SparTen: Leveraging Kokkos for On-node Parallelism in a Second-Order Method for Fitting Canonical Polyadic Tensor Models to Poisson Data.
Abstract not provided.
Teranishi, Keita↗
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Majorize-Minimize Algorithms for Streaming Generalized Canonical Polyadic Tensor Decompositions.
Abstract not provided.
Gilman, Kyle↗
A new specification for std::generate_canonical
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C++, random numbers↗
Streaming Generalized Canonical Polyadic Tensor Decompositions
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Phipps, Eric T.↗
gRASPA
GPU Monte Carlo Simulation Code with a taste of RASPA We present enhancements in Monte Carlo simulation speed and functionality within an open-source code, gRASPA, which uses graphical processing units (GPUs) to achieve significant performance improvements compared to serial, CPU implementations of Monte Carlo. The code supports a wide range of Monte Carlo simulations, including canonical ensemble (NVT), grand canonical, NVT Gibbs, Widom test particle insertions, and continuous-fractional component Monte Carlo. Implementation of grand canonical transition matrix Monte Carlo (GC-TMMC) and a novel feature to allow different moves for the different components of metal-organic framework (MOF) structures exemplify the capabilities of gRASPA for precise free energy calculations and enhanced adsorption studies, respectively. The introduction of a High-Throughput Computing (HTC) mode permits many Monte Carlo simulations on a single GPU device for accelerated materials discovery. The code can incorporate machine learning (ML) potentials. The open-source nature of gRASPA promotes reproducibility and openness in science, and users may add features to the code and optimize it for their own purposes. The code is written in CUDA/C++ and SYCL/C++ to support different GPU vendors. The gRASPA code is publicly available at https://github.com/snurr-group/gRASPA.
Li, Zhao [Purdue/Northwestern/Notre Dame Universit↗
Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles
Abstract Non‐canonical interactions in DNA remain under‐explored in DNA nanotechnology. Recently, many structures with non‐canonical motifs have been discovered, notably a hexagonal arrangement of typically rhombohedral DNA tensegrity triangles that forms through non‐canonical sticky end interactions. Here, we find a series of mechanisms to program a hexagonal arrangement using: the sticky end sequence; triangle edge torsional stress; and crystallization condition. We showcase cross‐talking between Watson–Crick and non‐canonical sticky ends in which the ratio between the two dictates segregation by crystal forms or combination into composite crystals. Finally, we develop a method for reconfiguring the long‐range geometry of formed crystals from rhombohedral to hexagonal and vice versa. These data demonstrate fine control over non‐canonical motifs and their topological self‐assembly. This will vastly increase the programmability, functionality, and versatility of rationally designed DNA constructs.
Lu, Brandon↗
Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles
Non-canonical interactions in DNA remain under-explored in DNA nanotechnology. Recently, many structures with non-canonical motifs have been discovered, notably a hexagonal arrangement of typically rhombohedral DNA tensegrity triangles that forms through non-canonical sticky end interactions. Here, in this study, we find a series of mechanisms to program a hexagonal arrangement using: the sticky end sequence; triangle edge torsional stress; and crystallization condition. We showcase cross-talking between Watson–Crick and non-canonical sticky ends in which the ratio between the two dictates segregation by crystal forms or combination into composite crystals. Finally, we develop a method for reconfiguring the long-range geometry of formed crystals from rhombohedral to hexagonal and vice versa. These data demonstrate fine control over non-canonical motifs and their topological self-assembly. This will vastly increase the programmability, functionality, and versatility of rationally designed DNA constructs.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The determination of the core mass at the helium flash in globular cluster stars
Evolutionary sequences for the red giant branch (RGB) phase of a representative globular cluster star have been computed in order to investigate the reliability of the current canonical values of the core mass M(sub c) at the helium flash. These computations were motivated by recent suggestions that the canonical values of M(sub c) may be systematically too small due to the numerical algorithms for shifting the hydrogen shell and advancing the chemical composition during the RGB phase. Our results show that these algorithms do not, in fact, introduce a significant error in the values of M(sub c). Moreover, we demonstrate that a procedure for advancing the chemical composition which is implicit only in the hydrogen abundance will systematically underestimate the amount of hydrogen fuel consumption between RGB models and therefore should not be used in RGB computations. Overall we estimate the uncertainty in the core masses of Sweigart & Gross (1978) due to numerical effects to be approximately equals 0.003 solar mass. From a consideration of the available canonical models we conclude that a change in the canonical values of M(sub c) by a few 10(exp -2) solar mass would require either a substantial change in the canonical input physics or some noncanonical effect such as rotation. Finally our models show that the use of short time steps can significantly increase the extent of the inner tail of the hydrogen shell. This effect may enhance the likelihood of hydrogen mixing following a helium shell flash in an asymptotic giant branch star.
Sweigart, Allen V.↗
On‐site surrogates for large‐scale calibration
Abstract Motivated by a computer model calibration problem from the oil and gas industry, involving the design of a honeycomb seal, we develop a new Bayesian methodology to cope with limitations in the canonical apparatus stemming from several factors. We propose a new strategy of on‐site design and surrogate modeling for a computer simulator acting on a high‐dimensional input space that, although relatively speedy, is prone to numerical instabilities, missing data, and nonstationary dynamics. Our aim is to strike a balance between data‐faithful modeling and computational tractability in a calibration framework—tailoring the computer model to a limited field experiment. Situating our on‐site surrogates within the canonical calibration apparatus requires updates to that framework. We describe a novel yet intuitive Bayesian setup that carefully decomposes otherwise prohibitively large matrices by exploiting the sparse blockwise structure. Empirical illustrations demonstrate that this approach performs well on toy data and our motivating honeycomb example.
Huang, Jiangeng↗
A conservative discontinuous Galerkin algorithm for particle kinetics on smooth manifolds
A novel, conservative discontinuous Galerkin algorithm is presented for particle kinetics on manifolds. The motion of particles on the manifold is represented using both canonical and non-canonical Hamiltonian formulations. Our schemes apply to both formulations, but the canonical formulation results in a particularly efficient scheme that also conserves particle density and energy exactly. The collisionless update is coupled to a Bhatnagar-Gross-Krook (BGK) collision operator that provides a simplified model for relaxation to local thermodynamic equilibrium. An iterative scheme is constructed to ensure collisional invariants (density, momentum and energy) are preserved numerically. Rotation of the manifold is incorporated by modifying the Hamiltonian while ensuring a canonical formulation. Several test problems, including a kinetic version of the classical Sod shock problem, Kelvin-Helmholtz instability on the surfaces of a sphere and a hyperboloid, with and without rotations, are presented. A prospectus for further development of this approach to simulation of kinetic theory in general relativity is presented.
Discontinuous Galerkin↗
Koopman wavefunctions and Clebsch variables in Vlasov–Maxwell kinetic theory
Motivated by recent discussions on the possible role of quantum computation in plasma simulations, here, we present different approaches to Koopman's Hilbert-space formulation of classical mechanics in the context of Vlasov–Maxwell kinetic theory. The celebrated Koopman–von Neumann construction is provided with two different Hamiltonian structures: one is canonical and recovers the usual Clebsch representation of the Vlasov density, the other is non-canonical and appears to overcome certain issues emerging in the canonical formalism. Furthermore, the canonical structure is restored for a variant of the Koopman–von Neumann construction that carries a different phase dynamics. Going back to van Hove's prequantum theory, the corresponding Koopman–van Hove equation provides an alternative Clebsch representation which is then coupled to the electromagnetic fields. Finally, the role of gauge transformations in the new context is discussed in detail.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Lectures on statistical mechanics
Presented here is a transcription of the lecture notes from Professor Allan N. Kaufman’s graduate statistical mechanics course Physics 212A and 212B at the University of California Berkeley from the 1972–1973 academic year. 212A addressed equilibrium statistical mechanics with topics: fundamentals (micro-canonical and sub-canonical ensembles, adiabatic law and action conservation, fluctuations, pressure, and virial theorem), classical fluids and other systems (equation of state, deviations from ideality, virial coefficients and van der Waals potential, canonical ensemble and partition function, quasistatic evolution, grand-canonical ensemble and partition function, chemical potential, simple model of a phase transition, quantum virial expansion, numerical simulation of equations of state, and phase transition), chemical equilibrium (systems with multiple species and chemical reactions, law of mass action, Saha equation, chemical equilibrium including ionization and excited states), and long-range interactions (including Coulomb, dipole, and gravitational interactions, Debye–Hückel theory, and shielding). 212B addressed nonequilibrium statistical mechanics with topics: fundamentals (definitions: realizations, moments, characteristic function, and discrete variables), Brownian motion (Langevin equation, fluctuation–dissipation theorem, spatial diffusion, Boltzmann’s H-theorem), Liouville and Klimontovich equations, Landau equation (derivation, elaboration, and H-theorem, and irreversibility), Markov processes and Fokker–Planck equation (derivations of the Fokker–Planck equation and a master equation), linear response and transport theory (linear Boltzmann equation, linear response theory of Kubo and Mori, relation of entropy production to electrical conductivity, transport relations and coefficients, normal mode solutions of the transport equations, sketch of a generalized Langevin equation method for transport theory), and an introduction to nonequilibrium quantum statistical mechanics.
plasma dynamics↗
An Improved Top-Down Mass Spectrometry Characterization of Chlamydomonas reinhardtii Histones and Their Post-translational Modifications
We present an updated analysis of the linker and core histone proteins and their proteoforms in the green microalga Chlamydomonas reinhardtii by top-down mass spectrometry (TDMS). The combination of high-resolution liquid chromatographic separation, robust fragmentation high, mass spectral resolution, the application of a custom search algorithm, and extensive manual analysis enabled the characterization of 86 proteoforms across all four core histones H2A, H2B, H3 and H4, and the linker histone H1. All canonical H2A paralogs, which vary in their C-termini, were identified, along with an unreported non-canonical variant that had both high levels of acetylation and C-terminal truncations. Similarly, a majority of the canonical H2B paralogs were identified, along with a smaller non-canonical variant, H2B.v, that was highly acetylated. Histone H4 exhibited a novel acetylation profile that differs significantly from that found in other organisms. A majority of H3 was monomethylated at K4, while a small fraction of H3 was trimethylated at K4 and also highly acetylated.
59 BASIC BIOLOGICAL SCIENCES↗
Structure of the Wnt–Frizzled–LRP6 initiation complex reveals the basis for coreceptor discrimination
Wnt morphogens are critical for embryonic development and tissue regeneration. Canonical Wnts form ternary receptor complexes composed of tissue-specific Frizzled (Fzd) receptors together with the shared LRP5/6 coreceptors to initiate β-catenin signaling. The cryo-EM structure of a ternary initiation complex of an affinity-matured XWnt8–Frizzled8–LRP6 complex elucidates the basis of coreceptor discrimination by canonical Wnts by means of their N termini and linker domains that engage the LRP6 E1E2 domain funnels. Chimeric Wnts bearing modular linker “grafts” were able to transfer LRP6 domain specificity between different Wnts and enable non-canonical Wnt5a to signal through the canonical pathway. Synthetic peptides comprising the linker domain serve as Wnt-specific antagonists. The structure of the ternary complex provides a topological blueprint for the orientation and proximity of Frizzled and LRP6 within the Wnt cell surface signalosome.
59 BASIC BIOLOGICAL SCIENCES↗
Nonenzymatic RNA copying with a potentially primordial genetic alphabet
Nonenzymatic RNA copying is thought to have been responsible for the replication of genetic information during the origin of life. However, chemical copying with the canonical nucleotides (A, U, G, and C) strongly favors the incorporation of G and C and disfavors the incorporation of A and especially U because of the stronger G:C vs. A:U base pair and the weaker stacking interactions of U. Recent advances in prebiotic chemistry suggest that the 2-thiopyrimidines were precursors to the canonical pyrimidines, raising the possibility that they may have played an important early role in RNA copying chemistry. Furthermore, 2-thiouridine (s 2 U) and inosine (I) form by deamination of 2-thiocytidine (s 2 C) and A, respectively. We used thermodynamic and crystallographic analyses to compare the I:s 2 C and A:s 2 U base pairs. We find that the I:s 2 C base pair is isomorphic and isoenergetic with the A:s 2 U base pair. The I:s 2 C base pair is weaker than a canonical G:C base pair, while the A:s 2 U base pair is stronger than the canonical A:U base pair, so that a genetic alphabet consisting of s 2 U, s 2 C, I, and A generates RNA duplexes with uniform base pairing energies. Consistent with these results, kinetic analysis of nonenzymatic template-directed primer extension reactions reveals that s 2 C and s 2 U substrates bind similarly to I and A in the template, and vice versa. Our work supports the plausibility of a potentially primordial genetic alphabet consisting of s 2 U, s 2 C, I, and A and offers a potential solution to the long-standing problem of biased nucleotide incorporation during nonenzymatic template copying.
Science & Technology - Other Topics↗
An ascomycete H4 variant with an unknown function
Histone variants leading to altered nucleosome structure, dynamics and DNA accessibility occur frequently, albeit rarely for H4. We carried out a comprehensive in silico scrutiny of fungal genomes, which revealed the presence of a novel H4 variant (H4E) in the ascomycetes, throughout the Pezizomycotina, in basal species of the Taphrinomycotina and also in the Glomeromycota. The coding cognate genes show a specific intron/exon organization, different from H4 canonical genes. H4Es diverge from canonical H4s mainly in the N- and C-terminal extensions, showing marked differences in the distribution and number of Lys and Arg residues, which may result in novel post-translational modifications. In Aspergillus nidulans (Pezizomycotina, Eurotiomycetes) the H4E variant protein level is low in mycelia. However, the encoding gene is well expressed at 37°C under nitrogen starvation. H4E localizes to the nucleus and interacts with H3, but its absence or overexpression does not result in any detectable phenotype. Deletion of only one of the of the two canonical H4 genes results in a strikingly impaired growth phenotype, which indicates that H4E cannot replace this canonical histone. Thus, an H4 variant is present throughout a whole subphylum of the ascomycetes, but with hitherto no experimentally detectable function.
59 BASIC BIOLOGICAL SCIENCES↗
Quantum Joule expansion of one-dimensional systems
Here, we investigate the Joule expansion of nonintegrable quantum systems that contain bosons or spinless fermions in one-dimensional lattices. A barrier initially confines the particles to be in half of the system in a thermal state described by the canonical ensemble and is removed at time t = 0. We investigate the properties of the time-evolved density matrix, the diagonal ensemble density matrix, and the corresponding canonical ensemble density matrix with an effective temperature determined by the total energy conservation using exact diagonalization. The weights for the diagonal ensemble and the canonical ensemble match well for high initial temperatures that correspond to negative effective final temperatures after the expansion. At long times after the barrier is removed, the time-evolved Rényi entropy of subsystems bigger than half can equilibrate to the thermal entropy with exponentially small fluctuations. The time-evolved reduced density matrix at long times can be approximated by a thermal density matrix for small subsystems. Few-body observables, like the momentum distribution function, can be approximated by a thermal expectation of the canonical ensemble with strongly suppressed fluctuations. The negative effective temperatures for finite systems go to non-negative temperatures in the thermodynamic limit for bosons, but there is a true thermodynamic effect for fermions, which is confirmed by finite-temperature density matrix renormalization group calculations. We propose the Joule expansion as a way to dynamically create negative temperature states for fermion systems with repulsive interactions.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Developing a pipeline to expand the genetic code of diverse bacteria for microbial engineering
Microbial biotechnologies are key to addressing grand challenges to promote human health, reverse carbon emissions, recycle mixed plastic waste, remediate contaminated soils, and achieve sustainable economies. Synthetic biology has enabled design of diverse microbes and their proteins for useful purposes, but the narrowness of the natural genetic code limits functional diversity (e.g., biosynthesis) of engineered microbes. The natural genetic code defines the fundamental rules of translating genetic information into proteins comprised of 22 ‘canonical’ amino acids. However, using a technique called genetic code expansion (GCE), the chemical properties and therefore functions of proteins can be transformed by incorporation of one or more of ~200 chemically diverse ‘non-canonical’ amino acids. The effective application of genetic code expansion in diverse microbes has the potential to revolutionize biotechnology. However, despite over 50 years of research and its transformative potential, the application of genetic code expansion has been limited to a handful of bacterial species. In this project, we will perform three tasks to both overcome the barriers that prevent wide spread adoption of GCE as molecular tool and demonstrate its potential for biotechnological applications. Specifically, we will (1) develop a genetic engineering methodology that will enable use of GCE in a broad range of bacterial hosts, (2) use high-throughput functional genomics methods to identify physiological responses to both genetic code expansion and exposure to non-canonical amino acids in three different bacteria, and (3) demonstrate an application of GCE by selectively incorporate non-canonical amino acids into surface displayed peptides such as those used for biomining.
59 BASIC BIOLOGICAL SCIENCES↗