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Forces, Stresses, and the (Thermo?) Dynamics of Active Matter: The Swim Pressure
Get PDFA core feature of many living systems is their ability to move, self-propel, and be active. From bird flocks to bacteria swarms, to even cytoskeletal networks, active matter systems exhibit collective and emergent dynamics owing to their constituents' ability to convert chemical fuel into mechanical activity. Active matter systems generate their own internal stress, which drives them far from equilibrium and thus frees them from conventional thermodynamic constraints, and by so doing they can control and direct their own behavior and that of their surrounding environment. This gives rise to fascinating behaviors such as spontaneous self-assembly and pattern formation, but also makes the theoretical understanding of their complex dynamical behaviors a challenging problem in the statistical physics of soft matter.
In this thesis, I present a new principle that all active matter systems display---namely, through their self-motion they generate an intrinsic `swim pressure' that impacts their dynamic and collective behavior. I combine experimental and computational methods to demonstrate how intrinsic activity imparts new behaviors to soft materials that explain a variety of complex phenomena, including the collective motion of self-propelled particles and the complete loss of shear viscosity in fluid suspensions. These nonequilibrium phenomena are driven fundamentally by the active constituent's tendency to diffuse, undergo a random walk, and exert a mechanical force or a pressure on a confining wall. The swim pressure theory is conceptually similar to the kinetic theory of gases, where molecular collisions with the container walls exert a pressure, or to the Brownian osmotic pressure exerted by molecular or colloidal solutes in solution. In contrast to thermodynamic quantities such as the chemical potential and free energy, the mechanical pressure (or stress) is valid out of equilibrium because it comes directly from the micromechanical equations of motion. I apply this swim pressure framework in a broad context to interpret living matter as a material and understand its complex behavior using tools of hydrodynamics, kinetic theory, and nonequilibrium statistical mechanics. The present theory is applied to active systems that are driven by self-propulsion and motility, but there are other types of nonequilibrium driving work that may fit into this general theoretical framework, like driven autocatalytic reactions in electrochemical and biochemical systems.</p
Revolution in Large-Area Curved Surface Lithography: Nanofilm Sculpting by Thermocapillary Modulation
Get PDFConventional lithography excels in producing blocky structures but has difficulty producing out-of-plane curvature. Such curvature is necessary for optical elements such as microlens arrays. Spatiotemporal control of the surface tension of liquid films offers a powerful method for sculpting myriad 3D shapes, thereby meeting this deficiency. In the Thermocapillary Lithography (TCL) project, we modulate thermocapillary forces by local control of surface temperature to deform a flat nanofilm into a variety of structures, which are then solidified in situ. In this thesis, we present two facile means of projecting the required temperature field, which we call Conduction TCL and Laser-induced TCL. In the former, which is a detailed expansion of the work performed in this group, the Laboratory of Interfacial and Small Scale Transport {LIS2T}, we place an array of chilled, prefabricated pins in close proximity to the film to provide precise thermal control via conduction. In the latter, which is new and has not been realized in literature yet, we project a spatially-modulated laser light field onto a horizontal heated fluid to achieve the same film deformation. Laser-induced TCL is shown to be a fully non-contact means of fabrication that admits real-time monitoring of the film profile. We demonstrate that the resultant temperature gradient field is capable of sculpting complex structures such as refractive optical elements, multiscale protrusions and depressions, arbitrary 2D images, as well as waveguides. By varying the pattern width, pitch and evolution time, we have also fabricated plano-convex, plano-concave, caldera-like, and hierarchical Microlens Arrays (MLAs) with ultrasmooth surfaces. As a proof of concept, the diverging arrays were incorporated in an adaptive optics component for wavefront sensing. This is the first functional optical device fabricated by modulation of the thermocapillary instability. Furthermore, the ultrasmooth out-of-plane curvature accessible through TCL is ideal for fabricating curved mirrors at the microscale. We exploit this property to fabricate the first large-scale optical microcavity array with curved mirrors for optical filtration. In the process, we developed a conformal, room-temperature metallization protocol for thermosensitive surfaces. In all, TCL is shown to be a facile, single-step means of fabricating complex ultrasmooth topologies, and opens up the possibility of printing planar optical circuit elements and beam shaping topologies on demand
Radiative Processes in Astrophysical Gases: From the Intergalactic and Interstellar Medium to Exoplanetary Atmospheres
Get PDFThis thesis presents theoretical investigations in three areas of astrophysics, all related to radiative processes and interactions between stellar radiation and gaseous media in the Universe, ranging from the intergalactic and interstellar medium to planetary atmospheres.
Part I of the thesis consists of two independent investigations in which we study the effects of stellar feedback in high-redshift environments. The topic of Chapter 2 is the intergalactic medium (IGM) in the epoch just after the formation of the first stars in the Universe, but before the cosmic reionization was completed. This epoch is of great interest for the ongoing and future experiments aimed at observing the neutral IGM via the redshifted 21 cm line of hydrogen. We study the effects of resonant scattering of Lyman-α photons produced by early stars on the structure of temperature fluctuations in the IGM. In Chapter 3, we use cosmological hydrodynamic simulations of galaxy evolution to study the effects of stellar feedback on the clumpy structure of star-forming galaxies at z ~ 2. Observations of high-redshift galaxies show that their morphology is often dominated by a few giant clumps of intense star formation, but the nature and the importance of these clumps for the evolution of their host galaxies are uncertain. We present a detailed analysis of the properties of giant clumps in a high-redshift simulated galaxy from the FIRE project.
Part II of the thesis is devoted to the effects of Raman scattering of stellar radiation in the atmospheres of extrasolar planets. Spectral signatures of Raman scattering imprinted in the geometric albedo spectrum of a gaseous planet carry information about the properties of the planet's atmosphere---its composition, temperature, and the radiation-penetration depth. In Chapter 5, we present the results of radiative transfer calculations including the treatment of Raman scattering for different types of planetary atmospheres and analyze the feasibility of detecting the spectral signatures of Raman scattering in nearby exoplanets. The structure and the intensity of Raman spectral features depends on both the atmospheric properties and the shape of the stellar spectrum irradiating the atmosphere. In Chapter 6, we analyze the diversity of Raman features in the geometric albedo spectra of planets hosted by different types of stars.</p
Mechanisms of Drp1 Recruitment to Mitochondria
Get PDFDynamin-related protein 1 (Drp1) is a GTPase of the dynamin superfamily that catalyzes mitochondrial fission in the cell. Cytosolic Drp1 is recruited to mitochondria by receptors anchored to the outer mitochondrial membrane. Once there, Drp1 assembles into a complex around the mitochondrial circumference to drive division via a GTP-dependent constriction process. The four known receptors of Drp1 are Fis1, Mff, MiD51, and MiD49, but stable interactions between Drp1 and these proteins have not been established. In addition, though mounting evidence suggests these receptors have non-redundant roles in their interaction with Drp1, mechanistic details explaining these distinctions are lacking. Here we address these questions, and show that the Insert B domain of Drp1 inhibits its interaction with Mff. Removal of this domain stabilizes a complex of Drp1 and Mff in vitro. In addition, we show that Drp1 oligomerization is a requirement for Mff recruitment, but not for MiD51 or MiD49-mediated recruitment. Together the results suggest a model in which Drp1 recruitment to mitochondria is regulated by the oligomeric state of Drp1, such that Mff, MiD51, and MiD49 recruit different subpopulations of Drp1 from the cytosol.
With this model as a framework, we analyze the effect that a Drp1 R403C mutant, identified in several human patients presenting with encephalopathy and refractory epilepsy, has on mitochondrial morphology in cultured cells. We find that the loss of Drp1 oligomerization in these mutants impedes its ability to be recruited by Mff, leading to abnormal elongation of the mitochondrial population.</p
Coding for Security and Reliability in Distributed Systems
Get PDFThis dissertation studies the use of coding techniques to improve the reliability and security of distributed systems. The first three parts focus on distributed storage systems, and study schemes that encode a message into n shares, assigned to n nodes, such that any n - r nodes can decode the message (reliability) and any colluding z nodes cannot infer any information about the message (security). The objective is to optimize the computational, implementation, communication and access complexity of the schemes during the process of encoding, decoding and repair. These are the key metrics of the schemes so that when they are applied in practical distributed storage systems, the systems are not only reliable and secure, but also fast and cost-effective.
Schemes with highly efficient computation and implementation are studied in Part I. For the practical high rate case of r ≤ 3 and z ≤ 3, we construct schemes that require only r + z XORs to encode and z XORs to decode each message bit, based on practical erasure codes including the B, EVENODD and STAR codes. This encoding and decoding complexity is shown to be optimal. For general r and z, we design schemes over a special ring from Cauchy matrices and Vandermonde matrices. Both schemes can be efficiently encoded and decoded due to the structure of the ring. We also discuss methods to shorten the proposed schemes.
Part II studies schemes that are efficient in terms of communication and access complexity. We derive a lower bound on the decoding bandwidth, and design schemes achieving the optimal decoding bandwidth and access. We then design schemes that achieve the optimal bandwidth and access not only for decoding, but also for repair. Furthermore, we present a family of Shamir's schemes with asymptotically optimal decoding bandwidth.
Part III studies the problem of secure repair, i.e., reconstructing the share of a (failed) node without leaking any information about the message. We present generic secure repair protocols that can securely repair any linear schemes. We derive a lower bound on the secure repair bandwidth and show that the proposed protocols are essentially optimal in terms of bandwidth.
In the final part of the dissertation, we study the use of coding techniques to improve the reliability and security of network communication.
Specifically, in Part IV we draw connections between several important problems in network coding. We present reductions that map an arbitrary multiple-unicast network coding instance to a unicast secure network coding instance in which at most one link is eavesdropped, or a unicast network error correction instance in which at most one link is erroneous, such that a rate tuple is achievable in the multiple-unicast network coding instance if and only if a corresponding rate is achievable in the unicast secure network coding instance, or in the unicast network error correction instance. Conversely, we show that an arbitrary unicast secure network coding instance in which at most one link is eavesdropped can be reduced back to a multiple-unicast network coding instance. Additionally, we show that the capacity of a unicast network error correction instance in general is not (exactly) achievable. We derive upper bounds on the secrecy capacity for the secure network coding problem, based on cut-sets and the connectivity of links. Finally, we study optimal coding schemes for the network error correction problem, in the setting that the network and adversary parameters are not known a priori.</p
Development of a Synthetic Strategy Toward Trans-Cyclobutane-Containing Natural Products: Enantioselective Total Synthesis of (+)-Psiguadial B
Get PDFTrans-cyclobutane-containing meroterpenoids are a structurally intriguing class of natural products with a diverse array of pharmacologically interesting properties. Herein, the development of a synthetic strategy for de novo construction of the trans-cyclobutane motif is described, which has enabled the first enantioselective total synthesis of the cytotoxic natural product, (+)-psiguadial B. Specifically, we have developed a photochemical Wolff rearrangement with tandem catalytic, asymmetric addition to a ketene generated in situ. To our knowledge, this work represents the first example of this methodology used to prepare enantioenriched amides. A palladium-catalyzed, directed C(sp3)–H alkenylation reaction is used to quickly build molecular complexity, and two distinct epimerization strategies permit access to either enantiomer of the natural product from a single enantiomer of organocatalyst.
In the course of this work, three different synthetic routes toward (+)-psiguadial B were investigated and each is discussed. These studies have led to the execution of several challenging key transformations, including an ortho-quinone methide hetero–Diels–Alder cycloaddition with a cyclohexanone-derived enol ether, a vinyl sulfide-mediated Prins cyclization, and a modified Norrish–Yang cyclization. Ultimately, the successful synthetic strategy was realized by employing a ring-closing metathesis to form the strained, 7-membered terpene framework, and a late-stage benzylic oxidation/arylation strategy to complete the core of the natural product. Finally, in an effort to apply these key strategy concepts in the context of other bioactive trans-cyclobutane-containing natural products, initial results toward a concise total synthesis of (+)-rumphellaone A are presented.</p
Computational Methods for Behavior Analysis
Get PDFBehavioral scientists strive to decode the functional relationship between sensory input and motor output of the brain, which requires quantitive measurement of animal behavior. Artificial intelligence researchers aim to build intelligent systems, capable of understanding, predicting, and generating behavior. Our research lies on the intersection of the two fields; our goal is to automate measurement of animal behavior and to model their sensory-motor relationship using machine learning.
We have developed a tool that tracks the pose of multiple fruit flies and aims to maintain their identity throughout a video. It outputs motion trajectories that can be used to quantify behavioral differences between individuals, for example by comparing histograms of velocities and wing angles. We show that the tool also works well on non-fly-like animals such as zebrafish larvae.
Embedded in these motion trajectories are temporal patterns that constitute actions. We developed two supervised learning frameworks for action detection: a sliding window framework and a structured output framework. Both frameworks learn to classify actions from motion trajectories and expert annotated action intervals. Our results show that the simpler sliding window framework achievers better results in spite of being much faster to train, reaching 90% of human performance.
Supervised learning requires a lot of training data which involves time consuming and painstaking annotation. To alleviate that we have built a semi-supervised neural network framework that, in addition to classifying actions, learns to predict how an animal will move next given its motion and sensory inputs so far. Our model archives as good results as its supervised counterpart with only half of the expert labels.
In addition, we show that motion prediction can be used to generate convincing simulations of fruit fly behavior and handwritten text, and that our model learns to represent high level information, such as identity, when trained unsupervised.
Although developed for animal behavior, our methods are general and could be applied to other motion data. We hope that this thesis demonstrates the value of studying animal behavior for the development of artificial intelligence.</p
Investigating Quantum Speedups through Numerical Simulations
Get PDFIt has been recently noted in a paper by Brandao et al. that the structure of a linear program in a classical semidefinite programming algorithm lends itself to quantization, such that the classical algorithm may experience a quantum speedup if the step of solving a linear program is replaced with the preparation of a Gibbs state of classical Hamiltonian on a quantum computer, where the Hamiltonian is given by a linear combination of the semidefinite program's constraint matrices. The quantum speedup would be exponential if the complexity of the Gibbs sampler used to execute the update step is polynomial in system size. The Gibbs samplers with explicitly defined runtimes are exponential in system size; however, while the quantum Metropolis sampling algorithm by Temme et al. does not have a runtime bounded explicitly in system size, the algorithm heuristically runs in polylogarithmic time. Since the inverse spectral gap of the quantum Metropolis map varies inversely with the running time of the algorithm, we simulate the behavior of the quantum Metropolis map's spectral gap as a function of system size and row sparsity. We also examine how different definitions of fixed row sparsity affect the spectral gap's behavior when the system size is increased linearly. While more numerical evidence is needed to draw a definitive conclusion, the current results appear to indicate that for system sizes ranging from three to ten qubits, if fixed row sparsity is defined as a fixed polynomial function of the system size, then the quantum Metropolis spectral gap behaves as a polynomial function of system size
Advances in Selectivity and Reactivity in Transition Metal Catalysis: Carbon–Silicon Bond Formation, Wacker Oxidation, and Olefin Metathesis
Get PDFThe development of reaction methodology and catalysts that promote challenging transformations with high yields and selectivities is presented in Chapters 2–4 of this thesis. The three projects discussed address challenges in cross-coupling, olefin oxidation, and olefin metathesis.
Chapter 2 describes a nickel-catalyzed cross-coupling strategy for the formation of C–Si bonds using unactivated alkyl halides as substrates. Reaction optimization, exploration of the substrate scope, and mechanistic studies are described. This method is unique in its compatibility with not only secondary alkyl bromides, but tertiary alkyl bromides as well. Low loadings of the nickel catalyst, the absence of an added ligand, and relative tolerance of air and moisture contribute to the efficiency and robustness of this reaction. Mechanistic studies suggest that oxidative addition proceeds through a radical intermediate, consistent with previous studies of C–C bond formation.
Chapter 3 describes the application of an aldehyde-selective Wacker oxidation to allylic fluoride substrates to produce beta-fluorinated aldehydes with remarkably high regioselectivities. Efficient anti-Markovnikov oxidation of allylic fluorides bearing a variety of functional groups was possible with reduced loadings of palladium, copper, and nitrite catalysts. In order to highlight the utility of this methodology, further derivatization of the aldehyde products to diverse fluorinated products is described. Mechanistic studies demonstrate the role of inductive effects in enhancing the regioselectivity of oxidation.
Chapter 4 investigates the synthesis, characterization, and reactivity studies of a new class of second-generation ruthenium olefin metathesis catalysts bearing aminophosphine ligands. The incorporation of P–N bonds into the dissociating phosphine ligand results in trends in catalyst initiation rates and catalyst activity that reveal important considerations for ligand design. The results from kinetics experiments correlate well with computational studies, which indicate that there are significant effects derived from sterics, electronic induction, orbital overlap from the nitrogen (aminophosphine) lone pair, and ligand distortion energies that contribute to trends in phosphine dissociation.</p
The Faint Intergalactic-Medium Redshifted Emission Balloon: FIREBall-2 Scientific Camera and Cooling System
Get PDFThe FIREBall-2 instrument provides a means of investigating both the processes responsible for building cosmic structure and the galaxies that trace it. By studying the inflow and outflow of gaseous hydrogen, we can better explain galaxy formation and evolution. Each individual galaxy lies within a dense gaseous region called the circumgalactic medium (CGM), itself surrounded by the diffuse intergalactic medium (IGM). Thin gaseous filaments connect galaxies to each other in space and time and they can be found at nodes of these filaments at the center of dark matter halos.
This large-scale structure, called the cosmicweb, has been modeled and corroborated with absorption line studies. To understand the structure of the galaxy environment, we need to map the extremely faint emission from the CGM and these filaments.
FIREBall-2 is a 1-meter-class, balloon-borne, UV telescope that will be launched from Texas in the fall of 2017. The instrument includes a vacuum tank, which houses an all-reflective, wide-field multislit spectrograph, guide camera, and UV optimized EMCCD sensor. The scientific camera sensor has to be operated near -110°C and is cooled with a mechanical cryocooler, which also powers a charcoal getter to maintain high vacuum during flight.
The scientific camera includes a Printed Circuit Board (PCB), which I use as a rigid harness that holds the sensor in place. The sensor (CCD201-20 from e2v) is a delta-doped, electron-multiplying charge-coupled device (EMCCD) that has been modified to be used as a 1K x 2K (1024 x 2048 pixels) sensor. The EMCCD has been developed at the Jet Propulsion Laboratory’s Micro Devices Laboratory. I operate this next-generation UV detector (NEXUS) at 10 MHz with read-out electronics from Nüvü Camēras. Nüvü’s controller for counting photons (CCCP) was chosen to achieve extremely low detector noise by reducing clock induced charge (CIC) and it is attached to the PCB with a SAMTEC EQCD high-speed coaxial cable. To reduce dark current, the other relevant detector noise source, the EMCCD is supported by a gold-plated copper clamp and cooled with a CryoTel MT mechanical cooler (Stirling engine) from Sunpower. The CCD operating temperature is -110°C, with a required heat lift of about 7 Watts at a 30°C reject temperature. Two 10-Watt Omega heaters are used to regulate the temperature. The cryocooler will be operated at a constant input cooling power of about 70 Watts, which corresponds to 110-Watts of battery power. The cooler is mounted to the side of the vacuum tank and I have incorporated the Sunpower active vibration cancellation system (AVC) to reduce the vibrational noise. A flexible copper ribbon conducts heat from the bottom of the CCD via the solid copper clamp. The detector is operated in a vacuum of about 10-6 Torr, initially started by a turbo pump, with the pressure then lowered and maintained by activated charcoal adsorption during flight. The flight hardware has been integrated into the flight vacuum tank and is currently undergoing testing.</p