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Mechanisms of Dorsal Root Ganglion Stimulation in Pain Suppression: A computational modeling Analysis

NEUROMODULATION 2018年第3期21卷 234-246页

作者： Kent, Alexander R. Min, Xiaoyi Hogan, Quinn H. Kramer, Jeffery M. Abbott Appl Res 645 Almanor Ave Sunnyvale CA 94085 USA Med Coll Wisconsin Dept Anesthesiol Milwaukee WI 53226 USA

Objective: The mechanisms of dorsal root ganglion (DRG) stimulation for chronic pain remain unclear. The objective of this work was to explore the neurophysiological effects of DRG stimulation using computational modeling. Methods: Electrical fields produced during DRG stimulation were calculated with finite element models, and were coupled to a validated biophysical model of a C-type primary sensory neuron. Intrinsic neuronal activity was introduced as a 4 Hz afferent signal or somatic ectopic firing. The transmembrane potential was measured along the neuron to determine the effect of stimulation on intrinsic activity across stimulation parameters, cell location/orientation, and membrane properties. Results: The model was validated by showing close correspondence in action potential (AP) characteristics and firing patterns when compared to experimental measurements. Subsequently, the model output demonstrated that T-junction filtering was amplified with DRG stimulation, thereby blocking afferent signaling, with cathodic stimulation at amplitudes of 2.8-5.5 3 stimulation threshold and frequencies above 2 Hz. This amplified filtering was dependent on the presence of calcium and calciumdependent small-conductance potassium channels, which produced a hyperpolarization offset in the soma, stem, and T-junction with repeated somatic APs during stimulation. Additionally, DRG stimulation suppressed somatic ectopic activity by hyperpolarizing the soma with cathodic or anodic stimulation at amplitudes of 3-11 3 threshold and frequencies above 2 Hz. These effects were dependent on the stem axon being relatively close to and oriented toward a stimulating contact. Conclusions: These results align with the working hypotheses on the mechanisms of DRG stimulation, and indicate the importance of stimulation amplitude, polarity, and cell location/orientation on neuronal responses.

关键词： computational modeling DRG stimulation ectopic activity mechanisms of action T-junction filtering

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Towards operando computational modeling in heterogeneous catalysis

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CHEMICAL SOCIETY REVIEWS 2018年第22期47卷 8307-8348页

作者： Grajciar, Lukas Heard, Christopher J. Bondarenko, Anton A. Polynski, Mikhail V. Meeprasert, Jittima Pidko, Evgeny A. Nachtigall, Petr Charles Univ Prague Fac Sci Dept Phys & Macromol Chem Prague 12843 2 Czech Republic ITMO Univ TheoMAT Grp Lomonosova 9 St Petersburg 191002 Russia Delft Univ Technol Dept Chem Engn Fac Appl Sci Inorgan Syst Engn Grp Van der Maasweg 9 NL-2629 HZ Delft Netherlands

An increased synergy between experimental and theoretical investigations in heterogeneous catalysis has become apparent during the last decade. Experimental work has extended from ultra-high vacuum and low temperature towards operando conditions. These developments have motivated the computational community to move from standard descriptive computational models, based on inspection of the potential energy surface at 0 K and low reactant concentrations (0 K/UHV model), to more realistic conditions. The transition from 0 K/UHV to operando models has been backed by significant developments in computer hardware and software over the past few decades. New methodological developments, designed to overcome part of the gap between 0 K/UHV and operando conditions, include (i) global optimization techniques, (ii) ab initio constrained thermodynamics, (iii) biased molecular dynamics, (iv) microkinetic models of reaction networks and (v) machine learning approaches. The importance of the transition is highlighted by discussing how the molecular level picture of catalytic sites and the associated reaction mechanisms changes when the chemical environment, pressure and temperature effects are correctly accounted for in molecular simulations. It is the purpose of this review to discuss each method on an equal footing, and to draw connections between methods, particularly where they may be applied in combination.

关键词： computational modeling temperature effects Chpher(0) Computer hardware Heterogeneous catalysis Active Site Reaction Mechanisms ULTRAHIGH VACUUM Molecular Dynamics potential energy surfaces

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EXPERIMENTAL AND computational modeling OF THE PROCESSES OF SUPERSONIC OUTFLOW FROM A HALF-CLOSED CHANNEL

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JOURNAL OF ENGINEERING PHYSICS AND THERMOPHYSICS 2018年第2期91卷 339-348页

作者： Abashev, V. M. Eremkin, I. N. Zhivotov, N. P. Zamuraev, V. P. Kalinina, A. P. Tret'tyakov, P. K. Tupikin, A., V Natl Res Univ MAI 4 Volokolamskoye ShosseGSP 3A-80 Moscow 125993 Russia Russian Acad Sci ITPM SO RAN Siberian Branch SA Khristianovich Inst Theoret & Appl Mech 4-1 Inst Skaya Str Novosibirsk 630090 Russia Novosibirsk State Univ NGU 2 Pirogov Str Novosibirsk 630090 Russia

This article is devoted to the investigation of the thermo-gas-dynamic processes in half-closed channels, into which air is fed through holes focused on the axis. We have investigated the influence of the size of holes, their arrangement, and the orientation of jets flowing out through them, as well as of the settling chamber pressure on the pressure at various points of the channel wall and on the fields of flow parameters (the field of Mach numbers and the pressure and temperature fields). Experimental investigations were accompanied by numerical 2D and 3D calculations.

关键词： supersonic flow half-closed channel cold and hot jets experiment computational modeling Euler equation temperature distribution

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Neural Networks-Based computational modeling of Bilinear Control Systems for Conservation Laws: Application to the Control of Cogeneration

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IEEE TRANSACTIONS ON INDUSTRY APPLICATIONS 2018年第6期54卷 6498-6507页

作者： Danciu, Daniela Popescu, Dan Bobasu, Eugen Univ Craiova Dept Automat & Elect Craiova 200585 Romania

This paper considers the computational modeling of the class of bilinear control systems for hyperbolic conservation laws with nonstandard boundary conditions. These systems arise from (control) engineering applications of systems displaying propagation phenomena, i.e., integrating steam, water, and gas pipes. The aim of this paper is achieved by means of a systematic computational procedure previously introduced and adapted here for the class of systems under consideration. The procedure, based on a convergent Method of Lines ensures the convergence of the approximate numerical solution and also the preservation of the basic properties of the "true" solution as well as its Lyapunov stability. Thus, the approximate computational model allows numerical quantitative and qualitative analysis relevant to a specific problem. The computational efficiency of the procedure is ensured by its implementation based on some, possibly massively, parallel-structured devices belonging to the Artificial Intelligence field-the cell-based recurrent neural networks. As a case study, we consider a control system occurring in the cogeneration process (combined heat and electricity generation). A comparison between the results of the qualitative analysis and those of the numerical simulations demonstrates the correctness and effectiveness of the computational procedure for the dynamics and transients analysis. The paper ends with some conclusions and a list of open problems.

关键词： Bilinear control system cellular neural networks (CNNs) cogeneration computational modeling conservation laws heat and electricity generation process hyperbolic partial differential equations (hPDEs) method of lines (MoL)

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computational modeling of Tumor-Induced Angiogenesis

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ARCHIVES OF computational METHODS IN ENGINEERING 2017年第4期24卷 1071-1102页

作者： Vilanova, Guillermo Colominas, Ignasi Gomez, Hector Univ A Coruna Dept Metodos Matemat & Representac Grp Metodos Numer Ingn Campus Elvina La Coruna 15071 Spain Purdue Univ Sch Mech Engn 585 Purdue Mall W Lafayette IN 47907 USA

Angiogenesis is the growth of new capillaries from preexisting ones. The ability to trigger angiogenesis is one of the hallmarks of cancer, and is a necessary step for a tumor to become malignant. This paper discusses computational modeling of tumor-induced angiogenesis with particular reference to mathematical modeling, numerical simulation, and comparison with experiments. We describe the basic biological phenomena associated with angiogenesis, and discuss how they can be incorporated into mathematical models. We emphasize the crucial role of numerical methods for model development. In particular, computational methods for tumor angiogenesis need to be geometrically flexible and capable of dealing with higher-order derivatives, which suggests isogeometric analysis as an ideal candidate. Finally, we propose an algorithm based on graph theory as a potential method for quantitative validation of tumor angiogenesis models.

关键词： computational modeling Graph theory Tumor Angiogenesis Biological Phenomena Numerical methods model design Angiogenesis Higher order derivative Hallmarking

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computational modeling and Simulation of CO₂ Capture by Aqueous Amines

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CHEMICAL REVIEWS 2017年第14期117卷 9524-9593页

作者： Yang, Xin Rees, Robert J. Conway, William Puxty, Graeme Yang, Qi Winkler, David A. CSIRO Mfg Bayview Ave Clayton Vic 3169 Australia Data61 CSIRO Door 34 Goods ShedVillage St Docklands Vic 3008 Australia Sichuan Univ Coll Chem Key Lab Green Chem & Technol Minist Educ Chengdu 610064 Sichuan Peoples R China CSIRO Energy Mayfield West NSW 2304 Australia Monash Inst Pharmaceut Sci 392 Royal Parade Parkville Vic 3052 Australia Latrobe Inst Mol Sci Bundoora Vic 3046 Australia Flinders Univ S Australia Sch Chem & Phys Sci Bedford Pk SA 5042 Australia

We review the literature on the use of computational methods to study the reactions between carbon dioxide and aqueous organic amines used to capture CO2 prior to storage, reuse, or sequestration. The focus is largely on the use of high level quantum chemical methods to study these reactions, although the review also summarizes research employing hybrid quantum mechanics/molecular mechanics Methods and molecular dynamics. We critically review the effects of basis set size, quantum chemical method) solvent models, and other factors on the accuracy of calculations to provide guidance on the most appropriate methods, the expected performance, method limitations, and future needs and trends. The review also discusses,experimental studies of amine-CO2 equilibria, kinetics, measurement and prediction of amine plc values, and degradation reactions of aqueous organic amines. computational simulations of carbon capture reaction mechanisms are also comprehensively described, and the relative merits of the zwitterion, termolecular, carbamic acid, and bicarbonate mechanisms are discussed in the context of computational and experimental studies:. computational methods will become an increasingly valuable and complementary adjunct to experiments for understanding mechanisms of amine-CO2 reactions and in the design of more efficient carbon capture agents with acceptable cost and toxicities.

关键词： computational modeling computational methods Carbon capture aqueous Carbon Dioxide simulating Carbon Capture Storage Amines Toxicity capture chemical technique

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computational modeling for prediction of the shear stress of three-dimensional isotropic and aligned fiber networks

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COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2017年 148卷 91-98页

作者： Park, Seungman Johns Hopkins Univ Dept Mech Engn Baltimore MD 21218 USA

Background and objective: Interstitial flow (IF) is a creeping flow through the interstitial space of the extracellular matrix (ECM). IF plays a key role in diverse biological functions, such as tissue homeostasis, cell function and behavior. Currently, most studies that have characterized IF have focused on the permeability of ECM or shear stress distribution on the cells, but less is known about the prediction of shear stress on the individual fibers or fiber networks despite its significance in the alignment of matrix fibers and cells observed in fibrotic or wound tissues. In this study, I developed a computational model to predict shear stress for different structured fibrous networks. Methods: To generate isotropic models, a random growth algorithm and a second-order orientation tensor were employed. Then, a three-dimensional (3D) solid model was created using computer-aided design (CAD) software for the aligned models (i.e., parallel, perpendicular and cubic models). Subsequently, a tetrahedral unstructured mesh was generated and flow solutions were calculated by solving equations for mass and momentum conservation for all models. Through the flow solutions, I estimated permeability using Darcy's law. Average shear stress (ASS) on the fibers was calculated by averaging the wall shear stress of the fibers. By using nonlinear surface fitting of permeability, viscosity, velocity, porosity and ASS, I devised new computational models. Results: Overall, the developed models showed that higher porosity induced higher permeability, as previous empirical and theoretical models have shown. For comparison of the permeability, the present computational models were matched well with previous models, which justify our computational approach. ASS tended to increase linearly with respect to inlet velocity and dynamic viscosity, whereas permeability was almost the same. Finally, the developed model nicely predicted the ASS values that had been directly estimated from computati

关键词： Interstitial flow (IF) Extracellular matrix (ECM) Permeability Average shear stress (ASS) computational modeling

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Dual Compartment computational modeling of Cortical Neurons in the Zebra Finch

Dual Compartment Computational Modeling of Cortical Neurons ...

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International Conference on Advances in Biomedical Engineering (ICABME)

作者： Ahmad Sibahi Arij Daou Biomedical Engineering Program American University of Beirut Beirut Lebanon

While the nonlinearity and complexity of biological phenomena keeps much of the intricate details of science mysterious, computational modeling can help unveil the dynamics and functionalities of such complex phenomena by studying the various parts orchestrating the system and leading eventually to its overall behavior. In this work, we develop a dual-compartment conductance-based model to replicate the neurophysiological firing patterns and properties seen in cortical neurons of the zebra finch, which are responsible for the bird's song. The model's aim is to capture the timing of the action potentials in the spike train for various stimuli and the intricate details of spikes' morphology.

关键词： Neurons Biological system modeling Mathematical model Brain modeling computational modeling Biological information theory Adaptation models

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Neural Networks-Based computational modeling of Bilinear Control Systems for Conservation Laws: Application to the Control of Cogeneration

Neural Networks-Based Computational Modeling of Bilinear Con...

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16th International Carpathian Control Conference (ICCC)

作者： Danciu, Daniela Popescu, Dan Bobasu, Eugen Univ Craiova Dept Automat & Elect Craiova 200585 Romania

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Tutorial 1: computational modeling of the Dividing Human Cell

Tutorial 1: Computational Modeling of the Dividing Human Cel...

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International Conference on Informatics, Electronics & Vision (ICIEV)

作者： M. Julius Hossain European Molecular Biology Laboratory (EMBL) Germany

Cell division/mitosis is a fundamental process of life where a mother cell undergoes profound morphological transformations to divide into two daughter cells. This process is driven by tight coordination of a large number of essential proteins in space and time. Recent publication from our group (Cai Y. and Hossain MJ et al., Nature 2018) utilized four-dimensional (3D+time) image data to construct a canonical model of the morphological change of human cells during the cell division in order to quantify spatio-temporal dynamics of essential mitotic proteins. We also constructed a dynamic protein atlas containing 28 mitotic proteins where user can visualize distributions of mitotic proteins during cell division within the cell model and obtain various parameters such absolute number proteins and average concentration inside different cellular compartments. During this tutorial, I will first introduce the project and the computation framework briefly. Then with a simpler version of source code, mostly developed in MATLAB, I will demonstrate various steps needed such as segmentation, parameters extraction, registration, cylindrical axis based representation and averaging in order to construct a canonical model of mitosis using a small set of data. The model is used to integrate proteins of interest from different cells to obtain average distributions. I will also demonstrate the functionality of the protein atlas.

关键词： Proteins computational modeling Mathematical model Tutorials Data models Matlab Europe

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