Thesis (Ph. D.)--Ohio State University, 2007. / Full text release at OhioLINK's ETD Center delayed at author's request

Proliferating cell nuclear antigen (PCNA) is a key factor involved in Eukaryotic DNA replication and repair, as well as other cellular pathways. Its importance comes mainly from two aspects: the large numbers of interacting partners and the mechanism of facilitated diffusion along the DNA. The large numbers of interacting partners makes PCNA a necessary factor to consider when studying DNA replication, either in vitro or in vivo. The mechanism of facilitated diffusion along the DNA, i.e. sliding along the duplex, reduces the six degrees of freedom of the molecule, three degrees of freedom of translation and three degrees of freedom of rotation, to only two, translation along the duplex and rotational tracking of the helix. Through this mechanism PCNA can recruit its partner proteins and localize them to the right spot on the DNA, maybe in the right spatial orientation, more effectively and in coordination with other proteins. Passive loading of the closed PCNA ring on the DNA without free ends is a topologically forbidden process. Replication factor C (RFC) uses energy of ATP hydrolysis to mechanically open the PCNA ring and load it on the dsDNA. The first half of the introduction gives overview of PCNA and RFC and the loading mechanism of PCNA on dsDNA. The second half is dedicated to a diffusion model and to an algorithm for analyzing PCNA sliding. PCNA and RFC were successfully purified, simulations and a mean squared displacement analysis algorithm were run and showed good stability and experimental PCNA sliding data was analyzed and led to parameters similar to the ones in literature.

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DNA encodes the genetic information of the cell, therefore, every single living organism has a precise DNA damage response mechanism to safeguard DNA integrity. Base mismatches are endogenous DNA lesions introduced by the replicative polymerase during DNA replication. The conserved DNA mismatch repair pathway corrects these base mismatches. Mismatch repair initiation is orchestrated by two proteins, MutS and MutL. MutS recognizes and binds to base mismatches and relays the presence of the lesion to MutL. MutL, in turn, interacts with downstream factors to coordinate mismatch excision. The processivity clamp, typically known for its role in tethering the DNA polymerase to DNA during replication, is also involved in several steps of this repair process including MutL endonuclease activation and strand resynthesis. The dynamics of the MutS-MutL and MutL-processivity clamp interactions present one of the bottlenecks to uncovering the spatial and time organization of these protein assemblies. Therefore, little is known about the interactions that orchestrate the early steps of mismatch repair. The biochemical and structural work included in this thesis outlines a precise series of molecular cues that activate MutL. / Thesis / Doctor of Philosophy (PhD)

This report evaluates the option of using an equal slip controller, an effective rolling radius and rolling resistance force observer in a 4WD wheel loader. The vehicle studied is an under development- vehicle designed by Volvo CE. A wheel loader is an over actuated, articulated vehicle that is mainly used with low velocities in construction operations. The efficiency subject has been studied earlier by many manufacturers in order to analyze the environmental and economical losses and profits. This has provided research opportunities of optimizing efficiency of different kinds. Since the tire is the only part of a vehicle that is in contact with the ground, the characteristic of the tire effects the dynamics. The analysis shows that the efficiency of a tire is directly connected to the slip ratio which in turn is a component of the overall efficiency ratio. Studies show that the slip ratio should be controlled in such a way that the highest value of efficiency rate is obtained. This optimal value is dependent on all four wheel’s slip conditions. Therefore a strategy should be formulated in order to apply changes to all wheels and not only one. Further analysis shows that the maximum efficiency in a 4WD wheel loader is obtained when the vehicle runs in such a way that the slip ratio is equal for all wheels. I order to maintain same amount of slip for all wheels a control strategy is required. In the control strategy the current amount of slip of each wheel is determined. Further, the average value of slip ratio is calculated. Finally the equal amount of slip is achieved using corresponding optimal torque inputs for each individual wheel. Thus a stable, robust controller is required. The controller used to achieve this goal is a sliding mode controller that is popular among control engineers for its stability, robustness against uncertainties, speed and easy implementation. For an accurate control, states of the rolling resistance and the effective rolling radius need to be determined. The pressure acting on the tire will cause deformation on the tire itself. This leads to a dynamic radius of the tire. This deformation is highly dependent on vertical stress and the structure of tire. Further more velocity, inflation pressure, vertical load etc. also have effect on rolling resistance. Rolling resistance has a great impact on the fuel consumption of the vehicle and the driving characteristics. These estimated variations of effective radius and rolling resistance build a feedback system to the controller which in turn derives the system to the desired slip ratio. As it turns out, the slip efficiency is increased using an equal slip controller. However, it is highly dependent on the ratio of thrust between front and rear wheels. / Denna rapport utvärderar möjligheten att använda en olinjär regulator i syfte att sätta lika stor ’slip’ på fordonets alla fyra hjul. Vidare ska en olinjär observerare modelleras för att uppskatta den så kallad hjulets effektiva radie samt rollmoståndskraften som verkar på däcket. Det studerade fordonet är en hjullastare konstruerad av Volvo CE och som i nuläget är under utveckling. En hjullastare är ett overmanövrerat fordon som huvudsakligen används i låga hastigheter i bygg- och transportverksamheter. Effektivitet är ett ämne som har studerats tidigare av många tillverkare för att analysera miljörelaterade och ekonomiska förluster och vinster. Detta har gett forskarna möjligheten att studera effektivitet av olika slag. Eftersom däcket är den enda delen av ett fordon som kommer i kontakt med marken, påverkar dess karaktär fordonets dynamika beteende i helhet. Analysen visar att däckets effektivitet är direkt kopplad till slipförhållande som i sin tur är en del av det totala effektivitetsförhållandet. Studier visar att slipförhållandet bör kontrolleras på ett sådant sätt att det högsta värdet av effektivitet uppnås. Detta optimala värde är beroende av slipförhållanden hos alla fyra hjul och därför bör en strategi formuleras för att nå optimalt slipeffektivitet på alla hjul. Ytterligare analys visar att maximal slipeffektivitet i en 4WD hjullastare erhålls när fordonet går så att slipförhållandet är lika för alla hjul. I kontrollstrategin bestäms det nuvarande slipförhållandet för varje hjul. Av dessa beräknas medelvärdet som skall presentera referensvärdet av slipförhållandet. Slutligen upp-nås detta värde med motsvarande optimala momentinmatningar för varje enskilt hjul. Styralgoritmen som används för att uppnå detta mål är en Sliding mode regulator som är populär bland kontrollingenjörer för dess stabilitet, robusthet mot osäkerhet, snabbhet och enkel implementering. För en noggrann kontroll måste tillstånden av rullmotståndskraften och effektiv rull-radien observeras. De verkande krafterna på hjulet orsakar deformation på däcket som ger upphov till däckets dynamiska radie. Denna deformation är starkt beroende av vertikal spänning och däckets struktur. Vidare har hastighet, däckets lufttryck, vertikal belastning etc. också effekt på rullmotståndskraften. Rullmotstånd har stor inverkan på fordonets bränsleförbrukning och drivegenskaper. Dessa variationer av effektivradie och rullmotstånd bygger ett återkopplat system till regulatorn som i sin tur leder systemet till önskat slipförhållande. Som det visar sig, ökar slipeffektiviteten med hjälp av "equal slip" styralgoritm. Detta är emellertid mycket beroende av förhållandet av momentinmatningar mellan fram och bakhjulet.

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This thesis is divided in two parts. The first part is devoted to the micro-macro modeling of the behavior of concrete under cyclic loading. Correlations between microscopic (frictional sliding of mesocracks) and macroscopic (energy dissipation) properties are investigated. The second part focuses on the description of a series of uniaxial cyclic tests on concrete and concrete-like materials performed in the "Rock Mechanics Laboratory" of Virginia Polytechnic Institute and State University, Virginia, USA. Data deriving from these experiments are analyzed on the basis of the micro-macro identification theory. Interesting predictions of the real mechanical behavior of concrete can be found by means of the aforementioned theory and are presented in the last part of the thesis. / Master of Science