A Dynamic Migration Model for Self-adaptive Genetic Algorithms

In this paper, we propose a self Adaptive Migration Model for Genetic Algorithms, where parameters of population size, the number of points of crossover and mutation rate for each population are fixed adaptively. Further, the migration of individuals between populations is decided dynamically. This paper gives a mathematical schema analysis of the method stating and showing that the algorithm exploits previously discovered knowledge for a more focused and concentrated search of heuristically high yielding regions while simultaneously performing a highly explorative search on the other regions of the search space. The effective performance of the algorithm is then shown using standard testbed functions, when compared with Island model GA(IGA) and Simple GA(SGA).

A Dynamic Migration Model for self-adaptive Genetic Algorithms

In this paper, we propose a self Adaptive Migration Model for Genetic Algorithms, where parameters of population size, the number of points of crossover and mutation rate for each population are fixed adaptively. Further, the migration of individuals between populations is decided dynamically. This paper gives a mathematical schema analysis of the method stating and showing that the algorithm exploits previously discovered knowledge for a more focused and concentrated search of heuristically high yielding regions while simultaneously performing a highly explorative search on the other regions of the search space. The effective performance of the algorithm is then shown using standard testbed functions, when compared with Island model GA(IGA) and Simple GA(SGA).

Monte Carlo simulations of molecular clusters in nucleation

A better understanding of the limiting step in a first order phase transition, the nucleation process, is of major importance to a variety of scientific fields ranging from atmospheric sciences to nanotechnology and even to cosmology. This is due to the fact that in most phase transitions the new phase is separated from the mother phase by a free energy barrier. This barrier is crossed in a process called nucleation. Nowadays it is considered that a significant fraction of all atmospheric particles is produced by vapor-to liquid nucleation. In atmospheric sciences, as well as in other scientific fields, the theoretical treatment of nucleation is mostly based on a theory known as the Classical Nucleation Theory. However, the Classical Nucleation Theory is known to have only a limited success in predicting the rate at which vapor-to-liquid nucleation takes place at given conditions. This thesis studies the unary homogeneous vapor-to-liquid nucleation from a statistical mechanics viewpoint. We apply Monte Carlo simulations of molecular clusters to calculate the free energy barrier separating the vapor and liquid phases and compare our results against the laboratory measurements and Classical Nucleation Theory predictions. According to our results, the work of adding a monomer to a cluster in equilibrium vapour is accurately described by the liquid drop model applied by the Classical Nucleation Theory, once the clusters are larger than some threshold size. The threshold cluster sizes contain only a few or some tens of molecules depending on the interaction potential and temperature. However, the error made in modeling the smallest of clusters as liquid drops results in an erroneous absolute value for the cluster work of formation throughout the size range, as predicted by the McGraw-Laaksonen scaling law. By calculating correction factors to Classical Nucleation Theory predictions for the nucleation barriers of argon and water, we show that the corrected predictions produce nucleation rates that are in good comparison with experiments. For the smallest clusters, the deviation between the simulation results and the liquid drop values are accurately modelled by the low order virial coefficients at modest temperatures and vapour densities, or in other words, in the validity range of the non-interacting cluster theory by Frenkel, Band and Bilj. Our results do not indicate a need for a size dependent replacement free energy correction. The results also indicate that Classical Nucleation Theory predicts the size of the critical cluster correctly. We also presents a new method for the calculation of the equilibrium vapour density, surface tension size dependence and planar surface tension directly from cluster simulations. We also show how the size dependence of the cluster surface tension in equimolar surface is a function of virial coefficients, a result confirmed by our cluster simulations.

Melting and superheating of nanowires-a nanotube approach

We have investigated the size-dependent melting of nanotubes based on a thermodynamic approach and shown that the melting temperature of nanotubes depends on the outer radius and on the inner radius through the thickness of the nanotubes. Size-dependent melting of nanowires and thin films has been derived from that of nanotubes. We validate the size-dependent melting of nanotubes, nanowires and thin films by comparing the results with available molecular dynamic simulations and experimental results. It has also been inferred that superheating occurs when the melting starts from the inner surface and proceeds towards the outer surface, while melting point depression occurs when the melting starts from the outer surface and proceeds towards the inner surface.

A simple classical approach for the melting temperature of inert-gas nanoparticles

Like the metal and semiconductor nanoparticles, the melting temperature of free inert-gas nanoparticles decreases with decreasing size. The variation is linear with the inverse of the particle size for large nanoparticles and deviates from the linearity for small nanoparticles. The decrease in the melting temperature is slower for free nanoparticles with non-wetting surfaces, while the decrease is faster for nanoparticles with wetting surfaces. Though the depression of the melting temperature has been reported for inert-gas nanoparticles in porous glasses, superheating has also been observed when the nanoparticles are embedded in some matrices. By using a simple classical approach, the influence of size, geometry and the matrix on the melting temperature of nanoparticles is understood quantitatively and shown to be applicable for other materials. It is also shown that the classical approach can be applied to understand the size-dependent freezing temperature of nanoparticles.

On the paradoxical relation between the melting temperature and forbidden energy gap of nanoparticles

We comment on the paradox that seems to exist about a correlation between the size-dependent melting temperature and the forbidden energy gap of nanoparticles. By analyzing the reported expressions for the melting temperature and the band gap of nanoparticles, we conclude that there exists a relation between these two physical quantities. However, the variations of these two quantities with size for semiconductors are different from that of metals. (C) 2010 American Institute of Physics.[doi:10.1063/1.3466920].

Kymmenen koirarodun perinnöllinen monimuotoisuus

Tämän tutkimuksen tavoitteena oli selvittää koirarotujen sisäistä ja välistä perinnöllistä muuntelua ja populaatioiden rakenteita. Tutkimuksessa käytettiin Finnzymes Oy:ltä saatua koirien mikrosatelliittimerkkeihin perustuvaa genotyypitysaineistoa. Lopullisessa aineistossa oli 395 koiraa kymmenestä keskenään varsin erilaisesta rodusta. Koirien määrä rotua kohti vaihteli 31:stä 53:een. Tutkimuksessa käytettiin 18 mikrosatelliittilokusta. Alleelirikkaus vaihteli mikrosatelliittilokuksissa välillä 2,0 – 9,9. Kaikkein muuntelevin lokus oli AHT137 ja vähiten muunteleva AHTk211. Jackrussellinterrierin alleelirikkaus oli yli kaikkien lokusten tarkasteltuna suurinta ja cavalier kingcharlesinspanielin pienintä. Eniten Hardy-Weinbergin tasapainosta poikkeavia mikrosatelliittilokuksia oli schipperke- rodulla. Coton de tulearin, saksanpaimenkoiran ja suomenlapinkoiran kaikki mikrosatelliittilokukset olivat Hardy-Weinbergin tasapainossa. Cavalier kingcharlesinspanielin havaittu heterotsygotia-aste oli matalin kaikkien lokusten yli tarkasteltuna (0,50) ja suomenlapinkoiran korkein (0,73). Ainoat tilastollisesti merkitsevät FIS-arvot olivat schipperken lokuksessa INU030 (0,39) ja kaikkien lokusten yli tarkasteltuna (0,11). Eniten populaatioiden välisiin eroihin perustuvaa muuntelua oli cavalier kingcharlesinspanielin ja pitkäkarvaisen collien välillä (FST = 0,34) ja vähiten chihuahuan ja coton de tulearin välillä (FST = 0,07). Koko aineistossa noin 17,7 % populaatioiden välisestä geneettisestä muuntelusta johtui populaatioiden välisistä eroista. Rodut ovat tulosten perusteella selvästi erillisiä populaatioita. Coton de tulearin alleeliparit olivat selvästi eniten kytkentäepätasapainossa keskenään (94) ja tiibetinspanielin vähiten (15). Pitkäkarvaisen collien tehollinen populaatiokoko oli pienin (35) ja chihuahuan suurin (86). U seiden populaatiogeneettisten tunnuslukujen perusteella nousivat esiin cavalier kingcharlesinspanieli, pitkäkarvainen collie ja schipperke perinnöllisen muuntelun vähäisyyden perusteella ja chihuahua, jackrussellinterrieri ja suomenlapinkoira keskimääräistä suuremman perinnöllisen muuntelun perusteella. Selityksiä geneettisen monimuotoisuuden vaihteluun näillä roduilla löytyy rotujen historiasta.

Design of speaker identification schemes for large number of speakers (A)

Design of speaker identification schemes for a small number of speakers (around 10) with a high degree of accuracy in controlled environment is a practical proposition today. When the number of speakers is large (say 50–100), many of these schemes cannot be directly extended, as both recognition error and computation time increase monotonically with population size. The feature selection problem is also complex for such schemes. Though there were earlier attempts to rank order features based on statistical distance measures, it has been observed only recently that the best two independent measurements are not the same as the combination in two's for pattern classification. We propose here a systematic approach to the problem using the decision tree or hierarchical classifier with the following objectives: (1) Design of optimal policy at each node of the tree given the tree structure i.e., the tree skeleton and the features to be used at each node. (2) Determination of the optimal feature measurement and decision policy given only the tree skeleton. Applicability of optimization procedures such as dynamic programming in the design of such trees is studied. The experimental results deal with the design of a 50 speaker identification scheme based on this approach.

Estimating Frequencies of Minority Nevirapine-Resistant Strains in Chronically HIV-1-Infected Individuals Naive to Nevirapine by Using Stochastic Simulations and a Mathematical Model

Nevirapine forms the mainstay of our efforts to curtail the pediatric AIDS epidemic through prevention of mother-to-child transmission of HIV-1. A key limitation, however, is the rapid selection of HIV-1 strains resistant to nevirapine following the administration of a single dose. This rapid selection of resistance suggests that nevirapine-resistant strains preexist in HIV-1 patients and may adversely affect outcomes of treatment. The frequencies of nevirapine-resistant strains in vivo, however, remain poorly estimated, possibly because they exist as a minority below current assay detection limits. Here, we employ stochastic simulations and a mathematical model to estimate the frequencies of strains carrying different combinations of the common nevirapine resistance mutations K103N, V106A, Y181C, Y188C, and G190A in chronically infected HIV-1 patients naive to nevirapine. We estimate the relative fitness of mutant strains from an independent analysis of previous competitive growth assays. We predict that single mutants are likely to preexist in patients at frequencies (similar to 0.01% to 0.001%) near or below current assay detection limits (>0.01%), emphasizing the need for more-sensitive assays. The existence of double mutants is subject to large stochastic variations. Triple and higher mutants are predicted not to exist. Our estimates are robust to variations in the recombination rate, cellular superinfection frequency, and the effective population size. Thus, with 10(7) to 10(8) infected cells in HIV-1 patients, even when undetected, nevirapine-resistant genomes may exist in substantial numbers and compromise efforts to prevent mother-to-child transmission of HIV-1, accelerate the failure of subsequent antiretroviral treatments, and facilitate the transmission of drug resistance.

The management of large mammals in relation to male strategies and conflict with people

Many large mammals such as elephant, rhino and tiger often come into conflict with people by destroying agricultural crops and even killing people, thus providing a deterrent to conservation efforts. The males of these polygynous species have a greater variance in reproductive success than females, leading to selection pressures favouring a ‘high risk-high gain’ strategy for promoting reproductive success. This brings them into greater conflict with people. For instance, adult male elephants are far more prone than a member of a female-led family herd to raid agricultural crops and to kill people. In polygynous species, the removal of a certain proportion of ‘surplus’ adult males is not likely to affect the fertility and growth rate of the population. Hence, this could be a management tool which would effectively reduce animal-human conflict, and at the same time maintain the viability of the population. Selective removal of males would result in a skewed sex ratio. This would reduce the ‘effective population size’ (as opposed to the total population or census number), increase the rate of genetic drift and, in small populations, lead to inbreeding depression. Plans for managing destructive mammals through the culling of males will have to ensure that the appropriate minimum size in the populations is being maintained.

Language universals and linguistic complexity : Three case studies in core argument marking

In this dissertation I study language complexity from a typological perspective. Since the structuralist era, it has been assumed that local complexity differences in languages are balanced out in cross-linguistic comparisons and that complexity is not affected by the geopolitical or sociocultural aspects of the speech community. However, these assumptions have seldom been studied systematically from a typological point of view. My objective is to define complexity so that it is possible to compare it across languages and to approach its variation with the methods of quantitative typology. My main empirical research questions are: i) does language complexity vary in any systematic way in local domains, and ii) can language complexity be affected by the geographical or social environment? These questions are studied in three articles, whose findings are summarized in the introduction to the dissertation. In order to enable cross-language comparison, I measure complexity as the description length of the regularities in an entity; I separate it from difficulty, focus on local instead of global complexity, and break it up into different types. This approach helps avoid the problems that plagued earlier metrics of language complexity. My approach to grammar is functional-typological in nature, and the theoretical framework is basic linguistic theory. I delimit the empirical research functionally to the marking of core arguments (the basic participants in the sentence). I assess the distributions of complexity in this domain with multifactorial statistical methods and use different sampling strategies, implementing, for instance, the Greenbergian view of universals as diachronic laws of type preference. My data come from large and balanced samples (up to approximately 850 languages), drawn mainly from reference grammars. The results suggest that various significant trends occur in the marking of core arguments in regard to complexity and that complexity in this domain correlates with population size. These results provide evidence that linguistic patterns interact among themselves in terms of complexity, that language structure adapts to the social environment, and that there may be cognitive mechanisms that limit complexity locally. My approach to complexity and language universals can therefore be successfully applied to empirical data and may serve as a model for further research in these areas.

Tuning the interfacial properties of supported metal nanoclusters

Nanoclusters are objects made up of several to thousands of atoms and form a transitional state of matter between single atoms and bulk materials. Due to their large surface-to-volume ratio, nanoclusters exhibit exciting and yet poorly studied size dependent properties. When deposited directly on bare metal surfaces, the interaction of the cluster with the substrate leads to alteration of the cluster properties, making it less or even non-functional. Surfaces modified with self-assembled monolayers (SAMs) were shown to form an interesting alternative platform, because of the possibility to control wettability by decreasing the surface reactivity and to add functionalities to pre-formed nanoclusters. In this thesis, the underlying size effects and the influence of the nanocluster environment are investigated. The emphasis is on the structural and magnetic properties of nanoclusters and their interaction with thiol SAMs. We report, for the first time, a ferromagnetic-like spin-glass behaviour of uncapped nanosized Au islands tens of nanometres in size. The flattening kinetics of the nanocluster deposition on thiol SAMs are shown to be mediated mainly by the thiol terminal group, as well as the deposition energy and the particle size distribution. On the other hand, a new mechanism for the penetration of the deposited nanoclusters through the monolayers is presented, which is fundamentally different from those reported for atom deposition on alkanethiols. The impinging cluster is shown to compress the thiol layer against the Au surface and subsequently intercalate at the thiol-Au interface. The compressed thiols try then to straighten and push the cluster away from the surface. Depending on the cluster size, this restoring force may or may not enable a covalent cluster-surface bond formation, giving rise to various cluster-surface binding patterns. Compression and straightening of the thiol molecules pinpoint the elastic nature of the SAMs, which has been investigated in this thesis using nanoindentation. The nanoindenation method has been applied to SAMs of varied tail groups, giving insight into the mechanical properties of thiol modified metal surfaces.

Patterning Nanoroads and Quantum Dots on Fluorinated Graphene

Using ab initio methods we have investigated the fluorination of graphene and find that different stoichiometric phases can be formed without a nucleation barrier, with the complete “2D-Teflon” CF phase being thermodynamically most stable. The fluorinated graphene is an insulator and turns out to be a perfect matrix-host for patterning nanoroads and quantum dots of pristine graphene. The electronic and magnetic properties of the nanoroads can be tuned by varying the edge orientation and width. The energy gaps between the highest occupied and lowest unoccupied molecular orbitals (HOMO-LUMO) of quantum dots are size-dependent and show a confinement typical of Dirac fermions. Furthermore, we study the effect of different basic coverage of F on graphene (with stoichiometries CF and C4F) on the band gaps, and show the suitability of these materials to host quantum dots of graphene with unique electronic properties.

Endemic malaria: an 'indoor' disease in northern Europe

Background: Endemic northern malaria reached 68°N latitude in Europe during the 19th century, where the summer mean temperature only irregularly exceeded 16°C, the lower limit needed for sporogony of Plasmodium vivax. Because of the available historical material and little use of quinine, Finland was suitable for an analysis of endemic malaria and temperature. Methods: Annual malaria death frequencies during 1800–1870 extracted from parish records were analysed against long-term temperature records in Finland, Russia and Sweden. Supporting data from 1750–1799 were used in the interpretation of the results. The life cycle and behaviour of the anopheline mosquitoes were interpreted according to the literature. Results: Malaria frequencies correlated strongly with the mean temperature of June and July of the preceding summer, corresponding to larval development of the vector. Hatching of imagoes peaks in the middle of August, when the temperature most years is too low for the sporogony of Plasmodium. After mating some of the females hibernate in human dwellings. If the female gets gametocytes from infective humans, the development of Plasmodium can only continue indoors, in heated buildings. Conclusion: Northern malaria existed in a cold climate by means of summer dormancy of hypnozoites in humans and indoor transmission of sporozoites throughout the winter by semiactive hibernating mosquitoes. Variable climatic conditions did not affect this relationship. The epidemics, however, were regulated by the population size of the mosquitoes which, in turn, ultimately was controlled by the temperatures of the preceding summer.

Gas-liquid nucleation at large metastability: unusual features and a new formalism

Nucleation at large metastability is still largely an unsolved problem, even though it is a problem of tremendous current interest, with wide-ranging practical value, from atmospheric research to materials science. It is now well accepted that the classical nucleation theory (CNT) fails to provide a qualitative picture and gives incorrect quantitative values for such quantities as activation-free energy barrier and supersaturation dependence of nucleation rate, especially at large metastability. In this paper, we present an alternative formalism to treat nucleation at large supersaturation by introducing an extended set of order parameters in terms of the kth largest liquid-like clusters, where k = 1 is the largest cluster in the system, k = 2 is the second largest cluster and so on. At low supersaturation, the size of the largest liquid-like cluster acts as a suitable order parameter. At large supersaturation, the free energy barrier for the largest liquid-like cluster disappears. We identify this supersaturation as the one at the onset of kinetic spinodal. The kinetic spinodal is system-size-dependent. Beyond kinetic spinodal many clusters grow simultaneously and competitively and hence the nucleation and growth become collective. In order to describe collective growth, we need to consider the full set of order parameters. We derive an analytic expression for the free energy of formation of the kth largest cluster. The expression predicts that, at large metastability (beyond kinetic spinodal), the barrier of growth for several largest liquid-like clusters disappears, and all these clusters grow simultaneously. The approach to the critical size occurs by barrierless diffusion in the cluster size space. The expression for the rate of barrier crossing predicts weaker supersaturation dependence than what is predicted by CNT at large metastability. Such a crossover behavior has indeed been observed in recent experiments (but eluded an explanation till now). In order to understand the large numerical discrepancy between simulation predictions and experimental results, we carried out a study of the dependence on the range of intermolecular interactions of both the surface tension of an equilibrium planar gas-liquid interface and the free energy barrier of nucleation. Both are found to depend significantly on the range of interaction for the Lennard-Jones potential, both in two and three dimensions. The value of surface tension and also the free energy difference between the gas and the liquid phase increase significantly and converge only when the range of interaction is extended beyond 6-7 molecular diameters. We find, with the full range of interaction potential, that the surface tension shows only a weak dependence on supersaturation, so the reason for the breakdown of CNT (with simulated values of surface tension and free energy gap) cannot be attributed to the supersaturation dependence of surface tension. This remains an unsettled issue at present because of the use of the value of surface tension obtained at coexistence.