Virtual Poster Session
Welcome to the Virtual Poster Session. Posters have been provided by various graduate research groups throughout the chemistry engineering option. If you have any questions on the research being presented, we encourage you to reach out to the respective group contacts.
Our work focuses on integration of machine learning to solve limitations of traditional directed enzyme evolution. This specific poster details our work on using machine learning for more effective and efficient optimization of protein activity over epistatic fitness landscapes.
Description: The Arnold group uses directed evolution to solve problems in synthetic chemistry and biocatalysis. We focus on four main areas: carbene transfer, nitrene transfer, non-canonical amino acid synthesis, and machine learning for directed evolution, and seek to perform chemistry that can not be done with traditional chemo-catalysts, including enantio- and stereo-selective reactions.
We study phase behavior of suspensions of active particles using a combination of analytic theory, computer simulation, and machine learning.
Locomotion of self-propelled particles such as motile bacteria or phoretic swimmers often takes place in the presence of applied flows and confining boundaries. Interactions of these active swimmers with the flow environment are important for the understanding of many biological processes, including infection by motile bacteria and the formation of biofilms. Recent experimental and theoretical work have shown that active particles in a Poiseuille flow exhibit interesting dynamics including accumulation at the wall and upstream swimming. Compared to the well-studied Taylor dispersion of passive Brownian particles, a theoretical understanding of the transport of active Brownian particles (ABPs) in a pressure-driven flow is relatively less developed. In this paper, employing a small wavenumber expansion of the Smoluchowski equation describing the particle distribution, we explicitly derive an effective advection-diffusion equation for the cross-sectional average of the particle number density in Fourier space. We characterize the average drift (specifically upstream swimming) and effective longitudinal dispersion coefficient of active particles in relation to the flow speed, the intrinsic swimming speed of the active particles, their Brownian diffusion and the degree of confinement. In contrast to passive Brownian particles, both the average drift and the longitudinal dispersivity of ABPs exhibit a non-monotonic variation as a function of the flow speed. In particular, the dispersion of ABPs includes the classical shear-enhanced (Taylor) dispersion and an active contribution called the swim diffusivity. While the pressure-driven flow always enhances particle diffusion through the classical Taylor dispersion process, it has a bidirectional effect on the swim diffusivity. Our continuum theory is corroborated by a direct Brownian dynamics simulation of the Langevin equations governing the motion of each ABP.
In nonequilibrium active matter systems a spatial variation in activity can lead to a spatial variation in concentration of active particles satisfying, at steady state, nU = const., where n is the number density and U is the active (swim) speed. We show that this condition holds even in the presence of thermal Brownian motion provided that the Peclet number is large. This spatial variation in swim speed and concentration produces a fluid pressure distribution that drives a reverse osmotic flow - fluid flows from regions of high concentration to low.
We aim to determine how nanoscale confinement can be used to tune the transport properties and thermodynamic stability of superionic sublattice melts. We use an anodic aluminum oxide platform to study confinement effects in a precisely controlled geometry.
Li-S batteries are poised to outcompete Li-ion batteries in key sectors such as transportation and grid storage due to their use of low cost and earth abundant materials. However, improving energy density and mitigating degradation in Li-S batteries is necessary before these tantalizing applications can be realized. Well-designed solid or solvate electrolyte systems have been shown to mitigate the widely known Li-S degradation mechanisms of electrolyte reactivity, polysulfide shuttling, and lithium dendrite growth. The most significant remaining degradation mechanism in these systems is mechanical failure and detachment of insulating Li2S from the conductive matrix in the cathode, causing irreversible capacity fade. However, the mechanisms of mechanical degradation and stress evolution in the cathode during the nucleation and growth of Li2S are not well understood. In particular, nothing is known about local stresses that could cause detachment or fracture within composite cathodes. Moreover, fundamental material properties of Li2S such as the Young's modulus, stiffness tensor, yield/failure stress and deformation mechanisms are unknown. Understanding these basic properties is a first step towards rational design of mechanically resilient sulfur cathodes with high energy density and long cycling lifetimes.
We report a novel methodology to investigate these previously unknown material properties and deformation mechanisms of Li2S via in situ SEM mechanical experiments. Our preliminary results from compression of micron sized Li2S grains help elucidate some of the deformation mechanisms of this material. During compression of Li2S particles we observe elastic loading consistent with a Hertzian contact model, followed by plastic deformation and catastrophic failure marked by crack initiation and propagation through the particle.
We additionally report he development of 3D structured Li2S-carbon composite cathodes with tunable features from the nm to cm scale using a novel technique called emulsion stereolithography. We use this technique to fabricate low tortuosity cathodes with three times better resolution than previously reported additively manufactures Li-S cathodes which demonstrate improved capacity retention after cycling.
Polymers abound the gut in the form of host secretions and dietary fibers. These polymers can aggregate particulate matter in the small intestine, which can affect the uptake of food and drugs and the function and behavior of microorganisms. In this poster, we show how particles spontaneously aggregate in the small intestinal lumen fluid ex vivo, and that chemically mediated interactions from mucins and immunoglobulins are not required for this aggregation. Furthermore, we show that aggregation can be controlled with dietary fibers through a mechanism qualitatively consistent with depletion-type interactions, demonstrating a polymer molecular weight and concentration dependence on particle aggregation. Finally, we show that motile E. coli can aggregate via depletion-type interactions, and that their motility enables aggregation in highly viscous environments where nonmotile bacteria and particles cannot aggregate due to lack of collision from hindered Brownian motion.
Contact: Michael Porter
We know that the 3-dimensional genome structure plays a role in regulating gene expression. We know there is heterogeneity in gene expression at the single cell level, which would likely result in heterogeneity in single cell genome structure. However current single cell methods are limited in looking at comprehensive single cell genome organization. As a result, our lab has collaborated with Mitch Guttman's lab at Caltech to develop scSPRITE (single cell split-pool recognition of interactions by tag extension) to look at comprehensive genome organization of DNA at the single cell level.
Contact: Mary Arrastia
Designing diagnostic tools to detect phenotypic antibiotic resistance at the point-of-care is vital to tackling the global threat of antibiotic resistance. Due to the slow growth rate of N. gonorrhoeaeand the mechanism of action of β-lactams, measuring the effect on the cell wall with nucleic acids can be challenging. By adding specific perturbations in succession with short antibiotic exposures and using nucleic acid accessibility as a readout, we are able to measure these effects. This poster details the development of a rapid, phenotypic antibiotic susceptibility test (AST), which is an active field of research in the Ismagilov lab.
Using megasupramolecules (long end-associative telechelic polymers) to study turbulence, mist control, and changes in rheology, including increased extensional viscosity.
Bubble nucleation is the least-understood part of polymer foaming due to the challenging of measuring such a fast, stochastic process. The Wang group has developed a model of bubble nucleation that predicts a dramatically lower nucleation energy barrier by adding an additional component, but lacks experimental means to demonstrate it. We developed a microfluidic instrument for measuring bubble nucleation at millisecond time scales and (ultimately) nanometer length scales under high-pressure (100 bar) conditions relevant for polyurethane thermally insulating foams, which has applications in improving energy efficiency of refrigerators, freezers, and buildings. Our collaboration among Dow, U. Naples, and Caltech developed additional custom instrumentation test other key aspects of the model and explore phase behavior.
Our research spans from single materials to fully integrated, operational devices and focuses on solving present-day issues in energy and chemical sensing by controlling interactions between light, semiconductors, catalysts, and liquids.
We are developing stochastic methods for gene expression systems, with applications to gene inference from single-cell sequencing datasets.
The See Group focuses on understanding fundamental processes governing performance in relevant electrochemical devices. We combine expertise in materials chemistry, analytical chemistry, and electrochemistry to gain a thorough understanding of the bulk and interfacial structure of active materials during and as a result of charge transfer processes in electrochemical devices.
Our research is broadly aimed at improving our understanding of the physics and chemistry of the atmosphere and of atmospheric aerosols, at scales ranging from the urban to the global atmosphere. This improved understanding will lead to more accurate representations of these processes in urban, regional, and global atmospheric models. We focus on the fundamental processes of atmospheric chemistry and aerosol formation and growth in the atmosphere. Of these, both the most important and the most uncertain are those involving the organic fraction of the atmospheric aerosol, which can be as large at 90% in some regions. Aerosol formation and evolution processes involve detailed gas-phase atmospheric chemistry and gas-particle interactions. We also focus on developing and evaluating the representation of aerosol-cloud-precipitation interactions in atmospheric models. Our research is broadly divided into three strongly overlapping areas:
- Laboratory chamber studies of atmospheric chemistry and the formation and evolution of atmospheric organic aerosols.
- Airborne field measurement of atmospheric aerosols and clouds.
- Urban, regional, and global modeling of air quality and climate.
Research description: Research in the Shapiro Group revolves around developing tools to non-invasively communicate with cells deep inside the body. To this end, we focus on two parallel research efforts: imaging and control of cellular function. The former effort involves developing genetically encoded contrast agents that can provide real-time information about cellular processes, and the latter involves engineering cells to respond to signals that can be delivered non-invasively to deep tissues. For more information, please see the "Research" section of our group's website: http://shapirolab.caltech.edu/?page_id=89.
Diblock copolymers are polymers consisting of a block of A-type monomers covalently linked to a block of B-type monomers. These polymers are known to microphase separate into spherical phases such as body-centered cubic (BCC) and the Frank-Kasper sigma phase. Several theoretical and experimental studies have examined factors that drive the formation of these phases; however, few studies have examined the kinetic pathway of the orderdisorder transition (ODT) to these spherical phases. For this reason, we investigated the nucleation behavior of a diblock copolymer melt as it undergoes a phase transition from a uniform, metastable disordered (DIS) phase to a BCC phase using self-consistent field theory in tandem with the string method. We found that the critical nucleus size and energy barrier grow as the ODT temperature is approached. We also found that, under certain conditions, the nucleus goes through a small energy barrier before the critical nucleus barrier, corresponding to the formation of a single micelle, which is consistent with previous theoretical studies. We concluded that composition fluctuations are significant near the disordered phase spinodal and cannot be ignored. Lastly, we found that the nucleation site matters for the A15 phase: nucleating at different sites yields strings with drastically different shapes and energy barrier heights.
Polyelectrolyte and electrolyte adsorption on charged surfaces and polymer mediated surface interactions for applications in colloidal stability and emerging energy materials.