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.

Nanocrystal Assemblies: Current Advances and Open Problems.

We explore the potential of nanocrystals (a term used equivalently to nanoparticles) as building blocks for nanomaterials, and the current advances and open challenges for fundamental science developments and applications. Nanocrystal assemblies are inherently multiscale, and the generation of revolutionary material properties requires a precise understanding of the relationship between structure and function, the former being determined by classical effects and the latter often by quantum effects. With an emphasis on theory and computation, we discuss challenges that hamper current assembly strategies and to what extent nanocrystal assemblies represent thermodynamic equilibrium or kinetically trapped metastable states.

Effect of Pressure on the Conformational Landscape of Human γD-Crystallin from Replica Exchange Molecular Dynamics Simulations.

Human γD-crystallin belongs to a crucial family of proteins known as crystallins located in the fiber cells of the human lens. Since crystallins do not undergo any turnover after birth, they need to possess remarkable thermodynamic stability. However, their sporadic misfolding and aggregation, triggered by environmental perturbations or genetic mutations, constitute the molecular basis of cataracts, which is the primary cause of blindness in the globe according to the World Health Organization.

Divergence among Local Structure, Dynamics, and Nucleation Outcome in Heterogeneous Nucleation of Close-Packed Crystals.

Heterogeneous crystal nucleation is the dominant mechanism of crystallization in most systems, yet its underlying physics remains an enigma. While emergent interfacial crystalline order precedes heterogeneous nucleation, its importance in the nucleation mechanism is unclear. Here, we use path sampling simulations of two model systems to demonstrate that crystalline order in its traditional sense is not predictive of the outcome of the heterogeneous nucleation of close-packed crystals.

Ideal conductor/dielectric model (ICDM): A generalized technique to correct for finite-size effects in molecular simulations of hindered ion transport.

Molecular simulations serve as indispensable tools for investigating the kinetics and elucidating the mechanism of hindered ion transport across nanoporous membranes. In particular, recent advancements in advanced sampling techniques have made it possible to access translocation timescales spanning several orders of magnitude. In our prior study [Shoemaker et al.

Correlations in Charged Multipore Systems: Implications for Enhancing Selectivity and Permeability in Nanoporous Membranes.

Nanoporous membranes have emerged as powerful tools for diverse applications, including gas separation and water desalination. Achieving high permeability for desired molecules alongside exceptional rejection of other species presents a significant design challenge. One potential strategy involves optimizing the chemistry and geometry of isolated nanopores to enhance permeability and selectivity while maximizing their density within a membrane.

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.

Robust Estimation of Position-Dependent Anisotropic Diffusivity Tensors from Stochastic Trajectories.

Materials under confinement can possess properties that deviate considerably from their bulk counterparts. Indeed, confinement makes all physical properties position-dependent and possibly anisotropic, and characterizing such spatial variations and directionality has been an intense area of focus in experimental and computational studies of confined matter. While this task is fairly straightforward for simple mechanical observables, it is far more daunting for transport properties such as diffusivity that can only be estimated from autocorrelations of mechanical observables.

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.

How to quantify and avoid finite size effects in computational studies of crystal nucleation: The case of homogeneous crystal nucleation.

Finite size artifacts arise in molecular simulations of nucleation when critical nuclei are too close to their periodic images. A rigorous determination of what constitutes too close is, however, a major challenge. Recently, we devised rigorous heuristics for detecting such artifacts based on our investigation of how system size impacts the rate of heterogeneous ice nucleation [S.

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.

How to quantify and avoid finite size effects in computational studies of crystal nucleation: The case of heterogeneous ice nucleation.

Computational studies of crystal nucleation can be impacted by finite size effects, primarily due to unphysical interactions between crystalline nuclei and their periodic images. It is, however, not always feasible to systematically investigate the sensitivity of nucleation kinetics and mechanism to system size due to large computational costs of nucleation studies. Here, we use jumpy forward flux sampling to accurately compute the rates of heterogeneous ice nucleation in the vicinity of square-shaped model structureless ice nucleating particles (INPs) of different sizes and identify three distinct regimes for the dependence of rate on the INP dimension, L.

Studying rare events using forward-flux sampling: Recent breakthroughs and future outlook.

Rare events are processes that occur upon the emergence of unlikely fluctuations. Unlike what their name suggests, rare events are fairly ubiquitous in nature, as the occurrence of many structural transformations in biology and material sciences is predicated upon crossing large free energy barriers. Probing the kinetics and uncovering the molecular mechanisms of possible barrier crossings in a system is critical to predicting and controlling its structural and functional properties.

Single crystal texture by directed molecular self-assembly along dual axes.

Creating well-defined single-crystal textures in materials requires the biaxial alignment of all grains into desired orientations, which is challenging to achieve in soft materials. Here we report the formation of single crystals with rigorously controlled texture over macroscopic areas (>1 cm) in a soft mesophase of a columnar discotic liquid crystal. We use two modes of directed self-assembly, physical confinement and magnetic fields, to achieve control of the orientations of the columnar axes and the hexagonal lattice along orthogonal directions.

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.

Forward-flux sampling with jumpy order parameters.

Forward-flux sampling (FFS) is a path sampling technique that has gained increased popularity in recent years and has been used to compute rates of rare event phenomena such as crystallization, condensation, hydrophobic evaporation, DNA hybridization, and protein folding. The popularity of FFS is not only due to its ease of implementation but also because it is not very sensitive to the particular choice of an order parameter. The order parameter utilized in conventional FFS, however, still needs to satisfy a stringent smoothness criterion in order to assure sequential crossing of FFS milestones.

Forward flux sampling calculation of homogeneous nucleation rates from aqueous NaCl solutions.

We used molecular dynamics simulations and the path sampling technique known as forward flux sampling to study homogeneous nucleation of NaCl crystals from supersaturated aqueous solutions at 298 K and 1 bar. Nucleation rates were obtained for a range of salt concentrations for the Joung-Cheatham NaCl force field combined with the Extended Simple Point Charge (SPC/E) water model. The calculated nucleation rates are significantly lower than the available experimental measurements.

Perspective: Surface freezing in water: A nexus of experiments and simulations.

Surface freezing is a phenomenon in which crystallization is enhanced at a vapor-liquid interface. In some systems, such as n-alkanes, this enhancement is dramatic and results in the formation of a crystalline layer at the free interface even at temperatures slightly above the equilibrium bulk freezing temperature. There are, however, systems in which the enhancement is purely kinetic and only involves faster nucleation at or near the interface.

Computational investigation of surface freezing in a molecular model of water.

Water freezes in a wide variety of low-temperature environments, from meteors and atmospheric clouds to soil and biological cells. In nature, ice usually nucleates at or near interfaces, because homogenous nucleation in the bulk can only be observed at deep supercoolings. Although the effect of proximal surfaces on freezing has been extensively studied, major gaps in understanding remain regarding freezing near vapor-liquid interfaces, with earlier experimental studies being mostly inconclusive.

Effect of material flexibility on the thermodynamics and kinetics of hydrophobically induced evaporation of water.

The evaporation of water induced by confinement between hydrophobic surfaces has received much attention due to its suggested functional role in numerous biophysical phenomena and its importance as a general mechanism of hydrophobic self-assembly. Although much progress has been made in understanding the basic physics of hydrophobically induced evaporation, a comprehensive understanding of the substrate material features (e.g.

Computational investigation of structure, dynamics and nucleation kinetics of a family of modified Stillinger-Weber model fluids in bulk and free-standing thin films.

In recent years, computer simulations have found increasingly widespread use as powerful tools for studying phase transitions in wide variety of systems. In the particular and very important case of aqueous systems, the commonly used force-fields tend to offer quite different predictions with respect to a wide range of thermodynamic and kinetic properties, including the ease of ice nucleation, the propensity to freeze at a vapor-liquid interface, and the existence of a liquid-liquid phase transition. It is thus of fundamental and practical interest to understand how different features of a given water model affect its thermodynamic and kinetic properties.

Thermodynamic and kinetic anisotropies in octane thin films.

Confinement breaks the translational symmetry of materials, making all thermodynamic and kinetic quantities functions of position. Such symmetry breaking can be used to obtain configurations that are not otherwise accessible in the bulk. Here, we use computer simulations to explore the effect of substrate-liquid interactions on thermodynamic and kinetic anisotropies induced by a solid substrate.