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Creators/Authors contains: "Kumar, Saurabh"

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  1. Abstract

    The Universe is neither homogeneous nor isotropic, but it is close enough that we can reasonably approximate it as such on suitably large scales.The inflationary-Λ-Cold Dark Matter (ΛCDM) concordance cosmology builds on these assumptions to describe the origin and evolution of fluctuations. With standard assumptions about stress-energy sources, this system is specified by just seven phenomenological parameters,whose precise relations to underlying fundamental theories are complicated and may depend on details of those fields.Nevertheless, it is common practice to set the parameter that characterizes the spatial curvature, ΩK, exactly to zero.This parameter-fixed ΛCDM is awarded distinguished status as separate model, “flat ΛCDM.”Ipso factothis places the onus on proponents of “curved ΛCDM” to present sufficient evidence that ΩK≠ 0, and is needed as a parameter.While certain inflationary model Lagrangians, with certain values of their parameters, and certain initial conditions, will lead to a present-day universe well-described as containing zero curvature, this does not justify distinguishing that subset of Lagrangians, parameters and initial conditions into a separate model.Absent any theoretical arguments, we cannot use observations that suggest small ΩKto enforce ΩK= 0.Our track record in picking inflationary models and their parametersa priorimakes such a choice dubious, andconcerns about tensions in cosmological parameters and large-angle cosmic-microwave-background anomalies strengthens arguments against this choice.We argue that ΩKmust not be set to zero, and that ΛCDM remains a phenomenological model with at least 7 parameters.

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    Free, publicly-accessible full text available February 1, 2024
  2. We present a fully-coupled, implicit-in-time framework for solving a thermodynamically-consistent Cahn-Hilliard Navier-Stokes system that models two-phase flows. In this work, we extend the block iterative method presented in Khanwale et al. [Simulating two-phase flows with thermodynamically consistent energy stable Cahn-Hilliard Navier-Stokes equations on parallel adaptive octree based meshes, J. Comput. Phys. (2020)], to a fully-coupled, provably second-order accurate scheme in time, while maintaining energy-stability. The new method requires fewer matrix assemblies in each Newton iteration resulting in faster solution time. The method is based on a fully-implicit Crank-Nicolson scheme in time and a pressure stabilization for an equal order Galerkin formulation. That is, we use a conforming continuous Galerkin (cG) finite element method in space equipped with a residual-based variational multiscale (RBVMS) procedure to stabilize the pressure. We deploy this approach on a massively parallel numerical implementation using parallel octree-based adaptive meshes. We present comprehensive numerical experiments showing detailed comparisons with results from the literature for canonical cases, including the single bubble rise, Rayleigh-Taylor instability, and lid-driven cavity flow problems. We analyze in detail the scaling of our numerical implementation. 
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  3. Efficiently and accurately simulating partial differential equations (PDEs) in and around arbitrarily defined geometries, especially with high levels of adaptivity, has significant implications for different application domains. A key bottleneck in the above process is the fast construction of a ‘good’ adaptively-refined mesh. In this work, we present an efficient novel octree-based adaptive discretization approach capable of carving out arbitrarily shaped void regions from the parent domain: an essential requirement for fluid simulations around complex objects. Carving out objects produces an incomplete octree. We develop efficient top-down and bottom-up traversal methods to perform finite element computations on incomplete octrees. We validate the framework by (a) showing appropriate convergence analysis and (b) computing the drag coefficient for flow past a sphere for a wide range of Reynolds numbers (0(1-10 6 )) encompassing the drag crisis regime. Finally, we deploy the framework on a realistic geometry on a current project to evaluate COVID-19 transmission risk in classrooms. 
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  4. Abstract With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at 
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