arXiv subjects

David Baker

Publications and source records attributed to David Baker.

25 records · Page 2Linked to original sources

arXiv2020

Quantifying the dynamics of protein self-organization using deep learning analysis of atomic force microscopy data

Dynamics of protein self-assembly on the inorganic surface and the resultant geometric patterns are visualized using high-speed atomic force microscopy. The time dynamics of the classical macroscopic descriptors such as 2D Fast Fourier Transforms (FFT), correlation and pair distribution function are explored using the unsupervised linear unmixing, demonstrating the presence of static ordered and dynamic disordered phases and establishing their time dynamics. The deep learning (DL)-based workflow is developed to analyze detailed particle dynamics on the particle-by-particle level. Beyond the macroscopic descriptors, we utilize the knowledge of local particle geometries and configurations to explore the evolution of local geometries and reconstruct the interaction potential between the particles. Finally, we use the machine learning-based feature extraction to define particle neighborhood free of physics constraints. This approach allowed separating the possible classes of particle behavior, identify the associated transition probabilities, and further extend this analysis to identify slow modes and associated configurations, allowing for systematic exploration and predictive modeling of the time dynamics of the system. Overall, this work establishes the DL based workflow for the analysis of the self-organization processes in complex systems from observational data and provides insight into the fundamental mechanisms.

physics.comp-ph↗

arXiv2019

A Hot Saturn Orbiting An Oscillating Late Subgiant Discovered by TESS

We present the discovery of TOI-197.01, the first transiting planet identified by the Transiting Exoplanet Survey Satellite (TESS) for which asteroseismology of the host star is possible. TOI-197 (HIP116158) is a bright (V=8.2 mag), spectroscopically classified subgiant which oscillates with an average frequency of about 430 muHz and displays a clear signature of mixed modes. The oscillation amplitude confirms that the redder TESS bandpass compared to Kepler has a small effect on the oscillations, supporting the expected yield of thousands of solar-like oscillators with TESS 2-minute cadence observations. Asteroseismic modeling yields a robust determination of the host star radius (2.943+/-0.064 Rsun), mass (1.212 +/- 0.074 Msun) and age (4.9+/-1.1 Gyr), and demonstrates that it has just started ascending the red-giant branch. Combining asteroseismology with transit modeling and radial-velocity observations, we show that the planet is a "hot Saturn" (9.17+/-0.33 Rearth) with an orbital period of ~14.3 days, irradiance of 343+/-24 Fearth, moderate mass (60.5 +/- 5.7 Mearth) and density (0.431+/-0.062 gcc). The properties of TOI-197.01 show that the host-star metallicity - planet mass correlation found in sub-Saturns (4-8 Rearth) does not extend to larger radii, indicating that planets in the transition between sub-Saturns and Jupiters follow a relatively narrow range of densities. With a density measured to ~15%, TOI-197.01 is one of the best characterized Saturn-sized planets to date, augmenting the small number of known transiting planets around evolved stars and demonstrating the power of TESS to characterize exoplanets and their host stars using asteroseismology.

astro-ph.EP↗

arXiv2018

The KELT Follow-Up Network and Transit False Positive Catalog: Pre-vetted False Positives for TESS

The Kilodegree Extremely Little Telescope (KELT) project has been conducting a photometric survey for transiting planets orbiting bright stars for over ten years. The KELT images have a pixel scale of ~23"/pixel---very similar to that of NASA's Transiting Exoplanet Survey Satellite (TESS)---as well as a large point spread function, and the KELT reduction pipeline uses a weighted photometric aperture with radius 3'. At this angular scale, multiple stars are typically blended in the photometric apertures. In order to identify false positives and confirm transiting exoplanets, we have assembled a follow-up network (KELT-FUN) to conduct imaging with higher spatial resolution, cadence, and photometric precision than the KELT telescopes, as well as spectroscopic observations of the candidate host stars. The KELT-FUN team has followed-up over 1,600 planet candidates since 2011, resulting in more than 20 planet discoveries. Excluding ~450 false alarms of non-astrophysical origin (i.e., instrumental noise or systematics), we present an all-sky catalog of the 1,128 bright stars (6<V<10) that show transit-like features in the KELT light curves, but which were subsequently determined to be astrophysical false positives (FPs) after photometric and/or spectroscopic follow-up observations. The KELT-FUN team continues to pursue KELT and other planet candidates and will eventually follow up certain classes of TESS candidates. The KELT FP catalog will help minimize the duplication of follow-up observations by current and future transit surveys such as TESS.

astro-ph.EP↗

arXiv2016

Structure, Function, and Control of the Musculoskeletal Network

The human body is a complex organism whose gross mechanical properties are enabled by an interconnected musculoskeletal network controlled by the nervous system. The nature of musculoskeletal interconnection facilitates stability, voluntary movement, and robustness to injury. However, a fundamental understanding of this network and its control by neural systems has remained elusive. Here we utilize medical databases and mathematical modeling to reveal the organizational structure, predicted function, and neural control of the musculoskeletal system. We construct a whole-body musculoskeletal network in which single muscles connect to multiple bones via both origin and insertion points. We demonstrate that a muscle's role in this network predicts susceptibility of surrounding components to secondary injury. Finally, we illustrate that sets of muscles cluster into network communities that mimic the organization of motor cortex control modules. This novel formalism for describing interactions between the muscular and skeletal systems serves as a foundation to develop and test therapeutic responses to injury, inspiring future advances in clinical treatments.

q-bio.TO↗

arXiv2016

Observing the carbon-climate system

Increases in atmospheric CO2 and CH4 result from a combination of forcing from anthropogenic emissions and Earth System feedbacks that reduce or amplify the effects of those emissions on atmospheric concentrations. Despite decades of research carbon-climate feedbacks remain poorly quantified. The impact of these uncertainties on future climate are of increasing concern, especially in the wake of recent climate negotiations. Emissions, long concentrated in the developed world, are now shifting to developing countries, where the emissions inventories have larger uncertainties. The fraction of anthropogenic CO2 remaining in the atmosphere has remained remarkably constant over the last 50 years. Will this change in the future as the climate evolves? Concentrations of CH4, the 2nd most important greenhouse gas, which had apparently stabilized, have recently resumed their increase, but the exact cause for this is unknown. While greenhouse gases affect the global atmosphere, their sources and sinks are remarkably heterogeneous in time and space, and traditional in situ observing systems do not provide the coverage and resolution to attribute the changes to these greenhouse gases to specific sources or sinks. In the past few years, space-based technologies have shown promise for monitoring carbon stocks and fluxes. Advanced versions of these capabilities could transform our understanding and provide the data needed to quantify carbon-climate feedbacks. A new observing system that allows resolving global high resolution fluxes will capture variations on time and space scales that allow the attribution of these fluxes to underlying mechanisms.

physics.ao-ph↗

arXiv2004

Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness

We develop a simple but rigorous model of protein-protein association kinetics based on diffusional association on free energy landscapes obtained by sampling configurations within and surrounding the native complex binding funnels. Guided by results obtained on exactly solvable model problems, we transform the problem of diffusion in a potential into free diffusion in the presence of an absorbing zone spanning the entrance to the binding funnel. The free diffusion problem is solved using a recently derived analytic expression for the rate of association of asymmetrically oriented molecules. Despite the required high steric specificity and the absence of long-range attractive interactions, the computed rates are typically on the order of 10^4-10^6 M-1 s-1, several orders of magnitude higher than rates obtained using a purely probabilistic model in which the association rate for free diffusion of uniformly reactive molecules is multiplied by the probability of a correct alignment of the two partners in a random collision. As the association rates of many protein-protein complexes are also in the 10^5-10^6 M-1 s-1, our results suggest that free energy barriers arising from desolvation and/or side-chain freezing during complex formation or increased ruggedness within the binding funnel, which are completely neglected in our simple diffusional model, do not contribute significantly to the dynamics of protein-protein association. The transparent physical interpretation of our approach that computes association rates directly from the size and geometry of protein-protein binding funnels makes it a useful complement to Brownian dynamics simulations.

q-bio.BM↗

arXiv2004

A general expression for bimolecular association rates with orientational constraints

We present a general expression for the association rate for partially diffusion-controlled reactions between spherical molecules with an asymmetric reactive patch on each surface. Reaction can occur only if the two patches are in contact and properly aligned to within specified angular tolerances. This extends and generalizes previous approaches that considered only axially symmetric patches; the earlier solutions are shown to be limiting cases of our general expression. Previous numerical results on the rate of protein-protein association with high steric specificity are in very good agreement with the value computed from our analytic expression. Using the new expression, we investigate the influence of orientational constraints on the rate constant. We find that for angular constraints of ~5-15 degrees, a typical range for example in the case of protein-protein interactions, the reaction rate is about 2 to 3 orders of magnitude higher than expected from a simple geometric model.

physics.chem-ph↗