Greetings Visitor. My name is HE Chong (贺翀). I am a ph.D in Physics that
somehow ended up working as a Software Engineer specialized in Cryptography.
Study complex system with Math and computation is interesting, (help) building
up practical systems with which people can create value feels even better. I
guess that's why I am having fun working in a Software company (V-Key) that creates Virtual Secure Element
to help our customers securing their digital assets / transactions.
For pasttime, I like making various kinds of soft drinks. Coffee and Matcha are my favorites.
A Vim plugin for user to lookup synonyms of any word under cursor or phrase covered in visual mode, and replace it with an user chosen synonym. It also accepts word/phrases from manual input for synonym checkup.
This plugin is aimed to be a decent thesaurus query and replacing plugin for Vim that is easy to customise and expand its functionalities. Currently it supports multiple thesaurus sources, both online and offline, of English, German, Russian and Chinese. At this point this plugin is already quite powerful and does its thing well. So, if you use Vim, give it a try!
Feedback and new suggestions are always welcomed~ XD
A toolkit that can be used to simulate a biochemical network. It provides routines for both deterministic (by adaptive stepsize Runge-Kutta algorithm) and stochastic (by Gillespie algirithm) for biochemical network composed of simple reactions and composite reactions (like Michaelis-Menten equation and Hill equation). The work of my paper Comparison of cellular oscillations driven by noise or deterministic mechanisms under cell-size scaling is done with this toolkit.
Ultradian cycles are frequently observed in biological systems. They serve important roles in regulating, for example, cell fate and the development of the organism. Many mathematical models have been developed to analyze their behavior. Generally, these models can be classified into two classes: Deterministic models that generate oscillatory behavior by incorporating time delays or Hopf bifurcations, and stochastic models that generate oscillatory behavior by noise driven resonance. However, it is still unclear which of these two mechanisms applies to cellular oscillations. In this paper, we show through theoretical analysis and numerical simulation that we can distinguish which of these two mechanisms govern cellular oscillations, by measuring statistics of oscillation amplitudes for cells of different sizes. We found that, for oscillations driven deterministically, the normalized average amplitude is constant with respect to cell size, while the coefficient of variation of the amplitude scales with cell size with an exponent of −0.5 . On the other hand, for oscillations driven stochastically, the coefficient of variation of the amplitude is constant with respect to cell size, while the normalized average amplitude scales with cell size with an exponent of −0.5 . Our results provide a theoretical basis to discern whether a particular oscillatory behavior is governed by a deterministic or stochastic mechanism.
In short, we accidentally noticed a phenomena, as we later had proven theoretically, that could very likely help us distinguishing biochemical oscillation's mechanism using statistical correlation between amplitude distribution and cell size. After the publication of this paper, we applied this method on several sets of sample data. Some yields quite promising results. We are eager to know how far this method can go and what we can do with the new results.