A comparison of the value of viscosity for several water models using Poiseuille flow in a nano-channel

Rocket Dynamics of Capped Nanotubes: A Molecular Dynamics Study

The study of nanoparticle motion has fundamental relevance in a wide range of nanotechnology-based fields. Molecular dynamics simulations offer a powerful tool to elucidate the dynamics of complex systems and derive theoretical models that facilitate the invention and optimization of novel devices. This research contributes to this ongoing effort by investigating the motion of one-end capped carbon nanotubes within an aqueous environment through extensive molecular dynamics simulations. By exposing the carbon nanotubes to localized heating, propelled motion with velocities reaching up to ≈0.08 nm ps-1 was observed. Through systematic exploration of various parameters such as temperature, nanotube diameter, and size, we were able to elucidate the underlying mechanisms driving propulsion. Our findings demonstrate that the propulsive motion predominantly arises from a rocket-like mechanism facilitated by the progressive evaporation of water molecules entrapped within the carbon nanotube. Therefore, this study focuses on the complex interplay between nanoscale geometry, environmental conditions, and propulsion mechanisms in capped nanotubes, providing relevant insights into the design and optimization of nanoscale propulsion systems with various applications in nanotechnology and beyond.

Interlink between Abnormal Water Imbibition in Hydrophilic and Rapid Flow in Hydrophobic Nanochannels

Nanoscale extension and refinement of the Lucas-Washburn model is presented with a detailed analysis of recent experimental data and extensive molecular dynamics simulations to investigate rapid water flow and water imbibition within nanocapillaries. Through a comparative analysis of capillary rise in hydrophilic nanochannels, an unexpected reversal of the anticipated trend, with an abnormal peak, of imbibition length below the size of 3 nm was discovered in hydrophilic nanochannels, surprisingly sharing the same physical origin as the well-known peak observed in flow rate within hydrophobic nanochannels. The extended imbibition model is applicable across diverse spatiotemporal scales and validated against simulation results and existing experimental data for both hydrophilic and hydrophobic nanochannels.

Liquid-Liquid Crossover in Water Model: Local Structure vs Kinetics of Hydrogen Bonds

In equilibrium and supercooled liquids, polymorphism is manifested by thermodynamic regions defined in the phase diagram, which are predominantly of different short- and medium-range order (local structure). It is found that on the phase diagram of the water model, the thermodynamic region corresponding to the equilibrium liquid phase is divided by a line of the smooth liquid-liquid crossover. In the case of the water model TIP4P/2005, this crossover is revealed by various local order parameters and corresponds to pressures on the order of 3150 ± 350 atm at ambient temperature. In the vicinity of the crossover, the dynamics of water molecules change significantly, which is reflected, in particular, in the fact that the self-diffusion coefficient reaches its maximum values. In addition, changes in the structure also manifest themselves in changes in the kinetics of hydrogen bonding, which are captured by values of such quantities as the average lifetime of hydrogen bonding, the average lifetimes of different local coordination numbers, and the frequencies of changes in different local coordination numbers. An interpretation of the hydrogen bond kinetics in terms of the free energy landscape concept in the space of possible coordination numbers is proposed.

Salinity-Driven Structural and Viscosity Modulation of Confined Polar Oil Phases by Carbonated Brine Films: Novel Insights from Molecular Dynamics

The structural and dynamic properties of fluids under confinement in a porous medium differ from their bulk properties. This study delves into the surface structuring and hydrodynamic characteristics of oil/thin film carbonated brine two-phase within a calcite channel upon salinity variation. To this end, both equilibrium and non-equilibrium molecular dynamics simulations are utilized to unveil the effect of the carboxylic acid component (benzoic acid) in a simple model oil (decane) confined between two thin films of carbonated brine on the oil-brine-calcite characteristics. The salinity effect was scrutinized under four saline carbonated waters, deionized carbonated water (DCW), carbonated low-salinity brine (CLSB, 30,000 ppm), carbonated seawater (CSW, 60,000 ppm), and carbonated high-salinity brine (CHSB, 180,000 ppm). An electrical double layer (EDL) is observed at varying salinities, comprising a Stern-like positive layer (formed by Na+ ions) followed by a negative one (formed by Cl- ions primarily residing on top of the adsorbed sodium cations). By lowering the salinity, the Na+ ions cover the interface regions (brine-calcite and brine-oil), depleting within the brine bulk region. The lowest positive surface charge on the rock surface was found in salinity corresponding to seawater. Two distinct Na+ peaks at the oleic phase interface have been observed in the carbonated high-salinity brine system, enhancing the adsorption of polar molecules at the thin brine film interfaces. There is a pronounced EDL formation at the oleic phase interface in the case of CSW, resulting in a strong interface region containing ions and functional fractions. Likewise, the oil region confined by CSW exhibited the lowest apparent viscosity, attributed to the optimized salinity distribution and inclination of benzoic acid fractions uniformly at the brine-oil interface, acting as a slippery surface. Moreover, the results reveal that the presence of polar fractions could increase the oil phase's apparent viscosity, and introducing ions to this system reduces the polar molecules' destructive effect on the apparent viscosity of the oil region. Therefore, the fluidity of confined systems is modulated by both composition of the brine and oil phases.

Unexpected Behavior in Thermal Conductivity of Confined Monolayer Water

Monolayer water can be formed under extreme confinement and will present distinctive thermodynamic properties compared with bulk water. In this work, we perform molecular dynamics simulations to study the thermal conductivity of monolayer water confined in graphene channels, finding an unexpected way of thermal conductivity of monolayer water dependent on its number density, which has a close correlation with the structure of water. The monolayer water is in an amorphous state, and its thermal conductivity increases linearly with the area density when the water density is low at first. Then, the thermal conductivity increases as the number density of water rises, which is attributed to the formation of a crystal structure and the reduction of crystal defects as the number of water molecules increases. After reaching the zenith, the thermal conductivity decreases rapidly owing to the formation of a wrinkle structure of monolayer water with excessive water molecules, which weakens the phonon dispersion. Moreover, we further investigate the remarkable effects of the channel height on both the structure and thermal conductivity of monolayer water. In summary, this study demonstrates the close connection between the thermal conductivity of monolayer water and its structure, contributing to not only expanding the understanding of the thermodynamic property of nanoconfined water but also benefiting the engineering applications for nanofluidics.

Electrokinetic, electrochemical, and electrostatic surface potentials of the pristine water liquid-vapor interface

Although conceptually simple, the air-water interface displays rich behavior and is subject to intense experimental and theoretical investigations. Different definitions of the electrostatic surface potential as well as different calculation methods, each relevant for distinct experimental scenarios, lead to widely varying potential magnitudes and sometimes even different signs. Based on quantum-chemical density-functional-theory molecular dynamics (DFT-MD) simulations, different surface potentials are evaluated and compared to force-field (FF) MD simulations. As well explained in the literature, the laterally averaged electrostatic surface potential, accessible to electron holography, is dominated by the trace of the water molecular quadrupole moment, and using DFT-MD amounts to +4.35 V inside the water phase, very different from results obtained with FF water models which yield negative values of the order of -0.4 to -0.6 V. Thus, when predicting potentials within water molecules, as relevant for photoelectron spectroscopy and non-linear interface-specific spectroscopy, DFT simulations should be used. The electrochemical surface potential, relevant for ion transfer reactions and ion surface adsorption, is much smaller, less than 200 mV in magnitude, and depends specifically on the ion radius. Charge transfer between interfacial water molecules leads to a sizable surface potential as well. However, when probing electrokinetics by explicitly applying a lateral electric field in DFT-MD simulations, the electrokinetic ζ-potential turns out to be negligible, in agreement with predictions using continuous hydrodynamic models. Thus, interfacial polarization charges from intermolecular charge transfer do not lead to significant electrokinetic mobility at the pristine vapor-liquid water interface, even assuming these transfer charges are mobile in an external electric field.

Connection between water's dynamical and structural properties: Insights from ab initio simulations

SignificanceFirst-principles calculations, which explicitly account for the electronic structure of matter, can shed light on the molecular structure and dynamics of water in its supercooled state. In this work, we use density functional theory, which relies on a functional to describe electronic exchange and correlations, to evaluate which functional best describes the temperature evolution of bulk water transport coefficients. We also assess the validity of the Stokes-Einstein relation for all the functionals in the temperature range studied, and explore the link between structure and dynamics. Based on these results, we show how transport coefficients can be computed from structural descriptors, which require shorter simulation times to converge, and we point toward strategies to develop better functionals.

Oxygen Quenching-Resistant Nanoaggregates with Aggregation-Induced Delayed Fluorescence for Time-Resolved Mapping of Intracellular Microviscosity

Microviscosity is a fundamental parameter in the biophysics of life science and governs numerous cellular processes. Thus, the development of real-time quantitative monitoring of microviscosity inside cells is important. The traditional probes for detecting microviscosity via time-resolved luminescence imaging (TRLI) are generally disturbed by autofluorescence or surrounding oxygen in cells. Herein, we developed loose packing nanoaggregates with aggregation-induced delayed fluorescence (FKP-POA and FKP-PTA) and free from the effect of oxygen and autofluorescence for viscosity mapping via TRLI. The feasibility of FKP-PTA nanoparticles (NPs) for microviscosity mapping through TRLI was demonstrated by monitoring the variation of microviscosity inside HepG2 cancer cells, which demonstrated a value change from 14.9 cP to 216.9 cP during the apoptosis. This indicates that FKP-PTA NP can be used as a probe for cellular microviscosity mapping to help people to understand the physiologically dynamic microenvironment. The present results are expected to promote the advancement of diagnostic and therapeutic methods to cope with related diseases.

Demonstrating the Interfacial Polymer Thermal Transition from Coil-to-Globule to Coil-to-Stretch under Shear Flow Using SFG and MD Simulation

Revealing interfacial shear-induced structural responsiveness has long been an important topic in that most fluids in nature and human life are in motion and cause interesting boundary phenomena. It is amazing how the polymer chain conformation or local structural features at a boundary change under the effective shear condition. In this study, microfluidic-assisted sum frequency generation (SFG) vibrational spectroscopy and all-atom molecular dynamics (MD) simulation are combined to reveal that the shear flow can effectively block the so-called thermal coil-to-globule transition of the poly(N-isopropylacrylamide) (PNIPAM) brushes on the solid substrate, and the normal coil-to-globule transition transfers to a coil-to-stretch one under shear flow with increasing ambient temperature. Such findings are attributed to the balance between the shear flow and the molecular interaction with respect to the polymer chains and adjacent water molecules, thus demonstrating the significant effect of the shear flow on the structural and dynamic behaviors of the polymer chains at the boundaries from the molecular level.

Effect of charge inversion on nanoconfined flow of multivalent ionic solutions

A comprehensive understanding of fluid dynamics of dilute electrolyte solutions in nanoconfinement is essential to develop more efficient nanofluidic devices. In nanoconduits, the electrical double layer can occupy a considerable...

Machine learning for reparameterization of four-site water models: TIP4P-BG and TIP4P-BGT

Parameterizing an effective water model is a challenging issue because of the difficulty in maintaining a comprehensive balance among the diverse physical properties of water with a limited number of parameters. The advancement in machine learning provides a promising path to search for a reliable set of parameters. Based on the TIP4P water model, hence, about 6000 molecular dynamics (MD) simulations for pure water at 1 atm and in the range of 273-373 K are conducted here as the training data. The back-propagation (BP) neural network is then utilized to construct an efficient mapping between the model parameters and four crucial physical properties of water, including the density, vaporization enthalpy, self-diffusion coefficient and viscosity. Without additional time-consuming MD simulations, this mapping operation could result in sufficient and accurate data for high-population genetic algorithm (GA) to optimize the model parameters as much as possible. Based on the proposed parameterizing strategy, TIP4P-BG (a conventional four-site water model) and TIP4P-BGT (an advanced model with temperature-dependent parameters) are established. Both the water models exhibit excellent performance with a reasonable balance among the four crucial physical properties. The relevant mean absolute percentage errors are 3.53% and 3.08%, respectively. Further calculations on the temperature of maximum density, isothermal compressibility, thermal expansion coefficient, radial distribution function and surface tension are also performed and the resulting values are in good agreement with the experimental values. Through this water modeling example, the potential of the proposed data-driven machine learning procedure has been demonstrated for parameterizing a MD-based material model.

Machine Learning Techniques for Fluid Flows at the Nanoscale

Simulations of fluid flows at the nanoscale feature massive data production and machine learning (ML) techniques have been developed during recent years to leverage them, presenting unique results. This work facilitates ML tools to provide an insight on properties among molecular dynamics (MD) simulations, covering missing data points and predicting states not previously located by the simulation. Taking the fluid flow of a simple Lennard-Jones liquid in nanoscale slits as a basis, ML regression-based algorithms are exploited to provide an alternative for the calculation of transport properties of fluids, e.g., the diffusion coefficient, shear viscosity and thermal conductivity and the average velocity across the nanochannels. Through appropriate training and testing, ML-predicted values can be extracted for various input variables, such as the geometrical characteristics of the slits, the interaction parameters between particles and the flow driving force. The proposed technique could act in parallel to simulation as a means of enriching the database of material properties, assisting in coupling between scales, and accelerating data-based scientific computations.

Wall friction should be decoupled from fluid viscosity for the prediction of nanoscale flow

The accurate determination of fluid viscosity based on the microscopic information of molecules is very crucial for the prediction of nanoscale flow. Despite the challenge of this problem, researchers have done a lot of meaningful work and developed several distinctive methods. However, one of the common approaches to calculate the fluid viscosity is using the Green-Kubo formula by considering all the fluid molecules in nanospace, inevitably causing the involvement of the frictional interaction between fluid and the wall into the fluid viscosity. This practice is certainly not appropriate because viscosity is essentially related only to the interactions among fluid molecules. Here, we clarify that the wall friction should be decoupled from fluid viscosity by distinguishing the frictional region and the viscous region for the accurate prediction of nanoscale flow. By comparing the fluid viscosities calculated from the Green-Kubo formula in the whole region and viscous region and the viscosity obtained from the velocity profile through the Hagen-Poiseuille equation, it is found that only the calculated viscosity in the viscous region agrees well with the viscosity from the velocity profile. To demonstrate the applicability of this clarification, the Lennard-Jones fluid and water confined between Lennard-Jones, graphene, and silica walls, even with different fluid-wall interactions, are extensively tested. This work clearly defines the viscosity of fluids at nanoscales from the inherent nature of physics, aiming at the accurate prediction of nanoscale flow from the classical continuum hydrodynamic theory.

Thermo-osmosis in hydrophilic nanochannels: mechanism and size effect

Understanding thermo-osmosis in nanoscale channels and pores is essential for both theoretical advances of thermally induced mass flow and a wide range of emerging industrial applications. We present a new mechanistic understanding and quantification of thermo-osmosis at nanometric/sub-nanometric length scales and link the outcomes with the non-equilibrium thermodynamics of the phenomenon. The work is focused on thermo-osmosis of water in quartz slit nanochannels, which is analysed by molecular dynamics (MD) simulations of mechano-caloric and thermo-osmotic systems. We investigate the applicability of Onsager reciprocal relation, irreversible thermodynamics, and continuum fluid mechanics at the nanoscale. Further, we analyse the effects of channel size on the thermo-osmosis coefficient, and show, for the first time, that these arise from specific liquid structures dictated by the channel size. The mechanical conditions of the interfacial water under different temperatures are quantified using a continuum approach (pressure tensor distribution) and a discrete approach (body force per molecule) to elucidate the underlying mechanism of thermo-osmosis. The results show that the fluid molecules located in the boundary layers adjacent to the solid surfaces experience a driving force which generates the thermo-osmotic flow. While the findings provide a fundamental understanding of thermo-osmosis, the methods developed provide a route for analysis of the entire class of coupled heat and mass transport phenomena in nanoscale structures.

Hierarchical thermal transport in nanoconfined water

The structure of nanoconfined fluids is particularly non-uniform owing to the wall interaction, resulting in the distinctive characteristic of thermal transport compared to bulk fluids. We present the molecular simulations on the thermal transport of water confined in nanochannels with a major investigation of its spatial distribution under the effects of wall interaction. The results show that the thermal conductivity of nanoconfined water is inhomogeneous and its layered distribution is very similar to the density profile. The layered thermal conductivity is the coupling result of inhomogeneous density and energy distributions that are generally diametrical, and their contributions to the thermal conductivity compensate with each other. However, the accumulative effect of water molecules is really dominating, resulting in a high thermal conductivity in the high-density layers with the low-energy molecules, and vice versa. Moreover, it is found that the adsorptive and repulsive interactions from solid walls have different roles in the hierarchical thermal transport in nanoconfined water. The adsorptive interaction is only responsible for the layered distribution of thermal conductivity, while the repulsive interaction is responsible for the overall thermal conductivity; accordingly, the thermal conductivity is independent of the strength of water-solid interactions. The identified hierarchical thermal transport in nanoconfined water and its underlying mechanisms have a great significance for the understanding of nanoscale thermal transport and even the mass and energy transport of nanoconfined fluids.

Molecular Dynamics Simulations of Ion Drift in Nanochannel Water Flow

The present paper employs Molecular Dynamics (MD) simulations to reveal nanoscale ion separation from water/ion flows under an external electric field in Poiseuille-like nanochannels. Ions are drifted to the sidewalls due to the effect of wall-normal applied electric fields while flowing inside the channel. Fresh water is obtained from the channel centerline, while ions are rejected near the walls, similar to the Capacitive DeIonization (CDI) principles. Parameters affecting the separation process, i.e., simulation duration, percentage of the removal, volumetric flow rate, and the length of the nanochannel incorporated, are affected by the electric field magnitude, ion correlations, and channel height. For the range of channels investigated here, an ion removal percentage near 100% is achieved in most cases in less than 20 ns for an electric field magnitude of E = 2.0 V/Å. In the nutshell, the ion drift is found satisfactory in the proposed nanoscale method, and it is exploited in a practical, small-scale system. Theoretical investigation from this work can be projected for systems at larger scales to perform fundamental yet elusive studies on water/ion separation issues at the nanoscale and, one step further, for designing real devices as well. The advantages over existing methods refer to the ease of implementation, low cost, and energy consumption, without the need to confront membrane fouling problems and complex electrode material fabrication employed in CDI.

Fast increase of nanofluidic slip in supercooled water: the key role of dynamics

Nanofluidics is an emerging field offering innovative solutions for energy harvesting and desalination. The efficiency of these applications depends strongly on liquid-solid slip, arising from a favorable ratio between viscosity and interfacial friction. Using molecular dynamics simulations, we show that wall slip increases strongly when water is cooled below its melting point. For water on graphene, the slip length is multiplied by up to a factor of five and reaches 230 nm at the lowest simulated temperature, T ∼ 225 K; experiments in nanopores can reach much lower temperatures and could reveal even more drastic changes. The predicted fast increase in water slip can also be detected at supercoolings reached experimentally in bulk water, as well as in droplets flowing on anti-icing surfaces. We explain the anomalous slip behavior in the supercooled regime by a decoupling between viscosity and bulk density relaxation dynamics, and we rationalize the wall-type dependence of the enhancement in terms of interfacial density relaxation dynamics. While providing fundamental insights on the molecular mechanisms of hydrodynamic transport in both interfacial and bulk water in the supercooled regime, this study is relevant to the design of anti-icing surfaces, could help explain the subtle phase and dynamical behaviors of supercooled confined water, and paves the way to explore new behaviors in supercooled nanofluidic systems.

Surface Nanostructure-Wettability Coupling Leads to Unique Topological Evolution Dictating Water Transport over Nanometer Scales

Surface nanostructure, either designed or generated as an artifact of the fabrication procedure, is known to influence interfacial phenomena intriguingly. While surface roughness-wettability coupling over nanometer scales has been addressed to some extent, the explicit interplay of hydrodynamics and confinement toward dictating the underlying characteristics for practically relevant material interfaces remains unexplored. Here, we bring out unique roles of surface nanostructures toward altering flow of water in a copper nanochannel, by capturing an exclusive interplay of confinement, roughness, wettability and flow dynamics. Toward this, non-equilibrium molecular dynamics (NEMD) simulations are performed to examine the effect of nanoscale triangular roughness. The width and height of the triangular microgroove are varied along with different driving forces at the channel inlet, and the results are compared with those corresponding to smooth-walled nanochannels. We also unveil the nontrivial characteristics of the interfacial topology as a consequence of spontaneous phase separation at the fluid-solid interface. For a constant driving force, we show that the interface may exhibit concave or convex topology, depending on the nanogroove geometry. Our results provide new vistas on how designed nanoscale roughness structures can be harnessed toward controlling the transport of water in a practically engineered nanosystem, as demanded by the specific application on hand.

The nano-structural inhomogeneity of dynamic hydrogen bond network of TIP4P/2005 water

A method for studying the time dependence of the short-range molecular order of water has been proposed. In the present study, water is considered as a dynamic network between molecules at distances not exceeding 3.2 Å. The instantaneous configurations obtained with the molecular dynamics method have been sequentially analyzed. The mutual orientation of each molecule with its neighboring molecules has been studied and the interaction energy of each pair of neighbor molecules has been calculated. The majority of mutual orientation angles between molecules lie in the interval [0°; 20°]. More than 85% of the molecular pairs in each instantaneous configuration form H-bonds and the H-bond network includes all water molecules in the temperature range 233-293 K. The number of H-bonds fluctuates near the mean value and increases with decreasing temperature, and the energy of the vast majority of such bonds is much higher than the thermal energy. The interaction energy of 80% of the H-bonding molecular pairs lies in the interval [-7; -4] kcal/mol. The interaction energy of pairs that do not satisfy the H-bond angle criterion lies in the interval [-5; 4] kcal/mol; the number of such bonds does not exceed 15% and decreases with decreasing temperature. For the first time it has been found that in each instantaneous configuration the H-bond network contains built-in nanometric structural heterogeneities formed by shorter H-bonds. The fraction of molecules involved in the structural heterogeneities increases from 40% to 60% with a temperature decrease from 293 K to 233 K. Each heterogeneity has a finite lifetime and changeable structure, but they are constantly present during the entire simulation time.

Molecular dynamics simulations of nano-confined methanol and methanol-water mixtures between infinite graphite plates: Structure and dynamics

Molecular dynamics simulations are used to investigate microscopic structures and dynamics of methanol and methanol-water binary mixture films confined between hydrophobic infinite parallel graphite plate slits with widths, H, in the range of 7-20 Å at 300 K. The initial geometric densities of the liquids were chosen to be the same as bulk methanol at the same temperature. For the two narrowest slit widths, two smaller initial densities were also considered. For the nano-confined system with H = 7 Å and high pressure, a solid-like hexagonal arrangement of methanol molecules arranged perpendicular to the plates is observed which reflects the closest packing of the molecules and partially mirrors the structure of the underlying graphite structure. At lower pressures and for larger slit widths, in the contact layer, the methanol molecules prefer having the C-O bond oriented parallel to the walls. Layered structures of methanol parallel to the wall were observed, with contact layers and additional numbers of central layers depending on the particular slit width. For methanol-water mixtures, simulations of solutions with different composition were performed between infinite graphite slits with H = 10 and 20 Å at 300 K. For the nanoslit with H = 10 Å, in the solution mixtures, three layers of molecules form, but for all mole fractions of methanol, methanol molecules are excluded from the central fluid layer. In the nanopore with H = 20 Å, more than three fluid layers are formed and methanol concentrations are enhanced near the confining plates walls compared to the average solution stoichiometry. The self-diffusion coefficients of methanol and water molecules in the solution show strong dependence on the solution concentration. The solution mole fractions with minimal diffusivity are the same in confined and non-confined bulk methanol-water mixtures.

VP, Sathian SP. Water flow in carbon nanotubes: the role of tube chirality

Flow rate of water in CNTs of different types.

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 flow in carbon nanotubes: The effect of tube flexibility and thermostat

Although the importance of temperature control in nonequilibrium molecular dynamics simulations is widely accepted, the consequences of the thermostatting approach in the case of strongly confined fluids are underappreciated. We show the strong influence of the thermostatting method on the water transport in carbon nanotubes (CNTs) by considering simulations in which the system temperature is controlled via the walls or via the fluid. Streaming velocities and mass flow rates are found to depend on the tube flexibility and on the thermostatting algorithm, with flow rates up to 20% larger when the walls are flexible. The larger flow rates in flexible CNTs are explained by a lower friction coefficient between water and the wall. Despite the lower friction, a larger solid-fluid interaction energy is found for flexible CNTs than for rigid ones. Furthermore, a comparison of thermostat schemes has shown that the Berendsen and Nosé-Hoover thermostats result in very similar transport rates, while lower flow rates are found under the influence of the Langevin thermostat. These findings illustrate the significant influence of the thermostatting methods on the simulated confined fluid transport.

Thermodynamics at Solid-Liquid Interfaces

The variation of the liquid properties in the vicinity of a solid surface complicates the description of heat transfer along solid-liquid interfaces. Using Molecular Dynamics simulations, this investigation aims to understand how the material properties, particularly the strength of the solid-liquid interaction, affect the thermal conductivity of the liquid at the interface. The molecular model consists of liquid argon confined by two parallel, smooth, solid walls, separated by a distance of 6.58 σ. We find that the component of the thermal conductivity parallel to the surface increases with the affinity of the solid and liquid.

Simulation of protein diffusion: a sensitive probe of protein-solvent interactions

Aqueous solutions of Candida antarctica lipase B (CALB) were simulated considering three different water models (SPC/E, TIP3P, TIP4P) by a series of molecular dynamics (MD) simulations of three different box sizes (L = 9, 14, and 19 nm) to determine the diffusion coefficient, the water viscosity and the protein density. The protein-water systems were equilibrated for 500 ns, followed by 100 ns production runs which were analysed. The diffusional properties of CALB were characterized by the Stokes radius (R_S), which was derived from the diffusion coefficient and the viscosity. R_S was compared to the geometric radius (R_G) of CALB, which was derived from the protein density. R_S and R_G differed by 0.27 nm for SPC/E and by 0.40 and 0.39 nm for TIP3P and TIP4P, respectively, which characterizes the thickness of the diffusive hydration layer on the protein surface. The simulated hydration layer of CALB resulted in agreement with those experimentally determined for other seven different proteins of comparable size. By avoiding the most common pitfalls, protein diffusion can be reliably simulated: simulating different box sizes to account for the finite size effect, equilibrating the protein-water system sufficiently, and using the complete production run for the determination of the diffusion coefficient.

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

Water desalination using graphene nanopores was studied using different water models. The water permeation was found to be influenced by the bulk transport properties and the hydrogen-bond dynamics of the simulated water.

What Controls Thermo-osmosis? Molecular Simulations Show the Critical Role of Interfacial Hydrodynamics

Thermo-osmotic and related thermophoretic phenomena can be found in many situations from biology to colloid science, but the underlying molecular mechanisms remain largely unexplored. Using molecular dynamics simulations, we measure the thermo-osmosis coefficient by both mechanocaloric and thermo-osmotic routes, for different solid-liquid interfacial energies. The simulations reveal, in particular, the crucial role of nanoscale interfacial hydrodynamics. For nonwetting surfaces, thermo-osmotic transport is largely amplified by hydrodynamic slip at the interface. For wetting surfaces, the position of the hydrodynamic shear plane plays a key role in determining the amplitude and sign of the thermo-osmosis coefficient. Finally, we measure a giant thermo-osmotic response of the water-graphene interface, which we relate to the very low interfacial friction displayed by this system. These results open new perspectives for the design of efficient functional interfaces for, e.g., waste-heat harvesting.

Negative effect of nanoconfinement on water transport across nanotube membranes

Nanoconfinement environments are commonly considered advantageous for ultrafast water flow across nanotube membranes. This study illustrates that nanoconfinement has a negative effect on water transport across nanotube membranes based on molecular dynamics simulations. Although water viscosity and the friction coefficient evidently decrease because of nanoconfinement, water molecular flux and flow velocity across carbon nanotubes decrease sharply with the pore size of nanotubes. The enhancement of water flow across nanotubes induced by the decreased friction coefficient and water viscosity is markedly less prominent than the negative effect induced by the increased flow barrier as the nanotube size decreases. The decrease in water flow velocity with the pore size of nanotubes indicates that nanoconfinement is not essential for the ultrafast flow phenomenon. In addition, the relationship between flow velocity and water viscosity at different temperatures is investigated at different temperatures. The results indicate that flow velocity is inversely proportional to viscosity for nanotubes with a pore diameter above 1 nm, thereby indicating that viscosity is still an effective parameter for describing the effect of temperature on the fluid transport at the nanoscale.

Electro-osmosis at surfactant-laden liquid-gas interfaces: beyond standard models

Electro-osmosis (EO) is a powerful tool to manipulate liquids in micro and nanofluidic systems. While EO has been studied extensively at liquid-solid interfaces, the case of liquid-vapor interfaces, found e.g. in foam films and bubbles, remains to be explored. Here we perform molecular dynamics (MD) simulations of EO in a film of aqueous electrolyte covered with fluid layers of ionic surfactants and surrounded by gas. Following the experimental procedure, we compute the zeta potential from the EO velocity, defined as the velocity difference between the middle of the liquid film and the surrounding gas. We show that the zeta potential can be smaller or larger than existing predictions depending on the surfactant coverage. We explain the failure of previous descriptions by the fact that surfactants and bound ions move as rigid bodies and do not transmit the electric driving force to the liquid locally. Considering the reciprocal streaming current effect, we then develop an extended model, which can be used to predict the experimental zeta potential of surfactant-laden liquid-gas interfaces.

On the hydrogen-bond network and the non-Arrhenius transport properties of water

We study the structural and dynamic transformations of SPC/E water with temperature, through molecular dynamics (MD), and discuss the non-Arrhenius behavior of the transport properties and orientational dynamics, and the magnitude of the breakdown of the Stokes-Einstein (SE) and the Stokes-Einstein-Debye (SED) relations, in the light of these transformations. Our results show that deviations from Arrhenius behavior of the self-diffusion at low temperatures cannot be exclusively explained by the reduction of water defects (interstitial waters) and the increase of the local tetrahedrality, thus, suggesting the importance of the slowdown of collective rearrangements. Interestingly we find that at high temperatures (T  ⩾  340 K) water defects lead to a slight increase of the tetrahedrality and a decrease of the self-diffusion, opposite to water at low temperatures. The relative magnitude of the breakdown of the SE and the SED relations is found to be in accord with recent experiments (Dehaoui et al 2015 Proc. Natl Acad. Sci. USA 112 12020) resolving the discrepancy with previous MD results. Further, we show that SPC/E hydrogen-bond (HB) lifetimes deviate from Arrhenious behaviour at low temperatures in contrast with some previous MD studies. This deviation is nevertheless much smaller than that observed for the orientational dynamics and the transport properties of water, consistent with the relaxation times measured by several experimental methods. The HB acceptor exchange dynamics defined here by the acceptor switch and reform (librational dynamics) frequencies exhibit similar Arrhenius deviations, thus explaining to some extent the non-Arrhenius behavior of the transport properties and of the orientational dynamics of water. Our results also show that the fraction of HB switches through a bifurcated pathway follow a power law with the temperature decrease. Thus, at low temperatures HB acceptor switches are less frequent but occur on a faster time scale consistent with the temperature dependence of the ratio of the rotational relaxation times for the different Legendre polynomial ranks.

Decoupling of viscosity and relaxation processes in supercooled water: a molecular dynamics study with the TIP4P/2005f model

We show that the TIP4P/2005f water model describes accurately the experimental viscosity and self-diffusion over a large temperature range. We then show the decoupling of viscosity and structural relaxation time in supercooled water.

A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and time

A new 3D implementation of a hybrid model based on the analogy with two-phase hydrodynamics has been developed for the simulation of liquids at microscale. The idea of the method is to smoothly combine the atomistic description in the molecular dynamics zone with the Landau-Lifshitz fluctuating hydrodynamics representation in the rest of the system in the framework of macroscopic conservation laws through the use of a single "zoom-in" user-defined function s that has the meaning of a partial concentration in the two-phase analogy model. In comparison with our previous works, the implementation has been extended to full 3D simulations for a range of atomistic models in GROMACS from argon to water in equilibrium conditions with a constant or a spatially variable function s. Preliminary results of simulating the diffusion of a small peptide in water are also reported.

Ion-specific adsorption and electroosmosis in charged amorphous porous silica

Aqueous electrolyte solutions (NaCl, KCl, CsCl, and SrCl₂) confined in a negatively charged amorphous silica slit pore.

COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids

We describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in both its protonated and neutral forms; nonbonded potential functions were derived from 1 μs MD simulations of every possible pairing of the amino acids (231 different systems). The angle and dihedral probability distributions and radial distribution functions sampled during MD were used to optimize a set of CG potential functions through use of the iterative Boltzmann inversion (IBI) method. The optimized set of potential functions—which we term COFFDROP (COarse-grained Force Field for Dynamic Representation Of Proteins)—quantitatively reproduced all of the “target” MD distributions. In a first test of the force field, it was used to predict the clustering behavior of concentrated amino acid solutions; the predictions were directly compared with the results of corresponding all-atom explicit-solvent MD simulations and found to be in excellent agreement. In a second test, BD simulations of the small protein villin headpiece were carried out at concentrations that have recently been studied in all-atom explicit-solvent MD simulations by Petrov and Zagrovic (PLoS Comput. Biol.2014, 5, e1003638). The anomalously strong intermolecular interactions seen in the MD study were reproduced in the COFFDROP simulations; a simple scaling of COFFDROP’s nonbonded parameters, however, produced results in better accordance with experiment. Overall, our results suggest that potential functions derived from simulations of pairwise amino acid interactions might be of quite broad applicability, with COFFDROP likely to be especially useful for modeling unfolded or intrinsically disordered proteins.