| 351. |
- Geng, Zeyang, 1991, et al.
(författare)
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Validity of solid-state Li + diffusion coefficient estimation by electrochemical approaches for lithium-ion batteries
- 2022
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Ingår i: Electrochimica Acta. - : Elsevier BV. - 0013-4686 .- 1873-3859. ; 404
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Tidskriftsartikel (refereegranskat)abstract
- The solid-state diffusion coefficient of the electrode active material is one of the key parameters in lithium-ion battery modelling. Conventionally, this diffusion coefficient is estimated through the galvanostatic intermittent titration technique (GITT). In this work, the validity of GITT and a faster alternative technique, intermittent current interruption (ICI), are investigated regarding their effectiveness through a black-box testing approach. A Doyle-Fuller-Newman model with parameters for a LiNi0.8Mn0.1Co0.1O2 electrode is used as a fairly faithful representation as a real battery system, and the GITT and ICI experiments are simulated to extract the diffusion coefficient. With the parameters used in this work, the results show that both the GITT and ICI methods can identify the solid-state diffusion coefficient very well compared to the value used as input into the simulation model. The ICI method allows more frequent measurement but the experiment time is 85% less than what takes to perform a GITT test. Different fitting approaches and fitting length affected the estimation accuracy, however not significantly. Moreover, a thinner electrode, a higher C-rate and a greater electrolyte diffusion coefficient will lead to an estimation of a higher solid-state diffusion coefficient, generally closer to the target value.
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| 352. |
- Gennemark, Peter, 1974, et al.
(författare)
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Benchmarks for identification of ordinary differential equations from time series data
- 2009
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1460-2059 .- 1367-4803 .- 1367-4811. ; 25:6, s. 780-786
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: In recent years, the biological literature has seen a significant increase of reported methods for identifying both structure and parameters of ordinary differential equations (ODEs) from time series data. A natural way to evaluate the performance of such methods is to try them on a sufficient number of realistic test cases. However, weak practices in specifying identification problems and lack of commonly accepted benchmark problems makes it difficult to evaluate and compare different methods. Results: To enable better evaluation and comparisons between different methods, we propose how to specify identification problems as optimization problems with a model space of allowed reactions (e.g. reaction kinetics like Michaelis - Menten or S-systems), ranges for the parameters, time series data and an error function. We also define a file format for such problems. We then present a collection of more than 40 benchmark problems for ODE model identification of cellular systems. The collection includes realistic problems of different levels of difficulty w.r.t. size and quality of data. We consider both problems with simulated data from known systems, and problems with real data. Finally, we present results based on our identification algorithm for all benchmark problems. In comparison with publications on which we have based some of the benchmark problems, our approach allows all problems to be solved without the use of supercomputing.
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| 353. |
- Gennemark, Peter, 1974, et al.
(författare)
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Modeling energy intake by adding homeostatic feedback and drug intervention
- 2015
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Ingår i: Journal of Pharmacokinetics and Pharmacodynamics. - : Springer Science and Business Media LLC. - 1567-567X .- 1573-8744. ; 42:1, s. 79-96
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Tidskriftsartikel (refereegranskat)abstract
- Energy intake (EI) is a pivotal biomarker used in quantification approaches to metabolic disease processes such as obesity, diabetes, and growth disorders. Eating behavior is however under both short-term and long-term control. This control system manifests itself as tolerance and rebound phenomena in EI, when challenged by drug treatment or diet restriction. The paper describes a model with the capability to capture physiological counter-regulatory feedback actions triggered by energy imbalances. This feedback is general as it handles tolerance to both increases and decreases in EI, and works in both acute and chronic settings. A drug mechanism function inhibits (or stimulates) EI. The deviation of EI relative to a reference level (set-point) serves as input to a non-linear appetite control signal which in turn impacts EI in parallel to the drug intervention. Three examples demonstrate the potential usefulness of the model in both acute and chronic dosing situations. The model shifts the predicted concentration-response relationship rightwardly at lower concentrations, in contrast to models that do not handle functional adaptation. A fourth example further shows that the model may qualitatively explain differences in rate and extent of adaptation in observed EI and its concomitants in both rodents and humans.
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| 354. |
- Gennemark, Peter, 1974, et al.
(författare)
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ODEion- a software module for structural identification of ordinary differential equations
- 2014
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Ingår i: Journal of Bioinformatics and Computational Biology. - 0219-7200 .- 1757-6334. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- In the systems biology field, algorithms for structural identification of ordinary differential equations (ODEs) have mainly focused on fixed model spaces like S-systems and/or on methods that require sufficiently good data so that derivatives can be accurately estimated. There is therefore a lack of methods and software that can handle more general models and realistic data. We present ODEion, a software module for structural identification of ODEs. Main characteristic features of the software are: • The model space is defined by arbitrary user-defined functions that can be nonlinear in both variables and parameters, such as for example chemical rate reactions. • ODEion implements computationally efficient algorithms that have been shown to efficiently handle sparse and noisy data. It can run a range of realistic problems that previously required a supercomputer. • ODEion is easy to use and provides SBML output. We describe the mathematical problem, the ODEion system itself, and provide several examples of how the system can be used. Read More: http://www.worldscientific.com/doi/abs/10.1142/S0219720013500157
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| 355. |
- Gennemark, Peter, 1974, et al.
(författare)
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Optimal Design in Population Kinetic Experiments by Set-Valued Methods
- 2011
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Ingår i: AAPS Journal. - : Springer Science and Business Media LLC. - 1550-7416. ; 13:4, s. 495-507
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Tidskriftsartikel (refereegranskat)abstract
- We propose a new method for optimal experimental design of population pharmacometric experiments based on global search methods using interval analysis; all variables and parameters are represented as intervals rather than real numbers. The evaluation of a specific design is based on multiple simulations and parameter estimations. The method requires no prior point estimates for the parameters, since the parameters can incorporate any level of uncertainty. In this respect, it is similar to robust optimal design. Representing sampling times and covariates like doses by intervals gives a direct way of optimizing with rigorous sampling and dose intervals that can be useful in clinical practice. Furthermore, the method works on underdetermined problems for which traditional methods typically fail.
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| 356. |
- Georgiou, P., et al.
(författare)
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Picosecond calorimetry: Time-resolved x-ray diffraction studies of liquid CH2Cl2
- 2006
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 124:23, s. 234507-
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Tidskriftsartikel (refereegranskat)abstract
- Liquid phase time-resolved x-ray diffraction with 100 ps resolution has recently emerged as a powerful technique for probing the structural dynamics of transient photochemical species in solution. It is intrinsic to the method, however, that a structural signal is observed not only from the photochemical of interest but also from the embedding solvent matrix. To experimentally characterize the x-ray diffraction signal deriving from the solvent alone we performed time-resolved diffraction studies of a pure liquid sample over a time domain from -250 ps to 2.5 mu s. Multiphoton excitation was used to rapidly heat liquid CH2Cl2 using UV pulses of 100 fs duration. A significant x-ray diffraction signal is visible prior to the onset of thermal expansion, which characterizes a highly compressed superheated liquid. Liquid CH2Cl2 then expands as a shock wave propagates through the sample and the temporal dependence of this phenomenon is in good agreement with theory. An unexpectedly slow initial release of energy into the liquid as heat is observed from multiphoton excited CH2Cl2, revealing the presence of a metastable state of multiphoton excited CH2Cl2.
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| 357. |
- Gerdin Hulkko, Johan, et al.
(författare)
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Kinetics of the low-pressure chemical vapor deposited tungsten nitride process using tungsten hexafluoride and ammonia precursors
- 2021
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Ingår i: Journal of Vacuum Science and Technology A. - : American Vacuum Society. - 1520-8559 .- 0734-2101. ; 39:6, s. 063403-
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Tidskriftsartikel (refereegranskat)abstract
- Tungsten nitride (WNx) is a hard refractory material with low electrical resistance that can be deposited using multiple methods. This study focuses on the microstructrual development of low pressure chemical vapor deposition grown WNx coatings. Also, the growth kinetics is studied and discussed in terms of the resulting microstructures. Samples of WNx were deposited using WF6, NH3, and Ar at 592–887 K in a hot-wall reactor with variable gas mixture compositions (NH3:WF6 = 0.5–25). The coatings were nitrogen-rich (x ∼ 1.65) and oxygen-free as determined by time-of-flight-elastic recoil detection analysis. X-ray diffraction showed that the coatings transformed from being amorphous to crystallizing as β-W2N at 641–690 K. The morphologies changed with deposition temperature. Being very fine grained and nodular at deposition temperatures 740 K and below, increasing the deposition temperature to 789 K while employing a NH3:WF6 molar ratio of 1, large disc-shaped protrusions were formed. When increasing the NH3:WF6 molar ratio to 25, striped facets became increasingly dominant. Investigating the latter by transmission electron microscopy, a microstructure of smaller ridges formed by twinning, oriented as <211> in the out-of-plane direction, was revealed across the facet surfaces. Transmission Kikuchi diffraction confirmed that <211> was the texture of these coatings. The partial reaction order of WF6 and NH3 at 740 K was determined to be close to 1/6 and 1/2, respectively. The apparent activation energy ranged from 82 to 12 kJ/mol corresponding to deposition temperatures from 592 to 887 K.
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| 358. |
- Gerken, Jan, 1991, et al.
(författare)
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Towards closed strings as single-valued open strings at genus one
- 2022
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Ingår i: Journal of Physics A: Mathematical and Theoretical. - : IOP Publishing. - 1751-8121 .- 1751-8113. ; 55:2
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Tidskriftsartikel (refereegranskat)abstract
- We relate the low-energy expansions of world-sheet integrals in genus-one amplitudes of open- and closed-string states. The respective expansion coefficients are elliptic multiple zeta values (eMZVs) in the open-string case and non-holomorphic modular forms dubbed 'modular graph forms (MGFs)' for closed strings. By inspecting the differential equations and degeneration limits of suitable generating series of genus-one integrals, we identify formal substitution rules mapping the eMZVs of open strings to the MGFs of closed strings. Based on the properties of these rules, we refer to them as an elliptic single-valued map which generalizes the genus-zero notion of a single-valued map acting on MZVs seen in tree-level relations between the open and closed string.
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| 359. |
- Gerlee, Philip, 1980, et al.
(författare)
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Autocrine signaling can explain the emergence of Allee effects in cancer cell populations
- 2022
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Ingår i: Plos Computational Biology. - : Public Library of Science (PLoS). - 1553-734X .- 1553-7358. ; 18:3
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Tidskriftsartikel (refereegranskat)abstract
- In many human cancers, the rate of cell growth depends crucially on the size of the tumour cell population. Low, zero, or negative growth at low population densities is known as the Allee effect; this effect has been studied extensively in ecology, but so far lacks a good explanation in the cancer setting. Here, we formulate and analyze an individual-based model of cancer, in which cell division rates are increased by the local concentration of an autocrine growth factor produced by the cancer cells themselves. We show, analytically and by simulation, that autocrine signaling suffices to cause both strong and weak Allee effects. Whether low cell densities lead to negative (strong effect) or reduced (weak effect) growth rate depends directly on the ratio of cell death to proliferation, and indirectly on cellular dispersal. Our model is consistent with experimental observations from three patient-derived brain tumor cell lines grown at different densities. We propose that further studying and quantifying population-wide feedback, impacting cell growth, will be central for advancing our understanding of cancer dynamics and treatment, potentially exploiting Allee effects for therapy.
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| 360. |
- Gerlee, Philip, 1980, et al.
(författare)
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Searching for Synergies: Matrix Algebraic Approaches for Efficient Pair Screening
- 2013
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:7
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Tidskriftsartikel (refereegranskat)abstract
- Functionally interacting perturbations, such as synergistic drugs pairs or synthetic lethal gene pairs, are of key interest in both pharmacology and functional genomics. However, to find such pairs by traditional screening methods is both time consuming and costly. We present a novel computational-experimental framework for efficient identification of synergistic target pairs, applicable for screening of systems with sizes on the order of current drug, small RNA or SGA (Synthetic Genetic Array) libraries (>1000 targets). This framework exploits the fact that the response of a drug pair in a given system, or a pair of genes' propensity to interact functionally, can be partly predicted by computational means from (i) a small set of experimentally determined target pairs, and (ii) pre-existing data (e.g. gene ontology, PPI) on the similarities between targets. Predictions are obtained by a novel matrix algebraic technique, based on cyclical projections onto convex sets. We demonstrate the efficiency of the proposed method using drug-drug interaction data from seven cancer cell lines and gene-gene interaction data from yeast SGA screens. Our protocol increases the rate of synergism discovery significantly over traditional screening, by up to 7-fold. Our method is easy to implement and could be applied to accelerate pair screening for both animal and microbial systems.
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