Design of an Electrostatic Frequency Map for the NH Stretch of the Protein Backbone and Application to Chiral Sum Frequency Generation Spectroscopy.

We develop an electrostatic map for the vibrational NH stretch (amide A) of the protein backbone with a focus on vibrational chiral sum frequency generation spectroscopy (chiral SFG). Chiral SFG has been used to characterize protein secondary structure at interfaces using the NH stretch and to investigate chiral water superstructures around proteins using the OH stretch. Interpretation of spectra has been complicated because the NH stretch and OH stretch overlap spectrally. Although an electrostatic map for water OH developed by Skinner and co-workers was used previously to calculate the chiral SFG response of water structures around proteins, a map for protein NH that is directly responsive to biological complexity has yet to be developed. Here, we develop such a map, linking the local electric field to vibrational frequencies and transition dipoles. We apply the map to two protein systems and achieve much better agreement with experiment than was possible in our previous studies. We show that couplings between NH and OH vibrations are crucial to the line shape, which informs the interpretation of chiral SFG spectra, and that the chiral NH stretch response is sensitive to small differences in structure. This work increases the utility of the NH stretch in biomolecular spectroscopy.

Chiral Sum Frequency Generation Spectroscopy Detects Double-Helix DNA at Interfaces.

Many DNA-based technologies involve the immobilization of DNA and therefore require a fundamental understanding of the DNA structure-function relationship at interfaces. We present three immobilization methods compatible with chiral sum frequency generation (SFG) spectroscopy at interfaces. They are the "anchor" method for covalently attaching DNA on a glass surface, the "island" method for dropcasting DNA on solid substrates, and the "buoy" method using a hydrocarbon moiety for localizing DNA at the air-water interface. Although SFG was previously used to probe DNA, the chiral and achiral SFG responses of single-stranded and double-stranded DNA have not been compared systemically. Using the three immobilization methods, we obtain the achiral and chiral C-H stretching spectra. The results introduce four potential applications of chiral SFG. First, chiral SFG gives null response from single-stranded DNA but prominent signals from double-stranded DNA, providing a simple binary readout for label-free detection of DNA hybridization. Second, with heterodyne detection, chiral SFG gives an opposite-signed spectral response useful for distinguishing native (D-) right-handed double helix from non-native (L-) left-handed double helix. Third, chiral SFG captures the aromatic C-H stretching modes of nucleobases that emerge upon hybridization, revealing the power of chiral SFG to probe highly localized molecular structures within DNA. Finally, chiral SFG is sensitive to macroscopic chirality but not local chiral centers and thus can detect not only canonical antiparallel double helix but also other DNA secondary structures, such as a poly-adenine parallel double helix. Our work benchmarks the SFG responses of DNA immobilized by the three distinct methods, building a basis for new chiral SFG applications to solve fundamental and biotechnological problems.

Molecular Transport across Oil-Brine Interfaces Impacts Interfacial Tension: Time-Effects in Buoyant and Pendant Drop Measurements.

The buoyant drop method is a ubiquitous tool for addressing phenomena at the liquid-liquid interface via the determination of the interfacial tension (IFT) between two immiscible phases. Here, the focus is on how electrolytes (in an aqueous phase) and carboxylic acids (in a decane phase) impact the interfacial layer between the two phases. The IFT measurement provides a single number, which is not fulfilling when it comes to deducing information about a complex multiparameter system. Furthermore, the temporal evolution of IFT does not always reach a steady-state value on a time scale, which is realistic to use for comparative studies. We have investigated the temporal evolution of IFT in a series of experiments with varying compositions of the decane-carboxylic acid phase and the brine phase. The results show that there are at least two opposing effects in play. For water-soluble acids, the IFT initially increases with time until a turnover point is reached from where there is a gradual decay. The IFT at the turnover point is close to that of the pure water-decane system. For a poorly water-soluble acid, the IFT shows a much smaller increase and the turnover happens much faster. For a water-soluble acid, there is a high degree of sensitivity toward the electrolyte; it determines the position (in time) of the IFT peak and the steepness of the subsequent decay. Now, if the phases are reversed, that is, by placing a drop of brine in the decane-surfactant phase, the IFT decreases with time regardless of the acid and with little impact of the electrolyte and its concentration in the brine. We propose an explanation for the observed behavior (supported by COSMO-RS calculations), which is based on diffusion in and out of the two phases, solubility, and interfacial reactivity (i.e., aggregation between electrolytes and carboxylic acids).

Decision support for diagnosis of lyme disease.

This paper describes the development of a Bayesian model for diagnosis of patients suspected of Lyme disease, and the integration of such a model into a medical information system. A Bayesian network incorporating the clinical history and laboratory results has been constructed. Because many of the symptoms are not exclusive to Lyme disease and they develop over time, the clinical history is important for making the correct diagnosis. The model is based on time slices, where each time slice contains the observed pathological picture from one consultation with for example, the general practitioner. Since the time intervals between consultations typically are not equivalent, we have developed a novel method that can handle non-equivalent time intervals between the time slices in the network. The method is based on a description of the general development pattern of Lyme disease, which is implemented in a model that states the conditional probabilities of experiencing a certain pathological picture given time since infection. The model has been integrated into a web-based medical information system, called Borrelia Systems, which has enabled us to evaluate the model during a progressive diagnostic process. The integration has been accomplished through the development of a Bayesian Application Framework. This framework specifies a communication data structure in XML providing a graphical user interface and database components, which can be used when developing systems that are based on Bayesian networks. The framework generalizes the integration of Bayesian networks so that it is possible to switch network without manually having to update or change the system.