BINA

In this opinion, we review some recent work on terpene biosynthesis using multiscale simulation approaches, with special focus on contributions from our group. Terpene synthases generate terpenes employing rich carbocation chemistry, including highly specific ring formations, proton, hydride, methyl, and methylene migrations, followed by reaction quenching. In these enzymes, the main catalytic challenge is not rate enhancement, but rather control of intrinsically reactive carbocations and the resulting product distribution. Herein, we review multiscale simulations of selected mono-, sesqui-, and diterpene synthases. We point to the many tools adopted by terpene synthases to achieve correct substrate fold, carbocation formation, carbocation reaction environment, and reaction quenching. A better understanding of the toolbox employed by terpene synthases is expected to aid in the search for new enzymatic and …

Due to strong electron-phonon interactions, strain engineering is a powerful tool to control quantum critical phenomena in strongly correlated oxides. Exploring this possibility requires understanding the nanoscale structure of quantum materials and the role it plays in forming the strain landscape. Here, we used a combination of x-ray nanoimaging and reciprocal space mapping to study the nanostructure of the archetypal Mott insulator VO 2, featuring an insulator-to-metal and structural phase transitions. We found that VO 2 thin films grown on r-cut sapphire consist of two intertwined crystal lattices, permanently inclined with respect to each other. This persistent pattern of twin domains stands out from the symmetry breaking induced by the structural phase transition and conceivably originates from the post-growth strain relaxation process. We propose a model explaining the formation of twin domains and the …

The Rosenzweig-Porter model has seen a resurgence in interest as it exhibits a nonergodic extended phase between the ergodic extended metallic phase and the localized phase. Such a phase is relevant to many physical models from the Sachdev-Ye-Kitaev model in high-energy physics and quantum gravity to the interacting many-body localization in condensed-matter physics and quantum computing. This phase is characterized by fractal behavior of the wave functions and a postulated correlated miniband structure of the energy spectrum. Here we will seek evidence for the latter in the spectrum. Since this behavior is expected on intermediate energy scales, spectral rigidity or number variance is a natural way to tease it out. Nevertheless, due to the Thouless energy and ambiguities in the unfolding procedure, the results are inconclusive. On the other hand, by using the singular-value decomposition method …

Arginine homeostasis in lysosomes is critical for the growth and metabolism of mammalian cells. Phagolysosomes of macrophages are the niche where the parasitic protozoan Leishmania resides and causes human leishmaniasis. During infection, parasites encounter arginine deprivation, which is monitored by a sensor on the parasite cell surface. The sensor promptly activates a mitogen-activated protein kinase 2 (MAPK2)-mediated arginine deprivation response (ADR) pathway, resulting in upregulating the abundance and activity of the Leishmania arginine transporter (AAP3). Significantly, the ADR is also activated during macrophage infection, implying that arginine levels within the host phagolysosome are limiting for growth. We hypothesize that ADR-mediated upregulation of AAP3 activity is necessary to withstand arginine starvation, suggesting that the ADR is essential for parasite intracellular development …

The adaptive immune system stores invaluable information about current and past immune responses and may serve as an ultrasensitive biosensor. Given the immune system’s critical role in a wide variety of disease types, this has broad implications for biomedicine. Machine and deep learning is being leveraged to decipher how information is encoded in adaptive immune receptor repertoires to enable prediction from adaptive immune responses and fast-track vaccine, therapeutics, and diagnostics development. Recent advances include predicting the presence of immunity post-vaccination or infection, predicting the presence of disease, and designing antibody-based therapeutics. Outstanding challenges encompass increasing our knowledge of the feature space structure that encodes relevant immune information, addressing the lack of ground-truth-labeled data, and improving our handling of genetic and …

By growing CuInSe2 with the traveling heater method, from an In melt (at a temperature below that of the sphalerite-chalcopyrite transition), twinning in the resulting single crystals was suppressed. The resulting crystals were n-type and could be converted to p-type by Se anneal. Both types were characterized structurally by X-ray diffraction, for composition by microprobe analyses, morphologically by AFM and SEM, and electrically. They were found to be mostly homogeneous, with mirror-like cleavage and without twins.

A doped semiconductor can be viewed as a mixed electronic-ionic conductor, with the dopants as mobile ions. Normally the temperature range where this becomes true is not even close to that where the (opto)electronic properties of the material are of interest. However notable exceptions exist and some examples of these are reviewed here. We limit ourselves to those cases where semiconductivity is preserved when the (mobile) dopant concentration changes and ambipolar behaviour can be obtained by dopant mobility. Dopant diffusion and drift are of interest not only in materials such as Si:Li, known from its use in radiation detectors, but also in ternary semiconductors, such as (Hg,Cd)Te and CuInSe2. Understanding the phenomena is important not only for low-temperature doping, but also because of the implications that it has for device miniaturization, as dopant diffusion and drift impose chemical limits on …

Capacitive deionization (CDI) has emerged as a novel desalination technology due to its cleanliness and low energy consumption. Despite being based on the principle of an electric double layer for ion adsorption on porous carbon materials, the inevitable faradaic reaction and the existence of co-ion repulsion reduce the charge efficiency (CE), leading to a low salt adsorption capacity (SAC). Herein, an integrated membrane electrode (IME), prepared by spray-coating a thin layer of an ion exchange polymer on the activated carbon (AC) electrode, effectively improves the selectivity of the electrode to the counter-ion, resulting in a high CE and high SAC with good stability. The results show that the CE of CDI performed using IMEs is between 70% and 98% during multiple adsorption-desorption cycles, and the SAC is up to 14–20 mg g−1, which is much higher than CE (35–65%) and SAC (7–13 mg g−1) of traditional …

We fabricate sub-micron sized diode and transistor structures (down to 100 nm in diameter) inside CuInSe2 crystals by inducing thermally assisted electromigration of mobile dopants. This is achieved by applying an electric field via a small area contact to the crystals, using a conducting Atomic Force Microscope tip. The structures are characterized by nm scale scanning spreading resistance - and scanning capacitance measurements to reveal the inhomogeneous doping profiles, that result from the electric field action. Calculations suggest that the smallest of the structures that we made are very close to the lower size limit of possible p/n/p devices.

The Aharonov-Casher effect is the analogue of the Aharonov-Bohm effect that applies to neutral particles carrying a magnetic moment. This effect can be manifested by vortices or fluxons flowing in trajectories that encompass an electric charge. These vortices have been predicted to result in a persistent voltage that fluctuates for different sample realizations. Here, we show that disordered superconductors exhibit reproducible voltage fluctuation, which is antisymmetrical with respect to the magnetic field, as a function of various parameters such as the magnetic field amplitude, field orientations, and gate voltage. These results are interpreted as the vortex equivalent of the universal conductance fluctuations typical of mesoscopic disordered metallic systems. We analyze the data in the framework of random matrix theory and show that the fluctuation correlation functions and curvature distributions exhibit behavior that …

Long-term monitoring of Rn-222 and CO2 at a depth of several dozen meter at the Sde-Eliezer site, located within one of the Dead Sea Fault Zone segments in northern Israel, has led to the discovery of the clear phenomenon that both gases are affected by underground tectonic activity along the Dead Sea Fault Zone. It may relate to pre-seismic processes associated with the accumulation and relaxation of lithospheric stress and strain producing earthquakes. This approach assumes that meteorological influences on physico-chemical parameters are limited at depth since its strength diminishes with the increase of the overlay layer thickness. Hence, the monitoring of natural gases in deep boreholes above the water table enables to reduce the climatic-induced periodic contributions, and thus to identify the specific portion of the radon signals that could be related to regional tectonic pre-seismic activity. The plausible pre-seismic local movement of the two gases at depthis identified by the appearance of discrete, random, non-cyclical signals, wider in time duration than 20 h and clearly wider than the sum of the width of the periodic diurnal and semidiurnal signals driven by ambient meteorological parameters. These non-cyclical signals may precede, by one day or more, a forthcoming seismic event. Hence, it is plausible to conclude that monitoring of any other natural gas that is present at depth may show a similar broadening signal and may serve as a precursor too. The necessary technical conditions enabling to distinguish between anomalous signals of gases that may be induced locally by pre-seismic processes at depth, and the relatively low …

In this paper we present a new technique for a fiber-based temporal super resolving system allowing to improve the resolution of a temporal imaging system. The proposed super resolving concept is based upon translating the field of view multiplexing method that is used to increase resolution in spatial imaging systems from the spatial domain to the temporal domain. In this paper, an optical realization of our proposed system is presented, using optical fibers and electro-optic modulators. In addition, we show how one can apply this method using low-rate electronics for the required modulation. We also show simulation results that demonstrate the high resolution accepted in our method compares to the basic temporal imaging system. Experimental results which demonstrate resolution improvement by a factor of 1.5 based on the proposed method are presented together with an additional experiment that shows the …

Amorphous tungsten oxide has been prepared by ultrasound irradiation of a solution of tungsten hexacarbonyl W (CO) 6 in diphenylmethane (DPhM) in the presence of an Ar (80%) â O2 (20%) gaseous mixture at 90 ÂC. Heating this amorphous powder at 550 ÂC under Ar yields snowflake-like dendritic particles consisting of a mixture of monoclinic and orthorhombic WO2 crystals. Annealing of the as-prepared product in Ar at 1000 ÂC causes the formation of a WO2â WO3 mixture containing nanorods (around 50 nm in diameter) and packs of these nanorods. Heating the product in air for 3 hours leads to triclinic WO3 crystal formation, with a basic size of 50â 70 nm. The prepared oxides have been characterized by elemental analysis, X-ray powder diffraction measurements, FTIR spectroscopy, differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), transmission electron microscopy (TEM), scanning electron microscopy (SEM), and energy dispersive X-ray analysis (EDX).

Neurons are diverse and can be differentiated by their morphological, electrophysiological, and molecular properties. Current morphology-based classification approaches largely rely on the dendritic tree structure or on the overall axonal projection layout. Here, we use data from public databases of neuronal reconstructions and membrane properties to study the characteristics of the axonal and dendritic trees for interneuron classification. We show that combining signal propagation patterns observed by biophysical simulations of the activity along ramified axonal trees with morphological parameters of the axonal and dendritic trees, significantly improve classification results compared to previous approaches. The classification schemes introduced here can be utilized for robust neuronal classification. Our work paves the way for understanding and utilizing form-function principles in realistic neuronal …

Discrete time, integrated microwave photonic filters with narrow bandwidths are realized in standard silicon on insulator. Long delays are achieved using slow moving surface acoustic waves. The complex magnitude of each tap is chosen arbitrarily. © 2020 The Author(s)

Light scattering and localization in strongly scattering disordered systems is governed by the nature of the underlying eigenmodes, specially their spatial extension within the system. One of the main challenges in studying experimentally Anderson like localized states resides in the difficulty to excite these states independently and observe them individually anywhere in the sample. The modes mutual interaction and their coupling to the sample boundaries makes it extremely challenging to isolate them spectrally and image them alone. In the presence of gain, random lasing occurs above threshold and lasing modes are excited. It was shown recently that shaping the intensity profile of the optical pump is a very effective way to control and force random lasing in singlemode regime at any desired emission wavelength. Active random media therefore offer a unique platform to select modes individually. By using pump shaping technique in a strongly scattering random laser, we successfully select localized lasing modes individually. Direct imaging of the light distribution within the random laser confirms the confined nature of the modes and enables us to elucidate long standing questions on the role of non-Hermiticity in active scattering media and the influence of nonlinearities on Anderson wave localization.

RNA-binding proteins, particularly splicing factors, localize to sub-nuclear domains termed nuclear speckles. During certain viral infections, as the nucleus fills up with replicating virus compartments, host cell chromatin distribution changes, ending up condensed at the nuclear periphery. In this study we wished to determine the fate of nucleoplasmic RNA-binding proteins and nuclear speckles during the lytic cycle of the Kaposi’s sarcoma associated herpesvirus (KSHV). We found that nuclear speckles became fewer and dramatically larger, localizing at the nuclear periphery, adjacent to the marginalized chromatin. Enlarged nuclear speckles contained splicing factors, whereas other proteins were nucleoplasmically dispersed. Polyadenylated RNA, typically found in nuclear speckles under regular conditions, was also found in foci separated from nuclear speckles in infected cells. Poly (A) foci did not contain lncRNAs known to colocalize with nuclear speckles but contained the poly (A)-binding protein PABPN1. Examination of the localization of spliced viral RNAs revealed that some spliced transcripts could be detected within the nuclear speckles. Since splicing is required for the maturation of certain KSHV transcripts, we suggest that the infected cell does not dismantle nuclear speckles but rearranges their components at the nuclear periphery to possibly serve in splicing and transport of viral RNAs into the cytoplasm. View Full-Text

We showed theoretically that the phase modulation of the output of a single optical parametric oscillator can be used to generate a square-grid cluster state, a key resource for universal quantum computing.

Olivine LiCoPO 4 (LCP) exhibits a rare combination of high theoretical capacity (167 mAh g− 1), excellent thermal stability, and high redox potential (4.8 V vs vs Li/Li+), making it a promising candidate for high voltage lithium batteries. Despite these attractive properties, practical implementation of this electrode chemistry has been limited by stability issues at the cathode-electrolyte interface, including parasitic electrolyte reactions, surface decomposition of the electrode material, and Co dissolution. Carbon coating and substitutions of Co by Fe and other cations improve the performance, however the cycling stability needs further improvement. In an effort to address these issues, we deposited thin, conformal metal oxide surface coatings on substituted LCP powder and investigated the effects of these coatings on the performance of carbon-coated substituted LCP/MCMB graphite full cells with a standard carbonate …

Coupled parametric oscillators were recently employed as simulators of artificial Ising networks, with the potential to solve computationally hard minimization problems. We demonstrate a new dynamical regime within the simplest network—two coupled parametric oscillators, where the oscillators never reach a steady state, but show persistent, full-scale, coherent beats, whose frequency reflects the coupling properties and strength. We present a detailed theoretical and experimental study and show that this new dynamical regime appears over a wide range of parameters near the oscillation threshold and depends on the nature of the coupling (dissipative or energy preserving). Thus, a system of coupled parametric oscillators transcends the Ising description and manifests unique coherent dynamics, which may have important implications for coherent computation machines.

RNA-binding proteins, particularly splicing factors, localize to sub-nuclear domains termed nuclear speckles. During certain viral infections, as the nucleus fills up with replicating virus compartments, host cell chromatin distribution changes, ending up condensed at the nuclear periphery. In this study we wished to determine the fate of nucleoplasmic RNA-binding proteins and nuclear speckles during the lytic cycle of the Kaposi’s sarcoma associated herpesvirus (KSHV). We found that nuclear speckles became fewer and dramatically larger, localizing at the nuclear periphery, adjacent to the marginalized chromatin. Enlarged nuclear speckles contained splicing factors, whereas other proteins were nucleoplasmically dispersed. Polyadenylated RNA, typically found in nuclear speckles under regular conditions, was also found in foci separated from nuclear speckles in infected cells. Poly (A) foci did not contain lncRNAs known to colocalize with nuclear speckles but contained the poly (A)-binding protein PABPN1. Examination of the localization of spliced viral RNAs revealed that some spliced transcripts could be detected within the nuclear speckles. Since splicing is required for the maturation of certain KSHV transcripts, we suggest that the infected cell does not dismantle nuclear speckles but rearranges their components at the nuclear periphery to possibly serve in splicing and transport of viral RNAs into the cytoplasm. View Full-Text