Probing Surface Chemistry at an Atomic Level; Decomposition of 1-Propanethiol on GaP(001)(2×4) Investigated by STM, XPS, and DFT

The adsorption and decomposition mechanisms for 1-propanethiol on a Ga-rich GaP(001) (2 × 4) surface are investigated at an atomic level using scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy, and density functional theory (DFT) calculations. Using a combination of experimental and theoretical tools, we probe the detailed structures and energetics of a series of reaction intermediates in the thermal decomposition pathway from 130 to 773 K. At 130 K, the propanethiolate adsorbates are observed at the edge gallium sites, with the thiolate–Ga bonding configuration maintained up to 473 K. Further decomposition produces two new surface features, Ga–S–Ga and P-propyl species at 573 K. Finally, S-induced (1 × 1) and (2 × 1) reconstructions are observed at 673–773 K, which are reportedly associated with arrays of surface Ga–S–Ga bonds and subsurface diffusion of S. To understand the observed site-selectivity on the hydrogen dissociation of the thiol molecule at 130 K, the two most likely dissociation pathways (Ga–P vs Ga–Ga dimer sites) are investigated using DFT Gibbs energy calculations. While the theory predicts the kinetic advantage for the dissociation reaction occurring on the Ga–P dimer (Lewis acid–base combination), we only observed dissociation products on the Ga–Ga dimer (Lewis acid). The DFT calculations clarify that the reversible thiolate diffusion along the Ga dimer row prevents recombinative desorption, which is probable on the Ga–P dimer. Together with experimental and theoretical results, we suggest a thermal decomposition mechanism for the thiol molecule with atomic-level structural details

Probing Surface Chemistry at an Atomic Level; Decomposition of 1-Propanethiol on GaP(001)(2×4) Investigated by STM, XPS, and DFT

The adsorption and decomposition mechanisms for 1-propanethiol on a Ga-rich GaP(001) (2 × 4) surface are investigated at an atomic level using scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy, and density functional theory (DFT) calculations. Using a combination of experimental and theoretical tools, we probe the detailed structures and energetics of a series of reaction intermediates in the thermal decomposition pathway from 130 to 773 K. At 130 K, the propanethiolate adsorbates are observed at the edge gallium sites, with the thiolate–Ga bonding configuration maintained up to 473 K. Further decomposition produces two new surface features, Ga–S–Ga and P-propyl species at 573 K. Finally, S-induced (1 × 1) and (2 × 1) reconstructions are observed at 673–773 K, which are reportedly associated with arrays of surface Ga–S–Ga bonds and subsurface diffusion of S. To understand the observed site-selectivity on the hydrogen dissociation of the thiol molecule at 130 K, the two most likely dissociation pathways (Ga–P vs Ga–Ga dimer sites) are investigated using DFT Gibbs energy calculations. While the theory predicts the kinetic advantage for the dissociation reaction occurring on the Ga–P dimer (Lewis acid–base combination), we only observed dissociation products on the Ga–Ga dimer (Lewis acid). The DFT calculations clarify that the reversible thiolate diffusion along the Ga dimer row prevents recombinative desorption, which is probable on the Ga–P dimer. Together with experimental and theoretical results, we suggest a thermal decomposition mechanism for the thiol molecule with atomic-level structural details

Software engineering to sustain a high-performance computing scientific application: QMCPACK

We provide an overview of the software engineering efforts and their impact in QMCPACK, a production-level ab-initio Quantum Monte Carlo open-source code targeting high-performance computing (HPC) systems. Aspects included are: (i) strategic expansion of continuous integration (CI) targeting CPUs, using GitHub Actions runners, and NVIDIA and AMD GPUs in pre-exascale systems, using self-hosted hardware; (ii) incremental reduction of memory leaks using sanitizers, (iii) incorporation of Docker containers for CI and reproducibility, and (iv) refactoring efforts to improve maintainability, testing coverage, and memory lifetime management. We quantify the value of these improvements by providing metrics to illustrate the shift towards a predictive, rather than reactive, sustainable maintenance approach. Our goal, in documenting the impact of these efforts on QMCPACK, is to contribute to the body of knowledge on the importance of research software engineering (RSE) for the sustainability of community HPC codes and scientific discovery at scale.Comment: Accepted at the first US-RSE Conference, USRSE2023, https://us-rse.org/usrse23/, 8 pages, 3 figures, 4 table

A microfluidics and agent-based modeling framework for investigating spatial organization in bacterial colonies: The case of Pseudomonas Aeruginosa amd H1-type VI secretion interactions

The factors leading to changes in the organization of microbial assemblages at fine spatial scales are not well characterized or understood. However, they are expected to guide the succession of community development and function toward specific outcomes that could impact human health and the environment. In this study, we put forward a combined experimental and agent-based modeling framework and use it to interpret unique spatial organization patterns of H1-Type VI secretion system (T6SS) mutants of P. aeruginosa under spatial confinement. We find that key parameters, such as T6SS-mediated cell contact and lysis, spatial localization, relative species abundance, cell density and local concentrations of growth substrates and metabolites are influenced by spatial confinement. The model, written in the accessible programming language NetLogo, can be adapted to a variety of biological systems of interest and used to simulate experiments across a broad parameter space. It was implemented and run in a high-throughput mode by deploying it across multiple CPUs, with each simulation representing an individual well within a high-throughput microwell array experimental platform. The microfluidics and agent-based modeling framework we present in this paper provides an effective means by which to connect experimental studies in microbiology to model development. The work demonstrates progress in coupling experimental results to simulation while also highlighting potential sources of discrepancies between real-world experiments and idealized models

Evaluating the Potential Effectiveness of Compensatory Mitigation Strategies for Marine Bycatch

Conservationists are continually seeking new strategies to reverse population declines and safeguard against species extinctions. Here we evaluate the potential efficacy of a recently proposed approach to offset a major anthropogenic threat to many marine vertebrates: incidental bycatch in commercial fisheries operations. This new approach, compensatory mitigation for marine bycatch (CMMB), is conceived as a way to replace or reduce mandated restrictions on fishing activities with compensatory activities (e.g., removal of introduced predators from islands) funded by levies placed on fishers. While efforts are underway to bring CMMB into policy discussions, to date there has not been a detailed evaluation of CMMB's potential as a conservation tool, and in particular, a list of necessary and sufficient criteria that CMMB must meet to be an effective conservation strategy. Here we present a list of criteria to assess CMMB that are tied to critical ecological aspects of the species targeted for conservation, the range of possible mitigation activities, and the multi-species impact of fisheries bycatch. We conclude that, overall, CMMB has little potential for benefit and a substantial potential for harm if implemented to solve most fisheries bycatch problems. In particular, CMMB is likely to be effective only when applied to short-lived and highly-fecund species (not the characteristics of most bycatch-impacted species) and to fisheries that take few non-target species, and especially few non-seabird species (not the characteristics of most fisheries). Thus, CMMB appears to have limited application and should only be implemented after rigorous appraisal on a case-specific basis; otherwise it has the potential to accelerate declines of marine species currently threatened by fisheries bycatch

Associations of body mass index and waist circumference with: energy intake and percentage energy from macronutrients, in a cohort of australian children

Background: It is evident from previous research that the role of dietary composition in relation to the development of childhood obesity remains inconclusive. Several studies investigating the relationship between body mass index (BMI), waist circumference (WC) and/or skin fold measurements with energy intake have suggested that the macronutrient composition of the diet (protein, carbohydrate, fat) may play an important contributing role to obesity in childhood as it does in adults. This study investigated the possible relationship between BMI and WC with energy intake and percentage energy intake from macronutrients in Australian children and adolescents

Go4it; study design of a randomised controlled trial and economic evaluation of a multidisciplinary group intervention for obese adolescents for prevention of diabetes mellitus type 2

<p>Abstract</p> <p>Background</p> <p>In the Netherlands, the first adolescents with diabetes mellitus type 2 as a result of obesity have recently been diagnosed. Therefore, it is very important that programs aiming at the prevention of type 2 diabetes of obese adolescents are developed and evaluated.</p> <p>Methods</p> <p>Go4it is a multidisciplinary group treatment that focuses on: 1) increasing awareness of the current dietary and physical activity behaviour (i.e. energy balance behaviour), 2) improving diet, 3) decreasing sedentary behaviour, 4) increasing levels of physical activity, and 5) coping with difficult situations. Go4it consists of 7 sessions with an interval of 2–3 weeks.</p> <p>The effectiveness of the multidisciplinary group treatment compared with usual care (i.e. referral to a dietician) was evaluated in a randomised controlled trial. We examined effects on BMI(sds), body composition, energy expenditure, glucose tolerance and insulin resistance (primary outcome measure), as well as dietary and physical activity behaviour and quality of life. An economic evaluation from a societal perspective was conducted alongside the randomised trial to evaluate the cost-effectiveness of the multidisciplinary treatment program vs. usual care.</p> <p>Discussion</p> <p>In this paper we described a multidisciplinary treatment program (Go4it) for obese adolescents and the design of a randomised controlled trial and economic evaluation to evaluate its effectiveness and cost-effectiveness.</p> <p>Trial registration</p> <p>Netherlands Trial Register (ISRCTN27626398).</p

DCA++ project: Sustainable and scalable development of a high-performance research code

Scientific discoveries across all fields, from physics to biology, are increasingly driven by computer simulations. At the same time, the computational demand of many problems necessitates large-scale calculations on high-performance supercomputers. Developing and maintaining the underlying codes, however, has become a challenging task due to a combination of factors. Leadership computer systems require massive parallelism, while their architectures are diversifying. New sophisticated algorithms are continuously developed and have to be implemented efficiently for such complex systems. Finally, the multidisciplinary nature of modern science involves large, changing teams to work on a given codebase. Using the example of the DCA++ project, a highly scalable and efficient research code to solve quantum many-body problems, we explore how computational science can overcome these challenges by adopting modern software engineering approaches. We present our principles for scientific software development and describe concrete practices to meet them, adapted from agile software development frameworks.ISSN:1742-6588ISSN:1742-659

Thermodynamic Control of Two-Dimensional Molecular Ionic Nanostructures on Metal Surfaces

Bulk molecular ionic solids exhibit fascinating electronic properties, including electron correlations, phase transitions, and superconducting ground states. In contrast, few of these phenomena have been observed in low-dimensional molecular structures, including thin films, nanoparticles, and molecular blends, not in the least because most of such structures have been composed of nearly closed-shell molecules. It is therefore desirable to develop low-dimensional ionic molecular structures that can capture potential applications. Here, we present detailed analysis of monolayer-thick structures of the canonical TTF–TCNQ (tetrathiafulvalene 7,7,8,8-tetracyanoquinodimethane) system grown on low-index gold and silver surfaces. The most distinctive property of the epitaxial growth is the wide abundance of stable TTF/TCNQ ratios, in sharp contrast to the predominance of a 1:1 ratio in the bulk. We propose the existence of the surface phase diagram that controls the structures of TTF–TCNQ on the surfaces and demonstrate phase transitions that occur upon progressively increasing the density of TCNQ while keeping the surface coverage of TTF fixed. Based on direct observations, we propose the binding motif behind the stable phases and infer the dominant interactions that enable the existence of the rich spectrum of surface structures. Finally, we also show that the surface phase diagram will control the epitaxy beyond monolayer coverage. Multiplicity of stable surface structures, the corollary rich phase diagram, and the corresponding phase transitions present an interesting opportunity for low-dimensional molecular systems, particularly if some of the electronic properties of the bulk can be preserved or modified in the surface phases

A microfluidics and agent-based modeling framework for investigating spatial organization in bacterial colonies: the case of Pseudomonas Aeruginosa and H1-Type VI secretion interactions

The factors leading to changes in the organization of microbial assemblages at fine spatial scales are not well characterized or understood. However, they are expected to guide the succession of community development and function toward specific outcomes that could impact human health and the environment. In this study, we put forward a combined experimental and agent-based modeling framework and use it to interpret unique spatial organization patterns of H1-Type VI secretion system (T6SS) mutants of P. aeruginosa under spatial confinement. We find that key parameters, such as T6SS-mediated cell contact and lysis, spatial localization, relative species abundance, cell density and local concentrations of growth substrates and metabolites are influenced by spatial confinement. The model, written in the accessible programming language NetLogo, can be adapted to a variety of biological systems of interest and used to simulate experiments across a broad parameter space. It was implemented and run in a high-throughput mode by deploying it across multiple CPUs, with each simulation representing an individual well within a high-throughput microwell array experimental platform. The microfluidics and agent-based modeling framework we present in this paper provides an effective means by which to connect experimental studies in microbiology to model development. The work demonstrates progress in coupling experimental results to simulation while also highlighting potential sources of discrepancies between real-world experiments and idealized models