Chemical and Biomolecular Engineering

Metallic materials under high stress often exhibit deformation localization, manifesting as slip banding. Over seven decades ago, Frank and Read introduced the well-known model of dislocation multiplication at a source, explaining slip band formation. Here, we reveal two distinct types of slip bands (confined and extended) in compressed CrCoNi alloys through multi-scale testing and modeling from microscopic to atomic scales. The confined slip band, characterized by a thin glide zone, arises from the conventional process of repetitive full dislocation emissions at Frank-Read source. Contrary to the classical model, the extended band stems from slip-induced deactivation of dislocation sources, followed by consequent generation of new sources on adjacent planes, leading to rapid band thickening. Our findings provide insights into atomic-scale collective dislocation motion and microscopic deformation instability in advanced structural materials.

As an emerging technology, polymer electrolyte fuel cells (PEFCs) powered by clean hydrogen can be a great source of renewable power generation with flexible utilization because of high gravimetric energy density of hydrogen. To be used in real-life applications, PEFCs need to maintain their performance for long-term use under a wide range of conditions. Therefore, it's important to understand the degradation of the PEFC under protocols that are closely related to the catalyst lifetime. Alloying Pt with transitional metal improves catalyst activity. It is also crucial to understand Pt alloys degradation mechanisms to improve their durability. To study durability of Pt alloys, accelerated stress tests (ASTs) are performed on Pt−Co catalyst supported on two types of carbon. Two different AST protocols were being studied: Membrane Electrolyte Assembly (MEA) AST based on the protocol introduced by the Million Mile Fuel Cell Truck consortium in 2023 and Catalyst AST, adopted from the U.S. Department of Energy (DoE).

Oxide-based ferroelectric tunnel junctions (FTJs) show promise for nonvolatile memory and neuromorphic applications, making their integration with existing semiconductor technologies highly desirable. Furthermore, resistance fatigue in current silicon-based integration remains a critical issue. Understanding this fatigue mechanism in semiconductor-integrated FTJ is essential yet unresolved. Here, we systematically investigate the fatigue performance of ultrathin bismuth ferrite BiFeO3 (BFO)-based FTJs integrated with various semiconductors. Notably, the BFO/gallium arsenide FTJ exhibits superior fatigue resistance characteristics (>108 cycles), surpassing the BFO/silicon FTJ (>106 cycles) and even approaching epitaxial oxide FTJs (>109 cycles). The atomic-scale fatigue mechanism is revealed as lattice structure collapse caused by oxygen vacancy accumulation in BFO near semiconductors after repeated switching. The enhanced fatigue-resistant behavior in BFO/gallium arsenide FTJ is due to gallium arsenides weak oxygen affinity, resulting in fewer oxygen vacancies. These findings provide deeper insights into the atomic-scale fatigue mechanism of semiconductor-integrated FTJs and pave the way for fabricating fatigue-resistant oxide FTJs for practical applications.

Biology provides many sources of inspiration for synthetic and multifunctional nanomaterials. Naturally evolved proteins exhibit specialized, sequence-defined functions and self-assembly behavior. Recapitulating their molecularly defined self-assembly behavior, however, is challenging in de novo proteins. Peptides, on the other hand, represent a more well-defined and rationally designable space with the potential for sequence-programmable, stimuli-responsive design for structure and function, making them ideal building blocks of bioelectronic interfaces. In this work, we design peptides that exhibit stimuli-responsive self-assembly and the capacity to transport electrical current over micrometer-long distances. A lysine-lysine (KK) motif inserted at solvent-exposed positions of a coiled-coil-forming peptide sequence introduces pH-dependent control over a transition from unordered to α-helical peptide structure. The ordered state of the peptide serves as a building block for the assembly of coiled coils and higher-order assemblies. Cryo-EM structures of these structures reveal a hierarchical organization of α-helical peptides in a cross coiled coil (CCC) arrangement. Structural analysis also reveals a β-sheet fiber phase under certain conditions and placements of the KK motif, revealing a complex and sensitive self-assembly pathway. Both solid-state and solution-based electrochemical characterizations show that CCC fibers are electronically conductive. Single-fiber conductive AFM measurement indicates that the solid-state electrical conductivity is comparable with bacterial cytochrome filaments. Solution-deposited fiber films approximately doubled the electroactive surface area of the electrode, confirming their conductivity in aqueous environments. This work establishes a stimuli-responsive peptide sequence element for balancing the order-disorder transitions in peptides to control their self-assembly into highly organized electronically conductive nanofibers.

Understanding bacterial physiology in real-world environments requires noninvasive approaches and is a challenging yet necessary endeavor to effectively treat infectious disease. Bacteria evolve strategies to tolerate chemical gradients associated with infections. The DIVER (Deep Imaging Via Enhanced Recovery) microscope can image autofluorescence and fluorescence lifetime throughout samples with high optical scattering, enabling the study of naturally formed chemical gradients throughout intact biofilms. Using the DIVER, a long fluorescent lifetime signal associated with reduced pyocyanin, a molecule for electron cycling in low oxygen, was detected in low-oxygen conditions at the surface of Pseudomonas aeruginosa biofilms and in the presence of fermentation metabolites from Rothia mucilaginosa, which cocolonizes infected airways with P. aeruginosa. These findings underscore the utility of the DIVER microscope and fluorescent lifetime for noninvasive studies of bacterial physiology within complex environments, which could inform on more effective strategies for managing chronic infection.

Understanding bacterial physiology in real-world environments requires noninvasive approaches and is a challenging yet necessary endeavor to effectively treat infectious disease. Bacteria evolve strategies to tolerate chemical gradients associated with infections. The DIVER (Deep Imaging Via Enhanced Recovery) microscope can image autofluorescence and fluorescence lifetime throughout samples with high optical scattering, enabling the study of naturally formed chemical gradients throughout intact biofilms. Using the DIVER, a long fluorescent lifetime signal associated with reduced pyocyanin, a molecule for electron cycling in low oxygen, was detected in low-oxygen conditions at the surface of Pseudomonas aeruginosa biofilms and in the presence of fermentation metabolites from Rothia mucilaginosa, which cocolonizes infected airways with P. aeruginosa. These findings underscore the utility of the DIVER microscope and fluorescent lifetime for noninvasive studies of bacterial physiology within complex environments, which could inform on more effective strategies for managing chronic infection.

Recent studies have reported long-range charge transport in peptide- and protein-based fibers and wires, rendering this class of materials as promising charge-conducting interfaces between biological systems and electronic devices. In the complex molecular environment of biomolecular building blocks, however, it is unclear which chemical and structural dynamic features support electronic conductivity. Here, we investigate the role of finite temperature fluctuations on the electronic structure and its implications for conductivity in a peptide-based fiber material composed of an antiparallel coiled coil hexamer, ACC-Hex, building block. All-atom classical molecular dynamics (MD) and first-principles density functional theory (DFT) are combined with interpretable machine learning (ML) to understand the relationship between physical and electronic structure of the peptide dimer subunit of ACC-Hex. For 1101 unique MD "snapshots" of the ACC peptide dimer, hybrid DFT calculations predict a significant variation of near-gap orbital energies among snapshots, with an increase in the predicted number of nearly degenerate states near the highest occupied molecular orbital (HOMO), which suggests improved conductivity. Interpretable ML is then used to investigate which nuclear conformations increase the number of nearly degenerate states. We find that molecular conformation descriptors of interphenylalanine distance and orientation are, as expected, highly correlated with increased state density near the HOMO. Unexpectedly, we also find that descriptors of tightly coiled peptide backbones, as well as those describing the change in the electrostatic environment around the peptide dimer, are important for predicting the number of hole-accessible states near the HOMO. Our study illustrates the utility of interpretable ML as a tool for understanding complex trends in large-scale ab initio simulations.

The reactions critical for the energy transition center on the chemistry of hydrogen, oxygen, carbon, and the heterogeneous catalyst surfaces that make up electrochemical energy conversion systems. Together, the surface-adsorbate interactions constitute the electrochemical interphase and define reaction kinetics of many clean energy technologies. Practical devices introduce high levels of complexity where surface roughness, structure, composition, and morphology combine with electrolyte, pH, diffusion, and system level limitations to challenge our ability to deconvolute underlying phenomena. To make significant strides in materials design, a structured approach based on well-defined surfaces is necessary to selectively control distinct parameters, while complexity is added sequentially through careful application of nanostructured surfaces. In this review, we cover advances made through this approach for key elements in the field, beginning with the simplest hydrogen oxidation and evolution reactions and concluding with more complex organic molecules. In each case, we offer a unique perspective on the contribution of well-defined systems to our understanding of electrochemical energy conversion technologies and how wider deployment can aid intelligent materials design.

Atomic polarizabilities are considered to be fundamental parameters in polarizable molecular mechanical force fields that play pivotal roles in determining model transferability across different electrostatic environments. In an earlier work, the atomic polarizabilities were obtained by fitting them to the B3LYP/aug-cc-pvtz molecular polarizability tensors of mainly small molecules. Taking advantage of the recent PCMRESPPOL method, we refine the atomic polarizabilities for condensed-phase simulations using a polarizable Gaussian Multipole (pGM) force field. Departing from earlier works, in this work, we incorporated polarizability tensors of a large number of dimers and electrostatic potentials (ESPs) in multiple solvents. We calculated 1565 × 4 ESPs of small molecule monomers and dimers of noble gas and small molecules and 4742 × 4 ESPs of small molecule dimers in four solvents (diethyl ether, ε = 4.24, dichloroethane, ε = 10.13, acetone, ε = 20.49, and water, ε = 78.36). For the gas-phase polarizability tensors, we supplemented the molecule set that was used in our earlier work by adding both the 4252 monomer and dimer sets studied by Shaw and co-workers and the 7211 small molecule monomers listed in the QM7b database to a combined total of 13,523 molecular polarizability tensors of monomers and dimers. The QM7b polarizability set was obtained from quantum-machine.org and was calculated at the LR-CCSD/d-aug-cc-pVDZ level of theory. All other polarizability tensors and all ESPs were calculated at the ωB97X-D/aug-cc-pVTZ level of theory. The atomic polarizabilities were developed using all polarizability tensors and the 1565 × 4 ESPs of small molecule monomers and were then assessed by comparing them to the 4742 × 4 ab initio ESPs of small molecule dimers. The predicted dimer ESPs had an average relative root-mean-square error (RRMSE) of 9.30%, which was only slightly larger than the average fitting RRMSE of 9.15% of the monomer ESPs. The transferability of the polarizability set was further evaluated by comparing the ESPs calculated using parameters developed in another dielectric environment for both tetrapeptide and DES monomer data sets. It was observed that the polarizabilities of this work retained or slightly improved the transferability over the one discussed in earlier work even though the number of parameters in the present set is about half of that in the earlier set. Excluding the gas-phase data, for the DES monomer set, the average transfer RRMSEs were 16.25% and 10.83% for pGM-ind and pGM-perm methods, respectively, comparable to the average fitting RRMSEs of 16.03% and 10.54%; for tetrapeptides, the average transfer RRMSEs were 5.62% and 3.95% for pGM-ind and pGM-perm methods, respectively, slightly larger than 5.41% and 3.61% of the fitting RRMSEs. Therefore, we conclude that the pGM methods with updated polarizabilities achieved remarkable transferability from monomer to dimer and from one solvent to another.

Abstract: In-situ two-dimensional X-ray absorption spectroscopy (XAS) imaging was employed to analyze cerium ion (Ce3+) migration in the through-plane direction in proton exchange membrane fuel cells (PEMFCs), offering fundamental insights supporting improvement of their power density and membrane durability. The transport of Ce3+ was visualized in both unreinforced thick Nafion membranes (Nafion 115, 127 µm) and reinforced thin (12 µm) perfluorosulfonic acid (PFSA) membranes under either an electrical potential gradient or a water activity gradient. The diffusion coefficients of Ce3+ were ascertained based on its behavior after removal of these gradients in both membrane types. Additionally, using a one-dimensional cation transport model, the mobility and electroosmotic drag coefficients of Ce3+ were derived from experimentally obtained data of the thick Nafion membrane. Our measurements also demonstrate that the migration of Ce3+ in the thick membranes was notably impeded by the presence of ferrous ion (Fe2+) impurities. Because Fe2+ is known to accelerate membrane degradation by promoting hydroxyl radical formation, this effect might further exacerbate membrane degradation. It therefore warrants careful consideration.