Showing 1–10 of 10 results for author: Ortiz, D

Bayesian umbrella quadrature accelerates free-energy calculations across diverse molecular systems and processes

Authors: Eline K. Kempkes, Alberto Pérez de Alba Ortíz

Abstract: Biased sampling in molecular dynamics simulations overcomes timescale limitations and delivers free-energy landscapes, essential to understand complex atomistic phenomena. However, when applied across diverse systems and processes, biasing protocols often require time- and resource-consuming fine-tuning. In search for robustness, we boost a prominent biasing method, Umbrella Sampling. To estimate… ▽ More Biased sampling in molecular dynamics simulations overcomes timescale limitations and delivers free-energy landscapes, essential to understand complex atomistic phenomena. However, when applied across diverse systems and processes, biasing protocols often require time- and resource-consuming fine-tuning. In search for robustness, we boost a prominent biasing method, Umbrella Sampling. To estimate the value of an integral, i.e., the free energy, our Bayesian Umbrella Quadrature (BUQ) method iteratively selects gradient samples, i.e., bias locations, that most reduce the posterior integral variance based on a noise-tolerant Gaussian process model, which also effectively interpolates between samples. We validate the method for a conformational change in a small peptide, a water-to-ice phase transition, and a substitution chemical reaction; obtaining excellent accuracies and speedups. To ease adoption of this more automated and universal free-energy method, we interface BUQ with wide-spread simulation packages and share hyperparametrization guidelines. △ Less

Submitted 13 January, 2026; originally announced January 2026.

Comments: 42 pages, 8 figures, SI included

Confinement-induced collective motion in suspensions of run-and-tumble particles

Authors: José Martín-Roca, Daniel Escobar Ortiz, Chantal Valeriani, Horacio Serna

Abstract: Collective motion is ubiquitous in active systems at all length and time scales. The mechanisms behind such collective motion usually are alignment interactions between active particles, effective alignment after collisions between agents or symmetry-breaking fluctuations induced by passive species in active suspensions. In this article, we introduce a new type of collective motion in the shape of… ▽ More Collective motion is ubiquitous in active systems at all length and time scales. The mechanisms behind such collective motion usually are alignment interactions between active particles, effective alignment after collisions between agents or symmetry-breaking fluctuations induced by passive species in active suspensions. In this article, we introduce a new type of collective motion in the shape of a traveling band induced purely by confinement, where no explicit or effective alignment are prescribed among active agents. We study a suspension of run-and-tumble particles confined in microchannels comprising asymmetric boundaries: one flat wall and one array of funnel-like obstacles. We study the phase behavior of the confined active suspension upon changes in the packing fraction and the persistence length to define the stability region of the traveling band. We characterize the traveling band structurally and dynamically and study its stability with respect to the tilt angle of the obstacles. Lastly, we describe the mechanism of motion of the band, which resembles the tracked locomotion of some heavy vehicles like tractors, finding that a counter-flux of active particles in the lower part of the band, explained in terms of source-sink and vacancy diffusion mechanisms, is the facilitator of the traveling band and sustains its motion. We name this new collective phenomenon confinement-induced tracked locomotion △ Less

Submitted 29 January, 2026; v1 submitted 11 November, 2025; originally announced November 2025.

Journal ref: J. Chem. Phys. 164, 074901 (2026)

The bcc coating of Lennard-Jones crystal nuclei vanishes with a change of local structure detection algorithm

Authors: Willem Gispen, Alberto Pérez de Alba Ortíz, Marjolein Dijkstra

Abstract: Since the influential work of ten Wolde, Ruiz-Montero, and Frenkel [Phys. Rev. Lett. 75, 2714 (1995)], crystal nucleation from a Lennard-Jones fluid has been regarded as a paradigmatic example of metastable crystal ordering at the surface of a critical nucleus. We apply seven commonly used local structure detection algorithms to characterize crystal nuclei obtained from transition path sampling si… ▽ More Since the influential work of ten Wolde, Ruiz-Montero, and Frenkel [Phys. Rev. Lett. 75, 2714 (1995)], crystal nucleation from a Lennard-Jones fluid has been regarded as a paradigmatic example of metastable crystal ordering at the surface of a critical nucleus. We apply seven commonly used local structure detection algorithms to characterize crystal nuclei obtained from transition path sampling simulations. The polymorph composition of these nuclei varies significantly depending on the algorithm used. Our results indicate that one should be very careful when characterizing the local structure near solid-solid and solid-fluid interfaces. Particles near such interfaces exhibit a local structure distinct from that of bulk fluid or bulk crystal phases. We argue that incorporating outlier detection into the local structure detection method is beneficial, leading to greater confidence in the classification results. Interestingly, the bcc coating nearly disappears when adopting a machine learning method with outlier detection. △ Less

Submitted 4 December, 2024; originally announced December 2024.

Inverse Design Method with Enhanced Sampling for Complex Open Crystals: Application to Novel Zeolite Self-Assembly in a Coarse-Grained Model

Authors: Chaohong Wang, Alberto Pérez de Alba Ortíz, Marjolein Dijkstra

Abstract: Optimizing the synthesis of zeolites and exploring novel frameworks offer pivotal opportunities and challenges in materials design. While inverse design proves highly effective for simpler crystals, its application to intricate structures like zeolites poses severe challenges. Here, we introduce an innovative inverse design workflow tailored to efficiently reproduce target zeolite frameworks in a… ▽ More Optimizing the synthesis of zeolites and exploring novel frameworks offer pivotal opportunities and challenges in materials design. While inverse design proves highly effective for simpler crystals, its application to intricate structures like zeolites poses severe challenges. Here, we introduce an innovative inverse design workflow tailored to efficiently reproduce target zeolite frameworks in a binary coarse-grained model using enhanced sampling molecular dynamics simulations. This workflow integrates an evolutionary parameter optimization strategy with a variant of the seeding approach. Using this method, we successfully reproduce Z1 and SGT zeolites, and Type-I clathrates, find new optimal parameters for known phases, such as the SOD and CFI, and even discover novel frameworks, such as Z5. This is done within a simple coarse-grained model for a tetrahedra-forming component and a structure-directing agent. Our methodology not only enables the screening of synthesis protocols but also facilitates the discovery of hypothetical zeolites. △ Less

Submitted 29 October, 2024; originally announced October 2024.

Comments: 17 pages, 13 figures

Inverse Design of Crystals and Quasicrystals in a Non-Additive Binary Mixture of Hard Disks

Authors: Edwin A. Bedolla-Montiel, Jochem T. Lange, Alberto Pérez de Alba Ortíz, Marjolein Dijkstra

Abstract: The development of new materials typically involves a process of trial and error, guided by insights from past experimental and theoretical findings. The inverse design approach for soft-matter systems has the potential to optimize specific physical parameters such as particle interactions, particle shape, or composition and packing fraction. This optimization aims to facilitate the spontaneous fo… ▽ More The development of new materials typically involves a process of trial and error, guided by insights from past experimental and theoretical findings. The inverse design approach for soft-matter systems has the potential to optimize specific physical parameters such as particle interactions, particle shape, or composition and packing fraction. This optimization aims to facilitate the spontaneous formation of specific target structures through self-assembly. In this study, we expand upon a recently introduced inverse design protocol for monodisperse systems to identify the required conditions and interactions for assembling crystal and quasicrystal phases within a binary mixture of two distinct species. This method utilizes an evolutionary algorithm to identify the optimal state point and interaction parameters, enabling the self-assembly of the desired structure. Additionally, we employ a convolutional neural network (CNN) that classifies different phases based on their diffraction patterns, serving as a fitness function for the desired structure. Using our protocol, we successfully inverse design two-dimensional crystalline structures, including a hexagonal lattice, and a dodecagonal quasicrystal, within a non-additive binary mixture of hard disks. Finally, we introduce a symmetry-based order parameter that leverages the encoded symmetry within the diffraction pattern. This order parameter circumvents the need for training a CNN, and is used as a fitness function to inverse design an octagonal quasicrystal. △ Less

Submitted 22 March, 2024; originally announced March 2024.

Comments: 12 pages, 5 figures

A Boltzmann generator for the isobaric-isothermal ensemble

Authors: Steyn van Leeuwen, Alberto Pérez de Alba Ortíz, Marjolein Dijkstra

Abstract: Boltzmann generators (BGs) are now recognized as forefront generative models for sampling equilibrium states of many-body systems in the canonical ensemble, as well as for calculating the corresponding Helmholtz free energy. Furthermore, BGs can potentially provide a notable improvement in efficiency compared to conventional techniques such as molecular dynamics (MD) and Monte Carlo (MC) methods.… ▽ More Boltzmann generators (BGs) are now recognized as forefront generative models for sampling equilibrium states of many-body systems in the canonical ensemble, as well as for calculating the corresponding Helmholtz free energy. Furthermore, BGs can potentially provide a notable improvement in efficiency compared to conventional techniques such as molecular dynamics (MD) and Monte Carlo (MC) methods. By sampling from a clustered latent space, BGs can circumvent free-energy barriers and overcome the rare-event problem. However, one major limitation of BGs is their inability to sample across phase transitions between ordered phases. This is due to the fact that new phases may not be commensurate with the box dimensions, which remain fixed in the canonical ensemble. In this work, we present a novel BG model for the isothermal-isobaric (NPT) ensemble, which can successfully overcome this limitation. This unsupervised machine-learning model can sample equilibrium states at various pressures, as well as pressure-driven phase transitions. We demonstrate that the samples generated by this model are in good agreement with those obtained through MD simulations of two model systems. Additionally, we derive an estimate of the Gibbs free energy using samples generated by the NPT BG. △ Less

Submitted 15 May, 2023; originally announced May 2023.

Simultaneous sampling of multiple transition channels using adaptive paths of collective variables

Authors: Alberto Pérez de Alba Ortíz, Bernd Ensing

Abstract: We present a molecular simulation method to simultaneously find multiple transition pathways, and their associated free-energy profiles. The scheme extends path-metadynamics (PMD) [Phys. Rev. Lett. 109, 020601 (2012)] with multiple paths and repulsive walkers (multiPMD). We illustrate multiPMD for two C7eq-to-C7ax paths in Ace-Ala-Nme and six PPII-to-PPII paths in Ace-(Pro)4-Nme. We also show a sc… ▽ More We present a molecular simulation method to simultaneously find multiple transition pathways, and their associated free-energy profiles. The scheme extends path-metadynamics (PMD) [Phys. Rev. Lett. 109, 020601 (2012)] with multiple paths and repulsive walkers (multiPMD). We illustrate multiPMD for two C7eq-to-C7ax paths in Ace-Ala-Nme and six PPII-to-PPII paths in Ace-(Pro)4-Nme. We also show a scheme to render an interpretable "PathMap", showing the free energy ridges between paths, as well as the branching and merging of the transition channels. MultiPMD is a flexible and promising method for systems with competing or controversial pathways, which appear in many biomolecular systems, including proteins and nucleic acids. △ Less

Submitted 20 June, 2025; v1 submitted 7 December, 2021; originally announced December 2021.

Confinement effects on the configurational order of monodisperse disk packings

Authors: Bjoern Arnold, Ayse Turak, Alejandro Diaz Ortiz

Abstract: Monodisperse circular disks have been collectively packed in confined geometries using a Monte Carlo method where the compaction is propelled by two- dimensional stochastic agitation. We have found that confinement (i.e., finite-size plus surface effects) determines the symmetry of the packed configurations together with the size evolution of the probability density of the packing fraction. For th… ▽ More Monodisperse circular disks have been collectively packed in confined geometries using a Monte Carlo method where the compaction is propelled by two- dimensional stochastic agitation. We have found that confinement (i.e., finite-size plus surface effects) determines the symmetry of the packed configurations together with the size evolution of the probability density of the packing fraction. For the particular case of small systems in square containers, the probability density of the packing fraction shows several well-defined peaks, depending on the system size, for both hard- wall and periodic boundary conditions. High-symmetry configurations (other than the n\timesn square arrays) with non-negligible occurrence probabilities are found as a direct consequence of monodispersity and confinement. △ Less

Submitted 30 January, 2012; originally announced January 2012.

Comments: 9 pages, 2 figures, submitted to J. Phys. Condens. Mater

Electric-field-controlled directional growth of ferroelectric domains in multiferroic BiFeO3 films

Authors: T. H. Kim, S. -H. Baek, S. M. Yang, S. Y. Jang, D. Ortiz, T. K. Song, J. -S. Chung, C. -B. Eom, T. W. Noh, J. -G. Yoon

Abstract: We describe the directional growth of ferroelectric domains in a multiferroic BiFeO3 thin film, which was grown epitaxially on a vicinal (001) SrTiO3 substrate. A detailed structural analysis of the film shows that a strain gradient, which can create a symmetry breaking in a ferroelectric double well potential, causes ferroelectric domains to grow with preferred directionality under the influenc… ▽ More We describe the directional growth of ferroelectric domains in a multiferroic BiFeO3 thin film, which was grown epitaxially on a vicinal (001) SrTiO3 substrate. A detailed structural analysis of the film shows that a strain gradient, which can create a symmetry breaking in a ferroelectric double well potential, causes ferroelectric domains to grow with preferred directionality under the influence of an electric field. Our results suggest the possibility of controlling the direction of domain growth with an electric field by imposing constraints on ferroelectric films, such as a strain gradient. △ Less

Submitted 30 September, 2009; originally announced September 2009.

Comments: 16 pages, 3 figures

D-wave overlapping band model for cuprate superconductors

Authors: Susana Orozco, Rosa María Méndez-Moreno, María de los Angeles Ortiz, Gabriela Murguía

Abstract: Within the BCS framework a multiband model with d-wave symmetry is considered. Generalized Fermi surface topologies via band overlapping are introduced. The band overlap scale is of the order of the Debye energy. The order parameters and the pairing have d-wave symmetry. Experimental values reported for the critical temperatures $T_c(x)$ and the order parameters, $Δ_0(x)$, in terms of dopping… ▽ More Within the BCS framework a multiband model with d-wave symmetry is considered. Generalized Fermi surface topologies via band overlapping are introduced. The band overlap scale is of the order of the Debye energy. The order parameters and the pairing have d-wave symmetry. Experimental values reported for the critical temperatures $T_c(x)$ and the order parameters, $Δ_0(x)$, in terms of dopping $x$ are used. Numerical results for the coupling and the band overlapping parameters in terms of the doping are obtained for the cuprate superconductor $La_{2-x}Sr_xCuO_4$. △ Less

Submitted 17 June, 2009; originally announced June 2009.

Comments: 5 pages, 4 Postscript figures