Description Of Configuration Research Articles

A Detailed View on the (Re)isomerization Dynamics in Microbial Rhodopsins Using Complementary Near‐UV and IR Readouts

AbstractIsomerization is a key process in many (bio)chemical systems. In microbial rhodopsins, the photoinduced isomerization of the all‐trans retinal to the 13‐cis isomer initiates a cascade of structural changes of the protein. The interplay between these changes and the thermal relaxation of the isomerized retinal is one of the crucial determinants for rhodopsin functionality. It is therefore important to probe this dynamic interplay with chromophore specific markers that combine gapless temporal observation with spectral sensitivity. Here we utilize the near‐UV and mid‐IR fingerprint region in the framework of a systematic (time‐resolved) spectroscopic study on H+‐ (HsBR, (G)PR), Na+‐ (KR2, ErNaR) and Cl−‐(NmHR) pumps. We demonstrate that the near‐UV region is an excellent probe for retinal configuration and—being sensitive to the electrostatic environment of retinal—even transient ion binding, which allows us to pinpoint protein specific mechanistic nuances and chromophore‐charge interactions. The combination of the near‐UV and mid‐IR fingerprint region hence provides a spectroscopic analysis tool that allows a detailed, precise and temporally fully resolved description of retinal configurations during all stages of the photocycle.

Influence of the turbulent magnetic pressure on isothermal jet emitting disks

The theory of jet emitting disks (JEDs) provides a mathematical framework for a self-consistent treatment of steady-state accretion and ejection. A large-scale vertical magnetic field threads the accretion disk where magnetic turbulence occurs in a strongly magnetized plasma. A fraction of mass leaves the disk and feeds the two laminar super-Alfv\'enic jets. In previous treatments of JEDs, the disk turbulence has been considered to provide only anomalous transport coefficients, namely magnetic diffusivities and viscosity. However, 3D numerical experiments show that turbulent magnetic pressure also sets in. We analyze how this turbulent magnetic pressure modifies the classical picture of JEDs and their parameter space. We included this additional pressure term using a prescription that is consistent with the latest 3D global (and local) simulations. We then solved the complete system of self-similar magnetohydrodynamic (MHD) equations, accounting for all dynamical terms. The magnetic surfaces are assumed to be isothermal, limiting the validity of our results to cold outflows. We explored the effects of the disk thickness and the level of magnetic diffusivities on the JED response to turbulent magnetic pressure. The disk becomes puffier and less electrically conductive, causing radial and toroidal electric currents to flow at the disk surface. Field lines within the disk become straighter, with their bending and shearing occurring mainly at the surface. Accretion remains supersonic, but becomes faster at the disk surface. Large values of both turbulent pressure and magnetic diffusivities allow powerful jets to be driven, and their combined effects have a constructive influence. Nevertheless, cold outflows do not seem to be able to reproduce mass-loss rates as large as those observed in numerical simulations. Our results are a major upgrade of the JED theory, allowing a direct comparison with full 3D global numerical simulations. We argue that JEDs provide a state-of-the-art mathematical description of the disk configurations observed in numerical simulations, commonly referred to as magnetically arrested disks (MADs). However, further efforts from both theoretical and numerical perspectives are needed to firmly establish this point.

A Detailed View on the (Re)isomerization Dynamics in Microbial Rhodopsins Using Complementary Near-UV and IR Readouts.

Isomerization is a key process in many (bio)chemical systems. In microbial rhodopsins, the photoinduced isomerization of the all-trans retinal to the 13-cis isomer initiates a cascade of structural changes of the protein. The interplay between these changes and the thermal relaxation of the isomerized retinal is one of the crucial determinants for rhodopsin functionality. It is therefore important to probe this dynamic interplay with chromophore specific markers that combine gapless temporal observation with spectral sensitivity. Here we utilize the near-UV and mid-IR fingerprint region in the framework of a systematic (time-resolved) spectroscopic study on H+- (HsBR, (G)PR), Na+- (KR2, ErNaR) and Cl--(NmHR) pumps. We demonstrate that the near-UV region is an excellent probe for retinal configuration and-being sensitive to the electrostatic environment of retinal-even transient ion binding, which allows us to pinpoint protein specific mechanistic nuances and chromophore-charge interactions. The combination of the near-UV and mid-IR fingerprint region hence provides a spectroscopic analysis tool that allows a detailed, precise and temporally fully resolved description of retinal configurations during all stages of the photocycle.

Evacuation from Cramped Interiors with Aisle Seats: Uncertainty Induced by the Random Choice of Initial Positions

Considering evacuation from cramped interiors with aisle seats, the initial seating positions of pedestrians represent a non-negligible source of variance in total evacuation time. By means of Pathfinder simulations, this uncertainty is quantitatively investigated for a train and lecture hall geometry with homogeneous and heterogeneous groups of agents. Furthermore, an energy-inspired description of the occupation configuration is introduced that enables a proper numerical representation of the configuration space of the initial seating positions.

Real-Time Surveillance with AI: A Comprehensive Approach to Security and Monitoring

The last ten years have been quite phenomenal for artificial intelligence and computer vision. For the past few years, it was unstoppable, with outstanding breakthroughs that moved towards advanced real-time surveillance systems-that wholesome approach to real-time surveillance through the power of AI in technological advancement for accuracy, scalability, and responsiveness. The system integrates facial recognition, object detection, and anomaly detection algorithms to give a very stable, adaptive response to the various facets of surveillance needs, such as public safety, institutional monitoring, and private security. Through deep learning models extracted from comprehensive datasets, the system is able to identify known individuals in real time and trace the movements and unusual behaviors of these people. A discussion of challenges in data privacy, computational efficiency, and false positives goes hand in hand with an in-depth analysis of system architecture, which includes thorough hardware and software configuration descriptions. The experimental results show the potential of the system in real-world environments as an alternate scalable solution for future security infrastructures.

Review of Experimental Activities and Recent Developments of Spouted Bed Reactors at Different Operational Scales

Recent research advances and technological developments of spouted bed reactors (SBRs) have been discussed in this work. SBR has aroused increasing interest since their invention in 1955 due to its flexibility in processing different feedstocks and the high process yields that can be achieved due to its characteristic fluid dynamics. However, even though highly satisfactory results have been obtained at the laboratory scale for different applications (i.e., drying or thermochemical reactions, among others), their full implementation at an industrial level is still scarce, mainly due to the challenges encountered for their scale-up. In this work, an initial short description of SBR and configurations is followed by a review of the main experimental activities that have been conducted at different scales in the period 2013–2023. Advanced solutions such as multi-unit reactors and the use of rectangular geometries instead of the classical cylindrical ones have arisen as potential areas for further study and development to achieve a reliable implementation of the spouted bed technology at an industrial scale.

Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics.

The structure and dynamics of the eukaryotic genome are intimately linked to gene regulation and transcriptional activity. Many chromosome conformation capture experiments like Hi-C have been developed to detect genome-wide contact frequencies and quantify loop/compartment structures for different cellular contexts and time-dependent processes. However, a full understanding of these events requires explicit descriptions of representative chromatin and chromosome configurations. With the exponentially growing amount of data from Hi-C experiments, many methods for deriving 3D structures from contact frequency data have been developed. Yet, most reconstruction methods use polymer models with low resolution to predict overall genome structure. Here we present a Brownian Dynamics (BD) approach termed Hi-BDiSCO for producing 3D genome structures from Hi-C and Micro-C data using our mesoscale-resolution chromatin model based on the Discrete Surface Charge Optimization (DiSCO) model. Our approach integrates reconstruction with chromatin simulations at nucleosome resolution with appropriate biophysical parameters. Following a description of our protocol, we present applications to the NXN, HOXC, HOXAand Fbn2 mouse genes ranging in size from 50 to 100kb. Such nucleosome-resolution genome structures pave the way for pursuing many biomedical applications related to the epigenomic regulation of chromatin and control of human disease.

Reducing the impact of degradation causes on electrical power sources in the photovoltaic water pumping system

The availability and accessibility of water are the main issues for irrigation in most desert areas, especially in Jerid Tunisia. One of the best alternative methods for irrigation is the use of Photovoltaic Water Pumping Systems (PVWPS). Despite the considerable improvements in the design and performance of PVWPS, the presence of the peak load current, unsuitable battery charging control as well as inefficient energy management remain the major impediments to its evolution. In this context, the main focus of this paper is to improve the PVWPS reliability by reducing the occurrence and impact of degradation causes on electrical power sources. Firstly, a description of PVWPS configuration and its operation for irrigation is provided. Then, the critical causes generating the degradation of the various electrical power sources such as the Photovoltaic (PV) generator and the battery pack are identified. In order to minimize the impact of the peak load current on the electrical power sources, the authors propose the integration of a Hybrid Energy Storage System (HESS). In addition, the minimization of gassing phenomenon, no-cohesion of the active mass and sulfating of the electrode of the battery pack is ensured by using optimized multi-steps charging current profile. This study is completed by the integration of an Energy Management System (EMS) able to monitor, control and optimize the use of the various electrical power sources. The simulation results highlight the effectiveness of the proposed HESS and the optimized multi-steps battery charging current profile to ensure maximum availability and reliability of the PVWPS.

New exact plasma equilibria with axial and helical symmetry

We derive new exact closed-form solutions of magnetohydrodynamics equations, with and without dynamics, which model astrophysical jets and other prolonged plasma configurations. The solutions are obtained in static and dynamic incompressible equilibrium settings, in axial and helical symmetry assumptions, and are given in terms of Whittaker, Coulomb, and Heun special functions. For each symmetry, two distinct families of physical solutions arise, corresponding to two distinct pressure profiles. One pressure profile models plasmas supported by an external pressure and is suitable for the description of plasma configurations in a medium, such as atmosphere. The second profile features higher pressure inside the plasma domain and can model plasmas residing in a vacuum. Examples of static and dynamic solutions in axially and helically symmetric settings, including solutions with boundary current sheets, are presented and discussed.

On the Intermolecular Interactions in Thiophene-Cored Single-Stacking Junctions.

There have been attempts, both experimental and based on density-functional theory (DFT) modeling, at understanding the factors that govern the electronic conductance behavior of single-stacking junctions formed by pi-conjugated materials in nanogaps. Here, a reliable description of relevant stacked configurations of some thiophene-cored systems is provided by means of high-level quantum chemical approaches. The minimal structures of these configurations, which are found using the dispersion-corrected DFT approach, are employed in calculations that apply the coupled cluster method with singles, doubles and perturbative triples [CCSD(T)] and extrapolations to the complete basis set (CBS) limit in order to reliably quantify the strength of intermolecular binding, while their physical origin is investigated using the DFT-based symmetry-adapted perturbation theory (SAPT) of intermolecular interactions. In particular, for symmetrized S-Tn dimers (where "S" and "T" denote a thiomethyl-containing anchor group and a thiophene segment comprising "n" units, respectively), the CCSD(T)/CBS interaction energies are found to increase linearly with n ≤ 6, and significant conformational differences between the flanking 2-thiophene group in S-T1 and S-T2 are described by the CCSD(T)/CBS and SAPT/CBS computations. These results are put into the context of previous work on charge transport properties of S-Tn and other types of supramolecular junctions.

An enhanced absolute nodal coordinate formulation for efficient modeling and analysis of long torsion-free cable structures

Long cable structures can be accurately modeled in the absolute nodal coordinate formulation (ANCF), but often at the expense of using too many degrees of freedom (DOFs). This research refines the section of node coordinates and configuration description of the element and forms an enhanced ANCF that required modeling DOFs are greatly reduced. In this formulation, the cable is treated as an elastic line and discretized with two-node elements. The gradients of all nodes and the absolute positions of only head node are selected as generalized coordinates. The gradient field of the element is linearly interpolated in nodal gradients. Unlike the traditional ANCFs, the absolute position vector of an arbitrary point of the element is calculated by evaluating an integral of the element gradient over the element length plus the position vector of the starting node of the element, instead of cubic polynomial interpolation of nodal position and gradient vectors of the element. This leads to considerable DOFs saving. Governing motion equations of the cable are derived. Benchmark examples are used to show the performance of the enhanced formulation against with the classical ANCF cable element. Comparative studies show the validity and the efficiency of the enhanced formulation.

On a quaternary nonlocal isoperimetric problem

We study a two-dimensional quaternary inhibitory system. This free energy functional combines an interface energy favoring micro-domain growth with a Coulomb-type long range interaction energy which prevents micro-domains from unlimited spreading. Here we consider a limit in which three species are vanishingly small, but interactions are correspondingly large to maintain a nontrivial limit. In this limit two energy levels are distinguished: the highest order limit encodes information on the geometry of local structures as a three-component isoperimetric problem, while the second level describes the spatial distribution of components in global minimizers. Geometrical descriptions of limit configurations are derived.

A Highly Sensitive Model Based on Graph Neural Networks for Enzyme Key Catalytic Residue Prediction.

Determining the catalytic site of enzymes is a great help for understanding the relationship between protein sequence, structure, and function, which provides the basis and targets for designing, modifying, and enhancing enzyme activity. The unique local spatial configuration bound to the substrate at the active center of the enzyme determines the catalytic ability of enzymes and plays an important role in the catalytic site prediction. As a suitable tool, the graph neural network can better understand and identify the residue sites with unique local spatial configurations due to its remarkable ability to characterize the three-dimensional structural features of proteins. Consequently, a novel model for predicting enzyme catalytic sites has been developed, which incorporates a uniquely designed adaptive edge-gated graph attention neural network (AEGAN). This model is capable of effectively handling sequential and structural characteristics of proteins at various levels, and the extracted features enable an accurate description of the local spatial configuration of the enzyme active site by sampling the local space around candidate residues and special design of amino acid physical and chemical properties. To evaluate its performance, the model was compared with existing catalytic site prediction models using different benchmark datasets and achieved the best results on each benchmark dataset. The model exhibited a sensitivity of 0.9659, accuracy of 0.9226, and area under the precision-recall curve (AUPRC) of 0.9241 on the independent test set constructed for evaluation. Furthermore, the F1-score of this model is nearly four times higher than that of the best-performing similar model in previous studies. This research can serve as a valuable tool to help researchers understand protein sequence-structure-function relationships while facilitating the characterization of novel enzymes of unknown function.

Конфигурация COSMO-Ru2By модели COSMO: успешность и методология оценки численных прогнозов - и γ-мезомасштабных атмосферных процессов

The paper gives а brief description of the COSMO-Ru2By configuration (the grid spacing is 2.2 km) of the COSMO model, which provides numerical weather forecasts for up to 48 hours for the European part of Russia and for the Republic of Belarus, as well the methodology and results of skill of these forecasts. The COSMO-Ru2By was realized in the Hydrometcentre of Russia and operates as an element of the COSMO-Ru operational limited-area numerical weather prediction system on the CRAY XС40-LC supercomputer. The features of the COSMO-Ru2By are: 1) a vast calculation domain with a grid spacing that allows an explicit description of large (over 5-6 km high) convective motions and considering in detail the features of terrain; 2) the “embedded” technology for assimilation of DMRL-C Doppler weather radar data providing more accurate forecasts of rapidly developing weather processes for the next few hours; 3) coupled visualization system providing a great number of maps for different regions with a cascade image detailing. Operational trials in 2020-2021 showed a high skill of forecasts of the basic weather parameters with the COSMO-Ru2By. For comparison with forecasts of highly variable weather parameters (wind gusts, hourly precipitation, parameters in mountain areas, etc.) based on mesoscale models with lower resolution (e.g., COSMO-Ru6ENA, the grid size is 6.6 km), it was proposed to apply expanded trial approaches and criteria: e.g., the estimation over geographically homogeneous areas, the use of special criteria for predicting rare events, the comparison with radar data. Keywords: numerical weather prediction, mesoscale atmospheric modeling, radar data assimilation, weather forecast skill estimation, non-hydrostatic atmosphere models

Working it Out Together: Toilets, Tourists, and an Interdisciplinary Experience

Abstract In 2019, interdisciplinary teams of anthropology and environmental engineering PhD students went to Placencia Village, Belize to study stakeholder-driven issues related to coastal resilience. Our team explored wastewater management on a few of the more than 400 small cayes peppering the Belize Barrier Reef. These islands have transitioned from temporary sites for overnight fishers to crowded tourism destinations. Wastewater management has struggled to keep pace with these changes, spurring concerns about the health of the reef. Our task was to construct contextualized system dynamic models which would be useful to those concerned. Along the way however, we ran into tensions related to the underlying logic, and representations of people, in mathematical descriptions of social and technical configurations. This article lays out the context and lessons learned from our encounter with interdisciplinary systems modeling.

New lower bounds for optimal horoball packing density in hyperbolic n-space for 6 le n le 9

Koszul type Coxeter simplex tilings exist in hyperbolic n-space mathbb {H}^n up to n = 9, and their horoball packings achieve the highest known regular ball packing densities for n = 3, 4, 5. In this paper we determine the optimal horoball packing densities of Koszul simplex tilings in dimensions 6 le n le 9, which give new lower bounds for optimal packing density in each dimension. The symmetries of the packings are given by Coxeter simplex groups, and a parameter related to the Busemann function gives an isometry invariant description of different optimal horoball packing configurations.

Toward Accurate Prediction of Ion Mobility in Organic Semiconductors by Atomistic Simulation.

A multiscale scheme (MLMS: Multi-Level Multi-Scale) to predict the ion mobility (μ) of amorphous organic semiconductors is proposed, which was successfully applied to the hole mobility predictions of 14 organic systems. An inverse relationship between μ and reorganization energy is observed due to local polaronic distortions. Another moderate inverse correlation between μ and distribution of site energy change exists, representing the effects of geometric flexibility. The former and the latter represent the intramolecular and intermolecular geometric effects, respectively. In addition, a linear correlation between transfer coupling and μ is observed, showing the importance of orbital overlaps between monomers. Especially, the highest hole mobility of C6-2TTN is due to its large transfer coupling. On the other hand, another high hole mobility of CBP turned out to come from the high first neighbor density (ρFND) of its first self-solvation, emphasizing the proper description of amorphous structural configurations with a sufficiently large number of monomers. In general, systems with either unusually high transfer coupling or high first neighbor density can potentially have high μ regardless of geometric effects. Especially, the newly suggested design parameter, ρFND, is pointing to a new direction as opposed to the traditional π-conjugation strategy.

Incoherent color holography lattice light-sheet for subcellular imaging of dynamic structures

The purpose of the article is to explore the need and advantages of using the incoherent color holography lattice light-sheet (ICHLLS) to provide multiwavelength quantitative monitoring of 3D cellular dynamics in live tissue to further understand complex functions of cells and cellular compartments. We have explored the use of incoherent color holography lattice light-sheet to investigate colocalization of fluorescent markers in live cells in intact tissue. Neuronal structures provide an attractive target for incoherent color holography lattice light-sheet. The cells show a complex architecture in 3D space in which signaling both between cells and within subcellular structures requires colocalization of proteins and lipids to function. During activity and over long periods it is important in understanding these signaling functions in Parkinson’s, Alzheimer’s and motoneuron diseases within live cells in intact tissue. As a proof of concept this article recalls the key aspects in lattice light-sheet imaging and provides a description of the incoherent detection system configuration to actively control dual diffractive lenses phase-shifting at multiple excitation wavelengths sequentially, and per each z-galvo scanning level, with extended field-of-view. The incoherent color holography lattice light-sheet system will allow simultaneous recording of multidimensional object waves that contain intensity in 3D space, phase, and wavelength information. We measure colocalization of fluorescence indicators introduced into live cells in intact neural tissue.

Configuration Information System for online processing and data monitoring in the NICA experiments

The collection, storage and processing of experimental data are an integral part of modern high-energy physics experiments. The Configuration Information System (CIS) based on the Configuration Database (ConfigDb) is an essential element of a complex of information systems developed for the NICA experiments. The CIS is used to store and provide data on the configuration of the experiment hardware and software systems when collecting data from the detectors in online mode. The ConfigDb stores both a set of various configuration parameters and descriptions of a sequence of online software tasks to be started and run during experiment sessions. The system allows loading configuration information, activating hardware setups and launching all necessary software applications with the required parameters on the specified distributed nodes. The CIS architecture mainly contains the ConfigDb and Configuration Manager, which uses the Dynamic Deployment System API for managing tasks and providing intercommunication. The manager loads configuration data from the database, starts software tasks in a described sequence and supports task process management. The client-server architecture of the CIS is presented. The client has been implemented as a Web service to manage configuration parameters by users.

Quantum Configuration and Phase Spaces: Finsler and Hamilton Geometries

In this paper, we reviewtwo approaches that can describe, in a geometrical way, the kinematics of particles that are affected by Planck-scale departures, named Finsler and Hamilton geometries. By relying on maps that connect the spaces of velocities and momenta, we discuss the properties of configuration and phase spaces induced by these two distinct geometries. In particular, we exemplify this approach by considering the so-called q-de Sitter-inspired modified dispersion relation as a laboratory for this study. We finalize with some points that we consider as positive and negative ones of each approach for the description of quantum configuration and phases spaces.