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We report simulation studies on the self-assembly of a binary mixture of snowman and dumbbell shaped lobed particles. Depending on the lobe size and temperature, different types of self-assembled structures (random aggregates, spherical aggregates, liquid droplets, amorphous wire-like structures, amorphous ring structures, crystalline structures) are observed. At lower temperatures, heterogeneous structures are formed for lobed particles of both shapes. At higher temperatures, homogeneous self-assembled structures are formed mainly by the dumbbell shaped particles, while the snowman shaped particles remain in a dissociated state. We also investigated the porosities of self-assembled structures. The pore diameters in self-assemblies increased with an increase in temperature for a given lobe size. The particles having smaller lobes produced structures with larger pores than the particles having larger lobes. We further investigated the effect of σ , a parameter in the surface-shifted Lennard-Jones potential, on the self-assembled morphologies and their porosities. The self-assembled structures formed at a higher σ value are found to produce larger pores than those at a lower σ . 

Base flipping is a key biophysical event involved in recognition of various ligands by ribonucleic acid (RNA) molecules. However, the mechanism of base flipping in RNA remains poorly understood, in part due to the lack of atomistic details on complex rearrangements in neighboring bases. In this work, we applied transition path sampling (TPS) methods to study base flipping in a double-stranded RNA (dsRNA) molecule that is known to interact with RNA-editing enzymes through this mechanism. We obtained an ensemble of 1000 transition trajectories to describe the base-flipping process. We used the likelihood maximization method to determine the refined reaction coordinate (RC) consisting of two collective variables (CVs), a distance and a dihedral angle between nucleotides that form stacking interactions with the flipping base. The free energy profile projected along the refined RC revealed three minima, two corresponding to the initial and final states and one for a metastable state. We suggest that the metastable state likely represents a wobbled conformation of nucleobases observed in NMR studies that is often characterized as the flipped state. The analyses of reactive trajectories further revealed that the base flipping is coupled to a global conformational change in a stem-loop of dsRNA. 

Entropy plays a key role in the self-assembly of colloidal particles. Specifically, in the case of hard particles, which do not interact or overlap with each other during the process of self-assembly, the free energy is minimized due to an increase in the entropy of the system. Understanding the contribution of entropy and engineering it is increasingly becoming central to modern colloidal self-assembly research, because the entropy serves as a guide to design a wide variety of self-assembled structures for many technological and biomedical applications. In this work, we highlight the importance of entropy in different theoretical and experimental self-assembly studies. We discuss the role of shape entropy and depletion interactions in colloidal self-assembly. We also highlight the effect of entropy in the formation of open and closed crystalline structures, as well as describe recent advances in engineering entropy to achieve targeted self-assembled structures. 

We report simulation studies on the self-assembly behavior of five different types of lobed patchy particles of different shapes (snowman, dumbbell, trigonal planar, square planar, and tetrahedral). Inspired by an experimental method of synthesizing patchy particles (Wang et al., Nature, 2012, 491:51-55), we control the lobe size indirectly by gradually varying the seed diameter and study its effect on self-assembled structures at different temperatures. Snowman shaped particles self-assemble only at a lower temperature and form two-dimensional sheets, elongated micelles, and spherical micelles, depending on the seed diameter. Each of the four other lobed particles self-assemble into four distinct morphologies (random aggregates, spherical aggregates, liquid droplets, and crystalline structures) for a given lobe size and temperature. We observed temperature-dependent transitions between two morphologies depending on the type of the lobed particle. The self-assembled structures formed by these four types of particles are porous. We show that their porosities can be tuned by controlling the lobe size and temperature. 

We report simulation studies on the self-assembly of hard-lobed particles (patchy particles where patches appear as lobes around a seed) of different shapes and show that various types of self-assembled morphologies can be achieved by tuning inter-lobe interactions. On self-assembly, the linear building blocks having two lobes around the seed formed rings, the trigonal planar building blocks formed cylindrical hollow tubes and two-dimensional sheets, and the square planar building blocks formed spherical clathrates. The tetrahedral, trigonal bipyramidal, and the octahedral-shaped particles formed compact porous crystalline structures which are constituted by either hexagonal close packed or face centered cubic lattices. The pore size distributions revealed that linear, trigonal planar, and square planar building blocks create highly porous self-assembled structures. Our results suggest that these self-assembled morphologies will potentially find applications in tissue engineering, host-guest chemistry, adsorption, and catalysis.