Hello,
A change in allocation has been requested:
Requester: abelardo (Abelardo Ramirez-Hernandez)
Project: nano-soft-assembly
Title: Modeling Self Assembly in Nanostructured Soft Materials
Description: Liquid Crystals. Liquid crystals are fascinating materials in that molecular-level events can reorganize the ordering at mesoscopic length scales. The long-range orientational order and anisotropic fluid properties of nematic LCs make them ideal candidates for a variety of applications including LC displays, thermometers, optical imaging devices, and sensors. The orientation of LC molecules can be manipulated through the application of external fields such as surface and electric fields. A surface field, for example, may create local disordered regions (defects) where the inherent orientation of the mesophase is lost. Interestingly, nanoparticles or small molecules can be localized in such defects, thus opening the possibility for creating hierarchical functional structures. Also, local orientation can be changed rapidly near aqueous interfaces by using external electric fields. Such unique responsive behavior introduces a large number of technologically attrac
tive features to this class of materials. However, despite rigorous experimental and theoretical efforts, the molecular nature of defects and atomic-scale mechanisms of adaptive oil-water interfacial organizations remain largely unknown. In this trust, our main goal is to employ advanced computational algorithms and large-scale molecular simulations to understand the behavior of LC molecules near, and inside, defects and at aqueous interfacial regions. The detailed proposed projects associated to this trust are described below:
1) In recent years, there has been a growing interest in controlling the assembly of molecules and nanoparticles within nematic LCs for creating materials with tunable mechanical, optical, and electronic properties. Theoretical and experimental work have shown that the physics of defects play an important role in the self-assembly of nanoparticles. Introducing nanoparticles into nematic LCs disturbs the nematic field and generates defects. The presence of defects costs elastic energy and therefore gives rise to anisotropic, long-range effective interactions between particles. The nanoparticles assemble into an arrangement which reduces or eliminates high elastic energy regions. However, the underlying mechanisms of such interactions remains elusive. The microscopic organization of LC defects are often too complex to be treated with standard experimental and analytical tools. By using the computer capabilities provided by the Blues cluster, we have recently characterized, for
the first time, defects in a nematic LC with atomistic resolution. We performed molecular dynamics (MD) simulations of a system consisting of 328000 atoms. Two disclination line defects have been stabilized by introducing a cylinder with homeotropic anchoring into the system. These preliminary results are very encouraging, we are currently finishing the analysis of this system. Based on this, we propose to explore the interaction of LC material with nanoparticles, or small molecules, close to these created defects. The energetically stable location of a small particle will be determined by computing the potential of mean force (PMF) as a function of distance from LC defects.
2) Ions and ionic pairs are ubiquitous in many different phenomena including tailoring molecular interactions at the interfaces. While some properties of the ions might be trivial to measure or calculate, some are harder to evaluate. A simple electrolyte solution such as sodium salts, for example, can modulate the orientation of LC molecules at aqueous interfaces. Importantly, the underlying microscopic mechanisms of such modulation remains poorly understood. It is postulated that ions at the interface of LC and water form an electric double layer which in turn create an external electric field to regulate the orientation of molecules at the interface. However, such mechanism remains to be confirmed using atomistic simulations and supplementary experiments. Here, we aim to unveil the atomistic details of such modular interfacial orientations using large-scale molecular dynamics simulations in a LC/water/air hybrid channel. To avoid finite-size effects large thickness of the c
hannel will be required (> 30-50 nm). Slabs of 8CB and 5CB will be brought in contact with water (~ 24,000 water molecules) to form the water/oil interface while two other ends of LC and water will remain in contact with vacuum to resemble the oil-air interface. We will then calculate the energetically preferred spatial location of cations and anions across the LC/water/air channel. Such calculations will make use of advanced computational algorithms to compute free energies. In particular, PMF of a single ion (sodium, chloride, and iodide) which explores the bulk water and gradually moves to the interfacial LC/water region and eventually lands in the neat LC region will be obtained.
In the projects described above, we will employ umbrella sampling methodology with a biasing center-of-mass harmonic potential applied to ions and small particles. In this technique, a series of molecular dynamics simulation are performed between two thermodynamic states with a bias potential applied along a reaction coordinate. The bias potentials drive the system from one thermodynamic state to another. The change in free energy in each simulation can be calculated from the sampled distribution of the system along the reaction coordinate. We will generate initial configurations by inserting small particles (or molecules) and ions into previously equilibrated configurations along the reaction coordinate. These pre-equilibrated initial configurations reduces the equilibration time of new systems significantly, and since the umbrella sampling must be carried out in an equilibrium state, such setup saves computational time substantially. We will run 100 independent simulations
for at least 100 ns with biasing potential applied to the center-of-mass of the ions and small the molecules. Simulation of 100 copies of a system this large (> 1 000 000 CPU hours) is only possible in a leadership class facility such as Blues.
Block Copolymers. Block copolymer molecules are chains composed of two or more chemically different polymers covalently bonded together. These materials self-assemble into structures whose dimensions range from 5 to 100 nm. Lithographic applications of block copolymer films in the microelectronics and memory device industries require formation of morphologies with perpendicularly oriented domains and long-range order. Although there has been significant progress in the directed self-assembly of block polymers for lithographic patterning applications, important challenges remain with regards to development of materials and processes leading to perfect, defect-free assembly. We have demonstrated the importance of kinetics on the elimination of defects, where an extraordinarily large thermodynamic driving force is not necessarily sufficient for defect removal. This latter point is highlighted in calculations of the minimum free-energy pathway for defect annihilation in block cop
olymer melt thin films using a string procedure. Kinetic energy barrier heights are shown to strongly depend on the defect type and on processing conditions such as the type of chemical pattern or the strength of the segregation force between blocks. Thus, kinetics plays a very important role defining the structure that finally will appear under specific conditions. Thus a model which is able to quantitatively predict rheological response of polymer materials is highly desired. We have developed a coarse grained simulation approach that faithfully represents both entangled and unentangled dynamics of homopolymers, our TIEPOS approach. We have demonstrated the ability of the TIEPOS approach to quantitatively predict the rheological behavior of polymer melts, both in linear as non-linear regimes. We have shown that by fitting only two scaling factors for a single sample, it is possible to predict the rheology of other samples, both at equilibrium as non-equilibrium conditions,
without any further parameter adjustments. So far our TIEPOS approach has been used to demonstrate that the model is able to reproduce the rheology of homopolymers in the bulk. However, there are not studies addressing the question about the rheology of BCP thin films and the effect of entanglements on the directed assembly of these materials. We will perform simulations using TIEPOS approach to explore how confinement and entanglements affect the kinetics of assembly in the presence of chemical patterns directing the structure formation.
We have also started the study of liquid crystalline polymers. By incorporating nematic motifs into the polymer backbones, we expand the palette of BCP morphologies and responses to external fields. In this situation, orientational order and microphase separation will cooperate and dictate how polymer chains will self-organize. We will explore the equilibrium and far from equilibrium behavior of these liquid crystalline BCP by using our generalized TICG model for these systems. Both bulk as thin films are systems to be considered.
Our recent work utilizing LCRC resources has contributed to the following publications. Several more are currently being finished to be submitted.
1. Surface Adsorption in Nonpolarizable Atomic Models
J. K. Whitmer, A. A. Joshi, R. J. Carlton, N. L. Abbott and J. J. de Pablo
J. Chem. Theory Comput. 10, 5616 (2014).
2. Basis Function Sampling: A New Paradigm for Material Property Computation
J. K. Whitmer, C. Chiu, A. A. Joshi, and J. J. de Pablo
Phys. Rev. Lett. 113, 190602 (2014).
3. Simulation of Defect Reduction in Block Copolymer Thin Films by Solvent Annealing
S. M. Hur, G. S. Khaira, A. Ramirez-Hernandez, M. Muller, P. F. Nealey and J. J. de Pablo
ACS Macro Lett. 4, 11 (2015).
4. Characterizing the Three-Dimensional Structure of Block Copolymers via Sequential Infiltration Synthesis and Scanning Transmission Electron Tomography
T. Segal-Peretz, J. Winterstein, M. Doxastakis, A. Ramirez-Hernandez, N. Zaluzec, M. Biswas, J. Ren, A. J. Liddle, J. W. Elam, J. J. de Pablo and P. F. Nealey
ACS Nano 9, 5333 (2015).
5. Theoretically Informed Monte Carlo Simulation of Liquid Crystals by Sampling of Alignment-Tensor Fields
J. C. Armas-Perez, A. Londono-Hurtado, O. Guzman, J. P. Hernandez-Ortiz and J. J. de Pablo
J. Chem. Phys. 143, 044107 (2015).
6. Interplay of Surface Energy and Bulk Thermodynamic Forces in Ordered Block Copolymer Droplets
S.M. Hur, M. S. Onses, A. Ramirez-Hernandez, P. F. Nealey, J. A. Rogers and J. J. de Pablo
Macromolecules 48, 4717 (2015).
7. Self-consistent description of electrokinetic phenomena in particle-based simulations
J. P. Hernandez-Ortiz and J. J. de Pablo
J. Chem. Phys. 143, 014108 (2015).
8. Sculpting bespoke mountains: Determining free energies with basis expansions
J. K. Whitmer, A. M. Fluitt, L. Antony, J. Qin, M. McGovern and J. J. de Pablo
J. Chem. Phys. 143, 044101 (2015).
9. Molecular Pathways for Defect Annihilation in Directed Self-Assembly
S. M. Hur, V. Thapar, A. Ramirez-Hernandez, G. S. Khaira, T. Segal-Peretz, P. A. Rincon-Delgadillo, M. Muller, P. F. Nealey and J. J. de Pablo
Proc. Natl. Acad. Sci. USA, Under Review (2015).
10. Liquid crystal free energy relaxation by a theoretically-informed Monte Carlo using a finite element quadrature approach
J. C. Armas-Perez, J. P. Hernandez-Ortiz and J. J. de Pablo
J. Chem. Phys. Under Review (2015).
11. A Multichain Polymer Slip-Spring Model with Fluctuating Number of Entanglements for Linear and Nonlinear Rheology
A. Ramirez-Hernandez, B. L. Peters, M. Andreev, J. D. Schieber and J. J. de Pablo
J. Chem. Phys. Under Review (2015).
12. Liquid crystal bi-stable induced phases by chemical control of anchoring surfaces
J. C. Armas-Perez, X. Li, J. A. Martinez-Gonzalez, J. P. Hernandez-Ortiz, P. F. Nealey and J. J. de Pablo
Phys. Rev. Lett. Under Review (2015).
Current: undetermined amount
Justification: Over the past year of LCRC supported research we have optimized the efficiency of our codes. For these projects, we will made use of NAMD, LAMMPS and in-house codes using these software packages. We have achieved excellent scaling, and make near-optimal use of LCRC resources. For example, we have tested the efficiency of NAMD for the atomistic simulations and found that the best performance is obtained by using 20 nodes (320 cores) per job. With this number of nodes we can simulate these huge systems for ~15 ns per day.
---- Table of NAMD efficiency ----
nodes days/ns
1 0.59
2 0.31
4 0.17
6 0.13
10 0.1
20 0.063
40 0.041
60 0.038
Requested: 500000
A specific reason has been given:
Dear LCRC Allocations Committee,
Our request for an additional half million core hours is based on the following: By using the previous allocation, we have been able to complete several papers with important results on the behavior of liquid crystalline and polymeric materials. These manuscripts have been submitted to review in high-impact journals, in a couple cases additional simulations have been requested and it would be important to have those results ready in the shortest possible time. Moreover, we have been able to develop an atomistic model for charged block copolymers with important usefulness for the understanding and developing of Li-based high energy density devices. We are in the process of testing such a model under different specific conditions to demonstrate its potential as a reliable model. Given the number of conditions to be studied and the scales to be explored, we estimate we will need ~ 400k core hours, the rest will be used to complete the work on LC. LCRC resources have been critica
l on the success on these works, allowing us to perform atomistic simulations of large systems for long times, impossible to achieve with other resources.
This needs to be approved and the final allocation amount decided upon.
Thank You,
The LCRC Accounts System
