Theoretical Biophysics(English)


Dah-Yen Yang

Theoretical biophysics (chinese) 

Principal Investigator
Institute of Atomic and Molecular Science
Academia Sinica, Taipei, Taiwan
Tel:886-2-2366-8239 
Fax:886-2-2362-0200
E_mail:dyyang@po.iams.sinica.edu.tw
  • Research Statement
  • Selected Publication
  • Online Journal
  • Physical Constants and Conventions

    •  

    　                                                                                                              27 May 2008

               在未來三年,我們將著重於發展分子導線的計算與生物物理的
    的大 型計算 (large-scale computation)。歡迎有興趣的學生或 post Dr. 加入我們的行列。 
    A. 生物物理方面:
            工作內容主要包括蛋白質分子, DNA模型及細胞分裂過程的運算

    1. 蛋白質分子:
            我們主要集中於了解蛋白質分子的功能(function), 如:呼吸過程, 電子轉換
            過程, 分子機器(molecular motor), 蛋白質間的交互作用, 光合作用, 蛋白質
            分子折疊現象等。

    2. DNA模型:
            主要是藉由簡單的模型計算DNA的supercoiling。
    3. 細胞分裂:
            利用數值方法, 計算細胞膜的分裂(fission) 及結合(fusion) 過程是如何進行
            的 。 希望能了解癌細胞分裂過程的物理機制。

    　

    B. 其他:
            我們將利用蛋白質分子之計算方法於
    1. 設計分子導線(molecular wire) 所需的分子電子零件(molecular electronics)。
    2. 設計原子機器(atomic engine) 的應用上。
    　
       
    　
    　

                 

    ________________________________________________________________________________________________________________________________________________

    Research Statement

       We develop various analytical theories to investigate biomolecular behaviors that include:
   
   1. Protein folding
     a. The protein folding time and construct the entropy barrier(manuscript in preparation).
     b. Solving the relationship between radius of gyration vs. pH value
     c. The onset of protein cooperativity.
   
   2. Protein-ligand interaction
     a. Unified kinetic theory of ligand recombination of myoglobin(published)
     b. Escaping from a spherical cavity with gate(published)
     c. We plan to study the effect of ligand interaction on the conformation change of protein.
   
   3. Protein-protein interaction
     a. cooperativity
     b. kinetic theory
   
   4. Membrane
     a. static scaling theory(published)
     b. dynamic scaling theory(published)
     c. static renormalization group theory
     d. dynamic renormalization group theory
     e. membrane folding time and entropy barrier
     f. static topology change problem
     g. simulation of dynamic topology change problem
   
   5. DNA supercoiling
     a. Brownian dynamic simulation of knotted DNA(manuscript in preparation)
     b. Brownian dynamic simulation of linked DNA
    ________________________________________________________________________________________________________________________________________________

    　

    Selected Publication

    last revised in Sep.21,2006.

       
    Electron transfer 
     1. Dah-Yen Yang and R.I. Cukier," The transition from non-adiabatic to solvent controlled

       adiabatic electron transfer: Solvent dynamical effects in the inverted regime",J. Chem.

       Phys.,91(1989)281.[pdf]
   
     2. M. Morillo, D.Y. Yang and R. I. Cukier," Solvent dynamical effects on non-adiabatic 

       electron transfer reactions at low temperature",J. Chem.Phys., 90(1989)5711.[pdf]

     3. Sheh-Yi Sheu and Dah-Yen Yang, "Mean first-passage time and multi- exponential relaxation 

       of the activationless nonadiabatic electron transfer reaction",Phys. Rev., E49(1994)4704.[pdf]

   
 4. Dah-Yen Yang," Generalized moment expansion for nonadiabatic transition reaction", 

       J. Stat. Phys., 74(1994)631.

     5. A.M. Berezhknovskii, V. Yu. Zitserman, D.Y. Yang, C.J. Guo and S.H. Lin, "Heavy-Particle 

       charge transfer reactions under slow adjustment of polar solvents", in "Electron and Ion transfer 

       in Condensed Media",eds A.A. Kornysheu, M.P. Tosi and J. Ulstrup, World Scientific, Singapore, 1997.
     6. Dah-Yen Yang, Sheh-Yi Sheu," Pump-probe Spectroscopy of Photoinduced charge transfer reactions

       in solution",J. Chem.Phys., 106(1997)9427.[pdf]
    
 7. Dah-Yen Yang and Sheh-Yi Sheu, "Dwell time of non-adiabatic transition reaction: solvent dynamic 

       effects",J. Chem.Phys.,107(1997)9361.[pdf]

     8. Sheh-Yi Sheu and Dah-Yen Yang, "Coherence motion of photoinduced non-adiabatic charge transfer
          reaction in solution: a numerical study of Pump-Probe spectroscopy", J. Chem. Phys., 109(1998)5524.[pdf]
     9. E.W. Schlag, Sheh-Yi Sheu, Dah-Yen Yang, H.L. Selzle and S.H.Lin,"Molecular dynamic simulations
         for a new mechanism of charge transport in polypeptides",Proc. Natl. Sci. Acad. USA,
         97(2000)1068-1072.[pdf]
     
    10. E.W. Schlag, Sheh-Yi Sheu, Dah-Yen Yang, H.L. Selzle and S.H.Lin, "Theory of charge transport in polypeptides",
         J. Phys. Chem., B104(2000)7790-7794.[pdf]
    
11. E.W. Schlag, Dah-Yen Yang, Sheh-Yi Sheu, H.L. Selzle and S.H.Lin and P.M.Rentzepis, "Dynamical principles
         in biological processes; a model of chage migration proteins and DNA",Proc. Natl. Acad. Sci. USA,
         97(2000)9849-9854.[pdf]
    
 12. S.Y Sheu,E.W.Schlag,D.Y.Yang and H.L.Selzle,"Efficiency of charge transport in polypeptide chain: the isolated system",
          J. Phys.Chem.,A105(2001)6353.[pdf]
    
 13. Sheh-Yi Sheu, Dah-Yen Yang, H.L.Selzle,and E.W.Schlag, "Charge transport in a polypeptide chain", European Physical 
          Journal D20(2002)557,( invited paper). [pdf]
     14. Sheh-Yi Sheu, Dah-Yen Yang, H.L.Selzle, and E.W.Schlag, "Efficiency of charge transport in a polypeptide chain: the 
          hydrated system", J. Phys. Chem.,A106(2002)9390. [pdf]
     
    　
    　
    Biological processes: escape process
     
    1. D.W. Liao, Dah-Yen Yang, S.Y.Sheu, M. Hayashi, C.K. Tang, S. Suzuki. R.G.Alden and S.H. Lin,

       " Effect of temperature and inhomogeneities on binding of a ligand to haeme proteins",

       J. Chinese Chem. Soc., 41(1994)401.
     2. A.M. Berezhkovskii, Dah-Yen Yang,Shen-Yi Sheu and S. H. Lin,"Stochastic gating in diffusion-

       influenced ligand binding to proteins: gated protein versus gated ligands", Phys. Rev.,

       E54(1996)4462.[pdf]
     3. Wen-Shyan Sheu, Dah-Yen Yang and Sheh-Yi Sheu, "Survival of a walker in gated trapping systems"

       ,J. Chem.Phys.,106(1997)9050.[pdf]
 
     4. Dah-Yen Yang, Wen-Shyan Sheu, Sheh-Yi Sheu and S.H. Lin, "Theory of ligand recombination of Myoglobin: 
    
        a combination of entropic and enthalphic effects", Mol. Phys., 93(1998)159.
     5. Y.A. Makhnovskii, A.M. Berezhkovskii, Sheh-Yi Sheu, Dah-Yen Yang, J. Kuo and S.H. Lin, "Stochastic
          gating influence on the kinetics of diffusion-limited reactions", J. Chem. Phys., 108(1998)971..[pdf]
     
     6. Sheh-Yi Sheu and Dah-Yen Yang," Gated escaping of ligand out of protein", J. Chem. Phys.,
         112(2000)408-415 [pdf]
     
     7. Sheh-Yi Sheu, Dah-Yen Yang, H.L.Selzle, and E.W.Schlag, "Energetics of hydrogen bonds in peptides", Proc. Natl. Acad. 
         Sci. USA ,100(2003)12683.[pdf]
     
     8. E.W.Schlag, Sheh-Yi Sheu, H.L.Selzle,and D.Y.Yang,"Interaction of adjacent amino acids", 
         J.Chinese Chem. Soc. 53(2006)265-270 [pdf]
     
    　
        Molecular motor
    
1. Sheh-Yi Sheu and Dah-Yen Yang, "Entropy driven uni-direction motion of Brownian particle inside three-dimensional
          tube", J. Chem. Phys.,114(2001)3325.[pdf]
    
2. Sheh-Yi Sheu, Dah-Yen Yang, H.L.Selzle, and E.W.Schlag, "Entropy driven rotary molecular motor", (in preparation).
    3. Yu. A. Makhnovskii, V.M. Rozenbaum, D.Y. Yang, S.H. Lin and T.Y. Tsong, "Flashing ratchet model with high efficiency",
         Phys. Rev. E69(2004)021102.[pdf]
    4. Rozenbaum, V. M.; Yang, D.-Y.; Lin, S. H.; Tsong, T. Y., "Catalytic Wheel as a Brownian Motor", J. Phys. Chem. B, 
         108(2004)15880. [pdf]
     
    5.V.M.Rozenbaum, T. Ye. Korochkova, D.Y.Yang, S.H.Lin and T.Y.Tsong,"Two approaches toward a high-efficiency 
       flashing ratchet", Phys. Rev. E71(2005)041102 [pdf]
     
    　
    6.V.M.Rozenbaum, D.Y.Yang, S.H.Lin and T.Y. Tsong,"Energy losses in a flashing ratchet with different
       potential well shapes",Physica A363(2006)211-216 [pdf]
    　
    7.Yu.A.Makhnovskii, V.M. Rozenbaum, D.Y. Yang, S.H.Lin and Y.T.Tsong,"Reciprocating nanoengine",Euro.Phys.J.,
       B(2006)501-505 [pdf]
    　
    Membrane
    1. Dah-Yen Yang and Sheh-Yi Sheu, "Scaling theory of self-avoiding crumpled membrane in solution",

       Phys. Rev. E, 56(1997)3346.[pdf]
    
2. Sheh-Yi Sheu and Dah-Yen Yang, "Dynamic scaling theory for a tethered membrane in solution", Phys. Rev.,
          E63(2001)061207-1.[pdf]
     
    　
    Diffusion controlled reaction
    1. Dah-Yen Yang and R.I.Cukier," Concentration dependent fluorescence quenching with ionic
      
       reactants",J. Chem. Phys., 86(1987)2833. [pdf]
    2. A.M. Berezhkovskii, Dah-Yen Yang, S. H. Lin, Yu. A. Maknovskii and Sheh-Yi Sheu,"Smoluchowski-

        type theory of stochastic gated diffusion- influenced reaction",J. Chem. Phys., 106(1997)6985.[pdf]

    3. A.M. Berezhkovskii, V. Yu. Zitserman, S.Y. Sheu, D.Y. Yang, J. Kuo and S.H.Lin, "Kramers theory of 
  
        chemical reactions in slowly adjusting environment",J. Chem. Phys.,107(1997)10539.[pdf]

    4. A.M. Berezhkovskii, V. Yu. Zitzerman, D.Y. Yang, J. Kuo and S.H. Lin, "Activated rate processes
          in many dimensions: energy diffusion under slow adjustment of the nonreactive mode". Physica,
          A251(1998)399.
     
    5. A.M. Brezehkovskii, V. Yu. Zitserman, D.Y. Yang and S.H. Lin, "Kramers theory of chemical reactions
          in slowly relaxing environment with allowence made  for the long-distance recrossings". Chem. Phys.,
          235(1998)201.[pdf]
     
    6. Yu. A. Makhnovskii, D.Y. Yang, A. M. Berezhkovskii, S. Y. Sheu and S.H.Lin," Effect of trap clustering
          on Brownian particle trapping rate, Phys. Rev., E58(1998)4340.[pdf]

    7. Y.A. Makhnovskii,A.M. Berezhkovskii, Sheh-Yi Sheu,Dah-Yen Yang and Sheng- Hsien Lin, "Role of trap
          clustering in the trapping kinetics", J. Chem. Phys., 111(1999)711  [pdf]
    
 8. A.M. Berezhkovskii,V.Yu. Zitserman,D. Yang and S. H.Lin,"Reversible reactions attended by energy diffusion
         and slow solvent relaxation",Chem. Phys. Reports, 18(1999)121
     9. Yu. A. Makhnovskii, A.M. Berezhkovskii, D.Y. Yang, Sheh-Yi Sheu and S.H.Lin," Trapping by clusters of traps",
          Phys. Rev., E61(2000)6302-6307.[pdf]
    
10. D.Y.Yang, Yu. A. Makhnovskii, Sheh-Yi Sheu and S.H. Lin, "Simulation of the Wiener sauager", Phys. Rev.,
          E62(2000)3116-3120.[pdf]
    11. Yu. A. Makhnovskii, Sheh-Yi Sheu, Dah-Yen Yang, and Sheng Hsien Lin, "Effect of polydispersity on Brownian-particle 
          trapping by clusters of traps", J. Chem. Phys.117(2002)897. [pdf]
     
    　
    Else 
    1. G.C. Lie, S. Grigoras, L. X. Dang, Dah-Yen Yang and A. D. Mclean," Monte-Carlo simulation 

       of the liquid-vapor interface of water using an ab initio potential",J. Chem.Phys.,99(1993)3933.[pdf]

2. B. Fain, T.C. Chang, H.T. Liou, D.Y. Yang, K.L. Huang, M.C. Chan and S.H.Lin, "Dual-
 
       frequency pump-probe time-resolved spectroscopy",Chem.Phys. Lett., 216(1993)551.

    
3. J. Yu, W.S. Fann, F.J. Kao, D.Y. Yang and S.H.Lin," Molecular orbital calculations of 

       electronic excited states in poly(p-phenylene vinylene)",Synthetic Metals, 66(1994)143.

4. S.H. Lin, M. Hayashi, R. Islampour, J. Yu, D.Y. Yang and George Y.C. Wu, "Molecular theory

       of second-order sum-frequency generation", Physica, B222(1996)191-208.[pdf]
     
5. The 2nd Cross-Strait Theoretical and Computational Chemistry Conference (CTCC-2)  第二屆海峽兩岸理論化學與計算會議 [pdf] [建議事項]