Non-local correlation in Density Functional Theory

In this thesis we present several advancements in the field of non-local Density Functional Theory (DFT). After a short theoretical introduction, both on DFT and some of its extensions, we introduce the non-local functional formalism as proposed by Dion et al. [PRL 92, 246401 (2004)] discussing the most important implementations. Then three main contributions are presented, starting from the stress derivation, with an application on aminoacid crystal; a new non-local functional formulation, the rVV10, derived from the original Vydrov and Van Voorhis implementation [JCP 133, 244103 (2010)], and in conclusion the extension of Density Functional Perturbation Theory for non-local functional is introduced, showing the results obtained on graphite. In the appendix we also present for the first time Moka (MOdeling pacKage for Atomistic simulations) an open-source modeling GUI for atomistic simulations

AiiDA: Automated Interactive Infrastructure and Database for Computational Science

Computational science has seen in the last decades a spectacular rise in the scope, breadth, and depth of its efforts. Notwithstanding this prevalence and impact, it is often still performed using the renaissance model of individual artisans gathered in a workshop, under the guidance of an established practitioner. Great benefits could follow instead from adopting concepts and tools coming from computer science to manage, preserve, and share these computational efforts. We illustrate here our paradigm sustaining such vision, based around the four pillars of Automation, Data, Environment, and Sharing. We then discuss its implementation in the open-source AiiDA platform (http://www.aiida.net), that has been tuned first to the demands of computational materials science. AiiDA's design is based on directed acyclic graphs to track the provenance of data and calculations, and ensure preservation and searchability. Remote computational resources are managed transparently, and automation is coupled with data storage to ensure reproducibility. Last, complex sequences of calculations can be encoded into scientific workflows. We believe that AiiDA's design and its sharing capabilities will encourage the creation of social ecosystems to disseminate codes, data, and scientific workflows.Comment: 30 pages, 7 figure

Metabolic profiling reveals reprogramming of lipid metabolic pathways in treatment of polycystic ovary syndrome with 3-iodothyronamine

Complex diseases such as polycystic ovary syndrome (PCOS) are associated with intricate pathophysiological, hormonal, and metabolic feedbacks that make their early diagnosis challenging, thus increasing the prevalence risks for obesity, cardiovascular, and fatty liver diseases. To explore the crosstalk between endocrine and lipid metabolic pathways, we administered 3-iodothyronamine (T1AM), a natural analog of thyroid hormone, in a mouse model of PCOS and analyzed plasma and tissue extracts using multidisciplinary omics and biochemical approaches. T1AM administration induces a profound tissue-specific antilipogenic effect in liver and muscle by lowering gene expression of key regulators of lipid metabolism, PTP1B and PLIN2, significantly increasing metabolites (glucogenic, amino acids, carnitine, and citrate) levels, while enhancing protection against oxidative stress. In contrast, T1AM has an opposing effect on the regulation of estrogenic pathways in the ovary by upregulating STAR, CYP11A1, and CYP17A1. Biochemical measurements provide further evidence of significant reduction in liver cholesterol and triglycerides in post-T1AM treatment. Our results shed light onto tissue-specific metabolic vs. hormonal pathway interactions, thus illuminating the intricacies within the pathophysiology of PCOS. This study opens up new avenues to design drugs for targeted therapeutics to improve quality of life in complex metabolic diseases

Thermodynamic stability of alkali metal/zinc double-cation borohydrides at low temperatures

We study the thermodynamic stability at low temperatures of a series of alkali metal/zinc double-cation borohydrides, including LiZn(BH$_4$)$_3$, LiZn$_2$(BH$_4$)$_5$, NaZn(BH$_4$)$_3$, NaZn$_2$(BH$_4$)$_5$, KZn(BH$_4$)$_3$, and KZn$_2$(BH$_4$)$_5$. While LiZn$_2$(BH$_4$)$_5$, NaZn(BH$_4$)$_3$, NaZn$_2$(BH$_4$)$_5$ and KZn(BH$_4$)$_3$ were recently synthesized, LiZn(BH$_4$)$_3$ and KZn$_2$(BH$_4$)$_5$ are hypothetical compounds. Using the minima-hopping method, we discover two new lowest-energy structures for NaZn(BH$_4$)$_3$ and KZn$_2$(BH$_4$)$_5$ which belong to the $C2/c$ and $P2$ space groups, respectively. These structures are predicted to be both thermodynamically stable and dynamically stable, implying that their existence may be possible. On the other hand, the lowest-energy $P1$ structure of LiZn(BH$_4$)$_3$ is predicted to be unstable, suggesting a possible reason elucidating why this compound has not been experimentally identified. In exploring the low-energy structures of these compounds, we find that their energetic ordering is sensitive to the inclusion of the van der Waals interactions. We also find that a proper treatment of these interactions, e.g., as given by a non-local density functional such as vdW-DF2, is necessary to address the stability of the low-energy structures of these compounds.Comment: Final versio

A PHABULOSA-Controlled Genetic Pathway Regulates Ground Tissue Patterning in the Arabidopsis Root

In both animals and plants, development involves anatomical modifications. In the root of Arabidopsis thaliana, maturation of the ground tissue (GT)—a tissue comprising all cells between epidermal and vascular ones—is a paradigmatic example of these modifications, as it generates an additional tissue layer, the middle cortex (MC).1, 2, 3, 4 In early post-embryonic phases, the Arabidopsis root GT is composed of one layer of endodermis and one of cortex. A second cortex layer, the MC, is generated by asymmetric cell divisions in about 80% of Arabidopsis primary roots, in a time window spanning from 7 to 14 days post-germination (dpg). The cell cycle regulator CYCLIN D6;1 (CYCD6;1) plays a central role in this process, as its accumulation in the endodermis triggers the formation of MC.5 The phytohormone gibberellin (GA) is a key regulator of the timing of MC formation, as alterations in its signaling and homeostasis result in precocious endodermal asymmetric cell divisions.3,6,7 However, little is known on how GAs are regulated during GT maturation. Here, we show that the HOMEODOMAIN LEUCINE ZIPPER III (HD-ZIPIII) transcription factor PHABULOSA (PHB) is a master regulator of MC formation, controlling the accumulation of CYCD6;1 in the endodermis in a cell non-autonomous manner. We show that PHB activates the GA catabolic gene GIBBERELLIN 2 OXIDASE 2 (GA2ox2) in the vascular tissue, thus regulating the stability of the DELLA protein GIBBERELLIN INSENSITIVE (GAI)—a GA signaling repressor—in the root and, hence, CYCD6;1 expression in the endodermis

New Insights into the Potential Roles of 3-Iodothyronamine (T1AM) and Newly Developed Thyronamine-Like TAAR1 Agonists in Neuroprotection

3-Iodothyronamine (T1AM) is an endogenous high-affinity ligand of the trace amine-associated receptor 1 (TAAR1), detected in mammals in many organs, including the brain. Recent evidence indicates that pharmacological TAAR1 activation may offer a novel therapeutic option for the treatment of a wide range of neuropsychiatric and metabolic disorders. To assess potential neuroprotection by TAAR1 agonists, in the present work, we initially investigated whether T1AM and its corresponding 3-methylbiaryl-methane analog SG-2 can improve learning and memory when systemically administered to mice at submicromolar doses, and whether these effects are modified under conditions of MAO inhibition by clorgyline. Our results revealed that when i.p. injected to mice, both T1AM and SG-2 produced memory-enhancing and hyperalgesic effects, while increasing ERK1/2 phosphorylation and expression of transcription factor c-fos. Notably, both compounds appeared to rely on the action of ubiquitous enzymes MAO to produce the corresponding oxidative metabolites that were then able to activate the histaminergic system. Since autophagy is key for neuronal plasticity, in a second line of experiments we explored whether T1AM and synthetic TAAR1 agonists SG1 and SG2 were able to induce autophagy in human glioblastoma cell lines (U-87MG). After treatment of U-87MG cells with 1 μM T1AM, SG-1, SG-2 transmission electron microscopy (TEM) and immunofluorescence (IF) showed a significant time-dependent increase of autophagy vacuoles and microtubule-associated protein 1 light chain 3 (LC3). Consistently, Western blot analysis revealed a significant increase of the LC3II/LC3I ratio, with T1AM and SG-1 being the most effective agents. A decreased level of the p62 protein was also observed after treatment with T1AM and SG-1, which confirms the efficacy of these compounds as autophagy inducers in U-87MG cells. In the process to dissect which pathway induces ATG, the effects of these compounds were evaluated on the PI3K-AKT-mTOR pathway. We found that 1 μM T1AM, SG-1 and SG-2 decreased pAKT/AKT ratio at 0.5 and 4 h after treatment, suggesting that autophagy is induced by inhibiting mTOR phosphorylation by PI3K-AKT-mTOR pathway. In conclusion, our study shows that T1AM and thyronamine-like derivatives SG-1 and SG-2 might represent valuable tools to therapeutically intervene with neurological disorder

Metabolic reprogramming by 3-Iodothyronamine (T1AM): a new perspective to reverse obesity through co-regulation of sirtuin 4 and 6 expression

Obesity is a complex disease associated with environmental and genetic factors. 3-Iodothyronamine (T1AM) has revealed great potential as an effective weight loss drug. We used metabolomics and associated transcriptional gene and protein expression analysis to investigate the tissue specific metabolic reprogramming effects of subchronic T1AM treatment at two pharmacological daily doses (10 and 25 mg/kg) on targeted metabolic pathways. Multi-analytical results indicated that T1AM at 25 mg/kg can act as a novel master regulator of both glucose and lipid metabolism in mice through sirtuin-mediated pathways. In liver, we observed an increased gene and protein expression of Sirt6 (a master gene regulator of glucose) and Gck (glucose kinase) and a decreased expression of Sirt4 (a negative regulator of fatty acids oxidation (FAO)), whereas in white adipose tissue only Sirt6 was increased. Metabolomics analysis supported physiological changes at both doses with most increases in FAO, glycolysis indicators and the mitochondrial substrate, at the highest dose of T1AM. Together our results suggest that T1AM acts through sirtuin-mediated pathways to metabolically reprogram fatty acid and glucose metabolism possibly through small molecules signaling. Our novel mechanistic findings indicate that T1AM has a great potential as a drug for the treatment of obesity and possibly diabetes

Inhibition of Polycomb Repressive Complex2 activity reduces trimethylation of H3K27 and affects development in Arabidopsis seedlings

Background: Polycomb repressive complex 2 (PRC2) is an epigenetic transcriptional repression system, whose catalytic subunit (ENHANCER OF ZESTE HOMOLOG 2, EZH2 in animals) is responsible for trimethylating histone H3 at lysine 27 (H3K27me3). In mammals, gain-of-function mutations as well as overexpression of EZH2 have been associated with several tumors, therefore making this subunit a suitable target for the development of selective inhibitors. Indeed, highly specific small-molecule inhibitors of EZH2 have been reported. In plants, mutations in some PRC2 components lead to embryonic lethality, but no trial with any inhibitor has ever been reported. Results: We show here that the 1,5-bis (3-bromo-4-methoxyphenyl)penta-1,4-dien-3-one compound (RDS 3434), previously reported as an EZH2 inhibitor in human leukemia cells, is active on the Arabidopsis catalytic subunit of PRC2, since treatment with the drug reduces the total amount of H3K27me3 in a dose-dependent fashion. Consistently, we show that the expression level of two PRC2 targets is significantly increased following treatment with the RDS 3434 compound. Finally, we show that impairment of H3K27 trimethylation in Arabidopsis seeds and seedlings affects both seed germination and root growth. Conclusions: Our results provide a useful tool for the plant community in investigating how PRC2 affects transcriptional control in plant development

Hit-to-Lead Optimization of Mouse Trace Amine Associated Receptor 1 (mTAAR1) Agonists with a Diphenylmethane-Scaffold: Design, Synthesis, and Biological Study

The trace amine-associated receptor 1 (TAAR1) is a G-protein-coupled receptors (GPCR) potently activated by a variety of molecules besides trace amines (TAs), including thyroid hormone-derivatives like 3-iodothyronamine (T1AM), catechol-O-methyltransferase products like 3-methoxytyramine, and amphetamine-related compounds. Accordingly, TAAR1 is considered a promising target for medicinal development. To gain more insights into TAAR1 physiological functions and validation of its therapeutic potential we recently developed a new class of thyronamine-like derivatives. Among them compound SG2 showed high affinity and potent agonist activity at mouse TAAR1. In the present work we describe design, the synthesis and SAR study of a new series of compounds (1-16) obtained by introducing specific structural changes at key points of our lead-compound SG2 skeleton. Five of the newly synthesized compounds displayed mTAAR1 agonist activity higher than both SG2 and T1AM. Selected diphenylmethane analogs, namely 1 and 2, showed potent functional activity in in vitro and in vivo models

ATLASPIX3 Modules for Experiments at Electron-Positron Colliders

High-voltage CMOS detectors are being developed for application in High-Energy Physics. ATLASPIX3 is a full-reticle size monolithic pixel detector, consisting of 49000 pixels of dimension 50×150 μm$^2$. It has been realized in in TSI 180 nm HVCMOS technology. In view of applications at future electron-positron colliders, multi-chip-modules are built. The module design and its characterization by electrical test and radiation sources will be illustrated, including characterization of shunt regulators for serial chain powering. Lightweight long structure to support and to cool multiple-module chain are also being realized. The multi-chip-modules performance shows no degradation with respect to single-chip devices and the level of integration achieved is suitable for tracking at future e+e- accelerators