Parameter estimation methods for biological systems

The inverse problem of modeling biochemical processes mathematically from measured time course data falls into the category of system identification and parameter estimation. Analyzing the time course data would provide valuable insights into the model structure and dynamics of the biochemical system. Based on the types of biochemical reactions, such as metabolic networks and genetic networks, several modeling frameworks have been proposed, developed and proved effective, including the Michaelis-Menten equation, the Biochemical System Theory (BST), etc. One bottleneck in analyzing the obtained data is the estimation of parameter values within the system model. As most models for molecular biological systems are nonlinear with respect to both parameters and system state variables, estimation of parameters in these models from experimental measurement data is thus a nonlinear estimation problem. In principle, all algorithms for nonlinear optimization can be used to deal with this problem, for example, the Gauss-Newton iteration method and its variants. However, these methods do not take the special structures of biological system models into account. When the number of parameters to be determined increases, it will be challenging and computationally expensive to apply these conventional methods. In this research, several methods are proposed for estimating parameters in two classes of widely used biological system models: the S-system model and the linear fractional model (LFM), by utilizing their structure specialties. For the S-system, two estimation methods are designed. 1) Based on the two-term structure (production and degradation) of the model, an alternating iterative least squares method is proposed. 2) A separation nonlinear least squares method is proposed to deal with the partially linear structure of the model. For the LFM, two estimation methods are provided. 1) The separation nonlinear least squares method can also be adopted to treat the partially linear structure of the LFM, and moreover a modified iterative version is included. 2) A special strategy using the separation principle and the weighted least squares method is implemented to turn the cost function into a quadratic form and thus the estimates for parameters can be analytically solved. Simulation results have demonstrated the effectiveness of the proposed methods, which have shown better performance in terms of estimation accuracy and computation time, compared with those conventional nonlinear estimation methods

Synthesizing and characterization of hole doped nickel based layer superconductor (La1−x_{1-x}Srx_{x})ONiAs

We report the synthesizing and characterization of the hole doped Ni-based superconductor ($La_{1-x}Sr_{x})ONiAs$. By substituting La with Sr, the superconducting transition temperature $T_c$ is increased from 2.75 K of the parent phase $LaONiAs$ to 3.7 K at the doping levels x= 0.1 - 0.2. The curve $T_c$ versus hole concentration shows a symmetric behavior as the electron doped samples $La(O_{1-x}F_{x})NiAs$. The normal state resistivity in Ni-based samples shows a good metallic behavior and reveals the absence of an anomaly which appears in the Fe-based system at about 150 K, suggesting that this anomaly is not a common feature for all systems. Hall effect measurements indicate that the electron conduction in the parent phase $LaONiAs$ is dominated by electron-like charge carriers, while with more Sr doping, a hole-like band will emerge and finally prevail over the conduction, and accordingly the superconducting transition temperature $T_c$ increases.Comment: 4 pages, 5 figure

Physical properties of noncentrosymmetric superconductor Ru7_7B3_3

Transition metal boride Ru$_7$B$_3$ was found to be a noncentrosymmetric superconductor with $T_{C}$ equal to 3.3 K. Superconducting and normal state properties of Ru$_7$B$_3$ were determined by a self-consistent analysis through resistivity($\rho_{xx}$ and $\rho_{xy}$), specific heat, lower critical field measurement and electronic band structure calculation. It is found that Ru$_7$B$_3$ belongs to an s-wave dominated single band superconductor with energy gap 0.5 meV and could be categorized into type II superconductor with weak electron-phonon coupling. Unusual 'kink' feature is clearly observed in field-broadening resistivity curves, suggesting the possible mixture of spin triplet induced by the lattice without inversion symmetry.Comment: 11 pages, 16 figures. submitted to Phys. Rev.

Specific-Heat Measurement of Residual Superconductivity in the Normal State of Underdoped Cuprate Superconductors

We have measured the magnetic field and temperature dependence of specific heat on $Bi_2Sr_{2-x}La_xCuO_{6+\delta}$ single crystals in wide doping and temperature regions. The superconductivity related specific heat coefficient $\gamma_{sc}$ and entropy $S_{sc}$ are determined. It is found that $\gamma_{sc}$ has a hump-like anomaly at $T_c$ and behaves as a long tail which persists far into the normal state for the underdoped samples, but for the heavily overdoped samples the anomaly ends sharply just near $T_c$. Interestingly, we found that the entropy associated with superconductivity is roughly conserved when and only the long tail part in the normal state is taken into account for the underdoped samples, indicating the residual superconductivity above T$_c$.Comment: 4 pages, 4 figures, Accepted for publication in Physical Review Letter

Temporary Structures in Shangai EXPO2010 - Structural Design Specification and Example

p. 790-798Many temporary buildings and structures are constructed in the Expo Park, Shanghai as pavilions and facilities of EXPO2010. New materials and new structural systems are expected to be used and appear. The structural design specification for temporary structures of EXPO2010 is summarized and the structural design of Norwegian pavilion is described in this paper.Wu, M.; Meng, L.; Mu, T. (2010). Temporary Structures in Shangai EXPO2010 - Structural Design Specification and Example. Editorial Universitat Politècnica de València. http://hdl.handle.net/10251/694

A comment on "Ab initio calculations of pressure-dependence of high-order elastic constants using finite deformations approach" by I. Mosyagin, A.V. Lugovskoy, O.M. Krasilnikov, Yu.Kh. Vekilov, S.I. Simak and I.A. Abrikosov

Recently, I. Mosyagin, A.V. Lugovskoy, O.M. Krasilnikov, Yu.Kh. Vekilov, S.I. Simak and I.A. Abrikosov in the paper: "Ab initio calculations of pressure-dependence of high-order elastic constants using finite deformations approach"[Computer Physics Communications 220 (2017) 2030] presented a description of a technique for ab initio calculations of the pressure dependence of second- and third-order elastic constants. Unfortunately, the work contains serious and fundamental flaws in the field of finite-deformation solid mechanics.Comment: 3 pages, 0 figure

No-compressing of quantum phase information

We raise a general question of quantum information theory whether the quantum phase information can be compressed and retrieved. A general qubit contains both amplitude and phase information, while an equatorial qubit contains only a phase information. We study whether it is possible to compress the phase information of n equatorial qubits into m general qubits with m being less than n, and still those information can be retrieved perfectly. We prove that this process is not allowed by quantum mechanics.Comment: 4 pages, 1 figur

Effects of Arbuscular Mycorrhizal Fungi on Root Growth and Architecture of Tulip Gesneriana

Arbuscular mycorrhizal fungi(AMF) can promote the absorption of soil water and mineral nutrients, improve photosynthesis, and make host attain higher quality finally by establishing symbiotic relationship between AMF and host root. To improve Tulip gesneriana quality have practical meaning under no bad affect to cultivation soil, in the light of its economical and ecological values. However, some AMF may be diverse from others, the concrete function of AMF on commercial tulip varieties need to explore. Therefore, three different sets of  arbuscular mycorrhizal fungi were inoculated into tulip rhizosphere soil, which were set as 4(Diversispora versiformis), 7(Diversispora spurca) and 1 + 3 + 4 (Rhizophagus intraradias + Funneliformis mosseae + Diversispora versiformis), respectively. The results showed that the activity of most of the measured indices increased, the average root diameter and sucrose content decreased in those three mycorrhizal treatments. Our research provide some theoretical basis for the application of AMF on T.gesneriana ecological cultivation in future