Dynamics of Nanoparticles in Solutions of Semiflexible Ring Polymers.

We use hybrid molecular dynamics-multiparticle collision dynamics (MD-MPCD) simulations to investigate the influence of chain stiffness on the transport of nanoparticles (NPs) through solutions of semiflexible ring polymers. The NPs exhibit subdiffusive dynamics on short time scales before transitioning to normal diffusion at longer times. The terminal NP diffusivity decreases with increasing ring stiffness, similar to the behavior observed in solutions of semiflexible linear chains.

Sequence-dependent conformational transitions of disordered proteins during condensation.

Intrinsically disordered proteins (IDPs) can form biomolecular condensates through phase separation. It is recognized that the conformation of IDPs in the dense and dilute phases, as well as at the interfaces of condensates, can critically impact their functionality. However, a residue-level understanding of the conformational transitions of IDPs during condensation remains elusive.

Multicompartmentalized Micellar Structures by Gold Nanoparticles Grafted with Diblock-Copolymer Ligands.

We study the formation of hybrid polymer/inorganic colloidal particles with multicompartmentalized structure, comprising gold nanoparticles grafted with polystyrene-block-poly(methacrylic acid) (PSt-block-PMAA) diblock copolymer ligands, through experiments and molecular dynamics simulations. The PMAA blocks segregate into small satellite-like domains that are separated by the polystyrene spacer from the gold nanoparticle core. Dialysis against water leads to the re-configuration of the formed structures into unique, kinetically trapped pinned-micelle-decorated nanoparticles with internal structure.

Coarse-Grained Simulations of Columnar Ionic Liquid Crystals: Comparison with Experiments.

We simulate a homologous series of guanidinium-based columnar ionic liquid crystals (ILCs) using coarse-grained molecular dynamics (MD) simulations with the Martini force field. We systematically vary the length of alkyl side chains, ILC- ( = 8, 12, 16), and compare our results with previous experimental findings. Experimentally, ILC-8 exhibits a narrow mesophase window and weak columnar order, while ILC-12 and ILC-16 display a broad mesophase window and high columnar order.

Nanocrystal Assemblies: Current Advances and Open Problems.

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

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.

Sequence-dependent material properties of biomolecular condensates and their relation to dilute phase conformations.

Material properties of phase-separated biomolecular condensates, enriched with disordered proteins, dictate many cellular functions. Contrary to the progress made in understanding the sequence-dependent phase separation of proteins, little is known about the sequence determinants of condensate material properties. Using the hydropathy scale and Martini models, we computationally decipher these relationships for charge-rich disordered protein condensates.

Sequence-Dependent Conformational Transitions of Disordered Proteins During Condensation.

Intrinsically disordered proteins (IDPs) can form biomolecular condensates through phase separation. It is recognized that the conformation of IDPs in the dense and dilute phases as well as at the interfaces of condensates can critically impact the resulting properties associated with their functionality. However, a comprehensive understanding of the conformational transitions of IDPs during condensation remains elusive.

Structure Formation in Supraparticles Composed of Spherical and Elongated Particles.

We studied the evaporation-induced formation of supraparticles from dispersions of elongated colloidal particles using experiments and computer simulations. Aqueous droplets containing a dispersion of ellipsoidal and spherical polystyrene particles were dried on superamphiphobic surfaces at different humidity values that led to varying evaporation rates. Supraparticles made from only ellipsoidal particles showed short-range lateral ordering at the supraparticle surface and random orientations in the interior regardless of the evaporation rate.

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 confinement-induced heterogeneity of polymers also emerges in single-component polymer solutions.

Confined Dynamics in Spherical Polymer Brushes.

We investigate the dynamics of polymers grafted to spherical nanoparticles in solution using hybrid molecular dynamics simulations with a coarse-grained solvent modeled via the multiparticle collision dynamics algorithm. The mean-square displacements of monomers near the surface of the nanoparticle exhibit a plateau on intermediate time scales, indicating confined dynamics reminiscent of those reported in neutron spin-echo experiments. The confined dynamics vanish beyond a specific radial distance from the nanoparticle surface that depends on the polymer grafting density.

Conformational Properties of Polymers at Droplet Interfaces as Model Systems for Disordered Proteins.

Polymer models serve as useful tools for studying the formation and physical properties of biomolecular condensates. In recent years, the interface dividing the dense and dilute phases of condensates has been discovered to be closely related to their functionality, but the conformational preferences of the constituent proteins remain unclear. To elucidate this, we perform molecular simulations of a droplet formed by phase separation of homopolymers as a surrogate model for the prion-like low-complexity domains.

Conformational Properties of Polymers at Droplet Interfaces as Model Systems for Disordered Proteins.

Polymer models serve as useful tools for studying the formation and physical properties of biomolecular condensates. In recent years, the interface dividing the dense and dilute phases of condensates has been discovered to be closely related to their functionality, but the conformational preferences of the constituent proteins remain unclear. To elucidate this, we perform molecular simulations of a droplet formed by liquid‒liquid phase separation of homopolymers, as a surrogate model for the prion-like low-complexity domains.

Aggregation of amphiphilic nanocubes in equilibrium and under shear.

We investigate the self-assembly of amphiphilic nanocubes into finite-sized aggregates in equilibrium and under shear, using molecular dynamics (MD) simulations and kinetic Monte Carlo (KMC) calculations. These patchy nanoparticles 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.

Sequence-Dependent Material Properties of Biomolecular Codensates and their Relation to Dilute Phase Conformations.

Material properties of phase-separated biomolecular assemblies, enriched with disordered proteins, dictate their ability to participate in many cellular functions. Despite the significant effort dedicated to understanding how the sequence of the disordered protein drives its phase separation to form condensates, little is known about the sequence determinants of condensate material properties. Here, we computationally decipher these relationships for charged disordered proteins using model sequences comprised of glutamic acid and lysine residues as well as naturally occurring sequences of LAF1's RGG domain and DDX4's N-terminal domain.

Role of Strong Localized vs Weak Distributed Interactions in Disordered Protein Phase Separation.

Interaction strength and localization are critical parameters controlling the single-chain and condensed-state properties of intrinsically disordered proteins (IDPs). Here, we decipher these relationships using coarse-grained heteropolymers comprised of hydrophobic (H) and polar (P) monomers as model IDPs. We systematically vary the fraction of P monomers and employ two distinct particle-based models that include either strong localized attractions between only H-H pairs (HP model) or weak distributed attractions between both H-H and H-P pairs (HP+ model).

Effect of Surfactant Selectivity on Shape and Inner Morphology of Triblock Terpolymer Microparticles.

The confined assembly of block copolymers (BCPs) has become a useful tool to prepare microparticles with controlled anisotropy and inner structure. While a solid understanding of the behavior of AB diblock copolymers exists, knowledge on the parameters affecting ABC triblock terpolymer assembly is much more limited. In this work, the effect of block-selective surfactants, sodium-4-vinylbenzenesulfonate (VBS) and sodium dodecylsulfate (SDS), is analyzed in the evaporation-induced confined assembly (EICA) of a polystyrene-block-polybutadiene-block-poly(methyl methacrylate) triblock terpolymer (SBM).

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 aggregates 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 better understand the physical mechanisms driving condensation in cellular environments, we perform molecular simulations of binary polymer mixtures in spherical droplets, considering both monodisperse and polydisperse molecular weight distributions for the longer polymer species.

Rapid Precipitation of Ionomers for Stabilization of Polymeric Colloids.

Polymeric colloids have shown potential as "building blocks" in applications ranging from formulations of Pickering emulsions and drug delivery systems to advanced materials, including colloidal crystals and composites. However, for applications requiring tunable properties of charged colloids, obstacles in fabrication can arise through limitations in process scalability and chemical versatility. In this work, the capabilities of flash nanoprecipitation (FNP), a scalable nanoparticle (NP) fabrication technology, are expanded to produce charged polystyrene colloids using sulfonated polystyrene ionomers as a new class of NP stabilizers.

Effect of Charge Distribution on the Dynamics of Polyampholytic Disordered Proteins.

The stability and physiological function of many biomolecular coacervates depend on the structure and dynamics of intrinsically disordered proteins (IDPs) that typically contain a significant fraction of charged residues. Although the effect of relative arrangement of charged residues on IDP conformation is a well-studied problem, the associated changes in dynamics are far less understood. In this work, we systematically interrogate the effects of charge distribution on the chain-level and segmental dynamics of polyampholytic IDPs in dilute solutions.

Single-chain and condensed-state behavior of hnRNPA1 from molecular simulations.

Intrinsically disordered proteins (IDPs) are essential components for the formation of membraneless organelles, which play key functional and regulatory roles within biological systems. These complex assemblies form and dissolve spontaneously over time via liquid-liquid phase separation of IDPs. Mutations in their amino acid sequence can alter their phase behavior, which has been linked to the emergence of severe diseases.

Crystal Prediction via Genetic Algorithms in a Model Chiral System.

Chiral crystals and their constituent molecules play a prominent role in theories about the origin of biological homochirality and in drug discovery, design, and stability. Although the prediction and identification of stable chiral crystal structures is crucial for numerous technologies, including separation processes and polymorph selection and control, predictive ability is often complicated by a combination of many-body interactions and molecular complexity and handedness. In this work, we address these challenges by applying genetic algorithms to predict the ground-state crystal lattices formed by a chiral tetramer molecular model, which we have previously shown to exhibit complex fluid-phase behavior.

Understanding Gas Transport in Polymer-Grafted Nanoparticle Assemblies.

We rationalize the unusual gas transport behavior of polymer-grafted nanoparticle (GNP) membranes. While gas permeabilities depend specifically on the chemistry of the polymers considered, we focus here on permeabilities relative to the corresponding pure polymer which show interesting, "universal" behavior. For a given NP radius, R, and for large enough areal grafting densities, σ, to be in the dense brush regime we find that gas permeability enhancements display a maximum as a function of the graft chain molecular weight, M.

Self-Assembly of Amphiphilic Cubes in Suspension.

We study the self-assembly of amphiphilic cubic colloids using molecular dynamics as well as rejection-free kinetic Monte Carlo simulations. We vary both the number and location of the solvophobic faces (patches) on the cubes at several colloid volume fractions and determine the resulting size and shape distributions of the self-assembled aggregates. When the binding energy is comparable to the thermal energy of the system, aggregates typically consist of only few spontaneously associating/dissociating colloids.