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The shape of the combustion chamber plays an important role in the formation of the air-fuel mixture in the chamber, which has a great influence on the combustion efficiency and emission formation. The pip is a protruding shape at the center of the combustion chamber, and its importance has been evaluated to be relatively low. There has also been little research on off-highway diesel engines in comparison with on-highway diesel engines. When a high-pressure injection system is used in an off-highway diesel engine, which injects more fuel than on-highway engines, the shape of the pip greatly affects the mixture spray momentum and air flow in the combustion chamber. In this study, the pip geometry of a 2.4-liter off-highway engine was modified using three shapes: a step cone, W shape, and egg shape. We used 3-D combustion simulations to analyze the effects of the pip geometry on the mixture formation and combustion efficiency. We also analyzed the influence of the height and corner angle of the pip on the combustion and emission based on the egg shape, which was the most efficient. The results of this study could be used as a guide in designing combustion chambers for diesel engines. [ABSTRACT FROM AUTHOR]

In this paper, we address the problem of boundary image matching that supports symmetric invariance. Supporting the symmetric invariance is an important factor to provide more intuitive and more correct results in boundary image matching. Previous boundary image matching methods, however, deal with mainly image rotations without consideration of symmetric transformations. In this paper, we propose a time-series-based boundary image matching that supports the symmetric invariance as well as the previous rotation invariance. For this, we first formally define the concept of a boundary time-series and its symmetric time-series. We then present a novel notion of symmetric-rotation property that the rotation-invariant matching result is always the same for all possible symmetric angles. We next discuss how to efficiently extract a symmetric time-series from an image boundary by presenting the domain independent property that both time-series domain and image domain methods produce the same symmetric time-series. Experimental results show that the proposed symmetric-invariant matching provides the more intuitive result compared with the previous rotation-invariant matching. To our best knowledge, this is the first attempt that solves the symmetric-invariant boundary matching problem in the simple time-series domain rather than in the complex image domain. [ABSTRACT FROM AUTHOR]

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We report a surface passivation method based on dichlorodimethylsilane (DDS)-Tween-20 for in vitro single-molecule studies, which, under the conditions tested here, more efficiently prevented nonspecific binding of biomolecules than the standard poly(ethylene glycol) surface. The DDS-Tween-20 surface was simple and inexpensive to prepare and did not perturb the behavior and activities of tethered biomolecules. It can also be used for single-molecule imaging in the presence of high concentrations of labeled species in solution. [ABSTRACT FROM AUTHOR]

The assembly of 30S ribosomes requires the precise addition of 20 proteins to the 16S ribosomal RNA. How early binding proteins change the ribosomal RNA structure so that later proteins may join the complex is poorly understood. Here we use single-molecule fluorescence resonance energy transfer (FRET) to observe real-time encounters between Escherichia coli ribosomal protein S4 and the 16S 5′ domain RNA at an early stage of 30S assembly. Dynamic initial S4-RNA complexes pass through a stable non-native intermediate before converting to the native complex, showing that non-native structures can offer a low free-energy path to protein-RNA recognition. Three-colour FRET and molecular dynamics simulations reveal how S4 changes the frequency and direction of RNA helix motions, guiding a conformational switch that enforces the hierarchy of protein addition. These protein-guided dynamics offer an alternative explanation for induced fit in RNA-protein complexes. [ABSTRACT FROM AUTHOR]

Sequence recognition through base-pairing is essential for DNA repair and gene regulation, but the basic rules governing this process remain elusive. In particular, the kinetics of annealing between two imperfectly matched strands is not well characterized, despite its potential importance in nucleic acid-based biotechnologies and gene silencing. Here we use single-molecule fluorescence to visualize the multiple annealing and melting reactions of two untethered strands inside a porous vesicle, allowing us to precisely quantify the annealing and melting rates. The data as a function of mismatch position suggest that seven contiguous base pairs are needed for rapid annealing of DNA and RNA. This phenomenological rule of seven may underlie the requirement for seven nucleotides of complementarity to seed gene silencing by small noncoding RNA and may help guide performance improvement in DNA- and RNA-based bio- and nanotechnologies, in which off-target effects can be detrimental. [ABSTRACT FROM AUTHOR]

Controlling efficiency and fidelity in the early stage of mitochondrial DNA transcription is crucial for regulating cellular energy metabolism. Conformational transitions of the transcription initiation complex must be central for such control, but how the conformational dynamics progress throughout transcription initiation remains unknown. Here, we use single-molecule fluorescence resonance energy transfer techniques to examine the conformational dynamics of the transcriptional system of yeast mitochondria with single-base resolution. We show that the yeast mitochondrial transcriptional complex dynamically transitions among closed, open, and scrunched states throughout the initiation stage. Then abruptly at position +8, the dynamic states of initiation make a sharp irreversible transition to an unbent conformation with associated promoter release. Remarkably, stalled initiation complexes remain in dynamic scrunching and unscrunching states without dissociating the RNA transcript, implying the existence of backtracking transitions with possible regulatory roles. The dynamic landscape of transcription initiation suggests a kinetically driven regulation of mitochondrial transcription. Conformational dynamics during the early stage of transcription is crucial to understanding the regulation of transcription efficiency and fidelity. Here the authors, by single-molecule fluorescence resonance energy transfer approaches, examine the conformational dynamics of the two-component transcription system of yeast mitochondria with single-base resolution. [ABSTRACT FROM AUTHOR]

Replication-Factor-C (RFC) and RFC-like complexes (RLCs) mediate chromatin engagement of the proliferating cell nuclear antigen (PCNA). It remains controversial how RFC and RLCs cooperate to regulate PCNA loading and unloading. Here, we show the distinct PCNA loading or unloading activity of each clamp loader. ATAD5-RLC possesses the potent PCNA unloading activity. ATPase motif and collar domain of ATAD5 are crucial for the unloading activity. DNA structures did not affect PCNA unloading activity of ATAD5-RLC. ATAD5-RLC could unload ubiquitinated PCNA. Through single molecule measurements, we reveal that ATAD5-RLC unloaded PCNA through one intermediate state before ATP hydrolysis. RFC loaded PCNA through two intermediate states on DNA, separated by ATP hydrolysis. Replication proteins such as Fen1 could inhibit the PCNA unloading activity of Elg1-RLC, a yeast homolog of ATAD5-RLC in vitro. Our findings provide molecular insights into how PCNA is released from chromatin to finalize DNA replication/repair. Replication-Factor-C (RFC) and RFC-like complexes (RLCs) mediate chromatin engagement of the proliferating cell nuclear antigen (PCNA). Here authors use biochemical and single molecule measurements to show that ATAD5-RLC has the most potent PCNA unloading activity and forms structurally distinct intermediates compared to RFC-PCNA. [ABSTRACT FROM AUTHOR]