Sarveiskalvon permeabiliteetin ennustaminen QSPR-mallin avulla

QSPR-malli kuvaa kvantitatiivista riippuvuutta muuttujien ja biologisen ominaisuuden välillä. Näin ollen QSPR mallit ovat käyttökelpoisia lääkekehityksen apuvälineitä. Kirjallisessa osassa kerrotaan sarveiskalvon, suoliston ja veriaivoesteen permeabiliteetin malleista. Useimmin käytettyjä muuttujia ovat yhdisteen rasvaliukoisuus, polaarinen pinta-ala, vetysidosten muodostuminen ja varaus. Myös yhdisteen koko vaikuttaa läpäisevyyteen, vaikka tutkimuksissa onkin erilaista tietoa tämän merkittävyydestä. Malliin vaikuttaa myös muiden kuin mallissa mukana olevien muuttujien suuruusluokka esimerkkinä Lipinskin ‖rule of 5‖ luokittelu. Tässä luokittelussa yhdisteen ominaisuus ei saa ylittää tiettyjä raja-arvoja. Muussa tapauksessa sen imeytyminen suun kautta otettuna todennäköisesti vaarantuu. Lisäksi kirjallisessa osassa tutustuttiin kuljetinproteiineihin ja niiden toimintaan silmän sarveiskalvossa, suolistossa ja veriaivoesteessä. Nykyisin on kehitetty erilaisia QSAR-malleja kuljetinproteiineille ennustamaan mahdollisten substraatittien tai inhibiittorien vuorovaikutuksia kuljetinproteiinin kanssa. Kokeellisen osan tarkoitus oli rakentaa in silico -malli sarveiskalvon passiiviselle permeabiliteetille. Työssä tehtiin QSPR-malli 54 yhdisteen ACDLabs-ohjelmalla laskettujen muuttujien arvojen avulla. Permeabiliteettikertoimien arvot saatiin kirjallisuudesta kanin sarveiskalvon läpäisevyystutkimuksista. Lopullisen mallin muuttujina käytettiin oktanoli-vesijakaantumiskerrointa (logD) pH:ssa 7,4 ja vetysidosatomien kokonaismäärää. Yhtälö oli muotoa log10(permeabiliteettikerroin) = -3,96791 - 0,177842Htotal + 0,311963logD(pH7,4). R2-korrelaatiokerroin oli 0,77 ja Q2-korrelaatiokerroin oli 0,75. Lopullisen mallin hyvyyttä arvioitiin 15 yhdisteen ulkoisella testijoukolla, jolloin ennustettua permeabiliteettia verrattiin kokeelliseen permeabiliteettiin. QSPR-malli arvioitiin myös farmakokineettisen simulaation avulla. Simulaatiossa laskettiin seitsemän yhdisteen kammionestepitoisuudet in vivo vakaassa tilassa käyttäen simulaatioissa QSPR mallilla ennustettuja permeabiliteettikertoimia. Lisäksi laskettiin sarveiskalvon imeytymisen nopeusvakio (Kc) 13 yhdisteelle farmakokineettisen simulaation avulla ja verrattiin tätä lopullisella mallilla ennustettuun permeabiliteettiin. Tulosten perusteella saatiin tilastollisesti hyvä QSPR-malli kuvaamaan sarveiskalvon passiivista permeabiliteettia, jolloin tätä mallia voidaan käyttää lääkekehityksen alkuvaiheessa. QSPR-malli ennusti permeabiliteettikertoimet hyvin, mikä nähtiin vertaamalla mallilla ennustettuja arvoja kokeellisiin tuloksiin. Lisäksi yhdisteiden kammionestepitoisuudet voitiin simuloida käyttäen apuna QSPR-mallilla ennustettuja permeabiliteettikertoimien arvoja.

A molecular dynamics study of cage-to-cage migration in sodium Y zeolite: role of surface-mediated diffusion

The details of cage-to-cage migration have been obtained from an analysis of the molecular dynamics trajectory of a probe adsorbate. It is observed that particles utilize the region within a radius of 2 angstrom from the window center but with diffusion taking place predominantly at 1.6 angstrom from the window center and a potential energy of nearly -12 kJ/mol. A barrier of about 0.5 kJ/mol is observed for surface-mediated diffusion. Surprisingly, for diffusion without surface mediation for a particle going from one cage center to another, there is an attractive well near the window instead of a barrier. At low adsorbate concentrations and room temperature, the predominant mode for cage-to-cage migration is surface-mediated diffusion. The analysis suggests that particles slide along the surface of the inner walls of the alpha-cages during migration from one cage to another.

Brownian motion of spins; generalized spin Langevin equation

We derive the Langevin equations for a spin interacting with a heat bath, starting from a fully dynamical treatment. The obtained equations are non-Markovian with multiplicative fluctuations and concommitant dissipative terms obeying the fluctuation-dissipation theorem. In the Markovian limit our equations reduce to the phenomenological equations proposed by Kubo and Hashitsume. The perturbative treatment on our equations lead to Landau-Lifshitz equations and to other known results in the literature.

Diffusion coefficients for selected binary liquid systems: cyclohexanes and n-alkyl alcohols

In the present work the integral diffusion coefficients are estimated by using the diaphragm cell technique. The diffusion coefficients are measured at various compositions for two sets binary systems: one of cyclohexane and n-paraffinic alcohols and the other of methylcyclohexane and n-paraffinic alcohols. The alcohols used are seven members of homologous series of n-paraffinic alcohols from ethanol to octanol. The maximum possible error in the experimental diffusion coefficient could be 8% for both the cyclohexane-n-alkyl alcohol system and methylcyclohexane-n-alkyl alcohol system. A correlation for each of the two sets of binary systems is given. The maximum deviation in the correlations was less than 6.5 and 3.5% for cyclohexane-n-alkyl alcohols and methylcyclohexane-n-alkyl alcohols, respectively.

Mutual diffusion coefficients of some binary liquid systems: benzene-n-alkyl alcohol

The mutual diffusion coefficients for binary liquid systems of benzene-n-alkyl alcohol at various compositions have been determined by the diaphragm cell method at 28-degrees-C. The alcohols used were the members of n-paraffinic alcohols ranging from C1 to C8. The maximum possible experimental error is 14%. The data were fitted with a generalized correlation, giving the deviation from the experimental data to within 2.75%, on average.

Rocking response of rectangular rigid blocks under random noise base excitations

The response of a rigid rectangular block resting on a rigid foundation and acted upon simultaneously by a horizontal and a vertical random white-noise excitation is considered. In the equation of motion, the energy dissipation is modeled through a viscous damping term. Under the assumption that the body does not topple, the steady-state joint probability density function of the rotation and the rotational velocity is obtained using the Fokker-Planck equation approach. Closed form solution is obtained for a specific combination of system parameters. A more general but approximate solution to the joint probability density function based on the method of equivalent non-linearization is also presented. Further, the problem of overturning of the block is approached in the framework of the diffusion methods for first passage failure studies. The overturning of the block is deemed incipient when the response trajectories in the phase plane cross the separatrix of the conservative unforced system. Expressions for the moments of first passage time are obtained via a series solution to the governing generalized Pontriagin-Vitt equations. Numerical results illustra- tive of the theoretical solutions are presented and their validity is examined through limited amount of digital simulations.

Large-amplitude chirped coherent phonons in tellurium mediated by ultrafast photoexcited carrier diffusion

We report femtosecond time-resolved reflectivity measurements of coherent phonons in tellurium performed over a wide range of temperatures (3-296 K) and pump-laser intensities. A totally symmetric A(1) coherent phonon at 3.6 THz responsible for the oscillations in the reflectivity data is observed to be strongly positively chirped (i.e., phonon time period decreases at longer pump-probe delay times) with increasing photoexcited carrier density, more so at lower temperatures. We show that the temperature dependence of the coherent phonon frequency is anomalous (i.e, increasing with increasing temperature) at high photoexcited carrier density due to electron-phonon interaction. At the highest photoexcited carrier density of (1.4 x 10(21) cm(-3) and the sample temperature of 3 K, the lattice displacement of the coherent phonon mode is estimated to be as high as similar to 0.24 angstrom. Numerical simulations based on coupled effects of optical absorption and carrier diffusion reveal that the diffusion of carriers dominates the nonoscillatory electronic part of the time-resolved reflectivity. Finally, using the pump-probe experiments at low carrier density of 6 x 10(18) cm(-3), we separate the phonon anharmonicity to obtain the electron-phonon coupling contribution to the phonon frequency and linewidth.

Impurity diffusion in bismuth single-crystals

Measurements of impurity diffusion of 86Rb, 90Sr, 133Ba, and 137Cs in single crystal Bi were carried out. Diffusion samples were prepared from single crystal Bi by ion implantation. About 1012-1013 ions were implanted, resulting in surface activities approx =104 cpm. After implantation, specimens were annealed for specified times at 220-265 deg C, and tracer penetration profiles were determined by an electrolytic method. A typical penetration profile for 137Cs in Bi showed a linear relationship for log C vs x in with Fick's law for volume diffusion. Laws of grain boundary diffusion were not obeyed and the order of magnitude of the penetration distances was much less than on a grain boundary mechanism. Results were interpreted in terms of a modified Fischer analysis using a kinetic trapping term. Effective half lengths for trapping at a twin boundary were determined for each impurity.

Alfvén waves in inhomogeneous magnetic fields: An integrodifferential equation formulation

An integrodifferential formulation for the equation governing the Alfvén waves in inhomogeneous magnetic fields is shown to be similar to the polyvibrating equation of Mangeron. Exploiting this similarity, a time‐dependent solution for smooth initial conditions is constructed. The important feature of this solution is that it separates the parts giving the Alfvén wave oscillations of each layer of plasma and the interaction of these oscillations representing the phase mixing.

Inverse problem for the wave equation : partial data and novel boundary sources

An inverse problem for the wave equation is a mathematical formulation of the problem to convert measurements of sound waves to information about the wave speed governing the propagation of the waves. This doctoral thesis extends the theory on the inverse problems for the wave equation in cases with partial measurement data and also considers detection of discontinuous interfaces in the wave speed. A possible application of the theory is obstetric sonography in which ultrasound measurements are transformed into an image of the fetus in its mother's uterus. The wave speed inside the body can not be directly observed but sound waves can be produced outside the body and their echoes from the body can be recorded. The present work contains five research articles. In the first and the fifth articles we show that it is possible to determine the wave speed uniquely by using far apart sound sources and receivers. This extends a previously known result which requires the sound waves to be produced and recorded in the same place. Our result is motivated by a possible application to reflection seismology which seeks to create an image of the Earth s crust from recording of echoes stimulated for example by explosions. For this purpose, the receivers can not typically lie near the powerful sound sources. In the second article we present a sound source that allows us to recover many essential features of the wave speed from the echo produced by the source. Moreover, these features are known to determine the wave speed under certain geometric assumptions. Previously known results permitted the same features to be recovered only by sequential measurement of echoes produced by multiple different sources. The reduced number of measurements could increase the number possible applications of acoustic probing. In the third and fourth articles we develop an acoustic probing method to locate discontinuous interfaces in the wave speed. These interfaces typically correspond to interfaces between different materials and their locations are of interest in many applications. There are many previous approaches to this problem but none of them exploits sound sources varying freely in time. Our use of more variable sources could allow more robust implementation of the probing.

Analytical solution of the laminar mean flow wave equation in a lined or unlined two-dimensional rectangular duct

The prediction of the sound attenuation in lined ducts with sheared mean flow has been a topic of research for many years. This involves solving the sheared mean flow wave equation, satisfying the relevant boundary condition. As far as the authors' knowledge goes, this has always been done using numerical techniques. Here, an analytical solution is presented for the wave propagation in two-dimensional rectangular lined ducts with laminar mean flow. The effect of laminar mean flow is studied for both the downstream and the upstream wave propagation. The attenuation values predicted for the laminar mean flow case are compared with those for the case of uniform mean flow. Analytical expressions are derived for the transfer matrices.

A new approach to the kinetics of size reduction in ball milling

The rate of breakage of feed in ball milling is usually represented in the form of a first-order rate equation. The equation was developed by treating a simple batch test mill as a well mixed reactor. Several case of deviation from the rule have been reported in the literature. This is attributed to the fact that accumulated fines interfere with the feed material and breaking events are masked by these fines. In the present paper, a new rate equation is proposed which takes into account the retarding effect of fines during milling. For this purpose the analogy of diffusion of ions through permeable membranes is adopted, with suitable modifications. The validity of the model is cross checked with the data obtained in batch grinding of ?850/+600 ?m size quartz. The proposed equation enables calculation of the rate of breakage of the feed at any instant of time.

Relaxation system based sub-grid scale modelling for large eddy simulation of Burgers' equation

An implicit sub-grid scale model for large eddy simulation is presented by utilising the concept of a relaxation system for one dimensional Burgers' equation in a novel way. The Burgers' equation is solved for three different unsteady flow situations by varying the ratio of relaxation parameter (epsilon) to time step. The coarse mesh results obtained with a relaxation scheme are compared with the filtered DNS solution of the same problem on a fine mesh using a fourth-order CWENO discretisation in space and third-order TVD Runge-Kutta discretisation in time. The numerical solutions obtained through the relaxation system have the same order of accuracy in space and time and they closely match with the filtered DNS solutions.