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At least 955 records · Page 53

A majority of Rhodobacter sphaeroides promoters lack a crucial RNA polymerase recognition feature, enabling coordinated transcription activation

Using an in vitro transcription system with purified RNA polymerase (RNAP) to investigate rRNA synthesis in the photoheterotrophic α-proteobacterium Rhodobacter sphaeroides, we identified a surprising feature of promoters recognized by the major holoenzyme. Transcription from R. sphaeroides rRNA promoters was unexpectedly weak, correlating with absence of 7T, the very highly conserved thymine found at the last position in –10 elements of promoters in most bacterial species. Thymine substitutions for adenine at position –7 in the three rRNA promoters strongly increased intrinsic promoter activity, indicating that R. sphaeroides RNAP can utilize –7T when present. rRNA promoters were activated by purified R. sphaeroides CarD, a transcription factor found in many bacterial species but not in β- and γ-proteobacteria. Overall, CarD increased the activity of 15 of 16 native R. sphaeroides promoters tested in vitro that lacked –7T, whereas it had no effect on three of the four native promoters that contained –7T. Genome-wide bioinformatic analysis of promoters from R. sphaeroides and two other α-proteobacterial species indicated that 30 to 43% contained –7T, whereas 90 to 99% of promoters from non–α-proteobacteria contained –7T. Thus, promoters lacking –7T appear to be widespread in α-proteobacteria and may have evolved away from consensus to enable their coordinated regulation by transcription factors like CarD. We observed a strong reduction in R. sphaeroides CarD levels when cells enter stationary phase, suggesting that reduced activation by CarD may contribute to inhibition of rRNA transcription when cells enter stationary phase, the stage of growth when bacterial ribosome synthesis declines.

59 BASIC BIOLOGICAL SCIENCES↗

Photo-exfoliation of MoS 2 quantum dots from nanosheets: an in-situ transmission electron microscopy study

Fabrication of transition metal dichalcogenide (TMD) quantum dots (QDs) is complex and requires submerging of powders in binary solvents and the constant tuning of wavelength and pulsed frequency of light to achieve a desired reaction. Here,iInstead of liquid state photoexfoliation, we utilize infrared laser irradiation of free-standing MoS 2 flakes in transmission electron microscope (TEM) to achieve solid-state multi-level photoexfoliation of QDs. By investigating the steps involved in photochemical reaction between the surface of MoS 2 and the laser beam, we gain insight into each step of the photoexfoliation mechanism and observe high yield production of QDs, led by an inhomogeneous crystalline size distribution. Additionally, by using a laser with a lower energy than the indirect optical transition of bulk MoS 2 , we conclude that the underlying phenomena behind the photoexfoliation is from multi-photon absorption achieved at high optical outputs from the laser source. These findings provide an environmentally friendly synthesis method to fabricate QDs for potential applications in biomedicine, optoelectronics, and fluorescence sensing.

36 MATERIALS SCIENCE↗

Will high-entropy carbides and borides be enabling materials for extreme environments?

Abstract The concept of multi-principal component has created promising opportunities for the development of novel high-entropy ceramics for extreme environments encountered in advanced turbine engines, nuclear reactors, and hypersonic vehicles, as it expands the compositional space of ceramic materials with tailored properties within a single-phase solid solution. The unique physical properties of some high-entropy carbides and borides, such as higher hardness, high-temperature strength, lower thermal conductivity, and improved irradiation resistance than the constitute ceramics, have been observed. These promising properties may be attributed to the compositional complexity, atomic-level disorder, lattice distortion, and other fundamental processes related to defect formation and phonon scattering. This manuscript serves as a critical review of the recent progress in high-entropy carbides and borides, focusing on synthesis and evaluations of their performance in extreme high-temperature, irradiation, and gaseous environments.

36 MATERIALS SCIENCE↗

Guiding Self-Assembly of Active Colloids by Temporal Modulation of Activity

Self-organization phenomena in ensembles of self-propelled particles open pathways to the synthesis of new dynamic states not accessible by traditional equilibrium processes. The challenge is to develop a set of principles that facilitate the control and manipulation of emergent active states. In this study, we report that dielectric rolling colloids energized by a pulsating electric field self-organize into alternating square lattices with a lattice constant controlled by the parameters of the field. We combine experiments and simulations to examine spatiotemporal properties of the emergent collective patterns and investigate the underlying dynamics of the self-organization.We reveal the resistance of the dynamic lattices to compression and expansion stresses leading to a hysteretic behavior of the lattice constant. The general mechanism of pattern synthesis and control in active ensembles via temporal modulation of activity can be applied to other active colloidal systems.

36 MATERIALS SCIENCE↗

Decontamination and Sterilization of Surfaces using Low Cost Ionic Liquids (CRADA Final Report)

The current study made a comprehensive literature review of the structure activity relationship (SAR) for microcidal and virucidal influence of ionic liquids. It summarized the key structure parameters that have close correlation to the antimicrobial and antiviral properties of the ILs. It proposed an experimental plan on developing and testing an effective ionic liquid from renewable lignocellulosic biomass. The goal is to understand the structure activity relationship (SAR) for virucidal influence of ionic liquids through comprehensive literature search and data analysis. A full experimental plan will be drafted based on the literature summary. Perform a comprehensive literature search to aid the development of an effective and easily deployable method to inactivate SARS-CoV-2 and decontaminate surfaces based on low-cost functional ionic liquids. These designer solvents have the potential to be a compelling and environmentally friendly alternative to common chemical disinfectants. Literature summary report including reported ionic liquid structures, synthesis and testing methods, and the structure activity relationship. Experimental plan on developing a low cost effective antiviral ionic liquid.

59 BASIC BIOLOGICAL SCIENCES↗

The role of defects and solid/liquid interfacial interactions on controlling anisotropic growth of novel two-dimensional materials

Atomic-scale understanding about how interfacial properties are modified in the presence of defects and how they are correlated to the properties of nucleation and growth is critical for controlled materials growth on solid/liquid interfaces. The goal of this proposal is to establish preliminary data on the critical role of surface defects and chemical compositions of solvent on the structure, dynamics, reactivity, and free energetics at graphene/ionic liquid (IL) interfaces and their impact on two-dimensional (2D) growth of transition metal oxides on the surface. This study aims to develop generalized physical/chemical principles for directional growth at solid/liquid interfaces to achieve atomic-level control of two-dimensional materials synthesis. The proposed study of the effects of surface defects on the interfacial structure and reactivity will improve our understanding of the critical roles of heterogeneity, disorder, and solvents on 2D materials synthesis and lead to better control of directional growth of materials at solid/liquid interfaces.

36 MATERIALS SCIENCE↗

EFRC PTL: Photonics at Thermodynamic Limits

The Photonics at Thermodynamic Limits (PTL) EFRC strives to achieve photonic operations at thermodynamic limits by controlling the flow of photons, electrons, and phonons in atomically architected materials, enabling entirely new energy conversion systems. To achieve this mission, the EFRC united leading researchers in layered and nanostructured materials synthesis, electromagnetic theory, first‐principles quantum theory of materials, and advanced characterization of excited state phenomena.

36 MATERIALS SCIENCE↗

Fullerene Negative Ions: Formation and Catalysis

We first explore negative-ion formation in fullerenes C 44 to C 136 through low-energy electron elastic scattering total cross sections calculations using our Regge-pole methodology. Then, the formed negative ions C 44 – to C 136 – are used to investigate the catalysis of water oxidation to peroxide and water synthesis from H 2 and O 2 . The exploited fundamental mechanism underlying negative-ion catalysis involves hydrogen bond strength-weakening/breaking in the transition state. Density Functional Theory transition state calculations found C 60 – optimal for both water and peroxide synthesis, C 100 – increases the energy barrier the most, and C 136 – the most effective catalyst in both water synthesis and oxidation to H 2 O 2 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Investigating the Origin of Bright Materials on Vesta: Synthesis, Conclusions, and Implications

The Dawn spacecraft started orbiting the second largest asteroid (4) Vesta in August 2011, revealing the details of its surface at an unprecedented pixel scale as small as approx.70 m in Framing Camera (FC) clear and color filter images and approx.180 m in the Visible and Infrared Spectrometer (VIR) data in its first two science orbits, the Survey Orbit and the High Altitude Mapping Orbit (HAMO) [1]. The surface of Vesta displays the greatest diversity in terms of geology and mineralogy of all asteroids studied in detail [2, 3]. While the albedo of Vesta of approx.0.38 in the visible wavelengths [4, 5] is one of the highest among all asteroids, the surface of Vesta shows the largest variation of albedos found on a single asteroid, with geometric albedos ranging at least from approx.0.10 to approx.0.67 in HAMO images [5]. There are many distinctively bright and dark areas observed on Vesta, associated with various geological features and showing remarkably different forms. Here we report our initial attempt to understand the origin of the areas that are distinctively brighter than their surroundings. The dark materials on Vesta clearly are different in origin from bright materials and are reported in a companion paper [6].

Li, Jian-Yang↗

DOE Energy Frontier Research Centers Center for Direct Catalytic Conversion of Biomass to Biofuels (C3Bio)

New capabilities to predict, design and control the chemistries of carbon could answer a global imperative to transition from fossil-based to sustainable transportation fuels. While the use of inexpensive hydrocarbons has been an unparalleled achievement and enabler of economic prosperity for many nations, singular dependence upon crude oil has given rise to systemic vulnerabilities in climate, energy, economic, and national security. Lignocellulosic biomass, a renewable and carbon-neutral resource, has the potential to displace an estimated annual equivalent of three billion barrels of oil in the U.S. alone (National Research Council 2009, U. S. Department of Energy, 2011). However, biomass has only one-third the energy density of crude oil (Agrawal and Singh 2009, Richard 2010) and lacks petroleum’s versatility as a feedstock for fuels and chemicals. These limitations keep biomass conversion below the efficiency level needed for strategic impact while the scientific challenge of routing carbon from one molecular context to another remains unmet. In 2009, the Center for Direct Catalytic Conversion of Biomass to Biofuels (C3Bio) recognized the potential of chemical catalysis and fast pyrolysis to overcome such limitations by transforming the main components of biomass (cellulose, xylan, and lignin) from grasses and trees directly to liquid hydrocarbons and aromatic co-products. Enabled by the EFRC high-risk, high-reward approach to grand challenge science, C3Bio researchers have been key national players in disrupting the conventional paradigm of the cellulosic biorefinery into a new future of “no carbon left behind”—the full utilization of carbon from plant cell walls in energy-dense fuels (Fig. 1). We identified catalytic and fast-pyrolytic pathways that utilize cellulose, xylan and, most significantly, lignin. We developed catalytic processes that deoxygenate and transform monomers and isolated polymers into useful products and tested their use with intact biomass. We gained control of lignin synthesis within plants and initiated tailoring biomass to its end-use through the tools of plant molecular biology and genetic engineering. C3Bio breakthroughs have increased the energy density of biomass-derived substrates via catalytic and pyrolytic conversions into products such as benzoquinones, furfural and hydroxymethylfurfural, levoglucosan and levulinic acid, methoxypropylphenols and propylbenzene. Such advances in biomass conversion would not have been possible without simultaneous advances in analytical instrumentation and methodologies, and imaging technologies and applications. The legacy science developed by C3Bio enables design and control strategies for achieving a targeted product portfolio of fuel and chemical feedstocks from a diverse range of native and tailored biomass. Our research provides the knowledge base required for a bio-economy with product streams as diverse in functionality as those of the petrochemical industry. Coupling targeted computational modeling with experimentation, we achieved: (1) fundamental understanding of biopolymers and cell wall architecture assembly, (2) discovery of new chemistries that allow the development of highly selective pathways to fuels and desirable chemicals, and (3) an integrated systems-level understanding to control catalytic and pyrolytic pathways.

09 BIOMASS FUELS↗

Normality of I-V Measurements Using ML

There is an increased interest in instrument-computing ecosystems (ICEs) that support science workflows empowered by AI-automated experiments and computations in diverse areas. In particular, electrochemistry ICEs are promising for accelerating the design and discovery of electrochemical systems for energy storage and conversion, by automating significant parts of workflows that combine synthesis and characterization experiments with computations. They require the integration of flow controllers, solvent containers, pumps, fraction collectors, and potentiostats, all connected to an electrochemical cell, as illustrated in Fig. 1. These are specialized instruments with custom software that is not originally designed for network integration. We developed network and software solutions for electrochemical workflows that adapt system and instrument settings in real-time for multiple rounds of experiments. In particular, we developed Python wrappers for Application Programming Interfaces (APIs) of instrument commands and Pyro client-server modules that enable them to be executed from remote computers. The entire workflow is orchestrated by a Jupyter notebook running on a remote computer.

Al Najjar, Anees↗

Beyond sequence similarity: toward function-based screening of nucleic acid synthesis

Synthetic nucleic acids are a key input to modern biotechnology, yet they represent dual-use materials that require robust screening to mitigate biosecurity risks. The prevailing screening paradigm, which identifies sequences of concern (SoCs) through sequence similarity to controlled pathogens and toxins, may not fully capture risks posed by AI tools that can decouple biomolecular function from reliance on known sequences. Rapidly advancing biodesign capabilities enable the generation of genes and proteins that might evade sequence-based detection. We highlight the critical need for function-based screening approaches that can detect sequences capable of hazardous biological functions, regardless of similarity to known SoCs. We examine the feasibility of function-based screening with an initial focus on proteins, arguing that, while protein sequence space is vast, biologically functional proteins are significantly constrained by biophysical and biochemical requirements that can be learned and modeled. We propose a concrete implementation framework organized along a continuum of complexity, starting with toxins as the most tractable targets before expanding to more complex pathogenic functions. We then discuss open challenges and describe a research and development strategy to address them.

59 BASIC BIOLOGICAL SCIENCES↗

Science-based Acceleration of the Full Value Stream for Metal Additive Manufacturing: Expedited Powder Development in the Area of Aluminum Powder Alloys and their End Use (Final Report)

The overall Science-based Acceleration of the Full Value Stream for Metal Additive Manufacturing (AM): Expedited Powder Development (“X-P4AM”) project objective is to drastically reduce the time-to-market barriers for new additive alloys of interest in automotive and aerospace applications, through computational alloy design with rapid screening and down- selection via synthesis of candidate alloys with rapid solidification. The project will also refine the technology in high pressure gas atomization to improve the production of commercial quantities of selected powders with high powder yields and enhanced powder quality. A new aluminum (Al) alloy based on high entropy composition, enhanced powder production, and optimized AM build parameterization provided a critical step in widespread adoption of AM technology for automotive applications, in this case. The individual backgrounds and capabilities of the Parties are ideally suited to the successful execution of this work. The included work enhanced the Contractors’ AM capabilities, a core competency of the Contractors, and develop a close working relationship with the Participant in the area of aluminum powder alloys and their end use.

36 MATERIALS SCIENCE↗