
During the summer, the Molecular Foundry supports several summer undergraduate students from the UC Berkeley, primarily from the College of Chemistry and College of Engineering, for a paid full-time summer internship (student benefits are the same as for the SULI program operated by LBNL. Transfer students are particularly encouraged to apply).
The internship program period spans 10 weeks from June 2, 2025 through August 8, 2025 and is administered by the Berkeley Lab Workforce Development and Education Office. Interns will participate in the same summer professional development programming as the SULI program. As an intern, participants will not only conduct research, but will participate in tours of Berkeley Lab facilities, lunchtime talks with researchers from across the lab, and more. The program culminates with a poster session where the interns present their research.
Continuing research opportunities after this time period may be available.
The deadline to apply for the summer 2025 program is January 31, 2025.
Eligibility:
- Must be a United States Citizen or Lawful Permanent Resident at the time of applying.
- Applicants must have an undergraduate cumulative minimum grade point average (GPA) of at least 3.0 on a 4.0 scale for all completed courses taken as a matriculated student at the applicant’s current (or recently graduated) institution and at any undergraduate institutions attended as a matriculated post-secondary student during the five years preceding the start of the current year.
- The FUSE internship is for rising juniors and seniors
- Interns cannot take classes while participating in the program.
Program Requirements:
The FUSE program is administered by the Berkeley Lab WDE office, which means that all FUSE interns will be required to complete all tasks associated with the SULI program.
- Complete the full 10-week program.
- Complete entrance and exit surveys.
- Make a poster presentation and submit a six- to eight-page research project report on the outcome of research activities.
- Attend all scheduled events, including lectures, tours, and group activities.
- Complete all Berkeley Lab safety and procedural requirements.
- Must behave in a responsible and professional manner. Interns must adhere to the Ethics and Conduct at Berkeley Lab Requirements and Policies Manual (RPM).
- Complete all assignments and deliverables including intern/mentor photos.
Application Information
The application for the 2025 FUSE program is now open with a deadline of January 31, 2025. If you have questions about the program or application, please contact us.
The application asks for 3 short essays (uploaded as a PDF), college transcripts, and project preferences, as well as demographic data for administrative purposes. This guidance document provides information about the essays so that applicants can draft them before completing the form.
Opportunities for the 2025 Summer Program
Project listings, as available, will be posted below. Interested students are welcome and encouraged to reach out to the PIs to discuss their interest in a particular project, or to learn more about a project. (Note that there may be a few late additions to this project list.)
Characterization of xanthine and uric acid biocrystals in unicellular microorganisms
Principal Investigators: Crysten Blaby-Haas
Other Mentor: Jana Pilatova
The recent discovery of new purine biocrystals that function as either nitrogen stores or as optically active photonic mirrors has engendered many questions about their chemical structures, biological functions, and biosynthesis. We are studying the in situ structure of diverse purine crystals using advanced microscopy techniques, such as optical and electron microscopy imaging.
Project Description:
Based on our published study, Pilátová et al. (2022, ISME J.), some protists produce purine crystals with as-yet-uncharacterized structures and chemical properties. Purines are either end products of nitrogen metabolism and are excreted or function as photonic mirror in various optically active interfaces or organs (Wright, 1995; Gur et al., 2017). Among the diversity of purines found in living organisms, the most well characterized are guanine crystals found in optically active organs of diverse animals – from the reflective background on the eyeballs of nocturnal mammals and insects to the glittery camouflage of fish scales and tunable photonic mirrors in the skin of chameleons (Wagner et al., 2021). Only a few others purines have been found to have similar functions in animals. One of them is uric acid found in some fish models, providing them with a white color, e.g., medaka fish (Oryzias latipes), or on butterfly wings and firefly light organs (Goda et al., 2023; Goh et al., 2013; Tojo and Yushima, 1972). The other one, recently found in the eyes of an invertebrate known as jumping bristletails (Archaeognatha), is formed by xanthine biocrystals (Friedman et al., 2022). In both cases, their structural and crystallographic characterization is missing so far. In our case, we will leverage unicellular microorganisms recently found to produce these crystals in protists, amoebae, photosynthetic microalgae, opportunist pathogens etc. To describe their morphology, we will conduct a correlative light and scanning electron microscopy.
Main project goal or research question to be address by the intern:
Our aim is to find the growth conditions suitable for purine biocrystallization in cells of diverse unicellular microorganisms that we have recently found to produce the new uncharacterized crystals. The growth conditions require aseptic handling of phototrophic microalgae and heterotrophic amoebae. The preparation of cells and crystal release will be optimized for both optical and electron microscopy.
Intern’s role:
The intern will learn how to make growth media for diverse microorganisms, understand variable growth conditions for heterotrophic and phototrophic microbes. Additionally, will learn how to design experiments for purine biocrystallization induction, how to handle cells, and extract crystals for subsequent imaging. Will get a proper training to operate optical and electron microscopes. Will process the data using simple morphometric statistics.
What can the intern expect to learn?
Aseptic microbiological work for routine handling of diverse microorganisms
Cell disruption and sample preparation for microscopy
Microscopy – optical and electron microscopy
Data processing
Synthesis of 2D TMDs for next generation optics and electronics
Principal Investigator: Tevye Kuykendall
Other Mentor: Aidar Kemelbay
In the Inorganic Facility of the Molecular Foundry we develop methods for gas-phase synthesis of compound semiconductor nanostructures such as nanowires, nanotubes, and 2D films. Recently, we have focused on 2D transition metal dichalcogenides (TMDs), inspired by the discovery of emergent properties when reduced from bulk crystals to 2D layers. Transition to direct band gap, emerging charge density waves, high mobility, and valley polarization are some of the many exciting properties that have been reported in the TMD literature recently.
Project Description:
Transition metal dichalcogenides (TMDs) are an interesting class of semiconductor materials due to their emergent properties when reduced to thin two-dimensional (2D) layers. While exfoliation and vapor phase growth produce extremely high-quality 2D materials, direct fabrication at wafer scale remains a significant challenge. In previously published results, we demonstrated a method that we call “lateral conversion,” which employs chemical conversion of a metal-oxide film to TMD layers by diffusion of precursor propagating laterally between lithographically defined silica layers, resulting in patterned TMD structures with control over the thickness down to a few layers. The intern will work on further development of this synthetic and related methods. The synthesis has two distinct components: 1) Micro lithography and substrate preparation, and 2) sample annealing and conversion to the resulting TMD. The intern will focus on processing lithographically patterned substrates using chemical vapor deposition (CVD) under a variety of conditions to optimize the growth strategy and control their morphology and crystalline quality. The main goal of the internship is to explore and optimize different synthetic conditions for growing 2D TMD semiconductor films. They will study the effect of precursor conditioning, pressure, temperature, and reactive gasses on the TMD growth. Using a variety of characterization techniques, they will narrow down the process, through successive experiments and characterization, to control size, thickness, and size distribution, producing high-quality TMD materials.
Main project goal or research question to be addressed by the intern:
The main goal is to explore and optimize different synthetic conditions for growing 2D TMD semiconductor films. The synthesis portion of the project will study the effect of precursor conditioning, pressure, temperature, and reactive gasses on the TMD growth.
Intern’s role:
The intern will learn how to conduct independent research on solid state materials synthesis.
• They will be responsible for synthesizing 2D TMD films using a variety of techniques.
• They will learn how to characterize their samples using a variety of analytic techniques.
• They will learn how to interpret results, and make improvements to the synthetic process using feedback for successive experiments.
They will receive careful oversight and training during the first month, until they are qualified to work independently. Additional training will be given as needed. Regular discussions will be had to interpret results and gauge progress.
What can the intern expect to learn?
The intern will learn a variety of synthetic and analytic techniques, such as:
• Chemical vapor deposition (CVD) synthesis
• Raman spectroscopy
• Optical microscopy
• They will learn about the lithographic process and microfabrication techniques
• They will be mentored in the creation of a final poster project and will learn how to present their data using written text, plots, photographic images, and illustrations.
Thermodynamic computing in and out of equilibrium
Principal Investigator: Steve Whitelam
Other Mentor: Corneel Casert
My group uses statistical mechanics and machine learning to study nanoscale dynamics and phenomena, including molecular-self assembly, driven nanoscale devices, and unconventional types of computing.
Project Description:
In classical computing, the energy scales of even the smallest devices, such as transistors and gates, are large compared to that of the thermal energy, k_B T. As a result, there is a clear separation of scales between signal and noise, enabling deterministic computation. This determinism comes with an energy cost: classical computers operate far above the limits of thermodynamic efficiency, and require large amounts of power and heat dissipation to ensure their reliability.
As devices shrink to the nanoscale, the energy associated with computation becomes comparable to that of thermal fluctuations, making computation more energy efficient. On these scales, thermodynamic computing makes use of the tendency of physical systems to evolve toward thermal equilibrium to do computation. The thermal bath contributes to computation by providing the fluctuations necessary for state changes, and in some modes of operation the signal the noise, with the equilibrium fluctuations of the degrees of freedom of the thermodynamic computer being the output of the calculation.
This project will involve the exploration of a classical digital computer model of a thermodynamic computer.
Main project goal or research question to be address by the intern
To become familiar with the notion of thermodynamic computing, and to choose a direction in this field to explore. Thermodynamic computing is a new field, and there’s lots to explore! [Look up “Normal Computing” to get an idea of what one startup in this field is working on]. The point of departure for this project could be this paper: https://arxiv.org/abs/2410.12211
Intern’s role:
Numerical simulations of physical systems, statistical mechanics, machine learning, learning to identify interesting research questions.
What can the intern expect to learn?
See above!
Digital Infrastructure for Biopolymer EUV Photoresist Discovery
Principal Investigator: Michael Connolly
Other Mentor: Morgan Wall
The Connolly lab focuses on the synthesis and applications of sequence-defined peptoid biopolymers to address diverse problems ranging from biomedicine to rare earth element separation and novel materials for lithographic patterning.
Morgan Wall leads efforts in the Molecular Foundry’s Data Infrastructure group to build data infrastructure to support automated data ingestion, processing, and analysis pipelines.
Project Description:
This proposal details includes efforts to develop data infrastructure to support the development of a material discovery platform for the accelerated development of hybrid peptoid metal oxide photoresists for the next generation of extreme ultraviolet lithography enabling the future of microelectronics. The miniaturization of semiconductor devices has been the key driver behind the continuous improvement in performance and energy efficiency of microelectronics. A cutting-edge technology called “extreme ultra-violet lithography” (EUVL) has enabled extreme downscaling to the sub-nanometer node––i.e., the angstrom era. This project leverages automated peptoid biopolymer synthesis and nanofabrication capabilities of the Molecular Foundry to produce large libraries of novel hybrid biopolymer metal oxide photoresists. These photoresist libraries will be analyzed by multimodal characterization techniques based on soft X-ray, EUV, and electron sources available at the Advanced Light Source (ALS) of LBNL. This characterization data will then be analyzed by artificial intelligence and machine learning (AI/ML) strategies to predict crucial EUV patterning performance parameters, thus accelerating the materials discovery process to continue the advancement of semiconductor manufacturing.
Main goal of the project:
To develop digital infrastructure to support the Molecular Foundry’s Crucible data infrastructure and an interdisciplinary team of scientist working to create rich data sets from combinatorial biopolymer libraries to produce new EUV photoresist materials. Data infrastructure tools developed by this project will include a cloud database, scientific instrument to cloud data transfer software, data organization for AI/ML processing, meta data tagging and user interface/data entry tool development.
Intern’s role:
Assist in the development of a suite of data infrastructure tools to support a complex interdisciplinary project to identify new biopolymer EUV photoresist materials.
What can the intern expect to learn?
- • Scientific software development best practices
- • Scientific programming in Python
- • Data organization for AI / ML
- Depending on the intern’s interest there will also be opportunities to learn about:
- • Implementation and deployment of cloud based microservices
- • CI/CD tools and processes
- • Containerization technologies including Docker and Kubernetes
- • API design and deployment using FastAPI
- • Designing and implementing message queues using RabbitMQ
- • Database technologies including postgreSQL and MongoDB
Machine learning methods for X-ray spectroscopic predictions
Principal Investigator: David Prendergast
Other mentor: Fabrice Roncoroni
The Prendergast Group’s focus is on computational science at the intersection of physics, materials science and chemistry developing and employing methods that explore electronic structure theory, molecular dynamics, continuum modeling, and machine learning for prediction and analysis of complex data. We are particularly interested in nanoscale processes at functional interfaces of relevance to energy conversion processes.
Project Description:
Theoretical models can simulate experimental measurements but accurate predictions may require the support of significant supercomputing resources. Machine learning methods can provide accurate predictions based on training data. Ideally, we want to minimize the required (and expensive) training data and, ideally, enable predictions that extend far beyond the original training data. We aim to apply such techniques to make predictions of X-ray spectroscopy measurements, which can be made at the Advanced Light Source, on nanoscale materials and devices fabricated or synthesized at the Molecular Foundry.
Main research question
The goal of the project is to employ various machine learning methods to accurately predict measured X-ray spectroscopy based on learning from a minimal set of first-principles calculations, thereby reducing the necessary computational workload. Additionally, such predictive models will be dissected to provide further analysis and interpretation of the measurements in terms of the atomic and electronic structure and dynamics of a given system.
Intern’s role:
Within the project you will be writing computational software (most likely in python) that can take existing data sets of computed X-ray spectra and train ML models to predict them. You will be expected to present your work to your colleagues providing regular progress updates, providing graphical presentation of results and building descriptive presentations on the algorithms developed and tested.
What can the intern expect to learn?
Ideally, this project will build on existing experience with python programming and data science techniques; provide experience with the application of machine learning methods and education and domain knowledge related to spectroscopy, molecular dynamics and electronic structure.
Interactive Visualization of Nanoscale Chemical Maps
Principal Investigator: Katherine Sytwu
Other mentor: Morgan Wall, Tara Mishra
This project is a collaboration between the NCEM floor and the Data Infrastructure group at the Foundry. NCEM specializes in advanced electron microscopy and spectroscopy to understand the relationship between material function and nano- to atomic-scale properties. The Data Infrastructure group develops systems and infrastructure to support scientific data management, analysis, and visualization across all Foundry facilities.
Project Description:
Understanding the distribution of chemical elements at the nanoscale is crucial for scientists that grow and synthesize new materials. Using electron spectroscopy signals in a transmission electron microscope (TEM), we’re able to map out chemical composition with nano- to atomic-scale resolution. However, in order to fully verify our results, we need data analysis and visualization capabilities that can not only handle experimental and data artifacts (i.e. overlapping spectral peaks, background subtraction, and spectral misalignment) but also make these issues transparent to the researcher.
Main project goal or research question to be addressed by the intern
The intern will adapt the Foundry’s current hyperspectral viewer widget for handling and processing energy-dispersive spectroscopy (EDS) datasets. The intern will create a user-friendly interface, with the expectation that this becomes a tool for Foundry users. If there is time, the intern will also develop interactive Jupyter notebooks for more advanced, quantitative chemical analysis.
Intern’s role:
• Develop code in Python (or language of choice) for interactive viewing of EDS datasets
• Adapt Crucible’s hyperspectral viewer for elemental mapping and creation of publication-quality figures
• Testing out the new EDS viewer with experimental EDS datasets
What can the intern expect to learn?
• General materials characterization with transmission electron microscopy
• Electron spectroscopy, specifically energy-dispersive spectroscopy (EDS)
• Data analysis of hyperspectral and multidimensional datasets
• Visual, oral, and written science communication skills
• Scientific programming and data visualization in Python
• Deployment of cloud based applications using CI/CD tools and frameworks
• Containerization technologies including Docker and Kubernetes
Long-wavelength fluorescent antibody conjugates
Principal Investigator: Bruce Cohen
Other mentor: Yazhi Liu
Optical microscopy is the primary means of studying complex living systems, enabling real-time analysis of individual cellular components at high spatial and temporal resolution. The Cohen lab develops novel optical probes as biosensors, improving bioconjugation and targeting chemistries, and imaging live systems with these reagents. We aim to integrate the development of novel luminescent nanomaterials into multidisciplinary efforts to address significant biological questions of cell function.
Project Description:
Labeling of antibodies with organic fluorophores is a cornerstone of bioimaging, but there are ongoing challenges with current antibody bioconjugation techniques. One problem is that many organic fluorophores are unstable under the reaction conditions needed to form stable fluorescent antibody conjugates. These include novel fluorophores that emit past 1000 nm, in the NIR-II range. We are developing a simple method for labeling clinically relevant IgG antibodies with fluorophores that are unstable under standard reaction conditions, and a goal of this internship is to contribute to the synthesis of these long-wavelength fluorophores.
Main research question
This project then entails synthesis of organic fluorophores in the NIR-II region, past 1000 nm.
Intern’s role:
The intern will learn and perform the basics of organic synthesis, chemical and optical characterization, and some bioconjugation chemistry. In addition to these techniques, the intern will learn about fluorescence, immunotargeting, and the science of bioimaging.
What can the intern expect to learn?
The intern will learn and perform the basics of organic synthesis, chemical and optical characterization, and some bioconjugation chemistry. In addition to these techniques, the intern will learn about fluorescence, immunotargeting, and the science of bioimaging.
Probing the physics of structuring liquids
Principal Investigator: Paul Ashby
Other mentors: Preetika Rastogi
The complexity of living systems inspires the Ashby group to create and characterize soft matter systems that use polymers and information rich molecules to create functional assemblies. We specialize in using in-situ microscopy methods to characterize the functional properties that arise from nanoscale composition and structure.
Project Description:
We create persistent liquid structures of specific shape, Structured Liquids, that are unlike normal liquids, which are known to minimize their surface area and lose their shape. By harnessing complementary chemical functionalities of nanoparticles and surfactants at the interface we can tailor dense assemblies of nanoparticle-surfactants (NPS) to lock-in non-equilibrium shapes and achieve desired structure and function. The innovative chemistry in the Structured Liquids collaboration has enabled generation of prescribed shapes for several applications such as all liquid encapsulants for drug delivery, energy storage, liquid electronics, liquid-in-liquid printing, microfluidics, and all-liquid reaction vessels. We will optimize the stability of nanoparticle-surfactants (NPS) by developing an understanding of the binding energy of NPSs at the liquid interface to impart remarkably high structural integrity to these all-liquid structures.
Main project goal or research question to be address by the intern:
The intern will contribute to the understanding of the high stability of nanoparticle-surfactant (NPS) systems at the liquid-liquid interface and compare them to traditional nanoparticle stabilized films. This direct comparison will augment our understanding of the NPS assemblies and the ability to lock-in non-equilibrium shapes, which is not possible using the traditional nanoparticles.
Intern’s role:
The intern will use microscopy techniques to characterize the 3D structure of the nanoparticles comprising the films to understand the adsorption of nanoparticles to the interface. The intern will also synthesize grafted nanoparticles in the laboratory with different grafting densities to alter the surface chemistry. The surface chemistry will be characterized using spectroscopic techniques including FT-IR and thermogravimetric analysis (TGA). They will also use pendant drop tensiometers to probe macroscopic properties of the interfacial films.
What can the intern expect to learn?
The intern can expect to learn high-precision microscopy for imaging the nanoparticles on advanced microscopes such as super resolution optical microscopy and in-situ Atomic Force Microscopy (AFM) in the Molecular Foundry. The intern will learn chemical analysis techniques such as TGA and FT-IR used in the synthesis and characterization of nanoparticles. Pendent drop tensiometry will be used to correlate macroscopic properties with the microscopic picture developed by AFM and super resolution optical microscopy.
Design and Synthesis of Crystallization Chaperones for Structural Determination of Organic Molecules via Co-crystallization
Principal Investigator: Jian Zhang
The Zhang group at the Foundry investigates the synthesis and emerging properties of self-assembly of molecular building blocks. The resulting close packed molecular crystals or porous framework materials exhibit tunable chemical, physical, optical, or mechanical properties for potential energy related applications, which requires a deep understanding the structure-property relationship across the spatial and temporal scale.
Project Description:
Single crystal X-ray diffraction (sc-XRD) is a well-known technique to provide accurate structural information of a crystalline material at the atomic level with unambiguous structural determination including absolute stereochemical assignment. However, a key experimental bottleneck in molecular and structural analysis by sc-XRD is the growth or preparation of high-quality single crystals, containing the target compound. However, it could take several days or weeks to successfully obtain high-quality single crystals. In addition, certain organic molecules tend to be oily, so the crystallization process to grow a good single crystal is challenging. Recently, co-crystallization using crystalline chaperones has emerged as a simple approach to obtaining the atomic structural information of small molecules. In this thermal co-crystallization method, a mixture of a chaperone and liquid guest molecule is heated until transparent and then cooled to room temperature to obtain the co-crystals for structural analysis by sc-XRD. Due to the co-crystallizing nature of this technique, its success largely depends on the ability of the chaperones to be matched with the analyte, especially when applying in the analysis of larger molecules. Thus, it is critical to develop new classes of crystallization chaperones.
Main project goal or research question to be address by the intern:
The main goal of the project is to design and synthesis new N,N′-bicarbazole-based crystallization chaperones for the structural determination of the guest with X-ray crystallography. N,N′-Bicarbazole is chosen here due to its tetrahedral-like symmetry, rich aromatic groups, four anchoring position to incorporating additional aromatic groups, allowing for versatile encapsulation of guest molecules based on pi–pi (face-to-face) or CH–pi (edge-to-face) interactions in the 3D space. Ultimately, it aims to expand the toolbox for single-crystal X-ray diffraction (XRD) technique for challenging small molecules. Understanding the crystallization habits would guide the future design and new general crystallization chaperones for a wide scope of molecules.
Intern’s role:
• Optimize crystallization conditions for growing large single crystals of crystallization chaperones and their host-guest co-crystals.
• Determine crystal structure of a wide range of guests using single crystal XRD using in house X-ray diffractometer and ALS beamline.
• Quantify intermolecular interaction energy between the host and guest molecules and rationalize the inclusion mechanism for future design of new crystallization chaperones.
What can the intern expect to learn?
• Hands-on experience on synthesis and characterization of organic molecular frameworks.
• Basic principles of chemical crystallography and hands-on experience on single crystal X-ray diffraction technique for structure solution and refinement
• Methods to execute a research project through daily task planning and outlining scientific questions
• Skills for scientific communication and presentation via interactions with PI and coworkers, group meetings, and poster session
Hybrid organic–inorganic photoresists for EUV lithography
Principal Investigator: Brett Helms
Other mentor: Declan McCarthy
We design and develop new materials to solve problems in energy and sustainability. We harness synthetic chemistry, X-ray characterization, and engineering to forge a molecular-level understanding of materials to realize performance advantages with them in photoresists, batteries, adaptive and reconfigurable energy materials, and chemically recyclable polymers for the circular economy. Helms Group website.
Project Description:
Microelectronics is a $442B/year industry that underpins nearly every sector of the U.S. and global economy.Research in microelectronics supports U.S. advanced manufacturing leadership through the development of smaller patterns at length scales beyond the limitations of current methods to enable high performance and energy efficient microelectronics.
We will design and synthesize new extreme ultraviolet (EUV) patternable materials with innovative compositions and architectures for photolithography. In this work, we will prepare new metal–organic hybrid resist materials and characterize EUV absorption and low-energy electron-responsive properties for high resolution nanopatterning via EUV lithography (EUVL).
Main project goal or research question to be addressed by the intern:
Explore synthesized ligands, metal salts, and the effects of their resultant nanostructures on photo-patternable materials in lithography.
Intern’s role (i.e., what kinds of things will they be doing):
Student will carry out synthesis and experimental work using a wide range of equipment/instrumentation relevant to modern synthetic organic/inorganic chemistry, materials science, and chemical engineering, and lithography.
What can the intern expect to learn?:
Organic synthesis; thin-film deposition; Absorption Spectroscopy; X-ray diffraction; profilometry; interdisciplinary research; interpretation of scientific results; Scientific communication and data presentation
Understanding the effect of the microplastic on the mammalian cell culture
Principal Investigator: Natalia Molchanova
Our research group focuses on studying the effects of microplastics on specific mammalian cell cultures (e.g., intestinal epithelial cells, lung epithelial cells) to understand the potential health risks posed by environmental contamination. Microplastics, made up of different materials, have been found in various ecosystems, raising concerns about their impact on living organisms.
Project Description:
This project aims to understand the effect of plastic particle exposure on human intestinal and lung cell cultures. We currently use fluorescent polystyrene beads (200 nm to 5 µm) in our experiments. We assess cellular responses (oxidative stress, inflammation, toxicity, gene expression) after exposing cells to microplastics for 24-72 hours. These studies provide insights into how microplastics might affect cellular function, potentially leading to long-term health consequences, including cancer, endocrine disruption, or immune system dysfunction.
Main project goal or research question to be address by the intern:
The primary objective is to investigate how different human cell types respond to microplastic exposure. We aim to use microscopy to identify microplastic accumulation within cells and determine the affected cellular processes. The intern will grow different types of cell cultures and expose them to a range of microplastic concentrations and sizes. Initial experiments have shown significant changes in cell behavior after microplastic exposure, and we are interested in further investigating the underlying causes.
Intern’s role (i.e., what kinds of things will they be doing):
The intern will be actively involved in laboratory experiments, working with several mammalian cell cultures and using imaging techniques to localize microplastics within cells. The intern will also assist with literature reviews on microplastic research.
What can the intern expect to learn?
This internship provides hands-on experience in cellular biology, including sterile technique and microscopy. The intern will develop a comprehensive understanding of cell culture and gain knowledge of the potential effects of microplastics on human health.
Image Segmentation of Cellular Organelles for Materials Synthesis
Principal Investigator: Behzad Rad
We use molecular biology and nanoscale optical methods to engineer and visualize complex biological systems to synthesize nano-scale materials. These engineered systems allow us to make green and energy efficient systems for materials synthesis from low nutrient sources.

Project description
Microorganisms provide a wonderfully complex system to engineer for materials synthesis. Typically, prokaryotes such as bacteria are used in these endeavors due to their simply organization and fast growth rates. Eukaryotic microbes like yeast and plants, however, provide organelles, membrane bound compartments within the cell, that can precisely control several environmental parameters. Understanding how organelle are organized and adapt to changes could allow us to modify them and create custom materials from sources like waste water.
Because organelles measure a few hundred nanometers in size, we use fluorescence microscopy to visualize the organization of organelles over time. We are interested in developing image processing methods to identify organelles within images over time. By training Neural Networks (NN) with imaging data, we plan to develop a model that would automatically track the location, size, and shape of these structures from many images. In this project, we will create data sets from yeast, Saccharomyces cerevisiae, cells to track their main organelle, the vacuole, and develop a NN model to identify its properties.
Main research question
We hypothesize that we can generate fluorescence images to train NN models to identify organelles. These models could be generalizable to other structures within the cell.
Intern’s role
The internship will involve microbial culture, working on a fluorescence microscope to acquire images and using commercial or open source software to develop models for image tracking.
What can the intern expect to learn?
The intern should expect to learn microbial culture, sample preparation for imaging, fluorescence imaging using state of the are microscopes, and image analysis methods.
Polymer brushes for high-precision surface patterning
PI Name: Ricardo Ruiz
Other Mentor Name: Beihang Yu, Emma Vargo
The Soft-Nano Research Group, led by Dr. Ricardo Ruiz in the Nanofabrication Facility, uses soft matter physics to overcome specific challenges in assembling and manipulating matter at the nanometer-length scale. This covers a variety of nanofabrication techniques such as block copolymer lithography, nanoparticle and colloidal self-assembly and biomolecular lithography for applications in nanoelectronics, memory, and semiconductor synthetic biology.
Project Description:
Polymer brushes are an ideal platform for nanoscale surface modification of semiconductor and other inorganic substrates. Conventional surface functionalization approaches such as silane chemistries and self-assembled monolayers may offer only a limited level of customization for surface chemistry, while polymer brushes offer a wider range of chemistries and maintain compatibility with lithographic techniques. In our group, we routinely leverage established and develop new fabrication approaches using both traditional polymer (PS, PMMA) brushes and bioinspired, sequence-defined polymer (polypeptoids) brushes to create surface nanopatterns for selective immobilization of biomolecules, as well as for pattern rectification and pattern transfer to augment state-of-the-art extreme ultraviolet lithography. In this project, the intern will investigate the diffusion behavior of polymer brushes through a resist layer and their subsequent grafting onto substrates. The goal is to capture the diffusion process (e.g., by experimentally determining the diffusion constant) as a function of annealing temperature, polymer–resist chemistry pair, polymer brush concentration gradient. The establishment of a diffusion model will inform and expand our fabrication approaches that utilize polymer brushes for nanoscale surface modification of various substrates.
Main project goal or research question to be address by the intern:
Investigate the diffusion behavior of polymer brushes through a resist layer as a function of annealing temperature, polymer–resist chemistry pair, and polymer brush concentration gradient.
Intern’s role (i.e., what kinds of things will they be doing):
● Prepare and characterize samples in a cleanroom setting: polymer thin-film and monolayer deposition, ellipsometry, water contact angle measurements, X-ray photoelectron spectroscopy (XPS) data analysis, and atomic force microscopy (AFM, potentially depending on project progress).
● Analyze results and develop scientific conclusions, and compare with existing literature.
● Conduct an independent research project while working closely with postdocs and the mentor; interact with team members through group meetings and other scientists at the Foundry.
● Observe and contribute to the safety working culture of the Molecular Foundry and LBL.
What can the intern expect to learn?
● Learn about polymer brushes, resists, and the cutting edge of high-precision patterning science
● Learn about the Molecular Foundry’s nanofabrication facility and gain experience with cleanroom work. Get hands-on experience with advanced fabrication and characterization techniques.
● Learn how to work on a research project from developing an overall research plan to planning daily tasks, practice asking good scientific questions.
● Practice scientific communication and presentation skills through daily interaction with scientists, group meetings, and at the end-of-program poster session.
Miniaturization of biological assays using digital microfluidic devices
PI Name:
Aeron Tynes Hammack
Other Mentor Name: Harika Dechiraju
Short description of research group’s focus:
The Tynes Hammack group focuses on developing single-particle sensing devices to better understand self-assembly processes in single and multicellular life. By creating nanofluidic integrated circuits and digital microfluidic devices, we aim to enable precise optical and electrical analysis of nanoparticles and biological materials. This approach bridges nanofabrication and biological nanostructures to unlock transformative insights in microbiology and molecular biology.
Project Description:
This project focuses on miniaturizing standard biological assays to explore host-pathogen interactions between bacteria and bacteriophages using advanced digital microfluidic (DMF) devices. By integrating wet lab techniques with microfluidic technologies, we aim to characterize individual interactions between living organisms and viruses at unprecedented scale. These DMF devices will enable precise small-volume analyses of bacterial and phage interactions, genetic and protein-level changes, and metabolic activity. The research extends to leveraging these platforms for broader applications, including studies on liquid-solid interactions and combinatorial chemical reactions, emphasizing their versatility in biological and quantum systems.
Main Project Goal or Research Question to Be Addressed by the Intern:
How can digital microfluidic devices be employed to miniaturize and improve the precision of biological assays, specifically in studying host-pathogen dynamics.
Intern’s Role:
- Assist in testing DMF devices for bacterial and bacteriophage assays.
- Perform wet lab tasks, including culturing bacteria and bacteriophage, conducting PCR, and long-read sequencing.
- Participate in imaging and spectroscopic characterization using optical and fluorescence microscopy.
- Conduct an independent research project while working closely with postdocs and the mentor.
What Can the Intern Expect to Learn?
- Operating digital microfluidic systems for biological assays.
- Techniques, including bacterial cell culture, DNA/RNA handling, sequencing and microscopy.
- Learn how to work on a research project and practice asking good scientific questions.
- Practice scientific communication and presentation skills through interaction with scientists, group meetings, and at the end-of-program poster session.