Laser-Induced Cavitation for Controlling Crystallization from Solution.

We demonstrate that a cavitation bubble initiated by a Nd:YAG laser pulse below breakdown threshold induces crystallization from supersaturated aqueous solutions with supersaturation and laser-energy-dependent nucleation kinetics. Combining high-speed video microscopy and simulations, we argue that a competition between the dissipation of absorbed laser energy as latent and sensible heat dictates the solvent evaporation rate and creates a momentary supersaturation peak at the vapor-liquid interface. The number and morphology of crystals correlate to the characteristics of the simulated supersaturation peak.

A Review of Laser-Induced Crystallization from Solution.

Crystallization abounds in nature and industrial practice. A plethora of indispensable products ranging from agrochemicals and pharmaceuticals to battery materials are produced in crystalline form in industrial practice. Yet, our control over the crystallization process across scales, from molecular to macroscopic, is far from complete. This bottleneck not only hinders our ability to engineer the properties of crystalline products essential for maintaining our quality of life but also hampers progress toward a sustainable circular economy in resource recovery. In recent years, approaches leveraging light fields have emerged as promising alternatives to manipulate crystallization. In this review article, we classify laser-induced crystallization approaches where light-material interactions are utilized to influence crystallization phenomena according to proposed underlying mechanisms and experimental setups. We discuss nonphotochemical laser-induced nucleation, high-intensity laser-induced nucleation, laser trapping-induced crystallization, and indirect methods in detail. Throughout the review, we highlight connections among these separately evolving subfields to encourage the interdisciplinary exchange of ideas.

Low-cost fluorescence microscope with microfluidic device fabrication for optofluidic applications.

Optofluidic devices have revolutionized the manipulation and transportation of fluid at smaller length scales ranging from micrometers to millimeters. We describe a dedicated optical setup for studying laser-induced cavitation inside a microchannel. In a typical experiment, we use a tightly focused laser beam to locally evaporate the solution laced with a dye resulting in the formation of a microbubble. The evolving bubble interface is tracked using high-speed microscopy and digital image analysis. Furthermore, we extend this system to analyze fluid flow through fluorescence-Particle Image Velocimetry (PIV) technique with minimal adaptations. In addition, we demonstrate the protocols for the in-house fabrication of a microchannel tailored to function as a sample holder in this optical setup. In essence, we present a complete guide for constructing a fluorescence microscope from scratch using standard optical components with flexibility in the design and at a lower cost compared to its commercial analogues.

Electro-osmotic Drag and Thermodynamic Properties of Water in Hydrated Nafion Membranes from Molecular Dynamics.

One of the important parameters in water management of proton exchange membranes is the electro-osmotic drag (EOD) coefficient of water. The value of the EOD coefficient is difficult to justify, and available literature data on this for Nafion membranes show scattering from in experiments and simulations. Here, we use a classical all-atom model to compute the EOD coefficient and thermodynamic properties of water from molecular dynamics simulations for temperatures between 330 and 420 K, and for different water contents between λ = 5 and λ = 20. λ is the ratio between the moles of water molecules to the moles of sulfonic acid sites. This classical model does not capture the Grotthuss mechanism; however, it is shown that it can predict the EOD coefficient within the range of experimental values for λ = 5 where the vehicular mechanism dominates proton transfer. For λ > 5, the Grotthuss mechanism becomes dominant. To obtain the EOD coefficient, average velocities of water and ions are computed by imposing different electric fields to the system. Our results show that the velocities of water and hydronium scale linearly with the electric field, resulting in a constant ratio of ca. 0.4 within the error bars. We find that the EOD coefficient of water linearly increases from 2 at λ = 5 to 8 at λ = 20 and the results are not sensitive to temperature. The EOD coefficient at λ = 5 is within the range of experimental values, confirming that the model can capture the vehicular transport of protons well. At λ = 20, due to the absence of proton hopping in the model, the EOD coefficient is overestimated by a factor of 3 compared to experimental values. To analyze the interactions between water and Nafion, the partial molar enthalpies and partial molar volumes of water are computed from molecular dynamics simulations. At different water uptakes, multiple linear regression is used on raw simulation data within a narrow composition range of water inside the Nafion membrane. The partial molar volumes and partial molar excess enthalpies of water asymptotically approach the molar volumes and molar excess enthalpies of pure water for water uptakes above 5. This confirms the model can capture the bulklike behavior of water in the Nafion at high water uptakes.

Coupling mesoscale transport to catalytic surface reactions in a hybrid model.

In heterogeneous catalysis, reactivity and selectivity are not only influenced by chemical processes occurring on catalytic surfaces but also by physical transport phenomena in the bulk fluid and fluid near the reactive surfaces. Because these processes take place at a large range of time and length scales, it is a challenge to model catalytic reactors, especially when dealing with complex surface reactions that cannot be reduced to simple mean-field boundary conditions. As a particle-based mesoscale method, Stochastic Rotation Dynamics (SRD) is well suited for studying problems that include both microscale effects on surfaces and transport phenomena in fluids. In this work, we demonstrate how to simulate heterogeneous catalytic reactors by coupling an SRD fluid with a catalytic surface on which complex surface reactions are explicitly modeled. We provide a theoretical background for modeling different stages of heterogeneous surface reactions. After validating the simulation method for surface reactions with mean-field assumptions, we apply the method to non-mean-field reactions in which surface species interact with each other through a Monte Carlo scheme, leading to island formation on the catalytic surface. We show the potential of the method by simulating a more complex three-step reaction mechanism with reactant dissociation.

Surface Protolysis and Its Kinetics Impact the Electrical Double Layer.

Surface conductivity in the electrical double layer (EDL) is known to be affected by proton hopping and diffusion at solid-liquid interfaces. Yet, the role of surface protolysis and its kinetics on the thermodynamic and transport properties of the EDL are usually ignored as physical models consider static surfaces. Here, using a novel molecular dynamics method mimicking surface protolysis, we unveil the impact of such chemical events on the system's response. Protolysis is found to strongly affect the EDL and electrokinetic aspects with major changes in ζ potential and electro-osmotic flow.

Real-time temperature measurement in stochastic rotation dynamics.

Many physical and chemical processes involve energy change with rates that depend sensitively on local temperature. Important examples include heterogeneously catalyzed reactions and activated desorption. Because of the multiscale nature of such systems, it is desirable to connect the macroscopic world of continuous hydrodynamic and temperature fields to mesoscopic particle-based simulations with discrete particle events. In this work we show how to achieve real-time measurement of the local temperature in stochastic rotation dynamics (SRD), a mesoscale method particularly well suited for problems involving hydrodynamic flows with thermal fluctuations. We employ ensemble averaging to achieve local temperature measurement in dynamically changing environments. After validation by heat diffusion between two isothermal plates, heating of walls by a hot strip, and by temperature programed desorption, we apply the method to a case of a model flow reactor with temperature-sensitive heterogeneously catalyzed reactions on solid spherical catalysts. In this model, adsorption, chemical reactions, and desorption are explicitly tracked on the catalyst surface. This work opens the door for future projects where SRD is used to couple hydrodynamic flows and thermal fluctuations to solids with complex temperature-dependent surface mechanisms.

The importance of specifically adsorbed ions for electrokinetic phenomena: Bridging the gap between experiments and MD simulations.

Molecular Dynamics (MD) simulations are uniquely suitable for providing molecular-level insights into the Electric Double Layer (EDL) that forms when a charged surface is in contact with an aqueous solution. However, simulations are only as accurate in predicting EDL properties as permitted by the atomic interaction models. Experimental ζ-potential values and surface charges could provide a potentially suitable reference to validate and tune the interaction models, if not for the fact that they themselves are a product of imperfect models used to interpret the raw measurement data. Here, we present an approach to tune an interaction model by comparing Electro-Osmotic Flow (EOF) MD simulations against experimental Streaming Current (SC) measurements while minimizing potential modeling errors arising from both approaches. The point that is least susceptible to interpretation and modeling errors is argued to be at the concentration for which zero flow velocity is observed in EOF simulations and a net zero electric current is measured in SC experiments. At this concentration, the ζ-potential is also zero. We were able to match the experimental concentration at which ζ = 0 in MD simulations for a CaCl2 solution at pH 7.5 in contact with fused silica by tuning the ion-surface Lennard-Jones cross interactions. These interactions were found to greatly affect the ion distribution within the EDL and particularly the formation of inner-sphere surface-complexes, which, in turn, affects the electrokinetic flow. With the ion distribution determined explicitly, a series of properties can be calculated unambiguously, such as the capacitance needed for surface complexation models.

Scale-Dependent Friction-Coverage Relations and Nonlocal Dissipation in Surfactant Monolayers.

Surfactant molecules, known as organic friction modifiers (OFMs), are routinely added to lubricants to reduce friction and wear between sliding surfaces. In macroscale experiments, friction generally decreases as the coverage of OFM molecules on the sliding surfaces increases; however, recent nanoscale experiments with sharp atomic force microscopy (AFM) tips have shown increasing friction. To elucidate the origin of these opposite trends, we use nonequilibrium molecular dynamics (NEMD) simulations and study kinetic friction between OFM monolayers and an indenting nanoscale asperity. For this purpose, we investigate various coverages of stearamide OFMs on iron oxide surfaces and silica AFM tips with different radii of curvature. We show that the differences between the friction-coverage relations from macroscale and nanoscale experiments are due to molecular plowing in the latter. For our small tip radii, the friction coefficient and indentation depth both have a nonmonotonic dependence on OFM surface coverage, with maxima occurring at intermediate coverage. We rationalize the nonmonotonic relations through a competition of two effects (confinement and packing density) that varying the surface coverage has on the effective stiffness of the OFM monolayers. We also show that kinetic friction is not very sensitive to the sliding velocity in the range studied, indicating that it originates from instabilities. Indeed, we find that friction predominately originates from plowing of the monolayers by the leading edge of the tip, where gauche defects are created, while thermal dissipation is mostly localized in molecules toward the trailing edge of the tip, where the chains return to a more extended conformation.

How do ions contribute to brine-hydrophobic hydrocarbon Interfaces? An in silico study.

HYPOTHESIS: The saltwater-oil interface is of broad implication in geochemistry and petroleum disciplines. To date, the main focus has been on the surface contribution of polar, heavy compounds of crude oil, widely neglecting the role of non-polar hydrocarbons. However, non-polar compounds are expected to contribute to characteristics of oil-brine interfaces. METHODOLOGY: Utilizing molecular dynamics simulation, we aim to characterize ion behavior adjacent to hydrophobic organic phases. Concerning natural environments, NaCl, CaCl2 and Na2SO4 electrolytes at low (5 wt%) and high (15 wt%) concentrations were brought in contact with heptane and/or toluene which account for aliphatic and aromatic constituents of typical crude oils, respectively. The reproduced experimental data for interfacial tension, brines density and ions' diffusivities adequately verify our molecular calculations. FINDINGS: Ions accumulate nearby the intrinsically charge-neutral oil surfaces. A disparate surface-favoring propensity of ions causes the interfacial region to resemble an electrical layer and impose an effective surface charge onto the oil surface. Despite absence of any polar site, the effective surface charge density is hydrocarbon-dependent, with the highest and lowest values observed for toluene and heptane interfaces, respectively. Due to accumulation of toluene molecules nearby the brines, the interfacial characteristics of heptol (toluene-heptane mixture) is comparable to that of the toluene phase.

Inclusion Complexation of Organic Micropollutants with ß-Cyclodextrin.

Recently, ß-cyclodextrin (ßCD)-based polymers with enhanced adsorption kinetics and high removal capacity of organic micropollutants (OMPs) and uptake rates have been synthesized and tested experimentally. Although the exact physical-chemical mechanisms via which these polymers capture the various types of OMPs are not yet fully understood, it is suggested that the inclusion complex formation of OMPs with ßCD is very important. In this study, the inclusion complex formation of OMPs with ßCD in an aqueous solution is investigated by using the well-established attach-pull-release method in force field-based molecular dynamics simulations. A representative set of OMPs is selected based on the measured occurrences in surface and ground waters and the directives published by the European Union. To characterize the formation of the inclusion complex, the binding free energies, enthalpies, and entropies are computed and compared to experimental values. It is shown that computations using the q4md-CD/GAFF/Bind3P force field combination yield binding free energies that are in reasonable agreement with the experimental results for all OMPs studied. The binding enthalpies are decomposed into the main contributing interaction types. It is shown that, for all studied OMPs, the van der Waals interactions are favorable for the inclusion complexion and the hydrogen bond formation of the guest with the solvent and ßCD plays a crucial role in the binding mechanism. Our findings show that MD simulations can adequately describe the inclusion complex formation of ßCD with OMPs, which is the first step toward understanding the underlying mechanisms via which the ßCD-based polymers capture OMPs.

On the transferability of ion parameters to the TIP4P/2005 water model using molecular dynamics simulations.

Countless molecular dynamics studies have relied on available ion and water force field parameters to model aqueous electrolyte solutions. The TIP4P/2005 model has proven itself to be among the best rigid water force fields, whereas many of the most successful ion parameters were optimized in combination with SPC/E, TIP3P, or TIP4P/Ew water. Many researchers have combined these ions with TIP4P/2005, hoping to leverage the strengths of both parameter sets. To assess if this widely used approach is justified and to provide a guide in selecting ion parameters, we investigated the transferability of various commonly used monovalent and multivalent ion parameters to the TIP4P/2005 water model. The transferability is evaluated in terms of ion hydration free energy, hydration radius, coordination number, and self-diffusion coefficient at infinite dilution. For selected ion parameters, we also investigated density, ion pairing, chemical potential, and mean ionic activity coefficients at finite concentrations. We found that not all ions are equally transferable to TIP4P/2005 without compromising their performance. In particular, ions optimized for TIP3P water were found to be poorly transferable to TIP4P/2005, whereas ions optimized for TIP4P/Ew water provided nearly perfect transferability. The latter ions also showed good overall agreement with experimental values. The one exception is that no combination of ion parameters and water model considered here was found to accurately reproduce experimental self-diffusion coefficients. Additionally, we found that cations optimized for SPC/E and TIP3P water displayed consistent underpredictions in the hydration free energy, whereas anions consistently overpredicted the hydration free energy.

The Impact of Salinity on the Interfacial Structuring of an Aromatic Acid at the Calcite/Brine Interface: An Atomistic View on Low Salinity Effect.

This study aims to elucidate the impact of salinity on the interactions governing the adsorption of polar aromatic oil compounds onto calcite. To this end, molecular dynamics simulations were employed to assess adsorption of a model polar organic molecule (deprotonated benzoic acid, benzoate) on the calcite surface in NaCl brines of different concentration levels, namely, deionized water (DW), low-salinity water (LS, 5000 ppm), and sea water (SW; 45,000 ppm). Calcite was found to be completely covered by several well-ordered water layers. The top hydration layer is very compact and prevents direct adsorption of benzoates onto the substrate. Instead, Na+ ions form a distinct positively charged layer by adhering on the calcite substrate through inner-sphere complexion mode. Cl- ions mostly lodge on top of the adsorbed sodium cations, forming a negatively charged layer. The distribution of ions at the calcite/brine interface thus exhibits the features of an electrical double layer, composed of a Stern-like positive layer followed by a negative one. The positive charged layer attracts benzoates toward the surface. As such, the sodium ions attached onto the calcite can act as adsorption sites to connect benzoates to the surface. By increasing the salinity, more Na+ ions adsorb onto the calcite surface, and the density of benzoate molecules at the interface is enhanced as a result of more Na+ bridging ions. The monotonic salinity-dependent adsorption of benzoate molecules on calcite offers a mechanism driving additional oil recovery upon injection of diluted brine into subsurface carbonate reservoirs.

The role of water models on the prediction of slip length of water in graphene nanochannels.

Slip lengths reported from molecular dynamics (MD) simulations of water flow in graphene nanochannels show significant scatter in the literature. These discrepancies are in part due to the used water models. We demonstrate self-consistent comparisons of slip characteristics between the SPC, SPC/E, SPC/Fw, TIP3P, TIP4P, and TIP4P/2005 water models. The slip lengths are inferred using an analytical model that employs the shear viscosity of water and channel average velocities obtained from nonequilibrium MD simulations. First, viscosities for each water model are quantified using MD simulations of counterflowing, force-driven flows in periodic domains in the absence of physical walls. While the TIP4P/2005 model predicts water viscosity at the specified thermodynamic state with 1.7% error, the predictions of SPC/Fw and SPC/E models exhibit 13.9% and 23.1% deviations, respectively. Water viscosities obtained from SPC, TIP4P, and TIP3P models show larger deviations. Next, force-driven water flows in rigid (cold) and thermally vibrating (thermal) graphene nanochannels are simulated, resulting in pluglike velocity profiles. Large differences in the flow velocities are observed depending on the used water model and to a lesser extent on the choice of rigid vs thermal walls. Depending on the water model, the slip length of water on cold graphene walls varied between 34.2 nm and 62.9 nm, while the slip lengths of water on thermal graphene walls varied in the range of 38.1 nm-84.3 nm.

Influence of Single-Stranded DNA Coatings on the Interaction between Graphene Nanoflakes and Lipid Bilayers.

Using molecular dynamics simulations, it is demonstrated that a partial coating of single-stranded DNA (ssDNA) reduces the penetration depth of a graphene nanoflake (GNF) into a phospholipid bilayer by attenuating the hydrophobic force that drives the penetration. As the GNF penetrates the bilayer, the ssDNA remains adsorbed to the GNF outside of the bilayer where it shields the graphene from the surrounding water. The penetration depth is found to be controlled by the amount of ssDNA coating the GNF, with a sparser coating resulting in a deeper penetration since the ssDNA shields less of the GNF surface. As the coating density is increased, the likelihood of the GNF entering the bilayer is reduced where it instead tends to lie flat on the bilayer surface with the sugar phosphate backbone of ssDNA interacting with the hydrophilic lipid head groups. While no bilayer disruption is observed for a partially inserted ssDNA-coated GNF, a larger, bare, partially inserted GNF is found to preferentially extract phospholipids from the bilayer, offering further evidence of lipid extraction as a main cytotoxicity mechanism of GNFs. Therefore, a coating of ssDNA may reduce the cytotoxicity of GNFs by shielding the unfavorable graphene-water interaction, thus preventing graphene penetration and lipid extraction.

Macroscopic relations for microscopic properties at the interface between solid substrates and dense fluids.

Strongly confined fluids exhibit inhomogeneous properties due to atomistic structuring in close proximity to a solid surface. State variables and transport coefficients at a solid-fluid interface vary locally and become dependent on the properties of the confining walls. However, the precise mechanisms for these effects are not known as of yet. Here, we make use of nonequilibrium molecular dynamics simulations to scrutinize the local fluid properties at the solid-fluid interface for a range of surface conditions and temperatures. We also derive microscopic relations connecting fluid viscosity and density profiles for dense fluids. Moreover, we propose empirical ready-to-use relations to express the average density and viscosity in the channel as a function of temperature, wall interaction strength, and bulk density or viscosity. Such relations are key to technological applications such as micro-/nanofluidics and tribology but also natural phenomena.

OCTP: A Tool for On-the-Fly Calculation of Transport Properties of Fluids with the Order- n Algorithm in LAMMPS.

We present a new plugin for LAMMPS for on-the-fly computation of transport properties (OCTP) in equilibrium molecular dynamics. OCTP computes the self- and Maxwell-Stefan diffusivities, bulk and shear viscosities, and thermal conductivities of pure fluids and mixtures in a single simulation. OCTP is the first implementation in LAMMPS that uses the Einstein relations combined with the order- n algorithm for the efficient sampling of dynamic variables. OCTP has low computational requirements and is easy to use because it follows the native input file format of LAMMPS. A tool for calculating the radial distribution function (RDF) of the fluid beyond the cutoff radius, while taking into account the system size effects, is also part of the new plugin. The RDFs computed from OCTP are needed to obtain the thermodynamic factor, which relates Maxwell-Stefan and Fick diffusivities. To demonstrate the efficiency of the new plugin, the transport properties of an equimolar mixture of water-methanol were computed at 298 K and 1 bar.

Shear Viscosity Computed from the Finite-Size Effects of Self-Diffusivity in Equilibrium Molecular Dynamics.

A method is proposed for calculating the shear viscosity of a liquid from finite-size effects of self-diffusion coefficients in Molecular Dynamics simulations. This method uses the difference in the self-diffusivities, computed from at least two system sizes, and an analytic equation to calculate the shear viscosity. To enable the efficient use of this method, a set of guidelines is developed. The most efficient number of system sizes is two and the large system is at least four times the small system. The number of independent simulations for each system size should be assigned in such a way that 50%-70% of the total available computational resources are allocated to the large system. We verified the method for 250 binary and 26 ternary Lennard-Jones systems, pure water, and an ionic liquid ([Bmim][Tf2N]). The computed shear viscosities are in good agreement with viscosities obtained from equilibrium Molecular Dynamics simulations for all liquid systems far from the critical point. Our results indicate that the proposed method is suitable for multicomponent mixtures and highly viscous liquids. This may enable the systematic screening of the viscosities of ionic liquids and deep eutectic solvents.

Prediction of fluid slip in cylindrical nanopores using equilibrium molecular simulations.

We introduce an analytical method to predict the slip length (L s) in cylindrical nanopores using equilibrium molecular dynamics (EMD) simulations, following the approach proposed by Sokhan and Quirke for planar channels [39]. Using this approach, we determined the slip length of water in carbon nanotubes (CNTs) of various diameters. The slip length predicted from our method shows excellent agreement with the results obtained from nonequilibrium molecular dynamics (NEMD) simulations. The data show a monotonically decreasing slip length with an increasing nanotube diameter. The proposed EMD method can be used to precisely estimate slip length in high slip cylindrical systems, whereas, L s calculated from NEMD is highly sensitive to the velocity profile and may cause large statistical errors due to large velocity slip at the channel surface. We also demonstrated the validity of the EMD method in a BNNT-water system, where the slip length is very small compared to that in a CNT pore of similar diameter. The developed method enables us to calculate the interfacial friction coefficient directly from EMD simulations, while friction can be estimated using NEMD by performing simulations at various external driving forces, thereby increasing the overall computational time. The EMD analysis revealed a curvature dependence in the friction coefficient, which induces the slip length dependency on the tube diameter. Conversely, in flat graphene nanopores, both L s and friction coefficient show no strong dependency on the channel width.

Water desalination using graphene nanopores: influence of the water models used in simulations.

Molecular dynamics simulations are widely employed to analyze water and ion permeation through nanoporous membranes for reverse osmosis applications. In such simulations, water models play an important role in accurately reproducing the properties of water. We investigated the water and ion transport across a hydroxyl (OH) functionalized graphene nanopore using six water models: SPC, SPC/E, SPC/Fw, TIP3P, TIP4P, and TIP4P/2005. The water flux thus obtained varied up to 84% between the models. The water and ion flux showed a correlation with the bulk transport properties of the models such as the diffusion coefficient and shear viscosity. We found that the hydrogen-bond lifetime, resulting from the partial charges of the model, influenced the flux. Our results are useful in the selection of a water model for computer simulations of desalination using nanomembranes. Our findings also suggest that lowering the hydrogen-bond lifetime and enhancing the rate of diffusion of water would lead to enhanced water/ion flux.