Multiscale dissection of bacterial proteome optimization
Lalanne, Jean-Benoît.
The quantitative composition of proteomes results from biophysical and biochemical selective pressures acting under system-level resource allocation constraints. The nature and strength of these evolutionary driving forces remain obscure. Through the development of analytical tools and precision measurement platforms spanning biological scales, we found evidence of optimization in bacterial gene expression programs. We compared protein synthesis rates across distant lineages and found tight conservation of in-pathway enzyme expression stoichiometry, suggesting generic selective pressures on expression setpoints. Beyond conservation, we used high-resolution transcriptomics to identify numerous examples of stoichiometry preserving cis-elements compensation in pathway operons. Genome-wide mapping of transcription termination sites also led to the discovery of a phylogenetically widespread mode of bacterial gene expression, 'runaway transcription', whereby RNA polymerases are functionally uncoupled from pioneering ribosomes on mRNAs. To delineate biophysical rationales underlying these pressures, we formulated a parsimonious ribosome allocation model capturing the trade-off between reaction flux and protein production cost. The model correctly predicts the expression hierarchy of key translation factors. We then directly measured the quantitative relationship between expression and fitness for specific translation factors in the Gram-positive species Bacillus subtilis. These precision measurements confirmed that endogenous expression maximizes growth rate. Idiosyncratic transcriptional changes in regulons were however observed away from endogenous expression. The resulting physiological burdens sharpened the fitness landscapes. Spurious system-level responses to targeted expression perturbations, called 'regulatory entrenchment', thus exacerbate the requirement for precisely set expression stoichiometry.
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Physics, May, 2020; Cataloged from student-submitted PDF version of thesis.; Includes bibliographical references (pages 315-348).
Multiscale dissection of bacterial proteome optimization
↧
↧
Dynamic polarizability and collective modes in narrow-band electron systems
Dynamic polarizability and collective modes in narrow-band electron systems
Lewandowski, Cyprian(Cyprian Krzysztof)
The family of moiré materials, in particular the magic angle twisted bilayer graphene, has emerged recently as a platform to study strongly interacting physics. This thesis analyzes the impact of the ultranarrow Bloch bands and strong electron-electron interactions on the dynamical polarization response of these systems. Strong interactions alter the collective charge dynamics in a number of interesting ways, in particular by stiffening the frequency-momentum dispersion of surface plasmons and making it much stronger than that of the underlying narrow-band carriers. Strongly dispersing plasmons pierce through the particle-hole continuum and extend in the forbidden energy band above it. This behavior enables decoupling of plasmons from particle-hole excitations. Such over-the-band plasmons are unable to decay into particle-hole pairs and thus are not subject to Landau damping. As a result, plasmons acquire longer lifetimes as well as an enhanced spatial optical coherence. The optical coherence manifests itself in spatial interference patterns that provide telltale signatures of over-the-band plasmons that are readily accessible in near-field imaging experiments. We further show that the over-the-band plasmon dispersion remains robust in the presence of ordering of the narrow-band carriers. The specific examples of a Wigner crystal and a Mott-Hubbard order, worked out in detail, show that interaction-driven gap opening has no impact on the over-the-band plasmon dispersion. Lastly, we consider the implications of the mechanisms behind the over-the-band behavior for achieving of unidirectional collective modes. We present a new mechanism for plasmon nonreciprocity the magnitude of which is controllable through the strength of electron-electron interactions, which makes it particularly pronounced in the moiré materials.
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Physics, May, 2020; Cataloged from student-submitted PDF version of thesis.; Includes bibliographical references (pages 114-123).
↧
From strongly-interacting Bose-Fermi mixtures to ultracold molecules
From strongly-interacting Bose-Fermi mixtures to ultracold molecules
Yan, Zoe Z.(Zoe Ziyue)
This thesis describes experiments on ultracold quantum gases. First, I discuss quantum simulation involving mixtures of bosonic and fermionic atoms. Second, I present work on creating and controlling ultracold dipolar molecules of ²³Na⁴⁰K. The rich phase diagram of Bose-Fermi mixtures was studied with our system of bosonic ²³Na and fermionic ⁴⁰K atoms. When the fermions were immersed as a minority species within a Bose-Einstein condensate, the system realized the canonical Bose polaron quasiparticle, which is an important paradigm in condensed matter physics. We investigated the strongly-coupled Bose polaron as it approached the quantum critical regime of the Bose-Fermi mixture. Using radiofrequency spectroscopy, we probed the binding energy and decay rate as a function of temperature.; In particular, the decay rate was found to scale linearly with temperature near the Planckian rate k[subscript B]T/h⁻ in the unitarity-limited regime, a hallmark of quantum critical behavior. Bose-Fermi mixtures host a complex spectrum of collective excitations, which can shed light on their properties such as collisional relaxation rates, equilibrium equations of state, and kinetic coefficients. We probed the low-lying collective modes of a Bose-Fermi mixture across different interaction strengths and temperatures. The spin-polarized fermions were observed to transition from ballistic to hydrodynamic flow induced by interactions with the bosonic excitations. Our measurements establish Bose-Fermi mixtures as a fruitful arena to understand hydrodynamics of fermions, with important connections to electron hydrodynamics in strongly-correlated 2D materials. The second part of this thesis describes the creation and manipulation of ultracold molecules in their ground state.; Molecules have more tunable degrees of freedom compared to atoms, paving the way for studies of quantum state-controlled chemistry, quantum information, and exotic phases of matter. We created loosely-bound Feshbach molecules from ultracold atoms, then transferred those molecules to their absolute electronic, vibrational, rotational, and hyperfine ground state by stimulated Raman adiabatic passage. The rotational level structure, sample lifetimes, and coherence properties were studied, culminating in a demonstration of second-scale nuclear spin coherence times in an ensemble of NaK. Controlling the intermolecular interactions - which can be tunable, anisotropic, and long range - is an outstanding challenge for our field. We induced strong dipolar interactions via the technique of microwave dressing, an alternative to using static electric fields to polarize the molecules.; The origin of these dipolar collisions was the resonant alignment of the approaching molecules' dipoles along their intermolecular axis, resulting in strong attraction. Our observations were explained by a conceptually simple two-state picture based on the Condon approximation.
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Physics, May, 2020; Cataloged from student-submitted PDF version of thesis.; Includes bibliographical references (pages 193-213).
↧
Experimental studies of internal dark currents in high gradient accelerator structures at 17 GHz
Experimental studies of internal dark currents in high gradient accelerator structures at 17 GHz
Xu, Haoran,Ph. D.Massachusetts Institute of Technology.
This thesis presents the measurement of the internal dark current in normal conducting single cell standing wave disk-loaded waveguide (DLWG) accelerator structures that operate at 17 GHz, and its comparison with theory. Dark current is the unwanted current of electrons generated by field emission, multipactor on the accelerator inner surfaces, or both. It is in distinction from the primary beam propagating along the accelerator axis. Dark current that propagates to the ends of the accelerator has been extensively studied, but this is the first detailed study of the internal dark current generated at the structure sidewalls by multipactor. Theoretical calculations indicate that the collision of electrons on the accelerator sidewall will lead to secondary electron emission and subsequent resonant multipactor discharges. Simulations of the multipactor modes were carried out with both our inhouse particle tracking code and with the commercial CST PIC code.; Multipactor modes of different orders were predicted to appear at the sidewall with increasing acceleration gradient. The first tested cavities were fabricated from copper and had a sidewall that was either uncoated or coated with diamond-like carbon or titanium nitride. The dark current was measured by a downstream current monitor and by current monitors behind two thin slits opened on the cavity sidewall. With increasing gradient, the downstream dark current increased monotonically, as expected for field emission. The variation of the internal, side dark current was not monotonic but showed the onset of peaks at gradients near 45 and 65 MV/m, in good agreement with simulations using the CST code as well as the in-house code. These were identified as the N = 2 and N = 1 single surface one-point multipactor resonances. The total internal dark current was estimated at ~15 - 30 A. The coated sidewall cavities showed the same multipactor resonances as the uncoated structure.; A second set of tests was conducted with a structure with an axisymmetric elliptical central cell sidewall, which was predicted to suppress the internal dark current. After conditioning with 2.2x10⁵ pulses to 93 MV/m, the multipactor modes were completely suppressed and no multipactor resonances were observed. Studies of internal dark current may help to understand the rf conditioning and the ultimate breakdown performance of high gradient rf accelerator structures.
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Physics, May, 2020; Cataloged from student-submitted PDF version of thesis.; Includes bibliographical references (pages 169-180).
↧
More Pages to Explore .....
