A physics-informed AI method for calculating melting points with uncertainty control and optimal sampling

We present an artificial intelligence (AI) method for automatically computing the melting point based on coexistence simulations in the NPT ensemble. Given the interatomic interaction model, the method makes decisions regarding the number of atoms and temperature at which to conduct simulations, and based on the collected data predicts the melting point along with the uncertainty, which can be systematically improved with more data. We demonstrate how incorporating physical models of the solid-liquid coexistence evolution enhances the AI method's accuracy and enables optimal decision-making to effectively reduce predictive uncertainty. To validate our approach, we compare our results with approximately 20 melting point calculations from the literature. Remarkably, we observe significant deviations in about one-third of the cases, underscoring the need for accurate and reliable AI-based algorithms for materials property calculations.Comment: 9 figure

Bayesian inference of composition-dependent phase diagrams

Phase diagrams serve as a highly informative tool for materials design, encapsulating information about the phases that a material can manifest under specific conditions. In this work, we develop a method in which Bayesian inference is employed to combine thermodynamic data from molecular dynamics (MD), melting point simulations, and phonon calculations, process these data, and yield a temperature-concentration phase diagram. The employed Bayesian framework yields us not only the free energies of different phases as functions of temperature and concentration but also the uncertainties of these free energies originating from statistical errors inherent to finite-length MD trajectories. Furthermore, it extrapolates the results of the finite-atom calculations to the infinite-atom limit and facilitates the choice of temperature, chemical potentials, and the number of atoms conducting the next simulation with which will be the most efficient in reducing the uncertainty of the phase diagram. The developed algorithm was successfully tested on two binary systems, Ge-Si and K-Na, in the full range of concentrations and temperatures

Impacts of urbanization on green infrastructure ecosystem services: the case study of post-soviet Moscow

Green infrastructure (GI) and ecosystem services (ES) improve the quality of urban life and aid city’s sustainable development. During the Soviet period, GI was an important part of spatial planning. Today, many post-Soviet cities face the problem of its deterioration due to the rapid economic growth and subsequent urban sprawl. Moscow is an exceptional case of a European city that both inherits features of central planning and integrates modern methods of greening. This paper aims to define the role of urban expansion in GI and ES transformation in Moscow during the last 25 years. Our method is based on combining spatial data on land-use from Open Street Map and Atlas of Urban Expansion, and reclassified Landsat images. The research revealed that the most important for ES provision land categories have gradually shrunk, especially in old Moscow, where the share of built-up area has increased by 18%. Considering the results, we stress that recent GI development mostly concerns small GI elements that do not provide regulating or supporting ES, while large GI massifs continue to deteriorate, thus resulting in a misbalance of urban ES provision.Les infrastructures vertes et les services écosystémiques améliorent la qualité de vie dans les villes et contribuent à leur développement durable. Sous le régime soviétique, les infrastructures vertes formaient une part considérable du développement territorial. Aujourd'hui, la plupart des villes post-soviétiques sont confrontées à leur détérioration en raison du développement économique fulgurant et de l'expansion urbaine qui s'ensuit. La ville de Moscou représente un cas particulier en Europe dans la mesure où elle doit combiner les caractéristiques d'un aménagement centralisé et la nécessité d'intégrer les méthodes modernes d'écologisation. Cet article tente de définir le rôle de l'expansion urbaine dans la transformation des infrastructures vertes et des services écosystémiques à Moscou au cours de ces 25 dernières années. Notre méthode se base sur la combinaison des données spatiales relatives à l'occupation du territoire à partir d'Open Street Map, de l'Atlas de l'expansion urbaine, ainsi que d'images Landsat reclassifiées.Notre recherche a révélé que l'utilisation des sols en faveur d'écosystèmes verts s'est peu à peu restreinte, en particulier dans l'ancien Moscou où la part des zones bâties s'est accrue de 18%.Au vu de ces résultats, nous soulignons le fait que le développement d'infrastructures vertes récent concerne principalement les petites entités où il n'existe ni régulation ni soutien aux services écosystémiques, alors que beaucoup d'infrastructures vertes continuent de se détériorer, ce qui crée un déséquilibre de la fourniture de services économiques urbains

Time- and dose dependent actions of cardiotonic steroids on transcriptome and intracellular content of Na+ and K+: a comparative analysis

Recent studies demonstrated that in addition to Na+,K+-ATPase inhibition cardiotonic steroids (CTSs) affect diverse intracellular signaling pathways. This study examines the relative impact of [Na+]i/[K+]i-mediated and -independent signaling in transcriptomic changes triggered by the endogenous CTSs ouabain and marinobufagenin (MBG) in human umbilical vein endothelial cells (HUVEC). We noted that prolongation of incubation increased the apparent affinity for ouabain estimated by the loss of [K+]i and gain of [Na+]i. Six hour exposure of HUVEC to 100 and 3,000 nM ouabain resulted in elevation of the [Na+]i/[K+]i ratio by ~15 and 80-fold and differential expression of 258 and 2185 transcripts, respectively. Neither [Na+]i/[K+]i ratio nor transcriptome were affected by 6-h incubation with 30 nM ouabain. The 96-h incubation with 3 nM ouabain or 30 nM MBG elevated the [Na+]i/[K+]i ratio by ~14 and 3-fold and led to differential expression of 880 and 484 transcripts, respectively. These parameters were not changed after 96-h incubation with 1 nM ouabain or 10 nM MBG. Thus, our results demonstrate that elevation of the [Na+]i/[K+]i ratio is an obligatory step for transcriptomic changes evoked by CTS in HUVEC. The molecular origin of upstream [Na+]i/[K+]i sensors involved in transcription regulation should be identified in forthcoming studies

Green infrastructure indicators for urban planning: applying the integrated approach for Russian largest cities

Modern approaches to urban planning assume the dualistic nature of urban green infrastructure (GI). On the one hand, green infrastructure is as an integrated network of natural and semi-natural areas, featuring a delivery of various benefits to humans. On the other hand, GI is multifunctional and provides the residents by complex of ecosystem services to be user-oriented. Most official reports and programs use common indicators that do not characterize distribution, dynamics or state of GI. In our research, we assessed the quality of GI in 15 largest Russian cities by using an integrated assessment of 13 indicators that make up three groups: the ones 1) characterizing general GI availability; 2) supporting a comfortable urban environment («recreational indicators»); and 3) forming a stable ecosystem («integrity indicators»). The cities were ranked by values of every indicator from 1 to 15 and then the results were summed and normalized to get a total mark (max. 100). To assess the development of GI elements of each group, we also ranked cities separately by values of different groups indicators. Thus, our study revealed that satisfactory marks for both recreational and integrity indicators have Ufa, Nizhny Novgorod, Kazan, Ekaterinburg, Perm and Voronezh. In contrast, Saint Petersburg, being a densely built-up city in an auspicious natural zone, got the worst result. According to the final assessment, the quality of green infrastructure in Krasnoyarsk, a large industrial city, and four cities from the steppe zone (Rostov-on-Don, Samara, Omsk, Novosibirsk) is also unsatisfactory. Our method does not cover all GI aspects (like vegetation health) and since it is based solely on remote sensing data and statistics data, there is definitely a room for improvement. However, this method, while being relatively quick and simple to accomplish, allows to assess not only general availability of GI, but its quality and distribution as well, which are essential for urban spatial planning

Green Infrastructure, Urbanization, and Ecosystem Services: The Main Challenges for Russia’s Largest Cities

Globally, the process of urbanization is transforming land use and, as a consequence, reducing the efficiency of ecosystem services (ESs), which ensure a healthy and comfortable urban environment. In cities, green infrastructure (GI) is a key source of urban ESs. Russia is a highly urbanized country: 70% of its population live in towns or cities. As cities continue to expand, they are swallowing unsealed lands that support ESs. In this paper, we present the results of an analysis of the current state and recent changes in urban GI in Russia’s 16 largest cities, including a biophysical evaluation of key urban ESs, using remote sensing data and freely available statistics. Our analysis identifies a weak correlation between GI area, ES volume, and favorable climate conditions as well as a stronger correlation between ESs and the increasing rate of urbanization. Considering Russia’s high level of urbanization, the key importance of ESs for the well-being of citizens, and ongoing reductions of urban GI, major revisions to urban planning policy are required. Indicators of urban biodiversity, GI, and ESs should be incorporated into decision-making processes. In particular, it is vital that the accounting and monitoring of GI and ESs are established in all of Russia’s larger cities

Green Infrastructure, Urbanization, and Ecosystem Services: The Main Challenges for Russia’s Largest Cities

Globally, the process of urbanization is transforming land use and, as a consequence, reducing the efficiency of ecosystem services (ESs), which ensure a healthy and comfortable urban environment. In cities, green infrastructure (GI) is a key source of urban ESs. Russia is a highly urbanized country: 70% of its population live in towns or cities. As cities continue to expand, they are swallowing unsealed lands that support ESs. In this paper, we present the results of an analysis of the current state and recent changes in urban GI in Russia’s 16 largest cities, including a biophysical evaluation of key urban ESs, using remote sensing data and freely available statistics. Our analysis identifies a weak correlation between GI area, ES volume, and favorable climate conditions as well as a stronger correlation between ESs and the increasing rate of urbanization. Considering Russia’s high level of urbanization, the key importance of ESs for the well-being of citizens, and ongoing reductions of urban GI, major revisions to urban planning policy are required. Indicators of urban biodiversity, GI, and ESs should be incorporated into decision-making processes. In particular, it is vital that the accounting and monitoring of GI and ESs are established in all of Russia’s larger cities

Transcriptomic changes in C2C12 myotubes triggered by electrical stimulation: Role of Ca2+i-mediated and Ca2+i-independent signaling and elevated [Na+]i/[K+]i ratio

Elevation of Ca2+i and AMP-activated protein kinase (AMPK) are considered as major signals triggering transcriptomic changes in exercising skeletal muscle. Electrical pulse stimulation (EPS) of cultured myotubes is widely employed as an in vitro model of muscle contraction. This study examines the impact of Ca2+i-mediated and Ca2+i-independent signaling in transcriptomic changes in EPS-treated C2C12 myotubes. Electrical pulse stimulation (40 V, 1 Hz, 10 ms, 2 h) resulted in [Ca2+]i oscillations, gain of Na+i, loss of K+i, and differential expression of 3215 transcripts. Additions of 10 μM nicardipine abolished [Ca2+]i oscillations but did not affect elevation of the [Na+]i/[K+]i ratio seen in EPS-treated myotubes. Differential expression of 1018 transcripts was preserved in the presence of nicardipine, indicating a Ca2+i-independent mechanism of excitation–transcription coupling. Among nicardipine-resistant transcripts, we noted 113 transcripts whose expression was also affected by partial Na+,K+-ATPase inhibition with 30 μM ouabain providing the same elevation of the [Na+]i/[K+]i ratio as in EPS-treated cells. Electrical pulse stimulation increased phosphorylation of CREB, ATF-1, Akt, ERK, and p38 MAPK without any impact on phosphorylation of acetyl-CoA carboxylase and Unc-51 like autophagy activating kinase-1, i.e. downstream markers of AMPK activation. Unlike CREB, ATF-1, and MAPKs, an increment in Akt phosphorylation was abolished by nicardipine. Thus, our results show that Ca2+i-independent signaling plays a key role in altered expression of 30% of studied genes in EPS-treated myotubes. This signaling pathway is at least partially triggered by dissipation of transmembrane gradients of monovalent cations

Transcriptomic changes in C2C12 myotubes triggered by electrical stimulation: Role of Ca2+i-mediated and Ca2+i-independent signaling and elevated [Na+]i/[K+]i ratio

Elevation of Ca2+i and AMP-activated protein kinase (AMPK) are considered as major signals triggering transcriptomic changes in exercising skeletal muscle. Electrical pulse stimulation (EPS) of cultured myotubes is widely employed as an in vitro model of muscle contraction. This study examines the impact of Ca2+i-mediated and Ca2+i-independent signaling in transcriptomic changes in EPS-treated C2C12 myotubes. Electrical pulse stimulation (40 V, 1 Hz, 10 ms, 2 h) resulted in [Ca2+]i oscillations, gain of Na+i, loss of K+i, and differential expression of 3215 transcripts. Additions of 10 μM nicardipine abolished [Ca2+]i oscillations but did not affect elevation of the [Na+]i/[K+]i ratio seen in EPS-treated myotubes. Differential expression of 1018 transcripts was preserved in the presence of nicardipine, indicating a Ca2+i-independent mechanism of excitation–transcription coupling. Among nicardipine-resistant transcripts, we noted 113 transcripts whose expression was also affected by partial Na+,K+-ATPase inhibition with 30 μM ouabain providing the same elevation of the [Na+]i/[K+]i ratio as in EPS-treated cells. Electrical pulse stimulation increased phosphorylation of CREB, ATF-1, Akt, ERK, and p38 MAPK without any impact on phosphorylation of acetyl-CoA carboxylase and Unc-51 like autophagy activating kinase-1, i.e. downstream markers of AMPK activation. Unlike CREB, ATF-1, and MAPKs, an increment in Akt phosphorylation was abolished by nicardipine. Thus, our results show that Ca2+i-independent signaling plays a key role in altered expression of 30% of studied genes in EPS-treated myotubes. This signaling pathway is at least partially triggered by dissipation of transmembrane gradients of monovalent cations

Effect of Reduction of Redox Modifications of Cys-Residues in the Na,K-ATPase α1-Subunit on Its Activity

Sodium-potassium adenosine triphosphatase (Na,K-ATPase) creates a gradient of sodium and potassium ions necessary for the viability of animal cells, and it is extremely sensitive to intracellular redox status. Earlier we found that regulatory glutathionylation determines Na,K-ATPase redox sensitivity but the role of basal glutathionylation and other redox modifications of cysteine residues is not clear. The purpose of this study was to detect oxidized, nitrosylated, or glutathionylated cysteine residues in Na,K-ATPase, evaluate the possibility of removing these modifications and assess their influence on the enzyme activity. To this aim, we have detected such modifications in the Na,K-ATPase α1-subunit purified from duck salt glands and tried to eliminate them by chemical reducing agents and the glutaredoxin1/glutathione reductase enzyme system. Detection of cysteine modifications was performed using mass spectrometry and Western blot analysis. We have found that purified Na,K-ATPase α1-subunit contains glutathionylated, nitrosylated, and oxidized cysteines. Chemical reducing agents partially eliminate these modifications that leads to the slight increase of the enzyme activity. Enzyme system glutaredoxin/glutathione reductase, unlike chemical reducing agents, produces significant increase of the enzyme activity. At the same time, the enzyme system deglutathionylates native Na,K-ATPase to a lesser degree than chemical reducing agents. This suggests that the enzymatic reducing system glutaredoxin/glutathione reductase specifically affects glutathionylation of the regulatory cysteine residues of Na,K-ATPase α1-subunit