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.

Enabling complex nanoscale pattern customization using directed self-assembly.

Block copolymer directed self-assembly is an attractive method to fabricate highly uniform nanoscale features for various technological applications, but the dense periodicity of block copolymer features limits the complexity of the resulting patterns and their potential utility. Therefore, customizability of nanoscale patterns has been a long-standing goal for using directed self-assembly in device fabrication. Here we show that a hybrid organic/inorganic chemical pattern serves as a guiding pattern for self-assembly as well as a self-aligned mask for pattern customization through cotransfer of aligned block copolymer features and an inorganic prepattern.

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.

Two-dimensional pattern formation using graphoepitaxy of PS-b-PMMA block copolymers for advanced FinFET device and circuit fabrication.

Directed self-assembly (DSA) of lamellar phase block-co-polymers (BCPs) can be used to form nanoscale line-space patterns. However, exploiting the potential of this process for circuit relevant patterning continues to be a major challenge. In this work, we propose a way to impart two-dimensional pattern information in graphoepitaxy-based lamellar phase DSA processes by utilizing the interactions of the BCP with the template pattern.

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.

Supramolecular high-aspect ratio assemblies with strong antifungal activity.

Efficient and pathogen-specific antifungal agents are required to mitigate drug resistance problems. Here we present cationic small molecules that exhibit excellent microbial selectivity with minimal host toxicity. Unlike typical cationic polymers possessing molecular weight distributions, these compounds have an absolute molecular weight aiding in isolation and characterization.

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.

Pattern placement accuracy in block copolymer directed self-assembly based on chemical epitaxy.

The realization of viable designs for circuit patterns using the dense features formed by block copolymer directed self-assembly (DSA) will require a precise and quantitative understanding of self-assembled feature registration to guiding templates or chemical prepatterns. Here we report measurements of DSA placement error for lamellar block copolymer domains indexed to specific lines in the surface chemical prepattern for spatial frequency tripling and quadrupling. These measurements are made possible by the use of an inorganic domain-selective prepattern material that may be imaged upon polymer removal after DSA and a prepattern design incorporating a single feature serving as an in situ registration mark that is identifiable by pattern symmetry in both the prepattern and resulting self-assembled pattern.

On the Use of Experimental Observations to Bias Simulated Ensembles.

Historically, experimental measurements have been used to bias biomolecular simulations toward structures compatible with those observations via the addition of ad hoc restraint terms. We show how the maximum entropy formalism provides a principled approach to enforce concordance with these measurements in a minimally biased way, yielding restraints that are linear functions of the target observables and specifying a straightforward scheme to determine the biasing weights. These restraints are compared with instantaneous and ensemble-averaged harmonic restraint schemes, illustrating their similarities and limitations.

Broad-spectrum antimicrobial supramolecular assemblies with distinctive size and shape.

With the increased prevalence of antibiotic-resistant infections, there is an urgent need for innovative antimicrobial treatments. One such area being actively explored is the use of self-assembling cationic polymers. This relatively new class of materials was inspired by biologically pervasive cationic host defense peptides.

Reducing lambda repressor to the core.

Lambda repressor fragment λ(*)(6-85) is one of the fastest folding small protein fragments known to date. We hypothesized that removal of three out of five helices of λ(*)(6-85) would further reduce this protein to its smallest folding core. Molecular dynamics simulations singled out two energetically stable reduced structures consisting of only helices 1 and 4 connected by a short glycine/serine linker, as well as a less stable control.

Current developments in and importance of high-performance computing in drug discovery.

A number of current trends that are being adopted to reshape the field of high-performance computing exist, including multi-core systems, accelerators, and software frameworks for large-scale intrinsically parallel applications. These trends intersect with recent developments in computational chemistry to provide new capabilities for computer-aided drug discovery. Although this review focuses primarily on the application domains of molecular modeling and biomolecular simulation, these computing changes are relevant for other computationally intensive tasks, such as instrument data processing and chemoinformatics.

Comparison of computational approaches for predicting the effects of missense mutations on p53 function.

We applied our recently developed kinetic computational mutagenesis (KCM) approach [L.T. Chong, W.

Observation of noncooperative folding thermodynamics in simulations of 1BBL.

One of the predictions of the energy landscape theory of protein folding is the possibility of barrierless, "downhill" folding under certain conditions. The protein 1BBL has been proposed to fold by such a downhill mechanism, though this is a matter of some dispute. We carried out extensive replica exchange molecular dynamics simulations on 1BBL in explicit solvent to address this controversy and provide a microscopic picture of its folding thermodynamics.

Soft patchy nanoparticles from solution-phase self-assembly of binary diblock copolymers.

The fabrication of highly ordered, defect-free nanostructures is a key challenge in nanotechnology. Bottom-up fabrication approaches require nanobuilding blocks of precisely defined size and shape. In this work we propose a simple approach to obtain one type of building block--soft patchy nanoparticles--suggested by a series of coarse grain molecular dynamics simulations.

Interfacial fluctuations of block copolymers: a coarse-grain molecular dynamics simulation study.

The lamellar and cylindrical phases of block copolymers have a number of technological applications, particularly when they occur in supported thin films. One such application is block copolymer lithography, the use of these materials to subdivide or enhance submicrometer patterns defined by optical or electron beam methods. A key parameter of all lithographic methods is the line edge roughness (LER), because the electronic or optical activities of interest are sensitive to small pattern variations.

Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations.

The growing adoption of generalized-ensemble algorithms for biomolecular simulation has resulted in a resurgence in the use of the weighted histogram analysis method (WHAM) to make use of all data generated by these simulations. Unfortunately, the original presentation of WHAM by Kumar et al. is not directly applicable to data generated by these methods.

Absence of reptation in the high-temperature folding of the trpzip2 beta-hairpin peptide.

We have carried out extensive all atom explicit solvent simulations of the high-temperature folding and unfolding of the trpzip2 beta-hairpin peptide and examined the resulting trajectories for evidence of folding via a reptation mechanism. Over 300 microcanonical simulations of 10 ns each were initiated from a Boltzmann ensemble of conformations at 425 K. Though we observed numerous folding and unfolding events, no evidence of reptation was found.

Kinetic computational alanine scanning: application to p53 oligomerization.

We have developed a novel computational alanine scanning approach that involves analysis of ensemble unfolding kinetics at high temperature to identify residues that are critical for the stability of a given protein. This approach has been applied to dimerization of the oligomerization domain (residues 326-355) of tumor suppressor p53. As validated by experimental results, our approach has reasonable success in identifying deleterious mutations, including mutations that have been linked to cancer.

Characterization of the TIP4P-Ew water model: vapor pressure and boiling point.

The liquid-vapor-phase equilibrium properties of the previously developed TIP4P-Ew water model have been studied using thermodynamic integration free-energy simulation techniques in the temperature range of 274-400 K. We stress that free-energy results from simulations need to be corrected in order to be compared to the experiment. This is due to the fact that the thermodynamic end states accessible through simulations correspond to fictitious substances (classical rigid liquids and classical rigid ideal gases) while experiments operate on real substances (liquids and real gases, with quantum effects).

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew.

A re-parameterization of the standard TIP4P water model for use with Ewald techniques is introduced, providing an overall global improvement in water properties relative to several popular nonpolarizable and polarizable water potentials. Using high precision simulations, and careful application of standard analytical corrections, we show that the new TIP4P-Ew potential has a density maximum at approximately 1 degrees C, and reproduces experimental bulk-densities and the enthalpy of vaporization, DeltaH(vap), from -37.5 to 127 degrees C at 1 atm with an absolute average error of less than 1%.

Heterogeneous folding of the trpzip hairpin: full atom simulation and experiment.

The beta-hairpin trpzip2 can be tuned continuously from a two-state folder to folding on a rough energy landscape without a dominant refolding barrier. At high denaturant concentration, this extremely stable peptide exhibits a single apparent "two-state" transition temperature when monitored by different spectroscopic techniques. However, under optimal folding conditions the hairpin undergoes an unusual folding process with three clusters of melting transitions ranging from 15 degrees C to 160 degrees C, as monitored by 12 different experimental and computational observables.

Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins.

Replica-exchange molecular dynamics simulations in implicit solvent have been carried out to study the folding thermodynamics of a designed 20-residue peptide, or "miniprotein." The simulations in this study used the amber (parm94) force field along with the generalized Born/solvent-accessible surface area implicit solvent model, and they spanned a range of temperatures from 273 to 630 K. Starting from a completely extended initial conformation, simulations of one peptide sequence sample conformations that are <1.