Expected Distributions of Root-Mean-Square Positional Deviations in Proteins

The atom positional root-mean-square deviation (RMSD) is a standard tool for comparing the similarity of two molecular structures. It is used to characterize the quality of biomolecular simulations, to cluster conformations, and as a reaction coordinate for conformational changes. This work presents an approximate analytic form for the expected distribution of RMSD values for a protein or polymer fluctuating about a stable native structure. The mean and maximum of the expected distribution are independent of chain length for long chains and linearly proportional to the average atom positional root-mean-square fluctuations (RMSF̅). To approximate the RMSD distribution for random-coil or unfolded ensembles, numerical distributions of RMSD were generated for ensembles of self-avoiding and non-self-avoiding random walks. In both cases, for all reference structures tested for chains more than three monomers long, the distributions have a maximum distant from the origin with a power-law dependence on chain length. The purely entropic nature of this result implies that care must be taken when interpreting stable high-RMSD regions of the free-energy landscape as “intermediates” or well-defined stable states

Determination of the Internal Morphology of Nanostructures Patterned by Directed Self Assembly

The directed self-assembly (DSA) of block copolymers (BCP) is an emerging resolution enhancement tool that can multiply or subdivide the pitch of a lithographically defined chemical or topological pattern and is a resolution enhancement candidate to augment conventional lithography for patterning sub-20 nm features. Continuing the development of this technology will require an improved understanding of the polymer physics involved as well as experimental confirmation of the simulations used to guide the design process. Both of these endeavors would be greatly facilitated by a metrology, which is capable of probing the internal morphology of a DSA film. We have developed a new measurement technique, resonant critical-dimension small-angle X-ray scattering (res-CDSAXS), to evaluate the 3D buried features inside the film. This is an X-ray scattering measurement where the sample angle is varied to probe the 3D structure of the film, while resonant soft X-rays are used to enhance the scattering contrast. By measuring the same sample with both res-CDSAXS and traditional CDSAXS (with hard X-rays), we are able to demonstrate the dramatic improvement in scattering obtained through the use of resonant soft X-rays. Analysis of the reciprocal space map constructed from the res-CDSAXS measurements allowed us to reconstruct the complex buried features in DSA BCP films. We studied a series of DSA BCP films with varying template widths, and the internal morphologies for these samples were compared to the results of single chain in mean-field simulations. The measurements revealed a range of morphologies that occur with changing template width, including results that suggest the presence of mixed morphologies composed of both whole and necking lamella. The development of res-CDSAXS will enable a better understanding of the fundamental physics behind the formation of buried features in DSA BCP films

Programmable Nanoparticle Ensembles via High-Throughput Directed Self-Assembly

We present a simple and facile strategy for the directed self-assembly of nanoparticles into complex geometries using a minimal set of post guiding features patterned on a substrate. This understanding is based on extensive studies of nanoparticle self-assembly into linear, dense-packed, circular, and star-shaped ensembles when coated onto patterned substrates of predefined post arrays. We determined the conditions under which nanoparticles assemble and “connect” two adjacent post features, thereby forming the desired shapes. We demonstrate that with rational design of the post patterns to enforce the required pairwise interactions with posts, we can create arbitrary arrangements of nanoparticlesfor example, to write “IBM” in a deterministic manner. This demonstration of programmable, high-throughput directed self-assembly of nanoparticles shows an alternative route to generate functional nanoparticle assemblies

Orientation Control of Block Copolymers Using Surface Active, Phase-Preferential Additives

Orientation control of thin film nanostructures derived from block copolymers (BCPs) are of great interest for various emerging technologies like separation membranes, nanopatterning, and energy storage. While many BCP compositions have been developed for these applications, perpendicular orientation of these BCP domains is still very challenging to achieve. Herein we report on a new, integration-friendly approach in which small amounts of a phase-preferential, surface active polymer (SAP) was used as an additive to a polycarbonate-containing BCP formulation to obtain perpendicularly oriented domains with 19 nm natural periodicity upon thermal annealing. In this work, the vertically oriented BCP domains were used to demonstrate next generation patterning applications for advanced semiconductor nodes. Furthermore, these domains were used to demonstrate pattern transfer into a hardmask layer via commonly used etch techniques and graphoepitaxy-based directed self-assembly using existing lithographic integration schemes. We believe that this novel formulation-based approach can easily be extended to other applications beyond nanopatterning