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Register a new userTrans-cis molecular photoswitching in interstellar Space
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As many organic molecules, formic acid (HCOOH) has two conformers (trans and cis). The energy barrier to internal conversion from trans to cis is much higher than the thermal energy available in molecular clouds. Thus, only the most stable conformer (trans) is expected to exist in detectable amounts. We report the first interstellar detection of cis-HCOOH. Its presence in ultraviolet (UV) irradiated gas exclusively (the Orion Bar photodissociation region), with a low trans-to-cis abundance ratio of 2.8+-1.0, supports a photoswitching mechanism: a given conformer absorbs a stellar photon that radiatively excites the molecule to electronic states above the interconversion barrier. Subsequent fluorescent decay leaves the molecule in a different conformer form. This mechanism, which we specifically study with ab initio quantum calculations, was not considered in Space before but likely induces structural changes of a variety of interstellar molecules submitted to UV radiation.
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We numerically study the implementation of a NOT gate by laser pulses in a model molecular system presenting two electronic surfaces coupled by non adiabatic interactions. The two states of the bit are the fundamental states of the cis-trans isomers of the molecule. The gate is classical in the sense that it involves a one-qubit flip so that the encoding of the outputs is based on population analysis which does not take the phases into account. This gate can also be viewed as a double photo-switch process with the property that the same electric field controls the two isomerizations. As an example, we consider one-dimensional cuts in a model of the retinal in rhodopsin already proposed in the literature. The laser pulses are computed by the Multi Target Optimal Control Theory with chirped pulses as trial fields. Very high fidelities are obtained. We also examine the stability of the control when the system is coupled to a bath of oscillators modelled by an Ohmic spectral density. The bath correlation time scale being smaller than the pulse duration the dynamics is carried out in the Markovian approximation.
During polymer translocation driven by e.g. voltage drop across a nanopore, the segments in the cis-side is incessantly pulled into the pore, which are then pushed out of it into the trans-side. This pulling and pushing polymer segments are described in the continuum level by nonlinear transport processes known, respectively, as fast and slow diffusions. By matching solutions of both sides through the mass conservation across the pore, we provide a physical basis for the cis and trans dynamical asymmetry, a feature repeatedly reported in recent numerical simulations. We then predict how the total driving force is dynamically allocated between cis (pulling) and trans (pushing) sides, demonstrating that the trans-side event adds a finite-chain length effect to the dynamical scaling, which may become substantial for weak force and/or high pore friction cases.
A better understanding of sulphur chemistry is needed to solve the interstellar sulphur depletion problem. A way to achieve this goal is to study new S-bearing molecules in the laboratory, obtaining accurate rest frequencies for an astronomical search. We focus on dithioformic acid, HCSSH, which is the sulphur analogue of formic acid. The aim of this study is to provide an accurate line list of the two HCSSH $trans$ and $cis$ isomers in their electronic ground state and a comprehensive centrifugal distortion analysis with an extension of measurements in the millimetre and submillimetre range. We studied the two isomers in the laboratory using an absorption spectrometer employing the frequency-modulation technique. The molecules were produced directly within a free-space cell by glow discharge of a gas mixture. We measured lines belonging to the electronic ground state up to 478 GHz, with a total number of 204 and 139 new rotational transitions, respectively, for $trans$ and $cis$ isomers. The final dataset also includes lines in the centimetre range available from literature. The extension of the measurements in the mm and submm range lead to an accurate set of rotational and centrifugal distortion parameters. This allows us to predict frequencies with estimated uncertainties as low as 5 kHz at 1 mm wavelength. Hence, the new dataset provided by this study can be used for astronomical search.
Deciphering gene regulatory networks is a central problem in computational biology. Here, we explore the use of multi-modal neural networks to learn predictive models of gene expression that include cis and trans regulatory components. We learn models of stress response in the budding yeast Saccharomyces cerevisiae. Our models achieve high performance and substantially outperform other state-of-the-art methods such as boosting algorithms that use pre-defined cis-regulatory features. Our model learns several cis and trans regulators including well-known master stress response regulators. We use our models to perform in-silico TF knock-out experiments and demonstrate that in-silico predictions of target gene changes correlate with the results of the corresponding TF knockout microarray experiment.
The local cosmic-ray (CR) spectra are calculated for typical characteristic regions of a cold dense molecular cloud, to investigate two so far neglected mechanisms of dust charging: collection of suprathermal CR electrons and protons by grains, and photoelectric emission from grains due to the UV radiation generated by CRs. The two mechanisms add to the conventional charging by ambient plasma, produced in the cloud by CRs. We show that the CR-induced photoemission can dramatically modify the charge distribution function for submicron grains. We demonstrate the importance of the obtained results for dust coagulation: While the charging by ambient plasma alone leads to a strong Coulomb repulsion between grains and inhibits their further coagulation, the combination with the photoemission provides optimum conditions for the growth of large dust aggregates in a certain region of the cloud, corresponding to the densities $n(mathrm{H_2})$ between $sim10^4$ cm$^{-3}$ and $sim10^6$ cm$^{-3}$. The charging effect of CR is of generic nature, and therefore is expected to operate not only in dense molecular clouds but also in the upper layers and the outer parts of protoplanetary discs.
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