCP) is introduced as a powerful new spectroscopic method for the analysis of complex dielectric functions and anisotropic samples in the mid-IR range. IR DCP enables novel hyperspectral and time-resolved applications far beyond the technical possibilities of classical Fourier-transform IR (FTIR) approaches. The method unravels structure–spectra relations at high spectral bandwidth (100 cm–1) and short integration times of 65 µs, with previously unattainable time resolutions for spectral IR polarimetric measurements for potential studies of noncyclic and irreversible processes. The polarimetric capabilities of IR-DCP are demonstrated by investigating an anisotropic inhomogeneous free-standing nanofiber scaffold for neural tissue applications. Polarization sensitive multi-angle dual-comb transmission amplitude and absolute phase measurements (separately for ss-, pp-, ps- and sp-polarized light) allow the in-depth probing of the samples’ orientation dependent vibrational absorption properties. Mid-IR anisotropies can be quickly identified by cross-polarized IR-DCP polarimetry.
There is a pseudo-embryology existing today, well nourished by popular science, religious ideologies, and the public media. Just as eugenics was a pseudoscience that influenced (and still influences) American popular culture and which was responsible for racist anti-immigration laws (such as the Immigration Restriction Act of 1924), pseudo-embryology is also influencing popular culture and legislation. This new pseudoscience promotes the belief that science supports current zygotic and fetal personhood movements and anti-abortion legislation. However, what often passes for science are actually ideological myths, often grounded in and supporting male superiority. Indeed, the first myth of pseudo-embryology is that fertilization is a masculine act that can be viewed as a classical hero narrative. The second myth is that fertilization is ensoulment, allowing it to displace the feminine act of birth as to when life begins. Here, DNA is seen to play the secular analogue of soul. The third myth is that the fetus in the womb is an independent autonomous entity and that birth merely moves the fetus from the womb to the outside world. This expresses the “seed-in-the-soil” myth that was also prevalent in ancient cultures. In this manner, masculine stories of fertilization are valorized while feminine narratives of birth are suppressed. So when public narratives discuss what “science” says about when human life begins, we are not really discussing science. Rather, we are allowing our discussions to fall back into tenacious ancient misogynist myths that have nothing to do with the conclusions of modern developmental biology.
End stage renal disease (ESRD), characterized by cessation in kidney function, has been linked to severe metabolic disturbances, caused by buildup of toxic solutes in blood. To remove these solutes, ESRD patients undergo dialysis. As a proof of concept, we tested whether ESRD-related metabolic signatures can be detected in perspiration samples using a combined methodology. Our rapid methodology involves swabbing a glass slide across the patient’s forehead, detecting the metabolites in the imprint using desorption electrospray ionization mass spectrometry, and identifying the key differences using machine learning methods. Based on collecting 42 healthy and 27 ESRD samples, we find saturated fatty acids are consistently suppressed in ESRD patients, with little change after dialysis. Also, our method enables the detection of uremic solutes, where we find elevated levels of uric acid (6.7 fold higher on average) that sharply decrease after dialysis. Beyond the study of individual metabolites, we find that a lasso model, which selects for 8 m/z fragments from 24,602 detected analytes, achieves area under the curve performance of 0.85 and 0.87 on training (n=52) and validation sets (n=17) respectively. Together, these results suggest that this methodology is promising for detecting signatures relevant for Precision Health.
Preface by Prof. Titia de Lange, Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA The 19th Annual Wiley Prize in Biomedical Sciences celebrated a breakthrough in cell biology: how membrane-less cellular compartments are formed. The existence of membrane-less organelles, often called bodies or puncta, have been known for a long time, but what exactly they represented and how they were formed was not known. This problem was solved by a physicist, Clifford Brangwynne, a cell biologist, Anthony Hyman and a chemist, Michael Rosen. Each, synergistically, made groundbreaking contributions to the discovery that membrane-less organelles are liquid-liquid phase-separated entities. The two independent discoveries leading to the principle that multivalent low-affinity interactions between selected sets of macromolecules, some containing intrinsically disordered regions, formed a molecular condensate with unique dynamic properties, gave birth to the large, blossoming field of biomolecular condensates. The implications of those findings have influenced almost all further research of intracellular processes, including RAS signaling, immune synapses, DNA repair, transcriptional activation, and the functions of nuclear pores, the nucleolus and centrosomes. In this Perspective article, the laureates of the award take us on their personal and professional trip that led to their scientific discoveries. Their stories are a celebration of the interdisciplinary essence of Natural Sciences and the potential unlocked when scientists from different fields work together to solve mysteries.
Hot excitons are usually neglected in optical spectroscopy in 2D semiconductors for the sake of momentum conservation, as the majority of hot excitons are out of light cones. In this letter, we elaborate the contribution of hot excitons to optical properties of monolayer MoSe2 with photoluminescence (PL) and photoluminescence excitation (PLE) spectroscopy. With the excitation-intensity-dependent PL, temperature-dependent PL and PLE experiments combined with the simulations, we experimentally distinguish the influences of the exciton temperature and the lattice temperature in the PL spectrum. It is concluded that the acoustic phonon assisted photoluminescence accounts for the non-Lorentzian high energy tail in the PL spectrum and the hot exciton effect is significant to linear optical properties of TMDs. Besides, the effective exciton temperature is found to be several tens of Kelvin higher than the lattice temperature at non-resonant optical excitation. It indicates that the exciton temperature needs to be carefully taken into account when considering the exciton related quantum phase phenomena such as exciton condensation. It is experimentally demonstrated that the effective exciton temperature can be tuned by excitation energy.
Since a polyvalent strategy has recently been assumed to be adopted by Deinococcus radiodurans that can generate various resistance against many different detrimental sources of oxidative damage (e.g. reactive oxygen species, heavy metal ions and ionising radiation), investigating more than one restorative metabolic activities and their interrelation of the very same entities of Deinococcus radiodurans is of great significance for exploring its polyextremophile nature, which will be insightful for obtaining fundamental generic insights into life sustainability. Herein, we apply mainly fluorescence microscopy and back reflection microscopy to visibly assess the respective activities of superoxide radical generation and silver ion metabolism for individual Deinococcus radiodurans. Strikingly, only a minority (<20%) of the bacteria which show low superoxide radical levels is revealed to exhibit considerable formation of silver nanoparticles whilst those containing more superoxide radicals all show minimum silver ion metabolism. The discovery of the strong negative correlation for the small subpopulation between the two visualised different metabolic activities not only provides direct experimental evidence in terms of bacterial functionality for the inferred survival regime of the extreme microbe, but also suggests a new way of chemically examining biology from the perspective of inter-functional relationship.
Mitochondria continuously undergo morphologically dynamic processes of fusion and fission to maintain their size, shape, amount, and function; yet the precise molecular mechanisms by which mitochondrial dynamics is regulated remain to be fully elucidated. Here, we report a previous unappreciated but critical role of eukaryotic elongation factor 2 (eEF2) in regulating mitochondrial fission. eEF2, a G-protein superfamily member encoded by EEF2 gene in human, has long been appreciated as a promoter of the GTP-dependent translocation of the ribosome during protein synthesis. We found unexpectedly in several types of cells that eEF2 was not only present in the cytosol but also in the mitochondria. Furthermore, we showed that mitochondrial length was significantly increased when the cells were subjected to silencing of eEF2 expression, suggesting a promotive role for eEF2 in the mitochondrial fission. Inversely, overexpression of eEF2 decreased mitochondrial length, suggesting an increase of mitochondrial fission. Inhibition of mitochondrial fission caused by eEF2 depletion was accompanied by alterations of cellular metabolism, as evidenced by a reduction of oxygen consumption and an increase of oxidative stress in the mitochondria. We further demonstrated that eEF2 and Drp1, a key driver of mitochondrial fission, co-localized at the mitochondria, as evidenced by microscopic observation, co-immunoprecipitation, and GST pulldown assay. Deletion of the GTP binding motif of eEF2 decreased its association with Drp1 and abrogated its effect on mitochondria fission. Moreover, we showed that wild-type eEF2 stimulated GTPase activity of Drp1, whereas deletion of the GTP binding site of eEF2 diminished its stimulatory effect on GTPase activity. This work not only reveals a previously unrecognized function of eEF2 (i.e., promoting mitochondrial fission), but also uncovers the interaction of eEF2 with Drp1 as a novel regulatory mechanism of the mitochondrial dynamics. Therefore, eEF2 warrants further exploration for its potential as a therapeutic target for the mitochondria-related diseases.
This Research Highlight showcases the two Research Papers entitled, A precise photometric ratio via laser excitation of the sodium layer – I. One-photon excitation using 342.78 nm light, https://doi.org/10.1093/mnras/stab1621 and A precise photometric ratio via laser excitation of the sodium layer – II. Two-photon excitation using lasers detuned from 589.16 nm and 819.71 nm resonances, https://doi.org/10.1093/mnras/stab1619.
Silicon-based anodes with lithium ions as charge carriers have the highest predicted theoretical specific capacity of 3579 mA h g-1 (for Li15Si4). Contemporary electrodes do not achieve this theoretical value largely because conventional production paradigms rely on the mixing of weakly coordinated components. In this paper, a semi-conductive triazine-based graphdiyne polymer network is grown around silicon nanoparticles directly on the current collector, a copper sheet. The porous, semi-conducting organic framework (i) adheres to the current collector on which it grows via cooperative van der Waals interactions, (ii) acts effectively as conductor for electrical charges and binder of silicon nanoparticles via conjugated, covalent bonds, and (iii) enables selective transport of electrolyte and Li-ions through pores of defined size. The resulting anode shows extraordinarily high capacity at the theoretical limit of fully lithiated silicon. Finally, we combine our anodes in proof-of-concept battery assemblies using a conventional layered Ni-rich oxide cathode.