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Rotational Gating Mechanisms of an Ion Channel with a Negative Hydrophobic Mismatch
이공주복 한국물리학회 2006 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.49 No.1
We analyze the energetics of three rotational gating mechanisms of an ion channel in the presence of a negative hydrophobic mismatch. To evaluate the free energy of the membrane deformation during the gating process, we use the continuum model imposing a strong hydrophobic interaction at the interface of the channel proteins and the nearby lipid molecules. Three gating mechanisms describe three different transitions from a conical closed state to one bottle-neck and two cylindrical open states. Differently from the situation of a positive hydrophobic mismatch, all three open states can be energetically favorable without introducing a spontaneous curvature although a quite strong surface tension of the membrane is required if the thickness change of the membrane does not cost any energy. We also discuss the effect of the thickness change of the membrane on the gating energy.
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이공주복,박병준,안민정,최새롬 한국물리학회 2014 새물리 Vol.64 No.7
Active motion is ubiquitous in nature, ranging from macroscopic flocking of birds to the microscopic stepping motion of molecular motors, and needs processes of energy supply and of conversion to mechanical work. The active Brownian-particle model describes the motion of a particle that has an internal depot to store energy supplied from the environment and is able to convert that internal energy into mechanical work. In this article, we introduce active Brownian-particle models with several variations and discuss their dynamic properties briefly. An active model in an overdamped limit is also built and applied to study the dynamics of on molecular motor and of cargo transport by many molecular motors. Also, our recent results which were simulated by using biologically-known values of the parameters are presented. 농동적 운동은 새들의 거시적 집단운동에서 분자모터의 미시적 걸음운동에 이르기까지 자연 도처에 존재하며, 에너지 공급과정과 에너지를 역학적 일로 전환하는 과정을 필요로 한다. 활성 브라운 입자 모형은 내부 에너지저장고를 갖고 있어 외부에서 공급된 에너지를 저장하고, 내부 에너지를 역학적 일로 전환할 수 있는 입자의 운동을 기술한다. 본 논고에서는 다양한 활성 브라운 입자 모형들을 소개하고 각 모형의 동역학 성질을 간단히 논의한다. 또한, 과도감쇠영역에서의 활성 모형을 구축하여 분자모터의 동역학과 다중분자모터에 의한 카고 수송 동역학 연구에 적용하고, 실제 알려진 생물학적 변수들을 이용하여 전산 모사한 최근의 우리 결과도 제시한다.
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Active Dynamics Model with Asymmetric Energy Conversion Rate
박병준,이공주복 한국물리학회 2018 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.72 No.3
We consider an energy depot model with an asymmetric energy conversion mechanism where theenergy conversion rate depends not only on the particle's speed but also on the particle's directionof motion. The e®ects of the asymmetric energy conversion on the dynamics are examined, and thedynamic phase diagram is constructed in terms of the energy conversion apparatus and the externalforces. We ¯nd a new dynamical state in the phase diagram as well as a discontinuous transitionamong the dynamical phases, which are absent in the symmetric active dynamics model. Moreover,we found a dynamical state with a negative energy conversion rate, which can be applied to themodeling of the energy storage from the work done by external forces as in chemisomosis.
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Jiyeon Oh,이공주복 한국물리학회 2007 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.51 No.III
The free energy of membrane deformation when a tilted ion channel is imbedded in a membrane is analyzed using a well-known continuum model. The ion channel is assumed to be closed when tilted and open when untilted. When the energetics of the membrane deformation is analyzed with the continuum model, explicit boundary conditions are usually adopted at a contact position between the channel and the membrane and at a position far from the channel. However, it is difficult to determine the contact position when the channel has a tilted orientation. Depending on the tilt angle, the difference in the contact position between the upper and the lower parts of the membrane could be as large as the thickness of the membrane. Hence, in this work, the dependence of the free energy of membrane deformation on the contact position is investigated in detail. Analysis shows that the contact position significantly affects the energetics of the ion channel gating when the energy cost for a thickness change of the membrane is not negligible. The analysis also shows that the energetics of rotational gating mechanisms, as discussed in a previous article using a decoupled model, can be reproduced for some reasonable values of the contact position.
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