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Sublattice melting is the loss of order of one lattice component in binary or ternary ionic crystals upon increase in temperature. A related transition has been predicted in colloidal crystals. To understand the nature of this transition, we study delocalization in self-assembled, size asymmetric binary colloidal crystals using a generalized molecular dynamics model. Focusing on BCC lattices, we observe a smooth change from localized-to-delocalized interstitial particles for a variety of interaction strengths. Thermodynamic arguments, mainly the absence of a discontinuity in the heat capacity, suggest that the passage from localization-to-delocalization is continuous and not a phase transition. This change is enhanced by lattice vibrations, and the temperature of the onset of delocalization can be tuned by the strength of the interaction between the colloid species. Therefore, the localized and delocalized regimes of the sublattice are dominated by enthalpic and entropic driving forces, respectively. This work sets the stage for future studies of sublattice melting in colloidal systems with different stoichiometries and lattice types, and it provides insights into superionic materials, which have potential for application in energy storage technologies., Hector Lopez-Rios and Ali Ehlen contributed equally

Label-free in situ X-ray scattering from protein spherical nucleic acids (Pro-SNAs, consisting of protein cores densely functionalized with covalently bound DNA) was used to elucidate the enzymatic reaction pathway for the DNase I-induced degradation of DNA. Time-course small-angle X-ray scattering (SAXS) and gel electrophoresis reveal a two-state system with time-dependent populations of intact and fully degraded DNA in the Pro-SNAs. SAXS shows that in the fully degraded state, the DNA strands forming the outer shell of the Pro-SNA were completely digested. SAXS analysis of reactions with different Pro-SNA concentrations reveals a reaction pathway characterized by a slow, rate determining DNase I-Pro-SNA association, followed by rapid DNA hydrolysis. Molecular dynamics (MD) simulations provide the distributions of monovalent and divalent ions around the Pro-SNA, relevant to the activity of DNase I. Taken together, in situ SAXS in conjunction with MD simulations yield key mechanistic and structural insights into the interaction of DNA with DNase I. The approach presented here should prove invaluable in probing other enzyme-catalyzed reactions on the nanoscale.

Polydispersity and random sequences are ubiquitous features of polymers, and molecular dynamics simulations can help elucidate the impact of disorder in polymer systems. However, currently available packages for building polymer topologies do not enable the user to include randomness in a straightforward fashion. Here, we introduce Hoobas, a molecular builder package that easily handles polydispersity using a prototype-builder design pattern. This enables fast and easy building of systems comprised of thousands of distinct objects. It is written in the Python programming language, which ensures compatibility with a wide range of molecular dynamics packages and tools, as well as easy integration into most workflows.

Colloidal crystals formed by size-asymmetric binary particles co-assemble into a wide variety of colloidal compounds with lattices akin to ionic crystals. Recently, a transition from a compound phase with a sublattice of small particles to a metal-like phase in which the small particles are delocalized has been predicted computationally and observed experimentally. In this colloidal metallic phase, the small particles roam the crystal maintaining the integrity of the lattice of large particles, as electrons do in metals. A similar transition also occurs in superionic crystals, termed sublattice melting. Here, we use energetic principles and a generalized molecular dynamics model of a binary system of functionalized nanoparticles to analyze the transition to sublattice delocalization in different co-assembled crystal phases as a function of T, number of grafted chains on the small particles, and number ratio between the small and large particles $n_s$:$n_l$. We find that $n_s$:$n_l$ is the primary determinant of crystal type due to energetic interactions and interstitial site filling, while the number of grafted chains per small particle determines the stability of these crystals. We observe first-order sublattice delocalization transitions as T increases, in which the host lattice transforms from low- to high-symmetry crystal structures, including A20 to BCT to BCC, Ad to BCT to BCC, and BCC to BCC/FCC to FCC transitions and lattices. Analogous sublattice transitions driven primarily by lattice vibrations have been seen in some atomic materials exhibiting an insulator-metal transition also referred to as metallization. We also find minima in the lattice vibrations and diffusion coefficient of small particles as a function of $n_s$:$n_l$, indicating enhanced stability of certain crystal structures for $n_s$:$n_l$ values that form compounds., Comment: AE and HL-R contributed equally to this work