Acceleration Schemes for Ab-Initio Molecular Dynamics and Electronic Structure Calculations

We study the convergence and the stability of fictitious dynamical methods for electrons. First, we show that a particular damped second-order dynamics has a much faster rate of convergence to the ground-state than first-order steepest descent algorithms while retaining their numerical cost per time step. Our damped dynamics has efficiency comparable to that of conjugate gradient methods in typical electronic minimization problems. Then, we analyse the factors that limit the size of the integration time step in approaches based on plane-wave expansions. The maximum allowed time step is dictated by the highest frequency components of the fictitious electronic dynamics. These can result either from the large wavevector components of the kinetic energy or from the small wavevector components of the Coulomb potential giving rise to the so called {\it charge sloshing} problem. We show how to eliminate large wavevector instabilities by adopting a preconditioning scheme that is implemented here for the first-time in the context of Car-Parrinello ab-initio molecular dynamics simulations of the ionic motion. We also show how to solve the charge-sloshing problem when this is present. We substantiate our theoretical analysis with numerical tests on a number of different silicon and carbon systems having both insulating and metallic character.Comment: RevTex, 9 figures available upon request, to appear in Phys. Rev.

Quantum dynamics of local phase differences between reservoirs of driven interacting bosons separated by simple aperture arrays

We present a derivation of the effective action for the relative phase of driven, aperture-coupled reservoirs of weakly-interacting condensed bosons from a (3+1)-D microscopic model with local U(1) gauge symmetry. We show that inclusion of local chemical potential and driving velocity fields as a gauge field allows derivation of the hydrodynamic equations of motion for the driven macroscopic phase differences across simple aperture arrays. For a single aperture, the current-phase equation for driven flow contains sinusoidal, linear, and current-bias contributions. We compute the renormalization group (RG) beta function of the periodic potential in the effective action for small tunneling amplitudes and use this to analyze the temperature dependence of the low-energy current-phase relation, with application to the transition from linear to sinusoidal current-phase behavior observed in experiments by Hoskinson et al. \cite{packard} for liquid $^{4}$He driven through nanoaperture arrays. Extension of the microscopic theory to a two-aperture array shows that interference between the microscopic tunneling contributions for individual apertures leads to an effective coupling between apertures which amplifies the Josephson oscillations in the array. The resulting multi-aperture current-phase equations are found to be equivalent to a set of equations for coupled pendula, with microscopically derived couplings.Comment: 16 pages, 5 figures v2: typos corrected, RG phase diagram correcte

First principles study of strain/electronic interplay in ZnO; Stress and temperature dependence of the piezoelectric constants

We present a first-principles study of the relationship between stress, temperature and electronic properties in piezoelectric ZnO. Our method is a plane wave pseudopotential implementation of density functional theory and density functional linear response within the local density approximation. We observe marked changes in the piezoelectric and dielectric constants when the material is distorted. This stress dependence is the result of strong, bond length dependent, hybridization between the O $2p$ and Zn $3d$ electrons. Our results indicate that fine tuning of the piezoelectric properties for specific device applications can be achieved by control of the ZnO lattice constant, for example by epitaxial growth on an appropriate substrate.Comment: accepted for publication in Phys. Rev.

First Principles Investigation of Ferromagnetism and Ferroelectricity in Bismuth Manganite

We present results of local spin density approximation (LSDA) pseudopotential calculations for the perovskite structure oxide, bismuth manganite (BiMnO3). The origin of the differences between bismuth manganite and other perovskite manganites is determined by first calculating total energies and band structures of the high symmetry cubic phase, then sequentially lowering the magnetic and structural symmetry. Our results indicate that covalent bonding between bismuth cations and oxygen anions stabilizes different magnetic and structural phases compared with the rare earth manganites. This is consistent with recent experimental results showing enhancement of charge ordering in doped bismuth manganite

Theoretical Aspects of Charge Ordering in Molecular Conductors

Theoretical studies on charge ordering phenomena in quarter-filled molecular (organic) conductors are reviewed. Extended Hubbard models including not only the on-site but also the inter-site Coulomb repulsion are constructed in a straightforward way from the crystal structures, which serve for individual study on each material as well as for their systematic understandings. In general the inter-site Coulomb interaction stabilizes Wigner crystal-type charge ordered states, where the charge localizes in an arranged manner avoiding each other, and can drive the system insulating. The variety in the lattice structures, represented by anisotropic networks in not only the electron hopping but also in the inter-site Coulomb repulsion, brings about diverse problems in low-dimensional strongly correlated systems. Competitions and/or co-existences between the charge ordered state and other states are discussed, such as metal, superconductor, and the dimer-type Mott insulating state which is another typical insulating state in molecular conductors. Interplay with magnetism, e.g., antiferromagnetic state and spin gapped state for example due to the spin-Peierls transition, is considered as well. Distinct situations are pointed out: influences of the coupling to the lattice degree of freedom and effects of geometrical frustration which exists in many molecular crystals. Some related topics, such as charge order in transition metal oxides and its role in new molecular conductors, are briefly remarked.Comment: 21 pages, 19 figures, to be published in J. Phys. Soc. Jpn. special issue on "Organic Conductors"; figs. 4 and 11 replaced with smaller sized fil

Population-based plasma lipidomics reveals developmental changes in metabolism and signatures of obesity risk : a mother-offspring cohort study

Publisher Copyright: © 2022, The Author(s).Background: Lipids play a vital role in health and disease, but changes to their circulating levels and the link with obesity remain poorly characterized in expecting mothers and their offspring in early childhood. Methods: LC-MS/MS-based quantitation of 480 lipid species was performed on 2491 plasma samples collected at 4 time points in the mother-offspring Asian cohort GUSTO (Growing Up in Singapore Towards healthy Outcomes). These 4 time points constituted samples collected from mothers at 26–28 weeks of gestation (n=752) and 4–5 years postpartum (n=650), and their offspring at birth (n=751) and 6 years of age (n=338). Linear regression models were used to identify the pregnancy and developmental age-specific variations in the plasma lipidomic profiles, and their association with obesity risk. An independent birth cohort (n=1935), the Barwon Infant Study (BIS), comprising mother-offspring dyads of Caucasian origin was used for validation. Results: Levels of 36% of the profiled lipids were significantly higher (absolute fold change > 1.5 and Padj < 0.05) in antenatal maternal circulation as compared to the postnatal phase, with phosphatidylethanolamine levels changing the most. Compared to antenatal maternal lipids, cord blood showed lower concentrations of most lipid species (79%) except lysophospholipids and acylcarnitines. Changes in lipid concentrations from birth to 6 years of age were much higher in magnitude (log2FC=−2.10 to 6.25) than the changes observed between a 6-year-old child and an adult (postnatal mother) (log2FC=−0.68 to 1.18). Associations of cord blood lipidomic profiles with birth weight displayed distinct trends compared to the lipidomic profiles associated with child BMI at 6 years. Comparison of the results between the child and adult BMI identified similarities in association with consistent trends (R2=0.75). However, large number of lipids were associated with BMI in adults (67%) compared to the children (29%). Pre-pregnancy BMI was specifically associated with decrease in the levels of phospholipids, sphingomyelin, and several triacylglycerol species in pregnancy. Conclusions: In summary, our study provides a detailed landscape of the in utero lipid environment provided by the gestating mother to the growing fetus, and the magnitude of changes in plasma lipidomic profiles from birth to early childhood. We identified the effects of adiposity on the circulating lipid levels in pregnant and non-pregnant women as well as offspring at birth and at 6 years of age. Additionally, the pediatric vs maternal overlap of the circulating lipid phenotype of obesity risk provides intergenerational insights and early opportunities to track and intervene the onset of metabolic adversities. Clinical trial registration: This birth cohort is a prospective observational study, which was registered on 1 July 2010 under the identifier NCT01174875.Peer reviewe

13C labeling experiments at metabolic nonstationary conditions: An exploratory study

<p>Abstract</p> <p>Background</p> <p>Stimulus Response Experiments to unravel the regulatory properties of metabolic networks are becoming more and more popular. However, their ability to determine enzyme kinetic parameters has proven to be limited with the presently available data. In metabolic flux analysis, the use of ¹³C labeled substrates together with isotopomer modeling solved the problem of underdetermined networks and increased the accuracy of flux estimations significantly.</p> <p>Results</p> <p>In this contribution, the idea of increasing the information content of the dynamic experiment by adding ¹³C labeling is analyzed. For this purpose a small example network is studied by simulation and statistical methods. Different scenarios regarding available measurements are analyzed and compared to a non-labeled reference experiment. Sensitivity analysis revealed a specific influence of the kinetic parameters on the labeling measurements. Statistical methods based on parameter sensitivities and different measurement models are applied to assess the information gain of the labeled stimulus response experiment.</p> <p>Conclusion</p> <p>It was found that the use of a (specifically) labeled substrate will significantly increase the parameter estimation accuracy. An overall information gain of about a factor of six is observed for the example network. The information gain is achieved from the specific influence of the kinetic parameters towards the labeling measurements. This also leads to a significant decrease in correlation of the kinetic parameters compared to an experiment without ¹³C-labeled substrate.</p

Reconnecting with nature for sustainability

Calls for humanity to ‘reconnect to nature’ have grown increasingly louder from both scholars and civil society. Yet, there is relatively little coherence about what reconnecting to nature means, why it should happen and how it can be achieved. We present a conceptual framework to organise existing literature and direct future research on human–nature connections. Five types of connections to nature are identified: material, experiential, cognitive, emotional, and philosophical. These various types have been presented as causes, consequences, or treatments of social and environmental problems. From this conceptual base, we discuss how reconnecting people with nature can function as a treatment for the global environmental crisis. Adopting a social–ecological systems perspective, we draw upon the emerging concept of ‘leverage points’—places in complex systems to intervene to generate change—and explore examples of how actions to reconnect people with nature can help transform society towards sustainability

A Novel Signaling Network Essential for Regulating Pseudomonas aeruginosa Biofilm Development

The important human pathogen Pseudomonas aeruginosa has been linked to numerous biofilm-related chronic infections. Here, we demonstrate that biofilm formation following the transition to the surface attached lifestyle is regulated by three previously undescribed two-component systems: BfiSR (PA4196-4197) harboring an RpoD-like domain, an OmpR-like BfmSR (PA4101-4102), and MifSR (PA5511-5512) belonging to the family of NtrC-like transcriptional regulators. These two-component systems become sequentially phosphorylated during biofilm formation. Inactivation of bfiS, bfmR, and mifR arrested biofilm formation at the transition to the irreversible attachment, maturation-1 and -2 stages, respectively, as indicated by analyses of biofilm architecture, and protein and phosphoprotein patterns. Moreover, discontinuation of bfiS, bfmR, and mifR expression in established biofilms resulted in the collapse of biofilms to an earlier developmental stage, indicating a requirement for these regulatory systems for the development and maintenance of normal biofilm architecture. Interestingly, inactivation did not affect planktonic growth, motility, polysaccharide production, or initial attachment. Further, we demonstrate the interdependency of this two-component systems network with GacS (PA0928), which was found to play a dual role in biofilm formation. This work describes a novel signal transduction network regulating committed biofilm developmental steps following attachment, in which phosphorelays and two sigma factor-dependent response regulators appear to be key components of the regulatory machinery that coordinates gene expression during P. aeruginosa biofilm development in response to environmental cues