Physiochemical Effects of Nanoparticles on Cell Nuclear Complex Pore Transport: A Coarse-Grained Computational Model

2019 ◽  
Vol 15 (11) ◽  
pp. 6382-6392 ◽  
Author(s):  
Liuyang Zhang ◽  
Matthew D. Becton ◽  
Ning Liu ◽  
Rodney D. Averett ◽  
Ramana M. Pidaparti ◽  
...  
Keyword(s):  
Computational Model ◽  
Coarse Grained ◽  
Nuclear Complex

scholarly journals Computer simulation of knotted proteins unfold and translocation through nano-pores

2018 ◽  
Author(s):  
M. A. Shahzad
Keyword(s):  
Computer Simulation ◽  
Computational Model ◽  
Coarse Grained ◽  
Kinetic Properties ◽  
Constant Force ◽  
Translocation Mechanism ◽  
Translocation Time ◽  
Knotted Protein ◽  
Knotted Proteins ◽  
Pulling Force

We study the unfold and translocation of knotted protein, YibK and YbeA, through α-hemolysin nano-pore via a coarse grained computational model. We observe that knot of protein unfold in advance before the translocation take place. We also characterized the translocation mechanism by studying the thermodynamical and kinetic properties of the process. In particular, we study the average of translocation time, and the translocation probability as a function of pulling force F acting in the channel. In limit of low pulling inward constant force acting along the axis of the pore, the YibK knotted protein takes longer average translocation time as compare to YbeA knotted protein.

scholarly journals Superlattice assembly by interpolymer complexation

Soft Matter ◽  
2019 ◽  
Vol 15 (47) ◽  
pp. 9690-9699 ◽  
Author(s):  
Nathan Horst ◽  
Srikanth Nayak ◽  
Wenjie Wang ◽  
Surya Mallapragada ◽  
David Vaknin ◽  
...  
Keyword(s):  
Computational Model ◽  
Coarse Grained ◽  
Interpolymer Complexation

We present a coarse-grained computational model that describes superlattice assembly via interpolymer complexation.

scholarly journals A coarse-grained computational model of the nuclear pore complex predicts Phe-Gly nucleoporin dynamics

2017 ◽  
Vol 149 (10) ◽  
pp. 951-966 ◽  
Author(s):  
Joan Pulupa ◽  
Manas Rachh ◽  
Michael D. Tomasini ◽  
Joshua S. Mincer ◽  
Sanford M. Simon
Keyword(s):  
Computational Model ◽  
Nuclear Pore Complex ◽  
Coarse Grained ◽  
Nuclear Pore ◽  
Experimental Measurements ◽  
Central Channel ◽  
Computational Simulations ◽  
Cargo Transport ◽  
And Function

The phenylalanine-glycine–repeat nucleoporins (FG-Nups), which occupy the lumen of the nuclear pore complex (NPC), are critical for transport between the nucleus and cytosol. Although NPCs differ in composition across species, they are largely conserved in organization and function. Transport through the pore is on the millisecond timescale. Here, to explore the dynamics of nucleoporins on this timescale, we use coarse-grained computational simulations. These simulations generate predictions that can be experimentally tested to distinguish between proposed mechanisms of transport. Our model reflects the conserved structure of the NPC, in which FG-Nup filaments extend into the lumen and anchor along the interior of the channel. The lengths of the filaments in our model are based on the known characteristics of yeast FG-Nups. The FG-repeat sites also bind to each other, and we vary this association over several orders of magnitude and run 100-ms simulations for each value. The autocorrelation functions of the orientation of the simulated FG-Nups are compared with in vivo anisotropy data. We observe that FG-Nups reptate back and forth through the NPC at timescales commensurate with experimental measurements of the speed of cargo transport through the NPC. Our results are consistent with models of transport where FG-Nup filaments are free to move across the central channel of the NPC, possibly informing how cargo might transverse the NPC.

Numerical Simulation of Void Growth Induced Creep Rupture in HAZ at Elevated Temperature

2008 ◽  
Vol 33-37 ◽  
pp. 441-448
Author(s):  
Tao Yu ◽  
Masataka Yatomi ◽  
Hui Ji Shi
Keyword(s):  
Numerical Simulation ◽  
Elevated Temperature ◽  
Computational Model ◽  
Void Growth ◽  
Welded Joints ◽  
Material Properties ◽  
Creep Damage ◽  
Coarse Grained ◽  
Damage Development ◽  
Fine Grained

In structural welded joints after long-term service under elevated temperature, fracture occurred mainly in the heat affected zone (HAZ). Recently, the nucleation and growth of creep voids in the fine-grained HAZ of weldments, recognized as Type IV fracture, has become an important problem for ferritic heat resisting steel. In this paper, a new computational model was presented to analyse the void growth induced creep damage development in HAZ. The new constitutive model based on continuum damage mechanics (CDM) equations is combined with a micromechanism-based model in order to account for the void growth process, which is different from the previous studies of creep damage. Material properties used for the creep damage computations are fitted from actual creep test data. Basic benchmark tests were performed to verify the new computational model. Then the model was used to study the creep damage development in the welded joints where four different material properties, base material, coarse-grained HAZ, fine-grained HAZ, and weld material, are taken into account. The numerical simulation results for creep lifetimes agreed well with the experimental results.

scholarly journals Frequency-control of protein translocation across an oscillating nanopore

2017 ◽  
Vol 19 (18) ◽  
pp. 11260-11272 ◽  
Author(s):  
Fabio Cecconi ◽  
Muhammad Adnan Shahzad ◽  
Umberto Marini Bettolo Marconi ◽  
Angelo Vulpiani
Keyword(s):  
Computational Model ◽  
Protein Translocation ◽  
Binding Protein ◽  
Frequency Control ◽  
Lipid Binding ◽  
Coarse Grained ◽  
Pore Geometry ◽  
Lipid Binding Protein

The translocation of a lipid binding protein (LBP) is studied using a phenomenological coarse-grained computational model that simplifies both chain and pore geometry.

The Alteration of the Pore Spaces in Sandstones

1973 ◽  
Vol 31 ◽  
pp. 210-211
Author(s):  
R. E. Ferrell ◽  
G. G. Paulson
Keyword(s):  
Electron Microscope ◽  
Scanning Electron Microscope ◽  
The Other ◽  
Coarse Grained ◽  
Depositional Fabric ◽  
Soluble Components ◽  
Scanning Electron ◽  
Shape And Size

The pore spaces in sandstones are the result of the original depositional fabric and the degree of post-depositional alteration that the rock has experienced. The largest pore volumes are present in coarse-grained, well-sorted materials with high sphericity. The chief mechanisms which alter the shape and size of the pores are precipitation of cementing agents and the dissolution of soluble components. Each process may operate alone or in combination with the other, or there may be several generations of cementation and solution.The scanning electron microscope has ‘been used in this study to reveal the morphology of the pore spaces in a variety of moderate porosity, orthoquartzites.

On the Origin of the Microscystalline Structure in Rapidly Solidified IN-100 Powder

1977 ◽  
Vol 35 ◽  
pp. 260-261
Author(s):  
J. M. Walsh ◽  
K. P. Gumz ◽  
J. C. Whittles ◽  
B. H. Kear
Keyword(s):  
The Other ◽  
Coarse Grained ◽  
Microcrystalline Structure ◽  
Routine Examination ◽  
Atomization Process ◽  
Centrifugal Atomization ◽  
Splat Quenching ◽  
Powder Particles ◽  
Dendritic Microstructures ◽  
Rapidly Solidified

During a routine examination of the microstructure of rapidly solidified IN-100 powder, produced by a newly-developed centrifugal atomization process1, essentially two distinct types of microstructure were identified. When a high melt superheat is maintained during atomization, the powder particles are predominantly coarse-grained, equiaxed or columnar, with distinctly dendritic microstructures, Figs, la and 4a. On the other hand, when the melt superheat is reduced by increasing the heat flow to the disc of the rotary atomizer, the powder particles are predominantly microcrystalline in character, with typically one dendrite per grain, Figs, lb and 4b. In what follows, evidence is presented that strongly supports the view that the unusual microcrystalline structure has its origin in dendrite erosion occurring in a 'mushy zone' of dynamic solidification on the disc of the rotary atomizer.The critical observations were made on atomized material that had undergone 'splat-quenching' on previously solidified, chilled substrate particles.

Correlation between dislocation, grain boundary and interface of duplex SS in stress corrosion cracking(SCC)

1990 ◽  
Vol 48 (4) ◽  
pp. 928-929
Author(s):  
Wang Zheng-fang ◽  
Z.F. Wang
Keyword(s):  
Stainless Steel ◽  
Thermal Cycle ◽  
Secondary Phase ◽  
Corrosion Cracking ◽  
Coarse Grained ◽  
Test Environment ◽  
Fine Grained ◽  
Evaluation Test ◽  
Welding Thermal Cycle ◽  
Micro Analysis

The main purpose of this study highlights on the evaluation of chloride SCC resistance of the material,duplex stainless steel,OOCr18Ni5Mo3Si2 (18-5Mo) and its welded coarse grained zone(CGZ).18-5Mo is a dual phases (A+F) stainless steel with yield strength:512N/mm2 .The proportion of secondary Phase(A phase) accounts for 30-35% of the total with fine grained and homogeneously distributed A and F phases(Fig.1).After being welded by a specific welding thermal cycle to the material,i.e. Tmax=1350°C and t8/5=20s,microstructure may change from fine grained morphology to coarse grained morphology and from homogeneously distributed of A phase to a concentration of A phase(Fig.2).Meanwhile,the proportion of A phase reduced from 35% to 5-10°o.For this reason it is known as welded coarse grained zone(CGZ).In association with difference of microstructure between base metal and welded CGZ,so chloride SCC resistance also differ from each other.Test procedures:Constant load tensile test(CLTT) were performed for recording Esce-t curve by which corrosion cracking growth can be described, tf,fractured time,can also be recorded by the test which is taken as a electrochemical behavior and mechanical property for SCC resistance evaluation. Test environment:143°C boiling 42%MgCl2 solution is used.Besides, micro analysis were conducted with light microscopy(LM),SEM,TEM,and Auger energy spectrum(AES) so as to reveal the correlation between the data generated by the CLTT results and micro analysis.

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