Journal Club for stochastic analysis of biochemical systems
Sep 3rd 2024, Jinsu Kim
Asymptotic Evaluation of Certain Markov Process Expectations for Large Time, I by M. D. DONSKER AND S. R. S. VARADHAN.
Sep 10th 2024, Minjoon Kim
Anderson, David F., and Desmond J. Higham. “Multilevel Monte Carlo for continuous time Markov chains, with applications in biochemical kinetics.” Multiscale Modeling & Simulation 10.1 (2012): 146-179.
Oct 8th 2024, Jeongwoon Kim
Gao, Xuefeng, Zuo Quan Xu, and Xun Yu Zhou. “State-dependent temperature control for Langevin diffusions.” SIAM Journal on Control and Optimization 60.3 (2022): 1250-1268.
Oct 15th 2024, Seokhwan Moon
Lestas, I., Vinnicombe, G. & Paulsson, J. Fundamental limits on the suppression of molecular fluctuations. Nature 467, 174–178 (2010). https://doi.org/10.1038/nature09333
Oct 22nd 2024, Jinsu Kim
Caputo, P., Sinclair, A. Nonlinear Dynamics for the Ising Model. Commun. Math. Phys. 405, 260 (2024)
Oct 29th 2024, Minji Kang
Clamons, Samuel, Lulu Qian, and Erik Winfree. “Programming and simulating chemical reaction networks on a surface.” Journal of the Royal Society Interface 17.166 (2020): 20190790.
Nov 5th 2024, Minjoon Kim
Prevalence of deficiency-zero reaction networks in an Erdös–Rényi framework
DF Anderson, TD Nguyen, Journal of Applied Probability, 2022
Nov 12th 2024, Jeongwoon Kim
Updating Markov Chains with an Eye on Google’s PageRank, Amy N. Langville and Carl D. Meyer, 2006, SIAM Journal on Matrix Analysis and Applications, Vol. 27, Iss. 4
Nov 19th 2024, Dr. Devanand
Nakao, Hiroya, and Alexander S. Mikhailov. “Turing patterns in network-organized activator–inhibitor systems.” Nature Physics 6.7 (2010): 544-550.
Nov 26th 2024, Junho Lim
Owen, J. A., Gingrich, T. R. & Horowitz, J. M. “Universal Thermodynamic Bounds on Nonequilibrium Response with Biochemical Applications” Phys. Rev. X, 10, 011066(2020)
Dec 3rd 2024, Hoejin Kim
Dresch, Jacqueline M., et al. “Two-layer mathematical modeling of gene expression: incorporating dna-level information and system dynamics.” SIAM Journal on Applied Mathematics 73.2 (2013): 804-826.
Dec 10th 2024 Dr. Devanand
Talks in previous semesters
3/14/2024
Speaker: Jinsu Kim
Paper: Thomas Kurtz, “Solutions of Ordinary Differential Equations as Limits of Pure Jump Markov Processes”, Journal of Applied Probability (1970).
3/7/2024
Speaker: Minjoon Kim
Paper: Chen Mufa. “Analytic proof of dual variational formula for the first eigenvalue in dimension one. Science in China Series A: Mathematics 42.8 (1999): 805-815
11/21/2023
Speaker: Jinsu Kim
Paper: Rao, Riccardo, and Massimiliano Esposito. “Nonequilibrium thermodynamics of chemical reaction networks: Wisdom from stochastic thermodynamics.” Physical Review X 6.4 (2016): 041064.
11/14/2023
No journal club, but we will participate in a probability seminar as an alternative plan: https://snu-ac-kr.zoom.us/my/snuinsukseo
11/7/2023
Speaker: Seokhwan Moon
Paper: Corentin Briat*, Ankit Gupta* and Mustafa Khammash. Antithetic proportional-integral feedback for reduced variance and improved control performance of stochastic reaction networks. Journal of the Royal Society Interface, 2018, Vol. 15 (143)
10/31/2023
Speaker: Minjoon Kim
Paper: Hirono, Yuji, and Ryo Hanai. “Squeezing stationary distributions of stochastic chemical reaction systems.” Journal of Statistical Physics 190.4 (2023): 86.
10/24/2023
Speaker: Jinyoung Kim
Paper: Hansen, Mads Christian, and Wiuf Carsten. “Existence of a unique quasi-stationary distribution in stochastic reaction networks.” (2020): 1-30.
10/17/2023
Speaker: Jeongwoon Kim
Paper: Whi, W., Ha, S., Kang, H., & Lee, D. S. (2022). Hyperbolic disc embedding of functional human brain connectomes using resting-state fMRI. Network Neuroscience
We will go to a restaurant for dinner after this journal club
9/19/2023
Speaker: Minjoon Kim
Paper: Hirono, Yuji, and Ryo Hanai. “Squeezing stationary distributions of stochastic chemical reaction systems.” Journal of Statistical Physics 190.4 (2023): 86.
9/12/2023
Speaker: Jinsu Kim
Paper: Meng, X. Flora, et al. “Recursively constructing analytic expressions for equilibrium distributions of stochastic biochemical reaction networks.” Journal of The Royal Society Interface 14.130 (2017): 20170157.
4/21/2023 (Friday) 2pm
Speaker: Minjoon Kim
Paper: Tweedie, Richard L. “Criteria for ergodicity, exponential ergodicity and strong ergodicity of Markov processes.” Journal of Applied Probability 18, no. 1 (1981): 122-130.
Note: We will have pizzas before the journal club starts.
5/26/2023
Speaker: Jinyoung Kim
Paper: Hong, Hyukpyo, Jinsu Kim, M. Ali Al-Radhawi, Eduardo D. Sontag, and Jae Kyoung Kim. “Derivation of stationary distributions of biochemical reaction networks via structure transformation.” Communications biology 4, no. 1 (2021): 620.
3/3 and 3/10/2023
Speaker: Jinsu Kim
Paper: Kurtz, Thomas G. “The relationship between stochastic and deterministic models for chemical reactions.” The Journal of Chemical Physics 57.7 (1972): 2976-2978.
3/24/2023
Speaker: Seokhwan Moon
Paper: Lee, Chang Hyeong, Kyeong-Hun Kim, and Pilwon Kim. “A moment closure method for stochastic reaction networks.” The Journal of chemical physics 130.13 (2009): 134107.
mathjinsukim.com 