We investigate the effect of the electron wave function producing permittivity (epsilon) near zero in sub-nanometer gaps and at surfaces. The field enhancement is calculated for gaps and nanoparticles, as well as the absorption from nanoparticles. Our modified quantum corrected model shows reduced absorption for nanoparticles due to "cloaking" of the epsilon near zero region, which has lower loss than the bulk region. We demonstrate that a modified quantum corrected model finite-difference time-domain simulation of metal slits with sub-nanometer gaps are in good agreement with the analytic expression for the quantum corrected plasmonic resonance wavelength as a function of gap size coming from Re{ε} = 0.

Here we experimentally demonstrate temperature dependent dynamics of streptavidin by using double nanohole optical trapping. The distinct fluctuations of streptavidin in transmission signal at room temperature vanish with an increase in temperature.

Nanohole optical trapping is a tool that has been shown to analyze proteins at the single molecule level using pure samples. The next step is to detect and study single molecules with dirty samples. We demonstrate that using our double nanohole optical tweezing configuration, single particles in an egg white solution can be classified when trapped. Different sized molecules provide different signal variations in their trapped state, allowing the proteins to be statistically characterized. Root mean squared variation and trap stiffness are methods used on trapped signals to distinguish between the different proteins. This method to isolate and determine single molecules in heterogeneous samples provides huge potential to become a reliable tool for use within biomedical and scientific communities.

We present a method for computing waveguide eigenmodes based on complex coupled mode theory (CCMT). This approach generalizes Fourier transform methods by allowing an arbitrary but convenient basis set to be used for the expansion. In the presented approach, one is free to choose an arbitrary basis representation; for example, we show the use of electromagnetic modes of a cylindrical metal waveguide. CCMT-computed modes are compared with modes computed using analytic expressions and results obtained using a finite difference solver. In cases where the basis set is small, the method can efficiently re-compute modes after structural refinements are made, and can efficiently compute dispersion. The parallel nature of the algorithm makes it well suited to a graphics processing unit implementation, as demonstrated here.

We present a theoretical analysis that associates the resonances of extraordinary acoustic Raman (EAR) spectroscopy [Wheaton et al., Nat. Photonics 9, 68 (2015)] with the collective modes of proteins. The theory uses the anisotropic elastic network model to find the protein acoustic modes, and calculates Raman intensity by treating the protein as a polarizable ellipsoid. Reasonable agreement is found between EAR spectra and our theory. Protein acoustic modes have been extensively studied theoretically to assess the role they play in protein function; this result suggests EAR spectroscopy as a new experimental tool for studies of protein acoustic modes.

Escherichia coli HisJ is a type II periplasmic binding protein that functions to reversibly capture histidine and transfer it to its cognate inner membrane ABC permease. Here, we used NMR spectroscopy to determine the structure of apo-HisJ (26.5 kDa) in solution. HisJ is a bilobal protein in which domain 1 (D1) is made up of two noncontiguous subdomains, and domain 2 (D2) is expressed as the inner domain. To better understand the roles of D1 and D2, we have isolated and characterized each domain separately. Structurally, D1 closely resembles its homologous domain in apo- and holo-HisJ, whereas D2 is more similar to the holo-form. NMR relaxation experiments reveal that HisJ becomes more ordered upon ligand binding, whereas isolated D2 experiences a significant reduction in slower (millisecond to microsecond) motions compared with the homologous domain in apo-HisJ. NMR titrations reveal that D1 is able to bind histidine in a similar manner as full-length HisJ, albeit with lower affinity. Unexpectedly, isolated D1 and D2 do not interact with each other in the presence or absence of histidine, which indicates the importance of intact interdomain-connecting elements (i.e. hinge regions) for HisJ functioning. Our results shed light on the binding mechanism of type II periplasmic binding proteins where ligand is initially bound by D1, and D2 plays a supporting role in this dynamic process.

ABSTRACTThe Escherichia coli histidine binding protein HisJ is a type II periplasmic binding protein (PBP) that preferentially binds histidine and interacts with its cytoplasmic membrane ABC transporter, HisQMP2, to initiate histidine transport. HisJ is a bilobal protein where the larger Domain 1 is connected to the smaller Domain 2 via two linking strands. Type II PBPs are thought to undergo “Venus flytrap” movements where the protein is able to reversibly transition from an open to a closed conformation. To explore the accessibility of the closed conformation to the apo state of the protein, we performed a set of all‐atom molecular dynamics simulations of HisJ starting from four different conformations: apo‐open, apo‐closed, apo‐semiopen, and holo‐closed. The simulations reveal that the closed conformation is less dynamic than the open one. HisJ experienced closing motions and explored semiopen conformations that reverted to closed forms resembling those found in the holo‐closed state. Essential dynamics analysis of the simulations identified domain closing/opening and twisting as main motions. The formation of specific inter‐hinge strand and interdomain polar interactions contributed to the adoption of the closed apo‐conformations although they are up to 2.5‐fold less prevalent compared with the holo‐closed simulations. The overall sampling of the closed form by apo‐HisJ provides a rationale for the binding of unliganded PBPs with their cytoplasmic membrane ABC transporters. Proteins 2014; 82:386–398. © 2013 Wiley Periodicals, Inc.

Researchers have been using single element transducers for photoacoustic microscopy (PAM), but such systems have limited depth of field due to a single focus. The aim for this project was to develop a high-frequency annular array transducer for improved depth-of-field PAM. We have designed a concave 40 MHz ultrasound transducer which has 8 annular array elements with equal area. The outer ring is 12 mm in diameter, the geometric focus is 12 mm, and the space between each annulus is 100 μm. The array was fabricated by lithographically patterning metalized polyimide film to define back electrodes and signal leads. 9-micron-PVDF film was then press-fit into the array pattern with epoxy as a backing material and a single drop of epoxy as a bonding layer. The array exhibits high sensitivity to high-frequency photoacoustic signals. Dynamic focusing of amplified and digitized signals permits extended depth-of-field imaging compared to the single-element transducer case. Dark-field light-delivery and 3-axis motorized scanning permits 3-D photoacoustic microscopy. Imaging performance in phantoms is discussed.