arXiv subjects

Arash Nikoubashman

Publications and source records attributed to Arash Nikoubashman.

At least 19 recordsLinked to original sources

arXiv2026

Controlling Porosity in Supraparticles Composed of Colloidal Rods and Spheres

Supraparticles (SPs) are assemblies of colloidal particles whose properties can be tuned by modifying the chemistry, shape, and size of the colloidal particles as well as their arrangement in the SP. SPs with internal porosity are of particular interest for catalysis, photonics, and adsorption applications because of their high surface area and tunable pore size distribution. SPs are often fabricated by droplet drying, and the nonequilibrium nature of drying processes may provide an additional handle to control particle arrangement within the SP. Here, we use mesoscale particle-based simulations to explore the drying-induced assembly of SPs made from rod-shaped and spherical colloidal particles. We selectively remove one type of particle after drying and characterize the structure of the resulting porous SP. We find that the remaining particles form connected networks for most compositions, with rods percolating at lower volume fractions than spheres. Most of the resulting void volume forms a single contiguous space whose surface area closely follows the total surface area of the remaining component. The pore-size distribution, however, depends strongly on sphere size and on the removed component, reflecting differences in sphere-clustering and rod-bundling before removal. This work provides new insight into how particle size and shape, as well as processing conditions, might be used to manipulate porosity in SPs.

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arXiv2025

Accurate coarse-graining of small organic molecules in melts and thin films using density-dependent potentials

Conjugated organic molecules play a central role in a wide range of optoelectronic devices, including organic light-emitting diodes, organic field-effect transistors, and organic solar cells. A major bottleneck in the computational design of these materials is the discrepancy between simulation and experimental time and length scales. Coarse-graining (CG) offers a promising solution to bridge this gap by reducing redundant degrees of freedom and smoothing the potential energy landscape, thereby significantly accelerating molecular dynamics simulations. However, standard CG models are typically parameterized from homogeneous bulk simulations and assume density-independent effective interactions. As a consequence, they often fail to replicate inhomogeneous systems, such as (free-standing) thin films, due to an incorrect representation of liquid-vacuum interfacial properties. In this work, we develop a CG parametrization strategy that incorporates local-density-dependent potentials to capture material heterogeneities. We evaluate the methodology by simulating free-standing films and comparing interfacial orientational order parameters between all-atom and CG simulations. The resulting CG models accurately reproduce bulk densities and radial distribution functions as well as molecular orientations at the liquid-vacuum interface. This work paves the way for reliable, computation-driven predictions of atomically resolved interfacial ordering in organic molecular systems.

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arXiv2025

Molecular simulations of phase separation in elastic polymer networks

Phase separation within polymer networks plays a central role in shaping the structure and mechanics of both synthetic materials and living cells, including the formation of biomolecular condensates within cytoskeletal networks. Previous experiments and theoretical studies indicate that network elasticity can regulate demixing and stabilize finite-sized domains, yet the microscopic origin of this size selection remains elusive. Here, we use coarse-grained molecular dynamics simulations with implicit solvent to investigate how network architecture controls phase separation and limits domain growth. By systematically varying chain contour length, chain rigidity, and network topology, we uncover that finite domains emerge when intrinsic chain- or network-level length scales, such as persistence length or entanglement length, impose local constraints on coarsening. Further, the size of these finite domains is highly correlated with these microscopic network properties, but depends surprisingly little on bulk elasticity. Taken together, our findings establish a molecular basis for understanding droplet formation in polymer networks, and provide guiding principles for engineering materials and interpreting condensate behavior in cells.

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arXiv2025

Cation accumulation drives the preferential partitioning of DNA in an aqueous two-phase system

Mixtures of polyethylene glycol (PEG) and dextran (Dex) represent a widely used class of aqueous two-phase systems (ATPS), with applications ranging from the purification of various biomolecules such as nucleic acids to the synthesis of protocells. A key feature underlying these applications is the selective accumulation of biomolecules within Dex-rich droplets in an aqueous PEG phase, but the physical origin of this partitioning remains unclear. Entropic interactions were long assumed to be the primary driving force; however, our systematic experiments using DNA of different lengths indicate that entropy alone cannot fully explain the observed behavior. We identify an additional and previously underappreciated contribution from electrostatic interactions: Dex carries a slightly more negative charge than PEG, which drives preferential cation accumulation in the Dex-rich phase. These counterions facilitate the selective partitioning of DNA inside the Dex-rich droplets. This mechanism explains the dependency of DNA uptake in Dex-rich droplets on polymer length and salt concentration. Our findings establish that Donnan-type ion partitioning plays a crucial role in the localization of long nucleic acids in Dex-rich droplets, offering a unified explanation for this long-standing phenomenon. They lay the foundation for designing ATPS-based systems and help elucidate the physicochemical principles of biomolecular partition upon phase separation in cells.

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arXiv2025

From Heteropolymer Stiffness Distributions to Effective Homopolymers: A Conformational Analysis of Intrinsically Disordered Proteins

Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To investigate these effects, we employ a discretized heterogeneous worm-like chain model, where the local persistence lengths are drawn from a Gaussian distribution. In the first part, we develop a theoretical model that maps such heterogeneous chains to homogeneous chains with a single effective persistence length. For uncorrelated disorder, our model predicts that this effective stiffness is systematically smaller than the arithmetic mean of the local persistence lengths, indicating that flexible segments have a bigger influence on the overall chain stiffness than rigid segments. We validate our model predictions using off-lattice Monte Carlo simulations, considering both ideal and self-avoiding chains in good solvent, and find excellent agreement in the regime, where the persistence lengths are on the order of a few bond lengths, consistent with typical values observed in polypeptides. In the second part, we performed simulations using various coarse-grained models of intrinsically disordered proteins (IDPs), finding that the simulated IDPs have similar shapes like the corresponding homogeneous and heterogeneous worm-like chains. However, the IDPs are systematically larger than ideal worm-like chains, yet slightly more compact when excluded volume interactions are considered. We attribute these differences to intramolecular interactions between non-bonded monomers, which our theoretical models do not account for.

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arXiv2025

Exploring the role of hydrodynamic interactions in spherically-confined drying colloidal suspensions

We study the distribution of colloidal particles confined in drying spherical droplets using both dynamic density functional theory (DDFT) and particle-based simulations. In particular, we focus on the advection-dominated regime typical of aqueous droplets drying at room temperature and systematically investigate the role of hydrodynamic interactions during this nonequilibrium process. In general, drying produces transient particle concentration gradients within the droplet in this regime, with a considerable accumulation of particles at the droplet's liquid-vapor interface. We find that these gradients become significantly larger with pairwise hydrodynamic interactions between colloidal particles instead of a free-draining hydrodynamic approximation; however, the solvent's boundary conditions at the droplet's interface (unbounded, slip, or no-slip) do not have a significant effect on the particle distribution. DDFT calculations leveraging radial symmetry of the drying droplet are in excellent agreement with particle-based simulations for free-draining hydrodynamics, but DDFT unexpectedly fails for pairwise hydrodynamic interactions after the particle concentration increases during drying, manifesting as an ejection of particles from the droplet. We hypothesize that this unphysical behavior originates from an inaccurate approximation of the two-body density correlations based on the bulk pair correlation function, which we support by measuring the confined equilibrium two-body density correlations using particle-based simulations. We identify some potential strategies for addressing this issue in DDFT.

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arXiv2024

Effects of Ligand vs. Linker on Phase Behavior and Mechanical Properties of Nanoparticle Gels

Nanoparticle gels have attracted considerable attention due to their highly tunable properties. One strategy for producing nanoparticle gels involves using strong local attractions between polymeric molecules, such as DNA hybridization or dynamic covalent chemistry, to form percolated nanoparticle networks. These molecules can be used in two distinct roles: as "ligands" with one end grafted to a nanoparticle or as "linkers" with both ends free. Here, we explore how these roles shape the phase behavior and mechanical properties of gel-like nanoparticle assemblies using coarse-grained simulations. We systematically vary the interaction strength and bending stiffness of both ligands and linkers. We find that phase separation can be limited to low nanoparticle volume fractions by making the ligands rigid, consistent with previous studies on linked nanoparticle gels. At fixed interaction strength and volume fraction, both ligand- and linker-mediated nanoparticle assemblies show similar mechanical responses as bending stiffness is varied. However, a comparison between the two association schemes reveals that the linked nanoparticles form rigid percolated networks that are less stretchable than the ligand-grafted gels, despite exhibiting similar tensile strength. We attribute these differences between ligands and linkers to the distinct structural arrangement of nanoparticles within the gel. Our findings highlight the potential to use different association schemes to tune specific mechanical properties.

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arXiv2024

Mesoscale simulations of diffusion and sedimentation in shape-anisotropic nanoparticle suspensions

We determine the long-time self-diffusion coefficient and sedimentation coefficient for suspensions of nanoparticles with anisotropic shapes (octahedra, cubes, tetrahedra, and spherocylinders) as a function of nanoparticle concentration using mesoscale simulations. We use a discrete particle model for the nanoparticles, and we account for solvent-mediated hydrodynamic interactions between nanoparticles using the multiparticle collision dynamics method. Our simulations are compared to theoretical predictions and experimental data from existing literature, demonstrating good agreement in the majority of cases. Further, we find that the self-diffusion coefficient of the regular polyhedral shapes can be estimated from that of a sphere whose diameter is average of their inscribed and circumscribed sphere diameters.

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arXiv2023

Simulations of Thin Polymer Films on Flat and Curved Substrates

We report molecular dynamics simulation results on the equilibrium properties of polymer thin films adsorbed onto flat and curved substrates. We first systematically determine the contact angle of polymer droplets on flat substrates as a function of the substrate-monomer adsorption strength and degree of polymerization. Focussing on the fully wetted regime, we then investigate the effect of the substrate's topography on the polymer film configuration by using substrates with varying mean curvature. We find that polymer chains close to the substrate are significantly stretched (compressed) in regions of high negative (positive) mean curvature. Further, we find partial dewetting near regions of high mean curvature for thin polymer films. For thicker films, the polymers fully cover the substrate and the shape of the liquid-vapor interface largely follows the shape of the substrate. As the film thickness is increased further, the liquid-vapor interface becomes completely flat. These simulation results are corroborated by analytic calculations using a simplified continuum model that treats the adsorbed polymers as an incompressible medium. Our findings show how the substrate topography influences the conformation of individual chains as well as the shape of the entire film.

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arXiv2023

Viscosity of flexible and semiflexible ring melts -- molecular origins and flow-induced segregation

We investigate with numerical simulations the molecular origin of viscosity in melts of flexible and semiflexible oligomer rings in comparison to corresponding systems with linear chains. The strong increase of viscosity with ring stiffness is linked to the formation of entangled clusters, which dissolve under shear. This shear-induced breakup and alignment of rings in the flow direction lead to pronounced shear-thinning and non-Newtonian behavior. In melts of linear chains, the viscosity can be associated with the (average) number of entanglements between chains, which also dissolve under shear. While blends of flexible and semiflexible rings are mixed at rest, the two species separate under flow. This phenomenon has potential applications in microfluidic devices to segregate ring polymers of similar mass and chemical composition by their bending rigidity.

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arXiv2023

Structure Formation of Amphiphilic Nanocubes at Rest and Under Shear

We investigate the self-assembly of amphiphilic nanocubes under rest and shear using molecular dynamics (MD) simulations and kinetic Monte Carlo (KMC) calculations. These particles combine both interaction and shape anisotropy, making them valuable models for studying folded proteins and DNA-functionalized nanoparticles. The nanocubes can self-assemble into various finite-sized aggregates ranging from rods to self-avoiding random walks, depending on the number and placement of the hydrophobic faces. Our study focuses on suspensions containing multi- and one-patch cubes, with their ratio systematically varied. When the binding energy is comparable to the thermal energy, the aggregates consist of only few cubes that spontaneously associate/dissociate. However, highly stable aggregates emerge when the binding energy exceeds the thermal energy. Generally, the mean aggregation number of the self-assembled clusters increases with the number of hydrophobic faces and decreases with the fraction of one-patch cubes. In sheared suspensions, the more frequent collisions between nanocube clusters lead to faster aggregation dynamics but also to smaller terminal steady-state mean cluster sizes. The MD and KMC simulations are in excellent agreement, and the analysis of the rate kernels enables the identification of the primary mechanisms responsible for the (shear-induced) cluster growth and breakup.

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arXiv2023

Cell-sized confinements alter molecular diffusion in concentrated polymer solutions due to length-dependent wetting of polymers

Living cells are characterized by the micrometric confinement of various macromolecules at high concentrations. Using droplets containing binary polymer blends as artificial cells, we previously showed that cell-sized confinement causes phase separation of the binary polymer solutions because of the length-dependent wetting of the polymers. Here we demonstrate that the wetting-induced heterogeneity of polymers also emerges in single-component polymer solutions. The resulting heterogeneity leads to a slower transport of small molecules at the center of cell-sized droplets than that in bulk solutions. This heterogeneous distribution is observed when longer polymers with lower wettability are localized at the droplet center. Molecular simulations support this wetting-induced heterogeneous distribution by polymer length. Our results suggest that cell-sized confinement functions as a structural regulator for polydisperse polymer solutions that specifically manipulate the diffusion of molecules, particularly those with sizes close to the correlation length of the polymer chains.

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arXiv2022

Confinement-induced fractionation and liquid-liquid phase separation of polymer mixtures

The formation of (bio)molecular condensates via liquid-liquid phase separation in cells has received increasing attention, as these coacervates play important functional and regulatory roles within biological systems. However, the majority of studies focused on the behavior of pure systems in bulk solutions, thus neglecting confinement effects and the interplay between the numerous molecules present in cells. To advance our knowledge, we perform simulations of binary polymer mixtures in droplets, considering both monodisperse and polydisperse molecular weight distributions for the longer polymer species. We find that confinement induces a spatial separation of the polymers by length, with the shorter ones moving to the droplet surface. This partitioning causes a distinct increase of the local polymer concentration in the droplet center, which is more pronounced in polydisperse systems. Consequently, the systems exhibit liquid-liquid phase separation at average polymer concentrations where bulk systems are still in the one-phase regime.

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arXiv2021

Wetting transitions of polymer solutions: Effects of chain length and chain stiffness

Wetting and drying phenomena are studied for flexible and semiflexible polymer solutions via coarse-grained molecular dynamics simulations and density functional theory calculations. The study is based on the use of Young's equation for the contact angle, determining all relevant surface tensions from the anisotropy of the pressure tensor. The solvent quality (or effective temperature, equivalently) is varied systematically, while all other interactions remain unaltered. For flexible polymers, the wetting transition temperature $T_{\rm w}$ increases monotonically with chain length $N$, while the contact angle at temperatures far below $T_{\rm w}$ is independent of $N$. For semiflexible polymer solutions, $T_{\rm w}$ varies non-monotonically with the persistence length: Initially, $T_{\rm w}$ increases with increasing chain stiffness and reaches a maximum, but then a sudden drop of $T_{\rm w}$ is observed, which is associated with the isotropic-nematic transition of the system.

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arXiv2021

Diffusion and sedimentation in colloidal suspensions using multiparticle collision dynamics with a discrete particle model

We study self-diffusion and sedimentation in colloidal suspensions of nearly-hard spheres using the multiparticle collision dynamics simulation method for the solvent with a discrete mesh model for the colloidal particles (MD+MPCD). We cover colloid volume fractions from 0.01 to 0.40 and compare the MD+MPCD simulations to Brownian dynamics simulations with free-draining hydrodynamics (BD) as well as pairwise far-field hydrodynamics described using the Rotne--Prager--Yamakawa mobility tensor (BD+RPY). The dynamics in MD+MPCD suggest that the colloidal particles are only partially coupled to the solvent at short times. However, the long-time self-diffusion coefficient in MD+MPCD is comparable to that in BD and BD+RPY, and the sedimentation coefficient in MD+MPCD is in good agreement with that in BD+RPY, suggesting that MD+MPCD gives a reasonable description of the hydrodynamic interactions in colloidal suspensions. The discrete-particle MD+MPCD approach is convenient and readily extended to more complex shapes, and we determine the long-time self-diffusion coefficient in suspensions of nearly-hard cubes to demonstrate its generality.

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arXiv2020

BoltzmaNN: Predicting effective pair potentials and equations of state using neural networks

Neural networks (NNs) are employed to predict equations of state from a given isotropic pair potential using the virial expansion of the pressure. The NNs are trained with data from molecular dynamics simulations of monoatomic gases and liquids, sampled in the $NVT$ ensemble at various densities. We find that the NNs provide much more accurate results compared to the analytic low-density limit estimate of the second virial coefficient. Further, we design and train NNs for computing (effective) pair potentials from radial pair distribution functions, $g(r)$, a task which is often performed for inverse design and coarse-graining. Providing the NNs with additional information on the forces greatly improves the accuracy of the predictions, since more correlations are taken into account; the predicted potentials become smoother, are significantly closer to the target potentials, and are more transferable as a result.

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arXiv2020

Entropic Unmixing in Nematic Blends of Semiflexible Polymers

Binary mixtures of semiflexible polymers with the same chain length but different persistence lengths separate into two coexisting different nematic phases when the osmotic pressure of the lyotropic solution is varied. Molecular Dynamics simulations and Density Functional Theory predict phase diagrams either with a triple point, where the isotropic phase coexists with two nematic phases, or a critical point of unmixing within the nematic mixture. The difference in locally preferred bond angles between the constituents drives this unmixing without any attractive interactions between monomers.

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arXiv2020

Stratification of polymer mixtures in drying droplets: hydrodynamics and diffusion

We study the evaporation-induced stratification of a mixture of short and long polymer chains in a drying droplet using molecular simulations. We systematically investigate the effects of hydrodynamic interactions (HI) on this process by comparing hybrid simulations accounting for HI between polymers through the multiparticle collision dynamics technique with free-draining Langevin dynamics simulations neglecting the same. We find that the dried supraparticle morphologies are homogeneous when HI are included but are stratified in core--shell structures (with the short polymers forming the shell) when HI are neglected. The simulation methodology unambiguously attributes this difference to the treatment of the solvent in the two models. We rationalize the presence (or absence) of stratification by measuring phenomenological multicomponent diffusion coefficients for the polymer mixtures. The diffusion coefficients show the importance of not only solvent backflow but also HI between polymers in controlling the dried supraparticle morphology.

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