Calculation of wood volume and stem taper using terrestrial single-image close-range photogrammetry and contemporary software tools

Abstract

Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions

Single-stranded DNA (ssDNA) plays a major role in several biological processes. It is therefore of fundamental interest to understand how the elastic response and the formation of secondary structures are modulated by the interplay between base pairing and electrostatic interactions. Here we measure force-extension curves (FECs) of ssDNA molecules in optical tweezers set up over two orders of magnitude of monovalent and divalent salt conditions, and obtain its elastic parameters by fitting the FECs to semiflexible models of polymers. For both monovalent and divalent salts, we find that the electrostatic contribution to the persistence length is proportional to the Debye screening length, varying as the inverse of the square root of cation concentration. The intrinsic persistence length is equal to 0.7 nm for both types of salts, and the effectivity of divalent cations in screening electrostatic interactions appears to be 100-fold as compared with monovalent salt, in line with what has been recently reported for single-stranded RNA. Finally, we propose an analysis of the FECs using a model that accounts for the effective thickness of the filament at low salt condition and a simple phenomenological description that quantifies the formation of non-specific secondary structure at low forces.

Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions

Single-stranded DNA (ssDNA) plays a major role in several biological processes. It is therefore of fundamental interest to understand how the elastic response and the formation of secondary structures are modulated by the interplay between base pairing and electrostatic interactions. Here we measure force-extension curves (FECs) of ssDNA molecules in optical tweezers set up over two orders of magnitude of monovalent and divalent salt conditions, and obtain its elastic parameters by fitting the FECs to semiflexible models of polymers. For both monovalent and divalent salts, we find that the electrostatic contribution to the persistence length is proportional to the Debye screening length, varying as the inverse of the square root of cation concentration. The intrinsic persistence length is equal to 0.7 nm for both types of salts, and the effectivity of divalent cations in screening electrostatic interactions appears to be 100-fold as compared with monovalent salt, in line with what has been recently reported for single-stranded RNA. Finally, we propose an analysis of the FECs using a model that accounts for the effective thickness of the filament at low salt condition and a simple phenomenological description that quantifies the formation of non-specific secondary structure at low forces.

Oxidation rates of carbon and nitrogen in char residues from solid fuels

Computational fluid dynamics (CFD) modeling is an important tool in designing new combustion systems. By using CFD modeling, entire combustion systems can be modeled and the emissions and the performance can be predicted. CFD modeling can also be used to develop new and better combustion systems from an economical and environmental point of view. In CFD modeling of solid fuel combustion, the combustible fuel is generally treated as single fuel particles. One of the limitations with the CFD modeling concerns the sub-models describing the combustion of single fuel particles. Available models in the scientific literature are in many cases not suitable as submodels for CFD modeling since they depend on a large number of input parameters and are computationally heavy. In this thesis CFD-applicable models are developed for the combustion of single fuel particles. The single particle models can be used to improve the combustion performance in various combustion devices or develop completely new technologies. The investigated fields are oxidation of carbon (C) and nitrogen (N) in char residues from solid fuels. Modeled char-C oxidation rates are compared to experimental oxidation rates for a large number of pulverized solid fuel chars under relevant combustion conditions. The experiments have been performed in an isothermal plug flow reactor operating at 1123-1673 K and 3-15 vol.% O2. In the single particle model, the char oxidation is based on apparent kinetics and depends on three fuel specific parameters: apparent pre-exponential factor, apparent activation energy, and apparent reaction order. The single particle model can be incorporated as a sub-model into a CFD code. The results show that the modeled char oxidation rates are in good agreement with experimental char oxidation rates up to around 70% of burnout. Moreover, the results show that the activation energy and the reaction order can be assumed to be constant for a large number of bituminous coal chars under conditions limited by the combined effects of chemical kinetics and pore diffusion. Based on this, a new model based on only one fuel specific parameter is developed (Paper III). The results also show that reaction orders of bituminous coal chars and anthracite chars differ under similar conditions (Paper I and Paper II); reaction orders of bituminous coal chars were found to be one, while reaction orders of anthracite chars were determined to be zero. This difference in reaction orders has not previously been observed in the literature and should be considered in future char oxidation models. One of the most frequently used comprehensive char oxidation models could not explain the difference in the reaction orders. In the thesis (Paper II), a modification to the model is suggested in order to explain the difference in reaction orders between anthracite chars and bituminous coal chars. Two single particle models are also developed for the NO formation and reduction during the oxidation of single biomass char particles. In the models the char-N is assumed to be oxidized to NO and the NO is partly reduced inside the particle. The first model (Paper IV) is based on the concentration gradients of NO inside and outside the particle and the second model is simplified to such an extent that it is based on apparent kinetics and can be incorporated as a sub-model into a CFD code (Paper V). Modeled NO release rates from both models were in good agreement with experimental measurements from a single particle reactor of quartz glass operating at 1173-1323 K and 3-19 vol.% O2. In the future, the models can be used to reduce NO emissions in new combustion systems.

Antinociceptive potency of aminoglycoside antibiotics and magnesium chloride: a comparative study on models of phasic and incisional pain in rats

A close relationship exists between calcium concentration in the central nervous system and nociceptive processing. Aminoglycoside antibiotics and magnesium interact with N- and P/Q-type voltage-operated calcium channels. In the present study we compare the antinociceptive potency of intrathecal administration of aminoglycoside antibiotics and magnesium chloride in the tail-flick test and on incisional pain in rats, taken as models of phasic and persistent post-surgical pain, respectively. The order of potency in the tail-flick test was gentamicin (ED50 = 3.34 µg; confidence limits 2.65 and 4.2) > streptomycin (5.68 µg; 3.76 and 8.57) = neomycin (9.22 µg; 6.98 and 12.17) > magnesium (19.49 µg; 11.46 and 33.13). The order of potency to reduce incisional pain was gentamicin (ED50 = 2.06 µg; confidence limits 1.46 and 2.9) > streptomycin (47.86 µg; 26.3 and 87.1) = neomycin (83.17 µg; 51.6 and 133.9). The dose-response curves for each test did not deviate significantly from parallelism. We conclude that neomycin and streptomycin are more potent against phasic pain than against persistent pain, whereas gentamicin is equipotent against both types of pain. Magnesium was less potent than the antibiotics and effective in the tail-flick test only.

Emission, kinetic and magnetic phenomena in rare-earth and transition metal doped ZnSe single crystals

In this work emission, optical, electrical and magnetic properties of the d- and f- elements doped zinc selenide crystals were investigated within a wide temperature range. Doping was performed in various technological processes: during the growth by chemical vapor transport method; by thermal diffusion from the Bi or Zn melt. Concentration of the doping impurity in the crystals was controlled by amount of the dopant in the source material or by its concentration in the doping media. Special interest in the work was paid to the influence of the different concentrations of Cr and Yb impurities on ZnSe crystals’ properties, correlations between observed effects and similarities with the Ni, Mn and Gd dopants are analysed. Possibility of formation of the excitons bound to the doping d-ions was shown. In contrast to this, it was observed that f-elements do not bound excitons, but prevent formation of excitons bound to some uncontrolled impurities. A mechanism of Cr doping impurity interaction with background impurities and zinc selenide structural defects was proposed based on experimental data. An assumption about resonant energy transfer between double charged chromium ions and complexes based on crystals’ vacancy defects was made. A correlation between emission and magnetic properties of the d- ions doped samples was established. Based on this correlation a mechanism explaining the concentration quench of the emission was proposed. It was found that f-ions bind electrically active shallow and deep donor and acceptor states of background impurity to electrically neutral complexes. This may be observed as “purification” of ZnSe crystals by doping with the rare-earth elements, resulting i tendency of the properties of f-ion doped crystals to the properties of intrinsic crystals, but with smaller concentration of uncontrolled native and impurity defects. A possible interpretation of this effect was proposed. It was shown that selenium substituting impurities decrease efficiency of the Yb doping. Based on this experimental results an attempt to determine ytterbium ion surroundings in the crystal lattice was made. It was shown that co-doping of zinc selenide crystals with the d- and f- ions leads to the combination of the impurities influence on the material’s properties. On the basis of obtained data an interaction mechanism of the d- and f-elements co-dopants was proposed. Guided by the model of the ytterbium ion incorporation in the selenide sublattice of the ZnSe crystals, an assumption about stabilization of single charged chromium ions in the zinc sublattice crystal nodes, by means of formation of the local charge compensating clusters, was made.

Percutaneous sciatic nerve block with tramadol induces analgesia and motor blockade in two animal pain models

Local anesthetic efficacy of tramadol has been reported following intradermal application. Our aim was to investigate the effect of perineural tramadol as the sole analgesic in two pain models. Male Wistar rats (280-380 g; N = 5/group) were used in these experiments. A neurostimulation-guided sciatic nerve block was performed and 2% lidocaine or tramadol (1.25 and 5 mg) was perineurally injected in two different animal pain models. In the flinching behavior test, the number of flinches was evaluated and in the plantar incision model, mechanical and heat thresholds were measured. Motor effects of lidocaine and tramadol were quantified and a motor block score elaborated. Tramadol, 1.25 mg, completely blocked the first and reduced the second phase of the flinching behavior test. In the plantar incision model, tramadol (1.25 mg) increased both paw withdrawal latency in response to radiant heat (8.3 ± 1.1, 12.7 ± 1.8, 8.4 ± 0.8, and 11.1 ± 3.3 s) and mechanical threshold in response to von Frey filaments (459 ± 82.8, 447.5 ± 91.7, 320.1 ± 120, 126.43 ± 92.8 mN) at 5, 15, 30, and 60 min, respectively. Sham block or contralateral sciatic nerve block did not differ from perineural saline injection throughout the study in either model. The effect of tramadol was not antagonized by intraperitoneal naloxone. High dose tramadol (5 mg) blocked motor function as well as 2% lidocaine. In conclusion, tramadol blocks nociception and motor function in vivo similar to local anesthetics.

Impact of Self-generation of Priorities and Non-preemptive Service in Single/Multiserver Queues

In this thesis we have studied a few models involving self-generation of priorities. Priority queues have been extensively discussed in literature. However, these are situations involving priority assigned to (or possessed by) customers at the time of their arrival. Nevertheless, customers generating into priority is a common phenomena. Such situations especially arise at a physicians clinic, aircrafts hovering over airport running out of fuel but waiting for clearance to land and in several communication systems. Quantification of these are very little seen in literature except for those cited in some of the work indicated in the introduction. Our attempt is to quantify a few of such problems. In doing so, we have also generalized the classical priority queues by introducing priority generation ( going to higher priorities and during waiting). Systematically we have proceeded from single server queue to multi server queue. We also introduced customers with repeated attempts (retrial) generating priorities. All models that were analyzed in this thesis involve nonpreemptive service. Since the models are not analytically tractable, a large number of numerical illustrations were produced in each chapter to get a feel about the working of the systems.

Systematic trends in self-consistent calculations of linear quantum wires

Systematic trends in the properties of a linear split-gate heterojunction are studied by solving iteratively the Poisson and Schrödinger equations for different gate potentials and temperatures. A two-dimensional approximation is presented that is much simpler in the numerical implementation and that accurately reproduces all significant trends. In deriving this approximation, we provide a rigorous and quantitative basis for the formulation of models that assumes a two-dimensional character for the electron gas at the junction.

Magnetic properties and domain-wall motion in single-crystal BaFe10.2Sn0.74Co0.66O19

The magnetic properties of BaFe12O19 and BaFe10.2Sn0.74Co0.66O19 single crystals have been investigated in the temperature range (1.8 to 320 K) with a varying field from -5 to +5 T applied parallel and perpendicular to the c axis. Low-temperature magnetic relaxation, which is ascribed to the domain-wall motion, was performed between 1.8 and 15 K. The relaxation of magnetization exhibits a linear dependence on logarithmic time. The magnetic viscosity extracted from the relaxation data, decreases linearly as temperature goes down, which may correspond to the thermal depinning of domain walls. Below 2.5 K, the viscosity begins to deviate from the linear dependence on temperature, tending to be temperature independent. The near temperature independence of viscosity suggests the existence of quantum tunneling of antiferromagnetic domain wall in this temperature range.