An Integrated In Silico Simulation and Biomatter Compilation Approach to Cellular Computation

2016 ◽  
pp. 655-676 ◽  
Author(s):  
Savas Konur ◽  
Harold Fellermann ◽  
Larentiu Marian Mierla ◽  
Daven Sanassy ◽  
Christophe Ladroue ◽  
...  
Keyword(s):  
In Silico ◽  
Cellular Computation ◽  
In Silico Simulation

Entry of water into the distal heme pocket of soluble guanylate cyclase β1 H-NOX domain alters the ligated CO structure: a resonance Raman and in silico simulation study

RSC Advances ◽  
2016 ◽  
Vol 6 (49) ◽  
pp. 43707-43714
Author(s):  
Haoran Xu ◽  
Yuebin Zhang ◽  
Lei Chen ◽  
Yan Li ◽  
Chen Li ◽  
...  
Keyword(s):  
Guanylate Cyclase ◽  
Simulation Study ◽  
In Silico ◽  
Soluble Guanylate Cyclase ◽  
Resonance Raman ◽  
Heme Pocket ◽  
In Silico Simulation

Water accessing into the heme pocket and alters the structures of CO–sGC (heme), exhibiting two different vFe–CO stretching modes.

scholarly journals Allosteric modulation of alternatively spliced Ca2+-activated Cl−channels TMEM16A by PI(4,5)P2and CaMKII

2020 ◽  
Vol 117 (48) ◽  
pp. 30787-30798
Author(s):  
Woori Ko ◽  
Seung-Ryoung Jung ◽  
Kwon-Woo Kim ◽  
Jun-Hee Yeon ◽  
Cheon-Gyu Park ◽  
...  
Keyword(s):  
Binding Site ◽  
In Silico ◽  
Single Channel ◽  
Splice Variants ◽  
Noise Analysis ◽  
Mechanistic Explanation ◽  
Intracellular Loop ◽  
Open Probability ◽  
In Silico Simulation ◽  
Alternatively Spliced

Transmembrane 16A (TMEM16A, anoctamin1), 1 of 10 TMEM16 family proteins, is a Cl−channel activated by intracellular Ca2+and membrane voltage. This channel is also regulated by the membrane phospholipid phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2]. We find that two splice variants of TMEM16A show different sensitivity to endogenous PI(4,5)P2degradation, where TMEM16A(ac) displays higher channel activity and more current inhibition by PI(4,5)P2depletion than TMEM16A(a). These two channel isoforms differ in the alternative splicing of the c-segment (exon 13). The current amplitude and PI(4,5)P2sensitivity of both TMEM16A(ac) and (a) are significantly strengthened by decreased free cytosolic ATP and by conditions that decrease phosphorylation by Ca2+/calmodulin-dependent protein kinase II (CaMKII). Noise analysis suggests that the augmentation of currents is due to a rise of single-channel current (i), but not of channel number (N) or open probability (PO). Mutagenesis points to arginine 486 in the first intracellular loop as a putative binding site for PI(4,5)P2, and to serine 673 in the third intracellular loop as a site for regulatory channel phosphorylation that modulates the action of PI(4,5)P2. In silico simulation suggests how phosphorylation of S673 allosterically and differently changes the structure of the distant PI(4,5)P2-binding site between channel splice variants with and without the c-segment exon. In sum, our study reveals the following: differential regulation of alternatively spliced TMEM16A(ac) and (a) by plasma membrane PI(4,5)P2, modification of these effects by channel phosphorylation, identification of the molecular sites, and mechanistic explanation by in silico simulation.

Comparison of in vivo and in silico growth performance and variability in pigs when applying a feeding strategy designed by simulation to control the variability of slaughter weight

2014 ◽  
Vol 54 (12) ◽  
pp. 1939 ◽  
Author(s):  
L. Brossard ◽  
B. Vautier ◽  
J. van Milgen ◽  
Y. Salaun ◽  
N. Quiniou
Keyword(s):  
Growth Performance ◽  
Coefficient Of Variation ◽  
In Silico ◽  
Feeding Strategy ◽  
Feeding Strategies ◽  
Net Energy ◽  
Two Phase ◽  
In Silico Simulation ◽  
Ad Libitum

Variability in bodyweight (BW) among pigs complicates the management of feeding strategies and slaughter. Including variability among individuals in modelling approaches can help to design feeding strategies to control performance level, but also its variability. The InraPorc model was used to perform simulations on 10 batches of 84 crossbred pigs each to characterise the effect of feeding strategies differing in amino acid supply or feed allowance on the mean and variation in growth rate. Results suggested that a feed restriction reduces the coefficient of variation of BW at first departure for slaughter (BW1) by 34%. Growth performance obtained from an in silico simulation using ad libitum and restricted feeding plans was compared with results obtained in an in vivo experiment on a batch of 168 pigs. Pigs were offered feed ad libitum or were restricted (increase in feed allowance by 27 g/day up to a maximum of 2.4 and 2.7 kg/day for gilts and barrows, respectively). A two-phase feeding strategy was applied, with 0.9 and 0.7 g of digestible lysine per MJ of net energy (NE) in diets provided before or after 65 kg BW, respectively. Actual growth was similar to that obtained by simulation. Coefficient of variation of BW1 was similar in vivo and in silico for the ad libitum feeding strategy but was underestimated by 1 percentage point in silico for the restriction strategy. This study confirms the relevance of using simulations performed to predict the level and variability in performance of group housed pigs.

scholarly journals In silico simulation of liver crack detection using ultrasonic shear wave imaging

2018 ◽  
Vol 18 (1) ◽  
Author(s):  
Erwei Nie ◽  
Jiao Yu ◽  
Debaditya Dutta ◽  
Yanying Zhu
Keyword(s):  
Shear Wave ◽  
In Silico ◽  
Crack Detection ◽  
Shear Wave Imaging ◽  
Wave Imaging ◽  
In Silico Simulation ◽  
Ultrasonic Shear

scholarly journals The emergence of DNA in the RNA world: an in silico simulation study of genetic takeover

2015 ◽  
Vol 15 (1) ◽  
Author(s):  
Wentao Ma ◽  
Chunwu Yu ◽  
Wentao Zhang ◽  
Sanmao Wu ◽  
Yu Feng
Keyword(s):  
Simulation Study ◽  
In Silico ◽  
Rna World ◽  
In Silico Simulation ◽  
Genetic Takeover
Sign in / Sign up

Export Citation Format

Share Document