Pub Date : 2024-03-23DOI: 10.1109/TNB.2024.3404396
Bosheng Song;Chuanlong Hu;Xiangxiang Zeng
A variant of tissue-like P systems is known as monodirectional tissue P systems, where objects only have one direction to move between two regions. In this article, a special kind of objects named proteins are added to monodirectional tissue P systems, which can control objects moving between regions, and such computational models are named as monodirectional tissue P systems with proteins on cells (PMT P systems). We discuss the computational properties of PMT P systems. In more detail, PMT P systems employing two cells, one protein controlling a rule, and at most one object used in each symport rule are capable of achievement of Turing universality. In addition, PMT P systems using one protein controlling a rule, and at most one object used in each symport rule can effectively solve the Boolean satisfiability problem (simply SAT ).
类组织 P 系统的一个变种被称为单向组织 P 系统，即物体在两个区域之间只有一个移动方向。本文在单向组织 P 系统中加入了一种名为蛋白质的特殊物体，它可以控制物体在区域间移动，这种计算模型被命名为细胞上有蛋白质的单向组织 P 系统（PMT P 系统）。我们将讨论 PMT P 系统的计算特性。更详细地说，采用两个细胞、一个蛋白质控制一个规则、每个交会规则最多使用一个对象的 PMT P 系统能够实现图灵普遍性。此外，使用一个蛋白质控制一个规则、每个交会规则中最多使用一个对象的 PMT P 系统可以有效地解决布尔可满足性问题（简称 SAT）。
{"title":"Monodirectional Tissue P Systems With Proteins on Cells","authors":"Bosheng Song;Chuanlong Hu;Xiangxiang Zeng","doi":"10.1109/TNB.2024.3404396","DOIUrl":"10.1109/TNB.2024.3404396","url":null,"abstract":"A variant of tissue-like P systems is known as monodirectional tissue P systems, where objects only have one direction to move between two regions. In this article, a special kind of objects named proteins are added to monodirectional tissue P systems, which can control objects moving between regions, and such computational models are named as monodirectional tissue P systems with proteins on cells (PMT P systems). We discuss the computational properties of PMT P systems. In more detail, PMT P systems employing two cells, one protein controlling a rule, and at most one object used in each symport rule are capable of achievement of Turing universality. In addition, PMT P systems using one protein controlling a rule, and at most one object used in each symport rule can effectively solve the Boolean satisfiability problem (simply \u0000<monospace>SAT</monospace>\u0000).","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141086513","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}
Pub Date : 2024-03-21DOI: 10.1109/TNB.2024.3379976
Jae-Won Kim;Jaeho Jeong;Hee-Youl Kwak;Jong-Seon No
In this paper, we propose a new coding scheme for DNA storage using low-density parity-check (LDPC) codes and interleaving techniques. While conventional coding schemes generally employ error correcting codes in both inter and intra-oligo directions, we show that inter-oligo LDPC codes, optimized by differential evolution, are sufficient in ensuring the reliability of DNA storage due to the powerful soft decoding of LDPC codes. In addition, we apply interleaving techniques for handling non-uniform error characteristics of DNA storage to enhance the decoding performance. Consequently, the proposed coding scheme reduces the required number of oligo reads for perfect recovery by 26.25% ~ 38.5% compared to existing state-of-the-art coding schemes. Moreover, we develop an analytical DNA channel model in terms of non-uniform binary symmetric channels. This mathematical model allows us to demonstrate the superiority of the proposed coding scheme while isolating the experimental variation, as well as confirm the independent effects of LDPC codes and interleaving techniques.
在本文中，我们利用低密度奇偶校验（LDPC）码和交织技术提出了一种新的 DNA 存储编码方案。传统的编码方案一般在oligo间和oligo内两个方向都采用纠错码，而我们的研究表明，通过差分进化优化的oligo间LDPC码足以确保DNA存储的可靠性，因为LDPC码具有强大的软解码功能。此外，我们还应用了交错技术来处理 DNA 存储的非均匀错误特性，以提高解码性能。因此，与现有的最先进编码方案相比，所提出的编码方案将完美恢复所需的寡核苷酸读数减少了 26.25% ~ 38.5%。此外，我们还根据非均匀二进制对称信道建立了 DNA 信道分析模型。通过这个数学模型，我们可以证明拟议编码方案的优越性，同时隔离实验变化，并确认 LDPC 码和交织技术的独立影响。
{"title":"Design of DNA Storage Coding Scheme With LDPC Codes and Interleaving","authors":"Jae-Won Kim;Jaeho Jeong;Hee-Youl Kwak;Jong-Seon No","doi":"10.1109/TNB.2024.3379976","DOIUrl":"10.1109/TNB.2024.3379976","url":null,"abstract":"In this paper, we propose a new coding scheme for DNA storage using low-density parity-check (LDPC) codes and interleaving techniques. While conventional coding schemes generally employ error correcting codes in both inter and intra-oligo directions, we show that inter-oligo LDPC codes, optimized by differential evolution, are sufficient in ensuring the reliability of DNA storage due to the powerful soft decoding of LDPC codes. In addition, we apply interleaving techniques for handling non-uniform error characteristics of DNA storage to enhance the decoding performance. Consequently, the proposed coding scheme reduces the required number of oligo reads for perfect recovery by 26.25% ~ 38.5% compared to existing state-of-the-art coding schemes. Moreover, we develop an analytical DNA channel model in terms of non-uniform binary symmetric channels. This mathematical model allows us to demonstrate the superiority of the proposed coding scheme while isolating the experimental variation, as well as confirm the independent effects of LDPC codes and interleaving techniques.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140184322","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}
Pub Date : 2024-03-20DOI: 10.1109/TNB.2024.3379588
K. Ramya;K. S. Jaya Lakshmi;Khairunnisa Amreen;Sanket Goel
L-Tyrosine (L-Tyr), a critical amino acid whose aberrant levels impact melanin and dopamine levels in human body while also increasing insulin resistance thereby increasing the risk of type 2 diabetes. The objective of this study was to detect the amount of L-Tyr in human fluids by tailored electrochemical synthesis of well adhered, homogenous and thin molecularly imprinted polymers (MIPs) by the electro-polymerization of pyrrole on glassy carbon electrode modified functionalized multi-walled carbon nanotubes. The key benefits of this procedure over previous imprinting techniques were the elimination of expensive materials like Au and tedious multi-step synthesis, for L-Tyr detection using a handheld potentiostat. The developed particles were characterized using Fourier Transform Infrared Spectroscopy, Scanning Electron Microscope, Chronoamperometry, and Cyclic Voltammetry. With strong reproducibility and stability, this optimized approach provides a rapid and effective method of preparing and sensing MIPs for the target analyte with a broad linear range of $1~mu text{M}$ to $2000~mu text{M}$ . The Limit of Detection and Limit of Quantification were $0.4~mu text{M}$ and $1.47~mu text{M}$ , respectively. The engineered sensor was validated for quantifying the concentrations of L-Tyr in human blood and serum samples, yielding satisfactory recovery and can be expanded in future to detect analytes simultaneous.
{"title":"Electrochemical Synthesis of Molecularly Imprinted Polymers for L-Tyrosine Detection","authors":"K. Ramya;K. S. Jaya Lakshmi;Khairunnisa Amreen;Sanket Goel","doi":"10.1109/TNB.2024.3379588","DOIUrl":"10.1109/TNB.2024.3379588","url":null,"abstract":"L-Tyrosine (L-Tyr), a critical amino acid whose aberrant levels impact melanin and dopamine levels in human body while also increasing insulin resistance thereby increasing the risk of type 2 diabetes. The objective of this study was to detect the amount of L-Tyr in human fluids by tailored electrochemical synthesis of well adhered, homogenous and thin molecularly imprinted polymers (MIPs) by the electro-polymerization of pyrrole on glassy carbon electrode modified functionalized multi-walled carbon nanotubes. The key benefits of this procedure over previous imprinting techniques were the elimination of expensive materials like Au and tedious multi-step synthesis, for L-Tyr detection using a handheld potentiostat. The developed particles were characterized using Fourier Transform Infrared Spectroscopy, Scanning Electron Microscope, Chronoamperometry, and Cyclic Voltammetry. With strong reproducibility and stability, this optimized approach provides a rapid and effective method of preparing and sensing MIPs for the target analyte with a broad linear range of \u0000<inline-formula> <tex-math>$1~mu text{M}$ </tex-math></inline-formula>\u0000 to \u0000<inline-formula> <tex-math>$2000~mu text{M}$ </tex-math></inline-formula>\u0000. The Limit of Detection and Limit of Quantification were \u0000<inline-formula> <tex-math>$0.4~mu text{M}$ </tex-math></inline-formula>\u0000 and \u0000<inline-formula> <tex-math>$1.47~mu text{M}$ </tex-math></inline-formula>\u0000, respectively. The engineered sensor was validated for quantifying the concentrations of L-Tyr in human blood and serum samples, yielding satisfactory recovery and can be expanded in future to detect analytes simultaneous.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140174505","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}
Pub Date : 2024-03-14DOI: 10.1109/TNB.2024.3375933
Dongliang Jing;Lin Lin;Andrew W. Eckford
In molecular communication (MC), molecules are released from the transmitter to convey information. This paper considers a realistic molecule shift keying (MoSK) scenario with two species of molecule in two reservoirs, where the molecules are harvested from the environment and placed into different reservoirs, which are purified by exchanging molecules between the reservoirs. This process consumes energy, and for a reasonable energy cost, the reservoirs cannot be pure; thus, our MoSK transmitter is imperfect, releasing mixtures of both molecules for every symbol, resulting in inter-symbol interference (ISI). To mitigate ISI, the properties of the receiver are analyzed and a detection method based on the ratio of different molecules is proposed. Theoretical and simulation results are provided, showing that with the increase of energy cost, the system achieves better performance. The good performance of the proposed detection scheme is also demonstrated.
{"title":"Performance Analysis and ISI Mitigation With Imperfect Transmitter in Molecular Communication","authors":"Dongliang Jing;Lin Lin;Andrew W. Eckford","doi":"10.1109/TNB.2024.3375933","DOIUrl":"10.1109/TNB.2024.3375933","url":null,"abstract":"In molecular communication (MC), molecules are released from the transmitter to convey information. This paper considers a realistic molecule shift keying (MoSK) scenario with two species of molecule in two reservoirs, where the molecules are harvested from the environment and placed into different reservoirs, which are purified by exchanging molecules between the reservoirs. This process consumes energy, and for a reasonable energy cost, the reservoirs cannot be pure; thus, our MoSK transmitter is imperfect, releasing mixtures of both molecules for every symbol, resulting in inter-symbol interference (ISI). To mitigate ISI, the properties of the receiver are analyzed and a detection method based on the ratio of different molecules is proposed. Theoretical and simulation results are provided, showing that with the increase of energy cost, the system achieves better performance. The good performance of the proposed detection scheme is also demonstrated.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140101512","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}
Pub Date : 2024-03-13DOI: 10.1109/TNB.2024.3376824
Sanjeev Kumar Raghuwanshi
A numerical model based on the Transfer matrix method (TMM) is proposed for the first time to study the gold coated tapered fibre optic surface plasmon resonance (SPR) with eight different types of taper profiles namely linear, exponential-linear, Gaussian, quadratic, sinusoidal, error function type and highly perturbed taper profile so-called chirp type of profile. The performance in terms of sensitivity, full width at half maximum (FWHM), detection accuracy (D.A.), amplitude dip, and half power points are estimated with respect to tapering ratio and choices of taper profile. It is found that sensitivity increased almost linearly with the taper ratio of each taper choice for the account of the reduction of detection accuracy. It has been found that sensitivity is highest for the case of chirp taper profile and lowest for the case of quadratic taper profile at low taper ratio. In this study, the aqueous solution is considered for sensor development which is adulterated by biomolecules species like DNA, blood samples, etc.
{"title":"Analysis of Tapered Fibre Optic Surface Plasmon Resonance Bio-Sensor Chip With Highly Perturbed Taper Profiles","authors":"Sanjeev Kumar Raghuwanshi","doi":"10.1109/TNB.2024.3376824","DOIUrl":"10.1109/TNB.2024.3376824","url":null,"abstract":"A numerical model based on the Transfer matrix method (TMM) is proposed for the first time to study the gold coated tapered fibre optic surface plasmon resonance (SPR) with eight different types of taper profiles namely linear, exponential-linear, Gaussian, quadratic, sinusoidal, error function type and highly perturbed taper profile so-called chirp type of profile. The performance in terms of sensitivity, full width at half maximum (FWHM), detection accuracy (D.A.), amplitude dip, and half power points are estimated with respect to tapering ratio and choices of taper profile. It is found that sensitivity increased almost linearly with the taper ratio of each taper choice for the account of the reduction of detection accuracy. It has been found that sensitivity is highest for the case of chirp taper profile and lowest for the case of quadratic taper profile at low taper ratio. In this study, the aqueous solution is considered for sensor development which is adulterated by biomolecules species like DNA, blood samples, etc.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140119348","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}
Zinc oxide (ZnO) and magnesium-doped zinc oxide (Mg-doped ZnO) nanoparticles (NPs) were synthesized using Ziziphus oxyphylla ’s aqueous leaf extract as reducing agent. UV-Vis absorption peaks at 324 nm and 335 nm were indicative of ZnO and Mg-doped ZnO, respectively. FTIR absorption bands observed at 3238, 1043, 1400, 1401, 2186 and 2320 cm $^{-1}$ suggested the presence of phenols, alcohols, saturated hydrocarbons, and possibly alkynes. X-ray diffraction (XRD), scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) spectroscopy revealed pure, spherical and agglomerated NPs with average size of 35.9 nm (ZnO) and 56.8 nm (Mg-doped ZnO). Both NPs remained active against all bacterial strains with the highest inhibition zones observed against Proteus vulgaris (21.16±1.25 mm for ZnO and 24.1±0.76 mm for Mg-doped ZnO. EtBr fluorescence (cartwheel assay) indicated efflux pump blockage, suggesting its facilitation in the bacterial growth inhibition. Antioxidant potential, determined via DPPH radical scavenging assay, revealed stronger antioxidant potential for Mg-doped ZnO (IC $_{{50}}~21.53pm 0.76~mu text{g}$ /mL) than pure ZnO (IC $_{{50}}~30.32pm 0.73~mu text{g}$ /mL). Furthermore, both NPs showed antileishmanial activity against Leishmania tropica promastigotes (IC $_{{50}}~47.23pm 3.22~mu text{g}$ /mL for Mg-doped ZnO and 64.34±6.56 for ZnO), while neither NP exhibited significant hemolysis, indicating biocompatibility and further assessment for their drugability.
{"title":"Biomedical Applications of Green Synthesized Zinc Oxide and Magnesium-Doped Zinc Oxide Nanoparticles Using Aqueous Extract of Ziziphus Oxyphylla Leaves","authors":"Suliman Syed;Arshad Islam;Muhammad Shabeer;Akhtar Nadhman;Farhan Ahmad;Nadia Irfan;Shaila Mehwish;Ajmal Khan","doi":"10.1109/TNB.2024.3373777","DOIUrl":"10.1109/TNB.2024.3373777","url":null,"abstract":"Zinc oxide (ZnO) and magnesium-doped zinc oxide (Mg-doped ZnO) nanoparticles (NPs) were synthesized using Ziziphus oxyphylla ’s aqueous leaf extract as reducing agent. UV-Vis absorption peaks at 324 nm and 335 nm were indicative of ZnO and Mg-doped ZnO, respectively. FTIR absorption bands observed at 3238, 1043, 1400, 1401, 2186 and 2320 cm\u0000<inline-formula> <tex-math>$^{-1}$ </tex-math></inline-formula>\u0000 suggested the presence of phenols, alcohols, saturated hydrocarbons, and possibly alkynes. X-ray diffraction (XRD), scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) spectroscopy revealed pure, spherical and agglomerated NPs with average size of 35.9 nm (ZnO) and 56.8 nm (Mg-doped ZnO). Both NPs remained active against all bacterial strains with the highest inhibition zones observed against Proteus vulgaris (21.16±1.25 mm for ZnO and 24.1±0.76 mm for Mg-doped ZnO. EtBr fluorescence (cartwheel assay) indicated efflux pump blockage, suggesting its facilitation in the bacterial growth inhibition. Antioxidant potential, determined via DPPH radical scavenging assay, revealed stronger antioxidant potential for Mg-doped ZnO (IC\u0000<inline-formula> <tex-math>$_{{50}}~21.53pm 0.76~mu text{g}$ </tex-math></inline-formula>\u0000/mL) than pure ZnO (IC\u0000<inline-formula> <tex-math>$_{{50}}~30.32pm 0.73~mu text{g}$ </tex-math></inline-formula>\u0000/mL). Furthermore, both NPs showed antileishmanial activity against Leishmania tropica promastigotes (IC\u0000<inline-formula> <tex-math>$_{{50}}~47.23pm 3.22~mu text{g}$ </tex-math></inline-formula>\u0000/mL for Mg-doped ZnO and 64.34±6.56 for ZnO), while neither NP exhibited significant hemolysis, indicating biocompatibility and further assessment for their drugability.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140049315","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}
A fiber-optic urea sensor based on surface plasmon resonance (SPR) and Mach-Zehnder interference (MZI) combined principle was designed and implemented. By plating gold film on the single-mode-no-core-thin-core-single-mode fiber structure, we successfully excited both SPR and MZI, and constructed two parallel detection channels for simultaneously measurement of urea concentration and temperature. Urease was immobilized on the gold film by metal-organic zeolite skeleton (ZIF-8), which can not only fix a large number of urease to improve measurement sensitivity of urea, but also protect urease activity to ensure the sensor stability. Experimental results indicate that the designed urea sensor with temperature compensation function can detect urea solution with concentration of 1-9 mM, and the sensitivity is 1.4 nm/mM. The proposed measurement method provides a new choice for monitoring urea concentration in the field of medical diagnosis and human health monitoring.
我们设计并实现了一种基于表面等离子体共振（SPR）和马赫-泽恩德干涉（MZI）相结合原理的光纤尿素传感器。通过在单模-无芯-细芯-单模光纤结构上镀金膜，我们成功地激发了 SPR 和 MZI，并构建了两个并行检测通道，可同时测量尿素浓度和温度。利用金属有机沸石骨架（ZIF-8）将尿素酶固定在金膜上，既能固定大量尿素酶，提高尿素的测量灵敏度，又能保护尿素酶的活性，保证传感器的稳定性。实验结果表明，所设计的具有温度补偿功能的尿素传感器可以检测浓度为 1-9 mM 的尿素溶液，灵敏度为 1.4 nm/mM。所提出的测量方法为医疗诊断和人体健康监测领域监测尿素浓度提供了新的选择。
{"title":"In Situ Measurement of Urea Concentration With an In-Fiber SPR-MZI Sensor","authors":"Liangliang Cheng;Wanlu Zheng;Ya-Nan Zhang;Xuegang Li;Yong Zhao","doi":"10.1109/TNB.2024.3398807","DOIUrl":"10.1109/TNB.2024.3398807","url":null,"abstract":"A fiber-optic urea sensor based on surface plasmon resonance (SPR) and Mach-Zehnder interference (MZI) combined principle was designed and implemented. By plating gold film on the single-mode-no-core-thin-core-single-mode fiber structure, we successfully excited both SPR and MZI, and constructed two parallel detection channels for simultaneously measurement of urea concentration and temperature. Urease was immobilized on the gold film by metal-organic zeolite skeleton (ZIF-8), which can not only fix a large number of urease to improve measurement sensitivity of urea, but also protect urease activity to ensure the sensor stability. Experimental results indicate that the designed urea sensor with temperature compensation function can detect urea solution with concentration of 1-9 mM, and the sensitivity is 1.4 nm/mM. The proposed measurement method provides a new choice for monitoring urea concentration in the field of medical diagnosis and human health monitoring.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140898232","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}
Pub Date : 2024-03-09DOI: 10.1109/TNB.2024.3399188
Nithin V. Sabu;Abhishek K. Gupta
A network of nanomachines (NMs) can be used to build a target detection system for a variety of promising applications. They have the potential to detect toxic chemicals, infectious bacteria, and biomarkers of dangerous diseases such as cancer within the human body. Many diseases and health disorders can be detected early and efficiently treated in the future by utilizing these systems. To fully grasp the potential of these systems, mathematical analysis is required. This paper describes an analytical framework for modeling and analyzing the performance of target detection systems composed of multiple mobile nanomachines of varying sizes with passive/absorbing boundaries. We consider both direct contact detection, in which NMs must physically contact the target to detect it, and indirect sensing, in which NMs must detect the marker molecules emitted by the target. The detection performance of such systems is calculated for degradable and non-degradable targets, as well as mobile and stationary targets. The derived expressions provide various insights, such as the effect of NM density and target degradation on detection probability.
{"title":"On the Target Detection Performance of a Molecular Communication Network With Multiple Mobile Nanomachines","authors":"Nithin V. Sabu;Abhishek K. Gupta","doi":"10.1109/TNB.2024.3399188","DOIUrl":"10.1109/TNB.2024.3399188","url":null,"abstract":"A network of nanomachines (NMs) can be used to build a target detection system for a variety of promising applications. They have the potential to detect toxic chemicals, infectious bacteria, and biomarkers of dangerous diseases such as cancer within the human body. Many diseases and health disorders can be detected early and efficiently treated in the future by utilizing these systems. To fully grasp the potential of these systems, mathematical analysis is required. This paper describes an analytical framework for modeling and analyzing the performance of target detection systems composed of multiple mobile nanomachines of varying sizes with passive/absorbing boundaries. We consider both direct contact detection, in which NMs must physically contact the target to detect it, and indirect sensing, in which NMs must detect the marker molecules emitted by the target. The detection performance of such systems is calculated for degradable and non-degradable targets, as well as mobile and stationary targets. The derived expressions provide various insights, such as the effect of NM density and target degradation on detection probability.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140898236","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}
Pub Date : 2024-03-07DOI: 10.1109/TNB.2024.3373597
Jiayu Sun;Yang Jiao;Fei Pan;Shuk Han Cheng;Dong Sun
The efficient application of the newly developed gene-editing method CRISPR/Cas9 requires more accurate intracellular gene delivery. Traditional delivery approaches, such as lipotransfection and non-viral delivery methods, must contend with major problems to overcome the drawbacks of low efficiency, high toxicity, and cell-type dependency. The high-throughput microdroplet-based single-cell transfection method presented herein provides an alternative method for delivering genome-editing reagents into single living cells. By accurately controlling the number of exogenous plasmids in microdroplets, this method can achieve high-efficiency delivery of nucleic acids to different types of single cells. This paper presents a high-throughput quantitative DNA transfection method for single cells and explores the optimal DNA transfection conditions for specific cell lines. The transfection efficiency of cells at different concentrations of DNA in microdroplets is measured. Under the optimized transfection conditions, the method is used to construct gene-knockout cancer cell lines to determine specific gene functions through the CRISPR/Cas9 knockout system. In a case study, the migration ability of TRIM72 knockout cancer cells is inhibited, and the tumorigenicity of cells in a zebrafish tumor model is reduced. A single-cell microfluidic chip is designed to achieve CRISPR/Cas9 DNA transfection, dramatically improving the transfection efficiency of difficult-to-transfect cells. This research demonstrates that the microdroplet method developed herein has a unique advantage in CRISPR/Cas9 gene-editing applications.
新开发的基因编辑方法 CRISPR/Cas9 的高效应用需要更精确的细胞内基因递送。传统的递送方法，如脂质转染和非病毒递送方法，必须克服低效率、高毒性和细胞类型依赖性等主要问题。本文介绍的基于微滴的高通量单细胞转染方法为向单个活细胞递送基因组编辑试剂提供了另一种方法。通过精确控制微滴中外源质粒的数量，这种方法可以实现向不同类型的单细胞高效递送核酸。本文介绍了一种高通量定量 DNA 单细胞转染方法，并探讨了特定细胞系的最佳 DNA 转染条件。测量了微滴中不同浓度 DNA 对细胞的转染效率。在优化的转染条件下，该方法被用于构建基因敲除癌症细胞系，通过 CRISPR/Cas9 基因敲除系统确定特定基因的功能。在一项案例研究中，TRIM72基因敲除癌细胞的迁移能力受到抑制，斑马鱼肿瘤模型中细胞的致瘤性降低。设计了一种单细胞微流控芯片来实现 CRISPR/Cas9 DNA 转染，大大提高了难以转染细胞的转染效率。这项研究表明，本文开发的微滴方法在 CRISPR/Cas9 基因编辑应用中具有独特的优势。
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Pub Date : 2024-03-06DOI: 10.1109/TNB.2024.3396142
Zhao-Cai Wang;Xian Wu;Kun Liang;Tun-Hua Wu
The traveling car renter problem (TCRP) is a variant of the Traveling Salesman Problem (TSP) wherein the salesman utilizes rented cars for travel. The primary objective of this problem is to identify a solution that minimizes the cumulative operating costs. Given its classification as a non-deterministic polynomial (NP) problem, traditional computers are not proficient in effectively resolving it. Conversely, DNA computing exhibits unparalleled advantages when confronted with NP-hard problems. This paper presents a DNA algorithm, based on the Adleman-Lipton model, as a proposed approach to address TCRP. The solution for TCRP can be acquired by following a series of fundamental steps, including coding, interaction, and extraction. The time computing complexity of the proposed DNA algorithm is $boldsymbol {O}(boldsymbol {n}^{boldsymbol {2}}boldsymbol {m})$ for TCRP with n cities and m types of cars. By conducting simulation experiments, the solutions for certain instances of TCRP are computed and compared to those obtained by alternative algorithms. The proposed algorithm further illustrates the potential of DNA computing, as a form of parallel computing, to address more intricate large-scale problems.
旅行汽车租赁问题（TCRP）是旅行推销员问题（TSP）的一种变体，其中推销员利用租赁的汽车进行旅行。该问题的主要目标是找出一个能使累计运营成本最小化的解决方案。鉴于该问题被归类为非确定性多项式 (NP) 问题，传统计算机无法有效解决该问题。相反，DNA 计算在面对 NP 难问题时却表现出无与伦比的优势。本文提出了一种基于 Adleman-Lipton 模型的 DNA 算法，作为解决 TCRP 的建议方法。通过一系列基本步骤，包括编码、交互和提取，可以获得 TCRP 的解决方案。对于有 n 个城市和 m 种汽车的 TCRP，所提出的 DNA 算法的时间计算复杂度为 O(n2m)。通过模拟实验，计算出了 TCRP 某些实例的解决方案，并与其他算法的解决方案进行了比较。所提出的算法进一步说明了 DNA 计算作为并行计算的一种形式，在解决更复杂的大规模问题方面的潜力。
{"title":"Exploring the Potential of DNA Computing for Complex Big Data Problems: A Case Study on the Traveling Car Renter Problem","authors":"Zhao-Cai Wang;Xian Wu;Kun Liang;Tun-Hua Wu","doi":"10.1109/TNB.2024.3396142","DOIUrl":"10.1109/TNB.2024.3396142","url":null,"abstract":"The traveling car renter problem (TCRP) is a variant of the Traveling Salesman Problem (TSP) wherein the salesman utilizes rented cars for travel. The primary objective of this problem is to identify a solution that minimizes the cumulative operating costs. Given its classification as a non-deterministic polynomial (NP) problem, traditional computers are not proficient in effectively resolving it. Conversely, DNA computing exhibits unparalleled advantages when confronted with NP-hard problems. This paper presents a DNA algorithm, based on the Adleman-Lipton model, as a proposed approach to address TCRP. The solution for TCRP can be acquired by following a series of fundamental steps, including coding, interaction, and extraction. The time computing complexity of the proposed DNA algorithm is \u0000<inline-formula> <tex-math>$boldsymbol {O}(boldsymbol {n}^{boldsymbol {2}}boldsymbol {m})$ </tex-math></inline-formula>\u0000 for TCRP with n cities and m types of cars. By conducting simulation experiments, the solutions for certain instances of TCRP are computed and compared to those obtained by alternative algorithms. The proposed algorithm further illustrates the potential of DNA computing, as a form of parallel computing, to address more intricate large-scale problems.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140854996","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}
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