부산대학교 도서관

국외단행본

Exploring Conformational Ensembles of Biomolecules Using Molecular Dynamics = 使用分子動力學模擬探究生物分子的構型系綜 [electronic resource].

University of Colorado at Boulder. Chemical and Biological Engineering.

[S.l.] : University of Colorado at Boulder. 2024 Ann Arbor : ProQuest Dissertations & Theses , 2024

1 online resource(266 p.)

Source: Dissertations Abstracts International, Volume: 85-11, Section: B.
Advisor: Shirts, Michael.

Thesis (Ph.D.)--University of Colorado at Boulder, 2024.

Conformational ensembles are Boltzmann-weighted collections of all possible configurations that the interested molecule can adopt. In biological contexts, conformational ensembles encode valuable insights into the structural landscape and underlying thermodynamics of biomolecules, which elucidate molecular mechanisms governing biological processes. However, obtaining accurate conformational ensembles is usually challenging, as most experimental methods are restricted to studying only a single snapshot of the system. Using molecular dynamics (MD), researchers are able to study a trajectory rather than just a snapshot, but it could still be difficult for simulations to sample the configurational space comprehensively to generate representative conformational ensembles.In light of the significance of conformational ensembles, and the difficulties in resolving them, this Ph.D. dissertation aims to study interesting biophysical phenomena from their relevant conformational ensembles derived from MD simulations, as well as to develop efficient simulation methods for such applications. Specifically, this dissertation carves out a trajectory of efforts in enhancing our understanding of biomolecular dynamics, from an investigation of the influence of glycosylation on insulin's properties, to the development of broad-reaching simulation methods such as alchemical metadynamics, and replica exchange of expanded ensemble, which collectively advancing alchemical free energy calculations in terms of improved flexibility, parallelizability, and configurational sampling.

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