Bongkeun Kim

Improving Brush Polymer Infrared One-Dimensional Photonic Crystals via Linear Polymer Additives

Brush block copolymers (BBCPs) enable the rapid fabrication of self-assembled one-dimensional photonic crystals with photonic band gaps that are tunable in the UV-vis-IR, where the peak wavelength of reflection scales with the molecular weight of the BBCPs. Due to the difficulty in synthesizing very large BBCPs, the fidelity of the assembled lamellar nanostructures drastically erodes as the domains become large enough to reflect IR light, severely limiting their performance as optical filters. To overcome this challenge, short linear homopolymers are used to swell the arrays to ∼180% of the initial domain spacing, allowing for photonic band gaps up to ∼1410 nm without significant opacity in the visible, demonstrating improved ordering of the arrays. Additionally, blending BBCPs with random copolymers enables functional groups to be incorporated into the BBCP array without attaching them directly to the BBCPs. The addition of short linear polymers to the BBCP arrays thus offers a facile means of improving the self-assembly and optical properties of these materials, as well as adding a route to achieving films with greater functionality and tailorability, without the need to develop or optimize the processing conditions for each new brush polymer synthesized.

The hole shrink problem: Theoretical studies of directed self-assembly in cylindrical confinement

We use self-consistent field theory (SCFT) to study the self-assembly of cylinder-forming diblock copolymers confined in a cylindrical prepattern. This situation arises in contact holes -the hole shrink problem- where the goal is to produce a cylindrical hole with reduced dimensions relative to a guiding prepattern. In this study, we focus on systems with a critical dimension (CD) ranging from 50nm to 100nm and which consequently lead to the formation of a single cylinder in the middle of the hole. We found that different morphologies arise from the self-assembly process and are strongly governed by the prepattern dimensions, wetting conditions as well as the polymer molecular weight. We also considered blends of diblock copolymers and homopolymers and determined optimal blending configurations that not only favor the formation of the desired cylindrical morphology but also extend the processing window relative to the pure diblock case.

Field-theoretic simulations of directed self-assembly in cylindrical confinement: placement and rectification aspects

We have investigated the directed self-assembly (DSA) of cylinder-forming block copolymers inside cylindrical guiding templates. To complement and corroborate our experimental study, we use field-theoretic simulations to examine the fluctuations-induced variations in the size and position of the cylindrical microdomain that forms in the middle of the guiding hole. Our study goes beyond the usual mean-field approximation and self-consistent field theory simulations (SCFT) and incorporates the effects of thermal fluctuations in the description of the self-assembly process using complex Langevin (CL) dynamics. In both our experimental and modeling efforts, we focus on minor-block-attractive sidewalls and bottom substrates and neutral top surfaces and explore the properties of the formed cylinders, including fluctuations in the center position and the size of the domain, for various prepattern conditions. Our results indicate robust critical dimensions (CD) of the DSA cylinders relative to the incoming CD, with a sigma CD < 0.9nm. Likewise, we find that the DSA cylinders are accurately registered in the center of the guiding hole, with deviations in the hole-inhole distance on the order of ≈ 0.7-1nm, translating to errors in the hole-to-hole distance of ≈ 1-1.5nm.

How water layers on graphene affect folding and adsorption of TrpZip2

We present a computational study of the folding of the Trp-rich β-hairpin TrpZip2 near graphene, a surface of interest as a platform for biosensors. The protein adsorbs to the surface, populating a new bound, folded state, coexisting with extended, adsorbed conformations. Adsorption and folding are modulated by direct interactions between the indole rings of TrpZip2 and the rings on the graphene surface, as well as by indirect water-mediated interactions. In particular, we observe strong layering of water near graphene, ice-like water configurations, and the formation of short lived hydrogen-bonds between water and protein. In order to study the effect of this layering in more detail, we modified the interactions between graphene and water to obtain two extreme cases: (1) enhanced layering of water that prevents the peptide from penetrating the water layer thereby enabling it to fold to a bulk-like structure, and (2) disruption of the water layer leading to adsorption and unfolding of the protein on the surface. These studies illuminate the roles of direct and solvent mediated interactions in modulating adsorption and folding of proteins on surfaces.

Defectivity study of directed self-assembly of cylindrical diblock copolymers in laterally confined thin channels

We use self-consistent field theory (SCFT) to study the directed self-assembly of cylinder-forming diblock copolymers laterally confined in narrow channels. The side walls and top/bottom surfaces of the channel are either all major block attractive, all minor block attractive, or a combination of major block attractive on the top surface and minor block attractive on the remaining film surfaces. We focus on systems in which the self-assembled cylinders form a monolayer oriented parallel to the sidewalls in a thin channel. Experimentally and theoretically, well-ordered perfect cylinders are observed in narrow channels, but undesirable defective structures are also found. We investigate the energetics of isolated, meta-stable defects and compare them with two types of defects (dislocations and disclinations) recently investigated in laterally confined lamellar block copolymer systems using SCFT. Our simulation results are also compared with defect energy estimates for lying down cylinder monolayers extracted from experimental work by Mishra and coworkers. Parametric studies include the effects of film thickness, domain spacing, χN, and composition on defect energies with various wall wetting conditions in narrow channels of varying widths. A major finding is that defects of cylindrical directed self-assembly in a confined channel have a smaller free energy cost (tens of kT) in comparison with defects in laterally confined, vertically oriented lamellae (many tens of kT). We also discovered a novel vertically branched cylinder defect in the case of neutral top and bottom surfaces with significantly lower defect energy than a corresponding dislocation defect. More broadly, this study reveals unexpected dependences of equilibrium defect densities on a wide range of parameters that must be carefully controlled in order to successfully implement a directed self-assembly process with block-copolymers.

Aggregation of Chameleon Peptides: Implications of α-Helicity in Fibril Formation

We investigate the relationship between the inherent secondary structure and aggregation propensity of peptides containing chameleon sequences (i.e., sequences that can adopt either α or β structure depending on context) using a combination of replica exchange molecular dynamics simulations, ion-mobility mass spectrometry, circular dichroism, and transmission electron microscopy. We focus on an eight-residue long chameleon sequence that can adopt an α-helical structure in the context of the iron-binding protein from Bacillus anthracis (PDB id 1JIG ) and a β-strand in the context of the baculovirus P35 protein (PDB id 1P35 ). We show that the isolated chameleon sequence is intrinsically disordered, interconverting between α-helical and β-rich conformations. The inherent conformational plasticity of the sequence can be constrained by addition of flanking residues with a given secondary structure propensity. Intriguingly, we show that the chameleon sequence with helical flanking residues aggregates rapidly into fibrils, whereas the chameleon sequence with flanking residues that favor β-conformations has weak aggregation propensity. This work sheds new insights into the possible role of α-helical intermediates in fibril formation.

Computational studies of shape rectification in directed self-assembly

We use self-consistent field theory (SCFT) to study shape rectification in overlapped cylindrical and non-cylindrical prepatterns. Specifically, we examine the potential of directed self-assembly (DSA) of block copolymers to not only reduce critical dimensions relative to the template, but also repair defects in the guiding prepatterns and produce defectfree contact holes. In our study over a wide range of prepattern dimensions, we found that defects in the central minorblock domain arise with decreasing center-to-center distance of the prepattern. Increasing the minor-block fraction in the block copolymer was observed to remove some of the defects. We also studied the effect of adding homopolymer to the block copolymer melt and show how blends can successfully eliminate defects and increase the range of the process window relative to the neat diblock case without influencing domain properties such as the critical dimension and the hole-to-hole distance.

Effects of thermal fluctuations on directed self-assembly in cylindrical confinement

Abstract. We investigate the directed self-assembly (DSA) of cylinder-forming block copolymers inside cylindrical guiding templates. To complement and corroborate our experimental investigations, we use field-theoretic simulations to examine the fluctuation-induced variations in the size and position of the cylindrical microdomain that forms in the middle of the guiding hole. Our study goes beyond the usual mean-field approximation and self-consistent field theory simulations (SCFT) and incorporates the effects of thermal fluctuations in the description of the self-assembly process using complex Langevin (CL) dynamics. In addition to CL simulations, we present an efficient SCFT-based approach that can inform about the positional error of the formed cylinders. In this new scheme, an external chemical-potential field is applied to displace the inner cylinder away from its centered, lowest energy configuration. In both our experimental and modeling efforts, we focus on two wall-wetting conditions: (1) minor-block-attractive sidewalls and bottom substrates and neutral top surfaces and (2) neutral sidewalls, substrates, and top surfaces. For both cases, we explore the properties of the formed cylinders, including fluctuations in the center position and the size of the domain, for various prepattern conditions. Our results indicate robust critical dimensions (CDs) of the DSA cylinders relative to the prepattern CD, with a standard deviation <0.9  nm. Likewise, we find that the DSA cylinders are accurately registered in the center of the guiding hole, with deviations in the hole-in-hole distance on the order of ∼0.7 to 1.4 nm, translating to errors in the hole-to-hole distance of ∼1 to 2 nm.

Directed self-assembly of diblock copolymers in laterally confining channels: line-edge-roughness and defectivity

The directed self-assembly (DSA) of diblock copolymers in laterally confining channels is a promising avenue to produce line-and-space patterns with a sub-25 nm pitch. In this study, we use self-consistent field theory (SCFT) to investigate the DSA of both cylinder- and lamella-forming diblock copolymers in narrow trenches with corrugated sidewalls. Specifically, we focus on systems that form lying-down cylinder monolayers or standing-up lamellae parallel to the sidewalls of the channel. While previous experimental and computational studies highlighted well-ordered cylinders and lamellae in smooth channels, undesirable defective structures are also observed. In the present study, the wetting sidewalls of the channels are no longer planar surfaces. Rather, we consider undulating sidewalls and investigate the effect of the rough surfaces on defectivity and line edge roughness (LER) in the self-assembled morphologies. We use SCFT to investigate the formation free energy of isolated, meta-stable defects of both cylindrical and lamellar block copolymers inside channels with sinusoidal corrugations along the sidewalls. Parametric studies include the effects of the amplitude and the frequency of the sinusoidal wall shape function, the placement of the defect core, as well as the number of cylinders and lamellae in channels of varying widths. Our simulations indicate that the relative decreases in defect formation energy in rough channels compared to smooth channels are strikingly similar in both cylinder- and lamella-forming melts. Furthermore, using a suitable order parameter and the center-to-center displacement of the self-assembled lines, our complex Langevin (CL) simulations (beyond SCFT) show that the propagation of the LER is sensitive to the amplitude and the wavelength of the sidewall shape function, with an even stronger dependence in the lamellar case compared to the cylindrical case. More broadly, our study reveals the dependence of line edge roughness propagation on a wide range of parameters that must be carefully controlled in order to successfully implement a directed self-assembly process with block copolymers.

Barriers to defect melting in chemo-epitaxial directed self-assembly of lamellar-forming diblock copolymer/homopolymer blends

We investigate energy barriers and minimum energy paths (MEPs) for transitions from dislocation-pair defects to perfect lamellae in self-assembly of AB-diblock copolymer plus A- or B-homopolymer blends using self-consistent field theory (SCFT) and the numerical string method. For neutral substrates, all minimum energy paths discovered by the string method show two successive energy barriers. The two-barrier qualitative nature of the MEPs appears not to depend on the presence or absence of small amounts of homopolymer. For the first energy barrier, the barrier height shows pronounced increase with addition of A-homopolymer due to localization of A-homopolymer on the T-junction core of the dislocation. For chemo-epitaxially patterned substrates (stripes of A-attractive substrate alternating with neutral substrate), the presence of A-attractive stripes helps draw the system towards a perfect lamellar configuration, and energy barriers along the MEP are reduced, in some cases disappearing entirely. Our findings provide guidance on how the presence of homopolymer and chemo-epitaxial prepatterns affect the stability of defective morphologies.