Modeling and Analysis of the Droplet Landing Process in Cell Direct-Writing

2013 ◽  
Vol 7 (3) ◽  
pp. 353-358 ◽  
Author(s):  
Cai Renye ◽  
◽  
Huang Jin ◽  
Keyword(s):  
Large Scale ◽  
Cell Damage ◽  
Three Dimensional ◽  
Smooth Particle Hydrodynamic ◽  
Direct Write ◽  
Direct Writing ◽  
Modeling And Analysis ◽  
Mesh Free ◽  
Hydrodynamic Method ◽  
The Impact

Cell direct-write, a promising technology for the creation of complex, three-dimensional tissue constructs, has great potential in tissue engineering, biological cytology, high-throughput drug screening and cell sensors. However, it has been found that cell damage due to the mechanical impact during cell direct-write is a possible hurdle for broad applications of fragile cell direct writing. The objective of this paper is to analyze the impact of the continuously jetted cell droplets on the hydro-gel coating substrate. In order to avoid the element distortion due to large-scale deformation, a mesh-free Smooth Particle Hydrodynamic method (SPH), is introduced to study the impact-induced cell mechanical loading profile during cell landing, including effective stress, plastic strain, velocity and acceleration, for better understanding and prediction of possible impact-induced cell damage. It is found that three important impact processes, cell-hydrogel, cellcell and cell-substrate impact, may occur during cell landing. It is concluded to decrease impact-induced cell damage, there are an appropriate firing period and jetting velocity.

Study of Impact-Induced Mechanical Effects in Cell Direct Writing Using Smooth Particle Hydrodynamic Method

2008 ◽  
Vol 130 (2) ◽  
Author(s):  
Wei Wang ◽  
Yong Huang ◽  
Mica Grujicic ◽  
Douglas B. Chrisey
Keyword(s):  
Shear Strain ◽  
Mechanical Loading ◽  
Cell Damage ◽  
Smooth Particle Hydrodynamic ◽  
Strain Component ◽  
Direct Writing ◽  
Maximum Shear Strain ◽  
Smooth Particle Hydrodynamic Method ◽  
Hydrodynamic Method ◽  
The Impact

Biomaterial direct-write technologies have been receiving more and more attention as rapid prototyping innovations in the area of tissue engineering, regenerative medicine, and biosensor∕actuator fabrication based on computer-aided designs. However, cell damage due to the mechanical impact during cell direct writing has been observed and is a possible hurdle for broad applications of fragile cell direct writing. The objective of this study is to investigate the impact-induced cell mechanical loading profile in cell landing in terms of stress, acceleration, and maximum shear strain component during cell direct writing using a mesh-free smooth particle hydrodynamic method. Such cell mechanical loading profile information can be used to understand and predict possible impact-induced cell damage. It is found that the cell membrane usually undergoes a relatively severe deformation and the cell mechanical loading profile is dependent on the cell droplet initial velocity and the substrate coating thickness. Two important impact processes may occur during cell direct writing: the first impact between the cell droplet and the substrate coating and the second impact between the cell and the substrate. It is concluded that the impact-induced cell damage depends not only on the magnitudes of stress, acceleration, and∕or shear strain but also the loading history that a cell experiences.

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.

scholarly journals Processing variables of direct-write, near-field electrospinning impact size and morphology of gelatin fibers

2020 ◽  
Author(s):  
Zachary G. Davis ◽  
Aasim F. Hussain ◽  
Matthew B. Fisher
Keyword(s):  
Acetic Acid ◽  
Acid Concentration ◽  
Near Field ◽  
Fiber Formation ◽  
Direct Write ◽  
Acetic Acid Concentration ◽  
Direct Writing ◽  
Fiber Morphology ◽  
Gelatin Concentration ◽  
The Impact

AbstractSeveral biofabrication methods are being investigated to produce scaffolds that can replicate the structure of the extracellular matrix. Direct-write, near-field electrospinning of polymer solutions and melts is one such method which combines fine fiber formation with computer-guided control. Research with such systems has focused primarily on synthetic polymers. To better understand the behavior of biopolymers used for direct-writing, this project investigated changes in fiber morphology, size, and variability caused by varying gelatin and acetic acid concentration, as well as, process parameters such as needle gauge and height, stage speed, and interfiber spacing. Increasing gelatin concentration at a constant acetic acid concentration improved fiber morphology from large, planar structures to small, linear fibers with a median of 2.3 µm. Further varying the acetic acid concentration at a constant gelatin concentration did not alter fiber morphology and diameter throughout the range tested. Varying needle gauge and height further improved the median fiber diameter to below 2 µm and variability of the first and third quartiles to within +/-1 µm of the median for the optimal solution combination of gelatin and acetic acid concentrations. Additional adjustment of stage speed did not impact the fiber morphology or diameter. Repeatable interfiber spacings down to 250 µm were shown to be capable with the system. In summary, this study illustrates the optimization of processing parameters for direct-writing of gelatin to produce fibers on the scale of collagen fibers. This system is thus capable of replicating the fibrous structure of musculoskeletal tissues with biologically relevant materials which will provide a durable platform for the analysis of single cell-fiber interactions to help better understand the impact scaffold materials and dimensions have on cell behavior.

scholarly journals Hybrid Analytical and Numerical Approach for Modeling Fluid Flow in Simplified Three-Dimensional Fracture Networks

Geofluids ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-14
Author(s):  
D. Roubinet ◽  
S. Demirel ◽  
E. B. Voytek ◽  
X. Wang ◽  
J. Irving
Keyword(s):  
Fluid Flow ◽  
Three Dimensional ◽  
Fracture Network ◽  
Numerical Approach ◽  
Fracture Networks ◽  
Surrounding Matrix ◽  
Mesh Free ◽  
Fracture Scale ◽  
The Impact ◽  
Numerical Approaches

Modeling fluid flow in three-dimensional fracture networks is required in a wide variety of applications related to fractured rocks. Numerical approaches developed for this purpose rely on either simplified representations of the physics of the considered problem using mesh-free methods at the fracture scale or complex meshing of the studied systems resulting in considerable computational costs. Here, we derive an alternative approach that does not rely on a full meshing of the fracture network yet maintains an accurate representation of the modeled physical processes. This is done by considering simplified fracture networks in which the fractures are represented as rectangles that are divided into rectangular subfractures such that the fracture intersections are defined on the borders of these subfractures. Two-dimensional analytical solutions for the Darcy-scale flow problem are utilized at the subfracture scale and coupled at the fracture-network scale through discretization nodes located on the subfracture borders. We investigate the impact of parameters related to the location and number of the discretization nodes on the results obtained, and we compare our results with those calculated using reference solutions, which are an analytical solution for simple configurations and a standard finite-element modeling approach for complex configurations. This work represents a first step towards the development of 3D hybrid analytical and numerical approaches where the impact of the surrounding matrix will be eventually considered.

Modeling of Thermoelastic Stress Wave in Laser-Assisted Cell Direct Writing

2009 ◽  
Author(s):  
Wei Wang ◽  
Yong Huang ◽  
Yafu Lin
Keyword(s):  
Stress Wave ◽  
Cell Damage ◽  
Optical Breakdown ◽  
Thermoelastic Stress ◽  
Laser Pulses ◽  
Stress Wave Propagation ◽  
Direct Write ◽  
Direct Writing ◽  
Coating Materials ◽  
Laser Focal Spot

Laser-assisted cell direct-write technique has been a promising biomaterial direct-write method. For safe and reproducible cell direct writing, the cell damage due to process-induced external stress must be understood in addition to biological property research. The objective of this study is to model the thermoelastic stress wave propagation inside the coating in laser-assisted cell direct writing when the vaporization or optical breakdown of coating materials is not available. It is found that a bipolar pressure pair has been developed within a finite thin coating medium, locations near the laser focal spot experience higher stresses, and shorter duration laser pulses lead to higher thermoelastic stresses. This study will help understand the photomechanical stress and its relevance with biomaterial damage in laser-assisted cell direct writing.

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).

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