IEEE Transactions on Molecular, Biological, and Multi-Scale Communications最新文献

{"title":"IEEE Communications Society Information","authors":"","doi":"10.1109/TMBMC.2025.3574832","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3574832","url":null,"abstract":"","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 2","pages":"C3-C3"},"PeriodicalIF":2.4,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=11033153","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144272804","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Special Feature: 15th EAI International Conference on Bio-Inspired Information and Communications Technologies and 1st Asia–Pacific Workshop on Molecular Communications","authors":"Yifan Chen","doi":"10.1109/TMBMC.2025.3574834","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3574834","url":null,"abstract":"","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 2","pages":"234-236"},"PeriodicalIF":2.4,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=11033161","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144272915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Publication Information","authors":"","doi":"10.1109/TMBMC.2025.3574830","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3574830","url":null,"abstract":"","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 2","pages":"C2-C2"},"PeriodicalIF":2.4,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=11033151","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144272953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extending Iterated, Spatialized Prisoner’s Dilemma to Understand Multicellularity: Game Theory With Self-Scaling Players","authors":"Lakshwin Shreesha;Federico Pigozzi;Adam Goldstein;Michael Levin","doi":"10.1109/TMBMC.2025.3562358","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3562358","url":null,"abstract":"Evolutionary developmental biology, biomedicine, neuroscience, and many aspects of the social sciences are impacted by insight into forces that facilitate the merging of active subunits into an emergent collective. The dynamics of interaction between agents are often studied in game theory, such as the popular Prisoner’s Dilemma (PD) paradigm, but the impact of these models on higher scales of organization, and their contributions to questions of how agents distinguish borders between themselves and the outside world, are not clear. Here we applied a spatialized, iterated PD model to understand the dynamics of the formation of large-scale tissues (colonies that act as one) out of single cell agents. In particular, we broke a standard assumption of PD: instead of a fixed number of players which can Cooperate or Defect on each round, we let the borders of individuality remain fluid, enabling agents to also Merge or Split. The consequences of enabling agents’ actions to change the number of agents in the world result in non-linear dynamics that are not known in advance: would higher-level (composite) individuals emerge? We characterized changes in collective formation as a function of memory size of the subunits. Our results show that when the number of agents is determined by the agents’ behavior, PD dynamics favor multicellularity, including the emergence of structured cell-groups, eventually leading to one single fully-merged tissue. These larger agents were found to have higher causal emergence than smaller ones. Moreover, we observed different spatial distributions of merged connectivity vs. of similar behavioral propensities, revealing that rich but distinct structures can coexist at the level of physical structure and the space of behavioral propensities. These dynamics raise a number of interesting and deep questions about decision-making in a self-modifying system that transitions from a metabolic to a morphological problem space, and how collective intelligences emerge, scale, and pattern.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 2","pages":"135-151"},"PeriodicalIF":2.4,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10970107","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144272882","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Joint DNA Encoding Approach Based on LZW and Arithmetic Encoding","authors":"Zhongyang Cheng;Qiang Liu;Kun Yang","doi":"10.1109/TMBMC.2025.3556858","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3556858","url":null,"abstract":"Molecular communication (MC) represents a novel approach to communication that employs nanoengineering and bioengineering technology to establish transient communication links in challenging environments. Deoxyribonucleic acid (DNA) molecular communication can transmit more and faster data than traditional molecular communication. Deoxyribonucleic acid (DNA) has been demonstrated to offer significant advantages over traditional information carriers, including its excellent storage density and structural stability, which renders it an ideal medium for information transmission. It is therefore imperative to investigate methods of increasing the data information density of DNA in order to reduce costs and enhance overall performance. LZW encoding is Lempel-Ziv–Welch encoding which creates a string table with shorter codes representing longer strings. Arithmetic coding is a compression process that involves the continuous refinement of probabilities of the input stream within an interval. A notable drawback of LZW coding is its suboptimal compression efficiency and the presence of data redundancy after dictionary mapping. Conversely, arithmetic coding attains compression efficiency that approaches the Shannon limit. In this study, we propose a novel DNA encoding method which is capable of adaptively generating coding streams in accordance with the characteristics of the stored content. The contribution of this paper is as follows: 1) A bespoke coding dictionary is constructed, which is capable of intelligently generating the corresponding coding stream in accordance with the specific characteristics of the file to be stored. 2) Utilising arithmetic coding techniques, these coding streams are converted into the final DNA sequence by means of compression techniques. Following comprehensive verification, it has been established that the information density of this encoding method is markedly superior to that of the prevailing mainstream encoding schemes.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 2","pages":"237-245"},"PeriodicalIF":2.4,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144272939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CDM in Neural Communication Based on Oscillatory Characteristics of Membrane Potential","authors":"Huiyu Luo;Yi Huang;Lin Lin","doi":"10.1109/TMBMC.2025.3556841","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3556841","url":null,"abstract":"With the advancement of the Internet of Nanothings (IoNT), information networks within organisms are becoming increasingly sophisticated, making the transmission of data from IoNT to the external environment a key research focus. Neural communication, as a promising solution, utilizes action potentials (APs) to carry information. However, enhancing the efficiency of data transmission for multiple IoNT nodes in a complex biological environment presents significant challenges. To address these challenges, this paper proposes an adaptive code division multiplexing (CDM) schemes in neural communication based on the oscillatory characteristics of membrane potential, enabling parallel information transmission for multiple IoNT nodes. This scheme assigns each signal an orthogonal code sequence and superimposes them onto a shared channel. To accommodate the oscillatory properties described by the resonate-and-fire (RF) neuron model, our approach further encodes the superimposed signals in CDM schemes, converting both symbolic and numerical bits into binary data for transmission. Simulation results demonstrate that the proposed scheme significantly enhances interference resistance while enabling multiple signals to share a single neuron channel. This paper paves the way for the implementation of IoNT applications.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 2","pages":"246-256"},"PeriodicalIF":2.4,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144272913","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Noise Characterization and Robust Signal Detection in Yeast Pheromone Molecular Communication","authors":"Nikolaos Ntetsikas;Styliana Kyriakoudi;Antonis Kirmizis Kirmizis;Ioannis Krikidis;Ian F. Akyildiz;Marios Lestas","doi":"10.1109/TMBMC.2025.3554640","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3554640","url":null,"abstract":"A critical aspect of Molecular Communications (MC) is the implementation of signal detection policies amidst noise. To date, noise characterizations within the MC field have predominantly drawn from methodologies found in wireless communications literature. In this study, we diverge from existing MC research by utilizing a newly developed experimental platform that employs yeast, allowing us to consider more realistic noise characterizations based on the relevant signaling pathways. We propose suitable signal detection mechanisms tailored to this experimental setup, which focuses on yeast cell-to-cell communications. Our analysis identifies gene transcription as the primary source of noise, and we utilize a Markov birth-death process model with Poisson arrivals and departures to characterize it. The noisy expression of the FUS1 gene is best represented using a mixed Gaussian distribution model. This model serves as a foundation for evaluating the performance of Maximum Likelihood Detection mechanisms in terms of Bit Error Rate (BER) for both symbol-by-symbol and sequence transmission schemes. Error analysis indicates that appropriate adjustments to the signal threshold can reduce errors to as low as 10%, which is not negligible. In contrast, the detection of symbol sequences demonstrates enhanced error performance, achieving error rates as low as 0.4%, albeit at the cost of increased computational complexity.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 2","pages":"218-227"},"PeriodicalIF":2.4,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144272884","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Anisotropic Diffusion Model of Communication in 2D Biofilm","authors":"Yanahan Paramalingam;Hamidreza Arjmandi;Freya Harrison;Tara Schiller;Adam Noel","doi":"10.1109/TMBMC.2025.3552991","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3552991","url":null,"abstract":"A biofilm is a microbial city. It consists of bacteria embedded in an extracellular polymeric substance (EPS) that functions as a protective barrier. Quorum sensing (QS) is a method of bacterial communication, where autoinducers (AIs) propagate via diffusion through the EPS and water channels within the biofilm. This diffusion process is anisotropic due to varying densities between the EPS and water channels. This study introduces a 2D anisotropic diffusion model for molecular communication (MC) within biofilms, analyzing information propagation between a point-to-point transmitter (TX) and receiver (RX) in bounded space. The channel impulse response is derived using Green’s function for concentration (GFC) and is validated with particle-based simulation (PBS). The outcomes reveal similar results for both isotropic and anisotropic diffusion when the TX is centrally located due to symmetry. However, anisotropic conditions lead to greater diffusion peaks when the TX is positioned off-center. Additionally, the propagation of AIs is inversely proportional to both overall biofilm size and diffusion coefficient values. It is hypothesized that anisotropic diffusion supports faster responses to hostile environmental changes because signals can propagate faster from the edge of the biofilm to the center.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 2","pages":"176-185"},"PeriodicalIF":2.4,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144272880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quorum Sensing Model Structures Inspire the Design of Quorum Quenching Strategies","authors":"Chiara Cimolato;Gianluca Selvaggio;Luca Marchetti;Giulia Giordano;Luca Schenato;Massimo Bellato","doi":"10.1109/TMBMC.2025.3554671","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3554671","url":null,"abstract":"Quorum Sensing (QS) is a bacterial cell-to-cell communication mechanism allowing to share information about cell density, to adjust gene expression accordingly. Pathogens leverage QS to coordinate virulence and antimicrobial resistance, leading to distinctive population-level behaviors. To support rational design of synthetic biology strategies counteracting these mechanisms, we first mathematically model and compare two common QS architectures: one based on a single positive feedback loop to auto-induce signal molecule synthesis, the other including an additional positive feedback to increase signal molecule receptors production. Our comprehensive analysis of these QS structures and their equilibria highlights the differences in their bistable and hysteretic behaviors. An extensive sensitivity analysis is then performed, highlighting how parameter variations may lead to phenotype alterations in system behavior. Finally, building on our sensitivity analysis, we mathematically model four distinct QS inhibition strategies - signal molecule degradation, pharmaceutical inhibition, CRISPRi, and RNAi - which lead to the design of Quorum-Quenching (QQ) therapeutic approaches. Despite the underlying complex mechanisms, we demonstrate that the effect of the proposed QQ strategies can be captured by varying specific parameters within the QS models. We numerically analyze how these strategies affect the steady-state behavior of both QS models, identifying critical parameter thresholds for effective QS suppression.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 2","pages":"201-217"},"PeriodicalIF":2.4,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10938711","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144272883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Molecular Communication Perspective of Alzheimer’s Disease: Impact of Amyloid Beta Oligomers on Glutamate Diffusion in the Synaptic Cleft","authors":"Nayereh FallahBagheri;Özgür B. Akan","doi":"10.1109/TMBMC.2025.3552959","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3552959","url":null,"abstract":"Molecular communication (MC) within the synaptic cleft is vital for neurotransmitter diffusion, a process critical to cognitive functions. In Alzheimer’s Disease (AD), beta-amyloid oligomers (A<inline-formula> <tex-math>$beta $ </tex-math></inline-formula>os) disrupt this communication, leading to synaptic dysfunction. This paper investigates the molecular interactions between glutamate, a key neurotransmitter, and A<inline-formula> <tex-math>$beta $ </tex-math></inline-formula>os within the synaptic cleft, aiming to elucidate the underlying mechanisms of this disruption. Through stochastic modeling, we simulate the dynamics of A<inline-formula> <tex-math>$beta $ </tex-math></inline-formula>os and their impact on glutamate diffusion. The findings, validated by comparing simulated results with existing experimental data, demonstrate that A<inline-formula> <tex-math>$beta $ </tex-math></inline-formula>os serve as physical obstacles, hindering glutamate movement and increasing collision frequency. This impairment of synaptic transmission and long-term potentiation (LTP) by binding to receptors on the postsynaptic membrane is further validated against known molecular interaction behaviors observed in similar neurodegenerative contexts. The study also explores potential therapeutic strategies to mitigate these disruptions. By enhancing our understanding of these molecular interactions, this research contributes to the development of more effective treatments for AD, with the ultimate goal of alleviating synaptic impairments associated with the disease.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 2","pages":"186-200"},"PeriodicalIF":2.4,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144272940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}