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Title | : Emergence of nonwhite noise in Langevin dynamics with magnetic Lorentz force |
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Author | : Noh, Jae Dong |
Journal | : PHYSICAL REVIEW E, 2018 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong |
TITLE | Emergence of nonwhite noise in Langevin dynamics with magnetic Lorentz force |
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JOURNAL | PHYSICAL REVIEW E, 2018 |
ABSTRACT | We investigate the low mass limit of Langevin dynamics for a charged Brownian particle driven by a magnetic Lorentz force. In the low mass limit, velocity variables relaxing quickly are coarse-grained out to yield effective dynamics for position variables. Without the Lorentz force, the low mass limit is equivalent to the high friction limit. Both cases share the same Langevin equation that is obtained by setting the mass to zero. The equivalence breaks down in the presence of the Lorentz force. The low mass limit cannot be achieved by setting the mass to zero. The limit is also distinct from the large friction limit. We derive the effective equations of motion in the low mass limit. The resulting stochastic differential equation involves a nonwhite noise whose correlation matrix has antisymmetric components. We demonstrate the importance of the nonwhite noise by investigating the heat dissipation by a driven Brownian particle, where the emergent nonwhite noise has a physically measurable effect. |
Title | : Microscopic theory for the time irreversibility and the entropy production |
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Author | : Noh, Jae Dong |
Journal | : JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, 2018 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong |
TITLE | Microscopic theory for the time irreversibility and the entropy production |
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JOURNAL | JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, 2018 |
ABSTRACT | In stochastic thermodynamics, the entropy production of a thermodynamic system is defined by the irreversibility measured by the logarithm of the ratio of the path probabilities in the forward and reverse processes. We derive the relation between the irreversibility and the entropy production starting from the deterministic equations of motion of the whole system consisting of a physical system and a surrounding thermal environment. The derivation assumes the Markov approximation that the environmental degrees of freedom equilibrate instantaneously. Our approach provides a guideline for the choice of the proper reverse process to a given forward process, especially when there exists a velocity-dependent force. We demonstrate our idea with an example of a charged particle in the presence of a time-varying magnetic field. |
Title | : Human bipedalism and body-mass index |
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Author | : Noh, Jae Dong |
Journal | : SCIENTIFIC REPORTS, 2017 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong |
TITLE | Human bipedalism and body-mass index |
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JOURNAL | SCIENTIFIC REPORTS, 2017 |
ABSTRACT | widely used as a useful proxy to measure a general health status of a human individual. We generalise BMI in the form of M/H-p and pursue to answer the question of the value of p for populations of animal species including human. We compare values of p for several different datasets for human populations with the ones obtained for other animal populations of fish, whales, and land mammals. All animal populations but humans analyzed in our work are shown to have p approximate to 3 unanimously. In contrast, human populations are different: As young infants grow to become toddlers and keep growing, the sudden change of p is observed at about one year after birth. Infants younger than one year old exhibit significantly larger value of p than two, while children between one and five years old show p approximate to 2, sharply different from other animal species. The observation implies the importance of the upright posture of human individuals. We also propose a simple mechanical model for a human body and suggest that standing and walking upright should put a clear division between bipedal human (p approximate to 2) and other animals (p approximate to 3). |
Title | : Time-Delay Induced Dimensional Crossover in the Voter Model |
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Author | : Noh, Jae Dong |
Journal | : PHYSICAL REVIEW LETTERS, 2017 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong |
TITLE | Time-Delay Induced Dimensional Crossover in the Voter Model |
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JOURNAL | PHYSICAL REVIEW LETTERS, 2017 |
ABSTRACT | We investigate the ordering dynamics of the voter model with time-delayed interactions. The dynamical process in the d-dimensional lattice is shown to be equivalent to the first passage problem of a random walker in the (d + 1)-dimensional strip of a finite width determined by the delay time. The equivalence reveals that the time delay leads to the dimensional crossover from the (d + 1)-dimensional scaling behavior at a short time to the d-dimensional scaling behavior at a long time. The scaling property in both regimes and the crossover time scale are obtained analytically, which are confirmed with the numerical simulation results. |
Title | : Tricritical behavior of nonequilibrium Ising spins in fluctuating environments |
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Author | : Noh, Jae Dong |
Journal | : PHYSICAL REVIEW E, 2017 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong |
TITLE | Tricritical behavior of nonequilibrium Ising spins in fluctuating environments |
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JOURNAL | PHYSICAL REVIEW E, 2017 |
ABSTRACT | We investigate the phase transitions in a coupled system of Ising spins and a fluctuating network. Each spin interacts with q neighbors through links of the rewiring network. The Ising spins and the network are in thermal contact with the heat baths at temperatures T-S and T-L, respectively, so the whole system is driven out of equilibrium for T-S not equal T-L. The model is a generalization of the q-neighbor Ising model [A. J. edrzejewski et al., Phys. Rev. E 92, 052105 (2015)], which corresponds to the limiting case of T-L = infinity. Despite the mean-field nature of the interaction, the q-neighbor Ising model was shown to display a discontinuous phase transition for q >= 4. Setting up the rate equations for the magnetization and the energy density, we obtain the phase diagram in the T-S-T-L parameter space. The phase diagram consists of a ferromagnetic phase and a paramagnetic phase. The two phases are separated by a continuous phase transition belonging to the mean-field universality class or by a discontinuous phase transition with an intervening coexistence phase. The equilibrium system with T-S = T-L falls into the former case while the q-neighbor Ising model falls into the latter case. At the tricritical point, the system exhibits the mean-field tricritical behavior. Our model demonstrates a possibility that a continuous phase transition turns into a discontinuous transition by a nonequilibrium driving. Heat flow induced by the temperature difference between two heat baths is also studied. |
Title | : Efficiency at maximum power and efficiency fluctuations in a linear Brownian heat-engine model |
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Author | : Noh, Jae Dong |
Journal | : PHYSICAL REVIEW E, 2016 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong |
TITLE | Efficiency at maximum power and efficiency fluctuations in a linear Brownian heat-engine model |
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JOURNAL | PHYSICAL REVIEW E, 2016 |
ABSTRACT | We investigate the stochastic thermodynamics of a two- particle Langevin system. Each particle is in contact with a heat bath at different temperatures T-1 and T-2 ( |
Title | : Optimal tuning of a confined Brownian information engine |
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Author | : Noh, Jae Dong,Lee, Jae Sung |
Journal | : PHYSICAL REVIEW E, 2016 |
NUMBER | Q17029 |
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AUTHOR | Noh, Jae Dong,Lee, Jae Sung |
TITLE | Optimal tuning of a confined Brownian information engine |
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JOURNAL | PHYSICAL REVIEW E, 2016 |
ABSTRACT | A Brownian information engine is a device extracting mechanical work from a single heat bath by exploiting the information on the state of a Brownian particle immersed in the bath. As for engines, it is important to find the optimal operating condition that yields the maximum extracted work or power. The optimal condition for a Brownian information engine with a finite cycle time tau has been rarely studied because of the difficulty in finding the nonequilibrium steady state. In this study, we introduce a model for the Brownian information engine and develop an analytic formalism for its steady-state distribution for any tau. We find that the extracted work per engine cycle is maximum when t approaches infinity, while the power is maximum when t approaches zero. |
Title | : Macroscopic time-reversal symmetry breaking at a nonequilibrium phase transition |
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Author | : Noh, Jae Dong |
Journal | : PHYSICAL REVIEW E, 2016 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong |
TITLE | Macroscopic time-reversal symmetry breaking at a nonequilibrium phase transition |
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JOURNAL | PHYSICAL REVIEW E, 2016 |
ABSTRACT | We study the entropy production in a globally coupled Brownian particles system that undergoes an order-disorder phase transition. Entropy production is a characteristic feature of nonequilibrium dynamics with broken detailed balance. We find that the entropy production rate is subextensive in the disordered phase and extensive in the ordered phase. It is found that the entropy production rate per particle vanishes in the disordered phase and becomes positive in the ordered phase following critical scaling laws. We derive the scaling relations for associated critical exponents. The disordered phase exemplifies a case where the entropy production is subextensive with the broken detailed balance. |
Title | : Hidden entropy production by fast variables |
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Author | : Noh, Jae Dong |
Journal | : PHYSICAL REVIEW E, 2015 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong |
TITLE | Hidden entropy production by fast variables |
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JOURNAL | PHYSICAL REVIEW E, 2015 |
ABSTRACT | We investigate nonequilibrium underdamped Langevin dynamics of Brownian particles that interact through a harmonic potential with coupling constant K and are in thermal contact with two heat baths at different temperatures. The system is characterized by a net heat flow and an entropy production in the steady state. We compare the entropy production of the harmonic system with that of Brownian particles linked with a rigid rod. The harmonic system may be expected to reduce to the rigid rod system in the infinite K limit. However, we find that the harmonic system in the K -> infinity limit produces more entropy than the rigid rod system. The harmonic system has the center-of-mass coordinate as a slow variable and the relative coordinate as a fast variable. By identifying the contributions of the degrees of freedom to the total entropy production, we show that the hidden entropy production by the fast variable is responsible for the extra entropy production. We discuss the K dependence of each contribution. |
Title | : Block renormalization study on the nonequilibrium chiral Ising model |
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Author | : Noh, Jae Dong |
Journal | : PHYSICAL REVIEW E, 2015 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong |
TITLE | Block renormalization study on the nonequilibrium chiral Ising model |
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JOURNAL | PHYSICAL REVIEW E, 2015 |
ABSTRACT | We present a numerical study on the ordering dynamics of a one-dimensional nonequilibrium Ising spin system with chirality. This system is characterized by a direction-dependent spin update rule. Pairs of +-spins can flip to ++ or -- with probability (1 - u) or to -+ with probability u while -+ pairs are frozen. The system was found to evolve into the ferromagnetic ordered state at any u < 1 exhibiting the power-law scaling of the characteristic length scale xi similar to t(1/z) and the domain-wall density rho similar to t(-delta). The scaling exponents z and d were found to vary continuously with the parameter u. To establish the anomalous power-law scaling firmly, we perform the block renormalization analysis proposed by Basu and Hinrichsen [U. Basu and H. Hinrichsen, J. Stat. Mech.: Theor. Exp. (2011) P11023]. The block renormalization method predicts, under the assumption of dynamic scale invariance, a scaling relation that can be used to estimate the scaling exponent numerically. We find the condition under which the scaling relation is justified. We then apply the method to our model and obtain the critical exponent z delta at several values of u. The numerical result is in perfect agreement with that of the previous study. This study serves as additional evidence for the claim that the nonequilibrium chiral Ising model displays power-law scaling behavior with continuously varying exponents. |
Title | : On the Steady-state Probability Distribution of Nonequilibrium Stochastic Systems |
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Author | : Noh, Jae Dong |
Journal | : JOURNAL OF THE KOREAN PHYSICAL SOCIETY, 2015 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong |
TITLE | On the Steady-state Probability Distribution of Nonequilibrium Stochastic Systems |
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JOURNAL | JOURNAL OF THE KOREAN PHYSICAL SOCIETY, 2015 |
ABSTRACT | A driven stochastic system in a constant temperature heat bath relaxes into a steady state that is characterized by the steady-state probability distribution. We investigate the relationship between the driving force and the steady-state probability distribution. We adopt the force decomposition method in which the force is decomposed as the sum of a gradient of a steady-state potential and the remaining part. The decomposition method allows one to find a set of force fields each of which is compatible with a given steady state. Such a knowledge provides useful insight into stochastic systems, especially those in a nonequilibrium situation. We demonstrate the decomposition method in stochastic systems under overdamped and underdamped dynamics and discuss the connection between them. |
Title | : Degree-ordered percolation on a hierarchical scale-free network |
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Author | : Noh, Jae Dong,Lee, Hyun Keun |
Journal | : PHYSICAL REVIEW E, 2014 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong,Lee, Hyun Keun |
TITLE | Degree-ordered percolation on a hierarchical scale-free network |
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JOURNAL | PHYSICAL REVIEW E, 2014 |
ABSTRACT | We investigate the critical phenomena of the degree-ordered percolation (DOP) model on the hierarchical (u, v) flower network with u <= v. Highest degree nodes are linked directly without intermediate nodes for u = 1, while this is not the case for u not equal 1. Using the renormalization-group-like procedure, we derive the recursion relations for the percolating probability and the percolation order parameter, from which the percolation threshold and the critical exponents are obtained. When u not equal 1, the DOP critical behavior turns out to be identical to that of the bond percolation with a shifted nonzero percolation threshold. When u = 1, the DOP and the bond percolation have the same vanishing percolation threshold but the critical behaviors are different. Implication to an epidemic spreading phenomenon is discussed. |
Title | : Stochastic echo phenomena in nonequilibrium systems |
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Author | : Noh, Jae Dong |
Journal | : JOURNAL OF THE KOREAN PHYSICAL SOCIETY, 2014 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong |
TITLE | Stochastic echo phenomena in nonequilibrium systems |
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JOURNAL | JOURNAL OF THE KOREAN PHYSICAL SOCIETY, 2014 |
ABSTRACT | A thermodynamic system is driven out of equilibrium by a time-dependent force or a nonconservative force represented with a protocol lambda(t). The dynamics of such a system is irreversible so that the ensemble of trajectories under a time-reversed protocol lambda(-t) is not equivalent to that of timereversed trajectories under lambda(t). We raise a question whether one can find a suitable protocol under which the system exhibits time-reversed motions of the original system. Such a phenomenon is referred to as a stochastic echo phenomenon. We derive a condition for the optimal protocol that leads to the stochastic echo phenomenon in Langevin systems. We find that any system driven by timeindependent nonconservative forces has a dual system exhibiting the stochastic echo phenomenon perfectly. The stochastic echo phenomena are also demonstrated for harmonic oscillator systems driven by time-dependent forces. Our study provides a novel perspective on the time-irreversibility of nonequilibrium systems. |
Title | : Fluctuations and correlations in nonequilibrium systems |
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Author | : Noh, Jae Dong |
Journal | : JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, 2014 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong |
TITLE | Fluctuations and correlations in nonequilibrium systems |
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JOURNAL | JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, 2014 |
ABSTRACT | Nonequilibrium systems exchange energy with an environment in the form of work and heat. The Work done on a system obeys the fluctuation theorem, while the dissipated heat. W hi c h differs from the work by the internal energy change, does not. We derive the modified fluctuation relation for the heat in an overdamped Lange in system. It shows that mutual correlations among the work, the heat and the internal energy change are responsible for the different fluctuation properties of the work and the heat. The mutual correlation is in in detail in a two-dimensional linear diffusion system. We develop an analytical method that allows one to calculate the large deviation function for the,joint probability distributions. We find that the heat and the internal energy change have a negative correlation, which explains the reason for the breakdown of the fluctuation theorem for the heat. |
Title | : Work fluctuations in a time-dependent harmonic potential: Rigorous results beyond the overdamped limit |
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Author | : Noh, Jae Dong,Park, Hyunggyu |
Journal | : PHYSICAL REVIEW E, 2013 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong,Park, Hyunggyu |
TITLE | Work fluctuations in a time-dependent harmonic potential: Rigorous results beyond the overdamped limit |
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JOURNAL | PHYSICAL REVIEW E, 2013 |
ABSTRACT | We investigate the stochastic motion of a Brownian particle in the harmonic potential with a time-dependent force constant. It may describe the motion of a colloidal particle in an optical trap where the potential well is formed by a time-dependent field. We use the path integral formalism to solve the Langevin equation and the associated Fokker-Planck (Kramers) equation. Rigorous relations are derived to generate the probability density function for the time-dependent nonequilibrium work production beyond the overdamped limit. We find that the work distribution exhibits an exponential tail with a power-law prefactor, accompanied by an interesting oscillatory feature (multiple pseudo-locking-unlocking transitions) due to the inertial effect. Some exactly solvable cases are discussed in the overdamped limit. |
Title | : Multiple Dynamic Transitions in Nonequilibrium Work Fluctuations |
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Author | : Noh, Jae Dong,Park, Hyunggyu |
Journal | : PHYSICAL REVIEW LETTERS, 2013 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong,Park, Hyunggyu |
TITLE | Multiple Dynamic Transitions in Nonequilibrium Work Fluctuations |
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JOURNAL | PHYSICAL REVIEW LETTERS, 2013 |
ABSTRACT | The time-dependent work probability distribution function P(W) is investigated analytically for a diffusing particle trapped by an anisotropic harmonic potential and driven by a nonconservative drift force in two dimensions. We find that the exponential tail shape of P(W) characterizing rare-event probabilities undergoes a sequence of dynamic transitions in time. These remarkable locking-unlocking type transitions result from an intricate interplay between a rotational mode induced by the nonconservative force and an anisotropic decaying mode due to the conservative attractive force. We expect that most of the high-dimensional dynamical systems should exhibit similar multiple dynamic transitions. |
Title | : Epidemic threshold of the susceptible-infected-susceptible model on complex networks |
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Author | : Noh, Jae Dong |
Journal | : PHYSICAL REVIEW E, 2013 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong |
TITLE | Epidemic threshold of the susceptible-infected-susceptible model on complex networks |
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JOURNAL | PHYSICAL REVIEW E, 2013 |
ABSTRACT | We demonstrate that the susceptible-infected-susceptible (SIS) model on complex networks can have an inactive Griffiths phase characterized by a slow relaxation dynamics. It contrasts with the mean-field theoretical prediction that the SIS model on complex networks is active at any nonzero infection rate. The dynamic fluctuation of infected nodes, ignored in the mean field approach, is responsible for the inactive phase. It is proposed that the question whether the epidemic threshold of the SIS model on complex networks is zero or not can be resolved by the percolation threshold in a model where nodes are occupied in degree-descending order. Our arguments are supported by the numerical studies on scale-free network models. |
Title | : Coarsening dynamics of nonequilibrium chiral Ising models |
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Author | : Noh, Jae Dong |
Journal | : PHYSICAL REVIEW E, 2013 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong |
TITLE | Coarsening dynamics of nonequilibrium chiral Ising models |
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JOURNAL | PHYSICAL REVIEW E, 2013 |
ABSTRACT | We investigate a nonequilibrium coarsening dynamics of a one-dimensional Ising spin system with chirality. Only spins at domain boundaries are updated so that the model undergoes a coarsening to either of equivalent absorbing states with all spins + or -. Chirality is imposed by assigning different transition rates to events at down (+-) kinks and up (-+) kinks. The coarsening is characterized by power-law scalings of the kink density rho similar to t(-delta) and the characteristic length scale xi similar to t(1/z) with time t. Surprisingly the scaling exponents vary continuously with model parameters, which is not the case for systems without chirality. These results are obtained from extensive Monte Carlo simulations and spectral analyses of the time evolution operator. Our study uncovers the novel universality class of the coarsening dynamics with chirality. DOI: 10.1103/PhysRevE.87.012129 |
Title | : Percolation transitions with nonlocal constraint |
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Author | : Noh, Jae Dong |
Journal | : PHYSICAL REVIEW E, 2012 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong |
TITLE | Percolation transitions with nonlocal constraint |
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JOURNAL | PHYSICAL REVIEW E, 2012 |
ABSTRACT | We investigate percolation transitions in a nonlocal network model numerically. In this model, each node has an exclusive partner and a link is forbidden between two nodes whose r-neighbors share any exclusive pair. The r-neighbor of a node x is defined as a set of at most N-r neighbors of x, where N is the total number of nodes. The parameter r controls the strength of a nonlocal effect. The system is found to undergo a percolation transition belonging to the mean-field universality class for r < 1/2. On the other hand, for r > 1/2, the system undergoes a peculiar phase transition from a nonpercolating phase to a quasicritical phase where the largest cluster size G scales as G similar to N-alpha with alpha = 0.74(1). In the marginal case with r = 1/2, the model displays a percolation transition that does not belong to the mean-field universality class. |
Title | : Fluctuation Relation for Heat |
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Author | : Noh, Jae Dong |
Journal | : PHYSICAL REVIEW LETTERS, 2012 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong |
TITLE | Fluctuation Relation for Heat |
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JOURNAL | PHYSICAL REVIEW LETTERS, 2012 |
ABSTRACT | We present a fluctuation relation for heat dissipation in a nonequilibrium system. A nonequilibrium work is known to obey the fluctuation theorem in any time interval t. Heat, which differs from work by an energy change, is shown to satisfy a modified fluctuation relation. Modification is brought about by the correlation between heat and energy change during nonequilibrium processes whose effect may not be negligible even in the t -> infinity limit. The fluctuation relation is derived for overdamped Langevin equation systems, and tested in a linear diffusion system. |
Title | : Phenomenology of aging in the Kardar-Parisi-Zhang equation |
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Author | : Noh, Jae Dong |
Journal | : PHYSICAL REVIEW E, 2012 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong |
TITLE | Phenomenology of aging in the Kardar-Parisi-Zhang equation |
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JOURNAL | PHYSICAL REVIEW E, 2012 |
ABSTRACT | We study aging during surface growth processes described by the one-dimensional Kardar-Parisi-Zhang equation. Starting from a flat initial state, the systems undergo simple aging in both correlators and linear responses, and its dynamical scaling is characterized by the aging exponents a = -1/3, b = -2/3, lambda(C) = lambda(R) = 1, and z = 3/2. The form of the autoresponse scaling function is well described by the recently constructed logarithmic extension of local scale invariance. |
Title | : Condensation and Clustering in the Driven Pair Exclusion Process |
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Author | : Noh, Jae Dong |
Journal | : JOURNAL OF THE KOREAN PHYSICAL SOCIETY, 2012 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong |
TITLE | Condensation and Clustering in the Driven Pair Exclusion Process |
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JOURNAL | JOURNAL OF THE KOREAN PHYSICAL SOCIETY, 2012 |
ABSTRACT | We investigate particle condensation in a driven pair exclusion process on one-and two-dimensional lattices under the periodic boundary condition. The model describes a biased hopping of particles subject to a pair exclusion constraint that each particle cannot stay at a same site with its pre-assigned partner. The pair exclusion causes a mesoscopic condensation characterized by the scaling of the condensate size m(con) similar to N-beta and the number of condensates N-con similar to N-alpha with the total number of sites N. Those condensates are distributed randomly without hopping bias. We find that the hopping bias generates a spatial correlation among condensates so that a cluster of condensates appears. Especially, the cluster has an anisotropic shape in the two-dimensional system. The mesoscopic condensation and the clustering are studied by means of numerical simulations. |
Title | : Scaling of cluster heterogeneity in percolation transitions |
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Author | : Noh, Jae Dong,Park, Hyunggyu |
Journal | : PHYSICAL REVIEW E, 2011 |
NUMBER | P11029 |
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AUTHOR | Noh, Jae Dong,Park, Hyunggyu |
TITLE | Scaling of cluster heterogeneity in percolation transitions |
ARCHIVE | arXiv:1106.0354 |
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JOURNAL | PHYSICAL REVIEW E, 2011 |
ABSTRACT | We investigate a critical scaling law for the cluster heterogeneity H in site and bond percolations in d-dimensional lattices with d = 2,...,6. The cluster heterogeneity is defined as the number of distinct cluster sizes. As an occupation probability p increases, the cluster size distribution evolves from a monodisperse distribution to a polydisperse one in the subcritical phase, and back to a monodisperse one in the supercritical phase. We show analytically that H diverges algebraically, approaching the percolation critical point p(c) as H similar to vertical bar p - p(c)vertical bar(-1/sigma) with the critical exponent sigma associated with the characteristic cluster size. Interestingly, its finite-size-scaling behavior is governed by a new exponent v(H) = (1 + d(f)/d)v, where d(f) is the fractal dimension of the critical percolating cluster and v is the correlation length exponent. The corresponding scaling variable defines a singular path to the critical point. All results are confirmed by numerical simulations. |
Title | : Nonequilibrium fluctuations for linear diffusion dynamics |
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Author | : Noh, Jae Dong,Park, Hyunggyu |
Journal | : PHYSICAL REVIEW E, 2011 |
NUMBER | P11018 |
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AUTHOR | Noh, Jae Dong,Park, Hyunggyu |
TITLE | Nonequilibrium fluctuations for linear diffusion dynamics |
ARCHIVE | 1102.2973 |
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JOURNAL | PHYSICAL REVIEW E, 2011 |
ABSTRACT | We present the theoretical study on nonequilibrium (NEQ) fluctuations for diffusion dynamics in high dimensions driven by a linear drift force. We consider a general situation in which NEQ is caused by two conditions: (i) drift force not derivable from a potential function, and (ii) diffusion matrix not proportional to the unit matrix, implying nonidentical and correlated multidimensional noise. The former is a well-known NEQ source and the latter can be realized in the presence of multiple heat reservoirs or multiple noise sources. We develop a statistical mechanical theory based on generalized thermodynamic quantities such as energy, work, and heat. The NEQ fluctuation theorems are reproduced successfully. We also find the time-dependent probability distribution function exactly as well as the NEQ work production distribution P(W) in terms of solutions of nonlinear differential equations. In addition, we compute low-order cumulants of the NEQ work production explicitly. In two dimensions, we carry out numerical simulations to check out our analytic results and also to get P(W). We find an interesting dynamic phase transition in the exponential tail shape of P(W), associated with a singularity found in solutions of the nonlinear differential equation. Finally, we discuss possible realizations in experiments. |
Title | : Asymmetric simple exclusion process in one-dimensional chains with long-range links |
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Author | : Noh, Jae Dong |
Journal | : JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, 2011 |
NUMBER | null |
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AUTHOR | Noh, Jae Dong |
TITLE | Asymmetric simple exclusion process in one-dimensional chains with long-range links |
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JOURNAL | JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, 2011 |
ABSTRACT | We study the boundary-driven asymmetric simple exclusion process (ASEP) in a one-dimensional chain with long-range links. Shortcuts are added to a chain by connecting pL different pairs of sites selected randomly where L and p denote the chain length and the shortcut density, respectively. Particles flow into a chain at one boundary at a rate a and out of a chain at the other boundary at a rate beta, while they hop inside a chain via nearest-neighbor bonds and long-range shortcuts. Without shortcuts, the model reduces to the boundary-driven ASEP in a one-dimensional chain which displays the low-density, high-density and maximal-current phases. Shortcuts lead to a drastic change. Numerical simulation studies suggest that there emerge three phases: an empty phase with rho = 0, a jammed phase with rho = 1 and a shock phase with 0 < rho < 1 where rho is the mean particle density. The shock phase is characterized with a phase separation between an empty region and a jammed region with a localized shock between them. The mechanism for the shock formation and the nonequilibrium phase transition are explained by an analytical theory based on a mean-field approximation and an annealed approximation. |
Title | : Finite-size scaling theory for explosive percolation transitions |
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Author | : Noh, J. D.,Kim, D.,Kahng, B. |
Journal | : PHYSICAL REVIEW E, 2010 |
NUMBER | null |
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AUTHOR | Noh, J. D.,Kim, D.,Kahng, B. |
TITLE | Finite-size scaling theory for explosive percolation transitions |
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JOURNAL | PHYSICAL REVIEW E, 2010 |
ABSTRACT | The finite-size scaling (FSS) theory for continuous phase transitions has been useful in determining the critical behavior from the size-dependent behaviors of thermodynamic quantities. When the phase transition is discontinuous, however, FSS approach has not been well established yet. Here, we develop a FSS theory for the explosive percolation transition arising in the Erdos and Renyi model under the Achlioptas process. A scaling function is derived based on the observed fact that the derivative of the curve of the order parameter at the critical point t(c) diverges with system size in a power-law manner, which is different from the conventional one based on the divergence of the correlation length at t(c). We show that the susceptibility is also described in the same scaling form. Numerical simulation data for different system sizes are well collapsed on the respective scaling functions. |
Title | : Deciphering Kinetic Information from Single-Molecule FRET Data That Show Slow Transitions |
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Author | : Hong, Seok-Cheol,Hyeon, Changbong |
Journal | : JOURNAL OF PHYSICAL CHEMISTRY B, 2015 |
NUMBER | C17037 |
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AUTHOR | Hong, Seok-Cheol,Hyeon, Changbong |
TITLE | Deciphering Kinetic Information from Single-Molecule FRET Data That Show Slow Transitions |
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JOURNAL | JOURNAL OF PHYSICAL CHEMISTRY B, 2015 |
ABSTRACT | Single-molecule: FRET is One Of the most powerful and widely used biophysical techniques in biological sciences. It, however often suffers from limitations such as weak signal and limited measurement time intrinsic to single- Molecule fluorescence measurements. Despite several ameliorative measures taken to increase- measurement time, it is nearly impossible to acquire meaningful kinetic information on a molecule if conformational transitions of the molecule are ultraslow such that transition times ( |
Title | : Destabilization of i-Motif by Submolar Concentrations of a Monovalent Cation |
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Author | : Hong, Seok-Cheol,Hyeon, Changbong |
Journal | : JOURNAL OF PHYSICAL CHEMISTRY B, 2014 |
NUMBER | C15010 |
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AUTHOR | Hong, Seok-Cheol,Hyeon, Changbong |
TITLE | Destabilization of i-Motif by Submolar Concentrations of a Monovalent Cation |
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JOURNAL | JOURNAL OF PHYSICAL CHEMISTRY B, 2014 |
ABSTRACT | Counterions are crucial for self-assembly of nucleic acids. Submolar monovalent cations are generally deemed to stabilize various types of base pairs in nucleic acids such as Watson-Crick and Hoogsteen base pairs via screening of electrostatic repulsion. Besides monovalent cations, acidic pH is required for i-motif formation because protons facilitate pairing between cytosines. Here we report that Li+ ions destabilize i-motif, whereas other monovalent cations, Na+ and K+, have the usual stabilizing effect. The thermodynamics data alone, however, cannot reveal which mechanism, enhanced unfolding or suppressed folding or both, is responsible for the Li+-induced destabilization. To gain further insight, we examined the kinetics of i-motif. To deal with slow kinetics of i-motif, we developed a method dubbed HaRP to construct a long FRET time trace to observe a sufficient number of transitions. Our kinetics analysis shows clearly that Li+ ions promote unfolding of i-motif but do not hinder its folding, lending strong support for our hypothesis on the origin of this unusual effect of Li+. Although the subangstrom size of Li+ ions allows them to infiltrate the space between cytosines in competition with protons, they cannot adequately fulfill the role of protons in mediating the hydrogen bonding of cytosine pairs. |
Title | : Direct observation of the formation of DNA triplexes by single-molecule FRET measurements |
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Author | : Hong, Seok-Cheol |
Journal | : CURRENT APPLIED PHYSICS, 2012 |
NUMBER | null |
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AUTHOR | Hong, Seok-Cheol |
TITLE | Direct observation of the formation of DNA triplexes by single-molecule FRET measurements |
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JOURNAL | CURRENT APPLIED PHYSICS, 2012 |
ABSTRACT | In this report we investigated the effects of various biological and chemical factors (DNA sequence, pH, ions, and molecularity) on the formation of DNA triplexes through single-molecule FRET technique. Using this method, we determined how the third strand bound to a DNA duplex and how stable the triplex structure was under various conditions. From this study, we not only verified a variety of well-known features of DNA triplex but also discovered or experimentally supported several interesting behaviors: at neutral pH, a pyrimidine-motif triplex can be formed; the parallel arrangement was not only possible but also dominant over the antiparallel arrangement for a purine-motif triplex. We demonstrated that our method is a versatile analytical tool in studying structural aspects of nucleic acids, particularly non-classical DNA structures, and provides insights into physical mechanism of such structures. (C) 2012 Elsevier B. V. All rights reserved. |