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Recent Publications

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

Physics Publications


 

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


 

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


 

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

 

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


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.