Search

A compact analytical form is derived via an integration approach for the interaction between a sphere and a thin rod of both finite and infinite lengths, with each object treated as a continuous medium of materials points interacting by the Lennard-Jones 12-6 potential. Expressions for the resultant forces and torques are obtained. Various asymptotic limits of the analytical sphere-rod potential are discussed., Comment: 6 pages, 2 figures

An analytical form has been derived using Ostrogradski's integration method for the interaction between two thin rods of finite lengths in arbitrary relative configurations in a 3-dimensional space, each treated as a line of material points interacting through the Lennard-Jones 12-6 potential. Simplified analytical forms for coplanar, parallel, and collinear rods are also derived. Exact expressions for the force and torque between the rods are obtained. Similar results for a point particle interacting with a thin rod are provided. These interaction potentials can be widely used for analytical descriptions and computational modeling of systems involving rod-like objects such as liquid crystals, colloids, polymers, elongated viruses and bacteria, and filamentous materials including carbon nanotubes, nanowires, biological filaments, and their bundles., Comment: 33 pages, 7 figures, including Supporting Information

Molecular dynamics simulations are used to demonstrate that a binary solvent can be used to stratify colloidal mixtures when the suspension is rapidly dried. The solvent consists of two components, one more volatile than the other. When evaporated at high rates, the more volatile component becomes depleted near the evaporation front and develops a negative concentration gradient from the bulk of the mixture to the liquid-vapor interface while the less volatile solvent is enriched in the same region and exhibit a positive concentration gradient. Such gradients can be used to drive a binary mixture of colloidal particles to stratify if one is preferentially attracted to the more volatile solvent and the other to the less volatile solvent. During solvent evaporation, the fraction of colloidal particles preferentially attracted to the less volatile solvent is enhanced at the evaporation front, whereas the colloidal particles having stronger attractions with the more volatile solvent are driven away from the interfacial region. As a result, the colloidal particles show a stratified distribution after drying, even if the two colloids have the same size., Comment: 11 pages, 6 figures, 1 page Supporting Information with 2 figures

A method of simulating the drying process of a soft matter solution with an implicit solvent model by moving the liquid-vapor interface is applied to various solution films and droplets. For a solution of a polymer and nanoparticles, we observe "polymer-on-top" stratification, similar to that found previously with an explicit solvent model. Furthermore, "polymer-on-top" is found even when the nanoparticle size is smaller than the radius of gyration of the polymer chains. For a suspension droplet of a bidisperse mixture of nanoparticles, we show that core-shell clusters of nanoparticles can be obtained via the "small-on-outside" stratification mechanism at fast evaporation rates. "Large-on-outside" stratification and uniform particle distribution are also observed when the evaporation rate is reduced. Polymeric particles with various morphologies, including Janus spheres, core-shell particles, and patchy particles, are produced from drying droplets of polymer solutions by combining fast evaporation with a controlled interaction between the polymers and the liquid-vapor interface. Our results validate the applicability of the moving interface method to a wide range of drying systems. The limitations of the method are pointed out and cautions are provided to potential practitioners on cases where the method might fail., Comment: 14 pages, 7 figures

Molecular dynamics simulations are used to investigate the conformations of a single polymer chain, represented by the Kremer-Grest bead-spring model, in a solution with a Lennard-Jones liquid as the solvent when the interaction strength between the polymer and solvent is varied. Results show that when the polymer-solvent interaction is unfavorable, the chain collapses as one would expect in a poor solvent. For more attractive polymer-solvent interactions, the solvent quality improves and the chain is increasingly solvated and exhibits ideal and then swollen conformations. However, as the polymer-solvent interaction strength is increased further to be more than about twice of the strength of the polymer-polymer and solvent-solvent interactions, the chain exhibits an unexpected collapsing behavior. Correspondingly, for strong polymer-solvent attractions, phase separation is observed in the solutions of multiple chains. These results indicate that the solvent becomes effectively poor again with very attractive polymer-solvent interactions. Nonetheless, the mechanism of chain collapsing and phase separation in this limit differs from the case with a poor solvent rendered by unfavorable polymer-solvent interactions. In the latter, the solvent is excluded from the domain of the collapsed chains while in the former, the solvent is still present in the pervaded volume of a collapsed chain or in the polymer-rich domain that phase separates from the pure solvent. In the limit of strong polymer-solvent attractions, the solvent behaves as a glue to stick monomers together, causing a single chain to collapse and multiple chains to aggregate and phase separate., Comment: 11 pages, 10 figures, 3-page Supporting Information

We investigate the behavior of hydrated sulfonated polysulfones over a range of ion contents through differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FTIR), and molecular dynamics (MD) simulations. Experimental evidence shows that at comparable ion contents, the spacing between the ionic groups along the polymer backbone can significantly impact the amount of melting water present in the polymer. When we only consider water molecules that can hydrogen bond to four neighboring water molecules as the melting water, the MD simulation results are found to agree with the experimental data. The states of water measured by DSC can therefore be described as "aggregated" (or bulk-like) for the melting component, and "isolated" for the nonmelting part. Using this physical picture, a polymer with more aggregated ions has a higher content of melting water, while a polymer at the same ion content but with more dispersed ions has a lower content of melting water. Therefore, ions should be well dispersed to minimize the amount of bulk-like water in ionic polymer membranes., Comment: 13 pages, 10 figures

We present the results of large scale molecular dynamics simulations aimed at understanding the origins of high friction coefficients in pure metals, and their concomitant reduction in alloys and composites. We utilize a series of targeted simulations to demonstrate that different slip mechanisms are active in the two systems, leading to differing frictional behavior. Specifically, we show that in pure metals, sliding occurs along the crystallographic slip planes, whereas in alloys shear is accommodated by grain boundaries. In pure metals, there is significant grain growth induced by the applied shear stress and the slip planes are commensurate contacts with high friction. However, the presence of dissimilar atoms in alloys suppresses grain growth and stabilizes grain boundaries, leading to low friction via grain boundary sliding., Comment: 8 pages, 7 figures, in a Topical Collection of Tribology Letters in memory of Prof. Mark O. Robbins

We use molecular dynamics simulations to probe hydration, ion spacing, and cation-anion interaction in two sulfonated polysulfones with different ion distributions along the polymer backbone. At room temperature, these polymers remain in a glassy state even with water contents more than 10%. At the equilibrium water uptake, the ions exhibit a similar level of hydration as they would in their saturated aqueous solution. The framework of Manning's limiting law for counterion condensation is used to examine ionic interactions in the simulated polysulfones. The dielectric constant that the ions experience can be well approximated by a volume-weighted average of the dielectric constants of the polymer backbone and water. Our results show that a reasonable estimate of the average inter-ion distance, b, is obtained by using the distance where the sulfonate-sulfonate coordination number reaches 1. The spacing of the sulfonate ions along the polysulfone backbone plays a role in determining their spatial distribution inside the hydrated polymer. As a result, the value of b is slightly larger for polymers where the sulfonate ions are more evenly spaced along the backbone, which is consistent with experimental evidence. The simulations reveal that the sulfonate ions and sodium counterions form fibrillar aggregates at water contents below the equilibrium water uptake. Such extensive ionic aggregates are expected to facilitate ion transport in sulfonated polysulfone membranes, without the need for long-range chain motion as in the case of traditional rubbery ionic polymers. Our estimates for the dielectric constant and b are used in conjunction with Manning's theory to estimate the fraction of counterions condensed to the fixed ions. The prediction of Manning's theory agrees well with the simulation result., Comment: 15 pages, 18 figures, 1-page Supporting Information

A coarse-grained model is developed to allow large-scale molecular dynamics (MD) simulations of a branched polyetherimide derived from two backbone monomers [4,4'-bisphenol A dianhydride (BPADA) and m-phenylenediamine (MPD)], a chain terminator [phthalic anhydride (PA)], and a branching agent [tris[4-(4-aminophenoxy)phenyl] ethane (TAPE)]. An atomistic model is first built for the branched polyetherimide. A systematic protocol based on chemistry-informed grouping of atoms, derivation of bond and angle interactions by direct Boltzmann inversion, and parameterization of nonbonded interactions by potential of mean force (PMF) calculations via gas-phase MD simulations of atomic group pairs, is used to construct the coarse-grained model. A six-pair geometry, with one atomic group at the center and six replicates of the other atomic group placed surrounding the central group in a NaCl structure, has been demonstrated to significantly speed up the PMF calculations and partially capture the many-body aspect of the PMFs. Furthermore, we propose a correction term to the PMFs that can make the resulting coarse-grained model transferable temperature-wise, by enabling the model to capture the thermal expansion property of the polymer. The coarse-grained model has been applied to explore the mechanical, structural, and rheological properties of the branched polyetherimide., Comment: 19 pages, 11 figures, 4-page Supporting Information

Glass transition temperature ($T_{\text{g}}$) plays an important role in controlling the mechanical and thermal properties of a polymer. Polyimides are an important category of polymers with wide applications because of their superior heat resistance and mechanical strength. The capability of predicting $T_{\text{g}}$ for a polyimide $a~priori$ is therefore highly desirable in order to expedite the design and discovery of new polyimide polymers with targeted properties and applications. Here we explore three different approaches to either compute $T_{\text{g}}$ for a polyimide via all-atom molecular dynamics (MD) simulations or predict $T_{\text{g}}$ via a mathematical model generated by using machine-learning algorithms to analyze existing data collected from literature. Our simulations reveal that $T_{\text{g}}$ can be determined from examining the diffusion coefficient of simple gas molecules in a polyimide as a function of temperature and the results are comparable to those derived from data on polymer density versus temperature and actually closer to the available experimental data. Furthermore, the predictive model of $T_{\text{g}}$ derived with machine-learning algorithms can be used to estimate $T_{\text{g}}$ successfully within an uncertainty of about 20 degrees, even for polyimides yet to be synthesized experimentally., Comment: 12 pages, 10 figures, 25-page Supporting Information

We report relaxation dynamics of glycerol-water mixtures as probed by megahertz-to-terahertz dielectric spectroscopy in a frequency range from 50 MHz to 0.5 THz at room temperature. The dielectric relaxation spectra reveal several polarization processes at the molecular level with different time constants and dielectric strengths, providing an understanding of the hydrogen-bonding network in glycerol-water mixtures. We have determined the structure of hydration shells around glycerol molecules and the dynamics of bound water as a function of glycerol concentration in solutions using the Debye relaxation model. The experimental results show the existence of a critical glycerol concentration of ~7.5 mol %, which is related to the number of water molecules in the hydration layer around a glycerol molecule. At higher glycerol concentrations, water molecules dispersed in a glycerol network become abundant and eventually dominate and four distinct relaxation processes emerge in the mixtures. The relaxation dynamics and hydration structure in glycerol-water mixtures are further probed with molecular dynamics simulations, which confirm the physical picture revealed by the dielectric spectroscopy., Comment: 15 pages

A Monte Carlo (MC) simulation method based on the Gillespie algorithm is developed for the polymerization of branched polyetherimides from two back-bone monomers [4,4'-bisphenol A dianhydride (BPADA) and m-phenylenediamine (MPD)], a chain terminator [phthalic anhydride (PA)], and a branching agent [tris[4-(4-aminophenoxy)phenyl] ethane (TAPE)]. This polymerization involves 4 reactions that all can be reduced to a condensation reaction between an amine group and a carboxylic anhydride group. By comparing the MC simulation results to the predictions of the Flory-Stockmayer theory on the molecular weight distribution, we show that the rates of the 4 reactions in the MC simulations should be set based on the concentrations of the functional groups on the monomers involved in each reaction. Using the MC simulations, we show that the Flory-Stockmayer theory predicts the molecular weight distribution well for systems below the gel point that is set by the functionality of the branching agent but starts to fail for systems around or above the gel point. However, for all the systems the MC simulations can be used to reliably predict the molecular weight distribution. Even for a macroscopic system, a converging distribution can be quickly obtained through the MC simulations on a system of only a few hundred to a few thousand monomers but with the same molar ratios of monomers as in the macroscopic system., Comment: 12 pages, 9 figures, 5 tables

Large scale molecular dynamics simulations are used to study drying suspensions of a binary mixture of large and small particles in explicit and implicit solvents. The solvent is first modeled explicitly and then mapped to a uniform viscous medium by matching the diffusion coefficients and the pair correlation functions of the particles. `Small-on-top' stratification of the particles, with an enrichment of the smaller ones at the receding liquid-vapor interface during drying, is observed in both models under the same drying conditions. With the implicit solvent model, we are able to model much thicker films and study the effect of the initial film thickness on the final distribution of particles in the dry film. Our results show that the degree of stratification is controlled by the P\'{e}clet number defined using the initial film thickness as the characteristic length scale. When the P\'{e}clet numbers of large and small particles are much larger than 1, the degree of `small-on-top' stratification is first enhanced and then weakens as the P\'{e}clet numbers are increased., Comment: 10 pages, 7 figures

A potential strategy for controlling stratification in a drying suspension of bidisperse particles is studied using molecular dynamics simulations. When the suspension is maintained at a constant temperature during fast drying, it can exhibit "small-on-top" stratification with an accumulation (depletion) of smaller (larger) particles in the top region of the drying film, consistent with the prediction of current theories based on diffusiophoresis. However, when only the region near the substrate is thermalized at a constant temperature, a negative temperature gradient develops in the suspension because of evaporative cooling at the liquid-vapor interface. Since the associated thermophoresis is stronger for larger nanoparticles, a higher fraction of larger nanoparticles migrate to the top of the drying film at fast evaporation rates. As a result, stratification is converted to "large-on-top". Very strong "small-on-top" stratification can be produced with a positive thermal gradient in the drying suspension. Here we explore a way to produce a positive thermal gradient by thermalizing the vapor at a temperature higher than that of the solvent. Possible experimental approaches to realize various thermal gradients in a suspension undergoing solvent evaporation, and thus to produce different stratification states in the drying film, are suggested., Comment: 10 pages, 4 figures, supporting information (17 pages, 15 figures)

We study the meniscus on the outside of a small spherical particle with radius $R$ at a liquid-vapor interface. The liquid is confined in a cylindrical container with a finite radius $L$ and has a contact angle $\pi/2$ at the container surface. The center of the particle is placed at various heights along the central axis of the container. By varying $L$, we are able to systematically study the crossover of the meniscus from nanometer to macroscopic scales. The meniscus rise or depression on the particle is found to grow as $\ln (2L/R)$ when $R\ll L\ll \kappa^{-1}$ with $\kappa^{-1}$ being the capillary length and saturate to a value predicted by the Derjaguin-James formula when $R \ll \kappa^{-1} \ll L$. The capillary force on the particle exhibits a linear dependence on the particle's displacement from its equilibrium position at the interface when the displacement is small. The associated spring constant is found to be $2\pi\gamma\ln^{-1} (2L/R)$ for $L\ll \kappa^{-1}$ and saturates to $2\pi\gamma\ln^{-1} (3.7\kappa^{-1}/R)$ for $L\gg \kappa^{-1}$. At nanometer scales, we perform molecular dynamics simulations of the described geometry and the results agree well with the predictions of the macroscopic theory of capillarity. At micrometer to macroscopic scales, comparison to experiments by Anachkov \textit{et al.} [Soft Matter {\bf 12}, 7632 (2016)] shows that the finite span of a liquid-vapor or liquid-liquid interface needs to be considered to interpret experimental data collected with $L \sim \kappa^{-1}$., Comment: 16 pages, 11 figures

The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus crucial to uncover the mystery of hydration structure and dynamics as well as their coupling to collective motions of proteins in aqueous solutions. Here we report dielectric properties of aqueous bovine serum albumin protein solutions as a model system using an extremely sensitive dielectric spectrometer with frequencies spanning from megahertz to terahertz. The dielectric relaxation spectra reveal several polarization mechanisms at the molecular level with different time constants and dielectric strengths, reflecting the complexity of protein-water interactions. Combining the effective-medium approximation and molecular dynamics simulations, we have determined collective vibrational modes at terahertz frequencies and the number of water molecules in the tightly-bound and loosely-bound hydration layers. High-precision measurements of the number of hydration water molecules indicate that the dynamical influence of proteins extends beyond the first solvation layer, to around 7 {\AA} distance from the protein surface, with the largest slowdown arising from water molecules directly hydrogen-bonded to the protein. Our results reveal critical information of protein dynamics and protein-water interfaces, which determine biochemical functions and reactivity of proteins., Comment: 16 pages, 5 figures, The Journal of Physical Chemistry B, 2018

Large scale molecular dynamics simulations for bidisperse nanoparticle suspensions with an explicit solvent are used to investigate the effects of evaporation rates and volume fractions on the nanoparticle distribution during drying. Our results show that ``small-on-top'' stratification can occur when ${\rm Pe}_s\phi_s \gtrsim c$ with $c\sim 1$, where ${\rm Pe}_s$ is the P\'{e}clet number and $\phi_s$ is the volume fraction of the smaller particles. This threshold of ${\rm Pe}_s\phi_s$ for ``small-on-top'' is larger by a factor of $\sim\alpha^2$ than the prediction of the model treating solvent as an implicit viscous background, where $\alpha$ is the size ratio between the large and small particles. Our simulations further show that when the evaporation rate of the solvent is reduced, the ``small-on-top'' stratification can be enhanced, which is not predicted by existing theories. This unexpected behavior is explained with thermophoresis associated with a positive gradient of solvent density caused by evaporative cooling at the liquid-vapor interface. For ultrafast evaporation the gradient is large and drives the nanoparticles toward the liquid/vapor interface. This phoretic effect is stronger for larger nanoparticles and consequently the ``small-on-top'' stratification becomes more distinct when the evaporation rate is slower (but not too slow such that a uniform distribution of nanoparticles in the drying film is produced), as thermophoresis that favors larger particles on the top is mitigated. A similar effect can lead to ``large-on-top'' stratification for ${\rm Pe}_s\phi_s$ above the threshold when ${\rm Pe}_s$ is large but $\phi_s$ is small. Our results reveal the importance of including the solvent explicitly when modeling evaporation-induced particle separation and organization and point to the important role of density gradients brought about by ultrafast evaporation., Comment: 11 pages, 4 figures, supporting information (19 pages, 19 figures)

We systematically study the meniscus on the outside of a small circular cylinder vertically immersed in a liquid bath in a cylindrical container that is coaxial with the cylinder. The cylinder has a radius $R$ much smaller than the capillary length, $\kappa^{-1}$, and the container radius, $L$, is varied from a small value comparable to $R$ to $\infty$. In the limit of $L \ll \kappa^{-1}$, we analytically solve the general Young-Laplace equation governing the meniscus profile and show that the meniscus height, $\Delta h$, scales approximately with $R\ln (L/R)$. In the opposite limit where $L \gg \kappa^{-1}$, $\Delta h$ becomes independent of $L$ and scales with $R\ln (\kappa^{-1}/R)$. We implement a numerical scheme to solve the general Young-Laplace equation for an arbitrary $L$ and demonstrate the crossover of the meniscus profile between these two limits. The crossover region has been determined to be roughly $0.4\kappa^{-1} \lesssim L \lesssim 4\kappa^{-1}$. An approximate analytical expression has been found for $\Delta h$, enabling its accurate prediction at any values of $L$ that ranges from microscopic to macroscopic scales., Comment: 9 pages, 6 figures

Ordering nanoparticles into a desired super-structure is often crucial for their technological applications. We use molecular dynamics simulations to study the assembly of nanoparticles in a polymer brush randomly grafted to a planar surface as the solvent evaporates. Initially, the nanoparticles are dispersed in a solvent that wets the polymer brush. After the solvent evaporates, the nanoparticles are either inside the brush or adsorbed at the surface of the brush, depending on the strength of the nanoparticle-polymer interaction. For strong nanoparticle-polymer interactions, a 2-dimensional ordered array is only formed when the brush density is finely tuned to accommodate a single layer of nanoparticles. When the brush density is higher or lower than this optimal value, the distribution of nanoparticles shows large fluctuations in space and the packing order diminishes. For weak nanoparticle-polymer interactions, the nanoparticles order into a hexagonal array on top of the polymer brush as long as the grafting density is high enough to yield a dense brush. An interesting healing effect is observed for a low-grafting-density polymer brush that can become more uniform in the presence of weakly adsorbed nanoparticles., Comment: 9 pages, 6 figures

A correlation is established between the macro-scale friction regimes of metals and a transition between two dominant atomistic mechanisms of deformation. Metals tend to exhibit bi-stable friction behavior -- low and converging or high and diverging. These general trends in behavior are shown to be largely explained using a simplified model based on grain size evolution, as a function of contact stress and temperature, and are demonstrated for pure copper and gold. Specifically, the low friction regime is linked to the formation of ultra-nanocrystalline surface films (10 to 20 nm), driving toward shear accommodation by grain boundary sliding. Above a critical combination of stress and temperature -- demonstrated to be a material property -- shear accommodation transitions to dislocation dominated plasticity and high friction. We utilize a combination of experimental and computational methods to develop and validate the proposed structure-property relationship. This quantitative framework provides a shift from phenomenological to mechanistic and predictive fundamental understanding of friction for crystalline materials, including engineering alloys., Comment: 26 pages, 11 figures

Molecular dynamics simulations are used to study capillary adhesion from a nanometer scale liquid bridge between two parallel flat solid surfaces. The capillary force and the meniscus shape of the bridge are computed as the separation between the solid surfaces is varied. Macroscopic theory predicts the meniscus shape and the contribution of liquid/vapor interfacial tension to the capillary force quite accurately for separations as small as 2 or 3 molecular diameters (1-2nm). However the total capillary force differs in sign and magnitude from macroscopic theory for separations less than about 5nm (8-10 diameters) because of molecular layering that is not included in macroscopic theory. For these small separations, the pressure tensor in the fluid becomes anisotropic. The components in the plane of the surface vary smoothly and are consistent with theory based on the macroscopic surface tension. Capillary adhesion is affected by only the perpendicular component, which has strong oscillations as the molecular layering changes., Comment: 9 pages, 6 figures, Langmuir, 2016

Large scale molecular dynamics simulations are used to study the dispersion of nanoparticles (NPs) in a polymer film during solvent evaporation. As the solvent evaporates, a dense polymer-rich skin layer forms at the liquid/vapor interface, which is either NP rich or poor depending on the strength of the NP/polymer interaction. When the NPs are strongly wet by the polymer, the NPs accumulate at the interface and form layers. However when the NPs are only partially wet by the polymer, most NPs are uniformly distributed in the bulk of the polymer film with the dense skin layer serving as a barrier to prevent the NPs from moving to the interface. Our results point to a possible route to employ less favorable NP/polymer interactions and fast solvent evaporation to uniformly disperse NPs in a polymer film, contrary to the common belief that strong NP/polymer attractions are needed to make NPs well dispersed in polymer nanocomposites., Comment: 7 pages, 6 figures

Molecular dynamics simulations are used to study the capillary adhesion from a nonvolatile liquid meniscus between a spherical tip and a flat substrate. The atomic structure of the tip, the tip radius, the contact angles of the liquid on the two surfaces, and the volume of the liquid bridge are varied. The capillary force between the tip and substrate is calculated as a function of their separation h. The force agrees with continuum predictions for h down to ~ 5 to 10nm. At smaller h, the force tends to be less attractive than predicted and has strong oscillations. This oscillatory component of the capillary force is completely missed in the continuum theory, which only includes contributions from the surface tension around the circumference of the meniscus and the pressure difference over the cross section of the meniscus. The oscillation is found to be due to molecular layering of the liquid confined in the narrow gap between the tip and substrate. This effect is most pronounced for large tip radii and/or smooth surfaces. The other two components considered by the continuum theory are also identified. The surface tension term, as well as the meniscus shape, is accurately described by the continuum prediction for h down to ~ 1nm, but the capillary pressure term is always more positive than the corresponding continuum result. This shift in the capillary pressure reduces the average adhesion by a factor as large as 2 from its continuum value and is found to be due to an anisotropy in the pressure tensor. The cross-sectional component is consistent with the capillary pressure predicted by the continuum theory (i.e., the Young-Laplace equation), but the normal pressure that determines the capillary force is always more positive than the continuum counterpart., Comment: 16 pages, 14 figures

The efficient and controlled assembly of complex structures from macromolecular building blocks is a critical open question in both biological systems and nanoscience. Using molecular dynamics simulations we study the self-assembly of tubular structures from model macromolecular monomers with multiple binding sites on their surfaces [Cheng et al., Soft Matter 8, 5666-5678 (2012)]. In this work we add chirality to the model monomer and a lock-and-key interaction. The self-assembly of free monomers into tubules yields a pitch value that often does not match the chirality of the monomer (including achiral monomers). We show that this mismatch occurs because of a twist deformation that brings the lateral interaction sites into alignment when the tubule pitch differs from the monomer chirality. The energy cost for this deformation is small as the energy distributions substantially overlap for small differences in the pitch and chirality. In order to control the tubule pitch by preventing the twist deformation, the interaction between the vertical surfaces must be increased without resulting in kinetically trapped structures. For this purpose, we employ the lock-and-key interactions and obtain good control of the self-assembled tubule pitch. These results explain some fundamental features of microtubules. The vertical interaction strength is larger than the lateral in microtubules because this yields a controlled assembly of tubules with the proper pitch. We also generally find that the control of the assembly into tubules is difficult, which explains the wide range of pitch and protofilament number observed in microtubule assembly., Comment: To appear in Soft Matter, 14 pages, 11 figures, 2 tables, Supplementary Material included

While evaporating solvent is a widely used technique to assemble nano-sized objects into desired superstructures, there has been limited work on how the assembled structures are affected by the physical aspects of the process. We present large scale molecular dynamics simulations of the evaporation-induced assembly of nanoparticles suspended in a liquid that evaporates in a controlled fashion. The quality of the nanoparticle crystal formed just below the liquid/vapor interface is found to be better at relatively slower evaporation rates, as less defects and grain boundaries appear. This trend is understood as the result of the competition between the accumulation and diffusion times of nanoparticles at the liquid/vapor interface. When the former is smaller, nanoparticles are deposited so fast at the interface that they do not have sufficient time to arrange through diffusion, which leads to the prevalence of defects and grain boundaries. Our results have important implications in understanding assembly of nanoparticles and colloids in non-equilibrium liquid environments., Comment: 8 pages, 5 figures, to appear in Journal of Chemical Physics

Large-scale molecular dynamics simulations are used to simulate a layer of nanoparticles diffusing on the surface of a liquid. Both a low viscosity liquid, represented by Lennard-Jones monomers, and a high viscosity liquid, represented by linear homopolymers, are studied. The organization and diffusion of the nanoparticles are analyzed as the nanoparticle density and the contact angle between the nanoparticles and liquid are varied. When the interaction between the nanoparticles and liquid is reduced the contact angle increases and the nanoparticles ride higher on the liquid surface, which enables them to diffuse faster. In this case the short range order is also reduced as seen in the pair correlation function. For the polymeric liquids, the out-of-layer fluctuation is suppressed and the short range order is slightly enhanced. However, the diffusion becomes much slower and the mean square displacement even shows sub-linear time dependence at large times. The relation between diffusion coefficient and viscosity is found to deviate from that in bulk diffusion. Results are compared to simulations of the identical nanoparticles in 2-dimensions., Comment: 8 pages, 9 figures

Understanding the complex self-assembly of biomacromolecules is a major outstanding question. Microtubules are one example of a biopolymer that possesses characteristics quite distinct from standard synthetic polymers that are derived from its hierarchical structure. In order to understand how to design and build artificial polymers that possess features similar to those of microtubules, we have initially studied the self-assembly of model monomers into a tubule geometry. Our model monomer has a wedge shape with lateral and vertical binding sites that are designed to form tubules. We used molecular dynamics simulations to study the assembly process for a range of binding site interaction strengths. In addition to determining the optimal regime for obtaining tubules, we have calculated a diagram of the structures that form over a wide range of interaction strengths. Unexpectedly, we find that the helical tubules form, even though the monomer geometry is designed for nonhelical tubules. We present the detailed dynamics of the tubule self-assembly process and show that the interaction strengths must be in a limited range to allow rearrangement within clusters. We extended previous theoretical methods to treat our system and to calculate the boundaries between different structures in the diagram., Comment: 15 pages, 11 figures

Evaporation and condensation at a liquid/vapor interface are ubiquitous interphase mass and energy transfer phenomena that are still not well understood. We have carried out large scale molecular dynamics simulations of Lennard-Jones (LJ) fluids composed of monomers, dimers, or trimers to investigate these processes with molecular detail. For LJ monomers in contact with a vacuum, the evaporation rate is found to be very high with significant evaporative cooling and an accompanying density gradient in the liquid domain near the liquid/vapor interface. Increasing the chain length to just dimers significantly reduces the evaporation rate. We confirm that mechanical equilibrium plays a key role in determining the evaporation rate and the density and temperature profiles across the liquid/vapor interface. The velocity distributions of evaporated molecules and the evaporation and condensation coefficients are measured and compared to the predictions of an existing model based on kinetic theory of gases. Our results indicate that for both monatomic and polyatomic molecules, the evaporation and condensation coefficients are equal when systems are not far from equilibrium and smaller than one, and decrease with increasing temperature. For the same reduced temperature $T/T_c$, where $T_c$ is the critical temperature, these two coefficients are higher for LJ dimers and trimers than for monomers, in contrast to the traditional viewpoint that they are close to unity for monatomic molecules and decrease for polyatomic molecules. Furthermore, data for the two coefficients collapse onto a master curve when plotted against a translational length ratio between the liquid and vapor phase., Comment: revised version, 15 pages, 15 figures, to appear in J. Chem. Phys

Molecular dynamics simulations are used to study different definitions of contact at the atomic scale. The roles of temperature, adhesive interactions and atomic structure are studied for simple geometries. An elastic, crystalline substrate contacts a rigid, atomically flat surface or a spherical tip. The rigid surface is formed from a commensurate or incommensurate crystal or an amorphous solid. Spherical tips are made by bending crystalline planes or removing material outside a sphere. In continuum theory the fraction of atomically flat surfaces that is in contact rises sharply from zero to unity when a load is applied. This simple behavior is surprisingly difficult to reproduce with atomic scale definitions of contact. Due to thermal fluctuations, the number of atoms making contact at any instant rises linearly with load over a wide range of loads. Pressures comparable to the ideal hardness are needed to achieve full contact at typical temperatures. A simple harmonic mean-field theory provides a quantitative description of this behavior and explains why the instantaneous forces on atoms have a universal exponential form. Contact areas are also obtained by counting the number of atoms with a time-averaged repulsive force. For adhesive interactions, the resulting area is nearly independent of temperature and averaging interval, but usually rises from zero to unity over a range of pressures that is comparable to the ideal hardness. The only exception is the case of two identical commensurate surfaces. For nonadhesive surfaces, the mean pressure is repulsive if there is any contact during the averaging interval $\Delta t$. The associated area is very sensitive to $\Delta t$ and grows monotonically. Similar complications are encountered in defining contact areas for spherical tips., Comment: 18 pages, 11 figures

An elastic membrane that is forced to reside in a container smaller than its natural size will deform and, upon further volume reduction, eventually crumple. The crumpled state is characterized by the localization of energy in a complex network of highly deformed crescent-like regions joined by line ridges. Previous studies have focused on the onset of the crumpled state by analyzing the mechanical response and stability of a conical dislocation, while others have simulated the highly packed regime neglecting the importance of the connectivity of the membrane. Here we show, through a combination of experiments, numerical simulations, and analytic approach, that the emergence of new regions of high stretching is a generic outcome when a self avoiding membrane is subject to a severe geometrical constraint. We demonstrate that, at moderate packing fraction, interlayer interactions produce a response equivalent to the one of a thicker membrane that has the shape of the deformed one. Evidence is found that friction plays a key role stabilizing the folded structures., Comment: 10 pages

Molecular dynamics simulations are used to study contact between a rigid, nonadhesive, spherical tip with radius of order 30nm and a flat elastic substrate covered with a fluid monolayer of adsorbed chain molecules. Previous studies of bare surfaces showed that the atomic scale deviations from a sphere that are present on any tip constructed from discrete atoms lead to significant deviations from continuum theory and dramatic variability in friction forces. Introducing an adsorbed monolayer leads to larger deviations from continuum theory, but decreases the variations between tips with different atomic structure. Although the film is fluid, it remains in the contact and behaves qualitatively like a thin elastic coating except for certain tips at high loads. Measures of the contact area based on the moments or outer limits of the pressure distribution and on counting contacting atoms are compared. The number of tip atoms making contact in a time interval grows as a power of the interval when the film is present and logarithmically with the interval for bare surfaces. Friction is measured by displacing the tip at a constant velocity or pulling the tip with a spring. Both static and kinetic friction rise linearly with load at small loads. Transitions in the state of the film lead to nonlinear behavior at large loads. The friction is less clearly correlated with contact area than load., Comment: RevTex4, 17 pages, 13 figures