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We introduce a mathematical modeling framework for the conformational dynamics of charged molecules (i.e., solutes) in an aqueous solvent (i.e., water or salted water). The solvent is treated as an incompressible fluid, and its fluctuating motion is described by the Stokes equation with the Landau–Lifschitz stochastic stress. The motion of the solutesolvent interface (i.e., the dielectric boundary) is determined by the fluid velocity together with the balance of the viscous force,hydrostatic pressure, surface tension, solutesolvent van der Waals interaction force, and electrostatic force. The electrostatic interactions are described by the dielectric Poisson–Boltzmann theory.Within such a framework, we derive a generalized Rayleigh–Plesset equation, a nonlinear stochastic ordinary differential equation (SODE), for the radius of a spherical charged molecule, such as anion. The spherical average of the stochastic stress leads to a multiplicative noise. We design and test numerical methods for solving the SODE and use the equation, together with explicit solvent molecular dynamics simulations, to study the effective radius of a single ion. Potentially, our general modeling framework can be used to efficiently determine the solutesolvent interfacial structures and predict the free energies of more complex molecular systems.

Abstract Oceanic oxygen minimum zones (OMZs) are globally significant sites of biogeochemical cycling where microorganisms deplete dissolved oxygen (DO) to concentrations <20 µM. Amid intense competition for DO in these metabolically challenging environments, aerobic nitrite oxidation may consume significant amounts of DO and help maintain low DO concentrations, but this remains unquantified. Using parallel measurements of oxygen consumption rates and^{15}Nnitrite oxidation rates applied to both water column profiles and oxygen manipulation experiments, we show that the contribution of nitrite oxidation to overall DO consumption systematically increases as DO declines below 2 µM. Nitrite oxidation can account for all DO consumption only under DO concentrations <393 nM found in and below the secondary chlorophyll maximum. These patterns are consistent across sampling stations and experiments, reflecting coupling between nitrate reduction and nitriteoxidizing
Nitrospina with high oxygen affinity (based on isotopic and omic data). Collectively our results demonstrate that nitrite oxidation plays a pivotal role in the maintenance and biogeochemical dynamics of OMZs. 
We explore and compare different ways largescale structure observables in redshiftspace and real space can be connected. These include direct computation in La grangian space, moment expansions and two formulations of the streaming model. We derive for the first time a Fourier space version of the streaming model, which yields an algebraic relation between the real and redshiftspace power spectra which can be compared to ear lier, phenomenological models. By considering the redshiftspace 2point function in both configuration and Fourier space, we show how to generalize the Gaussian streaming model to higher orders in a systematic and computationally tractable way. We present a closed form solution to the Zeldovich power spectrum in redshift space and use this as a framework for exploring convergence properties of different expansion approaches. While we use the Zeldovich approximation to illustrate these results, much of the formalism and many of the relations we derive hold beyond perturbation theory, and could be used with ingredients measured from Nbody simulations or in other areas requiring decomposition of Cartesian tensors times plane waves. We finish with a discussion of the redshiftspace bispectrum, bias and stochasticity and terms in Lagrangian perturbation theory up to 1loop order.

Faint starforming galaxies at z∼2–3 can be used as alternative background sources to probe the Lyα forest in addition to quasars, yielding high sightline densities that enable 3D tomographic reconstruction of the foreground absorption field. Here, we present the first data release from the COSMOS Lyα Mapping And Tomography Observations (CLAMATO) Survey, which was conducted with the LRIS spectrograph on the Keck I telescope. Over an observational footprint of 0.157 deg2 within the COSMOS field, we used 240 galaxies and quasars at 2.17<z<3.00, with a mean comoving transverse separation of 2.37 h1 Mpc, as background sources probing the foreground Lyα forest absorption at 2.05<z<2.55. The Lyα forest data was then used to create a Wiener filtered tomographic reconstruction over a comoving volume of 3.15 ́ 105 h3 Mpc3 with an effective smoothing scale of 2.5 h1 Mpc. In addition to traditional figures, this map is also presented as a virtualreality visualization and manipulable interactive figure. We see large overdensities and underdensities that visually agree with the distribution of coeval galaxies from spectroscopic redshift surveys in the same field, including overdensities associated with several recently discovered galaxy protoclusters in the volume. Quantitatively, the map signalto noise is S Nwiener » 3.4more »

In the next decade the peculiar velocities of SNe Ia in the local z<0.3 Universe will provide a measure of γ to ±0.01 precision that can definitively distinguish between General Relativity and leading models of alternative gravity.

Abstract The accurate simulation of additional interactions at the ATLAS experiment for the analysis of proton–proton collisions delivered by the Large Hadron Collider presents a significant challenge to the computing resources. During the LHC Run 2 (2015–2018), there were up to 70 inelastic interactions per bunch crossing, which need to be accounted for in Monte Carlo (MC) production. In this document, a new method to account for these additional interactions in the simulation chain is described. Instead of sampling the inelastic interactions and adding their energy deposits to a hardscatter interaction onebyone, the inelastic interactions are presampled, independent of the hard scatter, and stored as combined events. Consequently, for each hardscatter interaction, only one such presampled event needs to be added as part of the simulation chain. For the Run 2 simulation chain, with an average of 35 interactions per bunch crossing, this new method provides a substantial reduction in MC production CPU needs of around 20%, while reproducing the properties of the reconstructed quantities relevant for physics analyses with good accuracy.Free, publiclyaccessible full text available December 1, 2023

Abstract The ATLAS experiment at the Large Hadron Collider has a broad physics programme ranging from precision measurements to direct searches for new particles and new interactions, requiring ever larger and ever more accurate datasets of simulated Monte Carlo events. Detector simulation with Geant4 is accurate but requires significant CPU resources. Over the past decade, ATLAS has developed and utilized tools that replace the most CPUintensive component of the simulation—the calorimeter shower simulation—with faster simulation methods. Here, AtlFast3, the next generation of highaccuracy fast simulation in ATLAS, is introduced. AtlFast3 combines parameterized approaches with machinelearning techniques and is deployed to meet current and future computing challenges, and simulation needs of the ATLAS experiment. With highly accurate performance and significantly improved modelling of substructure within jets, AtlFast3 can simulate large numbers of events for a wide range of physics processes.Free, publiclyaccessible full text available December 1, 2023

Free, publiclyaccessible full text available May 1, 2023

Free, publiclyaccessible full text available May 1, 2023