Foundry Undergraduate Summer Experience (FUSE)

Principal Investigators: Michael Connolly, Ricardo Ruiz

This project is a collaborative effort involving two Molecular Foundry groups.

The Connolly group focuses on the synthesis and applications of sequence defined peptoid biopolymers to address diverse problems ranging from rare earth element separation to biomedicine.

The Ruiz group’s efforts revolve around using 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 bio-molecular lithography for applications in nanoelectronics, memory and semiconductor synthetic biology.

Project Description:

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. However, development of new EUV photoresists cannot come fast enough to keep pace with current demand. This project responds to this urgent need by building a materials development and characterization accelerator for materials discovery. Automated peptoid biopolymer synthesis and nanofabrication capabilities of the Molecular Foundry will be employed 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 project goal or research question to be address by the intern:

The main project goal is to develop new materials and to discover design rules to develop new EUV photoresists.

Intern’s role:

The intern will assist in the synthesis of peptoid biopolymers and production and characterization of metal infiltered peptoid thin films for EUV photoresists.  Additionally, they will collect and organize data, present results in group meetings and in a poster at the end of the program.

What can the intern expect to learn?

The intern will learn automated and manual solid-phase peptoid synthesis methods, how to use Atomic Layer Deposition (ALD) methods to prepare metal-biopolymer thin films using vapor-phase infiltration.  In addition, they will then work with team members to characterize these thin films employing multimodal characterization techniques such as soft X-ray, and EUV.  

Principal Investigator: Bruce Cohen

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:

The assembly of beta amyloid peptides (A-beta) into aggregates is a hallmark of Alzheimer’s disease, but major questions remain about how this happens and which aggregates, if any, are responsible for disease progression.  Micron-scale A-beta plaques are readily apparent in pathology of Alzheimer’s brain, but multiple lines of evidence suggest that earlier, nano-scale, aggregates are the critical neurotoxic agents.  Despite the apparent importance of A-beta oligomers, there is little experimental information on the structures or assembly process of these aggregates.  To address this, we have recently developed organic fluorescent probes able to bind and report on A-beta aggregation, including at the earliest timepoints. 

Main project goal or research question to be addressed by the intern: 

This project then entails optical characterization of labeled A-beta plaques optical microscopy, including kinetic studies, and imaging with therapeutic antibodies and microglial cells.

Intern’s role:

The intern will learn and perform confocal microscopy, fluorescence characterization, and cell culture.  In addition to these techniques, the intern will learn about fluorescence, protein/peptide biochemistry and the science underlying amyloid diseases.

What can the intern expect to learn?

The intern will learn and perform confocal microscopy, fluorescence characterization, and cell culture.  In addition to these techniques, the intern will learn about fluorescence, protein/peptide biochemistry and the science underlying amyloid diseases.

Principal Investigator: Natalia Molchanova
Other mentors: Behzad Rad, Crysten Blaby-Haas

Our research group focus is on developing living and regenerable systems to advance sustainable solutions for environmental challenges. To this end we harness the potential of microorganisms for biodegradation using cutting-edge genetic and biochemical approaches to enhance the efficiency of plastic-eating bacteria. Our work integrates molecular biology and biochemistry to address critical issues at the intersection of science and sustainability.

Project Description:

This project aims to understand and engineering polymer degradation pathways in bacteria as a sustainable solution for plastic waste management. The researcher will look into the enzymatic processes and metabolic pathways employed by these microorganisms to break down various types of plastic polymers to identify and enhance the efficiency of plastic-degrading bacteria.

Main project goal or research question to be address by the intern

The primary objective is to investigate the specific mechanisms employed by plastic-eating bacteria, with a focus on optimizing their performance in degrading PET and other common plastics. The intern will contribute to elucidating key genetic factors that influence the biodegradation process.

Intern’s role:

The intern will be actively involved in laboratory experiments: working with microbial culture, cloning, expression and purification of plastic degrading enzymes, and developing a high-through put assay for enzyme activity. The intern will also help check the efficacy of mutations to ensure their practical application and effectiveness and literature search of current advancements in plastic biodegradation.

What can the intern expect to learn?

This internship offers a unique opportunity for the candidate to gain hands-on experience in the field of molecular biology, synthetic biology, and biochemistry. Moreover, they will develop a comprehensive understanding of working with bacteria, and broaden their knowledge of the possible sustainable way of plastic recycling.

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 (XRD) technique provides accurate structural information at the atomic level and is perhaps the most reliable method to structure determination. However, many organic molecules tend to form oils due to low melting point or amorphous phases or be frustrated while growing larger single crystals with good crystallographic quality for XRD analysis. Recently, several strategies have been proposed to help study molecules that exhibit challenges in obtaining single crystals and address the limitations. One effective strategy is so-called “crystalline sponges” method first developed by the Fujita group. By this method, small organic guest molecules are absorbed into the pores or channels of porous metal–organic frameworks (MOFs); the absorption is driven by strong p-p, CH–p, and charge–transfer interactions between guest molecules and the electron-deficient p-plane of MOFs. However, the dominant metal–organic framework crystal sponge platforms typically face poor chemical stability, especially solvent instability, hampering their application in a larger domain.

Main goal of the project:

The main goal of the project is to design and synthesis new porous organic molecular frameworks as crystalline sponges for the structural determination of the guest with X-ray crystallography. 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 crystalline sponges for a wide scope of molecules.

Intern’s role:

• Optimize crystallization conditions for growing large single crystals of porous organic molecular frameworks.
• 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 porous framework host and guest molecules and rationalize the inclusion mechanism for future design of new crystalline sponges.

What can the intern expect to learn?

• Hands-on experience on synthesis and characterization of porous 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

Principal Investigator: Ricardo Ruiz
Other mentor: Emma Vargo, Beihang Yu

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 patterning of semiconductor devices and biomolecular building blocks alike. Conventional surface functionalization methods 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. This broad range of composition and processing options forms a rich parameter-space, which needs to be explored and mapped. In this project, the intern will work with other group members to measure brush properties (thickness, grafting density, surface energy) as a function of input variables (brush chemistry, surface activation, annealing temperature, substrate chemistry). The input variables are expected to have complex and interdependent effects on the final brush. Depending on the intern’s interests, the project can incorporate elements of data science and/or data visualization to build a better understanding of the brush parameter-space. Optimized brush monolayers will create high-fidelity surface guiding patterns for selective immobilization of biomolecules and state-of-the-art EUV lithography.

Main research question

Identify and separate the effects of chemistry and processing parameters on polymer brush grafting density and surface selectivity

Intern’s role:

• Prepare and characterize samples in a cleanroom setting: polymer thin-film and monolayer deposition, ellipsometry, water contact angle measurements, and atomic force microscopy (AFM).
• Analyze results and develop scientific conclusions, and compare with existing literature.
• Identify and apply appropriate data science techniques to extract key relationships
• 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 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 characterization techniques such as AFM.
• 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.

Principal Investigator: Rohan Dhall, John Turner
Other mentor: Karen Bustillo, Chengyu Song

The National Center for Electron Microscopy is focused on high resolution imaging of various material systems. However, high resolution imaging requires ultra-thin samples and image quality is often limited by damage to the sample during thinning. In this project, we hope to enable low temperature sample preparation, which would prevent damage, and improve sample quality, and enable high resolution imaging for certain material systems such as polymers, battery materials, and perovskite solar cells.

Project Description:

High resolution electron microscopy needs specimens of thicknesses below 100 nm to ensure electron transparency. Typically, samples are thinned down using a focused ion beam (FIB) of accelerated Gallium ions. Unfortunately, this process also leads to significant beam-induced damage, which is particularly troublesome in various materials of interest such as battery materials, polymers, biological samples, organic semiconductors, etc. The issue of beam damage can, however, be mitigated by cooling the sample during FIB milling, leading to the development of “cryo-FIB” techniques. Special instruments have been designed to cool specimens down during FIB milling, using a cryogen such as liquid nitrogen. This, however, adds significant cost and complexity to the instrument, and also creates various issues like vibration and drift during the FIB milling.

An alternative strategy to cool the specimen down could be to use thermo-electric cooling. Thermoelectric coolers are already used in various systems, and operate on the basis of the Peltier effect, where an electric current is used to create a temperature gradient across the thermoelectric. Samples for FIB milling could be attached to the cold side of this temperature gradient.  In this project, we hope to integrate a commercially purchased thermo-electric cooler into a custom built stage for the FIB instruments to enable low temperature milling. It is expected that this setup would be simpler and cheaper than cryogen based cooling, while also providing greater sample stability.

Main project goal or research question to be addressed by the intern

Design and development of a cryo-gen free cooling stage for FIB microscopes.

Intern’s role:

We would like the intern to be responsible for the design of the cryogen free cooling stage for FIBs. This would require 3D CAD skills, as well as calculations (either analytical, or based on finite element modeling) to optimize design parameters such as the stage dimensions, electrical power requirements, and the lowest achievable sample temperature. If the intern is able to produce a viable design for the instrument, we can also work with the machine shop at the Molecular Foundry to build a prototype of the stage, and test its performance in the Strata FIB at NCEM. If time permits, we would also like to design a software interface to control the Peltier cooled stage. 

What can the intern expect to learn?

The intern can expect to learn various skills for prototyping engineering projects, such as mechanical and electrical design. Additionally, the student will learn about thermoelectric cooling devices, as well as their integration into a system. Finite element modeling, and 3D CAD are going to be required for this work, using a tool such as Solid Works. Additionally, the student will learn how to operate a dual beam scanning electron/ion microscope , and learn how to prepare TEM samples. If interested, the student can also be involved in machining a prototype of the designed instrument, and  imaging prepared samples under a high resolution TEM to learn about materials characterization methods.

Principal Investigator: Sinéad Griffin
Other mentor: Bernard Field

The Griffin Group is multidisciplinary theory and computation team that solve the most
exciting problems ranging from future technologies to high-energy physics, bridging
disparate fields to solve grand challenges. We primarily use first-principles calculations
and phenomenological models to describe and design materials for quantum systems
(including dark matter detection), and next-generation microelectronics. Our work is
often combined with and inspires experimental investigations of candidate materials,
which is facilitated by our proximity to state-of-the-art materials synthesis and
characterization capabilities at LBNL and UC Berkeley.

Project Description:

To keep up with growing demand for computing, we must move electrons at the atomic scale. This requires new materials with structures just a few atoms across. Grain boundaries and line defects in 2D materials are nano-scale structures which can host special electronic states. Such states have unique properties which could be useful in next-generation electronics and computing. However, systematically identifying materials with such special defects is an ongoing challenge. This project will use state-of-the-art quantum mechanical calculations to analyze several candidate materials with line defects. In this project, you will identify electronic features of interest in these materials and possibly propose new materials which may be investigated further by experiments.

Main research question 

How can nanoscale defects have new properties not available in pristine materials?

Intern’s role:

• Carry out computational and theoretical studies on the materials
• Compare calculations to existing literature
• Deliver oral, written and poster presentations
• Collaborate and interact with scientists in the group and at LBL
• Write paper with results and conclusions

What can the intern expect to learn?

• How to perform first-principles calculations (Density Functional Theory)
• How to interpret results and understand advantages and drawbacks of methods
• How to plan research and ask good questions
• Scientific communication and presentation skills
• How to learn something new

Principal Investigator: Mary Scott
Other mentors: Katherine Sytwu, Luis Rangel DaCosta

Research in Scott lab uses advanced and high resolution electron microscopy methods to relate structure to function in a variety of materials. Much of the work occurs at the National Center for Electron Microscopy (NCEM), part of the Molecular Foundry at Lawrence Berkeley National Lab.

Project Description:

Recently, our lab has studied machine learning techniques for analyzing experimental atomic-scale images of nanoparticles taken with High-resolution Transmission Electron Microscopy (HRTEM). In particular, we’ve successfully developed and analyzed methods which use either experimental or simulated data to train neural network models, both of which can perform well but have their own performance limitations.

Main project goal or research question to be address by the intern:

In this project, an intern would join us in investigating how to best incorporate both sources of training data–experimental and simulated–for training neural network models to analyze HRTEM data, and how techniques such as transfer learning can be leveraged to further understand and analyze our experimental data.

Intern’s role:

They can expect to learn about HRTEM experiments and why we use HRTEM to study nanoparticle systems, about HRTEM simulations and how to perform them, and about various basic machine learning techniques and how they are used and deployed in scientific contexts. They would be involved in curating simulated and experimental datasets, training neural network models and analyzing some experimental HRTEM benchmark datasets, and developing and optimizing neural network training procedures.

What can the intern expect to learn?

They can expect to learn about HRTEM experiments and why we use HRTEM to study nanoparticle systems, about HRTEM simulations and how to perform them, and about various basic machine learning techniques and how they are used and deployed in scientific contexts. They would be involved in curating simulated and experimental datasets, training neural network models and analyzing some experimental HRTEM benchmark datasets, and developing and optimizing neural network training procedures.

Principal Investigator: Paul Ashby
Other mentor: 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:

Liquid in liquid structures can be created by assembling nanoparticles with surfactants at the phase boundary between two immiscible liquids.  The nanoparticle surfactant assemblies pack into a dense film that jams allowing the liquid boundary to maintain its shape. We use these structured liquids to create reconfigurable reaction vessels and probe the organization of active matter systems.  

Main project goal or research question to be address by the intern:

Theory predicts that film stability increases, reaches a maximum, then decreases as surfactant concentration increases. However, we observe a region of even higher stability after an initial decrease at very high surfactant concentrations. We seek to understand the structure of the nanoparticles in the film and why the film has anomalously high stiffness so that this phenomena can be harnessed for technological applications. 

Intern’s role:

The intern will use microscopy techniques to characterize the 3D structure of the nanoparticles comprising the films.  Super resolution optical microscopy and atomic force microscopy provide 3D descriptions of the material with resolution on order of 10 nanometers. 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 performance microscopy techniques and excellent laboratory techniques for high precision measurements. 

Principal Investigator: Crysten Blaby-Haas

The Blaby-Haas group studies how biology encodes functionality in genomes, proteins, complexes, and bioproducts. Using computational genomics approaches combined with hypothesis-based experimentation from reverse genetics to structural characterization, we aim to define the foundational design principles needed to build bio-based technologies for addressing challenges in energy and environmental sustainability.

Project Description:

The last decade has seen extraordinary advances in methods for manipulating biological systems. Technologies such as the CRISPR-Cas system for gene editing have enabled the understanding and control of biological systems at a level that was impossible even five years ago. At the same time, high-throughput genome sequencing has provided millions of biological blueprints, while new machine-learning-based methods have vastly improved the predictability of sequence-to-structure. Leveraging these recent advancements, we have identified a plethora of novel, naturally evolved, encodable, adhesion polymers with promising features for synthesizing bio-based programmable materials. By combining the natural light harvesting and carbon sequestration capabilities of cyanobacteria with these newly discovered biopolymers, we aim to design and build bio-based devices for capturing and converting CO2 from the atmosphere to help achieve climate resilience. 

Main project goal or research question to be address by the intern:

Acquire a predictive understanding of synthetic connective filament design and construction. 

Intern’s role (i.e., what kinds of things will they be doing):

Design a cell-to-cell adhesion matrix composed of genetically encoded biopolymers and, leveraging recombinant gene expression, build a photosynthetic biofilm.

What can the intern expect to learn?:

Bioinformatics, genomics, microbe culturing, transformation, concepts in bio-based materials.

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 method. 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 address 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 (i.e., what kinds of things will they be doing):

• 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 two-step “lateral conversion” synthesis method.
• They will learn how to characterize their samples using a variety of synthetic and 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.

Principal Investigator– Colin Ophus
2nd mentor – Karen Bustillo
Our group focuses on computational imaging methods applied to scanning transmission electron microscopy (STEM). We develop mathematical methods and software analysis pipelines for measuring material properties from datasets consisting of thousands or even millions of diffraction patterns.

Project description – In this project, the intern will develop methods and python analysis code to measure radial distribution functions from diffraction data. They will start by simulating diffraction patterns from thin, known materials and implementing existing algorithms to measure 2-atom pair distribution functions. They will extend these methods to 3-atom distribution functions and thicker samples. They will study materials ranging from liquids to amorphous glasses to nanocrystalline thin films.

Main research question – Can 3-atom distribution functions be recovered from electron diffraction patterns?

Intern’s role and skill development – The intern will learn how to build atomic models and simulate electron diffraction patterns using quantum-mechanical scattering algorithms. They will also learn how to load and analyze diffraction patterns using our group’s python code, py4DSTEM. They will learn how to write python in a collaborative software environment, and contribute to open source code development.

PI Name: David Prendergast
Other Mentor Name: Fabrice Roncoroni
The Prendergast group performs molecular dynamics simulations of interfaces for energy conversion and application of data science techniques to accelerate scientific insight.

Project Description: With the increased focus on electrification of infrastructure as a driver for weaning society off its dependence on fossil fuels, water electrolysis is viewed as an effective means of storing electrical energy (hopefully from renewable sources) in chemical carriers, such as hydrogen. Electrolyzers are the devices that enable this conversion but their expense presents a barrier to widespread utilization. This expense is driven in large part by materials limitations (precious metal catalysts, complex polymer membranes) and poor understanding of how harsh operating conditions (extreme pH, high voltage and current) lead to degradation in performance and reduced operation lifetimes. Understanding such processes at the molecular scale provides much needed feedback to synthesis and fabrication efforts to develop more efficient devices.

Main project goal or research question to be address by the intern: In this project, you will learn how to model and understand electrochemical processes at active interface and how to analyze the large volumes of data from molecular dynamics simulations using modern data science techniques to expand insight and create more accurate models of functioning electrolyzers.

Intern’s role (i.e., what kinds of things will they be doing): Data analysis and modeling using python notebooks, application of machine learning and data mining techniques, compilation and presentation of results in a collaborative group setting

What can the intern expect to learn? Data mining techniques (such as dimensionality reduction (UMAP), and clustering (HDBSCAN)), python-based workflows, domain knowledge on molecular dynamics, clean energy applications, water electrolysis.