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IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Publication Information 电气和电子工程师学会《分子、生物和多尺度通信论文集》(IEEE Transactions on Molecular, Biological, and Multi-Scale Communications)出版信息
IF 2.4 Q2 ENGINEERING, ELECTRICAL & ELECTRONIC Pub Date : 2024-09-25 DOI: 10.1109/TMBMC.2024.3458333
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引用次数: 0
Optical Polarization Evolution and Transmission in Multi-Ranvier-Node Axonal Myelin-Sheath Waveguides 多ranvier节点轴突髓鞘波导的光偏振演化与传输
IF 2.4 Q2 ENGINEERING, ELECTRICAL & ELECTRONIC Pub Date : 2024-09-19 DOI: 10.1109/TMBMC.2024.3464415
Emily Frede;Hadi Zadeh-Haghighi;Christoph Simon
In neuroscience, it is of interest to consider all possible modes of information transfer between neurons in order to fully understand processing in the brain. It has been suggested that photonic communication may be possible along axonal connections, especially through the myelin sheath as a waveguide, due to its high refractive index. There is already a good deal of theoretical and experimental evidence for light guidance in the myelin sheath; however, the question of how the polarization of light is transmitted remains largely unexplored. It is presently unclear whether polarization-encoded information could be preserved within the myelin sheath. We simulate guided mode propagation through a myelinated axon structure with multiple Ranvier nodes. This allows both to observe polarization change and to test the assumption of exponentiated transmission loss through multiple Ranvier nodes for guided light in myelin sheath waveguides. We find that the polarization can be well preserved through multiple nodes and that transmission losses through multiple nodes are approximately multiplicative. These results provide an important context for the hypothesis of neural information transmission facilitated by biophotons, strengthening the possibility of both classical and quantum photonic communication within the brain.
在神经科学中,考虑神经元之间信息传递的所有可能模式以充分理解大脑中的处理是很有兴趣的。由于髓鞘的高折射率,光子通信可能沿着轴突连接,特别是通过作为波导的髓鞘进行。已经有大量的理论和实验证据证明髓鞘中的光引导;然而,光的偏振是如何传播的问题在很大程度上仍未被探索。目前还不清楚极化编码的信息是否可以保存在髓鞘内。我们模拟引导模式传播通过有髓鞘的轴突结构与多个朗维耶节点。这既可以观察偏振变化,也可以测试在髓鞘波导中引导光通过多个朗维耶节点的指数传输损耗假设。我们发现,通过多个节点可以很好地保持极化,并且通过多个节点的传输损失近似为乘法。这些结果为生物光子促进神经信息传递的假设提供了重要的背景,加强了脑内经典和量子光子通信的可能性。
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引用次数: 0
Localization With Joint Diffusion-Based Molecular Communication and Sensing Systems: Fundamental Limits and Tradeoffs
IF 2.4 Q2 ENGINEERING, ELECTRICAL & ELECTRONIC Pub Date : 2024-09-19 DOI: 10.1109/TMBMC.2024.3463672
Flavio Zabini
This paper introduces and examines a novel joint communication and sensing system based on molecular diffusion. Using a configuration of at least four fully absorbing spherical receivers, the proposed system achieves precise 3D-localization of a pointwise transmitter by counting the same molecules emitted for communication purposes. We develop an analytical framework to explore the fundamental limits of communication and localization within this context. Exact closed-form expressions for the bit error probability and the Cramér-Rao bound on localization error are derived, considering both Poisson concentration and timing transmitter models, with and without accounting for molecule degradation. For the first time, theoretical trade-offs between communication and localization performance are established, taking inter-symbol interference and molecule degradation into account. In scenarios without molecule degradation, inter-symbol interference detrimentally affects communication but enhances localization. Conversely, the introduction of degradation improves communication performance but partially compromises localization effectiveness. These trade-offs are navigated by adjusting number of transmitted symbols or degradation rate, respectively. Furthermore, we compare communication and localization ranges, alongside the associated costs measured in terms of average emitted molecules required to meet performance requirements.
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引用次数: 0
Molecular Quantum (MolQ) Communication Channel in the Gut-Brain Axis Synapse 肠-脑轴突触中的分子量子(MolQ)通信通道
IF 2.4 Q2 ENGINEERING, ELECTRICAL & ELECTRONIC Pub Date : 2024-09-17 DOI: 10.1109/TMBMC.2024.3462727
Bitop Maitra;Ozgur B. Akan
The gut-brain axis is the communication link between the gut and the brain. Although it is known that the gut-brain axis plays a pivotal role in homeostasis, its overall mechanism is still not known. However, for neural synapses, classical molecular communication is described by the formation of ligand-receptor complexes, which leads to the opening of ion channels. Moreover, there are some conditions that need to be fulfilled before the opening of the ion channel. In this study, we consider the gut-brain axis, where neurotransmitters diffuse through the synaptic cleft, considering molecular communication. On the vagus nerve (VN) membrane, i.e., the post-synaptic membrane of the synapse, it undergoes a quantum communication (QC), which initiates the opening of the ion channel, thus initiating the communication signal from the gut to the brain. It evolves a new paradigm of communication approach, Molecular Quantum (MolQ) communication. Based on the QC model, we theoretically analyze the output states, and QC is simulated considering the incoming neurotransmitter’s concentration and validated by analyzing the entropy and the mutual information of the input, i.e., neurotransmitter’s concentration, and output, i.e., ion channel opening.
肠脑轴是肠和大脑之间的沟通纽带。虽然已知肠脑轴在体内平衡中起关键作用,但其整体机制尚不清楚。然而,对于神经突触来说,经典的分子通信是通过配体-受体复合物的形成来描述的,这导致离子通道的开放。此外,在离子通道打开之前还需要满足一些条件。在这项研究中,我们考虑肠-脑轴,神经递质通过突触间隙扩散,考虑分子通讯。在迷走神经(VN)膜上,即突触的突触后膜上,进行量子通信(QC),量子通信启动离子通道的打开,从而启动肠道到大脑的通信信号。它发展了一种新的通信方法范式——分子量子通信。在QC模型的基础上,从理论上分析了输出状态,考虑输入神经递质浓度对QC进行了仿真,并通过分析输入神经递质浓度和输出离子通道开度的熵和互信息进行了验证。
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引用次数: 0
Odor Perceptual Shift Keying (OPSK) for Odor-Based Molecular Communication
IF 2.4 Q2 ENGINEERING, ELECTRICAL & ELECTRONIC Pub Date : 2024-09-13 DOI: 10.1109/TMBMC.2024.3460708
Fatih Efe Bilgen;Ahmet Burak Kilic;Ozgur B. Akan
Molecular communication (MC) has promising potential and a wide range of applications. However, odor-based communication which is common in nature, has not been sufficiently examined within the context of MC, yet. In this paper, we introduce a novel approach for implementing odor-based molecular communication (OMC) systems. We propose a new modulation scheme called Odor Perceptual Shift Keying (OPSK), which encodes information by shifting the perceptual values of odor molecules in pleasantness, intensity and edibility dimensions. We construct a system which transmits OPSK modulated signals between a transmitter and receiver. We conduct analyses on the system parameters to simulate performance metrics such as bit error rate (BER) and symbol rate (SR). Our analyses indicate that OPSK has a potential for realizing OMC systems. We find that under certain conditions, reliable OMC systems can be implemented using OPSK across a variety of distance ranges from millimeters up to kilometers. Additionally, we introduce adaptive waveform generation to our system for input symbol sequences featuring symbols that occur with unequal probabilities. We further demonstrate that the proposed algorithm at the transmitter side can achieve extended operation times.
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引用次数: 0
The Method of Fictitious Negative Sources to Model Diffusive Channels With Absorbing Boundaries 用虚构负源法模拟有吸收边界的扩散通道
IF 2.4 Q2 ENGINEERING, ELECTRICAL & ELECTRONIC Pub Date : 2024-09-02 DOI: 10.1109/TMBMC.2024.3453808
Fardad Vakilipoor;Abdulhamid N. M. Ansari;Luca Barletta;Gian Guido Gentili;Maurizio Magarini
This paper presents an approach to address the diffusion equation in scenarios involving multiple absorbing boundary conditions, commonly found in diffusive molecular communication (MC) channels. Instead of using multiple mirror images of the source, fictitious sources with time-varying release rates are introduced to replace the boundaries. This transformation enables the calculation of the expected cumulative number of absorbed particles (CNAP) by multiple absorbing boundaries with finite volume. To compute the expected CNAP, the concept of barycenter, which represents the spatial mean of particles the receiver absorbs is introduced. Substituting absorbing objects with their barycenters leads to model the CNAP in scenarios with convex geometry of absorbers. In a one-dimensional (1D) space, the proposed approach yields the same expression as the method of images for describing the expected CNAP by an absorber. However, in three-dimensional (3D) space, where using the method of images is challenging or even impossible, the proposed approach enables substituting the objects with fictitious sources and compute the expected CNAP. In 1D, an extension of this approach to the case in which one boundary exhibits an absorption characteristic while the other has zero-flux characteristic is demonstrated. This research direction is valuable for modeling channels where not all objects are particle receptors.
本文提出了一种在涉及多个吸收边界条件的情况下处理扩散方程的方法,这种情况通常出现在扩散分子通讯(MC)通道中。该方法不使用多个源的镜像,而是引入具有时变释放率的虚构源来替代边界。通过这种转换,可以计算出具有有限体积的多个吸收边界的预期累积吸收粒子数(CNAP)。为了计算预期累积吸收粒子数,引入了 "原心 "的概念,它代表了接收器吸收粒子的空间平均值。用吸收物体的原心代替吸收物体,就能在吸收体具有凸几何形状的情况下建立 CNAP 模型。在一维(1D)空间中,所提出的方法与图像法描述吸收体预期 CNAP 的表达式相同。然而,在三维(3D)空间中,使用图像方法具有挑战性,甚至是不可能的,而所提出的方法可以用虚构源代替物体,并计算预期的 CNAP。在一维空间中,这种方法扩展到了一个边界显示吸收特性而另一个边界显示零流量特性的情况。这一研究方向对于模拟并非所有物体都是粒子受体的通道非常有价值。
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引用次数: 0
Quantitative Aspects, Engineering and Optimization of Bacterial Sensor Systems 定量方面,工程和优化细菌传感器系统
IF 2.4 Q2 ENGINEERING, ELECTRICAL & ELECTRONIC Pub Date : 2024-08-30 DOI: 10.1109/TMBMC.2024.3452066
Florian Anderl;Gabriela Salvadori;Mladen Veletic;Fernanda Cristina Petersen;Ilangko Balasingham
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.
细菌传感器系统可用于分子信号浓度的检测和测量。传感器的动力学直接取决于细菌传感器细胞的生物学特性;在湿实验室中对这些特征的操作可以实现细菌传感器动力学的工程和优化。这就需要为包含各种不同分子机制的细菌传感器开发具有生物学意义的计算模型,从而进一步促进对优化策略的系统和定量评估。在这项工作中,我们剖析了细菌传感器的检测链,重点是计算方面。作为一个案例,我们推导了一个基于变形链球菌的细菌传感器的完整计算模型,并得到了湿实验室数据的支持。我们通过数学研究改变的细菌细胞特性对传感器响应特性的影响,特别是传感器灵敏度和响应信号强度,来解决细菌传感器的工程问题。这是通过针对稳态和瞬态传感器响应特性的灵敏度分析来实现的。除了证明我们的方法方法的适用性之外,我们的分析表明,通过有针对性地操纵细菌生理学来增加传感器灵敏度通常是以传感器响应强度普遍降低为代价的。
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引用次数: 0
Half-Space Modeling With Reflecting Surface in Molecular Communication 分子通信中带有反射面的半空间模型
IF 2.4 Q2 ENGINEERING, ELECTRICAL & ELECTRONIC Pub Date : 2024-08-23 DOI: 10.1109/TMBMC.2024.3448353
Anil Kamber;H. Birkan Yilmaz;Ali E. Pusane;Tuna Tugcu
In molecular communication via diffusion (MCvD), messenger molecules are emitted by a transmitter and propagate randomly through the fluidic environment. In biological systems, the environment can be considered a bounded space, surrounded by various structures such as tissues and organs. The propagation of molecules is affected by these structures, which reflect the molecules upon collision. Deriving the channel response of MCvD systems with an absorbing spherical receiver requires solving the 3-D diffusion equation in the presence of reflecting and absorbing boundary conditions, which is extremely challenging. In this paper, the method of images is brought to molecular communication (MC) realm to find a closed-form solution to the channel response of a single-input single-output (SISO) system near an infinite reflecting surface. It is shown that a molecular SISO system in a 3-D half-space with an infinite reflecting surface could be approximated as a molecular single-input multiple-output (SIMO) system in a 3-D space, which consists of two symmetrically located, with respect to the reflecting surface, identical absorbing spherical receivers.
在通过扩散进行的分子通讯(MCvD)中,信使分子由发射器发射,并在流体环境中随机传播。在生物系统中,环境可被视为一个有边界的空间,周围环绕着各种结构,如组织和器官。分子的传播会受到这些结构的影响,这些结构会在碰撞时反射分子。要推导具有吸收球形接收器的 MCvD 系统的通道响应,需要在存在反射和吸收边界条件的情况下求解三维扩散方程,这极具挑战性。本文将图像方法引入分子通信(MC)领域,为无限反射面附近的单输入单输出(SISO)系统的信道响应寻找闭式解。研究表明,在具有无限反射面的三维半空间中的分子 SISO 系统可以近似为三维空间中的分子单输入多输出(SIMO)系统,该系统由两个相对于反射面对称的相同吸收球形接收器组成。
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引用次数: 0
From Multiscale Biophysics to Digital Twins of Tissues and Organs: Future Opportunities for in-silico Pharmacology 从多尺度生物物理学到组织和器官的数字孪生:计算机药理学的未来机遇
IF 2.4 Q2 ENGINEERING, ELECTRICAL & ELECTRONIC Pub Date : 2024-08-12 DOI: 10.1109/TMBMC.2024.3442083
Michael Taynnan Barros;Michelangelo Paci;Aapo Tervonen;Elisa Passini;Jussi T. Koivumäki;Jari A. K. Hyttinen;Kerstin Lenk
With many advancements in in silico multiscale biology in recent years, the paramount challenge is to translate the accumulated knowledge into exciting industry partnerships and clinical applications. Historically, the pharmaceutical industry has worked well with in silico models by leveraging their prediction capabilities for drug testing. However, the needed higher fidelity and higher resolution of models for efficient prediction of pharmacological phenomenon dictates that in silico approaches must account for the verifiable multiscale biophysical phenomena, as a spatial and temporal dimension variation for different processes and models. Our paper has two main goals: 1) To clarify to what extent detailed single- and multiscale modeling has been accomplished thus far, we provide a review on this topic focusing on the biophysics of epithelial, cardiac, and brain tissues; 2) To discuss the present and future role of multiscale biophysics in in silico pharmacology as a digital twin solution by defining a roadmap from simple biophysical models to powerful prediction tools. Digital twins have the potential to pave the way for extensive clinical and pharmaceutical usage of multiscale models, and our paper shows the fundamentals and opportunities for their accurate development, enabling the quantum leaps of future precise and personalized medical software.
随着近年来硅多尺度生物学的许多进步,最大的挑战是将积累的知识转化为令人兴奋的行业合作伙伴关系和临床应用。从历史上看,制药行业通过利用其药物测试的预测能力,与计算机模型合作得很好。然而,为了有效地预测药理学现象,需要更高的保真度和更高的分辨率的模型,这就要求计算机方法必须考虑可验证的多尺度生物物理现象,作为不同过程和模型的空间和时间维度变化。我们的论文有两个主要目标:1)为了澄清到目前为止详细的单尺度和多尺度建模已经完成的程度,我们对这一主题进行了回顾,重点是上皮组织、心脏组织和脑组织的生物物理学;2)通过定义从简单的生物物理模型到强大的预测工具的路线图,讨论多尺度生物物理在计算机药理学中作为数字孪生解决方案的现在和未来的作用。数字孪生体有可能为多尺度模型的广泛临床和制药应用铺平道路,我们的论文展示了它们精确发展的基础和机会,使未来精确和个性化的医疗软件实现飞跃。
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引用次数: 0
Investigation of Different Chemical Realizations for Molecular Matrix Multiplications 分子矩阵乘法的不同化学实现方式研究
IF 2.4 Q2 ENGINEERING, ELECTRICAL & ELECTRONIC Pub Date : 2024-08-01 DOI: 10.1109/TMBMC.2024.3436905
Stefan Angerbauer;Nunzio Tuccitto;Giuseppe Trusso Sfrazzetto;Rossella Santonocito;Werner Haselmayr
Intelligent nano-machines are a promising candidate technology for the next generation of health care. The realization of such units relies on novel, unconventional approaches, to navigate the challenges of this particular domain. In this work, we present three chemical processes, that can be used to realize a recently proposed molecular matrix multiplication unit on the lab-scale. The matrix multiplication is the fundamental operation for the realization of neural networks and, therefore, artificial intelligence. Hence, this work presents an important step towards practical realization of intelligent nano-machines for the next generation of health care.
智能纳米机器是下一代医疗保健领域一项前景广阔的候选技术。要实现这种装置,需要采用新颖、非常规的方法,以应对这一特定领域的挑战。在这项工作中,我们介绍了三种化学过程,可用于在实验室规模上实现最近提出的分子矩阵乘法单元。矩阵乘法是实现神经网络和人工智能的基本操作。因此,这项工作是为下一代医疗保健实际实现智能纳米机器迈出的重要一步。
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引用次数: 0
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IEEE Transactions on Molecular, Biological, and Multi-Scale Communications
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