Skip to main content
Open Access Publications from the University of California
Cover page of Simple and Accurate One-Body Energy and Dipole Moment Surfaces for Water and Beyond

Simple and Accurate One-Body Energy and Dipole Moment Surfaces for Water and Beyond


Water is often the testing ground for new, advanced force fields. While advanced functional forms for intermolecular interactions have been integral to the development of accurate water models, less attention has been paid to a transferable model for intramolecular valence terms. In this work, we present a one-body energy and dipole moment surface model, named 1B-UCB, that is simple yet accurate and can be feasibly adapted for both standard and advanced potentials. 1B-UCB for water is comparable in accuracy to those with much more complex functional forms, despite having drastically fewer parameters. The parametrization protocol has been implemented as part of the Q-Force automated workflow and requires only a quantum mechanical Hessian calculation as reference data, hence allowing it to be easily extended to a variety of molecular systems beyond water, which we demonstrate on a selection of small molecules with different symmetries.

Cover page of Operando Study Insights into Lithiation/Delithiation Processes in a Poly(ethylene oxide) Electrolyte of All-Solid-State Lithium Batteries by Grazing-Incidence X-ray Scattering.

Operando Study Insights into Lithiation/Delithiation Processes in a Poly(ethylene oxide) Electrolyte of All-Solid-State Lithium Batteries by Grazing-Incidence X-ray Scattering.


Poly(ethylene oxide) (PEO)-based composite electrolytes (PCEs) are considered as promising candidates for next-generation lithium-metal batteries (LMBs) due to their high safety, easy fabrication, and good electrochemical stability. Here, we utilize operando grazing-incidence small-angle and wide-angle X-ray scattering to probe the correlation of electrochemically induced changes and the buried morphology and crystalline structure of the PCE. Results show that the two irreversible reactions, PEO-Li+ reduction and TFSI- decomposition, cause changes in the crystalline structure, array orientation, and morphology of the PCE. In addition, the reversible Li plating/stripping process alters the inner morphology, especially the PEO-LiTFSI domain radius and distance between PEO-LiTFSI domains, rather than causing crystalline structure and orientation changes. This work provides a new path to monitor a working battery in real time and to a detailed understanding of the Li+ diffusion mechanism, which is essential for developing highly transferable and interface-stable PCE-based LMBs.

Cover page of Scanning electrochemical probe microscopy investigation of two-dimensional materials

Scanning electrochemical probe microscopy investigation of two-dimensional materials


Research interests in two-dimensional (2D) materials have seen exponential growth owing to their unique and fascinating properties. The highly exposed lattice planes coupled with tunable electronic states of 2D materials have created manifold opportunities in the design of new platforms for energy conversion and sensing applications. Still, challenges in understanding the electrochemical (EC) characteristics of these materials arise from the complexity of both intrinsic and extrinsic heterogeneities that can obscure structure-activity correlations. Scanning EC probe microscopic investigations offer unique benefits in disclosing local EC reactivities at the nanoscale level that are otherwise inaccessible with macroscale methods. This review summarizes recent progress in applying techniques of scanning EC microscopy (SECM) and scanning EC cell microscopy (SECCM) to obtain distinctive insights into the fundamentals of 2D electrodes. We showcase the capabilities of EC microscopies in addressing the roles of defects, thickness, environments, strain, phase, stacking, and many other aspects in the heterogeneous electron transfer, ion transport, electrocatalysis, and photoelectrochemistry of representative 2D materials and their derivatives. Perspectives for the advantages, challenges, and future opportunities of scanning EC probe microscopy investigation of 2D structures are discussed.

Cover page of A curated rotamer library for common post-translational modifications of proteins.

A curated rotamer library for common post-translational modifications of proteins.


MOTIVATION: Sidechain rotamer libraries of the common amino acids of a protein are useful for folded protein structure determination and for generating ensembles of intrinsically disordered proteins (IDPs). However, much of protein function is modulated beyond the translated sequence through the introduction of post-translational modifications (PTMs). RESULTS: In this work, we have provided a curated set of side chain rotamers for the most common PTMs derived from the RCSB PDB database, including phosphorylated, methylated, and acetylated sidechains. Our rotamer libraries improve upon existing methods such as SIDEpro, Rosetta, and AlphaFold3 in predicting the experimental structures for PTMs in folded proteins. In addition, we showcase our PTM libraries in full use by generating ensembles with the Monte Carlo Side Chain Entropy (MCSCE) for folded proteins, and combining MCSCE with the Local Disordered Region Sampling algorithms within IDPConformerGenerator for proteins with intrinsically disordered regions. AVAILABILITY AND IMPLEMENTATION: The codes for dihedral angle computations and library creation are available at

Cover page of Anion and Cation Migration at 2D/3D Halide Perovskite Interfaces

Anion and Cation Migration at 2D/3D Halide Perovskite Interfaces


This study explores the ionic dynamics in 2D/3D perovskite solar cells, which are known for their improved efficiency and stability. The focus is on the impact of halide choice in 3D perovskites treated with phenethylammonium halide salts (PEAX, X = Br and I). Our findings reveal that light and heat drive ionic migration in these structures, with PEA+ species diffusing into the 3D film in PEABr-treated samples. Mixed-halide 3D perovskites show halide interdiffusion, with bromine migrating to the surface and iodine diffusing into the film. Cathodoluminescence microscopy reveals localized 2D phases on the 3D perovskite, which become more evenly distributed after thermal treatment. Both PEAX salts enhance the performance of photovoltaic devices. This improvement is attributed to the passivation capabilities of the salts themselves and their respective Ruddlesden−Popper (RP) phases. Annealed PEAI-treated devices show a better balance between efficiency and statistical distribution of photovoltaic parameters.

Cover page of Surfactant Partitioning Dynamics in Freshly Generated Aerosol Droplets.

Surfactant Partitioning Dynamics in Freshly Generated Aerosol Droplets.


Aerosol droplets are unique microcompartments with relevance to areas as diverse as materials and chemical synthesis, atmospheric chemistry, and cloud formation. Observations of highly accelerated and unusual chemistry taking place in such droplets have challenged our understanding of chemical kinetics in these microscopic systems. Due to their large surface-area-to-volume ratios, interfacial processes can play a dominant role in governing chemical reactivity and other processes in droplets. Quantitative knowledge about droplet surface properties is required to explain reaction mechanisms and product yields. However, our understanding of the compositions and properties of these dynamic, microscopic interfaces is poor compared to our understanding of bulk processes. Here, we measure the dynamic surface tensions of 14-25 μm radius (11-65 pL) droplets containing a strong surfactant (either sodium dodecyl sulfate or octyl-β-D-thioglucopyranoside) using a stroboscopic imaging approach, enabling observation of the dynamics of surfactant partitioning to the droplet-air interface on time scales of 10s to 100s of microseconds after droplet generation. The experimental results are interpreted with a state-of-the-art kinetic model accounting for the unique high surface-area-to-volume ratio inherent to aerosol droplets, providing insights into both the surfactant diffusion and adsorption kinetics as well as the time-dependence of the interfacial surfactant concentration. This study demonstrates that microscopic droplet interfaces can take up to many milliseconds to reach equilibrium. Such time scales should be considered when attempting to explain observations of accelerated chemistry in microcompartments.

Cover page of Reinforcement learning pulses for transmon qubit entangling gates

Reinforcement learning pulses for transmon qubit entangling gates


The utility of a quantum computer is highly dependent on the ability to reliably perform accurate quantum logic operations. For finding optimal control solutions, it is of particular interest to explore model-free approaches, since their quality is not constrained by the limited accuracy of theoretical models for the quantum processor—in contrast to many established gate implementation strategies. In this work, we utilize a continuous control reinforcement learning algorithm to design entangling two-qubit gates for superconducting qubits; specifically, our agent constructs cross-resonance and CNOT gates without any prior information about the physical system. Using a simulated environment of fixed-frequency fixed-coupling transmon qubits, we demonstrate the capability to generate novel pulse sequences that outperform the standard cross-resonance gates in both fidelity and gate duration, while maintaining a comparable susceptibility to stochastic unitary noise. We further showcase an augmentation in training and input information that allows our agent to adapt its pulse design abilities to drifting hardware characteristics, importantly, with little to no additional optimization. Our results exhibit clearly the advantages of unbiased adaptive-feedback learning-based optimization methods for transmon gate design.

Diamond-lattice photonic crystals assembled from DNA origami.


Colloidal self-assembly allows rational design of structures on the micrometer and submicrometer scale. One architecture that can generate complete three-dimensional photonic bandgaps is the diamond cubic lattice, which has remained difficult to realize at length scales comparable with the wavelength of visible or ultraviolet light. In this work, we demonstrate three-dimensional photonic crystals self-assembled from DNA origami that act as precisely programmable patchy colloids. Our DNA-based nanoscale tetrapods crystallize into a rod-connected diamond cubic lattice with a periodicity of 170 nanometers. This structure serves as a scaffold for atomic-layer deposition of high-refractive index materials such as titanium dioxide, yielding a tunable photonic bandgap in the near-ultraviolet.

Cover page of Molecular beam scattering of ammonia from a dodecane flat liquid jet

Molecular beam scattering of ammonia from a dodecane flat liquid jet


The evaporation and scattering of ND3 from a dodecane flat liquid jet are investigated and the results are compared with previous studies on molecular beam scattering from liquid surfaces. Evaporation is well-described by a Maxwell-Boltzmann flux distribution with a cos θ angular distribution at the liquid temperature. Scattering experiments at Ei = 28.8 kJ mol-1 over a range of deflection angles show evidence for impulsive scattering and thermal desorption. At a deflection angle of 90°, the thermal desorption fraction is 0.49, which is higher than that of other molecules previously scattered from dodecane and consistent with work performed on NH3 scattering from a squalane-wetted wheel. ND3 scattering from dodecane results in super-specular scattering, as seen in previous experiments on dodecane. The impulsive scattering channel is fitted to a "soft-sphere" model, yielding an effective surface mass of 55 amu and an internal excitation of 5.08 kJ mol-1. Overall, impulsively scattered ND3 behaves similarly to other small molecules scattered from dodecane.