scholarly journals Evaluate the impact of hydrodynamic pressure on hydrologic exchange fluxes and resident time for a large-scale river section over a long-term period

2021 ◽  
Author(s):  
Jie Bao ◽  
Yunxiang Chen ◽  
Yilin Fang ◽  
Xuehang Song ◽  
William Perkins ◽  
...  
Keyword(s):  
Large Scale ◽  
Three Dimensional ◽  
Hydrodynamic Pressure ◽  
Subsurface Water ◽  
Flow Transport ◽  
Resident Time ◽  
Phase Surface ◽  
Hydrologic Exchange ◽  
Multi Phase ◽  
The Impact

Quantifying hydrologic exchange fluxes (HEF) and subsurface water residence times (RT) are important for managing the water quality and ecosystem health in dynamic river corridor systems. Laboratory-scale experiments and models have shown that hydrodynamic pressure variations on the riverbed induced by dynamic river flows can strongly impact HEFs and RTs. In this study, the impacts of hydrodynamic pressure on HEFs and RT for a 30 km section of the Columbia River in Washington State over a three-year period were quantitatively evaluated using a coupled transient three-dimensional (3D) multi-phase surface and subsurface water flow transport approach. Based on comparisons between model simulations with and without considering hydrodynamic pressure, we found that hydrodynamic pressure increase the net HEFs by 7% of flowing into river from subsurface domain, and also leads to a reduction of the area with long RT, and increase of area with short RT.

scholarly journals 3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome

2020 ◽  
Vol 49 (D1) ◽  
pp. D38-D46
Author(s):  
Kyukwang Kim ◽  
Insu Jang ◽  
Mooyoung Kim ◽  
Jinhyuk Choi ◽  
Min-Seo Kim ◽  
...  
Keyword(s):  
Cell Line ◽  
Large Scale ◽  
Three Dimensional ◽  
Cancer Cell Line ◽  
Cancer Genome ◽  
Structural Variations ◽  
3D Genome ◽  
Tightly Coupled ◽  
Regulatory Effects ◽  
The Impact

Abstract Three-dimensional (3D) genome organization is tightly coupled with gene regulation in various biological processes and diseases. In cancer, various types of large-scale genomic rearrangements can disrupt the 3D genome, leading to oncogenic gene expression. However, unraveling the pathogenicity of the 3D cancer genome remains a challenge since closer examinations have been greatly limited due to the lack of appropriate tools specialized for disorganized higher-order chromatin structure. Here, we updated a 3D-genome Interaction Viewer and database named 3DIV by uniformly processing ∼230 billion raw Hi-C reads to expand our contents to the 3D cancer genome. The updates of 3DIV are listed as follows: (i) the collection of 401 samples including 220 cancer cell line/tumor Hi-C data, 153 normal cell line/tissue Hi-C data, and 28 promoter capture Hi-C data, (ii) the live interactive manipulation of the 3D cancer genome to simulate the impact of structural variations and (iii) the reconstruction of Hi-C contact maps by user-defined chromosome order to investigate the 3D genome of the complex genomic rearrangement. In summary, the updated 3DIV will be the most comprehensive resource to explore the gene regulatory effects of both the normal and cancer 3D genome. ‘3DIV’ is freely available at http://3div.kr.

Can the Deforestation Breeze Change the Rainfall in Amazonia? A Case Study for the BR-163 Highway Region

2010 ◽  
Vol 14 (18) ◽  
pp. 1-25 ◽  
Author(s):  
Sandra I. Saad ◽  
Humberto R. da Rocha ◽  
Maria A. F. Silva Dias ◽  
Rafael Rosolem
Keyword(s):  
Boundary Layer ◽  
Large Scale ◽  
Three Dimensional ◽  
Atmospheric Modeling ◽  
Thermal Cell ◽  
Soil Wetness ◽  
Soil Dryness ◽  
Regional Atmospheric Modeling ◽  
The Impact

Abstract The authors simulated the effects of Amazonian mesoscale deforestation in the boundary layer and in rainfall with the Brazilian Regional Atmospheric Modeling System (BRAMS) model. They found that both the area and shape (with respect to wind incidence) of deforestation and the soil moisture status contributed to the state of the atmosphere during the time scale of several weeks, with distinguishable patterns of temperature, humidity, and rainfall. Deforestation resulted in the development of a three-dimensional thermal cell, the so-called deforestation breeze, slightly shifted downwind to large-scale circulation. The boundary layer was warmer and drier above 1000-m height and was slightly wetter up to 2000-m height. Soil wetness affected the circulation energetics proportionally to the soil dryness (for soil wetness below ∼0.6). The shape of the deforestation controlled the impact on rainfall. The horizontal strips lined up with the prevailing wind showed a dominant increase in rainfall, significant up to about 60 000 km2. On the other hand, in the patches aligned in the opposite direction (north–south), there was both increase and decrease in precipitation in two distinct regions, as a result of clearly separated upward and downward branches, which caused the precipitation to increase for patches up to 15 000 km2. The authors’ estimates for the size of deforestation impacting the rainfall contributed to fill up the low spatial resolution in other previous studies.

An Impact Assessment of GPS Radio Occultation Data on Prediction of a Rapidly Developing Cyclone over the Southern Ocean*

2014 ◽  
Vol 142 (11) ◽  
pp. 4187-4206 ◽  
Author(s):  
Shu-Ya Chen ◽  
Tae-Kwon Wee ◽  
Ying-Hwa Kuo ◽  
David H. Bromwich
Keyword(s):  
Data Assimilation ◽  
Southern Ocean ◽  
Large Scale ◽  
Radio Occultation ◽  
Three Dimensional ◽  
Wrf Model ◽  
The Other ◽  
Gps Radio Occultation ◽  
The Antarctic ◽  
The Impact

Abstract The impact of global positioning system (GPS) radio occultation (RO) data on an intense synoptic-scale storm that occurred over the Southern Ocean in December 2007 is evaluated, and a synoptic explanation of the assessed impact is offered. The impact is assessed by using the three-dimensional variational data assimilation scheme (3DVAR) of the Weather Research and Forecasting (WRF) Model Data Assimilation system (WRFDA), and by comparing two experiments: one with and the other without assimilating the refractivity data from four different RO missions. Verifications indicate significant positive impacts of the RO data in various measures and parameters as well as in the track and intensity of the Antarctic cyclone. The analysis of the atmospheric processes underlying the impact shows that the assimilation of the RO data yields substantial improvements in the large-scale circulations that in turn control the development of the Antarctic storm. For instance, the RO data enhanced the strength of a 500-hPa trough over the Southern Ocean and prevented the katabatic flow near the coast of East Antarctica from an overintensification. This greatly influenced two low pressure systems of a comparable intensity, which later merged together and evolved into the major storm. The dominance of one low over the other in the merger dramatically changed the track, intensity, and structure of the merged storm. The assimilation of GPS RO data swapped the dominant low, leading to a remarkable improvement in the subsequent storm’s prediction.

scholarly journals Using AlphaFold to predict the impact of single mutations on protein stability and function

2021 ◽  
Author(s):  
Marina A Pak ◽  
Karina A Markhieva ◽  
Mariia S Novikova ◽  
Dmitry S Petrov ◽  
Ilya S Vorobyev ◽  
...  
Keyword(s):  
Protein Folding ◽  
Protein Stability ◽  
Structure Prediction ◽  
Large Scale ◽  
3D Structure ◽  
Three Dimensional ◽  
Single Mutation ◽  
Before And After ◽  
And Function ◽  
The Impact

AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is "solved". However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the AlphaFold predictions on the impact of a single mutation on structure with a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold cannot be immediately applied to other problems or applications in protein folding.

scholarly journals Global-scale brittle plastic rheology at the cometesimals merging of comet 67P/Churyumov–Gerasimenko

2020 ◽  
Vol 117 (19) ◽  
pp. 10181-10187
Author(s):  
Marco Franceschi ◽  
Luca Penasa ◽  
Matteo Massironi ◽  
Giampiero Naletto ◽  
Sabrina Ferrari ◽  
...  
Keyword(s):  
Large Scale ◽  
Three Dimensional ◽  
Global Scale ◽  
Refractory Materials ◽  
High Porosity ◽  
A Minor ◽  
The Impact ◽  
Comet 67P ◽  
Dextral Strike Slip ◽  
Minor Extent

Observations of comet nuclei indicate that the main constituent is a mix of ice and refractory materials characterized by high porosity (70–75%) and low bulk strength (10−4–10−6 MPa); however, the nature and physical properties of these materials remain largely unknown. By combining surface inspection of comet 67P/Churyumov–Gerasimenko and three-dimensional (3D) modeling of the independent concentric sets of layers that make up the structure of its two lobes, we provide clues about the large-scale rheological behavior of the nucleus and the kinematics of the impact that originated it. Large folds in the layered structure indicate that the merging of the two cometesimals involved reciprocal motion with dextral strike–slip kinematics that bent the layers in the contact area without obliterating them. Widespread long cracks and the evidence of relevant mass loss in absence of large density variations within the comet’s body testify that large-scale deformation occurred in a brittle-plastic regime and was accommodated through folding and fracturing. Comparison of refined 3D geologic models of the lobes with triaxial ellipsoids that suitably represent the overall layers arrangement reveals characteristics that are consistent with an impact between two roughly ellipsoidal cometesimals that produced large-scale axial compression and transversal elongation. The observed features imply global transfer of impact-related shortening into transversal strain. These elements delineate a model for the global rheology of cometesimals that could be possible evoking a prominent bonding action of ice and, to a minor extent, organics.

scholarly journals Stellar Explosions in High-surface Density Galaxies

2015 ◽  
Vol 11 (A29B) ◽  
pp. 232-232
Author(s):  
Evan Scannapieco ◽  
Sharanya Sur ◽  
Eve C. Ostriker
Keyword(s):  
Star Formation ◽  
Surface Density ◽  
Energy Input ◽  
Large Scale ◽  
Star Formation Rate ◽  
High Surface ◽  
Formation Rate ◽  
Three Dimensional ◽  
Velocity Dispersions ◽  
The Impact

AbstractHigh surface density, rapidly star-forming galaxies are observed to have ≈ 50 - 100 km s−1 line-of-sight velocity dispersions, which are much higher than expected from supernova driving alone, but may arise from large-scale gravitational instabilities. Using three-dimensional simulations of local regions of the interstellar medium, we explore the impact of high velocity dispersions that arise from these disk instabilities. Parametrizing disks by their surface densities and epicyclic frequencies, we conduct a series of simulations that probe a broad range of conditions. Turbulence is driven purely horizontally and on large scales, neglecting any energy input from supernovae.We find that such motions lead to strong global outflows in the highly-compact disks that were common at high redshifts, but weak or negligible mass loss in the more diffuse disks that are prevalent today. Substantial outflows are generated if the one-dimensional horizontal velocity dispersion exceeds -35 km s−1, as occurs in the dense disks that have star formation rate densities above ≈ 0.1 M⊙ yr−1 kpc−2. These outflows are triggered by a thermal runaway, arising from the inefficient cooling of hot material coupled with successive heating from turbulent driving. Thus, even in the absence of stellar feedback, a critical value of the star-formation rate density for outflow generation can arise due to a turbulent heating instability. This suggests that in strongly self-gravitating disks, outflows may be enhanced by, but need not caused by, energy input from stellar explosions.These results are explained in more detailed in Sur, Scannapieco, & Ostriker (2015).

Three-Dimensional Dynamic Simulation System for Forest Surface Fire Spreading Prediction

2018 ◽  
Vol 32 (08) ◽  
pp. 1850026 ◽  
Author(s):  
Jianwei Li ◽  
Xiaowen Li ◽  
Chongchen Chen ◽  
Huiru Zheng ◽  
Naiyuan Liu
Keyword(s):  
Prediction Model ◽  
Forest Fire ◽  
Forest Fires ◽  
Large Scale ◽  
Three Dimensional ◽  
Simulation System ◽  
Dynamic Visualization ◽  
Surface Fire ◽  
Fire Spreading ◽  
The Impact

Forest fire is one of the most frequent, fast spreading and destructive natural disasters. Many countries have developed their own fire prediction model and computational systems to predict the fire spreading, however, the user interaction, display effect and prediction accuracy have not yet met the requirements for firefighting in real forest fire events. The forest fire spreading is a complex process affected by multi-factors. Understanding the relationships between these multi-factors and the forest fire spreading trend is vital to predicting the fire spreading promptly and accurately to make the strategy in extinguishing the forest fire. In this paper, we propose and develop a three-dimensional (3D) forest fire spreading simulation system, FFSimulator, to visualize the impact of multi-factors to the fire spread. FFSimultor integrates the multi-factor analysis approach with the FARSITE prediction model to improve the prediction. The FFSimulator developed applies 3D scene organization, template-based vector data mapping and overlaps visualization techniques to provide a 3D dynamic visualization of large-scale forest fire. The 3D multi-factors superposition analysis simulates the impacts of individual factor and multi-factors on the trend of surface fire spreading, which can be used to identify the key sites for the prevention and the control of forest fires. The system has been tested and evaluated using real data of Shanghan forest fire.

scholarly journals Simulating Groups and the IntraGroup Medium: The Surprisingly Complex and Rich Middle Ground between Clusters and Galaxies

Universe ◽  
2021 ◽  
Vol 7 (7) ◽  
pp. 209
Author(s):  
Benjamin D. Oppenheimer ◽  
Arif Babul ◽  
Yannick Bahé ◽  
Iryna S. Butsky ◽  
Ian G. McCarthy
Keyword(s):  
Galaxy Evolution ◽  
Large Scale ◽  
Cosmological Parameters ◽  
Cosmic Ray ◽  
Cosmological Simulations ◽  
Hydrodynamic Simulations ◽  
Galaxy Groups ◽  
Cooling Flows ◽  
Multi Phase ◽  
The Impact

Galaxy groups are more than an intermediate scale between clusters and halos hosting individual galaxies, they are crucial laboratories capable of testing a range of astrophysics from how galaxies form and evolve to large scale structure (LSS) statistics for cosmology. Cosmological hydrodynamic simulations of groups on various scales offer an unparalleled testing ground for astrophysical theories. Widely used cosmological simulations with ∼(100 Mpc)3 volumes contain statistical samples of groups that provide important tests of galaxy evolution influenced by environmental processes. Larger volumes capable of reproducing LSS while following the redistribution of baryons by cooling and feedback are the essential tools necessary to constrain cosmological parameters. Higher resolution simulations can currently model satellite interactions, the processing of cool (T≈104−5 K) multi-phase gas, and non-thermal physics including turbulence, magnetic fields and cosmic ray transport. We review simulation results regarding the gas and stellar contents of groups, cooling flows and the relation to the central galaxy, the formation and processing of multi-phase gas, satellite interactions with the intragroup medium, and the impact of groups for cosmological parameter estimation. Cosmological simulations provide evolutionarily consistent predictions of these observationally difficult-to-define objects, and have untapped potential to accurately model their gaseous, stellar and dark matter distributions.

scholarly journals Towards a predictive multi-phase model for alpine mass movements and process cascades

2022 ◽  
Author(s):  
Alessandro Cicoira ◽  
Lars Blatny ◽  
Xingyue Li ◽  
Bertil Trottet ◽  
Johan Gaume
Keyword(s):  
Complex Dynamics ◽  
Management Strategies ◽  
Three Dimensional ◽  
Mass Movements ◽  
Risk Management Strategies ◽  
Complex Events ◽  
Generate Process ◽  
Operational Models ◽  
Multi Phase ◽  
The Impact

Alpine mass movements can generate process cascades involving different materials including rock, ice, snow, and water. Numerical modelling is an essential tool for the quantification of natural hazards, but state-of-the-art operational models reach their limits when facing unprecedented or complex events. Here, we advance our predictive capabilities for process cascades on the basis of a three-dimensional numerical model, coupling fundamental conservation laws to finite strain elastoplasticity. Through its hybrid Eulerian-Lagrangian character, our approach naturally reproduces fractures and collisions, erosion/deposition phenomena, and multi-phase interactions, which finally grant very accurate simulations of complex dynamics. Four benchmark simulations demonstrate the physical detail of the model and its applicability to real-world full-scale events, including various materials and ranging through four orders of magnitude in volume. In the future, our model can support risk-management strategies through predictions of the impact of potentially catastrophic cascading mass movements at vulnerable sites.

Sign in / Sign up

Export Citation Format

Share Document