Computational biology of gene expression systems, including:
- Structure, function, evolution and coevolution with genomes
- Functional and evolutionary bioinformatics of RNA and proteins
- Evolutionary and comparative genomics
Professor Berhe's research is broadly focused on soil science and global change science. The main goal of her research is to understand the effect of changing environmental conditions on vital soil processes, most importantly the cycling and fate of essential elements in the critical zone. She studies soil processes in systems experiencing natural and/or anthropogenic perturbation in order to understand fundamental principles governed by geomorphology, and contemporary modifications introduced by changes in land use and climate.
Professor Berhe's general research themes are:
- Effect of climate changes (specifically rainfall and temperature) on storage and stabilization of soil organic matter and cation nutrient budgets
- Nano-scale biogeochemistry of iron oxides, especially how the size and concentration of oxides in soil control stabilization and destabilization of organic matter
- Erosion and terrestrial carbon sequestration, specifically temporal evolution of the erosion-induced terrestrial carbon sink and reconstruction of environmental history from sediments
- Political ecology of land degradation and ownership, particularly the contribution of armed conflicts to land degradation and ways people relate to their environment
- Delayed random walks and stochastic delay differential equations
- Option pricing
- Statistical analysis of financial data
- Optimization of circuits and networks
- Wave propagation in electromagnetic media and analog circuits
- Numerical analysis and scientific computing
Professor Blanchette is an applied mathematician primarily interested in problems involving fluid dynamics. A large portion of his research is concerned with problems related to sedimentation. The accumulation patterns, erosion potential and transport properties of such systems are of geophysical and environmental interest. He also studies systems where two immiscible fluids are present and surface tension plays a significant role, such as drops, bubbles and micro-fluidic devices. Professor Blanchette's approach is mostly theoretical and numerical, and he also values interactions with experimentalists so as to paint as complete a picture as possible of a given physical system.
Raymond Chiao is a professor jointly in the UC Merced schools of Natural Sciences and Engineering. Previously, he was a professor for 38 years at UC Berkeley, where he earned international acclaim (including the Willis E. Lamb Medal and the Einstein Prize for Laser Science) studying nonlinear and quantum optics. At UC Merced, is pursuing a new line of groundbreaking research on gravitational radiation.
Professor Cleary is interested in how complex tissues develop from relatively small populations of stem cells. Nervous system development in the fruit fly, Drosophila melanogaster, provides an excellent model system for studying this process. His lab focuses on how Drosophila neural stem cells, called neuroblasts, which produce the diversity of cell types found in the nervous system. His primary aim is to understand:
- How cell fate decisions are temporally regulated, so that distinct cell types are made at specific times during development
- How mitotic activity is regulated, so that neuroblasts stop and start dividing at the proper time
- How cell fate information is passed from a neuroblast to its progeny and the role of chromatin remodeling factors and other transcription factors in this process
His research team uses the many powerful molecular and genetic techniques available for Drosophila research to address these questions, with the ultimate goal of identifying mechanisms that are conserved in human stem cells.
Associate Dean for Academic Programs and Professor, Chemistry & Biochemistry
The past century has seen tremendous progress in determining the biochemical and biophysical processes that constitute life. One exciting consequence of this understanding is the possibility of developing mathematical models of biological function that are accurate and even predictive.
Professor Colvin's research uses a wide range of simulation methods to model biological systems at different levels. Much of his research uses molecular modeling to study biochemical problems, with a particular emphasis on modeling the activity of DNA-binding food mutagens and anticancer drugs. These methods involve computing the structures and energetics of biomolecules using either quantum or classical mechanics, and often require the use of supercomputers.
Other molecular modeling projects include studying:
- Synthetic analogs to nucleic acids and exotic nucleic acid structures
- The function of DNA-processing multiprotein complexes
- The mechanism of cytochrome P450 and other enzymes
More recently, his research interests have expanded to include simulations of biophysical and cellular processes using equations that describe the system as continuous (and sometime stochastic) dynamical systems. These projects include:
- Simulating the formation mutagenic compounds during cooking
- The operation of the nuclear pore complex
- Cell fate decisions
These projects offer a wide range of research projects for students interested in the application of mathematics and computers to understand the living world.
Millions of species demonstrate that evolution happens, but few illuminate the process. Professor Dawson's lab focuses on elucidating the origins, maintenance, and loss of marine biodiversity, from molecular to ecosystem levels. His specific interests are:
- How molecular variation explains and causes differences between individuals, populations, species, and higher taxa
- How the environment shapes and is shaped by genetic, organismal, population, and community variation
His lab's work scales from micro- to macro-evolution and integrates biological and physical sciences. Topic areas include:
- Adaptation, ecological genetics and evolutionary ecology
- Population genetics, phylogeography, biogeography and phylogenetics
- Speciation, systematics and taxonomy
- Behavior and morphology
- Climate change, invasive species and marine protected areas
Professor Edwards' research focuses on understanding how the environment affects the evolution of phenotype and behavior in reptiles. To do this, she incorporates ecological, genomic, behavioral and phenotypic information to look at:
- how the landscape affects evolutionary history;
- how shifts in ecological niche drive phenotypic evolution; and
- how ecological and sexual selection combine during speciation.
She is also interested in using integrative studies to inform conservation management strategies for endangered and vulnerable reptiles and amphibians.
Professor Frey’s research interests include effective instructional practices in STEM education. Frey also studies computational modeling of nonlinear elastic systems with applications in planetary science.
We study mechanisms of cell signaling in the developing brain, focusing on primary cilium, the antenna-like organelle that integrate signaling pathways in the cell. Our research aims to shed light on how signaling errors lead to brain developmental disorders.
Ge X*, Yang H, Bednarek MA, Galon-Tilleman H, Chen P, Chen M, Lichtman JS, Wang Y, Dalmas O, Yin Y, Tian H, Jermutus L, Grimsby J, Rondinone, CM, Konkar A, Kaplan, DD. (2018) LEAP2 is an endogenous Antagonist of the Ghrelin Receptor. Cell Metabolism. 27(2): 461-469. doi: 10.1016/j.cmet.2017.10.01 *Author of correspondence.
Ge X, Milenkovic L, Suyama K, Hartl T, Winan A, Meyer T, Scott MP. (2015) Integration of Neuropilin with Hedgehog signal transduction through control of Phosphodiesterase 4 and protein kinase A. eLife. 4:e07068. DOI: 10.7554/eLife.07068.
Ge X, Frank CL, Calderon de Anda F, Tsai LH. (2010) Hook3 and PCM1 regulate neurogenesis by controlling the centrosome dynamics and interkinetic nuclear migration. Neuron 65:191-203
Professor Ghezzehei's research interest is in the movement and transformation of mass and energy in porous media at a fundamental level, as well as their application to environmental- and energy-related problems. The scale of his interest ranges from sub-pore scale dynamics of water-gas interfaces to water flow and solute transport at scales of tens of meters. The scope of his research includes laboratory and field experiments, theory, and computational modeling.
Professor Ghosh's research interests span traditional topics in condensed matter physics such as correlated magnetic phases and coupled quantum systems, as well as emerging multi-disciplinary themes such as hybrid solar cells and plasmonics-based opto-electronic devices. Her group focuses on the physics of new materials and using ultra-fast time resolved spectroscopy, develops techniques and protocols to manipulate their properties for applications in energy storage and information processing devices.
The current research topics in her group include:
- Cooperative energy transfer dynamics in self-assembled nanostructured materials
- Directed assembly of metallic, magnetic and semiconducting nanostructures using liquid crystal based electro-optically active matrices
- Hybrid photovoltaic devices including solar cells and luminescent solar concentrators
- Exotic magnetic phases originating from geometric frustration in doped and undoped systems
In addition, Professor Ghosh is also the founding faculty and advisor of UC Merced Women in Science and Engineering (WiSE@UCM).
Professor Gopinathan's research focuses on a variety of problems in biophysics, soft condensed matter and the interface between the two fields. His group uses theoretical and computational techniques from different areas in soft matter and statistical mechanics including polymer physics, elasticity and anomalous transport.
The group's primary research area is Biological Transport which involves understanding how transport occurs in biological systems across different levels of organization and scale - ranging from macromolecules and vesicles being transported within the cell and across membranes to cells to communities of cells and higher animals across geographical scales. In the cellular context, the environment is structurally complex and exhibits unique dynamical properties. This results in novel types of transport phenomena and effects that in vivo systems manage to remarkably exploit. Examples include polymer transport across membrane pores, macromolecular transport through nuclear pores and motor driven intracellular transport. At higher levels, problems studied include eukaryotic cell motility, bacterial community motility and foraging in higher animals.
In addition, his group is involved in a number of other projects including drug design, colloidal dynamics, self-organization at surfaces, the geometry and dynamics of elastic sheets, transport in disordered systems and fluctuation induced forces.
The Grasis Lab researches in the following areas: viral metagenomics, systems immunology, microbiome regulation, and viral/antiviral discovery.
Grasis JA, Lachnit T, Anton-Erxleben F, Lim YW, Schmieder R, Fraune S, et al. (2014) Species-Specific Viromes in the Ancestral Holobiont Hydra. PLoS ONE 9(10): e109952. https://doi.org/10.1371/journal.pone.0109952
Grasis JA. The Intra-Dependence of Viruses and the Holobiont. Front Immunol. 2017;8:1501. Published 2017 Nov 9. doi:10.3389/fimmu.2017.01501
Professor Hart's research explores the controls of biogeochemical processes and productivity in managed and wildland terrestrial ecosystems using methods such as:
- Ecological genetics to isotopic analyses
- Computer simulation modeling
- Elucidate the biotic and abiotic factors that regulate terrestrial ecosystem structure and function
His research group is currently investigating:
- Biological and geochemical controls on ecosystem development along a three million year, semi-arid soil chronosequence
- Influence of the genetics of dominant plants on ecosystem processes
- Effects of forest restoration treatments (e.g., thinning with or without prescribed fire) and wildfire on ecosystem carbon and water balance, soil microbial communities, and belowground processes
- Efficacy of insect communities as indicators of forest ecosystem health
- Utility of the 15N natural abundance signature of soil microbes as an integrator of nitrogen cycling processes
- Impact of climatic change on soil-plant-atmosphere interactions; and the effects of water diversion on riparian forest
Professor Hirst's research interests focus on soft-condensed matter physics, with interests in both biophysics and liquid crystal materials. In general, her research group uses experimental techniques to characterize molecular assemblies and to understand the physics behind why they form. In a wider context, her group tries to uncover the common principles of how self-organization at a molecular level can transfer physical properties across length scales to define complex structures in real biological systems and soft phases.
Professor Hirst's group uses a wide variety of experimental techniques, with significant focus on:
- X-ray diffraction and scattering (both synchrotron and in-house)
- Confocal microscopy
- Atomic force microscopy
- Transmission electron microscopy
Current research projects include the:
- Influence of cholesterol and polyunsaturated lipids on cell membrane structure.
- Controlling Lipid phase behavior and raft formation for "soft microfluidics"
- Biopolymer networks
- Bent-core and novel ferroelectric liquid crystal materials
In addition to her research interests Prof. Hirst is also the creator of softmatterworld.org, a new educational networking site for the soft matter community around the world.
Professor Ilan's research interest lies in the mathematics involved with real-world phenomena, and its application to areas such as the control of intense lasers beams and harvesting solar energy. His research uses modeling physical systems in terms of ordinary and partial differential equations. Detailed studies are obtained using functional analytic, asymptotic and perturbation analysis, and numerical computation. The over-arching goal of this research is to connect between the mathematical and physical aspects arising from these problems and make useful predictions about physical systems.
Professor Kelley's research group uses ultrafast optical spectroscopy to examine the optical and electronic properties of semiconductor nanoparticles. He focuses on layered semiconductors - specifically gallium selenide and indium selenide - which have layered crystal structures and form two-dimensional, disk-like nanoparticles. The optical properties of indium selenide are very well suited for the absorption of sunlight; therefore, its nanoparticles hold considerable promise as the active media in photovoltaics.
Professor Kelley's group synthesizes nanoparticles that have diameters from 2 nm to tens of nanometers - all of which are four atoms thick - as the properties of such nanoparticles are strongly size dependent, due to quantum size effects. He is primarily interested controlling and optimizing the properties of the nanoparticles for solar energy conversion.
Professor Kelley's research uses the laser light scattering techniques of resonance Raman and hyper-Raman spectroscopy to study the atomic-level details of how materials interact with light. These studies reveal the detailed mechanisms of fast photochemical reactions such as those involved in human vision, photography, xerography, and solar energy conversion. Her group carries out experiments and also develops theoretical and computational tools for analyzing the data. Currently, her work focuses on using these techniques to understand how the vibrations (phonons) of semiconductor nanocrystals influence and are influenced by, absorption and emission of light in these materials.
Professor Kim is interested in interdisciplinary research problems at the interface between mathematics, science and engineering. In particular, he studies wave propagation in random media with applications to biomedical optics and wireless communications.
This research includes the study of differential and integral equations, asymptotic analysis, scientific computing and inverse problems.
The rising and setting of the sun causes dramatic oscillations in light and temperature each day. Most life forms involuntarily coordinate their lifestyles to these cyclic variations by means of an endogenous clock called the circadian clock. These circadian clocks have been identified in diverse organisms from cyanobacteria to humans, and studies suggest that the circadian clock has adaptive value.
Professor LiWang's laboratory is resolving the structural and biochemical basis of rhythmicity of the cyanobacterial circadian clock. The central oscillator of this clock is composed of only three proteins, which by themselves in a test tube with ATP generate a self-sustained circadian rhythm for several days. Their objective is to develop a comprehensive understanding of how a simple mixture of three proteins keeps time.
- Developmental and comparative genomics
- Transcriptional regulation
- Transgenic technologies
- Skeletal and limb development
- Bone and cartilage tissue engineering
- Genetics of bone disease — Sclerosteosis and Van Buchem Disease
Professor Manilay is a developmental immunologist, with research interest in the mechanisms that control cell fate decisions in the immune system. Her current topic of study is the development of T lymphocytes, important components of immune defense against pathogens.
Professor Menke addresses to broad questions through his research:
- How does one prepare solar cells that are both cheap and efficient?
- How does one use these solar cells to create chemical fuels?
To address these questions, he uses electrodeposition to prepare a variety of nanostructures to understand how the various properties, such as material, size, shape, and crystallinity, affect either their photovoltaic or catalytic properties.
Dr. Meza studies nonlinear optimization with an emphasis on methods for parallel computing. He has also worked on various scientific and engineering applications including scalable methods for nanoscience, power grid reliability, molecular conformation problems, optimal design of chemical vapor deposition furnaces, and semiconductor device modeling.
Photocatalysis of nanomaterials
Spectroscopic and mechanistic studies
Dr. Nguyen's research is focused on understanding and expanding the applications of nanoparticle photocatalyst to novel green synthesis and solar energy harvesting. These nanometer size catalysts have unique chemical reactivities that will lead to potential applications in chemical industry where chemical reactions will be driven by solar energy and hazardous wastes to the environment will be minimized.
Professor Nobile's research is directed toward understanding the molecular and mechanistic basis of microbial communities. Her lab is interested in investigating how transcriptional networks underlie the regulation of gene expression during biofilm development. Much of this work is carried out in the species Candida albicans, the most prevalent fungal pathogen of humans. The lab is also beginning to study interspecies interactions between different fungal and bacterial species. Questions that the lab is currently pursuing include: How are microbial communities regulated? How are microbial communities built? How are their unique and specialized properties maintained? How have microbial communities evolved?
- Molecular self-assembly in systems with reduced dimensionality
- Inorganic nanowires and carbon nanotubes
- Biophysics and measurement of biological forces using scanning probe microscopy
- Nanofluidics, and molecular transport at nanoscale
Peggy O'Day is environmental geochemist who studies the chemistry, reaction, and transport of inorganic contaminants and species, primarily metal and metalloid elements, in surface and subsurface systems. She specializes in the use of spectroscopic and microscopic methods, especially synchrotron X-ray techniques, to determine element speciation and molecular-scale mechanisms of biogeochemical reactions in natural systems and laboratory analogs. She develops and applies thermodynamic, kinetic and reactive transport models for synthesis and quantitative description of biogeochemical cycling, reactivity, transport, and bioavailability.
Current research projects include:
- Characterization of element speciation and solid phases in natural and engineered airborne particulates, and their impacts on human health through cellular response.
- Surface reactivity of mineral phases with respect to metal ion adsorption using molecular computational methods, spectroscopic characterizations, and geochemical modeling.
- Environmental influences on mercury speciation and methylation.
- Novel methods for remediation of soils and sediments through application of reactive amendments.
- Mechanisms and rates of abiotic and biotic uranium oxidation linked to nitrogen and iron cycling, and dissolution mechanisms and rates of uranyl oxide, silicate, and phosphate phases.
Professor Ojcius uses molecular and cell biological techniques to characterize interactions between epithelial cells and intracellular pathogens. He studies the bacteria, Chlamydia, as a model system because its species represent the world's leading cause of preventable blindness, and are a common cause of respiratory and sexually-transmitted infections in humans.
His current projects are focused on how the bacteria modify signal-transduction pathways that affect programmed cell death (apoptosis) and metabolism of the host cell. Whenever possible, the physiological relevance of results obtained with cell lines are tested in a mouse model of infection. Specifically, his group is investigating:
- Whether host-cell death plays a role in propagation of the infection
- How molecules released from dying infected-cells are recognized by the host immune system
- Effect of infection on metabolism of the host cell
Professor Ortiz's research focuses on the regulation of kidney function and metabolism in a variety of animal models, including seals and dolphins, with the intent that the data will have translative value to clinical medicine. These studies are conducted in collaboration with colleagues at:
- Sonoma State University
- University of Alaska, Fairbanks
- University of California, Santa Cruz
His lab - in conjunction with collaborators at Kagawa Medical University, SUNY Buffalo Medical School, and Tulane University HSC - investigate:
- Role of aldosterone plays in exacerbating high blood pressure
- Effects of aldosterone antagonism and hypercholesterolemia on renal sodium regulation
Professor Ortiz is also pursuing studies that address the link between diabetes and obesity with hypertension.
From an evolutionary perspective, he is interested in the physiological mechanisms marine-adapted vertebrates use to regulate water and electrolytes during a variety of altered environmental conditions, such as prolonged food deprivation or extended fresh water exposure.
Professor Sharping's research involves building a fundamental understanding of - and developing technology and applications for - ultrafast laser technology. These lasers have the potential to capture extremely short snapshots in time, as well as measure frequencies with unprecedented precision and accuracy. The applications are numerous in the areas of environmental science, biotechnology and national security. The research his group pursues will result in transferable technological advances (e.g., new optical sources), which will have a broad impact in:
- Physics - e.g., studies of atomic- and molecular-optical interactions
- Chemistry - e.g., ultra-sensitive spectroscopy
- Biology - e.g., time-resolved studies of biological processes
Developing and applying multi-scale modeling methods to understand the structure, dynamics and spectroscopy of complex condensed-phase molecular systems, such as
- novel optoelectronic materials (e.g., organic semiconductors and quantum dots)
- supercritical aqueous solutions
Professor Sistrom works broadly across a number of bacterial and viral systems to explore evolutionary hypotheses using high throughput sequencing and bioinformatics methods. In particular, he is interested in:
- How microbial populations change over space and time.
- What selective pressures lead to emergent disease.
- How the evolutionary properties of microbes can be exploited to manage or eliminate disease.
He is interested in collaborative projects that look at pertinent evolutionary questions in a range of biological systems using big data approaches.
Professor Tokman's research is focused on building mathematical models of physical phenomena and developing efficient numerical methods for problems in science and engineering. In particular, she has been developing numerical techniques, which allow fast integration of large nonlinear systems of differential equations with widely varying temporal scales. Professor Tokman has worked on modeling large scale behavior of astrophysical and laboratory plasmas, including evolution of coronal loops in the solar atmosphere and plasma configurations arising in fusion related experiments. Her research interests also include computational biology, in particular, modeling experimental manipulations of biomolecular structure of living cells.
Professor and Vice Chancellor for Research and Economic Development
Using a wide range of analytical methods (infra-red spectroscopy, electron microsocpy, x-ray absorption spectroscopy and mass spectroscopy), Professor Traina's group studies:
- Chemical transformations of pollutants in soils, surface and ground water
- Linkages between chemical form or speciation of particular pollutants and their relative toxicities in terrestrial and aquatic ecosystems
- Roles of geoparticle surfaces and bacteria in pollutant fate
Current projects include the study of:
- Contaminants at Department of Energy waste sites (Cr, Pu and U)
- Role of Fe(II) and HSe- in transformations of nitroaromatic pesticides in wetlands
- Fate of pharmaceuticals in the surface waters of National Parks
The Wolf lab studies the genetic and neural circuit mechanisms for coding simple behaviors, including motivated seeking and plasticity driven by addictive drugs. We also study the regulation of DNA damage repair.
Mef2 induction of the immediate early gene Hr38/Nr4a is terminated by Sirt1 to promote ethanol tolerance. Adhikari P, Orozco D, Randhawa H, Wolf FW. Genes Brain Behav. 2019 Mar;18(3):e12486. doi: 10.1111/gbb.12486. Epub 2018 May 28.
Satiation state-dependent dopaminergic control of foraging in Drosophila. Landayan D, Feldman DS, Wolf FW. Sci Rep. 2018 Apr 10;8(1):5777. doi: 10.1038/s41598-018-24217-1.
Perineurial Barrier Glia Physically Respond to Alcohol in an Akap200-Dependent Manner to Promote Tolerance. Parkhurst SJ, Adhikari P, Navarrete JS, Legendre A, Manansala M, Wolf FW. Cell Rep. 2018 Feb 13;22(7):1647-1656. doi: 10.1016/j.celrep.2018.01.049.
The Woo Lab is interested in how dynamic cellular processes such as cell migration and cell adhesion contribute to the formation of the gastrointestinal epithelium, using the zebrafish embryo as our model system. We are also interested in developing new tools to study in vivo cell biology.
Woo, S, Housley, MP, Weiner, OD, and Stainier DYR (2012) Nodal signaling regulates endodermal cell motility and actin dynamics via Rac1 and Prex1. J. Cell Biol. 198(5): 941- 952.
Reade, A, Motta-Mena, LB, Gardner, KH, Stainier, DY, Weiner, OD, and Woo, S (2017) TAEL: a zebrafish-optimized optogenetic gene expression system with fine spatial and temporal control. Development. 144(2): 345-355.
Professor Ye's research is focused on developing the nanoscale surface chemistry needed to manipulate and measure biomolecules and analogous systems. The nanoscale arrangements of biomolecules, such as proteins and DNA, underlie a wide spectrum of biological functions. Yet our ability to measure and control biomolecules at the nanoscale and single molecule level remains very limited. His group is using and developing sophisticated nanoscience tools to position and measure single molecules with nanometer resolution, dynamically activate the functions of individual biomolecules on surfaces, and develop artificial analogs of biological motors. The greatly improved understanding and control of biomolecules at the nanoscale have implications in unraveling key biological functions, creating artificial functional bimolecular structures, and developing ultra-sensitive biosensors.