Computational investigation of surface freezing in a molecular model of water

Multitwinned Ice Nanocrystals

Multitwinned nanocrystals are commonly found in substances that preferentially adopt tetrahedral local arrangements, but not yet in water crystals. Ice nanocrystals are pivotal in cloud microphysics, and their surfaces become increasingly prominent in determining structure as crystal size decreases. Nevertheless, discussions on nanocrystal structures have predominantly centered on ice polymorphs observed in bulk: hexagonal (Ih), cubic (Ic), and stacking-disordered (Isd) ices. Here, we demonstrate, through molecular dynamics (MD) simulations, that decahedral and icosahedral nanocrystals form from liquid water droplets of a few nanometers in size without violating the ice rule. The brute force spontaneous crystallization is conducted using the mW model, and the thermodynamic stability is examined using the TIP4P/Ice model. During the crystallization process, the formation of twin boundaries precedes the emergence of centers exhibiting 5-fold and icosahedral symmetry. The free energy calculation suggests the icosahedron has comparable stability with ice Ih nanocrystal. The frequent occurrence of these unreported ice nanocrystals aligns with the fact that natural polycrystalline snow crystals predominantly display a 70.5-degree angle between the Ih c-axes of adjacent branches. Moreover, we show that the formation of multitwinned ice nanocrystals is enhanced within a fullerene, providing a potential avenue for experimental observations.

Surface-induced water crystallisation driven by precursors formed in negative pressure regions

Ice nucleation is a crucial process in nature and industries; however, the role of the free surface of water in this process remains unclear. To address this, we investigate the microscopic freezing process using brute-force molecular dynamics simulations. We discover that the free surface assists ice nucleation through an unexpected mechanism. The surface-induced negative pressure enhances the formation of local structures with a ring topology characteristic of Ice 0-like symmetry, promoting ice nucleation despite the symmetry differing from ordinary ice crystals. Unlike substrate-induced nucleation via water-solid interactions that occurs directly on the surface, this negative-pressure-induced mechanism promotes ice nucleation slightly inward the surface. Our findings provide a molecular-level understanding of the mechanism and pathway behind free-surface-induced ice formation, resolving the longstanding debate. The implications of our discoveries are of substantial importance in areas such as cloud formation, food technology, and other fields where ice nucleation plays a pivotal role.

Estimating Position-Dependent and Anisotropic Diffusivity Tensors from Molecular Dynamics Trajectories: Existing Methods and Future Outlook

Confinement can substantially alter the physicochemical properties of materials by breaking translational isotropy and rendering all physical properties position-dependent. Molecular dynamics (MD) simulations have proven instrumental in characterizing such spatial heterogeneities and probing the impact of confinement on materials' properties. For static properties, this is a straightforward task and can be achieved via simple spatial binning. Such an approach, however, cannot be readily applied to transport coefficients due to lack of natural extensions of autocorrelations used for their calculation in the bulk. The prime example of this challenge is diffusivity, which, in the bulk, can be readily estimated from the particles' mobility statistics, which satisfy the Fokker-Planck equation. Under confinement, however, such statistics will follow the Smoluchowski equation, which lacks a closed-form analytical solution. This brief review explores the rich history of estimating profiles of the diffusivity tensor from MD simulations and discusses various approximate methods and algorithms developed for this purpose. Besides discussing heuristic extensions of bulk methods, we overview more rigorous algorithms, including kernel-based methods, Bayesian approaches, and operator discretization techniques. Additionally, we outline methods based on applying biasing potentials or imposing constraints on tracer particles. Finally, we discuss approaches that estimate diffusivity from mean first passage time or committor probability profiles, a conceptual framework originally developed in the context of collective variable spaces describing rare events in computational chemistry and biology. In summary, this paper offers a concise survey of diverse approaches for estimating diffusivity from MD trajectories, highlighting challenges and opportunities in this area.

The limit of macroscopic homogeneous ice nucleation at the nanoscale

Nucleation in small volumes of water has garnered renewed interest due to the relevance of pore condensation and freezing under conditions of low partial pressures of water, such as in the upper troposphere. Molecular simulations can in principle provide insight on this process at the molecular scale that is challenging to achieve experimentally. However, there are discrepancies in the literature as to whether the rate in confined systems is enhanced or suppressed relative to bulk water at the same temperature and pressure. In this study, we investigate the extent to which the size of the critical nucleus and the rate at which it grows in thin films of water are affected by the thickness of the film. Our results suggest that nucleation remains bulk-like in films that are barely large enough accommodate a critical nucleus. This conclusion seems robust to the presence of physical confining boundaries. We also discuss the difficulties in unambiguously determining homogeneous nucleation rates in nanoscale systems, owing to the challenges in defining the volume. Our results suggest any impact on a film's thickness on the rate is largely inconsequential for present day experiments.

Ice-Water Equilibrium in Nanoscale Confinement

We show that 2D ^{2}H NMR spectra enable valuable insights into the nature of an ice-water equilibrium in nanoscale confinement, which extends over a broad temperature range. In particular, 2D ^{2}H NMR line-shape analysis allows us to determine the timescale on which the coexisting ice and water phases exchange molecules. For D_{2}O in a silica nanopore with a diameter of 5.4 nm, we find that the residence time of a water molecule in either phase is characterized by an NMR exchange time of τ_{X}=5.7  ms at 220 K. Thus, the ice-water equilibrium is highly dynamic, which is an important aspect for an understanding of deeply cooled confined and, possibly, bulk waters.

Robust Estimation of Position-Dependent Anisotropic Diffusivity Tensors from Molecular Dynamics Trajectories

Confinement breaks translational and rotational symmetry in materials and makes all physical properties functions of position. Such spatial variations are key to modulating material properties at the nanoscale, and characterizing them accurately is therefore an intense area of research in the molecular simulations community. This is relatively easy to accomplish for basic mechanical observables. Determining spatial profiles of transport properties, such as diffusivity, is, however, much more challenging, as it requires calculating position-dependent autocorrelations of mechanical observables. In our previous paper (Domingues, T.S.; Coifman, R.; Haji-Akbari, A. J. Phys. Chem. B 2023, 127, 5273 10.1021/acs.jpcb.3c00670), we analytically derive and numerically validate a set of filtered covariance estimators (FCEs) for quantifying spatial variations of the diffusivity tensor from stochastic trajectories. In this work, we adapt these estimators to extract diffusivity profiles from MD trajectories and validate them by applying them to a Lennard-Jones fluid within a slit pore. We find our MD-adapted estimator to exhibit the same qualitative features as its stochastic counterpart, as it accurately estimates the lateral diffusivity across the pore while systematically underestimating the normal diffusivity close to hard boundaries. We introduce a conceptually simple and numerically efficient correction scheme based on simulated annealing and diffusion maps to resolve the latter artifact and obtain normal diffusivity profiles that are consistent with the self-part of the van Hove correlation functions. Our findings demonstrate the potential of this MD-adapted estimator in accurately characterizing spatial variations of diffusivity in confined materials.

Anomalous Vapor and Ice Nucleation in Water at Negative Pressures: A Classical Density Functional Theory Study

In contrast to the abundance of work on the anomalous behavior of water, the relationship between the water's thermodynamic anomalies and kinetics of phase transition from metastable water is relatively unexplored. In this work, we have employed classical density functional theory to provide a unified and coherent picture of nucleation (both vapor and ice) from metastable water at negative pressure conditions. Our results suggest a peculiar nonmonotonic temperature dependence of vapor-liquid surface tension at temperatures where vapor-liquid coexistence is metastable with respect to the ice phase. The vapor nucleation barrier on isochoric cooling also shows a nonmonotonic temperature dependence. We further report that, for low density isochores, the temperature of the minimum vapor nucleation barrier (TΔΩv/min*) does not coincide with the temperature of maximum density (TMD) where metastability is maximum. The difference between the TΔΩv/min* and the TMD, however, decreases with increasing the density of the isochore. The vapor nucleation barrier along isobars shows an interesting crossover behavior in the vicinity of the Widom line on lowering the temperature. Our results on the ice nucleation suggest an anomalous retracing behavior of the nucleation barrier along isotherms at negative pressures and theoretically validate the recent findings that the reentrant ice(Ih)-liquid coexistence line can induce a drastic change in the kinetics of ice nucleation. Thus, this study establishes a direct connection between the metastable water's thermodynamic anomalies and the (vapor and ice) nucleation kinetics. In addition, this study provides deeper insights into the origin of the isothermal compressibility maximum on isochoric cooling.

Minimum in the pressure dependence of the interfacial free energy between ice Ih and water

Despite the importance of ice nucleation, this process has been barely explored at negative pressures. Here, we study homogeneous ice nucleation in stretched water by means of molecular dynamics seeding simulations using the TIP4P/Ice model. We observe that the critical nucleus size, interfacial free energy, free energy barrier, and nucleation rate barely change between isobars from -2600 to 500 bars when they are represented as a function of supercooling. This allows us to identify universal empirical expressions for homogeneous ice nucleation in the pressure range from -2600 to 500 bars. We show that this universal behavior arises from the pressure dependence of the interfacial free energy, which we compute by means of the mold integration technique, finding a shallow minimum around -2000 bars. Likewise, we show that the change in the interfacial free energy with pressure is proportional to the excess entropy and the slope of the melting line, exhibiting in the latter a reentrant behavior also at the same negative pressure. Finally, we estimate the excess internal energy and the excess entropy of the ice Ih-water interface.

High-density liquid (HDL) adsorption at the supercooled water/vapor interface and its possible relation to the second surface tension inflection point

We investigate the properties of water along the liquid/vapor coexistence line in the supercooled regime down to the no-man's land. Extensive molecular dynamics simulations of the TIP4P/2005 liquid/vapor interface in the range 198-348 K allow us to locate the second surface tension inflection point with a high accuracy at 283 ± 5 K, close to the temperature of maximum density. This temperature also coincides with the appearance of a density anomaly at the interface known as the apophysis. We relate the emergence of the apophysis to the observation of high-density liquid (HDL) water adsorption in the proximity of the liquid/vapor interface.

Does twist angle affect the properties of water confined inside twisted bilayer graphene?

Graphene nanoslit pores are used for nanofluidic devices, such as, in water desalination, ion-selective channels, ionic transistors, sensing, molecular sieving, blue energy harvesting, and protein sequencing. It is a strenuous task to prepare nanofluidic devices, because a small misalignment leads to a significant alteration in various properties of the devices. Here, we focus on the rotational misalignment between two parallel graphene sheets. Using molecular dynamics simulation, we probe the structure and dynamics of monolayer water confined inside graphene nanochannels for a range of commensurate twist angles. With SPC/E and TIP4P/2005 water models, our simulations reveal the independence of the equilibrium number density- n ∼ 13 nm^-2 for SPC/E and n ∼ 11.5 nm^-2 for TIP4P/2005- across twists. Based on the respective densities of the water models, the structure and dielectric constant are invariant of twist angles. The confined water structure at this density shows square ice ordering for SPC/E water only. TIP4P/2005 shows ordering at the vicinity of a critical density (n ∼ 12.5 nm^-2). The average perpendicular dielectric constant of the confined water remains anomalously low (∼2 for SPC/E and ∼6 for TIP4P/2005) for the studied twist angles. We find that the friction coefficient of confined water molecules varies for small twist angles, while becoming independent for twists greater than 5.1°. Our results indicate that a small, angular misalignment will not impair the dielectric properties of monolayer water within a graphene slit-pore, but can significantly influence its dynamics.

Ideal Conductor Model: An Analytical Finite-Size Correction for Nonequilibrium Molecular Dynamics Simulations of Ion Transport through Nanoporous Membranes

Modulating ion transport through nanoporous membranes is critical to many important chemical and biological separation processes. The corresponding transport timescales, however, are often too long to capture accurately using conventional molecular dynamics (MD). Recently, path sampling techniques, such as forward-flux sampling (FFS), have emerged as attractive alternatives for efficiently and accurately estimating arbitrarily long ionic passage times. Here, we use non-equilibrium MD and FFS to explore how the kinetics and mechanisms of pressure-driven chloride transport through a nanoporous graphitic membrane are affected by its lateral dimensions. We not only find ionic passage times and free energy barriers to decrease dramatically upon increasing the membrane surface area but also observe an abrupt and discontinuous change in the locus of the transition state. These strong finite size effects arise due to the cumulative effect of the periodic images of the leading ion entering the pore on the distribution of the induced excess charge at the membrane surface in the feed. By assuming that the feed is an ideal conductor, we analytically derive a finite size correction term that can be computed from the information obtained from a single simulation and successfully use it to obtain corrected free energy profiles with no dependence on the system size. We then estimate ionic passage times in the thermodynamic limit by assuming an Eyring-type dependence of rates on barriers with a size-independent prefactor. This approach constitutes a universal framework for removing finite size artifacts in molecular simulations of ion transport through nanoporous membranes and biological channel proteins.

Anisotropic Molecular Organization at a Liquid/Vapor Interface Promotes Crystal Nucleation with Polymorph Selection

The molecules at the surface of a liquid have different organization and dynamics from those in the bulk, potentially altering the rate of crystal nucleation and polymorphic selection, but this effect remains poorly understood. Here we demonstrate that nucleation at the surface of a pure liquid, d-arabitol, is vastly enhanced, by 12 orders of magnitude, and selects a different polymorph. The surface effect intensifies with cooling and can be inhibited by a dilute, surface-active second component. This phenomenon arises from the anisotropic molecular packing at the interface and its similarity to the surface-nucleating polymorph. Our finding is relevant for controlling the crystallization and polymorphism in any system with a significant interface such as nanodroplets and atmospheric water.

Can molecular simulations reliably compare homogeneous and heterogeneous ice nucleation?

In principle, the answer to the posed titular question is undoubtedly "yes." But in practice, requisite reference data for homogeneous systems have been obtained with a treatment of intermolecular interactions that is different from that typically employed for heterogeneous systems. In this article, we assess the impact of the choice of truncation scheme when comparing water in homogeneous and inhomogeneous environments. Specifically, we use explicit free energy calculations and a simple mean field analysis to demonstrate that using the "cut-and-shift" version of the Lennard-Jones potential (common to most simple point charge models of water) results in a systematic increase in the melting temperature of ice I_h. In addition, by drawing an analogy between a change in cutoff and a change in pressure, we use existing literature data for homogeneous ice nucleation at negative pressures to suggest that enhancements due to heterogeneous nucleation may have been overestimated by several orders of magnitude.

How do interfaces alter the dynamics of supercooled water?

The structure of liquid water in the proximity of an interface can deviate significantly from that of bulk water, with surface-induced structural perturbations typically converging to bulk values at about ∼1 nm from the interface. While these structural changes are well established it is, in contrast, less clear how an interface perturbs the dynamics of water molecules within the liquid. Here, through an extensive set of molecular dynamics simulations of supercooled bulk and interfacial water films and nano-droplets, we observe the formation of persistent, spatially extended dynamical domains in which the average mobility varies as a function of the distance from the interface. This is in stark contrast with the dynamical heterogeneity observed in bulk water, where these domains average out spatially over time. We also find that the dynamical response of water to an interface depends critically on the nature of the interface and on the choice of interface definition. Overall these results reveal a richness in the dynamics of interfacial water that opens up the prospect of tuning the dynamical response of water through specific modifications of the interface structure or confining material.

Low Density Interior in Supercooled Aqueous Nanodroplets Expels Ions to the Subsurface

The interaction between water and ions within droplets plays a key role in the chemical reactivity of atmospheric and man-made aerosols. Here we report direct computational evidence that in supercooled aqueous nanodroplets a lower density core of tetrahedrally coordinated water expels the cosmotropic ions to the denser and more disordered subsurface. In contrast, at room temperature, depending on the nature of the ion, the radial distribution in the droplet core is nearly uniform or elevated toward the center. We analyze the spatial distribution of a single ion in terms of a reference electrostatic model. The energy of the system in the analytical model is expressed as the sum of the electrostatic and surface energy of a deformable droplet. The model predicts that the ion is subject to a harmonic potential centered at the droplet's center of mass. We name this effect "electrostatic confinement". The model's predictions are consistent with the simulation findings for a single ion at room temperature but not at supercooling. We anticipate this study to be the starting point for investigating the structure of supercooled (electro)sprayed droplets that are used to preserve the conformations of macromolecules originating from the bulk solution.

Molecular dynamics study of wetting of alkanes on water: from high temperature to the supercooled region and the influence of second inflection points of interfacial tensions

To explore the wetting behavior of alkanes on bulk water interfaces, molecular dynamics (MD) simulations were carried out for united-atom PYS alkane models, and for SPC/E and TIP4P/2005 water models over a wide temperature range. The MD results at each temperature were used to find (1) the surface tension of the alkanes (octane, nonane) and water, and (2) the interfacial tensions of the alkane-water systems. These quantities were then used to calculate the spreading coefficient (S) and contact angle (θc) for each alkane on water. At higher temperatures, the contact angle of octane and nonane on water is found to behave in accord with conventional expectations, i.e., it decreases with increasing temperature for both water models as each system approaches the usual high-temperature transition to perfect wetting. At lower temperatures, we found an unusual temperature dependence of S and θc for each PYS alkane on SPC/E water. In contrast to conventional expectations, θc decreases with a decrease in the temperature. For octane-SPC/E water, this unusual behavior of θc occurs due to the presence of second inflection points (SIP) in the vapor-water and the octane-water interfacial tensions, whereas the SIP effect is much less important for the nonane-water system. The unusual temperature dependence of θc observed for nonane on SPC/E water is also found for nonane on TIP4P/2005 water. On the other hand, such unusual wetting behavior has not been observed in the PYS octane-TIP4P/2005 water system, except possibly for the two lowest temperatures studied.

Is Ice Nucleation by Organic Crystals Nonclassical? An Assessment of the Monolayer Hypothesis of Ice Nucleation

Potent ice nucleating organic crystals display an increase in nucleation efficiency with pressure and memory effect after pressurization that set them apart from inorganic nucleants. These characteristics were proposed to arise from an ordered water monolayer at the organic-water interface. It was interpreted that ordering of the monolayer is the limiting step for ice nucleation on organic crystals, rendering their mechanism of nucleation nonclassical. Despite the importance of organics in atmospheric ice nucleation, that explanation has never been investigated. Here we elucidate the structure of interfacial water and its role in ice nucleation at ambient pressure on phloroglucinol dihydrate, the paradigmatic example of outstanding ice nucleating organic crystal, using molecular simulations. The simulations confirm the existence of an interfacial monolayer that orders on cooling and becomes fully ordered upon ice formation. The monolayer does not resemble any ice face but seamlessly connects the distinct hydrogen-bonding orders of ice and the organic surface. Although large ordered patches develop in the monolayer before ice nucleates, we find that the critical step is the formation of the ice crystallite, indicating that the mechanism is classical. We predict that the fully ordered, crystalline monolayer nucleates ice above -2 °C and could be responsible for the exceptional ice nucleation by the organic crystal at high pressures. The lifetime of the fully ordered monolayer around 0 °C, however, is too short to account for the memory effect reported in the experiments. The latter could arise from an increase in the melting temperature of ice confined by strongly ice-binding surfaces.

Role of Nanoscale Interfacial Proximity in Contact Freezing in Water

Contact freezing is a mode of atmospheric ice nucleation in which a collision between a dry ice nucleating particle (INP) and a water droplet results in considerably faster heterogeneous nucleation. The molecular mechanism of such an enhancement is, however, still a mystery. While earlier studies had attributed it to collision-induced transient perturbations, recent experiments point to the pivotal role of nanoscale proximity of the INP and the free interface. By simulating the heterogeneous nucleation of ice within INP-supported nanofilms of two model water-like tetrahedral liquids, we demonstrate that such nanoscale proximity is sufficient for inducing rate increases commensurate with those observed in contact freezing experiments, but only if the free interface has a tendency to enhance homogeneous nucleation. Water is suspected of possessing this latter property, known as surface freezing propensity. Our findings therefore establish a connection between the surface freezing propensity and kinetic enhancement during contact nucleation. We also observe that faster nucleation proceeds through a mechanism markedly distinct from classical heterogeneous nucleation, involving the formation of hourglass-shaped crystalline nuclei that conceive at either interface and that have a lower free energy of formation due to the nanoscale proximity of the interfaces and the modulation of the free interfacial structure by the INP. In addition to providing valuable insights into the physics of contact nucleation, our findings can assist in improving the accuracy of heterogeneous nucleation rate measurements in experiments and in advancing our understanding of ice nucleation on nonuniform surfaces such as organic, polymeric, and biological materials.

A Reactive Force Field with Coarse-Grained Electrons for Liquid Water

Nonreactive force fields are defined by perturbations of electron density that are relatively small, whereas chemical reactivity involves wholesale electronic rearrangements that make and break bonds. Thus, reactive force fields are incredibly difficult to develop compared to nonreactive force fields, yet at the same time, they fill a critical need when ab initio molecular dynamics methods are not affordable. We introduce a new reactive force field model for water that combines modified nonbonded terms of the ReaxFF model and its embedding in the electrostatic interactions described by our recently introduced coarse-grained electron model (C-GeM). The ReaxFF/C-GeM force field is characterized for many energetic and dissociative water properties for water clusters, structure, and dynamical properties under ambient conditions in the condensed phase, as well as the temperature dependence of density and water diffusion, with very good agreement with experiment. The ReaxFF/C-GeM force field should be more transferable and more broadly applicable to a range of reactive systems involving both proton and electron transfer in the condensed phase.

Replica exchange dissipative particle dynamics method on threadlike micellar aqueous solutions

The self-assembly of surfactant molecules can spontaneously result in a variety of micelle morphologies, such as spherical micelles, threadlike micelles, and vesicles, and it is therefore crucial to predict and control the self-assembly to achieve a helpful process in the fields of materials chemistry and engineering. A dissipative particle dynamics (DPD) method used in a coarse-grained molecular simulation is applied to simulate various self-assembling soft matter systems because it can handle greater length and time scales than a typical molecular dynamics simulation (MD). It should be noted that the thorough sampling of a system is not assured at low temperatures because of large complex systems with coarse-grained representations. In this article, we demonstrate that the replica exchange method (REM) is very effective for even a DPD in which the energy barrier is comparatively lower than that of a MD. A replica exchange on DPD (REDPD) simulation for threadlike micellar aqueous solutions was conducted, and the values of the potential energy and the mean aggregation number were compared. As a result, the correct values and a self-assembled structure within a low-temperature range can only be obtained through the REDPD.

Premelting of ice adsorbed on a rock surface

Considering ice-premelting on a quartz rock surface (i.e. silica) we calculate the Lifshitz excess pressures in a four layer system with rock–ice–water–air.

Entropic colloidal crystallization pathways via fluid-fluid transitions and multidimensional prenucleation motifs

Complex crystallization pathways are common in protein crystallization, tetrahedrally coordinated systems, and biomineralization, where single or multiple precursors temporarily appear before the formation of the crystal. The emergence of precursors is often explained by a unique property of the system, such as short-range attraction, directional bonding, or ion association. But, structural characteristics of the prenucleation phases found in multistep crystallization remain unclear, and models are needed for testing and expanding the understanding of fluid-to-solid ordering pathways. Here, we report 3 instances of 2-step crystallization of hard-particle fluids. Crystallization in these systems proceeds via a high-density precursor fluid phase with prenucleation motifs in the form of clusters, fibers and layers, and networks, respectively. The density and diffusivity change across the fluid-fluid phase transition increases with motif dimension. We observe crystal nucleation to be catalyzed by the interface between the 2 fluid phases. The crystals that form are complex, including, notably, a crystal with 432 particles in the cubic unit cell. Our results establish the existence of complex crystallization pathways in entropic systems and reveal prenucleation motifs of various dimensions.

Anomalous Stability of Two-Dimensional Ice Confined in Hydrophobic Nanopores

The freezing of water mostly proceeds via heterogeneous ice nucleation, a process in which an effective nucleation medium not only expedites ice crystallization but also may effectively direct the polymorph selection of ice. Here, we show that water confined within a hydrophobic slit nanopore exhibits a freezing behavior strongly distinguished from its bulk counterpart. Such a difference is reflected by a strong, non-monotonic pore-size dependence of freezing temperature but, more surprisingly, by an unexpected stacking ordering of crystallized two-dimensional ice containing just a few ice layers. In particular, confined trilayer ice is found to exclusively crystallize into a well-ordered, hexagonal stacking sequence despite the fact that nanopore exerts no explicit constraint on stacking order. The absence of cubic stacking sequence is found to be originated from the intrinsically lower thermodynamic stability of cubic ice over hexagonal ice at the interface, which contrasts sharply the nearly degenerated stability of bulk hexagonal and cubic ices. Detailed examination clearly reveals that the divergence is attributed to the inherent difference between the two ice polymorphs in their surface phonon modes, which is further found to generically occur at both hydrophobic and hydrophilic surfaces.

Water flow modeling through a graphene-based nanochannel: theory and simulation

Understanding the behavior of water molecule transport through artificial nano-channels is essential in designing novel nanofluidic devices that could be used especially in nanofiltration processes. In this study, using nonequilibrium molecular dynamics (MD) simulations, we simulated the water flow through different graphene-based channels to investigate the influences of some key factors such as the channel thickness and applied pressure on the water flow. It was demonstrated that the water flow was enhanced by increasing the applied pressure and channel thickness. Our results indicated that a third order polynomial curve could describe the variation of the water flow as a function of the channel thickness and the applied pressure. In addition, we improved the hydrodynamics equation used to consider the water flow through nano-channels, by adding two terms to describe the slip effect and the entrance/exit effect, in which the first term increased the water flow rate, while the second term reduced it. This study may be helpful in designing high-performance graphene-based membranes with some practical applications such as desalination.

Thermodynamically driven assemblies and liquid-liquid phase separations in biology

The sustenance of life depends on the high degree of organization that prevails through different levels of living organisms, from subcellular structures such as biomolecular complexes and organelles to tissues and organs. The physical origin of such organization is not fully understood, and even though it is clear that cells and organisms cannot maintain their integrity without consuming energy, there is growing evidence that individual assembly processes can be thermodynamically driven and occur spontaneously due to changes in thermodynamic variables such as intermolecular interactions and concentration. Understanding the phase separation in vivo requires a multidisciplinary approach, integrating the theory and physics of phase separation with experimental and computational techniques. This paper aims at providing a brief overview of the physics of phase separation and its biological implications, with a particular focus on the assembly of membraneless organelles. We discuss the underlying physical principles of phase separation from its thermodynamics to its kinetics. We also overview the wide range of methods utilized for experimental verification and characterization of phase separation of membraneless organelles, as well as the utility of molecular simulations rooted in thermodynamics and statistical physics in understanding the governing principles of thermodynamically driven biological self-assembly processes.

Second inflection point of water surface tension in the deeply supercooled regime revealed by entropy anomaly and surface structure using molecular dynamics simulations

The surface tension of supercooled water is of fundamental importance in physical chemistry and materials and atmospheric sciences. Controversy, however, exists over its temperature dependence in the supercooled regime, especially on the existence of the "second inflection point (SIP)". Here, we use molecular dynamics simulations of the SPC/E water model to study the surface tension of water (σw) as a function of temperature down to 198.15 K, and find a minimum point of surface excess entropy per unit area around ∼240-250 K. Additional simulations with the TIP4P/2005 water model also show consistent results. Hence, we predict an SIP of σw roughly in this region, at the boundary where the "no man's land" happens. The increase of surface entropy with decreasing temperature in the region below the inflection point is clearly an anomalous behavior, unknown for simple liquids. Furthermore, we find that σw has a near-linear correlation with the interfacial width, which can be well explained by the capillary wave theory. Deep in the supercooled regime, a compact water layer at the interface is detected in our simulations, which may be a key component that contributes to the deviation of surface tension from the International Association for the Properties of Water and Steam relationship. Our findings may advance the understanding of the origin of the anomalous properties of liquid water in the supercooled regime.

Does Local Structure Bias How a Crystal Nucleus Evolves?

The broad scientific and technological importance of crystallization has led to significant research probing and rationalizing crystal nucleation processes. Previous work has generally neglected the possibility of the molecular-level dynamics of individual crystal nuclei coupling to local structures. However, recent experimental work has conjectured that this can occur. Therefore, to address a deficiency in scientific understanding of crystallization, we have probed the nucleation of prototypical single and multicomponent crystals (specifically, ice and mixed gas hydrates). We establish that local structures can bias the evolution of nascent crystal phases on a nanosecond time scale by, for example, promoting the appearance or disappearance of specific crystal motifs and thus reveal a new facet of crystallization behavior. Moreover, we demonstrate structural biases are likely present during crystallization processes beyond ice and gas hydrate formation. Structurally biased dynamics are a lens for understanding existing computational and experimental results while pointing to future opportunities.

Unravelling the origins of ice nucleation on organic crystals

Organic molecules such as steroids or amino acids form crystals that can facilitate the formation of ice - arguably the most important phase transition on earth. However, the origin of the ice nucleating ability of organic crystals is still largely unknown. Here, we combine experiments and simulations to unravel the microscopic details of ice formation on cholesterol, a prototypical organic crystal widely used in cryopreservation. We find that cholesterol - which is also a substantial component of cell membranes - is an ice nucleating agent more potent than many inorganic substrates, including the mineral feldspar (one of the most active ice nucleating materials in the atmosphere). Scanning electron microscopy measurements reveal a variety of morphological features on the surfaces of cholesterol crystals: this suggests that the topography of the surface is key to the broad range of ice nucleating activity observed (from -4 to -20 °C). In addition, we show via molecular simulations that cholesterol crystals aid the formation of ice nuclei in a unconventional fashion. Rather than providing a template for a flat ice-like contact layer (as found in the case of many inorganic substrates), the flexibility of the cholesterol surface and its low density of hydrophilic functional groups leads to the formation of molecular cages involving both water molecules and terminal hydroxyl groups of the cholesterol surface. These cages are made of 6- and, surprisingly, 5-membered hydrogen bonded rings of water and hydroxyl groups that favour the nucleation of hexagonal as well as cubic ice (a rare occurrence). We argue that the phenomenal ice nucleating activity of steroids such as cholesterol (and potentially of many other organic crystals) is due to (i) the ability of flexible hydrophilic surfaces to form unconventional ice-templating structures and (ii) the different nucleation sites offered by the diverse topography of the crystalline surfaces. These findings clarify how exactly organic crystals promote the formation of ice, thus paving the way toward deeper understanding of ice formation in soft and biological matter - with obvious reverberations on atmospheric science and cryobiology.

Hybrid Monte Carlo with LAMMPS

We describe a strategy for performing canonical and isothermal-isobaric ensemble hybrid Monte Carlo (HMC) simulations with the widely-used Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) molecular dynamics (MD) software package. The overall workflow for the HMC simulations is handled using an external Python driver script, which invokes LAMMPS’ library interface to perform numerically intensive tasks such as MD integration. We document several rigorous consistency checks that have been used to validate our HMC implementation. We also demonstrate that our approach can be readily extended to implement biased HMC sampling schemes for computing free energies. Codes and input files from the documented examples are available on the web.

Phase Diagram of Water Confined by Graphene

The behavior of water confined at the nanoscale plays a fundamental role in biological processes and technological applications, including protein folding, translocation of water across membranes, and filtration and desalination. Remarkably, nanoscale confinement drastically alters the properties of water. Using molecular dynamics simulations, we determine the phase diagram of water confined by graphene sheets in slab geometry, at T = 300 K and for a wide range of pressures. We find that, depending on the confining dimension D and density σ, water can exist in liquid and vapor phases, or crystallize into monolayer and bilayer square ices, as observed in experiments. Interestingly, depending on D and σ, the crystal-liquid transformation can be a first-order phase transition, or smooth, reminiscent of a supercritical liquid-gas transformation. We also focus on the limit of stability of the liquid relative to the vapor and obtain the cavitation pressure perpendicular to the graphene sheets. Perpendicular cavitation pressure varies non-monotonically with increasing D and exhibits a maximum at D ≈ 0.90 nm (equivalent to three water layers). The effect of nanoconfinement on the cavitation pressure can have an impact on water transport in technological and biological systems. Our study emphasizes the rich and apparently unpredictable behavior of nanoconfined water, which is complex even for graphene.

Evaluating the Laplace pressure of water nanodroplets from simulations

We calculate the components of the microscopic pressure tensor as a function of radial distance r from the centre of a spherical water droplet, modelled using the TIP4P/2005 potential. To do so, we modify a coarse-graining method for calculating the microscopic pressure (Ikeshoji et al 2003 Mol. Simul. 29 101) in order to apply it to a rigid molecular model of water. As test cases, we study nanodroplets ranging in size from 776 to 2880 molecules at 220 K. Beneath a surface region comprising approximately two molecular layers, the pressure tensor becomes approximately isotropic and constant with r. We find that the dependence of the pressure on droplet radius is that expected from the Young-Laplace equation, despite the small size of the droplets.

How Cubic Can Ice Be?

Using an X-ray laser, we investigated the crystal structure of ice formed by homogeneous ice nucleation in deeply supercooled water nanodrops (r ≈ 10 nm) at ∼225 K. The nanodrops were formed by condensation of vapor in a supersonic nozzle, and the ice was probed within 100 μs of freezing using femtosecond wide-angle X-ray scattering at the Linac Coherent Light Source free-electron X-ray laser. The X-ray diffraction spectra indicate that this ice has a metastable, predominantly cubic structure; the shape of the first ice diffraction peak suggests stacking-disordered ice with a cubicity value, χ, in the range of 0.78 ± 0.05. The cubicity value determined here is higher than those determined in experiments with micron-sized drops but comparable to those found in molecular dynamics simulations. The high cubicity is most likely caused by the extremely low freezing temperatures and by the rapid freezing, which occurs on a ∼1 μs time scale in single nanodroplets.