Optical trapping: a review of essential concepts

Optical tweezers are an innovative technique for the non-contact, all-optical manipulation of small material samples, which has extraordinarily expanded and evolved since its inception in the mid-80s of the last century. Nowadays, the potential of optical tweezers has been clearly proven and a wide range of applications both from the physical and biological sciences have solidly emerged, turning the early ideas and techniques into a powerful paradigm for experimentation in the micro- and nanoworld. This review aims at highlighting the fundamental concepts that are essential for a thorough understanding of optical trapping, making emphasis on both its manipulation and measurement capabilities, as well as on the vast array of important biological applications appeared in the last years.

Split message-based anonymity for JXTA applications

JXTA is an open peer-to-peer (P2P) protocols specification that, in its about 10 years of history, has slowly evolved to appeal to a broad set of applications. As part of this process,some long awaited security improvements have been included in the latest versions. However, under some contexts, even more advanced security requirements should be met, such as anonymity. Several approaches exist to deploy anonymity in P2P networks, but no perfect solution exists. Even though path-based approaches are quite popular, it is considered that, in dynamicgroups, using a split message-based one is better. In this work, we propose an anonymity service for JXTA using such approach. The proposal takes advantage JXTA's core services, in a manner so that it can be easily integrated to existing end applications and services.

The effects of ICT on school: teachers’ and students’ perspectives

The purpose of this study was to investigate the effects of information and communication technology (ICT) on school from teachers’ and students’ perspectives. The focus was on three main subject matters: on ICT use and competence, on teacher and school community, and on learning environment and teaching practices. The study is closely connected to the national educational policy which has aimed strongly at supporting the implementation of ICT in pedagogical practices at all institutional levels. The phenomena were investigated using a mixed methods approach. The qualitative data from three cases studies and the quantitative data from three statistical studies were combined. In this study, mixed methods were used to investigate the complex phenomena from various stakeholders’ points of view, and to support validation by combining different perspectives in order to give a fuller and more complete picture of the phenomena. The data were used in a complementary manner. The results indicate that the technical resources for using ICT both at school and at homes are very good. In general, students are capable and motivated users of new technology; these skills and attitudes are mainly based on home resources and leisuretime use. Students have the skills to use new kinds of applications and new forms of technology, and their ICT skills are wide, although not necessarily adequate; the working habits might be ineffective and even wrong. Some students have a special kind of ICT-related adaptive expertise which develops in a beneficial interaction between school guidance and challenges, and individual interest and activity. Teachers’ skills are more heterogeneous. The large majority of teachers have sufficient skills for everyday and routine working practices, but many of them still have difficulties in finding a meaningful pedagogical use for technology. The intensive case study indicated that for the majority of teachers the intensive ICT projects offer a possibility for learning new skills and competences intertwined in the work, often also supported by external experts and a collaborative teacher community; a possibility that “ordinary” teachers usually do not have. Further, teachers’ good ICT competence help them to adopt new pedagogical practices and integrate ICT in a meaningful way. The genders differ in their use of and skills in ICT: males show better skills especially in purely technical issues also in schools and classrooms, whereas female students and younger female teachers use ICT in their ordinary practices quite naturally. With time, the technology has become less technical and its communication and creation affordances have become stronger, easier to use, more popular and motivating, all of which has increased female interest in the technology. There is a generation gap in ICT use and competence between teachers and students. This is apparent especially in the ICT-related pedagogical practices in the majority of schools. The new digital affordances not only replace some previous practices; the new functionalities change many of our existing conceptions, values, attitudes and practices. The very different conceptions that generations have about technology leads, in the worst case, to a digital gap in education; the technology used in school is boring and ineffective compared to the ICT use outside school, and it does not provide the competence needed for using advanced technology in learning. The results indicate that in schools which have special ICT projects (“ICT pilot schools”) for improving pedagogy, these have led to true changes in teaching practices. Many teachers adopted student-centred and collaborative, inquiry-oriented teaching practices as well as practices that supported students' authentic activities, independent work, knowledge building, and students' responsibility. This is, indeed, strongly dependent on the ICT-related pedagogical competence of the teacher. However, the daily practices of some teachers still reflected a rather traditional teacher-centred approach. As a matter of fact, very few teachers ever represented solely, e.g. the knowledge building approach; teachers used various approaches or mixed them, based on the situation, teaching and learning goals, and on their pedagogical and technical competence. In general, changes towards pedagogical improvements even in wellorganised developmental projects are slow. As a result, there are two kinds of ICT stories: successful “ICT pilot schools” with pedagogical innovations related to ICT and with school community level agreement about the visions and aims, and “ordinary schools”, which have no particular interest in or external support for using ICT for improvement, and in which ICT is used in a more routine way, and as a tool for individual teachers, not for the school community.

Photoelectric Measurements and Modeling of Bacteriorhodopsin

Recent technology has provided us with new information about the internal structures and properties of biomolecules. This has lead to the design of applications based on underlying biological processes. Applications proposed for biomolecules are, for example, the future computers and different types of sensors. One potential biomolecule to be incorporated in the applications is bacteriorhodopsin. Bacteriorhodopsin is a light-sensitive biomolecule, which works in a similar way as the light sensitive cells of the human eye. Bacteriorhodopsin reacts to light by undergoing a complicated series of chemical and thermal transitions. During these transitions, a proton translocation occurs inside the molecule. It is possible to measure the photovoltage caused by the proton translocations when a vast number of molecules is immobilized in a thin film. Also the changes in the light absorption of the film can be measured. This work aimed to develop the electronics needed for the voltage measurements of the bacteriorhodopsin-based optoelectronic sensors. The development of the electronics aimed to get more accurate information about the structure and functionality of these sensors. The sensors used in this work contain a thick film of bacteriorhodopsin immobilized in polyvinylalcohol. This film is placed between two transparent electrodes. The result of this work is an instrumentation amplifier which can be placed in a small space very close to the sensor. By using this amplifier, the original photovoltage can be measured in more detail. The response measured using this amplifier revealed two different components, which could not be distinguished earlier. Another result of this work is the model for the photoelectric response in dry polymer films.

Use of the Optical Cantilever Microphone in Photoacoustic Spectroscopy

A novel cantilever pressure sensor was developed in the Department of Physics at the University of Turku in order to solve the sensitivity problems which are encountered when condenser microphones are used in photoacoustic spectroscopy. The cantilever pressure sensor, combined with a laser interferometer for the measurement of the cantilever movements, proved to be highly sensitive. The original aim of this work was to integrate the sensor in a photoacoustic gas detector working in a differential measurement scheme. The integration was made successfully into three prototypes. In addition, the cantilever was also integrated in the photoacoustic FTIR measurement schemes of gas-, liquid-, and solid-phase samples. A theoretical model for the signal generation in each measurement scheme was created and the optimal celldesign discussed. The sensitivity and selectivity of the differential method were evaluated when a blackbody radiator and a mechanical chopper were used with CO₂, CH4, CO, and C2H4 gases. The detection limits were in the sub-ppm level for all four gases with only a 1.3 second integration time and the cross interference was well below one percent for all gas combinations other than those between hydrocarbons. Sensitivity with other infrared sources was compared using ethylene as an example gas. In the comparison of sensitivity with different infrared sources the electrically modulated blackbody radiator gave a 35 times higher and the CO2-laser a 100 times lower detection limit than the blackbody radiator with a mechanical chopper. As a conclusion, the differential system is well suited to rapid single gas measurements. Gas-phase photoacoustic FTIR spectroscopy gives the best performance, when several components have to be analyzed simultaneously from multicomponent samples. Multicomponent measurements were demonstrated with a sample that contained different concentrations of CO₂, H₂O, CO, and four different hydrocarbons. It required an approximately 10 times longer measurement time to achieve the same detection limit for a single gas as with the differential system. The properties of the photoacoustic FTIR spectroscopy were also compared to conventional transmission FTIR spectroscopy by simulations. Solid- and liquid-phase photoacoustic FTIR spectroscopy has several advantages compared to other techniques and therefore it also has a great variety of applications. A comparison of the signal-to-noise ratio between photoacoustic cells with a cantilever microphone and a condenser microphone was done with standard carbon black, polyethene, and sunflower oil samples. The cell with the cantilever microphone proved to have a 5-10 times higher signal-to-noise ratio than the reference detector, depending on the sample. Cantilever enhanced photoacoustics will be an effective tool for gas detection and analysis of solid- and liquid-phase samples. The preliminary prototypes gave good results in all three measurement schemes that were studied. According to simulations, there are possibilities for further enhancement of the sensitivity, as well as other properties, of each system.

Online Ultrasound Measurements of Membrane Compaction

There are several filtration applications in the pulp and paper industry where the capacity and cost-effectiveness of processes are of importance. Ultrafiltration is used to clean process water. Ultrafiltration is a membrane process that separates a certain component or compound from a liquid stream. The pressure difference across the membrane sieves macromolecules smaller than 0.001-0.02 μm through the membrane. When optimizing the filtration process capacity, online information about the conditions of the membrane is needed. Fouling and compaction of the membrane both affect the capacity of the filtration process. In fouling a “cake” layer starts to build on the surface of the membrane. This layer blocks the molecules from sieving through the membrane thereby decreasing the yield of the process. In compaction of the membrane the structure is flattened out because of the high pressure applied. The higher pressure increases the capacity but may damage the structure of the membrane permanently. Information about the compaction is needed to effectively operate the filters. The objective of this study was to develop an accurate system for online monitoring of the condition of the membrane using ultrasound reflectometry. Measurements of ultrafiltration membrane compaction were made successfully utilizing ultrasound. The results were confirmed by permeate flux decline, measurements of compaction with a micrometer, mechanical compaction using a hydraulic piston and a scanning electron microscope (SEM). The scientific contribution of this thesis is to introduce a secondary ultrasound transducer to determine the speed of sound in the fluid used. The speed of sound is highly dependent on the temperature and pressure used in the filters. When the exact speed of sound is obtained by the reference transducer, the effect of temperature and pressure is eliminated. This speed is then used to calculate the distances with a higher accuracy. As the accuracy or the resolution of the ultrasound measurement is increased, the method can be applied to a higher amount of applications especially for processes where fouling layers are thinner because of smaller macromolecules. With the help of the transducer, membrane compaction of 13 μm was measured in the pressure of 5 bars. The results were verified with the permeate flux decline, which indicated that compaction had taken place. The measurements of compaction with a micrometer showed compaction of 23–26 μm. The results are in the same range and confirm the compaction. Mechanical compaction measurements were made using a hydraulic piston, and the result was the same 13 μm as obtained by applying the ultrasound time domain reflectometry (UTDR). A scanning electron microscope (SEM) was used to study the structure of the samples before and after the compaction.

Application and validation of a warning system for grapevine downy mildew controlusing fungicides

Most warning systems for plant disease control are based on Vinho, in Bento Gonçalves - RS, during the growing seasons 2000/ weather models dependent on the relationships between leaf wetness 01, 2002/03 and 2003/2004, using the grape cultivar Isabel. The duration and mean air temperature in this period considering the conventional system used by local growers was compared with the target disease intensity. For the development of a warning system to new warning system by using different cumulative daily disease severity control grapevine downy mildew, the equation generated by Lalancette values (CDDSV) as the criterion to schedule fungicide application and et al. (7) was used. This equation was employed to elaborate a critical reapplication. In experiments conducted in 2003/04, CDDSV of 12 - period table and program a computerized device, which records, though 14 showed promising to schedule the first spraying and the interval electronic sensors, leaf wetness duration, mean temperature in this between fungicide applications, reducing by 37.5% the number of period and automatically calculates the daily value of probability of applications and maintaining the same control efficiency in leaves infection occurrence. The system was validated at Embrapa Uva e and bunches, similarly to the conventional system.

Structural and operational optimisation : applications in energy systems

In this work mathematical programming models for structural and operational optimisation of energy systems are developed and applied to a selection of energy technology problems. The studied cases are taken from industrial processes and from large regional energy distribution systems. The models are based on Mixed Integer Linear Programming (MILP), Mixed Integer Non-Linear Programming (MINLP) and on a hybrid approach of a combination of Non-Linear Programming (NLP) and Genetic Algorithms (GA). The optimisation of the structure and operation of energy systems in urban regions is treated in the work. Firstly, distributed energy systems (DES) with different energy conversion units and annual variations of consumer heating and electricity demands are considered. Secondly, district cooling systems (DCS) with cooling demands for a large number of consumers are studied, with respect to a long term planning perspective regarding to given predictions of the consumer cooling demand development in a region. The work comprises also the development of applications for heat recovery systems (HRS), where paper machine dryer section HRS is taken as an illustrative example. The heat sources in these systems are moist air streams. Models are developed for different types of equipment price functions. The approach is based on partitioning of the overall temperature range of the system into a number of temperature intervals in order to take into account the strong nonlinearities due to condensation in the heat recovery exchangers. The influence of parameter variations on the solutions of heat recovery systems is analysed firstly by varying cost factors and secondly by varying process parameters. Point-optimal solutions by a fixed parameter approach are compared to robust solutions with given parameter variation ranges. In the work enhanced utilisation of excess heat in heat recovery systems with impingement drying, electricity generation with low grade excess heat and the use of absorption heat transformers to elevate a stream temperature above the excess heat temperature are also studied.

Towards combining interactive mobile TV and smart spaces : architectures, tools and application development

Technological developments in microprocessors and ICT landscape have made a shift to a new era where computing power is embedded in numerous small distributed objects and devices in our everyday lives. These small computing devices are ne-tuned to perform a particular task and are increasingly reaching our society at every level. For example, home appliances such as programmable washing machines, microwave ovens etc., employ several sensors to improve performance and convenience. Similarly, cars have on-board computers that use information from many di erent sensors to control things such as fuel injectors, spark plug etc., to perform their tasks e ciently. These individual devices make life easy by helping in taking decisions and removing the burden from their users. All these objects and devices obtain some piece of information about the physical environment. Each of these devices is an island with no proper connectivity and information sharing between each other. Sharing of information between these heterogeneous devices could enable a whole new universe of innovative and intelligent applications. The information sharing between the devices is a diffcult task due to the heterogeneity and interoperability of devices. Smart Space vision is to overcome these issues of heterogeneity and interoperability so that the devices can understand each other and utilize services of each other by information sharing. This enables innovative local mashup applications based on shared data between heterogeneous devices. Smart homes are one such example of Smart Spaces which facilitate to bring the health care system to the patient, by intelligent interconnection of resources and their collective behavior, as opposed to bringing the patient into the health system. In addition, the use of mobile handheld devices has risen at a tremendous rate during the last few years and they have become an essential part of everyday life. Mobile phones o er a wide range of different services to their users including text and multimedia messages, Internet, audio, video, email applications and most recently TV services. The interactive TV provides a variety of applications for the viewers. The combination of interactive TV and the Smart Spaces could give innovative applications that are personalized, context-aware, ubiquitous and intelligent by enabling heterogeneous systems to collaborate each other by sharing information between them. There are many challenges in designing the frameworks and application development tools for rapid and easy development of these applications. The research work presented in this thesis addresses these issues. The original publications presented in the second part of this thesis propose architectures and methodologies for interactive and context-aware applications, and tools for the development of these applications. We demonstrated the suitability of our ontology-driven application development tools and rule basedapproach for the development of dynamic, context-aware ubiquitous iTV applications.

Design of RFID-system for industrial after-sale service

RFID-tekniikka on radiotaajuudella toimivaa etätunnistusta, jossa hyödynnetään RFID-tunnisteiksi kutsuttuja tageja, sekä RFID-lukijoita. RFID-tekniikan käyttökohteet ovat erittäin laajat. Tässä kandidaatintyössä tutkitaan RFID-tekniikan hyödyntämismahdollisuuksia teollisuuden huoltopalvelusuhteessa. Työ keskittyy huollettavien laitteiden etätunnistamiseen mobiileja RFID-lukijoita hyödyntäen. Laitteiden tiedot noudetaan olemassa olevasta tietokannasta web-käyttöliittymän kautta. Koska laitteet koostuvat pääosin metallista, joudutaan tunnistetyyppien valintaa pohtimaan tarkasti. Metallipinnat sekä nesteet vaikuttavat erittäin negatiivisesti useiden tunnisteiden lukuetäisyyteen. Työssä keskitytään vaadittavan järjestelmän suunnittelemiseen aikaisempia tutkimuksia hyödyntäen, mutta itse järjestelmän toteutus ei kuulu tähän kandidaatintyöhön. Lopussa järjestelmän alustava suunnitelma esitellään.

Application of cutting fluids in machining processes

In the last decade a lot has been discussed about the suitability of using cutting fluid in abundance to cool and lubricate machining processes. The use of cutting fluid generally causes economy of tools and it becomes easier to keep tight tolerances and to maintain workpiece surface properties without damages. In the other hand, it brings also some problems, like fluid residuals and human diseases. Because of them some alternatives has been sought to minimise or even avoid the use of cutting fluid in machining operations. Some of these alternatives are dry cutting and cutting with minimum quantity of fluid (MQF). The main goal of this work is to discuss these tendencies. Therefore, topics like kinds and methods of applications of modern cutting fluids and what are new in this area will unavoidably be considered. MQF and dry cutting techniques, their applications and where it is not possible to apply them will also be focused. To exemplify the topics, this work will describe some of the researches been developed in two important Brazilian Universities: State University of Campinas (UNICAMP) and Federal University of Uberlândia (UFU).

Methods of genetic diversity creation and functional display for directed evolution experiments

Protein engineering aims to improve the properties of enzymes and affinity reagents by genetic changes. Typical engineered properties are affinity, specificity, stability, expression, and solubility. Because proteins are complex biomolecules, the effects of specific genetic changes are seldom predictable. Consequently, a popular strategy in protein engineering is to create a library of genetic variants of the target molecule, and render the population in a selection process to sort the variants by the desired property. This technique, called directed evolution, is a central tool for trimming protein-based products used in a wide range of applications from laundry detergents to anti-cancer drugs. New methods are continuously needed to generate larger gene repertoires and compatible selection platforms to shorten the development timeline for new biochemicals. In the first study of this thesis, primer extension mutagenesis was revisited to establish higher quality gene variant libraries in Escherichia coli cells. In the second study, recombination was explored as a method to expand the number of screenable enzyme variants. A selection platform was developed to improve antigen binding fragment (Fab) display on filamentous phages in the third article and, in the fourth study, novel design concepts were tested by two differentially randomized recombinant antibody libraries. Finally, in the last study, the performance of the same antibody repertoire was compared in phage display selections as a genetic fusion to different phage capsid proteins and in different antibody formats, Fab vs. single chain variable fragment (ScFv), in order to find out the most suitable display platform for the library at hand. As a result of the studies, a novel gene library construction method, termed selective rolling circle amplification (sRCA), was developed. The method increases mutagenesis frequency close to 100% in the final library and the number of transformants over 100-fold compared to traditional primer extension mutagenesis. In the second study, Cre/loxP recombination was found to be an appropriate tool to resolve the DNA concatemer resulting from error-prone RCA (epRCA) mutagenesis into monomeric circular DNA units for higher efficiency transformation into E. coli. Library selections against antigens of various size in the fourth study demonstrated that diversity placed closer to the antigen binding site of antibodies supports generation of antibodies against haptens and peptides, whereas diversity at more peripheral locations is better suited for targeting proteins. The conclusion from a comparison of the display formats was that truncated capsid protein three (p3Δ) of filamentous phage was superior to the full-length p3 and protein nine (p9) in obtaining a high number of uniquely specific clones. Especially for digoxigenin, a difficult hapten target, the antibody repertoire as ScFv-p3Δ provided the clones with the highest affinity for binding. This thesis on the construction, design, and selection of gene variant libraries contributes to the practical know-how in directed evolution and contains useful information for scientists in the field to support their undertakings.

Effect of zone and crops rotation on Ischaemum rugosum and resistance to bispyribac-sodium in Ariari, Colombia

The objectives of this research were to evaluate (1) weed species presented in rice fields in relation to the geographical zone and crop rotation and (2) the resistance level of Ischaemum rugosum to the herbicide bispyribac-sodium. For the first objective, were sampled 79 commercial fields of rice to establish weed density, coverage, and rotation system in the evaluated fields with record of bispyribac-sodium application of at least five years. To reach the second objective, the seeds were collected from plants in commercial fields with different control levels of bispyribac-sodium herbicide. Seeds were germinated in trays under controlled conditions. When plants presented three leaves these were treated with bispyribac-sodium at different doses. Percentages of control and dry weight of plants were evaluated 12 days after treatments (dat). Dominant species in evaluated fields was I. rugosum, with a frequency of 100%, presenting escapes to different chemical commercial treatments. No significant differences were recorded between rotation systems, nevertheless, the most of I. rugosum population was found in the system rice-fallow-rice. The response of applications at different concentrations allows concluding that 65% of samples had resistance at different degrees reported as indexes from 2 to 42 which are related to rotation systems.

EFFECT OF TRINEXAPAC-ETHYL ON GROWTH AND YIELD OF SUGARCANE

ABSTRACT Growth regulators can be used to further retard or inhibit vegetative growth. In this sense, the objective of this study was to determine the effects of age and number of trinexapac-ethyl applications on the growth and yield of sugarcane. The experiment was in a randomized complete block design with four replications. The treatments were in a 3 x 2 + 2 factorial arrangement, where factor A corresponded to the application times of the plant growth regulator (120, 200 and 240 days after bud burst (DAB) of sugarcane) and factor B to the number of applications (one or two applications). In addition, two controls (one with three applications and another application without the regulator) were added. The application of trinexapac-ethyl decreased the number and the distance between buds, height, root volume and sugarcane yield. The sequential application (2 or 3 times) induced an increase in stem diameter and three applications of the product increased the number of plant tillers. The use of growth regulators applied at 240 DAB has reduced plant height, however without changing the number of buds. It can be concluded that trinexapac-ethyl changes sugarcane growth and yield, regardless of season and number of applications.

Integration of JINR Information Resources

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014