arXiv subjects

Rafael Delgado-Buscalioni

Publications and source records attributed to Rafael Delgado-Buscalioni.

At least 19 recordsLinked to original sources

arXiv2026

Unraveling Internal Friction in a Coarse-Grained Protein Model

Understanding the dynamic behavior of complex biomolecules requires simplified models that not only make computations feasible but also reveal fundamental mechanisms. Coarse-graining (CG) achieves this by grouping atoms into beads, whose stochastic dynamics can be derived using the Mori-Zwanzig formalism, capturing both reversible and irreversible interactions. In liquid, the dissipative bead-bead interactions have so far been restricted to hydrodynamic couplings. However, friction does not only arises from the solvent but notably, from the internal degrees of freedom missing in the CG beads. This leads to an additional ''internal friction'' whose relevance is studied in this contribution. By comparing with all-atom molecular dynamics (MD), we neatly show that in order to accurately reproduce the dynamics of a globular protein in water using a coarse-grained (CG) model, not only a precise determination of elastic couplings and the Stokesian self-friction of each bead is required. Critically, the inclusion of internal friction between beads is also necessary for a faithful representation of protein dynamics. We propose to optimize the parameters of the CG model through a self-averaging method that integrates the CG dynamics with an evolution equation for the CG parameters. This approach ensures that selected quantities, such as the radial distribution function and the time correlation of bead velocities, match the corresponding MD values.

cond-mat.soft↗

arXiv2026

Quantitative measurement of fluid inertial effects in confined Brownian motion

The hydrodynamic response of Brownian particles in liquids is fundamentally altered by inertial forces arising from unsteady momentum transport in the surrounding fluid. These forces are of two distinct types\,: the added mass and the history effect. While both are well understood in bulk and weakly-confined geometries, under deterministic driving, their respective behaviours under strong confinement and thermal fluctuations remain scarcely addressed, unclear and often entangled together. The goal of the present study is thus to fill this fundamental gap. The behaviours of the two distinct inertial contributions are quantitatively investigated in the vicinity of a flat, rigid wall, using a combination of broadrange thermal colloidal-probe atomic-force-microscopy experiments, advanced numerical simulations and theory. The separation of the added-mass and history-force contributions is achieved through their different frequency-scaling signatures within the measured high-resolution thermal spectra. Our results establish a complete picture of Brownian motion at interfaces, in the lubrication regime, with direct relevance to nanofluidics and interfacial biophysics.

cond-mat.soft↗

arXiv2026

Magnetic Nanoparticles as Label-Free Dual-Function Nanoheaters and Nanothermometers

Heat generation and temperature reading at the nanoscale have attracted increasing attention due to their direct relevance in thermal therapeutic approaches. Consequently, huge progress has been made toward the design of dual-function nanoplatforms that integrate heating and thermometry capabilities at the nanoscale. However, in most cases, dual nanoheater nanothermometer platforms rely either on specifically engineered materials or on complex readout schemes, which limits translational potential due to complex implementation procedures. To overcome these challenges, we present a methodology for directly extracting temperature information based on dynamical magnetization measurements of cobalt ferrite magnetic nanoflowers. We demonstrate that these nanocrystals monitor temperature changes through variations in their magnetization cycles measured under alternating magnetic fields. Importantly, this thermometric functionality is preserved after surface functionalization and under chemical variations in the nanoparticle environment. Interestingly, we show that we can simultaneously generate heat and report temperature changes within the same agent. This is thanks to the photothermal conversion of cobalt ferrite nanoparticles subjected to near infrared irradiation and the tight reported relationship between magnetization dynamics and Brownian relaxation. Together, these results establish cobalt ferrite magnetic nanoparticles as a label-free platform for simultaneous heat generation and intrinsic temperature readout, enabling real-time nanoscale thermal control.

physics.bio-ph↗

arXiv2026

libMobility: A Python library for hydrodynamics at the Smoluchowski level

Effective hydrodynamic modeling is crucial for accurately predicting fluid-particle interactions in diverse fields such as biophysics and materials science. Developing and implementing hydrodynamic algorithms is challenging due to the complexity of fluid dynamics, necessitating efficient management of large-scale computations and sophisticated boundary conditions. Furthermore, adapting these algorithms for use on massively parallel architectures like GPUs adds an additional layer of complexity. This paper presents the libMobility software library, which offers a suite of CUDA-enabled solvers for simulating hydrodynamic interactions in particulate systems at the Rotne-Prager-Yamakawa (RPY) level. The library facilitates precise simulations of particle displacements influenced by external forces and torques, including both the deterministic and stochastic components. Notable features of libMobility include its ability to handle linear and angular displacements, thermal fluctuations, and various domain geometries effectively. With an interface in Python, libMobility provides comprehensive tools for researchers in computational fluid dynamics and related fields to simulate particle mobility efficiently. This article details the technical architecture, functionality, and wide-ranging applications of libMobility. libMobility is available at https://github.com/stochasticHydroTools/libMobility.

cond-mat.soft↗

arXiv2025

Fast spectral solver for viscoelastic structures under oscillatory flow in free space or wall-bounded domains: applications to quartz crystal microbalance and force spectroscopy

We present a fast spectral solver for the linear response of viscoelastic structures under oscillatory flow either in free space or close to a flat moving wall. The scheme works in the frequency domain (using phasors) and couples the oscillatory Stokes equation with rigid or flexible structures, modeled by viscoelastic networks of immersed boundary kernels. The fluid-structure coupling can be solved by two routes. One route calculates the hydrodynamic mobility matrix required to solve the equation for the structure deformation rate in matrix form. The second route iteratively solves the coupled fluid-structure equations: fluid-induced forces on the structures create a tension field which is then transferred to the fluid, until convergence. The resulting fixed-point problem is solved iteratively using the Anderson acceleration method. The mobility route is optimal when dealing with one or few structures, while the iterative scheme is preferred for denser dispersions. In any case, the flow resulting from the body forces is solved by a recently developed scheme [J. Fluid. Mech. 1010 A57, 2025] which is spectral in space and time and deals with doubly periodic open domains (either free-space or wall-bounded) where meshing is restricted to the region of interest around the structures. We test the present scheme in two applied contexts: quartz-crystal-microbalance (QCM) of spheres, suspended, adsorbed or tethered to viscoelastic linkers; and force spectroscopy (via atomic force microscopy) reproducing the power spectra of vibrating microparticles near a solid boundary. In all cases, comparisons with analytical, numerical and experimental results show excellent agreement. We conclude by discussing new routes the scheme opens in force spectroscopy and QCM analyses of soft objects.

cond-mat.mes-hall↗

arXiv2024

Rolling vesicles: From confined rotational flows to surface-enabled motion

The interaction of surfaces in relative motion in wet environments is dominated by lubrication forces, which play a pivotal role in the dynamics of microscopic systems. Here, we develop motile vesicles that exploit lubrication forces to roll on substrates. The activity of the vesicle comes from the confined rotational flow generated by a driven rotating particle encapsulated within the vesicle by droplet-microfluidics. Lubrication forces driving vesicle rolling are controlled by membrane mechanics and its tribological properties. This provides the design principles for motile vesicles that exploit frictional forces to efficiently navigate through complex environments.

cond-mat.soft↗

arXiv2023

Boosting the efficiency of transient photoluminescence microscopy using cylindrical lenses

Transient Photoluminescence Microscopy (TPLM) allows for the direct visualization of carrier transport in semiconductor materials with sub nanosecond and few nanometer resolution. The technique is based on measuring changes in the spatial distribution of a diffraction limited population of carriers using spatiotemporal detection of the radiative decay of the carriers. The spatial resolution of TPLM is therefore primarily determined by the signal-to-noise-ratio (SNR). Here we present a method using cylindrical lenses to boost the signal acquisition in TPLM experiments. The resulting asymmetric magnification of the photoluminescence emission of the diffraction limited spot can increase the collection efficiency by more than a factor of 10, significantly reducing acquisition times and further boosting spatial resolution.

physics.app-ph↗

arXiv2021

Halide mixing inhibits exciton transport in two-dimensional perovskites despite phase purity

Metal-halide perovskites are a versatile material platform for light-harvesting and light-emitting applications as their variable chemical composition allows the optoelectronic properties to be tailored to specific applications. Halide mixing is one of the most powerful techniques to tune the optical bandgap of metal-halide perovskites across wide spectral ranges. However, halide mixing has commonly been observed to result in phase segregation, which reduces excited-state transport and limits device performance. While the current emphasis lies on the development of strategies to prevent phase segregation, it remains unclear how halide mixing may affect excited-state transport even if phase purity is maintained. In this work, we study excitonic excited-state transport in phase pure mixed-halide 2D perovskites. Using transient photoluminescence microscopy, we show that, despite phase purity, halide mixing inhibits exciton transport in these materials. We find a significant reduction even for relatively low alloying concentrations, with bromide-rich perovskites being particularly sensitive to the introduction of iodide ions. Performing Brownian dynamics simulations, we are able to reproduce our experimental results and attribute the decrease in diffusivity to the energetically disordered potential landscape that arises due to the intrinsic random distribution of alloying sites. Our results suggest that even in the absence of phase segregation, halide mixing may still impact carrier transport due to the local intrinsic inhomogeneities in the energy landscape.

physics.app-ph↗

arXiv2020

Mapping the Trap-State Landscape in 2D Metal-Halide Perovskites using Transient Photoluminescence Microscopy

Transient microscopy is of vital importance in understanding the dynamics of optical excited states in optoelectronic materials, as it allows for a direct visualization of the movement of energy carriers in space and time. Important information on the influence of trap-states can be obtained using this technique, typically observed as a slow-down of the energy transport as carriers are trapped at defect sites. To date, however, studies of the trap-state dynamics have been mostly limited to phenomenological descriptions of the early time-dynamics. In this report, we show how long-acquisition-time transient photoluminescence microscopy can be used to provide a detailed map of the trap-state landscape in 2D perovskites, in particular when used in combination with transient spectroscopy. We reveal anomalous spatial dynamics of excitons in 2D perovskites, which cannot be explained with existing models for trap limited exciton transport that only account for a single trap type. Instead, using a continuous diffusion model and performing Brownian dynamics simulations, we show that this behavior can be explained by accounting for a distinct distribution of traps in this material. Our results highlight the value of transient microscopy as a complementary tool to more common transient spectroscopy techniques in the characterization of the excited state dynamics in semiconductors.

cond-mat.mtrl-sci↗

arXiv2020

Exciton diffusion in two-dimensional metal-halide perovskites

Two-dimensional perovskites, in which inorganic layers are stabilized by organic spacer molecules, are attracting increasing attention as a more robust analogue to the conventional three-dimensional metal-halide perovskites. However, reducing the perovskite dimensionality alters their optoelectronic properties dramatically, yielding excited states that are dominated by bound electron-hole pairs known as excitons, rather than by free charge carriers common to their bulk counterparts. Despite the growing interest in two-dimensional perovskites for both light harvesting and light emitting applications, the full impact of the excitonic nature on their optoelectronic properties remains unclear, particularly regarding the spatial dynamics of the excitons within the two-dimensional (2D) plane. Here, we present direct measurements of in-plane exciton transport in single-crystalline layered perovskites. Using time-resolved fluorescence microscopy, we show that excitons undergo an initial fast, intrinsic normal diffusion through the crystalline plane, followed by a transition to a slower subdiffusive regime as excitons get trapped. Interestingly, the early intrinsic exciton diffusivity depends sensitively on the exact composition of the perovskite, such as the choice of organic spacer. We attribute these changes in exciton transport properties to strong exciton-phonon interactions and the formation of large exciton-polarons. Our findings provide a clear design strategy to optimize exciton transport in these systems.

physics.app-ph↗

arXiv2019

Sectoral Multipole Focused Beams

We discuss the properties of pure multipole beams with well-defined handedness or helicity, with the beam field a simultaneous eigenvector of the squared total angular momentum and its projection along the propagation axis. Under the condition of hemispherical illumination, we show that the only possible propagating multipole beams are `sectoral' multipoles. The sectoral dipole beam is shown to be equivalent to the non-singular time-reversed field of an electric and a magnetic point dipole Huygens' source located at the beam focus. Higher order multipolar beams are vortex beams vanishing on the propagation axis. The simple analytical expressions of the electric field of sectoral multipole beams, exact solutions of Maxwell's equations, and the peculiar behaviour of the Poynting vector and spin and orbital angular momenta in the focal volume could help to understand and model light-matter interactions under strongly focused beams.

physics.optics↗

arXiv2019

Optofluidic control of the dispersion of nanoscale dumbbells

Previous research has shown that gold nanoparticles immersed in water in an optical vortex lattice formed by the perpendicular intersection of two standing light waves with a π/2 rad phase difference will experience enhanced dispersion that scales with the intensity of the incident laser. We show that flexible nanoscale dumbbells (created by attaching two such gold particles by means of a polymer chain) in the same field display different types of motion depending on the chain length and field intensity. We have not disregarded the secondary optical forces due to light scattering. The dumbbells may disperse, rotate or remain trapped. For some values of the parameters, the (enhanced) dispersion possesses a displacement distribution with exponential tails, making the motion anomalous, though Brownian.

physics.optics↗

arXiv2018

Solvent hydrodynamics enhances the collective diffusion of membrane lipids

The collective motion of membrane lipids over hundred of nanometers and nanoseconds is essential for the formation of submicron complexes of lipids and proteins in the cell membrane. These dynamics are difficult to access experimentally and are currently poorly understood. One of the conclusions of the celebrated Saffman-Debrück (SD) theory is that lipid disturbances smaller than the Saffman length (microns) are not affected by the hydrodynamics of the embedding solvent. Using molecular dynamics and coarse-grained models with implicit hydrodynamics we show that this is not true. Hydrodynamic interactions between the membrane and the solvent strongly enhance the short-time collective diffusion of lipids at all scales. The momentum transferred between the membrane and the solvent in normal direction (not considered by the SD theory) propagates tangentially over the membrane inducing long-ranged repulsive forces amongst lipids. As a consequence the lipid collective diffusion coefficient increases proportionally to the disturbance wavelength. We find quantitative agreement with the predicted anomalous diffusion in quasi-two-dimensional dynamics, observed in colloids confined to a plane but embedded in 3D solvent.

physics.bio-ph↗

arXiv2018

Light induced "Mock Gravity" at the nanoscale

The origin of long-range attractive interactions has fascinated scientist along centuries. The remarkable Fatio-LeSage's corpuscular theory, introduced as early as in 1690 and generalized to electromagnetic waves by Lorentz, proposed that, due to their mutual shadowing, two absorbing particles in an isotropic radiation field experience an attractive force which follows a gravity-like inverse square distance law. Similar "Mock Gravity" interactions were later introduced by Spitzer and Gamow in the context of Galaxy formation but their actual relevance in Cosmology has never been unambiguously established. Here we predict the existence of Mock-Gravity, inverse square distance, attractive forces between two identical molecules or nanoparticles in a quasi monochromatic isotropic random light field, whenever the light frequency is tuned to an absorption line such that the real part of the particle's electric polarizability is zero, i.e. at the so-called Froehlich resonance. These interactions are scale independent, holding for both near and far-field separation distances.

physics.optics↗

arXiv2017

Application of the Eckart frame to soft matter: rotation of star polymers under shear flow

The Eckart co-rotating frame is used to analyze the dynamics of star polymers under shear flow, either in melt or solution and with different types of bonds. This formalism is compared with the standard approach used in many previous studies on polymer dynamics, where an apparent angular velocity $ω$ is obtained from relation between the tensor of inertia and angular momentum. A common mistake is to interpret $ω$ as the molecular rotation frequency, which is only valid for rigid-body rotation. The Eckart frame, originally formulated to analyze the infrared spectra of small molecules, dissects different kinds of displacements: vibrations without angular momentum, pure rotation, and vibrational angular momentum (leading to a Coriolis cross-term). The Eckart frame co-rotates with the molecule with an angular frequency $Ω$ obtained from the Eckart condition for minimal coupling between rotation and vibration. The standard and Eckart approaches are compared with a straight description of the star's dynamics taken from the time autocorrelation of the monomers positions moving around the molecule's center of mass. This is an underdamped oscillatory signal, which can be described by a rotation frequency $ω_R$ and a decorrelation rate $Γ$. We consistently find that $Ω$ coincides with $ω_R$, which determines the characteristic tank-treading rotation of the star. By contrast, the apparent angular velocity $ω< Ω$ does not discern between pure rotation and molecular vibrations. We believe that the Eckart frame will be useful to unveil the dynamics of semiflexible molecules where rotation and deformations are entangled, including tumbling, tank-treading motions and breathing modes.

cond-mat.soft↗

arXiv2016

Control of diffusion of nano-particles in an optical vortex lattice

A two-dimensional periodic optical force field, which combines conservative dipolar forces with vortices from radiation pressure, is proposed in order to influence the diffusion properties of optically susceptible nano-particles. The different deterministic flow patterns are identified. In the low noise limit, the diffusion coefficient is computed from a Mean First Passage Time (MFPT) and the Most Probable Escape Paths (MPEP) are identified for those flow patterns which possess an stable stationary point. Numerical simulations of the associated Langevin equations show remarkable agreement with the analytically deduced expressions. Modifications of the force field are proposed so that a wider range of phenomena could be tested.

cond-mat.mes-hall↗

arXiv2014

Statistical Mechanics of Hamiltonian Adaptive Resolution Simulations

The Adaptive Resolution Scheme (AdResS) is a hybrid scheme that allows one to treat a molecular system with different levels of resolution depending on the location of the molecules. The construction of a Hamiltonian based on the this idea (H-AdResS) allows one to formulate the usual tools of ensembles and statistical mechanics. We present a number of exact and approximate results that provide a statistical mechanics foundation for this simulation method. We also present simulation results that illustrate the theory.

cond-mat.stat-mech↗

arXiv2014

A multiblob approach to colloidal hydrodynamics with inherent lubrication

This work presents an intermediate resolution model of the hydrodynamics of colloidal particles based on a mixed Eulerian-Lagrangian formulation. The particle is constructed with a small set of overlapping Peskin's Immersed Boundary kernels (blobs) which are held together by springs to build up a particle impenetrable core. Here, we used 12 blobs placed in the vertexes of an icosahedron with an extra one in its center. Although the particle surface is not explicitly resolved, we show that the short-distance hydrodynamic responses (flow profiles, translational and rotational mobilities, lubrication, etc) agree with spherical colloids and provide consistent effective radii. A remarkable property of the present multiblob model is that it naturally presents a "divergent" lubrication force at finite inter-particle distance. This permits to resolve the large viscosity increase at dense colloidal volume fractions. The intermediate resolution model is able to recover highly non-trivial (many-body) hydrodynamics using small particles whose radii are similar to the grid size $h$ (in the range $[1.6-3.2]\,h$). Considering that the cost of the embedding fluid phase scales like the cube of the particle radius, this result brings about a significant computational speed-up. Our code Fluam works in Graphics Processor Units (GPU's) and uses Fast Fourier Transform for the Poisson solver, which further improves its efficiency.

cond-mat.soft↗