A strategic oscillation simheuristic for the Time Capacitated Arc Routing Problem with stochastic demands

[EN] The Time Capacitated Arc Routing Problem (TCARP) extends the classical Capacitated Arc Routing Problem by considering time-based capacities instead of traditional loading capacities. In the TCARP, the costs associated with traversing and servicing arcs, as well as the vehicle's capacity, are measured in time units. The increasing use of electric vehicles and unmanned aerial vehicles, which use batteries of limited duration, illustrates the importance of time-capacitated routing problems. In this paper, we consider the TCARP with stochastic demands, i.e.: the actual demands on each edge are random variables which specific values are only revealed once the vehicle traverses the arc. This variability affects the service times, which also become random variables. The main goal then is to find a routing plan that minimizes the expected total time required to service all customers. Since a maximum time capacity applies on each route, a penalty time-based cost arises whenever a route cannot be completed within that limit. In this paper, a strategic oscillation simheuristic algorithm is proposed to solve this stochastic problem. The performance of our algorithm is tested in a series of numerical experiments that extend the classical deterministic instances into stochastic ones.This work has been partially supported by the Spanish Ministry of Science (PID2019-111100RB-C21/AEI/10.13039/501100011033, RED2018102642T, PGC2018-0953322-B-C21/MCIU/AEI/FEDERUE) . The authors are also grateful to the Michael Smurfit Graduate Business School at University College Dublin, Ireland for supporting research stays that contributed to the development of this work.Keenan, P.; Panadero, J.; Juan, AA.; Martí, R.; Mcgarraghy, S. (2021). A strategic oscillation simheuristic for the Time Capacitated Arc Routing Problem with stochastic demands. Computers & Operations Research. 133:1-12. https://doi.org/10.1016/j.cor.2021.10537711213

Molecular beacons with intrinsically fluorescent nucleotides

We report the design, synthesis and characterization of a novel molecular beacon (MB-FB) which uses the fluorescent bases (FB) 2-aminopurine (AP) and pyrrolo-dC (P-dC) as fluorophores. Because the quantum yield of these FB depend on hybridization with complementary target, the fluorescent properties of MB-FB were tuned by placing the FB site specifically within the MB such that hybridization with complementary sequence switches from single strand to double strand for AP and vice versa for P-dC. The MB-FB produces a ratiometric fluorescence increase (the fluorescence emission of P-dC over that of AP in the presence and absence of complementary sequence) of 8.5 when excited at 310 nm, the maximum absorption of AP. This ratiometric fluorescence is increased to 14 by further optimizing excitation (325 nm). The fluorescence lifetime is also affected by the addition of target, producing a change in the long-lived component from 6.5 to 8.7 ns (Exc. 310 nm, Em. 450 nm). Thermal denaturation profiles monitored at 450 nm (P-dC emission) show a cooperative denaturation of the MB-FB with a melting temperature of 53°C. The thermal denaturation profile of MB-FB hybridized with its target shows a marked fluorescence reduction at 53°C, consistent with a transition from double stranded helix to random coil DNA

Luminogenic iridium azide complexes

The synthesis and characterization of luminogenic, bioorthogonal iridium probes is described. These probes exhibit long photoluminescence lifetimes amenable to time-resolved applications. A simple, modular synthesis via 5-azidophenanthroline allows structural variation and allows optimization of cell labeling

Inorganic−Organic Hybrid Luminescent Binary Probe for DNA Detection Based on Spin-Forbidden Resonance Energy Transfer

We describe the design of new fluorescent binary probe sensors for DNA detection based on spin-forbidden resonance energy transfer (SF-RET). Binary probes consist of a donor and acceptor fluorophores that are attached to two different oligonucleotides and serve as a resonance energy transfer (RET) donor−acceptor pair when hybridized to adjacent sites of a target sequence. In the absence of target, excitation of the donor results in fluorescence only from the donor, but when the probes hybridize to the target, the fluorophores are brought into close proximity favoring RET, yielding fluorescence mainly from the acceptor fluorophore. These new binary probes use the metal complex Ru(bpy‘)(DIP)_2^(2+) as the energy donor and an organic fluorophore (Cy5) as the energy acceptor. Energy transfer from the MLCT state of the Ru complex to singlet Cy5 is spin forbidden and produces a delayed fluorescence of Cy5. This paper demonstrates that fluorescence delay of Cy5 can be used to time resolve the emission of the probe from the intense fluorescence background of a model system for cellular background; this provides the reported system to overcome intense autofluorescence, an important and general advantage over “classical” spin-allowed steady-state probes

Combinatorial fluorescence energy transfer molecular beacons for probing nucleic acid sequences

We report the design, synthesis, and characterization of molecular beacons (MB) consisting of three distinct fluorophores, 6-carboxyfluorescein (Fam), N,N,N ,N -tetramethyl-6-carboxyrhodamine (Tam), and Cyanine-5 (Cy5). The primary light absorber/energy donor (Fam) is located on one terminus of the MB, whereas the primary energy acceptor/secondary donor (Tam) and secondary acceptor (Cy5) are located at the other terminus of the MB. In the absence of target DNA or RNA, the MB exists in the stem-closed form. Excitation of Fam initiates an energy transfer cascade from Fam to Tam and further to Cy5 generating unique fluorescence signatures defined as the ratio of the emission from each of the three fluorophores. This energy transfer cascade was investigated in detail by steady-state and time-resolved fluorescence spectroscopy, as well as fluorescence depolarization studies. In the presence of the complementary target DNA, the MB opened efficiently and hybridized with the target separating Fam and Tam by a large distance, so that energy transfer from Fam to Tam was blocked in the stem-open form. This opening of the MB generates a "bar code" fluorescence signature, which is different from the signature of the stem-closed MB. The fluorescence signature of this combinatorial fluorescence energy transfer MB can be tuned by variation of the spacer length between the individual fluorophores

A covalently linked phenanthridine-ruthenium(II) complex as a RNA probe

A phenanthridine derivative covalently linked to a ruthenium complex yields an imaging probe whose fluorescence intensity and lifetime change substantially in the presence of RNA

Pyrene binary probes for unambiguous detection of mRNA using time-resolved fluorescence spectroscopy

We report here the design, synthesis and application of pyrene binary oligonucleotide probes for selective detection of cellular mRNA. The detection strategy is based on the formation of a fluorescent excimer when two pyrene groups are brought into close proximity upon hybridization of the probes with the target mRNA. The pyrene excimer has a long fluorescence lifetime (>40 ns) compared with that of cellular extracts (∼7 ns), allowing selective detection of the excimer using time-resolved emission spectra (TRES). Optimized probes were used to target a specific region of sensorin mRNA yielding a strong excimer emission peak at 485 nm in the presence of the target and no excimer emission in the absence of the target in buffer solution. While direct fluorescence measurement of neuronal extracts showed a strong fluorescent background, obscuring the detection of the excimer signal, time-resolved emission measurements indicated that the emission decay of the cellular extracts is ∼8 times faster than that of the pyrene excimer probes. Thus, using TRES of the pyrene probes, we are able to selectively detect mRNA in the presence of cellular extracts, demonstrating the potential for application of pyrene excimer probes for imaging mRNAs in cellular environments that have background fluorescence

Low-temperature titania-graphene quantum dots paste for flexible dye-sensitised solar cell applications

Graphene possesses excellent mechanical strength and chemical inertness with high intrinsic carrier mobility and superior flexibility making them exceptional candidates for optoelectronic applications. Graphene quantum dots (GQDs) derived from graphene domains have been widely explored to study their photoluminescence properties which can be tuned by size. GQDs are biocompatible, low cytotoxic, strongly luminescent and disperse well in polar and non-polar solvents showing bright promise for the integration into devices for bioimaging, light emitting and photovoltaic applications. In the present study, graphene quantum dots were synthesized by an electrochemical cyclic voltammetry technique using reduced graphene oxide (rGO). GQDs have been incorporated into binder free TiO2 paste and studied as a photoelectrode material fabricated on ITO/PEN substrates for flexible dye sensitized solar cells (DSSCs). DSSC based on GQDs-TiO2 exhibited open circuit output potential difference (Voc) of 0.73 V, and short circuit current density (Jsc) of 11.54 mA cm-2 with an increment in power conversion efficiency by 5.48 %, when compared with those with DSSC build with just a TiO2 photoanode (open-circuit output potential difference (Voc) of 0.68 V and short circuit density (Jsc) of 10.67 mA cm-2). The results have been understood in terms of increased charge extraction and reduced recombination losses upon GQDs incorporation

Hydroxamate Titanium−Organic Frameworks and the Effect of Siderophore-Type Linkers over Their Photocatalytic Activity

The chemistry of Metal-Organic Frameworks (MOFs) relies on the controlled linking of organic molecules and inorganic secondary building units to assemble an unlimited number of reticular frameworks. However, the design of porous solids with chemical stability remains still limited to carboxylate or azolate groups. There is a timely opportunity to develop new synthetic platforms that make use of unexplored metal binding groups to produce metal-linker joints with hydrolytical stability. Living organisms use siderophores (iron carriers in greek) to effectively assimilate iron in soluble form. These compounds make use of hard oxodonors as hydroxamate or catecholate groups to coordinate metal Lewis acids like iron, aluminium or titanium to form metal complexes very stable in water. Inspired by the chemistry of these microorganisms, we report the first hydroxamate MOF prepared by direct synthesis. MUV-11 (MUV = Materials of Universidad de Valencia) is a crystalline, porous material (close to 800 m2·g-1) that combines photoactivity with good chemical stability in acid conditions. By using a high-throughput approach, we also demonstrate that this new chemistry is compatible with the formation of single crystalline phases for multiple titanium salts, thus expanding the scope of precursors accessible. Titanium frameworks are regarded as promising materials for photocatalytic applications. Our photoelectrochemical and catalytic tests suggests important differences for MUV-11. Compared to other Ti-MOFs, changes in the photoelectrochemical and photocatalytic activity have been rationalized with computational modelling revealing how the chemistry of siderophores can introduce changes to the electronic structure of the frontier orbitals, relevant to the photocatalytic activity of these solids

Monitoring the Formation of Amyloid Oligomers Using Photoluminescence Anisotropy

The formation of oligomeric soluble aggregates is related to the toxicity of amyloid peptides and proteins. In this manuscript, we report the use of a ruthenium polypyridyl complex ([Ru(bpy)2(dpqp)]2+) to track the formation of amyloid oligomers at different times using photoluminescence anisotropy. This technique is sensitive to the rotational correlation time of the molecule under study, which is consequently related to the size of the molecule. [Ru(bpy)2(dpqp)]2+ presents anisotropy values of zero when free in solution (due to its rapid rotation and long lifetime) but larger values as the size and concentration of amyloid-β (Aβ) oligomers increase. Our assays show that Aβ forms oligomers immediately after the assay is started, reaching a steady state at ∼48 h. SDS–PAGE, DLS, and TEM were used to confirm and characterize the formation of oligomers. Our experiments show that the rate of formation for Aβ oligomers is temperature dependent, with faster rates as the temperature of the assay is increased. The probe was also effective in monitoring the formation of α-synuclein oligomers at different timesAAM thanks the Welch Foundation (Grant C-1743) and JM thanks AEI (SAF2017-89890-R), ERC (DYNAP-677786) and HFSP (RGY0066/2017) for financial supportS