Enhancing Mechanical and Biological Properties of Zinc Phosphate Dental Cement with Akermanite and Hardystonite Nanoparticles: A Synthesis and Characterization Study.

This study investigates the potential of incorporating akermanite and hardystonite nanoparticles (NPs) into commercially available zinc phosphate cement. Akermanite and hardystonite NPs were synthesized through a mechanical route and characterized using X-ray diffraction (XRD), fourier transform infrared spectroscopy (FTIR), and scanning electron microscopy (SEM). The NPs were then added to the cement at a concentration of 5 wt%, and the physical and biological properties of the resulting composite were evaluated. The results showed that the incorporation of NPs led to a significant reduction in porosity (from 12.4% to 5.6%) and a notable improvement in compressive strength (from 90 to 120 MPa) compared to the control group. MTT assay revealed that the cement containing NPs exhibited no significant toxicity and even promoted cell growth and proliferation. Specifically, cell viability increased by 15%, and cell proliferation rate increased by 20% compared to the control group. These findings suggest that the designed cement has suitable mechanical and biological properties, making it a promising material for dental and orthopedic applications.

Self-Assembly of Model Three- and Four-Patch Colloidal Particles in Two Dimensions.

A coarse-grained effective solvent model of two-patch particles is extended to study the self-assembly of three- and four-patch particles to two-dimensional honeycomb and square lattices, respectively. Employing this model, grand canonical ensemble simulations are done to calculate vapor-liquid equilibria and the critical temperatures for patchy particles of various patch widths. The range of stability of the liquid, although very limited compared to isotropic particles, which interact through a longer-range potential, depends on the patch width and on the number of patches. Biased sampling and unbiased simulations are also done to investigate the mechanism of nucleation and crystal growth for honeycomb and square lattices, self-assembled from three- and four-patch particles, respectively. A two-step mechanism governs the nucleation of both lattices. In the first step, the particles form a dense amorphous network, and in the second step, the particles inside the amorphous network reorient to form crystalline nuclei. Barrier heights for the nucleation of honeycomb and square lattices are 7.8 kBT and 7.4 kBT, which are close to the reported values for the nucleation of the kagome lattice. In agreement with confocal microscopy experiments, the self-assembly in a honeycomb lattice involves the formation of 5- to 7-membered rings. The 5- and 7-membered rings hamper the nucleation of the honeycomb lattice, through defect formation and rotation of the symmetry planes of crystals that form at their surfaces. With the progress of self-assembly, a substantial amount of restructuring of the defects and crystals in their vicinity is needed to heal the defects.

Self-Assembly Pathways of Triblock Janus Particles into 3D Open Lattices.

The self-assembly of triblock Janus particles is simulated from a fluid to 3D open lattices: pyrochlore, perovskite, and diamond. The coarse-grained model explicitly takes into account the chemical details of the Janus particles (attractive patches at the poles and repulsion around the equator) and it contains explicit solvent particles. Hydrodynamic interactions are accounted for by dissipative particle dynamics. The relative stability of the crystals depends on the patch width. Narrow, intermediate, and wide patches stabilize the pyrochlore-, the perovskite-, and the diamond-lattice, respectively. The nucleation of all three lattices follows a two-step mechanism: the particles first agglomerate into a compact and disordered liquid cluster, which does not crystallize until it has grown to a threshold size. Second, the particles reorient inside this cluster to form crystalline nuclei. The free-energy barriers for the nucleation of pyrochlore and perovskite are ≈10 kBT, which are close to the nucleation barriers of previously studied 2D kagome lattices. The barrier height for the nucleation of diamond, however, is much larger (>20 kBT), as the symmetry of the triblock Janus particles is not perfect for a diamond structure. The large barrier is associated with the reorientation of particles, i.e., the second step of the nucleation mechanism.

Understanding Humidity-Enhanced Adhesion of Geckos: Deep Neural Network-Assisted Multi-Scale Molecular Modeling.

A higher relative humidity leads to an increased sticking power of gecko feet to surfaces. The molecular mechanism responsible for this increase, however, is not clear. Capillary forces, water mediating keratin-surface contacts and water-induced softening of the keratin are proposed as candidates. In previous work, strong evidence for water mediation is found but indirect effects via increased flexibility are not completely ruled out. This article studies the latter hypothesis by a bottom-up coarse-grained mesoscale model of an entire gecko spatula designed without explicit water particles, so that capillary action and water-mediation are excluded. The elasticity of this model is adjusted with a deep neural network to atomistic elastic constants, including water at different concentrations. Our results show clearly that on nanoscopic flat surfaces, the softening of keratin by water uptake cannot nearly account for the experimentally observed increase in gecko sticking power. Here, the dominant mechanism is the mediation of keratin-surface contacts by intervening water molecules. This mechanism remains important on nanostructured surfaces. Here, however, a water-induced increase of the keratin flexibility may enable the spatula to follow surface features smaller than itself and thereby increase the number of contacts with the surface. This leads to an appreciable but not dominant contribution to the humidity-increased adhesion. Recently, by atomistic grand-canonical molecular dynamics simulation, the room-temperature isotherm is obtained for the sorption of water into gecko keratin, to the authors' knowledge, the first such relation for any beta-keratin. In this work, it relates the equilibrium water content of the keratin to the ambient relative humidity.

Molecular Structure and Dynamics in Wet Gecko ß-Keratin.

Molecular dynamics simulations are performed to investigate the molecular picture of water sorption in gecko keratin and the influence of relative humidity (RH) on the local structure and dynamics in water-swollen keratin. At low RHs, water sorption occurs through hydrogen bonding of water with the hydrophilic groups of keratin. At high RHs (>80%), additional water molecules connect to the first "layer" of amide-connected water molecules (multimolecular sorption) through hydrogen bonds, giving rise to a sigmoidal shape of the sorption isotherm. This causes the formation of large chain-like clusters surrounding the hydrophilic groups of keratin, which upon a further increase of the RH form a percolating water network. An examination of the dynamics of water molecules sorbed in keratin demonstrates that there are two states, bound and free, for water. The dynamics of water in these states depends on the RH. At low RHs, large-scale translational motions of tightly bound water molecules to keratin are needed to remake the entire hydration shell of the keratin. At high RHs (>80%), the water molecules more quickly exchange between the two states. The center-of-mass mean-square displacement of water molecules indicates a hopping motion of water molecules in the keratin solvation shell. The hopping mechanism is more pronounced at RHs < 80%. At higher RHs, water translation through water clusters (water network) dominates. We have observed two regimes for the dependence of dynamical properties on the RH: a regime of gradual increase of the dynamics over 10% < RH < 80% and a regime of drastic dynamic acceleration at RH > 80%. The latter regime begins exactly where the water uptake and the volume swelling also increase much more and where a drastic change in the elastic properties of gecko keratin has been observed. A nearly linear relation between the relaxation times for all dynamical processes and the water content of gecko keratin is observed.

Water uptake by gecko ß-keratin and the influence of relative humidity on its mechanical and volumetric properties.

Grand canonical ensemble molecular dynamics simulations are done to calculate the water content of gecko ß-keratin as a function of relative humidity (RH). For comparison, we experimentally measured the water uptake of scales of the skin of cobra Naja nigricollis. The calculated sigmoidal sorption isotherm is in good agreement with experiment. To examine the softening effect of water on gecko keratin, we have calculated the mechanical properties of dry and wet keratin samples, and we have established relations between the mechanical properties and the RH. We found that a higher RH causes a decrease in the Young's modulus, the yield stress, the yield strain, the stress at failure and an increase in the strain at failure of the gecko keratin. At low RHs (less than 80%), the change in the mechanical properties is small, with most of the changes occurring at higher RHs. The changes in the macroscopic properties of the keratin are explained by the action of sorbed water on the molecular scale. It causes keratin to swell, thereby increasing the distances between amino acids. This has a weakening effect on amino acid interactions and softens the keratin material. The effect is more pronounced at higher RHs.

Supramolecular Self-Assembly of Dipalmitoylphosphatidylcholine and Carbon Nanotubes: A Dissipative Particle Dynamics Simulation Study.

Dissipative particle dynamics simulations were performed to investigate the self-assembly of dipalmitoylphosphatidylcholine (DPPC) as a model lipid membrane on the surface of carbon nanotubes (CNTs). The influence of surface curvature of CNTs on self-assembly was investigated by performing simulations on solutions of DPPC in water in contact with CNTs of different diameters: CNT (10, 10), CNT (14, 14), CNT (20, 20), and CNT (34, 34). DPPC solutions with a wide range of concentrations were chosen to allow for formation of lipid structures of various surface densities, ranging from a submonolayer to a well-organized monolayer and a CNT covered with a lipid monolayer immersed in a planar lipid bilayer. Our results are indicative of a sequence of phase-ordering processes for DPPC on the surface of CNTs. At low surface coverages, the majority of hydrocarbon tail groups of DPPC are in contact with the CNT surface. Increasing the surface coverage leads to the formation of hemimicellar aggregates, and at high surface coverages close to the saturation limit, an organized lipid monolayer self-assembles. An examination of the mechanism of self-assembly reveals a two-step mechanism. The first step involves densification of DPPC on the CNT surface. Here, the lipid molecules do not adopt the order of the target phase (lipid monolayer on the CNT surface). In the second step, when the lipid density on the CNT surface is above a threshold value (close to saturation), the lipid molecules reorient themselves to form an organized monolayer around the tube. Here, the DPPC molecules adopt stretched conformations normal to the surface, the end hydrocarbon groups adsorb on the surface, and the head groups occupy the outermost part of the monolayer. The saturation density and the degree of lipid ordering on the CNT surface depend on the surface curvature. The saturation density increases with increased surface curvature, and better-ordered structures are formed on less curved surfaces.

How is mechanobiology involved in bone regenerative medicine?

Regenerative medicine is recognized as one of the developing sciences in the world. Repair of bone injuries using stem cells and biomaterials has been considered by reconstructive medicine researchers in recent years. Biomechanical environments play a predominant role from cells to tissues and organs. These environments are also effective in the process of bone repair. Mechanical signals control biological activity at the site of injury. These signals regulate the formation, differentiation and proliferation of different cells. They are also responsible for the formation of connective tissue and the stabilization of damaged bone. Mechanical signals are applied to cells through external or internal factors. In this review, we first introduce and review the effective and active forces in determining the fate of stem cells such as Shear Stress, Tension, Elasticity, Stiffness, etc. Then we analyze the evidence from experimental studies and clinical observations about the effect of mechanobiology on bone repair or targeted differentiation of stem cells. We have also summarized the studies conducted in recent years in several tables.

How Ethanolic Disinfectants Disintegrate Coronavirus Model Membranes: A Dissipative Particle Dynamics Simulation Study.

We have developed dissipative particle dynamics models for pure dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), and dimyristoylphosphatidylcholine (DMPC) as well as their binary and ternary mixed membranes, as coronavirus model membranes. The stabilities of pure and mixed membranes, surrounded by aqueous solutions containing up to 70 mol % ethanol (alcoholic disinfectants), have been investigated at room temperature. We found that aqueous solutions containing 5-10 mol % ethanol already have a significant weakening effect on the pure and mixed membranes. The magnitude of the effect depends on the membrane composition and the ethanol concentration. Ethanol permeabilizes the membrane, causing its lateral swelling and thickness shrinking and reducing the orientational order of the hydrocarbon tail of the bilayer. The free energy barrier for the permeation of ethanol in the bilayers is considerably reduced by the ethanol uptake. The rupture-critical ethanol concentrations causing the membrane failure are 20.7, 27.5, and 31.7 mol % in the aqueous phase surrounding pure DMPC, DOPC, and DPPC membranes, respectively. Characterizing the failure of lipid membranes by a machine-learning neural network framework, we found that all mixed binary and/or ternary membranes disrupt when immersed in an aqueous solution containing a rupture-critical ethanol concentration, ranging from 20.7 to 31.7 mol %, depending on the composition of the membrane; the DPPC-rich membranes are more intact, while the DMPC-rich membranes are least intact. Due to the tight packing of long, saturated hydrocarbon tails in DPPC, increasing the DPPC content of the mixed membrane increases its stability against the disinfectant. At high DPPC concentrations, where the DOPC and DMPC molecules are confined between the DPPC lipids, the ordered hydrocarbon tails of DPPC also induce order in the DOPC and DMPC molecules and, hence, stabilize the membrane more. Our simulations on pure and mixed membranes of a diversity of compositions reveal that a maximum ethanol concentration of 32 mol % (55 wt %) in the alcohol-based disinfectants is enough to disintegrate any membrane composed of these three lipids.

Self-Assembly of Model Triblock Janus Colloidal Particles in Two Dimensions.

A simplified two-dimensional effective-solvent model of triblock Janus particles, consisting of three interaction sites in a linear configuration, a core particle, and two particles modeling the attractive patches at the poles, is developed to study the mechanism of nucleation and self-assembly in triblock Janus particles. The potential energy parameters are tuned against phase transition temperatures and free energy barriers to the nucleation of crystalline phases, calculated from our previous detailed model of Janus particles. Vapor-liquid equilibria and critical temperatures are calculated by grand-canonical molecular dynamics simulations for particles of different patch widths. With metadynamics, phase equilibria, mechanism of nucleation, and free energy barriers to nucleation are investigated. The minimum free energy path to nucleation indicates two steps. The first step, with a higher free energy increase, consists of the densification of the fluid into a disordered cluster. In the second step, of a lower free energy barrier, the inner particles of the disordered cluster reorient to form a crystalline nucleus. This two-step mechanism of nucleation of a kagome lattice is in complete agreement with the experiment and with our previous simulations using a detailed model of Janus particles. Large systems at a slight supersaturation generate multiple crystalline domains, which are misaligned at the grain boundaries. In complete agreement with the experiment and with previous simulation results, we observe a two-step mechanism for crystal growth: melting of the smaller (less stable) crystallites to a fluid followed by recrystallization at the surface of neighboring bigger (more stable) crystallites. A comparison of the present softer modeling of a Janus particle with harder models in the literature for self-assembly of Janus particles indicates that softer potentials stabilize open lattices (e.g., kagome) more than dense lattices (e.g., hexagonal). Also, experimental locations of phase transition points and barrier heights to nucleation are better reproduced by the present model than by the existing simple models.

Mechanisms of Nucleation and Solid-Solid-Phase Transitions in Triblock Janus Assemblies.

A model, including the chemical details of core nanoparticles as well as explicit surface charges and hydrophobic patches, of triblock Janus particles is employed to simulate nucleation and solid-solid phase transitions in two-dimensional layers. An explicit solvent and a substrate are included in the model, and hydrodynamic and many-body interactions were taken into account within many-body dissipative particle dynamics simulation. In order not to impose a mechanism a priori, we performed free (unbiased) simulations, leaving the system the freedom to choose its own pathways. In agreement with the experiment and previous biased simulations, a two-step mechanism for the nucleation of a kagome lattice from solution was detected. However, a distinct feature of the present unbiased versus biased simulations is that multiple nuclei emerge from the solution; upon their growth, the aligned and misaligned facets at the grain boundaries are introduced into the system. The liquid-like particles trapped between the neighboring nuclei connect them together. A mismatch in the symmetry planes of neighboring nuclei hinders the growth of less stable (smaller) nuclei. Unification of such nuclei at the grain boundaries of misaligned facets obeys a two-step mechanism: melting of the smaller nuclei, followed by subsequent nucleation of liquid-like particles at the interface of bigger neighboring nuclei. Besides, multiple postcritical nuclei are formed in the simulation box; the growth of some of which stops due to introduction of a strain in the system. Such an incomplete nucleation/growth mechanism is in complete agreement with the recent experiments. The solid-solid (hexagonal-to-kagome) phase transition, at weak superheatings, obeys a two-step mechanism: a slower step (formation of a liquid droplet), followed by a faster step (nucleation of kagome from the liquid droplet).

The potential of urban distributed solar energy in transition economies: The case of Beirut city.

In this paper, using Lebanon's capital, Beirut, as a case study, a methodology is proposed to assess the potential for solar photovoltaics (PV) in urban areas incorporating both economic and non-economic factors. Utilizing a rich spatial dataset of solar irradiation augmented with electricity bills at the building level, the cost and benefit of installing rooftop PV systems for each building is estimated. Additionally, incentives and barriers for adopting those systems are investigated using a probabilistic choice model. The results show that Beirut city has a potential for distributed rooftop solar PV to be between 195 and 295 MWp. However, adoption rates are low at 0.49% and 1.23% for residential and commercial buildings, respectively, reflecting the limitation of financial incentives alone to promote the deployment of distributed renewable energy systems in transition economies. The impact of different incentive policy instruments and the role of solar PV in today's economic crisis in Lebanon is analyzed. The biggest impact was achieved through removing (or lowering) electricity tariff subsidy, although this option remains highly constrained by political calculus. We argue that the Lebanese government should fast-track and implement the required legal framework to facilitate and incentivize distributed power generation from renewable sources to promote both green energy and its financial resilience. The proposed modeling framework together with the results obtained in this study will have important implications for energy policy makers in Lebanon and other transition economies.

How Alcoholic Disinfectants Affect Coronavirus Model Membranes: Membrane Fluidity, Permeability, and Disintegration.

Atomistic molecular dynamics simulations have been carried out with a view to investigating the stability of the SARS-CoV-2 exterior membrane with respect to two common disinfectants, namely, aqueous solutions of ethanol and n-propanol. We used dipalmitoylphosphatidylcholine (DPPC) as a model membrane material and did simulations on both gel and liquid crystalline phases of membrane surrounded by aqueous solutions of varying alcohol concentrations (up to 17.5 mol %). While a moderate effect of alcohol on the gel phase of membrane is observed, its liquid crystalline phase is shown to be influenced dramatically by either alcohol. Our results show that aqueous solutions of only 5 and 10 mol % alcohol already have significant weakening effects on the membrane. The effects of n-propanol are always stronger than those of ethanol. The membrane changes its structure, when exposed to disinfectant solutions; uptake of alcohol causes it to swell laterally but to shrink vertically. At the same time, the orientational order of lipid tails decreases significantly. Metadynamics and grand-canonical ensemble simulations were done to calculate the free-energy profiles for permeation of alcohol and alcohol/water solubility in the DPPC. We found that the free-energy barrier to permeation of the DPPC liquid crystalline phase by all permeants is significantly lowered by alcohol uptake. At a disinfectant concentration of 10 mol %, it becomes insignificant enough to allow almost free passage of the disinfectant to the inside of the virus to cause damage there. It should be noted that the disinfectant also causes the barrier for water permeation to drop. Furthermore, the shrinking of the membrane thickness shortens the gap needed to be crossed by penetrants from outside the virus into its core. The lateral swelling also increases the average distance between head groups, which is a secondary barrier to membrane penetration, and hence further increases the penetration by disinfectants. At alcohol concentrations in the disinfectant solution above 15 mol %, we reliably observe disintegration of the DPPC membrane in its liquid crystalline phase.

Molecular Dynamics Simulation of the Ionic Liquid 1-n-Butyl-3-Methylimidazolium Methylsulfate [Bmim][MeSO4 ]: Interfacial Properties at the Silica and Vacuum Interfaces.

Molecular dynamics simulations are done to investigate the structure and dynamics of a thin [Bmim][MeO4 ] film in contact with a hydroxylated silica surface on one side and with vacuum on the other. An examination of the microscopic structure of ionic liquid (IL) film shows that strong layered anionic/cationic structures are formed at both interfaces. At the silica interface, the imidazolium rings are closer to the silica surface (compared to anions) and are coplanar with it. At the vacuum interface, the charged imidazolium ring more concentrates in the interior of the film, but the butyl side chain stretches out toward the vacuum interface. While there exists an excess concentration of the cations at the silica interface, at the vacuum interface an excess concentration of anions (dissolved in the butyl chain) is found. The influence of the interface on the dynamical properties is shown to depend on their time scales. A short-time dynamical property, such as hydrogen bond formation is not noticeably perturbed at the interface. In contrary, long-time properties such as ion-pair formation/rupture and translation of ions across the film are largely decelerated at the silica interface but are accelerate at the vacuum interface. Our findings indicate that the structural relaxation time of ion-pairs, is comparable to diffusion time scale in the IL film. Therefore, ion-pairs are not stable species; the IL is composed of short-lived ion-pairs and freely diffusing ions. However, the structural relaxation times of ion-pairs is still long enough (comparable to the time scale of diffusion) to conclude that correlated motions of counterions influence the macroscopic properties of IL, such as diffusion and ionic conductivity. In this respect, we have shown that correcting the Nernst-Einstein equation for the joint translation of ion-pairs considerably improves the accuracy of calculated ionic conductivities.

Coarse-grained molecular dynamics simulations of poly(ethylene terephthalate).

We have constructed efficient coarse-grained (CG) models of poly(ethylene terephthalate) (PET), using three mapping schemes, in which a repeat unit is lumped into either three or four beads. The CG potentials are parameterized to reproduce target distributions of an underlying accurate atomistic model [H. Eslami and F. Müller-Plathe, Macromolecules 42, 8241-8250 (2009)]. The CG simulations allow equilibration of long PET chains at all length scales. The CG results on the density of PET in melt and glassy states, chain dimension, local packing, and structure factor are in good agreement with experiment. We have established a link between the glass transition temperature and the local movements including conformational transitions and mean-square displacements of chain segments. Temperature transferabilities of the three proposed models were studied by comparing CG results on the static and thermodynamic properties of a polymer with atomistic and experimental findings. One of the three CG models has a good degree of transferability, following all inter- and intra-structural rearrangements of the atomistic model, over a broad range of temperature. Furthermore, as a distinct point of strength of CG, over atomistic, simulations, we have examined the dynamics of PET long chains, consisting of 100 repeat units, over a regime where entanglements dominate the dynamics. Performing long-time (550 ns) CG simulations, we have noticed the signature of a crossover from Rouse to reptation dynamics. However, a clear separation between the Rouse and the reptation dynamics needs much longer time simulations, confirming the experimental findings that the crossover to full reptation dynamics is very protracted.

Thermal Conductivity of Polyamide-6,6/Carbon Nanotube Composites: Effects of Tube Diameter and Polymer Linkage between Tubes.

Reverse nonequilibrium molecular dynamics simulations were done to quantify the effect of the inclusion of carbon nanotubes (CNTs) in the Polyamide-6,6 matrix on the enhancement in the thermal conductivity of polymer. Two types of systems were simulated; systems in which polymer chains were in contact with a single CNT, and those in which polymer chains were in contact with four CNTs, linked together via polymer linkers at different linkage fractions. In both cases, heat transfer in both perpendicular and parallel (to the CNT axis) directions were studied. To examine the effect of surface curvature (area) on the heat transfer between CNT and polymer, systems containing CNTs of various diameters were simulated. We found a large interfacial thermal resistance at the CNT-polymer boundary. The interfacial thermal resistance depends on the surface area of the CNT (lower resistances were seen at the interface of flatter CNTs) and is reduced by linking CNTs together via polymer chains, with the magnitude of the reduction depending on the linkage fraction. The thermal conductivity of polymer in the perpendicular direction depends on the surface proximity; it is lower at closer distances to the CNT surface and converges to the bulk value at distances as large as 2 nm. The chains at the interface of CNT conduct heat more in the parallel than in the perpendicular directions. The magnitude of this thermal conductivity anisotropy reduces with decreasing the CNT diameter and increasing the linkage fraction. Finally, microscopic parameters obtained from simulations were used to investigate macroscopic thermal conductivities of polymer nanocomposites within the framework of effective medium approximation.

Gaussian Charge Distributions for Incorporation of Electrostatic Interactions in Dissipative Particle Dynamics: Application to Self-Assembly of Surfactants.

The point charges are distributed over the soft dissipative particle dynamics (DPD) beads using a Gaussian of tunable width. Screening the Gaussian smeared charge distributions, with wider Gaussians of opposite charge, splits the electrostatic interaction into the real- and the reciprocal-space contributions. This method is validated against model test systems in the literature. The method has also been employed to study self-assembly in solutions of sodium dodecyl sulfate (SDS) in water. The critical micelle concentration (CMC) and the equilibrium concentration of free surfactants, in solutions with SDS concentrations varying from CMC to ≈20 times larger than CMC, are in close agreement with experiment. The microscopic structure of the micelles and the distributions of its hydrophobic/hydrophilic groups and counterions at the water interface are in agreement with experiment. The dynamics of monomer exchange between micelles and solution is examined in terms of the intermittent and continuous correlation functions for the fluctuation of micelle size with time. Two discrete relaxation processes, whose relaxation times differ by 2 orders of magnitude are found. Using the natural DPD time unit, defined in terms of thermal velocity, the relaxation times are an order of magnitude shorter than experimental relaxation times for monomer exchange and establishment of equilibrium between surfactants in the solution and micelles through diffusion of surfactants. However, experimentally comparable relaxation times are obtained by defining the DPD time scale such that the calculated diffusion coefficient of water corresponds to its experimental value.

Self-Assembly Mechanisms of Triblock Janus Particles.

We present a detailed model to study the nucleation of triblock Janus particles from solution. The Janus particles are modeled as cross-linked polystyrene spheres whose poles are patched with sticky alkyl groups and their middle band is covered with negative charges. To mimic the experimental conditions, solvent, counterions, and a substrate, on which the crystallization takes place, are included in the model. A many-body dissipative particle dynamics simulation technique is employed to include hydrodynamic and many-body interactions. Metadynamics simulations are performed to explore the pathways for nucleation of Kagome and hexagonal lattices. In agreement with experiment, we found that nucleation of the Kagome lattice from solution follows a two-step mechanism. The connection of colloidal particles through their patches initially generates a disordered liquid network. Subsequently, orientational rearrangements in the liquid precursors lead to the formation of ordered nuclei. Biasing the potential energy of the largest crystal, a critical nucleus appears in the simulation box, whose further growth crystallizes the whole solution. The location of the phase transition point and its shift with patch width are in very good agreement with experiment. The structure of the crystallized phase depends on the patch width; in the limit of very narrow patches strings are stable aggregates, intermediate patches stabilize the Kagome lattice, and wide patches nucleate the hexagonal phase. The scaling behavior of the calculated barrier heights confirms a first-order liquid-Kagome phase transition.

Local bond order parameters for accurate determination of crystal structures in two and three dimensions.

Local order parameters for the characterization of liquid and different two- and three-dimensional crystalline structures are presented. The order parameters are expressed in terms of the angular correlations between a vector (defined in terms of the spherical harmonics, identifying the local environment around a central particle) and its neighboring vectors. For the three-dimensional systems, we have undertaken simulation of the Lennard-Jones (12-6) particles and metallic systems at the melting temperature. The proposed order parameters are shown to accurately discriminate between liquid, fcc, hcp, and bcc phases. The simulated two-dimensional systems consist of liquid, Kagome, square, honeycomb, and hexagonal phases formed from a solution of triblock Janus colloidal particles, sedimented on the top of a supporting surface. The presented order parameters resolve all phases. A comparison was made between the predictive ability of the present order parameters and the popular three-dimensional [Lechner and Dellago, J. Chem. Phys., 2008, 129, 114707] and two-dimensional [Mermin, Phys. Rev., 1968, 176, 250] order parameters in the literature in the identification of crystal structures. In both cases, advancements in the present scheme, over the existing methods in the literature, are seen.