Rice University Research Repository
The Rice Research Repository (R-3) provides access to research produced at Rice University, including theses and dissertations, journal articles, research center publications, datasets, and academic journals. Managed by Fondren Library, R-3 is indexed by Google and Google Scholar, follows best practices for preservation, and provides DOIs to facilitate citation. Woodson Research Center collections, including Rice Images and Documents and the Task Force on Slavery, Segregation, and Racial Injustice, have moved here.
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Cell behaviors underlying Myxococcus xanthus aggregate dispersal
(American Society for Microbiology, 2023) Murphy, Patrick; Comstock, Jessica; Khan, Trosporsha; Zhang, Jiangguo; Welch, Roy; Igoshin, Oleg A.; Center for Theoretical Physical Biology
The soil bacterium Myxococcus xanthus is a model organism with a set of diverse behaviors. These behaviors include the starvation-induced multicellular development program, in which cells move collectively to assemble multicellular aggregates. After initial aggregates have formed, some will disperse, with smaller aggregates having a higher chance of dispersal. Initial aggregation is driven by two changes in cell behavior: cells slow down inside of aggregates and bias their motion by reversing direction less frequently when moving toward aggregates. However, the cell behaviors that drive dispersal are unknown. Here, we use fluorescent microscopy to quantify changes in cell behavior after initial aggregates have formed. We observe that after initial aggregate formation, cells adjust the bias in reversal timings by initiating reversals more rapidly when approaching unstable aggregates. Using agent-based modeling, we then show dispersal is predominantly generated by this change in bias, which is strong enough to overcome slowdown inside aggregates. Notably, the change in reversal bias is correlated with the nearest aggregate size, connecting cellular activity to previously observed correlations between aggregate size and fate. To determine if this connection is consistent across strains, we analyze a second M. xanthus strain with reduced levels of dispersal. We find that far fewer cells near smaller aggregates modified their bias. This implies that aggregate dispersal is under genetic control, providing a foundation for further investigations into the role it plays in the life cycle of M. xanthus.
Stable reconstruction of simple Riemannian manifolds from unknown interior sources
(IOP Publishing Ltd, 2023) Hoop, Maarten V. de; Ilmavirta, Joonas; Lassas, Matti; Saksala, Teemu
Consider the geometric inverse problem: there is a set of delta-sources in spacetime that emit waves travelling at unit speed. If we know all the arrival times at the boundary cylinder of the spacetime, can we reconstruct the space, a Riemannian manifold with boundary? With a finite set of sources we can only hope to get an approximate reconstruction, and we indeed provide a discrete metric approximation to the manifold with explicit data-driven error bounds when the manifold is simple. This is the geometrization of a seismological inverse problem where we measure the arrival times on the surface of waves from an unknown number of unknown interior microseismic events at unknown times. The closeness of two metric spaces with a marked boundary is measured by a labeled Gromov–Hausdorff distance. If measurements are done for infinite time and spatially dense sources, our construction produces the true Riemannian manifold and the finite-time approximations converge to it in the metric sense
Bridging physical intuition and hardware efficiency for correlated electronic states: the local unitary cluster Jastrow ansatz for electronic structure
(Royal Society of Chemistry, 2023) Motta, Mario; Sung, Kevin J.; Whaley, K. Birgitta; Head-Gordon, Martin; Shee, James
A prominent goal in quantum chemistry is to solve the molecular electronic structure problem for ground state energy with high accuracy. While classical quantum chemistry is a relatively mature field, the accurate and scalable prediction of strongly correlated states found, e.g., in bond breaking and polynuclear transition metal compounds remains an open problem. Within the context of a variational quantum eigensolver, we propose a new family of ansatzes which provides a more physically appropriate description of strongly correlated electrons than a unitary coupled cluster with single and double excitations (qUCCSD), with vastly reduced quantum resource requirements. Specifically, we present a set of local approximations to the unitary cluster Jastrow wavefunction motivated by Hubbard physics. As in the case of qUCCSD, exactly computing the energy scales factorially with system size on classical computers but polynomially on quantum devices. The local unitary cluster Jastrow ansatz removes the need for SWAP gates, can be tailored to arbitrary qubit topologies (e.g., square, hex, and heavy-hex), and is well-suited to take advantage of continuous sets of quantum gates recently realized on superconducting devices with tunable couplers. The proposed family of ansatzes demonstrates that hardware efficiency and physical transparency are not mutually exclusive; indeed, chemical and physical intuition regarding electron correlation can illuminate a useful path towards hardware-friendly quantum circuits.
Denoising Non-Stationary Signals via Dynamic Multivariate Complex Wavelet Thresholding
(MDPI, 2023) Raath, Kim C.; Ensor, Katherine B.; Crivello, Alena; Scott, David W.
Over the past few years, we have seen an increased need to analyze the dynamically changing behaviors of economic and financial time series. These needs have led to significant demand for methods that denoise non-stationary time series across time and for specific investment horizons (scales) and localized windows (blocks) of time. Wavelets have long been known to decompose non-stationary time series into their different components or scale pieces. Recent methods satisfying this demand first decompose the non-stationary time series using wavelet techniques and then apply a thresholding method to separate and capture the signal and noise components of the series. Traditionally, wavelet thresholding methods rely on the discrete wavelet transform (DWT), which is a static thresholding technique that may not capture the time series of the estimated variance in the additive noise process. We introduce a novel continuous wavelet transform (CWT) dynamically optimized multivariate thresholding method (WaveL2E). Applying this method, we are simultaneously able to separate and capture the signal and noise components while estimating the dynamic noise variance. Our method shows improved results when compared to well-known methods, especially for high-frequency signal-rich time series, typically observed in finance.
Thickness-Dependent Terahertz Permittivity of Epitaxially Grown PbTe Thin Films
(MDPI, 2023) Kawahala, Nicolas M.; Matos, Daniel A.; Rappl, Paulo H. O.; Abramof, Eduardo; Baydin, Andrey; Kono, Junichiro; Hernandez, Felix G. G.; Smalley-Curl Institute
The exceptional thermoelectric properties of PbTe are believed to be associated with the incipient ferroelectricity of this material, which is caused by strong electron–phonon coupling that connects phononic and electronic dynamics. Here, we have used terahertz time-domain spectroscopy measurements to generate complex permittivity spectra for a set of epitaxially grown PbTe thin films with thicknesses between 100 nm and 500 nm at temperatures from 10 K to 300 K. Using a Drude–Lorentz model, we retrieved the physical parameters of both the phononic and electronic contributions to the THz permittivity. We observed a strong decrease, or softening, of the transverse optical phonon mode frequency with decreasing temperature, determining a thickness-independent negative ferroelectric-transition critical temperature, while we found a thickness-dependent anharmonic phonon decay lifetime. The electronic contribution to the permittivity was larger in thinner films, and both the carrier density and mobility increased with decreasing temperature in all films. Finally, we detected a thickness-dependent longitudinal optical phonon mode frequency, indicating the presence of plasmon–phonon coupling.