Pub Date : 2025-10-24DOI: 10.1109/TMBMC.2025.3625536
Russ White;Emily Brown Reeves;Gerald L. Fudge;Dagmar Zigackova;Joseph E. Deweese;James P. Keener
Engineers have developed abstract network models to better understand the recurring problems faced by communication systems. This paper argues that these models can be generalized to describe biological communications systems given that they share many requirements with human-designed systems, including functional requirements and physical constraints. Leveraging collaboration, biologists and engineers can work together to use well-understood communication systems, designed to carry data across a computer network, as a model for analyzing less well-understood biological communication systems in order to make predictions and uncover previously unknown functionalities. To illustrate this approach, we apply the Recursive Internet Network Architecture model (RINA) to two biological communications systems: DNA-to-ribosome signaling and phosphorylation signaling in bacterial chemotaxis. The RINA model categorizes biological observations as solutions to the familiar design requirements of multiplexing, marshaling, error control, and flow control. This approach offers a structured framework for analyzing biological communication systems that yields new insights into why they are structured as they are and how to further explore them.
{"title":"Using Network Models to Understand Biological Signaling Architecture","authors":"Russ White;Emily Brown Reeves;Gerald L. Fudge;Dagmar Zigackova;Joseph E. Deweese;James P. Keener","doi":"10.1109/TMBMC.2025.3625536","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3625536","url":null,"abstract":"Engineers have developed abstract network models to better understand the recurring problems faced by communication systems. This paper argues that these models can be generalized to describe biological communications systems given that they share many requirements with human-designed systems, including functional requirements and physical constraints. Leveraging collaboration, biologists and engineers can work together to use well-understood communication systems, designed to carry data across a computer network, as a model for analyzing less well-understood biological communication systems in order to make predictions and uncover previously unknown functionalities. To illustrate this approach, we apply the Recursive Internet Network Architecture model (RINA) to two biological communications systems: DNA-to-ribosome signaling and phosphorylation signaling in bacterial chemotaxis. The RINA model categorizes biological observations as solutions to the familiar design requirements of multiplexing, marshaling, error control, and flow control. This approach offers a structured framework for analyzing biological communication systems that yields new insights into why they are structured as they are and how to further explore them.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"12 ","pages":"47-68"},"PeriodicalIF":2.3,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=11217234","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145886635","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}
Pub Date : 2025-10-01DOI: 10.1109/TMBMC.2025.3615926
Ian F. Akyildiz;Selin Sayin;E. Ilker Saygili;Bige Deniz Unluturk
Algae, the ancient oxygenators of Earth, are increasingly recognized as dynamic communicative systems rather than passive photosynthetic organisms. This paper introduces a comprehensive framework for understanding algae communication and its implications for biotechnology and sustainability. We synthesize current knowledge of algae signaling, namely, chemical, optical, electrical, and physical and illustrate how these mechanisms underpin resilience, coordination, and ecosystem regulation. Building on this foundation, we highlight engineered applications where algae communication has been harnessed for bioenergy, bioremediation, medicine, and agriculture. Finally, we identify key research challenges, including decoding the algae interactome, designing biohybrid interfaces, and addressing ethical considerations in deploying communicative organisms. By connecting algae biology with principles of communication engineering and network theory, this work positions algae as living blueprints for robust, distributed, and programmable systems, offering a transformative path toward sustainable innovation. Our paper’s contributions are multidisciplinary: it provides biologists with a new network framework for algae behavior; offers engineers biological prototypes for distributed communication systems; gives interdisciplinary researchers a unifying bridge for collaboration; and supplies applied scientists with a roadmap for the next generation of communication-focused algae biotech.
{"title":"Algae Communication: Nature’s Oldest Networks for Sustainability and Biotechnology","authors":"Ian F. Akyildiz;Selin Sayin;E. Ilker Saygili;Bige Deniz Unluturk","doi":"10.1109/TMBMC.2025.3615926","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3615926","url":null,"abstract":"Algae, the ancient oxygenators of Earth, are increasingly recognized as dynamic communicative systems rather than passive photosynthetic organisms. This paper introduces a comprehensive framework for understanding algae communication and its implications for biotechnology and sustainability. We synthesize current knowledge of algae signaling, namely, chemical, optical, electrical, and physical and illustrate how these mechanisms underpin resilience, coordination, and ecosystem regulation. Building on this foundation, we highlight engineered applications where algae communication has been harnessed for bioenergy, bioremediation, medicine, and agriculture. Finally, we identify key research challenges, including decoding the algae interactome, designing biohybrid interfaces, and addressing ethical considerations in deploying communicative organisms. By connecting algae biology with principles of communication engineering and network theory, this work positions algae as living blueprints for robust, distributed, and programmable systems, offering a transformative path toward sustainable innovation. Our paper’s contributions are multidisciplinary: it provides biologists with a new network framework for algae behavior; offers engineers biological prototypes for distributed communication systems; gives interdisciplinary researchers a unifying bridge for collaboration; and supplies applied scientists with a roadmap for the next generation of communication-focused algae biotech.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 4","pages":"468-481"},"PeriodicalIF":2.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145760856","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}
Terahertz (THz) signalling, when tuned its frequency to the resonant frequency of target proteins, can induce conformational changes, which enables the design of interfaces for data exchange between external THz devices and intra-body protein-based molecular communication systems. Leveraging existing energy transfer models of the THz-excited protein resonance phenomenon, this work presents a THz-protein communication system, consisting of an inter-symbol interference (ISI)-free and an ISI-involved scenario. For ISI-free cases, we deduce the theoretical bit error rate (BER) and the optimal binary detection threshold. Then, a constrained BER optimization problem is created and solved to find optimal THz signalling variables, aiming at further improving the communication performance and mitigating the side-effects of THz signalling on undesired proteins. To address ISI contamination, we design a sequential maximizing a posteriori (MAP) signal detection scheme to recover the transmitted OOK sequences modulated onto the THz sinusoidal carrier. Numerical results show: (i) our constrained BER optimization provides optimal THz variables to simultaneously minimize BER and prevent THz side-effect on undesired proteins, and (ii) the designed sequential MAP scheme offers the best signal detection accuracy compared to other methods. This therefore, paves the way for the implementation of THz-protein communication systems to enable external to intra-body applications.
{"title":"Terahertz-Excited Protein Conformation-Based Communication: Optimization and Signal Detection","authors":"Zhuangkun Wei;Wenxiu Hu;Chenguang Liu;Tianhua Xu;Hongjian Sun;Yunfei Chen","doi":"10.1109/TMBMC.2025.3615930","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3615930","url":null,"abstract":"Terahertz (THz) signalling, when tuned its frequency to the resonant frequency of target proteins, can induce conformational changes, which enables the design of interfaces for data exchange between external THz devices and intra-body protein-based molecular communication systems. Leveraging existing energy transfer models of the THz-excited protein resonance phenomenon, this work presents a THz-protein communication system, consisting of an inter-symbol interference (ISI)-free and an ISI-involved scenario. For ISI-free cases, we deduce the theoretical bit error rate (BER) and the optimal binary detection threshold. Then, a constrained BER optimization problem is created and solved to find optimal THz signalling variables, aiming at further improving the communication performance and mitigating the side-effects of THz signalling on undesired proteins. To address ISI contamination, we design a sequential maximizing a posteriori (MAP) signal detection scheme to recover the transmitted OOK sequences modulated onto the THz sinusoidal carrier. Numerical results show: (i) our constrained BER optimization provides optimal THz variables to simultaneously minimize BER and prevent THz side-effect on undesired proteins, and (ii) the designed sequential MAP scheme offers the best signal detection accuracy compared to other methods. This therefore, paves the way for the implementation of THz-protein communication systems to enable external to intra-body applications.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"12 ","pages":"171-184"},"PeriodicalIF":2.3,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145929374","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}
Pub Date : 2025-09-30DOI: 10.1109/TMBMC.2025.3615932
Christopher J. Rourk
It has been hypothesized that the interaction of microtubules with photons via tryptophan arrays results in consciousness, and that inhibiting that behavior with anesthetics will provide proof of that hypothesis. Recently, evidence of superradiance in microtubules in tubo in response to UV stimulation and additional evidence of damping of electronic energy migration by the anesthetics isoflurane and etomidate have been proposed to provide evidentiary support for that model of consciousness. This minireview presents evidence that ferritin physically interacts with microtubules in samples obtained from live tissue. In addition, ferritin has relevant physical properties that are better for interacting with microtubules and damping electronic energy migration in microtubules than those of isoflurane and etomidate. This physical interaction and those properties would inhibit tryptophan fluorescence by 1) absorbing biophotons, as well as 2) additional mechanisms that result in electrical and magnetic interaction with microtubules and excited electrons in the microtubules. Therefore, the anesthetics isoflurane and etomidate would likely have no additional effect on microtubules in living cells than what is already present from ferritin, precluding the use of those test results as evidence for a microtubule theory of consciousness.
{"title":"The Interaction of Ferritin With Microtubules in Vivo Will Inhibit Microtubule Superradiance and Electronic Energy Migration Through Microtubules","authors":"Christopher J. Rourk","doi":"10.1109/TMBMC.2025.3615932","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3615932","url":null,"abstract":"It has been hypothesized that the interaction of microtubules with photons via tryptophan arrays results in consciousness, and that inhibiting that behavior with anesthetics will provide proof of that hypothesis. Recently, evidence of superradiance in microtubules in tubo in response to UV stimulation and additional evidence of damping of electronic energy migration by the anesthetics isoflurane and etomidate have been proposed to provide evidentiary support for that model of consciousness. This minireview presents evidence that ferritin physically interacts with microtubules in samples obtained from live tissue. In addition, ferritin has relevant physical properties that are better for interacting with microtubules and damping electronic energy migration in microtubules than those of isoflurane and etomidate. This physical interaction and those properties would inhibit tryptophan fluorescence by 1) absorbing biophotons, as well as 2) additional mechanisms that result in electrical and magnetic interaction with microtubules and excited electrons in the microtubules. Therefore, the anesthetics isoflurane and etomidate would likely have no additional effect on microtubules in living cells than what is already present from ferritin, precluding the use of those test results as evidence for a microtubule theory of consciousness.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"12 ","pages":"111-117"},"PeriodicalIF":2.3,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145929405","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}
We present a fluid-based experimental molecular communication (MC) testbed which uses media modulation. Motivated by the natural human cardiovascular system, the testbed operates in a closed-loop tube system. The proposed system is designed to be resource-efficient and controllable from outside the tube. As signaling molecule, the testbed employs the biocompatible green fluorescent protein variant “Dreiklang” (GFPD). GFPDs can be reversibly switched via light of different wavelengths between a bright fluorescent state and a less fluorescent state. GFPDs in solution are filled into the testbed prior to the start of information transmission and remain there for an entire experiment. For information transmission, an optical transmitter (TX) and an optical eraser (EX), which are located outside the tube, are used to write and erase the information encoded in the state of the GFPDs, respectively. At the receiver (RX), the state of the GFPDs is read out by fluorescence detection. In our testbed, due to the closed-loop setup and the long experiment durations of up to 125 hours, we observe new forms of inter-symbol interferences (ISI), which do not occur in short experiments and open-loop systems. In particular, up to four different forms of ISI, namely channel ISI, inter-loop ISI, offset ISI, and permanent ISI, occur in the considered system. For the testbed, we developed a communication scheme, which includes blind transmission start detection, symbol-by-symbol synchronization, and adaptive threshold detection, that supports higher order modulation. We comprehensively analyze our MC experiments using the absolute mean Euclidean distance (AMED), eye diagram, and bit error rate (BER) as performance metrics. Furthermore, we experimentally demonstrate the error-free transmission of 5,370 bit at a data rate of $36~mathrm {bit}{,}min ^{boldsymbol {-1}}$ using 8-ary modulation and the error-free binary transmission of around 90,000 bit at a data rate of $12~mathrm {bit}{,}min ^{boldsymbol {-1}}$ . For the latter experiment, data was transmitted continuously for a period of more than five days (125 hours) during which no signaling molecules were injected into or removed from the system. All signals recorded during the experiments, representing more than 250 kbit of data transmitted via MC, and parts of the evaluation code are publicly available on Zenodo and Github, respectively.
{"title":"Closed-Loop Long-Term Experimental Molecular Communication System","authors":"Maike Scherer;Lukas Brand;Louis Wolf;Teena Tom Dieck;Maximilian Schäfer;Sebastian Lotter;Andreas Burkovski;Heinrich Sticht;Robert Schober;Kathrin Castiglione","doi":"10.1109/TMBMC.2025.3615924","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3615924","url":null,"abstract":"We present a fluid-based experimental molecular communication (MC) testbed which uses media modulation. Motivated by the natural human cardiovascular system, the testbed operates in a closed-loop tube system. The proposed system is designed to be resource-efficient and controllable from outside the tube. As signaling molecule, the testbed employs the biocompatible green fluorescent protein variant “Dreiklang” (GFPD). GFPDs can be reversibly switched via light of different wavelengths between a bright fluorescent state and a less fluorescent state. GFPDs in solution are filled into the testbed prior to the start of information transmission and remain there for an entire experiment. For information transmission, an optical transmitter (TX) and an optical eraser (EX), which are located outside the tube, are used to write and erase the information encoded in the state of the GFPDs, respectively. At the receiver (RX), the state of the GFPDs is read out by fluorescence detection. In our testbed, due to the closed-loop setup and the long experiment durations of up to 125 hours, we observe new forms of inter-symbol interferences (ISI), which do not occur in short experiments and open-loop systems. In particular, up to four different forms of ISI, namely channel ISI, inter-loop ISI, offset ISI, and permanent ISI, occur in the considered system. For the testbed, we developed a communication scheme, which includes blind transmission start detection, symbol-by-symbol synchronization, and adaptive threshold detection, that supports higher order modulation. We comprehensively analyze our MC experiments using the absolute mean Euclidean distance (AMED), eye diagram, and bit error rate (BER) as performance metrics. Furthermore, we experimentally demonstrate the error-free transmission of 5,370 bit at a data rate of <inline-formula> <tex-math>$36~mathrm {bit}{,}min ^{boldsymbol {-1}}$ </tex-math></inline-formula> using 8-ary modulation and the error-free binary transmission of around 90,000 bit at a data rate of <inline-formula> <tex-math>$12~mathrm {bit}{,}min ^{boldsymbol {-1}}$ </tex-math></inline-formula>. For the latter experiment, data was transmitted continuously for a period of more than five days (125 hours) during which no signaling molecules were injected into or removed from the system. All signals recorded during the experiments, representing more than 250 kbit of data transmitted via MC, and parts of the evaluation code are publicly available on Zenodo and Github, respectively.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"12 ","pages":"22-41"},"PeriodicalIF":2.3,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145861191","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}
Molecular Communications (MC), transferring information via chemical signals, holds promise for transformative healthcare applications within the Internet of Bio-Nano Things (IoBNT) framework. Despite promising advances toward practical MC systems, progress has been constrained by experimental testbeds that are costly, difficult to customize, and require labor-intensive fabrication. Here, we address these challenges by introducing a low-cost ($sim {$}1$ per unit), rapidly fabricated (<1 hour), and highly customizable microfluidic testbed that integrates a cross-shaped, hydrodynamic gating-based microfluidic transmitter, and a screen-printed potentiometric sensor-based receiver. This platform enables precise spatiotemporal control over chemical signals and supports reconfigurable channel architectures along with on-demand sensor functionalization. As a proof of concept, we demonstrate a pH-based MC system combining a polyaniline (PANI)-functionalized screen printed sensor for real-time pH signal detection with a programmable hydrodynamic gating architecture, patterned in a double-sided adhesive tape, as the transmitter. By dynamically mixing phosphate-buffered saline (PBS) with an acidic solution (pH 3), the testbed reliably generates pH-encoded pulses. Experimental results confirm robust control over pulse amplitude and pulse width, enabling the simulation of end-to-end MC scenarios with 4-ary concentration shift keying (CSK) modulation. By combining affordability and rapid prototyping without compromising customizability, this platform is poised to accelerate the translation of MC concepts into practical IoBNT applications.
{"title":"Low-Cost Microfluidic Testbed for Molecular Communications With Integrated Hydrodynamic Gating and Screen-Printed Sensors","authors":"Maide Miray Albay;Eren Akyol;Fariborz Mirlou;Levent Beker;Murat Kuscu","doi":"10.1109/TMBMC.2025.3614382","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3614382","url":null,"abstract":"Molecular Communications (MC), transferring information via chemical signals, holds promise for transformative healthcare applications within the Internet of Bio-Nano Things (IoBNT) framework. Despite promising advances toward practical MC systems, progress has been constrained by experimental testbeds that are costly, difficult to customize, and require labor-intensive fabrication. Here, we address these challenges by introducing a low-cost (<inline-formula> <tex-math>$sim {$}1$ </tex-math></inline-formula> per unit), rapidly fabricated (<1 hour), and highly customizable microfluidic testbed that integrates a cross-shaped, hydrodynamic gating-based microfluidic transmitter, and a screen-printed potentiometric sensor-based receiver. This platform enables precise spatiotemporal control over chemical signals and supports reconfigurable channel architectures along with on-demand sensor functionalization. As a proof of concept, we demonstrate a pH-based MC system combining a polyaniline (PANI)-functionalized screen printed sensor for real-time pH signal detection with a programmable hydrodynamic gating architecture, patterned in a double-sided adhesive tape, as the transmitter. By dynamically mixing phosphate-buffered saline (PBS) with an acidic solution (pH 3), the testbed reliably generates pH-encoded pulses. Experimental results confirm robust control over pulse amplitude and pulse width, enabling the simulation of end-to-end MC scenarios with 4-ary concentration shift keying (CSK) modulation. By combining affordability and rapid prototyping without compromising customizability, this platform is poised to accelerate the translation of MC concepts into practical IoBNT applications.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 4","pages":"518-523"},"PeriodicalIF":2.3,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145760894","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}
Pub Date : 2025-09-22DOI: 10.1109/TMBMC.2025.3613268
Ben Cao;Yunzhu Zhao;Lei Xie;Qi Shao;Kun Wang;Bin Wang;Shihua Zhou;Pan Zheng
As the amount of data grows exponentially, traditional storage media face fundamental limitations in terms of density, lifespan, and energy consumption. DNA-based storage technology has become the most promising storage solution in recent years due to its ultra-high physical density, high stability, and low energy consumption. DNA sequencing is not only the core process of genomics, but is also a key step in reading data in DNA storage. However, sequencing errors are inevitable, and existing error correction codes can partially solve the problem, but they will introduce redundancy. In this work, we propose a Diversified Beam Search Path (DBSP) to process DNA sequencing data, aiming to improve nucleotide utilization in DNA storage and ensure data integrity. DBSP is a DNA storage data reconstruction pipeline from sequencing data that does not have additional redundancy. The scheme constructs the maximum node subgraph to cluster the sequencing data according to the similarity between sequences, finds the optimal solution of the candidate path set via a diverse beam search strategy, and finally introduces the consensus sequences into a nonredundant de Bruijn graph to solve the problem of path entanglement in the process of DNA sequence assembly. Experimental results show that DBSP outperforms multiple sequence alignment (MSA). The consensus sequence obtained by this scheme through multiple sequence alignment of diverse beam search has a smaller Levenshtein distance (LD) and Jaccard similarity closer to 1. It maintains a higher similarity to the encoded DNA at high error rates without redundancy. The nonredundant de Bruijn graph achieves over 68% sequence reconstruction rate. sequence recovery rate near 100% and the radians stable. In summary, this scheme can be an effective pre- or post-processing of error correction codes, and can realize end-to-end high-speed reconstruction of DNA storage data, and improve sequence reconstruction and sequence recovery rates, making DNA storage more reliable.
{"title":"DBSP: An End-to-End Pipeline for DNA Storage Data Reconstruction From DNA Sequencing","authors":"Ben Cao;Yunzhu Zhao;Lei Xie;Qi Shao;Kun Wang;Bin Wang;Shihua Zhou;Pan Zheng","doi":"10.1109/TMBMC.2025.3613268","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3613268","url":null,"abstract":"As the amount of data grows exponentially, traditional storage media face fundamental limitations in terms of density, lifespan, and energy consumption. DNA-based storage technology has become the most promising storage solution in recent years due to its ultra-high physical density, high stability, and low energy consumption. DNA sequencing is not only the core process of genomics, but is also a key step in reading data in DNA storage. However, sequencing errors are inevitable, and existing error correction codes can partially solve the problem, but they will introduce redundancy. In this work, we propose a Diversified Beam Search Path (DBSP) to process DNA sequencing data, aiming to improve nucleotide utilization in DNA storage and ensure data integrity. DBSP is a DNA storage data reconstruction pipeline from sequencing data that does not have additional redundancy. The scheme constructs the maximum node subgraph to cluster the sequencing data according to the similarity between sequences, finds the optimal solution of the candidate path set via a diverse beam search strategy, and finally introduces the consensus sequences into a nonredundant de Bruijn graph to solve the problem of path entanglement in the process of DNA sequence assembly. Experimental results show that DBSP outperforms multiple sequence alignment (MSA). The consensus sequence obtained by this scheme through multiple sequence alignment of diverse beam search has a smaller Levenshtein distance (LD) and Jaccard similarity closer to 1. It maintains a higher similarity to the encoded DNA at high error rates without redundancy. The nonredundant de Bruijn graph achieves over 68% sequence reconstruction rate. sequence recovery rate near 100% and the radians stable. In summary, this scheme can be an effective pre- or post-processing of error correction codes, and can realize end-to-end high-speed reconstruction of DNA storage data, and improve sequence reconstruction and sequence recovery rates, making DNA storage more reliable.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"12 ","pages":"157-170"},"PeriodicalIF":2.3,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145929467","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}
Pub Date : 2025-09-16DOI: 10.1109/TMBMC.2025.3610330
Franziska Weindel;Andreas L. Gimpel;Robert N. Grass;Reinhard Heckel
DNA is an attractive medium for digital data storage. When data is stored on DNA, errors occur, making error-correcting codes critical for reliable storage. A common approach to reduce errors is constrained coding, which avoids homopolymers (consecutive repeated nucleotides) and balances GC content, as they are associated with higher error rates. However, constrained coding comes at the cost of an increase in redundancy. An alternative is to randomize DNA sequences, embrace errors, and compensate with additional coding redundancy. In this paper, we identify the error regimes in which embracing substitution errors is more efficient than constrained coding. Our results indicate that constrained coding for substitution errors can be inefficient in current DNA data storage systems. Theoretical analysis shows that constrained coding would be efficient only under high error rates in homopolymers and GC-imbalanced sequences, while empirical data show that error-rate increases for these nucleotides are minimal in current systems.
{"title":"Embracing Errors Can Be More Efficient Than Avoiding Them Through Constrained Coding for DNA Data Storage","authors":"Franziska Weindel;Andreas L. Gimpel;Robert N. Grass;Reinhard Heckel","doi":"10.1109/TMBMC.2025.3610330","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3610330","url":null,"abstract":"DNA is an attractive medium for digital data storage. When data is stored on DNA, errors occur, making error-correcting codes critical for reliable storage. A common approach to reduce errors is constrained coding, which avoids homopolymers (consecutive repeated nucleotides) and balances GC content, as they are associated with higher error rates. However, constrained coding comes at the cost of an increase in redundancy. An alternative is to randomize DNA sequences, embrace errors, and compensate with additional coding redundancy. In this paper, we identify the error regimes in which embracing substitution errors is more efficient than constrained coding. Our results indicate that constrained coding for substitution errors can be inefficient in current DNA data storage systems. Theoretical analysis shows that constrained coding would be efficient only under high error rates in homopolymers and GC-imbalanced sequences, while empirical data show that error-rate increases for these nucleotides are minimal in current systems.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"12 ","pages":"146-156"},"PeriodicalIF":2.3,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145929465","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}
We investigate the application of semantic information theory to drug delivery systems (DDS) within the molecular communication (MC) framework. To operationalise this, we observe a DDS as a molecular concentration-based channel. Semantic information is defined as the amount of information required for a DDS to achieve its therapeutic goal in a dynamic environment. We derive it by introducing interventions, defined as modifications to DDS parameters, a viability function, and system-environment correlations quantified via the channel capacity. Here, the viability function represents DDS performance based on a drug dose-response relationship. Our model considers a system capable of inducing functional changes in a receiver cancer cell, where exceeding critical DDS parameter values can significantly reduce performance or cost-effectiveness. By analysing the MC-based DDS model through a semantic information perspective, we examine how correlations between the internalised particle concentration and the released particle concentration evolve under interventions. The final catalogue of results provides a quantitative basis for DDS design and optimisation, offering a method to determine optimal DDS parameter values under constraints such as chemical budget, desired effect and accuracy. Thus, the proposed framework can serve as a novel tool for guiding DDS design and optimisation.
{"title":"On Drug Delivery System Parameter Optimization via Semantic Information Theory","authors":"Milica Lekić;Mohammad Zoofaghari;Ilangko Balasingham;Mladen Veletić","doi":"10.1109/TMBMC.2025.3610350","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3610350","url":null,"abstract":"We investigate the application of semantic information theory to drug delivery systems (DDS) within the molecular communication (MC) framework. To operationalise this, we observe a DDS as a molecular concentration-based channel. Semantic information is defined as the amount of information required for a DDS to achieve its therapeutic goal in a dynamic environment. We derive it by introducing interventions, defined as modifications to DDS parameters, a viability function, and system-environment correlations quantified via the channel capacity. Here, the viability function represents DDS performance based on a drug dose-response relationship. Our model considers a system capable of inducing functional changes in a receiver cancer cell, where exceeding critical DDS parameter values can significantly reduce performance or cost-effectiveness. By analysing the MC-based DDS model through a semantic information perspective, we examine how correlations between the internalised particle concentration and the released particle concentration evolve under interventions. The final catalogue of results provides a quantitative basis for DDS design and optimisation, offering a method to determine optimal DDS parameter values under constraints such as chemical budget, desired effect and accuracy. Thus, the proposed framework can serve as a novel tool for guiding DDS design and optimisation.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"12 ","pages":"11-21"},"PeriodicalIF":2.3,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145861205","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":"Guest Editorial Understanding Communicable Diseases Through the Lens of Molecular Communications","authors":"Prabhat Kumar Sharma;Mauro Femminella;Sudhir Kumar","doi":"10.1109/TMBMC.2025.3601681","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3601681","url":null,"abstract":"","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 3","pages":"332-334"},"PeriodicalIF":2.3,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=11159554","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145036901","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}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：