Keyword Suggestions

Results
 
 
Account Login
 
 
 
 
 

Library Navigation

 
 

Browse Meetings

 
 
 
NN6.01 - Multi-Scale Modeling and Design of Sequence-Defined Biomimetic Polymers 
Date/Time:
December 3, 2014   8:00am - 8:15am
 
Speaker:
 
Taxonomy
 
 
 
Format:
       
  Synced Audio / Video / Slides
 
Share:
 

Biomimetic polymers (BMPs) are useful for materials science and bioenergy applications like CO2 separation because of a diverse availability of monomers, high thermostability, and resistance to biodegradation. We have been developing a multi-scale simulation framework to facilitate experimental design and development of BMP systems, with the goal of forming ordered structures and pore networks. These simulations also provide insights about the key forces governing folding and assembly in such systems, which are currently poorly understood.

For example, experiments show that amphiphilic peptoid BMPs form fibers in solution and/or micron-scale bilayers on a mica surface. Peptoids are challenging to simulate because the amide bonds between residues can isomerize between cis and trans and the peptoid amide cannot form backbone-backbone hydrogen bonds. In addition, replica-exchange molecular dynamics (REMD) atomistic simulations of dimers of these 12-residue peptoids do not reproduce the experimental structural forms. Thus, we are developing a MARTINI-based coarse-grained (CG) force field for the peptoid backbone to model cooperative assembly at larger length scales. For bonded terms, atomistic simulations show that the backbone Ni-Nj distance is consistently 0.37 nm, while the Ni-Nj-Nk pseudo-angle clearly distinguishes the cis and trans states of the amide bond between residues i and j. For non-bonded parameters, we create a new particle type from the MARTINI P3 type that reflects the unusual hydrogen bonding properties of the peptoid amide. CG simulations of all-trans sarcosine 12-mer recover the bonded potentials seen in a corresponding atomistic simulation, and they also qualitatively reproduces the atomistic radius of gyration (Rg) distribution.

In a parallel example, we are structurally modeling different sequences of a new polymer architecture, in which variable-length non-amide linkers connect core elements bearing sidechains, to inform experimental designs. The cores and linkers are parameterized using the generalized amber force field, and 500-ns REMD simulations are used to explore the conformational space of short polymers. K-means clustering is used to identify favored structures. Simulations of hexamers suggest several favored motifs with different backbone/backbone hydrogen bonding and π stacking configurations. The simulations also suggest that imine sidechains increase helical propensity, chiral linkers increase conformational order, and longer linkers promote more globular structures. We are currently performing experiments to test these simulation-based hypotheses. In simulations of 12-mers, more globular and elaborate tertiary structures form that are reminiscent of proteins. This suggests significant promise of the novel polymer architecture for applications where intramolecular conformational and structural order are functionally important.
 


 
 
Average Rating: (No Ratings)
  Was great, surpassed expectations, and I would recommend this
  Was good, met expectations, and I would recommend this
  Was okay, met most expectations
  Was okay but did not meet expectations
  Was bad and I would not recommend this
 



Submit
 
Performance Enhancement of Pentacene Based Organic Field-Effect Transistor through DNA Interlayer
Semiconducting Polymer-Dipeptide Nanostructures by Ultrasonically-Assisted Self-Assembling
DNA as a Molecular Wire: Distance and Sequence Dependence
Structure-Property Relationship in Biologically-Derived Eumelanin Cathodes Electrochemical Energy Storage
Artificial Physical and Chemical Awareness (proprioception) from Polymeric Motors