Browsing by Author "Chang, Cheng-Hung"

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A Markovian engine for a biological energy transducer: The catalytic wheel
(2007-04-01)
Tsong, Tian Yow
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Chang, Cheng-Hung
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物理研究所
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Institute of Physics
The molecular machines in biological cells are made of proteins, DNAs and other classes of molecules. The structures of these molecules are characteristically "soft", highly flexible, and yet their interactions with other molecules or ions are specific and selective. This chapter discusses a prevalent form, the catalytic wheel, or the energy transducer of cells, examines its mechanism of action, and extracts from it a set of simple but general rules for understanding the energetics of the biomolecular devices. These rules should also benefit design of manmade nanometer scale machines such as rotary motors or track-guided linear transporters. We will focus on an electric work that, by matching system dynamics and then enhancing the conformational fluctuation of one or several driver proteins, converts stochastic input of energy into rotation or locomotion of a receptor protein. The spatial (or barrier) and temporal symmetry breakings required for selected driver/receptor combinations are examined. This electric ratchet consists of a core engine that follows the Markovian dynamic, alleviates difficulties encountered in rigid mechanical model, and tailors to the soft-matter characteristics of the biomolecules. (c) 2006 Elsevier Ireland Ltd. All rights reserved.
Carrier-mediated exchange coupling and fermi surface topology
(2008-01-20)
Huang, Wen-Min
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Lai, Hsin-Hua
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Chang, Cheng-Hung
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Lin, Hsiu-Hau
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物理研究所
We investigate the carrier-mediated exchange coupling between two ferromagnets, sandwiching an intermediate thin layer with Rashba interaction. The effective exchange coupling is obtained by integrating out the itinerant carriers. It turns out that the magnetic trends depend sensitively upon the topology of the Fermi surface. As the topology changes from "wedding cake" to "donut", the mediated exchange goes from the oscillatory Ruderman-Kittel-Kasuya-Yosida to the non-collinear spiral interactions accordingly. It is rather surprising that the Fermi surface topology determines which type of magnetic interaction becomes dominant. Finally, we also discuss potential applications for carrier-mediated exchange coupling across the junction.
Chemical potential formalism for polymer entropic forces
(2019-03-01)
Xie, Hong-Qing
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Chang, Cheng-Hung
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物理研究所
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Institute of Physics
The entropic force is one of the most elusive interactions in macromolecules. It is clearly defined theoretically, but practically difficult to evaluate, thus restricting our knowledge of it often to a qualitative level. Here, we propose a formula for entropic force, f = f(-o) + T ln(alpha), for confined polymers and demonstrate its mathematical equivalence to the widely used chemical potential formula for solutions, mu = mu(-o) + R (T) over tilde ln(a). A systematic analysis based on this formalism clarifies the force magnitudes obtained in several recent experiments on polymers and granular chains and elucidates the common force scales for polymers studied in nanoscience and biological systems. This work provides a practical tool for instantaneously evaluating the entropic forces in polymer science and indicates the possibility of using a reference-based strategy to tackle general entropic problems beyond chemical solutions.
Collective flow dynamics across a bacterial carpet: Understanding the forces generated
(2014-11-17)
Hsiao, Yi-Teng
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Wang, Jing-Hui
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Wu, Kuan-Ting
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Tsai, Jengjan
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Chang, Cheng-Hung
Bacterial carpets consist of randomly anchored uni-polar-flagellated sodium-motive bacterial matrix are prepared by flow deposition. Collective flow dynamics across the bacterial carpets are probed with optical tweezers-microsphere assay. Around the center of a uniform bacterial cluster, collective forces that pull microsphere towards carpet surface are detected at a distance of 10 mu m away from carpets. At sodium-motive driving over a critical value, the force magnitudes increase abruptly, suggesting a threshold-like transition of hydrodynamic synchronization across bacterial carpet. The abrupt force increase is explained in term of bifurcation to phase synchronization in a noisy non-linearly coupled rotor array mediated by hydrodynamic interactions. (C) 2014 AIP Publishing LLC.
Energy transduction in molecular machines
(2007-10-01)
Chang, Cheng-Hung
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Tsong, Tian Yow
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交大名義發表
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物理研究所
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National Chiao Tung University
An applied force may cause the conformation and thus, the activity of a biological molecule to change. Here we consider a system in which an oscillating or fluctuating electric field is used to actuate membrane protein activities. Most proteins have electric dipoles and net charges in the structure and their conformations are susceptible to the electric and magnetic perturbation. The shape of a cell may also amplify an electric field across its plasma membrane. Therefore, a membrane integral protein such as an ion channel, an ion pump, or a molecular motor, is especially amenable to electric perturbation. The theory of electroconformational coupling addresses the functional implication of this field effect. When an alternating electric field or a fluctuating electric field is employed to actuate a two-state protein oscillator, the dynamics of the conformational change of the protein can be synchronized with the applied field. Through this two-state protein oscillator, we construct a four-state catalytic wheel by coupling an energy transducer mechanism to the two-state protein oscillator. Analysis shows that the catalytic wheel can extract energy from a disordered external energy source, be it electrical, mechanical, or chemical, and convert this stochastic energy source to a usable energy format. The catalytic wheel is tested with the experimental data on the electric field-stimulated cation pumping of Na, K-ATPase. A dipole ratchet model based on the electroconformational coupling concept will also be discussed and compared with the ATP-dependent rotation of a rotary motor F-1-ATPase. Since the working principle of this model is simpler than that of F-1-ATPase, it provides an easier way to realize a nanoscale rotary motor than artificially reconstructing a F-1-ATPase.
Fluctuation relations between hierarchical kinetically equivalent networks with Arrhenius-type transitions and their roles in systems and structural biology
(2017-06-02)
Deng, De-Ming
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Lu, Yi-Ta
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Chang, Cheng-Hung
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物理研究所
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Institute of Physics
The legality of using simple kinetic schemes to determine the stochastic properties of a complex system depends on whether the fluctuations generated from hierarchical equivalent schemes are consistent with one another. To analyze this consistency, we perform lumping processes on the stochastic differential equations and the generalized fluctuation-dissipation theorem and apply them to networks with the frequently encountered Arrhenius-type transition rates. The explicit Langevin force derived from those networks enables us to calculate the state fluctuations caused by the intrinsic and extrinsic noises on the free energy surface and deduce their relations between kinetically equivalent networks. In addition to its applicability to wide classes of network related systems, such as those in structural and systems biology, the result sheds light on the fluctuation relations for general physical variables in Keizer's canonical theory.
Fouling Elimination of PTFE Membrane under Precoagulation Process Combined with Ultrasound Irradiation
(2012-03-01)
Wan, Meng-Wei
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Yang, Hui-Ling
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Chang, Cheng-Hung
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Reguyal, Febelyn
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Kan, Chi-Chuan
Precoagulation is one of the effective pretreatments in membrane filtration. This process mitigates membrane fouling, which is the major drawback of membrane technology in drinking water and wastewater treatment. This study investigated the effects of precoagulation under different coagulation mechanisms on membrane fouling. Use of ultrasound in polytetrafluoroethylene (PTFE) membrane cleaning was also evaluated. In precoagulation, synthetic raw water was precoagulated using aluminum sulfate at different coagulation mechanisms, named electrostatic patch effect (EPE), charge neutralization (CN), and sweep flocculation (SW). Flocs produced from different coagulation mechanisms exhibited different sizes, structures, and strengths. Likewise, the fouling type generated from each mechanism was demonstrated as pore blocking for EPE, cake formation for SW, and combination phenomenon for CN. Moreover, this study indicated that the membrane flux was enhanced in the sequence of EPE > CN > SW. The flux recovery rate after ultrasonic cleaning was in the sequence of SW > CN > EPE. Finally, this study evidenced that the floc characteristics from various coagulation mechanisms affected membrane performance, fouling types, and ultrasonic cleaning efficiency. DOI: 10.1061/(ASCE)EE.1943-7870.0000406. (C) 2012 American Society of Civil Engineers.
Generalized path integral method for Elliott-Yafet spin relaxations in quantum wells and narrow wires
(2012-02-22)
Tsai, Jengjan
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Chang, Cheng-Hung
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物理研究所
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Institute of Physics
We generalized the semiclassical path integral method originally used in the D'yakonov-Perel' mechanism to study the spin relaxation of the Elliott-Yafet mechanism in low-dimensional systems. In quantum wells, the spin properties calculated by this method confirmed the experimental results. In two-dimensional narrow wires, size and impurity effects on the Elliott-Yafet relaxation were predicted, including the wire-width-dependent relaxation time, the polarization evolution on the sample boundaries, and the relaxation behavior during the diffusive-ballistic transition. These properties were compared with those of the D'yakonov-Perel' relaxation calculated under similar conditions. For ballistic narrow wires, we derived an exact relation between the Elliott-Yafet relaxation time and the wire width, which confirmed the above simulations.
Localization-delocalization transition of the instantaneous normal modes of liquid water
(2013-10-09)
Huang, Ban-Chiech
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Chang, Cheng-Hung
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物理研究所
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Institute of Physics
Despite the fact that the localization-delocalization transition (LDT) widely exists in wave systems, quantitative studies on its critical and multifractal properties are mainly focused on solids. In this work, these properties are investigated on the vibrational motions of liquid water. Simulations of up to 18 000 molecules on the flexible extended simple point charge water model provide nearly 10(6) instantaneous normal modes. They are shown to undergo an LDT close to the translational transition and exhibit multifractal fluctuations while approaching the LDT. In combination with finite-size scaling, multifractal analysis predicts the critical frequency Im(omega(c)) approximate to -131.6 cm(-1) for unstable modes at room temperature. The estimated critical exponent nu approximate to 1.60 is close to those of other calculated systems in the same Wigner-Dyson class. At the LDT, the fractal spectrum f (alpha) and the most probable local vibrational intensity alpha(mc) approximate to 4.04 coincide with those of the Anderson model, which might be additional universal properties of LDT in more general wave systems. The results extend the validity of the multifractal scaling approach beyond Andersonian systems to a Hessian system.
Non-collinear magnetic junction mediated by Rashba interaction
(2007-03-01)
Huang, Wen-Min
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Chang, Cheng-Hung
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Lin, Hsiu-Hau
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物理研究所
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Institute of Physics
We study the non-collinear exchange coupling across the trilayer magnetic junction composed of an intermediate layer with Rashba interaction and two sandwiching ferromagnetic ones. To compute the mediated exchange coupling between the ferromagnetic layers, one needs to go beyond the single-particle argument and numerically integrates over contributions from the whole Fermi surface. We found interesting competition between the oscillatory Ruderman-Kittel-Kasuya-Yosida and the non-collinear spiral interactions. Surprisingly, the Fermi surface topology determines which type of magnetic interaction becomes dominant. Finally, we also discuss potential applications for the non-collinear exchange coupling across the junction. (C) 2006 Elsevier B.V. All rights reserved.
Noncollinear exchange coupling in a trilayer magnetic junction and its connection to Fermi surface topology
(2006-06-01)
Huang, Wen-Min
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Chang, Cheng-Hung
;
Lin, Hsiu-Hau
;
物理研究所
;
Institute of Physics
We investigate the noncollinear exchange coupling across a trilayer magnetic junction composed of an intermediate layer with Rashba interaction and two sandwiching ferromagnetic layers. To compute the mediated exchange coupling, one needs to go beyond the single-particle argument and integrate over the contributions from the whole Fermi surface. Surprisingly, we find that the topology of the Fermi surface plays a crucial role in determining whether the oscillatory Ruderman-Kittel-Kasuya-Yosida or the spiral interactions will dominate. At the end, we discuss the connection of our numerical results to experiments and potential applications.
Quantisations of piecewise parabolic maps on the torus and their quantum limits
(2008-09-01)
Chang, Cheng-Hung
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Krueger, Tyll
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Schubert, Roman
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Troubetzkoy, Serge
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物理研究所
For general quantum systems the semiclassical behaviour of eigenfunctions in relation to the ergodic properties of the underlying classical system is quite difficult to understand. The Wignerfunctions of eigenstates converge weakly to invariant measures of the classical system, the so-called quantum limits, and one would like to understand which invariant measures can occur that way, thereby classifying the semiclassical behaviour of eigenfunctions. We introduce a class of maps on the torus for whose quantisations we can understand the set of quantum limits in great detail. In particular we can construct examples of ergodic maps which have singular ergodic measures as quantum limits, and examples of non-ergodic maps where arbitrary convex combinations of absolutely continuous ergodic measures can occur as quantum limits. The maps we quantise are obtained by cutting and stacking.
Semiclassical path integral approach for spin relaxations in narrow wires
(2009-03-01)
Chang, Cheng-Hung
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Tsai, Jengjan
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Lo, Hui-Fen
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Mal'shukov, A. G.
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數學建模與科學計算所(含中心)
The semiclassical path integral (SPI) method has been applied for studying spin relaxation in a narrow two-dimensional strip with the Rashba spin-orbit interaction. Our numerical calculations show good agreement with the experimental data, although some features of experimental results are not clear yet. We also calculated the relaxation of a uniform spin-density distribution in the ballistic regime of very narrow wires. With the decreasing wire width, the spin polarization exhibits a transition from the exponential decay to the oscillatory Bessel-type relaxation. The SPI method has also been employed to calculate the relaxation of the particularly long-lived helix mode. Good agreement has been found with calculations based on the diffusion theory.
Spectral properties and magneto-optical excitations in semiconductor double rings under Rashba spin-orbit interaction
(2007-04-01)
Kuan, Wen-Hsuan
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Tang, Chi-Shung
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Chang, Cheng-Hung
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物理研究所
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Institute of Physics
We have numerically solved the Hamiltonian of an electron in a semiconductor double ring subjected to the magnetic flux and Rashba spin-orbit interaction. It is found that the Aharonov-Bohm energy spectrum reveals multizigzag periodic structures. The investigations of spin-dependent electron dynamics via Rabi oscillations in two-level and three-level systems demonstrate the possibility of manipulating quantum states. Our results show that the optimal control of photon-assisted inter-ring transitions can be achieved by employing cascade-type and Lambda-type transition mechanisms. Under chirped pulse impulsions, a robust and complete transfer of an electron to the final state is shown to coincide with the estimation of the Landau-Zener formula.
Stochastic lumping analysis for linear kinetics and its application to the fluctuation relations between hierarchical kinetic networks
(2015-05-14)
Deng, De-Ming
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Chang, Cheng-Hung
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物理研究所
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Institute of Physics
Conventional studies of biomolecular behaviors rely largely on the construction of kinetic schemes. Since the selection of these networks is not unique, a concern is raised whether and under which conditions hierarchical schemes can reveal the same experimentally measured fluctuating behaviors and unique fluctuation related physical properties. To clarify these questions, we introduce stochasticity into the traditional lumping analysis, generalize it from rate equations to chemical master equations and stochastic differential equations, and extract the fluctuation relations between kinetically and thermodynamically equivalent networks under intrinsic and extrinsic noises. The results provide a theoretical basis for the legitimate use of low-dimensional models in the studies of macromolecular fluctuations and, more generally, for exploring stochastic features in different levels of contracted networks in chemical and biological kinetic systems. (C) 2015 AIP Publishing LLC.
The defect effects on the signal transport of an excitable soft cable
(2013-03-18)
Liu, Tang-Yu
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Chang, Cheng-Hung
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物理研究所
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Institute of Physics
How a local perturbation affects a propagating wave traveling in a homogeneous medium is a general physics question widely investigated in condensed materials. Intuitively, one might expect that a perturbation would suppress the transport ability of the medium if it is quasi one dimensional. This is generically true as defects and impurities influence numerous non-excitable systems such as carbon nanotubes, nanowires and DNA double helixes. However, if the system is excitable, such as a neuron, a defect may generate a highly non-trivial dynamical behavior. In this paper, using the Hodgkin-Huxley model, we explored this diversity generated by locally non-uniform ion channel densities caused by toxins, diseases, environmental disorders or artificial manipulations. These channel density defects could induce several exotic behaviors, in contrast with the normal destructive role of defects in solid-state physics. They may behave as an electric signal generator exhibiting spontaneous or stimulated emissions, as well as trap, reflect, rectify, delay or extinguish propagating signals or be switched to different functions by a signal. Nonlinear analysis and phase diagrams were used to quantify this dynamical complexity. The results may contribute to research on signal manipulation in biotechnology, neuronal diseases and damages, channel distribution-related cell functions and defect dynamics in general excitable mathematical models.
Unidirectional rotation driven by random fluctuations
(2011)
Chang, Cheng-Hung
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Tsong, Tian-Yow
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物理研究所
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Institute of Physics
Ratchet effect might be responsible for the unidirectional movement of a couple of systems. The theoretical study of ratchet mechanism usually focuses on the particle or state properties on a prescribed ratchet potential. In contrast, this work starts with a real system and shows how one can manipulate the system setup to have a ratchet potential for the system state. The model consists of a rotor surrounded by several drivers on a 2D plane. Both the rotor and drivers are furnished with electric dipoles, through which they can interact with each other. During the rotational fluctuations of the driver dipoles between two states, the rotor may rotate unidirectionally, independent of whether the driver fluctuations are periodic or completely random. If the driver fluctuations come from the conformational change of certain protein subunits consuming ATP, the rotor behavior would be similar to the rotation of the central gamma subunit of F0F1-ATPase in mitochondria. We compare the rotational properties of our model with that of the flashing ratchet and F0F1-ATPase. This model provides a feasible way for harvesting non-equilibrium energy from ambient noise, which could be used to design microscopic artificial machines.