分子馬達的工作環境是在奈米尺度下，利用ATP水解及水解產物的釋放，將化學能轉變成機械功，進而產生機械運動。受熱晃動而作機械化學耦合運動的分子馬達，可使用布朗馬達運動的理論來說明其是如何達成有方向性的運動。
　　本文使用兩狀態模型來模擬分子馬達的運動，假設此兩狀態的勢能圖形式是相同，但是相位則相差了半個週期，並且在每一個狀態內，各包含有兩個構型狀態。利用酵素動力學的概念，首先建構出分子馬達的Master equation，可以計算出每個構型狀態位置的機率密度，如此可進一步求得分子馬達的前進通量，以及依照勢能改變對分子馬達的輸入能量，和分子馬達抵抗外力所做的機械功，最後計算出分子馬達向前運動的效率。
　　本文採用MATLAB 7.0軟體，求解上述的Master equation。討論在各種不同切換速率情況下，分子馬達的通量會有什麼變化，以及切換速率與效率關係。當增大此兩狀態的順向切換速率的時候，分子馬達的通量會有提昇的效果，順向趨勢與逆向趨勢相比較，因為模型設計的關係，順向趨勢的通量改變程度會比逆向趨勢來得明顯；在不同切換速率下，分子馬達的效率都相當接近，其切換速率對效率影響甚小。

　The working environment of the molecular motor is in nano-scale, using hydrolysis and release processes bring chemically energy transfer to mechanical work, then starting mechanical motion. The molecular motor subjects to thermal fluctuation and makes mechanochemistry motion. We can use the theory of Brownian motor to illustrate how the molecular motor become the direction motion.
　This paper uses two state model to imitate molecular motor, supposedly two potentials are the same but shifted on a period to the right or to the left, and each state has two conformation states. Using enzyme kinetics concept, we first build up the Master equation of the molecular motor to calculate the probability density in each conformation state and then find the forward flux of the molecular motor. Because potential could change input energy of the molecular motor and the molecular motor made the mechanical work from resisting external force, we calculated the efficiency by input energy and mechanical work.
　This paper used MATLAB 7.0 to calculate the Master equation. We discussed the change of the flux of the molecular motor in different transition rates. When we increased the forward transition rates of two states, the flux of the molecular motor increased too. We compared forward with backward transition rates, because of the relationship of the model, the change of the flux of forward transition rates was more than the change of the flux of backward transition rates. The efficiency of the molecular motor is almost the same in different transition rates. The influence of transition rates on efficiency is very small.

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