Pub Date : 2025-08-19DOI: 10.1109/TMBMC.2025.3600516
Akshay Uttarkar;Vidya Niranjan
Protein folding is a fundamental process crucial for the functionality of biological molecules. Despite its significance, predicting protein structures accurately remains a challenging task due to the complex nature of folding pathways and interactions. In this study, we explore the application of quantum computing, specifically error mitigated VQE, in investigating the folding of disordered regions in Ubiquitin C. By integrating advanced simulation techniques and quantum algorithms, we aim to unravel the intricate dynamics of protein folding at a molecular level. We employ a combination of molecular dynamics simulations and quantum VQE algorithms to analyze the folding kinetics and stability of C-terminal region of Ubiquitin C. Utilizing state-of-the-art quantum simulators and computational tools, we track the evolution of protein conformations and assess ground state energy values to elucidate the folding process. Our results demonstrate the effectiveness of error mitigated VQE in providing accurate ground state energy values compared to traditional methods like MD simulations with difference less than −0.91 kcal/mol. The analysis reveals insights into the structural transitions and stability of Ubiquitin C during the folding process, shedding light on key interactions and conformational changes. This study underscores the potential of quantum computing in advancing our understanding of protein folding dynamics.
{"title":"Quantum-Enabled Protein Folding of Disordered Regions in Ubiquitin C via Error-Mitigated VQE Benchmarked on Tensor Network Simulator and Aria 1","authors":"Akshay Uttarkar;Vidya Niranjan","doi":"10.1109/TMBMC.2025.3600516","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3600516","url":null,"abstract":"Protein folding is a fundamental process crucial for the functionality of biological molecules. Despite its significance, predicting protein structures accurately remains a challenging task due to the complex nature of folding pathways and interactions. In this study, we explore the application of quantum computing, specifically error mitigated VQE, in investigating the folding of disordered regions in Ubiquitin C. By integrating advanced simulation techniques and quantum algorithms, we aim to unravel the intricate dynamics of protein folding at a molecular level. We employ a combination of molecular dynamics simulations and quantum VQE algorithms to analyze the folding kinetics and stability of C-terminal region of Ubiquitin C. Utilizing state-of-the-art quantum simulators and computational tools, we track the evolution of protein conformations and assess ground state energy values to elucidate the folding process. Our results demonstrate the effectiveness of error mitigated VQE in providing accurate ground state energy values compared to traditional methods like MD simulations with difference less than −0.91 kcal/mol. The analysis reveals insights into the structural transitions and stability of Ubiquitin C during the folding process, shedding light on key interactions and conformational changes. This study underscores the potential of quantum computing in advancing our understanding of protein folding dynamics.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"12 ","pages":"118-125"},"PeriodicalIF":2.3,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145929409","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 : 2025-07-30DOI: 10.1109/TMBMC.2025.3594064
Sunil Kumar;Prabhat Kumar Sharma;Anamika Singh;Adam Noel;Manav R. Bhatnagar
This study explores the collaborative behavior of engineered transmitter nano-machines (TNMs) in forming a network for efficient information transmission. The integrated units within TNMs enable them to monitor and regulate their behavior based on a system of punishments. Specifically, the research investigates how punishment impacts the system performance of TNM interacting to detect the region of interest (RoI) within a three-dimensional (3D) drift-diffusive channel. The TNMs communicate their observations about the RoI using information molecules (IMs) to a passive supervisor nano-machine (SNM), which makes RoI decisions comprehensively using AND and OR fusion rules. Inspired by nature, TNM opts for either cooperative or greedy strategies to produce IMs by consuming food from the environment. In the cooperative strategy, a TNM produces IMs and shares them equally among TNMs in the group, whereas in the greedy strategy, a TNM does not share the produced IMs, but it can continue receiving IMs shared by cooperative TNMs. A system of punishment for greedy TNMs is considered as per Tit-for-Tat and Grude policies. The study evaluates system performance in terms of the rate of success (RoS) of RoI detection, and the effects of factors such as diffusion coefficient, drift velocity, and the number of cooperating TNMs, on system performance. The results are validated using Monte Carlo simulation.
{"title":"Tit-for-Tat or Hold a Grudge: Impact of Punishment on Strategic Interactions of Nano-Machines","authors":"Sunil Kumar;Prabhat Kumar Sharma;Anamika Singh;Adam Noel;Manav R. Bhatnagar","doi":"10.1109/TMBMC.2025.3594064","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3594064","url":null,"abstract":"This study explores the collaborative behavior of engineered transmitter nano-machines (TNMs) in forming a network for efficient information transmission. The integrated units within TNMs enable them to monitor and regulate their behavior based on a system of punishments. Specifically, the research investigates how punishment impacts the system performance of TNM interacting to detect the region of interest (RoI) within a three-dimensional (3D) drift-diffusive channel. The TNMs communicate their observations about the RoI using information molecules (IMs) to a passive supervisor nano-machine (SNM), which makes RoI decisions comprehensively using AND and OR fusion rules. Inspired by nature, TNM opts for either cooperative or greedy strategies to produce IMs by consuming food from the environment. In the cooperative strategy, a TNM produces IMs and shares them equally among TNMs in the group, whereas in the greedy strategy, a TNM does not share the produced IMs, but it can continue receiving IMs shared by cooperative TNMs. A system of punishment for greedy TNMs is considered as per Tit-for-Tat and Grude policies. The study evaluates system performance in terms of the rate of success (RoS) of RoI detection, and the effects of factors such as diffusion coefficient, drift velocity, and the number of cooperating TNMs, on system performance. The results are validated using Monte Carlo simulation.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 4","pages":"600-609"},"PeriodicalIF":2.3,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145760895","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}
Recent experiments have demonstrated the feasibility of storing digital information in macromolecules such as DNA and proteins. While DNA storage systems benefit from extreme density and long durability, they suffer from various types of errors, including deletions, insertions, and substitutions. One way to address this problem is to store a sequence multiple times which can be modelled by sending a transmitted sequence over several identical channels that produce distinct outputs, allowing the receiver to collect the outputs and attempt to reconstruct the original sequence. The maximum number of possible outputs from the channels is referred to as the size of the error ball. The error ball encompasses all possible sequences that can arise from a limited number of errors applied to the original sequence. In this paper, we derive the size of the error ball generated by one deletion and two insertions. The method of derivation employs the inclusion-exclusion principle. We characterize the intersection size of any number of double-insertion balls of subsequences belong to single-deletion ball of a particular sequence. Furthermore, we generalize the notion of Type-B-confusable sequences for non-binary sequences and prove that the intersection size of two single-insertion balls of two sequences is one if and only if they are Type-B-confusable.
{"title":"On the Size of Error Ball in Single-Deletion Double-Insertion Channels","authors":"Aryan Abbasian;Mahtab Mirmohseni;Masoumeh Nasiri-Kenari","doi":"10.1109/TMBMC.2025.3590000","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3590000","url":null,"abstract":"Recent experiments have demonstrated the feasibility of storing digital information in macromolecules such as DNA and proteins. While DNA storage systems benefit from extreme density and long durability, they suffer from various types of errors, including deletions, insertions, and substitutions. One way to address this problem is to store a sequence multiple times which can be modelled by sending a transmitted sequence over several identical channels that produce distinct outputs, allowing the receiver to collect the outputs and attempt to reconstruct the original sequence. The maximum number of possible outputs from the channels is referred to as the size of the error ball. The error ball encompasses all possible sequences that can arise from a limited number of errors applied to the original sequence. In this paper, we derive the size of the error ball generated by one deletion and two insertions. The method of derivation employs the inclusion-exclusion principle. We characterize the intersection size of any number of double-insertion balls of subsequences belong to single-deletion ball of a particular sequence. Furthermore, we generalize the notion of Type-B-confusable sequences for non-binary sequences and prove that the intersection size of two single-insertion balls of two sequences is one if and only if they are Type-B-confusable.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 4","pages":"537-548"},"PeriodicalIF":2.3,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145760884","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 : 2025-07-03DOI: 10.1109/TMBMC.2025.3585798
Beyza E. Ortlek;Ozgur B. Akan
Molecular communication (MC) is a bio-inspired communication paradigm that utilizes molecules to transfer information and offers a robust framework for understanding biological signaling systems. This paper introduces a novel end-to-end MC framework for short-chain fatty acid (SCFA)-driven vagus nerve signaling within the gut-brain axis (GBA) to enhance our understanding of gut-brain communication mechanisms. SCFA molecules, produced by gut microbiota, serve as important biomarkers in physiological and psychological processes, including neurodegenerative and mental health disorders. The developed end-to-end model integrates SCFA binding to vagal afferent fibers, G protein-coupled receptor (GPCR)-mediated calcium signaling, and Hodgkin-Huxley-based action potential generation into a comprehensive vagus nerve signaling mechanism through GBA. Information-theoretic metrics such as mutual information and delay are used to evaluate the efficiency of this SCFA-driven signaling pathway model. Simulations demonstrate how molecular inputs translate into neural outputs, highlighting critical aspects that govern gut-brain communication. In this work, the integration of SCFA-driven signaling into the MC framework provides a novel perspective on gut-brain communication and paves the way for the development of innovative therapeutic advancements targeting neurological and psychiatric disorders.
{"title":"Modeling and Analysis of SCFA-Driven Vagus Nerve Signaling in the Gut-Brain Axis via Molecular Communication","authors":"Beyza E. Ortlek;Ozgur B. Akan","doi":"10.1109/TMBMC.2025.3585798","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3585798","url":null,"abstract":"Molecular communication (MC) is a bio-inspired communication paradigm that utilizes molecules to transfer information and offers a robust framework for understanding biological signaling systems. This paper introduces a novel end-to-end MC framework for short-chain fatty acid (SCFA)-driven vagus nerve signaling within the gut-brain axis (GBA) to enhance our understanding of gut-brain communication mechanisms. SCFA molecules, produced by gut microbiota, serve as important biomarkers in physiological and psychological processes, including neurodegenerative and mental health disorders. The developed end-to-end model integrates SCFA binding to vagal afferent fibers, G protein-coupled receptor (GPCR)-mediated calcium signaling, and Hodgkin-Huxley-based action potential generation into a comprehensive vagus nerve signaling mechanism through GBA. Information-theoretic metrics such as mutual information and delay are used to evaluate the efficiency of this SCFA-driven signaling pathway model. Simulations demonstrate how molecular inputs translate into neural outputs, highlighting critical aspects that govern gut-brain communication. In this work, the integration of SCFA-driven signaling into the MC framework provides a novel perspective on gut-brain communication and paves the way for the development of innovative therapeutic advancements targeting neurological and psychiatric disorders.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 4","pages":"588-599"},"PeriodicalIF":2.3,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145760932","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 : 2025-06-30DOI: 10.1109/TMBMC.2025.3584281
Ruifeng Zheng;Pit Hofmann;Pengjie Zhou;Juan A. Cabrera;Patrick Seeling;Martin Reisslein;Frank H. P. Fitzek
Molecular Communication via Diffusion (MCvD) is a viable communication paradigm for nanonetworks, particularly in fluidic biological environments where bio-nanonetworks operate. Two significant factors that degrade the MCvD signal are noise and Inter-Symbol Interference (ISI). The expected Channel Impulse Response (CIR) of MCvD exhibits a long, slowly attenuating tail due to molecular diffusion, leading to ISI and consequently limiting the data rate. The suppression of ISI and noise is crucial for enhancing the effectiveness of MCvD systems, especially at higher data rates. Although various ISI-suppression methods have been explored, they are often treated as secondary components in broader topics, such as signal detection or modulation. Moreover, most current ISI-suppression techniques subtract the estimated ISI from the total signal. In this study, we introduce a novel approach to ISI-suppression through the use of filters, which eliminate ISI without requiring an ISI estimation. We explore the principles underlying ISI-suppression filters in MCvD and propose the Anti-Noise ISI-Suppression (ANIS) filter with robust anti-noise capabilities, accompanied by a signal detection scheme tailored for MCvD scenarios afflicted by both ISI and noise. We compare our proposed ANIS filter against state-of-the-art detection approaches. The results demonstrate that our ANIS filter can effectively recover signals severely degraded by both ISI and noise.
{"title":"ANIS: Anti-Noise ISI-Suppression Filter for Molecular Communication via Diffusion","authors":"Ruifeng Zheng;Pit Hofmann;Pengjie Zhou;Juan A. Cabrera;Patrick Seeling;Martin Reisslein;Frank H. P. Fitzek","doi":"10.1109/TMBMC.2025.3584281","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3584281","url":null,"abstract":"Molecular Communication via Diffusion (MCvD) is a viable communication paradigm for nanonetworks, particularly in fluidic biological environments where bio-nanonetworks operate. Two significant factors that degrade the MCvD signal are noise and Inter-Symbol Interference (ISI). The expected Channel Impulse Response (CIR) of MCvD exhibits a long, slowly attenuating tail due to molecular diffusion, leading to ISI and consequently limiting the data rate. The suppression of ISI and noise is crucial for enhancing the effectiveness of MCvD systems, especially at higher data rates. Although various ISI-suppression methods have been explored, they are often treated as secondary components in broader topics, such as signal detection or modulation. Moreover, most current ISI-suppression techniques subtract the estimated ISI from the total signal. In this study, we introduce a novel approach to ISI-suppression through the use of filters, which eliminate ISI without requiring an ISI estimation. We explore the principles underlying ISI-suppression filters in MCvD and propose the Anti-Noise ISI-Suppression (ANIS) filter with robust anti-noise capabilities, accompanied by a signal detection scheme tailored for MCvD scenarios afflicted by both ISI and noise. We compare our proposed ANIS filter against state-of-the-art detection approaches. The results demonstrate that our ANIS filter can effectively recover signals severely degraded by both ISI and noise.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 4","pages":"572-587"},"PeriodicalIF":2.3,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145760880","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}
Intersymbol Interference (ISI) is one of the major bottlenecks in Molecular Communication via Diffusion (MCvD) systems resulting in degraded system performance. This paper first introduces two new families of linear channel codes to minimize the effect of ISI: linear Zero Pad Zero Start (ZPZS) and linear Zero Pad (ZP) codes, ensuring that every codeword is devoid of consecutive bit-1s. Subsequently, the ZPZS linear and ZP linear codes are combined to form a binary ZP code, aiming for a higher code rate compared to the linear ZP codes, which can be decoded with a simple Majority Location Rule (MLR) algorithm. Additionally, a linear Leading One Zero Pad (LOZP) code is proposed, which relaxes the zero padding constraints considering the placement of bit-1s in the codeword as an important metric to have an improved code rate than the ZP code. Finally, a closed-form expression is deduced to compute the expected ISI for the proposed codes and to demonstrate that the expected ISI is a function of the average bit-1 density of the codewords in a code. To compare the ISI and BER performance with average bit-1 density of the proposed codes, two types of MCvD channel are considered: (i) channel without refresh, where the previously transmitted bits persist for a longer duration and (ii) channel with refresh, where the channel is cleared after each successful reception of the message. The ISI comparison, across different sequence distributions for a given length and weight, shows that the linear LOZP code exhibits superior resilience against ISI in a channel with refresh due to the placement of bit-1s at the initial positions, whereas the ZP code performs better in channel without refresh by reducing the average bit-1 density of the code. The asymptotic upper bound of the code rate is derived for the proposed codes, which depicts that a trade-off exists between the ISI and code rate. The simulation results show that the proposed family of ZP and linear LOZP codes can improve the Bit Error Rate (BER) performance by controlling the bit-1 locations and the average bit-1 density of the code, specifically where the ISI is more pronounced over the channel noise, thus providing a better reliability compared to the conventional error correcting codes at different data rate regimes.
{"title":"ISI-Aware Code Design: A Linear Approach Toward Reliable Molecular Communication","authors":"Tamoghno Nath;Krishna Gopal Benerjee;Adrish Banerjee","doi":"10.1109/TMBMC.2025.3583543","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3583543","url":null,"abstract":"Intersymbol Interference (ISI) is one of the major bottlenecks in Molecular Communication via Diffusion (MCvD) systems resulting in degraded system performance. This paper first introduces two new families of linear channel codes to minimize the effect of ISI: linear Zero Pad Zero Start (ZPZS) and linear Zero Pad (ZP) codes, ensuring that every codeword is devoid of consecutive bit-1s. Subsequently, the ZPZS linear and ZP linear codes are combined to form a binary ZP code, aiming for a higher code rate compared to the linear ZP codes, which can be decoded with a simple Majority Location Rule (MLR) algorithm. Additionally, a linear Leading One Zero Pad (LOZP) code is proposed, which relaxes the zero padding constraints considering the placement of bit-1s in the codeword as an important metric to have an improved code rate than the ZP code. Finally, a closed-form expression is deduced to compute the expected ISI for the proposed codes and to demonstrate that the expected ISI is a function of the average bit-1 density of the codewords in a code. To compare the ISI and BER performance with average bit-1 density of the proposed codes, two types of MCvD channel are considered: (i) channel without refresh, where the previously transmitted bits persist for a longer duration and (ii) channel with refresh, where the channel is cleared after each successful reception of the message. The ISI comparison, across different sequence distributions for a given length and weight, shows that the linear LOZP code exhibits superior resilience against ISI in a channel with refresh due to the placement of bit-1s at the initial positions, whereas the ZP code performs better in channel without refresh by reducing the average bit-1 density of the code. The asymptotic upper bound of the code rate is derived for the proposed codes, which depicts that a trade-off exists between the ISI and code rate. The simulation results show that the proposed family of ZP and linear LOZP codes can improve the Bit Error Rate (BER) performance by controlling the bit-1 locations and the average bit-1 density of the code, specifically where the ISI is more pronounced over the channel noise, thus providing a better reliability compared to the conventional error correcting codes at different data rate regimes.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 4","pages":"549-571"},"PeriodicalIF":2.3,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145760908","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 : 2025-06-19DOI: 10.1109/TMBMC.2025.3581468
Alexander S. Moffett;Andrew W. Eckford
In an information-processing investment game, such as the growth of a population of organisms in a changing environment, Kelly betting maximizes the expected log rate of growth. In this paper, we show that Kelly bets are closely related to optimal single-letter codes (i.e., they can achieve the rate-distortion bound with equality). Thus, natural information processing systems with limited computational resources can achieve information-theoretically optimal performance. We show that the rate-distortion tradeoff for an investment game has a simple linear bound, and that the bound is achievable at the point where the corresponding single-letter code is optimal. This interpretation has two interesting consequences. First, we show that increasing the organism’s portfolio of potential strategies can lead to optimal performance over a continuous range of channels, even if the strategy portfolio is fixed. Second, we show that increasing an organism’s number of phenotypes (i.e., its number of possible behaviours in response to the environment) can lead to higher growth rate, and we give conditions under which this occurs. Examples illustrating the results in simplified biological scenarios are presented.
{"title":"Kelly Bets and Single-Letter Codes: Optimal Information Processing in Natural Systems","authors":"Alexander S. Moffett;Andrew W. Eckford","doi":"10.1109/TMBMC.2025.3581468","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3581468","url":null,"abstract":"In an information-processing investment game, such as the growth of a population of organisms in a changing environment, Kelly betting maximizes the expected log rate of growth. In this paper, we show that Kelly bets are closely related to optimal single-letter codes (i.e., they can achieve the rate-distortion bound with equality). Thus, natural information processing systems with limited computational resources can achieve information-theoretically optimal performance. We show that the rate-distortion tradeoff for an investment game has a simple linear bound, and that the bound is achievable at the point where the corresponding single-letter code is optimal. This interpretation has two interesting consequences. First, we show that increasing the organism’s portfolio of potential strategies can lead to optimal performance over a continuous range of channels, even if the strategy portfolio is fixed. Second, we show that increasing an organism’s number of phenotypes (i.e., its number of possible behaviours in response to the environment) can lead to higher growth rate, and we give conditions under which this occurs. Examples illustrating the results in simplified biological scenarios are presented.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 3","pages":"418-434"},"PeriodicalIF":2.3,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145036902","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 : 2025-06-19DOI: 10.1109/TMBMC.2025.3581470
Hongbin Ni;Ozgur B. Akan
Signal detection in diffusion-based molecular communication (MC) is challenged by stochastic propagation, inter-symbol interference (ISI), and rapidly varying microfluidic channels. This paper presents ART-Rx, an adaptive real-time threshold receiver that embeds a proportional–integral–derivative (PID) controller in a conceptual system-on-chip with the detection threshold updated once per symbol interval. Extensive Smoldyn and MATLAB simulations sweep the interferer molecule count, concentration-shift keying (CSK) levels, flow velocity, transmitter–receiver (Tx–Rx) distance, diffusion coefficient, and receptor binding rate. Averaged over the interferer molecule sweep, ART-Rx achieves a mean bit-error ratio (BER) of $1.8times 10^{-2}$ . Across −4 dB ≤ SNR ≤ 19 dB the BER remains below $6.0times 10^{-2}$ , and never exceeds $7.4times 10^{-2}$ for Tx–Rx distances up to $1times 10^{-2},mathrm {m}$ . The closed-loop strategy outperforms a statistical fixed-threshold detector and achieves a $2.6times $ lower BER than a prior non-machine learning (ML) baseline while retaining $mathcal {O}(1)$ operations per symbol. Gain scheduling, coupled with Ziegler—Nichols (Z–N) tuned PID gains and an integral windup clamp, preserves stability across strongly non-linear parameter regimes. These results position ART-Rx as a practical Rx front-end for small, resource-constrained Internet of Bio-Nano Things (IoBNT) nodes and implantable biosensors.
{"title":"ART-Rx: A Proportional-Integral-Derivative (PID) Controlled Adaptive Real-Time Threshold Receiver for Molecular Communication","authors":"Hongbin Ni;Ozgur B. Akan","doi":"10.1109/TMBMC.2025.3581470","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3581470","url":null,"abstract":"Signal detection in diffusion-based molecular communication (MC) is challenged by stochastic propagation, inter-symbol interference (ISI), and rapidly varying microfluidic channels. This paper presents ART-Rx, an adaptive real-time threshold receiver that embeds a proportional–integral–derivative (PID) controller in a conceptual system-on-chip with the detection threshold updated once per symbol interval. Extensive Smoldyn and MATLAB simulations sweep the interferer molecule count, concentration-shift keying (CSK) levels, flow velocity, transmitter–receiver (Tx–Rx) distance, diffusion coefficient, and receptor binding rate. Averaged over the interferer molecule sweep, ART-Rx achieves a mean bit-error ratio (BER) of <inline-formula> <tex-math>$1.8times 10^{-2}$ </tex-math></inline-formula>. Across −4 dB ≤ SNR ≤ 19 dB the BER remains below <inline-formula> <tex-math>$6.0times 10^{-2}$ </tex-math></inline-formula>, and never exceeds <inline-formula> <tex-math>$7.4times 10^{-2}$ </tex-math></inline-formula> for Tx–Rx distances up to <inline-formula> <tex-math>$1times 10^{-2},mathrm {m}$ </tex-math></inline-formula>. The closed-loop strategy outperforms a statistical fixed-threshold detector and achieves a <inline-formula> <tex-math>$2.6times $ </tex-math></inline-formula> lower BER than a prior non-machine learning (ML) baseline while retaining <inline-formula> <tex-math>$mathcal {O}(1)$ </tex-math></inline-formula> operations per symbol. Gain scheduling, coupled with Ziegler—Nichols (Z–N) tuned PID gains and an integral windup clamp, preserves stability across strongly non-linear parameter regimes. These results position ART-Rx as a practical Rx front-end for small, resource-constrained Internet of Bio-Nano Things (IoBNT) nodes and implantable biosensors.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 3","pages":"435-450"},"PeriodicalIF":2.3,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145036855","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 : 2025-06-13DOI: 10.1109/TMBMC.2025.3579530
Taha Sajjad;Andrew W. Eckford
Biomolecules exhibit a remarkable property of transforming signals from their environment. This paper presents a communication system design using a light-modulated protein channel: Synthetic Photoisomerizable Azobenzene-regulated K+ (SPARK). Our approach involves a comprehensive design incorporating the SPARK-based receiver, encoding methods, modulation techniques, and detection processes. By analyzing the resulting communication system, we determine how different parameters influence its performance. Furthermore, we explore the potential design in terms of bioengineering and demonstrate that the data rate scales up with the number of receptors, indicating the possibility of achieving high-speed communication.
{"title":"Communication System Design Using Synthetic Photoisomerizable Azobenzene-Regulated K+ (SPARK) Channel","authors":"Taha Sajjad;Andrew W. Eckford","doi":"10.1109/TMBMC.2025.3579530","DOIUrl":"https://doi.org/10.1109/TMBMC.2025.3579530","url":null,"abstract":"Biomolecules exhibit a remarkable property of transforming signals from their environment. This paper presents a communication system design using a light-modulated protein channel: Synthetic Photoisomerizable Azobenzene-regulated K+ (SPARK). Our approach involves a comprehensive design incorporating the SPARK-based receiver, encoding methods, modulation techniques, and detection processes. By analyzing the resulting communication system, we determine how different parameters influence its performance. Furthermore, we explore the potential design in terms of bioengineering and demonstrate that the data rate scales up with the number of receptors, indicating the possibility of achieving high-speed communication.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"11 3","pages":"451-461"},"PeriodicalIF":2.3,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145036900","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 : 2025-06-12DOI: 10.1109/TMBMC.2025.3574832
{"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}
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：