Systems biology of energetic and atomic costs in the yeast transcriptome, proteome, and metabolome

Proteins vary in their cost to the cell and natural selection may favour the use of proteins that are cheaper to produce. We develop a novel approach to estimate the amino acid biosynthetic cost based on genome-scale metabolic models, and directly investigate the effects of biosynthetic cost on transcriptomic, proteomic and metabolomic data in _Saccharomyces cerevisiae_. We find that our systems approach to formulating biosynthetic cost produces a novel measure that explains similar levels of variation in gene expression compared with previously reported cost measures. Regardless of the measure used, the cost of amino acid synthesis is weakly associated with transcript and protein levels, independent of codon usage bias. In contrast, energetic costs explain a large proportion of variation in levels of free amino acids. In the economy of the yeast cell, there appears to be no single currency to compute the cost of amino acid synthesis, and thus a systems approach is necessary to uncover the full effects of amino acid biosynthetic cost in complex biological systems that vary with cellular and environmental conditions

Lead-Chalcogenide Colloidal-Quantum-Dot Solids:Novel Assembly Methods, Electronic Structure Control, and Application Prospects

The quest for novel semiconductors with easy, cheap fabrication and tailorable properties has led to the development of several classes of materials, such as semiconducting polymers, carbon nanotubes, hybrid perovskites, and colloidal quantum dots. All these candidates can be processed from the liquid phase, enabling easy fabrication, and are suitable for different electronic and optoelectronic applications. Here, recent developments in the field of colloidal-quantum-dot solids are discussed, with a focus on lead-chalcogenide systems. These include novel deposition methods; the recent growing understanding of their fundamental properties, driven by major successes in the control of the nanostructured assembly and surface chemistry; and selected reports on lab-scale devices showing the technological prospects of these fascinating class of materials

Next-to-next-to-leading logarithmic corrections at small transverse momentum in hadronic collisions

We study the region of small transverse momenta in qqbar- and gg-initiated processes with no colored particle detected in the final state. We present the universal expression of the O(alpha_s^2) logarithmically enhanced contributions up to next-to-next-to-leading logarithmic accuracy. From there we extract the coefficients that allow the resummation of the large logarithmic contributions. We find that the coefficient known in the literature as B^{(2)} is process dependent, since it receives a hard contamination from the one loop correction to the leading order subprocess. We present the general result of B^{(2)} for both quark and gluon channels. In particular, in the case of Higgs production, this result will be relevant to improve the matching between resummed predictions and fixed order calculations.Comment: LaTeX, 8 pages. Few typos corrected, particularly Eq.(25). Two references added, to be published in PR

Stoichiometric control of the density of states in PbS colloidal quantum dot solids

Colloidal quantum dots, and nanostructured semiconductors in general, carry the promise of overcoming the limitations of classical materials in chemical and physical properties and in processability. However, sufficient control of electronic properties, such as carrier concentration and carrier mobility, has not been achieved until now, limiting their application. In bulk semiconductors, modifications of electronic properties are obtained by alloying or doping, an approach that is not viable for structures in which the surface is dominant. The electronic properties of PbS colloidal quantum dot films are fine-tuned by adjusting their stoichiometry, using the large surface area of the nanoscale building blocks. We achieve an improvement ofmore than two orders ofmagnitude in the holemobility, from below 10(-3) to above 0.1 cm(2)/N.s, by substituting the iodide ligands with sulfide while keeping the electron mobility stable (similar to 1 cm(2)/V.s). This approach is not possible in bulk semiconductors, and the developed method will likely contribute to the improvement of solar cell efficiencies through better carrier extraction and to the realization of complex (opto) electronic devices

Free carrier generation and recombination in PbS quantum dot solar cells

Time Delayed Collection Field and Bias Assisted Charge Extraction (BACE) experiments are used to investigate the charge carrier dynamics in PbS colloidal quantum dot solar cells. We find that the free charge carrier creation is slightly field dependent, thus providing an upper limit to the fill factor. The BACE measurements reveal a rather high effective mobility of 2 x 10(-3) cm(2)/Vs, meaning that charge extraction is efficient. On the other hand, a rather high steady state non-geminate recombination coefficient of 3 x 10(-10) cm(3)/s is measured. We, therefore, propose a rapid free charge recombination to constitute the main origin for the limited efficiency of the PbS colloidal quantum dots cells. (C) 2016 AIP Publishing LLC

Quantum Multibaker Maps: Extreme Quantum Regime

We introduce a family of models for quantum mechanical, one-dimensional random walks, called quantum multibaker maps (QMB). These are Weyl quantizations of the classical multibaker models previously considered by Gaspard, Tasaki and others. Depending on the properties of the phases parametrizing the quantization, we consider only two classes of the QMB maps: uniform and random. Uniform QMB maps are characterized by phases which are the same in every unit cell of the multibaker chain. Random QMB maps have phases that vary randomly from unit cell to unit cell. The eigenstates in the former case are extended while in the latter they are localized. In the uniform case and for large $\hbar$, analytic solutions can be obtained for the time dependent quantum states for periodic chains and for open chains with absorbing boundary conditions. Steady state solutions and the properties of the relaxation to a steady state for a uniform QMB chain in contact with ``particle'' reservoirs can also be described analytically. The analytical results are consistent with, and confirmed by, results obtained from numerical methods. We report here results for the deep quantum regime (large $\hbar$) of the uniform QMB, as well as some results for the random QMB. We leave the moderate and small $\hbar$ results as well as further consideration of the other versions of the QMB for further publications.Comment: 17 pages, referee's and editor's comments addresse

Casimir energy in multiply connected static hyperbolic Universes

We generalize a previously obtained result, for the case of a few other static hyperbolic universes with manifolds of nontrivial topology as spatial sections.Comment: accepted for publicatio

Fullerene derivatives with oligoethylene-glycol side chains:An investigation on the origin of their outstanding transport properties

For many years, fullerene derivatives have been the main n-type material of organic electronics and optoelectronics. Recently, fullerene derivatives functionalized with ethylene glycol (EG) side chains have been showing important properties such as enhanced dielectric constants, facile doping and enhanced self-assembly capabilities. Here, we have prepared field-effect transistors using a series of these fullerene derivatives equipped with EG side chains of different lengths. Transport data show the beneficial effect of increasing the EG side chain. In order to understand the material properties, full structural determination of these fullerene derivatives has been achieved by coupling the X-ray data with molecular dynamics (MD) simulations. The increase in transport properties is paired with the formation of extended layered structures, efficient molecular packing and an increase in the crystallite alignment. The layer-like structure is composed of conducting layers, containing of closely packed C60 balls approaching the inter-distance of 1 nm, that are separated by well-defined EG layers, where the EG chains are rather splayed with the chain direction almost perpendicular to the layer normal. Such a layered structure appears highly ordered and highly aligned with the C60 planes oriented parallel to the substrate in the thin film configuration. The order inside the thin film increases with the EG chain length, allowing the systems to achieve mobilities as high as 0.053 cm2 V−1 s−1. Our work elucidates the structure of these interesting semiconducting organic molecules and shows that the synergistic use of X-ray structural analysis and MD simulations is a powerful tool to identify the structure of thin organic films for optoelectronic applications

Exciton Recombination in Formamidinium Lead Triiodide:Nanocrystals versus Thin Films

The optical properties of the newly developed near-infrared emitting formamidinium lead triiodide (FAPbI3) nanocrystals (NCs) and their polycrystalline thin film counterpart are comparatively investigated by means of steady-state and time-resolved photoluminescence. The excitonic emission is dominant in NC ensemble because of the localization of electron–hole pairs. A promisingly high quantum yield above 70%, and a large absorption cross-section (5.2 × 10−13 cm−2) are measured. At high pump fluence, biexcitonic recombination is observed, featuring a slow recombination lifetime of 0.4 ns. In polycrystalline thin films, the quantum efficiency is limited by nonradiative trap-assisted recombination that turns to bimolecular at high pump fluences. From the temperature-dependent photoluminescence (PL) spectra, a phase transition is clearly observed in both NC ensemble and polycrystalline thin film. It is interesting to note that NC ensemble shows PL temperature antiquenching, in contrast to the strong PL quenching displayed by polycrystalline thin films. This difference is explained in terms of thermal activation of trapped carriers at the nanocrystal's surface, as opposed to the exciton thermal dissociation and trap-mediated recombination, which occur in thin films at higher temperaturesISSN:1613-6810ISSN:1613-682

Rationally designed immunogens enable immune focusing following SARS-CoV-2 spike imprinting

Eliciting antibodies to surface-exposed viral glycoproteins can generate protective responses that control and prevent future infections. Targeting conserved sites may reduce the likelihood of viral escape and limit the spread of related viruses with pandemic potential. Here we leverage rational immunogen design to focus humoral responses on conserved epitopes. Using glycan engineering and epitope scaffolding in boosting immunogens, we focus murine serum antibody responses to conserved receptor binding motif (RBM) and receptor binding domain (RBD) epitopes following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike imprinting. Although all engineered immunogens elicit a robust SARS-CoV-2-neutralizing serum response, RBM-focusing immunogens exhibit increased potency against related sarbecoviruses, SARS-CoV, WIV1-CoV, RaTG13-CoV, and SHC014-CoV; structural characterization of representative antibodies defines a conserved epitope. RBM-focused sera confer protection against SARS-CoV-2 challenge. Thus, RBM focusing is a promising strategy to elicit breadth across emerging sarbecoviruses without compromising SARS-CoV-2 protection. These engineering strategies are adaptable to other viral glycoproteins for targeting conserved epitopes