arXiv subjects

José Rafael Bordin

Publications and source records attributed to José Rafael Bordin.

At least 19 recordsLinked to original sources

arXiv2026

Density-Selected Topological Pathways in the Melting of Single-Particle-Thick Stripes

The melting of stripe-forming systems involves changes in connectivity that are not fully captured by conventional structural and orientational descriptors. We investigate a two-dimensional model with competing interactions whose low-temperature phase consists of one-particle-thick stripes. Molecular dynamics simulations along seven heating isochores are analyzed using thermodynamic, orientational, dynamical, and graph-based observables. Heating produces a multistage reconstruction in which the loss of stripe alignment and the reorganization of filament connectivity occur over distinct temperature ranges. Density controls whether the disordered filaments fragment into finite polymer-like clusters or remain joined in a dynamically fluid, system-spanning network. The topological observables distinguish these outcomes, which are not resolved by the thermodynamic and orientational responses alone. Thus, the same ordered stripe microphase can melt into topologically distinct fluids selected by density.

cond-mat.soft↗

arXiv2026

Activity and Competing Length Scales in an Anomalous Core-Softened Fluid

The interplay between activity and competing interaction length scales remains largely unexplored, despite its relevance to many soft and biological systems. Here, we study Active Brownian Particles interacting through a ramp-like core-softened potential that exhibits water-like anomalies in equilibrium. By varying the activity over a broad range of densities along two representative isotherms, one within the anomalous region and the other above it, we examine how self-propulsion modifies the structure and dynamics of the fluid. To gain microscopic insight into these changes, we construct effective interactions from the steady-state pair correlations using iterative Boltzmann inversion. We find that activity progressively suppresses the anomalies of the passive fluid, although signatures of the underlying structural crossover remain visible in normalized quantities. The effective interactions reveal that self-propulsion lowers the distinction between the local environments and facilitates population transfer between the two characteristic length scales. These results indicate that activity primarily acts by facilitating population transfer between the two local environments, thereby reducing the structural competition responsible for the anomalous response.

cond-mat.soft↗

arXiv2026

Amorphous Radial Frustration and Water-Like Anomalies in a Ramp-Shoulder Fluid

We investigate the thermodynamic, structural, and dynamic behavior of a three-dimensional coarse-grained ramp-shoulder fluid derived from effective interactions between polymer-grafted nanoparticles. The interaction combines a softened repulsive ramp with a shallow attractive shoulder, stabilizing competing local organizations over a broad pressure interval. Molecular dynamics simulations reveal density, diffusion, and structural anomalies together with crystalline, amorphous, and fluid regions in the phase diagram. Unlike conventional isotropic core-softened fluids, the anomalous hierarchy becomes partially decoupled: the density anomaly extends beyond the structural anomaly, while the diffusion anomaly becomes closely connected to amorphization and shell migration processes. Analysis of radial distribution functions, excess entropy, translational and orientational order, and coordination-shell organization shows that the anomalies are not controlled solely by shell competition. Instead, they emerge from cooperative radial restructuring in a regime where radial correlations increase without the development of crystalline orientational order. The results indicate that the detailed shape of the softened interaction region strongly influences the structural pathways explored under compression, leading to a regime of amorphous radial frustration associated with anomalous diffusion and frustrated shell reorganization.

cond-mat.soft↗

arXiv2026

Confinement-controlled chase-escape dynamics

We investigate a minimal chase-and-escape model on a two-dimensional square lattice with randomly distributed static obstacles, focusing on how geometric disorder controls collective pursuit dynamics. Chasers and escapers move according to short-range sensing rules, while the density of obstacles tunes the connectivity of the accessible space. Using a combination of geometric analysis, dynamical observables, survival statistics, and transport characterization, we establish a direct link between lattice connectivity and pursuit efficiency. A Breadth-First Search analysis reveals that obstacle-induced fragmentation leads to a progressive loss of accessibility before the percolation threshold, defining the effective initial conditions for the dynamics. The trapping time and capture cost exhibit a non-monotonic dependence on obstacle density, reflecting a competition between path elongation in connected environments and geometric confinement near the percolation threshold. Survival analysis shows that the decay of the escaper population follows a Weibull form, with characteristic time and shape parameters displaying clear crossovers as a function of obstacle density, signaling the coexistence of cooperative capture and confinement-dominated trapping. Transport properties, quantified through the mean-squared displacement exponent, further support this picture, revealing sub-diffusive dynamics and a convergence toward a geometry-controlled regime near percolation. Overall, our results demonstrate that chase--and--escape dynamics in disordered environments are governed by a geometry-driven crossover, where percolation and connectivity act as unifying control parameters for spatial, temporal, and collective behavior.

cond-mat.stat-mech↗

arXiv2025

Order-Disorder Transitions and Thermal Pathways in Frustrated 2D Colloidal Crystals

We employ extensive NPT molecular dynamics simulations to explore the thermal transitions of two-dimensional colloidal crystals interacting via a core-softened potential with competing length scales. The system stabilizes three distinct solid phases, namely low-density triangular (LDT), stripe, and kagome, which exhibit markedly different responses to heating and cooling. Our simulations reveal that the LDT and kagome phases melt via first-order transitions, but only the former recrystallizes smoothly. The kagome phase displays strong hysteresis and metastability, while the stripe phase undergoes a continuous and nearly reversible transformation. These results highlight the role of lattice geometry and frustration in shaping non-universal melting and freezing pathways in 2D soft matter.

cond-mat.soft↗

arXiv2025

How Soft is Too Soft? Tuning Order and Disorder in Dimeric Core-Soft Colloids with Bond Flexibility

We employ molecular dynamics simulations to explore how internal flexibility affects phase transitions in soft-matter systems composed of dimers interacting via a core-softened potential with two characteristic length scales. Monomers are connected by harmonic springs with varying stiffness, allowing us to tune the dimer rigidity from highly flexible to nearly rigid. Flexible dimers reproduce the behavior of monomeric systems, displaying well-defined BCC and HCP crystalline phases separated by a narrow amorphous region. As the bond stiffness increases, this amorphous phase gives way to a coexistence region between BCC and HCP structures. In the rigid limit, amorphous regions reemerge and expand, and high-density systems fail to crystallize completely, instead forming mixed phases with HCP-like and disordered local environments. This transition arises from geometric frustration: rigid dimers are unable to adjust their internal configuration to optimize local packing, thereby suppressing crystallization and promoting amorphization. Our findings reveal that bond flexibility is a key control parameter governing structural organization in core-softened colloidal and molecular systems, offering insights for the design of tunable soft materials.

cond-mat.soft↗

arXiv2025

Competing Length Scales and Symmetry Frustration Govern Non-Universal Melting in 2D Core-softened Colloidal Crystals

We investigate the melting behavior of two-dimensional colloidal crystals stabilized by a core-softened potential featuring two competing interaction length scales. Using molecular dynamics simulations, we analyze three polymorphic solid phases -- low-density triangular, stripe, and kagome -- and uncover distinct melting pathways. The triangular and kagome crystals undergo abrupt first-order transitions, driven by the interplay between energetic frustration and structural reorganization. In particular, the LDT phase melts through a sharp transition induced by a crossover between the two characteristic length scales. In contrast, the stripe phase exhibits a continuous transition with liquid-crystalline features: orientational and translational order decay gradually, while intra-stripe mobility persists, consistent with a KTHNY-like scenario. These findings demonstrate that melting in 2D soft-matter systems is inherently non-universal and governed by the competition between lattice symmetry, frustration, and multiple interaction scales. Our results provide microscopic insight into melting mechanisms beyond classical universality classes and offer guiding principles for the design of self-assembled materials with tunable phase behavior.

cond-mat.soft↗

arXiv2024

Nanoscale Water Behavior and Its Impact on Adsorption: A case study with CNTs and Diclofenac

Water is a fundamental component of life, playing a critical role in regulating metabolic processes and facilitating the dissolution and transport of essential molecules. However, the presence of emerging contaminants, such as pharmaceuticals, poses significant challenges to water quality and safety. Nanomaterials-based technologies arise as a promising tool to remove those contaminants from water. Nevertheless, interfacial water plays a major role in the adsorption of chemical compounds in the nanomaterials - as it plays in biological processes such as protein folding, enzyme activity, and drug delivery. To understand this role, in this study we employ Molecular Dynamics (MD) simulations to explore the adsorption dynamics of potassium diclofenac (K-DCF) on single-walled (SWCNT) and double-walled (DWCNT) carbon nanotubes, considering both dry and wet conditions. Our findings reveal that the structuring of water molecules around CNTs creates hydration layers that significantly influence the accessibility of active sites and the interaction strength between contaminants and adsorbents. Our analysis indicates higher energy barriers for adsorption in DWCNTs compared to SWCNTs, which is attributed to stronger water-surface interactions. This research highlights the importance of understanding nanoscale water behavior for optimizing the design and functionality of nanomaterials for water purification. These findings can guide the development of more efficient and selective nanomaterials, enhancing contaminant removal and ensuring safer water resources, while also contributing to a deeper understanding of fundamental biological interactions.

cond-mat.soft↗

arXiv2023

TrajPy: empowering feature engineering for trajectory analysis across domains

Trajectories, sequentially measured quantities that form a path, are an important presence in many different fields, from hadronic beams in physics to electrocardiograms in medicine. Trajectory anal-ysis requires the quantification and classification of curves either using statistical descriptors or physics-based features. To date, there is no extensive and user-friendly package for trajectory anal-ysis available, despite its importance and potential application across domains. We developed a free open-source python package named TrajPy as a complementary tool to empower trajectory analysis. The package showcases a friendly graphic user interface and provides a set of physical descriptors that help characterizing these intricate structures. In combina-tion with image analysis, it was already successfully applied to the study of mitochondrial motility in neuroblastoma cell lines and to the analysis of in silico models for cell migration. The TrajPy package was developed in Python 3 and released under the GNU GPL-3 license. Easy installation is available through PyPi and the development source code can be found in the repository https://github.com/ocbe-uio/TrajPy/. The package release is automatically archived under the DOI 10.5281/zenodo.3656044.

q-bio.QM↗

arXiv2023

Stripes polymorphism and water-like anomaly in hard core-soft corona dumbbells

In this paper we investigate the phase diagram of a dumbbell model composed of two hard-core soft-corona beads through $NpT$ simulations. This particular system was chosen due to its ability to exhibit a diverse range of stripe patterns. Analyzing the thermodynamic and structural changes along compression isotherms, we explore the transition between these distinct patterns. In addition to the stripe and Low-Density-Triangular solid phases obtained, we observed a Nematic Anisotropic phase characterized by a polymer-like pattern at high temperatures and intermediate pressures. Furthermore, we demonstrate the significant role played by the new characteristic length scale, which arises from the anisotropic geometry of the dumbbell structure, in the transition between the stripes patterns. Notably, not only do the structural properties exhibit intriguing behavior, but the diffusion and density in the nematic fluid phase also displays a water-like anomalous increase under compression. Those findings can be valuable in guiding the design of materials based on nanoparticles, with the aim of achieving specific mesopatterns.

cond-mat.soft↗

arXiv2023

Molecular Modeling of Aquaporins and Artificial Transmembrane Channels: a mini-review and perspective for plants

Aquaporins (AQPs) are a family of transmembrane channels that are found from archaea, eubacteria, and fungi kingdoms to plants and animals. These proteins play a major role in water and small solutes transport across biological cell membranes and maintain the osmotic balance of living cells. In this sense, many works in recent years have been devoted to understanding their behavior, including in plants, where 5 major groups of AQPs have been identified, whose physiological function details still have open questions waiting for an answer. In this direction, we observed in the literature very few Molecular Modeling studies focusing on plant AQPs. It creates a gap in the proper depiction of AQPs since Molecular Simulations allow us to get information that is usually inaccessible by experiments. Likewise, many efforts have been made to create artificial nanochannels with improved properties. It has the potential to help humanity (and plants) to face water stress -- a current problem that will be worsened by Climate Change. In this short review, we will revisit and discuss important computational studies about plant aquaporins and artificial transmembrane channels. With this, we aim to show how the Molecular Modeling community can (and should) help to understand plants' AQPs properties and function and how we can create new nanotechnology-based artificial channels.

cond-mat.soft↗

arXiv2023

Solid-amorphous transition is related to the waterlike anomalies in a fluid without liquid-liquid phase transition

The most accepted origin for the water anomalous behavior is the phase transition between two liquids (LLPT) in the supercooled regime connected to the glassy first order phase transition at lower temperatures. Two length scales potentials are an effective approach that have long being employed to understand the properties of fluids with waterlike anomalies and, more recently, the behavior of colloids and nanoparticles. These potentials can be parameterized to have distinct shapes, as a pure repulsive ramp, such as the model proposed by de Oliveira et al. [J. Chem. Phys. 124, 64901 (2006)]. This model has waterlike anomalies despite the absence of LLPT. To unravel how the waterlike anomalies are connected to the solid phases we employ Molecular Dynamics simulations. We have analyzed the fluid-solid transition under cooling, with two solid crystalline phases, BCC and HCP, and two amorphous regions being observed. We show how the competition between the scales creates an amorphous cluster in the BCC crystal that leads to the amorphization at low temperatures. A similar mechanism is found in the fluid phase, with the system changing from a BCC-like to an amorphous-like structure in the point where a maxima in $k_T$ is observed. With this, we can relate the competition between two fluid structures with the amorphous clusterization in the BCC phase.Those findings help to understand the origins of waterlike behavior in systems without liquid-liquid critical point.

cond-mat.soft↗

arXiv2022

Water inside charged nanoslits: Structure and Dielectric study with a novel water model FAB/$ε$

In this work, the dielectric behavior of water inside charged nanoslit of graphene is studied to analized the water molecules under electrical confinement; through polarizing the nanoslit of graphene, creating an electric field inside the nanopore. How the water molecules are structured under this type of electrical confinement is studied with two force fields of water, the three-site water models here used are the SCP/$ε$ and the FAB/$ε$, the first is a rigid model that improves the SPC model and the second is a flexible model that improves all the force fields of three sites non-polarizables and flexibles.

cond-mat.soft↗

arXiv2021

Hard core-soft shell particles near repulsive interfaces: interplay between adsorption, aggregation and diffusion

The behavior of colloidal particles with a hard core and a soft shell has attracted the attention for researchers in the physical-chemistry interface not only due the large number of applications, but due the unique properties of these systems in bulk and at interfaces. The adsorption at the boundary of two phases can provide information about the molecular arrangement. In this way, we perform Langevin Dynamics simulations of polymer-grafted nanoparticles. We employed a recently obtained core-softened potential to analyze the relation between adsorption, structure and dynamic properties of the nanoparticles near a solid repulsive surface. Two cases were considered: flat or structured walls. At low temperatures, a maxima is observed in the adsorption. It is related to a fluid to clusters transition and with a minima in the contact layer diffusion - and is explained by the competition between the scales in the core-softened interaction. Due the long range repulsion, the particles stay at the distance correspondent to this length scale at low densities, and overcome the repulsive barrier as the packing increases, However, increasing the temperature, the gain in kinetic energy allows the colloids to overcome the long range repulsion barrier even at low densities. As consequence, there is no competition and no maxima was observed in the adsorption.

cond-mat.soft↗

arXiv2020

Tracer diffusion in crowded solutions of sticky polymers

Macromolecular diffusion in strongly confined geometries and crowded environments is still to a large extent an open subject in soft matter physics and biology. In this paper, we employ large-scale Langevin dynamics simulations to investigate how the diffusion of a tracer is influenced by the combined action of excluded-volume and weak attractive crowder-tracer interactions. We consider two species of tracers, standard hard-core particles described by the Weeks-Chandler-Andersen (WCA) repulsive potential and core-softened (CS) particles, which model, e.g., globular proteins, charged colloids and nanoparticles covered by polymeric brushes. These systems are characterized by the presence of two length scales in the interaction and can show water-like anomalies in their diffusion, stemming from the inherent competition between different length scales. Here we report a comprehensive study of both diffusion and structure of these two tracer species in an environment crowded by quenched configurations of polymers at increasing density. We analyze in detail how the tracer-polymer affinity and the system density affect transport as compared to the emergence of specific static spatial correlations. In particular, we find that, while hardly any differences emerge in the diffusion properties of WCA and CS particles, the propensity to develop structural order for large crowding is strongly frustrated for CS particles. Surprisingly, for large enough affinity for the crowding matrix, the diffusion coefficient of WCA tracers display a non-monotonic trend as their density is increased when compared to the zero affinity scenario. This water-like anomaly turns out to be even larger than what observed for CS particle and appears to be rooted in a similar competition between excluded-volume and affinity effects.

cond-mat.soft↗

arXiv2020

Structural behavior of a two length scale core-softened fluid in two dimensions

2D competitive systems shows a large variety of solid and aggregate patterns, re-entrant fluid phase, a continuous melting as predicted by the KTHNY theory and, in some cases, waterlike anomalies. In this paper, we employ Langevin Dynamics simulations of a ramp-like core-softened fluid that have two characteristic length scales and all the features mentioned above. Analyzing the fluid phase of this system, Bordin and Barbosa [Phys. Rev. E 97, 022604 (2018)] reported the existence of two waterlike anomalous region. Now, we revisit this problem focusing in the low temperature regime and a larger range of densities looking for a relation between the origin of the anomalous behavior, the solid phases and the re-entrant melting. Now, not two, but three anomalous regions were observed. The extra anomalous regions are related to the re-entrant melting of a amorphous solid to a cluster fluid. They are ruled not only by the competition between the characteristic length scales in the potential, but also by extra competitions induced by the variety of particles conformations. These competitions extends from the solid to the fluid phase, reflecting in the structural waterlike anomaly. Our results shade some light in the complex behavior of two length scales competitive potential, and helps to elucidate the relation between the large number of solid phases and the existence of more than one waterlike anomalies region in these systems.

cond-mat.soft↗

arXiv2020

Salt parameterization can drastically affect the results from classical atomistic simulations of water desalination by MoS$_2$ nanopores

Water scarcity is a reality in our world, and scenarios predicted by leading scientists in this area indicate that it will worsen in the next decades. However, new technologies based in low-cost seawater desalination can prevent the worst scenarios, providing fresh water for humanity. With this goal, membranes based in nanoporous materials have been suggested in recent years. One of the materials suggested is MoS$_2$, and classical Molecular Dynamics (MD) simulation is one of the most powerful tools to explore these nanomaterials. However, distinct Force Fields employed in MD simulations are parameterized based on distinct experimental quantities. In this paper, we compare two models of salt that were build based on distinct properties of water-salt mixtures. One model fits the hydration free energy and lattice properties, the second fits the crystal density and the density and the dielectric constant of water and salt mixtures. To compare the models, MD simulations for salty water flow through two nanopores sizes were used -- one pore big enough to accommodate hydrated ions, and one smaller in which the ion has to dehydrate to enter, and two rigid water models from the TIP4P family -- the TIP4P/2005 and TIP4P/$ε$. Our results indicate that the water permeability and salt rejection by the membrane are more influenced by the salt model than by the water model, especially for the narrow pore. In fact, completely distinct mechanisms were observed, and they are related to the characteristics employed in the ion model parameterization. The results show that not only the water model can influence the outcomes, but the ion model plays a crucial role.

cond-mat.soft↗

arXiv2019

Waterlike anomalies in hard core-soft shell nanoparticles using a effective potential approach: pinned vs adsorbed polymers

In this work, a two dimensional system of polymer grafted nanoparticles is analyzed using large-scale Langevin Dymanics simulations. Effective core-softened potentials were obtained for two cases: one where the polymers are free to rotate around the nanoparticle core and a second where the polymers are fixed, with a $45^\circ$ angle between them. The use of effective core-softened potentials allow us to explore the complete system phase space. In this way, the $PT$, $Tρ$ and $Pρ$ phase diagrams for each potential were obtained, with all fluid and solid phases. The phase boundaries were defined analyzing the specific heat at constant pressure, the system mean square displacement, the radial distribution function and the discontinuities in the density-pressure phase diagram. Also, due the competition in the system we have observed the presence of waterlike anomalies, such as the temperature of maximum density - in addition with a tendency of the TMD to move to lower temperatures (negative slope)- and the diffusion anomaly. It was observed different morphologies (stripes, honeycomb, amorphous) for each nanoparticle. We observed that for the fixed polymers case the waterlike anomalies are originated by the competition between the potential characteristic length scales, while for the free to rotate case the anomalies arises due a smaller region of stability in the phase diagram and no competition between the scales was observed.

cond-mat.soft↗