171 Search Results

Silicon carbide (SiC) divacancies are attractive candidates for spin-defect qubits possessing long coherence times and optical addressability. The high activation barriers associated with SiC defect formation and motion pose challenges for their study by first-principles molecular dynamics. In this work, we develop and deploy machine learning interatomic potentials (MLIPs) to accelerate defect dynamics simulations while retaining ab initio accuracy. We employ an active learning strategy comprising symmetry-adapted collective variable discovery and enhanced sampling to compile configurationally diverse training data, calculation of energies and forces using density functional theory (DFT), and training of an E(3)-equivariant MLIP based on the Allegro model.more » Here, the trained MLIP reproduces DFT-level accuracy in defect transition activation free energy barriers, enables the efficient and stable simulation of multidefect 216-atom supercells, and permits an analysis of the temperature dependence of defect thermodynamic stability and formation/annihilation kinetics to propose an optimal annealing temperature to maximally stabilize VV divacancies.« less

Multidrug efflux pumps are dynamic molecular machines that drive antibiotic resistance by harnessing ion gradients to export chemically diverse substrates. Despite their clinical importance, the molecular principles underlying multidrug promiscuity and energy efficiency remain poorly understood. Using multiparametric deep mutational scanning across eight substrates and two energy conditions, we deconvolute the contributions of substrate recognition, energetic coupling, and protein stability, providing an integrated, high-resolution view of multidrug transport. We find that substrate specificity arises from a distributed network of residues extending beyond the binding site, with mutations that reshape binding, coupling, conformational flexibility, and membrane interactions. Further, we apply amore » pH-based selection scheme to measure the effect of mutation on pH-dependent transport efficiency. By integrating these data, we reveal a fundamental relationship between efficiency and promiscuity: Highly efficient variants exhibit broad substrate profiles, while inefficient variants are narrower. In conclusion, these findings establish a direct link between energy coupling and polyspecificity, uncovering the biochemical logic underlying multidrug transport.« less

We report a water-soluble conjugated oligoelectrolyte (COE) composed of carbazole-benzophenone, COE-CbzBP, that exhibits photogenerated spin-correlated radical pair (SCRP) behavior sensitive to static electric fields from DNA but not from lipid bilayers. The SCRP forms from a thermally activated, spin-polarized state enabled by partial π-conjugation disruption at the donor–acceptor (carbazole-benzophenone) nitrogen–carbon (N–C) junction, which facilitates a twisted intramolecular charge-transfer (TICT) geometry. This state minimizes the singlet–triplet energy gap (ΔE_ST = 0.12 eV), radical–pair exchange coupling (J_RP ∼ ΔE_ST/2), and charge separation free energy (ΔG_CS) in both DNA (−0.19 eV) and lipid bilayers (−0.55 eV). Room-temperature continuous-wave electron paramagnetic resonance (CW-EPR) revealsmore » a photogenerated spin-polarized singlet for COE-CbzBP that splits upon DNA association, consistent with modulation of J_RP and hyperfine coupling (A_x), presumably via electric field-spin coupling. No spin-polarized signal was observed under dark, cryogenic conditions, or in liposomes, but was quenched by the spin trap 4-POBN. Transient absorption and spectroelectrochemistry confirmed magnetic-field sensitive long-lived excited-state absorption features attributed to charge-separated states ³[Cbz^•+-BP^•–]*, which were lengthened by DNA, and quenched in lipid bilayers and 4-POBN. Quantum chemical simulations show that planar geometries (lipid-like) increase ΔE_ST by 0.31 eV compared to TICT-optimized structures. This geometry-dependent modulation explains the absence of SCRP signatures in rigid environments, underscoring the importance of TICT states, minimized ΔE_ST, and favorable ΔG_CS for achieving room-temperature SCRP generation. These findings establish design principles for TICT-enabled molecules exhibiting qubit-like behavior that operate under ambient and biologically relevant conditions, with direct implications for quantum information science (QIS).« less

Functional group migration (FGM) reactions represent a fundamental class of transformations in organic chemistry, enabling the repositioning of functional moieties in nonobvious ways. However, catalytic asymmetric radical-mediated FGMs remain rare due to the inherent challenges of achieving catalyst-controlled enantioselectivity over free radical intermediates. Herein, we repurpose imine reductases (IREDs), a class of biotechnologically important enzymes known for their substrate promiscuity, to enable the first examples of catalytic asymmetric cyano group migration via a radical mechanism. An orthogonal set of radical enzymes, including PbaIREDCym and SmiIREDCym, was engineered, allowing both 1,4- and 1,5-cyano group migration reactions to occur in an enantiodivergentmore » fashion. The use of the nonionic surfactant TPGS-1000 was found to improve both the yield and enantioselectivity of these cyano migration reactions. Furthermore, this biocatalytic process exhibited a broad substrate scope and is readily scalable, affording a rare example of chiral nonamine product assembly with imine reductases. More broadly, stereoselective radical biocatalysis with engineered IREDs and other versatile enzymes provides a potentially general solution to challenging asymmetric FGM reactions.« less

Achieving precise control over quantitative developmental phenotypes is a key objective in plant biology. Recent advances in synthetic biology have enabled tools to reprogram entire developmental pathways; however, the complexity of designing synthetic genetic programs and the inherent interactions between various signaling processes remains a critical challenge. Here, we leverage Type-B response regulators to modulate the expression of genes involved in cytokinin-dependent growth and development processes. We rationally engineered these regulators to modulate their transcriptional activity (i.e., repression or activation) and potency while reducing their sensitivity to cytokinin. By localizing the expression of these engineered transcription factors using tissue-specific promoters,more » we can predictably tune cytokinin-regulated traits. As a proof of principle, we deployed this synthetic system in Arabidopsis thaliana to either decrease or increase the number of lateral roots. The simplicity and modularity of our approach makes it an ideal system for controlling other developmental phenotypes of agronomic interest in plants.« less

DNA-programmable self-assembly enables the formation of nanoparticle crystals with controlled lattice symmetry. While this approach offers the formation of complexly ordered nanostructures for optical, mechanical, and biological applications, a mesoscale control over such nanomaterials is limited. Directing the material formation process through the assembly pathway or external fields allows for modulating crystal morphology, but achieving arbitrary morphology remains challenging. Here, we present a photothermal method for shaping 3D DNA-programmable crystals of gold nanoparticles. Through local heating of nanoparticles due to plasmonic light absorption, we induce targeted volumetric dissolution of specifically defined crystal areas with micron-scale accuracy. This technique effectively prescribesmore » crystal shaping and creates arbitrarily shaped voids within crystals. We further investigate both computationally and experimentally the key factors governing volumetric material subtraction. The developed automated light-milling platform enables the fabrication of nanomaterials exhibiting both DNA-programmable nanoscale order and custom-designed mesoscale architecture.« less

Cyanobacteria are promising microbial platforms for a diverse set of biotechnology applications, from living materials to photosynthetic chemical production, but are less well characterized than commonly engineered microbes such as Escherichia coli. This study facilitates genetic engineering in Synechococcus sp. PCC 7002, a fast-growing, halotolerant, and naturally competent strain, by identifying ten native methylation motifs and designing shuttle strains that mimic the native methylation state by expressing a subset of heterologous methyltransferases. DNA methylation in E. coli with as few as two active methyltransferases increased transformation efficiency up to 30-fold across four distinct integration sites in PCC 7002. This workmore » provides an experimental framework to bypass native restriction-modification systems for efficient genome editing and metabolic engineering in nonmodel bacteria.« less

Solid-state electrolytes (SSEs) require ionic conductivities that are competitive with liquid electrolytes to realize applications in all-solid-state batteries. Although candidate SSEs have been discovered, the underlying mechanisms enabling superionic conduction (>1 mS cm^–1) remain elusive. In particular, the role of ultrafast lattice dynamics in mediating ion migration, which involves couplings between ions, phonons, and electrons, is rarely explored experimentally at their corresponding time scales. To investigate the complex contributions of coupled lattice dynamics on ion migration, we modulate the charge density occupations within the crystal framework and then measure the time-resolved change in impedance on picosecond time scales for amore » candidate SSE, Li_0.5La_0.5TiO₃ (LLTO). Upon perturbation, we observe enhanced ion migration at ultrafast time scales. The respective transients match the time scales of optical and acoustic phonon vibrations, suggesting their involvement in ion migration. We further computationally evaluate the effect of a charge transfer from the O 2p to the Ti 3d band on the electronic and physical structure of LLTO. We hypothesize that the charge-transfer excitation distorts the TiO₆ polyhedra by altering the local charge density occupancy of the hopping site at the migration pathway saddle point, thereby causing a reduction in the migration barrier for the Li⁺ hop. We rule out the contribution of photogenerated electron carriers and laser heating. Overall, our investigation introduces a new spectroscopic tool to probe fundamental ion hopping mechanisms transiently at ultrafast time scales, which has previously only been achieved in a time-averaged manner or solely via computational methods.« less

Carboxysomes are polyhedral protein organelles that microorganisms use to facilitate carbon dioxide assimilation. They are composed of a modular protein shell that envelops an enzymatic core mainly composed of physically coupled Rubisco and carbonic anhydrase. While the modular construction principles of carboxysomes make them attractive targets as customizable metabolic platforms, their size and complexity can be a hindrance. In this work, we design and validate a plasmid set, the pXpressome toolkit, in which α-carboxysomes are robustly expressed and remain intact and functional after purification. We tested this toolkit by introducing mutations that influence carboxysome structure and performance. We find thatmore » deletion of vertex-capping genes results in formation of larger carboxysomes, while deletion of facet forming genes produces smaller particles, suggesting that adjusting the ratio of these proteins can rationally affect morphology. Through a series of fluorescently labeled constructs, we observe that this toolkit leads to more uniform expression and better cell health than previously published carboxysome expression systems. Overall, the pXpressome toolkit facilitates the study and redesign of carboxysomes with robust performance and improved phenotype uniformity. The pXpressome toolkit will support efforts to remodel carboxysomes for enhanced carbon fixation or serve as a platform for other nanoencapsulation goals.« less

Fabrication of ordered mesoporous materials (OMMs) has predominantly relied on templating-based methods. However, these methods are constrained by several limitations, especially the limited pore sizes attainable with commercially available surfactants used as structure-directing agents. To unlock the full potential of the OMMs, it is essential to develop synthetic strategies that facilitate the production of large-pore OMMs using scalable processes and cost-effective precursors. This work demonstrates the use of thermoplastic elastomer (TPE)-derived carbon replicas for synthesizing ordered mesoporous silica (OMS) and metal oxides (OMMOs) via precursor infiltration and template removal. The nanostructural evolution of the resulting inorganic materials was systematically investigated.more » Specifically, using tetraethyl orthosilicate (TEOS) as a silica precursor, this method can produce an OMS with relatively large pores. To establish the generalizability of this process, the fabrication approach was extended to other commercially available TPEs with varied chemical compositions and molecular weights while consistently resulting in ordered structures. Additionally, this synthetic strategy can be successfully applied to the production of OMMOs, including tin and titanium oxide matrix chemistries, yielding pore sizes of 16.0 and 19.2 nm, respectively. By developing a general method and using low-cost precursors, this work presents a scalable approach for fabricating large-pore OMMs with tunable pore textures and matrix chemistries.« less