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Browsing by Author "Arias González de la Aleja, José Ricardo"

Now showing items 1-20 of 25

A DNA-centered explanation of the DNA polymerase translocation mechanism

Arias-Gonzalez, J. R. (Nature Publishing Group, 2017-08-08)

[EN] DNA polymerase couples chemical energy to translocation along a DNA template with a specific directionality while it replicates genetic information. According to single-molecule manipulation experiments, the polymerase-DNA ...
A Temperature-Jump Optical Trap for Single-Molecule Manipulation

de Lorenzo, S.; Ribezzi-Crivellari, M.; Arias-Gonzalez, J. R.; Smith, S.B.; Ritort, F. (Elsevier, 2015-06-16)

[EN] To our knowledge, we have developed a novel temperature-jump optical tweezers setup that changes the temperature locally and rapidly. It uses a heating laser with a wavelength that is highly absorbed by water so it ...
Characterization of avoided crossings in acoustic superlattices: The Shannon entropy in acoustics

Sánchez-Dehesa Moreno-Cid, José; Arias-Gonzalez, J. R. (Frontiers Media, 2022-08-17)

[EN] We show that Shannon's information entropy provides a correct physical insight of localization effects taking place in structured fields fashioned by eigenmodes upon substrate. In particular, we find that the localization ...
Comment on "Information management in DNA replication modeled by directional, stochastic chains with memory" [J. Chem. Phys. 145, 185103 (2016)]

Arias-Gonzalez, J. R.; Aleja, D. (American Institute of Physics, 2020-01-31)
Diseño y caracterización experimental de sistemas de atrapamiento y manipulación de micro-objetos mediante técnicas ópticas, térmicas y acústicas

Muñoz Pérez, Francisco Misael (Universitat Politècnica de València, 2024-04-11)

[ES] La necesidad de confinar y manipular micro-objetos tiene aplicaciones en múltiples áreas de la ciencia y tecnología. Actualmente, existen diversas técnicas para lograr este objetivo, y una de las más destacadas es el ...
DNA synthesis determines the binding mode of the human mitochondrial single-stranded DNA-binding protein

Morin, J.A.; Cerrón, F.; Jarillo, J.; Beltran-Heredia, E.; Ciesielski, G.L.; Arias-Gonzalez, J. R.; Kaguni, L.S.; Cao, F.J.; Ibarra, B. (Oxford University Press, 2017-07-07)

[EN] Single-stranded DNA-binding proteins (SSBs) play a key role in genome maintenance, binding and organizing single-stranded DNA (ssDNA) intermediates. Multimeric SSBs, such as the human mitochondrial SSB (HmtSSB), present ...
Fluctuation relations for irreversible emergence of information

Arias-Gonzalez, J. R. (Nature Publishing Group, 2022-10-14)

[EN] Information theory and Thermodynamics have developed closer in the last years, with a growing application palette in which the formal equivalence between the Shannon and Gibbs entropies is exploited. The main barrier ...
Heat Generation in Single Magnetic Nanoparticles under Near-Infrared Irradiation

Rodríguez-Rodríguez, Héctor; Salas, Gorka; Arias-Gonzalez, J. R. (American Chemical Society, 2020-03-19)

[EN] Heat generation by pointlike structures is an appealing concept for its implications in nanotechnology and biomedicine. The way to pump energy that excites heat locally and the synthesis of nanostructures that absorb ...
Information management in DNA replication modeled by directional, stochastic chains with memory

Arias-Gonzalez, J. R. (American Institute of Physics, 2016-11-14)

[EN] Stochastic chains represent a key variety of phenomena in many branches of science within the context of information theory and thermodynamics. They are typically approached by a sequence of independent events or by ...
Laser Heating Tunability by Off-Resonant Irradiation of Gold Nanoparticles

Hormeño, S.; Gregorio-Godoy, P.; Pérez-Juste, J.; Liz-Marzán, L.M.; Juárez, B.H.; Arias-Gonzalez, J. R. (John Wiley & Sons, 2014-01-29)

[EN] Temperature changes in the vicinity of a single absorptive nanostructure caused by local heating have strong implications in technologies such as integrated electronics or biomedicine. Herein, the temperature changes ...
Luminescence Dynamics of Silica-Encapsulated Quantum Dots During Optical Trapping

Rodríguez-Rodríguez, H.; Acebrón, M.; Juárez, B.H.; Arias-Gonzalez, J. R. (American Chemical Society, 2017-05-11)

[EN] The trade-off between photobrightening and photobleaching controls the emission stability of colloidal quantum dots. This balance is critical in optical trapping configurations, where irradiances that confine and ...
Mechanical Identities of RNA and DNA Double Helices Unveiled at the Single-Molecule Level

Herrero-Galán, E.; Fuentes-Perez. M.E.; Carrasco, C.; Valpuesta, J.M.; Carrascosa, J.L.; Moreno-Herrero, F.; Arias-Gonzalez, J. R. (American Chemical Society, 2013-01-09)

[EN] Double-stranded (ds) RNA is the genetic material of a variety of viruses and has been recently recognized as a relevant molecule in cells for its regulatory role. Despite that the elastic response of dsDNA has been ...
Mechanical unfolding of long human telomeric RNA (TERRA)

Garavís, M.; Bocanegra, R.; Herrero-Galán, E.; González, C.; Villasante, A.; Arias-Gonzalez, J. R. (The Royal Society of Chemistry, 2013)

[EN] We report the first single molecule investigation of TERRA molecules. By using optical-tweezers and other biophysical techniques, we have found that long RNA constructions of up to 25 GGGUUA repeats form higher order ...
Mechano-chemical kinetics of DNA replication: identification of the translocation step of a replicative DNA polymerase

Morin, J.A.; Cao, F.J.; Lázaro, J.M.; Arias-Gonzalez, J. R.; Valpuesta, J.M.; Carrascosa, J.L.; Salas, M.; Ibarra, B. (Oxford University Press, 2015-04-20)

[EN] During DNA replication replicative polymerases move in discrete mechanical steps along the DNA template. To address how the chemical cycle is coupled to mechanical motion of the enzyme, here we use optical tweezers ...
Mesoscopic model for DNA G-quadruplex unfolding

Bergues-Pupo, A.E.; Gutiérrez, I.; Arias-Gonzalez, J. R.; Falo, F.; Fiasconaro, A. (Nature Publishing Group, 2017-09-18)

[EN] Genomes contain rare guanine-rich sequences capable of assembling into four-stranded helical structures, termed G-quadruplexes, with potential roles in gene regulation and chromosome stability. Their mechanical unfolding ...
Microscopically Reversible Pathways with Memory

Arias-Gonzalez, J. R. (MDPI AG, 2021-01)

[EN] Statistical mechanics is a physics theory that deals with ensembles of microstates of a system compatible with environmental constraints and that on average define a thermodynamic state. The evolution of a small system ...
Near-field distributions of resonant modes in small dielectric objects on flat surfaces

Arias-Gonzalez, J. R.; Nieto-Vesperinas, M. (The Optical Society, 2000-06-01)

[EN] We report numerical simulations of the coupling of waves, either propagating or evanescent, with the eigenmodes of dielectric nanocylinders and nanospheres upon substrates. The multiple interaction of light between ...
Optical multi-trapping by Kinoform m-Bonacci lenses

Muñoz-Pérez, Francisco M.; Ferrando, Vicente; Furlan, Walter D.; Monsoriu Serra, Juan Antonio; Arias-Gonzalez, J. R. (The Optical Society, 2022-09-12)

[EN] Optical manipulation is interfacing disciplines in the micro and nanoscale, from molecular biology to quantum computation. Versatile solutions for increasingly more sophisticated technological applications require ...
Optical Trapping of Single Nanostructures in a Weakly Focused Beam. Application to Magnetic Nanoparticles

Rodríguez-Rodríguez, H.; de Lorenzo, S.; de la Cueva, L.; Salas, G.; Arias-Gonzalez, J. R. (American Chemical Society, 2018-08-09)

[EN] Optical trapping of individual particles is believed to be only effective under highly focused beams because these conditions strengthen the gradient forces. This is especially critical in the beam propagating direction, ...
Photoluminescence Activation of Organic Dyes via Optically Trapped Quantum Dots

Rodríguez-Rodríguez, H.; Acebrón, M.; Iborra, F.J.; Arias-Gonzalez, J. R.; Juárez, B.H. (American Chemical Society, 2019-06-25)

[EN] Laser tweezers afford quantum dot (QD) manipulation for use as localized emitters. Here, we demonstrate fluorescence by radiative energy transfer from optically trapped colloidal QDs (donors) to fluorescent dyes ...