Internal Coordinate System Research Articles

Effect of choosing coordinate systems on computationally predicting nonradiative transition rates of flexible thermally activated delayed fluorescence molecules

AbstractUnderstanding nonradiative transition mechanisms is important in various situations. However, compared with radiative processes where temporal profiles of photon emission can be monitored in a straightforward manner, experimentally accessing the rate information may not be an easy task with nonradiative transitions. Hence, applying theoretical tools toward predicting the rates can be a useful tactic. Such predictions become very useful in designing optoelectronic materials as in the molecules adopted for constructing organic light‐emitting diodes (OLEDs). The correlation function formalism is a method that can fulfill the purpose of designing OLED materials. The formalism requires information regarding the vibrational normal modes of the two electronic states before and after the transition. Because the method is also based on harmonic oscillator approximation, it can actually fail to provide high reliability when there is a large geometric distortion between the initial and the final states. In fact, the harmonic normal mode picture is more prone to lose reliability in the Cartesian coordinates than in the internal ones even at a small distortion, and hence adopting internal coordinates may be more preferable for practical calculations. This is because normal mode mixing becomes less severe when molecular coordinates are described with internal degrees of freedom such as bond stretching, bending, and torsion. In this regard, how much more reliable the nonradiative rate predictions in OLED materials become with the use of internal coordinate system deserves a close inspection. In this account, we review on the derivation of the correlation function formalism and provide how it can be adapted toward the use of the internal coordinates. As a demonstration, we evaluate the intersystem crossing and the internal conversion rates of a series of thermally activated delayed fluorescence (TADF) molecules with both Cartesian and internal coordinate systems. Overall, handling transitions involving substantial structural changes is improved indeed with the internal coordinates. However, limitations are still apparent for the TADF systems with a flexible donor–acceptor type construct especially when the inevitable inter‐domain twisting takes place with the electronic transition. Future prospect for handling the issue is commented as a concluding remark.

Изучение концептосферы русского языка через поиск универсальной основы ее формирования

The aim of the research is to search for a universal basis for the formation and development of the conceptual sphere of the Russian language through the study of dictionaries of cultural concepts. Currently, there are several dictionaries that provide insight into the peculiarities of the Russian worldview through key concepts, however, the basis of the taxonomies they offer is different. The scientific novelty of the research lies in the search for a common basis that makes it possible to combine the taxonomies of concepts under consideration and determine the main ways to expand the common basis, including through a philosophical understanding of how reality reflected by consciousness is interpreted through these cultural concepts. As a result of the search for a universal basis for the formation and development of the conceptual sphere of the Russian language, four areas that serve as sources for the formation of the conceptual sphere have been identified: the noosphere, the psychosphere, the biosphere and the sociosphere. Their knowledge leads to the dynamic development of the conceptual sphere, the emergence of new concepts and changes in the existing ones. The cross of reality, according to which reality reflected in the conceptual sphere is interpreted in the direction of the past, future, internal and external, has been proposed as an internal coordinate system for the formation of the conceptual sphere.

Tools and Computational Machinery for Movement

This paper is a discussion of computational tools and circuits that deal with the internal and external worlds of the human body. The information processing avenues in the central nervous system (CNS) are an important part of the development.
 
 All sensory channels and the vision system are involved. It clarifies the role of the sensory system in internal coordinate systems and for all activities of the CNS. It includes the inherent redundancy aspects of the motor system as well. The visual system is involved in sports such as soccer and basketball and for being aware of and paying attention to both the internal world and the external reality surrounding the athlete.

Sella, an Open-Source Automation-Friendly Molecular Saddle Point Optimizer.

We present a new algorithm for the optimization of molecular structures to saddle points on the potential energy surface using a redundant internal coordinate system. This algorithm automates the procedure of defining the internal coordinate system, including the handling of linear bending angles, for example, through the addition of dummy atoms. Additionally, the algorithm supports constrained optimization using the null-space sequential quadratic programming formalism. Our algorithm determines the direction of the reaction coordinate through iterative diagonalization of the Hessian matrix and does not require evaluation of the full Hessian matrix. Geometry optimization steps are chosen using the restricted step partitioned rational function optimization method, and displacements are realized using a high-performance geodesic stepping algorithm. This results in a robust and efficient optimization algorithm suitable for use in automated frameworks. We have implemented our algorithm in Sella, an open-source software package designed to optimize atomic systems to saddle point structures. We also introduce a new benchmark test comprising 500 molecular structures that approximate saddle point geometries and show that our saddle point optimization algorithm outperforms the algorithms implemented in several leading electronic structure theory packages.

A new approach for extracting information from protein dynamics.

Increased ability to predict protein structures is moving research focus towards understanding protein dynamics. A promising approach is to represent protein dynamics through networks and take advantage of well-developed methods from network science. Most studies build protein dynamics networks from correlation measures, an approach that only works under very specific conditions, instead of the more robust inverse approach. Thus, we apply the inverse approach to the dynamics of protein dihedral angles, a system of internal coordinates, to avoid structural alignment. Using the well-characterized adhesion protein, FimH, we show that our method identifies networks that are physically interpretable, robust, and relevant to the allosteric pathway sites. We further use our approach to detect dynamical differences, despite structural similarity, for Siglec-8 in the immune system, and the SARS-CoV-2 spike protein. Our study demonstrates that using the inverse approach to extract a network from protein dynamics yields important biophysical insights.

METHOD AND ALGORITHMS FOR CALCULATING HIGH-PRECISION ORIENTATION AND MUTUAL BINDING OF COORDINATE SYSTEMS OF SPACECRAFT STAR TRACKERS CLUSTER BASED ON INACCURATE MEASUREMENTS

The problem of increasing the accuracy of determining the orientation of a spacecraft (SC) using a system of star trackers (ST) is considered. Methods are proposed that make it possible to use a joint field of view and refine the relative position of ST to improve the accuracy of orientation determination. The use of several star trackers leads to an increase in the angle between the directions to the stars into the joint field of view, which makes it possible to reduce the condition number of the matrices used in calculating the orientation parameters. The paper develops a combinatorial method for interval estimation of the SC orientation with an arbitrary number of star trackers. To calculate the ST orientation, a linear problem of interval estimation of the orthogonal orientation matrix for a sufficiently large number of stars is solved. The orientation quaternion is determined under the condition that the corresponding orientation matrix belongs to the obtained interval estimates. The case is considered when the a priori estimate of the mutual binding of star trackers can have an error comparable to or greater than the error in measuring the angular coordinates of stars. With inaccurately specified matrices of the mutual orientation of the star trackers, the errors in the mutual orientations of the STs are added to the errors of measuring the directions to the stars, which leads to an expansion of the uncertainty intervals of the right-hand sides of the system of linear algebraic equations used to determine the orientation parameters. A method is proposed for solving the problem of refining the mutual reference of the internal coordinate systems of a pair of ST as an independent task, after which the main problem of increasing the accuracy of spacecraft orientation is solved. The developed method and algorithms for solving such a complex problem are based on interval estimates of orthogonal orientation matrices. For additional narrowing of the intervals, the property of orthogonality of orientation matrices is used. The numerical simulation carried out made it possible to evaluate the advantages and disadvantages of each of the proposed methods.

Different mechanisms of magnitude and spatial representation for tactile and auditory modalities

The human brain creates an external world representation based on magnitude judgments by estimating distance, numerosity, or size. The magnitude and spatial representation are hypothesized to rely on common mechanisms shared by different sensory modalities. We explored the relationship between magnitude and spatial representation using two different sensory systems. We hypothesize that the interaction between space and magnitude is combined differently depending on sensory modalities. Furthermore, we aimed to understand the role of the spatial reference frame in magnitude representation. We used stimulus–response compatibility (SRC) to investigate these processes assuming that performance is improved if stimulus and response share common features. We designed an auditory and tactile SRC task with conflicting spatial and magnitude mapping. Our results showed that sensory modality modulates the relationship between space and magnitude. A larger effect of magnitude over spatial congruency occurred in a tactile task. However, magnitude and space showed similar weight in the auditory task, with neither spatial congruency nor magnitude congruency having a significant effect. Moreover, we observed that the spatial frame activated during tasks was elicited by the sensory inputs. The participants' performance was reversed in the tactile task between uncrossed and crossed hands posture, suggesting an internal coordinate system. In contrast, crossing the hands did not alter performance (i.e., using an allocentric frame of reference). Overall, these results suggest that space and magnitude interaction differ in auditory and tactile modalities, supporting the idea that these sensory modalities use different magnitude and spatial representation mechanisms.

Structure activity investigation, CT complex analysis and spectroscopic investigation on antibiotic drug; Sulfamethoxazole using quantum chemical calculations

The physico-chemical, structural and biological significance for the drug Sulfamethoxazole was analyzed by vibrational spectroscopic, biological assessment and theoretical tools. The structure activity on par with ligand group injection into the internal coordinate system was analyzed using the various spectroscopic techniques (FT-IR, FT-Raman, NMR and UV–Vis).The drug potential reside over molecular site was thoroughly studied by molecular charge depletion profile (protonic and electronic delocalization). In order to attain the proper drug function, the chemi-equivalent potential exchange was monitored on different entities of the molecule. The biological profile was keenly observed to find out the biological ambiance of the present molecule and to fabricate an advanced drug model of the molecule. The exchange of chemical potential in the core and allied carbons of the molecular skeleton was keenly noted to find the prearranged chemical environment for successful drug operation. The non-bonded transitions between Lewis acid and base of bonded molecular system were observed to determine the restoring potential to customize drug potential. The drug assistance for enantiomer characteristics of chirality sequence was displayed to expose the toxicity effect of the molecule. The hyperactive pressure was measured in terms of polarizability and corresponding biological properties were validated.

Determination of quantum labels based on projections of the total angular momentum on the molecule-fixed axis

Molecular line lists, particularly those computed for high temperature applications, often have very few states assigned local quantum numbers, i.e rotational and vibrational quantum labels. These are often important components for accurately determining line shape parameters required for radiative transfer simulations. Through variational calculations, the projection of the total angular momentum onto the molecule fixed axis (k) is investigated in the Radau internal coordinate system to determine when it can be considered a good quantum number. In the Radau coordinate system, when the square of the th component of the wavefunction is greater than one half, then we can classify k as a good quantum number in accordance with the theorem of Hose and Taylor, a quantum analogue of the Kolmogorov–Arnold–Moser theorem. When the theorem is satisfied, it is shown that k can reliably be used to determine oblate and prolate quantum labels Ka and Kc. This approach is tested on the states of the water and ozone molecules.

Molecular structure analysis and biological properties investigation on antiseptic drug; 2-amino-1-phenyl-1-propanol using spectroscopic and computational research analysis

The inducement of physical, chemical, structural and biological properties to entice of pharmaceutical property was analyzed by Vibrational spectroscopic, biological and theoretical tools. The structural arrangement for describing structure activity was investigated by injecting ligand groups in internal coordinate system by molecular tools (FT adopted IR, Raman, and NMR). Bond length and bond angle strain was pronounced much due to the chemical equivalent forces extension due to the injection of substitutional groups on base compound and thus non-Centro symmetry was processed. The molecular charge depletion profile was thoroughly studied to persuade protonic and electronic delocalization setup for arranging the drug potential. The chemi-equivalent potential exchange was monitored among different parts of the molecule for obtaining drug mechanism. The biological profile was keenly observed to look at the biological ambiance of the present molecule to fabricate advanced drug. The Lipinski five rule parameters; MV = 137.18, LogP = 0.27, HBD = 2, HBA = 2 and TPSA = 46.2 A2 showed the enhancement of additive drug quality. The exchange of oscillating chemical energy in the core and allied carbons of the base skeleton was keenly noted to find the prearranged chemical environment for successful drug mechanism. The non bonded transitions between Lewis acid and base of bonded molecular system were observed to determine the restoring potential to customize drug potential. The drug assistance for enantiomer characteristics of chirality sequence was displayed to expose the toxicity effect of the molecule. The active molecular bondings on different sites of molecule were measured by estimating polarizability and associated biological inhibition was validated.

LOCAL IDENTITY AND FEATURES OF THE ARCHITECTURE OF KYIV IN THE FIRST HALF OF THE TWENTIETH CENTURY

The article presents an analysis of the compilation of local and regional features of the development of Kyiv at the beginning of the last century, which arose as a reflection on global socio-political, economic and cultural transformations. In particular, successive iterations of the main city-forming function, "invented traditions" in their local manifestation, local decorative techniques ("brick style") and terrain subordination are studied. Mentioned as domestic (J. Yu. Karakis, P. F. Alyoshin, V. G. Krychevsky, V. G. Zabolotny, D. M. Dyachenko, and others) as all- Soviet architects (J. G. Langbard, I. O. Fomin and others).
 The concept of invented traditions according to E. Hobsbawm is extrapolated to the field of architecture through the prism of artistic and cultural context. The localization of traditions and the corresponding separation are presented in the concept of T. Eriksen: as a means of self-identification and response to the need to create an internal coordinate system for representatives of individual groups.
 The article summarizes a series of author's researches devoted to a detailed analysis of each of the mentioned artistic transitions in Kyiv architecture (from eclecticism and historical reminiscences to modernism, from Art Nouveau to avant-garde, from constructivism to Soviet neoclassicism and, finally, from Stalinist empire to modernism), being part of a global analysis of the genesis of city architecture in a global context. A detailed analysis of the objects identified in the article is presented in other works of the author.

Conformational stability of the bacterial adhesin, FimH, with an inactivating mutation.

Allostery governing two conformational states is one of the proposed mechanisms for catch-bond behavior in adhesive proteins. In FimH, a catch-bond protein expressed by pathogenic bacteria, separation of two domains disrupts inhibition by the pilin domain. Thus, tensile force can induce a conformational change in the lectin domain, from an inactive state to an active state with high affinity. To better understand allosteric inhibition in two-domain FimH (H2 inactive), we use molecular dynamics simulations to study the lectin domain alone, which has high affinity (HL active), and also the lectin domain stabilized in the low-affinity conformation by an Arg-60-Pro mutation (HL mutant). Because ligand-binding induces an allostery-like conformational change in HL mutant, this more experimentally tractable version has been proposed as a "minimal model" for FimH. We find that HL mutant has larger backbone fluctuations than both H2 inactive and HL active, at the binding pocket and allosteric interdomain region. We use an internal coordinate system of dihedral angles to identify protein regions with differences in backbone and side chain dynamics beyond the putative allosteric pathway sites. By characterizing HL mutant dynamics for the first time, we provide additional insight into the transmission of allosteric information across the lectin domain and build upon structural and thermodynamic data in the literature to further support the use of HL mutant as a "minimal model." Understanding how to alter protein dynamics to prevent the allosteric conformational change may guide drug development to prevent infection by blocking FimH adhesion.

A method of tunnel critical rock identification and stability analysis based on a laser point cloud

The role of 3D laser scanning technology in the identification of critical rock in engineering is becoming increasingly important. In order to improve the recognition efficiency and accuracy of this identification, it is particularly significant to propose an analytical method for matching critical rock with point cloud technology. Based on the research foundation of 3D laser scanning technology in the field of rock mass structural surface identification, this paper proposes a critical rock identification and stability analysis method based on laser point cloud technology. First, a calculation method for a closed critical rock body is proposed. Second, block theory and point cloud technology are combined. Then, by utilizing the high-density features of the point cloud, the vector analysis method of the traditional critical rock is converted into the space coordinates of the 3D point cloud, and the internal coordinate system of the 3D laser scanning system is directly used to extract the X, Y, and Z coordinate values of the corner points of the critical rock. Next, these coordinates are spatially compared and analyzed, and the key critical rock determination and its corresponding instability method are identified. Finally, the movable identification and stability analysis of the critical rock on the geometric scale is attained. This paper mainly summarizes the identification of closed critical rock bodies, the movable identification of key critical rock, and the determination methods of three types of critical rock instability modes as follows: falling type, single-sided sliding type, and double-sided sliding type. The method of the visual analysis process is implemented using C++ and OpenGL language programming. Eventually, the method is applied to practical engineering, and good results are obtained, which demonstrates the effectiveness of the method and makes it of great significance for future engineering applications.

Geometry optimization using Gaussian process regression in internal coordinate systems.

Locating the minimum energy structure of molecules, typically referred to as geometry optimization, is one of the first steps of any computational chemistry calculation. Earlier research was mostly dedicated to finding convenient sets of molecule-specific coordinates for a suitable representation of the potential energy surface, where a faster convergence toward the minimum structure can be achieved. More recent approaches, on the other hand, are based on various machine learning techniques and seem to revert to Cartesian coordinates instead for practical reasons. We show that the combination of Gaussian process regression with those coordinate systems employed by state-of-the-art geometry optimizers can significantly improve the performance of this powerful machine learning technique. This is demonstrated on a benchmark set of 30 small covalently bonded molecules.

How visual experience and task context modulate the use of internal and external spatial coordinate for perception and action.

Recent studies proposed that the use of internal and external coordinate systems for perception and action may be more flexible in congenitally blind when compared to sighted individuals. To investigate this hypothesis further, we asked congenitally blind and sighted people to perform, with the hands uncrossed and crossed over the body midline, a tactile temporal order judgment and an auditory Simon task. Crucially, both tasks were carried out under task instructions either favoring the use of an internal (left vs. right hand) or an external (left vs. right hemispace) frame of reference. In the internal condition of the temporal order judgment task, our results replicated previous findings (Röder, Rösler, & Spence, 2004) showing that hand crossing only impaired sighted participants' performance, suggesting that blind people did not activate by default a (conflicting) external frame of reference. However, under external instructions, a decrease of performance was observed in both groups, suggesting that even blind people activated an external coordinate system in this condition. In the Simon task, and in contrast with a previous study (Röder, Kusmierek, Spence, & Schicke, 2007), both groups responded more efficiently when the sound was presented from the same side of the response ("Simon effect") independently of the hands position. This was true under the internal and external conditions, therefore suggesting that blind and sighted by default activated an external coordinate system in this task. Together, these data demonstrated that both sighted and blind individuals were able to activate internal and external information for perception and action. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

Bead-Based Hydrodynamic Simulations of Rigid Magnetic Micropropellers.

The field of synthetic microswimmers, micro-robots moving in aqueous environments, has evolved significantly in the last years. Micro-robots actuated and steered by external magnetic fields are of particular interest because of the biocompatibility of this energy source and the possibility of remote control, features suited for biomedical applications. While initial work has mostly focused on helical shapes, the design space under consideration has widened considerably with recent works, opening up new possibilities for optimization of propellers to meet specific requirements. Understanding the relation between shape on the one hand and targeted actuation and steerability on the other hand requires an understanding of their propulsion behavior. Here we propose hydrodynamic simulations for the characterization of rigid micropropellers of any shape, actuated by rotating external magnetic fields. The method consists of approximating the propellers by rigid clusters of spheres. We characterize the influence of model parameters on the swimming behavior to identify optimal simulation parameters using helical propellers as a test system. We then explore the behavior of randomly shaped propellers that were recently characterized experimentally. The simulations show that the orientation of the magnetic moment with respect to the propeller's internal coordinate system has a strong impact on the propulsion behavior and has to be known with a precision of ≤ 5° to predict the propeller's velocity-frequency curve. This result emphasizes the importance of the magnetic properties of the micropropellers for the design of desired functionalities for potential biomedical applications, and in particular the importance of their orientation within the propeller's structure.

Molecular structure-associated pharmacodynamic investigation on benzoyl peroxide using spectroscopic and quantum computational tools

ABSTRACTThe pharmacodynamic activity on the organic structure of benzoyl peroxide has been analysed by molecular spectroscopical tools (IR, Raman, nuclear magnetic resonance and UV–visible). Simultaneously, the results obtained in the experimental process are verified by performing Quantum Gaussian computational calculations with higher-order basis sets. The actual positions of internal compositions and purity of the compound are verified with the observations of fundamental and group frequency of the recorded pattern of the FT-IR and FT-Raman spectra. The chemical environment of different carbons existing in various entities for approving a drug property is keenly identified and distinguished. The energy level degeneracy among different Frontier molecular orbitals is viewed from the orbital overlapping interaction contour. The biological activity of the present compound is emphasized and correlated with the hyperpolarizability profile of the internal coordinate system of a molecular structure arrangement. The involvement of non-bonding molecular orbital for the inducement of drug reactivity is monitored from the observation of cluster electron transitions. The Gibbs energy for chemical reaction with augmented temperature is relatively discussed, and the continuum of chemical reaction is observed.

Visuomotor Dissociation in Cerebral Scaling of Size.

Estimating size and distance is crucial in effective visuomotor control. The concept of an internal coordinate system implies that visual and motor size parameters are scaled onto a common template. To dissociate perceptual and motor components in such scaling, we performed an fMRI experiment in which 16 right-handed subjects copied geometric figures while the result of drawing remained out of sight. Either the size of the example figure varied while maintaining a constant size of drawing (visual incongruity) or the size of the examples remained constant while subjects were instructed to make changes in size (motor incongruity). These incongruent were compared to congruent conditions. Statistical Parametric Mapping (SPM8) revealed brain activations related to size incongruity in the dorsolateral prefrontal and inferior parietal cortex, pre-SMA / anterior cingulate and anterior insula, dominant in the right hemisphere. This pattern represented simultaneous use of a ‘resized’ virtual template and actual picture information requiring spatial working memory, early-stage attention shifting and inhibitory control. Activations were strongest in motor incongruity while right pre-dorsal premotor activation specifically occurred in this condition. Visual incongruity additionally relied on a ventral visual pathway. Left ventral premotor activation occurred in all variably sized drawing while constant visuomotor size, compared to congruent size variation, uniquely activated the lateral occipital cortex additional to superior parietal regions. These results highlight size as a fundamental parameter in both general hand movement and movement guided by objects perceived in the context of surrounding 3D space.

Robust patterning of gene expression based on internal coordinate system of cells

Cell-to-cell communication in multicellular organisms is established through the transmission of various kinds of chemical substances such as proteins. It is well known that gene expression triggered by a chemical substance in individuals has stable spatial patterns despite the individual differences in concentration patterns of the chemical substance. This fact reveals an important property of multicellular organisms called “robustness”, which allows the organisms to generate their forms while maintaining proportion. Robustness has been conventionally accounted for by the stability of solutions of dynamical equations that represent a specific interaction network of chemical substances. However, any biological system is composed of autonomous elements. In general, an autonomous element does not merely accept information on the chemical substance from the environment; instead, it accepts the information based on its own criteria for reaction. Therefore, this phenomenon needs to be considered from the viewpoint of cells. Such a viewpoint is expected to allow the consideration of the autonomy of cells in multicellular organisms. This study aims to explain theoretically the robust patterning of gene expression from the viewpoint of cells. For this purpose, we introduced a new operator for transforming a state variable of a chemical substance from an external coordinate system to an internal coordinate system of each cell, which describes the observation of the chemical substance by cells. We then applied this operator to the simplest reaction–diffusion model of the chemical substance to investigate observation effects by cells. Our mathematical analysis of this extended model indicates that the robust patterning of gene expression against individual differences in concentration pattern of the chemical substance can be explained from the viewpoint of cells if there is a regulation field that compensates for the difference between cells seen in the observation results. This result provides a new insight into the investigation of the mechanism of robust patterning in biological systems composed of individual elements.

Flexible docking-based molecular dynamics/steered molecular dynamics calculations of protein-protein contacts in a complex of cytochrome P450 1A2 with cytochrome b5.

Formation of transient complexes of cytochrome P450 (P450) with another protein of the endoplasmic reticulum membrane, cytochrome b5 (cyt b5), dictates the catalytic activities of several P450s. Therefore, we examined formation and binding modes of the complex of human P450 1A2 with cyt b5. Docking of soluble domains of these proteins was performed using an information-driven flexible docking approach implemented in HADDOCK. Stabilities of the five unique binding modes of the P450 1A2-cyt b5 complex yielded by HADDOCK were evaluated using explicit 10 ns molecular dynamics (MD) simulations in aqueous solution. Further, steered MD was used to compare the stability of the individual P450 1A2-cyt b5 binding modes. The best binding mode was characterized by a T-shaped mutual orientation of the porphyrin rings and a 10.7 Å distance between the two redox centers, thus satisfying the condition for a fast electron transfer. Mutagenesis studies and chemical cross-linking, which, in the absence of crystal structures, were previously used to deduce specific P450-cyt b5 interactions, indicated that the negatively charged convex surface of cyt b5 binds to the positively charged concave surface of P450. Our simulations further elaborate structural details of this interface, including nine ion pairs between R95, R100, R138, R362, K442, K455, and K465 side chains of P450 1A2 and E42, E43, E49, D65, D71, and heme propionates of cyt b5. The universal heme-centric system of internal coordinates was proposed to facilitate consistent classification of the orientation of the two porphyrins in any protein complex.