Search

In this paper, we study an optimal control problem for a stationary Navier–Stokes hemivariational inequality with control constraints and its numerical approximation. The hemivariational inequality is the weak formulation of a stationary incompressible fluid flow problem, modeled by the Navier-Stokes equations subject to a nonleak boundary condition and a subdifferential condition of friction type. We investigate the stability of the solution of the hemivariational inequality with respect to perturbations in the density of external force and superpotential, and demonstrate the existence of a solution for the optimal control problem with the external force density as the control. Moreover, we consider the numerical solution of the optimal control problem and show its convergence. As an example and for definiteness, the numerical solution is defined through the finite element method. [ABSTRACT FROM AUTHOR]

We numerically investigate the hydrodynamic interactions between two microswimmers in viscoelastic fluids at low Reynolds number regimes using the fictitious domain method. In the Newtonian fluid, after contact, pushers rotate toward each other and remain in a "trapped" state for a long time, induced by a counterclockwise viscous torque. We believe it is related to the asymmetrical surrounding vortexes. As the pushers approach, two positive vortexes merge into one, disrupting the vortex balance and inducing a net counterclockwise torque on the swimmers. But in the Giesekus viscoelastic fluids, an clockwise elastic torque modifies the pushers' rotations during early contact. Subsequently, two negative vortexes around the pushers merge, generating a clockwise torque that causes the swimmers to separate. Additionally, a huge elastic stretching effect is observed at the rear of the pullers, which restricts their swimming behavior through elastic force. Post-collision, the pullers rapidly separate with a large scattering angle in both Newtonian and viscoelastic fluids. However, neutral swimmers separate with unchanged orientations, and their trajectories remain consistently aligned across various Weissenberg numbers. Furthermore, the elastic force impedes the relative motions of the swimmers and alters the pressure and viscosity force. [ABSTRACT FROM AUTHOR]

The thermal-controlled fracture method has been increasingly focused upon in the high-quality cutting of advanced ceramic materials due to its excellent characteristics. The successful application of this method in cutting ceramics mainly depends on the volumetric heating effect. However, most ceramics are treated using the surface heating mode. For the surface heating mode, the processing quality, including fracture trajectory and fracture quality, is far lower than the industrial application standards. This work was conducted to reveal the mechanism of this processing quality. Experiments involving cutting ceramics in single-surface heating mode indicate that the fracture trajectories of the upper and lower surfaces display a significant inconsistency, and the fracture quality is worse than that using the dual-surface heating mode. A cutting model was established to calculate the thermal stress distribution and to simulate the crack-propagation behaviors. The simulation results show good agreement with the experiment and provide the stress distribution, and are used to understand the reason for the processing quality problem. The mechanism of the trajectory deviation and uneven distribution of the fracture quality is revealed based on the simulation and calculation results. This study helps provide a deep understanding of the processing problems arising from this method and thus helps to innovate high-quality processing methods in this field. [ABSTRACT FROM AUTHOR]

In this paper, we are concerned with a class of second-order hemivariational inequalities involving history-dependent operators. For the problem, we first derive a semidiscrete scheme by implicit Euler formula and prove its unique solvability. The existence and uniqueness of a solution to the inequality problem is given by Rothe method. As the core part of the paper, we propose a two-step semidiscrete approximation for the problem, provide its unique solvability and obtain its second-order error estimates. The two-step scheme is more accurate than the standard implicit Euler scheme. Finally, we apply the results to a dynamic frictionless contact problem with long memory. [ABSTRACT FROM AUTHOR]

Cost-effective hydrolysis of biomass into sugars for biofuel production requires high-performance low-cost glycoside hydrolase (GH) cocktails that are active under demanding process conditions. Improving the performance of GH cocktails depends on knowledge of many critical parameters, including individual enzyme stabilities, optimal reaction conditions, kinetics, and specificity of reaction. With this information, rate- and/or yield-limiting reactions can be potentially improved through substitution, synergistic complementation, or protein engineering. Given the wide range of substrates and methods used for GH characterization, it is difficult to compare results across a myriad of approaches to identify high performance and synergistic combinations of enzymes. Here, we describe a platform for systematic screening of GH activities using automatic biomass handling, bioconjugate chemistry, robotic liquid handling, and nanostructure-initiator mass spectrometry (NIMS). Twelve well-characterized substrates spanning the types of glycosidic linkages found in plant cell walls are included in the experimental workflow. To test the application of this platform and substrate panel, we studied the reactivity of three engineered cellulases and their synergy of combination across a range of reaction conditions and enzyme concentrations. We anticipate that large-scale screening using the standardized platform and substrates will generate critical datasets to enable direct comparison of enzyme activities for cocktail design.

Harnessing the biotechnological potential of the large number of proteins available in sequence databases requires scalable methods for functional characterization. Here we propose a workflow to address this challenge by combining phylogenomic guided DNA synthesis with high-throughput mass spectrometry and apply it to the systematic characterization of GH1 β-glucosidases, a family of enzymes necessary for biomass hydrolysis, an important step in the conversion of lignocellulosic feedstocks to fuels and chemicals. We synthesized and expressed 175 GH1s, selected from over 2000 candidate sequences to cover maximum sequence diversity. These enzymes were functionally characterized over a range of temperatures and pHs using nanostructure-initiator mass spectrometry (NIMS), generating over 10,000 data points. When combined with HPLC-based sugar profiling, we observed GH1 enzymes active over a broad temperature range and toward many different β-linked disaccharides. For some GH1s we also observed activity toward laminarin, a more complex oligosaccharide present as a major component of macroalgae. An area of particular interest was the identification of GH1 enzymes compatible with the ionic liquid 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), a next-generation biomass pretreatment technology. We thus searched for GH1 enzymes active at 70 °C and 20% (v/v) [C2mim][OAc] over the course of a 24-h saccharification reaction. Using our unbiased approach, we identified multiple enzymes of different phylogentic origin with such activities. Our approach of characterizing sequence diversity through targeted gene synthesis coupled to high-throughput screening technologies is a broadly applicable paradigm for a wide range of biological problems.

This paper is devoted to studying a dynamic adhesive contact model where the body is composed of a viscoelastic material with long memory. The adhesion process is modeled by a bonding field on part of the contact surface and on which the contact and the friction are modeled by nonmonotone Clarke subdifferential conditions with adhesion. Meanwhile, on another part of the contact surface, the contact is comprised of a normal compliance contact condition while the memory effects of the obstacle are considered, the friction is modeled by a version of Coulomb's law of dry friction and the friction bound is dependent on the normal stress. The variational form of the model generates a system of a doubly-history dependent variational–hemivariational inequality as well as a differential equation. Then, on the basis of the proof of abstract variational–hemivariational inequality, the existence and uniqueness results of the contact problem are established. [ABSTRACT FROM AUTHOR]

Motivation Topologically associating domains (TADs) are fundamental building blocks of 3D genome. TAD-like domains in single cells are regarded as the underlying genesis of TADs discovered in bulk cells. Understanding the organization of TAD-like domains helps to get deeper insights into their regulatory functions. Unfortunately, it remains a challenge to identify TAD-like domains on single-cell Hi-C data due to its ultra-sparsity. Results We propose scKTLD, an in silico tool for the identification of TAD-like domains on single-cell Hi-C data. It takes Hi-C contact matrix as the adjacency matrix for a graph, embeds the graph structures into a low-dimensional space with the help of sparse matrix factorization followed by spectral propagation, and the TAD-like domains can be identified using a kernel-based changepoint detection in the embedding space. The results tell that our scKTLD is superior to the other methods on the sparse contact matrices, including downsampled bulk Hi-C data as well as simulated and experimental single-cell Hi-C data. Besides, we demonstrated the conservation of TAD-like domain boundaries at single-cell level apart from heterogeneity within and across cell types, and found that the boundaries with higher frequency across single cells are more enriched for architectural proteins and chromatin marks, and they preferentially occur at TAD boundaries in bulk cells, especially at those with higher hierarchical levels. Availability and implementation scKTLD is freely available at https://github.com/lhqxinghun/scKTLD. [ABSTRACT FROM AUTHOR]

Mass spectrometry based technologies are promising as generalizable high-throughput assays for enzymatic activity. In one such technology, a specialized enzyme substrate probe is presented to a biological mixture potentially exhibiting enzymatic activity, followed by an in situ enrichment step using fluorous interactions and nanostructure-initiator mass spectrometry. This technology, known as Nimzyme, shows great potential but is limited by the need to synthesize custom substrate analogs. We describe a synthetic route that simplifies the production of these probes by fashioning their perfluorinated invariant portion as an alkylating agent. This way, a wide variety of compounds can be effectively transformed into enzyme activity probes. As a proof of principle, a chloramphenicol analog synthesized according to this methodology was used to detect chloramphenicol acetyltransferase activity in cell lysate. This verifies the validity of the synthetic strategy employed and constitutes the first reported application of Nimzyme to a non-carbohydrate-active enzyme. The simplified synthetic approach presented here may help advance the application of mass spectrometry to high-throughput enzyme activity determination.

Production of biofuels via enzymatic hydrolysis of complex plant polysaccharides is a subject of intense global interest. Microbial communities are known to express a wide range of enzymes necessary for the saccharification of lignocellulosic feedstocks and serve as a powerful reservoir for enzyme discovery. However, the growth temperature and conditions that yield high cellulase activity vary widely, and the throughput to identify optimal conditions has been limited by the slow handling and conventional analysis. A rapid method that uses small volumes of isolate culture to resolve specific enzyme activity is needed. In this work, a high throughput nanostructure-initiator mass spectrometry (NIMS)-based approach was developed for screening a thermophilic cellulolytic actinomycete, Thermobispora bispora, for β-glucosidase production under various growth conditions. Media that produced high β-glucosidase activity were found to be I/S + glucose or microcrystalline cellulose (MCC), Medium 84 + rolled oats, and M9TE + MCC at 45°C. Supernatants of cell cultures grown in M9TE + 1% MCC cleaved 2.5 times more substrate at 45°C than at all other temperatures. While T. bispora is reported to grow optimally at 60°C in Medium 84 + rolled oats and M9TE + 1% MCC, approximately 40% more conversion was observed at 45°C. This high throughput NIMS approach may provide an important tool in discovery and characterization of enzymes from environmental microbes for industrial and biofuel applications.