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TRACK 4 TRACK 4 Technical Program

moment, then those forces do not contribute to the dynamics and therefore Technical Presentation. NEMB2016-6134
may be eliminated from the model. The use of this method greatly reduces
the forward dynamics computational burden without significant deviation in Taha Goudarzi, Nahil A. Sobh, UIUC, Urbana, IL, United States
results. This method has previously been applied to dynamic simulations of
motor proteins and estrogen molecules. The analytical tools at our disposal for characterizing the mechanical behav-
ior of indented materials in a nanoindentation test with a spherical probe
The model used in this work is the Ebola virus glycoprotein. This virally en- (usually suitable for soft/bio materials) are limited to the Hertz’s contact solu-
coded glycoprotein is bound in the virion envelope and has been shown tion and its extensions. To overcome this deficiency many researchers have
to play a pivotal role in the mechanism of infection. Simulations of the in- used finite element simulations to model the nanoindentation tests.
teraction of this protein with host cell receptors could greatly aid on-going To characterize the behavior of indented materials in an inverse manner
research for effective treatments. using the finite element simulation, one needs to run the nanoindentation
simulation with a guess for the material properties which are the unknown of
The glycoprotein model has full atomic resolution and is assembled piece- the problem and then compare the simulation results with the experimental
wise from a user-input sequence of amino acids. Given the large number of data to see how good of a guess has been made. The computational cost
degrees of freedom, the Featherstone algorithm is used to numerically solve of such an approach has been an obstacle in development of inverse com-
the forward dynamics. This algorithm is ideal for biopolymer simulations putational methods and tools for material characterization based on results
as it precludes a symbolic model and is easily parallelizable. Active forces of nanoindentation tests. We have developed an online software (https://
include electrostatic and Lennard-Jones interaction potentials, viscous flu- nanohub.org/tools/nanoindentation) that can characterize the mechanical
idic damping, and stochastic Brownian motion arising from non-modeled behavior of indented materials in an iterative approach using finite element
collisions with the medium. This work is the first application of the multiscale simulations. In order to maintain the computational cost under a reasonable
method to a high-resolution protein model and a simulation using Feather- level very effective optimization methods have been utilized.
stone algorithms. In this online tool that is the first to a series of tools focusing on more com-
plicated problems (e.g. inelastic constitutive behavior and boundary condi-
4:20pm Adhesion Mechanisms of Curli Subunit CsgA tions) the concentration is on the nanoindentation of isotropic elastic materi-
als with spherical probes under arbitrary boundary conditions.
Technical Presentation. NEMB2016-5997
5:00pm Atomistic-to-continuum rod modeling of DNA mechanics
Elizabeth P. DeBenedictis, Jenny Liu, Sinan Keten, Northwestern
University, Evanston, IL, United States Technical Presentation. NEMB2016-5986

Naturally occurring and making up a large portion of the world’s biomass, Wonmuk Hwang, Xiaojing Teng, Texas A&M University, College
biofilms are present in a number of industrial and medical applications. They Station, TX, United States
comprise bacterial communities housed in a scaffold of proteins and poly-
saccharides, which along with water make a slime-like substance that is dif- Mechanical properties of DNA is crucial for genome organization and inter-
ficult to remove. Because of their strong adhesion and persistence, biofilms action with proteins. A challenge in modeling DNA mechanics arises due
are often associated with pathogenicity and nuisance, yet possess enviable to the co-existence of atomistic behaviors and mesoscale behavior of DNA
adhesive and survival properties. Curli is a specific fiber that grows on the as a chain molecule. For the latter, order parameters must be identified that
surface of E. Coli and plays a structural role in its biofilms, where it has been properly describe elastic deformation of DNA. We apply theory of elastic rod
shown to be critical for adhesion. Additionally, it has been shown that genet- to the atomistic molecular dynamics simulation of B-DNA oligos, to identify
ically engineered biofilms can be created to exploit the curli self-assembly local principal axes of bending. To achieve this, we perform a total of 0.9 mi-
process and to synthesize materials with molecularly precise features. Yet, crosecond all-atom molecular dynamics simulation of DNA oligos possess-
so far there is no clear link between the sequence, chemistry, and topolo- ing repeating sequences. For each base pair, we assign a local coordinate
gy of curli and resulting mechanical properties of their biofilms. Here, we basis (triad) and follow its trajectory relative to the triad of the neighboring
investigate the adhesion mechanisms of CsgA, the beta-helical subunit that dinucleotide step. In this way, major and minor bending axes are identified,
self-assembles into curli fibers. All-atomistic Molecular Dynamics simulations where the distributions of bending angles are well-approximated by Gauss-
of the protein subunit adsorbing on hydrophobic and charged surfaces in ian. For a given dinucleotide step (there are 10 possible dinucleotide steps
explicit water solvent are employed to assess adhesion. Using these, we ex- formed by G, C, A, T), we calculate the four elastic stiffness of the major/mi-
plore the connection between cooperative motion among residues, change nor bending, twist, and extension. DNA is the most compliant in major bend-
in secondary structure, and surface contact. Groups of residues in the struc- ing, and we find that traditional description based on helicoidal parameters
ture are seen to experience correlated changes in secondary structure and do not adequately capture conformational fluctuation around the equilibrium
flexibility, which can guide mutation location choices to induce changes in conformation. This is because the 16 helicoidal parameters, although they
subunit mechanical properties. While loss of secondary structure can result describe atomic structure of DNA well, they are not based on principal axes
in reduced stiffness, it often occurs in protein regions in contact with the of DNA. For any given oligo sequence, we can calculate the corresponding
surface. We find adhesion to be mediated by different mechanisms: aromatic persistence length that is consistent with experimental measurement. Based
residues facilitate adhesion onto graphene, while negatively charged resi- on our calculated parameters, we build coarse-grained model of DNA that
dues play a larger role in adhesion to silica. Additionally, rows of mutations effectively captures its sequence-dependent elastic properties. The coarse-
are incorporated within the subunit, with various compositions and positions. grained simulation of DNA oligos further reveals a finite size effect where
These are investigated in regard to changes in structural dependencies the persistence length measured by following the end to end distance fluc-
between residues, adhesion energy, and alignment between aromatic tuation and applying the wormlike chain model, is shorter than one for an
mutations. These results can be applied to determine optimal mutation lo- ideal, infinitely long DNA that is calculated based on their bending stiffness
cation and type for (1) enhancing adhesion and (2) facilitating pi-stacking for and sequence composition. This is due to the nonzero intrinsic curvature.
electron conduction and can be used as a guide for choices in genetically We also decompose elastic energy in 1381 x-ray structures of protein-DNA
modifications. These findings lend insight into the mechanisms governing complexes. In most cases, DNAs are only mildly deformed with the total
the impressive adhesive properties of curli, which can be applied to devel- elastic energy less than two times the thermal energy. In this case, twist is
opment of strong adhesives. Results concerning mutations set the stage for the dominant mode of deformation. For structures with total elastic energy
development of methods to enhance adhesion and use curli’s self-assem- greater than about four times thermal energy, major bending becomes dom-
bling power to create ordered nanostructures and microbial nanowires. inant. The present results elucidate the atomistic origin for the elastic be-
havior of DNA and how it is used for interaction with proteins. Our approach 57
4:40pm Computational characterization of materials response is applicable to DNAs in different conformational states as well as to other
based on results of nanoindentation tests filamentous proteins.