ParaCopasi : A package for parallel biochemical simulation and analysis

2021 ◽  
Author(s):  
Lihuan Yuan ◽  
Chengkun Wu ◽  
Xiaowei Guo ◽  
Canqun Yang
Keyword(s):  
Biochemical Simulation

scholarly journals Simulation of hypoxia of myocardial cells in microfluidic systems

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Anna Kobuszewska ◽  
Elżbieta Jastrzębska ◽  
Kamil Żukowski ◽  
Zbigniew Brzózka
Keyword(s):  
Fluorescent Dyes ◽  
Microfluidic System ◽  
Cardiac Cells ◽  
Human Cardiomyocytes ◽  
New Methods ◽  
Biochemical Simulation ◽  
Carbonyl Cyanide ◽  
Myocardial Hypoxia ◽  
Biochemical Approach ◽  
Methods Of Treatment

Abstract The paper presents a newly designed microfluidic system that allows simulation of myocardial hypoxia by biochemical method. The geometry of the microsystem was designed in such a way, that quantitative fluorescent measurements using a spectrofluorometric plate reader was possible. Biochemical simulation of hypoxia was carried out using potent mitochondrial oxidative phosphorylation uncoupler—Carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone (FCCP). Two cardiac cell lines were used in the study—rat cardiomyoblasts (H9C2) and human cardiomyocytes. The effectiveness of biochemical simulation of hypoxia was studied using two fluorescent dyes: carbocyanine iodide (JC-1) and Fluo-4. Changes in the mitochondrial membrane potential and concentration of intracellular calcium ions were tested. The major novelty of this research was the applying the microfluidic system to create hypoxia conditions for cardiac cells using the biochemical approach. In further studies, the presented hypoxia model could be used to develop new methods of treatment of ischemic heart disease for example in cell therapy based on stem cells.

scholarly journals Acceleration of discrete stochastic biochemical simulation using GPGPU

2015 ◽  
Vol 6 ◽  
Author(s):  
Kei Sumiyoshi ◽  
Kazuki Hirata ◽  
Noriko Hiroi ◽  
Akira Funahashi
Keyword(s):  
Biochemical Simulation

A biochemical simulation system

1977 ◽  
Vol 10 (4) ◽  
pp. 383-392 ◽  
Author(s):  
William F. Cassano
Keyword(s):  
Simulation System ◽  
Biochemical Simulation

scholarly journals BISEN: Biochemical Simulation Environment

2009 ◽  
Vol 25 (6) ◽  
pp. 836-837 ◽  
Author(s):  
J. Vanlier ◽  
F. Wu ◽  
F. Qi ◽  
K. C. Vinnakota ◽  
Y. Han ◽  
...  
Keyword(s):  
Simulation Environment ◽  
Biochemical Simulation

Applications of rare event dynamics on the free energy calculations for membrane protein systems

2013 ◽  
Vol 91 (9) ◽  
pp. 769-774 ◽  
Author(s):  
Yun-Kun Wang ◽  
Dong-Qing Wei ◽  
Ruo-Xu Gu ◽  
Huai-Meng Fan ◽  
Jakob Ulmschneider
Keyword(s):  
Free Energy ◽  
Rare Event ◽  
Free Energy Calculations ◽  
Drug Binding ◽  
Proton Channel ◽  
Active Peptides ◽  
Biochemical Simulation ◽  
Dynamics Simulations ◽  
Event Dynamics ◽  
Energy Information

Techniques of rare event dynamics were reviewed, including string methods, which will be implemented with the biochemical simulation packages. The existing methods were applied to study biological systems with relevance to drug design and drug metabolism. The rare event dynamics simulations were performed to understand the kinetic and thermodynamic free energy information on the drug binding sites in the M2 proton channel, the free energy of insertion and association of membrane proteins and membrane active peptides. Results give a theoretical framework to interpret and reconcile existing and often conflicting opinions.

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