MTSM Research Group
Research Highlights
Polymer Composites and Glasses
The many recent experiments have shown that the addition of nanoparticles (colloidal particles with nanometer dimensions) to
polymer fluids and polymer glasses can have dramatic effects on the transport and mechanical properties of these materials
that are not found through the use of micron-sized particles. By employing molecular simulations, we are trying to achieve
a fundamental-level understanding of how these nanoparticles are able to improve the properties of polymer glasses. By
performing calculations of the local mechanical properties, we have been able to show that a very stiff, glassy layer exists
near the surfaces of the nanoparticles. At sufficiently high concentrations, this glassy layer can form bridges of stiff
material between the particles, leading to an overall increase in the stiffness of the nanocomposite [1]. Currently, we are
studying how the addition of nanoparticles affects the dynamics and the rheological properties of glassy polymers. In very
high molecular weight polymeric systems, the polymer chains form entanglements with each other, which lead to slower
relaxation. We have recently shown how the addition of nanoparticles can increase the entanglement density in polymer
nanocomposites by behaving as "entanglement traps". Furthermore, we have shown that this effect is exacerbated
upon deformation of the polymer as shown in the image.
- George J. Papakonstantopoulos, Emmanouil Doxastakis,
Paul F. Nealey, Jean-Louis Barrat, and Juan J. de Pablo.
"Calculation of Local Mechanical Properties of Filled Polymers".
Physical Review E 75(3):031803, March 23, 2007. [doi:10.1103/PhysRevE.75.031803] [APS/PRE]
DNA Translocation
An exciting area of research we are pursuing involves the confinement of DNA in small spaces, such as a viral capsid.
Viruses utilize a protein shell, or capsid, to transport their DNA from one host to another. In bacteriophage, a preformed
capsid utilizes a molecular motor to translocate DNA from the capsid's environment (e.g. cytoplasm of the host bacterium)
into the capsid. These molecular motors are among the most powerful found in nature and are capable of packaging DNA to
very high volume fractions, over fifty percent in some cases. Due to the self-repelling nature of the negatively charge
phosphate backbone of DNA, this high volume fraction within the capsid generates pressures on the order of 100 atm. There
is mounting experimental evidence that this high internal pressure is at least partially responsible for ejection of the
genome during infection. Our current work focuses on elucidating the mechanisms of both internalization and ejection of the
genome at the molecular scale. Our primary tools to study this problem are molecular dynamics techniques used with
coarse-grained capsid and DNA models. In particular, our DNA model is capable of capturing the rich physics of DNA (such as
melting and hybridization) that are not possible with standard bead-spring models that have been used to date in studying
these phenomena.
Liquid Crystals
Liquid crystals (LCs) are a phase of matter that flows like a liquid, but the orientations of the molecules are highly
ordered over a very long range. This presence of long-range orientation results in interesting behavior of systems that
employ LCs. In our group, we model LCs on multiple scales in an effort to engineer new applications for the laboratory and
industry. At the atomistic level, we investigate the behavior of LCs near surfaces to determine the types and strength of
anchoring present at different surfaces. At a mesoscale, we study systems mixtures and determine the accessibility
different phases of LCs. On the largest scales, we investigate the behavior of particles, from the nanometer to micron
scale, and observe their behavior in an LC solvent; the presence of defects in the LC has a marked effect on particle
behavior, so by controlling the defect with fields (flow, electric, magnetic,etc.), we can dictate particle behavior in a
well controlled manner.
Block Copolymers
Block copolymers are made of two or more polymeric blocks, each a sequence of identical monomers, attached by covalent bonds. At a low enough temperature, the incompatibility between different blocks leads to a micro-phase separation, and the copolymer self-assembles into an ordered morphology, such as lamellae, cylinders or spheres. The extraordinary variety of possible morphologies and their molecular dimension (5-100 nm) make block copolymers ideal materials to create structures at the nanoscale.
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| Nanoparticle/block-copolymer self-assembled on patterned substrates | Example of morphologies obtained with an ABC triblock: (a) lamellae, (b) core-shell cylinders, (c) tetragonal cylinders, (d) spheres |
To predict the self-assembly of block-copolymers, we have developed Monte Carlo simulations of a coarse-grained model [1]. We focus on three different lines of research, often in close contact with the experimental work done in Prof. Nealey's group.
- The directed assembly of block copolymers is a promising approach to extend lithographic processes and fabricate devices with critical dimensions below 10 nm. However, morphologies produced through spontaneous self-assembly usually lack the long-range order which is desirable for applications. The use of patterned substrates, either chemically or topographically, are two proposed solutions to enforce long-range order. We use our simulation to compare those strategies and identify under which conditions a defect-free assembly is obtained.
- Incorporating nanoparticles into self-assembling copolymers could prove useful for design of new functional materials. We have investigated how a mixture of nanoparticles (8 nm in diameter) and copolymers self-assemble when deposited in a thin film over patterned substrate. The distribution of nanoparticles predicted by simulation is in good agreement with the experimental result.
- Our simulations are used to predict the phase diagram of triblock copolymers, which remains largely unexplored.
- François A. Detcheverry, Huiman Kang, Kostas Ch. Daoulas, Marcus Müller, Paul F. Nealey, and Juan J. de Pablo.
"Monte Carlo simulations of a coarse grain model for block copolymer systems".
Macromolecules, submitted, 2008.
Polyelectrolyte Gels
Polyelectrolyte gels are crosslinked networks of ionizable polymers swollen in water or aqueous salt solutions. These types
of hydrogels have very large swelling capacities and have found applications as superabsorbent materials in medical and
hygienic products (for example, sodium polyacrylate gel—shown in the photograph at right—in powder form is used
to make diapers), as water retainers and fertilizer capsules in agriculture, as flocculating agents in wastewater treatment,
as thickening agents in food and cosmetics, and as gel media for the separation and purification of biomacromolecules such
as proteins and DNA. In living organisms, natural polyelectrolyte gels regulate the storage and transport of water and
electrolytes (such as the mucopolysaccharide gel in aloe vera), provide structural and optical functions (the vitreous
humor in the eyes), and provide lubrication (the synovial fluid in bone joints and the mucin secreted by snails and
slugs). On a more theoretical level, polyelectrolyte gels have been used as models to help scientists understand
biophysical processes such as muscle contraction and nerve excitation.
An interesting property of polyelectrolyte gels is that they can undergo a discontinuous first-order volume phase transition
due to changes in the quality of the solvent surrounding the gel. This means that with a very slight change in the
salt concentration, temperature, or pH of the solvent, it can be possible to change the volume of the gel by a
factor of several hundred or more than a thousand times.
Many novel applications of polyelectrolyte gels, including the use of these gels as capsules for drug delivery and as motors
for microfluidic actuation, seek to exploit this discontinuous change in the gel volume as a means of implementing an on-off
switching device. To this end we are using molecular simulations to study the properties of polyelectrolyte gels, focusing
our effort on understanding the thermodynamic principles that causes the phase transition, so that this phenomenon can be
better controlled in real applications. The MPEG animation shown here was produced from simulation data generated using a
coarse-grained molecular model for a swollen polyelectrolyte gel, and shows that divalent cations (red) are much more
strongly attracted to the anionic polyelectrolyte network backbone (blue) than are the monovalent cations (white).
Quantitative analysis of the simulation data allows us to gain insight into the interplay between energetic and entropic
effects as the polyelectrolyte gel undergoes the volume phase transition and provide explanation for certain experimental
observations.
- Qiliang Yan and Juan J. de Pablo.
"Monte Carlo Simulation of a Coarse-Grained Model of Polyelectrolyte Networks".
Physical Review Letters 91(1) 018301, July 4, 2003. [doi:10.1103/PhysRevLett.91.018301] [APS/PRL] - De-Wei Yin, Qiliang Yan, and Juan J. de Pablo.
"Molecular Dynamics Simulation of Discontinuous Volume Phase Transitions in Highly-Charged Crosslinked Polyelectrolyte Networks with Explicit Counterions in Good Solvent".
Journal of Chemical Physics 123(17):174909, November 1, 2005. [doi:10.1063/1.2102827] [AIP/JCP] - De-Wei Yin, Ferenc Horkay, Jack F. Douglas, and Juan J. de Pablo.
"Molecular Simulation of the Swelling of Polyelectrolyte Gels by Monovalent and Divalent Counterions".
Journal of Chemical Physics, 129(15):154902, October 16, 2008. [doi:10.1063/1.2991179] [AIP/JCP]
Folding and Aggregation of Polyglutamines
The aim of this project is to study, at a molecular detail, the folding and aggregation of long polyglutamine (PolyQ)
chains. Under some circumstances, these peptides fold onto themselves adopting a metastable conformation that is believed to
be the nucleus for subsequent polymerization of additional chains. Our work is motivated by a desire to understand the
molecular mechanisms behind such a nucleated growth polymerization process, and by the fact that polyglutamine is of central
importance in a number of neurodegenerative disorders, most notably Huntington's Disease; literature studies concur in that
a better understanding of the thermodynamics and kinetics of PolyQ folding and aggregation will accelerate the development
of therapeutic treatments for Huntington's and other expanded PolyQ diseases.
With this goal in mind, the project has been divided into several sub-projects involving:
- the development of new simulation techniques that will enable efficient study of the PolyQ folding and aggregation processes, including a detailed analysis of the relevant transition states
- the study of the folding process of individual PolyQ chains into plausible, metastable candidate folded structures
- the study of the polymerization or aggregation process of multiple chains into stable oligomeric aggregates
- the study of the effects of additives (solutes) and site mutations on the folding of individual chains and the aggregation of multiple chains
A detailed, atomic-level understanding of the pathways through which polyglutamine folds and polymerizes will emerge out of these studies, as well as methodological and fundamental advances that will have a positive, wide-ranging impact on the scientific community's ability to understand protein misfolding and aggregation. Finally, the insights into PolyQ structure and dynamics under a variety of conditions will be of considerable use for development of therapeutic strategies.
