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Systems dynamics model

Mahmoud K Madi, Fadi N Karameh
Kalman filtering methods have long been regarded as efficient adaptive Bayesian techniques for estimating hidden states in models of linear dynamical systems under Gaussian uncertainty. Recent advents of the Cubature Kalman filter (CKF) have extended this efficient estimation property to nonlinear systems, and also to hybrid nonlinear problems where by the processes are continuous and the observations are discrete (continuous-discrete CD-CKF). Employing CKF techniques, therefore, carries high promise for modeling many biological phenomena where the underlying processes exhibit inherently nonlinear, continuous, and noisy dynamics and the associated measurements are uncertain and time-sampled...
2017: PloS One
Rui Yin, Mingzhu Zhao, Kangyu Wang, Yanping Lin, Yanfang Wang, Chunyu Sun, Yi Wang, Meiping Zhang
Ginseng, Panax ginseng C.A. Meyer, is one of the most important medicinal plants for human health and medicine. It has been documented that over 80% of genes conferring resistance to bacteria, viruses, fungi and nematodes are contributed by the nucleotide binding site (NBS)-encoding gene family. Therefore, identification and characterization of NBS genes expressed in ginseng are paramount to its genetic improvement and breeding. However, little is known about the NBS-encoding genes in ginseng. Here we report genome-wide identification and systems analysis of the NBS genes actively expressed in ginseng (PgNBS genes)...
2017: PloS One
Hiroshi Wada, Chisato Masumoto-Kubo, Koichi Tsutsumi, Hiroshi Nonami, Fukuyo Tanaka, Haruka Okada, Rosa Erra-Balsells, Kenzo Hiraoka, Taiken Nakashima, Makoto Hakata, Satoshi Morita
Grain filling ability is mainly affected by the translocation of carbohydrates generated from temporarily stored stem starch in most field crops including rice (Oryza sativa L.). The partitioning of non-structural stem carbohydrates has been recognized as an important trait for raising the yield ceiling, yet we still do not fully understand how carbohydrate partitioning occurs in the stems. In this study, two rice subspecies that exhibit different patterns of non-structural stem carbohydrates partitioning, a japonica-dominant cultivar, Momiroman, and an indica-dominant cultivar, Hokuriku 193, were used as the model system to study the relationship between turgor pressure and metabolic regulation of non-structural stem carbohydrates, by combining the water status measurement with gene expression analysis and a dynamic prefixed 13C tracer analysis using a mass spectrometer...
2017: PloS One
Gabor Nagy, Chris Oostenbrink, Jozef Hritz
The 14-3-3 protein family performs regulatory functions in eukaryotic organisms by binding to a large number of phosphorylated protein partners. Whilst the binding mode of the phosphopeptides within the primary 14-3-3 binding site is well established based on the crystal structures of their complexes, little is known about the binding process itself. We present a computational study of the process by which phosphopeptides bind to the 14-3-3ζ protein. Applying a novel scheme combining Hamiltonian replica exchange molecular dynamics and distancefield restraints allowed us to map and compare the most likely phosphopeptide-binding pathways to the 14-3-3ζ protein...
2017: PloS One
Xiangnan Zhong, Haibo He, Ding Wang, Zhen Ni
In this paper, we present a new model-free globalized dual heuristic dynamic programming (GDHP) approach for the discrete-time nonlinear zero-sum game problems. First, the online learning algorithm is proposed based on the GDHP method to solve the Hamilton-Jacobi-Isaacs equation associated with H∞ optimal regulation control problem. By setting backward one step of the definition of performance index, the requirement of system dynamics, or an identifier is relaxed in the proposed method. Then, three neural networks are established to approximate the optimal saddle point feedback control law, the disturbance law, and the performance index, respectively...
July 17, 2017: IEEE Transactions on Cybernetics
K T Gebre, M Wurzinger, S Gizaw, A Haile, B Rischkowsky, T Getachew, J Sölkner
A comprehensive dynamic simulation model was developed to describe a community-based breeding program for the Menz sheep population of Ethiopia. Selection of male and female animals based on their own and maternal performance was simulated. The breeding goal traits were 6-mo weight, preweaning survival, and fertility rate. The model input data were obtained from the flock book, questionnaires, and references. The simulation model used a mix of deterministic and stochastic procedures to model the complex system...
June 2017: Journal of Animal Science
Tereza Pereira de Souza, Guilherme Volpe Bossa, Pasquale Stano, Frank Steiniger, Sylvio May, Pier Luigi Luisi, Alfred Fahr
Primitive cell models help to understand the role that compartmentalization plays in origin of life scenarios. Here we present a combined experimental and modeling approach towards the construction of simple model systems for primitive cellular assemblies. Charged lipid vesicles aggregate in the presence of oppositely charged biopolymers, such as nucleic acids or polypeptides. Based on zeta potential measurements, dynamic light scattering and cryo-transmission electron-microscopy, we have characterized the behavior of empty and ferritin-filled large unilamellar POPC vesicles, doped with different amounts of cationic (DDAB, CTAB) and anionic (sodium oleate) surfactants, and their aggregation upon the addition of anionic (tRNA, poly-l-glutamic acid) and cationic (poly-l-arginine) biopolymers, respectively...
July 20, 2017: Physical Chemistry Chemical Physics: PCCP
Ignat Harczuk, Balazs Nagy, Frank Jensen, Olav Vahtras, Hans Ågren
We present a new way to compute the two-body contribution to the dispersion energy using ab initio theory. By combining the complex polarization propagator method and the LoProp transformation, local contributions to the Casimir-Polder interaction is obtained. The full dispersion energy in dimer systems consisting of pairs of molecules including H2, N2, CO, CH4, pyridine, and benzene is investigated, where anisotropic as well as isotropic models of dispersion are obtained using a decomposition scheme for the dipole-dipole polarizability...
July 20, 2017: Physical Chemistry Chemical Physics: PCCP
Sheng-Lun Yi, Xue-Bo Jin, Ting-Li Su, Zhen-Yun Tang, Fa-Fa Wang, Na Xiang, Jian-Lei Kong
Online denoising is motivated by real-time applications in the industrial process, where the data must be utilizable soon after it is collected. Since the noise in practical process is usually colored, it is quite a challenge for denoising techniques. In this paper, a novel online denoising method was proposed to achieve the processing of the practical measurement data with colored noise, and the characteristics of the colored noise were considered in the dynamic model via an adaptive parameter. The proposed method consists of two parts within a closed loop: the first one is to estimate the system state based on the second-order adaptive statistics model and the other is to update the adaptive parameter in the model using the Yule-Walker algorithm...
July 20, 2017: Sensors
Ibtisam Marey-Sarwan, Dorit Roer-Strier, Hiltrud Otto
This qualitative study utilizes ecological theory, a context-informed perspective, and an interactive model to study minority children, while considering structural factors, oppression, segregation, power dynamics, and awareness of the political context. It examines perceptions of risk and protection using "snowball" sampling of 33 Bedouin mothers, citizens of Israel, from the unrecognized villages (UVs) in the Naqab in Southern Israel. Data were collected via in-depth, semistructured interviews during 2011 to 2013...
July 20, 2017: American Journal of Orthopsychiatry
K R Krishnadas, Ananya Baksi, Atanu Ghosh, Ganapati Natarajan, Anirban Som, Thalappil Pradeep
Nanoparticles exhibit a rich variety in terms of structure, composition, and properties. However, reactions between them remain largely unexplored. In this Account, we discuss an emerging aspect of nanomaterials chemistry, namely, interparticle reactions in solution phase, similar to reactions between molecules, involving atomically precise noble metal clusters. A brief historical account of the developments, starting from the bare, gas phase clusters, which led to the synthesis of atomically precise monolayer protected clusters in solution, is presented first...
July 20, 2017: Accounts of Chemical Research
Cintia C Lobo, Nora C Bertola, Edgardo M Contreras, Noemí E Zaritzky
The aim of this study was to analyze the mechanisms, stoichiometry, and stability of 4-chlorophenol (4CP) biodegradation kinetics by phenol-acclimated activated sludge using open respirometry. While the removal of 4CP was higher than 98%, the removal of chemical oxygen demand (COD) ranged between 69 and 79% due to the accumulation of an intermediate metabolite. The value obtained from respirometric profiles for the stoichiometric ratio of O2 to 4CP (YO2/4CP) was 1.95 ± 0.04 mol of oxygen consumed per mol of 4CP removed...
July 20, 2017: Environmental Science and Pollution Research International
V E Dubrov, I A Kuz'kin, I M Shcherbakov, A L Matveev, A V Yudin
Volume model of transtrochanteric fracture of the femoral bone fixed by Targon PF dynamic fixator was studied by the finite element analysis. The following parameters were measured: magnitude and direction of displacement of system elements, pressure between fragments, and von Mises stress distribution in the fixator depending on support screw plunging into the sleeve. The results indicate that stability of the bone-nail system increases during fracture union and 10-mm shortening of the femoral neck axis, which is seen from a decrease in system deformation under load by 16...
July 18, 2017: Bulletin of Experimental Biology and Medicine
Arnaud Barré, Kamiar Aminian
Roentgen stereophotogrammetry analysis technique allows an accurate measurement of knee joint prosthesis position and orientation using two X-ray images. Although this technique is used generally during static procedure, it is possible to use it with a biplane fluoroscopic system to measure the prosthesis kinematics during functional tasks (e.g., gait, squat, jump) performed in a laboratory environment. However, the performance of the system in terms of errors for the measurements and the model-based matching algorithm are not well known for dynamic tasks such as walking...
July 18, 2017: Medical & Biological Engineering & Computing
Cheng Zhan, Cheng Lian, Yu Zhang, Matthew W Thompson, Yu Xie, Jianzhong Wu, Paul R C Kent, Peter T Cummings, De-En Jiang, David J Wesolowski
Supercapacitors such as electric double-layer capacitors (EDLCs) and pseudocapacitors are becoming increasingly important in the field of electrical energy storage. Theoretical study of energy storage in EDLCs focuses on solving for the electric double-layer structure in different electrode geometries and electrolyte components, which can be achieved by molecular simulations such as classical molecular dynamics (MD), classical density functional theory (classical DFT), and Monte-Carlo (MC) methods. In recent years, combining first-principles and classical simulations to investigate the carbon-based EDLCs has shed light on the importance of quantum capacitance in graphene-like 2D systems...
July 2017: Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
Birgit Schoeberl, Art Kudla, Kristina Masson, Ashish Kalra, Michael Curley, Gregory Finn, Emily Pace, Brian Harms, Jaeyeon Kim, Jeff Kearns, Aaron Fulgham, Olga Burenkova, Viara Grantcharova, Defne Yarar, Violette Paragas, Jonathan Fitzgerald, Marisa Wainszelbaum, Kip West, Sara Mathews, Rachel Nering, Bambang Adiwijaya, Gabriela Garcia, Bill Kubasek, Victor Moyo, Akos Czibere, Ulrik B Nielsen, Gavin MacBeath
The ErbB family of receptor tyrosine kinases comprises four members: epidermal growth factor receptor (EGFR/ErbB1), human EGFR 2 (HER2/ErbB2), ErbB3/HER3, and ErbB4/HER4. The first two members of this family, EGFR and HER2, have been implicated in tumorigenesis and cancer progression for several decades, and numerous drugs have now been approved that target these two proteins. Less attention, however, has been paid to the role of this family in mediating cancer cell survival and drug tolerance. To better understand the complex signal transduction network triggered by the ErbB receptor family, we built a computational model that quantitatively captures the dynamics of ErbB signaling...
2017: NPJ Systems Biology and Applications
Yu Matsuoka, Hiroyuki Kurata
BACKGROUND: Microbial production of biofuels and biochemicals from renewable feedstocks has received considerable recent attention from environmental protection and energy production perspectives. Many biofuels and biochemicals are produced by fermentation under oxygen-limited conditions following initiation of aerobic cultivation to enhance the cell growth rate. Thus, it is of significant interest to investigate the effect of dissolved oxygen concentration on redox regulation in Escherichia coli, a particularly popular cellular factory due to its high growth rate and well-characterized physiology...
2017: Biotechnology for Biofuels
Yonghui Zheng, Yan Cheng, Rong Huang, Ruijuan Qi, Feng Rao, Keyuan Ding, Weijun Yin, Sannian Song, Weili Liu, Zhitang Song, Songlin Feng
Phase change memory (PCM) is a promising nonvolatile memory to reform current commercial computing system. Inhibiting face-centered cubic (f-) to hexagonal (h-) phase transition of Ge2Sb2Te5 (GST) thin film is essential for realizing high-density, high-speed, and low-power PCM. Although the atomic configurations of f- and h-lattices of GST alloy and the transition mechanisms have been extensively studied, the real transition process should be more complex than previous explanations, e.g. vacancy-ordering model for f-to-h transition...
July 19, 2017: Scientific Reports
Lei Tao, Rouzbeh Shahsavari
Understanding the deformation mechanisms underlying the mechanical behavior of materials is the key to fundamental and engineering advances in materials' performance. Herein, we focus on crystalline calcium-silicate-hydrates (C-S-H) as a model system with applications in cementitious materials, bone-tissue engineering, drug delivery and refractory materials, and use molecular dynamics simulation to investigate its loading geometry dependent mechanical properties. By comparing various conventional (e.g. shear, compression and tension) and nano-indentation loading geometries, our findings demonstrate that the former loading leads to size-independent mechanical properties while the latter results in size-dependent mechanical properties at the nanometer scales...
July 19, 2017: Scientific Reports
Casey O Diekman, Peter J Thomas, Christopher G Wilson
How sensory information influences the dynamics of rhythm generation varies across systems, and general principles for understanding this aspect of motor control are lacking. Determining the origin of respiratory rhythm generation is challenging because the mechanisms in a central circuit considered in isolation may be different than those in the intact organism. We analyze a closed-loop respiratory control model incorporating a central pattern generator (CPG), the Butera-Rinzel-Smith (BRS) model, together with lung mechanics, oxygen handling, and chemosensory components...
July 19, 2017: Journal of Neurophysiology
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