Real Complexes Research Articles

Using Short Molecular Dynamics Simulations to Determine the Important Features of Interactions in Antibody-Protein Complexes.

The last few years have seen the rapid proliferation of machine learning methods to design binding proteins. Although these methods have shown large increases in experimental success rates compared to prior approaches, the majority of their predictions fail when they are experimentally tested. It is evident that computational methods still struggle to distinguish the features of real protein binding interfaces from false predictions. Short molecular dynamics simulations of 20 antibody-protein complexes were conducted to identify features of interactions that should occur in binding interfaces. Intermolecular salt bridges, hydrogen bonds, and hydrophobic interactions were evaluated for their persistences, energies, and stabilities during the simulations. It was found that only the hydrogen bonds where both residues are stabilized in the bound complex are expected to persist and meaningfully contribute to binding between the proteins. In contrast, stabilization was not a requirement for salt bridges and hydrophobic interactions to persist. Still, interactions where both residues are stabilized in the bound complex persist significantly longer and have significantly stronger energies than other interactions. Two hundred and twenty real antibody-protein complexes and 8194 decoy complexes were used to train and test a random forest classifier using the features of expected persistent interactions identified in this study and the macromolecular features of interaction energy (IE), buried surface area (BSA), IE/BSA, and shape complementarity. It was compared to a classifier trained only on the expected persistent interaction features and another trained only on the macromolecular features. Inclusion of the expected persistent interaction features reduced the false positive rate of the classifier by two- to five-fold across a range of true positive classification rates.

Morse theoretic signal compression and reconstruction on chain complexes

At the intersection of Topological Data Analysis (TDA) and machine learning, the field of cellular signal processing has advanced rapidly in recent years. In this context, each signal on the cells of a complex is processed using the combinatorial Laplacian, and the resultant Hodge decomposition. Meanwhile, discrete Morse theory has been widely used to speed up computations by reducing the size of complexes while preserving their global topological properties. In this paper, we provide an approach to signal compression and reconstruction on chain complexes that leverages the tools of algebraic discrete Morse theory. The main goal is to reduce and reconstruct a based chain complex together with a set of signals on its cells via deformation retracts, preserving as much as possible the global topological structure of both the complex and the signals. We first prove that any deformation retract of real degree-wise finite-dimensional based chain complexes is equivalent to a Morse matching. We will then study how the signal changes under particular types of Morse matchings, showing its reconstruction error is trivial on specific components of the Hodge decomposition. Furthermore, we provide an algorithm to compute Morse matchings with minimal reconstruction error.

К вопросу об отнесении линейных объектов к объектам капитального строительства, недвижимого имущества, категории единого недвижимого комплекса

This article examines the classification of linear objects within the context of capital construction, real estate, and single real estate complexes. The study reviews relevant provisions of the Urban Planning Code of the Russian Federation, the Land Code of the Russian Federation, the Civil Code of the Russian Federation, as well as other federal laws and subordinate regulations. The explanations of authorized authorities, acts of judi-cial authorities, opinions of researchers of civil law science on the concept of linear objects and their inherent characteristics, belonging of linear objects to capital construction objects, real estate, the ratio of these con-cepts, belonging of linear objects to the category of a single immovable complex, things of auxiliary purpose, the specifics of linear objects in comparison are analyzed with other objects of civil rights in terms of restrictions on the interests of land rights holders, necessary for the placement, maintenance and repair of linear objects, the extension of the protected zone of linear objects with a special legal regime to a certain part of the land plots. Conflicts of law, controversial issues of judicial practice are revealed, the author’s definition of linear ob-jects is formulated, including their inherent features. The directions of the development of regulatory regulation, including in terms of the unification of terminology and proposals to consolidate the types of linear objects re-lated to real estate by the norms of special legislation, are determined.

Assessment of the usefulness of β-cyclodextrin in the removal of progesterone from the environment

The paper presents the results and interpretation of theoretical calculations for the progesterone–β-cyclodextrin (P@β-CD; G4MP2) and progesterone–β-cyclodextrin–β-cyclodextrin (P@β-CD–β-CD; G2) systems. The geometry of the progesterone molecule was optimized on basis of the DFT theory using the B3LYP, PBE1PBE and M06-2X functionals, for selected Pople basis sets [6-31G, 6‐31++G, 6‐31++G(d,p), 6-311G, 6‐311++G, 6‐311++G(d,p)] and the Dunning basis set (aug-cc-pVDZ). Presented results of theoretical calculations provide insight into the mechanism of formation of supramolecular systems of progesterone and β-cyclodextrin, allowing us to understand the impact of differences in the polarizability of specific fragments of the “guest” molecule, through the analysis of the Mulliken population distribution, on the tendency for equilibrium inclusion by “host” molecules characterized by selective affinity towards hydrophilic and hydrophobic molecular systems. The comparison of model structures of “guest–host” systems with 1:1 and 1:2 stoichiometry allows us to assess the contribution of a given type of non-covalent interactions (hydrogen bonds, van der Waals interactions, London dispersion forces) in the formation of supramolecular complexes. Due to the complexity of the real research object, including interactions between large molecules in solution, in this work it was decided to choose an approximation that reflects only the key effects. The results presented in this paper constitute a starting point for both theoretical research on analogous supramolecular systems based on β-cyclodextrin derivatives, as well as instrumental studies (NMR, FT–IR, HPLC) of preparations of real inclusion complexes. The approach adopted now can contribute to a better understanding of the phenomenon used in the development of water purification technologies.

Территориальные комплексы недвижимости и новое законодательство об общей долевой собственности

The article analyses the meaning of the new norms of the Russian Civil Code on common shared ownership of common property of owners of real estate (buildings, structures and land plots) included in territorial complexes. It concludes that the norms of § 2 of Chapter 16 of the Civil Code cannot be considered as a legal basis for the emergence of shared ownership of common property in territorial real estate complexes. The norms of the Civil Code serve as the basis for the emergence of common shared ownership only for owners of premises and parking spaces in buildings and structures. For other real estate complexes consisting of buildings, structures, land plots, either a special law is required, which in this case acts as the basis for the emergence of shared ownership, or a joint expression of the will of all property owners — a transaction. At the same time, Art. 259.1 of the Civil Code opens up the possibility of carrying out such transactions, defines the conditions under which they can be concluded, and the characteristics of the object of such transactions — the common property of the owners of immovable things. The author criticises the conditions provided by law for the emergence of shared ownership of common property — the definition of the boundaries of the common territory and the physical or technological connection of the complex’s objects — and believes that such a condition should be the presence of common property. The proposal for the development of legislation is to establish a unified legal regulation of relations in any territorial real estate complexes, abandoning special laws on certain types of such complexes.

Creation of virtual models of buildings for the formation of unified real estate complexes as a part of land and cadastral works

The article presents the results of the research project to create 3D models of buildings from digital images using a smartphone camera and the Agisoft Photoscan Professional software, comparing them with data obtained with an electronic total station. The authors outlined the possibilities of using the described technologies for the development of 3D cadastre, which can simplify creation of virtual models through the adaptation of modern widgets. The technological sequence of creating a building model in a virtual format and the accuracy of linear measurements are considered here. The paper contains the results of determining the area and the value of the mean square error. The authors presume that these technologies can be used for the development of 3D cadastre in the formation of unified real estate complexes as a part of land cadastral works, as well as for design and reconstruction solutions.

Identifying influential nodes in spreading process in higher-order networks

Identifying influential nodes in spreading process in the network is an important step to control the speed and range of spreading, which can be used to accelerate the spread of beneficial information such as healthy behaviors, innovations and suppress the spread of epidemics, rumors and fake news. Existing researches on identification of influential spreaders are mostly based on low-order complex networks with pairwise interactions. However, interactions between individuals occur not only between pairwise nodes but also in groups of three or more nodes, which introduces complex mechanism of reinforcement and indirect influence. The higher-order networks such as simplicial complexes and hypergraphs, can describe features of interactions that go beyond the limitation of pairwise interactions. Currently, there are relatively few researches of identifying influential spreaders in higher-order networks. Some centralities of nodes such as higher-order degree centrality and eigenvector centrality are proposed, but they mostly consider only the network structure. As for identification of influential spreaders, the spreading influence of a node is closely related to the spreading process. In this paper, we work on identification of influential spreaders on simplicial complexes by taking both network structure and dynamical process into consideration. Firstly, we quantitatively describe the dynamics of disease spreading on simplicial complexes by using the Susceptible-Infected-Recovered microscopic Markov equations. Next, we use the microscopic Markov equations to calculate the probability that a node is infected in the spreading process, which is defined as the spreading centrality (SC) of nodes. This spreading centrality involves both the structure of simplicial complex and the dynamical process on it, and is then used to rank the spreading influence of nodes. Simulation results on two types of synthetic simplicial complexes and four real simplicial complexes show that compared with the existing centralities on higher-order networks and the optimal centralities of collective influence and nonbacktracking centrality in complex networks, the proposed spreading centrality can more accurately identify the most influential spreaders in simplicial complexes. In addition, we find that the probability of nodes infected is highly positively correlated with its influence, which is because disease preferentially reaches nodes with many contacts, who can in turn infect their many neighbors and become influential spreaders.

Topology and dynamics of higher-order multiplex networks

Higher-order networks are gaining significant scientific attention due to their ability to encode the many-body interactions present in complex systems. However, higher-order networks have the limitation that they only capture many-body interactions of the same type. To address this limitation, we present a mathematical framework that determines the topology of higher-order multiplex networks and illustrates the interplay between their topology and dynamics. Specifically, we examine the diffusion of topological signals associated not only to the nodes but also to the links and to the higher-dimensional simplices of multiplex simplicial complexes. We leverage on the ubiquitous presence of the overlap of the simplices to couple the dynamics among multiplex layers, introducing a definition of multiplex Hodge Laplacians and Dirac operators. We show that the spectral properties of these operators determine higher-order diffusion on higher-order multiplex networks and encode their multiplex Betti numbers. Our numerical investigation of the spectral properties of synthetic and real (connectome, microbiome) multiplex simplicial complexes indicates that the coupling between the layers can either speed up or slow down the higher-order diffusion of topological signals. This mathematical framework is very general and can be applied to study generic higher-order systems with interactions of multiple types. In particular, these results might find applications in brain networks which are understood to be both multilayer and higher-order.

Imaging and detecting intercellular tensile forces in spheroids and embryoid bodies using lipid-modified DNA probes.

Cells continuously experience and respond to different physical forces that are used to regulate their physiology and functions. Our ability to measure these mechanical cues is essential for understanding the bases of various mechanosensing and mechanotransduction processes. While multiple strategies have been developed to study mechanical forces within two-dimensional (2D) cell culture monolayers, the force measurement at cell-cell junctions in real three-dimensional (3D) cell models is still pretty rare. Considering that in real biological systems, cells are exposed to forces from 3D directions, measuring these molecular forces in their native environment is thus highly critical for the better understanding of different development and disease processes. We have recently developed a type of DNA-based molecular probe for measuring intercellular tensile forces in 2D cell models. Herein, we will report the further development and first-time usage of these molecular tension probes to visualize and detect mechanical forces within 3D spheroids and embryoid bodies (EBs). These probes can spontaneously anchor onto live cell membranes via the attached lipid moieties. By varying the concentrations of these DNA probes and their incubation time, we have first characterized the kinetics and efficiency of probe penetration and loading onto tumor spheroids and stem cell EBs of different sizes. After optimization, we have further imaged and measured E-cadherin-mediated forces in these 3D spheroids and EBs for the first time. Our results indicated that these DNA-based molecular tension probes can be used to study the spatiotemporal distributions of target mechanotransduction processes. These powerful imaging tools may be potentially applied to fill the gap between ongoing research of biomechanics in 2D systems and that in real 3D cell complexes.

PCGAN: a generative approach for protein complex identification from protein interaction networks.

Protein complexes are groups of polypeptide chains linked by non-covalent protein-protein interactions, which play important roles in biological systems and perform numerous functions, including DNA transcription, mRNA translation, and signal transduction. In the past decade, a number of computational methods have been developed to identify protein complexes from protein interaction networks by mining dense subnetworks or subgraphs. In this article, different from the existing works, we propose a novel approach for this task based on generative adversarial networks, which is called PCGAN, meaning identifying Protein Complexes by GAN. With the help of some real complexes as training samples, our method can learn a model to generate new complexes from a protein interaction network. To effectively support model training and testing, we construct two more comprehensive and reliable protein interaction networks and a larger gold standard complex set by merging existing ones of the same organism (including human and yeast). Extensive comparison studies indicate that our method is superior to existing protein complex identification methods in terms of various performance metrics. Furthermore, functional enrichment analysis shows that the identified complexes are of high biological significance, which indicates that these generated protein complexes are very possibly real complexes. https://github.com/yul-pan/PCGAN.

Evaluating planting strategies for outdoor thermal comfort in high-rise residential complexes: a computational fluid dynamics simulation study.

This study aims to examine the impact of planting strategies on improving thermal comfort in relation to the existing buildings within real high-rise residential complexes. Using numerical simulation via ENVI-met, we compare six planting scenarios characterized by two locational schemes-open-space planting and building-vicinity planting-and three tree quantities. The results highlight the importance of planting greater numbers of trees, and also of their locations, to moderate the thermal environment. The findings of the study demonstrated that increasing the number of trees in the open space by threefold of the advisory guidelines led to a significant reduction in the average air temperature by 0.87°C, mean radiant temperature (MRT) by 11.00°C, physiological equivalent temperature (PET) by 4.50°C, and wind speed by 0.30m/s. Planting the minimum number of trees under building-vicinity reduced air temperature by 0.07°C, MRT by 2.48°C, and PET by 0.92°C, while showing a slight increase in wind speed of approximately 0.01m/s. To achieve improvements in both thermal condition and air flow, we suggest planting rows of trees parallel to the prevailing wind direction in the ventilation corridors at some distance from buildings, to minimize overlap of shade from trees and from buildings. The findings of this study will provide useful guidelines for effective planting design in dense residential areas.

Using a Digital Twin of Hybrid Energy Complexes to Optimize Their Parameters and Operation Modes

The aim of the work is to develop a universal technique that will make it possible to determine -- both quickly and with high accuracy -- the optimal composition, parameters and operation modes of hybrid energy complexes containing power plants that use renewable energy sources and energy storage systems from the viewpoint of ensuring safe operation and guaranteed electricity and heat supply to isolated consumers and hard-to-reach areas. The article shows the effectiveness of research and development of recommendations on the choice of parameters and operation modes of hybrid energy complexes with a heterogeneous composition of generating plants and a high dependence on natural uncertain factors at all stages of the life cycle using the developed universal digital twin, which was verified on the example of real energy complexes with miscellaneous composition of equipment.

About Some Aspects of Finite State Machine Models Application to Group Control

The article discusses using discrete-event models to control the coordinated behavior of groups of agents and proposes a mechanism for organizing behavior control based on a hierarchy of finite state machines (FSM). The basic level of agent movement control uses a continuous model of joint movement — the method of potentials, in which the direction of movement is determined by the total sum of the forces of "repulsion", "attraction" and "course alignment". The paper describes a set of independent rules for the group movement of agents — cohesion, distribution, leader following, movement along a chain of landmarks, pursuit, etc. Moreover, all of them are interpreted in terms of the results of the operation of FSM models. Mathematical modeling of controlling a group of agents was carried out using the independent rules of group movement, which confirmed their efficacy. Computational experiments were also carried out using the Gazebo 3D simulator. In addition, the paper describes an experimental group of three underwater vehicles that were used to test the independent rules of group movement: cohesion, distribution, leader following. Communication between the devices was carried out using a system of infrared transceivers via a pseudo-analog channel. The experiments were carried out in a laboratory pool and were successful.The paper shows that the technology for creating group control systems based on the hierarchy of FSM (meta-FSM) allows solving control problems not only at the level of abstract models and simulation modeling, but also at the level of creating real robotic complexes.

SIMPLIFIED ASSESSMENT OF EARTHQUAKE DAMAGE RATIO FOR LOW- AND MID-RISE BUILDINGS BASED ON ENERGY BALANCE CONSIDERING SOIL-STRUCTURE INTERACTION

In order to easily assess the damage caused by earthquakes in low- and mid-rise building complexes, this paper proposes a simplified method for assessing the damage ratio in real building complexes by combining a seismic evaluation method based on the energy balance and reliability theory. This method enables the effect of dissipation damping to be taken into account, and is effective for the evaluation of the largest foreshocks and aftershocks in addition to the main shock. A comparison of the damage ratio calculated using this method with the actual damage ratio from the 1995 Hyogo-ken Nanbu Earthquake showed that the two ratios generally matched with each other. In terms of applications, this method provides a standard for calculating the base shear coefficient of low-rise reinforced concrete buildings for continued use after an earthquake from the viewpoint of performance design.

DECARBONIZATION MANAGEMENT: DEVELOPMENT OF A SYNERGY MODEL OF ELECTROMOBILITY FOR CLIMATE CONSERVATION

The work uses an integrated approach, methods of analysis and synthesis. The research is based on the official data of world economic statistics, the study of data from international news agencies and organizations. The changes in the planet's climate under the influence of emissions of harmful substances into the atmosphere are shown. The analysis of the existing processes allows us to judge that the world community is already fully aware of the severity and possible consequences of climate change, but is not yet ready for taking radical effective measures to stabilize the situation. The need for systemic measures to preserve the climate was noted. It is pointed out that in the process of decarbonization management, the development of electromobility, which should be combined with environmentally-friendly methods of generating electrical energy, occupies the most important place. The synergistic effect of the proposed model for the development of electromobility is manifested in the fact that it can receive support not only from supporters of electromobility, but also from those who support the construction of private houses to ensure comfortable living for people. The analysis of the calculated indicators of obtaining electrical energy for different conditions is carried out. It is shown that among many options for using the synergetic model, there are those that quite reliably provide electric vehicles and households with energy. A synergetic model is proposed, which includes the management of a set of factors to ensure the process of balanced development of electric mobility, which has a number of advantages: ease of placement of electric vehicles; no air pollution; the possibility in some cases of fully charging electric vehicles with their own energy, meeting the needs of households, as well as the supply of excess energy to the external electricity grid; the ability to charge electric cars at home with your own charger, while such charging is not limited in time. Such synergetic model of electric mobility development should contribute not only to the widespread use of electric vehicles, but also to the creation of comfortable living conditions for people, so it can be much more attractive for implementation. The results of the work can be used in practice in the process of managing the development of real complexes of objects associated with the operation of environmentally-friendly transport.

Scalable Architecture and Structure of Modules for Distributed Process Control System in Industrial Greenhouse Comp

With the growth of the population, the issue of food supply of cities with high-quality agricultural crops becomes urgent. Supply problems arising from this can be solved with the use of industrial greenhouse complexes with artificial lighting and groundless technologies. The development of these complexes makes the task of developing a control system to automate the cultivation processes urgent. Real industrial greenhouse complexes have a significant number of operations with the direct participation of personnel, which can be automated: control of the greenhouse microclimate, lighting, watering and preparation of the nutrient solution composition. This paper presents the architecture of a distributed control system for industrial greenhouse complexes. The system is built on a modular basis and is divided into three levels. The developed architecture is based on the use of standard modules, which makes the control system flexible and scalable. The paper also presents the basic design ratios, with the help of which it is possible to determine the required number of modules for the three levels of the proposed architecture. The use of wireless data transmission between modules based on LoRa technology allows you to abandon the laying of an information bus and at the same time deploy the system over large areas. Control of the system and its parameters is possible through direct human interaction with the interface of the control module or through remote interaction through the cloud. The architecture includes 3 types of executive modules, one combined sensor module and a control module. Each of the executive modules functions according to a given algorithm, and its parameters are controlled by a control module, based on a given growing program and information from sensors. This feature allows you to increase the reliability of the system and continue working in the event of a loss of communication with the cloud, as well as to exclude emergencies in the event of a loss of communication between the modules. The developed solutions make it possible to adapt the proposed control system for greenhouse complexes of various configurations and growing principles.

The cohomology rings of real toric spaces and smooth real toric varieties

We compute the cohomology rings of smooth real toric varieties and of real toric spaces, which are quotients of real moment-angle complexes by freely acting subgroups of the ambient 2-torus. The differential graded algebra (dga) we present is in fact an equivariant dga model, valid for arbitrary coefficients. We deduce from our description that smooth toric varieties are $\hbox{M}$-varieties.

Analysis of Non-innocence of Phosphaquinodimethane Ligands when Charge and Aromaticity Come into Play.

Several phosphaquinodimethanes and their M(CO)5 complexes (M=Cr, Mo, W) and model derivatives have been theoretically investigated regarding the quest of non‐innocence. Computed structural and electronic properties of the P‐Me/NH2 substituted phosphaquinodimethanes and tungsten complexes revealed an interesting non‐innocent ligand behaviour for the radical anion complexes with distonic ion character and a strong rearomatization of the middle phenyl ring. The latter was further probed taking also geometric aromaticity (HOMA) and quinoid distortion parameters (HOMQc) into account, as well as NICS(1). Furthermore, the effect of the P‐substitution was investigated for real (or plausible) complexes and their free ligands focusing on the resulting aromaticity at the middle phenyl ring and vertical one‐electron redox processes. The best picture of ligand engagement in redox changes was provided by representing NICS(1) values versus HOMA and the new geometric distortion parameter HOMQc8.

Expanding the capabilities of the ARCHICAD software package for effective solution of construction design tasks

Effective management of real estate complexes, which determines the minimum cost of ownership of constructed and operated objects, implies at the present stage the active introduction of information modeling technologies into the project life cycle. At the same time, in all the variety of modeling software and modeling formats offered by the national and foreign markets, those that have advanced controllability and adaptability to the changing conditions of the design or actual construction stages are the most effective for the purposes of managing the capital intensity of a non-movable asset. The ARCHICAD software package, which is a recognized leader in architectural modeling software, contains the necessary standard and additional tools for creating parameterized objects - elements of a real estate object that have the required properties, significantly accelerating and simplifying the work on adapting the model and optimizing space-planning solutions created on its basis. The authors created a universal parameterizing library feature of wall panel of precast technology in private residential construction, which implements a modular approach to parametric modeling using encapsulation basic library features to upgrade effectively the panel, to implement the specification of resources, visualize technology, including the virtual reality environment, providing the necessary visibility when training for line personnel of the construction site and technical quality control of construction products. The estimation to reduce the complexity and growth performance of work implementation of the proposed approach when designing a wall barrier of low-rise residential buildings.

SETS: A Seed-Dense-Expanding Model-Based Topological Structure for the Prediction of Overlapping Protein Complexes

Defining protein complexes by analysing the protein–protein interaction (PPI) networks is a crucial task in understanding the principles of a biological cell. In the last few decades, researchers have proposed numerous methods to explore the topological structure of a PPI network to detect dense protein complexes. In this paper, the overlapping protein complexes with different densities are predicted within an acceptable execution time using seed expanding model and topological structure of the PPI network (SETS). SETS depend on the relation between the seed and its neighbours. The algorithm was compared with six algorithms on six datasets: five for yeast and one for human. The results showed that SETS outperformed other algorithms in terms of F-measure, coverage rate and the number of complexes that have high similarity with real complexes.