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Using non-equilibrium molecular dynamics for thermal energy transfer, we investigate the interfacial thermal conductance between non-covalently interacting graphene nano-ribbons (GNRs) of varying lengths and widths in a cross-contact (x-shaped) geometry. Our results show that the out-of-plane conductance between GNRs can vary significantly (up to a factor of 4) depending upon their geometric parameters. We observe that when plotted against aspect ratio, the predicted interface thermal conductance values fit excellently on a single masterplot with a logarithmic scaling, suggesting the importance of GNR aspect ratio towards thermal conductance. We propose a model based on incorporating different thermal conductance characteristics of edge and inner interacting regions which predicts the observed logarithmic dependence on aspect ratio. We also study the effect of graphene edge roughness, temperature, and strain on out-of-plane thermal conductance and discuss the observed results based on local vibrational characteristics of atoms within interacting region, number of interacting phonons, and the degree to which they interact across the interaction zone., Journal article published in 2D Materials, v1, 025005, 2014. Prepared in collaboration with Universal Technology Corp., Dayton, OH.

Histone proteins are not only important due to their vital role in cellular processes such as DNA compaction, replication and repair but also show intriguing structural properties that might be exploited for bioengineering purposes such as the development of nano-materials. Based on their biological and technological implications, it is interesting to investigate the structural properties of proteins as a function of temperature. In this work, we study the spatial response dynamics of the histone H2AX, consisting of 143 residues, by a coarse-grained bond fluctuating model for a broad range of normalized temperatures. A knowledge-based interaction matrix is used as input for the residue-residue Lennard-Jones potential. We find a variety of equilibrium structures including global globular configurations at low normalized temperature (T*=0.014), combination of segmental globules and elongated chains (T*=0.016,0.017), predominantly elongated chains (T *=0.019,0.020), as well as universal SAW conformations at high normalized temperature (T* or = 0.023). The radius of gyration of the protein exhibits a non-monotonic temperature dependence with a maximum at a characteristic temperature (T*c=0.019) where a crossover occurs from a positive (stretching at T* or = T*c ) to negative (contraction at T* or =T*c) thermal response on increasing T*., Published in PloS ONE, v7 n3 article e32075, March 2012.

Monte Carlo simulations are used to model the self-organizing behavior of the biomineralizing peptide KSL (KKVVFKVKFK) in the presence of phosphate. Originally identified as an antimicrobial peptide, KSL also directs the formation of biosilica through a hypothetical supramolecular template that requires phosphate for assembly. Specificity of each residue and the interactions between the peptide and phosphate are considered in a coarse-grained model. Both local and global physical quantities are calculated as the constituents execute their stochastic motion in the presence and absence of phosphate. Ordered peptide aggregates develop after simulations reach thermodynamic equilibrium, wherein phosphates form bridging ligands with lysines and are found interdigitated between peptide molecules. Results demonstrate that interactions between the lysines and phosphate drive self-organization into lower energy conformations of interconnected peptide scaffolds that resemble the supramolecular structures of polypeptide- and polyamine-mediated silica condensation systems. Furthermore, the specific phosphate-peptide organization appears to mimic the zwitterionic structure of native silaffins (scaffold proteins of diatom shells), suggesting a similar template organization for silica deposition between the in vitro KSL and silaffin systems., Prepared in collaboration with the Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH. Prepared in cooperation with Universal Technology Corporation, Dayton, OH and the Univ of Southern Mississippi, Hattiesburg. Published in Physical Chemistry Chemical Physics, 2010.

Single-wall carbon nanotube field effect transistors (SWNT-FETs) are ideal candidates for fabricating sensors due to their unique electronic properties and have been widely investigated for chemical and biological sensing applications. The lack of selectivity of SWNT-FETs has prompted extensive research on developing ligands that exhibit specific binding as selective surface coating for SWNTs. Herein we describe the rational design of a peptide recognition element (PRE) that is capable of noncovalently attaching to SWNTs as well as binding to trinitrotoluene (TNT). The PRE contains two domains, a TNT binding domain derived from the binding pocket of the honeybee odor binding protein ASP1, and a SWNT binding domain previously identified from the phage peptide display library. The PRE structure in the presence of SWNT was investigated by performing classical all-atom molecular dynamics simulations, circular dichroism spectroscopy, and atomic force microscopy. Both computational and experimental analyses demonstrate that the peptide retains two functional domains for SWNT and TNT binding. The binding motif of the peptide to SWNT and to TNT was revealed from interaction energy calculations by molecular dynamics simulations. The potential application of the peptide for the detection of TNT is theoretically predicted and experimentally validated using a SWNT-FET sensor functionalized with a designer PRE. Results from this study demonstrate the creation of chemosensors using designed PRE as selective surface coatings for targeted., Published in ACS Nano, v4 p452-458, 28 Dec 2009.

In summary, we employ a classical atomistic molecular dynamics approach to analyze specific peptide binding to metal surfaces in comparison with thermochemical, IR, NMR, and TEM measurements. Modeling at all levels, molecular, coarse-grain, and bioinformatics, is ultimately important in identifying the most suitable peptide sequences for controlled binding and detachment. Quantum-mechanical approaches indicate approximate trends of the interaction of peptide fragments and a few solvent molecules with parts of a surface, and have shown that covalent interactions with metal surfaces are modest to small. However, such approaches cannot fully explain the mechanisms of binding due to limitations to static calculations. Coarse-grain approaches can be computationally -10(3) times more efficient and include certain specific peptide-surface interactions. A critical role can also be attributed to bioinformatics approaches such as simple numerical screening functions on the basis of molecular-level insight to help eliminate sequences of undesirable binding strength. The success of such higher-level approaches, however, yet depends on understanding the nature of the molecular interactions., Supports 'Nature of Molecular Interactions of Peptides with Gold, Palladium, and Pd-Au Bimetal Surfaces in Aqueous Solution' published in the Journal of the American Chemical Society, v131 n28 p9704-9714, 22 Jul 2009; published online 24 Jun 2009. See ADA509904. Prepared in cooperation with Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, OH and the Department of Physics and Astronomy, University of Southern Mississippi, Hattiesburg, MS.

We investigated molecular interactions involved in the selective binding of several short peptides derived from phage-display techniques (8-12 amino acids, excluding Cys) to surfaces of Au, Pd, and Pd-Au bimetal. Changes in chain conformation from the solution to the adsorbed state over the course of multiple nanoseconds suggest that the peptides preferably interact with vacant sites of the face-centered cubic lattice above the metal surface. Residues that contribute to binding are in direct contact with the metal surfaces, and less-binding residues are separated from the surface by one or two water layers. The strength of adsorption ranges from 0 to -100 kcal/(mol peptide) and scales with the surface energy of the metal, the affinity of individual residues versus the affinity of water, and conformation aspects, as well as polarization and charge transfer at the metal interface (only qualitatively considered here). A hexagonal spacing of approx. 1.6 angstrom between available lattice sites on the {111} surfaces accounts for the characteristic adsorption of aromatic side groups and various other residues, and a quadratic spacing of approximately 2.8 angstroms between available lattice sites on the {100} surface accounts for a significantly lower affinity to all peptides in favor of mobile water molecules. The combination of these factors suggests a "soft epitaxy" mechanism of binding. On a bimetallic Pd-Au {111} surface, binding patterns are similar, and the polarity of the bimetal junction can modify the binding energy by approximately 10 kcal/mol. The results are semiquantitatively supported by experimental measurements of the affinity of peptides and small molecules to metal surfaces as well as results from quantum-mechanical calculations on small peptide and surface fragments. Interfaces were modeled using the consistent valence force field extended for Lennard-Jones parameters for fcc metals which accurately reproduce surface and interface energies., Published in the Journal of the American Chemical Society, v131 n28 p9704-9714, 22 Jul 2009; published online 24 Jun 2009. Supporting information appears in ADA509904. Prepared in cooperation with Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, OH and the Department of Physics and Astronomy, University of Southern Mississippi, Hattiesburg, MS. The original document contains color images. All DTIC reproductions will be in black and white.

This research in support of the Air Force Research Laboratory Materials and Manufacturing Directorate was conducted at Wright-Patterson AFB, Ohio from 1 December 2005 through 1 April 2008. This task developed and validated Monte Carlo computational methods for the modeling of two-dimensional nanoplates in polymer/solvent matrix. Nano-particulate polymer composites consist of multi-component systems with such constituents as solvent, polymer chains, clay platelets etc. The vast parameter space includes molecular weight of constituents, their concentrations, temperature, and interaction apart from processing and driving mechanism (shearing, compression, etc.). The constitutive components can be described by particles, chains, and sheets in a coarse-grained modeling by computer simulations. Relaxation of each component and their cooperative dynamics lead to multi-scale responses resulting in self-organizing structures. While the stochastic dynamics of each component facilitate equilibration, the physical entanglement, local-crowding, and jamming cause entropic constraints that may hinder thermal equilibration. The evolving structure may or may not be in thermodynamics equilibrium depending on the time scales. Understanding the structure and dynamics of such a multi-component system is known for its complexities. Therefore, we proposed to address some of the issues by accelerated computational approach., Performed in cooperation with Universal Technology Corportation, Dayton, OH; and the Air Force Research Laboratory (AFRL), Wright-Patterson AFB, OH. The original document contains color images. All DTIC reproductions will be in black and white.

This research in support of the Air Force Research Laboratory Materials and Manufacturing Directorate was conducted at Wright-Patterson AFB, Ohio at the University of Southern Mississippi from 1 Apr 04 through 1 Oct 2005. The research investigated alternate computational approaches to simulating nanocomposites. The nanoparticulate polymer composites consisted of multicomponent constituents, such as large planar clay segments, polymer chains and colvent particles.