arXiv subjects

Martin Lopez-Garcia

Publications and source records attributed to Martin Lopez-Garcia.

12 recordsLinked to original sources

arXiv2026

Mechanistic mathematical model of the in vitro infection dynamics of Bunyamwera and Batai viruses including MOI-dependent shortening of the eclipse phase

We develop a deterministic mathematical model to quantify the distinct in vitro infection dynamics of Bunyamwera virus (BUNV) and Batai virus (BATV) in A549 cells, incorporating cell division and natural death, continued entry of virions into already-infected cells, and shortening of the eclipse phase driven by re-infection. The model parameters were estimated making use of viral decay data, growth curves at two different inoculum concentrations, and extra-cellular genome copy measurements (for BUNV) via Markov chain Monte Carlo. Genome copy measurements were essential for constraining estimates of the number of cells that can become infected per unit of infectious virus for BUNV. We found that BUNV exhibited substantially longer eclipse and infectious periods than BATV, while BATV showed a higher per-cell virus production rate. Re-infection was predicted to shorten the eclipse phase for both viruses, but the effect was markedly stronger for BUNV. Together, these results provide a quantitative comparison of the in vitro viral kinetics of BUNV and BATV and reveal substantial differences in their replication dynamics.

q-bio.QM↗

arXiv2025

Surface Exciton Polaritons and Near-Zero Permittivity Surface Waves Supported by Artificial Organic Hyperbolic Metamaterials

Hyperbolic metamaterials enable extreme light confinement and control of photonic states, but their realization has been restricted to inorganic architectures. Here, a fully organic route to fabricate artificial hyperbolic metamaterials based on multilayered thin films of J-aggregate carbocyanine dyes alternated with polyelectrolytes is introduced. These structures exhibit strong optical anisotropy and experimentally support hyperbolic surface exciton polaritons and, for selected dyes, additional surface waves in near-zero permittivity regimes. Spectroscopic ellipsometry confirms a uniaxial dielectric tensor with negative in-plane and positive out-of-plane components, close to the absorption peaks of the constituent J-aggregates. This anisotropy is preserved across individual layers, demonstrating the robustness of the layer-by-layer approach and enabling the coupling of surface exciton polaritons and near-zero permittivity modes even in films only a few nanometres thick. Transfer-matrix simulations based on the obtained dielectric tensor reproduce the coupling conditions for all thicknesses, validating the optical model. Structural characterization reveals the link between optical anisotropy and supramolecular order, with preferential in-plane molecular orientation and the evolution from discrete nanostructures to continuous films as deposition progresses. These organic hyperbolic metamaterial architectures, associated with narrow excitonic resonances from J-aggregates, offer a unique platform for tailoring emission, energy transport, and exploring polariton dynamics at the nanoscale.

cond-mat.mtrl-sci↗

arXiv2025

Room-Temperature Surface Exciton Polaritons in Colloidal J-Aggregate Flakes

J-aggregates are promising organic materials for nanophotonic applications due to their excitonic properties and ability to support surface exciton polaritons at room temperature, providing a robust platform for nanoscale light manipulation. While thin films composed of J-aggregates have demonstrated these advantages, colloidal J-aggregate nanoparticles remain underexplored. Herein, we report the synthesis of colloidal J-aggregate flakes by electrostatic interaction of cyanine molecules (TDBC) and oppositely charged polyelectrolytes (polydiallyldimethylammonium chloride, PDDA). These flakes exhibit colloidal stability maintaining the J-aggregate conformation even in solvents that favoured their monomeric state. The characterization of the colloidal J-aggregate flakes reveals their capability to support surface exciton polaritons at room temperature. This was further confirmed at single-particle level by observing an angular-independent Reststrahlen band near the excitonic resonance. In addition, the colloidal flakes exhibit a strong scattering component that broadens the extinction band and redshifts the photoluminescence, indicating that the colloidal architecture influences the optical response. These findings introduce a versatile colloidal system for constructing excitonic nanostructures tailored for advanced photonic applications.

physics.optics↗

arXiv2022

Bio-inspired polymers with polaritonic properties from visible to infrared: a material playground to mimic purple bacteria light-harvesting resonators

Light-harvesting complexes in natural photosynthetic systems, such as those in purple bacteria, consist of photo-reactive chromophores embedded in densely packed "antenna" systems organized in well-defined nanostructures. In the case of purple bacteria, the chromophore antennas are composed of natural J-aggregates such as bacteriochlorophylls and carotenoids. Inspired by the molecular composition of such biological systems, we create a library of organic materials composed of densely packed J-aggregates in a polymeric matrix, in which the matrix mimics a protein scaffold. This library of organic materials shows polaritonic properties which can be tuned from the visible to the infrared by choice of the model molecule. Inspired by the molecular architecture of the light-harvesting complexes of \textit{Rhodospirillum molischianum} bacteria, we study the light-matter interactions of J-aggregate-based nanorings with similar dimensions to the analogous natural nanoscale architectures. Electromagnetic simulations show that these nanorings of J-aggregates can act as resonators, with subwavelength confinement of light while concentrating the electric field in specific regions. These results open the door to bio-inspired building blocks for all-organic metamaterials while offering a new perspective on light-matter interactions at the nanoscale in densely packed organic matter in biological organisms including photosynthetic organelles.

physics.optics↗

arXiv2022

Tunable narrowband Excitonic Optical Tamm States enabled by a metal-free all-organic structure

Optical Tamm States (OTS) are confined optical modes that can occur at the interface between two highly reflective structures. However, due to the strong reflectance required, their implemen-tation with highly processable and metal-free flexible materials has proven challenging. Herein, we develop the first structure supporting OTS based only on organic polymeric materials, demon-strating a photonic platform based on non-critical, widely available, and easily processable mate-rials. The structures fabricated present large areas and consist of a narrowband multi-layered polymeric Distributed Bragg Reflector (DBR) followed by a thin film of J-aggregate molecular exci-tonic material that can act as a highly reflective surface within a narrowband range. We take ad-vantage of the narrowband spectral response of the DBR and of the reflective molecular layer to tune the OTS band by varying the periodicity of the multilayer, opening the door for the fabrica-tion of OTS structures based on lightweight integrable excitonic devices with cost-effective proce-dures.

physics.optics↗

arXiv2021

Enhanced light absorption in all-polymer biomimetic photonic structures by near-zero-index organic matter

Natural photosynthetic photonic nanostructures can show sophisticated light matter-interactions including enhanced light absorption by slow light even for highly pigmented systems. Beyond fundamental biology aspects these natural nanostructures are very attractive as blueprints for advanced photonic devices. But the soft-matter biomimetic implementations of such nanostructures is challenging due to the low refractive index contrast of most organic photonic structures. Excitonic organic material with near zero index (NZI) optical properties allow overcoming these bottlenecks. Here we demonstrate that the combination of NZI thin films into photonic multilayers like the ones found in nature enables broadband tuneable strong reflectance as well as slow light absorption enhancement and tailored photoluminescence properties in the full VIS spectrum. Moreover, it is shown that this complex optical response is tuneable, paving the way towards the development of active devices based on all polymer and near zero index materials photonic structures.

physics.optics↗

arXiv2021

Plasmonic crystals with highly ordered lattice geometries using continuous metal films on diatom bio-silica as both scaffolds and sources of tuneability

Diatoms are microscopic algae found in all of Earths water courses. They produce frustules, porous silica exoskeletons, grown by precipitation of silicic acid from water. Frustule components, known as girdles, from some diatom species also feature highly periodic pore arrays with properties on the same scale and quality of ordering as manufactured photonic crystals. Here, the girdles of two diatom species with various lattice constants are used as bio-silica scaffolds for plasmonic crystals, combined with metals chosen for spectral agreement between permittivity and photonic crystal properties. The use of frustules as scaffolds for plasmonic application has been tested earlier, as nano-porous features can enhance scattering and local hotspots, useful for sensing application or SERS. However, both the use of girdles and of continuous metal films are new approaches offering previously unseen plasmonic effects. Angularly resolved dispersions from reflection Fourier spectroscopy are provided for Coscinodiscus granii girdles, forming well-ordered square lattices, and Coscinodiscus wailesii, forming ordered hexagonal lattices, covered with a 40 nm film of silver or with 40 nm of gold, respectively. These were confirmed with optical modelling of the 3D systems, including both metal surface layers and internal frustule structures, allowing for the calculation of dispersions and electric fields. Measurements are further compared with structures produced via Focused Ion Beam microscopy, demonstrating the advantages of girdles as photonic crystal scaffolds and as an alternative to conventional plasmonic crystal fabrication. The results demonstrate that high-quality plasmonic crystal scaffolds from diatoms are available in nature, and their natural diversity can be applied in a controlled way to obtain plasmonic crystals with a wide range of behaviours and spectral responses.

physics.optics↗

arXiv2020

Quantification of Ebola virus replication kinetics in vitro

Mathematical modelling has successfully been used to provide quantitative descriptions of many viral infections, but for the Ebola virus, which requires biosafety level 4 facilities for experimentation, modelling can play a crucial role. Ebola modelling efforts have primarily focused on in vivo virus kinetics, e.g., in animal models, to aid the development of antivirals and vaccines. But, thus far, these studies have not yielded a detailed specification of the infection cycle, which could provide a foundational description of the virus kinetics and thus a deeper understanding of their clinical manifestation. Here, we obtain a diverse experimental data set of the Ebola infection in vitro, and then make use of Bayesian inference methods to fully identify parameters in a mathematical model of the infection. Our results provide insights into the distribution of time an infected cell spends in the eclipse phase (the period between infection and the start of virus production), as well as the rate at which infectious virions lose infectivity. We suggest how these results can be used in future models to describe co-infection with defective interfering particles, which are an emerging alternative therapeutic.

q-bio.CB↗

arXiv2018

Microstructure-Stabilized Blue Phase Liquid Crystals

We show that micron-scale two-dimensional (2D) honeycomb microwells can significantly improve the stability of blue phase liquid crystals (BPLCs). Polymeric microwells made by direct laser writing improve various features of the blue phase (BP) including a dramatic extension of stable temperature range and a large increase both in reflectivity and thermal stability of the reflective peak wavelength. These results are mainly attributed to the omni-directional anchoring of the isotropically oriented BP molecules at the polymer walls of the hexagonal microwells and at the top and bottom substrates. This leads to an omni-directional stabilization of the entire BPLC system. This study not only provides a novel insight into the mechanism for the BP formation in the 2D microwell but also points to an improved route to stabilize BP using 2D microwell arrays.

cond-mat.soft↗

arXiv2017

Direct Wide-angle Measurement of Photonic Band- structure in a Three-dimensional Photonic Crystal using Infrared Fourier Imaging Spectroscopy

We propose a method to directly visualize the photonic band-structure of micron size photonic crystals using wide angle spectroscopy. By extending Fourier Imaging Spectroscopy sensitivity into the infrared range we have obtained accurate measurements of the band-structures along the high-symmetry directions (X-W-K-L-U) of polymeric three-dimensional rod-connected diamond photonic crystals. Our implementation also allows us to record single-wavelength reflectance far field patterns showing a very good agreement with simulations of the same designs. This technique is suitable for the characterization of photonic structures working in the infrared and in particular, to obtain band-structure information of complete photonic band gap materials.

physics.optics↗

arXiv2016

Stochastic models of the binding kinetics of VEGF-A to VEGFR1 and VEGFR2 in endothelial cells

Vascular endothelial growth factor receptors (VEGFRs) are receptor tyrosine kinases (RTKs) that regulate proliferation, migration, angiogenesis and vascular permeability of endothelial cells. VEGFR1 and VEGFR2 bind vascular endothelial growth factors (VEGFs), inducing receptor dimerisation and activation, characterised by phosphorylation of tyrosine residues in their cytoplasmic domain. Although experimental evidence suggests that RTK signalling occurs both on the plasma membrane and intra-cellularly, and reveals the role of endocytosis in RTK signal transduction, we still lack knowledge of VEGFR phosphorylation-site use and of the spatiotemporal regulation of VEGFR signalling. In this paper, we introduce four stochastic mathematical models to study the binding kinetics of vascular endothelial growth factor VEGF-A to VEGFR1 and VEGFR2, and phosphorylation. The formation of phosphorylated dimers on the cell surface is a two-step process: diffusive transport and binding. The first two of our models only consider VEGFR2, which allows us to introduce new stochastic descriptors making use of a matrix-analytic approach. The two remaining models describe the competition of VEGFR1 and VEGFR2 for ligand availability, and are analysed making use of Gillespie simulations and the van Kampen approximation. Under the hypothesis that bound phosphorylated receptor dimers are the signalling units, we study the time to reach a threshold number of such complexes. Our results indicate that the presence of VEGFR1 does not only affect the timescale to reach a given signalling threshold, but it also affects the maximum attainable threshold. This result is consistent with the conjectured role of VEGFR1 as a decoy receptor, that prevents VEGF-A binding to VEGFR2, and thus, VEGFR2 attaining suitable phosphorylation levels. We identify an optimum range of ligand concentration for sustained dimer phosphorylation.

q-bio.BM↗

arXiv2015

Evidence of near-infrared partial photonic bandgap in polymeric rod-connected diamond structures

We present the simulation, fabrication, and optical characterization of low-index polymeric rod-connected diamond (RCD) structures. Such complex three-dimensional photonic crystal structures are created via direct laser writing by two-photon polymerization. To our knowledge, this is the first measurement at near-infrared wavelengths, showing partial photonic bandgaps for this structure. We characterize structures in transmission and reflection using angular resolved Fourier image spectroscopy to visualize the band structure. Comparison of the numerical simulations of such structures with the experimentally measured data show good agreement for both P- and S-polarizations.

physics.optics↗