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Recent Publications

By Department: Physics | Applied Math | Molecular and Cell Biology | Life & Environmental Sciences | Chemistry and Biochemistry

Physics Publications

Sayantani Ghosh, co-author. Complex Dependence of Optoelectronic Properties of Metal Halide Perovskite Thin Films on Quantum Dot Decoration Layers. Journal of Physical Chemistry.


David Strubbe, co-author. Exploring Newton’s Second Law and Kinetic Friction Using the Accelerometer Sensor in Smartphones. Phys. Teach.


Linda Hirst, co-author. Effect of internal energy depletion on active nematic texture and dynamics. Liquid Crystals. 


Sayantani Ghosh, co-author. Evaluation of oil sludge vermicompost for integrated nutrient management in rain fed wetland rice (Oryza sativa L.). Journal of Crop and Weed.


Dustin Kleckner, co-author. High-speed two-color scanning volumetric laser- induced fluorescence. Springer Nature.


David Strubbe, co-author. Development and Application of a ReaxFF Reactive Force Field for Ni-Doped MoS2. Journal of Physical Chemistry C.


Sayantani Ghosh, co-author. Evaluation of Hybrid Perovskite Prototypes After 10-Month Space Flight on the International Space Station. Advanced Energy Materials.


Ajay Gopinathan, co-author. Optimal foraging strategies for mutually avoiding competitors. Journal of Theoretical Biology.


Linda Hirst, co-author. Forming, Confining, and Observing Microtubule-Based Active Nematics. National Library of Medicine.


Jing Xu, co-author. Cholesterol in the cargo membrane amplifies tau inhibition of kinesin-1-based transport. PNAS.


Chih-Chun Chien, co-author. Atomic boson-fermion mixtures in one-dimensional box potentials: Few-body and mean-field many-body analyses. APS Physical Review A.


David Strubbe, co-author. One-dimensional organic metal halide nanoribbons with dual emission. Royal Society of Chemistry.


Sayantani Ghosh and Michael Scheibner, co-authors. Evaluation of Hybrid Perovskite Prototypes After 10-Month Space Flight on the International Space Station. Advanced Energy Materials.


Anna Nierenberg, co-author. PSFr: Point Spread Function reconstruction. Astrophysics Source Code Library.


David Strubbe, co-author. Intercalation leads to inverse layer dependence of friction on chemically doped MoS2. Nanotechnology.


Sayantani Ghosh, co-author. Synthesis and Properties of Stable Amino Metal Halide Molecular Clusters in the Solid State. The Journal of Physical Chemistry Letters.


David Strubbe, co-author. Structure, Thermodynamics, and Raman Spectroscopy of Rhenium-Doped Bulk MoS2 from First Principles. The Journal of Physical Chemistry Letters.


Chih-Chun Chien, co-author. Uhlmann phase of coherent states and the Uhlmann-Berry correspondence. SciPost Physics.


Sayantani Ghosh, co-author. Understanding the effect of irradiation temperature on microstructural evolution of 20MnMoNi55 steel. Scientific Reports.


David Strubbe, co-author. Intercalation leads to inverse layer dependence of friction on chemically doped MoS2. IOP Science Nanotechnology.


David Strubbe, co-author. Spinor GW/Bethe-Salpeter calculations in BerkeleyGW: Implementation, symmetries, benchmarking, and performance. APS Physical Review B. 


Anna Nierenberg, co-author. VizieR Online Data Catalog: AGN photoionization of gas in companion galaxies (Keel+, 2019). Monthly Notices of the Royal Astronomical Society.


Hui, Cai, co-author. Stabilized Synthesis of 2D Verbeekite: Monoclinic PdSe2Crystals with High Mobility and In-Plane Optical and Electrical Anisotropy. ACS NANO.


Chih-Chun Chien, co-author. Metamorphic dynamical quantum phase transition in double-quench processes at finite temperatures. APS Physical Review B.


Chih-Chun Chien, co-author. Topological classifications of quadratic bosonic excitations in closed and open systems with examples. Journal of Physics: Condensed Matter.


Chih-Chun Chien, co-author. Custodial Chiral Symmetry in a Su-Schrieffer-Heeger Electrical Circuit with Memory. Physical Review Letters.


Kevin Mitchell, co-author. Barriers Impeding Active Mixing of Swimming Microbes in a Hyperbolic Flow. Frontiers in Physics.


Hui Cai, co-author. Unusual Deformation and Fracture in Gallium Telluride Multilayers. The Journal of Physical Chemistry Letters.


Ajay Gopinathan, Kinjal Dasbiswas, Linda Hirst, co-authors. Active nematic order and dynamic lane formation of microtubules driven by membrane-bound diffusing motors. PNAS.


Ajay Gopinathan, Sayatani Ghosh and Ryan Baxter, co-authors. Tuning three-dimensional nano-assembly in the mesoscale via bis(imino)pyridine molecular functionalization. Scientific Reports.


Jing Xu, co-author. Tuning ensemble-averaged cargo run length via fractional change in mean kinesin number. Physical Biology.


Kinjal Dasbiswas, co-author. Matrix Stiffness Modulates Mechanical Interactions and Promotes Contact between Motile Cells. Biomedicines.


David Strubbe, co-author. Phase Stability and Raman/IR Signatures of Ni-Doped MoS2 from Density Functional Theory Studies. The Journal of Physical Chemistry C.


Sayantani Ghosh, co-author. Low-temperature energy transfer via self-trapped Excitons in Mn2+-Doped 2D Organometal Halide Perovskites. The Journal of Physical Chemistry Letters.


Maxime Theillard, Dustin Kleckner, and Shilpa Kahatri, co-authors. Retention of rising droplets in density stratification. Physical Review Fluids.


Chih-Chun Chien, co-author. Erratum: Dynamic process and Uhlmann process: incompatibility and dynamic phase of mixed quantum states. Physical Review B.


Daniel A. Beller, co-author. Fast, scalable, and interactive software for Landau-deGennes numerical modeling of nematic topological defects. Frontiers in Physics.


Linda S. Hirst and Sayantani Ghosh, co-authors. Directed assembly of magnetic and semiconducting nanoparticles with tunable and synergistic functionality. Scientific Reports.


Ajay Gopinathan, co-author. Chiral twisting in a bacterial cytoskeletal polymer affects filament size and orientation. Nature Communications.


Sayantani Ghosh, co-author. Enhancing charge carrier delocalization in perovskite quantum dot solids with energetically aligned conjugated capping ligands. ACS Energy Letters.


Kinjal Dasbiswas, co-author. Mechanical force-driven registry of non-muscle myosin in fibroblasts. Biophysical Journal.


Applied Math Publications

Chrysoula Tsogka, co-author. Statistical Stability of Correlation Based Imaging Algorithms. IEEE.


Tomas Rube, co-author. Boosting genome editing efficiency in human cells and plants with novel LbCas12a variants. BMC.


Arnold Kim and Chrysoula Tsogka, co-authors. Imaging in lossy media. Inverse Problems.


Noemi Petra, co-author. On global normal linear approximations for nonlinear Bayesian inverse problems. Inverse Problems.


Suzanne Sindi and Clarissa Nobile, co-authors. A Computational Workflow for Analysis of 3′ Tag-Seq Data. Current Protocols.


Camille Carvalho and Chrysoula Tsogka, co-authors. Boundary Integral Equation Methods for Optical Cloaking Models. WAVES 2022.


Roummel Marcia, co-author. Image classification and training with severe data loss. Applications of Machine Learning.


Arnold Kim and Chrysoula Tsogka, co-authors. High-resolution imaging for synthetic aperture radar. IEEE.


Chrysoula Tsogka, co-author. Computational Vibro-Acoustic Time Reversal for Source and Novelty Localization. Signals. 


Chrysoula Tsogka, Roummel Marcia and Arnold Kim, co-authors. Synthetic aperture radar inverse scattering reconstruction using convolutional neural networks. Applications of Machine Learning.


Suzanne Sindi, co-author. Mathematical Modeling to Identify Clotting Factor Combinations That Modify Thrombin Generation in Hemophilia. Blood.


Noemi Petra, co-author. On the implementation of a quasi-Newton interior-point method for PDE-constrained optimization using finite element discretizations. Optimization Methods and Software.


Erica Rutter, co-author. Traveling wave speed and profile of a “go or grow” glioblastoma multiforme model. Communications in Nonlinear Science and Numerical Simulation.


Arnold Kim and Camille Carvalho, co-authors. Capturing plasmonic behaviors in light scattering by spheres using finite element methods and asymptotic quadrature. WAVES 2022.

Arnold Kim and Camille Carvalho, co-authors. Asymptotic analysis for sound-hard acoustic scattering by two closely-situated spheres. WAVES 2022.


Arnold Kim and Camille Carvalho, co-authors. Quadrature by Parity Asymptotic eXpansions (QPAX) for light scattering by high aspect ratio plasmonic particle. WAVES 2022.


Suzanne Sindi, co-author. A structured model and likelihood approach to estimate yeast prion propagon replication rates and their asymmetric transmission. PLOS Computational Biology.


Arnold Kim and Boaz Ilan, co-authors. Radiance backscattered by a strongly scattering medium in the high spatial frequency limit. Journal of the Optical Society of America.


Suzanne Sindi, Clarissa Nobile, Aaron Hernday, co-authors. Genome-wide Profiling of Transcription Factor-DNA Binding Interactions in Candida albicans: A Comprehensive CUT&RUN Method and Data Analysis Workflow. JoVE Journal.


Harish S. Bhat, co-author. Resampling to address inequities in predictive modeling of suicide deaths. BMJ Health & Care Informatics.


Harish Bhat, co-author. Suicide Risk Among Hospitalized Versus Discharged Deliberate Self-Harm Patients: Generalized Random Forest Analysis Using a Large Claims Data Set. American Journal of Preventative Medicine.


Erica Rutter, co-author. Multitask neural networks for predicting bladder pressure with time series data. Biomedical Signal Processing and Control.


Harish Bhat and Christine Isborn, co-authors. Statistical Learning for Predicting Density-Matrix Based Electron Dynamics. Stat.


Harish Bhat, co-author. Equity-Weighted Bootstrapping: Examples and Analysis. Stat.


Chrysoula Tsogka, co-author. Stretching Method-Based Damage Detection Using Neural Networks. Sensors.


Suzanne Sindi and Miriam Barlow, co-authors. Distribution of β-Lactamase Genes in Clinical Isolates from California Central Valley Hospital Deviates from the United States Nationwide Trends. Antibiotics.


Maxime Theillard, author. A volume-preserving reference map method for the level set representation. Journal of Computational Physics.


Maxime Theillard, Dustin Kleckner, and Shilpa Kahatri, co-authors. Retention of rising droplets in density stratification. Physical Review Fluids.


Book Chapter: Boaz Ilan and Arnold D. Kim, co-authors. Radiative transfer of light in strongly scattering media. Springer Series in Light Scattering.


Camille Carvalho, co-author. A fully fourth order accurate energy stable finite difference method for Maxwell’s equations in metamaterials. IEEE Journal on Multiscale and Multiphysics Computational Techniques.


Molecular and Cell Biology Publications

Chris Amemiya, co-author. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature


Clarissa Nobile, co-author. Broad susceptibility of Candida auris strains to 8- hydroxyquinolines and mechanisms of resistance. American Society for Microbiology, Mycology.


Clarissa Nobile, co-author. Candida vulturna Outbreak Caused by Cluster of Multidrug-Resistant Strains, China. Europe PMC.


Clarissa Nobile, co-author. Worldwide emergence of fluconazole-resistant Candida parapsilosis: current framework and future research roadmap. The Lancet.


Clarissa Nobile, co-author. Atmospheric humidity regulates same-sex mating in Candida albicans through the trehalose and osmotic signaling pathways. Science China Life Sciences.


Chris Amemiya, co-author. Genome reveals how the skate got its wings. Nature. 

Rudy Ortiz, co-author. Exogenous Thyroxine Increases Cardiac Nrf2 and the Potential to Upregulate Nrf2-Mediated Antioxidant Defense Mechanisms in Insulin Resistant OLETF rats. APS.


Rudy Ortiz and Juris Grasis, co-authors. Increased dose and duration of infection with human adenovirus serotype 5 shifts amino acid, nucleic acid, TCA, and carbohydrate metabolism in human kidney cells. APS.


Rudy Ortiz, co-author. Angiotensin receptor blocker ameliorates hypertension, improves glucose intolerance, and reduces visceral fat in OLETF rats fed a high-cholesterol diet. APS.


Petra Kranzfelder, co-author. Breakout Rooms, Polling, and Chat, Oh COPUS! The Adaptation of COPUS for Online Synchronous Learning. Research and Practice in Assessment.


Maggie Sogin, co-author. Hawaiian coral holobionts reveal algal and prokaryotic host specificity, intraspecific variability in bleaching resistance, and common interspecific microbial consortia modulating thermal stress responses. Science of the Total Environment.


Maggie Sogin, co-author. Light-dependent metabolic shifts in the model diatom Thalassiosira pseudonana. Algal Research.


Gabriela Loots, co-author. Antibiotic Treatment Prior to Injury Abrogates the Detrimental Effects of LPS in STR/ort Mice Susceptible to Osteoarthritis Development. JMBR Plus.


Clarissa Nobile, co-author. Clinical isolates of Candida auris with enhanced adherence and biofilm formation due to genomic amplification of ALS4. PLOS Pathogens.


Gabriela Loots, co-author. Sostdc1 Suppression in the Absence of Sclerostin Potentiates Anabolic Action of Cortical Bone in Mice. JBMR.


Clarissa Nobile and Suzanne Sindi, co-authors. A Computational Workflow for Analysis of 3′ Tag-Seq Data. Current Protocols.


Gabriela Loots, co-author. Degradation-Resistant Hypoxia Inducible Factor-2α in Murine Osteocytes Promotes a High Bone Mass Phenotype. JBMR Plus.


Gabriella Loots, co-author. Single-cell RNA-Seq reveals changes in immune landscape in post-traumatic osteoarthritis. Frontiers in Immunology.


Rudy Ortiz, co-author. Improved lipogenesis gene expression in liver is associated with elevated plasma angiotensin 1-7 after AT1 receptor blockade in insulin-resistant OLETF rats. Molecular and Cellular Endocrinology.


Petra Kranzfelder, co-author. Predicting implementation of active learning by tenure-track teaching faculty using robust cluster analysis. International Journal of STEM Education.


Nestor Oviedo and Petra Kranzfelder, co-authors. Collaborative Teaching plus (CT+): A Timely, Flexible, and Dynamic Course Design Implemented during Emergency Remote Teaching in an Introductory Biology Course. CBE—Life Sciences Education, The American Society for Cell Biology.


Rudy Ortiz, co-author. Perilipin Isoforms and PGC-1 Are Regulated Differentially in Rat Heart during Pregnancy-Induced Physiological Cardiac Hypertrophy. Medicina.


Michael Cleary, co-author. mRNAs encoding neurodevelopmental regulators have equal N6-methyladenosine stoichiometry in Drosophila neuroblasts and neurons. Neural Development.


Rudy Ortiz, co-author. Angiotensin receptor blockade with olmesartan alleviates brain pathology in obese OLETF rats. Clinical and Experimental Pharmacology and Physiology.


Gabriella Loots, co-author. Isolation of Murine Articular Chondrocytes for Single-Cell RNA or Bulk RNA Sequencing Analysis. Methods in Molecular Biology.


Bercem Dutagaci, co-author. Molecular Dynamics Simulations of Rhodamine B Zwitterion Diffusion in Polyelectrolyte Solutions. The Journal of Physical Chemistry.


Clarissa Nobile, co-author. Antifungal drug-resistance mechanisms in Candida biofilms. Current Opinion in Microbiology.


Marcos García-Ojeda, co-author. An Upper-Division, Remote Microbiology Laboratory That Blends Virtual and Hands-on Components to Promote Student Success during the COVID-19 Pandemic. Journal of Microbiology and Biology Education.


Clarissa Nobile, co-author. Mucin O-glycans are natural inhibitors of Candida albicans pathogenicity. Nature Chemical Biology.  


Gabriela Loots, co-author. Pre‐existing Type 1 Diabetes Mellitus Blunts the Development of Post‐Traumatic Osteoarthritis. JBMR Plus.


Gabriela Loots, co-author. Interactions between diabetes mellitus and osteoarthritis; from animal studies to clinical data. JBMR Plus.


Suzanne Sindi, Clarissa Nobile, Aaron Hernday, co-authors. Genome-wide Profiling of Transcription Factor-DNA Binding Interactions in Candida albicans: A Comprehensive CUT&RUN Method and Data Analysis Workflow. JoVE Journal.


Nestor Oviedo, co-author. Analysis of DNA Double-Stranded Breaks Using the Comet Assay in Planarians. Methods in Molecular Biology.


Clarissa Nobile, co-author. Candida auris infections in China. Virulence.


Juris Grasis and Nestor Oviedo, co-authors. Non-traditional roles of immune cells in regeneration: an evolutionary perspective. Development.


Rudy Ortiz, co-author. Cardiac NF-κB Acetylation Increases While Nrf2-Related Gene Expression and Mitochondrial Activity Are Impaired during the Progression of Diabetes in UCD-T2DM Rats. Antioxidants.


Gabriela Loots, co-author. Synthetic antibacterial minerals: harnessing a natural geochemical reaction to combat antibiotic resistance. Scientific Reports.


Gabriela Loots, co-author. Extracellular matrix modulates T cell clearance of malignant cells in vitro. Biomaterials.


Clarissa Nobile, co-authorDiscovering the chlamydospore regulatory network in Candida albicans. Microbiology Society.


Chris Amemiya, co-author. The lungfish cocoon is a living tissue with antimicrobial functions. Science Advances.


Nestor J. Oviedo, co-author. Can neural signals override cellular decisions in the presence of DNA damage? DNA Repair.


David H. Ardell, co-author. tSFM 1.0: tRNA Structure–Function Mapper. Bioinformatics.


Suzanne Sindi and Miriam Barlow, co-authors. Distribution of β-Lactamase Genes in Clinical Isolates from California Central Valley Hospital Deviates from the United States Nationwide Trends. Antibiotics.


Fred W. Wolf, co-author. Thirst interneurons that promote water seeking and limit feeding behavior in Drosophila. eLife.


Maria E. Zoghbi, co-author. ABCB10 exports mitochondrial biliverdin, driving metabolic maladaptation in obesity. Science Translational Medicine.


Rudy Ortiz, co-author. Blood Transcriptome Profiling Reveals Diet-Induced Changes in Metabolic Pathway Gene Expression. Current Developments in Nutrition.


Gabriela Loots, co-author. Single-Cell RNA-Seq Reveals Transcriptomic Heterogeneity and Post-Traumatic Osteoarthritis-Associated Early Molecular Changes in Mouse Articular Chondrocytes. Cells.


Clarissa J. Nobile, co-author. Visible Lights Combined with Photosensitizing Compounds Are Effective against Candida albicans Biofilms. Microorganisms.


Clarissa J. Nobile, co-author. Filamentous growth is a general feature of Candida auris clinical isolates. Medical Mycology.


Clarissa J. Nobile, co-author. Candida auris: Epidemiology, biology, antifungal resistance and virulence. PLOS Pathogens.


Clarissa J. Nobile and Aaron D. Hernday, co-authors. The Roles of Chromatin Accessibility in Regulating the Candida albicans White-Opaque Phenotypic Switch. Journal of Fungi.


Nestor Oviedo, co-author. Whole planarian chromosome squash. STAR Protocols.


Ramendra N. Saha, co-author. Merits and limitations in studying neuronal depolorization-dependent processes using elevated external potassium. American Society for Neurochemistry.


Rudy M. Ortiz, co-author. Prolonged fasting does not increase oxidative damage or inflammation in post weaned northern elephant seal pups. Journal of Experimental Biology.


Maria E. Zoghbi, co-author. Production of a human mitochondrial ABC transporter in E. Coli. Protein Expression and Purification.


Chris T. Amemiya, co-author. Generation of lamprey monoclonal antibodies (lampribodies) using the phage display system. Biomolecules.


Rudy M. Ortiz, co-author. Simultaneous angiotensin receptor blockade and glucagon-like peptide-1 receptor activation ameliorate albuminuria in obese insulin-resistant rats. Clinical and Experimental Pharmacology and Physiology.


David H. Ardell, co-author. tRNA functional signatures classify plastids as late-branching cyanobacteria. BMC Evolutionary Biology


Ramendra N. Saha, co-author. Certain ortho-hydroxylated brominated ethers are promiscuous kinase inhibitors that impair neuronal signaling and neurodevelopmental processes. Journal of Biological Chemistry.



Life & Environmental Sciences Publications

Elizabeth Dumont, co-author. Neuronal scaling in the olfactory system of bats. The Anatomical Record.


Rebecca Ryals, Asmeret Asefaw Berhe and Jennifer Pett-Ridge, co-authors. The Deep Soil Organic Carbon Response to Global Change. Annual Review of Ecology, Evolution, and Systematics.


Adeyemi A. Adebiyi, co-author. The Misrepresentation of the Southern African Easterly Jet in Models and Its Implications for Aerosol, Clouds, and Precipitation Distributions. American Meteorological Society. 


Rebecca Ryals and Teamrat Ghezzehei, co-authors. The effects of different biochar-dairy manure co-composts on soil moisture and nutrients retention, greenhouse gas emissions, and tomato productivity: Observations from a soil column experiment. Agrosystems, Geosciences & Environment.


Rebecca Ryals and Asmeret Asefaw Berhe, co-author. Impacts of organic matter amendments on urban soil carbon and soil quality: A meta-analysis. Journal of Cleaner Production. 


Peggy O’Day, co-author. Operationalizing Real-Time Monitoring Data in Simulation Models Using the Public Domain HEC-DSSVue Software Platform. Journal of Water Resources Planning and Management.


Emily Moran, co-author. Masting is uncommon in trees that depend on mutualist dispersers in the context of global climate and fertility gradients. Nature Plants.


Peggy O’Day and Sam Traina, co-authors. Characterization of Manganese Oxide Modified Activated Carbon for Remediation of Redox-Sensitive Contaminants. ACS Earth Space Chem.


Jessica Blois, co-author. Strengthening global-change science by integrating aeDNA with paleoecoinformatics. Trends in Ecology & Evolution. 


Adeyemi Adebiyi, co-author. Observations suggest that North African dust absorbs less solar radiation than models estimate. Nature.


Steve Hart, co-author. Standardized Data to Improve Understanding and Modeling of Soil Nitrogen at Continental Scale. AGU.


Rebecca Ryals, co-author. Compost amendment to enhance carbon sequestration in rangelands. Journal of Soil and Water Conservation.


Emily Moran, co-author. Linking seed size and number to trait syndromes in trees. Global Ecology and Biogeography.


Emily Moran, co-author. Heritability of plastic trait changes in drought-exposed ponderosa pine seedlings. Ecosphere.


Gordon Bennett, co-author. Genomic Comparisons Reveal Selection Pressure
and Functional Variation Between Nutritional Endosymbionts of Cave-Adapted and Epigean Hawaiian Planthoppers.


Rebecca Ryals, co-author. Carbon farming can enhance pollinator resources. California Agriculture.


Adeyemi Adebiyi, co-author. Mineral dust aerosol impacts on global climate and climate change. Nature Reviews Earth and Environment.


Teamrat Ghezzehei and Rebecca Ryals, co-authors. Biochar co-compost improves nitrogen retention and reduces carbon emissions in a winter wheat cropping system. Wiley.


Jessica Blois, co-author. Phylogeography within the Peromyscus maniculatus species group: Understanding past distribution of genetic diversity and areas of refugia in western North America. Elsevier, Molecular Phylogenetics and Evolution.


Justin Yeakel and Sora Kim, co-authors. Supplementary Materials: Decoding the dynamics of dental distributions: insights from shark demography and dispersal. Royal Society Open Science. 


Stephen Hart and Asmeret Asefaw Berhe, co-authors. Impacts of climate and forest management on suspended sediment source and transport in montane headwater catchments. Hydrological Processes.


Jason Sexton, co-author. Environmental DNA (eDNA) detects temporal and habitat effects on community composition and endangered species in ephemeral ecosystems: a case study in vernal pools. Wiley.


Jessica Blois, co-author. A solution to the challenges
of interdisciplinary aggregation and use of specimen-level trait data.


Stephen Hart, co-author. Leaf endophytic microbiomes of different almond cultivars grafted to the same rootstock. Applied Microbiology International.


Peggy O’Day, co-author. Multimodal X-ray nano-spectromicroscopy analysis of chemically heterogeneous systems. Metallomics.


Michael Dawson, co-author. Species' attributes predict the relative magnitude of ecological and genetic recovery following mass mortality. Wiley Molecular Ecology.


Michael Beman, co-author. Multiple sources of aerobic methane production in aquatic ecosystems include bacterial photosynthesis. Nature Communications.


Stephen Hart and Asmeret Asefaw Berhe, co-authors. Climate Warming Alters Nutrient Storage in Seasonally Dry Forests: Insights From a 2,300 m Elevation Gradient. Global Biogeochemical Cycles.


Stephen Hart and Asmeret Asefaw Berhe, co-authors. Climatic controls on soil and saprock nitrogen distribution and persistence in the Sierra Nevada. Journal of Plant Nutrition and Soil Science.


Gordon Bennet, co-author. A complex interplay of evolutionary forces continues to shape ancient co-occurring symbiont genomes. iScience.


Emily Jane Mctavish, co-author. Approachable Case Studies Support Learning and Reproducibility in Data Science: An Example from Evolutionary Biology. Journal of Statistics and Data Science Education.


Rebecca Ryals, co-author. Dairy Manure Co-composting with Wood Biochar Plays a Critical Role in Meeting Global Methane Goals. Environmental Science and Technology.


Danielle Edwards and Jessica Blois, co-authors. Colour morph predicts social behaviour and contest outcomes in a polymorphic lizard (Podarciserhardii). USDA Pub Ag.


Justin Yeakel and Sora Kim, co-authors. Decoding the dynamics of dental distributions: insights from shark demography and dispersal. Proceedings of the Royal Society B Biological Sciences.


Peggy O’Day, co-author. Effects of flow on uranium speciation in soils impacted by acidic waste fluids. Journal of Environmental Radioactivity.


Michael Beman, co-author. Thousands of small, novel genes predicted in global phage genomes. Cell Reports.


Danielle Edwards, co-author. Environmental correlates of phenotypic evolution in ecologically diverse Liolaemus lizards. Ecology and Evolution.


Peggy O’Day, co-author.  Iron Speciation in Respirable Particulate Matter and Implications for Human Health. Environmental Science and Technology.


Stephen C. Hart, co-author. Ecological and genomic responses of soil microbiomes to high-severity wildfire: linking community assembly to functional potential. The ISME Journal.


Emily Moran, co-author. Globally, tree fecundity exceeds productivity gradients. Ecology Letters.


Emily Moran, co-author. Limits to reproduction and seed size-number trade-offs that shape forest dominance and future recovery. Nature Communications.


Jason Sexton, Carolin Frank and J. Michael Beman, co-authors. Archaeal and Bacterial Diversity and Distribution Patterns in Mediterranean-Climate Vernal Pools of Mexico and the Western USA. Microbial Ecology.


Emily Moran, co-author. North American tree migration paced by climate in the West, lagging in the East. PNAS.


Adeyemi Adebiyi, co-author. Parameterization for the Emission of Super Coarse Desert Dust. Geophysical Research Letters.


J. Michael Beman, co-author. Substantial oxygen consumption by aerobic nitrite oxidation in oceanic oxygen minimum zones. Nature Communications.


Peggy O’Day, co-authorCritical review of mercury methylation and methylmercury demethylation rate constants in aquatic sediments for biogeochemical modeling. Critical Reviews in Environmental Science and Technology.


Asmeret Asefaw Berhe and Stephen C. Hart, co-authors.  Impacts of climate and disturbance on nutrient fluxes and stoichiometry in mixed-conifer forests. Biogeochemstry.


Asmeret Asefaw Berhe and Stephen C. Hart, co-authorsDeep in the Sierra Nevada critical zone: saprock represents a large terrestrial organic carbon stock. Environmental Research Letters.


Stephen C. Hart and Asmeret Asefaw Berhe, co-authors. Stream Water Chemistry in Mixed-Conifer Headwater Basins: Role of Water Sources, Seasonality, Watershed Characteristics, and Disturbances. Ecosystems.


Justin D. Yeakel, co-author. Carbon and strontium isotope ratios shed new light on the paleobiology and collapse of Theropithecus, a primate experiment in graminivory. Palaeogeography, Palaeoclimatology, Palaeoecology.


Stephen C. Hart and J. Michael Beman, co-authors. Methane dynamics of high-elevation lakes in the Sierra Nevada California: the role of elevation, temperature, and inorganic nutrients. Inland Waters.


Elizabeth R. Dumont, co-author. Find the food first: An omnivorous sensory morphotype predates biomechanical specialization for plant based diets in phyllostomid bats. International Journal of Organic Evolution.


Peggy A. O’Day, co-author. Phosphate controls uranium release from acidic waste-weathered Hanford sediments. Journal of Hazardous Materials.


Michael N. Dawson and Emily Jane McTavish, co-authors. Landscape analyses using eDNA metabarcoding and Earth observation predict community biodiversity in California. Ecological Applications.


Danielle L. Edwards, co-author. A return-on-investment approach for prioritization of rigorous taxonomic research needed to inform responses to the biodiversity crisis. PLOS Biology.


Danielle Edwards, co-author. Environmental drivers of sexual dimorphism in a lizard with alternative mating strategies. Journal of Evolutionary Biology.


Emily Jane McTavish, co-author. Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life. BMC Bioinformatics.


Jason P. Sexton, co-author. The CALeDNA program: Citizen scientists and researchers inventory California's biodiversity. California Agriculture.


Rebecca R. Ryals, co-author.  Reducing climate impacts of beef production: A synthesis of life cycle assessments across management systems and global regions. Global Change Biology.


Emily Moran, co-author. Continent-wide tree fecundity driven by indirect climate effects. Nature Communications.


Jessica L. Blois, co-author. Occupancy models reveal regional differences in detectability and improve relative abundance estimations in fossil pollen assemblages. Quaternary Science Reviews.


Asmeret A. Berhe and Teamrat A. Ghezzehei, co-authors. Race and racism in soil science. European Journal of Social Science.


Danielle L. Edwards, co-author. Trait differences among discret morphs of a color polymorphic lizard, Podarcis erhardii. Peer J. Life & Environmental.


Asmeret A. Berhe and Teamrat A. Ghezzehei, co-authors. Towards diverse representation and inclusion in soil science in the United States. Social Science Society of America Journal.


Peggy A. O’Day, co-author. Effects of mercury, organic carbon, and microbial inhibition on methylmercury cycling at the profundal sediment-water interface of a sulfate-rich hypereutrophic reservoir. Environmental Pollution.


Justin D. Yeakel, co-author. Modern models of trophic meta-communities. Philosophical Transactions B.


Peggy A. O’Day, co-author. Iron speciation in particulate matter (PM2.5) from urban Los Angeles using spectro microscopy methods. Atmospheric Environment.


Stephen C. Hart, co-author. Montane meadows: A soil carbon sink or source? Ecosystems.


J. Michael Beaman and Michael N. Dawson, co-authors. Microbes and macro-invertebrates show parallel B-diversity but contrasting a-diversity patterns in a marine natural experiment. Proceedings of the Royal Society B.


J. Michael Beman, co-author. Climatic, physical and biogeochemical changes drive rapid oxygen loss and recovery in a marine ecosystem. Scientific Reports.


J. Michael Beman, co-author. Euphotic zone nitrification in the California current ecosystem. Limnology and Oceanography.


Jessica L. Blois, co-author. A protocol for differentiating late Quaternary leporids in southern California with remarks on Project 23 lagomorphs at Rancho La Brea, Los Angeles, California, USA. PaleoBios.


Stephan C. Hart, co-author. Climatic vulnerabilities and ecological preferences of soil invertebrates across biomes. Molecular Ecology.


Elizabeth R. Dumont, co-author. Intraspecific make combat behavior predicts morphology of cervical vertebrae in ruminant mammals. Proceeding of the Royal Society B.


Elizabeth R. Dumont, co-author. How moles walk; it’s all thumbs. Biology Letters.



Chemistry and Biochemistry Publications

Shahar Sukenik, co-author. Intrinsically disordered regions are poised to act as sensors of cellular chemistry. Trends in Biochemical Sciences.


Michael Findlater, co-author. Homogeneous and Recyclable Palladium Catalysts: Application in Suzuki–Miyaura Cross-Coupling Reactions. Organometallics


Son Nguyen, co-author. Photocatalysis of Metallic Nanoparticles: Interband vs Intraband Induced Mechanisms. Journal of Physical Chemistry.


Aleksandr Noy, co-author. Fabrication of Atomically Precise Nanopores in 2D Hexagonal Boron Nitride Using Electron and Ion Beam Microscopes. Microscopy and Microanalysis. 


Michael Findlater, co-author. Improved Syntheses of an Arseno-Fatty Acid (As-FA 362) and an Arseno-Hydrocarbon (As-HC 444). Thieme.


Andy Liwang, co-author. Protocols for in vitro reconstitution of the cyanobacterial circadian clock. Biopolymers


Tao Ye, co-author. Single molecule insights into interfacial molecular recognition for model electrochemical DNA biosensors. Science Direct.





Aleksandr Noy, co-author. Co-Assembly of Carbon Nanotube Porins into Biomimetic Peptoid Membranes. Small


Michael Findlater, co-author. Electrochemically Driven Hydrogen Atom Transfer Catalysis: A Tool for C(sp3)/Si–H Functionalization and Hydrofunctionalization of Alkenes. ACS Catalysis.


Shahar Sukenik, co-author. When Phased without Water: Biophysics of Cellular Desiccation, from Biomolecules to Condensates. ACS.


Andy LiWang, co-author. Synchronization of the circadian clock to the environment tracked in real time. PNAS.


Tao Ye, co-author. Simulations of Subnanometer Scale Image Contrast in Atomic Force Microscopy of Self-Assembled Monolayers in Water. Chemical and Biomedical Imaging.


Son Nguyen, co-author. Experimental and Thermodynamic Viewpoints on Claims of a Spontaneous H2O2 Formation at the Air–Water Interface. The Journal of Physical Chemistry B.


Aleksandr Noy, co-author. Fluids and Electrolytes under Confinement in Single-Digit Nanopores. ACS Chemical Reviews.


Aleksandr Noy, co-author. Co-Assembly of Carbon Nanotube Porins into Biomimetic Peptoid Membranes. Wiley Online Library.


Aleksandr Noy, co-author. Nanofluidic computing makes a splash. Science.


Christine Isborn and Liang Shi, co-authors. Incorporating Polarization and Charge Transfer into a Point Charge Model for Water using Machine Learning. ChemRxiv.


Aleksandr Noy, co-author. Breakdown of the Nernst–Einstein relation in carbon nanotube porins. Nature Nanotechnology.


Liang Shi, co-author. Molecular Property Prediction with Photonic Chip-Based Machine Learning. Wiley Online Library, Laser and Photonics Reviews.


Christine Isborn, co-author. Molecular polariton electroabsorption. Nature Communications.


Michael Findlater, co-author. Improved Syntheses of 4′-Vinylbenzo-3n-Crown-n Ethers (n = 5–7). The Journal of Organic Chemistry.


Tao Ye, co-author. One-Step Ligand-Exchange Method to Produce Quantum Dot–DNA Conjugates for DNA-Directed Self-Assembly. ACS Applied Materials and Interfaces.


Tao Ye, co-author. Potential-Dependent Adhesion Forces between dsDNA and Electroactive Surfaces. American Chemical Society.


Michael Findlater, co-author. Redox-Active BIAN-Based Iron Complexes in Catalysis. Chemistry Europe.


Andy LiWang, co-author. Coupling of distant ATPase domains in the circadian clock protein KaiC. Nature Structural & Molecular Biology.


Liang Shi, co-author. Epitope alteration by small molecules and applications in drug discovery. Royal Society of Chemistry.


Hrant Hratchian and Ryan Baxter co-authors. Enhanced Reactivity for Aromatic Bromination via Halogen Bonding with Lactic Acid Derivatives. Journal of Organic Chemistry.


Michael Findlater, co-author. Progress in Convergent Paired Electrolysis. Chemistry Europe.


Michael Findlater, co-author. Cobalt-Catalyzed Alkylation of Nitriles with Alcohols. Organometallics.


Aurora Pribram-Jones, co-author. Assessing Mg–Sc–(rare earth) ternary phase stability via constituent binary cluster expansions. Computational Materials.


Tao Ye, co-author. Hybridization and self‐assembly behaviors of surface‐immobilized DNA in close proximity: A single‐molecule perspective. Aggregate.


Michael Findlater, co-author. Catalyst-Dependent Direct and Deoxygenative Coupling of Alcohols by Convergent Paired Electrolysis. CCS Chemistry.


Son C. Nguyen, co-author. Revisiting the Effect of the Air–Water Interface of Ultrasonically Atomized Water Microdroplets on H2O2 Formation. The Journal of Physical Chemistry B.


Michael Findlater, co-author. Applications of catalysis in hydroboration of imines, nitriles, and carbodiimides. Organic & Biomolecular Chemistry.


Son C. Nguyen, co-author. Revisiting the Effect of the Air–Water Interface of Ultrasonically Atomized Water Microdroplets on H₂O₂ Formation. Journal of Physical Chemistry Letters.


Michael Findlater, co-author. Kolbe reaction goes reductive. Nature Synthesis.


Michael Findlater, co-author. Selective Removal of Barium and Hardness Ions from Brackish Water with Chemically Enhanced Electrodialysis. ACS ES&T Water.


Aurora Pribram-Jones and Hrant Hratchian, co-authors. Using projection operators with maximum overlap methods to simplify challenging self-consistent field optimization. Journal of Computational Chemistry.


Andy LiWang, co-author. A Night-Time Edge Site Intermediate in the Cyanobacterial Circadian Clock Identified by EPR Spectroscopy. Journal of the American Chemical Society.


Son C. Nguyen, co-author. Effect of Photocharging on Catalysis of Metallic Nanoparticles. Journal of Physical Chemistry Letters.


Aleksandr Noy, co-author. Early-Stage Aggregation and Crystalline Interactions of Peptoid Nanomembranes. Journal of Physical Chemistry Letters.


Shahar Sukenik, co-author. A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation. Cell.


Son C. Nguyen, co-author. Catalytic Mechanism of Interfacial Water in the Cycloaddition of Quadricyclane and Diethyl Azodicarboxylate. Journal of Physical Chemistry Letters.


Andy LiWang, co-author. A Cyanobacterial Component Required for Pilus Biogenesis Affects the Exoproteome. mBio.


Aurora Pribram-Jones, co-author. Predicting ductility in quaternary B2-like alloys. Physical Review Materials.


Christine M. Isborn, co-author. Explicit environmental and vibronic effects in simulations of linear and nonlinear optical spectroscopy. Journal of Chemical Physics.


Liang Shi and Christine M. Isborn, co-authors. Vibronic and environmental effects in simulations of optical spectroscopy. Annual Review of Physical Chemistry.


Aurora Pribram Jones, co-author. New density-functional approximations and beyond: general discussion. Faraday Discussions.


Shahar Sukenik, co-author. Revealing hidden sensitivity of intrinsically disordered proteins to their chemical environment. The Journal of Physical Chemistry Letters.


Liang Shi and Christine M. Isborn, co-authors. The influence of electronic polarization on the sprectral density. Journal of Physical Chemistry B.


Aleksandr Noy, co-author. Antifouling strategies for protecting bioelectronic devices. APL Materials.


Aurora Pribram Jones, co-author. Challenges for large scale simulation: general discussion. Faraday Discussions.


Hrant P. Hratchian, co-author. Exceptionally complex electronic structures of lanthanide oxides and small molecules. Accounts of Chemical Research.


Book Chapter: Michelle Leslie, Christine M. Isborn, Erik Menke, Benjamin J. Stokes and Hrant P. Hratchian, co-authors. Aiming towards an effective Hispanic-serving chemistry curriculum. Growing Diverse STEM Communities: Methodology, Impact and Evidence.


Aleksandr Noy, co-author. A new type of artificial water channels. Nature Nanotechnology.


Aleksandr Noy, co-author. Strong electroosmotic coupling dominates ion conductance of 1.5 nm diameter carbon nanotube porins. ACS Nano.


Christine M. Isborn, co-author. Molecular dynamics simulations of alkaline earth metal ions binding to DNA reveal ion size and hydration effects. Physical Chemistry Chemical Physics.


Tao Ye, co-author. Simulation of subnanometer contrast in synamic atomic force microscopy of hydrophilic alkanethiol self-assembled monolayers in water. Langmuir.