Correlation of macroscopic material properties and function with molecular structure and dynamics, particularly in heterogeneous macromolecular solids. Synthesis and characterization of self-assembled inorganic-organic and mesoporous materials for catalysis, separations, and opto-electronic applications. Molecular dynamics and structure in hierarchically ordered polymers, liquid crystals, nanocrystals, and biominerals. Development and application of nuclear magnetic resonance spectroscopy methods for characterizing structure, dynamics, adsorption, transport, and reaction properties of new solid-state materials.
Catalytic processes are relied upon globally for trillions of dollars per year of industry. The conversion of oil to gasoline, transformation of natural gas and nitrogen into fertilizer, and conversion of un-burnt fuels into less harmful gasses in the tail pipes of cars all rely on solid state catalysts. Increasing demands for efficient, environmentally friendly chemical processes, in concert with the push to utilize emerging natural resources, rely on the development novel catalytic materials and processes for success. We use principles from chemical engineering, materials science, physical chemistry and solid-state physics to engineer catalytic reactions towards these goals. We develop molecular level insights into governing phenomena of catalytic reactions by coupling quantum chemical calculations with an array of experimental and characterization techniques. Mechanistic insights are utilized to guide the synthesis of catalysts with targeted geometries, compositions and architectures.
The genome within all cells of a multicellular organism is identical, yet different cells within the heart, brain or small intestine for example, display varied functions and properties. Even the same tissue is composed of several distinct cell types that gives rise to a wide range of cellular heterogeneity. What makes these cells, with identical genomic blueprints, different? It has been shown that chemical modifications of DNA and certain other proteins associated with DNA, collectively termed as the epigenome, result in the same genome being read in different ways that results in cell-to-cell heterogeneity in the expression of genes. Thus, one of the central questions we will be addressing in our group is to understand how the genome or epigenome regulates gene expression, thereby influencing cellular functions. Regulation of the transcriptome, defined as the genome-wide distribution of mRNA molecules, can be viewed as the output of a complex network of chemical and physical processes, and understanding how these processes interact and integrate to govern cellular behaviors, or phenotypes, will be a major focus area of our research.
Over the last decade, understanding genome-wide correlations between the genome, epigenome and transcriptome typically involved starting from a large population of cells or complex tissues. However, as these measurements are made from a bulk population, they only provide an average description of the system. As individual cells can display dramatic cell-to-cell variability, to unambiguously understand how a particular gene expression program in a cell is regulated will require direct measurement of both the transcriptome together with the epigenome from the same cell. Therefore, in our group we will be developing novel integrated technologies that enable simultaneous genome-wide measurements of the epigenome and transcriptome from the same cell to gain insights into early mammalian development, maintenance and regeneration of adult tissues and mechanisms contributing to tumor progression. Finally, we will be employing tools from single-cell genomics to unravel the evolutionary relationship between cells, also known as developmental lineage trees, that are currently not well known in complex multicellular organisms. Reconstructing these lineage trees will offer significant new insights into cellular differentiation with important applications in regenerative medicine.
Protein synthesis and conceptual design of chemical process systems. Combining reactions and separations, crystallization of organic materials, and systems with complex chemistries. Applications: specialty chemical and pharmaceuticals.
Separation with chemical reaction. Potential to create quantum improvements in process technology through the enhancement of reactions by separation and by the improvement of separation by reaction. Developing new feasibility methods using geometric techniques such as residue curve maps, bifurcation analysis, and attainable regions. Applications: production of esters and ethers by reactive distillation, and antibiotics by reactive solvent extraction.
Crystallization of organic materials. Study the effect of process design and operation on crystal quality for organic-solids processes. The key measures of quality that we are interested in are, enantiomorph (for chiral mixtures), polymorph, and crystal shape. Developing new methods to account for solution effects, with the ultimate goal of using these new methods to account for crystal shape, as well as enantiomorph and polymorph selection in the conceptual design of solids processes.
Theoretical analysis of complex fluids and polymers including suspensions, polymer solutions, and melts, and especially block and graft copolymers. A major effort involves the development of new computer simulation tools for analyzing statistical field theory models of polymers and complex fluids -- "field theoretic simulations" -- and the application of such tools to the design of improved complex fluid formulations and high performance plastic materials.
- Polymers and complex fluids
- Thermodynamics and statistical mechanics
- Transport phenomena
Synthesis and characterization of nanoscale materials as well as the development of scanning probe microscopy (SPM) methods for optical, electrical, and mechanical interrogation of nanoscale systems found in different venues such as material science, microelectronics, catalysis, and biology. Our overall goal is to exploit the unique physicochemical properties of nanoscale systems by probing and understanding materials over a variety of length scales from nano to macro. Our research is "hands-on" experimental science involving a combination of scanning probe microscopy techniques (STM, AFM, SNOM), laser spectroscopy, nanofabrication, and traditional surface science. We build our own instruments and synthesize various nanostructured materials using plasmas, CVD, lithography, and traditional solution-based methods.
- Design/construction of scanning probe microscopy tools for chemical imaging of surfaces
- Using sub-wavelength optical interactions with matter to study physical, chemical, and biological processes
- Developing novel ways to identify/manipulate single molecules, nano-objects, and micro-scale systems using hybrid AFM techniques
- Synthesis and characterization of plasmonic and catalytic materials
- Spectroscopy of organic semiconductors for OLED and PV applications
In the Han Lab, we are developing novel techniques and innovative approaches, relying on electron and nuclear spin magnetic resonance concepts that enables one to detect structure, dynamics and interaction with unprecedented sensitivity, resolution and information content. Our lab takes a two-pronged approach: (1) to develop new instrumental capabilities, methodologies and concepts, and (2) to concurrently pursue important questions in biophysics and materials science using a new combination of the just developed, as well as existing set of, technologies. An important emphasis of the development in the Han lab lies on dynamic nuclear polarization that can amplify the nuclear magnetic resonance (NMR) signal by orders of magnitudes, by transferring polarization from highly polarized electron spin probes to surrounding nuclei.
We employ strategic spin probes at molecular or material sites of interest, and pursue ambient temperature Overhauser DNP enhanced study of hydration dynamics at 10 GHz, as well as below 20 Kelvin solid state DNP enhanced NMR spectroscopy at 200 GHz. Concurrently, we also develop cw and pulsed electron spin resonance (EPR) capabilities at 200 and 240 GHz, and arbitrary waveform-powered pulsed EPR spectroscopy at X-band for enhanced studies of molecular structure and dynamics. Questions of interest include, but are not limited to, the study of lipid membrane biophysics, functional role of hydration water dynamics, membrane protein structure-dynamics-function relationship, early stages of amyloid protein aggregation, polyelectrolyte coacervation for bioinspired materials and unraveling soft matter structure-dynamics-property relationships.
Our research is devoted to the design and processing of complex fluids, especially those involving colloidal species (nanoparticles, emulsions, proteins, etc.) in self-assembling & structured liquids. Specifically, we seek to understand how well-specified mesostructure can be obtained in these fluids, and how it can be used to control the mechanical and transport properties of soft materials. Our approach involves combining experimental and theoretical tools (scattering, microscopy, rheology, statistical & colloidal thermodynamics) for multi-scale characterization and description of fluid microstructure and dynamics, ultimately to inform the molecular-level design of mesoscale structure. We have particular expertise in developing methods for in situ monitoring of fluid microstructure during processing. Current projects include the design of functional and stimuli-responsive gels and particulates for applications in biotechnology, advanced materials and energy conversion.
McFarland’s research activities are focused on coupling fundamental processes at surfaces with novel material systems to enable economically and environmentally sustainable production of chemicals and power in real industrial processes. In particular, his group is working on use of new catalysts and materials for decarbonizing fossil fuels and producing chemicals without carbon dioxide. His group is also investigating novel nuclear reactor designs to reduce cost and increase safety and allow the opportunity for coupling chemical production with power production. McFarland teams with colleagues using state-of-the-art theoretical methods to guide and interpret experimental work using advanced theory and to develop conceptual process models to evaluate the technoeconomic potential of new processes making use of the chemistry.
Our ability to visualize biological activity inside living cells relies almost exclusively on genetically encoded light emitting proteins such as the green fluorescent protein (GFP) and luciferase. However, practical application of these bioluminescent proteins is often constrained by two transport restrictions that are a major factor in vivo: the limited diffusion of oxygen, which is an essential substrate for light emission; and the inability of light to access deep, opaque tissues. For these reasons, low-oxygen biological systems (e.g., the gut microbiome) as well as preclinical models of disease, injury, and therapy in optically opaque animals have remained largely “invisible” to investigations using existing biomolecular tools.
To address these challenges, the Mukherjee group will pursue fundamental advances at the intersection of molecular biology, biomedical imaging, and biophysics to discover and repurpose new classes of biomolecules into genetic reporters for studying cell function under low-oxygen conditions and inside deep tissues. Specifically, the group will explore biomolecular materials with interesting properties such as paramagnetism, photoreception, and water diffusion. Using advanced protein engineering techniques such as directed evolution, the Mukherjee lab will turn these proteins into “molecular spies” that can transduce biochemical signals inside a cell into an oxygen-independent optical readout (for fluorescence imaging) or a deep tissue-penetrant magnetic resonance signal (for magnetic resonance imaging). The biomolecular agents developed in the Mukherjee lab will be useful for studying a wide range of problems encompassing cancer, neurobiology, degenerative diseases, infections, biomechanics, anaerobic microbiology, and immunotherapy.
The O'Malley Lab works at the interface of engineering and biology to engineer microbes and consortia with novel functions. We are especially interested in deciphering how “unwieldy” microbes in the environment perform extraordinary tasks - many of these microbes have no available genomic sequence and are exceptionally difficult to manipulate. We seek a better understanding of how proteins are synthesized by cells, and how their three-dimensional structure informs their function would enhance our ability to engineer proteins (and cellular expression platforms) for diverse biomedical and biotechnology applications. To address these issues, our approach combines classical cell biology tools with cutting-edge technologies (genome sequencing, RNAseq, cellular reprogramming) that are rooted in the core biological sciences to interrogate and engineer molecular mechanisms that underlie protein production in eukaryotic cells. In addition, we rely on biophysical methods to elucidate protein-protein contacts, with the aim of controlling these interactions both in vivo and in vitro. Systems of interest to us have broad applicability to bioenergy and sustainability, as well as to drug development and detection.
Areas of interest:
- Genetic and cellular engineering of anaerobic gut fungi
- Synthetic anaerobic consortia for bioproduction and model development
- Engineering synthetic fungal cellulosomes and novel biocatalysts
- Membrane proteins for drug discovery, detection, and diagnostics
- New membrane proteins for synthetic biology
The kinetics of nucleation, electron transfer, and catalytic reactions depend on the properties of short-lived and rarely-visited transition states that cannot be directly observed in experiments. We gain insight into the properties of transition states using molecular simulation and electronic structure theory. Examples include the effects of solution additives on nucleation rates for crystallization, the dominant electron transfer conduits in realistic fluctuating environments, and catalytic reaction mechanisms. When applications pose new challenges beyond the scope of available techniques, we develop theories and algorithms to address those challenges. In particular, we specialize in path sampling methods for free energies and reaction coordinate identification, metrics for reaction coordinate error, methods to obtain accurate rate constants, and multiscale simulation approaches.
Areas of interest:
- Solute precipitate nucleation and polymorph selection
- Single atom catalysts on amorphous supports
- Simulation methods for mechanistic hypothesis testing
Chemical process monitoring and control: Chemical processes are inherently nonlinear and must operate at their design constraints to achieve optimal economic performance. We have developed methods of moving horizon estimation and model predictive control to monitor and control the operation of chemical processes. This research has provided new theoretical results as well as practical, implementable methods for industrial application.
Reaction engineering at the molecular level: When reacting systems are considered at small length scales (small catalyst particles, inside living cells, etc.), the concentrations are small enough that the stochastic fluctuations cannot be neglected, and the classical standard methods of chemical reaction engineering are not applicable. The focus of our research is to develop new systems tools to support chemical reaction engineering at this molecular level.
Computational modeling: Our group has developed Octave, a freely available, high-level computer language for numerical simulation and analysis of chemical engineering models. We use Octave in order to define models quickly, compute and analyze solutions, estimate model parameters from data, and solve controller design problems.
The Scott group conducts both fundamental and applied research in surface chemistry and catalysis. We aim to understand the interactions and transformations of molecules in solution and at gas-solid interfaces by creating highly uniform active sites. We apply techniques from organometallic and coordination chemistry, surface science, spectroscopy, kinetics, mechanistic analysis and modeling to investigate, design and re-engineer heterogeneous catalysts. A key element of our strategy is to synthesize well-defined molecular precursors and anchor them onto solid supports via self-limiting surface reactions. For example, organochromium complexes CrRx are precursors to active sites in the Phillips (Cr/SiO2) catalysts for ethylene polymerization, while perrhenates such as (CH3)3SiOReO3 and CH3ReO3 are precursors to supported olefin metathesis catalysts.
Structure control over soft matter on a molecular through nanoscopic lengthscale is a vital tool to optimizing properties for applications ranging from energy (solar and thermal) to biomaterials. For example, while molecular structure affects the electronic properties of semiconducting polymers, the crystal and grain structure greatly affect bulk conductivity, and nanometer lengthscale pattern of internal interfaces is vital to charge separation and recombination in photovoltaic and light emission effects. Similarly, biological materials gain functionality from structures ranging from monomeric sequence through chain shape through self-assembly. We work to both understand the effects of structure on properties and gain pattern control in these inherently multidimensional problems. We are particularly interested in materials for energy applications such as photovoltaics, fuel cells, and thermoelectrics.
We use molecular simulation and theory to understand multi-scale, hierarchical interactions in complex biomolecular systems, with a specific focus on proteins and peptides. In particular, our group develops general methods for predicting peptide structure and self-assembly behavior, and is designing new approaches for linking simulations and theories across multiple length and time scales in fundamental, rigorous ways. These efforts are used to understand (1) folding and design principles in proteins; (2) peptide structure, association, self-assembly, and aggregation; and (3) the role of water and the hydrophobic interaction in driving biological recognition and self-assembly processes.
Sho is interested in the statistical mechanics and fluid dynamics of biological soft matter systems. He combines techniques of computational and experimental soft matter to study how emergent biological properties emerge from collective activity of microbial and cellular communities. These insights will advance fundamental understanding of the properties of bacterial biofilms and biological tissues, and could also lead to the design of bio-inspired, adaptive complex fluids for applications in medicine, manufacturing, and biomaterials.
Transport science plays a role in all things dynamical - and can often play the crucial role. As such, it is an extremely versatile science. Learning to think effectively about fluids and transport enables one to understand and contribute to a wide range of interesting and important problems. Our group works various areas of micro-scale fluid mechanics and transport science - microfluidics and electrokinetics, active, nonlinear and interfacial microrheology of complex materials, polymer dynamics and sensors. Current theoretical and experimental projects include:
- Non-linear (induced-charge) electrokinetic flows, with an eye towards portable, self-contained and implantable microfluidic devices,
- Extending the capabilities of "microrheology" (which typically uses colliodal beads as passive tracers to measure the rheological properties of complex materials) by using active forcing to extract nonlinear material response properties;
- Developing and employing a novel technique for measuring the rheology of fluid-fluid interfaces, with particular emphasis on natural and synthetic lung surfactant layers and surfactant-laden polymer-polymer interfaces;
- Theoretical and experimental investigations into interfacial mobility of nanoparticle and copolymer surfactants (collaboration with Leal and MRL), and
- Understanding the self-assembly and transport properties of nanostructured materials, with applications in ultracapacitors for energy storage (collaboration with Chmelka).
This is a wide range of topics, loaded with interesting and important questions - underscoring the versatility of this fascinating field.
Our research group works at the interface of chemistry, chemical engineering and catalysis to address outstanding issues in energy science, sustainability and green chemistry. Much of modern life materials are based on nonrenewable petroleum. We are active in two areas of research, biomass conversion and bio-inspired chemistry, to discover and develop new transformations and molecules that can serve as monomers for new materials and/or precursors to renewable liquid fuels.
In catalytic conversion of nonfood biomass, we have demonstrated novel methods to convert lignin into two high value phenols. These molecules can be used as monomers to make thermoplastics, precursors to aromatic compounds, and they can be deoxygenated further to high octane hydrocarbon fuels. An attractive feature of our lignin first approach is the preservation of the cellulose, which we have shown can be upgraded via catalysis to value added chemicals or fuel precursors.
In our bioinspired project, we have prepared metal oxo complexes and investigated their use in small molecule activation such as dioxygen and chlorite. In a recent example we discovered and characterized unusual valence tautomerization in manganese oxo corrole that affords upon addition of a proton or a Lewis acid reactivity that spans seven orders of magnitude. These findings illuminate how nature’s enzymes work and provide insight on how we as molecular engineers can design and prepare catalysts tailored for function much like nature does in metalloproteins.
A common theme in our research is catalyst design based on mechanistic understanding on the molecular scale. To determine reaction mechanisms and structure-function relationships, we study chemical kinetics, characterize intermediates, and employ state-of-the art spectroscopy under operando conditions. Graduate students and postdoctoral scholars in the group are given the freedom to tailor their own projects and are encouraged to collaborate with their colleagues in the lab as well as peers in other groups on campus with whom we share common scientific interests.
Prof. Bates’s research sits at the intersection of chemistry, materials science, and physics, leveraging a variety of synthetic and physical experimental techniques to design, create, and probe the structure and properties of soft matter. Current endeavors span a variety of topics including polymer mesostructure and dynamics, energy storage, and crystallization. Students in his research group will gain proficiency with numerous techniques useful in both academic and industrial settings, including small molecule and macromolecule synthesis, scattering and diffraction, rheology, electrochemistry, and thin film engineering.
Molecular Recognition Tools: Molecular recognition discovery processes developed by the Daugherty group have provided fundamentally new capabilities to create peptides with remarkable specificity for their target(s) while simultaneously accelerating the pace of their discovery.
Antibody Repertoire Analysis: We have developed a new antibody biomarker discovery method that provides the opportunity to discover diagnostically useful biomarkers for unmet medical needs. With clinical collaborators, we are applying these methods to develop reagents suitable for clinical diagnostic development.
Therapeutic Protein Design: We are creating peptide-based probes that enable quantitative measurements of protease activity in living organisms. In particular we are constructing novel activity-based molecular probes to elucidate the functions of proteases involved in cancer progression.
Howard Zisser M.D. is director of clinical research at Sansum Diabetes Research Institute, where he conducts clinical trials on new and innovative therapies for type 1, type 2 and gestational diabetes. He currently manages trials investigating the safety and efficacy of inhaled insulin, of insulin that is absorbed in the cheek, of implantable insulin pumps and implantable glucose sensors.
Professor Israelachvili's research interests are in the general area of intermolecular and intersurface forces in complex fluid, biological and materials systems. He uses the Surface Forces Apparatus and other techniques for directly measuring the forces between surfaces in liquids and vapors, and for studying other interfacial and thin film phenomena at the molecular level. Specific projects currently include: non-equilibrium interactions (e.g., adhesion and friction), and developing new experimental techniques.
- Surfaces & thin films
- Adhesion & bioadhesion
- Molecular & hydrodynamic forces
My research is currently focused on the dynamics of complex fluids, such as polymeric liquids, emulsions, foams, polymer blends, and liquid crystalline polymers (LCPs). Much of this is related to the coupling between the influence of flow on the microstructure of these materials, and hence on the macroscopic material properties. Within this broad framework, we are working on: coalescence phenomena; the dynamics of thin liquid films and the control of the stability of such films due to additives such as copolymer surfactants, and nano- or micro-particles; the flow behavior of LCPs, including the formation of disclinations; and the dynamics of entangled polymers. Our tools encompass a spectrum of experimental methods (including several that are unique to our laboratory), as well as theoretical methods based primarily on large-scale computational studies.