• Emergence of nonwhite noise in Langevin dynamics with magnetic Lorentz force

  Title	: Emergence of nonwhite noise in Langevin dynamics with magnetic Lorentz force
  Author	: Noh, Jae Dong
  Journal	: PHYSICAL REVIEW E, 2018

  
  

  Emergence of nonwhite noise in Langevin dynamics with magnetic Lorentz force

  NUMBER	null
  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.

  
  

  

• Microscopic theory for the time irreversibility and the entropy production

  Title	: Microscopic theory for the time irreversibility and the entropy production
  Author	: Noh, Jae Dong
  Journal	: JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, 2018

  
  

  Microscopic theory for the time irreversibility and the entropy production

  NUMBER	null
  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.

  
  

  

• Human bipedalism and body-mass index

  Title	: Human bipedalism and body-mass index
  Author	: Noh, Jae Dong
  Journal	: SCIENTIFIC REPORTS, 2017

  
  

  Human bipedalism and body-mass index

  NUMBER	null
  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).

  
  

  

• Time-Delay Induced Dimensional Crossover in the Voter Model

  Title	: Time-Delay Induced Dimensional Crossover in the Voter Model
  Author	: Noh, Jae Dong
  Journal	: PHYSICAL REVIEW LETTERS, 2017

  
  

  Time-Delay Induced Dimensional Crossover in the Voter Model

  NUMBER	null
  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.

  
  

  

• Tricritical behavior of nonequilibrium Ising spins in fluctuating environments

  Title	: Tricritical behavior of nonequilibrium Ising spins in fluctuating environments
  Author	: Noh, Jae Dong
  Journal	: PHYSICAL REVIEW E, 2017

  
  

  Tricritical behavior of nonequilibrium Ising spins in fluctuating environments

  NUMBER	null
  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.

  
  

  

• Efficiency at maximum power and efficiency fluctuations in a linear Brownian heat-engine model

  Title	: Efficiency at maximum power and efficiency fluctuations in a linear Brownian heat-engine model
  Author	: Noh, Jae Dong
  Journal	: PHYSICAL REVIEW E, 2016

  
  

  Efficiency at maximum power and efficiency fluctuations in a linear Brownian heat-engine model

  NUMBER	null
  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 ( and increases monotonically until it reaches plateaus when eta <= eta(L) and eta >= eta(R) with model- dependent parameters eta(R) and eta(L).

  
  

  

• Optimal tuning of a confined Brownian information engine

  Title	: Optimal tuning of a confined Brownian information engine
  Author	: Noh, Jae Dong,Lee, Jae Sung
  Journal	: PHYSICAL REVIEW E, 2016

  
  

  Optimal tuning of a confined Brownian information engine

  NUMBER	Q17029
  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.

  
  

  

• Macroscopic time-reversal symmetry breaking at a nonequilibrium phase transition

  Title	: Macroscopic time-reversal symmetry breaking at a nonequilibrium phase transition
  Author	: Noh, Jae Dong
  Journal	: PHYSICAL REVIEW E, 2016

  
  

  Macroscopic time-reversal symmetry breaking at a nonequilibrium phase transition

  NUMBER	null
  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.

  
  

  

• Hidden entropy production by fast variables

  Title	: Hidden entropy production by fast variables
  Author	: Noh, Jae Dong
  Journal	: PHYSICAL REVIEW E, 2015

  
  

  Hidden entropy production by fast variables

  NUMBER	null
  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.

  
  

  

• Block renormalization study on the nonequilibrium chiral Ising model

  Title	: Block renormalization study on the nonequilibrium chiral Ising model
  Author	: Noh, Jae Dong
  Journal	: PHYSICAL REVIEW E, 2015

  
  

  Block renormalization study on the nonequilibrium chiral Ising model

  NUMBER	null
  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.

  
  

  

• On the Steady-state Probability Distribution of Nonequilibrium Stochastic Systems

  Title	: On the Steady-state Probability Distribution of Nonequilibrium Stochastic Systems
  Author	: Noh, Jae Dong
  Journal	: JOURNAL OF THE KOREAN PHYSICAL SOCIETY, 2015

  
  

  On the Steady-state Probability Distribution of Nonequilibrium Stochastic Systems

  NUMBER	null
  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.

  
  

  

• Degree-ordered percolation on a hierarchical scale-free network

  Title	: Degree-ordered percolation on a hierarchical scale-free network
  Author	: Noh, Jae Dong,Lee, Hyun Keun
  Journal	: PHYSICAL REVIEW E, 2014

  
  

  Degree-ordered percolation on a hierarchical scale-free network

  NUMBER	null
  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.

  
  

  

• Stochastic echo phenomena in nonequilibrium systems

  Title	: Stochastic echo phenomena in nonequilibrium systems
  Author	: Noh, Jae Dong
  Journal	: JOURNAL OF THE KOREAN PHYSICAL SOCIETY, 2014

  
  

  Stochastic echo phenomena in nonequilibrium systems

  NUMBER	null
  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.

  
  

  

• Fluctuations and correlations in nonequilibrium systems

  Title	: Fluctuations and correlations in nonequilibrium systems
  Author	: Noh, Jae Dong
  Journal	: JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, 2014

  
  

  Fluctuations and correlations in nonequilibrium systems

  NUMBER	null
  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.

  
  

  

• Work fluctuations in a time-dependent harmonic potential: Rigorous results beyond the overdamped limit

  Title	: Work fluctuations in a time-dependent harmonic potential: Rigorous results beyond the overdamped limit
  Author	: Noh, Jae Dong,Park, Hyunggyu
  Journal	: PHYSICAL REVIEW E, 2013

  
  

  Work fluctuations in a time-dependent harmonic potential: Rigorous results beyond the overdamped limit

  NUMBER	null
  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.

  
  

  

• Multiple Dynamic Transitions in Nonequilibrium Work Fluctuations

  Title	: Multiple Dynamic Transitions in Nonequilibrium Work Fluctuations
  Author	: Noh, Jae Dong,Park, Hyunggyu
  Journal	: PHYSICAL REVIEW LETTERS, 2013

  
  

  Multiple Dynamic Transitions in Nonequilibrium Work Fluctuations

  NUMBER	null
  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.

  
  

  

• Epidemic threshold of the susceptible-infected-susceptible model on complex networks

  Title	: Epidemic threshold of the susceptible-infected-susceptible model on complex networks
  Author	: Noh, Jae Dong
  Journal	: PHYSICAL REVIEW E, 2013

  
  

  Epidemic threshold of the susceptible-infected-susceptible model on complex networks

  NUMBER	null
  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.

  
  

  

• Coarsening dynamics of nonequilibrium chiral Ising models

  Title	: Coarsening dynamics of nonequilibrium chiral Ising models
  Author	: Noh, Jae Dong
  Journal	: PHYSICAL REVIEW E, 2013

  
  

  Coarsening dynamics of nonequilibrium chiral Ising models

  NUMBER	null
  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

  
  

  

• Percolation transitions with nonlocal constraint

  Title	: Percolation transitions with nonlocal constraint
  Author	: Noh, Jae Dong
  Journal	: PHYSICAL REVIEW E, 2012

  
  

  Percolation transitions with nonlocal constraint

  NUMBER	null
  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.

  
  

  

• Fluctuation Relation for Heat

  Title	: Fluctuation Relation for Heat
  Author	: Noh, Jae Dong
  Journal	: PHYSICAL REVIEW LETTERS, 2012

  
  

  Fluctuation Relation for Heat

  NUMBER	null
  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.

  
  

  

• Phenomenology of aging in the Kardar-Parisi-Zhang equation

  Title	: Phenomenology of aging in the Kardar-Parisi-Zhang equation
  Author	: Noh, Jae Dong
  Journal	: PHYSICAL REVIEW E, 2012

  
  

  Phenomenology of aging in the Kardar-Parisi-Zhang equation

  NUMBER	null
  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.

  
  

  

• Condensation and Clustering in the Driven Pair Exclusion Process

  Title	: Condensation and Clustering in the Driven Pair Exclusion Process
  Author	: Noh, Jae Dong
  Journal	: JOURNAL OF THE KOREAN PHYSICAL SOCIETY, 2012

  
  

  Condensation and Clustering in the Driven Pair Exclusion Process

  NUMBER	null
  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.

  
  

  

• Scaling of cluster heterogeneity in percolation transitions

  Title	: Scaling of cluster heterogeneity in percolation transitions
  Author	: Noh, Jae Dong,Park, Hyunggyu
  Journal	: PHYSICAL REVIEW E, 2011

  
  

  Scaling of cluster heterogeneity in percolation transitions

  NUMBER	P11029
  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.

  
  

  

• Nonequilibrium fluctuations for linear diffusion dynamics

  Title	: Nonequilibrium fluctuations for linear diffusion dynamics
  Author	: Noh, Jae Dong,Park, Hyunggyu
  Journal	: PHYSICAL REVIEW E, 2011

  
  

  Nonequilibrium fluctuations for linear diffusion dynamics

  NUMBER	P11018
  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.

  
  

  

• Asymmetric simple exclusion process in one-dimensional chains with long-range links

  Title	: Asymmetric simple exclusion process in one-dimensional chains with long-range links
  Author	: Noh, Jae Dong
  Journal	: JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, 2011

  
  

  Asymmetric simple exclusion process in one-dimensional chains with long-range links

  NUMBER	null
  AUTHOR	Noh, Jae Dong
  TITLE	Asymmetric simple exclusion process in one-dimensional chains with long-range links
  ARCHIVE
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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.

  
  

  

• Finite-size scaling theory for explosive percolation transitions

  Title	: Finite-size scaling theory for explosive percolation transitions
  Author	: Noh, J. D.,Kim, D.,Kahng, B.
  Journal	: PHYSICAL REVIEW E, 2010

  
  

  Finite-size scaling theory for explosive percolation transitions

  NUMBER	null
  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.

  
  

  

• Deciphering Kinetic Information from Single-Molecule FRET Data That Show Slow Transitions

  Title	: Deciphering Kinetic Information from Single-Molecule FRET Data That Show Slow Transitions
  Author	: Hong, Seok-Cheol,Hyeon, Changbong
  Journal	: JOURNAL OF PHYSICAL CHEMISTRY B, 2015

  
  

  Deciphering Kinetic Information from Single-Molecule FRET Data That Show Slow Transitions

  NUMBER	C17037
  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 ((orig)) are. comparable to or longer than measurement times (delta t) limited by the finite lifetime of fluorescent dye. Here, to extract a reliable and accurate mean transition time from, a series of short time traces with ultraslow kinetics, we suggest seheme called sHaRPer (serialized Handshaking Repeated Permutation with end removal) that concatenates multiple time traces because data acquisition frequency f and measurement time (delta t) affect the estimation of mean transition time (), we provide Mathematical criteria that f, delta t, and should satisfy to make close enough to (orig) Although application of the sHaRPer: methods a potential risk of distorting the time,constants of individual kinetic phases if the data are described with kinetic partitioning, We, also provide criteria to avoid such distortion. Our sHaRPer method is a useful way to handle single-molecule data:With,slow transition kinetics This,study:provides a practical vide to use sHaRPer.

  
  

  

• Destabilization of i-Motif by Submolar Concentrations of a Monovalent Cation

  Title	: Destabilization of i-Motif by Submolar Concentrations of a Monovalent Cation
  Author	: Hong, Seok-Cheol,Hyeon, Changbong
  Journal	: JOURNAL OF PHYSICAL CHEMISTRY B, 2014

  
  

  Destabilization of i-Motif by Submolar Concentrations of a Monovalent Cation

  NUMBER	C15010
  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.

  
  

  

• Direct observation of the formation of DNA triplexes by single-molecule FRET measurements

  Title	: Direct observation of the formation of DNA triplexes by single-molecule FRET measurements
  Author	: Hong, Seok-Cheol
  Journal	: CURRENT APPLIED PHYSICS, 2012

  
  

  Direct observation of the formation of DNA triplexes by single-molecule FRET measurements

  NUMBER	null
  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.