Applications of graphene have extended into areas of nanobio-technology such as nanobio-medicine, nanobio-sensing, as well as nanoelectronics with biomolecules. These applications involve interactions between proteins, peptides, DNA, RNA etc. and graphene, therefore understanding such molecular interactions is essential. For example, many applications based on using graphene and peptides require peptides to interact with (e.g., noncovalently bind to) graphene at one end, while simultaneously exposing the other end to the surrounding medium (e.g., to detect analytes in solution). To control and characterize peptide behavior on a graphene surface in solution is difficult. Here we successfully probed the molecular interactions between two peptides (cecropin P1 and MSI-78(C1)) and graphene in situ and in real-time using sum frequency generation (SFG) vibrational spectroscopy and molecular dynamics (MD) simulation. We demonstrated that the distribution of various planar (including aromatic (Phe, Trp, Tyr, and His)/amide (Asn and Gln)/Guanidine (Arg)) side-chains and charged hydrophilic (such as Lys) side-chains in a peptide sequence determines the orientation of the peptide adsorbed on a graphene surface. It was found that peptide interactions with graphene depend on the competition between both planar and hydrophilic residues in the peptide. Our results indicated that part of cecropin P1 stands up on graphene due to an unbalanced distribution of planar and hydrophilic residues, whereas MSI-78(C1) lies down on graphene due to an even distribution of Phe residues and hydrophilic residues. With such knowledge, we could rationally design peptides with desired residues to manipulate peptide-graphene interactions, which allows peptides to adopt optimized structure and exhibit excellent activity for nanobio-technological applications. This research again demonstrates the power to combine SFG vibrational spectroscopy and MD simulation in studying interfacial biological molecules.

Immobilization on solid supports provides an effective way to improve enzyme stability and simplify downstream processing for biotechnological applications, which has been widely used in research and in applications. However, surface immobilization may disrupt enzyme structure due to interactions between the enzyme and the supporting substrate, leading to a loss of the enzyme catalytic efficiency and stability. Here, we use a model enzyme, nitroreductase (NfsB), to demonstrate that engineered variants with two strategically positioned surface-tethering sites exhibit improved enzyme stability when covalently immobilized onto a surface. Tethering sites were designed based on molecular dynamics (MD) simulations, and enzyme variants containing cysteinyl residues at these positions were expressed, purified, and immobilized on maleimide-terminated self-assembled monolayer (SAM) surfaces. Sum frequency generation (SFG) vibrational spectroscopy and attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy were used to deduce the NfsB enzyme orientations, which were found to be consistent with those predicted from the MD simulations. Thermal stability analyses demonstrated that NfsB variants immobilized through two tethering sites exhibited generally improved thermal stability compared with enzymes tethered at only one position. For example, NfsB enzyme chemically immobilized via positions 423 and 111 exhibits at least 60% stability increase compared to chemically immobilized NfsB mutant via a single site. This research develops a generally applicable and systematic approach using a combination of simulation and experimental methods to rationally select protein immobilization sites for the optimization of surface-immobilized enzyme activity and stability.

Graphene-based biosensors have attracted considerable attention due to their advantages of label-free detection and high sensitivity. Many such biosensors utilize noncovalent van der Waals force to attach proteins onto graphene surface while preserving graphene's high conductivity. Maintaining the protein structure without denaturation/substantial conformational change and controlling proper protein orientation on the graphene surface are critical for biosensing applications of these biosensors fabricated with proteins on graphene. Based on the knowledge we obtained from our previous experimental study and computer modeling of amino acid residual level interactions between graphene and peptides, here we systemically redesigned an important protein for better conformational stability and desirable orientation on graphene. In this paper, immunoglobulin G (IgG) antibody-binding domain of protein G (protein GB1) was studied to demonstrate how we can preserve the protein native structure and control the protein orientation on graphene surface by redesigning protein mutants. Various experimental tools including sum frequency generation vibrational spectroscopy, attenuated total refection-Fourier transform infrared spectroscopy, fluorescence spectroscopy, and circular dichroism spectroscopy were used to study the protein GB1 structure on graphene, supplemented by molecular dynamics simulations. By carefully designing the protein GB1 mutant, we can avoid strong unfavorable interactions between protein and graphene to preserve protein conformation and to enable the protein to adopt a preferred orientation. The methodology developed in this study is general and can be applied to study different proteins on graphene and beyond. With the knowledge obtained from this research, one could apply this method to optimize protein function on surfaces (e.g., to enhance biosensor sensitivity).

Using terahertz time-domain spectroscopy, the real part of optical conductivity [σ1(ω)] of twisted bilayer graphene was obtained at different temperatures (10 -300 K) in the frequency range 0.3 -3 THz. On top of a Drude-like response, we see a strong peak in σ1(ω) at ∼2.7 THz. We analyze the overall Drude-like response using a disorder-dependent (unitary scattering) model, then attribute the peak at 2.7 THz to an enhanced density of states at that energy, that is caused by the presence of a van Hove singularity arising from a commensurate twisting of the two graphene layers.Compared to single-layer graphene (SLG), where there are two non-equivalent lattice sites (A and B), bilayer graphene (BLG) has two SLGs stacked in the third direction. In the most common Bernal (AB) stacking of BLG, adjacent layers are rotated by 60 • , so that the B atoms of layer 2 (B ′ ) sits directly on top of A atoms in layer 1 (A), and B and A ′ atoms are in the center of the hexagons of the opposing layer. Electrons can then hop between these two A sites with a hopping energy t ⊥ . In the undoped case, though both SLG and BLG are gapless semi-metals, carriers in SLG exhibit linear dispersion, while those in BLG show quadratic dispersion. An energy gap in SLG opens up due to finite geometry effects, but its control has proven to be unreliable [1]. On the other hand, the electronic gap in BLG can be reliably opened and controlled by an applied electric field, shown theoretically and demonstrated experimentally [2][3][4][5], and promises interesting applications. Both SLG and BLG however, are sensitive to disorder. Hence, to realize graphene-based optoelectronic devices, an understanding of the temperature and disorder effects in the transport and spectroscopic properties of BLG is needed. Temperature and disorder-dependent conductivity of BLG have been derived theoretically [1,6]. Experimentally, spectroscopies (from terahertz (THz) to visible) and ultrafast dynamics of various flavors of graphene have been reported, such as SLG, few and many-layer graphene, and graphite [7][8][9][10][11]. For example, Fourier-transform infrared spectroscopy (FTIR) on large-area SLG grown by chemical vapor deposition (CVD) revealed a Drude-like frequency dependence of the spectral density from THz to mid-infrared at different carrier concentrations [12]. In addition, graphene plasmons, which lie in the THz range, are strongly coupled to the interband electronic transitions and decay by exciting interband electron-hole pairs [13]. Hence knowledge of graphene's electromagnetic response, as a function of disorder, in the THz frequency range is critical for applications such as graphene-based THz oscillators [14].

Temperature-dependent terahertz conductivity of tin oxide (SnO 2) nanowire films was measured from 10 to 300 K using terahertz time-domain spectroscopy. The optical parameters, including the complex refractive index, optical conductivity and dielectric function, were obtained using a simple effective medium theory. The complex conductivity was fitted with the Drude-Smith model and the plasmon model. The results show that the carrier density (N) and plasmon resonance frequency (ω 0) increase while the scattering time decreases with increasing temperature. The reduced carrier mobility compared with bulk SnO 2 indicates the presence of carrier localization or trapping in these nanowires.