Quantum Simulations and Experimental Insights into Glyphosate Adsorption Using Graphene-Based Nanomaterials.

The increasing global demand for food and agrarian development brings to light a dual issue concerning the use of substances that are crucial for increasing productivity yet can be harmful to human health and the environment when misused. Herein, we combine insights from high-level quantum simulations and experimental findings to elucidate the fundamental physicochemical mechanisms behind developing graphene-based nanomaterials for the adsorption of emerging contaminants, with a specific focus on pesticide glyphosate (GLY). We conducted a comprehensive theoretical and experimental investigation of graphene-based supports as promising candidates for detecting, sensing, capturing, and removing GLY applications. By combining ab initio molecular dynamics and density functional theory calculations, we explored several chemical environments encountered by GLY during its interaction with graphene-based substrates, including pristine and punctual defect regions. Our results unveiled distinct interaction behaviors: physisorption in pristine and doped graphene regions, chemisorption leading to molecular dissociation in vacancy-type defect regions, and complex transformations involving the capture of N and O atoms from impurity-adsorbed graphene, resulting in the formation of new GLY-derived compounds. The theoretical findings were substantiated by FTIR and Raman spectroscopy, which proposed a mechanism explaining GLY adsorption in graphene-based nanomaterials. The comprehensive evaluation of adsorption energies and associated properties provides valuable insights into the intricate nature of these interactions, shedding light on potential applications and guiding future experimental investigations of graphene-based nanofilters for water decontamination.

Core-softened colloid under extreme geometrical confinement.

Geometrical constraints offer a promising strategy for assembling colloidal crystal structures that are not typically observed in bulk or under 2D conditions. Core-softened colloids, in particular, have emerged as versatile chemical building blocks with applications across various scientific and technological areas. In this study, we investigate the behavior of a core-softened model confined between two parallel walls. Employing molecular dynamics simulations, we analyze the system's response under extreme confinement, where only one or two layers of colloids are permitted. The system comprises particles modeled by a ramp-like potential confined within slit nanoslits created by two flat, purely repulsive walls with a lateral side L separated by a distance Lz. Through a systematic analysis of the phase behavior as Lz increases, or as the system undergoes decompression, for different values of L, we identified a mono-to-bilayer transition associated with changes in the colloidal structure. In the monolayer regime, we observed solid phases at lower densities than those observed in the 2D case. Importantly, we demonstrated that confinement at specific Lz values, allowing particle arrangement into two layers, can lead to the emergence of the square phase, which was not observed under monolayer or 2D conditions. By correlating thermodynamic, translational, and orientational ordering, as well as the dynamics of this confined colloidal system, our findings offer valuable insights into the utilization of geometrical constraints to induce and manipulate structural changes.

TrajPy: empowering feature engineering for trajectory analysis across domains.

Motivation: Trajectories, which are 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 analysis requires the quantification and classification of curves, either by using statistical descriptors or physics-based features. To date, no extensive and user-friendly package for trajectory analysis has been readily available, despite its importance and potential application across various domains. Results: We have developed TrajPy, a free, open-source Python package that serves as a complementary tool for empowering trajectory analysis. This package features a user-friendly graphical user interface and offers a set of physical descriptors that aid in characterizing these complex structures. TrajPy has already been successfully applied to studies of mitochondrial motility in neuroblastoma cell lines and the analysis of in silico models for cell migration, in combination with image analysis. Availability and implementation: The TrajPy package is developed in Python 3 and is released under the GNU GPL-3.0 license. It can easily be installed via PyPi, and the development source code is accessible at the repository: https://github.com/ocbe-uio/TrajPy/. The package release is also automatically archived with the DOI 10.5281/zenodo.3656044.

The ECM and tissue architecture are major determinants of early invasion mediated by E-cadherin dysfunction.

Germline mutations of E-cadherin cause Hereditary Diffuse Gastric Cancer (HDGC), a highly invasive cancer syndrome characterised by the occurrence of diffuse-type gastric carcinoma and lobular breast cancer. In this disease, E-cadherin-defective cells are detected invading the adjacent stroma since very early stages. Although E-cadherin loss is well established as a triggering event, other determinants of the invasive process persist largely unknown. Herein, we develop an experimental strategy that comprises in vitro extrusion assays using E-cadherin mutants associated to HDGC, as well as mathematical models epitomising epithelial dynamics and its interaction with the extracellular matrix (ECM). In vitro, we verify that E-cadherin dysfunctional cells detach from the epithelial monolayer and extrude basally into the ECM. Through phase-field modelling we demonstrate that, aside from loss of cell-cell adhesion, increased ECM attachment further raises basal extrusion efficiency. Importantly, by combining phase-field and vertex model simulations, we show that the cylindrical structure of gastric glands strongly promotes the cell's invasive ability. Moreover, we validate our findings using a dissipative particle dynamics simulation of epithelial extrusion. Overall, we provide the first evidence that cancer cell invasion is the outcome of defective cell-cell linkages, abnormal interplay with the ECM, and a favourable 3D tissue structure.

A DPD model of soft spheres with waterlike anomalies and poly(a)morphism.

Core-softened approaches have been employed to understand the behavior of a large variety of systems in soft condensed matter, from biological molecules to colloidal crystals, glassy phases, and water-like anomalies. At the same time, dissipative particle dynamics (DPD) is a powerful tool suitable for studying larger length and time scales. In this sense, we propose a simple model of soft molecules that exhibits a wide range of interesting phenomena: polyamorphism, with three amorphous phases, polymorphysm, including a recently found gyroid phase and a cubic diamond structure, reentrant liquid phase, and density, diffusion, and structural water-like anomalies. Each molecule is constituted by two collapsing beads, representing a harder central core and a softer corona. This induces a competition between distinct conformations that leads to their unique behavior. This provides a basis for the development of more accurate water-like DPD models that can then be parameterized for specific systems and even used to model and understand the self-assembly of colloidal crystals.

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 scale potentials are an effective approach that has long been 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 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 kT is observed. With this, we can relate the competition between two fluid structures with the amorphous clusterization in the BCC phase. These findings help to understand the origins of waterlike behavior in systems without the liquid-liquid critical point.

Phase classification using neural networks: application to supercooled, polymorphic core-softened mixtures.

Characterization of phases of soft matter systems is a challenge faced in many physical chemical problems. For polymorphic fluids it is an even greater challenge. Specifically, glass forming fluids, as water, can have, besides solid polymorphism, more than one liquid and glassy phases, and even a liquid-liquid critical point. In this sense, we apply a neural network algorithm to analyze the phase behavior of a mixture of core-softened fluids that interact through the continuous-shouldered well (CSW) potential, which have liquid polymorphism and liquid-liquid critical points, similar to water. We also apply the neural network to mixtures of CSW fluids and core-softened alcohols models. We combine and expand methods based on bond-orientational order parameters to study mixtures, applied to mixtures of hardcore fluids and to supercooled water, to include longer range coordination shells. With this, the trained neural network was able to properly predict the crystalline solid phases, the fluid phases and the amorphous phase for the pure CSW and CSW-alcohols mixtures with high efficiency. More than this, information about the phase populations, obtained from the network approach, can help verify if the phase transition is continuous or discontinuous, and also to interpret how the metastable amorphous region spreads along the stable high density fluid phase. These findings help to understand the behavior of supercooled polymorphic fluids and extend the comprehension of how amphiphilic solutes affect the phases behavior.

Core-softened water-alcohol mixtures: the solute-size effects.

Water is the most anomalous material on Earth, with a long list of thermodynamic, dynamic and structural behaviors that deviate from what is expected. Recent studies have indicated that these anomalies may be related to a competition between two liquids, which means that water has a potential liquid-liquid phase transition (LLPT) that ends at a liquid-liquid critical point (LLCP). In a recent study [J. Mol. Liq., 2020, 320, 114420], using molecular dynamics simulations and a core-softened potential approach, we have shown that adding a simple solute such as methanol can "kill" the density-anomalous behavior as the LLCP is suppressed by spontaneous crystallization in a hexagonal close packing (HCP) crystal near the LLPT. Now, we extend this work to realize how longer-chain alcohols will affect the complex behavior of water-alcohol mixtures in the supercooled regime. Besides core-softened (CS) methanol, ethanol and 1-propanol were added to a system of identical particles that interact through the continuous shouldered well (CSW) potential. We observed that the density anomaly gradually decreases its extension in phase diagrams until it disappears with the growth of the non-polar chain and the alcohol concentration, different from the liquid-liquid phase transition (and the LLCP), which remained present in all analyzed mixtures, according to Nature, 2001, 409, 692. For our model, the longer non-polar chains and higher concentrations gradually impact the competition between the scales in the CS potential, leading to a gradual disappearing of the anomalies until the TMD total disappearance is observed when the first coordination shell structure is also affected: short-range ordering is favored, leading to less competition between short- and long-range ordering and, consequently, to the extinction of anomalies. Also, the non-polar chain size and concentration have an effect on the solid phases, favoring the hexagonal close packed (HCP) solid and the amorphous solid phase over the body-centered cubic (BCC) crystal. These findings help to elucidate the behavior of water solutions in the supercooled regime and indicate that the LLCP can be observed in systems without density-anomalous behavior.

Correction: Salt parameterization can drastically affect the results from classical atomistic simulations of water desalination by MoS2 nanopores.

Correction for 'Salt parameterization can drastically affect the results from classical atomistic simulations of water desalination by MoS2 nanopores' by João P. K. Abal et al., Phys. Chem. Chem. Phys., 2020, 22, 11053-11061, DOI: 10.1039/d0cp00484g.

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 waterlike 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 nonmonotonic trend as their density is increased when compared to the zero affinity scenario. This waterlike 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.

Adhesion modulates cell morphology and migration within dense fibrous networks.

One of the most fundamental abilities required for the sustainability of complex life forms is active cell migration, since it is essential in diverse processes from morphogenesis to leukocyte chemotaxis in immune response. The movement of a cell is the result of intricate mechanisms, that involve the coordination between mechanical forces, biochemical regulatory pathways and environmental cues. In particular, epithelial cancer cells have to employ mechanical strategies in order to migrate through the tissue's basement membrane and infiltrate the bloodstream during the invasion stage of metastasis. In this work we explore how mechanical interactions such as spatial restriction and adhesion affect migration of a self-propelled droplet in dense fibrous media. We have performed a systematic analysis using a phase-field model and we propose a novel approach to simulate cell migration with dissipative particle dynamics modelling. With this purpose we have measured in our simulation the cell's velocity and quantified its morphology as a function of the fibre density and of its adhesiveness to the matrix fibres. Furthermore, we have compared our results to a previous in vitro migration assay of fibrosarcoma cells in fibrous matrices. The results show good agreement between the two methodologies and experiments in the literature, which indicates that these minimalist descriptions are able to capture the main features of the system. Our results indicate that adhesiveness is critical for cell migration, by modulating cell morphology in crowded environments and by enhancing cell velocity. In addition, our analysis suggests that matrix metalloproteinases (MMPs) play an important role as adhesiveness modulators. We propose that new assays should be carried out to address the role of adhesion and the effect of different MMPs in cell migration under confined conditions.

Salt parameterization can drastically affect the results from classical atomistic simulations of water desalination by MoS2 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 on low-cost seawater desalination can prevent the worst scenarios, providing fresh water for humanity. With this goal, membranes based on nanoporous materials have been suggested in recent years. One of the materials suggested is MoS2, 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 built based on distinct properties of water-salt mixtures. One model fits the hydration free energy and lattice properties, and 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 nanopores of two 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 - 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 can the water model influence the outcomes, but the ion model plays a crucial role when the pore is small enough.

2D nanoporous membrane for cation removal from water: Effects of ionic valence, membrane hydrophobicity, and pore size.

Using molecular dynamic simulations, we show that single-layers of molybdenum disulfide (MoS2) and graphene can effectively reject ions and allow high water permeability. Solutions of water and three cations with different valencies (Na+, Zn2+, and Fe3+) were investigated in the presence of the two types of membranes, and the results indicate a high dependence of the ion rejection on the cation charge. The associative characteristic of ferric chloride leads to a high rate of ion rejection by both nanopores, while the monovalent sodium chloride induces lower rejection rates. Particularly, MoS2 shows 100% of Fe3+ rejection for all pore sizes and applied pressures. On the other hand, the water permeation does not vary with the cation valence, having dependence only with the nanopore geometric and chemical characteristics. This study helps us to understand the fluid transport through a nanoporous membrane, essential for the development of new technologies for the removal of pollutants from water.

Waterlike anomalies in a two-dimensional core-softened potential.

We investigate the structural, thermodynamic, and dynamic behavior of a two-dimensional (2D) core-corona system using Langevin dynamics simulations. The particles are modeled by employing a core-softened potential which exhibits waterlike anomalies in three dimensions. In previous studies in a quasi-2D system a new region in the pressure versus temperature phase diagram of structural anomalies was observed. Here we show that for the two-dimensional case two regions in the pressure versus temperature phase diagram with structural, density, and diffusion anomalies are observed. Our findings indicate that, while the anomalous region at lower densities is due the competition between the two length scales in the potential at higher densities, the anomalous region is related to the reentrance of the melting line.

Breakdown of the Stokes-Einstein water transport through narrow hydrophobic nanotubes.

In this paper the transport properties of water confined inside hydrophobic and hydrophilic nanotubes are compared for different nanotube radii and densities. While for wider nanotubes the nature of the wall plays no relevant role in the water mobility, for small nanotubes the hydrophobic confinement presents a peculiar behavior. As the density is increased the viscosity shows a huge increase associated with a small increase in the diffusion coefficient. This breakdown in the Stokes-Einstein relation for diffusion and viscosity was observed in the hydrophobic, but not in the hydrophilic nanotubes. The mechanism underlying this behavior is explained in terms of the structure of water under confinement. This result indicates that some of the features observed for water inside hydrophobic carbon nanotubes cannot be observed in other nanopores.

How Competitive Interactions Affect the Self-Assembly of Confined Janus Dumbbells.

We explore the self-assembled morphologies of Janus nanoparticles under cylindrical confinement. Langevin dynamics simulations are employed to study the behavior of two types of dimers inside cylinders with distinct radius. The first type of nanoparticle was modeled using one monomer that interacts by a standard Lennard-Jones potential and another monomer that is modeled using a purely repulsive two length scale shoulder potential. The second type is composed by a Lennard-Jones monomer and a repulsive monomer which interacts by the purely repulsive Weeks-Chandler-Andersen potential, which have only one length scale. The two length scale potential used in the first type of nanoparticle models a monomer with competitive interaction. Our results show that the aggregated structures are completely distinct for each type of nanoparticle. Also, our simulations indicate that the cylinder radius can be used to control the type of self-assembled cluster. Small clusters, tubular and donut-like micelles with central holes, with potential application to molecule encapsulation were observed regarding the nanoparticle specificities and the cylinder radii. Also, bilayer lamellae structures were obtained depending on the type of nanoparticle and the cylinder size.

Confinement effects on the properties of Janus dimers.

Confinement has been suggested as a tool to tune the self-assembly properties of nanoparticles, surfactants, polymers and colloids. In this way, we explore the phase diagram of Janus nanoparticles confined between two parallel walls using molecular dynamics simulations. A nanoparticle was modeled as a dimer made by one monomer that interacts via a standard Lennard Jones potential and another monomer that is modeled using a two-length scale shoulder potential. This specific design of the nanoparticle exhibits distinct self-assembled structures and a water-like diffusion anomaly in the bulk. Our results indicate that besides the aggregates observed in bulk, new structures are observed under confinement. Also, the dynamic and thermodynamic behavior of the fluid phase is affected. The systems show a reentrant fluid phase and density anomaly. None of these two features were observed in bulk. Our results show that geometrical confinement leads to new structural, thermodynamical and dynamical behavior for this Janus nanoparticle.

Anomalous diffusion and diffusion anomaly in confined Janus dumbbells.

Self-assembly and dynamical properties of Janus nanoparticles have been studied by molecular dynamic simulations. The nanoparticles are modeled as dimers and they are confined between two flat parallel plates to simulate a thin film. One monomer from the dumbbells interacts by a standard Lennard-Jones potential and the other by a two-length scales shoulder potential, typically used for anomalous fluids. Here, we study the effects of removing the Brownian effects, typical from colloidal systems immersed in aqueous solution, and consider a molecular system, without the drag force and the random collisions from the Brownian motion. Self-assembly and diffusion anomaly are preserved in relation to the Brownian system. Additionally, a superdiffusive regime associated to a collective reorientation in a highly structured phase is observed. Diffusion anomaly and anomalous diffusion are explained in the two length scale framework.

Self-Assembly and Water-like Anomalies in Janus Nanoparticles.

We explore the pressure versus temperature phase diagram of a system of dimeric Janus nanoparticles using molecular dynamics simulations. Each nanoparticle is modeled as a dumbbell which has one monomer that interacts by a standard Lennard-Jones potential while the other monomer interacts by a core-softened potential. The systems composed by particles interacting only by core-softened potential exhibit the density and the diffusion anomalous behavior observed in water while if the particles interact only by the Lennard-Jones potential no anomaly is present. Here we explore if the anomalous behavior is present when half of the particles are modeled by a core-softened potential and half with Lennard-Jones potential. We show that the diffusion anomaly is preserve, while the density anomaly can disappear depending on the nonanomalous monomer characteristics. We also show that the self-assembly structures characteristics of the dumbbell systems are affected by the balance between core-softened and non-core-softened monomers.

Effects of confinement on anomalies and phase transitions of core-softened fluids.

We use molecular dynamics simulations to study how the confinement affects the dynamic, thermodynamic, and structural properties of a confined anomalous fluid. The fluid is modeled using an effective pair potential derived from the ST4 atomistic model for water. This system exhibits density, structural, and dynamical anomalies, and the vapor-liquid and liquid-liquid critical points similar to the quantities observed in bulk water. The confinement is modeled both by smooth and structured walls. The temperatures of extreme density and diffusion for the confined fluid show a shift to lower values while the pressures move to higher amounts for both smooth and structured confinements. In the case of smooth walls, the critical points and the limit between fluid and amorphous phases show a non-monotonic change in the temperatures and pressures when the nanopore size is increase. In the case of structured walls, the pressures and temperatures of the critical points varies monotonically with the pore size. Our results are explained on basis of the competition between the different length scales of the fluid and the wall-fluid interaction.