The Role of Nonlinear Dynamics in Quantitative Atomic Force Microscopy

Various methods of force measurement with the Atomic Force Microscope (AFM) are compared for their ability to accurately determine the tip-surface force from analysis of the nonlinear cantilever motion. It is explained how intermodulation, or the frequency mixing of multiple drive tones by the nonlinear tip-surface force, can be used to concentrate the nonlinear motion in a narrow band of frequency near the cantilevers fundamental resonance, where accuracy and sensitivity of force measurement are greatest. Two different methods for reconstructing tip-surface forces from intermodulation spectra are explained. The reconstruction of both conservative and dissipative tip-surface interactions from intermodulation spectra are demonstrated on simulated data.Comment: 25 pages (preprint, double space) 7 figure

Probing the role of single defects on the thermodynamics of electric-field induced phase transitions

The kinetics and thermodynamics of first order transitions is universally controlled by defects that act as nucleation sites and pinning centers. Here we demonstrate that defect-domain interactions during polarization reversal processes in ferroelectric materials result in a pronounced fine structure in electromechanical hysteresis loops. Spatially-resolved imaging of a single defect center in multiferroic BiFeO3 thin film is achieved, and the defect size and built-in field are determined self-consistently from the single-point spectroscopic measurements and spatially-resolved images. This methodology is universal and can be applied to other reversible bias-induced transitions including electrochemical reactions.Comment: 34 pages,4 figures, high quality figures are available upon request, submitted to Phys. Rev. Let

Classification and energetics of the base-phosphate interactions in RNA

Structured RNA molecules form complex 3D architectures stabilized by multiple interactions involving the nucleotide base, sugar and phosphate moieties. A significant percentage of the bases in structured RNA molecules in the Protein Data Bank (PDB) hydrogen-bond with phosphates of other nucleotides. By extracting and superimposing base-phosphate (BPh) interactions from a reduced-redundancy subset of 3D structures from the PDB, we identified recurrent phosphate-binding sites on the RNA bases. Quantum chemical calculations were carried out on model systems representing each BPh interaction. The calculations show that the centers of each cluster obtained from the structure superpositions correspond to energy minima on the potential energy hypersurface. The calculations also show that the most stable phosphate-binding sites occur on the Watson–Crick edge of guanine and the Hoogsteen edge of cytosine. We modified the ‘Find RNA 3D' (FR3D) software suite to automatically find and classify BPh interactions. Comparison of the 3D structures of the 16S and 23S rRNAs of Escherichia coli and Thermus thermophilus revealed that most BPh interactions are phylogenetically conserved and they occur primarily in hairpin, internal or junction loops or as part of tertiary interactions. Bases that form BPh interactions, which are conserved in the rRNA 3D structures are also conserved in homologous rRNA sequence alignments

Classification and energetics of the base-phosphate interactions in RNA

Structured RNA molecules form complex 3D architectures stabilized by multiple interactions involving the nucleotide base, sugar and phosphate moieties. A significant percentage of the bases in structured RNA molecules in the Protein Data Bank (PDB) hydrogen-bond with phosphates of other nucleotides. By extracting and superimposing base-phosphate (BPh) interactions from a reduced-redundancy subset of 3D structures from the PDB, we identified recurrent phosphate-binding sites on the RNA bases. Quantum chemical calculations were carried out on model systems representing each BPh interaction. The calculations show that the centers of each cluster obtained from the structure superpositions correspond to energy minima on the potential energy hypersurface. The calculations also show that the most stable phosphate-binding sites occur on the Watson–Crick edge of guanine and the Hoogsteen edge of cytosine. We modified the ‘Find RNA 3D' (FR3D) software suite to automatically find and classify BPh interactions. Comparison of the 3D structures of the 16S and 23S rRNAs of Escherichia coli and Thermus thermophilus revealed that most BPh interactions are phylogenetically conserved and they occur primarily in hairpin, internal or junction loops or as part of tertiary interactions. Bases that form BPh interactions, which are conserved in the rRNA 3D structures are also conserved in homologous rRNA sequence alignments

Ultrafast Resonant Polarization Interferometry: Towards the First Direct Detection of Vacuum Polarization

Vacuum polarization, an effect predicted nearly 70 years ago, is still yet to be directly detected despite significant experimental effort. Previous attempts have made use of large liquid-helium cooled electromagnets which inadvertently generate spurious signals that mask the desired signal. We present a novel approach for the ultra-sensitive detection of optical birefringence that can be usefully applied to a laboratory detection of vacuum polarization. The new technique has a predicted birefringence measurement sensitivity of $\Delta n \sim 10^{20}$ in a 1 second measurement. When combined with the extreme polarizing fields achievable in this design we predict that a vacuum polarization signal will be seen in a measurement of just a few days in duration.Comment: 9 pages, 2 figures. submitted to PR

Recellularization of Porcine Internal Thoracic Arteries as a Tissue Engineered Small-Diameter Vascular Graft Alternative

Small-diameter vascular grafts are the leading treatment for myocardial infarctions resulting from atherosclerosed coronary vasculature. A potential alternative to using patient-derived grafts is the use of tissue engineered vessels. The removal of native cells from xenogenic vessels allows for recellularization with human cells types; however, the decellularization process depends on the use of cytotoxic reagents that must be removed prior to recellularization. The recellularization process must produce a functional graft that contains the multiple cell types found within arteries. We hypothesized that porcine internal thoracic arteries decellularized using a combination of detergents could be processed to support human endothelial and smooth muscle cell growth. We also hypothesized that in order to optimize in vitro co-culture conditions during recellularization, a mix of media types would be necessary to simultaneously support endothelial and smooth muscle cell growth. A cytotoxicity assay was performed to assess the effects of residual detergents on endothelial cells seeded onto the scaffolds. A relationship between the degree of detergent rinsing and cellular viability was identified via a resazurin reduction assay with more extensive rinsing significantly enhancing cell viability. This same cell viability assay was used to identify media combinations that supported growth of both endothelial and smooth muscle cells. Both cell types were able to grow in a 50:50 mixture of their media types without any loss of viability or effect on morphology. Furthermore, endothelial cells grown in the mixed medium maintained their characteristic CD31 expression. Taken together, these results show that human cells native to arteries can remain viable within the extracellular matrix of porcine internal thoracic artery scaffolds after thorough scaffold detoxification. Additionally, the co-culture conditions established can support the growth of both endothelial and smooth muscle cell types found within arteries. Future work will focus on simultaneously culturing the cells within scaffolds to build toward the goal of tissue engineering small-diameter vascular graft alternatives.https://digitalcommons.winthrop.edu/sureposters/1005/thumbnail.jp

Natural variation in abiotic stress responsive gene expression and local adaptation to climate in Arabidopsis thaliana.

Gene expression varies widely in natural populations, yet the proximate and ultimate causes of this variation are poorly known. Understanding how variation in gene expression affects abiotic stress tolerance, fitness, and adaptation is central to the field of evolutionary genetics. We tested the hypothesis that genes with natural genetic variation in their expression responses to abiotic stress are likely to be involved in local adaptation to climate in Arabidopsis thaliana. Specifically, we compared genes with consistent expression responses to environmental stress (expression stress responsive, "eSR") to genes with genetically variable responses to abiotic stress (expression genotype-by-environment interaction, "eGEI"). We found that on average genes that exhibited eGEI in response to drought or cold had greater polymorphism in promoter regions and stronger associations with climate than those of eSR genes or genomic controls. We also found that transcription factor binding sites known to respond to environmental stressors, especially abscisic acid responsive elements, showed significantly higher polymorphism in drought eGEI genes in comparison to eSR genes. By contrast, eSR genes tended to exhibit relatively greater pairwise haplotype sharing, lower promoter diversity, and fewer nonsynonymous polymorphisms, suggesting purifying selection or selective sweeps. Our results indicate that cis-regulatory evolution and genetic variation in stress responsive gene expression may be important mechanisms of local adaptation to climatic selective gradients

Direct Improvement of Hamiltonian Lattice Gauge Theory

We demonstrate that a direct approach to improving Hamiltonian lattice gauge theory is possible. Our approach is to correct errors in the Kogut-Susskind Hamiltonian by incorporating additional gauge invariant terms. The coefficients of these terms are chosen so that the order $a^2$ classical errors vanish. We conclude with a brief discussion of tadpole improvement in Hamiltonian lattice gauge theory.Comment: 9 page

A comparison of GC-FID and PTR-MS toluene measurements in ambient air under conditions of enhanced monoterpene loading

Toluene was measured using both a gas chromatographic system (GC), with a flame ionization detector (FID), and a proton transfer reaction-mass spectrometer (PTR-MS) at the AIRMAP atmospheric monitoring station Thompson Farm (THF) in rural Durham, NH during the summer of 2004. Simultaneous measurements of monoterpenes, including alpha- and beta-pinene, camphene, Delta(3)-carene, and d-limonene, by GC-FID demonstrated large enhancements in monoterpene mixing ratios relative to toluene, with median and maximum enhancement ratios of similar to 2 and similar to 30, respectively. A detailed comparison between the GC-FID and PTR-MS toluene measurements was conducted to test the specificity of PTR-MS for atmospheric toluene measurements under conditions often dominated by biogenic emissions. We derived quantitative estimates of potential interferences in the PTR-MS toluene measurements related to sampling and analysis of monoterpenes, including fragmentation of the monoterpenes and some of their primary carbonyl oxidation products via reactions with H(3)O(+), O(2)(+) and NO(+) in the PTR-MS drift tube. The PTR-MS and GC-FID toluene measurements were in good quantitative agreement and the two systems tracked one another well from the instrumental limits of detection to maximum mixing ratios of similar to 0.5 ppbv. A correlation plot of the PTR-MS versus GC-FID toluene measurements was described by the least squares regression equation y=(1.13 +/- 0.02)x-(0.008 +/- 0.003) ppbv, suggesting a small similar to 13% positive bias in the PTR-MS measurements. The bias corresponded with a similar to 0.055 ppbv difference at the highest measured toluene level. The two systems agreed quantitatively within the combined 1 sigma measurement precisions for 60% of the measurements. Discrepancies in the measured mixing ratios were not well correlated with enhancements in the monoterpenes. Better quantitative agreement between the two systems was obtained by correcting the PTR-MS measurements for contributions from monoterpene fragmentation in the PTR-MS drift tube; however, the improvement was minor (\u3c10%). Interferences in the PTRMS measurements from fragmentation of the monoterpene oxidation products pinonaldehyde, caronaldehyde and alpha-pinene oxide were also likely negligible. A relatively large and variable toluene background in the PTR-MS instrument likely drove the measurement bias; however, the precise contribution was difficult to accurately quantify and thus was not corrected for in this analysis. The results from THF suggest that toluene can be reliably quantified by PTR-MS using our operating conditions (drift tube pressure, temperature and voltage of 2.0 mbar, 45 degrees C and 600V, respectively) under the ambient compositions probed. This work extends the range of field conditions under which PTR-MS validation studies have been conducted