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THERMAL RESPONSE MODEL OF A SIMULATED CRANIAL STRUCTURE EXPOSED TO RADIOFREQUENCY RADIATION

IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING 1980年第8期27卷 452-460页

作者： BURR, JG COHOON, DK BELL, EL PENN, JW USAF DIV DATA SCIBIOMATH MODELING BRANCHBROOKS AFBTX 78235

A thermal response model of a simulated cranial structure (multilayered sphere) exposed to radiofrequency radiation (RFR) has been developed and experimentally verified for the no blood flow case. The thermal response model considers the RFR energy absorption distribution as predicted through use of the Mie theory, the thermal properties of the many layers, the blood flow to the central core area, and surface cooling through the application of a nonhomogeneous Newton cooling law. The model was preliminarily verified using homogeneous muscle equivalent spheres and a Vitek, Inc., model 101, electrothermia monitor.

关键词： Cranial Radio frequency Blood flow Cooling Temperature distribution biological system modeling Predictive models Electromagnetic modeling Temperature measurement Liquid crystal devices

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Optimality of Motion Camouflage Under Escape Uncertainty

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IEEE CONTROL systemS LETTERS 2024年 8卷 2613-2618页

作者： Gaspard, Mallory E. Cornell Univ Ctr Appl Math Ithaca NY 14853 USA

This letter proposes a novel continuous-time dynamic programming framework to determine when it is optimal for a pursuer to use motion camouflage (MC) amidst uncertainty in the evader's escape attempt time. We motivate this framework through the model problem of an energy-optimizing male hover fly pursuing a female hover fly for mating. The time at which the female fly initiates an escape is modeled to occur as the result of a non-homogeneous Poisson point process with a biologically informed rate function, and we obtain and solve two Hamilton-Jacobi-Bellman (HJB) PDEs which encode the pursuer's optimal trajectories. Our numerical experiments and statistics illustrate when it is optimal to use MC pursuit tactics amidst uncertainty and how MC optimality is affected by certain properties of the evader's sensing abilities.

关键词： Trajectory Optimal control biological system modeling Visual systems Uncertainty Visualization Planning Mathematical models Energy loss Costs biological systems switched systems pursuer-evader interactions

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modeling Variability in Populations of Cells Using Approximated Multivariate Distributions

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IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020年第5期17卷 1691-1702页

作者： Pichene, Matthieu Palaniappan, Sucheendra K. Fabre, Eric Genest, Blaise Univ Rennes INRIA Team SUMO F-35000 Rennes France Syst Biol Inst Tokyo 1410022 Japan Univ Rennes CNRS F-75016 Paris France

We are interested in studying the evolution of large homogeneous populations of cells, where each cell is assumed to be composed of a group of biological players (species) whose dynamics is governed by a complex biological pathway, identical for all cells. modeling the inherent variability of the species concentrations in different cells is crucial to understand the dynamics of the population. In this work, we focus on handling this variability by modeling each species by a random variable that evolves over time. This appealing approach runs into the curse of dimensionality since exactly representing a joint probability distribution involving a large set of random variables quickly becomes intractable as the number of variables grows. To make this approach amenable to biopathways, we explore different techniques to (i) approximate the exact joint distribution at a given time point, and (ii) to track its evolution as time elapses. We start with the problem of approximating the probability distribution of biological species in a population of cells at some given time point. Data come from different fine-grained models of biological pathways of increasing complexities, such as (perturbed) Ordinary Differential Equations (ODEs). Classical approximations rely on the strong and unrealistic assumption that variables/species are independent, or that they can be grouped into small independent clusters. We propose instead to use the Chow-Liu tree representation, based on overlapping clusters of two variables, which better captures correlations between variables. Our experiments show that the proposed approximation scheme is more accurate than existing ones to model probability distributions deriving from biopathways. Then we address the problem of tracking the dynamics of a population of cells, that is computing from an initial distribution the evolution of the (approximate) joint distribution of species over time, called the inference problem. We evaluate several approximate

关键词： Sociology Statistics biological system modeling Computational modeling Random variables Probability distribution biological pathways population of cells multivariate distributions

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IDENTIFICATION OF VIABLE biological STRATEGIES FOR PEST MANAGEMENT BY SIMULATION STUDIES

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IEEE TRANSACTIONS ON systemS MAN AND CYBERNETICS 1974年第4期SMC4卷 379-386页

作者： MENKE, WW UNIV FLORIDA COLL BUSINESS ADM DEPT MANAGEMENT GAINESVILLE FL 32611 USA

Interdisciplinary research has developed a stochastic computer model for studying interactions between an insect population, its host food crop, and other variables. This population growth model, highly adaptable to any insect and any host crop, is technically characterized by discrete arrivals, infinite servers, and multistage continuous service-time distribution functions. Because steady state is seldom achieved in nature, this paper identifies combinations of critical starting conditions (number of insects and disparate start times for insects and host crops), and critical stages for induced survival rate reductions to minimize crop damage. Sensitivity analyses serve to identify the most promising areas for future entomological research in pest management strategies.

关键词： biological system modeling Crops Insects Stochastic processes Ecosystems Computational modeling Disaster management Environmental economics Computer simulation Biology computing

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modeling Control of Supercoiling Dynamics and Transcription Using DNA-Binding Proteins

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IEEE CONTROL systemS LETTERS 2024年 8卷 2253-2258页

作者： Clark, Harris Taylor, Aleczander Yeung, Enoch Univ Calif Santa Barbara Dept Mech Engn Biol Control Lab Santa Barbara CA 93106 USA

Nearly all natural and synthetic gene networks rely on the fundamental process of transcription to enact biological feedback, genetic programs, and living circuitry. In this letter, we investigate the efficacy of controlling transcription using a new biophysical mechanism, control of localized supercoiling near a gene of interest. We postulate a basic reaction network model for describing the general phenomenon of transcription and introduce a separate set of equations to describe the dynamics of supercoiling. We show that supercoiling and transcription introduce a shared reaction flux term in the model dynamics and illustrate how the modulation of supercoiling can be used to control transcription rates. We show the supercoiling-transcription model can be written as a nonlinear state-space model, with a radial basis function nonlinearity to capture the empirical relationship between supercoiling and transcription rates. We show the system admits a single, globally exponentially stable equilibrium point. Notably, we show that mRNA steady-state levels can be controlled directly by increasing a length-scale parameter for genetic spacing. Finally, we build a mathematical model to explore the use of a DNA binding protein, to define programmable boundary conditions on supercoiling propagation, which we show can be used to control transcriptional bursting or pulsatile transcriptional response. We show there exists a stabilizing control law for mRNA tracking, using the method of control Lyapunov functions and illustrate these results with numerical simulations.

关键词： DNA Proteins Mathematical models Degradation biological system modeling RNA Polymers Biomolecular systems biological systems nonlinear control

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AN ITERATIVE EXTENDED BOUNDARY-CONDITION METHOD FOR SOLVING THE ABSORPTION CHARACTERISTICS OF LOSSY DIELECTRIC OBJECTS OF LARGE ASPECT RATIOS

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IEEE TRANSACTIONS ON MICROWAVE THEORY AND TECHNIQUES 1983年第8期31卷 640-647页

作者： LAKHTAKIA, A ISKANDER, MF DURNEY, CH Department of Electrical Engineering University of Utah Salt Lake UT USA

The recently developed iterative extended boundary condition method (IEBCM) has been used to compute the internal fields induced in homogeneous, axisymmetric, lossy dielectric objects of large aspect ratios when exposed to incident planewave radiation. Calculations were made for both the E- and k-polarization cases. The computed results for a prolate spheroidal model of an average man are found to be accurate for frequencies up to 300 MHz, while the use of the popular EBCM [1] was found to be essentially restricted to frequencies less than 70 MHz for these models and exposure conditions. The applicability of the IEBCM to composite bodies has also been examined by studying the irradiation of a capped cylindrical object. This composite object was first partitioned into several overlapping spherical subregions, and, alternatively, into two spherical subregions overlapping with a central cylindrical subregion. Spherical harmonics were used to represent the internal fields in the spherical subregions, while cylindrical expansions were utilized in the cylindrical subregions. It is shown that the second partitioning scheme is more computationally efficient and thereby suggests that the basis functions used to represent the subregional fields should be compatible with the subregional geometry. The new IEBCM, therefore, is a very valuable procedure which provides the opportunity of using the mixed basis functions in the solution.

关键词： Dielectric losses Iterative methods Boundary conditions Electromagnetic wave absorption Electromagnetic scattering Computational geometry Microwave frequencies biological system modeling Context modeling Humans

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Quantitative Aspects, Engineering and Optimization of Bacterial Sensor systems

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IEEE TRANSACTIONS ON MOLECULAR biological AND MULTI-SCALE COMMUNICATIONS 2024年第4期10卷 517-533页

作者： Anderl, Florian Salvadori, Gabriela Veletic, Mladen Petersen, Fernanda Cristina Balasingham, Ilangko Norwegian Univ Sci & Technol Dept Elect Syst N-7491 Trondheim Norway Oslo Univ Hosp Intervent Ctr N-0424 Oslo Norway Univ Oslo Inst Oral Biol Fac Dent N-0317 Oslo Norway

Bacterial sensor systems can be used for the detection and measurement of molecular signal concentrations. The dynamics of the sensor directly depend on the biological properties of the bacterial sensor cells;manipulation of these features in the wet lab enables the engineering and optimization of the bacterial sensor kinetics. This necessitates the development of biologically meaningful computational models for bacterial sensors comprising a variety of different molecular mechanisms, which further facilitates a systematic and quantitative evaluation of optimization strategies. In this work, we dissect the detection chain of bacterial sensors, focusing on computational aspects. As a case example, we derive, supported by wet-lab data, a complete computational model for a Streptococcus mutans-based bacterial sensor. We address the engineering of bacterial sensors by mathematically investigating the impact of altered bacterial cell properties on the sensor response characteristics, specifically sensor sensitivity and response signal intensity. This is achieved through a sensitivity analysis targeting both the steady-state and transient sensor response characteristics. Alongside the demonstration of the suitability of our methodological approach, our analysis shows that an increase in sensor sensitivity through targeted manipulation of bacterial physiology often comes at the cost of generally diminished sensor response intensity.

关键词： Microorganisms Biosensors Mathematical models Sensors biological system modeling Analytical models Computational modeling Bacterial sensor biosensors biochemical systems theory sensitivity analysis

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A Multi-Market Trading Framework for Low-Latency Service Provision at the Edge of Networks

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IEEE TRANSACTIONS ON SERVICES COMPUTING 2023年第1期16卷 27-39页

作者： Shih, Yuan-Yao Pang, Ai-Chun He, Tian Chiu, Te-Chuan Natl Chung Cheng Univ Dept Commun Engn Chiayi 62102 Taiwan Natl Taiwan Univ Grad Inst Networking & Multimedia Taipei 10617 Taiwan Natl Taiwan Univ Dept Comp Sci & Informat Engn Taipei 10617 Taiwan Univ Minnesota Dept Comp Sci & Engn Minneapolis MN 55455 USA Acad Sin Res Ctr Informat Technol Innovat CITI Taipei 115024 Taiwan

Along with the Ultra-Reliable and Low-Latency Communications (URLLC) of 5G, edge computing enables many potential low-latency IoT applications and has recently gained widespread attention. Addressing edge computing's economic issues is critical as we need to motivate edge devices as resource providers to devote their computing resources to the service. There are multiple users and resource providers in most edge computing service scenarios. The communication delays between users and providers are not the same since their physical distances are different. However, most existing works on edge computing regarding network economics adopt single market models that do not consider the influence of communication delay. Some researchers advocate using multi-market models to overcome this issue by grouping users who connect to the same access point or base station and letting each host its auction for resource trading. However, due to the high cost of deploying 5G ultra-dense small cells, barely a network operator can reach full network coverage. Users cannot rely on a single network, but these models do not allow resource trading between different groups. Thus, this article proposes a novel multi-market trading (MMT) framework to address these shortcomings. The framework combines the double auction at each group and a market selection game to enable the resource providers to participate in multiple auctions and analyze their choice of markets. We present the framework's detailed design and propose a theory-based learning algorithm to approximate each provider's optimal strategies. Through extensive simulations using real-world datasets of vehicular networks, we show that the proposed framework can improve the social welfare by $14.45\%$14.45% and $36.74\%$36.74%, respectively, compared with classic multi-market and single market models.

关键词： Performance evaluation 5G mobile communication Computational modeling biological system modeling Games Ultra reliable low latency communication Approximation algorithms Double auction edge computing multi-market fictitious play

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Electromagnetic absorption in the human head from experimental 6-GHz handheld transceivers

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IEEE TRANSACTIONS ON ELECTROMAGNETIC COMPATIBILITY 1995年第4期37卷 547-558页

作者： Gandhi, OP Chen, JY Department of Electrical Engineering University of Utah Salt Lake UT USA

We have used a new millimeter-resolution MRI-based model of the human body to calculate the electromagnetic absorption in the head and neck for three experimental Yagi antennas suggested for the handheld transceivers of a proposed 6-GHz personal communication network (PCN) system, The SAR distributions are obtained with a resolution of 1.974 x 1.974 x 1.5 mm for the transceivers that are held against the ears and tilted forward by 33 degrees. The finite-difference time-domain technique is used to calculate the EM fields and SAR's for the transceiver, antenna, and head and neck coupled region that is divided into 158 x 84 x 188 or nearly 2.5 million cells. The highlights of the numerical calculations are verified by means of a head-shaped experimental model made of tissue-equivalent materials simulating the electrical properties (epsilon(r),sigma) of skull, brain, muscle, eyes, and ears developed for use at 6 GHz. Because of the proximity to the antenna, the highest SAR's are obtained for the upper part of the ear, For a planned radiated power of 0.6 W, the peak SAR's averaged over any 1 g of tissue defined as a tissue volume in the shape of a cube are on the order of 0.5-1.0 W/kg for two of the proposed antennas and considerably higher (2.06 W/kg) far the third antenna using a narrower off-axis reflector, Low SAR's for the first two antennas are likely due to the shielding provided by the relatively wider strip reflector plates used for these antennas.

关键词： Electromagnetic wave absorption Humans Reflector antennas Transceivers Ear Neck Personal communication networks Brain modeling biological system modeling Electromagnetic modeling

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Deep Collaborative Filtering for Prediction of Disease Genes

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IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020年第5期17卷 1639-1647页

作者： Zeng, Xiangxiang Lin, Yinglai He, Yuying Lu, Linyuan Min, Xiaoping Rodriguez-Paton, Alfonso Xiamen Univ Dept Comp Sci Xiamen 361005 Peoples R China Univ Politecn Madrid Dept Inteligencia Artificial Campus Montegancedo Madrid 28660 Spain Univ Elect Sci & Technol China Inst Fundamental & Frontier Sci Chengdu 610054 Sichuan Peoples R China Hangzhou Normal Univ Alibaba Business Coll Alibaba Res Ctr Complex Sci Hangzhou 311121 Peoples R China

Accurate prioritization of potential disease genes is a fundamental challenge in biomedical research. Various algorithms have been developed to solve such problems. Inductive Matrix Completion (IMC) is one of the most reliable models for its well-established framework and its superior performance in predicting gene-disease associations. However, the IMC method does not hierarchically extract deep features, which might limit the quality of recovery. In this case, the architecture of deep learning, which obtains high-level representations and handles noises and outliers presented in large-scale biological datasets, is introduced into the side information of genes in our Deep Collaborative Filtering (DCF) model. Further, for lack of negative examples, we also exploit Positive-Unlabeled (PU) learning formulation to low-rank matrix completion. Our approach achieves substantially improved performance over other state-of-the-art methods on diseases from the Online Mendelian Inheritance in Man (OMIM) database. Our approach is 10 percent more efficient than standard IMC in detecting a true association, and significantly outperforms other alternatives in terms of the precision-recall metric at the top-k predictions. Moreover, we also validate the disease with no previously known gene associations and newly reported OMIM associations. The experimental results show that DCF is still satisfactory for ranking novel disease phenotypes as well as mining unexplored relationships. The source code and the data are available at https://***/xzenglab/DCF.

关键词： Diseases Collaboration biological system modeling Loss measurement Noise reduction Feature extraction Deep learning Disease genes prediction data integration deep learning PU learning matrix completion

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