41 research outputs found

    PRACTICE OF CAD AND CAE DESIGN IN THE FIELD OF PLASMA TECHNOLOGIES

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    The effectiveness of automated plasma torch design methods can be improved by integrating design and engineering analysis technologies. The features of CAD and CAE technologies for designing plasma torches are considered. Shows examples of the design of plasma torches for cutting metals and waste treatment with the use of digital technologies.Эффективность автоматизированных методов проектирования плазмотронов можно повысить за счет интеграции технологий проектирования и инженерного анализа. Рассмотрены особенности CAD и CAE технологий проектирования плазмотронов. Показаны примеры проектирования плазмотронов для резки металлов и обезвреживания отходов с применением цифровых технологий

    Structural Characterization and Function Prediction of Immunoglobulin-like Fold in Cell Adhesion and Cell Signaling

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    Domains that belong to an immunoglobulin (Ig) fold are extremely abundant in cell surface receptors, which play significant roles in cell–cell adhesion and signaling. Although the structures of domains in an Ig fold share common topology of β-barrels, functions of receptors in adhesion and signaling are regulated by the very heterogeneous binding between these domains. Additionally, only a small number of domains are directly involved in the binding between two multidomain receptors. It is challenging and time consuming to experimentally detect the binding partners of a given receptor and further determine which specific domains in this receptor are responsible for binding. Therefore, current knowledge in the binding mechanism of Ig-fold domains and their impacts on cell adhesion and signaling is very limited. A bioinformatics study can shed light on this topic from a systematic point of view. However, there is so far no computational analysis on the structural and functional characteristics of the entire Ig fold. We constructed nonredundant structural data sets for all domains in Ig fold, depending on their functions in cell adhesion and signaling. We found that data sets of domains in adhesion receptors show different binding preference from domains in signaling receptors. Using structural alignment, we further built a common structural template for each group of a domain data set. By mapping the protein–protein binding interface of each domain in a group onto the surface of its structural template, we found binding interfaces are highly overlapped within each specific group. These overlapped interfaces, we called consensus binding interfaces, are distinguishable among different data sets of domains. Finally, the residue compositions on the consensus interfaces were used as indicators for multiple machine learning algorithms to predict if they can form homotypic interactions with each other. The overall performance of the cross-validation tests shows that our prediction accuracies ranged between 0.6 and 0.8

    To evaluate how spatial organization of a multi-specific ligand affects its binding with receptors, we fixed the binding affinity between receptor C and ligand D as -9kT.

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    <p>The affinity between receptor A and ligand B were changed from -5kT (black), -7kT (red) to -9kT (blue). The simulation results for the first scenario are shown in <b>(a)</b> and <b>(b)</b>; the simulation results for the second scenario are shown in <b>(c)</b> and <b>(d)</b>; and the simulation results for the third scenario are shown in <b>(e)</b> and <b>(f)</b>. The figure indicates that when ligands B and D are tethered, the interaction between receptor C and ligand D can be affected by the interaction between receptor A and ligand B, although the CD affinity remains unchanged.</p

    Wnt stimulation and β-catenin degradation module.

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    <p>The module is divided into four parts: <b>a)</b> (1) formation of destruction complex and retention of β-catenins by APC and Axin; (2) destruction complex cycle; <b>b)</b> (3) Wnt stimulation and (4) Wnt signal transduction.</p

    Design, Synthesis, and Isomerization Studies of Light-Driven Molecular Motors for Single Molecular Imaging

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    The design of a multicomponent system that aims at the direct visualization of a synthetic rotary motor at the single molecule level on surfaces is presented. The synthesis of two functional motors enabling photochemical rotation and fluorescent detection is described. The light-driven molecular motor is found to operate in the presence of a fluorescent tag if a rigid long rod (32 Å) is installed between both photoactive moieties. The photochemical isomerization and subsequent thermal helix inversion steps are confirmed by <sup>1</sup>H NMR and UV–vis absorption spectroscopies. In addition, the tetra-acid functioned motor can be successfully grafted onto amine-coated quartz and it is shown that the light responsive rotary motion on surfaces is preserved

    We changed the relative concentrations of two receptors on cell surfaces.

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    <p>The second scenario was applied, in which the total number of receptor A was fixed and the total number of receptor C was changed from 0 to 100. We first fixed both AB and CD binding affinities <b>(a)</b>. The figure shows that higher surface densities of receptors C lead to more interactions between receptor A and its ligand. In the second test <b>(b)</b>, we changed the affinity between receptor A and ligand B from -7kT to -11kT. The x index of the figure is the number of receptors C on cell surfaces. The relative increment of AB interactions between 0 and a given concentration of receptors C is recorded in the y axis. The simulation results of the figure demonstrate that the ligands with reduced affinity have higher specificity to distinguish different types of cells based on the concentrations of their receptors.</p

    In order to investigate the functional role of binding site organization, four different topologies were designed.

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    <p>Each topology includes two ligands B and two ligands D, as shown in the bottom row. The binding of all four types of topology were simulated. The average numbers of interactions between ligands and receptors are plotted as striped bars, while the deviations in total number of interactions are plotted as black bars. The first two topologies show similar average and deviation. Moreover, the fourth model has higher deviations than the third model, although they have very close average number of interactions.</p

    The 2D phase diagram gives the number of ABC in cytoplasm under different adhesion condition after 0.5 hr Wnt treatment.

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    <p>The diagram is plotted along the ratio between numbers of Cad/Cat in “<i>cis</i>” and “<i>trans</i>” statues (Y/X), and the ratio between number of Cad/Cat in “<i>trans</i>” and “free” status (X). The value of each point is the average of 50 simulation trajectories. The figure illustrates that cell adhesion negatively contributes to Wnt signaling through competition for cytoplasmic ABCs.</p

    The overall representation of our network model.

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    <p>There are three modules in the network. These modules are connected by two distinctive forms of β-catenin. In additional to the normal form of β-catenins, a second form, active β-catenin, is presented in our model. Only the active β-catenins can activate the gene expression. The activated genetic pathways further affect expressions of proteins in both cadherin adhesion and β-catenin degradation modules through genetic feedback loops. The interplay between Wnt signaling and cell adhesion is captured by inter-module crosstalk, which are labeled with numbers.</p

    Multiscale Model for the Assembly Kinetics of Protein Complexes

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    The assembly of proteins into high-order complexes is a general mechanism for these biomolecules to implement their versatile functions in cells. Natural evolution has developed various assembling pathways for specific protein complexes to maintain their stability and proper activities. Previous studies have provided numerous examples of the misassembly of protein complexes leading to severe biological consequences. Although the research focusing on protein complexes has started to move beyond the static representation of quaternary structures to the dynamic aspect of their assembly, the current understanding of the assembly mechanism of protein complexes is still largely limited. To tackle this problem, we developed a new multiscale modeling framework. This framework combines a lower-resolution rigid-body-based simulation with a higher-resolution Cα-based simulation method so that protein complexes can be assembled with both structural details and computational efficiency. We applied this model to a homotrimer and a heterotetramer as simple test systems. Consistent with experimental observations, our simulations indicated very different kinetics between protein oligomerization and dimerization. The formation of protein oligomers is a multistep process that is much slower than dimerization but thermodynamically more stable. Moreover, we showed that even the same protein quaternary structure can have very diverse assembly pathways under different binding constants between subunits, which is important for regulating the functions of protein complexes. Finally, we revealed that the binding between subunits in a complex can be synergistically strengthened during assembly without considering allosteric regulation or conformational changes. Therefore, our model provides a useful tool to understand the general principles of protein complex assembly
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