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Item Spectral study of photon pairs generated in dispersion shifted fiber with a pulsed pump(Optical Society of America, 2008-01-07) Li, Xiaoying; Ma, Xiaoxin; Ou, Zhe Yu; Yang, Lei; Cui, Liang; Yu, Daoyin; Physics, School of ScienceSpectral correlation of photon pairs generated in dispersion shifted fiber by a pulsed pump is theoretically analyzed and experimentally investigated. We first calculate the spectral function of photon pairs according to the deduced two-photon state generated by spontaneous four wave mixing under the assumptions close to the real experimental conditions. We then experimentally study the spectral property of the signal and idler photon pairs generated in optical fiber by photon correlation measurements, and the experimental results agree with the calculation. The investigation is useful for developing fiber-based sources of entangled photon pairs and for studying multi-photon quantum interference with multiple photon pairs.Item Biophysics of Zebrafish (Danio rerio) Sperm(Elsevier, 2009-02) Hagedorn, M.; Ricker, J.; McCarthy, M.; Meyers, S.A.; Tiersch, T.R.; Varga, Z. M.; Kleinhans, F.W.; Physics, School of ScienceIn the past two decades, laboratories around the world have produced thousands of mutant, transgenic, and wild-type zebrafish lines for biomedical research. Although slow-freezing cryopreservation of zebrafish sperm has been available for 30 years, current protocols lack standardization and yield inconsistent post-thaw fertilization rates. Cell cryopreservation cannot be improved without basic physiological knowledge, which was lacking for zebrafish sperm. The first goal was to define basic cryobiological values for wild-type zebrafish sperm and to evaluate how modern physiological methods could aid in developing improved cryopreservation protocols. Coulter counting methods measured an osmotically inactive water fraction (Vb) of 0.37 ± 0.02 (SEM), an isosmotic cell volume (Vo) of 12.1 ± 0.2 μm3 (SEM), a water permeability (Lp) in 10% dimethyl sulfoxide of 0.021 ± 0.001(SEM) um/min/atm, and a cryoprotectant permeability (Ps) of 0.10 +/− 0.01 (SEM) × 10−3 cm/min. Fourier transform infrared spectroscopy indicated that sperm membranes frozen without cryoprotectant showed damage and lipid reorganization, while those exposed to 10% glycerol demonstrated decreased lipid phase transition temperatures, which would stabilize the cells during cooling. The second goal was to determine the practicality and viability of shipping cooled zebrafish sperm overnight through the mail. Flow cytometry demonstrated that chilled fresh sperm can be maintained at 92% viability for 24 h at 0°C, suggesting that it can be shipped and exchanged between laboratories. Additional methods will be necessary to analyze and improve cryopreservation techniques and post-thaw fertility of zebrafish sperm. The present study is a first step to explore such techniques.Item Strong Casimir force reduction through metallic surface nanostructuring(Springer Nature, 2013) Intravaia, Francesco; Koev, Stephan; Jung, Il Woong; Talin, A. Alec; Davids, Paul S.; Decca, Ricardo S.; Aksyuk, Vladimir A.; Dalvit, Diego A. R.; López, Daniel; Physics, School of ScienceThe Casimir force between bodies in vacuum can be understood as arising from their interaction with an infinite number of fluctuating electromagnetic quantum vacuum modes, resulting in a complex dependence on the shape and material of the interacting objects. Becoming dominant at small separations, the force has a significant role in nanomechanics and object manipulation at the nanoscale, leading to a considerable interest in identifying structures where the Casimir interaction behaves significantly different from the well-known attractive force between parallel plates. Here we experimentally demonstrate that by nanostructuring one of the interacting metal surfaces at scales below the plasma wavelength, an unexpected regime in the Casimir force can be observed. Replacing a flat surface with a deep metallic lamellar grating with sub-100 nm features strongly suppresses the Casimir force and for large inter-surfaces separations reduces it beyond what would be expected by any existing theoretical prediction.Item Endoglucanases: insights into thermostability for biofuel applications(Springer Nature, 2013-09-27) Yennamalli, Ragothaman M.; Rader, Andrew J.; Kenny, Adam J.; Wolt, Jeffrey D.; Sen, Taner Z.; Physics, School of ScienceObtaining bioethanol from cellulosic biomass involves numerous steps, among which the enzymatic conversion of the polymer to individual sugar units has been a main focus of the biotechnology industry. Among the cellulases that break down the polymeric cellulose are endoglucanases that act synergistically for subsequent hydrolytic reactions. The endoglucanases that have garnered relatively more attention are those that can withstand high temperatures, i.e., are thermostable. Although our understanding of thermostability in endoglucanases is incomplete, some molecular features that are responsible for increased thermostability have been recently identified. This review focuses on the investigations of endoglucanases and their implications for biofuel applications.Item Quantum metrology with parametric amplifier-based photon correlation interferometers(Springer Nature, 2014) Hudelist, F.; Kong, Jia.; Liu, Cunjin; Jing, Jietai; Ou, Z. Y.; Zhang, Weiping; Physics, School of ScienceConventional interferometers usually utilize beam splitters for wave splitting and recombination. These interferometers are widely used for precision measurement. Their sensitivity for phase measurement is limited by the shot noise, which can be suppressed with squeezed states of light. Here we study a new type of interferometer in which the beam splitting and recombination elements are parametric amplifiers. We observe an improvement of 4.1±0.3 dB in signal-to-noise ratio compared with a conventional interferometer under the same operating condition, which is a 1.6-fold enhancement in rms phase measurement sensitivity beyond the shot noise limit. The improvement is due to signal enhancement. Combined with the squeezed state technique for shot noise suppression, this interferometer promises further improvement in sensitivity. Furthermore, because nonlinear processes are involved in this interferometer, we can couple a variety of different waves and form new types of hybrid interferometers, opening a door for many applications in metrology.Item Effects of Lipid Interactions on Model Vesicle Engulfment by Alveolar Macrophages(Elsevier B.V., 2014-02-04) Justice, Matthew J.; Petrusca, Daniela N.; Rogozea, Adriana L.; Williams, Justin A.; Schweitzer, Kelly S.; Petrache, Irina; Wassall, Stephen R.; Petrache, Horia I.; Department of Physics, School of ScienceThe engulfment function of macrophages relies on complex molecular interactions involving both lipids and proteins. In particular, the clearance of apoptotic bodies (efferocytosis) is enabled by externalization on the cell target of phosphatidylserine lipids, which activate receptors on macrophages, suggesting that (local) specific lipid-protein interactions are required at least for the initiation of efferocytosis. However, in addition to apoptotic cells, macrophages can engulf foreign bodies that vary substantially in size from a few nanometers to microns, suggesting that nonspecific interactions over a wide range of length scales could be relevant. Here, we use model lipid membranes (made of phosphatidylcholine, phosphatidylserine, and ceramide) and rat alveolar macrophages to show how lipid bilayer properties probed by small-angle x-ray scattering and solid-state 2H NMR correlate with engulfment rates measured by flow cytometry. We find that engulfment of protein-free model lipid vesicles is promoted by the presence of phosphatidylserine lipids but inhibited by ceramide, in accord with a previous study of apoptotic cells. We conclude that the roles of phosphatidylserine and ceramide in phagocytosis is based, at least in part, on lipid-mediated modification of membrane physical properties, including interactions at large length scales as well as local lipid ordering and possible domain formation.Item How does Water Pass through a Sugar Transporter?(Elsevier B.V., 2014-03-18) Zhu, Fangqiang; Department of Physics, School of ScienceItem Constraints On Spin Independent Forces At The ~100 Nm Range By Means Of A Micromechanical Oscillator(2014-06) Decca, Ricardo S.; Physics, School of SciencePreliminary data from improvements made in our experimental setup are presented. Forces measured with our setup are presented and possible origins for the systematics observed are discussed. The observed signal is most likely induced by an impulsive oscillation of the motor.Item Survivals of mouse oocytes approach 100% after vitrification in 3-fold diluted media and ultra-rapid warming by an IR laser pulse(Elsevier, 2014-06) Jin, Bo; Kleinhans, F.W.; Mazur, Peter; Department of Physics, School of ScienceVitrification is the most sought after route to the cryopreservation of animal embryos and oocytes and other cells of medical, genetic, and agricultural importance. Current thinking is that successful vitrification requires that cells be suspended in and permeated by high concentrations of protective solutes and that they be cooled at very high rates to below − 100°C. We report here that neither of these beliefs holds for mouse oocytes. Rather, we find that if mouse oocytes are suspended in media that produce considerable osmotic dehydration before vitrification and are subsequently warmed at ultra high rates (10,000,000°C/min) achieved by a laser pulse, nearly 100% will survive even when cooled rather slowly and when the concentration of solutes in the medium is only 1/3rd of standard.Item Single Molecule Conformational Memory Extraction: P5ab RNA Hairpin(American Chemical Society, 2014-06-19) Pressé, Steve; Peterson, Jack; Lee, Julian; Elms, Phillip; MacCallum, Justin L.; Marqusee, Susan; Bustamante, Carlos; Dill, Ken; Department of Physics, School of ScienceExtracting kinetic models from single molecule data is an important route to mechanistic insight in biophysics, chemistry, and biology. Data collected from force spectroscopy can probe discrete hops of a single molecule between different conformational states. Model extraction from such data is a challenging inverse problem because single molecule data are noisy and rich in structure. Standard modeling methods normally assume (i) a prespecified number of discrete states and (ii) that transitions between states are Markovian. The data set is then fit to this predetermined model to find a handful of rates describing the transitions between states. We show that it is unnecessary to assume either (i) or (ii) and focus our analysis on the zipping/unzipping transitions of an RNA hairpin. The key is in starting with a very broad class of non-Markov models in order to let the data guide us toward the best model from this very broad class. Our method suggests that there exists a folding intermediate for the P5ab RNA hairpin whose zipping/unzipping is monitored by force spectroscopy experiments. This intermediate would not have been resolved if a Markov model had been assumed from the onset. We compare the merits of our method with those of others.