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Open Access Publications from the University of California

Chemical and Biomolecular Engineering - Open Access Policy Deposits

This series is automatically populated with publications deposited by UC Irvine Samueli School of Engineering Chemical and Biomolecular Engineering researchers in accordance with the University of California’s open access policies. For more information see Open Access Policy Deposits and the UC Publication Management System.

Cover page of Proton-Transfer Kinetics at Liquid–Liquid Interfaces

Proton-Transfer Kinetics at Liquid–Liquid Interfaces

(2025)

Proton transfer at electrochemical interfaces is fundamentally important across science and technology, yet kinetic measurements of this elementary step at electrode|electrolyte interfaces are convoluted with other electron-transfer steps and by inhomogeneous electrode surfaces. We use facilitated proton transfer at the interface between two immiscible electrolyte solutions (ITIES) as a platform to study proton-transfer kinetics in the absence of interfacial electron transfer and without the defects at solid|electrolyte interfaces. Diffusion-controlled micropipette voltammetry revealed that 2,6-diphenylpyridine (DPP) facilitates proton transfer across the HCl(aq)|trifluorotoluene interface, while voltammetry at nanopipette-supported interfaces yielded activation-controlled ion-transfer currents. We extract kinetic parameters kapp0 and αapp, 3.0 ± 1.8 cm/s and 0.3 ± 0.2, respectively, for DPP-facilitated proton transfer by fitting quasi-reversible voltammograms to a mixed diffusive-kinetic model. Finite-element simulations highlighted regimes of direct proton transfer and sequential proton transfer, where the current divided between these two possible pathways was shown to favor direct proton transfer when the neutral partitioning step DPP(org) → DPP(aq) was rate-determining. Atomistic molecular-dynamics simulations were used to compute the free energy change to move DPP and its protonated analogue within, and across, the liquid|liquid interface. The most-likely location for proton transfer is predicted to be in the surface region where significant interpenetration of the two liquids occurs. Understanding the kinetics of ion transfer at the ITIES illustrated here is important in the development of general theories of ion transfer in electrochemical science and technology.

Cover page of Chemical Mapping of Nanoparticle-Ligand Interfaces in Optical Nanocavities.

Chemical Mapping of Nanoparticle-Ligand Interfaces in Optical Nanocavities.

(2025)

Understanding processes in photon-phonon scattering, absorption, and chemical reactions in optical nanocavities is important for single-molecule sensors, single-photon emitters, and photocatalysis. However, the influence of electromagnetic fields, charge transfer, and molecular geometry is challenging to probe by ensemble-averaged spectroscopic techniques over multiple nanocavities. Photoinduced force microscopy (PiFM), which measures photoinduced polarizability under infrared excitation of a sample in the nanocavity between the scanning probe microscopy tip and sample surface, is used here for simultaneous nanoscale topological and chemical characterization. First-principles density functional theory (DFT) simulations of the vibrational spectra of gold nanoparticle surfaces functionalized with benzenedithiol (Au-BDT) elucidate molecular orientation, charge transfer, and oxidation state for understanding molecular and adatom reconfiguration in optical nanocavities in response to external fields.

Cover page of Structured light imaging mesoscopy: detection of embedded morphological changes in superficial tissues

Structured light imaging mesoscopy: detection of embedded morphological changes in superficial tissues

(2025)

Significance

Current paradigms for the optical characterization of layered tissues involve explicit consideration of an inverse problem which is often ill-posed and whose resolution may retain significant uncertainty. Here, we present an alternative approach, structured light imaging mesoscopy (SLIM), that leverages the inherent sensitivity of raw spatial frequency domain (SFD) reflectance measurements for the detection of embedded subsurface scattering changes in tissue.

Aim

We identify wavelength-spatial frequency ( λ-fx ) combinations that provide optimal sensitivity of SFD reflectance changes originating from scattering changes in an embedded tissue layer. We specifically consider the effects of scattering changes in the superficial dermis which is a key locus of pathology for diverse skin conditions such as cancer, aging, and scleroderma.

Approach

We used Monte Carlo simulations in a four-layer skin model to analyze the SFD reflectance changes resulting from changes in superficial dermal scattering across wavelength ( λ=471 to 851 nm) and spatial frequency ( fx=0 to 0.5/mm). Within this model, we consider different values for epidermal melanin concentration to simulate variations in skin tone.

Results

Monte Carlo simulations revealed that scattering changes within the superficial dermis produce SFD reflectance changes which are maximized at specific ( λ-fx ) pairs and vary with skin tone. For light skin tones, SFD reflectance changes due to scattering reductions in the superficial dermis are maximized at λ=621  nm and spatial frequency fx≈0.33/mm . By contrast, for darker skin tones, maximal SFD reflectance changes occur at wavelengths in the near-infrared ( λ≥811  nm ) at a spatial frequency of fx≈0.25/mm . Interestingly, the change in SFD reflectance produced by such scattering changes is most uniform across all skin tones when using the longest wavelength tested ( λ=851  nm ) and a spatial frequency of fx≈0.22/mm . Taken together, our computational model identifies specific ( λ-fx ) pairs to optimally detect embedded structural alterations in the superficial dermis.

Conclusions

The findings establish the SLIM methodology as a means to detect morphological changes in an embedded subsurface tissue layer by leveraging inherent sensitivities of spatial frequency domain reflectance. This approach promises to enable simplified clinical tracking of subsurface microstructural alterations without the explicit need to consider an inverse problem approach.

Cover page of Divergent evolution of slip banding in CrCoNi alloys.

Divergent evolution of slip banding in CrCoNi alloys.

(2025)

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.

Cover page of Durability of Pt‐Alloy Catalyst for Heavy‐Duty Polymer Electrolyte Fuel Cell Applications under Realistic Conditions

Durability of Pt‐Alloy Catalyst for Heavy‐Duty Polymer Electrolyte Fuel Cell Applications under Realistic Conditions

(2025)

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).

Cover page of Ferroelectric tunnel junctions integrated on semiconductors with enhanced fatigue resistance.

Ferroelectric tunnel junctions integrated on semiconductors with enhanced fatigue resistance.

(2025)

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.

Cover page of Structured light imaging mesoscopy for detection of embedded morphological changes in superficial tissues

Structured light imaging mesoscopy for detection of embedded morphological changes in superficial tissues

(2025)

This study introduces Structured Light Imaging Mesoscopy (SLIM), a novel non-contact optical method for detecting subsurface morphological tissue alterations. By leveraging the inherent sensitivity of spatial frequency domain (SFD) reflectance measurements, SLIM identifies specific wavelength-spatial frequency combinations that optimize the detection of scattering changes in the superficial dermis, a key area for various skin conditions. Monte Carlo simulations across a range of skin tones revealed that these optimal combinations vary with melanin concentration. Specifically, in subjects with lighter skin tones optimal sensitivity is achieved using shorter wavelengths and higher spatial frequencies, while for darker skin tones longer wavelengths and lower spatial frequencies are preferred. This approach simplifies clinical tracking of subsurface microstructural changes by eliminating the need for complex inverse problem solving, enabling rapid data acquisition and minimal processing.

Cover page of Hierarchical Assembly of Conductive Fibers from Coiled-Coil Peptide Building Blocks

Hierarchical Assembly of Conductive Fibers from Coiled-Coil Peptide Building Blocks

(2025)

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.

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Cover page of Fluorescence Lifetime Imaging Detects Long-Lifetime Signal Associated with Reduced Pyocyanin at the Surface of Pseudomonas aeruginosa Biofilms and in Cross-Feeding Conditions

Fluorescence Lifetime Imaging Detects Long-Lifetime Signal Associated with Reduced Pyocyanin at the Surface of Pseudomonas aeruginosa Biofilms and in Cross-Feeding Conditions

(2025)

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.

Cover page of Fluorescence Lifetime Imaging Detects Long-Lifetime Signal Associated with Reduced Pyocyanin at the Surface of Pseudomonas aeruginosa Biofilms and in Cross-Feeding Conditions

Fluorescence Lifetime Imaging Detects Long-Lifetime Signal Associated with Reduced Pyocyanin at the Surface of Pseudomonas aeruginosa Biofilms and in Cross-Feeding Conditions

(2025)

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.