Mechanics Force Research Articles

Numerical simulations of a subsonic round jet with transverse acoustic and mechanical forcing

The results of numerical experiments on the bifurcation effects for a free round jet caused by acoustic or vibrational excitations are presented. The three-dimensional distributions of the instantaneous and time-averaged velocity vector components have been obtained and analyzed. The effects of Strouhal and Reynolds numbers on the jet splitting angle, as well as those of the amplitude and type of jet perturbations is discussed in such a comparative parametric study.

QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations.

Understanding the interaction of ligands with biomolecules is an integral component of drug discovery and development. Challenges for computing thermodynamic and kinetic quantities for pharmaceutically relevant receptor-ligand complexes include the size and flexibility of the ligands, large-scale conformational rearrangements of the receptor, accurate force field parameters, simulation efficiency, and sufficient sampling associated with rare events. Our recently developed multiscale milestoning simulation approach, SEEKR2 (Simulation Enabled Estimation of Kinetic Rates v.2), has demonstrated success in predicting unbinding (koff) kinetics by employing molecular dynamics (MD) simulations in regions closer to the binding site. The MD region is further subdivided into smaller Voronoi tessellations to improve the simulation efficiency and parallelization. To date, all MD simulations are run using general molecular mechanics (MM) force fields. The accuracy of calculations can be further improved by incorporating quantum mechanical (QM) methods into generating system-specific force fields through reparameterizing ligand partial charges in the bound state. The force field reparameterization process modifies the potential energy landscape of the bimolecular complex, enabling a more accurate representation of the intermolecular interactions and polarization effects at the bound state. We present QMrebind (Quantum Mechanical force field reparameterization at the receptor-ligand binding site), an ORCA-based software that facilitates reparameterizing the potential energy function within the phase space representing the bound state in a receptor-ligand complex. With SEEKR2 koff estimates and experimentally determined kinetic rates, we compare and interpret the receptor-ligand unbinding kinetics obtained using the newly reparameterized force fields for model host-guest systems and HSP90-inhibitor complexes. This method provides an opportunity to achieve higher accuracy in predicting receptor-ligand koff rate constants.

The Application of Thermomechanical Dynamics (TMD) to the Analysis of Nonequilibrium Irreversible Motion and a Low-Temperature Stirling Engine

We applied the method of Thermomechanical Dynamics (TMD) to a low-temperature Stirling engine, and the dissipative equation of motion and time-evolving physical quantities are self-consistently calculated for the first time in this field. The thermomechanical states of the heat engine are in Nonequilibrium Irreversible States (NISs), and time-dependent thermodynamic work W(t), internal energy E(t), energy dissipation or entropy Qd(t), and temperature T(t), are precisely studied and computed in TMD. We also introduced the new formalism, Q(t)-picture of thermodynamic heat-energy flows, for consistent analyses of NISs. Thermal flows in a long-time uniform heat flow and in a short-time heat flow are numerically studied as examples. In addition to the analysis of time-dependent physical quantities, the TMD analysis suggests that the concept of force and acceleration in Newtonian mechanics should be modified. The acceleration is defined as a continuously differentiable function of Class C2 in Newtonian mechanics, but the thermomechanical dynamics demands piecewise continuity for acceleration and thermal force, required from physical reasons caused by frictional variations and thermal fluctuations. The acceleration has no direct physical meaning associated with force in TMD. The physical implications are fundamental for the concept of the macroscopic phenomena in NISs composed of systems in thermal and mechanical motion.

Kinematic modeling and analysis of transmission mechanism with joint clearance for flapping wing micro aerial vehicle

A theoretical model is built to reveal the effect of the joint clearance on the kinematic performance of the transmission mechanism of a flapping wing micro aerial vehicle (FWMAV). Massless link approach is used to model the joint clearance and the reciprocal screw is introduced to solve the kinematic model. Finite element method simulations are also performed to validate the model. The kinematic model reveals that the inertia force of the transmission mechanism contributes little to the flapping motion whereas the sign of the resultant moment of aerodynamic drag and wing inertia force plays decisive role. Besides, the joint clearance can either increase or decrease the flapping angle of the wing during a flapping period and it will significantly affect the flapping amplitude while involves little in the mean flapping angle. The effects of the positions of the joint with clearance and its magnitude on the flapping motion are also revealed.

Інфляція в системі суспільно-економічних відносин

The article examines the essential features, deep causes and main forms of inflation as a multifactorial phenomenon that inevitably accompanies the economic development of almost all countries of the world. It is shown that the sources and consequences of inflation are not only of a monetary nature, but rather are deeply rooted in structural problems and affect directly and indirectly the totality of social relations. It is noted that the nature of inflation is rooted in the social conflict regarding the distribution of the social product between different social groups of the society. It is justified that inflation itself is complex and heterogeneous in its causes of origin, general features of the inflationary process, its mechanism of action, and consequences. It is argued that inflation is a monetary phenomenon, as it is caused by an excess of money in circulation. However, it should be noted that non-monetary factors can also be the cause of inflation. Regardless of the area in which inflation originates – monetary or non-monetary – monetary and non-monetary factors are interdependent, as they interact in a reproductive process. It is emphasized that one of the driving forces of the inflationary mechanism is the unevenness of price increases, as a result of which some economic subjects are interested in the existence of inflation. It is found that the nature of the national economy and the market has a significant impact on the inflationary process. The dominance of monopolistic structures of the economy, the majority of imperfect competition in the markets is a favorable environment in which inflationary tendencies are quite easily picked up and become strengthened. It is identified that inflationary processes of the national economy can also arise as a result of international exchange, through the price mechanism of foreign trade, when the increase in the price of imported resources creates an impulse for inflationary costs within the country.

Simulation Reveals the Chameleonic Behavior of Macrocycles.

Conformational analysis is central to the design of bioactive molecules. It is particularly challenging for macrocycles due to noncovalent transannular interactions, steric interactions, and ring strain that are often coupled. Herein, we simulated the conformations of five macrocycles designed to express a progression of increasing complexity in environment-dependent intramolecular interactions and verified the results against NMR measurements in chloroform and dimethyl sulfoxide. Molecular dynamics using an explicit solvent model, but not the Monte Carlo method with implicit solvation, handled both solvents correctly. Refinement of conformations at the ab initio level was fundamental to reproducing the experimental observations─standard state-of-the-art molecular mechanics force fields were insufficient. Our simulations correctly predicted the intramolecular interactions between side chains and the macrocycle and revealed an unprecedented solvent-induced conformational switch of the macrocyclic ring. Our results provide a platform for the rational, prospective design of molecular chameleons that adapt to the properties of the environment.

Solid-State Dewetting as a Driving Force for Structural Transformation and Magnetization Reversal Mechanism in FePd Thin Films.

In this work, the process of solid-state dewetting in FePd thin films and its influence on structural transformation and magnetic properties is presented. The morphology, structure and magnetic properties of the FePd system subjected to annealing at 600 °C for different times were studied. The analysis showed a strong correlation between the dewetting process and various physical phenomena. In particular, the transition between the A1 phase and L10 phase is strongly influenced by and inextricably connected with solid-state dewetting. Major changes were observed when the film lost its continuity, including a fast growth of the L10 phase, changes in the magnetization reversal behavior or the induction of magnetic spring-like behavior.

Framing climate strategy of the oil industry of China: A tailored approach to ecological modernization

China has announced its ambitious targets of attaining a carbon peak before 2030 and achieving carbon neutrality by 2060. Although China is a developing country, its oil sector plays a key role in carbon emissions and thus has a responsibility toward climate change. It is very important to understand the role of the oil industry of China in climate governance. This raises the following question: how have oil companies in China framed and tailored their climate strategies? By employing the concept of ecological modernization as a theoretical framework, this study observes the driving forces of climate policies, low-carbon energy, advanced technologies, and market mechanisms by collecting and analyzing reports published by three oil companies. The main findings are that state-owned oil companies in China have adopted the ideas and institutions of national climate strategies, low-carbon energy systems, and emerging financial and market tools. The analysis of the reports reveals that the main motives for the climate strategies of the companies are China’s administrative system, international climate cooperation, the transformation of the energy mix, and emerging market mechanisms.

How does dextran sulfate promote the egg white protein to form transparent hydrogel?the gelation mechanism and molecular force changes

Most globular protein solutions will form turbid gels when heated and exhibit unsatisfactory mechanical strength. Our previous study found that highly charged dextran sulfate (DS) has the potential to induce egg white protein (EWP) to form transparent hydrogel with excellent gelation properties. However, the mechanism is not clear. Therefore, the effect of DS on the gelation characteristics of EWP was investigated, including rheological properties, microstructures, water distributions, molecule conformation, and intermolecular forces. Results showed that DS addition significantly prevented the formation of large insoluble aggregates of EWP during heating, which is the prerequisite for forming a transparent gel. The EWP/DS hydrogel possesses remarkably higher gel strength and water holding capacity compared to EWP. The microstructure analysis showed that EWP/DS has a highly ordered fibrous mesh structure after heat treatment. Fourier transform infrared spectroscopy (FT-IR) revealed that DS addition promotes the denaturation of EWP (decrease in α-helices and increase in β-sheets). In addition, hydrophobic interactions are confirmed to be the major intermolecular force in EWP/DS, rather than disulfide bonds in EWP and EWP/dextran gels. Overall, combining the data from turbidity, FT-IR, and microstructure analysis, we found that the EWP/DS complex formation effectively suppresses the further disordered aggregation process of denatured protein by electrostatic repulsion. This work will be beneficial to understand the mechanism of DS on the gelation of EWP after thermal treatment, which will expand the application of sulfated polysaccharides on food structure design. • Dextran sulfate (DS) addition induced egg white protein (EWP) to form a transparent hydrogel under heat treatment. • The EWP/DS composite hydrogel possesses excellent gelation properties compared to that of the native EWP. • The improvement was largely due to high electrostatic repulsion of EWP/DS coacervates which suppress the formation of insoluble protein aggregates. • Hydrophobic interactions were the major intermolecular force in EWP/DS composite hydrogel.

Influence of beta cyclodextrin on amlodipine-BSA interaction: A spectroscopic and molecular docking study

• Thermodynamic study revealed the static quenching mechanism and Van der Waals force, hydrogen bond and hydrophobic interactions are involved in the ALDP-BSA binding • Spectroscopic and molecular docking results demonstrated that β-CD incorporates ALDP, within its moiety thereby reducing its interaction with BSA • β-CD-ALDP inclusion complex enhanced solubility and bioavailability of ALDP • Inclusion complex interaction with BSA leads to increased therapeutic effect of ALDP Interaction behaviour of amlodipine (ALDP) with bovine serum albumin (BSA) in beta cyclodextrin (β-CD) environment has been studied in this work. Absorbance, steady-state fluorescence, three-dimensional fluorescence, circular dichroism and molecular docking techniques have been followed to monitor the BSA-(β-CD-ALDP) interaction. Thermodynamic study by steady-state fluorescence has shown spontaneous reaction between BSA-ALDP with static quenching, involving Van der Waals forces and hydrogen bonding interaction. Stern-Volmer equation has been employed to compute quenching constant and binding constant values for BSA-ALDP system in β-CD media. Reduction in the binding constant values for BSA-ALDP in β-CD media compared to BSA-ALDP suggests the formation of an inclusion complex. Spectroscopic experimental results are found to be in good agreement with molecular docking, which has demonstrated that β-CD incorporates ALDP within its moiety thereby reducing its interaction with BSA.

Molecular mechanics simulations of lattice dynamical properties of the spin crossover complex [Fe(pyrazine)][Ni(CN)4

An empirical molecular mechanics force field has been built for the [Fe(pyrazine)][Ni(CN)4] spin crossover complex using Raman spectroscopic and nuclear inelastic scattering data. Based on this force field, molecular dynamics simulations were conducted to investigate the lattice dynamical properties of the complex in the high-spin and low-spin states. The extracted thermodynamic and mechanical parameters match well with the corresponding experimental data. Most importantly, the force field can successfully reproduce the low-frequency acoustic part of the partial densities of vibrational states, which is vital for the understanding the thermodynamic analysis of the spin crossover phenomenon in crystalline solids and which would be difficult to tackle by quantum mechanical methods.

Ginkgo seed shell provides a unique model for bioinspired design

Natural structural materials typically feature complex hierarchical anisotropic architectures, resulting in excellent damage tolerance. Such highly anisotropic structures, however, also provide an easy path for crack propagation, often leading to catastrophic fracture as evidenced, for example, by wood splitting. Here, we describe the weakly anisotropic structure of Ginkgo biloba (ginkgo) seed shell, which has excellent crack resistance in different directions. Ginkgo seed shell is composed of tightly packed polygonal sclereids with cell walls in which the cellulose microfibrils are oriented in a helicoidal pattern. We found that the sclereids contain distinct pits, special fine tubes like a "screw fastener," that interlock the helicoidal cell walls together. As a result, ginkgo seed shell demonstrates crack resistance in all directions, exhibiting specific fracture toughness that can rival other highly anisotropic natural materials, such as wood, bone, insect cuticle, and nacre. In situ characterization reveals ginkgo's unique toughening mechanism: pit-guided crack propagation. This mechanism forces the crack to depart from the weak compound middle lamella and enter into the sclereid, where the helicoidal cell wall significantly inhibits crack growth by the cleavage and breakage of the fibril-based cell walls. Ginkgo's toughening mechanism could provide guidelines for a new bioinspired strategy for the design of high-performance bulk materials.

Physical effects of gravitational waves: pedagogical examples

General relativity describes gravitation in terms of the geometry of spacetime. It predicts the existence of gravitational waves (GWs) that stretch and compress spacetime and were detected recently by state-of-the-art interferometer observations. Yet, for those who are not familiar with general relativity, it may be difficult to understand how the GWs actually stretch and compress spacetime. In this paper, after reviewing the fact that the effects of GWs can be understood as a force in Newtonian mechanics, we consider extreme and readily perceivable situations where large-amplitude GWs pass through the human body and the Earth, and demonstrate that GWs cause phenomena that commonly occur in daily life by back-of-the-envelope calculations. Our analysis provides intellectual and pedagogical materials for understanding the nature of GWs for nonexperts in general relativity.

Enhancing Biomolecular Simulations with Hybrid Potentials Incorporating NMR Data.

Some recent advances in biomolecular simulation and global optimization have used hybrid restraint potentials, where harmonic restraints that penalize conformations inconsistent with experimental data are combined with molecular mechanics force fields. These hybrid potentials can be used to improve the performance of molecular dynamics, structure prediction, energy landscape sampling, and other computational methods that rely on the accuracy of the underlying force field. Here, we develop a hybrid restraint potential based on NapShift, an artificial neural network trained to predict protein nuclear magnetic resonance (NMR) chemical shifts from sequence and structure. In addition to providing accurate predictions of experimental chemical shifts, NapShift is fully differentiable with respect to atomic coordinates, which allows us to use it for structural refinement. By employing NapShift to predict chemical shifts from the protein conformation at each simulation step, we can compute an energy penalty and the corresponding hybrid restraint forces based on the difference between the predicted values and the experimental chemical shifts. The performance of the hybrid restraint potential was benchmarked using both basin-hopping global optimization and molecular dynamics simulations. In each case, the NapShift hybrid potential improved the accuracy, leading to better structure prediction via basin-hopping and increased local stability in molecular dynamics simulations. Our results suggest that neural network hybrid potentials based on NMR observables can enhance a broad range of molecular simulation methods, and the prediction accuracy will improve as more experimental training data become available.

Phenomenological rate-independent uniaxial hysteretic models: A mini-review

A great variety of phenomenological models has been proposed over the years to model rate-independent hysteretic forces in structural mechanics. The classification of such models is usually based on the type of equation that needs to be solved to evaluate the output variable. In particular, we distinguish among algebraic, transcendental, differential and integral models. For algebraic (transcendental) models, an algebraic (a transcendental) equation needs to be solved to compute the output variable; conversely, differential equations are employed for differential models, whereas equations expressed in integral form characterize integral models. This paper provides a mini-review of the most adopted phenomenological rate-independent uniaxial hysteretic models. Such models are selected in order to provide a complete overview of the four types of previously mentioned models, currently available in the literature. In particular, we illustrate the fundamental characteristics of each model and discuss their peculiarities in terms of 1) number of adopted parameters and variables, 2) physical interpretation of parameters and related calibration procedures, 3) type of hysteresis loop shapes that can be simulated.

Defect suppression mechanism of ultrasonic vibration-assisted drilling carbon fiber/bismaleimide composite

Ultrasonic vibration-assisted drilling (UVAD) has recently been successfully applied in the drilling of carbon fiber reinforced polymer/plastic (CFRP) due to its high reliability. Multiple defects have been observed in the CFRP drilling process which negatively affects the quality of the hole. The carbon fiber/bismaleimide (BMI) composites is an advanced kind of CFRPs with greater strength and heat resistance, having been rapidly applied in lightweight and high temperature resistant structures in the aerospace field. To suppress the defect during the drilling of carbon fiber/BMI composites, it is necessary to comprehensively understand the defect formation and suppression mechanism at different positions. In this study, the defects formation in both conventional drilling (CD) and UVAD were observed and analyzed. The variation trend in the defect factor and thrust force with the spindle speed and feed rate were acquired. The results revealed that the UVAD could significantly enhance the hole’s quality with no delamination and burr. Meanwhile, the defect suppression mechanism and thrust force in UVAD were analyzed and verified, where the method of rod chip removal affected the exit defect formation. In summary, UVAD can be considered a promising and competitive technique for drilling carbon fiber/BMI composites.

Atomic-Resolution Experimental Structural Biology and Molecular Dynamics Simulations of Hyaluronan and Its Complexes.

This review summarizes the atomic-resolution structural biology of hyaluronan and its complexes available in the Protein Data Bank, as well as published studies of atomic-resolution explicit-solvent molecular dynamics simulations on these and other hyaluronan and hyaluronan-containing systems. Advances in accurate molecular mechanics force fields, simulation methods and software, and computer hardware have supported a recent flourish in such simulations, such that the simulation publications now outnumber the structural biology publications by an order of magnitude. In addition to supplementing the experimental structural biology with computed dynamic and thermodynamic information, the molecular dynamics studies provide a wealth of atomic-resolution information on hyaluronan-containing systems for which there is no atomic-resolution structural biology either available or possible. Examples of these summarized in this review include hyaluronan pairing with other hyaluronan molecules and glycosaminoglycans, with ions, with proteins and peptides, with lipids, and with drugs and drug-like molecules. Despite limitations imposed by present-day computing resources on system size and simulation timescale, atomic-resolution explicit-solvent molecular dynamics simulations have been able to contribute significant insight into hyaluronan's flexibility and capacity for intra- and intermolecular non-covalent interactions.

Mid-Holocene climate of the Tibetan Plateau and hydroclimate in three major river basins based on high-resolution regional climate simulations

Abstract. The Tibetan Plateau (TP) contains the headwaters of major Asian rivers that sustain billions of people and plays an important role in both regional and global climate through thermal and mechanical forcings. Understanding the characteristics and changes to the hydrological regimes on the TP during the mid-Holocene (MH) will help in understanding the expected future changes. Here, an analysis of the hydroclimates over the headwater regions of three major rivers originating in the TP, namely the Yellow, Yangtze, and Brahmaputra rivers, is presented, using dynamically downscaled climate simulations constructed using the Weather Research and Forecasting Model (WRF) coupled to the hydrological model WRF-Hydro. Green Sahara (GS) boundary conditions have also been incorporated into the global model so as to capture the remote feedbacks between the Saharan vegetation and the river hydrographs over the TP. Model–data comparisons show that the dynamically downscaled simulations significantly improve the regional climate simulations over the TP in both the modern day and the MH, highlighting the crucial role of downscaling in both present-day and past climates. TP precipitation is also strongly affected by the greening of the Sahara, with a particularly large increase over the southern TP, as well as a delay in the monsoon withdrawal. The simulation results were first validated over the upper basins of the three rivers before the hydrological responses to the MH forcing for the three basins were quantified. Both the upper Yellow and Yangtze rivers exhibit a decline in streamflow during the MH, especially in summer, which is a combined effect of less snowmelt and stronger evapotranspiration. The GS forcing caused a rise in temperature during the MH, as well as larger rainfall but less snowfall and greater evaporative water losses. The Brahmaputra River runoff is simulated to increase in the MH due to greater net precipitation.

Structural Investigation of Aaptourinamine by a Novel Module-Assembly-Based Calculation.

Natural products have various and complicated structures, which is still a challenge for elucidating these compounds, especially for those lacking two-dimensional nuclear magnetic resonance (2D NMR) correlations mainly caused by high C/H ratios or proton-deficient and multiple heteroatoms through the conventional structural analytical methods. We reported a novel module-assembly calculation method named Dooerafa, which included constructing the meta-structures by a grafting method based on the crucial and the limited 2D NMR correlations, ring-contraction strategy based on mechanic force field and quantum chemical theory, and self-assemble calculation in Python programming for shaping up the structural candidates along with DFT-GIAO calculation. This new method, verified by a known alkaloid spiroreticulatine with the structure determined by X-ray diffraction, was performed for the structural elucidation of aaptourinamine isolated from marine sponge Aaptos suberitoides, showing us a brand new scaffold of imidazo [4,5,1-ij]pyrrolo [3,2-f]quinolin-7(8H)-one, which has a biosynthetic relationship with the bioactive and structurally unique aaptamine alkaloid.

A Planar Underactuated Compaction Mechanism with Self-Adaptability for Automated Fiber Placement Heads

Automated fiber placement (AFP) systems accommodate complex-shaped structures by pressing fibers against the non-planar surfaces of mandrels, in which compaction mechanisms are of crucial significance. A conventional compaction mechanism utilizes an independent actuator with compacting rollers to conform surfaces. Compared with these mechanisms, underactuated mechanisms can improve self-adjustability and functionality. This research introduces the concept design and the analysis of a planar underactuated compaction mechanism for automated fiber placement heads. Firstly, the requirements and design premise are determined. Then, a novel planar underactuated compaction mechanism with a bistable structure is constructed based on the metamorphic design theory. Secondly, the analytical models are established to give insight into the motion characteristics of the mechanism. Moreover, the example and simulation results are presented to verify the conceptual design. Furthermore, the standard deviation of the contact force of the planar underactuated compaction mechanism is much lower than that of a conventional compaction mechanism under equal conditions. Finally, the potential application of the underactuated mechanisms is discussed. Thus, this research shows that the designed compaction mechanism increases the adjustability, robustness, and high repeatability in positioning and can be used to simplify the motion planning for AFP systems when producing complex structures.