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At least 325 records · Page 18

Parallel Runtime Interface for Fortran (PRIF) Specification (Rev. 0.6)

This document specifies an interface to support the multi-image parallelism features of Fortran, named the Parallel Runtime Interface for Fortran (PRIF). PRIF is a solution in which a runtime library is primarily responsible for implementing coarray allocation, deallocation and accesses, image synchronization, atomic operations, events, teams and collective subroutines. The Fortran compiler is responsible for transforming the invocation of Fortran-level multi-image parallelism features into procedure calls to the necessary PRIF subroutines. The interface is designed for portability across shared- and distributed-memory machines, different operating systems, and multiple architectures. Implementations of this interface are intended as an augmentation for the compiler's own runtime library. With an implementation-agnostic interface, alternative parallel runtime libraries may be developed that support the same interface. One benefit of this approach is the ability to vary the communication substrate. A central aim of this document is to define a parallel runtime interface in standard Fortran syntax, which enables us to leverage Fortran to succinctly express various properties of the procedure interfaces, including argument attributes.

97 MATHEMATICS AND COMPUTING↗

Parallel Runtime Interface for Fortran (PRIF) Specification (Rev. 0.4)

This document specifies an interface to support the parallel features of Fortran, named the Parallel Runtime Interface for Fortran (PRIF). PRIF is a proposed solution in which the runtime library is responsible for coarray allocation, deallocation and accesses, image synchronization, atomic operations, events, and teams. In this interface, the compiler is responsible for transforming the invocation of Fortran-level parallel features into procedure calls to the necessary PRIF procedures. The interface is designed for portability across shared- and distributed-memory machines, different operating systems, and multiple architectures. Implementations of this interface are intended as an augmentation for the compiler's own runtime library. With an implementation-agnostic interface, alternative parallel runtime libraries may be developed that support the same interface. One benefit of this approach is the ability to vary the communication substrate. A central aim of this document is to define a parallel runtime interface in standard Fortran syntax, which enables us to leverage Fortran to succinctly express various properties of the procedure interfaces, including argument attributes.

97 MATHEMATICS AND COMPUTING↗

Towards interpretable Cryo-EM: disentangling latent spaces of molecular conformations

Molecules are essential building blocks of life and their different conformations (i.e., shapes) crucially determine the functional role that they play in living organisms. Cryogenic Electron Microscopy (cryo-EM) allows for acquisition of large image datasets of individual molecules. Recent advances in computational cryo-EM have made it possible to learn latent variable models of conformation landscapes. However, interpreting these latent spaces remains a challenge as their individual dimensions are often arbitrary. The key message of our work is that this interpretation challenge can be viewed as an Independent Component Analysis (ICA) problem where we seek models that have the property of identifiability. That means, they have an essentially unique solution, representing a conformational latent space that separates the different degrees of freedom a molecule is equipped with in nature. Thus, we aim to advance the computational field of cryo-EM beyond visualizations as we connect it with the theoretical framework of (nonlinear) ICA and discuss the need for identifiable models, improved metrics, and benchmarks. Moving forward, we propose future directions for enhancing the disentanglement of latent spaces in cryo-EM, refining evaluation metrics and exploring techniques that leverage physics-based decoders of biomolecular systems. Moreover, we discuss how future technological developments in time-resolved single particle imaging may enable the application of nonlinear ICA models that can discover the true conformation changes of molecules in nature. The pursuit of interpretable conformational latent spaces will empower researchers to unravel complex biological processes and facilitate targeted interventions. This has significant implications for drug discovery and structural biology more broadly. More generally, latent variable models are deployed widely across many scientific disciplines. Thus, the argument we present in this work has much broader applications in AI for science if we want to move from impressive nonlinear neural network models to mathematically grounded methods that can help us learn something new about nature.

59 BASIC BIOLOGICAL SCIENCES↗

Observation of critical scaling in spin glasses below T c using thermoremanent magnetization

Time-dependent thermoremanent magnetization (TRM) studies have been instrumental in probing energy dynamics within the spin glass phase. In this paper, we review the evolution of the TRM experiment over the last half century and discuss some aspects related to how it has been used in the understanding of spin glasses. We also report on recent experiments using high-resolution DC SQUID magnetometry to probe the TRM at temperatures less than but near to the transition temperature T c . These experiments have been performed as a function of waiting time, temperature, and five different magnetic fields. We find that as the transition temperature is approached from below, the characteristic time scale of TRM is suppressed up to several orders of magnitude in time. In the highest-temperature region, we find that the waiting time effect subsides, and a waiting time-independent crossover line is reached. We also find that increasing the magnetic field further suppresses the crossover line. Using a first-principles energy argument across the crossover line, we derive an equation that is an excellent fit to the crossover lines for all magnetic fields probed. The data show strong evidence for critical slowing down and an H = 0 Oe phase transition.

36 MATERIALS SCIENCE↗

Weak Scale Supersymmetry Emergent from the String Landscape

Superstring flux compactifications can stabilize all moduli while leading to an enormous number of vacua solutions, each leading to different 4−d laws of physics. While the string landscape provides at present the only plausible explanation for the size of the cosmological constant, it may also predict the form of weak scale supersymmetry which is expected to emerge. Rather general arguments suggest a power-law draw to large soft terms, but these are subject to an anthropic selection of a not-too-large value for the weak scale. The combined selection allows one to compute relative probabilities for the emergence of supersymmetric models from the landscape. Models with weak scale naturalness appear most likely to emerge since they have the largest parameter space on the landscape. For finetuned models such as high-scale SUSY or split SUSY, the required weak scale finetuning shrinks their parameter space to tiny volumes, making them much less likely to appear compared to natural models. Probability distributions for sparticle and Higgs masses from natural models show a preference for Higgs mass mh∼125 GeV, with sparticles typically beyond the present LHC limits, in accord with data. From these considerations, we briefly describe how natural SUSY is expected to be revealed at future LHC upgrades. This article is a contribution to the Special Edition of the journal Entropy, honoring Paul Frampton on his 80th birthday.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

The Baby Universe is Fine and the CFT Knows It: On Holography for Closed Universes

Big bang/big crunch closed universes can be realized in AdS/CFT, even though they lack asymptotically AdS boundaries. With enough bulk entanglement, the bulk Hilbert space of a closed universe can be holographically encoded in the CFT. We clarify the relation of this encoding to observer-clone proposals and refute recent arguments about the breakdown of semiclassical physics in such spaces. In the limit of no bulk entanglement, the holographic encoding breaks down. The oft-cited one-dimensional nature of the closed universe Hilbert space represents the limitation of the external (CFT) Hilbert space to access the quantum information in the closed universe, similar to the limitations imposed on observers outside a perfectly isolated quantum lab. We advocate that the CFT nevertheless continues to determine the physical properties of the closed universe in this regime, showing how to interpret this relationship in terms of a final state projection in the closed universe. We provide a dictionary between the final state wavefunction and CFT data. We propose a model of the emergence of an arrow of time in the universe with a given initial or final state projection. Finally, we show that the conventional EFT in the closed universe, without any projection, can be recovered as a maximally ignorant description of the final state. This conventional EFT is encoded in CFT data, and it can be probed by computing coarse-grained observables. We provide an example of one such observable. Taken together, these results amount to a clean bill of health for baby universes born of AdS/CFT.

FOS: Physical sciences↗

Holographic codes and bulk RG flows

We consider the coarse-graining of holographic quantum error correcting codes under a generalized notion of bulk renormalization-group flow. In particular, we study the renormalization under this flow of the $A/4G$ term in the Faulkner-Lewkowycz-Maldacena formula and in its Rényi generalization. This provides a general quantum code perspective on the arguments of Susskind and Uglum. Specifically, given a 'UV' code with two-sided recovery and appropriately flat entanglement spectrum together with a set of 'seed' states in the UV code, we explicitly construct an 'IR' code with corresponding properties which contains the given seed states and is of minimal size in a sense we describe.

FOS: Physical sciences↗

Clearing up the Strong $CP$ problem

The absence of a neutron electric dipole moment (EDM) constrains the quantum chromodynamics (QCD) theta angle to be less than one part in ten billion, posing the Strong $CP$ problem. We revisit two classes of proposed solutions. First, we show that when $P$ or $CP$ is realized as a gauged discrete symmetry - as can arise in quantum gravity - the vacuum necessarily preserves $CP$, contrary to recent claims that discrete-symmetry solutions fail. Gauged discrete models face model-building challenges, such as avoiding contributions to the neutron EDM after spontaneous $P$ or $CP$ breaking, but in principle have no fundamental obstructions. Second, we critically examine recent arguments that the Strong $CP$ problem is illusory, demonstrating that a nonzero neutron EDM at finite $\barθ$ follows directly from well-understood QCD dynamics. Taken together, our results reinforce the reality of the Strong $CP$ problem and highlight gauged discrete-symmetry realizations of $P$ or $CP$ as plausible solutions.

FOS: Physical sciences↗

Synthesis of epitaxial TaO$_2$ thin films on Al$_2$O$_3$ by suboxide molecular-beam epitaxy and thermal laser epitaxy

Tantalum dioxide (TaO2) is a metastable tantalum compound. Here, we report the epitaxial stabilization of TaO2 on Al2O3 (1-102) (r-plane sapphire) substrates using suboxide molecular-beam epitaxy (MBE) and thermal laser epitaxy (TLE), demonstrating single-oriented, monodomain growth of anisotropically strained thin films. Microstructural investigation is performed using synchrotron X-ray diffraction and scanning transmission electron microscopy. The tetravalent oxidation state of tantalum is confirmed using X-ray absorption and photoemission spectroscopy as well as electron energy-loss spectroscopy. Optical properties are investigated via spectroscopic ellipsometry and reveal a 0.3 eV Mott gap of the tantalum 5d electrons. Density-functional theory and group theoretical arguments are used to evaluate the limited stability of the rutile phase and reveal the potential to unlock a hidden metal-insulator transition concomitant with a structural phase transition to a distorted rutile phase, akin to NbO2. Our work expands the understanding of tantalum oxides and paves the way for their integration into next-generation electronic and photonic devices.

FOS: Physical sciences↗

Alquimia v1.0: a generic interface to biogeochemical codes – a tool for interoperable development, prototyping and benchmarking for multiphysics simulators

Alquimia v1.0 is a generic interface to geochemical solvers that facilitates development of multiphysics simulators by enabling code coupling, prototyping and benchmarking. The interface enforces the function arguments and their types for setting up, solving, serving up output data and carrying out other common auxiliary tasks while providing a set of structures for data transfer between the multiphysics code driving the simulation and the geochemical solver. Alquimia relies on a single-cell approach that permits operator splitting coupling and parallel computation. We describe the implementation in Alquimia of two widely used open-source codes that perform geochemical calculations: PFLOTRAN and CrunchFlow. We then exemplify its use for the implementation and simulation of reactive transport in porous media by two open-source flow and transport simulators: Amanzi and ParFlow. We also demonstrate its use for the simulation of coupled processes in novel multiphysics applications including the effect of multiphase flow on reaction rates at the pore scale with OpenFOAM, the role of complex biogeochemical processes in land surface models such as the E3SM Land Model (ELM) and the impact of surface–subsurface hydrological interactions on hydrogeochemical export from watersheds with the Advanced Terrestrial Simulator (ATS). These applications make it apparent that the availability of a well-defined yet flexible interface has the potential to improve the software development workflow, freeing up resources to focus on advances in process models and mechanistic understanding of coupled problems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗