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To address the challenge of performance portability and facilitate the implementation of electronic structure solvers, we developed the basic matrix library (BML) and Parallel, Rapid O(N), and Graph-based Recursive Electronic Structure Solver (PROGRESS) library. The BML implements linear algebra operations necessary for electronic structure kernels using a unified user interface for various matrix formats (dense and sparse) and architectures (CPUs and GPUs). Focusing on density functional theory and tight-binding models, PROGRESS implements several solvers for computing the single-particle density matrix and relies on BML. In this paper, we describe the general strategies used for these implementations on various computer architectures, using OpenMP target functionalities on GPUs, in conjunction with third-party libraries to handle performance critical numerical kernels. We demonstrate the portability of this approach and its performance in benchmark problems. [ABSTRACT FROM AUTHOR]

Matrix diagonalization is almost always involved in computing the density matrix needed in quantum chemistry calculations. In the case of modest matrix sizes (≲4000), performance of traditional dense diagonalization algorithms on modern GPUs is underwhelming compared to the peak performance of these devices. This motivates the exploration of alternative algorithms better suited to these types of architectures. We newly derive, and present in detail, an existing Chebyshev expansion algorithm [Liang et al., J. Chem. Phys. 119, 4117–4125 (2003)] whose number of required matrix multiplications scales with the square root of the number of terms in the expansion. Focusing on dense matrices of modest size, our implementation on GPUs results in large speed ups when compared to diagonalization. Additionally, we improve upon this existing method by capitalizing on the inherent task parallelism and concurrency in the algorithm. This improvement is implemented on GPUs by using CUDA and HIP streams via the MAGMA library and leads to a significant speed up over the serial-only approach for smaller (≲1000) matrix sizes. Finally, we apply our technique to a model system with a high density of states around the Fermi level, which typically presents significant challenges. [ABSTRACT FROM AUTHOR]

Cephalopods camouflage abilities arise from highly specialized chromatic elements in their skin, chromatophores, iridophores, and leucophores, that enable them to display complex and rapidly changing color patterns. Despite the extensive study of these chromatic elements in squid and cuttlefish, full characterization of their individual optical response is still elusive in the Octopus species. We present here detailed multispectral analysis and mapping of the Octopus bimaculoides skin that allows to precisely identify the spatial distribution of the animal’s pigmented and structural elements. The mutual interaction of chromatophores and iridophores is also characterized both in terms of spectral response and spatial localization. The spectral information obtained through this analysis helps to understand the complexity and behavior of these natural tissues while continuing to serve as an inspiration for the fabrication of advanced, chromatically adaptable materials.

In light of the recently published complete set of statistically correct Grønbech–Jensen (GJ) methods for discrete-time thermodynamics, we revise a differential operator splitting method for the Langevin equation in order to comply with the basic GJ thermodynamic sampling features, namely, the Boltzmann distribution and Einstein diffusion, in linear systems. This revision, which is based on the introduction of time scaling along with flexibility of a discrete-time velocity attenuation parameter, provides a direct link between the ABO splitting formalism and the GJ methods. This link brings about the conclusion that any GJ method has at least weak second order accuracy in the applied time step. It further helps identify a novel half-step velocity, which simultaneously produces both correct kinetic statistics and correct transport measures for any of the statistically sound GJ methods. Explicit algorithmic expressions are given for the integration of the new half-step velocity into the GJ set of methods. Numerical simulations, including quantum-based molecular dynamics (QMD) using the QMD suite Los Alamos Transferable Tight-Binding for Energetics, highlight the discussed properties of the algorithms as well as exhibit the direct application of robust, time-step-independent stochastic integrators to QMD. [ABSTRACT FROM AUTHOR]

In light of the recently developed complete GJ set of single random variable stochastic, discrete-time Størmer–Verlet algorithms for statistically accurate simulations of Langevin equations [N. Grønbech-Jensen, Mol. Phys. 118, e1662506 (2020)], we investigate two outstanding questions: (1) Are there any algorithmic or statistical benefits from including multiple random variables per time step and (2) are there objective reasons for using one or more methods from the available set of statistically correct algorithms? To address the first question, we assume a general form for the discrete-time equations with two random variables and then follow the systematic, brute-force GJ methodology by enforcing correct thermodynamics in linear systems. It is concluded that correct configurational Boltzmann sampling of a particle in a harmonic potential implies correct configurational free-particle diffusion and that these requirements only can be accomplished if the two random variables per time step are identical. We consequently submit that the GJ set represents all possible stochastic Størmer–Verlet methods that can reproduce time step-independent statistics of linear systems. The second question is thus addressed within the GJ set. Based on numerical simulations of complex molecular systems, as well as on analytic considerations, we analyze apparent friction-induced differences in the stability of the methods. We attribute these differences to an inherent, friction-dependent discrete-time scaling, which depends on the specific method. We suggest that the method with the simplest interpretation of temporal scaling, the GJ-I/GJF-2GJ method, be preferred for statistical applications. [ABSTRACT FROM AUTHOR]

[Display omitted] • Bioelectrosynthesis systems have the potential to increase substrate to product conversion yields and reduce CO 2 emissions. • Increasing the rate of NAD(P)H supply can shift metabolism to favor the production of more reduced compounds. • Extracellular electron transfer is a multistep process that warrants consideration of the limitations at each step. • Bioelectrosynthesis can be conducted with intact microorganisms, cell extracts or purified enzymes. • Reduced electron mediators and energy source substrates can be generated ex situ and fed into the process. Bioelectrosynthesis (BES) systems exploit extracellular electron transport pathways to augment cellular metabolism. This strategy can be used to improve the economic viability of bio-based syntheses versus conventional methods, most notably petrochemical-based syntheses. It also has the potential to reduce the carbon footprint of biomanufacturing processes. Efficient channeling of cathode-derived electrons towards biosynthesis requires a better understanding of the biological mechanisms of electron transport as well as detailed evaluation of all aspects of process performance. More advanced solutions may deploy cell free systems that use ex situ generated reducing equivalents to improve economic performance. [ABSTRACT FROM AUTHOR]

The Facilitative Interpersonal Skills (FIS) task is a performance test of therapists' use of common relational skills (e.g. empathy, building expectations). The FIS method includes (a) materials that simulate difficult client moments on video, which are used to collect therapists' responses to these situations; and (b) independent ratings of these responses. Many of the FIS items are informed by psychotherapy processes that have been linked to outcome and facilitative conditions that have been reframed as individual therapist skills (e.g. alliance bond capacity). Overall, the FIS has predicted psychotherapy outcome. A single study is described in which FIS predicted the therapist effect using multilevel modelling of a large sample of clients who were nested within therapists. We also summarise two additional outcome studies that used experimental designs. One future direction is to better understand how therapists form responses to these difficult moments. We conclude that forming an optimal therapeutic response during challenging, emergent in‐session situations involves responsiveness (Stiles et al., 1998), or finding a response that fits the clients' needs within any moment. [ABSTRACT FROM AUTHOR]

Author(s): Joshua Finkelstein [1]; Alex Eccleston [1]; Sadaf Shadan [1] [illus. 1] Our understanding of how proteins fold into distinct shapes and catalyse a broad range of chemical transformations has [...]

Living systems exhibit remarkable abilities to self-assemble, regenerate, and remodel complex shapes. How cellular networks construct and repair specific anatomical outcomes is an open question at the heart of the next-generation science of bioengineering. Developmental bioelectricity is an exciting emerging discipline that exploits endogenous bioelectric signaling among many cell types to regulate pattern formation. We provide a brief overview of this field, review recent data in which bioelectricity is used to control patterning in a range of model systems, and describe the molecular tools being used to probe the role of bioelectrics in the dynamic control of complex anatomy. We suggest that quantitative strategies recently developed to infer semantic content and information processing from ionic activity in the brain might provide important clues to cracking the bioelectric code. Gaining control of the mechanisms by which large-scale shape is regulated in vivo will drive transformative advances in bioengineering, regenerative medicine, and synthetic morphology, and could be used to therapeutically address birth defects, traumatic injury, and cancer. [ABSTRACT FROM AUTHOR]

Regeneration is regulated not only by chemical signals but also by physical processes, such as bioelectric gradients. How these may change in the absence of the normal gravitational and geomagnetic fields is largely unknown. Planarian flatworms were moved to the International Space Station for 5 weeks, immediately after removing their heads and tails. A control group in spring water remained on Earth. No manipulation of the planaria occurred while they were in orbit, and space-exposed worms were returned to our laboratory for analysis. One animal out of 15 regenerated into a double-headed phenotype-normally an extremely rare event. Remarkably, amputating this double-headed worm again, in plain water, resulted again in the double-headed phenotype. Moreover, even when tested 20 months after return to Earth, the space-exposed worms displayed significant quantitative differences in behavior and microbiome composition. These observations may have implications for human and animal space travelers, but could also elucidate how microgravity and hypomagnetic environments could be used to trigger desired morphological, neurological, physiological, and bacteriomic changes for various regenerative and bioengineering applications. [ABSTRACT FROM AUTHOR]

Memories of alien abduction present researchers with a unique opportunity to explore memories for events which, in all likelihood, did not occur. In this review of the literature, the factors which can lead to the development of abduction memories are explored. These include personality and psychopathology variables, as well as instances of sleep paralysis, and the effects of hypnosis and memory implantation. In the end, while the events abductees report are unlikely to have occurred, the earnestness with which they endorse these memories is a strong indicator that memory is a malleable and complicated phenomenon, with implications for a wide range of psychological topics. [ABSTRACT FROM AUTHOR]

Proteins can catalyse a remarkably wide range of chemical reactions. Yet the main differences among polypeptides are in the side chains of naturally occurring amino acids, which account for only [...]

Author(s): Tanguy Chouard [1]; Joshua Finkelstein [1] How are innumerable protein functions integrated so that a living cell interacts coherently with its environment? This question is central to an emerging [...]

Research into the construction of a varied library of synthetic heterodimers made up of an invariant ligand that targets the FK506-binding protein linked to 320 substituted tetrahydrooxazepines is presented. It must still be established whether any of the 320 library members reported in this research will act as heterodimerizers.

The article discuses the effect guanine nucleotide methylation in protecting the messenger RNA (mRNA) from unexpected degradation.

The article offers several information related to drug discovery. Two groups have described high-throughput screens for compounds that inhibit the development of asexual blood-stage Plasmodium falciparum at low micromolar concentrations. Researchers offer evidence in Arabidopsis thaliana that the redox state of plastoquinone results in alterations in the plastid sigma factors' phosphorylation state.

The article discusses the research which focued on the use of Nuclear magnetic resonance (NMR) spectroscopy, to examine the movment of Nucleoporin 153 (Nup153) protein through nuclear pore complex (NPC), and discusses how Phenylalanine-glycine-rich nucleoporins (FG-Nups) line up around NPC.

The article discusses research on a method to rapidly and comprehensively screen different parameters that affect the stability of protein complexes, referencing a study published in the journal "Nature Methods" in 2015.

The article offers information on an analyses of biological processes at the single-cell level revealing that cells with identical genotypes can behave quite differently, which makes it difficult to study complex systems like tumors.

The article reports a study which identifies the natural leucine-rich repeat (LRR) modules with well-defined shapes, and their potential use as building blocks to construct larger, non-natural proteins with predictable three-dimensional structures.

The article focuses on role played by uridine in metabolism of RNA and discusses the catalyses of mRNA through Terminal uridylyl transferases (TUTs), TUTs acting on short poly(A) tail mRNAs and depletion of TUT4 and TUT7 in HeLa cells leading to increased half-lives of most mRNAs.

The article discusses the zinc uptake regulator (Zur) protein, which is a transcription factor that maintains zinc homeostasis in Escherichia coli, and expands on a study that solved the X-ray crystal structure of two Zur dimers bound to a DNA duplex derived from the znuABC operator gene.

The article discusses a study published in the journal "Nature Structural and Molecular Biology" which identified sites of small ubiquitin-like modifier (SUMO) proteins in cells using a purification strategy and examined its attachment to the lysine side chains of specific proteins.

The article offers the research by Teufel and colleagues to reconstitute biosynthetic pathway for synthesis of Merochlorins A and B terpenoids from dimethylallyl diphosphate (DMAPP), geranyldiphosphate (GPP) and malonyl?CoA and state production of complex natural products with the help of enzymes.

The article discusses the use of SHAPE -MaP methods in generating an accurate models of ribonucleic acid (RNA) structures through incorporating information from chemical probes.

The article focuses on a research, which probe the physiological functions of four enzymes in the pseurotin biosynthetic gene cluster from Aspergillus fumigatu including methyltransferases and FAD-containing monooxygenases (FMOs).

The article focuses on a research regarding the modification of the split ubiquitin two-hybrid assay, which can be used to detect interactions between a membrane protein and other proteins in mammalian cells along with the role in G protein-coupled receptors (GPCRs)-&#946-arrestin interaction.

The article focuses on a study which shows that a highly conserved stretch of positively charged amino acids, found between thermo sensor containing transmemberane (TM) domain and the cytoplasmic catalytic domain of DesK, adopts conformations in response to temperature change.

The article presents information on a study related to secondary metabolites which are produced by a broad range of microorganisms and many of them are used clinically as antibiotics or anticancer agents.