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Open Access Publications from the University of California

LBL Publications

Lawrence Berkeley National Laboratory (Berkeley Lab) has been a leader in science and engineering research for more than 70 years. Located on a 200 acre site in the hills above the Berkeley campus of the University of California, overlooking the San Francisco Bay, Berkeley Lab is a U.S. Department of Energy (DOE) National Laboratory managed by the University of California. It has an annual budget of nearly $480 million (FY2002) and employs a staff of about 4,300, including more than a thousand students.

Berkeley Lab conducts unclassified research across a wide range of scientific disciplines with key efforts in fundamental studies of the universe; quantitative biology; nanoscience; new energy systems and environmental solutions; and the use of integrated computing as a tool for discovery. It is organized into 17 scientific divisions and hosts four DOE national user facilities. Details on Berkeley Lab's divisions and user facilities can be viewed here.

Cover page of Efficient separation of carbon dioxide and methane in high-pressure and wet gas mixtures using Zr-MOF-808

Efficient separation of carbon dioxide and methane in high-pressure and wet gas mixtures using Zr-MOF-808

(2025)

The capture and separation of carbon dioxide (CO2) has been the focus of a plethora of research in order to mitigate its emissions and contribute to global development. Given that CO2 is commonly found in natural gas streams, there have been efforts to seek more efficient materials to separate gaseous mixtures such as CO2/CH4. However, there are only a few reports regarding adsorption processes within pressurized systems. In the offshore scenario, natural gas streams still exhibit high moisture content, necessitating a greater understanding of processes in moist systems. In this article, a metal-organic framework synthesis based on zirconium (MOF-808) was carried out through a conventional solvothermal method and autoclave for the adsorption of CO2 and CH4 under different temperatures (45–65 °C) and pressures up to 100 bar. Furthermore, the adsorption of humid CO2 was evaluated using thermal analyses. The MOF-808 synthesized in autoclave showed a high surface area (1502 m2/g), a high capacity for CO2 adsorption at 50 bar and 45 °C and had a low selectivity to capture CH4 molecules. It also exhibited a fine stability after five cycles of CO2 adsorption and desorption at 50 bar and 45 °C − as confirmed by structural post-adsorption analyses while maintaining its adsorption capacity and crystallinity. Furthermore, it can be observed that the adsorption capacity increased in a humid environment, and that the adsorbent remained stable after adsorption cycles in the presence of moisture. Finally, it was possible to confirm the occurrence of physisorption processes through nuclear magnetic resonance (NMR) analyses, thus validating the choice of mild temperatures for regeneration and contributing to the reduction of energy consumption in processing plants.

Cover page of The EGS Collab project: Outcomes and lessons learned from hydraulic fracture stimulations in crystalline rock at 1.25 and 1.5 km depth

The EGS Collab project: Outcomes and lessons learned from hydraulic fracture stimulations in crystalline rock at 1.25 and 1.5 km depth

(2025)

With the goal of better understanding stimulation in crystalline rock for improving enhanced geothermal systems (EGS), the EGS Collab Project performed a series of stimulations and flow tests at 1.25 and 1.5 km depths. The tests were performed in two well-instrumented testbeds in the Sanford Underground Research Facility in Lead, South Dakota, United States. The testbed for Experiment 1 at 1.5 km depth contained two open wells for injection and production and six instrumented monitoring wells surrounding the targeted stimulation zone. Four multi-step stimulation tests targeting hydraulic fracturing and nearly year-long ambient temperature and chilled water flow tests were performed in Experiment 1. The testbed for Experiments 2 and 3 was at 1.25 km depth and contained five open wells in an outwardly fanning five-spot pattern and two fans of well-instrumented monitoring wells surrounding the targeted stimulation zone. Experiment 2 targeted shear stimulation, and Experiment 3 targeted low-flow, high-flow, and oscillating pressure stimulation strategies. Hydraulic fracturing was successful in Experiments 1 and 3 in generating a connected system wherein injected water could be collected. However, the resulting flow was distributed dynamically, and not entirely collected at the anticipated production well. Thermal breakthrough was not observed in the production well, but that could have been masked by the Joule-Thomson effect. Shear stimulation in Experiment 2 did not occur – despite attempting to pressurize the fractures most likely to shear – because of the inability to inject water into a mostly-healed fracture, and the low shear-to-normal stress ratio. The EGS Collab experiments are described to provide a background for lessons learned on topics including induced seismicity, the correlation between seismicity and permeability, distributed and dynamic flow systems, thermoelastic and pressure effects, shear stimulation, local geology, thermal breakthrough, monitoring stimulation, grouting boreholes, modeling, and system management.

Cover page of Magnetic order in nanogranular iron germanium (Fe0.53Ge0.47) films

Magnetic order in nanogranular iron germanium (Fe0.53Ge0.47) films

(2025)

We study the effect of strain on the magnetic properties and magnetization configurations in nanogranular FexGe1-xfilms (x=0.53±0.05) with and without B20 FeGe nanocrystals surrounded by an amorphous structure. Relaxed films on amorphous silicon nitride membranes reveal a disordered skyrmion phase while films near and on top of a rigid substrate favor ferromagnetism and an anisotropic hybridization of Fedlevels and spin-polarized Gespband states. The weakly coupled topological states emerge at room temperature and become more abundant at cryogenic temperatures without showing indications of pinning at defects or confinement to individual grains. These results demonstrate the possibility to control magnetic exchange and topological magnetism by strain and inform magnetoelasticity-mediated voltage control of topological phases in amorphous quantum materials.

Cover page of Aqueous solution-based synthesis approach for carbon-disordered rocksalt composite cathode development and its limitations

Aqueous solution-based synthesis approach for carbon-disordered rocksalt composite cathode development and its limitations

(2025)

Disordered rocksalt cathodes exhibit high specific capacities and high energy density; however, their low electronic conductivity poses a great challenge. Herein, we explored an aqueous-solution-based synthesis route that involves controlling the surface charges of Li1.2Mn0.6Ti0.2O1.8F0.2 (LMTOF) to be anchored by a few-layer reduced graphene oxide (rGO) for the first time. The uniform rGO wrapping on the surface of the LMTOF particles is achieved by electrostatic attraction between the negatively charged rGO and positively charged LMTOF particles. Although the initial specific capacity of rGO-LMTOF composite increased by 58 % compared to the pristine LMTOF, the composite experienced a severe capacity fade over cycling. The synthesis process in an aqueous medium resulted in Li+/H+ exchange and TM dissolution as evidenced from inductively coupled plasmon analysis and X-ray diffraction analysis. Therefore, this work suggests the search for alternative media or conditions for the synthesis of carbon-disordered rock salt cathode composite.

Cover page of Acetaminophen production in the edible, filamentous cyanobacterium Arthrospira platensis.

Acetaminophen production in the edible, filamentous cyanobacterium Arthrospira platensis.

(2025)

Spirulina is the common name for the edible, nonheterocystous, filamentous cyanobacterium Arthrospira platensis that is grown industrially as a food supplement, animal feedstock, and pigment source. Although there are many applications for engineering this organism, until recently no genetic tools or reproducible transformation methods have been published. While recent work showed the production of a diversity of proteins in A. platensis, including single-domain antibodies for oral delivery, there remains a need for a modular, characterized genetic toolkit. Here, we independently establish a reproducible method for the transformation of A. platensis and engineer this bacterium to produce acetaminophen as proof-of-concept for small molecule production in an edible host. This work opens A. platensis to the wider scientific community for future engineering as a functional food for nutritional enhancement, modification of organoleptic traits, and production of pharmaceuticals for oral delivery.

Cover page of Genetic and microbial determinants of azoxymethane-induced colorectal tumor susceptibility in Collaborative Cross mice and their implication in human cancer

Genetic and microbial determinants of azoxymethane-induced colorectal tumor susceptibility in Collaborative Cross mice and their implication in human cancer

(2024)

The insights into interactions between host genetics and gut microbiome (GM) in colorectal tumor susceptibility (CTS) remains lacking. We used Collaborative Cross mouse population model to identify genetic and microbial determinants of Azoxymethane-induced CTS. We identified 4417 CTS-associated single nucleotide polymorphisms (SNPs) containing 334 genes that were transcriptionally altered in human colorectal cancers (CRCs) and consistently clustered independent human CRC cohorts into two subgroups with different prognosis. We discovered a set of genera in early-life associated with CTS and defined a 16-genus signature that accurately predicted CTS, the majority of which were correlated with human CRCs. We identified 547 SNPs associated with abundances of these genera. Mediation analysis revealed GM as mediators partially exerting the effect of SNP UNC3869242 within Duox2 on CTS. Intestine cell-specific depletion of Duox2 altered GM composition and contribution of Duox2 depletion to CTS was significantly influenced by GM. Our findings provide potential novel targets for personalized CRC prevention and treatment.

Cover page of Evolving to Find Optimizations Humans Miss: Using Evolutionary Computation to Improve GPU Code for Bioinformatics Applications

Evolving to Find Optimizations Humans Miss: Using Evolutionary Computation to Improve GPU Code for Bioinformatics Applications

(2024)

GPUs are used in many settings to accelerate large-scale scientific computation, including simulation, computational biology, and molecular dynamics. However, optimizing codes to run efficiently on GPUs requires developers to have both detailed understanding of the application logic and significant knowledge of parallel programming and GPU architectures. This paper shows that an automated GPU program optimization tool, GEVO, can leverage evolutionary computation to find code edits that reduce the runtime of three important applications, multiple sequence alignment, agent-based simulation and molecular dynamics codes, by 28.9%, 29%, and 17.8% respectively. The paper presents an in-depth analysis of the discovered optimizations, revealing that (1) several of the most important optimizations involve significant epistasis, (2) the primary sources of improvement are application-specific, and (3) many of the optimizations generalize across GPU architectures. In general, the discovered optimizations are not straightforward even for a GPU human expert, showcasing the potential of automated program optimization tools to both reduce the optimization burden for human domain experts and provide new insights for GPU experts.

Cover page of Parallel Runtime Interface for Fortran (PRIF) Specification, Revision 0.5

Parallel Runtime Interface for Fortran (PRIF) Specification, Revision 0.5

(2024)

This document specifies an interface to support the parallel features of Fortran, named the Parallel Runtime Interface for Fortran (PRIF). PRIF is a proposed solution in which the runtime library is primarily responsible for implementing coarray allocation, deallocation and accesses, image synchronization, atomic operations, events, teams and collective subroutines. In this interface, the compiler is responsible for transforming the invocation of Fortran-level parallel features into procedure calls to the necessary PRIF subroutines. The interface is designed for portability across shared- and distributed-memory machines, different operating systems, and multiple architectures. Implementations of this interface are intended as an augmentation for the compiler's own runtime library. With an implementation-agnostic interface, alternative parallel runtime libraries may be developed that support the same interface. One benefit of this approach is the ability to vary the communication substrate. A central aim of this document is to define a parallel runtime interface in standard Fortran syntax, which enables us to leverage Fortran to succinctly express various properties of the procedure interfaces, including argument attributes.

Cover page of High-precision chemical quantum sensing in flowing monodisperse microdroplets.

High-precision chemical quantum sensing in flowing monodisperse microdroplets.

(2024)

A method is presented for high-precision chemical detection that integrates quantum sensing with droplet microfluidics. Using nanodiamonds (ND) with fluorescent nitrogen-vacancy (NV) centers as quantum sensors, rapidly flowing microdroplets containing analyte molecules are analyzed. A noise-suppressed mode of optically detected magnetic resonance is enabled by pairing controllable flow with microwave control of NV electronic spins, to detect analyte-induced signals of a few hundredths of a percent of the ND fluorescence. Using this method, paramagnetic ions in droplets are detected with low limit-of-detection using small analyte volumes, with exceptional measurement stability over >103 s. In addition, these droplets are used as microconfinement chambers by co-encapsulating ND quantum sensors with various analytes such as single cells, suggesting wide-ranging applications including single-cell metabolomics and real-time intracellular measurements from bioreactors. Important advances are enabled by this work, including portable chemical testing devices, amplification-free chemical assays, and chemical imaging tools for probing reactions within microenvironments.