Exploring the Potential of DNA Computing for Complex Big Data Problems: A Case Study on the Traveling Car Renter Problem.

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 O(n2m) 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.

A Novel Algorithm for Solving the Prize Collecting Traveling Salesman Problem Based on DNA Computing.

DNA computing is a new pattern of computing that combines biotechnology and information technology. As a new technology born in less than three decades, it has developed at an extremely rapid rate, which can be attributed to its advantages, including high parallelism, powerful data storage capacity, and low power consumption. Nowadays, DNA computing has become one of the most popular research fields worldwide and has been effective in solving certain combinatorial optimization problems. In this study, we use the Adleman-Lipton model based on DNA computing for solving the Prize Collecting Traveling Salesman Problem (PCTSP) and demonstrate the feasibility of this model. Then, we design a simulation experiment of the model to solve some open instances of PCTSP. The results illustrate that the model can satisfactorily solve these instances. Finally, the comparison with the results of the Clustering Search algorithm and the Greedy Stochastic Adaptive Search Procedure/Variable Neighborhood Search method reveals that the optimal solutions obtained by this simulation experiment are significantly superior to those of the other two algorithms in all instances. This research also provides a method for proficiently solving additional combinatorial optimization problems.

A Parallel DNA Algorithm for Solving the Quota Traveling Salesman Problem Based on Biocomputing Model.

The quota traveling salesman problem (QTSP) is a variant of the traveling salesman problem (TSP), which is a classical optimization problem. In the QTSP, the salesman visits some of the n cities to meet a given sales quota Q while having minimized travel costs. In this paper, we develop a DNA algorithm based on Adleman-Lipton model to solve the quota traveling salesman problem. Its time complexity is O(n 2+Q), which is a significant improvement over previous algorithms with exponential complexity. A coding scheme of element information is pointed out, and a reasonable biological algorithm is raised by using limited conditions, whose feasibility is verified by simulation experiments. The innovation of this study is to propose a polynomial time complexity algorithm to solve the QTSP. This advantage will become more obvious as the problem scale increases compared with the algorithm of exponential computational complexity. The proposed DNA algorithm also has the significant advantages of having a large storage capacity and consuming less energy during the operation. With the maturity of DNA manipulation technology, DNA computing, as one of the parallel biological computing methods, has the potential to solve more complex NP-hard problems.

Solving the Family Traveling Salesperson Problem in the Adleman-Lipton Model Based on DNA Computing.

The Family Traveling Salesperson Problem (FTSP) is a variant of the Traveling Salesperson Problem (TSP), in which all vertices are divided into several different families, and the goal of the problem is to find a loop that concatenates a specified number of vertices with minimal loop overhead. As a Non-deterministic Polynomial Complete (NP-complete) problem, it is difficult to deal with it by the traditional computing. On the contrary, as a computer with strong parallel ability, the DNA computer has incomparable advantages over digital computers when dealing with NP problems. Based on this, a DNA algorithm is proposed to deal with FTSP based on the Adleman-Lipton model. In the algorithm, the solution of the problem can be obtained by executing several basic biological manipulations on DNA molecules with O ( N2 ) computing complexity ( N is the number of vertices in the problem without the origin). Through the simulation experiments on some benchmark instances, the results show that the parallel DNA algorithm has better performance than traditional computing. The effectiveness of the algorithm is verified by deducing the algorithm process in detail. Furthermore, the algorithm further proves that DNA computing, as one of the parallel computing methods, has the potential to solve more complex big data problems.

New Enhanced Method for Determination of Trace Sulfamethodxazole Based on the Fluorescence Behaviors of Cyclodextrins in Water Solutions.

The widespread occurrence of sulfonamides (SAs) in the environment water has rasied great concerns about their potential to antibiotics resistance. In this study, the fluorescence behaviors of sulfamethoxazole (SMZ) representing certain properties of the SAs mixed with three different kinds of cyclodextrins (CDs) in water solutions were investigated, respectively. The result reported that the shapes of the fluorescence peak and its position for the SMZ that were mixed with the CDs were almost the same as those of the standard SMZ, respectively. In addition, compared with the identical control sample the fluorescence of SMZ mixed with each of the CD was greatly enhanced. Therefore, a new simple, and sensitive spectrofluorimetric method for the determination of SMZ was established in water solutions. and the dynamic linear ranges varied from 0.01 to 0.7 mg/L with the detection limit of 7.1 ng/L. And the correlation coefficient was more than 99.9%. Significantly, this new method was successfully applied to direct determination of SMZ in pharmaceutical compounds. Moreover, the results showed that the SMZ could separately form the 1:1 supramolecular compound with each of the CD.

Novel methods for the rapid detection of trace tetracyclines based on the fluorescence behaviours of Maillard reaction fluorescent nanoparticles.

The Maillard reaction and its fluorescent products have attracted widespread attention in the field of food safety and biology. Herein, the novel Maillard reaction fluorescent nanoparticles (MRFNs) as a fluorescent probe were synthesized via a "green" method with simple technical processes. In addition, the effects of tetracycline (TC) and chlorotetracycline (CTC) representing certain properties of tetracyclines (TCs) on the fluorescence behaviour of MRFNs were studied, respectively. The present study showed that the fluorescence intensity of MRFNs greatly enhanced with a linear increase in the CTC concentration. However, with the gradual increase in the TC concentration, the intensity of MRFNs tended to significantly decrease linearly. Based on this, novel fluorescence analysis methods for the simple and rapid detection of TC and CTC in water bodies were established, respectively. Significantly, the proposed detection methods were successfully adopted for detecting TC and CTC in some environmental water samples. Besides, the possible mechanisms for TC-induced fluorescence quenching and CTC-induced fluorescence enhancement of MRFNs were also discussed, respectively.

A novel bio-heuristic computing algorithm to solve the capacitated vehicle routing problem based on Adleman-Lipton model.

DNA computing, as one of potential means to solve complicated computational problems, is a new field of interdisciplinary research, including computational mathematics, parallel algorithms, bioinformatics. Capacitated vehicle routing problem is one of famous NP-hard problems, which includes determining the path of a group same vehicles serving a set of clients, while minimizing the total transportation cost. Based on the bio-heuristic computing model and DNA molecular manipulations, parallel biocomputing algorithms for solving capacitated vehicle routing problem are proposed in this paper. We appropriately use different biological chains to mean vertices, edges, weights, and adopt appropriate biological operations to search the solutions of the problem with O(n2) time complexity. We enrich the application scope of biocomputing, reduce computational complexity, and verify practicability of DNA parallel algorithms through simulations.

A new parallel DNA algorithm to solve the task scheduling problem based on inspired computational model.

As a promising approach to solve the computationally intractable problem, the method based on DNA computing is an emerging research area including mathematics, computer science and molecular biology. The task scheduling problem, as a well-known NP-complete problem, arranges n jobs to m individuals and finds the minimum execution time of last finished individual. In this paper, we use a biologically inspired computational model and describe a new parallel algorithm to solve the task scheduling problem by basic DNA molecular operations. In turn, we skillfully design flexible length DNA strands to represent elements of the allocation matrix, take appropriate biological experiment operations and get solutions of the task scheduling problem in proper length range with less than O(n2) time complexity.

Novel metal nanoparticle-enhanced fluorescence for determination of trace amounts of fluoroquinolone in aqueous solutions.

Metal-enhanced fluorescence of fluoroquinolones (FQs) was first observed in aqueous solutions. In addition, a new type of silver nanoparticles (AgNP) was synthesized with simple and easy synthetic processes and environmentally friendly compounds. The effects of different concentrations of AgNPs on the fluorescence behaviours of ciprofloxacin (CIP), enrofloxacin (ENR) and lomefloxacin (LMF) in aqueous solutions were investigated, respectively. The experimental results demonstrated that the fluorescence peak shapes and the locations of the features in the excitation and emission spectra for each FQ that was mixed with AgNPs were almost the same as those of the standard FQs. An enhancement or quenching of the fluorescence can also be observed, depending on the exact conditions. Compared with the identical control samples that lack AgNPs, the fluorescence of each FQ in aqueous solutions was greatly enhanced by AgNPs with concentrations at a volume ratio of 5%. Moreover, at the optimum AgNP concentration, novel sensitive fluorometric methods for the separate determination of trace amounts of CIP, ENR and LMF in aqueous solutions were established. Under optimal experimental conditions, the linear dynamic ranges for the determination of CIP, ENR and LMF concentrations varied from 0.025 to 1.0mgL-1, 5.0 to 160ngL-1 and 0.01 to 0.8mgL-1, and the limits of detection were 90, 5 and 6ngL-1, respectively; the relative standard deviation was less than 1.2% (n = 9). The experimental recovery results for the determination of CIP, ENR and LMF in aqueous solutions ranged from 99% to 102%, 90% to 103% and 92% to 107%, respectively. Compared with the established method in which no AgNPs were added, the quantitation limits of the silver nanoparticle-enhanced fluorometric methods were approximately 2-fold lower for CIP, 2.6-fold lower for ENR and 4-fold lower for LMF. Significantly, the novel silver nanoparticle-enhanced fluorometric methods were successfully applied to directly determine CIP, ENR and LMF concentrations in pharmaceutical preparations, demonstrating the methods' advantages of simplicity, sensitivity and low cost.

Novel silver nanoparticle-enhanced fluorometric determination of trace tetracyclines in aqueous solutions.

Metal-enhanced fluorescence (MEF) has exhibited promise for applications in fluorometric assays. The effects of silver nanoparticles (AgNP) on the fluorescence behaviours of tetracycline hydrochloride (TCH) and chlortetracycline hydrochloride (CTC) in aqueous solutions were investigated. The experimental results demonstrated that the fluorescence intensities of each tetracycline in water solutions were greatly enhanced by AgNP through the MEF effect. In addition, a novel silver nanoparticle-enhanced fluorometric method was established for the direct determination of TCH and CTC in aqueous solutions. Under optimum experimental conditions, the linear dynamic ranges for the determination of TCH and CTC in aqueous solutions varied from 0.10 to 6.0 mg L(-1) and 0.050 to 3.0 mg L(-1) with detection limits of 0.63 µg L(-1) and 0.19 µg L(-1), respectively, and with the relative standard deviation of less than 1.9% (n=9). The experimental recovery results for the determination of TCH and CTC in aqueous solutions ranged from 93-106% and 95-104%, respectively. Compared with the established method without the addition of AgNP, the limits of quantitation of the silver nanoparticle-enhanced fluorometric method were approximately 5-fold lower for TCH and 3-fold lower for CTC. Moreover, the newly established silver nanoparticle-enhanced fluorometric method was successfully applied to the direct determination of TCH and CTC in pharmaceutical preparations.

Direct observation of the photodegradation of anthracene and pyrene adsorbed onto mangrove leaves.

An established synchronous fluorimetry method was used for in situ investigation of the photodegradation of pyrene (PYR) and anthracene (ANT) adsorbed onto fresh leaves of the seedlings of two mangrove species, Aegiceras corniculatum (L.) Blanco (Ac) and Kandelia obovata (Ko) in multicomponent mixtures (mixture of the ANT and PYR). Experimental results indicated that photodegradation was the main transformation pathway for both ANT and PYR in multicomponent mixtures. The amount of the PAHs volatilizing from the leaf surfaces and entering the inner leaf tissues was negligible. Over a certain period of irradiation time, the photodegradation of both PYR and ANT adsorbed onto the leaves of Ac and Ko followed first-order kinetics, with faster rates being observed on Ac leaves. In addition, the photodegradation rate of PYR on the leaves of the mangrove species in multicomponent mixtures was much slower than that of adsorbed ANT. Compared with the PAHs adsorbed as single component, the photodegradation rate of ANT adsorbed in multicomponent mixtures was slower, while that of PYR was faster. Moreover, the photodegradation of PYR and ANT dissolved in water in multicomponent mixtures was investigated for comparison. The photodegradation rate on leaves was much slower than in water. Therefore, the physical-chemical properties of the substrate may strongly influence the photodegradation rate of adsorbed PAHs.

In situ investigation the photolysis of the PAHs adsorbed on mangrove leaf surfaces by synchronous solid surface fluorimetry.

An established synchronous solid surface fluorimetry (S-SSF) was utilized for in situ study the photolysis processes of anthracene (An) and pyrene (Py) adsorbed on the leaf surfaces of Kandelia obovata seedlings (Ko) and Aegiceras corniculata (L.) Blanco seedlings (Ac). Experimental results demonstrated that the photolysis of An and Py adsorbed on the leaf surfaces of two mangrove species under the laboratory conditions, followed first-order kinetics with their photolysis rates in the order of Ac>Ko. In addition, with the same amount of substances, the photolysis rate of An adsorbed on the same mangrove leaf surfaces was much faster than the adsorbed Py. In order to investigate further, the photolysis processes of An and Py in water were also studied for comparison. And the photolysis of An and Py in water also followed first-order kinetics. Moreover, for the same initial amount, the photolysis rate of the PAH in water was faster than that adsorbed on the leaf surfaces of two mangrove species. Therefore, photochemical behaviors of PAHs were dependent not only on their molecular structures but also the physical-chemical properties of the substrates on which they are adsorbed.

Monitoring and visualizing of PAHs into mangrove plant by two-photon laser confocal scanning microscopy.

In this paper, we described the applications of two-photon laser confocal scanning microscopy (TPLCSM) for in situ monitoring and visualizing the localizations and movements of naphthalene, phenanthrene, and pyrene into living Aegiceras corniculata (L.) Blanco seedlings (A. corniculata). Experimental results demonstrated that all of the polycyclic aromatic hydrocarbons (PAHs) were observed entering into the root of A. corniculata and being transmitted to the stem. The transport processes and subsequent storages of the three typical PAHs into A. corniculata were similar. Further studies indicated that the transmission rates of the PAHs in A. corniculata were in the order of naphthalene>phenanthrene>pyrene. Compared with the control group, the growth of the A. corniculata was inhibited by these three specific PAHs, and the inbibitional effect of naphthalene was the most obvious (P<0.05). Furthermore, without the need for sample manipulation or modification this TPLCSM provides us a real-time tool for direct observation of organic chemicals within plants.