Cooperative Motion Research Articles

Friends in need: How chaperonins recognize and remodel proteins that require folding assistance.

Chaperonins are biological nanomachines that help newly translated proteins to fold by rescuing them from kinetically trapped misfolded states. Protein folding assistance by the chaperonin machinery is obligatory in vivo for a subset of proteins in the bacterial proteome. Chaperonins are large oligomeric complexes, with unusual seven fold symmetry (group I) or eight/nine fold symmetry (group II), that form double-ring constructs, enclosing a central cavity that serves as the folding chamber. Dramatic large-scale conformational changes, that take place during ATP-driven cycles, allow chaperonins to bind misfolded proteins, encapsulate them into the expanded cavity and release them back into the cellular environment, regardless of whether they are folded or not. The theory associated with the iterative annealing mechanism, which incorporated the conformational free energy landscape description of protein folding, quantitatively explains most, if not all, the available data. Misfolded conformations are associated with low energy minima in a rugged energy landscape. Random disruptions of these low energy conformations result in higher free energy, less folded, conformations that can stochastically partition into the native state. Two distinct mechanisms of annealing action have been described. Group I chaperonins (GroEL homologues in eubacteria and endosymbiotic organelles), recognize a large number of misfolded proteins non-specifically and operate through highly coordinated cooperative motions. By contrast, the less well understood group II chaperonins (CCT in Eukarya and thermosome/TF55 in Archaea), assist a selected set of substrate proteins. Sequential conformational changes within a CCT ring are observed, perhaps promoting domain-by-domain substrate folding. Chaperonins are implicated in bacterial infection, autoimmune disease, as well as protein aggregation and degradation diseases. Understanding the chaperonin mechanism and the specific proteins they rescue during the cell cycle is important not only for the fundamental aspect of protein folding in the cellular environment, but also for effective therapeutic strategies.

Design and Testing of Cooperative Motion Controller for UAV-UGV System

Unmanned ground vehicles (UGVs) and quadrotor unmanned aerial vehicles (UAVs) can work together to solve challenges like intelligent transportation, thanks to their excellent performance complements in perception, loading, and endurance. This study presents a UAV-UGV system cooperative control mechanism. To achieve collaborative trajectory tracking, the leader-follower strategy based on a centralized control structure is firstly established in conjunction with the application scenario. The fuzzy robust controller is created to control the quadrotor UAV and improve attitude stability. Meanwhile, the UGV's controller uses the pure pursuit algorithm and a proportional integral derivative (PID) controller. In order to evaluate the cooperative control strategy and algorithm, the UAV-UGV experimental platform is set up based on the QDrone and QCar, and the experimental results show the viability of the suggested plan.

Analysis of Kinematic Characteristics of Saanen Goat Spine under Multi-Slope.

In order to improve the slope movement stability and flexibility of quadruped robot, a theoretical design method of a flexible spine of a robot that was based on bionics was proposed. The kinematic characteristics of the spine were analyzed under different slopes with a Saanen goat as the research object. A Qualisys track manager (QTM) gait analysis system was used to obtain the trunk movement of goats under multiple slopes, and linear time normalization (LTN) was used to calibrate and match typical gait cycles to characterize the goat locomotion gait under slopes. Firstly, the spatial angle changes of cervical thoracic vertebrae, thoracolumbar vertebrae, and lumbar vertebrae were compared and analyzed under 0°, 5°, 10°, and 15° slopes, and it was found that the rigid and flexible coupling structure between the thoraco-lumbar vertebrae played an obvious role when moving on the slope. Moreover, with the increase in slope, the movement of the spine changed to the coupling movement of thoraco-lumbar coordination movement and a flexible swing of lumbar vertebrae. Then, the Gaussian mixture model (GMM) clustering algorithm was used to analyze the changes of the thoraco-lumbar vertebrae and lumbar vertebrae in different directions. Combined with anatomical knowledge, it was found that the motion of the thoraco-lumbar vertebrae and lumbar vertebrae in the goat was mainly manifested as a left-right swing in the coronal plane. Finally, on the basis of the analysis of the maximin and variation range of the thoraco-lumbar vertebrae and lumbar vertebrae in the coronal plane, it was found that the coupling motion of the thoraco-lumbar cooperative motion and flexible swing of the lumbar vertebrae at the slope of 10° had the most significant effect on the motion stability. SSE, R2, adjusted-R2, and RMSE were used as evaluation indexes, and the general equations of the spatial fitting curve of the goat spine were obtained by curve fitting of Matlab software. Finally, Origin software was used to obtain the optimal fitting spatial equations under eight movements of the goat spine with SSE and adjusted-R2 as indexes. The research will provide an idea for the bionic spine design with variable stiffness and multi-direction flexible bending, as well as a theoretical reference for the torso design of a bionic quadruped robot.

Cooperative control strategy of wheel-legged robot based on attitude balance

AbstractTo integrate the uneven terrain adaptivity of legged robots and the fast capacity of wheeled robots on even terrains, a four wheel-legged robot is addressed and the cooperative control strategy of wheels and legs based on attitude balance is investigated. Firstly, the kinematics of wheel-legged robot is analyzed, which contains the legged and wheeled motion modal. Secondly, the cooperative control strategy of wheel-legged robot based on attitude balance is proposed. The attitude is calculated by using the quaternion method and complementary filtering, and the attitude stability control of the wheel-legged robot is studied. The trajectory planning of leg motion including walk and trot gait is implemented, and the differential control of wheeled motion is deduced. And then, the cooperative motion control of wheels and legs is achieved by keeping the attitude balance of robot body. Finally, a small prototype is set up to validate the feasibility and effectiveness of proposed method. The experimental results show that the established wheel-legged robot can do walk, trot, and wheel-leg compound motion to overcome many complex terrains and environments.

Synchronized motion of two camphor disks on a water droplet levitated under microgravity

Two camphor disks, as self-propelled objects, were placed on a water droplet levitated under microgravity to understand the nature of their self-propelled motion on a sphere field without a boundary. When a single camphor disk was placed on the droplet, unidirectional rotation with a constant speed was observed. When two camphor disks were placed on the droplet, synchronized motion occurred; that is, the two disks exhibited unidirectional motion while the distance between them was maintained. The characteristic features of the self-propelled motion are discussed in relation to the camphor molecules developed from the disk as the source of both the driving force of motion and the repulsive force between the disks. The present study suggests that self-propelled objects can exhibit cooperative motion in a field without boundary.

Thermal properties of polymer with intrinsic microporosity membranes

The thermal behavior of a polymer with intrinsic microporosity (PIM-1) membrane was investigated via thermomechanical analysis and differential scanning calorimetry. The coefficient of thermal expansion (CTE) was almost constant at 70*106 K−1 below 110 °C and inflection points were observed over the range 120–150 °C, regardless of the fabrication conditions. The CTE after the inflection point strongly depended on the membrane formation conditions and the thermal history. Although the CTE increased with a methanol treatment, the CTE of other membranes decreased because of shrinkage attributed to internal stress. This behavior indicated cooperative molecular motion below 200 °C. In the calorimetry measurements, a specific-heat discontinuity from the glass transition was not observed. However, an extremely broad endothermic peak, which may have been caused by enthalpy relaxation, was observed for a membrane that exhibited advanced physical aging.

Scalable Learned Geometric Feasibility for Cooperative Grasp and Motion Planning

This letter proposes a novel learned feasibility estimator that considers multi-modal grasp poses for grasp and motion planning. Grasp poses inherently have multi-modal structures, that is, continuous and discrete parameters. Mixed-integer programming (MIP) is one method that solves these multi-modal problems. However, searching for all the discrete parameters costs considerable time. Therefore, by learning the feasibility of each mode from the geometric variables, the problem can be solved efficiently within a given time limit. The feasibility of grasp poses is related to the pose of the object and nearby obstacles. Utilizing this information, we introduce learned geometric feasibility (LGF), which prioritizes the integer search of MIP. LGF is scalable to multiple robots and environments because it learns the feasibility using object-oriented information. It has been demonstrated to improve the number of solved MIP problems within the time limit and to be applicable to various environmental settings.

Dual-Loop Dynamic Control of Cable-Driven Parallel Robots Without Online Tension Distribution

Achieving high-precision position control while maintaining positive cable tensions is the most challenging issue for the motion control of cable-driven parallel robots, which should be considered significantly. Different from the existing control schemes with online tension distribution that needs real-time computing in each control cycle, a novel dual-loop dynamic control scheme is proposed in this article, where a paralleled dual-loop tracking strategy is introduced to provide a more compatible scheme, which consists of two tracking loops: 1) the tension control loop and 2) the position control loop. In the former loop, the offline tension distribution is adopted to avoid cable hanging loosely and the real-time feasibility of the distribution method is no longer a necessary demand. In the latter loop, due to the complex dynamics characterized by the cable-driven form, the cooperative motion relation among multiple cables and inevitable external disturbances are investigated comprehensively, and the robust synchronization method is included to guarantee the high-precision position control. Afterward, the Lyapunov method is adopted to analyze the strict stability of the whole closed-loop system with both the position and tension control feedback. The experiments indicate that by synthesizing the two control loops, the proposed scheme can dramatically reduce the tracking errors in the trajectory tracking while avoiding the cable relaxation, and particularly, has a satisfactory control effect when the velocity and acceleration of the trajectory have significant oscillations. Additionally, the strong disturbance rejection ability is also validated via robustness experiments.

Two-Stage Structural and Slowing-Down Percolation Transitions in the Densifying Cancer Cell Monolayer.

We experimentally demonstrate the two-stage structural and slowing-down percolating transitions, followed by the confluent transition in the densifying cancer cell monolayers from the dilute state, and investigate their impacts on collective cell dynamics. It is found that cells aggregate into clusters at low cell density. With increasing cell number density, the structural percolation through the formation of a large cell cluster percolating through the space precedes the dynamical percolation transition of forming a percolating cluster of slow cell elements. Both percolating transitions exhibit scale-free scaling behaviors of cluster size distributions and fractal structures, similar to those of the universality class of 2D nonequilibrium systems governed by percolation theory. Dynamically, at low cell density, cell aggregation enhances cooperative motion. The structural percolation leads to slower motion, especially with stronger suppression for the high-frequency modes in the turbulent-like velocity power spectra. The following slowing-down percolation associated with the onset of cell crowding in regions occupied by cells further enhances dynamical slowing-down, and suppresses the increasing trend of dynamical heterogeneity and the steepening of the power spectrum of motion, until their reversions after the confluent transition.

Synergistic Motion Stability of a Scorpion-like Composite Robot

In this paper, a compliant control scheme based on the optimization of the contact force of the robot leg is proposed to improve the stability of the whole moving process of the robot. Firstly, according to the motion state of the robot, the change of its center of gravity is analyzed, then the stable gait of the robot is determined by the stability margin, and the smooth control of the robot’s foot trajectory is realized. Finally, the compliant control model of the robot leg is established. In the process of moving, the contact force between the legs and the ground is optimized in real-time, so that the composite robot can walk steadily on uneven terrain. The 3-D model of the scorpion composite robot was built with ADAMS software, and dynamics simulation was carried out according to the compliant control scheme. This paper takes the robot’s walking speed and torso angle as performance evaluation indexes and verifies the effectiveness of the compliant control scheme. The cooperative motion stability test is carried out on the actual uneven terrain. The test results show that the robot’s pitch angle and roll angle are between ±0.5°, which meets the motion stability requirements of the robot and verifies the correctness of the compliant control scheme and control model proposed in this paper.

On Molecular Dynamics and Charge Transport in a Flexible Epoxy Resin Network.

An epoxy based on diglycidyl ether of bisphenol A was reacted with a long-chain poly(oxypropylene diamine) hardener in the presence of an accelerator, resulting in a flexible epoxy network. Tensile properties were tested as a function of accelerator concentration. All systems exhibited high levels of extensibility, with strain at failure values in excess of 65%. Molecular dynamics in a formulation containing 10 phr of accelerator were then examined using dielectric spectroscopy over the temperature range of 103–433 K. At low temperatures, a molecular relaxation process (γ relaxation) was observed and shown to conform well to both the Arrhenius equation and activated tunnelling. A stronger relaxation appeared (203–303 K) just before the onset of charge transport, which dominated the behaviour at higher temperatures. The former takes an unusual bimodal form, which we consider a result of overlapping β and α relaxations, consequently termed αβ mode. Analysis of this mechanism revealed a Vogel–Fulcher–Tammann (VFT) behaviour. The temperature-dependent DC conductivity, σDC (deduced from the low-frequency charge transport contribution to εr″), also revealed VFT behaviour with an onset statistically equivalent to that of the αβ mode, therefore suggesting that charge transport, at this temperature regime, is strongly affiliated with cooperative molecular motion.

Screening and collective effects in randomly pinned fluids: a new theoretical framework

We propose a theoretical framework for the dynamics of bulk isotropic hard-sphere systems in the presence of randomly pinned particles and apply this theory to supercooled water to validate it. Structural relaxation is mainly governed by local and non-local activated process. As the pinned fraction grows, a local caging constraint becomes stronger and the long range collective aspect of relaxation is screened by immobile obstacles. Different responses of the local and cooperative motions results in subtle predictions for how the alpha relaxation time varies with pinning and density. Our theoretical analysis for the relaxation time of water with pinned molecules quantitatively well describe previous simulations. In addition, the thermal dependence of relaxation for unpinned bulk water is also consistent with prior computational and experimental data.

Molecular basis of secondary relaxation in stiff-chain glassy polymers.

Recent progress in establishing local order in polycarbonate-like glasses using rotational echo double resonance and centerband-only detection of exchange solid-state nuclear magnetic resonance (NMR) has stimulated a renewed attempt to connect molecular motion within glassy polymers and the mechanical properties of the glass. We have in fact established a correlation between molecular motion characterized by NMR and the mechanical secondary relaxation (tan δ) for nine polycarbonate-like glasses. All of the NMR and mechanical data are for T ≪ Tg. The resulting structural insights suggest that the chains of these polymers are simultaneously both Flory random coils and Vol'kenstein bundles. The cooperative motions of groups of bundles can be described qualitatively by a variety of constrained-kinetics models of the glass. All of the models share a common trait for large-amplitude motion: an exponential increase in the time required for an inter-bundle dilation event with a linear increase in bundle group size. This dependence and a locally ordered Vol'kenstein bundle lead to an understanding of the surprising 60° (K) shift of tan δ to higher temperature for ring-fluoro-polycarbonate relative to that of polycarbonate by the apparently minor substitution of a fluorine for a hydrogen on every fourth ring.

Evolution path of metallic glasses under extensive cryogenic thermal cycling: Rejuvenation or relaxation?

Rejuvenation of metallic glasses (MGs) under Cryogenic thermal cycling (CTC) has aroused attention due to its prospect of fundamental and practical interest in recent years. However, not all MGs could be rejuvenated by CTC. For some system, obvious rejuvenation is achieved under few number of cycles. While for other system, rejuvenation is hard to achieve and relaxation to lower energy states occurs. The responses of MGs to CTC are so complicated and the inherent dominat factors leading to this situation remains unclear. By extensive CTC (∼800 cycles), the present work discovered quasi periodic characteristics of two typical evolution paths (rejuvenation and relaxation) in MGs, and revealed the different structural origins between them by experimental and simulation. It has been verified that the rejuvenation process induced by CTC comes mainly from local atomic motion in loosely packed regions (LPRs), while the cooperative motion of atoms in densely packed regions (DPRs) is responsible for the other evolution path, i.e., relaxation. Besides, the relaxation path induced by CTC could stabilize the supercooled liquids, with a mechanism different from that underlying the general effect of annealing on marginal MGs. Our finding explains why MGs (even with the same composition) have diverse responses to CTC. It also provides a comprehensive understanding for the mechanism of rejuvenation and a new strategy for modulating the properties of MGs by controlling microstructures by CTC.

In Situ Electron Microscopy Study of the Dynamics of Liquid Flow in Confined Cells.

Confined liquid has attracted great attention due to its potential applications in nanofluidic devices. With the development of liquid-cell transmission electron microscopy (LC-TEM), investigating the behaviors of confined liquid can be realized in real time. However, the dynamics of the liquid layer in liquid cells have not been fully understood. Here, nanoparticles (NPs) adhered to the cell window membranes are used as reference objects to study the flow regime of the liquid layer, which causes cooperative motion of the membranes and the NPs. Two categories of motion behaviors are investigated. One is the contraction of NPs toward the interior viewing area which results from the spreading out of the liquid to the surrounding region, with the bending of the membranes increasing with the loss of liquid in the viewing area. The other motion behavior is the occasional movement of all the NPs in the same direction with the directional movement of the liquid layer. This work offers a new method to study the dynamics of liquids by LC-TEM, the discoveries of which are valuable for understanding the confined liquid dynamics.

Relaxation and Aging of Nanosphere Assemblies at a Water-Oil Interface.

The relaxation and aging of an assembly of spherical nanoparticles (NPs) at a water-oil interface are characterized in situ by grazing incidence X-ray photon correlation spectroscopy. The dynamics of the interfacial assembly is measured while the interface saturates with NPs. Weak attractions between NPs lead to gel-like structures in the assembly, where the in-plane ordering is inhibited by the broad size distribution of the NPs. Structural rearrangements on the length scale of the NP-NP center-to-center distances proceed by intermittent fluctuations instead of continuous cooperative motions. The coexistence of rapid and slow NP populations is confirmed, as commonly observed in soft glass-forming materials. Dynamics are increasingly slowed as the NPs initially segregate to the locally clustered interface. The structural relaxation of the NPs in these localized clusters is 5 orders of magnitude slower than that of free particles in the bulk. When the interface is nearly saturated, the time for relaxation increases suddenly due to the onset of local jamming, and the dynamics slow exponentially afterward until the system reaches collective jamming by cooperative rearrangements. This investigation provides insights into structural relaxations near the glass transition and the evolution of the structure and dynamics of the assemblies as they transition from an isotropic liquid to a dense disordered film.

Effect of amplitude and wavelength in the cooperative motion of Taylor lines

In the present study, we have modeled the clustering of binary Taylor line swimmers in a Newtonian fluid. The fluid is modeled using the particle-based simulation method multiparticle collision dynamics, while for the Taylor line, we use a bead spring arrangement with a sine wave passing through it using a bending wave potential. The binary swimmers have the same propulsion speed, but they differ from each other in the shape of the Taylor line ensured by different amplitudes and lengths. We observe that an optimal amplitude exists for the Taylor line swimmer leading to large clusters formation. The size distribution of the clusters was observed to follow a power-law behavior followed by an exponential cutoff. We also calculated the probability of finding a bead of the swimmer as a function of the fractional distance from the center of the bounding circle and observed that when the amplitude is close to the optimal value, the swimmer forms clusters closer to the walls; otherwise, the swimmer stays almost uniformly distributed around the bounding area. When the ratio of the amplitude is high, the clusters formed at the center of the bounding area become stable and have a wedge-shape. By calculating the speed of the swimmer as a function of the fractional distance from the center of the bounding area, we show that the swimmers speed increases with the maximum at the walls. The simulation with a smaller system has revealed that the maximum clustering happens for an amplitude parameter of ∼0.17.

Structural and computational investigation of MMP‐3 affinity improvements with an engineered TIMP‐1 inhibitor

Matrix metalloproteinases (MMPs) are a family of zinc‐dependent endopeptidases that function to mediate tissue remodeling; however, they are also implicated in pathological conditions such as cancer, inflammatory and degenerative diseases. There are 23 human MMPs and significant sequence and structural homology exists among them and with other metalloproteinases. This represents a substantial challenge in developing therapeutically viable selective inhibitors due to off‐target effects. Tissue inhibitors of metalloproteinases (TIMPs) are a family of four endogenous protein protease inhibitors that regulate MMP activity. Our lab and others have utilized TIMPs as scaffolds, engineering them to selectively target specific MMPs for potential therapeutic applications. We previously employed a yeast surface display platform to identify TIMP‐1 variants possessing enhanced MMP‐3 affinity. In the current study, we used structures of MMP‐3 co‐crystallized with either WT TIMP‐1 or an engineered TIMP‐1 variant as seeds for molecular dynamics simulations. Simulations were also conducted on unbound WT and engineered TIMP‐1 to examine MMP‐independent dynamics that distinguish the engineered variant. The simulation data were analyzed with root‐mean‐square deviation/fluctuation, time‐dependent secondary structure, temporally resolved hydrogen bonding, conformational clustering, and dynamical network algorithms to discern structural and dynamical determinants of the increased affinity. Key observations that demonstrate the increased effectiveness of engineered TIMP‐1 as an MMP‐3 inhibitor were secondary structural changes in the MMP‐binding loops in proximity to mutations, attenuated global and mutation‐adjacent dynamics, decreased conformational dynamics, and increased persistence of MMP‐3‐compatible conformations. There were also indications of greater interdomain cooperativity within the engineered TIMP‐1 variant: increased interdomain hydrogen bonding, coordinated motions of the N‐terminal region with the C‐terminal domain, and increased intercommunity information flow/motion transfer. From these observations, we hypothesize the increased interdomain interactions represent a mechanism of dynamical stabilization such that mainly cooperative motion between domains presides, rather than random independent motions. Our findings suggest propagated motions between domains may influence the MMP affinity of TIMPs. Furthermore, these data suggest future strategies to design next‐generation mutant TIMP libraries by targeting regions dynamically coupled to the MMP binding loops for variation, thus exploiting natural protein dynamics to achieve desired selectivity.

Mean-field model for the Curie-Weiss temperature dependence of coherence length in metallic liquids

The coherence length of the medium-range order (MRO) in metallic liquids is known to display a Curie-Weiss temperature dependence; its inverse is linearly related to temperature, and when extrapolated from temperatures above the glass transition, the coherence length diverges at a negative temperature with a critical exponent of unity. We propose a mean-field pseudospin model that explains this behavior. Specifically, we model the atoms and their local environment as Ising spins with antiferromagnetic exchange interactions. We further superimpose an exchange interaction between dynamical heterogeneities, or clusters of atoms undergoing cooperative motion. The coherence length in the metallic liquid is thus the correlation length between dynamical heterogeneities. Our results reaffirm the idea that the MRO coherence length is a measure of point-to-set correlations, and that local frustrations in the interatomic interactions are prominent in metallic liquids.

Autonomous vehicles’ intended cooperative motion planning for unprotected turning at intersections

Turning behaviour is one of the most challenging driving manoeuvres that take place at intersections. Autonomous vehicles (AVs) are often overly conservative in these scenarios as they compromised to others’ behaviour to realize behavioural consistency. This paper proposes an intended cooperative motion planning (ICMP) that can actively predict the intentions of interacting participants. This helps achieve socially compliant cooperation and enables each vehicle to converge upon a set of consistent behaviours. The ICMP framework divides the integrated driving process into two related modules: prediction and planning. These modules are integrated using the mechanism of intended cooperation, which first introduces the criteria for a cooperative response and then maps them in the motion planning space. The prediction module applies a Gaussian mixture model to learn human drivers’ behaviour to determine conflict points, which helps to narrow down the solution spaces. In the planning module, paths are represented by quartic Bézier curves and speed is modelled as a polynomial function. Optimizations can then be used that maximize the efficiency and smoothness for path planning, and comfort and efficiency for speed planning. The test results show that ICMP-based AVs had consistent interactions with other vehicles. Moreover, when compared with a potential field-based method, the ICMP-based method had better performance in terms of safety, comfort and efficiency, especially when interacting with multiple oncoming vehicles.