Optimization of the PID coefficients for the line-follower mobile robot controller employing genetic algorithm

O b j e c t i v e s. To develop a control system for the movement of a mobile robot along a color-contrast line, as well as to find the values of the coefficients of a proportional-integral-differentiating (PID) controller that allows the robot to move along the line at a given speed.M e t ho d s. To adjust the values of the coefficients of the PID controller, methods of enumeration, automatic tuning and a genetic algorithm are used.Re s u l t s. A software package for tuning the PID controller of the educational mobile robot RoboCake, designed to move along a closed color-contrast line at a given speed, has been developed. The software package consists of a simulation model of the specified robot in the Simulink environment, several virtual traces-polygons and a specialized solver based on the developed genetic algorithm. With the help of the proposed fitness function, a mobile robot control system that satisfies the stated conditions is implemented. Based on the conducted model experiments, the desired values of the parameters of the PID controller are obtained.Co n c l u s i o n. A comparison of the effectiveness of various methods of tuning the PID controller is carried out. The developed software package is designed to solve the practical problem of moving a mobile robot along a color-contrast line at a speed of 1 m/s. The results obtained can be used to study methods of evolutionary tuning of stabilization systems for transport robots, ensuring their movement without overshoot.

Insertions in the SARS-CoV-2 Spike N-Terminal Domain May Aid COVID-19 Transmission

Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 is an ongoing pandemic that causes significant health/socioeconomic burden. Variants of concern (VOCs) have emerged which may affect transmissibility, disease severity and re-infection risk. Most studies focus on the receptor-binding domain (RBD) of the Spike protein. However, some studies suggest that the Spike N-terminal domain (NTD) may have a role in facilitating virus entry via sialic-acid receptor binding. Furthermore, most VOCs include novel NTD variants. Recent analyses demonstrated that NTD insertions in VOCs tend to lie close to loop regions likely to be involved in binding sialic acids. We extended the structural characterisation of these putative sugar binding pockets and explored whether variants could enhance the binding to sialic acids and therefore to the host membrane, thereby contributing to increased transmissibility. We found that recent NTD insertions in VOCs (i.e., Gamma, Delta and Omicron variants) and emerging variants of interest (VOIs) (i.e., Iota, Lambda, Theta variants) frequently lie close to known and putative sugar-binding pockets. For some variants, including the recent Omicron VOC, we find increases in predicted sialic acid binding energy, compared to the original SARS-CoV-2, which may contribute to increased transmission. We examined the similarity of NTD across a range of related Betacoronaviruses to determine whether the putative sugar-binding pockets are sufficiently similar to be exploited in drug design. Despite global sequence and structure similarity, most sialic-acid binding pockets of NTD vary across related coronaviruses. Typically, SARS-CoV-2 possesses additional loops in these pockets that increase contact with polysaccharides. Our work suggests ongoing evolutionary tuning of the sugar-binding pockets in the virus. Whilst three of the pockets are too structurally variable to be amenable to pan Betacoronavirus drug design, we detected a fourth pocket that is highly structurally conserved and could therefore be investigated in pursuit of a generic drug. Our structure-based analyses help rationalise the effects of VOCs and provide hypotheses for experiments. For example, the Omicron variant, which has increased binding to sialic acids in pocket 3, has a rather unique insertion near pocket 3. Our work suggests a strong need for experimental monitoring of VOC changes in NTD.

Stabilization and tracking control of an x-z type inverted pendulum system using Lightning Search Algorithm tuned nonlinear PID controller

Inverted pendulum systems (IPSs) are mostly used to demonstrate the control rules for keeping the pendulum at a balanced upright position due to a slight force applied to the cart system. This paper presents an application for nonlinear control of an x-z type IPS by using a proportional-integral-derivative (PID) controller with newly established evolutionary tuning method Lightning Search Algorithm (LSA). A single, double and triple PID controller system is tested with the conventional and the self-tuning controllers to get a better understanding of the performance of the given system. The mathematical modelling of the x-z type IPS, the theoretical explanation of the LSA and the simulation analysis of the x-z type IPS is put forward entirely. The LSA algorithm solves the optimization problem of PID controller in an evolutionary way. The most effective way of making comparisons is evaluating the performance results with a well-known optimization technique or with the previous accepted results. We have compared the system’s performance with particle swarm optimization and with a classical control study in the literature. According to the simulation results, LSA-tuned PID controller has the ability to decrease the overshoot better than the conventional-tuned controllers. Finally, it can be concluded that the LSA-supported PID can better stabilize the pendulum angle and track the reference better for non-disturbed and the slightly disturbed systems.

Characterisation of B.1.1.7 and Pangolin coronavirus spike provides insights on the evolutionary trajectory of SARS-CoV-2

The recent emergence of SARS-CoV-2 variants with increased transmission, pathogenesis and immune resistance has jeopardised the global response to the COVID-19 pandemic. Determining the fundamental biology of viral variants and understanding their evolutionary trajectories will guide current mitigation measures, future genetic surveillance and vaccination strategies. Here we examine virus entry by the B.1.1.7 lineage, commonly referred to as the UK/Kent variant. Pseudovirus infection of model cell lines demonstrate that B.1.1.7 entry is enhanced relative to the Wuhan-Hu-1 reference strain, particularly under low expression of receptor ACE2. Moreover, the entry characteristics of B.1.1.7 were distinct from that of its predecessor strain containing the D614G mutation. These data suggest evolutionary tuning of spike protein function. Additionally, we found that amino acid deletions within the N-terminal domain (NTD) of spike were important for efficient entry by B.1.1.7. The NTD is a hotspot of diversity across sarbecoviruses, therefore, we further investigated this region by examining the entry of closely related CoVs. Surprisingly, Pangolin CoV spike entry was 50-100 fold enhanced relative to SARS-CoV-2; suggesting there may be evolutionary pathways by which SARS-CoV-2 may further optimise entry. Swapping the NTD between Pangolin CoV and SARS-CoV-2 demonstrates that changes in this region alone have the capacity to enhance virus entry. Thus, the NTD plays a hitherto unrecognised role in modulating spike activity, warranting further investigation and surveillance of NTD mutations.

Evolution and expansion of the RUNX2 QA repeat corresponds with the emergence of vertebrate complexity

Runt-related transcription factor 2 (RUNX2) is critical for the development of the vertebrate bony skeleton. Unlike other RUNX family members, RUNX2 possesses a variable poly-glutamine, poly-alanine (QA) repeat domain. Natural variation within this repeat is able to alter the transactivation potential of RUNX2, acting as an evolutionary ‘tuning knob’ suggested to influence mammalian skull shape. However, the broader role of the RUNX2 QA repeat throughout vertebrate evolution is unknown. In this perspective, we examine the role of the RUNX2 QA repeat during skeletal development and discuss how its emergence and expansion may have facilitated the evolution of morphological novelty in vertebrates.

Evolution of dynamical networks enhances catalysis in a designer enzyme

Activation heat capacity is emerging as a crucial factor in enzyme thermoadaptation, as shown by non-Arrhenius behaviour of many natural enzymes1,2. However, its physical origin and relationship to evolution of catalytic activity remain uncertain. Here, we show that directed evolution of a computationally designed Kemp eliminase introduces dynamical changes that give rise to an activation heat capacity absent in the original design3. Extensive molecular dynamics simulations show that evolution results in the closure of solvent exposed loops and better packing of the active site with transition state stabilising residues. Remarkably, these changes give rise to a correlated dynamical network involving the transition state and large parts of the protein. This network tightens the transition state ensemble, which induces an activation heat capacity and thereby nonlinearity in the temperature dependence. Our results have implications for understanding enzyme evolution (e.g. in explaining the role of distal mutations and evolutionary tuning of dynamical responses) and suggest that integrating dynamics with design and evolution will accelerate the development of efficient novel enzymes.