Rafael Delgado-Buscalioni
Current Organizations / Institutes
The organizations/institutes from the scholar's latest article
Rafael Delgado-Buscalioni has a total of 197 co-authors. Here are the top co-authors by number of shared publications:
- Marc Meléndez
Universidad Autónoma de Madrid
12 shared publications - Peter Vivian Coveney
University College London
12 shared publications - Gianni De Fabritiis
Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C Dr. Aiguader 88, 08003 Barcelona, Spain
9 shared publications - Florencio Balboa Usabiaga
Basque Center for Applied Mathematics, BCAM 1 , Alameda de Mazarredo 14, Bilbao 48400
8 shared publications - Matej Praprotnik
Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
7 shared publications - Ferry Prins
Universidad Autónoma de Madrid
5 shared publications
Latest Publications
- Open Access
Three‐Dimensional Optical and Computational Reconstruction of Colloidal Electrokinetic Flows via Multiplane Imaging and Multiscale Modeling
Sorting, filtering, and controlling colloidal particles is crucial in many fields, ranging from chemistry to biology and physics. Dielectrophoresis (DEP) enables selective manipulation of colloids by non‐uniform AC electric fields, yet the associated three‐dimensional nanoparticle dynamics and electrokinetic flows remain difficult to access experimentally. Here, we combine real‐time multiplane widefield microscopy (> 100 fps), 3D single‐particle tracking, and multiscale modeling to reconstruct the motion of 200 nm fluorescent polystyrene nanoparticles around a quadrupolar electrode under positive and negative DEP. This optical–computational approach provides volumetric trajectories and flow maps, revealing particle trapping, depletion, and three‐dimensional vortical motion. A model including DEP and AC electro‐osmotic flow quantitatively reproduces the positive DEP dynamics, demonstrating direct agreement between experiment and theory. Under negative DEP, the model captures particle depletion near the electrodes but not all observed flow structures, pointing to additional electrokinetic or electrothermal contributions. This framework provides a route to validate and refine AC electrokinetic models for complex colloidal and microfluidic systems.
Open AccessThree‐Dimensional Optical and Computational Reconstruction of Colloidal Electrokinetic Flows via Multiplane Imaging and Multiscale Modeling
Sorting, filtering, and controlling colloidal particles is crucial in many fields, ranging from chemistry to biology and physics. Dielectrophoresis (DEP) enables selective manipulation of colloids by non‐uniform AC electric fields, yet the associated three‐dimensional nanoparticle dynamics and electrokinetic flows remain difficult to access experimentally. Here, we combine real‐time multiplane widefield microscopy (> 100 fps), 3D single‐particle tracking, and multiscale modeling to reconstruct the motion of 200 nm fluorescent polystyrene nanoparticles around a quadrupolar electrode under positive and negative DEP. This optical–computational approach provides volumetric trajectories and flow maps, revealing particle trapping, depletion, and three‐dimensional vortical motion. A model including DEP and AC electro‐osmotic flow quantitatively reproduces the positive DEP dynamics, demonstrating direct agreement between experiment and theory. Under negative DEP, the model captures particle depletion near the electrodes but not all observed flow structures, pointing to additional electrokinetic or electrothermal contributions. This framework provides a route to validate and refine AC electrokinetic models for complex colloidal and microfluidic systems.
- 9 April 2026
- Published by AIP Publishing in The Journal of Chemical Physics
- Vol. 164 (14)
Quantitative description of protein configuration and viscoelasticity using first-principles hydrodynamics applied to quartz crystal microbalance experiments
The quartz crystal microbalance (QCM) is one of the few label-free techniques capable of sampling the response of proteins and their aggregates. However, QCM signals come encrypted by a complicated interaction between the biomolecular viscoelastic response and their hydrodynamic perturbations. This has hampered the quantitative interpretation of QCM signals of biomolecules. In addition, the large size disparity between proteins and the QCM flow penetration length of 100 nm creates a deadlock for standard simulation packages. Using first-principles modeling and adaptive schemes, we show that the ultrasensitive QCM sensor can be upgraded to a high-precision quantitative tool for protein analysis. We present a “Virtual-QCM” (VQCM) framework to introduce viscoelastic structures in a hydrodynamic solver for semi-infinite wall-bounded oscillatory flow. The fluid solver [R. P. Peláez, P. Palacios-Alonso, and R. Delgado-Buscalioni, J. Fluid Mech. 1010, A57 (2025)] is spectral in time and space and implements open boundaries focusing on the relevant fluid layer around proteins with ∼104 speed-up. Biomolecules are modeled as viscoelastic networks connected to the atomistic level via coarse-graining theory. Integrating VQCM with experiments allows us to predict the physicochemical properties of FtsZ and ZipA; bacterial proteins with intrinsically disordered regions (IDRs) tethered to lipid membrane substrates. Quantitative match with experiments at all coverages permits us to measure substrate binding affinities, IDR extension ℓ, stiffness k, and intrinsic friction ξ. We find the polypeptide chains to be extremely sensitive to the buffer ionic strength, with protein friction affected by Mg+2. Measured intrinsic relaxation times ξ/k ∼ [3–30] ns are consistent with FRET analyses. Access to microscopic information using standard QCM sensors will help decipher the IDR structure–function and other protein aggregates.
- 9 April 2026
- Published by AIP Publishing in The Journal of Chemical Physics
- Vol. 164 (14)
Quantitative description of protein configuration and viscoelasticity using first-principles hydrodynamics applied to quartz crystal microbalance experiments
The quartz crystal microbalance (QCM) is one of the few label-free techniques capable of sampling the response of proteins and their aggregates. However, QCM signals come encrypted by a complicated interaction between the biomolecular viscoelastic response and their hydrodynamic perturbations. This has hampered the quantitative interpretation of QCM signals of biomolecules. In addition, the large size disparity between proteins and the QCM flow penetration length of 100 nm creates a deadlock for standard simulation packages. Using first-principles modeling and adaptive schemes, we show that the ultrasensitive QCM sensor can be upgraded to a high-precision quantitative tool for protein analysis. We present a “Virtual-QCM” (VQCM) framework to introduce viscoelastic structures in a hydrodynamic solver for semi-infinite wall-bounded oscillatory flow. The fluid solver [R. P. Peláez, P. Palacios-Alonso, and R. Delgado-Buscalioni, J. Fluid Mech. 1010, A57 (2025)] is spectral in time and space and implements open boundaries focusing on the relevant fluid layer around proteins with ∼104 speed-up. Biomolecules are modeled as viscoelastic networks connected to the atomistic level via coarse-graining theory. Integrating VQCM with experiments allows us to predict the physicochemical properties of FtsZ and ZipA; bacterial proteins with intrinsically disordered regions (IDRs) tethered to lipid membrane substrates. Quantitative match with experiments at all coverages permits us to measure substrate binding affinities, IDR extension ℓ, stiffness k, and intrinsic friction ξ. We find the polypeptide chains to be extremely sensitive to the buffer ionic strength, with protein friction affected by Mg+2. Measured intrinsic relaxation times ξ/k ∼ [3–30] ns are consistent with FRET analyses. Access to microscopic information using standard QCM sensors will help decipher the IDR structure–function and other protein aggregates.
- 27 January 2026
- Published by AIP Publishing in The Journal of Chemical Physics
- Vol. 164 (4)
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 such as 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 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.
- 27 January 2026
- Published by AIP Publishing in The Journal of Chemical Physics
- Vol. 164 (4)
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 such as 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 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.
- Open Access
- 30 December 2025
- Published by Royal Society of Chemistry (RSC) in Nanoscale Advances
- Vol. 8 (4) , 1251-1259
Tunable optical matter: electrostatic repulsion modulates near- and far-field gold nanoparticle arrangements
Experiments and simulations reveal that salt-dependent electrostatic repulsion modulates near- and far-field optical binding of gold nanoparticles, with a simple model reproducing observed configurations and highlighting electrostatics' key role.
- 30 December 2025
- Published by Royal Society of Chemistry (RSC) in Nanoscale Advances
- Vol. 8 (4) , 1251-1259
Open AccessTunable optical matter: electrostatic repulsion modulates near- and far-field gold nanoparticle arrangements
Experiments and simulations reveal that salt-dependent electrostatic repulsion modulates near- and far-field optical binding of gold nanoparticles, with a simple model reproducing observed configurations and highlighting electrostatics' key role.
- Open Access
- 18 November 2025
- Published by AIP Publishing in The Journal of Chemical Physics
- Vol. 163 (19)
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 a 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 [R. P. Peláez, P. Palacios-Alonso, and R. Delgado-Buscalioni, 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.
- 18 November 2025
- Published by AIP Publishing in The Journal of Chemical Physics
- Vol. 163 (19)
Open AccessFast 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 a 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 [R. P. Peláez, P. Palacios-Alonso, and R. Delgado-Buscalioni, 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.
- Open Access
- 20 October 2025
- Published by American Chemical Society (ACS) in ChemRxiv
Tunable Optical Matter: Electrostatic Repulsion Governs Near- and Far-Field Gold Nanoparticle Arrangements
The dynamics and equilibrium configurations of immersed optically-bound particles are complex phenomena involving several physical mechanisms such as optical forces, electrostatic interactions, and fluid dynamics. In this work, we unravel, using experiments and numerical simulations, the key role played by short-range electrostatic forces. The repulsive interaction among gold nanoparticles is adjusted by changing the salt concentration. When the electrostatic interaction is reduced, near-field (NF) optical binding with particles oriented along the polarization direction is promoted, while, for low values of the salt concentration, inter-particle repulsion induces far-field (FF) optical binding configurations oriented perpendicular to the polarization. The importance of electrostatic force is confirmed by a theoretical model in which the repulsive effect is explicitly tuned. The numerical results reproduce the measured particle configurations and highlight the dominant role of electrostatic interactions, particularly in FF optical binding configurations.
- 20 October 2025
- Published by American Chemical Society (ACS) in ChemRxiv
Open AccessTunable Optical Matter: Electrostatic Repulsion Governs Near- and Far-Field Gold Nanoparticle Arrangements
The dynamics and equilibrium configurations of immersed optically-bound particles are complex phenomena involving several physical mechanisms such as optical forces, electrostatic interactions, and fluid dynamics. In this work, we unravel, using experiments and numerical simulations, the key role played by short-range electrostatic forces. The repulsive interaction among gold nanoparticles is adjusted by changing the salt concentration. When the electrostatic interaction is reduced, near-field (NF) optical binding with particles oriented along the polarization direction is promoted, while, for low values of the salt concentration, inter-particle repulsion induces far-field (FF) optical binding configurations oriented perpendicular to the polarization. The importance of electrostatic force is confirmed by a theoretical model in which the repulsive effect is explicitly tuned. The numerical results reproduce the measured particle configurations and highlight the dominant role of electrostatic interactions, particularly in FF optical binding configurations.
- Open Access
- 8 May 2025
- Published by Cambridge University Press (CUP) in Journal of Fluid Mechanics
- Vol. 1010, A57
Spectral solver for the oscillatory Stokes frequency-based equation in doubly periodic confined domains
Oscillatory flows induced by a monochromatic forcing frequency $\omega$ close to a planar surface are present in many applications involving fluid–matter interaction such as ultrasound, vibrational spectra by microscopic pulsating cantilevers, nanoparticle oscillatory magnetometry, quartz crystal microbalance and more. Numerical solution of these flows using standard time-stepping solvers in finite domains present important drawbacks. First, hydrodynamic finite-size effects scale as $1/L_{\parallel }^2$ close to the surface and extend several times the penetration length $\delta \sim \omega ^{-1/2}$ in the normal $z$ direction and second, they demand rather long transient times $O(L_z^2)$ to allow vorticity to diffuse over the computational domain. We present a new frequency-based scheme for doubly periodic (DP) domains in free or confined spaces which uses spectral-accurate solvers based on fast Fourier transform in the periodic $(xy)$ plane and Chebyshev polynomials in the aperiodic $z$ direction. Following the ideas developed for the steady Stokes solver (Hashemi et al. J. Chem. Phys. vol. 158, 2023, p. 154101), the computational system is decomposed into an ‘inner’ domain (where forces are imposed) and an outer domain (where the flow is solved analytically using plane-wave expansions). Matching conditions leads to a solvable boundary value problem. Solving the equations in the frequency domain using complex phasor fields avoids time-stepping and permits a strong reduction in computational time. The spectral scheme is validated against analytical results for mutual and self-mobility tensors, including the in-plane Fourier transform of the Green function. Hydrodynamic couplings are investigated as a function of the periodic lattice length. Applications are finally discussed.- 8 May 2025
- Published by Cambridge University Press (CUP) in Journal of Fluid Mechanics
- Vol. 1010, A57
Open AccessSpectral solver for the oscillatory Stokes frequency-based equation in doubly periodic confined domains
Oscillatory flows induced by a monochromatic forcing frequency $\omega$ close to a planar surface are present in many applications involving fluid–matter interaction such as ultrasound, vibrational spectra by microscopic pulsating cantilevers, nanoparticle oscillatory magnetometry, quartz crystal microbalance and more. Numerical solution of these flows using standard time-stepping solvers in finite domains present important drawbacks. First, hydrodynamic finite-size effects scale as $1/L_{\parallel }^2$ close to the surface and extend several times the penetration length $\delta \sim \omega ^{-1/2}$ in the normal $z$ direction and second, they demand rather long transient times $O(L_z^2)$ to allow vorticity to diffuse over the computational domain. We present a new frequency-based scheme for doubly periodic (DP) domains in free or confined spaces which uses spectral-accurate solvers based on fast Fourier transform in the periodic $(xy)$ plane and Chebyshev polynomials in the aperiodic $z$ direction. Following the ideas developed for the steady Stokes solver (Hashemi et al. J. Chem. Phys. vol. 158, 2023, p. 154101), the computational system is decomposed into an ‘inner’ domain (where forces are imposed) and an outer domain (where the flow is solved analytically using plane-wave expansions). Matching conditions leads to a solvable boundary value problem. Solving the equations in the frequency domain using complex phasor fields avoids time-stepping and permits a strong reduction in computational time. The spectral scheme is validated against analytical results for mutual and self-mobility tensors, including the in-plane Fourier transform of the Green function. Hydrodynamic couplings are investigated as a function of the periodic lattice length. Applications are finally discussed. - Open Access
- 29 April 2025
- Published by Royal Society of Chemistry (RSC) in Nanoscale
- Vol. 17 (20) , 12963-12980
Fast and accurate characterization of bioconjugated particles and solvent properties by a general nonlinear analytical relationship for the AC magnetic hysteresis area
A nonlinear relationship for the magnetic hysteresis area of Brownian nanoparticles permits fast and accurate characterization of bioconjugated particles and solvent properties by an automated method.
- 29 April 2025
- Published by Royal Society of Chemistry (RSC) in Nanoscale
- Vol. 17 (20) , 12963-12980
Open AccessFast and accurate characterization of bioconjugated particles and solvent properties by a general nonlinear analytical relationship for the AC magnetic hysteresis area
A nonlinear relationship for the magnetic hysteresis area of Brownian nanoparticles permits fast and accurate characterization of bioconjugated particles and solvent properties by an automated method.
- Open Access
- 6 April 2025
- Published by Elsevier in Acta Biomaterialia
- Vol. 198, 356-365
The tubular cavity of tobacco mosaic virus shields mechanical stress and regulates disassembly
- 6 April 2025
- Published by Elsevier in Acta Biomaterialia
- Vol. 198, 356-365
Open AccessThe tubular cavity of tobacco mosaic virus shields mechanical stress and regulates disassembly
- Open Access
- 25 March 2025
- Published by National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 122 (13)
Rolling vesicles: From confined rotational flows to surface-enabled motion
Friction forces are essential for cell movement, yet they also trigger numerous active cellular responses, complicating their measurement in vivo. Here, we introduce a synthetic model designed to measure friction forces between biomimetic membranes and substrates. The model consists of a vesicle with precisely controlled properties, fabricated via microfluidics, encapsulating a single ferromagnetic particle that is magnetically driven to rotate. The rotation of the particle generates a confined rotational flow, setting the vesicle membrane into motion. By adjusting the magnetic field frequency and vesicle size, the rotation frequency of the vesicle can be finely controlled, resulting in a rolling vesicle that functions as an effective tribological tool across a wide frequency range. At low frequencies, molecular contact between the membrane and substrate dominates frictional interactions, which enables determination of the contact friction coefficient. At higher frequencies, lubrication becomes predominant, causing the vesicles to slip rather than roll. Adjusting membrane fluidity and incorporating specific ligand–receptor interactions within this model will enable detailed studies of frictional forces in more complex biomimetic systems, providing key insights into the mechanisms of cell movement and mechanotransduction.
- 25 March 2025
- Published by National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 122 (13)
Open AccessRolling vesicles: From confined rotational flows to surface-enabled motion
Friction forces are essential for cell movement, yet they also trigger numerous active cellular responses, complicating their measurement in vivo. Here, we introduce a synthetic model designed to measure friction forces between biomimetic membranes and substrates. The model consists of a vesicle with precisely controlled properties, fabricated via microfluidics, encapsulating a single ferromagnetic particle that is magnetically driven to rotate. The rotation of the particle generates a confined rotational flow, setting the vesicle membrane into motion. By adjusting the magnetic field frequency and vesicle size, the rotation frequency of the vesicle can be finely controlled, resulting in a rolling vesicle that functions as an effective tribological tool across a wide frequency range. At low frequencies, molecular contact between the membrane and substrate dominates frictional interactions, which enables determination of the contact friction coefficient. At higher frequencies, lubrication becomes predominant, causing the vesicles to slip rather than roll. Adjusting membrane fluidity and incorporating specific ligand–receptor interactions within this model will enable detailed studies of frictional forces in more complex biomimetic systems, providing key insights into the mechanisms of cell movement and mechanotransduction.