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Visiting Faculty
 Bae, Myoungjean
 Affiliate Professor
 Partial Differential equations, Calculus of Variations, Mathematical fluid dynamics
 Office
 Tel / Fax 3786


 Cha, Jae Choon
 Affiliate Professor
 Geometric Topology
 Office 1410
 Tel 3848 / Fax 3786

 Ha, SeungYeal
 Affiliate Professor
 Analysis, Hyperbolic Conservation Laws, Kinetic Theory
 Office 1410
 Tel 3848 / Fax 3786


 Hong, SeokCheol
 Affiliate Professor
 Theoretical and Computational Biophysics
 Office 8214
 Tel 2660 / Fax 3820



Deciphering Kinetic Information from SingleMolecule FRET Data That Show Slow Transitions
NUMBER  C17037 
AUTHOR  Hong, SeokCheol,Hyeon, Changbong 
TITLE  Deciphering Kinetic Information from SingleMolecule FRET Data That Show Slow Transitions 
ARCHIVE  
FILE  
JOURNAL  JOURNAL OF PHYSICAL CHEMISTRY B, 2015 
ABSTRACT  Singlemolecule: 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 singlemolecule data:With,slow transition kinetics This,study:provides a practical vide to use sHaRPer. 

Destabilization of iMotif by Submolar Concentrations of a Monovalent Cation
NUMBER  C15010 
AUTHOR  Hong, SeokCheol,Hyeon, Changbong 
TITLE  Destabilization of iMotif by Submolar Concentrations of a Monovalent Cation 
ARCHIVE  
FILE  
JOURNAL  JOURNAL OF PHYSICAL CHEMISTRY B, 2014 
ABSTRACT  Counterions are crucial for selfassembly of nucleic acids. Submolar monovalent cations are generally deemed to stabilize various types of base pairs in nucleic acids such as WatsonCrick and Hoogsteen base pairs via screening of electrostatic repulsion. Besides monovalent cations, acidic pH is required for imotif formation because protons facilitate pairing between cytosines. Here we report that Li+ ions destabilize imotif, 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 imotif. To deal with slow kinetics of imotif, 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 imotif 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. 
 Ki, Haseo
 Affiliate Professor
 Number Theory
 Office 1404B
 Tel 3715 / Fax 3786


 Kwak, Sijong
 Affiliate Professor
 Algebraic geometry & commutative algebra
 Office
 Tel / Fax


 Kwon, Chulan
 Affiliate Professor
 Office 8410
 Tel 2594 / Fax

 Lee, KiAhm
 Affiliate Professor
 Analysis, Partial Differential Equations
 Office 1410
 Tel 3848 / Fax 3786


 Lee, Yongnam
 Affiliate Professor
 Algebraic Geometry
 Office 1404B
 Tel 3715 / Fax 3786


 Noh, Jae Dong
 Affiliate Professor
 Fluctuations, correlations, and collective phenomena in complex systems
 Office 1231
 Tel 3758, 3868 / Fax



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 
ARCHIVE  
FILE  
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 steadystate 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. 

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 
FILE  
JOURNAL  PHYSICAL REVIEW E, 2011 
ABSTRACT  We investigate a critical scaling law for the cluster heterogeneity H in site and bond percolations in ddimensional 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 finitesizescaling 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
NUMBER  P11018 
AUTHOR  Noh, Jae Dong,Park, Hyunggyu 
TITLE  Nonequilibrium fluctuations for linear diffusion dynamics 
ARCHIVE  1102.2973 
FILE  
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 wellknown 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 timedependent 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 loworder 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. 
 Oum, Sangil
 Affiliate Professor
 Graph Theory, Combinatorics, Combinatorial Optimization
 Office
 Tel / Fax 3786


 Park, Jongil
 Affiliate Professor
 Topology
 Office 1521
 Tel 2521 / Fax 3786


 Bae, Sunghan
 KIAS Visiting Professor
 Algebra, Number theory
 Office 1411
 Tel 3857 / Fax


 Cho, Sangbum
 KIAS Visiting Professor
 geometric topology
 Office 8305
 Tel / Fax

 Han, Jongmin
 KIAS Visiting Professor
 Partial Differential Equations
 Office 1530
 Tel / Fax

 Jeong, HyeongChai
 KIAS Visiting Professor
 Office
 Tel 2593 / Fax

 Kyeonghee Jo
 KIAS Visiting Professor
 Geometric structures on manifolds
 Office 8306
 Tel / Fax


 Lee, Hyunho
 KIAS Visiting Professor
 operator algebra, anticommutative geometry
 Office 1411
 Tel / Fax

 Lee, Jaehyouk
 KIAS Visiting Professor
 Differential geometry, Symplectic geometry, Algebraic geometry
 Office 1544
 Tel / Fax

 Lee, SangJin
 KIAS Visiting Professor
 Geometric Topology
 Office 8305
 Tel / Fax

 Lee, Yongnam
 KIAS Visiting Professor
 Algebraic Geometry
 Office 1404B
 Tel / Fax

 Moon, Dongho
 KIAS Visiting Professor
 Representation theory of Lie algebras
 Office 8306
 Tel / Fax

 Shin, Heayong
 KIAS Visiting Professor
 Differential geometry
 Office 1410
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 Sohn, SungIk
 KIAS Visiting Professor
 Fluid Dynamics, Scientific Computing
 Office 1530
 Tel / Fax
