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1. Density-Dependent Selection

   https://doi.org/10.1146/annurev-ecolsys-110321-055345  

   Travis, Joseph; Bassar, Ronald D.; Coulson, Tim; Reznick, David; Walsh, Matthew (November 2023, Annual Review of Ecology, Evolution, and Systematics)

   Density-dependent selection, which promotes contrasting patterns of trait means at different population densities, has a long history in population genetics and ecology. The unifying principle from theory is that density-dependent selection operates on phenotypic traits whose values counter the effects of whatever ecological agent is limiting population growth, be it resource competition, predators, or pathogens. However, the complexity inherent in density dependence means that the same selective process can generate multiple outcomes, depending upon the details of how population density affects vital rates and the age or size structure of a population. Failure to appreciate the potential for multiple outcomes confounded many early studies of the process. Nonetheless, careful empirical work in laboratory studies, long-term field studies, and studies of sexual selection demonstrates the wide reach of density-dependent selection. The inconsistent outcomes observed in these studies call for renewed research into how the details of density dependence channel adaptive responses. 

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2. A continuum of amorphous ices between low-density and high-density amorphous ice

   https://doi.org/10.1038/s42004-024-01117-2  

   Eltareb, Ali; Lopez, Gustavo E; Giovambattista, Nicolas (February 2024, Communications Chemistry)

   Abstract Amorphous ices are usually classified as belonging to low-density or high-density amorphous ice (LDA and HDA) with densitiesρ_LDA ≈ 0.94 g/cm³andρ_HDA ≈ 1.15−1.17 g/cm³. However, a recent experiment crushing hexagonal ice (ball-milling) produced amedium-density amorphous ice (MDA,ρ_MDA ≈ 1.06 g/cm³) adding complexity to our understanding of amorphous ice and the phase diagram of supercooled water. Motivated by the discovery of MDA, we perform computer simulations where amorphous ices are produced by isobaric cooling and isothermal compression/decompression. Our results show that, depending on the pressure employed, isobaric cooling can generate a continuum of amorphous ices with densities that expand in between those of LDA and HDA (briefly, intermediate amorphous ices, IA). In particular, the IA generated atP ≈ 125 MPa has a remarkably similar density and average structure as MDA, implying that MDA is not unique. Using the potential energy landscape formalism, we provide an intuitive qualitative understanding of the nature of LDA, HDA, and the IA generated at different pressures. In this view, LDA and HDA occupy specific and well-separated regions of the PEL; the IA prepared atP = 125 MPa is located in the intermediate region of the PEL that separates LDA and HDA. 

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3. Data Structures for Density Estimation

   Aamand, Anders; Andoni, Alexandr; Chen, Justin; Indyk, Piotr; Narayanan, Shyam; Silwal, Sandeep (January 2023, International Conference on Machine Learning)

   We study statistical/computational tradeoffs for the following density estimation problem: given kdistributionsv1,...,vk overadiscretedomain of size n, and sampling access to a distribution p, identify vi that is “close” to p. Our main result is the first data structure that, given a sublinear (in n) number of samples from p, identifies vi in time sublinear in k. We also give an improved version of the algorithm of (Acharya et al., 2018) that reports vi in time linear in k. The experimental evaluation of the latter algorithm shows that it achieves a significant reduction in the number of operations needed to achieve a given accuracy compared to prior work. 

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4. Tunable noninteracting free-energy density functionals for high-energy-density physics applications

   https://doi.org/10.1063/5.0191091  

   Karasiev, Valentin_V; Mihaylov, Deyan_I; Zhang, Shuai; Hinz, Joshua_P; Goshadze, R_M_N; Hu, S_X (July 2024, Physics of Plasmas)

   In this work, we introduce the concept of a tunable noninteracting free-energy density functional and present two examples realized: (i) via a simple one-parameter convex combination of two existing functionals and (ii) via the construction of a generalized gradient approximation (GGA) enhancement factor that contains one free parameter and is designed to satisfy a set of incorporated constraints. Functional (i), constructed as a combination of the local Thomas–Fermi and a pseudopotential-adapted GGA for the noninteracting free-energy, has already demonstrated its practical usability for establishing the high temperature end of the equation of state of deuterium [Phys. Rev. B 104, 144104 (2021)] and CHON resin [Phys. Rev. E 106, 045207 (2022)] for inertial confinement fusion applications. Hugoniot calculations for liquid deuterium are given as another example of how the application of computationally efficient orbital-free density functional theory (OF-DFT) can be utilized with the employment of the developed functionals. Once the functionals have been tuned such that the OF-DFT Hugoniot calculation matches the Kohn–Sham solution at some low-temperature point, agreement with the reference Kohn–Sham results for the rest of the high temperature Hugoniot path is very good with relative errors for compression and pressure on the order of 2% or less. 

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5. Emergence of the temperature–density relation in the low-density intergalactic medium

   https://doi.org/10.1093/mnras/stae401  

   Wells, Alexandra; Robinson, David; Avestruz, Camille; Gnedin, Nickolay Y. (February 2024, Monthly Notices of the Royal Astronomical Society)

   ABSTRACT We examine the evolution of the phase diagram of the low-density intergalactic medium during the Epoch of Reionization in simulation boxes with varying reionization histories from the Cosmic Reionization on Computers project. The probability density function (PDF) of gas temperature at fixed density exhibits two clear modes: a warm and a cold temperature mode, corresponding to the gas inside and outside of ionized bubbles. We find that the transition between the two modes is ‘universal’ in the sense that its timing is accurately parametrized by the value of the volume-weighted neutral fraction for any reionization history. This ‘universality’ is more complex than just a reflection of the fact that ionized gas is warm and neutral gas is cold: it holds for the transition at a fixed value of gas density, and gas at different densities transitions from the cold to the warm mode at different values of the neutral fraction, reflecting a non-trivial relationship between the ionization history and the evolving gas density PDF. Furthermore, the ‘emergence’ of the tight temperature–density relation in the warm mode is also approximately ‘universally’ controlled by the volume-weighted neutral fraction for any reionization history. In particular, the ‘emergence’ of the temperature–density relation (as quantified by the rapid decrease in its width) occurs when the neutral fraction is 10−4 ≲ XH i ≲ 10−3 for any reionization history. Our results indicate that the neutral fraction is a primary quantity controlling the various properties of the temperature–density relation, regardless of reionization history. 

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