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Non-additive mixing plays a key role in the properties of molecular fluids and solids. In this work, the potential for athermal order-disorder phase transitions is explored in non-additive binary colloidal nanoparticles that form substitutionally ordered compounds, namely, for equimolar mixtures of octahedra + spheres, which form a CsCl lattice compound, and cubes + spheres, which form a NaCl crystal. Monte Carlo simulations that target phase coexistence conditions were used to examine the effect on compound formation of varying degrees of negative non-additivity created by component size asymmetry and by size-tunable indentations in the polyhedra's facets, intended to allow the nestling of neighboring spheres. Our results indicate that the stabilization of the compound crystal requires a relatively large degree of negative non-additivity, which depends on particle geometry and the packing of the relevant phases. It is found that negative non-additivity can be achieved in mixtures of large spheres and small cubes having no indentations and lead to the athermal crystallization of the NaCl lattice. For similarly sized components, athermal congruent transitions are attainable and non-additivity can be generated through indentations, especially for the cubes + spheres system. Increasing indentation leads to lower phase coexistence free energy and pressure in the cubes + spheres system but has the opposite effect in the octahedra + spheres system. These results indicate a stronger stabilizing effect on the athermal compound phase by the cubes' indentations, where a deeper nestling of the spheres leads to a denser compound phase and a larger reduction in the associated pressure-volume free-energy term., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Upon osmotic compression, rotationally symmetric faceted colloidal particles can form translationally ordered, orientationally disordered rotator mesophases. This study explores the mechanism of rotator-to-crystal phase transitions where orientational order is gained in a translationally ordered phase, using rotator-phase forming truncated cubes as a testbed. Monte Carlo simulations were conducted for two selected truncations (s), one for s = 0.527 where the rotator and crystal lattices are dissimilar and one for s = 0.572 where the two phases have identical lattices. These differences set the stage for a qualitative difference in their rotator-crystal transitions, highlighting the effect of lattice distortion on phase transition kinetics. Our simulations reveal that significant lattice deviatoric effects could hinder the rotator-to-crystal transition and favor arrangements of lower packing fraction instead. Indeed, upon compression, it is found that for s = 0.527, the rotator phase does not spontaneously transition into the stable, densely packed crystal due to the high lattice strains involved but instead transitions into a metastable solid phase to be colloquially referred to as "orientational salt" for short, which has a similar lattice as the rotator phase and exhibits two distinct particle orientations having substitutional order, alternating regularly throughout the system. This study paves the way for further analysis of diffusionless transformations in nanoparticle systems and how lattice-distortion could influence crystallization kinetics., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

This work aims to deepen our understanding of the molecular origin of the recently observed phenomenon of polymer cooperative adsorption onto faceted nanoparticle (NP) surfaces. By exploring a large parameter space for polymer/NP interactions through coarse-grained (CG) molecular dynamics (MD) simulations, it is found that consistent with experiments the presence or absence of cooperativity is related to solvent quality and relative interaction strengths between the polymer and the adsorbent. Specifically, positive cooperativity is associated with stronger polymer-polymer interaction than polymer-surface interactions and vice versa for negative cooperativity. This contrast in interaction energies manifests in positive cooperativity (i.e., increased affinity) and negative cooperativity (i.e., decreased affinity) as concentration increases. It is also found that increasing chain length strengthens cooperativity effects and that the nanoscale confinement of polymer chains to the adsorbing facet (due to weaker affinity to corners and edges) enhances positive cooperativity but weakens negative cooperativity. Moreover, adsorption onto a spherical NP shows stronger positive cooperativity but weaker negative cooperativity compared with adsorption onto a cubic NP of equal surface area. It was further found that as polymer bulk concentration increases, the free energy of adsorption decreases in positive cooperativity, increases in negative cooperativity, and is independent of concentration in noncooperative systems consistent with the phenomenological explanation of cooperativity. We further found that positive cooperativity is associated with growing fluctuations in the adsorption density at critical bulk polymer concentrations. This behavior can be attributed to the competition between enthalpic gains and entropic losses upon adsorption. Overall, our results shed light on the microscopic origin of cooperative adsorption and the role of solvent quality, which can be leveraged in, for example, controlling NP growth into target shapes and designing NP catalysts with improved performance.

Bolapolyphiles constitute a versatile class of materials with a demonstrated potential to form a wide variety of complex ordered mesophases. In particular, cubic network phases (like the gyroid, primitive, and diamond phases) have been a target of many studies for their ability to create percolating 3D nanosized channels. In this study, molecular simulations are used to explore the phase behavior of bolapolyphiles containing a rigid rodlike core, associating hydrophilic core ends and a hydrophobic side chain with a multident architecture, i.e., where the branching pattern can vary from bident (two branches) to hexadent (six branches). Upon network phase formation, its skeleton is made up of "nodes" populated by the core ends and "struts" populated by the cores. It is shown that, by varying the side chain length, branching pattern, and attachment point to the core, one can alter the crowding around the cores and hence tune the nodal size and nodal valence (i.e., number of connecting struts) which lead to different types of network morphologies. For example, for a fixed total side chain length, having more branches generates a stronger crowding around the molecular core, driving them to form bundlelike domains with curvier interfaces that result in thinner struts. Also, attaching the lateral chain closer to one core end breaks the symmetry between the environments around the two core ends, leading to networks with bimodal nodal sizes. Importantly, since the characterization of (ordered or partially ordered) network phases is challenging given the potential incompatibilities between the simulation box size with the structure's space group periodic symmetry and the effect of morphological defects, a detailed framework is presented to analyze and fully characterize the unit cell parameters and structure factor of such systems.

Mixtures of nanoparticles (NPs) with hybridizing grafted DNA or DNA-like strands have been of particular interest because of the tunable selectivity provided for the interactions between the NP components. A richer self-assembly behavior would be accessible if these NP-NP interactions could be designed to give nonadditive mixing (in analogy to the case of molecular components). Nonadditive mixing occurs when the mixed-state volume is smaller (negative) or larger (positive) than the sum of the individual components' volumes. However, instances of nonadditivity in colloidal/NP mixtures are rare, and systematic studies of such mixtures are nonexistent. This work focuses on patchy NPs whose patches (coarsely representing grafted hybridizing DNA strands) not only encode selectivity across components but also impart a tunable nonadditivity by varying their extent of protrusion. To guide the exploration of the relationship between phase behavior and nonadditivity for different patches' designs, the NP-NP potential of mean force (PMF) and a nonadditive parameter were first calculated. For one-patch NPs, different lamellar morphologies were predominantly observed. In contrast, for mixtures of two-patch NPs and (fully grafted) spherical particles, a rich phase behavior was found depending on patch-patch angle and degree of nonadditivity, resulting in phases such as the gyroid, cylinder, honeycomb, and two-layered crystal. Our results also show that both minimum positive nonadditivity and multivalent interactions are necessary for the formation of ordered network mesophases in the class of models studied.

Mixtures of nanoparticles (NPs) with hybridizing grafted DNA or DNA-like strands have been shown to create highly tunable NP-NP interactions, which, if designed to give nonadditive mixing, could lead to a richer self-assembly behavior. While nonadditive mixing is known to result in nontrivial phase behavior in molecular fluids, its effects on colloidal/NP materials have been much less studied. Such effects are explored here via molecular simulations for a binary system of tetrahedral patchy NPs, known to self-assemble into the diamond phase. The NPs are modeled with raised patches that interact through a coarse-grained interparticle potential representing DNA hybridization between grafted strands. It was found that these patchy NPs spontaneously nucleate into the diamond phase, and that hard-interacting NP cores eliminated the competition between the diamond and BCC phases at the conditions studied. Our results also showed that while higher nonadditivity had a small effect on phase behavior, it kinetically enhanced the formation of the diamond phase. Such a kinetic enhancement is argued to arise from changes in phase packing densities and how these modulate the interfacial free energy of the crystalline nucleus by favoring high-density motifs in the isotropic phase and larger NP vibrations in the diamond phase.

Monte Carlo simulations were used to study the influence of particle aspect ratio on the kinetics and phase behavior of hard gyrobifastigia (GBF). First, the formation of a highly anisotropic nucleus shape in the isotropic-to-crystal transition in regular GBF is explained by the differences in interfacial free energies of various crystal planes and the nucleus geometry predicted by the Wulff construction. GBF-related shapes with various aspect ratios were then studied, mapping their equations of state, determining phase coexistence conditions via interfacial pinning, and computing nucleation free-energy barriers via umbrella sampling using suitable order parameters. Our simulations reveal a reduction of the kinetic barrier for isotropic-crystal transition upon an increase in aspect ratio, and that for highly oblate and prolate aspect ratios, an intermediate nematic phase is stabilized. Our results and observations also support two conjectures for the formation of the crystalline state from the isotropic phase: that low phase free energies at the ordering phase transition correlate with low transition barriers and that the emergence of a mesophase provides a steppingstone that expedites crystallization.

Leveraging the self-assembling behavior of liquid crystals designed for controlling ion transport is of both fundamental and technological significance. Here, we have designed and prepared a liquid crystal that contains 2,5-bis(thien-2-yl)thieno[3,2- b ]thiophene (BTTT) as mesogenic core and conjugated segment and symmetric tetra(ethylene oxide) (EO4) as polar side chains for ion-conducting regions. Driven by the crystallization of the BTTT cores, BTTT/dEO4 exhibits well-ordered smectic phases below 71.5 °C as confirmed by differential scanning calorimetry, polarized optical microscopy, temperature-dependent wide-angle X-ray scattering, and grazing incidence wide-angle X-ray scattering (GIWAXS). We adopted a combination of experimental GIWAXS and molecular dynamics (MD) simulations to better understand the molecular packing of BTTT/dEO4 films, particularly when loaded with the ion-conducting salt lithium bis(trifluoromethanesulfonyl)imide (LiTFSI). Ionic conduction of BTTT/dEO4 is realized by the addition of LiTFSI, with the material able to maintain smectic phases up to r = [Li + ]/[EO] = 0.1. The highest ionic conductivity of 8 × 10 -3 S/cm was attained at an intermedium salt concentration of r = 0.05. It was also found that ion conduction in BTTT/dEO4 is enhanced by forming a smectic layered structure with irregular interfaces between the BTTT and EO4 layers and by the lateral film expansion upon salt addition. This can be explained by the enhancement of the misalignment and configurational entropy of the side chains, which increase their local mobility and that of the solvated ions. Our molecular design thus illustrates how, beyond the favorable energetic interactions that drive the assembly of ion solvating domains, modulation of entropic effects can also be favorably harnessed to improve ion conduction.

Non-equilibrium molecular dynamics simulations are used to probe the driving forces behind the formation of highly ordered, epitaxially connected superlattices of polyhedral-shaped nanoparticles (NPs) at fluid-fluid interfaces. By explicitly modeling coarse-grained ligands that cap the NP surface, it is shown that differences in NP shapes and time-dependent facet-specific ligand densities give rise to drastically different transformation mechanisms. Our results indicate that the extent of screening of the inter-particle interactions by the surrounding solvation environment has a significant impact on reversibility and ultimately the coherence of the final two-dimensional superlattice obtained. For the particle shapes examined, a hexagonal pre-assembly and a square superlattice final assembly (upon preferential ligand desorption from {100} facets) were prevalent; however, cuboctahedral NPs formed intermediate epitaxially bonded branched clusters, which eventually grew and rearranged into a square lattice; in contrast, truncated octahedral NPs exhibited an abrupt rhombic-to-square transition driven by the clustering of their numerous {111}-ligands that favored the stacking of linear NP rods. To track the incipient order in the system, we also outline a set of novel order parameters that measure the local orientation alignment between nearest-neighbor pairs. The simulation protocols advanced in this work could pave the way forward for exploration of the vast phase space associated with the interfacial self-assembly of NPs.

The entropy-driven monolayer assembly of hexagonal prisms and cylinders was studied under hard slit confinement. At the conditions investigated, the particles have two distinct and dynamically disconnected rotational states: unflipped and flipped, depending on whether their circular/hexagonal face is parallel or perpendicular to the wall plane. Importantly, these two rotational states cast distinct projection areas over the wall plane that favor either hexagonal or tetragonal packing. Monte Carlo simulations revealed a re-entrant melting transition where an intervening disordered Flipped-Unflipped (FUN) phase is sandwiched between a fourfold tetratic phase at high concentrations and a sixfold triangular solid at intermediate concentrations. The FUN phase contains a mixture of flipped and unflipped particles and is translationally and orientationally disordered. Complementary experiments were conducted with photolithographically fabricated cylindrical microparticles confined in a wedge cell. Both simulations and experiments show the formation of phases with comparable fraction of flipped particles and structure, i.e., the FUN phase, triangular solid, and tetratic phase, indicating that both approaches sample analogous basins of particle-orientation phase-space. The phase behavior of hexagonal prisms in a soft-repulsive wall model was also investigated to exemplify how tunable particle-wall interactions can provide an experimentally viable strategy to dynamically bridge the flipped and unflipped states., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier Inc. All rights reserved.)

A previously introduced framework to identify local order parameters (OPs) distinctive of incipient complex mesophases, such as bicontinuous network phases, is used in this work to evaluate nucleation free-energy barriers. The sampling techniques considered are the mean-first-passage-time (MFPT) method and novel variants of umbrella sampling, including Hybrid Monte Carlo (HMC) and a dual-OP-method that uses a blunter global OP for the umbrella bias while keeping record of configurations for analysis with a local OP. These methods were chosen for their ability to minimize or avoid frequent calculation of the expensive local OP, which makes their continuous on-the-fly tracking computationally very inefficient. These techniques were first validated by studying phase-transition barriers of model systems, i.e., the vapor-liquid nucleation of Lennard-Jones argon and a binary nanoparticle model. The disorder-to-order free energy barrier was then traced for the double gyroid and single diamond formed by mesoscopic bead-spring macromolecular models. The dual OP method was found to be the most robust and computationally efficient, since, unlike HMC, it does not require the expensive local OP to be computed on-the-fly, and unlike the MFPT method, it can negotiate large barriers aided by the biased sampling. The dual OP method requires, however, that a cheap global OP be identified and correlated (in a post-processing step) with the local OP that describes the structure of the critical nucleus, a process that can be aided by machine learning.

In this work, complementary formulas are presented to compute free-energy differences via perturbation (FEP) methods and thermodynamic integration (TI). These formulas are derived by selecting only the most statistically significant data from the information extractable from the simulated points involved. On the one hand, commonly used FEP techniques based on overlap sampling leverage the full information contained in the overlapping macrostate probability distributions. On the other hand, conventional TI methods only use information on the first moments of those distributions, as embodied by the first derivatives of the free energy. Since the accuracy of simulation data degrades considerably for high-order moments (for FEP) or free-energy derivatives (for TI), it is proposed to consider, consistently for both methods, data up to second-order moments/derivatives. This provides a compromise between the limiting strategies embodied by common FEP and TI and leads to simple, optimized expressions to evaluate free-energy differences. The proposed formulas are validated with an analytically solvable harmonic Hamiltonian (for assessing systematic errors), an atomistic system (for computing the potential of mean force with coordinate-dependent order parameters), and a binary-component coarse-grained model (for tracing a solid-liquid phase diagram in an ensemble sampled through alchemical transformations). It is shown that the proposed FEP and TI formulas are straightforward to implement, perform similarly well, and allow robust estimation of free-energy differences even when the spacing of successive points does not guarantee them to have proper overlapping in phase space.

Many hard faceted nanoparticles are known to undergo disorder-to-order phase transitions following a classical nucleation and growth mechanism. In a previous study [ J. Phys. Chem. B 2018 , 122 , 9264-9273], it was shown that hard cubes undergo a nonclassical phase transition with a bulk character instead of originating from consolidated nuclei. Significantly, an unusually high fraction of ordered particles was observed in the metastable basin of the disordered phase, even for very low degrees of supersaturation. This work aims to substantiate the conjecture that these unique properties originate from a comparatively low interfacial free energy between the disordered and ordered phases for hard cubes relative to other hard particle systems. Using the cleaving wall method to directly measure the interfacial free energy for cubes, it is found that its values are indeed small; e.g., at phase coexistence conditions, it is only one-fifth that for hard spheres. A theoretical nucleation model is used to explore the broader implications of low interfacial tension values and how this could result in a bulk ordering mechanism.

This study outlines the development of an implicit-solvent model that reproduces the behavior of colloidal nanoparticles at a fluid-fluid interface. The center point of this formulation is the generalized quaternion-based orientational constraint (QOCO) method. The model captures three major energetic characteristics that define the nanoparticle configuration-position (orthogonal to the interfacial plane), orientation, and inter-nanoparticle interaction. The framework encodes physically relevant parameters that provide an intuitive means to simulate a broad spectrum of interfacial conditions. Results show that for a wide range of shapes, our model is able to replicate the behavior of an isolated nanoparticle at an explicit fluid-fluid interface, both qualitatively and often nearly quantitatively. Furthermore, the family of truncated cubes is used as a test bed to analyze the effect of changes in the degree of truncation on the potential-of-mean-force landscape. Finally, our results for the self-assembly of an array of cuboctahedra provide corroboration to the experimentally observed honeycomb and square lattices.

We use molecular dynamics simulations to study the phase behavior of a coarse-grained lamella-forming A- b -B diblock copolymer under thin-film soft confinement for different heating cycle lengths, film thicknesses, and substrate-polymer affinities. This model describes the effect on thin-film morphology with a free surface (air-polymer interface) and a solid substrate. Our simulation results were first validated by showing that they capture changes for the order-disorder transition temperature with annealing conditions consistent with those found in laser spike annealing experiments, when the vertical lamella phase formed on neutral substrates. In addition, simulations with a substrate selective for a particular block revealed the formation of other phases, including a mixed vertical-horizontal lamella and a metastable island phase having horizontal but incomplete lamella layers. The nanoscale roughness features of this island phase, and hence its surface wettability, can be tuned with suitable choices of chemistry and annealing conditions.

This work represents a joint computational and experimental study on a series of n -ethylene glycol (PEO n )-terminated quaterthiophene (4T) oligomers for 1 < n < 10 to elucidate their self-assembly behavior into a smectic-like lamellar phase. This study builds on an earlier study for n = 4 that showed that our model predictions were consistent with experimental data on the melting behavior and structure of the lamellar phase, with the latter consisting of crystal-like 4T domains and liquid-like PEO4 domains. The present study aims to understand how the length of the terminal PEO n chains modulates the disordering temperature of the lamellar phase and hence the relative stability of the ordered structure. A simplified bilayer model, where the 4T domains are not explicitly described, is put forward to efficiently estimate the disordering effect of the PEO domains with increasing n ; this method is first validated by correctly predicting that layers of alkyl (PE)-capped 4T oligomers (for 1 < n < 10) stay ordered at room temperature. Both 4T-domain implicit and explicit model simulations reveal that the order-disorder temperature decreases with the length of the PEO capping chains, as the associated increase in conformational entropy drives a tendency toward disorder that overtakes the cohesive energy, keeping the ordered packing of the 4T domains.

Coarse-grained (CG) models have allowed molecular simulations to access large enough time and length scales to elucidate relationships between macroscale properties and microscale molecular interactions. However, an unaddressed inverse-design problem concerns the identification of an optimal chemistry-specific (CS) molecule that the generic CG model represents. This has been addressed here by introducing new tools for automatically generating and refining the mapping of CS-molecule candidates to the constraints of a CG model, based on representative optimization criteria. With these tools, for each CS-molecule from a candidate group, the best mapping of that molecule onto the CG model is found and their fit is assessed by an objective function designed to emphasize matching key properties of the CG model. We employ this methodology to a range of CG models from small solvent molecules up to block copolymer systems to show its ability to find optimal candidates and to uncover the underlying length scale of some of the CG models. For instances where the identity of the CG model is known a priori, the methodology identifies the correct AA chemistry. For instances where the identity is unknown and a pool of candidates is provided, the method selects a chemistry that aligns well with physical intuition. The best candidate chemistry is also found to be sensitive to changes to the CG model.

Developing soft materials with both ion and electron transport functionalities is of broad interest for energy-storage and bioelectronics applications. Rational design of these materials requires a fundamental understanding of interactions between ion and electron conducting blocks along with the correlation between the microstructure and the conduction characteristics. Here, we investigate the structure and mixed ionic/electronic conduction in thin films of a liquid crystal (LC) 4T/PEO4, which consists of an electronically conducting quarterthiophene (4T) block terminated at both ends by ionically conducting oligoethylenoxide (PEO4) blocks. Using a combined experimental and simulation approach, 4T/PEO4 is shown to self-assemble into smectic, ordered, or disordered phases upon blending the materials with the ionic dopant bis(trifluoromethane)sulfonimide lithium (LiTFSI) under different LiTFSI concentrations. Interestingly, at intermediate LiTFSI concentration, ordered 4T/PEO4 exhibits an electronic conductivity as high as 3.1 × 10 -3 S/cm upon being infiltrated with vapor of the 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ) molecular dopant while still maintaining its ionic conducting functionality. This electronic conductivity is superior by an order of magnitude to the previously reported electronic conductivity of vapor co-deposited 4T/F4TCNQ blends. Our findings demonstrate that structure and electronic transport in mixed conduction materials could be modulated by the presence of the ion transporting component and will have important implications for other more complex mixed ionic/electronic conductors.

Ordered intermetallic nanoparticles are promising electrocatalysts with enhanced activity and durability for the oxygen-reduction reaction (ORR) in proton-exchange membrane fuel cells (PEMFCs). The ordered phase is generally identified based on the existence of superlattice ordering peaks in powder X-ray diffraction (PXRD). However, after employing a widely used postsynthesis annealing treatment, we have found that claims of "ordered" catalysts were possibly/likely mixed phases of ordered intermetallics and disordered solid solutions. Here, we employed in situ heating, synchrotron-based, X-ray diffraction to quantitatively investigate the impact of a variety of annealing conditions on the degree of ordering of large ensembles of Pt 3 Co nanoparticles. Monte Carlo simulations suggest that Pt 3 Co nanoparticles have a lower order-disorder phase transition (ODPT) temperature relative to the bulk counterpart. Furthermore, we employed microscopic-level in situ heating electron microscopy to directly visualize the morphological changes and the formation of both fully and partially ordered nanoparticles at the atomic scale. In general, a higher degree of ordering leads to more active and durable electrocatalysts. The annealed Pt 3 Co/C with an optimal degree of ordering exhibited significantly enhanced durability, relative to the disordered counterpart, in practical membrane electrode assembly (MEA) measurements. The results highlight the importance of understanding the annealing process to maximize the degree of ordering in intermetallics to optimize electrocatalytic activity., Competing Interests: The authors declare no conflict of interest.

Molecular simulations of coarse-grained diblock copolymers (DBP) were conducted to study the effect of segregation strength and morphology on transport properties. It was found that in the strong segregation limit (i.e., high χN, where χ is the Flory-Huggins parameter and N is the degree of polymerization), the presence of the DBP interfaces imposes topological constraints similar to those of entanglements as manifested in the rheological signature of the polymer (i.e., a plateau modulus). Furthermore, compared to the behavior of isotropic melts, the crossover from Rouse to reptation scaling of the self-diffusion coefficient (D) parallel to the DBP interface takes place at a smaller N, an effect that depends on temperature and is more pronounced in the Lamellae morphology than in the hexagonal cylinder morphology. Additionally, it is shown that for an entangled melt (i.e., N ≫ Ne where Ne is the entanglement length) block retraction is instrumental for chains to diffuse parallel to the interface of lamellar layers. Lastly, it is found that the anisotropic viscosity of different morphologies is mostly affected by the orientation of the chains relative to the shear flow direction, exhibiting reduced values when chains align in the neutral or flow directions.

Improving the affinity of protein-protein interactions is a challenging problem that is particularly important in the development of antibodies for diagnostic and clinical use. Here, we used structure-based computational methods to optimize the binding affinity of V H NAC1, a single-domain intracellular antibody (intrabody) from the camelid family that was selected for its specific binding to the nonamyloid component (NAC) of human α-synuclein (α-syn), a natively disordered protein, implicated in the pathogenesis of Parkinson's disease (PD) and related neurological disorders. Specifically, we performed ab initio modeling that revealed several possible modes of V H NAC1 binding to the NAC region of α-syn as well as mutations that potentially enhance the affinity between these interacting proteins. While our initial design strategy did not lead to improved affinity, it ultimately guided us towards a model that aligned more closely with experimental observations, revealing a key residue on the paratope and the participation of H4 loop residues in binding, as well as confirming the importance of electrostatic interactions. The binding activity of the best intrabody mutant, which involved just a single amino acid mutation compared to parental V H NAC1, was significantly enhanced primarily through a large increase in association rate. Our results indicate that structure-based computational design can be used to successfully improve the affinity of antibodies against natively disordered and weakly immunogenic antigens such as α-syn, even in cases such as ours where crystal structures are unavailable.

The stability of the gyroid phase in a coarse-grained model of rod-coil block copolymers is ascertained by using a field-based thermodynamic integration method to calculate free-energy differences between competing phases. The scope of the original methodology is expanded in terms of both its implementation by designing guiding fields suitable for molecular dynamics simulations (besides Monte Carlo simulations) and its applications by describing the formation of bicontinuous phases with linear rod-coil amphiphilic chains and with bolaamphiphilic molecules. For both types of systems, results are presented that complement those from previous studies, providing a quantitative metric to pinpoint the conditions and molecular parameters that render the gyroid phase more stable than other competing morphologies.

Monte Carlo simulations are used to investigate the mechanism of the disorder-to-order phase transition for a bulk system of colloidal hard cubes. It is observed that the structure of the ordered state is foreshadowed in the disordered state through multiple spontaneously occurring ordered domains. Such domains arise due to the entropic preference for local facet alignment between particles and occur transiently and sparsely throughout the system even in the stable isotropic phase. At pressures (and degrees of supersaturation) where the isotropic phase becomes marginally metastable, a classical nucleation process is never observed; instead, the ordered domains increase in number and size, eventually reaching a critical point where they percolate the entire system and spontaneously consolidate to form the ordered phase. The critical number of particles and the per particle free-energy barrier both decrease with pressure. Using the total number of locally ordered particles as a global order parameter, it is predicted that for large systems the ordering transition would only be spontaneous above a critical pressure. Finally, a test designed to probe the ability of the system to favor a single monodomain solid from initially misaligned-ordered domains, reveals that an active interdomain zone mediates the concerted reorientation of particles.

Classical Nucleation Theory (CNT) has recently been used in conjunction with a seeding approach to simulate nucleation phenomena at small-to-moderate supersaturation conditions when large free-energy barriers ensue. In this study, the conventional seeding approach [J. R. Espinosa et al., J. Chem. Phys. 144, 034501 (2016)] is improved by a novel, more robust method to estimate nucleation barriers. Inspired by the interfacial pinning approach [U. R. Pedersen, J. Chem. Phys. 139, 104102 (2013)] used before to determine conditions where two phases coexist, the seed of the incipient phase is pinned to a preselected size to iteratively drive the system toward the conditions where the seed becomes a critical nucleus. The proposed technique is first validated by estimating the critical nucleation conditions for the disorder-to-order transition in hard spheres and then applied to simulate and characterize the highly non-trivial (prolate) morphology of the critical crystal nucleus in hard gyrobifastigia. A generalization of CNT is used to account for nucleus asphericity and predict nucleation free-energy barriers for gyrobifastigia. These predictions of nuclei shape and barriers are validated by independent umbrella sampling calculations.

The nucleation of ordered phases from the bulk isotropic phase of octahedron-like particles has been studied via Monte Carlo simulations and umbrella sampling. In particular, selected shapes that form ordered (plastic) phases with various symmetries (cubic and tetragonal) are chosen to unveil trends in the free-energy barrier heights (ΔG*'s) associated with disorder to order transitions. The shapes studied in this work have truncation parameter (s) values of 0.58, 0.75, 0.8 and 1. The case of octahedra (s = 1.0) is studied to provide a counter-example where the isotropic phase nucleates directly into a (Minkowski) crystal phase rather than a rotator phase. The simulated ΔG*'s for these systems are compared with those previously reported for hard spheres and truncated cubes with s = 0.5 (cuboctahedra, CO) and s = 2/3 (truncated octahedra, TO). The comparison shows that, for comparable degrees of supersaturation, all rotator phases nucleate with smaller ΔG*'s than that of the hard sphere crystal, whereas the octahedral crystal nucleates with a larger ΔG*. Our analysis of near-critical translationally ordered nuclei of octahedra shows a strong bias towards an orientational alignment which is incompatible with the tendency to form facet-to-facet contacts in the disordered phase, thus creating an additional entropic penalty for crystallization. For rotator phases of octahedra-like particles, we observe that the strength of the localized orientational order correlates inversely with ΔG*. We also observe that for s > 0.66 shapes and similar to octahedra, configurations with high facet alignment do not favor high orientational order, and thus ΔG*'s increase with truncation.

By introducing favorable inter-species interactions, stoichiometric compound phases (C*), akin to intermetallic alloys, can be formed by binary mixtures of nanoparticle components of different shapes. The stability of such C* phases is expected to be affected by asymmetries in both the energetics of like vs. unlike species contacts, and the packing entropy of components, as captured by their shapes and relative sizes. Using Monte Carlo simulations, we explore the effect of changes in size ratio (for fixed contact energy) and in binding energy (for fixed size ratio) in the stability of the CsCl compound phase for equimolar mixtures of octahedra and spheres and of the NaCl compound for equimolar mixtures of cubes and spheres. As a general design rule, it is proposed that enhanced compound stability is associated with inter-species interactions that minimize the free-energy of the C* phase at coexistence with the (disordered) phase that is stable at lower concentrations. For the systems studied, this rule identifies optimal relative particle sizes and inter-species binding energies that are consistent with physically grounded expectations.

T-shaped bolaamphiphiles (TBA) with a swallow-tail lateral chain have been found to provide a fertile platform to produce complex liquid crystalline phases that are accessible through changes of temperature and lateral chain length and design. In this work, we use molecular simulations of a simple coarse-grained model to map out the phase behavior of this type of molecules. This model is based on the premise that the crucial details of the fluid structure stem from close range repulsions and the strong directional forces typical of hydrogen bonds. Our simulations confirm that TBAs exhibit a rich phase behavior upon increasing the length of their lateral chain. The simulations detect a double gyroid phase and an axial-bundle columnar phase which bear some structural resemblance to those found in the experiment. In addition, simulations predict two cocontinuous phases with 3D-periodicity: the "single" diamond and the "single" plumber's nightmare phase. Our analysis of energetic and entropic contributions to the free energy of phases formed by TBA with either swallow-tail or linear side-chains suggest that the 3D-periodic network phases formed by the former are stabilized by the large conformation entropy of the side-chains.

In chain-growth polymerization, a chain grows continually to reach thousands of subunits. However, the real-time dynamics of chain growth remains unknown. Using magnetic tweezers, we visualized real-time polymer growth at the single-polymer level. Focusing on ring-opening metathesis polymerization, we found that the extension of a growing polymer under a pulling force does not increase continuously but exhibits wait-and-jump steps. These steps are attributable to the formation and unraveling of conformational entanglements from newly incorporated monomers, whose key features can be recapitulated with molecular dynamics simulations. The configurations of these entanglements appear to play a key role in determining the polymerization rates and the dispersion among individual polymers., (Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

A key challenge to engineer ordered solids from the co-assembly of two differently shaped building blocks is to predict the key particle characteristics that lead to maximal mutual ordered-phase compatibility (MaxOC). While both entropy disparity, as captured by the relative size of the components, and energetic inter-species selectivity affect MaxOC, it is the former whose effect is less intuitive and the main focus of this work. Such MaxOC predictive rules are formulated and validated by using Monte Carlo simulation results for hard-core mixtures of octahedra and spheres and of other previously studied mixtures. Specifically, it is proposed that component size ratios should maximize their "substitutional symmetry" and hence minimize the combined free-energy cost associated with mutating a host-particle into a guest-particle in each of the solid phases. For the hard-core mixtures examined, packing entropy stabilizes substitutionally disordered solid solutions but not stoichiometric compounds. Additional molecular simulations were hence used to demonstrate, consistent with recent experimental findings, that such compounds can be formed by strengthening the inter-species compatibility via orientation-dependent attractions.

The phase behavior and the homogeneous nucleation of an equimolar mixture of octahedra and cuboctahedra are studied using thermodynamic integration, Gibbs-Duhem integration, and umbrella sampling simulations. The components of this mixture are modeled as polybead objects of equal edge lengths so that they can assemble into a space-filling compound with the CsCl crystal structure. Taking as reference the hard-core system where the compound crystal does not spontaneously nucleate, we quantified the effect of inter-species selective interactions on facilitating the disorder-to-order transition. Facet selective and facet non-selective inter-species attractions were considered, and while the former was expectedly more favorable toward the target tessellating structure, the latter was found to be similarly effective in nucleating the crystal compound. Ranges for the strength of attractions and degree of supersaturation were identified where the nucleation free-energy barrier was small enough to foretell a fast process but large enough to prevent spinodal fluctuations that can trap the system in dense metastable states lacking long-range order. At those favorable conditions, the tendency toward the local orientational order favored by packing entropy is amplified and found to play a key role seeding nuclei with the CsCl structure.

Materials comprising porous structures, often in the form of interconnected concave cavities, are typically assembled from convex molecular building blocks. The use of nanoparticles with a characteristic nonconvex shape provides a promising strategy to create new porous materials, an approach that has been recently used with cagelike molecules to form remarkable liquids with "scrabbled" porous cavities. Nonconvex mesogenic building blocks can be engineered to form unique self-assembled open structures with tunable porosity and long-range order that is intermediate between that of isotropic liquids and of crystalline solids. Here we propose the design of highly open liquid-crystalline structures from rigid nanorings with ellipsoidal and polygonal geometry. By exploiting the entropic ordering characteristics of athermal colloidal particles, we demonstrate that high-symmetry nonconvex rings with large internal cavities interlock within a 2D layered structure leading to the formation of distinctive liquid-crystalline smectic phases. We show that these smectic phases possess uniquely high free volumes of up to ∼95%, a value significantly larger than the 50% that is typically achievable with smectic phases formed by more conventional convex rod- or disklike mesogenic particles., Competing Interests: The authors declare no conflict of interest.

Adhesion energies for sub-micron particles cannot be accurately calculated with macro-scale theories, in part because heterogeneities in surface morphology and chemistry play a significant role. Atomistic models have been used previously to quantify adhesion energies in wet environments for pure silica surfaces. To extend such modeling to more complex glass materials, we adopt a more comprehensive amorphous glass potential, and use a simplified approach to define the interaction between the hydroxylated surface and SPC/E water. We compute adhesion energies for pure SiO2, and 90mol% SiO2+10mol% B2O3, in dry and humid conditions. We find that the addition of B2O3 reduces adhesion, due to multiple effects which result in reduced hydrogen bonding. At high RH, the water between the plates forms a clear liquid bridge, whereas at the lowest RH, the water connects in chains of hydrogen bonded molecules that form and break during the adhesion process, so that capillary forces do not come into play. We also find that for under-hydroxylated pure SiO2 surfaces, a transitional state which may be found after heating or during glass formation, adhesion energies are the highest., (Copyright © 2015 Elsevier Inc. All rights reserved.)

Monte Carlo simulations are used to investigate the phase behavior of hard cubes, truncated cubes, cuboctahedra and truncated octahedra when confined between two parallel hard walls. The walls are separated by a distance H* which is varied to accommodate a different number of layers, from a monolayer up to approximately 5 layers, hence allowing us to probe the transitional phase behavior as the system goes from a quasi-2D geometry to a quasi-3D bulk behavior. While our results do reveal some phases whose structures resemble those that have been observed before for such systems in 2D and 3D spaces, other phases are also detected, including buckled phases, rotator plastic phases, and solids with significant translational disorder. Ordered phases formed for H* values that are a little too narrow to accommodate an additional particle layer are particularly interesting as they tend to have complex structures. The maximum density for such frustrated phases is low compared to that of non-frustrated ones for the same system at different H*. As the asphericity in the shapes is reduced, the simulated phases show structural features that approach those of the phases that have been reported for hard spheres under similar confinement.

In this work, a method is proposed to simultaneously compute the transition rate constant and the free energy profile of a rare event along an order parameter connecting two well-defined regions of phase space. The method employs a forward flux sampling technique in combination with a mean first passage time approach to estimate the steady state probability and mean first passage times. These quantities are fitted to a Markovian model that allows the estimation of the free energy along the chosen order parameter. The proposed technique is first validated with two test systems (an Ising model and a model potential energy surface) and then used to study the solid-phase homogeneous nucleation of selected polyhedral particles.

The structure and transport properties of physisorbed and chemisorbed CO2 in model polyamine liquids (hexamethylenediamine and diethylenetriamine) are studied via molecular dynamics simulations. Such systems are relevant to CO2 absorption processes where nonaqueous amines are used as absorbents (e.g., when impregnated or grafted onto mesoporous media or misted in the gas phase). It is shown that accounting for the ionic speciation resulting from CO2 chemisorption enabled us to capture the qualitative changes in extent of absorption and fluidity with time that are observed in thermogravimetric experiments. Simulations reveal that high enough concentration of reacted CO2 leads to strong intermolecular ionic interactions and the arrest of molecular translations. The transport properties obtained from the simulations of the ionic speciated mixtures are also used to construct an approximate continuum-level model for the CO2 absorption process that mimics thermogravimetric experiments.

The self-assembly of hard polyhedral particles confined to a flat interface is studied using Monte Carlo simulations. The particles are pinned to the interface by restricting their movement in the direction perpendicular to it while allowing their free rotations. The six different polyhedral shapes studied in this work are selected from a family of truncated cubes defined by a truncation parameter, s, which varies from cubes (s = 0) via cuboctahedra (s = 0.5) to octahedra (s = 1). Our results suggest that shapes with small values of s show square-like behavior whereas shapes with large values of s tend to show more disc-like behavior. At an intermediate value of s = 0.4, the phase behavior of the system shows both square-like and disc-like features. The results are also compared with the phase behavior of 3D bulk polyhedra and of 2D rounded hard squares. Both comparisons reveal key similarities in the number and sequence of mesophases and solid phases observed. These insights on 2D entropic self-assembly of polyhedral particles is a first step toward understanding the self-assembly of particles at fluid-fluid interfaces, which is driven by a complex interplay of entropic and enthalpic forces. A first-order analysis of the particle-surface energies associated with a fluid-fluid interface indicates that such enthalpic interactions will be particularly important in determining particle orientation behavior at low to intermediate concentrations.

Colloidal aperiodic phases (i.e., entropy stabilized degenerate crystals, DCs) are realized via self-assembly of hollow fluorescent silica dimers under wedge-cell confinement. The dimer building blocks approximate two tangent spheres and their arrangements are studied via laser scanning confocal microscopy. In the DCs, the individual lobes tile a lattice and five distinct DC arrangements with square, triangular or rectangular layer symmetry are determined as a function of confinement height. Moreover, Monte Carlo simulations are used to construct the phase diagram for DCs up to two layer confinements and to analyze structural order in detail. Just as for spheres, the DC structural transitions under confinement are attributed to the ability or frustration to accommodate an integral number of particle layers between hard walls. Unlike spheres, dimers can also experience transitions involving changes in orientation. DCs are among the unconventional structures (e.g., semi-regular tilings, quasicrystals, plastic crystals) expected to enhance the properties of photonic solids.

The role of entropic interactions, often subtle and sometimes crucial, on the structure and properties of soft matter has a well-recognized place in the classic and modern scientific literature. However, the lessons learned from many of those studies do not always form part of the standard arsenal of strategies that are taught or used for de novo studies relevant to the engineering of new materials. Fortunately, a growing number of examples exist where entropic effects have been designed a priori to achieve a desired or new outcome. This tutorial review describes some recent such examples, selected to illustrate the potential benefits of a more pro-active approach to harnessing the often overlooked power of entropy.

Sought-after ordered structures of mixtures of hard anisotropic nanoparticles can often be thermodynamically unfavorable due to the components' geometric incompatibility to densely pack into regular lattices. A simple compatibilization rule is identified wherein the particle sizes are chosen such that the order-disorder transition pressures of the pure components match (and the entropies of the ordered phases are similar). Using this rule with representative polyhedra from the truncated-cube family that form pure-component plastic crystals, Monte Carlo simulations show the formation of plastic-solid solutions for all compositions and for a wide range of volume fractions.

The precise estimation of the location of phase transitions is an essential task in the study of many condensed matter systems. A recently developed technique denoted interface pinning (IP) [U. R. Pedersen, F. Hummel, G. Kresse, G. Kahl, and C. Dellago, Phys. Rev. B. 88, 094101 (2013); U. R. Pedersen, J. Chem. Phys. 139, 104102 (2013)] can accurately estimate the location of fluid-solid transition using the NP(z)T ensemble for single-component systems by computing the free energy difference between a solid and a fluid. The IP method is extended here to be applicable to different ensembles for both single-component systems and binary mixtures. A more general scheme is also proposed for the extrapolation of properties targeting coexistence conditions. This framework is used to estimate the coexistence pressure for the isotropic-rotator phase transition for three single-component polyhedral systems and to estimate isotropic-crystal coexistence compositions for a binary mixture of hard cubes and spheres. In addition, by exploring various choices for the order parameter used to distinguish between the isotropic and ordered phases, it is found that volume provides a reasonable alternative to translational order parameters which can be either more expensive to calculate or unable to pin a two-phase interfacial state.

Self-consistent field theory is used to model the self-assembly of a symmetric PMMA-block-PHEMA in the presence of two solvents, methanol and tetrahydrofuran (THF). The model predictions are compared to our experimental results of solvent-vapour annealing of thin polymer films, where the sequence of cylinder to gyroid (or micelles) to lamellar phases was found upon increasing the methanol-THF ratio and for particular extents of film swelling. The Hansen solubility parameters are used to estimate the Flory-Huggins interaction parameters (χ) needed in the theoretical model. However, because enacting the experimental range of high (χ)N values is computationally prohibitive, the use of moderate (χ)N values is compensated by employing larger values of the solvent-to-polymer size ratio (α). This approach is validated by showing that the predicted phase diagrams exhibit qualitatively similar trends whether (χ)N or α is increased. Using such an approach, the theory predicts a cylinder to gyroid to lamellar transition on increasing the THF-methanol ratio, a trend consistent with that observed in the experiments.

In this work, a variant of the Gibbs-Duhem integration (GDI) method is proposed to trace phase coexistence lines that combines some of the advantages of the original GDI methods such as robustness in handling large system sizes, with the ability of histogram-based methods (but without using histograms) to estimate free-energies and hence avoid the need of on-the-fly corrector schemes. This is done by fitting to an appropriate polynomial function not the coexistence curve itself (as in GDI schemes) but the underlying free-energy function of each phase. The availability of a free-energy model allows the post-processing of the simulated data to obtain improved estimates of the coexistence line. The proposed method is used to elucidate the phase behavior for two non-trivial hard-core mixtures: a binary blend of spheres and cubes and a system of size-polydisperse cubes. The relative size of the spheres and cubes in the first mixture is chosen such that the resulting eutectic pressure-composition phase diagram is nearly symmetric in that the maximum solubility of cubes in the sphere-rich solid (∼20%) is comparable to the maximum solubility of spheres in the cube-rich solid. In the polydisperse cube system, the solid-liquid coexistence line is mapped out for an imposed Gaussian activity distribution, which produces near-Gaussian particle-size distributions in each phase. A terminal polydispersity of 11.3% is found, beyond which the cubic solid phase would not be stable, and near which significant size fractionation between the solid and isotropic phases is predicted.

The nucleation kinetics of the rotator phase in hard cuboctahedra, truncated octahedra, and rhombic dodecahedra is simulated via a combination of forward flux sampling and umbrella sampling. For comparable degrees of supersaturation, the polyhedra are found to have significantly lower free-energy barriers and faster nucleation rates than hard spheres. This difference primarily stems from localized orientational ordering, which steers polyhedral particles to pack more efficiently. Orientational order hence fosters here the growth of orientationally disordered nuclei.

Using high-speed confocal microscopy, we measure the particle positions in a colloidal suspension under large-amplitude oscillatory shear. Using the particle positions, we quantify the in situ anisotropy of the pair-correlation function, a measure of the Brownian stress. From these data we find two distinct types of responses as the system crosses over from equilibrium to far-from-equilibrium states. The first is a nonlinear amplitude saturation that arises from shear-induced advection, while the second is a linear frequency saturation due to competition between suspension relaxation and shear rate. In spite of their different underlying mechanisms, we show that all the data can be scaled onto a master curve that spans the equilibrium and far-from-equilibrium regimes, linking small-amplitude oscillatory to continuous shear. This observation illustrates a colloidal analog of the Cox-Merz rule and its microscopic underpinning. Brownian dynamics simulations show that interparticle interactions are sufficient for generating both experimentally observed saturations.

We consider an atomistic model to investigate the flux of water through thin Linde type A (LTA) zeolite membranes with differing surface chemistries. Using molecular dynamics, we have studied the flow of water under hydrostatic pressure through a fully hydrated LTA zeolite film (~2.5 nm thick) capped with hydrophilic and hydrophobic moieties. Pressure drops in the 50-400 MPa range were applied across the membrane, and the flux of water was monitored for at least 15 ns of simulation time. For hydrophilic membranes, water molecules adsorb at the zeolite surface, creating a highly structured fluid layer. For hydrophobic membranes, a depletion of water molecules occurs near the water/zeolite interface. For both types of membranes, the water structure is independent of the pressure drop established in the system and the flux through the membranes is lower than that observed for the bulk zeolitic material; the latter allows an estimation of surface barrier effects to pressure-driven water transport. Mechanistically, it is observed that (i) bottlenecks form at the windows of the zeolite structure, preventing the free flow of water through the porous membrane, (ii) water molecules do not move through a cage in a single-file fashion but rather exhibit a broad range of residence times and pronounced mixing, and (iii) a periodic buildup of a pressure difference between inlet and outlet cages takes place which leads to the preferential flow of water molecules toward the low-pressure cages.

Nanobodies are single-domain antibodies found in camelids. These are the smallest naturally occurring binding domains and derive functionality via three hypervariable loops (H1-H3) that form the binding surface. They are excellent candidates for antibody engineering because of their favorable characteristics like small size, high solubility, and stability. To rationally engineer antibodies with affinity for a specific target, the hypervariable loops can be tailored to obtain the desired binding surface. As a first step toward such a goal, we consider the design of loops with a desired conformation. In this study, we focus on the H1 loop of the anti-hCG llama nanobody that exhibits a noncanonical conformation. We aim to "tilt" the stability of the H1 loop structure from a noncanonical conformation to a (humanized) type 1 canonical conformation by studying the effect of selected mutations to the amino acid sequence of the H1, H2, and proximal residues. We use all-atomistic, explicit-solvent, biased molecular dynamic simulations to simulate the wild-type and mutant loops in a prefolded framework. We thus find mutants with increasing propensity to form a stable type 1 canonical conformation of the H1 loop. Free energy landscapes reveal the existence of conformational isomers of the canonical conformation that may play a role in binding different antigenic surfaces. We also elucidate the approximate mechanism and kinetics of transitions between such conformational isomers by using a Markovian model. We find that a particular three-point mutant has the strongest thermodynamic propensity to form the H1 type 1 canonical structure but also to exhibit transitions between conformational isomers, while a different, more rigid three-point mutant has the strongest propensity to be kinetically trapped in such a canonical structure.

The self-assembly of polyhedral particles has been a topic of interest in both experimental and simulation studies due to its potential to help engineer novel materials from colloidal nanoparticles. An important extension to the study of single species of polyhedral particles is the case of binary mixtures. Mixtures that tessellate space are particularly interesting because they are expected to form high-pressure ordered structures. Here, we study three such binary tessellating mixtures; namely, cuboctahedra + octahedra (Mixture 1), octahedra + tetrahedra (Mixture 2), and truncated cubes + octahedra (Mixture 3). We use Monte Carlo methods to first determine their phase behavior when driven by hard-core interactions (i.e., entropic self-assembly). We observe that upon gradual compression of the isotropic system, none of the three cases exhibits a spontaneous ordering into the expected tessellated structure: Mixtures 1 and 2 form a glassy disordered state that is shown to be metastable with respect to the tessellated phase via interfacial simulations; Mixture 3 demixes into a disordered phase and an unusual ordered phase where truncated cubes arrange in a cubic lattice while the octahedra remain disordered occupying interstitial pockets. Using polybead models for Mixtures 1 and 2, we show that the large free-energy barrier that precludes the spontaneous nucleation of the tessellating structure from the isotropic state can be overcome by introducing favorable enthalpic interactions. Our results allow identifying some relations between properties of individual species and the phase behavior of their mixtures, providing a first step toward a "chemistry" of polyhedral compounds, while also raising key questions regarding the kinetics of the pseudo "reactions" involved.

When in contact with a rough solid surface, fluids with low surface tension, such as oils and alkanes, have their lowest free energy in the fully wetted state. For applications where nonwetting by these phillic fluids is desired, some barrier must be introduced to maintain the nonwetted composite state. One way to create this free-energy barrier is to fabricate roughness with reentrant geometry, but the question remains as to whether the free-energy barrier is sufficiently high to prevent wetting. Our goal is to quantify the free-energy landscape for the wetting transition of an oily fluid on a surface of nails and identify significant surface features and conditions that maximize the wetting free-energy barrier (ΔGfwd*). This is a departure from most work on wetting, which focuses on the equilibrium composite and wetted states. We use boxed molecular dynamics (BXD) (Glowacki, D. R.; Paci, E.; Shalashilin, D. V. J. Phys. Chem. B2009, 113, 16603-16611) with a modified control scheme to evaluate both the thermodynamics and kinetics of the transition over a range of surface affinities (chemistry). We find that the reentrant geometry of the nails does create a free-energy barrier to transition for phillic chemistry whereas a corresponding system on straight posts wets spontaneously and, that doubling the nail height more than doubles ΔGfwd*. For neutral to phillic chemistry, the dewetting free-energy barrier is at least an order of magnitude higher than that for wetting, indicating an essentially irreversible wetting transition. Transition rates from BXD simulations and the associated trends agree well with those in our previous study that used forward flux sampling to compute transition rates for similar systems.

The simulation of homogeneous liquid to vapor nucleation is investigated using three rare-event algorithms, boxed molecular dynamics, hybrid umbrella sampling Monte Carlo, and forward flux sampling. Using novel implementations of these methods for efficient use in the isothermal-isobaric ensemble, the free energy barrier to nucleation and the kinetic rate are obtained for a Lennard-Jones fluid at stretched and at superheated conditions. From the free energy surface mapped as a function of two order parameters, the global density and largest bubble volume, we find that the free energy barrier height is larger when projected over bubble volume. Using a regression analysis of forward flux sampling results, we show that bubble volume is a more ideal reaction coordinate than global density to quantify the progression of the metastable liquid toward the stable vapor phase and the intervening free energy barrier. Contrary to the assumptions of theoretical approaches, we find that the bubble takes on cohesive non-spherical shapes with irregular and (sometimes highly) undulating surfaces. Overall, the resulting free energy barriers and rates agree well between the methods, providing a set of complementary algorithms useful for studies of different types of nucleation events.