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Perylene-3,4,9,10-tetracarboxylic diimides (PTCDIs) are a well-known class of organic materials. Recently, these molecules have been incorporated within DNA as base surrogates, finding ready applications as probes of DNA structure and function. However, the assembly dynamics and kinetics of PTCDI DNA base surrogates have received little attention to date. Herein, we employ constant temperature molecular dynamics simulations to gain an improved understanding of the assembly of PTCDI dimers and trimers. We also use replica-exchange molecular dynamics simulations to elucidate the energetic landscape dictating the formation of stacked PTCDI structures. Our studies provide insight into the equilibrium configurations of multimeric PTCDIs and hold implications for the construction of DNA-inspired systems from perylene-derived organic semiconductor building blocks.

A novelcoarse-grained model is developed to elucidate thermodynamicsand kinetic mechanisms of DNA self-assembly. It accounts for sequenceand solvent conditions to capture key experimental results such assequence-dependent thermal property and salt-dependent persistencelength of ssDNA and dsDNA. Moreover, constant-temperature simulationson two single strands of a homogeneous sequence show two main mechanismsof hybridization: a slow slithering mechanism and a one-order fasterzippering mechanism. Furthermore, large-scale simulations at a highDNA strand concentration demonstrate that DNA self-assembly is a robustand enthalpically driven process in which the formation of doublehelices is deciphered to occur via multiple self-assembly pathwaysincluding the strand displacement mechanism. However, sequence playsan important role in shifting the majority of one pathway over theothers and controlling size distribution of self-assembled aggregates.This study yields a complex picture on the role of sequence on programmableself-assembly and demonstrates a promising simulation tool that issuitable for studies in DNA nanotechnology. [ABSTRACT FROM AUTHOR]

Peptideamphiphiles are known to form a variety of distinctiveself-assembled nanostructures (including cylindrical nanofibers inhydrogels) dependent upon the solvent conditions. Using a novel coarse-grainedmodel, large-scale molecular dynamics simulations are performed ona system of 800 peptide amphiphiles (sequence, palmitoyl-Val3Ala3Glu3) to elucidate kinetic mechanisms ofmolecular assembly as a function of the solvent conditions. The assemblyprocess is found to occur via a multistep process with transient intermediatesthat ultimately leads to the stabilized nanostructures including opennetworks of β-sheets, cylindrical nanofibers, and elongatedmicelles. Different kinetic mechanisms are compared in terms of peptidesecondary structures, solvent-accessible surface area, radius of gyration,relative shape anisotropy, intra/intermolecular interactions, andaggregate size dynamics to provide insightful information for thedesign of functional biomaterials. [ABSTRACT FROM AUTHOR]

Using a novel coarse-grained model,large-scale molecular dynamicssimulations were performed to examine self-assembly of 800 peptideamphiphiles (sequence palmitoyl-V3A3E3). Under suitable physiological conditions, these molecules readilyassemble into nanofibers leading to hydrogel construction as observedin experiments. Our simulations capture this spontaneous self-assemblyprocess, including formation of secondary structure, to identifymorphological transitions of distinctive nanostructures. As the hydrophobicinteraction is increased, progression from open networks of secondarystructures toward closed cylindrical nanostructures containing eitherβ-sheets or random coils are observed. Moreover, temperatureeffects are also determined to play an important role in regulating formation of secondary structures within those nanostructures. Theseunderstandings of the molecular interactions involved and the roleof environmental factors on hydrogel formation provide useful insightfor development of innovative smart biomaterials for biomedical applications. [ABSTRACT FROM AUTHOR]