Including residual contact information into replica-exchange MD simulations significantly enriches native-like conformations

Proteins are complex biomolecules which perform critical tasks in living organisms. Knowledge of a protein’s structure is essential for understanding its physiological function in detail. Despite the incredible progress in experimental techniques, protein structure determination is still expensive, time-consuming, and arduous. That is why computer simulations are often used to complement or interpret experimental data. Here, we explore how in silico protein structure determination based on replica-exchange molecular dynamics (REMD) can benefit from including contact information derived from theoretical and experimental sources, such as direct coupling analysis or NMR spectroscopy. To reflect the influence from erroneous and noisy data we probe how false-positive contacts influence the simulated ensemble. Specifically, we integrate varying numbers of randomly selected native and non-native contacts and explore how such a bias can guide simulations towards the native state. We investigate the number of contacts needed for a significant enrichment of native-like conformations and show the capabilities and limitations of this method. Adhering to a threshold of approximately 75% true-positive contacts within a simulation, we obtain an ensemble with native-like conformations of high quality. We find that contact-guided REMD is capable of delivering physically reasonable models of a protein’s structure

Automated visual inspection algorithm for the reflection detection and removing in image sequences

Specular reflections are undesirable phenomena that can impair overall perception and subsequent image analysis. In this paper, we propose a modern solution to this problem, based on the latest achievements in this field. The proposed method includes three main steps: image enhancement, detection of specular reflections, and reconstruction of damaged areas. To enhance and equalize the brightness characteristics of the image, we use the alpha-rooting method with an adaptive choice of the optimal parameter alpha. To detect specular reflections, we apply morphological filtering in the HSV color space. At the final stage, there is a reconstruction of damaged areas using adversarial neural networks. This combination makes it possible to quickly and effectively detect and remove specular reflections, which is confirmed by a series of experiments given by the experimental section of this work

Information model of green building research in the Arctic: methodological aspects

The article raises the question of the need to create a tool for complex scientific research based on an information model. The sphere of green construction in the northern and Arctic regions was chosen as the sphere of comprehensive scientific research. The paper defines the tasks of a comprehensive study, its stages, as well as a set of models used in the study. The methodology of complex scientific research has been developed. Scientific research methods are defined for each stage and the model used. An information model of a comprehensive scientific study of green construction in the Arctic has been developed. The necessity of using research information model (RIM) for the implementation of a set of tasks is substantiated

Factors influencing the rating of low-rise wooden houses as “green” buildings

The article presents a program of scientific and practical research on the assessment of “green” technologies in wooden low-rise housing construction in the field of energy efficiency and resource conservation. The objects of research are two identical experimental buildings built in 2020 in Murmansk and Petrozavodsk using different technologies of wooden housing construction and various thermal insulation materials. Attention is focused on assessing the factors affecting the energy efficiency class and the internal microclimate of a wooden building, taking into account the changing environmental conditions and operating modes of buildings in cold climates. The stages of the study were determined, the tasks for each type of experiment and the expected results were formulated. Methods fixed in the regulatory documents of the Russian Federation are considered as the main ones. A method for monitoring the parameters of the internal microclimate, environment and temperature and humidity in the layers of the enclosing structures of model objects is proposed and implemented. The implementation of the research program will allow assessing the influence of the factors under study on the energy efficiency class of a wooden building and developing recommendations for the design, construction and operation of low-rise wooden buildings in a cold climate, taking into account the criteria of “green” construction

Light-emitting-diode Fourier-transform spectroscopy of HD16O between 11200 and 12400 cm-1

The absorption spectrum of monodeuterated water, HDO has been investigated between 11200 and 12400 cm-1. The spectrum has been recorded using IFS-125M interferometer with spectral resolution of 0.05 cm-1. For measurements White’s-type cell were used. The bright light emitting diode (LED) EDEI-1LS3-R was applied as a source of radiation. Signal to noise ratio was about 104. The spectral line parameters - line positions, intensities and half-widths were obtained by least square fitting. As a result of the spectrum analysis the line list containing more than 1500 lines was created. The spectral line parameters have been compared with the previous measured and calculated data. © (2015) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only

Modelling parameters of traffic flows in a traffic simulation model with the priority of public transport

The article defines the importance of simulation modeling of traffic flows for the development of both individual territories and the entire city. The object of the study is a transport artery connecting two major districts of the city of Moscow: Strogino and Shchukino. As part of the work, the key quantitative and qualitative parameters of the object are highlighted, allowing to determine the input parameters for the simulation model of the real object in order to implement a scenario of reducing the number of lanes for personal road transport and adding a dedicated lane for public transport

CAG-Repeat RNA Hairpin Folding and Recruitment to Nuclear Speckles with a Pivotal Role of ATP as a Cosolute

A hallmark of Huntington’s disease (HD) is a prolonged polyglutamine sequence in the huntingtin protein and, correspondingly, an expanded cytosine, adenine, and guanine (CAG) triplet repeat region in the mRNA. A majority of studies investigating disease pathology were concerned with toxic huntingtin protein, but the mRNA moved into focus due to its recruitment to RNA foci and emerging novel therapeutic approaches targeting the mRNA. A hallmark of CAG-RNA is that it forms a stable hairpin in vitro which seems to be crucial for specific protein interactions. Using in-cell folding experiments, we show that the CAG-RNA is largely destabilized in cells compared to dilute buffer solutions but remains folded in the cytoplasm and nucleus. Surprisingly, we found the same folding stability in the nucleoplasm and in nuclear speckles under physiological conditions suggesting that CAG-RNA does not undergo a conformational transition upon recruitment to the nuclear speckles. We found that the metabolite adenosine triphosphate (ATP) plays a crucial role in promoting unfolding, enabling its recruitment to nuclear speckles and preserving its mobility. Using in vitro experiments and molecular dynamics simulations, we found that the ATP effects can be attributed to a direct interaction of ATP with the nucleobases of the CAG-RNA rather than ATP acting as “a fuel” for helicase activity. ATP-driven changes in CAG-RNA homeostasis could be disease-relevant since mitochondrial function is affected in HD disease progression leading to a decline in cellular ATP levels

Unique cellular organization in the oldest root meristem

Roots and shoots of plant bodies develop from meristems—cell populations that self-renew and produce cells that undergo differentiation—located at the apices of axes [1].The oldest preserved root apices in which cellular anatomy can be imaged are found in nodules of permineralized fossil soils called coal balls [2], which formed in the Carboniferous coal swamp forests over 300 million years ago [3, 4, 5, 6, 7, 8 and 9]. However, no fossil root apices described to date were actively growing at the time of preservation [3, 4, 5, 6, 7, 8, 9 and 10]. Because the cellular organization of meristems changes when root growth stops, it has been impossible to compare cellular dynamics as stem cells transition to differentiated cells in extinct and extant taxa [11]. We predicted that meristems of actively growing roots would be preserved in coal balls. Here we report the discovery of the first fossilized remains of an actively growing root meristem from permineralized Carboniferous soil with detail of the stem cells and differentiating cells preserved. The cellular organization of the meristem is unique. The position of the Körper-Kappe boundary, discrete root cap, and presence of many anticlinal cell divisions within a broad promeristem distinguish it from all other known root meristems. This discovery is important because it demonstrates that the same general cellular dynamics are conserved between the oldest extinct and extant root meristems. However, its unique cellular organization demonstrates that extant root meristem organization and development represents only a subset of the diversity that has existed since roots first evolved.</p