FINDING SADDLE-POINTS;
POLYMER TRANSLOCATION;
PROTEIN TRANSLOCATION;
COMPUTER-SIMULATIONS;
FORCE SPECTROSCOPY;
TRAJECTORIES;
NANOPORE;
PATHS;
TIME;
MECHANICS;
D O I:
10.1063/1.3459058
中图分类号:
O64 [物理化学(理论化学)、化学物理学];
学科分类号:
070304 ;
081704 ;
摘要:
Motivated by recent experimental efforts to measure the time a molecular system spends in transit between the reactants and the products of a chemical reaction, here we study the properties of the distribution of such transit times for the case of conservative dynamics on a multidimensional energy landscape. Unlike reaction rates, transit times are not invariant with respect to the order parameter (a.k.a. the experimental signal) used to monitor the progress of a chemical reaction. Nevertheless, such order parameter dependence turns out to be relatively weak. Moreover, for several model systems we find that the probability distribution of transit times can be estimated analytically, with reasonable accuracy, by assuming that the order parameter coincides with the direction of the unstable normal mode at the transition state. Although this approximation tends to overestimate the actual mean transit time measured using other order parameters, it yields asymptotically correct long-time behavior of the transit time distribution, which is independent of the order parameter. (C) 2010 American Institute of Physics. [doi:10.1063/1.3459058]
机构:
NIH, Ctr Informat Technol, Div Computat Biosci, Math & Stat Comp Lab, Bethesda, MD 20892 USANIH, Ctr Informat Technol, Div Computat Biosci, Math & Stat Comp Lab, Bethesda, MD 20892 USA
Berezhkovskii, A
;
Szabo, A
论文数: 0引用数: 0
h-index: 0
机构:NIH, Ctr Informat Technol, Div Computat Biosci, Math & Stat Comp Lab, Bethesda, MD 20892 USA
机构:
Natl Inst Hlth, Math & Stat Comp Lab, Div Computat Biosci, Bethesda, MD 20892 USANatl Inst Hlth, Math & Stat Comp Lab, Div Computat Biosci, Bethesda, MD 20892 USA
Berezhkovskii, A. M.
;
Pustovoit, M. A.
论文数: 0引用数: 0
h-index: 0
机构:Natl Inst Hlth, Math & Stat Comp Lab, Div Computat Biosci, Bethesda, MD 20892 USA
Pustovoit, M. A.
;
Bezrukov, S. M.
论文数: 0引用数: 0
h-index: 0
机构:Natl Inst Hlth, Math & Stat Comp Lab, Div Computat Biosci, Bethesda, MD 20892 USA
机构:
NIH, Math & Stat Comp Lab, Div Computat Biosci, Ctr Informat Technol, Bethesda, MD 20892 USANIH, Math & Stat Comp Lab, Div Computat Biosci, Ctr Informat Technol, Bethesda, MD 20892 USA
Berezhkovskii, Alexander M.
;
Hummer, Gerhard
论文数: 0引用数: 0
h-index: 0
机构:NIH, Math & Stat Comp Lab, Div Computat Biosci, Ctr Informat Technol, Bethesda, MD 20892 USA
Hummer, Gerhard
;
Bezrukov, Sergey M.
论文数: 0引用数: 0
h-index: 0
机构:NIH, Math & Stat Comp Lab, Div Computat Biosci, Ctr Informat Technol, Bethesda, MD 20892 USA
机构:
NIDDK, Chem Phys Lab, NIH, Bethesda, MD 20892 USANIH, Math & Stat Comp Lab, Div Computat Biosci, Ctr Informat Technol, Bethesda, MD 20892 USA
Best, Robert B.
;
Paci, Emanuele
论文数: 0引用数: 0
h-index: 0
机构:
Univ Leeds, Sch Phys & Astron, Leeds, W Yorkshire, EnglandNIH, Math & Stat Comp Lab, Div Computat Biosci, Ctr Informat Technol, Bethesda, MD 20892 USA
Paci, Emanuele
;
Hummer, Gerhard
论文数: 0引用数: 0
h-index: 0
机构:
NIDDK, Chem Phys Lab, NIH, Bethesda, MD 20892 USANIH, Math & Stat Comp Lab, Div Computat Biosci, Ctr Informat Technol, Bethesda, MD 20892 USA
Hummer, Gerhard
;
Dudko, Olga K.
论文数: 0引用数: 0
h-index: 0
机构:
NIH, Math & Stat Comp Lab, Div Computat Biosci, Ctr Informat Technol, Bethesda, MD 20892 USANIH, Math & Stat Comp Lab, Div Computat Biosci, Ctr Informat Technol, Bethesda, MD 20892 USA
机构:
Univ Calif San Diego, Dept Phys, La Jolla, CA 92093 USA
Univ Calif San Diego, Ctr Theoret Biol Phys, La Jolla, CA 92093 USAUniv Calif San Diego, Dept Phys, La Jolla, CA 92093 USA
Dudko, Olga K.
;
Hummer, Gerhard
论文数: 0引用数: 0
h-index: 0
机构:
NIDDK, Chem Phys Lab, NIH, Bethesda, MD 20892 USAUniv Calif San Diego, Dept Phys, La Jolla, CA 92093 USA
Hummer, Gerhard
;
Szabo, Attila
论文数: 0引用数: 0
h-index: 0
机构:
NIDDK, Chem Phys Lab, NIH, Bethesda, MD 20892 USAUniv Calif San Diego, Dept Phys, La Jolla, CA 92093 USA
机构:
NIH, Ctr Informat Technol, Div Computat Biosci, Math & Stat Comp Lab, Bethesda, MD 20892 USANIH, Ctr Informat Technol, Div Computat Biosci, Math & Stat Comp Lab, Bethesda, MD 20892 USA
Berezhkovskii, A
;
Szabo, A
论文数: 0引用数: 0
h-index: 0
机构:NIH, Ctr Informat Technol, Div Computat Biosci, Math & Stat Comp Lab, Bethesda, MD 20892 USA
机构:
Natl Inst Hlth, Math & Stat Comp Lab, Div Computat Biosci, Bethesda, MD 20892 USANatl Inst Hlth, Math & Stat Comp Lab, Div Computat Biosci, Bethesda, MD 20892 USA
Berezhkovskii, A. M.
;
Pustovoit, M. A.
论文数: 0引用数: 0
h-index: 0
机构:Natl Inst Hlth, Math & Stat Comp Lab, Div Computat Biosci, Bethesda, MD 20892 USA
Pustovoit, M. A.
;
Bezrukov, S. M.
论文数: 0引用数: 0
h-index: 0
机构:Natl Inst Hlth, Math & Stat Comp Lab, Div Computat Biosci, Bethesda, MD 20892 USA
机构:
NIH, Math & Stat Comp Lab, Div Computat Biosci, Ctr Informat Technol, Bethesda, MD 20892 USANIH, Math & Stat Comp Lab, Div Computat Biosci, Ctr Informat Technol, Bethesda, MD 20892 USA
Berezhkovskii, Alexander M.
;
Hummer, Gerhard
论文数: 0引用数: 0
h-index: 0
机构:NIH, Math & Stat Comp Lab, Div Computat Biosci, Ctr Informat Technol, Bethesda, MD 20892 USA
Hummer, Gerhard
;
Bezrukov, Sergey M.
论文数: 0引用数: 0
h-index: 0
机构:NIH, Math & Stat Comp Lab, Div Computat Biosci, Ctr Informat Technol, Bethesda, MD 20892 USA
机构:
NIDDK, Chem Phys Lab, NIH, Bethesda, MD 20892 USANIH, Math & Stat Comp Lab, Div Computat Biosci, Ctr Informat Technol, Bethesda, MD 20892 USA
Best, Robert B.
;
Paci, Emanuele
论文数: 0引用数: 0
h-index: 0
机构:
Univ Leeds, Sch Phys & Astron, Leeds, W Yorkshire, EnglandNIH, Math & Stat Comp Lab, Div Computat Biosci, Ctr Informat Technol, Bethesda, MD 20892 USA
Paci, Emanuele
;
Hummer, Gerhard
论文数: 0引用数: 0
h-index: 0
机构:
NIDDK, Chem Phys Lab, NIH, Bethesda, MD 20892 USANIH, Math & Stat Comp Lab, Div Computat Biosci, Ctr Informat Technol, Bethesda, MD 20892 USA
Hummer, Gerhard
;
Dudko, Olga K.
论文数: 0引用数: 0
h-index: 0
机构:
NIH, Math & Stat Comp Lab, Div Computat Biosci, Ctr Informat Technol, Bethesda, MD 20892 USANIH, Math & Stat Comp Lab, Div Computat Biosci, Ctr Informat Technol, Bethesda, MD 20892 USA
机构:
Univ Calif San Diego, Dept Phys, La Jolla, CA 92093 USA
Univ Calif San Diego, Ctr Theoret Biol Phys, La Jolla, CA 92093 USAUniv Calif San Diego, Dept Phys, La Jolla, CA 92093 USA
Dudko, Olga K.
;
Hummer, Gerhard
论文数: 0引用数: 0
h-index: 0
机构:
NIDDK, Chem Phys Lab, NIH, Bethesda, MD 20892 USAUniv Calif San Diego, Dept Phys, La Jolla, CA 92093 USA
Hummer, Gerhard
;
Szabo, Attila
论文数: 0引用数: 0
h-index: 0
机构:
NIDDK, Chem Phys Lab, NIH, Bethesda, MD 20892 USAUniv Calif San Diego, Dept Phys, La Jolla, CA 92093 USA