sequence dependent
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2022 ◽  
Vol 18 (1) ◽  
pp. e1009749
Author(s):  
Benjamin Martin ◽  
Pablo D. Dans ◽  
Milosz Wieczór ◽  
Nuria Villegas ◽  
Isabelle Brun-Heath ◽  
...  

We have used a variety of theoretical and experimental techniques to study the role of four basic amino acids–Arginine, Lysine, Ornithine and L-2,4-Diaminobutyric acid–on the structure, flexibility and sequence-dependent stability of DNA. We found that the presence of organic ions stabilizes the duplexes and significantly reduces the difference in stability between AT- and GC-rich duplexes with respect to the control conditions. This suggests that these amino acids, ingredients of the primordial soup during abiogenesis, could have helped to equalize the stability of AT- and GC-rich DNA oligomers, facilitating a general non-catalysed self-replication of DNA. Experiments and simulations demonstrate that organic ions have an effect that goes beyond the general electrostatic screening, involving specific interactions along the grooves of the double helix. We conclude that organic ions, largely ignored in the DNA world, should be reconsidered as crucial structural elements far from mimics of small inorganic cations.


2022 ◽  
Vol 12 (2) ◽  
pp. 607
Author(s):  
Fredy Juárez-Pérez ◽  
Marco Antonio Cruz-Chávez ◽  
Rafael Rivera-López ◽  
Erika Yesenia Ávila-Melgar ◽  
Marta Lilia Eraña-Díaz ◽  
...  

In this paper, a hybrid genetic algorithm implemented in a grid environment to solve hard instances of the flexible flow shop scheduling problem with sequence-dependent setup times is introduced. The genetic algorithm takes advantage of the distributed computing power on the grid to apply a hybrid local search to each individual in the population and reach a near optimal solution in a reduced number of generations. Ant colony systems and simulated annealing are used to apply a combination of iterative and cooperative local searches, respectively. This algorithm is implemented using a master–slave scheme, where the master process distributes the population on the slave process and coordinates the communication on the computational grid elements. The experimental results point out that the proposed scheme obtains the upper bound in a broad set of test instances. Also, an efficiency analysis of the proposed algorithm indicates its competitive use of the computational resources of the grid.


2021 ◽  
Author(s):  
Sophie Hertel ◽  
Richard Spinney ◽  
Stephanie Xu ◽  
Thomas E Ouldridge ◽  
Richard Morris ◽  
...  

The kinetics of DNA hybridisation are fundamental to biological processes and DNA-based technologies. However, the precise physical mechanisms that determine why different DNA sequences hybridise at different rates are not well understood. Secondary structure is one predictable factor that influences hybridisation rates but is not sufficient on its own to fully explain the observed sequence-dependent variance. Consequently, to achieve a good correlation with experimental data, current prediction algorithms require many parameters that provide little mechanistic insight into DNA hybridisation. In this context, we measured hybridisation rates of 43 different DNA sequences that are not predicted to form secondary structure and present a parsimonious physically justified model to quantify their hybridisation rates. Accounting only for the combinatorics of complementary nucleating interactions and their sequence-dependent stability, the model achieves good correlation with experiment with only two free parameters, thus providing new insight into the physical factors underpinning DNA hybridisation rates.


2021 ◽  
Author(s):  
Shih-Wei Lin ◽  
Kuo-Ching Ying

Abstract Sequence-dependent setup times (SDSTs) and delayed precedence (DP) occur commonly in various manufacturing settings. This study investigated the single machine scheduling problem with SDSTs and DP constraints arising in an amplifier assembly company. A mixed-integer linear programming model and a lean iterated greedy (LIG) algorithm is proposed to search for the best job sequence with minimum makespan. Based on the characteristic of delayed precedence constraints of the problem, the proposed LIG algorithm implements a straightforward but effective lean construction mechanism, which can keep the search process within the feasible solution space and quickly converge toward the (near-) global optimum. Computational results reveal that LIG significantly outperforms the state-of-the-art algorithm in terms of solution quality and computational efficiency. This study mainly contributes to providing a simple, effective, and efficient algorithm that can facilitate industrial applications and act as a new benchmark approach for future research.


2021 ◽  
Author(s):  
Salvatore Assenza ◽  
Rubén Pérez

AbstractWe introduce MADna, a sequence-dependent coarse-grained model of double-stranded DNA (dsDNA), where each nucleotide is described by three beads localized at the sugar and base moieties, and at the phosphate group. The sequence dependence is included by considering a step-dependent parameterization of the bonded interactions, which are tuned in order to reproduce the values of key observables obtained from exhaustive atomistic simulations from literature. The predictions of the model are benchmarked against an independent set of all-atom simulations, showing that it captures with high fidelity the sequence dependence of conformational and elastic features beyond the single step considered in its formulation. A remarkably good agreement with experiments is found for both sequence-averaged and sequence-dependent conformational and elastic features, including the stretching and torsion moduli, the twist-stretch and twist-bend couplings, the persistence length and the helical pitch. Overall, for the inspected quantities, the model has a precision comparable to atomistic simulations, hence providing a reliable coarse-grained description for the rationalization of singlemolecule experiments and the study of cellular processes involving dsDNA. Owing to the simplicity of its formulation, MADna can be straightforwardly included in common simulation engines.


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