IEEE Transactions on NanoBioscience最新文献

{"title":"Synthesis of Biodegradable Cell-Laden Microgels Assembly by Stop-Flow Lithography","authors":"Jakub Zlatník;Eliška Pazderková;Alina Mamedova;Jindřich Kropáček;Mario Rothbauer;Zdeněk Slouka;Ondřej Kašpar;Viola Tokárová;Ivan Řehoř","doi":"10.1109/TNB.2025.3644496","DOIUrl":"10.1109/TNB.2025.3644496","url":null,"abstract":"This study presents a novel approach for the synthesis of biodegradable cell-laden microgels using stop-flow lithography (SFL), addressing critical challenges in the field of tissue engineering. Traditional methods for creating 3D cell cultures often rely on non-biodegradable materials, which limit their application and raise concerns about cell viability. In this work, we successfully replace poly(ethylene glycol) diacrylate (PEGDA) with dextran-2-hydroxyethyl methacrylate (dex-HEMA), a biocompatible and biodegradable alternative. Furthermore, we introduce a technical solution for sterile cell encapsulation, validated through assessments of cell growth and viability alongside the biodegradation rate of the microgel matrix. Our results demonstrate the potential of the self-assembly technique to form organized structures with high spatial resolution. By encapsulating relevant cell lines, Caco-2 and HT-29, within distinct microgel types, we pave the way for the development of sophisticated 3D co-culture models. These advancements hold significant promise for replicating the structural and functional complexities found in native tissues, thereby enhancing the relevance of in vitro studies in biomedical research.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"25 2","pages":"232-240"},"PeriodicalIF":4.4,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=11301805","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145774202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"FDCSNPS: A Fast Division Calculation SNP System","authors":"Ping Guo;Xiong Chen;Xiaotong Liu;Hongsen Zhang;Ye Yan","doi":"10.1109/TNB.2025.3649201","DOIUrl":"10.1109/TNB.2025.3649201","url":null,"abstract":"Spiking Neural P system (SNP system) is a distributed parallel computing model inspired by the information processing of biological neurons. The SNP system has emerged as a research hotspots in the field of membrane computing, being utilized to tackle NP-hard problems and widely applied in solving practical issues. In this paper, we introduce a SNP system, Fast Division Calculation Spiking Neural P System (FDCSNPS), which is designed to reduce division operation time and minimize the number of spiking neurons. The system flow, input, control, and functional modules of FDCSNPS are discussed in detail. At the same time, the complexity of the system is analyzed, and its feasibility is verified by an example. Compared with the division SNP system based on multiple subtractions, which requires a time slice O(<inline-formula> <tex-math>$2^{mathbf {k}}$ </tex-math></inline-formula>), FDCSNPS only needs O(k<inline-formula> <tex-math>${}^{mathbf {{2}}}$ </tex-math></inline-formula>) time slices to complete k-bit binary division.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"25 2","pages":"249-258"},"PeriodicalIF":4.4,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145855860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design and Analysis of Two-Layer Coding Scheme for DNA-Based Data Storage","authors":"Jiayao Zhang;Shancheng Zhao","doi":"10.1109/TNB.2025.3648790","DOIUrl":"10.1109/TNB.2025.3648790","url":null,"abstract":"DNA-based data storage has emerged as a compelling alternative to traditional media due to its ultra-high information density and long-term stability. However, the high read cost caused by the error-prone synthesis, storage, and sequencing processes remains a major bottleneck for practical deployment. To address this challenge, this paper proposes a read-cost-efficient coding framework that enhances reliability without increasing total redundancy. First, a novel two-layer intra-oligo coding scheme based on Bose–Chaudhuri–Hocquenghem (BCH) codes is presented, where index bits and data bits are respectively protected to mitigate base-level errors. Second, a semi-analytical optimization method based on the normal approximation of the finite-length coding rate is developed to allocate redundancy between index and data bits optimally under a fixed total code rate. The inter-oligo protection is further achieved through low-density parity-check (LDPC) codes to combat sequence-level errors. We then present extensive analytical and numerical results to show the effectiveness of the proposed analysis. Finally, we present numerical results to demonstrate that the concatenated code based on the optimized two-layer coding scheme significantly outperforms the concatenated code based on the single-layer coding scheme in terms of frame error rate (FER) under the same sequencing depth and total redundancy. These results underscore the advantages of the two-layer coding scheme and the optimization method for DNA-based data storage systems.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"25 2","pages":"259-269"},"PeriodicalIF":4.4,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145843774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Variational Bayesian-Based Correntropy Cubature Kalman Filter for Drug Release Estimation Using a Second-Order Model","authors":"Samer S. Sarkis;Sherif Ismail;Ali Wadi;Mamoun F. Abdel-Hafez;Ghaleb A. Husseini","doi":"10.1109/TNB.2025.3641838","DOIUrl":"10.1109/TNB.2025.3641838","url":null,"abstract":"Ultrasound-triggered liposomes designed for specific targeting show promise as a drug delivery system, with the potential to enhance the effectiveness of chemotherapy while minimizing related side effects in clinical settings. This paper aims to model the drug release rate of seven targeted liposomes using a second-order discrete equation rather than the previously used first-order equation. By modeling the rate as second-order, different variants of the Kalman Filter can be applied to estimate the drug release rate. After modeling the equations and fitting the data to a second-order model, the Kalman filter variants, including the Extended Kalman Filter (EKF), Cubature Kalman Filter (CKF), and the Variational Bayesian-Based Correntropy Cubature Kalman Filter (VBMCCKF), were used to estimate the drug release rate. By applying those variants, we can see that the VBMCCKF yields the best tracking performance, combining the Variational Bayesian KF (VBKF’s) adaptive estimation of measurement noise with the MCCKF’s setting of the filter gain to a very small value when an abnormal measurement is detected. As a result, the VBMCCKF yielded the lowest Mean Squared Error (MSE) and Root Mean Squared Error (RMSE).","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"25 2","pages":"203-212"},"PeriodicalIF":4.4,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=11284883","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145708145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improved Destaining and Antimicrobial Potential of Pepsin Cross-Linked HPMC-Se Nanoparticles","authors":"Taleeha Roheen;Nazia Perveen;Nasir Assad;Muhammad Fayyaz ur Rehman;Muhammad Nadeem;Farhan Ahmad Atif;Humaira Yasmeen Gondal;Fozia Batool;Mehvish Bibi;Shahzad;Ahmad Bilal;Rehana Kousar;Noor ul Ain Zafar;Daneen Gondal","doi":"10.1109/TNB.2025.3648368","DOIUrl":"10.1109/TNB.2025.3648368","url":null,"abstract":"In this study, Hydroxypropyl methyl cellulose-stabilized selenium nanoparticles (HPMC-SeNPs) were successfully synthesized and utilized as a support for pepsin immobilization via glutaraldehyde crosslinking. Characterization through SEM, FTIR, and XRD confirmed their structural integrity, while zeta potential (- 12.61 mV) and DLS (PDI: 0.1818) indicated good colloidal stability and uniform size distribution. The immobilized pepsin (HPMC/Se-Pep) demonstrated high immobilization efficiency (81.25%) and yield (78.73%). The enzymatic system exhibited enhanced stability over a wider pH (2–6) and temperature range (20–<inline-formula> <tex-math>$60~^{circ }$ </tex-math></inline-formula>C), with improved kinetic parameters—lower K_m (0.16 mM) and higher V_max (<inline-formula> <tex-math>$0.94~mu $ </tex-math></inline-formula>mol/min)—indicating stronger substrate affinity and better catalytic performance than free pepsin. Functional assays revealed significantly enhanced caseinolytic and antimicrobial activities, with inhibition zones of <inline-formula> <tex-math>$22~pm ~0.05$ </tex-math></inline-formula> mm (<italic>S. aureus</i>) and <inline-formula> <tex-math>$21~pm ~0.12$ </tex-math></inline-formula> mm (<italic>E. coli</i>), outperforming both native NPs and free enzyme. Notably, the immobilized pepsin achieved complete removal of blood stains within 30–40 min and retained 60.2% of its activity after five reuse cycles, confirming excellent operational stability. However, a gradual decline in enzymatic activity was observed after repeated reuse and prolonged storage, indicating the need for further optimisation to enhance long-term stability. These results demonstrate that HPMC-SeNPs are an effective platform for enzyme immobilization, offering improved performance, reusability, and multifunctionality. The developed system holds strong potential for applications in biocatalysis, textile processing, and healthcare industries.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"25 2","pages":"213-221"},"PeriodicalIF":4.4,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145843778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unified Analysis of Spatio-temporal Anomalous Diffusion for Nano-Bio Molecular Communication.","authors":"Neha Bhusari, Prabhat Kumar Sharma, Avinash G Keskar","doi":"10.1109/TNB.2026.3679584","DOIUrl":"https://doi.org/10.1109/TNB.2026.3679584","url":null,"abstract":"<p><p>In this paper, we analyze molecular communication (MC) channels governed by spatio-temporal anomalous diffusion (STAD), a phenomenon commonly observed in complex biological environments such as intracellular transport and microfluidic systems. We consider that information molecules (IMs) undergo anomalous diffusion while the mobile nanomachines, transmitter (TX) and passive observer follow Brownian mobility. A unified mathematical framework is developed to characterize this time varying stochastic channel via the channel impulse response (CIR) across diverse observer geometries: point and bar shaped in one-dimensional (1-D) settings, and cuboidal, spherical, and cylindrical in three-dimensional (3-D) environments. Classical diffusion is included as a special case of the STAD model. Performance is evaluated using average error probability (AEP), receiver operating characteristics (ROC), and area under the curve (AUC) metrics to study the impact of mobility and space-time anomalies. Analytical results are validated through Monte Carlo simulations, offering insights relevant to nano-bio communication and drug delivery systems.</p>","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"PP ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147591767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MSGTrans: circRNA-disease association prediction with cluster-based negative sampling and multi-scale graph transformer.","authors":"Jing Yang, Xiujuan Lei","doi":"10.1109/TNB.2026.3679349","DOIUrl":"https://doi.org/10.1109/TNB.2026.3679349","url":null,"abstract":"<p><p>Circular RNAs (circRNAs) contribute significantly to various biological processes, with their stable structures and regulatory functions, circRNAs are gaining attention for their biomarker potential and therapeutic applications in human diseases. However, the wet-lab experiments for identifying the associations between circRNAs and diseases are time-consuming and expensive, necessitating the development of efficient computational methods. Here, a novel computational method, MSGTrans, is developed for predicting circRNA-disease associations, specifically, the model integrates multi-source nodes and cluster-based negative sampling is applied to address the imbalance of associations, then multi-scale graph transformers and cross-scale attention mechanism are designed to capture both local and global features of nodes, finally, LightGBM is introduced to predict the associations between circRNAs and diseases. Experimental results demonstrate that MSGTrans outperforms several state-of-the-art methods, offering reliable circRNA candidates for specific diseases.</p>","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"PP ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147591718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ion Transmitter for Molecular Communication.","authors":"Shaojie Zhang, Ozgur B Akan","doi":"10.1109/TNB.2026.3676352","DOIUrl":"https://doi.org/10.1109/TNB.2026.3676352","url":null,"abstract":"<p><p>Molecular communication (MC) is an emerging paradigm that takes inspiration from biological processes, enabling communication at the nanoscale and facilitating the development of the Internet of Bio-Nano Things (IoBNT). Traditional models of MC often rely on idealized assumptions that overlook practical challenges related to noise and signal behavior. This paper proposes and evaluates the first physical MC ion transmitter (ITX) using an ion exchange membrane. The circuit network model is used to simulate ion transport and analyze both transient and steady-state behavior. This analysis includes the effects of noise sources such as thermal and shot noise on signal integrity and SNR. The main contributions of this paper are to demonstrate how a practical MC ITX can produce a realistic waveform and to highlight future research challenges associated with a physical membrane-based ITX.</p>","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"PP ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147503773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recurrent Neural Network Based on DNA Strand Displacement Circuits and Its Application in Location Prediction.","authors":"Yanfeng Wang, Pengpeng Zhao, Junwei Sun","doi":"10.1109/TNB.2026.3673367","DOIUrl":"https://doi.org/10.1109/TNB.2026.3673367","url":null,"abstract":"<p><p>With the rapid development of science and technology, various intelligent devices continuously generate large amounts of real-time location data. Efficiently utilizing this data for accurate location prediction has become a critical issue in fields such as intelligent transportation and smart logistics. To realize low-power location prediction, this paper constructs a molecular recurrent neural network (RNN) model based on DNA strand displacement (DSD) technology. The RNN model can process sequence data and accurately predict the next position. Firstly, multiple modules are designed based on DSD circuits, including dual-channel weighted summation module, dual-domain data module and Tanh activation function module. Secondly, a RNN model for processing sequence data is constructed using the above modules. Finally, the constructed RNN model successfully achieves position prediction for multiple inputs and a single output. The robustness and accuracy of the neural network are verified through data experiment. It has been demonstrated that DNA molecules can effectively process complex sequence data. This method holds significant potential in the field of path planning. This method holds significant potential in the field of path planning. This paper uses MAE and RMSE to evaluate the experimental data. The results prove that the RNN model constructed in this paper demonstrates strong accuracy and stability.</p>","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"PP ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147443685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dispersion Control in Stochastic Biomolecular Systems Without Peak Shifts.","authors":"Taishi Kotsuka, Enoch Yeung","doi":"10.1109/TNB.2026.3670609","DOIUrl":"https://doi.org/10.1109/TNB.2026.3670609","url":null,"abstract":"<p><p>Intracellular biomolecular circuits often exhibit multimodal stationary distributions due to intrinsic noise, and the dispersion around each peak governs phenotypic robustness and adaptability. However, tuning dispersion by changing reaction parameters typically shifts peak positions or even alters modality. In this paper, we derive conditions that enable peak-shape control without peak shifts using the Chemical Fokker-Planck Equation. First, we formalize sharpness as a peak-local measure via probability ratios and show that the positions of peaks and valleys remain invariant as a control parameter varies. Second, we prove that sharpness varies monotonically as the control parameter increases, while the modality and the positions of extrema remain fixed. We validate these results with Monte Carlo simulations of two univariate networks: the burst-and-trickle gene expression system (unimodal) and the Schlögl system (bimodal), achieving dispersion tuning without peak shifts. Finally, we present preliminary multivariate evidence on the Genetic Toggle Switch, where the marginal distribution of one protein exhibits similar sharpness control. Our results provide structural design rules for engineering stochastic phenotypes while safeguarding the desired modal structure.</p>","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"PP ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147354870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}