Intelligent robust control of redundant smart robotic arm Pt I: Soft computing KB optimizer - deep machine learning IT

Redundant robotic arm models as a control object discussed. Background of computational intelligence IT based on soft computing optimizer of knowledge base in smart robotic manipulators introduced. Soft computing optimizer is the toolkit of deep machine learning SW platform with optimal fuzzy neural network structure. The methods for development and design technology of intelligent control systems based on the soft computing optimizer presented in this Part 1 allow one to implement the principle of design an optimal intelligent control systems with a maximum reliability and controllability level of a complex control object under conditions of uncertainty in the source data, and in the presence of stochastic noises of various physical and statistical characters. The knowledge bases formed with the application of a soft computing optimizer produce robust control laws for the schedule of time dependent coefficient gains of conventional PID controllers for a wide range of external perturbations and are maximally insensitive to random variations of the structure of control object. The robustness of control laws is achieved by application a vector fitness function for genetic algorithm, whose one component describes the physical principle of minimum production of generalized entropy both in the control object and the control system, and the other components describe conventional control objective functionals such as minimum control error, etc. The application of soft computing technologies (Part I) for the development a robust intelligent control system that solving the problem of precision positioning redundant (3DOF and 7 DOF) manipulators considered. Application of quantum soft computing in robust intelligent control of smart manipulators in Part II described

Robotic Smart Prosthesis Arm with BCI and Kansei / Kawaii / Affective Engineering Approach. Pt I: Quantum Soft Computing Supremacy

A description of the design stage and results of the development of the conceptual structure of a robotic prosthesis arm is given. As a result, a prototype of manmade prosthesis on a 3D printer as well as a foundation for computational intelligence presented. The application of soft computing technology (the first step of IT) allows to extract knowledge directly from the physical signal of the electroencephalogram, as well as to form knowledge-based intelligent robust control of the lower performing level taking into account the assessment of the patient’s emotional state. The possibilities of applying quantum soft computing technologies (the second step of IT) in the processes of robust filtering of electroencephalogram signals for the formation of mental commands and quantum supremacy simulation of robotic prosthetic arm discussed

Intelligent control of mobile robot with redundant manipulator & stereovision: quantum / soft computing toolkit

The task of an intelligent control system design applying soft and quantum computational intelligence technologies discussed. An example of a control object as a mobile robot with redundant robotic manipulator and stereovision introduced. Design of robust knowledge bases is performed using a developed computational intelligence – quantum / soft computing toolkit (QC/SCOptKBTM). The knowledge base self-organization process of fuzzy homogeneous regulators through the application of end-to-end IT of quantum computing described. The coordination control between the mobile robot and redundant manipulator with stereovision based on soft computing described. The general design methodology of a generalizing control unit based on the physical laws of quantum computing (quantum information-thermodynamic trade-off of control quality distribution and knowledge base self-organization goal) is considered. The modernization of the pattern recognition system based on stereo vision technology presented. The effectiveness of the proposed methodology is demonstrated in comparison with the structures of control systems based on soft computing for unforeseen control situations with sensor system

The mRubyFT Protein, Genetically Encoded Blue-to-Red Fluorescent Timer.

peer reviewedGenetically encoded monomeric blue-to-red fluorescent timers (mFTs) change their fluorescent color over time. mCherry-derived mFTs were used for the tracking of the protein age, visualization of the protein trafficking, and labeling of engram cells. However, the brightness of the blue and red forms of mFTs are 2-3- and 5-7-fold dimmer compared to the brightness of the enhanced green fluorescent protein (EGFP). To address this limitation, we developed a blue-to-red fluorescent timer, named mRubyFT, derived from the bright mRuby2 red fluorescent protein. The blue form of mRubyFT reached its maximum at 5.7 h and completely transformed into the red form that had a maturation half-time of 15 h. Blue and red forms of purified mRubyFT were 4.1-fold brighter and 1.3-fold dimmer than the respective forms of the mCherry-derived Fast-FT timer in vitro. When expressed in mammalian cells, both forms of mRubyFT were 1.3-fold brighter than the respective forms of Fast-FT. The violet light-induced blue-to-red photoconversion was 4.2-fold less efficient in the case of mRubyFT timer compared to the same photoconversion of the Fast-FT timer. The timer behavior of mRubyFT was confirmed in mammalian cells. The monomeric properties of mRubyFT allowed the labeling and confocal imaging of cytoskeleton proteins in live mammalian cells. The X-ray structure of the red form of mRubyFT at 1.5 Å resolution was obtained and analyzed. The role of the residues from the chromophore surrounding was studied using site-directed mutagenesis

Demonstration of a parity-time symmetry breaking phase transition using superconducting and trapped-ion qutrits

Scalable quantum computers hold the promise to solve hard computational problems, such as prime factorization, combinatorial optimization, simulation of many-body physics, and quantum chemistry. While being key to understanding many real-world phenomena, simulation of non-conservative quantum dynamics presents a challenge for unitary quantum computation. In this work, we focus on simulating non-unitary parity-time symmetric systems, which exhibit a distinctive symmetry-breaking phase transition as well as other unique features that have no counterpart in closed systems. We show that a qutrit, a three-level quantum system, is capable of realizing this non-equilibrium phase transition. By using two physical platforms - an array of trapped ions and a superconducting transmon - and by controlling their three energy levels in a digital manner, we experimentally simulate the parity-time symmetry-breaking phase transition. Our results indicate the potential advantage of multi-level (qudit) processors in simulating physical effects, where additional accessible levels can play the role of a controlled environment.Comment: 14 pages, 9 figure

Combined Structural and Computational Study of the mRubyFT Fluorescent Timer Locked in Its Blue Form

The mRubyFT is a monomeric genetically encoded fluorescent timer based on the mRuby2 fluorescent protein, which is characterized by the complete maturation of the blue form with the subsequent conversion to the red one. It has higher brightness in mammalian cells and higher photostability compared with other fluorescent timers. A high-resolution structure is a known characteristic of the mRubyFT with the red form chromophore, but structural details of its blue form remain obscure. In order to obtain insight into this, we obtained an S148I variant of the mRubyFT (mRubyFTS148I) with the blocked over time blue form of the chromophore. X-ray data at a 1.8 Å resolution allowed us to propose a chromophore conformation and its interactions with the neighboring residues. The imidazolidinone moiety of the chromophore is completely matured, being a conjugated π-system. The methine bridge is not oxidized in the blue form bringing flexibility to the phenolic moiety that manifests itself in poor electron density. Integration of these data with the results of molecular dynamic simulation disclosed that the OH group of the phenolic moiety forms a hydrogen bond with the side chain of the T163 residue. A detailed comparison of mRubyFTS148I with other available structures of the blue form of fluorescent proteins, Blue102 and mTagBFP, revealed a number of characteristic differences. Molecular dynamic simulations with the combined quantum mechanic/molecular mechanic potentials demonstrated that the blue form exists in two protonation states, anion and zwitterion, both sharing enolate tautomeric forms of the C=C–O− fragment. These two forms have similar excitation energies, as evaluated by calculations. Finally, excited state molecular dynamic simulations showed that excitation of the chromophore in both protonation states leads to the same anionic fluorescent state. The data obtained shed light on the structural features and spectral properties of the blue form of the mRubyFT timer

Elucidation of the Conformational Transition of Oligopeptidase B by an Integrative Approach Based on the Combination of X-ray, SAXS, and Essential Dynamics Sampling Simulation

Oligopeptidase B (OPB) is the least studied group from the prolyl oligopeptidase family. OPBs are found in bacteria and parasitic protozoa and represent pathogenesis factors of the corresponding infections. OPBs consist of two domains connected by a hinge region and have the characteristics of conformational dynamics, which include two types of movements: the bridging/separation of α/β-hydrolase catalytic and β-propeller-regulatory domains and the movement of a loop carrying catalytic histidine, which regulates an assembly/disassembly of the catalytic triad. In this work, an elucidation of the interdomain dynamics of OPB from Serratia proteamaculans (SpOPB) with and without modification of the hinge region was performed using a combination of X-ray diffraction analysis and small-angle X-ray scattering, which was complemented with an essential dynamics sampling (EDS) simulation. The first crystal structure of catalytically deficient SpOPB (SpOPBS532A) with an intact hinge sequence is reported. Similarly to SpOPB with modified hinges, SpOPBS532A was crystallized in the presence of spermine and adopted an intermediate conformation in the crystal lattice. Despite the similarity of the crystal structures, a difference in the catalytic triad residue arrangement was detected, which explained the inhibitory effect of the hinge modification. The SpOPBS532A structure reconstituted to the wild-type form was used as a starting point to the classical MD followed by EDS simulation, which allowed us to simulate the domain separation and the transition of the enzyme from the intermediate to open conformation. The obtained open state model was in good agreement with the experimental SAXS data

Blue-to-Red TagFT, mTagFT, mTsFT, and Green-to-FarRed mNeptusFT2 Proteins, Genetically Encoded True and Tandem Fluorescent Timers

True genetically encoded monomeric fluorescent timers (tFTs) change their fluorescent color as a result of the complete transition of the blue form into the red form over time. Tandem FTs (tdFTs) change their color as a consequence of the fast and slow independent maturation of two forms with different colors. However, tFTs are limited to derivatives of the mCherry and mRuby red fluorescent proteins and have low brightness and photostability. The number of tdFTs is also limited, and there are no blue-to-red or green-to-far-red tdFTs. tFTs and tdFTs have not previously been directly compared. Here, we engineered novel blue-to-red tFTs, called TagFT and mTagFT, which were derived from the TagRFP protein. The main spectral and timing characteristics of the TagFT and mTagFT timers were determined in vitro. The brightnesses and photoconversions of the TagFT and mTagFT tFTs were characterized in live mammalian cells. The engineered split version of the TagFT timer matured in mammalian cells at 37 °C and allowed the detection of interactions between two proteins. The TagFT timer under the control of the minimal arc promoter, successfully visualized immediate-early gene induction in neuronal cultures. We also developed and optimized green-to-far-red and blue-to-red tdFTs, named mNeptusFT and mTsFT, which were based on mNeptune-sfGFP and mTagBFP2-mScarlet fusion proteins, respectively. We developed the FucciFT2 system based on the TagFT-hCdt1-100/mNeptusFT2-hGeminin combination, which could visualize the transitions between the G1 and S/G2/M phases of the cell cycle with better resolution than the conventional Fucci system because of the fluorescent color changes of the timers over time in different phases of the cell cycle. Finally, we determined the X-ray crystal structure of the mTagFT timer and analyzed it using directed mutagenesis

Elucidation of the Conformational Transition of Oligopeptidase B by an Integrative Approach Based on the Combination of X-ray, SAXS, and Essential Dynamics Sampling Simulation

Oligopeptidase B (OPB) is the least studied group from the prolyl oligopeptidase family. OPBs are found in bacteria and parasitic protozoa and represent pathogenesis factors of the corresponding infections. OPBs consist of two domains connected by a hinge region and have the characteristics of conformational dynamics, which include two types of movements: the bridging/separation of α/β-hydrolase catalytic and β-propeller-regulatory domains and the movement of a loop carrying catalytic histidine, which regulates an assembly/disassembly of the catalytic triad. In this work, an elucidation of the interdomain dynamics of OPB from Serratia proteamaculans (SpOPB) with and without modification of the hinge region was performed using a combination of X-ray diffraction analysis and small-angle X-ray scattering, which was complemented with an essential dynamics sampling (EDS) simulation. The first crystal structure of catalytically deficient SpOPB (SpOPBS532A) with an intact hinge sequence is reported. Similarly to SpOPB with modified hinges, SpOPBS532A was crystallized in the presence of spermine and adopted an intermediate conformation in the crystal lattice. Despite the similarity of the crystal structures, a difference in the catalytic triad residue arrangement was detected, which explained the inhibitory effect of the hinge modification. The SpOPBS532A structure reconstituted to the wild-type form was used as a starting point to the classical MD followed by EDS simulation, which allowed us to simulate the domain separation and the transition of the enzyme from the intermediate to open conformation. The obtained open state model was in good agreement with the experimental SAXS data

Blue-to-Red TagFT, mTagFT, mTsFT, and Green-to-FarRed mNeptusFT2 Proteins, Genetically Encoded True and Tandem Fluorescent Timers

True genetically encoded monomeric fluorescent timers (tFTs) change their fluorescent color as a result of the complete transition of the blue form into the red form over time. Tandem FTs (tdFTs) change their color as a consequence of the fast and slow independent maturation of two forms with different colors. However, tFTs are limited to derivatives of the mCherry and mRuby red fluorescent proteins and have low brightness and photostability. The number of tdFTs is also limited, and there are no blue-to-red or green-to-far-red tdFTs. tFTs and tdFTs have not previously been directly compared. Here, we engineered novel blue-to-red tFTs, called TagFT and mTagFT, which were derived from the TagRFP protein. The main spectral and timing characteristics of the TagFT and mTagFT timers were determined in vitro. The brightnesses and photoconversions of the TagFT and mTagFT tFTs were characterized in live mammalian cells. The engineered split version of the TagFT timer matured in mammalian cells at 37 °C and allowed the detection of interactions between two proteins. The TagFT timer under the control of the minimal arc promoter, successfully visualized immediate-early gene induction in neuronal cultures. We also developed and optimized green-to-far-red and blue-to-red tdFTs, named mNeptusFT and mTsFT, which were based on mNeptune-sfGFP and mTagBFP2-mScarlet fusion proteins, respectively. We developed the FucciFT2 system based on the TagFT-hCdt1-100/mNeptusFT2-hGeminin combination, which could visualize the transitions between the G1 and S/G2/M phases of the cell cycle with better resolution than the conventional Fucci system because of the fluorescent color changes of the timers over time in different phases of the cell cycle. Finally, we determined the X-ray crystal structure of the mTagFT timer and analyzed it using directed mutagenesis