Physically Based Modeling
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Lidská chůze je dynamický rys, který je složitý a unikátní pro každou osobu. Její analýze je věnováno stále velké úsilí, neboť porozumnění faktorům, které ji ovlivňují, a jejich vzájemným závislostem, napomáhá k diagnóze i léčení abnormalit chůze. Nalezení příčin postižení a funkčních omezení může vést k optimalizaci rehabilitací či simulaci výsledků chirurgického zákroku. Tento článek se zabývá právě přehledem přístupů k modelování chůze. Obsahuje klasifikaci modelů dle různých kritérií a zaměřuje se jak na širokou škálu minimalistických modelů založených na jednoduchém fyzikálním modelu obráceného kyvadla, tak i komplexní analytické modely, reflektujících skutečnou stavbu dolních končetin.
Human gait is dynamic feature, which is unique, complex and difficult to mimic. Understanding of factors that affect it and their mutual dependencies, helps to diagnose and treat abnormalities of gait. Defining the causes of impairment and functional limitation can lead to optimization of rehabilitation treatment and simulation of surgical intervention. Therefore, gait modeling is devoted great effort. This article deals with an overview of approaches to gait modeling. It contains classes accroding to various criteria. Further, review of minimalistic physics-based models and complex analytical models is included.
During pregnancy, oxygen diffuses from maternal to fetal blood through villous trees in the placenta. In this paper, we simulate blood flow and oxygen transfer in feto-placental capillaries by converting three-dimensional representations of villous and capillary surfaces, reconstructed from confocal laser scanning microscopy, to finite-element meshes, and calculating values of vascular flow resistance and total oxygen transfer. The relationship between the total oxygen transfer rate and the pressure drop through the capillary is shown to be captured across a wide range of pressure drops by physical scaling laws and an upper bound on the oxygen transfer rate. A regression equation is introduced that can be used to estimate the oxygen transfer in a capillary using the vascular resistance. Two techniques for quantifying the effects of statistical variability, experimental uncertainty and pathological placental structure on the calculated properties are then introduced. First, scaling arguments are used to quantify the sensitivity of the model to uncertainties in the geometry and the parameters. Second, the effects of localized dilations in fetal capillaries are investigated using an idealized axisymmetric model, to quantify the possible effect of pathological placental structure on oxygen transfer. The model predicts how, for a fixed pressure drop through a capillary, oxygen transfer is maximized by an optimal width of the dilation. The results could explain the prevalence of fetal hypoxia in cases of delayed villous maturation, a pathology characterized by a lack of the vasculo-syncytial membranes often seen in conjunction with localized capillary dilations.
- MeSH
- biologické modely * MeSH
- choriové klky embryologie MeSH
- difuze MeSH
- kapiláry metabolismus fyziologie MeSH
- krevní oběh * MeSH
- kyslík metabolismus MeSH
- lidé MeSH
- placenta krevní zásobení MeSH
- plod krevní zásobení MeSH
- těhotenství MeSH
- zobrazování trojrozměrné * MeSH
- Check Tag
- lidé MeSH
- těhotenství MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
Accurate estimates of intermolecular interaction energy, ΔE, are crucial for modeling the properties of organic electronic materials and many other systems. For a diverse set of 50 dimers comprising up to 50 atoms (Set50-50, with 7 of its members being models of single-stacking junctions), benchmark ΔE data were compiled. They were obtained by the focal-point strategy, which involves computations using the canonical variant of the coupled cluster theory with singles, doubles, and perturbative triples [CCSD(T)] performed while applying a large basis set, along with extrapolations of the respective energy components to the complete basis set (CBS) limit. The resulting ΔE data were used to gauge the performance for the Set50-50 of several density-functional theory (DFT)-based approaches, and of one of the localized variants of the CCSD(T) method. This evaluation revealed that (1) the proposed "silver standard" approach, which employs the localized CCSD(T) method and CBS extrapolations, can be expected to provide accuracy better than two kJ/mol for absolute values of ΔE, and (2) from among the DFT techniques, computationally by far the cheapest approach (termed "ωB97X-3c/vDZP" by its authors) performed remarkably well. These findings are directly applicable in cost-effective yet reliable searches of the potential energy surfaces of noncovalent complexes.
- MeSH
- benchmarking * MeSH
- dimerizace MeSH
- elektronika * MeSH
- fyzikální jevy MeSH
- polymery MeSH
- Publikační typ
- časopisecké články MeSH
On the basis of new examination of ancient DNA and craniometric analyses, Neolithic dispersal in Central Europe has been recently explained as reflecting colonization or at least a major influx of near eastern farmers. Given the fact that Neolithic dispersal in Central Europe was very rapid and extended into a large area, colonization would have to be associated with high population growth and fertility rates of an expanding Neolithic population. We built three demographic models to test whether the growth and fertility rates of Neolithic farmers were high enough to allow them to colonize Central Europe without admixture with foragers. The principle of the models is based on stochastic population projections. Our results demonstrate that colonization is an unlikely explanation for the Neolithic dispersal in Central Europe, as the majority of fertility and growth rate estimates obtained in all three models are higher than levels expected in the early Neolithic population. On the basis of our models, we derived that colonization would be possible only if (1) more than 37% of women survived to mean age at childbearing, (2) Neolithic expansion in Central Europe lasted more than 150 years, and (3) the population of farmers grew in the entire settled area. These settings, however, represent very favorable demographic conditions that seem unlikely given current archaeological and demographic evidence. Therefore, our results support the view that Neolithic dispersal in Central Europe involved admixture of expanding farmers with local foragers. We estimate that the admixture contribution from foragers may have been between 55% and 72%.
- MeSH
- analýza přežití MeSH
- antropologie fyzická MeSH
- biologické modely MeSH
- dějiny starověku MeSH
- DNA analýza genetika MeSH
- emigrace a imigrace MeSH
- kefalometrie MeSH
- lidé MeSH
- parita MeSH
- populační dynamika dějiny MeSH
- regresní analýza MeSH
- stochastické procesy MeSH
- zemědělství MeSH
- Check Tag
- dějiny starověku MeSH
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- historické články MeSH
- Geografické názvy
- Evropa MeSH
Lipid-mediated delivery of active pharmaceutical ingredients (API) opened new possibilities in advanced therapies. By encapsulating an API into a lipid nanocarrier (LNC), one can safely deliver APIs not soluble in water, those with otherwise strong adverse effects, or very fragile ones such as nucleic acids. However, for the rational design of LNCs, a detailed understanding of the composition-structure-function relationships is missing. This review presents currently available computational methods for LNC investigation, screening, and design. The state-of-the-art physics-based approaches are described, with the focus on molecular dynamics simulations in all-atom and coarse-grained resolution. Their strengths and weaknesses are discussed, highlighting the aspects necessary for obtaining reliable results in the simulations. Furthermore, a machine learning, i.e., data-based learning, approach to the design of lipid-mediated API delivery is introduced. The data produced by the experimental and theoretical approaches provide valuable insights. Processing these data can help optimize the design of LNCs for better performance. In the final section of this Review, state-of-the-art of computer simulations of LNCs are reviewed, specifically addressing the compatibility of experimental and computational insights.
- MeSH
- léčivé přípravky chemie MeSH
- lékové transportní systémy metody MeSH
- lidé MeSH
- lipidy * chemie MeSH
- nanočástice chemie MeSH
- nosiče léků chemie MeSH
- počítačová simulace MeSH
- simulace molekulární dynamiky * MeSH
- strojové učení MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
The human dopamine, norepinephrine, and serotonin transporters (hDAT, hNET, and hSERT) are carriers of neurotransmitters and targets for many drugs. Pioneering works in the past three years to elucidate experimental models of the Drosophila dDAT and human hSERT structures will rapidly impact the field of neuroscience. Here, we evaluated automated homology-based human models of these transporters, employing systematic physics-based, knowledge-based, and empirical-based check. Modeling guidelines were conveyed with attention to the central binding site (S1), secondary binding site (S2), and the extracellular loops EL2 and EL4. Application of new experimental models (dDAT and hSERT) will improve the accuracy of homology models, previously utilizing prokaryotic leucine transporter (LeuT) structure, and provide better predictions of ligand interactions, which is required for understanding of cellular mechanisms and for development of novel therapeutics.
- MeSH
- acetyltransferasy genetika metabolismus MeSH
- Drosophila MeSH
- konformace proteinů MeSH
- lidé MeSH
- membránové transportní proteiny pro serotonin genetika metabolismus MeSH
- molekulární modely * MeSH
- proteiny Drosophily genetika metabolismus MeSH
- proteiny přenášející dopamin přes plazmatickou membránu genetika metabolismus MeSH
- proteiny přenášející noradrenalin přes plazmatickou membránu genetika metabolismus MeSH
- rozpoznávání automatizované MeSH
- sekvenční homologie aminokyselin * MeSH
- vazebná místa MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- hodnotící studie MeSH
OBJECTIVES: The aim was to assess the association between physical activity and screen-based activities in adolescents and selected school factors and urbanization and whether these associations were modified by degree of urbanization. METHODS: We obtained data regarding the fifth-ninth grade students from 130 schools in 2014 via the Health Behaviour in School-aged Children cross-sectional study in Slovakia (n = 9743, mean age = 13.5, 50.3% boys). We explored the associations using multilevel logistic regression. RESULTS: We found significant associations between physical activity and the accessibility of an area for skating/tennis court [odds ratio (OR) = 1.20 and 95% confidence interval (CI) 1.01-1.42], and between physical activity and active breaks (OR = 0.83 and 95% CI 0.69-0.99). The rates of screen-based activities were higher in small towns (OR = 1.63, 95% CI 1.29-2.06), towns (OR = 1.30, 95% CI 1.08-1.57), and cities (OR = 1.40, 95% CI 1.04-1.87) than in villages. CONCLUSIONS: School environment and degree of urbanization are associated with adolescents' physical activity and screen-based activities. This holds positively for access to an area for skating/tennis court and negatively for active breaks regarding physical activity and for living in villages regarding less use of screens.
- MeSH
- cvičení * MeSH
- dítě MeSH
- lidé MeSH
- logistické modely MeSH
- mladiství MeSH
- odds ratio MeSH
- průřezové studie MeSH
- sedavý životní styl * MeSH
- školy statistika a číselné údaje MeSH
- urbanizace * MeSH
- velkoměsta MeSH
- veřejná zařízení MeSH
- životní prostředí MeSH
- Check Tag
- dítě MeSH
- lidé MeSH
- mladiství MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Slovenská republika epidemiologie MeSH
- velkoměsta MeSH
BACKGROUND: Physically based tier-II models may serve as possible alternatives to expensive field and laboratory leaching experiments required for pesticide approval and registration. The objective of this study was to predict pesticide fate and transport at five different sites in Hawaii using data from an earlier field leaching experiment and a one-dimensional tier-II model. As the predicted concentration profiles of pesticides did not provide close agreement with data, inverse modeling was used to obtain adequate reactive transport parameters. The estimated transport parameters of pesticides were also utilized in a tier-I model, which is currently used by the state authorities to evaluate the relative leaching potential. RESULTS: Water flow in soil profiles was simulated by the tier-II model with acceptable accuracy at all experimental sites. The observed concentration profiles and center of mass depths predicted by the tier-II simulations based on optimized transport parameters provided better agreements than did the non-optimized parameters. With optimized parameters, the tier-I model also delivered results consistent with observed pesticide center of mass depths. CONCLUSION: Tier-II numerical modeling helped to identify relevant transport processes in field leaching of pesticides. The process-based modeling of water flow and pesticide transport, coupled with the inverse procedure, can contribute significantly to the evaluation of chemical leaching in Hawaii soils.
- MeSH
- chemické látky znečišťující vodu analýza chemie MeSH
- chemické modely MeSH
- látky znečišťující půdu analýza chemie MeSH
- monitorování životního prostředí metody MeSH
- pesticidy analýza chemie MeSH
- počítačová simulace MeSH
- pohyb vody MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Havajské ostrovy MeSH
Binary and ternary amorphous transition metal (TM) nitrides and oxides are of great interest because of their suitability for diverse applications ranging from high-temperature machining to the production of optical filters or electrochromic devices. However, understanding of bonding in, and electronic structure of, these materials represents a challenge mainly due to the d electrons in their valence band. In the present work, we report ab initio calculations of the structure and electronic structure of ZrSiN materials. We focus on the methodology needed for the interpretation and automatic analysis of the bonding structure, on the effect of the length of the calculation on the convergence of individual quantities of interest and on the electronic structure of materials. We show that the traditional form of the Wannier function center-based algorithm fails due to the presence of d electrons in the valence band. We propose a modified algorithm, which allows one to analyze bonding structure in TM-based systems. We observe an appearance of valence p states of TM atoms in the electronic spectra of such systems (not only ZrSiN but also NbO(x) and WAuO), and examine the importance of the p states for the character of the bonding as well as for facilitating the bonding analysis. The results show both the physical phenomena and the computational methodology valid for a wide range of TM-based ceramics.
