使用DMRG进行化学总方程参数探索
John P Zima1, Schuyler B Nicholson1, Todd R Gingrich1
1Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA.
The Journal of chemical physics
|August 7, 2025
概括
张量网络近似化学反应网络分布,在基因切换开关模型中揭示了双稳定性. 该方法捕获超出平均场分析的随机波动,用于更广泛的CRN应用.
科学领域:
- 计算化学是一种计算化学.
- 生物物理学的生物物理.
- 系统生物学 系统生物学
背景情况:
- 化学反应网络 (CRN) 具有复杂的动态,与相关的物种波动相关.
- 蒙特卡洛方法是分析CRN随机轨迹的标准.
- 使用张量网络在大型状态空间上近似的联合分布是一个新兴的领域.
研究的目的:
- 应用张量网络方法来分析七种基因切换开关CRN的稳定状态分布.
- 在CRN模型中确定双稳定性的条件作为分解速率的函数.
- 为了证明张量网络在捕获随机效应和实现参数探索方面的能力.
主要方法:
- 使用张量网络策略,特别是密度矩阵重规范化组 (DMRG) 算法,来计算稳定状态分布.
- 分析七个物种的基因切换开关CRN模型.
- 使用兴奋状态DMRG来计算放松时间表.
主要成果:
- 张量网络方法成功确定了基因切换开关CRN的稳定状态分布.
- 双稳定性被确定为两个分解速率的函数,张量网络捕捉了超出平均场近似的随机效应.
- 该方法证明了对订单参数进行有效投射以识别双模性,并计算了放松时间表.
结论:
- 张量网络为计算CRN的稳态分布提供了强大的工具,为随机动态提供了洞察力.
- 这种方法对具有显著波动的系统的准确性超过了平均场分析.
- 开发的技术有助于参数探索和分析复杂的CRN模型,包括可比式系统.
相关概念视频
01:21Chemical Equilibria: Systematic Approach to Equilibrium Calculations
826
Equilibrium calculations for systems involving multiple equilibria are often complex. For example, to calculate the solubility of a sparingly soluble salt in an aqueous solution in the presence of a common ion, one must consider all the equilibria in this solution. Calculations for these systems can be complicated and tedious, so a systematic approach with a series of steps is often helpful. The process is detailed below.
The first step is to identify all the chemical reactions involved, The...
The first step is to identify all the chemical reactions involved, The...
826
01:20Chemical Equilibria: Redefining Equilibrium Constant
698
The effect of an inert salt on the solubility of a sparingly soluble salt is known as the salt effect. The degree of the salt effect varies with the ionic strength of the solution, which in turn depends on the activity of the species in the solution. The activity is expressed as the product of concentration and the activity coefficient of the species.
To calculate the equilibrium constants of solutions of moderately high ionic strength, one must account for the salt effect. This redefined...
To calculate the equilibrium constants of solutions of moderately high ionic strength, one must account for the salt effect. This redefined...
698
02:21Chemical and Solubility Equilibria
4.2K
The free energy change associated with dissolving a solute in a liter of solvent is called the free energy of a solution, ΔGsolution. The overall ΔGsolution is expressed as the balance of ΔGinteraction against the always-favorable free-energy of mixing, ΔGmixing. Solution formation is favorable if ΔGsolution is less than zero, whereas it is unfavorable if ΔGsolution is greater than zero. In short, for a solution to form and complete dissolution to take place,...
4.2K
01:32Radical Anti-Markovnikov Addition to Alkenes: Thermodynamics
2.1K
The anti-Markovnikov addition of hydrogen halides to an alkene is thermodynamically feasible only with HBr. The radical addition reaction with other hydrogen halides like HCl and HI is thermodynamically unfavorable.
2.1K
03:08Rate-Determining Steps
33.4K
Relating Reaction Mechanisms
In a multistep reaction mechanism, one of the elementary steps progresses significantly slower than the others. This slowest step is called the rate-limiting step (or rate-determining step). A reaction cannot proceed faster than its slowest step, and hence, the rate-determining step limits the overall reaction rate.
The concept of rate-determining step can be understood from the analogy of a 4-lane freeway with a short-stretch of traffic-bottleneck caused due to...
In a multistep reaction mechanism, one of the elementary steps progresses significantly slower than the others. This slowest step is called the rate-limiting step (or rate-determining step). A reaction cannot proceed faster than its slowest step, and hence, the rate-determining step limits the overall reaction rate.
The concept of rate-determining step can be understood from the analogy of a 4-lane freeway with a short-stretch of traffic-bottleneck caused due to...
33.4K
01:17Chemical Shift: Internal References and Solvent Effects
769
In an NMR sample, precise measurement of the absolute absorption frequencies of nuclei is difficult. A standard internal reference compound is added, and the frequency difference between the reference signal and sample signals is measured.
The internal reference compound generally used in NMR spectroscopy is tetramethylsilane (TMS). TMS is preferred because it is chemically inert, soluble in NMR solvents, and easily removable. Also, the highly shielded methyl protons in TMS yield an intense...
The internal reference compound generally used in NMR spectroscopy is tetramethylsilane (TMS). TMS is preferred because it is chemically inert, soluble in NMR solvents, and easily removable. Also, the highly shielded methyl protons in TMS yield an intense...
769