Maria Stepanova

Fundamentals of Electron Beam Exposure and Development

Electron Beam Lithography (EBL) is a fundamental technique of nanofabrication, allowing not only the direct writing of structures down to sub-10 nm dimensions, but also enabling high volume nanoscale patterning technologies such as (DUV and EUV) optical lithography and nanoimprint lithography through the formation of masks and templates. This chapter summarizes the key principles of EBL and explores some of the complex interactions between relevant parameters and their effects on the quality of the resulting lithographic structures. The use of low energy exposure and cold development is discussed, along with their impacts on processing windows. Applications of EBL are explored for the fabrication of very small isolated bridge structures and for high density master masks for nanoimprint lithography. Strategies for using both positive and negative tone resists are explored.

Effects of temperature on the p53-DNA binding interactions and their dynamical behavior: comparing the wild type to the R248Q mutant.

Background The protein p53 plays an active role in the regulation of cell cycle. In about half of human cancers, the protein is inactivated by mutations located primarily in its DNA-binding domain. Interestingly, a number of these mutations possess temperature-induced DNA-binding characteristics. A striking example is the mutation of Arg248 into glutamine or tryptophan. These mutants are defective for binding to DNA at 310 K although they have been shown to bind specifically to several p53 response elements at sub-physiological temperatures (298–306 K). Methodology/Principal Findings This important experimental finding motivated us to examine the effects of temperature on the structure and configuration of R248Q mutant and compare it to the wild type protein. Our aim is to determine how and where structural changes of mutant variants take place due to temperature changes. To answer these questions, we compared the mutant to the wild-type proteins from two different aspects. First, we investigated the systems at the atomistic level through their DNA-binding affinity, hydrogen bond networks and spatial distribution of water molecules. Next, we assessed changes in their long-lived conformational motions at the coarse-grained level through the collective dynamics of their side-chain and backbone atoms separately. Conclusions The experimentally observed effect of temperature on the DNA-binding properties of p53 is reproduced. Analysis of atomistic and coarse-grained data reveal that changes in binding are determined by a few key residues and provide a rationale for the mutant-loss of binding at physiological temperatures. The findings can potentially enable a rescue strategy for the mutant structure.

Understanding Interactions of Functionalized Nanoparticles with Proteins: A Case Study on Lactate Dehydrogenase

Nanomaterials in biological solutions are known to interact with proteins and have been documented to affect protein function, such as enzyme activity. Understanding the interactions of nanoparticles with biological components at the molecular level will allow for rational designs of nanomaterials for use in medical technologies. Here we present the first detailed molecular mechanics model of functionalized gold nanoparticle (NP) interacting with an enzyme (L-lactate dehydrogenase (LDH) enzyme). Molecular dynamics (MD) simulations of the response of LDH to the NP binding demonstrate that although atomic motions (dynamics) of the main chain exhibit only a minor response to the binding, the dynamics of side chains are significantly constrained in all four active sites that predict alteration in kinetic properties of the enzyme. It is also demonstrated that the 5 nm gold NPs cause a decrease in the maximal velocity of the enzyme reaction (V(max)) and a trend towards a reduced affinity (increased K(m)) for the β-NAD binding site, while pyruvate enzyme kinetics (K(m) and V(max)) are not significantly altered in the presence of the gold NPs. These results demonstrate that modeling of NP:protein interactions can be used to understand alterations in protein function.

Comparison between ZEP and PMMA resists for nanoscale electron beam lithography experimentally and by numerical modeling

A modern alternative to the positive-tone PMMA resist is the ZEP 520A (Nippon Zeon) brand co-polymer resist, which offers a higher sensitivity and etch durability for electron beam lithography. However, the molecular mechanisms are not entirely understood, and the relative performance of two resists for various process conditions of nanofabrication is not readily predictable. The authors report a thorough experimental comparison of the performance of PMMA 950k and ZEP 520A resists in MIBK:IPA, ZED, and IPA:water developers. Interestingly, ZEP resist performance was found to depend significantly on the developer. ZED developer increases the sensitivity, whereas IPA:water optimizes line edge roughness and conceivably the resolution at the expense of sensitivity. The authors also describe two alternative numerical models, one assuming an enhancement of the main chain scission in ZEP as a result of electronic excitations in side groups, and another without such enhancement. In the second case, the differences...

Study of Development Processes for ZEP-520 as a High-Resolution Positive and Negative Tone Electron Beam Lithography Resist

ZEP brand electron beam resists are well-known for their high sensitivity and etch durability. The various performance metrics such as sensitivity, contrast, and resolution of ZEP resist depend strongly on the development process. In this work, we investigate the development of ZEP-520 resist through contrast curves, dense gratings, and surface roughness measurements using three different classes of developer systems of varying solvation strength, ZED-N50, methyl isobutyl ketone (MIBK) : isopropyl alcohol (IPA) 1:3, and IPA : H2O 7:3, at the ambient temperature (22 °C) and cold (-15 °C) development conditions. In order to provide a deeper insight into the ZEP development process, we propose a novel kinetic model of dissolution for ZEP, and develop an efficient analytical method that allows determining the microscopic parameters of ZEP dissolution based on experimental contrast curves. We also observe experimentally and characterize the negative tone behavior of ZEP for dense grating patterning and compare its performance with positive tone behavior.

Nanopatterning of PMMA on insulating surfaces with various anticharging schemes using 30 keV electron beam lithography

As a low cost and high throughput method for nanoscale pattern replication, step and flash imprint lithography (SFIL) with UV transparent masters is gaining prominence for its potential in photonics and integrated-circuit fabrication. However, dielectric materials appropriate for fabricating nanostructured SFIL masters present a challenge when employing electron beam lithography (EBL) because insulator substrates covered by polymeric resists such as PMMA tend to accumulate charge during EBL exposures, thereby degrading the process. In this work we explore the performance of four different EBL anticharging schemes for nanofabrication of dense arrays of dots having diameters 16–30 nm in PMMA on UV transparent fused silica (FS) substrates. These include overlayers of aluminum or a water-soluble conducting polymer, as well as sandwiching of Al or Cr thin films between the substrate and PMMA. The quality of patterns transferred from PMMA into the underlying metallic layers was analyzed, and the grain size of t...

Exploring the essential collective dynamics of interacting proteins: Application to prion protein dimers

Essential collective dynamics is a promising and robust approach for analysing the slow motions of macromolecules from short molecular dynamics trajectories. In this study, an extension of the method to treat a collection of interacting protein molecules is presented. The extension is applied to investigate the effects of dimerization on the collective dynamics of ovine prion protein molecules in two different arrangements. Examination of the structural plasticity shows that aggregation has a restricting effect on the local mobility of the prion protein molecules in the interfacial regions. Domain motions of the two dimeric ovine prion protein conformations are distinctly different and can be related to interatomic correlations at the interface. Correlated motions are among the slow collective modes extensively analysed by considering both main‐chain and side‐chain atoms. Correlation maps reveal the existence of a vast network of dynamically correlated side groups, which extends beyond individual subunits via interfacial interconnections. The network is formed by a core of hydrophobic side chains surrounded by hydrophilic groups at the periphery. The relevance of these findings are discussed in the context of mutations associated with prion diseases. The binding free energy of the dimeric conformations is evaluated to probe their thermodynamic stability. The descriptions afforded by the analysis of the essential collective dynamics of the prion dimers are consistent with their binding free energies. The agreement validates the extension of the methodology and provides a means of interpreting the collective dynamics in terms of the thermodynamic stability of ovine prion proteins. Proteins 2012.

Nanomachining and clamping point optimization of silicon carbon nitride resonators using low voltage electron beam lithography and cold development

The authors report the nanomachining of sub-20-nm wide doubly clamped silicon carbon nitride resonators using low keV electron beam lithography with polymethyl methacrylate resist and cold development. Methodologies are developed for precisely controlling the resonator widths in the ultranarrow regime of 11–20 nm. Resonators with lengths of 1–20 μm and widths of 16–280 nm are characterized at room temperature in vacuum using piezoelectric actuation and optical interferometry. Clamping and surface losses are identified as the dominant energy loss mechanisms for a range of resonator widths. The resonator clamping points are optimized using an original electron beam lithography simulator. Various alternative clamping point designs are also modeled and fabricated in order to reduce the clamping losses.

Interdependence of optimum exposure dose regimes and the kinetics of resist dissolution for electron beam nanolithography of polymethylmethacrylate

The authors report a systematic experimental study of dense nanostructures in polymethylmethacrylate (PMMA) created by low-energy electron beam lithography (EBL) with varying duration and temperature of the resist dissolution. They observe that decreasing the development temperature not only yields the widest favorable exposure dose regimes but also requires highest exposure doses to fabricate dense nanopatterns. They interpret the observed interdependence of the exposure doses and the development temperatures in terms of a simple kinetic model describing the diffusion mobility of fragments in exposed PMMA during dissolution and discuss the corresponding molecular mechanisms that determine the resolution and sensitivity of EBL nanofabrication.

Molecular mechanisms in the activation of abscisic acid receptor PYR1.

The pyrabactin resistance 1 (PYR1)/PYR1-like (PYL)/regulatory component of abscisic acid (ABA) response (RCAR) proteins comprise a well characterized family of ABA receptors. Recent investigations have revealed two subsets of these receptors that, in the absence of ABA, either form inactive homodimers (PYR1 and PYLs 1–3) or mediate basal inhibition of downstream target type 2C protein phosphatases (PP2Cs; PYLs 4–10) respectively in vitro. Addition of ABA has been shown to release the apo-homodimers yielding ABA-bound monomeric holo-receptors that can interact with PP2Cs; highlighting a competitive-interaction process. Interaction selectivity has been shown to be mediated by subtle structural variations of primary sequence and ligand binding effects. Now, the dynamical contributions of ligand binding on interaction selectivity are investigated through extensive molecular dynamics (MD) simulations of apo and holo-PYR1 in monomeric and dimeric form as well as in complex with a PP2C, homology to ABA insensitive 1 (HAB1). Robust comparative interpretations were enabled by a novel essential collective dynamics approach. In agreement with recent experimental findings, our analysis indicates that ABA-bound PYR1 should efficiently bind to HAB1. However, both ABA-bound and ABA-extracted PYR1-HAB1 constructs have demonstrated notable similarities in their dynamics, suggesting that apo-PYR1 should also be able to make a substantial interaction with PP2Cs, albeit likely with slower complex formation kinetics. Further analysis indicates that both ABA-bound and ABA-free PYR1 in complex with HAB1 exhibit a higher intra-molecular structural stability and stronger inter-molecular dynamic correlations, in comparison with either holo- or apo-PYR1 dimers, supporting a model that includes apo-PYR1 in complex with HAB1. This possibility of a conditional functional apo-PYR1-PP2C complex was validated in vitro. These findings are generally consistent with the competitive-interaction model for PYR1 but highlight dynamical contributions of the PYR1 structure in mediating interaction selectivity suggesting added degrees of complexity in the regulation of the competitive-inhibition.