Quantum behavior of water nano-confined in beryl.

The proton mean kinetic energy, Ke(H), of water confined in nanocavities of beryl (Be3Al2Si6O18) at 5 K was obtained by simulating the partial vibrational density of states from density functional theory based first-principles calculations. The result, Ke(H) = 104.4 meV, is in remarkable agreement with the 5 K deep inelastic neutron scattering (DINS) measured value of 105 meV. This is in fact the first successful calculation that reproduces an anomalous DINS value regarding Ke(H) in nano-confined water. The calculation indicates that the vibrational states of the proton of the nano-confined water molecule distribute much differently than in ordinary H2O phases, most probably due to coupling with lattice modes of the hosting beryl nano-cage. These findings may be viewed as a promising step towards the resolution of the DINS controversial measurements on other H2O nano-confining systems, e.g., H2O confined in single and double walled carbon nanotubes.

On the mean kinetic energy of the proton in strong hydrogen bonded systems.

The mean atomic kinetic energies of the proton, Ke(H), and of the deuteron, Ke(D), were calculated in moderate and strongly hydrogen bonded (HB) systems, such as the ferro-electric crystals of the KDP type (XH2PO4, X = K, Cs, Rb, Tl), the DKDP (XD2PO4, X = K, Cs, Rb) type, and the X3H(SO4)2 superprotonic conductors (X = K, Rb). All calculations utilized the simulated partial phonon density of states, deduced from density functional theory based first-principle calculations and from empirical lattice dynamics simulations in which the Coulomb, short range, covalent, and van der Waals interactions were accounted for. The presently calculated Ke(H) values for the two systems were found to be in excellent agreement with published values obtained by deep inelastic neutron scattering measurements carried out using the VESUVIO instrument of the Rutherford Laboratory, UK. The Ke(H) values of the M3H(SO4)2 compounds, in which the hydrogen bonds are centro-symmetric, are much lower than those of the KDP type crystals, in direct consistency with the oxygen-oxygen distance ROO, being a measure of the HB strength.

Determining the band gap and mean kinetic energy of atoms from reflection electron energy loss spectra.

Reflection electron energy loss spectra from some insulating materials (CaCO3, Li2CO3, and SiO2) taken at relatively high incoming electron energies (5-40 keV) are analyzed. Here, one is bulk sensitive and a well-defined onset of inelastic excitations is observed from which one can infer the value of the band gap. An estimate of the band gap was obtained by fitting the spectra with a procedure that includes the recoil shift and recoil broadening affecting these measurements. The width of the elastic peak is directly connected to the mean kinetic energy of the atom in the material (Doppler broadening). The experimentally obtained mean kinetic energies of the O, C, Li, Ca, and Si atoms are compared with the calculated ones, and good agreement is found, especially if the effect of multiple scattering is taken into account. It is demonstrated experimentally that the onset of the inelastic excitation is also affected by Doppler broadening. Aided by this understanding, we can obtain a good fit of the elastic peak and the onset of inelastic excitations. For SiO2, good agreement is obtained with the well-established value of the band gap (8.9 eV) only if it is assumed that the intensity near the edge scales as (E - Egap)(1.5). For CaCO3, the band gap obtained here (7 eV) is about 1 eV larger than the previous experimental value, whereas the value for Li2CO3 (7.5 eV) is the first experimental estimate.

Assignment of Colletotrichum coccodes isolates into vegetative compatibility groups using infrared spectroscopy: a step towards practical application.

Colletotrichum coccodes (C. coccodes) is a pathogenic fungus that causes anthracnose on tomatoes and black dot disease in potatoes. It is considered as a seed tuber and soil-borne pathogen that is difficult to control. C. coccodes isolates are classified into Vegetative Compatibility Groups (VCGs). Early classification of isolates into VCGs is of great importance for a better understanding of the epidemiology of the disease and improving its control. Moreover, the differentiation among these isolates and the assignment of newly-discovered isolates enable control of the disease at its early stages. Distinguishing between isolates using microbiological or genetic methods is time-consuming and not readily available. Our results show that it is possible to assign the isolates into their VCGs and to classify them at the isolate level with a high success rate using Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA).

Classification of Colletotrichum coccodes isolates into vegetative compatibility groups using infrared attenuated total reflectance spectroscopy and multivariate analysis.

In this study the potential of infrared (IR) spectroscopy for the classification of Colletotrichum coccodes (C. coccodes) isolates into vegetative compatibility groups (VCGs) was evaluated. Isolates which belong to the same VCG may have similar pathological and physiological traits that differ from those that are not assigned to the same VCG. Early classification of isolates into VCGs is of a great importance for a better understanding of the epidemiology of the disease and improves its control. The main goal of the present study was to classify 14 isolates of C. coccodes into VCGs and differentiate between them, based on their IR absorption spectra as obtained by the FTIR-ATR sampling technique. Advanced statistical and mathematical methods, including Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA), were applied to the spectra after manipulation. The results show that it is possible to assign the isolates into VCGs with more than 90% success based on the wavenumber low region (1800-800 cm(-1)) and using 15 PCs. However, on the isolate level, the best differentiation results were obtained using PCA (15 PCs) and LDA for the combined regions (2990-2800 cm(-1), 1800-800 cm(-1)), with identification success rates of 87.2%.

Proton dynamics in ice VII at high pressures.

We calculated the proton kinetic energies Ke(H) of ice under high pressures up to 63 GPa by assuming the harmonic approximation. The input measured optical frequencies of vibration, libration, and translation of ice VII versus pressure as well as the H2O geometry and the distances R(OH) necessary for calculating Ke(H) (at 298 K) were taken from the literature. The resulting Ke(H) values were found to decrease gradually with increasing pressure, approaching the region where the H-atom is symmetrically hydrogen bonded between two oxygens in the OH-O system. Interestingly, the Ke(H) results were found to be consistent with those of other materials such as Rb3H(PO4)2 and KH2PO4 having similar R(OH) and R(OO) distances in the OH-O system. Similar calculations were also carried out for D2O.

Elastic electron scattering from water vapor and ice at high momentum transfer.

We compare the area, peak separation, and width of the H and O elastic peak for light and heavy water, as observed in spectra of keV electrons scattered over large angles. Peak separation is well reproduced by the theory, but the O:H area ratio is somewhat larger than expected and is equal to the O:D area ratio. Thus no anomalous scattering from H was observed. Only minor differences are observed for scattering from a gaseous or a solid target. The extracted mean kinetic energy of H and D agreed within 5% with the calculated ones for ice. For the more difficult vapor measurements agreement was on a 12% level. A preliminary attempt to extract the O kinetic energy in ice agreed within 10% with the calculated values.

Utilizing FTIR-ATR spectroscopy for classification and relative spectral similarity evaluation of different Colletotrichum coccodes isolates.

Colletotrichum coccodes (C. coccodes) is a pathogenic fungus which causes anthracnose on tomatoes and black dot disease in potatoes. It is important to differentiate among these isolates and to detect the origin of newly discovered isolates, in order to treat the disease in its early stages. However, distinguishing between isolates using common biological methods is time-consuming, and not always available. We used Fourier Transform Infra-Red (FTIR)-Attenuated Total Reflectance (ATR) spectroscopy and advanced mathematical and statistical methods to distinguish between different isolates of C. coccodes. To our knowledge, this is the first time that FTIR-ATR spectroscopy was used, combined with multivariate analysis, to classify such a large number of 15 isolates belonging to the same species. We obtained a success rate of approximately 90% which was achieved using the region 800-1775 cm(-1). In addition we succeeded in determining the relative spectral similarity between different fungal isolates by developing a new algorithm. This method could be an important potential diagnostic tool in agricultural research, since it may outline the extent of the biological similarity between fungal isolates. Based on the PCA calculations, we grouped the fifteen isolates included in this study into four different degrees of similarity.

The use of electron scattering for studying atomic momentum distributions: the case of graphite and diamond.

The momentum distributions of C atoms in polycrystalline diamond (produced by chemical vapor deposition) and in highly oriented pyrolitic graphite (HOPG) are studied by scattering of 40 keV electrons at 135°. By measuring the Doppler broadening of the energy of the elastically scattered electrons, we resolve a Compton profile of the motion of the C atoms. The aim of the present work is to resolve long-standing disagreements between the calculated kinetic energies of carbon atoms in HOPG and in diamond films and the measured ones, obtained both by neutron Compton scattering (NCS) and by nuclear resonance photon scattering (NRPS). The anisotropy of the momentum distribution in HOPG was measured by rotating the HOPG sample relative to the electron beam. The obtained kinetic energies for the motion component along, and perpendicular to, the graphite planes were somewhat higher than those obtained from the most recent NCS data of HOPG. Monte Carlo simulations indicate that multiple scattering adds about 2% to the obtained kinetic energies. The presence of different isotopes in carbon affects the measurement at a 1% level. After correcting for these contributions, the kinetic energies are 3%-6% larger than the most recent NCS results for HOPG, but 15%-25% smaller than the NRPS results. For diamond, the corrected direction-averaged kinetic energy is ≈ 6% larger than the calculated value. This compares favorably to the ≈25% discrepancy between theory and both the NCS and NRPS results for diamond.

Grading of intrinsic and acquired cisplatin-resistant human melanoma cell lines: an infrared ATR study.

Attenuated total reflection (ATR) spectroscopy is used as an in vitro optical approach for the diagnosis and characterization of cell and tissue pathology. In comparison with the more conventional FTIR microspectroscopy that relies on transmission of IR radiation, ATR spectroscopy uses the evanescent wave technique, which is a step forward toward in vivo research. The aim of the present investigation was to examine the potential of ATR spectroscopy to differentiate between drug-resistant and drug-sensitive melanoma cell lines. We studied two human melanoma parental cell lines, GA and BG, and their cisplatin-resistant counterparts, GAC and BGC, respectively, which were derived by survival selection with this anticancer drug. Cisplatin cytotoxicity was measured on the four cell lines, and their relative resistance to cisplatin was established: BGC > BG > GAC > GA. Different resistance mechanisms were noticed between the two parental groups in accordance with their spectrum. ATR spectra-based cluster analysis of the selective biomarkers, such as phosphate and RNA/DNA, were found useful in differentiating sensitive from resistant cells. Normalized and absolute values of the differences between spectra were employed to compare between the two parental groups. It was possible to predict the relative cisplatin resistance between the cell lines using the discriminant classifying function. The success rates in predicting cisplatin resistance in these cells was 88 and 81% for GA versus GAC and BG versus BGC, respectively. These results support the further development of the ATR technique as a simple, in vitro, reagent-free method to identify drug resistance in cancer cells.

Distinction of Fusarium oxysporum fungal isolates (strains) using FTIR-ATR spectroscopy and advanced statistical methods.

Fusarium is a large fungi genus of a large variety of species and strains which inhabits soil and vegetation. It is distributed worldwide and affiliated to both warm and cold weather. Fusarium oxysporum species, for instance, cause the Fusarium wilt disease of plants, which appears as a leaf wilting, yellowing and eventually plant death. Early detection and identification of these pathogens are very important and might be critical for their control. Previously, we have managed to differentiate among different fungi genera (Rhizoctonia, Colletotrichum, Verticillium and Fusarium) using FTIR-ATR spectroscopy methods and cluster analysis. In this study, we used Fourier-transform infrared (FTIR) attenuated total reflection (ATR) spectroscopy to discriminate and differentiate between different strains of F. oxysporum. The result obtained was of spectral patterns distinct to each of the various examined strains, which belong to the same species. These differences were not as significant as those found between the different genera species. We applied advanced statistical techniques: principal component analysis (PCA) and linear discriminant analysis (LDA) on the FTIR-ATR spectra in order to examine the feasibility of distinction between these fungi strains. The results are encouraging and indicate that the FTIR-ATR methodology can differentiate between the different examined strains of F. oxysporum with a high success rate. Based on our PCA and LDA calculations performed in the regions [900-1775 cm(-1), 2800-2990 cm(-1), with 9 PCs], we were able to classify the different strains with high success rates: Foxy1 90%, Foxy2 100%, Foxy3 100%, Foxy4 92.3%, Foxy5 83.3% and Foxy6 100%.

On the proton kinetic energy in H2O and in nanotube water.

We calculated the kinetic energies of the H-atom in ice Ih between 5 and 269 K and in water in the range 293-673 K. To do so we used the literature optical vibration frequencies of ice and water of the different phases assuming the harmonic approximation and decoupling between the degrees of freedom of translation, rotation (libration), and internal vibrations. Apart for ice at 269 K, good agreement was obtained with published experimental values for both cases. Similar agreement with experiment was found for the case of water confined in 14 A diameter carbon nanotubes at 268 K. However, serious deviations from measured values were found in nanotube water in the range 5-230 K. Possible reasons for those deviations are discussed.

Attenuated total reflectance spectroscopy: a promising technique for early detection of premalignancy.

In last decades infrared spectroscopy has demonstrated potential as a novel technology for early cancer diagnosis. Among the various IR spectroscopic techniques special interest has arisen from methods based on evanescent wave absorbance due to the possibility for in situ and in vivo implementation. The goal of the present study is to examine the potential of Attenuated Total Reflectance (ATR) spectroscopy for early detection of premalignant changes. As a model we used both cell lines and primary cells, which were transformed to be malignant by a retrovirus. Spectral measurements were performed at various post infection stages in parallel with morphological observations. Our results showed gradual and consistent spectral alterations in both cell cultures due to carcinogenesis, which were outlined using Principal Component Analysis (PCA). The main spectral differences appeared in three spectral ranges: at 3000-2800 cm(-1) (attributed to stretching vibrational modes of lipids and proteins), at 1470-1300 cm(-1)(attributed to bending overlapping modes of lipids and proteins) and also at the highly overlapping spectral range at 1000-1200 cm(-1) (attributed to bending and starching vibrational modes corresponding to all types of biological macromolecules). In order to obtain robust unsupervised classifications of the malignant progression we applied approaches of Linear Discriminant Analysis (LDA). The classifications based on Mahalanobis distances allowed us to discern that the accuracy of successful identification of premalignant stages varied between 86.5-97.2%. Our results show that ATR spectroscopy in tandem with proper statistical tools may provide a promising technique for early detectable signals of malignant progression.

On anomalies in elastic electron scattering cross sections from protons.

A critical examination of recent elastic electron scattering reports on H-containing samples is carried out. We show that all results are consistent with the conclusion that no anomaly exists in the measured e-H scattering intensities as compared to e-scattering from other light atoms such as D or C. The scattering results are, in fact, in agreement with the classical Rutherford formula and there is no need to invoke short-lived quantum entanglement of the protons to explain the existing data. The neutron-proton scattering intensities on H-containing samples were also examined and found to agree with standard cross sections. Also no theoretical evidence was found supporting the existence of the reported anomalies.

Doppler widths in electron quasielastic scattering from molecular gases.

Recent quasielastic electron scattering experiments on some molecular gases at E(e) > or = 1.8 keV have shown that the scattering is from single isotopes of the atomic components of the gas. The scattered electron lines at definite angles are Doppler broadened by the instantaneous kinetic energy (KE) of the scattering atoms. We calculated the KE of the scattering atoms by accounting for translation, rotation, and all normal modes of vibrations of the molecule. The results reveal some large and fundamental differences from literature estimates.

Distinction of malignant melanoma and epidermis using IR micro-spectroscopy and statistical methods.

Infrared spectroscopy is widely perceived as a future technology for cancer detection and grading. Malignant melanoma, an aggressive skin cancer, is accessible to non-invasive IR radiation based surface probes for its identification and grading. The present work examines the differences in the IR spectra of melanoma tissues and the surrounding epidermis in skin biopsies with the objective of identifying diagnostic parameters and suitable computational/statistical methods of analysis. Melanoma could be differentiated from the epidermis in biopsies of 55 patients, using parameters derived from absorbance bands originating from molecular vibrations of nucleic acids and/or their bases. Additionally, absorbances from tyrosine and phosphate that are abnormally elevated in malignant melanoma could be used as markers. Two-dimensional plots of these parameters in tandem with advanced statistical methods successfully demonstrate the potential of IR spectroscopy to distinguish between epidermal and melanoma regions with a high classification success. The work underlines the importance of developing data analysis methods in FTIR based diagnosis using melanoma as a model system.

Potential of 'flat' fibre evanescent wave spectroscopy to discriminate between normal and malignant cells in vitro.

The present study focuses on evaluating the potential of flattened AgClBr fibre-optic evanescent wave spectroscopy (FTIR-FEWS) technique for detection and identification of cancer cells in vitro using cell culture as a model system. The FTIR-FEWS results are compared to those from FTIR-microspectroscopy (FTIR-MSP) method extensively used to identify spectral properties of intact cells. Ten different samples of control and malignant cells were measured in parallel by the above two methods. Our results show a significant similarity between the results obtained by the two methodologies. The absorbance level of Amide I/Amide II, phosphates and carbohydrates were significantly altered in malignant compared to the normal cells using both systems. Thus, common biomarkers such as Amide I/Amide II, phosphate and carbohydrate levels can be derived to discern between normal and cancer cells. However, marked differences are also noted between the two methodologies in the protein bands due to CH3 bending vibration (1480-1350 cm(-1)). The spectral differences may be attributed to the variation in the penetration depth of the two methodologies. The use of flattened fibre rather than the standard cylindrical fibre has several practical advantages and is considered as an important step towards in vivo measurements in real time, such as that of skin nevi and melanoma using special designs of fibre-optic-based sensors.

Scattering of 64 eV to 3 keV neutrons from polyethylene and graphite and the coherence length problem.

We measured the neutron scattering intensity ratios from polyethylene (CH2) relative to graphite (C) at several discrete final energies, of narrow widths (approximately 3 eV) between 64 eV and 3 keV. The final energies were selected using a 238U filter. This experiment was carried out to search for any anomaly in the n-p scattered intensities from CH2 caused by the neutron coherence length. The scattered intensity ratios were found to conform to conventional expectations and no anomaly was observed.

Search for anomalous scattering of keV neutrons from H2O-D2O mixtures.

We measured the neutron scattering intensities from pure liquid H2O relative to that of pure D2O and also relative to H2O-D2O mixtures, at room temperature. This study is relevant to the problem of quantum entanglement. The neutrons were generated from an electron Linac and the final energy of the scattered neutrons was fixed at 24.3 keV using a 20 cm thick pure iron filter. The scattering intensity ratios were found to agree with expected values deduced from the tabulated total cross sections within an accuracy of 3%. Thus no anomaly was observed.

Nuclear Resonance Photon Scattering Studies of N 2 Adsorbed on Grafoil and of NaNO 2 Single Crystal.

The nuclear resonance photon scattering (NRPS) from (15)N2 adsorbed on graphite was investigated. The resonantly scattered intensities from the 6324 keV level of (15)N with the photon beam parallel and perpendicular to the adsorbing grafoil planes was measured at 140 K and coverages below 0.7 monolayers (ML), where the (15)N2 occur in the vapor phase. The data were used for deducing the out-of-plane tilt angle of adsorbed N2 relative to the graphite surface and the results were compared with grand canonical Monte Carlo (GCMC) calculations. Using the same method, a single crystal of NaNO2 was studied by measuring the scattering intensities with the nitrite planes aligned parallel and perpendicular to the photon beam. At 80 K, a huge anisotropy (R≈3.6) was observed, caused by the anisotropy in the zero-point motion of the internal modes of vibration of the NO2 ion. The variation of the scattering intensity from a powdered isotopic (15)NaNO2 sample versus T in the range 12 K to 297 K was also measured and explained by accounting for the internal and external vibrational modes in NaNO2.