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# Systems Dynamics

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#1
REVIEW
Alessandro Solimeno, Joan García
The search for environmentally neutral alternative fuels had revived the interest for microalgae-bacteria wastewater treatment systems. The potential achieving of bioproducts from microalgae biomass has also greatly contributed. The reactions that occur in these systems are complex, and the degree of scientific knowledge is still scarce compared to that of conventional bacteria wastewater treatments. Mathematical models offer a great opportunity to study the simultaneous effect of the multiple factors affecting microalgae and bacteria, thus allowing for the prediction of final biomass production, and contributing to the system design optimization in terms of operation and control...
July 17, 2017: Science of the Total Environment
#2
Tahir Maqbool, Jinwoo Cho, Jin Hur
In this study, the spectroscopic indices of soluble microbial products (SMP) were explored using absorption and fluorescence spectroscopy to identify different distinctive biomass growth phases (i.e., exponential phase, pseudo-endogenous phase, and endogenous phase) and to describe the microbial activity of activated sludge in a batch type bioreactor under prolonged starvation. The optical descriptors, including UV absorption at 254 nm (UVA254), spectral slope, absorbance slope index (ASI), biological index (BIX), humification index (HIX), and the ratio of tryptophan-like to humic-like components (C1/C2), were examined to describe the dynamic changes in SMP...
July 15, 2017: Water Research
#3
Quanchao Zeng, Shaoshan An, Yang Liu
Natural succession is an important process in terrestrial system, playing an important role in enhancing soil quality and plant diversity. Soil bacteria is the linkage between soil and plant, has an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems, driving the decomposition of soil organic matter and plant litter. However, the role of soil bacteria in the secondary succession has not been well understood, particularly in the degraded soil of Loess Plateau...
July 18, 2017: Science of the Total Environment
#4
REVIEW
Carmen Sánchez-Cañizares, Beatriz Jorrín, Philip S Poole, Andrzej Tkacz
The holobiont is composed by the plant and its microbiome. In a similar way to ecological systems of higher organisms, the holobiont shows interdependent and complex dynamics [1,2]. While plants originate from seeds, the microbiome has a multitude of sources. The assemblage of these communities depends on the interaction between the emerging seedling and its surrounding environment, with soil being the main source. These microbial communities are controlled by the plant through different strategies, such as the specific profile of root exudates and its immune system...
July 18, 2017: Current Opinion in Microbiology
#5
Dolores Jiménez-Rubio, Pilar García-Gómez
While many countries worldwide are shifting responsibilities for their health systems to local levels of government, there is to date insufficient evidence about the potential impact of these policy reforms. We estimate the impact of decentralization of the health services on infant and neonatal mortality using a natural experiment: the devolution of health care decision making powers to Spanish regions. The devolution was implemented gradually and asymmetrically over a twenty-year period (1981-2002). The order in which the regions were decentralized was driven by political factors and hence can be considered exogenous to health outcomes...
July 1, 2017: Social Science & Medicine
#6
Yunduan Cui, Takamitsu Matsubara, Kenji Sugimoto
We propose a new value function approach for model-free reinforcement learning in Markov decision processes involving high dimensional states that addresses the issues of brittleness and intractable computational complexity, therefore rendering the value function approach based reinforcement learning algorithms applicable to high dimensional systems. Our new algorithm, Kernel Dynamic Policy Programming (KDPP) smoothly updates the value function in accordance to the Kullback-Leibler divergence between current and updated policies...
June 29, 2017: Neural Networks: the Official Journal of the International Neural Network Society
#7
Jonas Elm, Monica Passananti, Theo Kurtén, Hanna Vehkamaki
Recent experimental evidence suggests that diamines can enhance atmospheric new particle formation more efficiently compared to monoamines such as dimethylamine. Here we investigate the molecular interactions between sulfuric acid (sa) and the di- amine putrescine (put) using computational methods. The molecular structure of up to four sulfuric acid molecules and up to four putrescine molecules were obtained at the ωB97X-D/6-31++G(d,p) level of theory. We utilized a domain local pair natural orbital coupled cluster method - DLPNO-CCSD(T)/aug-cc-pVTZ - to obtain highly accurate binding energies of the clusters...
July 21, 2017: Journal of Physical Chemistry. A
#8
Owing to properties of magnetic nanoparticles and elegant three-dimensional macromolecule architectural features, dendrimeric structures have been investigated as nanoscale drug delivery systems. In this paper, a novel magnetic nanocarrier, generation two (G2) triazine dendrimer modified Fe3O4@SiO2 magnetic nanoparticles (MNP-G2), was designed, fabricated and characterized by Fourier transform infrared (FT-IR), thermal gravimetric analysis (TGA), vibrating sample magnetometer (VSM), field emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM) and dynamic light scattering (DLS)...
July 21, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
#9
Warren D Anderson, Danielle DeCicco, James S Schwaber, Rajanikanth Vadigepalli
Multiple physiological systems interact throughout the development of a complex disease. Knowledge of the dynamics and connectivity of interactions across physiological systems could facilitate the prevention or mitigation of organ damage underlying complex diseases, many of which are currently refractory to available therapeutics (e.g., hypertension). We studied the regulatory interactions operating within and across organs throughout disease development by integrating in vivo analysis of gene expression dynamics with a reverse engineering approach to infer data-driven dynamic network models of multi-organ gene regulatory influences...
July 2017: PLoS Computational Biology
#10
Hiroshi Imada, Kuniyuki Miwa, Miyabi Imai-Imada, Shota Kawahara, Kensuke Kimura, Yousoo Kim
We investigate the near-field interaction between an isolated free-base phthalocyanine molecule and a plasmon localized in the gap between an NaCl-covered Ag(111) surface and the tip apex of a scanning tunneling microscope. When the tip is located in the close proximity of the molecule, asymmetric dips emerge in the broad luminescence spectrum of the plasmon generated by the tunneling current. The origin of the dips is explained by energy transfer between the plasmon and molecular excitons and a quantum mechanical interference effect, where molecular vibrations provide additional degrees of freedom in the dynamic process...
July 7, 2017: Physical Review Letters
#11
Shreya Vardhan, Giuseppe De Tomasi, Markus Heyl, Eric J Heller, Frank Pollmann
We study the effects of local perturbations on the dynamics of disordered fermionic systems in order to characterize time irreversibility. We focus on three different systems: the noninteracting Anderson and Aubry-André-Harper (AAH) models and the interacting spinless disordered t-V chain. First, we consider the effect on the full many-body wave functions by measuring the Loschmidt echo (LE). We show that in the extended or ergodic phase the LE decays exponentially fast with time, while in the localized phase the decay is algebraic...
July 7, 2017: Physical Review Letters
#12
Michele Ceotto, Giovanni Di Liberto, Riccardo Conte
A new semiclassical "divide-and-conquer" method is presented with the aim of demonstrating that quantum dynamics simulations of high dimensional molecular systems are doable. The method is first tested by calculating the quantum vibrational power spectra of water, methane, and benzene-three molecules of increasing dimensionality for which benchmark quantum results are available-and then applied to C_{60}, a system characterized by 174 vibrational degrees of freedom. Results show that the approach can accurately account for quantum anharmonicities, purely quantum features like overtones, and the removal of degeneracy when the molecular symmetry is broken...
July 7, 2017: Physical Review Letters
#13
Wen Wei Ho, Soonwon Choi, Mikhail D Lukin, Dmitry A Abanin
We analyze the quantum dynamics of periodically driven, disordered systems in the presence of long-range interactions. Focusing on the stability of discrete time crystalline (DTC) order in such systems, we use a perturbative procedure to evaluate its lifetime. For 3D systems with dipolar interactions, we show that the corresponding decay is parametrically slow, implying that robust, long-lived DTC order can be obtained. We further predict a sharp crossover from the stable DTC regime into a regime where DTC order is lost, reminiscent of a phase transition...
July 7, 2017: Physical Review Letters
#14
Alan Celestino, Alexander Eisfeld
We show that molecular aggregation can strongly influence the nonradiative decay (NRD) lifetime of an electronic excitation. As a demonstrative example, we consider a transition-dipole-dipole-interacting dimer whose monomers have harmonic potential energy surfaces (PESs). Depending on the position of the NRD channel ($q_{\rm nr}$), we find that the NRD lifetime ($\tau_{\rm nr}^{\rm dim}$) can exhibit a completely different dependence on the intermolecular-interaction strength. We observe that (i) for $q_{\rm nr}$ near the Franck-Condon region, $\tau_{\rm nr}^{\rm dim}$ increases with the interaction strength; (ii) for $q_{\rm nr}$ near the minimum of the monomer excited PES, the intermolecular interaction has little influence on $\tau_{\rm nr}^{\rm dim}$; (iii) for $q_{\rm nr}$ near the classical turning point of the monomer nuclear dynamics, on the other side of the minimum, $\tau_{\rm nr}^{\rm dim}$ decreases with the interaction strength...
July 21, 2017: Journal of Physical Chemistry. A
#15
Cristina M Herren, Katherine D McMahon
The ability to predict microbial community dynamics lags behind the quantity of data available in these systems. Most predictive models use only environmental parameters, although a long history of ecological literature suggests that community complexity should also be an informative parameter. Thus, we hypothesize that incorporating information about a community's complexity might improve predictive power in microbial models. Here, we present a new metric, called community 'cohesion,' that quantifies the degree of connectivity of a microbial community...
July 21, 2017: ISME Journal
#16
Mary X Wang, Jeffrey D Brodin, Jaime A Millan, Soyoung E Seo, Martin Girard, Monica Olvera de la Cruz, Byeongdu Lee, Chad A Mirkin
Colloidal crystal engineering with DNA can be used to realize precise control over nanoparticle (NP) arrangement. Here, we investigate a case of DNA-based assembly where the properties of DNA as a polyelectrolyte brush are employed to alter a hybridization-driven NP crystallization pathway. Using the coassembly of DNA-conjugated proteins and spherical gold nanoparticles (AuNPs) as a model system, we explore how steric repulsion between noncomplementary, neighboring NPs due to overlapping DNA shells can influence their ligand-directed behavior...
July 21, 2017: Nano Letters
#17
Zarko Krkeljas
The objective of the study was to determine whether a relationship exists between the two common methods for assessing postural stability in athletes: the time-to-stabilisation (TTS) via force-plate and the Biodex Balance System (BBS). The conditions under which these measurements assess dynamic postural control may not provide sufficient feedback to practitioners. Fourty-four amateur soccer players with no history of musculoskeletal disorders volunteered for the study. Pearson correlation was used to compare the anterior-posterior (AP), medio-lateral (ML), and the overall stability indexes measured by BBS, with the corresponding parameters of TTS assessed via force plate...
July 21, 2017: Sports Biomechanics
#18
Rachel S Gabor, Steven J Hall, David Eiriksson, Yusuf Jameel, Mallory Millington, Trinity Stout, Michelle L Barnes, Andrew Gelderloos, Hyrum Tennant, Gabriel J Bowen, Bethany T Neilson, Paul D Brooks
Growing urban environments stress hydrologic systems and impact downstream water quality. We examined a third-order catchment that transitions from an undisturbed mountain environment into urban Salt Lake City, Utah. We performed synoptic surveys during a range of seasonal baseflow conditions and utilized multiple lines of evidence to identify mechanisms by which urbanization impacts water quality. Surface water chemistry did not change appreciably until several kilometers into the urban environment, where concentrations of solutes such as chloride and nitrate increase quickly in a gaining reach...
July 21, 2017: Environmental Science & Technology
#19
Dirk Fey, Edita Aksamitiene, Anatoly Kiyatkin, Boris N Kholodenko
The advent of systems biology has convincingly demonstrated that the integration of experiments and dynamic modelling is a powerful approach to understand the cellular network biology. Here we present experimental and computational protocols that are necessary for applying this integrative approach to the quantitative studies of receptor tyrosine kinase (RTK) signaling networks. Signaling by RTKs controls multiple cellular processes, including the regulation of cell survival, motility, proliferation, differentiation, glucose metabolism, and apoptosis...
2017: Methods in Molecular Biology
#20
Faraz K Mardakheh
A major challenge in systems biology is comprehensive mapping of protein interaction networks. Crucially, such interactions are often dynamic in nature, necessitating methods that can rapidly mine the interactome across varied conditions and treatments to reveal change in the interaction networks. Recently, we described a fast mass spectrometry-based method to reveal functional interactions in mammalian cells on a global scale, by revealing spatial colocalizations between proteins (COLA) (Mardakheh et al., Mol Biosyst 13:92-105, 2017)...
2017: Methods in Molecular Biology
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