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At least 595 records · Page 33

Orthogonal replication with optogenetic selection evolves yeast JEN1 into a mevalonate transporter

Abstract The in vivo continuous evolution system OrthoRep (orthogonal replication) is a powerful strategy for rapid enzyme evolution inSaccharomyces cerevisiaethat diversifies genes at a rate exceeding the endogenous genome mutagenesis rate by several orders of magnitude. However, it is difficult to neofunctionalize genes using OrthoRep partly because of the way selection pressures are applied. Here we combine OrthoRep with optogenetics in a selection strategy we call OptoRep, which allows fine-tuning of selection pressure with light. With this capability, we evolved a truncated form of the endogenous monocarboxylate transporterJEN1 (JEN1t)into a de novo mevalonate importer. We demonstrate the functionality of the evolvedJEN1t(JEN1t Y180C/G ) in the production of farnesene, a renewable aviation biofuel, from mevalonate fed to fermentation media or produced by microbial consortia. This study shows that the light-induced complementation of OptoRep may improve the ability to evolve functions not currently accessible for selection, while its fine tunability of selection pressure may allow the continuous evolution of genes whose desired function has a restrictive range between providing effective selection and cellular viability.

Biochemistry & Molecular Biology↗

Tree-based solvers for adaptive mesh refinement code $\scriptsize{FLASH}$ – IV. An X-ray radiation scheme to couple discrete and diffuse X-ray emission sources to the thermochemistry of the interstellar medium

X-ray radiation, in particular radiation between 0.1 and 10 keV, is evident from both point-like sources, such as compact objects and T-Tauri young stellar objects, and extended emission from hot, cooling gas, such as in supernova remnants. The X-ray radiation is absorbed by nearby gas, providing a source of both heating and ionization. While protoplanetary chemistry models now often include X-ray emission from the central young stellar object, simulations of star-forming regions have yet to include X-ray emission coupled to the chemo-dynamical evolution of the gas. We present an extension of the $\scriptsize{TREERAY}$ reverse ray trace algorithm implemented in the flash magnetohydrodynamic code which enables the inclusion of X-ray radiation from 0.1 keV < E γ < 100 keV, dubbed $\scriptsize{XRAYTHESPOT}$. $\scriptsize{XRAYTHESPOT}$ allows for the use of an arbitrary number of bins, minimum and maximum energies, and both temperature-independent and temperature-dependent user-defined cross-sections, along with the ability to include both point and extended diffuse emission and is coupled to the thermochemical evolution. We demonstrate the method with several multibin benchmarks testing the radiation transfer solution and coupling to the thermochemistry. Finally, we show two example star formation science cases for this module: X-ray emission from protostellar accretion irradiating an accretion disc and simulations of molecular clouds with active chemistry, radiation pressure, and protostellar radiation feedback from infrared to X-ray radiation.

79 ASTRONOMY AND ASTROPHYSICS↗

Mixing of Condensable Constituents with H–He during the Formation and Evolution of Jupiter

Simulations of Jupiter's formation are presented that incorporate mixing of H–He with denser material entering the planet as solids. Heavy compounds and gas mix substantially when the planet becomes roughly as massive as Earth, because incoming planetesimals can fully vaporize. Supersaturation of vaporized silicates causes the excess to sink as droplets, but water remains at higher altitudes. Because the mean molecular weight decreases rapidly outward, some of the compositional inhomogeneities produced during formation can survive for billions of years. After 4.57 Gyr, our Jupiter model retains compositional gradients; proceeding outward, one finds (i) an inner heavy-element core, the outer part derived from hot supersaturated rain-out; (ii) a composition-gradient region, containing most of the heavy elements, where H–He abundance increases outward, reaching about 0.9 mass fraction at 0.3 of the radius, with silicates enhanced relative to water in the lower parts and depleted in the upper parts; (iii) a uniform-composition region (neglecting He immiscibility) that is enriched over protosolar and contains most of the planet’s mass; and (iv) an outer region where cloud formation (condensation) of heavy constituents occurs. This radial compositional profile has heavy elements more broadly distributed than predicted by classical formation models but less diluted than suggested by Juno-constrained gravity models. The compositional gradients in the region containing the bulk of the heavy elements prevent convection, in both our models and those fitting current gravity, resulting in a hot interior where much of the accretion energy remains trapped.

79 ASTRONOMY AND ASTROPHYSICS↗

Fullerene Promotes CO 2 Reduction to Methanol by a Cobalt(II) Phthalocyanine Electrocatalyst

Heterogenization of molecular electrocatalysts offers an attractive way to improve the catalytic selectivity and efficiency of CO 2 conversion to liquid fuels. Herein, we employ density functional theory to compare the mechanism of CO 2 RR by a cobalt(II) tetra(amino)phthalocyanine (Co(II)Pc(NH 2 ) 4 ) electrocatalyst with and without the presence of fullerene support. Our DFT calculations suggest that the CO 2 reduction mechanism is initiated by a metal-based electron reduction followed by subsequent CO 2 nucleophilic addition, electron transfer, proton transfer, water dissociation, and proton-coupled electron transfer steps that lead to CO and methanol formation. We show that graphitic interactions between the Co(II)Pc(NH 2 ) 4 electrocatalyst and C 60 support selectively improve the CO 2 RR to methanol at mild potentials. The undesirable hydrogen evolution reaction (HER) was also investigated for both electrocatalysts and proceeds via the protonation of the cobalt metal center over the nitrogen atom in the inner ring. The competition between the HER and the CO 2 RR was improved in favor of CO and methanol formation using the Co(II)Pc(NH 2 ) 4 @C 60 electrocatalyst. Overall, our results suggest C 60 as a promising graphitic support for molecular electrocatalysts integration for CO 2 catalysis.

Alcohols↗

Connectivity between Static Field and Continuous Wave Field Effects on Excitation-Induced H 2 Activation

Due to the tremendous applications of the plasmon resonance excitation process, such as improvements in catalytic efficiency due to plasmonic enhancement and/or hot-electron processes, understanding the mechanism behind these processes has become a popular topic in recent years. In this work, we focus on unraveling the mechanism of excitation-induced H 2 activation using a simplified triangular Au 6 /Ag 6 cluster to investigate the effects of the electric field on electron redistribution and bond activation. We applied both static and continuous wave fields to investigate how these fields affect the systems. Geometrical changes (such as bond lengthening), molecular orbital reordering (affecting the relative energies of orbitals corresponding to hot-electron and charge-transfer excited states), and electronic charge redistribution between the cluster and the adsorbate occur upon application of a static electric field. To study H 2 activation, we apply Ehrenfest dynamics with real-time time-dependent density functional theory and examine how different excitation frequencies and polarizations affect bond activation. Moreover, electron-only dynamics are examined with real-time time-dependent density functional theory, and the time-dependent variations in the orbital populations and electronic transitions provide information about the excitation and relaxation processes of hot electrons with applied electric fields. Here, the static field results represent structures that can be accessed during the evolution of the systems when applying continuous wave fields. Through these studies, the effects of static and continuous wave field effects on plasmon-induced H 2 activation can be understood.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Emergence of two distinct phase transitions in monolayer CoSe2 on graphene

Abstract Dimensional modifications play a crucial role in various applications, especially in the context of device miniaturization, giving rise to novel quantum phenomena. The many-body dynamics induced by dimensional modifications, including electron-electron, electron-phonon, electron-magnon and electron-plasmon coupling, are known to significantly affect the atomic and electronic properties of the materials. By reducing the dimensionality of orthorhombic CoSe 2 and forming heterostructure with bilayer graphene using molecular beam epitaxy, we unveil the emergence of two types of phase transitions through angle-resolved photoemission spectroscopy and scanning tunneling microscopy measurements. We disclose that the 2 × 1 superstructure is associated with charge density wave induced by Fermi surface nesting, characterized by a transition temperature of 340 K. Additionally, another phase transition at temperature of 160 K based on temperature dependent gap evolution are observed with renormalized electronic structure induced by electron-boson coupling. These discoveries of the electronic and atomic modifications, influenced by electron-electron and electron-boson interactions, underscore that many-body physics play significant roles in understanding low-dimensional properties of non-van der Waals Co-chalcogenides and related heterostructures. Graphical Abstract

36 MATERIALS SCIENCE↗

Directly Probing the Fracture Behavior of Ultrathin Polymeric Films

Understanding fracture mechanics of ultrathin polymeric films is crucial for modern technologies, including semiconductor and coating industries. However, up to now, the fracture behavior of sub-100 nm polymeric thin films is rarely explored due to challenges in handling samples and limited testing methods available. In this work, we report a new testing methodology that can not only visualize the evolution of the local stress distribution through wrinkling patterns and crack propagation during the deformation of ultrathin films but also directly measure their fracture energies. Using ultrathin polystyrene films as a model system, we both experimentally and computationally investigate the effect of the film thickness and molecular weight on their fracture behavior, both of which show a ductile-to-brittle transition. Furthermore, we demonstrate the broad applicability of this testing method in semicrystalline semiconducting polymers. We anticipate our methodology described here could provide new ways of studying the fracture behavior of ultrathin films under confinement.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Newly identified sex chromosomes in the Sphagnum (peat moss) genome alter carbon sequestration and ecosystem dynamics

Peatlands are crucial sinks for atmospheric carbon but are critically threatened due to warming climates. Sphagnum (peat moss) species are keystone members of peatland communities where they actively engineer hyperacidic conditions, which improves their competitive advantage and accelerates ecosystem-level carbon sequestration. To dissect the molecular and physiological sources of this unique biology, we generated chromosome-scale genomes of two Sphagnum species: S. divinum and S. angustifolium. Sphagnum genomes show no gene colinearity with any other reference genome to date, demonstrating that Sphagnum represents an unsampled lineage of land plant evolution. The genomes also revealed an average recombination rate an order of magnitude higher than vascular land plants and short putative U/V sex chromosomes. These newly described sex chromosomes interact with autosomal loci that significantly impact growth across diverse pH conditions. This discovery demonstrates that the ability of Sphagnum to sequester carbon in acidic peat bogs is mediated by interactions between sex, autosomes and environment.

59 BASIC BIOLOGICAL SCIENCES↗

Practical quantum computation of chemical and nuclear energy levels using quantum imaginary time evolution and Lanczos algorithms

Various methods have been developed for the quantum computation of the ground and excited states of physical and chemical systems, but many of them require either large numbers of ancilla qubits or high-dimensional optimization in the presence of noise. The quantum imaginary-time evolution (QITE) and quantum Lanczos (QLanczos) methods proposed in Motta et al. (2020) eschew the aforementioned issues. In this study, we demonstrate the practical application of these algorithms to challenging quantum computations of relevance for chemistry and nuclear physics, using the deuteron-binding energy and molecular hydrogen binding and excited state energies as examples. With the correct choice of initial and final states, we show that the number of timesteps in QITE and QLanczos can be reduced significantly, which commensurately simplifies the required quantum circuit and improves compatibility with NISQ devices. We have performed these calculations on cloud-accessible IBM Q quantum computers. With the application of readout-error mitigation and Richardson error extrapolation, we have obtained ground and excited state energies that agree well with exact results obtained from diagonalization.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Simultaneous velocity and density measurements of fully developed Rayleigh-Taylor mixing

Here, the dynamics of molecular mixing and the energy transfer process in the Rayleigh-Taylor instability (RTI) are studied through the collection of simultaneous density-velocity measurements. These experiments provide simultaneous density-velocity field measurements, in contrast to previous point measurements. Statistically stationary experiments are performed in a “convective-type” gas tunnel facility, with density contrast achieved through the injection of helium into the bottom stream. Three experiments at Atwood number ≈ 0.1 are captured at three outer scale Reynolds numbers Re = 520, 2260, and 4050. Particle image velocimetry and laser induced fluorescence are employed simultaneously. Statistics of the density and velocity show self-similar collapse of RTI profiles at large Reynolds number Re >2000. Flat velocity profiles indicate homogeneous turbulence characteristics in the core of the mixing region. Significant anisotropy develops in the flow, with horizontal velocity fluctuations being only 60% of the vertical velocity fluctuations. The turbulent mass flux is found to be asymmetric about the centerline, with increased peak towards the spike. Measurements of the molecular mixing show that mixing is maximized at the core of the flow and increases with increased Reynolds number. The transport equation of density-specific-volume correlation b shows that it is mostly produced in the core of the mixing region, and that the spatial evolution of its profile is the result of transport by bulk motion of the bubble and spike. Energy transfer from gravitational potential energy to turbulent kinetic energy and viscous dissipation is observed to occur in the experiment with a ratio of dissipated energy to potential energy released of 38%. The analysis of the turbulent kinetic energy transport equation budget reveals that production is the primary mechanism towards the growth of turbulent kinetic energy in the core of the flow, and is asymmetrically slightly skewed towards the spike. However, it is through the transport that the strong advection at the edges of the mixing region is maintained.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Guanosine Dianions Hydrated by One to Four Water Molecules

Intermolecular interactions as those present in molecule…water complexes may profoundly influence the physico-chemical properties of molecules. Here, we carried out an experimentally-computational study on the doubly-deprotonated guanosine monophosphate…water clusters, [dGMP-2H] 2- •nH 2 O (n=1–4), using a combination of negative anion photoelectron spectroscopy (NIPES) with molecular dynamics (MD) and quantum chemical (QM) calculations. Successive addition of water molecules to [dGMP-2H] 2- increases the experimental adiabatic detachment (ADE) and vertical detachment energy (VDE) by 0.5 to 0.1 eV, depending on the cluster size. In order to choose the representative conformations, we combined MD simulations with a clustering procedure to identify low energy geometries for which ADEs and VDEs were computed at the CAM-B3LYP/6-31++G(d,p) level. Our results demonstrate that the assumed approach lead to the sound geometries and energetics of the studied micro-solvates since the calculated ADEs and VDEs are in pretty good agreement with the experimental characteristics. The evolution of hydrogen bonding with cluster size indicates possibility of the occurrence of proton transfer for clusters comprising a larger number of water molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multiscale Modeling and Experimental Insights into High-Temperature Soil Biodegradation Dynamics of Semi-Crystalline Poly(Lactic Acid) Nonwoven Fabrics

This study investigates the biodegradation of semi-crystalline poly(lactic acid) (PLA) nonwovens (NWs) in soil at 58 °C using both experimental and mathematical modeling approaches. The model utilizes a system of parabolic diffusion-reaction partial differential equations (PDEs) to elucidate chemical transformations over time and in space. It accounts for phenomena such as the diffusion of water and lactic acid monomers through the polymer matrix and into the surrounding soil, along with their microbial breakdown. It also accounts for the initial PLA crystallinity and predicts its evolution in time. The model is solved numerically for a single filament, and the results were used to shed light on PLA NW transformations observed in soil over a 180-day incubation period. Various characterization techniques, including scanning electron microscopy (SEM), differential scanning calorimetry (DSC), and Raman spectroscopy, were employed to assess morphological changes, crystallinity, and molecular changes in the NWs throughout the experiment. By comparing the experimental data with the model predictions, the hydrolysis rate coefficient was found to be 3.37 × 10 -7 s -1 , while the rate of microbial degradation of lactic acid monomers was faster, of the order of 9.63 × 10 -7 s -1 . The findings highlight the significant role of crystallinity in the biodegradation process. The PLA degradation ceases when no amorphous material remains, and the crystallinity reaches 0.8, as observed in the experiments by day 120. Furthermore, this research contributes to a deeper understanding of PLA biodegradation dynamics and offers insights for effectively managing biodegradable materials in environmental settings.

Diffusion−reaction modeling↗

Investigation of the Origins of Comets as Revealed through Infrared High-resolution Spectroscopy I. Molecular Abundances

We report and analyze updated molecular abundances in 20 comets obtained by employing modern data reduction procedures and molecular models. Using box and scatter plots, we examine how the different molecular species are distributed among the comet population, while by means of pie charts, we investigate the relative proportions of these molecular species in each comet. We compare these results with the orbital parameters of the selected comets to identify trends related to their dynamical history. With these analyses, we tentatively identify at least three chemical classes based mainly on relative abundances of CO, CH{sub 3}OH, CH{sub 4}, C{sub 2}H{sub 6}, HCN, and NH{sub 3}. The combination of relative abundances and orbital parameters is then compared with recent chemical models of planetary system formation. This approach may help in investigating the origins and evolution of the material in cometary nuclei. Among other aspects, we underline the need to increase our sample size, especially for hypervolatiles (i.e., CH{sub 4} and CO) in Jupiter family comets.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure–property relationships of reduced graphene oxide membranes intercalated with polycyclic aromatics

Graphene oxide (GO) membranes intercalated with various organic moieties have shown excellent potential for a range of water processing applications. However, microstructure–functional property relationships in these structurally disordered membranes are not well understood. We demonstrate a practical methodology for developing such relationships for GO membranes intercalated with molecular species, with polycyclic aromatic toluidine blue O (TBO) as an example functional intercalant. We use solid-state UV–vis absorbance and fluorescence measurements to quantitatively track the arrangements of TBO in a series of TBO-loaded reduced GO (rGO) membranes. This study reveals the evolution of diverse arrangements including TBO monomers, lateral and stacked dimers, and other aggregates, as a function of overall TBO loading. These microstructures are then correlated to changes in overall properties such as interlayer d-spacings, permeate fluxes, and solute rejections. The characterization of these different intercalant microstructures explains non-intuitive flux and rejection trends, which can circumvent flux and solute rejection trade-offs.

02 PETROLEUM↗

Concerted Proton–Electron Transfer Minimizes Substituent Effects on Adsorbed Phthalocyanine Electrocatalysis

Molecularly modified electrodes (MMEs) are potent electrocatalysts, but few principles exist for their rational design. Electrocatalysis by soluble molecules depends strongly on substituents that tune the catalyst redox potential (E 1/2 ), but it is unclear if this parameter similarly impacts MME catalysis. Herein, we employ the hydrogen evolution reaction (HER) as a test case for comparing carbon-adsorbed cobalt phthalocyanine (CoPc/C) and cobalt hexadecafluoro-phthalocyanine (CoFPc/C). By correlating HER activity and voltammetric data to total Co surface concentration across a wide range of catalyst loadings, we find that only 5–25% of adsorbed Co sites contribute to the Co(II/I) redox wave and that this subpopulation poorly correlates with catalytic activity. Instead, in the low-loading limit, catalytic activity correlates linearly with the majority Co(II/I)-silent Co population, revealing per-site turnover frequency (TOF) values for HER. Despite a 230 mV difference in Co(II/I) redox potentials, CoPc/C and CoFPc/C display TOF values differing by less than a factor of 3 when compared over a wide potential range. Mechanistic studies point to an inner-sphere concerted proton–electron transfer step as rate-determining, suggesting that the Co–H bond dissociation free energy (BDFE) rather than the Co(II/I) E 1/2 is thermodynamically relevant. Computational studies indicate that the fluoro-substituents lead to compensatory changes in Co(II/I) E 1/2 and Co(I) basicity, leaving the Co–H BDFE largely unchanged between CoPc and CoFPc and thereby manifesting in similar catalytic rates. Furthermore, these results highlight the limited effect of E 1/2 -tuning on MME catalytic activity and motivate the development of methods to directly alter active site–substrate BDFE.

Catalysts↗

Role of the Character of the Excited State of Singly Reduced Rh 2 (II,II) Intermediates on Photocatalytic Activity

Singly reduced intermediates have recently been implicated as photoactive intermediates in a number of important reactions; however, their photophysical properties remain poorly understood. A series of dirhodium(II,II) complexes, cis-[Rh 2 (p-R-Form) 2 (bncn) 2 ] 2+ (bncn = benzo[c]cinnoline; p-R-Form = N,N′-di-p-R-phenylformamidinate), where R = −OCH 3 (1), −CH 3 (2), −H (3), −F (4), −Cl (5), and −CF 3 (6), and their respective radical anions were prepared and their excited state properties were investigated. Complex 3 acted as a singlemolecule photocatalyst for H 2 production with red light. Substitution on the formamidinate ligands in 1−6 affected the energy of the Rh 2 (δ*)/Form(π,nb) highest occupied molecular orbital (HOMO), consistent with the metal/ligand-to-ligand charge transfer ( 1 ML-LCT) absorption maxima and the 3 ML-LCT excited state lifetime, ranging from 1.6 ns in 1 to 54 ns in 6 in CH 3 CN. The highest turnover number for photocatalytic H 2 evolution was observed for 3, and the lowest values were for 1 and 6. The radical anion, [Rh 2 ] − , formed during photocatalysis, was shown to absorb a photon and undergo a second reduction. The lifetimes of the doublet excited states of [3] − and [6] − were 0.49 and 0.24 ns, respectively. Calculations showed that the lowest energy excited state in [3] − was 2 ML-LCT, whereas that in [6] − was a bncn − → Rh 2 (σ*) ligand-to-metal charge transfer ( 2 LMCT) state. The 2 LMCT state stabilized across the series from [1] − to [6] − , pointing at its role in modulating the photophysical properties. This work highlights the importance of the reductive quenching of [Rh 2 ] − and the generation of the doubly reduced species to effectively catalyze hydrogen evolution.

Absorption↗

Fundamental Investigations into the Properties and Performance of Advanced Materials

Intelligent engineering designs require an accurate understanding of material behavior, since any uncertainties or gaps in knowledge must be counterbalanced with heightened factors of safety, leading to overdesign. Therefore, building better structures and pushing the performance of new components requires an improved understanding of the thermomechanical response of advanced materials under service conditions. This dissertation provides fundamental investigations of several advanced materials: thermoset polymers, a common matrix material for fiber-reinforced composites and nanocomposites; aluminum alloy 7075-T6 (AA7075-T6), a high-performance aerospace material; and ceramic matrix composites (CMCs), an advanced composite for extreme-temperature applications. To understand matrix interactions with various interfaces and nanoinclusions at their fundamental scale, the properties of thermoset polymers are studied at the atomistic scale. An improved proximity-based molecular dynamics (MD) technique for modeling the crosslinking of thermoset polymers is carefully established, enabling realistic curing simulations through its ability to dynamically and probabilistically perform complex topology transformations. The proximity-based MD curing methodology is then used to explore damage initiation and the local anisotropic evolution of mechanical properties in thermoset polymers under uniaxial tension with an emphasis on changes in stiffness through a series of tensile loading, unloading, and reloading experiments. Aluminum alloys in aerospace applications often require a fatigue life of over 109 cycles, which is well over ii the number of cycles that can be practically tested using conventional fatigue testing equipment. In order to study these high-life regimes, a detailed ultrasonic cycle fatigue study is presented for AA7075-T6 under fully reversed tension-compression loading. The geometric sensitivity, frequency effects, size effects, surface roughness effects, and the corresponding failure mechanisms for ultrasonic fatigue across different fatigue regimes are investigated. Finally, because CMCs are utilized in extreme environments, oxidation plays an important role in their degradation. A multiphysics modeling methodology is thus developed to address the complex coupling between oxidation, mechanical stress, and oxygen diffusion in heterogeneous carbon fiber-reinforced CMC microstructures.

Schichtel, Jacob J.↗

Coordinate transformation methodology for simulating quasistatic elastoplastic solids

Molecular dynamics simulations frequently employ periodic boundary conditions where the positions of the periodic images are manipulated in order to apply deformation to the material sample. For example, Lees-Edwards conditions use moving periodic images to apply simple shear. Here, we examine the problem of precisely comparing this type of simulation to continuum solid mechanics. We employ a hypo-elastoplastic mechanical model, and develop a projection method to enforce quasi-static equilibrium. We introduce a simulation framework that uses a fixed Cartesian computational grid on a reference domain, and imposes deformation via a time-dependent coordinate transformation to the physical domain. As a test case for our method, we consider the evolution of shear bands in a bulk metallic glass using the shear transformation zone theory of amorphous plasticity. We examine the growth of shear bands in simple shear and pure shear conditions as a function of the initial preparation of the bulk metallic glass.

74 ATOMIC AND MOLECULAR PHYSICS↗