東華大學圖書館 |

語系: 繁體中文

說明(常見問題)

回圖書館首頁

手機版館藏查詢

登入

回首頁

切換: 標籤 | MARC模式 | ISBD

Optimal Network Generation for the S...

Reidelbach, Marco.

FindBook

Google Book

Amazon

博客來

Optimal Network Generation for the Simulation of Proton Transfer Processes = = Optimale Bestimmung von Netzwerken fur die Simulation von Protonen Transfer Prozessen.

紀錄類型:	書目-電子資源 : Monograph/item
正題名/作者:	Optimal Network Generation for the Simulation of Proton Transfer Processes =/
其他題名:	Optimale Bestimmung von Netzwerken fur die Simulation von Protonen Transfer Prozessen.
作者:	Reidelbach, Marco.
出版者:	Ann Arbor : ProQuest Dissertations & Theses, : 2018,
面頁冊數:	246 p.
附註:	Source: Dissertations Abstracts International, Volume: 81-10, Section: B.
Contained By:	Dissertations Abstracts International81-10B.
標題:	Biochemistry. -
電子資源:	https://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=27605798
ISBN:	9781687930347

Optimal Network Generation for the Simulation of Proton Transfer Processes = = Optimale Bestimmung von Netzwerken fur die Simulation von Protonen Transfer Prozessen.
Reidelbach, Marco.

Optimal Network Generation for the Simulation of Proton Transfer Processes =Optimale Bestimmung von Netzwerken fur die Simulation von Protonen Transfer Prozessen. - Ann Arbor : ProQuest Dissertations & Theses, 2018 - 246 p.

Source: Dissertations Abstracts International, Volume: 81-10, Section: B.

Thesis (Ph.D.)--Freie Universitaet Berlin (Germany), 2018.

This item must not be sold to any third party vendors.

The oxidative phosphorylation is the most important step of the aerobic respiration. Here, electrons are transferred along several membrane-embedded enzyme complexes to finally reduce molecular oxygen to water in Cytochrome c Oxidase. The energy released by the electron flow and the oxygen reduction is used to translocate protons across the membrane. Thereby, an electro-chemical gradient is established which subsequently drives the synthesis of the biological energy carrier Adenosine Triphosphate. Numerous diseases, e.g. Alzheimer or Parkinson, are partially assigned to malfunctions of the oxidative phosphorylation, rendering a detailed understanding of this step indispensable. Common computational investigations, employing Molecular Dynamics simulations, enhanced sampling techniques, or transition pathway finding algorithms, are limited in their description of quantum effects and often only provide a limited, or biased, description of complex reactions. The alternative Transition Network approach, divides a complex reaction of interest into numerous simpler transitions, connecting various local potential energy minima of the potential energy surface by minimum energy pathways, yielding a Transition Network, or simple graph, which can be analyzed in terms of optimal transition pathways by standard graph theoretical algorithms. A major drawback of the Transition Network approach is the exponential increase of stationary points of the potential energy surface with increasing numbers of degrees of freedom to sample, rendering the Transition Network approach infeasible for most complex reactions. Within the framework of this thesis two methods optimizing the Transition Network approach are developed and extensively tested in small proton transfer model systems. These are: 1) the TN-MD method coupling the discrete sampling of states separated by substantial energy barriers with Molecular Dynamics simulations for the sampling of states separated by minor energy barriers, e.g. amino acid side chain dihedral angle rotations or water molecule translations, respectively, and 2) the TN prediction method using a known, initial Transition Network and an excessive two-step coarse-graining procedure for the determination of an unknown Transition Network in a perturbed environment, e.g. different protonation states. Both methods provide significant cost reductions, while important properties of the proton transfer reactions, e.g. rate-determining, maximal transition barriers and the variability of transition pathways or mechanisms, are maintained. Furthermore, the TN-MD method is used to investigate the proton transfer through the D-channel of Cytochrome c Oxidase in a minimal model system, providing various proton transfer pathways with rate-determining, maximal transition barriers which are in agreement to computational results from Liang et al using a much more involved model and simulation setup. Other decisive aspects of previous proton transfer investigations along the D-channel, e.g. the identity of the rate-determining, maximal transition state and the behavior of the proposed asparagine gate, are reproduced and extended. Overall, this thesis provides a methodical leap forward in terms of the Transition Network approach as well as another piece of analysis required for the understanding of the proton translocation along the oxidative phosphorylation.

ISBN: 9781687930347Subjects--Topical Terms:

518028
Biochemistry.
Subjects--Index Terms:

Cytochrome c oxidase

Optimal Network Generation for the Simulation of Proton Transfer Processes = = Optimale Bestimmung von Netzwerken fur die Simulation von Protonen Transfer Prozessen.
LDR:04602nmm a2200337 4500 001 2275406
005 20210209133255.5
008 220723s2018 ||||||||||||||||| ||eng d
020 $a 9781687930347
035 $a (MiAaPQ)AAI27605798
035 $a (MiAaPQ)FreiBerlin_fub18824601
035 $a AAI27605798
040 $a MiAaPQ $c MiAaPQ
100 1 $a Reidelbach, Marco. $3 3553655
245 1 0 $a Optimal Network Generation for the Simulation of Proton Transfer Processes = $b Optimale Bestimmung von Netzwerken fur die Simulation von Protonen Transfer Prozessen.
260 1 $a Ann Arbor : $b ProQuest Dissertations & Theses, $c 2018
300 $a 246 p.
500 $a Source: Dissertations Abstracts International, Volume: 81-10, Section: B.
500 $a Advisor: Weber, Marcus.
502 $a Thesis (Ph.D.)--Freie Universitaet Berlin (Germany), 2018.
506 $a This item must not be sold to any third party vendors.
520 $a The oxidative phosphorylation is the most important step of the aerobic respiration. Here, electrons are transferred along several membrane-embedded enzyme complexes to finally reduce molecular oxygen to water in Cytochrome c Oxidase. The energy released by the electron flow and the oxygen reduction is used to translocate protons across the membrane. Thereby, an electro-chemical gradient is established which subsequently drives the synthesis of the biological energy carrier Adenosine Triphosphate. Numerous diseases, e.g. Alzheimer or Parkinson, are partially assigned to malfunctions of the oxidative phosphorylation, rendering a detailed understanding of this step indispensable. Common computational investigations, employing Molecular Dynamics simulations, enhanced sampling techniques, or transition pathway finding algorithms, are limited in their description of quantum effects and often only provide a limited, or biased, description of complex reactions. The alternative Transition Network approach, divides a complex reaction of interest into numerous simpler transitions, connecting various local potential energy minima of the potential energy surface by minimum energy pathways, yielding a Transition Network, or simple graph, which can be analyzed in terms of optimal transition pathways by standard graph theoretical algorithms. A major drawback of the Transition Network approach is the exponential increase of stationary points of the potential energy surface with increasing numbers of degrees of freedom to sample, rendering the Transition Network approach infeasible for most complex reactions. Within the framework of this thesis two methods optimizing the Transition Network approach are developed and extensively tested in small proton transfer model systems. These are: 1) the TN-MD method coupling the discrete sampling of states separated by substantial energy barriers with Molecular Dynamics simulations for the sampling of states separated by minor energy barriers, e.g. amino acid side chain dihedral angle rotations or water molecule translations, respectively, and 2) the TN prediction method using a known, initial Transition Network and an excessive two-step coarse-graining procedure for the determination of an unknown Transition Network in a perturbed environment, e.g. different protonation states. Both methods provide significant cost reductions, while important properties of the proton transfer reactions, e.g. rate-determining, maximal transition barriers and the variability of transition pathways or mechanisms, are maintained. Furthermore, the TN-MD method is used to investigate the proton transfer through the D-channel of Cytochrome c Oxidase in a minimal model system, providing various proton transfer pathways with rate-determining, maximal transition barriers which are in agreement to computational results from Liang et al using a much more involved model and simulation setup. Other decisive aspects of previous proton transfer investigations along the D-channel, e.g. the identity of the rate-determining, maximal transition state and the behavior of the proposed asparagine gate, are reproduced and extended. Overall, this thesis provides a methodical leap forward in terms of the Transition Network approach as well as another piece of analysis required for the understanding of the proton translocation along the oxidative phosphorylation.
590 $a School code: 0693.
650 4 $a Biochemistry. $3 518028
650 4 $a Biophysics. $3 518360
653 $a Cytochrome c oxidase
653 $a Proton translocation
690 $a 0786
690 $a 0487
710 2 $a Freie Universitaet Berlin (Germany). $3 1900748
773 0 $t Dissertations Abstracts International $g 81-10B.
790 $a 0693
791 $a Ph.D.
792 $a 2018
793 $a English
856 4 0 $u https://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=27605798