Stochastic chemical kinetics : A review of the modelling and simulation approaches

Biophysics Reviews
Paola Lecca

Abstract

A review of the physical principles that are the ground of the stochastic formulation of chemical kinetics is presented along with a survey of the algorithms currently used to simulate it. This review covers the main literature of the last decade and focuses on the mathematical models describing the characteristics and the behavior of systems of chemical reactions at the nano- and micro-scale. Advantages and limitations of the models are also discussed in the light of the more and more frequent use of these models and algorithms in modeling and simulating biochemical and even biological processes.

References

Mar 1, 2003·Biophysical Journal·R BundschuhC Jayaprakash
Jun 5, 2003·Chaos·Jeff HastyJ. J. Collins
Feb 13, 2004·Bioinformatics·Thomas R KiehlMelvin K Simmons
Aug 31, 2004·The Journal of Chemical Physics·Yang CaoLinda Petzold
Feb 9, 2005·Bioinformatics·Abhijit ChatterjeeDionisios G Vlachos
Aug 20, 2005·The Journal of Chemical Physics·Yang CaoLinda R Petzold
Feb 8, 2006·The Journal of Chemical Physics·Yang CaoLinda R Petzold
Oct 14, 2006·Annual Review of Physical Chemistry·Daniel T Gillespie
Oct 21, 2006·Systems Biology·T LuJ Hasty
Feb 13, 2008·The Journal of Chemical Physics·David F Anderson
Dec 3, 2008·IET Systems Biology·Z Liu, Y Cao
Jan 20, 2009·Briefings in Bioinformatics·Jürgen Pahle
Feb 17, 2009·Methods in Enzymology·Yang Cao, David C Samuels
Apr 22, 2009·Methods in Molecular Biology·Haluk ResatMichel F Pettigrew
May 6, 2009·Computational Biology and Chemistry·Georgios Kalantzis
May 14, 2009·Bioinformatics·G L PapadopoulosA G Hatzigeorgiou
Jul 2, 2009·The Journal of Chemical Physics·Rajesh RamaswamyIvo F Sbalzarini

❮ Previous
Next ❯

Citations

Aug 10, 2017·Microcirculation : the Official Journal of the Microcirculatory Society, Inc·Joseph WalpoleJohn C Chappell
Feb 15, 2020·PLoS Computational Biology·Jordan DouglasAlexei J Drummond
Feb 23, 2020·PLoS Computational Biology·Natacha Comandante-LouMohammad Fallahi-Sichani
Oct 28, 2019·Essays in Biochemistry·George ButlerPhilip R Dash
Apr 22, 2018·Environmental Science and Pollution Research International·Zhonghao WanFrancis Verpoort
Apr 29, 2021·Computers in Biology and Medicine·Manuel JuradoAntonio Zorzano
Jun 25, 2021·Chemical Science·Jack W JordanAndrei N Khlobystov

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Journal of Photochemistry and Photobiology. B, Biology
Shakeel AhmedSalprima Yudha S
Nature Nanotechnology
© 2022 Meta ULC. All rights reserved