Systematic Generation of Anisotropic Coarse-Grained Lennard-Jones Potentials and Their Application to Ordered Soft Matter

Systematic bottom-up molecular coarse-graining via force and torque matching using anisotropic particles

We derive a systematic and general method for parametrizing coarse-grained molecular models consisting of anisotropic particles from fine-grained (e.g. all-atom) models for condensed-phase molecular dynamics simulations. The method, which we call anisotropic force-matching coarse-graining (AFM-CG), is based on rigorous statistical mechanical principles, enforcing consistency between the coarse-grained and fine-grained phase-space distributions to derive equations for the coarse-grained forces, torques, masses, and moments of inertia in terms of properties of a condensed-phase fine-grained system. We verify the accuracy and efficiency of the method by coarse-graining liquid-state systems of two different anisotropic organic molecules, benzene and perylene, and show that the parametrized coarse-grained models more accurately describe properties of these systems than previous anisotropic coarse-grained models parametrized using other methods that do not account for finite-temperature and many-body effects on the condensed-phase coarse-grained interactions. The AFM-CG method will be useful for developing accurate and efficient dynamical simulation models of condensed-phase systems of molecules consisting of large, rigid, anisotropic fragments, such as liquid crystals, organic semiconductors, and nucleic acids.

High-viscosity Pickering emulsion stabilized by amphiphilic alginate/SiO2 via multiscale methodology for crude oil-spill remediation

The separation of crude oil from oily water and collection of the emulsion constituents has attracted significant attention. We demonstrate that the relationships between inherent dynamic factors and the performance of a Pickering emulsion stabilized by SiO₂ particles with adsorbed hydrophobically modified sodium alginate derivatives (HMSA), a natural pH-sensitive polysaccharide, can be clarified via a multi-scale methodology. Functionalization of the silica surface with HMSA controls particle dispersibility, as verified by turbidity and stability analyses, the zeta potential, and transmission electron microscopy measurements. The interaction mechanism between HMSA and SiO₂ nanoparticles was elucidated by both experimental adsorption measurements and computer simulations, which showed qualitative consistency. The aggregation/disaggregation of HMSA/SiO₂ particles achieved by tuning the pH of the solution facilitated reversible dispersibility/collectability behavior. Overall, a high-viscosity Pickering emulsion system based on particle-particle and droplet-droplet interactions, which can be filtered for the recovery of spilled crude oil, was demonstrated.

Backbone oriented anisotropic coarse grains for efficient simulations of polymers

Despite the fact that anisotropic particles have been introduced to describe molecular interactions for decades, they have been poorly used for polymers because of their computing time overhead and the absence of a relevant proof of their impact in this field. We first report a method using anisotropic beads for polymers, which solves the computing time issue by considering that beads keep their principal orientation alongside the mean local backbone vector of the polymer chain, avoiding the computation of torques during the dynamics. Applying this method to a polymer bulk, we study the effect of anisotropic interactions vs isotropic ones for various properties such as density, pressure, topology of the chain network, local structure, and orientational order. We show that for different classes of potentials traditionally used in molecular simulations, those backbone oriented anisotropic beads can solve numerous issues usually encountered with isotropic interactions. We conclude that the use of backbone oriented anisotropic beads is a promising approach for the development of realistic coarse-grained potentials for polymers.

Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu

Although the fast association between DNA-binding proteins (DBPs) and DNA is explained by a facilitated diffusion mechanism, in which DBPs adopt a weighted combination of three-dimensional diffusion and one-dimensional (1D) sliding and hopping modes of transportation, the role of cellular environment that contains many nonspecifically interacting proteins and other biomolecules is mostly overlooked. By performing large-scale computational simulations with an appropriately tuned model of protein and DNA in the presence of nonspecifically interacting bulk and DNA-bound crowders (genomic crowders), we demonstrate the structural basis of the enhanced facilitated diffusion of DBPs inside a crowded cellular milieu through, to our knowledge, novel 1D scanning mechanisms. In this one-dimensional scanning mode, the protein can float along the DNA under the influence of nonspecific interactions of bulk crowder molecules. The search mode is distinctly different compared to usual 1D sliding and hopping dynamics in which protein diffusion is regulated by the DNA electrostatics. In contrast, the presence of genomic crowders expedites the target search process by transporting the protein over DNA segments through the formation of a transient protein-crowder bridged complex. By analyzing the ruggedness of the associated potential energy landscape, we underpin the molecular origin of the kinetic advantages of these search modes and show that they successfully explain the experimentally observed acceleration of facilitated diffusion of DBPs by molecular crowding agents and crowder-concentration-dependent enzymatic activity of transcription factors. Our findings provide crucial insights into gene regulation kinetics inside the crowded cellular milieu.

Structural Correlations and Percolation in Twisted Perylene Diimides Using a Simple Anisotropic Coarse-Grained Model

Large, twisted, and fused conjugated molecular architectures have begun to appear more prominently in the organic semiconductor literature. From a modeling perspective, such structures present a challenge to conventional simulation techniques; atomistic resolutions are computationally inefficient, while traditional isotropic coarse-grained models do not capture the inherent anisotropies of the molecules. In this work, we develop a simple coarse-grained model that explicitly incorporates the anisotropy of these molecular architectures, thereby providing a route toward analyzing π-stacking, and thus qualitative electronic structure, at a computationally efficient coarse-grained resolution. Our simple coarse-grained model maintains relative orientations of conjugated rings, as well as inter-ring dihedrals, that are critical for understanding electronic and excitonic transport in bulk systems. We apply this model to understand structural correlations in several recently synthesized perylene diimide (PDI)-based organic semiconductors. Twisted and nonplanar molecular architectures are found to promote amorphous morphologies while maintaining local π-stacking. A graph theoretical network analysis demonstrates that these twisted molecules are more likely to form percolating three-dimensional pathways for charge motion than strictly planar molecules, which show connectivity in only one dimension.

Nonlinearities of organic electro-optic materials in nanoscale slots and implications for the optimum modulator design

The performance of highly nonlinear organic electro-optic (EO) materials incorporated into nanoscale slots is examined. It is shown that EO coefficients as large as 190 pm/V can be obtained in 150 nm wide plasmonic slot waveguides but that the coefficients decrease for narrower slots. Possible mechanism that lead to such a decrease are discussed. Monte-Carlo computer simulations are performed, confirming that chromophore-surface interactions are one important factor influencing the EO coefficient in narrow plasmonic slots. These highly nonlinear materials are of particular interest for applications in optical modulators. However, in modulators the key parameters are the voltage-length product U_πL and the insertion loss rather than the linear EO coefficients. We show record-low voltage-length products of 70 Vµm and 50 Vµm for slot widths in the order of 50 nm for the materials JRD1 and DLD164, respectively. This is because the nonlinear interaction is enhanced in narrow slot and thereby compensates for the reduced EO coefficient. Likewise, it is found that lowest insertion losses are observed for slot widths in the range 60 to 100 nm.

Dynamics and thermodynamics of the coronene octamer described by coarse-grained potentials

Coarse-grained models developed for polycyclic aromatic hydrocarbons based on the Paramonov–Yaliraki potential have been employed to investigate the finite temperature thermodynamics, out-of-equilibrium dynamics, energy landscapes, and rearrangement pathways of the coronene octamer.