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Enhanced Sampling Methodologies for Free Energy Calculations in Biomolecular Systems
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| 자료유형 | 학위논문 |
|---|---|
| 서명/저자사항 | Enhanced Sampling Methodologies for Free Energy Calculations in Biomolecular Systems. |
| 개인저자 | Suh, Donghyuk. |
| 단체저자명 | The University of Chicago. Chemistry. |
| 발행사항 | [S.l.]: The University of Chicago., 2019. |
| 발행사항 | Ann Arbor: ProQuest Dissertations & Theses, 2019. |
| 형태사항 | 93 p. |
| 기본자료 저록 | Dissertations Abstracts International 81-02B. Dissertation Abstract International |
| ISBN | 9781085606554 |
| 학위논문주기 | Thesis (Ph.D.)--The University of Chicago, 2019. |
| 일반주기 |
Source: Dissertations Abstracts International, Volume: 81-02, Section: B.
Advisor: Roux, Benoit. |
| 이용제한사항 | This item must not be sold to any third party vendors. |
| 요약 | We developed two enhanced sampling methods, one for configurational sampling of small molecules/peptides, and the other for calculating protein-protein binding free energies to solve interaction/recognition problems.To enhance the configurational sampling which can be very computationally demanding with conventional Molecular Dynamics (MD) simulations, a Hybrid non-equilibrium MD/Monte Carlo propagator is developed in which we apply non-equilibrium work to the system in order to boost the Hamiltonian while a Metropolis-Hastings Monte Carlo (MC) step ensures sampling from the correct Boltzmann distribution. When the sampling of a biomolecular system gets stuck in a kinetic trap (metastable state), the Hybrid neMD/MC propagator helps it to escape. Specific biomolecular peptide systems were used to test validity and performance of the method.We put forth a novel theoretical framework for binding free energy calculations between two proteins, leaning on the optimal curvilinear minimum free-energy path (MFEP) determined from the string method. The curvilinear path connects the fully bound state to the unbound state and is generated from quick simulations using an implicit solvent model, followed by application of the dynamic histogram analysis method (DHAM). In each of the simulations DHAM finds the free energy minimum |
| 일반주제명 | Chemistry. Theoretical physics. Physical chemistry. |
| 언어 | 영어 |
| 바로가기 | 
: 이 자료의 원문은 한국교육학술정보원에서 제공합니다. |
