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Several molecular simulations of different computational models are conducted to explain the mechanisms involved in the disease and nondisease protein aggregation. The aggregation mechanisms of different proteins are shown to be dependent on the protein sequence, concentration and solution conditions of the system.

The physical properties of matter rely fundamentally on the symmetry of constituent building blocks. This is particularly true for structures that interact with light via the collective motion of their conduction electrons (i.e., plasmonic materials), where the observation of exotic optical effects, such as negative refraction and electromagnetically induced transparency, require the coupling of modes that are only present in systems with nontrivial broken symmetries. Lithography has been the predominant fabrication technique for constructing plasmonic metamaterials, as it can be used to form patterns of arbitrary complexity, including those with broken symmetry. Here, we show that low-symmetry, one-dimensional plasmonic structures that would be challenging to make using traditional lithographic techniques can be assembled using DNA as a programmable surface ligand. We investigate the optical properties that arise as a result of systematic symmetry breaking and demonstrate the appearance of π-type coupled modes formed from both dipole and quadrupole nanoparticle sources. These results demonstrate the power of DNA assembly for generating unusual structures that exhibit both fundamentally insightful and technologically important optical properties. [ABSTRACT FROM AUTHOR]

With the abundant variety and increasing chemical complexity of conjugated polymers proliferating the field of organic semiconductors, it has become increasingly important to correlate the polymer molecular structure with its mesoscale conformational and morphological attributes. For instance, it is unknown which combinations of chemical moieties and periodicities predictably produce mesoscale ordering. Interestingly, not all ordered morphologies result in efficient devices. In this work we have parametrized accurate classical force-fields and used these to compute the conformational and aggregation characteristics of single strands of common conjugated polymers. Molecular dynamics trajectories are shown to reproduce experimentally observed polymeric ordering, concluding that efficient organic photovoltaic devices span a range of polymer conformational classes, and suggesting that the solution-phase morphologies have far-reaching effects. Encouragingly, these simulations indicate that despite the wide-range of conformational classes present in successful devices, local molecular ordering, and not long-range crystallinity, appears to be the necessary requirement for efficient devices. Finally, we examine what makes a "good" solvent for conjugated polymers, concluding that dispersive π-electron solvent-polymer interactions, and not the electrostatic potential of the backbone interacting with the solvent, are what primarily determine a polymer's solubility in a particular solvent, and consequently its morphological characteristics. [ABSTRACT FROM AUTHOR]

Two-dimensional covalent organic frameworks (COFs) are an emerging class of photocatalytic materials for solar energy conversion. In this work, we report a pair of structurally isomeric COFs with reversed imine bond directions, which leads to drastic differences in their physical properties, photophysical behaviors, and photocatalytic CO 2 reduction performance after incorporating a Re(bpy)(CO) 3 Cl molecular catalyst through bipyridyl units on the COF backbone (Re-COF). Using the combination of ultrafast spectroscopy and theory, we attributed these differences to the polarized nature of the imine bond that imparts a preferential direction to intramolecular charge transfer (ICT) upon photoexcitation, where the bipyridyl unit acts as an electron acceptor in the forward imine case (f-COF) and as an electron donor in the reverse imine case (r-COF). These interactions ultimately lead the Re-f-COF isomer to function as an efficient CO 2 reduction photocatalyst, while the Re-r-COF isomer shows minimal photocatalytic activity. These findings not only reveal the essential role linker chemistry plays in COF photophysical and photocatalytic properties but also offer a unique opportunity to design photosensitizers that can selectively direct charges.

The end-capping group (EG) is the essential electron-withdrawing component of nonfullerene acceptors (NFAs) in bulk heterojunction (BHJ) organic solar cells (OSCs). To systematically probe the impact of two frequent EG functionalization strategies, π-extension and halogenation, in A-DAD-A type NFAs, we synthesized and characterized four such NFAs: BT-BIC , LIC , L4F , and BO-L4F . To assess the relative importance of these strategies, we contrast these NFAs with the baseline acceptors, Y5 and Y6 . Up to 16.6% power conversion efficiency (PCE) in binary inverted OSCs with BT-BO - L4F combining π-extension and halogenation was achieved. When these two factors are combined, the effect on optical absorption is cumulative. Single-crystal π-π stacking distances are similar for the EG strategies of π-extension. Increasing the alkyl substituent length from BT-L4F to BT-BO-L4F significantly alters the packing motif and eliminates the EG core interactions of BT-L4F . Electronic structure computations reveal some of the largest NFA π-π electronic couplings observed to date, 103.8 meV in BT-L4F and 47.5 meV in BT-BO-L4F . Computed electronic reorganization energies, 132 and 133 meV for BT-L4F and BT-BO-L4F , respectively, are also lower than Y6 (150 meV). BHJ blends show preferential π-face-on orientation, and both fluorination and π-extension increase NFA crystallinity. Femto/nanosecond transient absorption spectroscopy (fs/nsTA) and integrated photocurrent device analysis (IPDA) indicate that π-extension modifies the phase separation to enhance film ordering and carrier mobility, while fluorination suppresses unimolecular recombination. This systematic study highlights the synergistic effects of NFA π-extension and fluorination in affording efficient OSCs and provides insights into designing next-generation materials.

The design of materials needed for the storage, delivery, and conversion of (re)useable energy is still hindered by the lack of new, hierarchical molecular screening methodologies that encode information on more than one length scale. Using a molecular network theory as a foundation, we show that to describe charge transport in disordered materials the network methodology must be scaled-up. We detail the scale-up through the use of adjacency lists and depth first search algorithms for during operations on the adjacency matrix. We consider two types of electronic acceptors, perylenediimide (PDI) and the fullerene derivative phenyl-C61-butyric acid methyl ester (PCBM), and we demonstrate that the method is scalable to length scales relevant to grain boundary and trap formations. Such boundaries lead to a decrease in the percolation ratio of PDI with system size, while the ratio for PCBM remains constant, further quantifying the stable, diverse transport pathways of PCBM and its success as a charge-accepting material.

The hybridization of free oligonucleotides to densely packed, oriented arrays of DNA modifying the surfaces of spherical nucleic acid (SNA)-gold nanoparticle conjugates occurs with negative cooperativity; i.e., each binding event destabilizes subsequent binding events. DNA hybridization is thus an ever-changing function of the number of strands already hybridized to the particle. Thermodynamic quantification of this behavior reveals a 3 orders of magnitude decrease in the binding constant for the capture of a free oligonucleotide by an SNA conjugate as the fraction of pre-hybridized strands increases from 0 to ∼30%. Increasing the number of pre-hybridized strands imparts an increasing enthalpic penalty to hybridization that makes binding more difficult, while simultaneously decreasing the entropic penalty to hybridization, which makes binding more favorable. Hybridization of free DNA to an SNA is thus governed by both an electrostatic barrier as the SNA accumulates charge with additional binding events and an effect consistent with allostery, where hybridization at certain sites on an SNA modify the binding affinity at a distal site through conformational changes to the remaining single strands. Leveraging these insights allows for the design of conjugates that hybridize free strands with significantly higher efficiencies, some of which approach 100%.

Herein, we report the synthesis of structurally uniform gold circular disks as two-dimensional plasmonic nanostructures that complement the well-established one-dimensional rod and three-dimensional shell structures. We show that a Au conproportionation reaction can be used to etch a collection of nonuniform triangular prisms into a uniform circular disk product with thickness and diameter varying <10%. These new particles have broadly tunable plasmon resonances (650-1000 nm) with narrow bandwidths (0.23-0.28 eV) and can be described as "effectively two-dimensional" plasmonic structures, as they do not support a significant transverse mode.

Spherical nucleic acid (SNA) nanostructures assemble into a large variety of well-defined crystalline superlattices via DNA-directed hybridization. Crystallities of SNA with various shapes emerge during the assembly process, which coalesce during coarsening, leading to polycrystalline materials. Here, we investigate the growth dynamics of SNAs into body-centered cubic superlattices and the coalescence of SNA aggregates using a colloidal model formulated from the competition of electrostatic core repulsions and localized DNA hybridization attractions. We find that the growth law of isolated SNA crystallities is well-described by the power law t(1/2), in agreement with experimental observations. At later times, coalescence slows the growth dynamics considerably and is dependent on the orientational mismatch (misorientation angle) of the coalescing crystallites. Molecular dynamics simulations show that the misorientation angle decreases continually during the coalescence, which is a signature of the grain rotation induced coalescence mechanism. This mechanism is followed by the coarsening of a "neck" that develops at the boundary between the coalescing crystallites. Remarkably, we find faster coalescence dynamics for larger SNAs compared to smaller SNAs due to their enhanced surface diffusion, which more effectively reduces curvature at the boundary of two superlattices. These findings provide fundamental insight into the relationship between nanoparticle surface chemistry and its crystallite growth and coalescence.

We report a method to synthesize and image Janus spheroid and "kayak" shaped patchy particles that combine both shape and interaction anisotropy. These particles are fabricated by sequentially combining evaporative deposition of chrome and gold with the uniaxial deformation of the colloidal particles into spheroids. We introduce combined reflection and fluorescence confocal microscopy to image each component of the patchy particle. Image analysis algorithms that resolve patch orientation from these image volumes are described and used to characterize self-assembly behavior. Assemblies of the Janus spheroid and kayak particles produced at different salt concentrations demonstrate the functional nature of the patch-to-patch interactions between the particles. Selective gold-to-gold patch bonding is observed at intermediate salt concentrations, while higher salt concentrations yield gel-like structures with nonselective patch-to-patch bonding. At intermediate salt concentrations, differences in the orientational order of the assemblies indicate that both the preferential gold-to-gold patch bonding and the particles' shape anisotropy influence the self-assembled structure.

Multivalent nanostructures are becoming an increasingly important player in the self-assembly of supramolecular lattices. Understanding the role that shape plays in the coordination of the assemblies is crucial for the functional response of the material. We develop a simple design rule for the assembly of multivalent Au triangular nanoprisms into 1-D ordered arrays based on both the length of the valent DNA and the aspect ratio of the prism. Using MD simulations, we describe an order parameter that captures the short-range order of the assembly controlled by the design parameters. The order parameter shows that even short chains (N = 4) of prisms have a high degree of orientational order that transitions to no orientational order when the DNA length is similar to the prism length. Unlike isotropic polyvalent assemblies, we find that the highly oriented chains of prisms lose orientational order in discrete steps during melting as the prisms in the arrays dissociate.