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Seung-Yeon Kim

Publications and source records attributed to Seung-Yeon Kim.

At least 19 recordsLinked to original sources
arXiv2012

Collapse transition of a square-lattice polymer with next nearest-neighbor interaction

We study the collapse transition of a polymer on a square lattice with both nearest-neighbor and next nearest-neighbor interactions, by calculating the exact partition function zeros up to chain length 36. The transition behavior is much more pronounced than that of the model with nearest-neighbor interactions only. The crossover exponent and the transition temperature are estimated from the scaling behavior of the first zeros with increasing chain length. The results suggest that the model is of the same universality class as the usual theta point described by the model with only nearest-neighbor interaction.

cond-mat.stat-mech↗
arXiv2012

Exact Partition Function Zeros of a Polymer on a Simple-Cubic Lattice

We study conformational transitions of a polymer on a simple-cubic lattice by calculating the zeros of the exact partition function, up to chain length 24. In the complex temperature plane, two loci of the partition function zeros are found for longer chains, suggesting the existence of both the coil-globule collapse transition and the melting-freezing transition. The locus corresponding to coil-globule transition clearly approaches the real axis as the chain length increases, and the transition temperature could be estimated by finite-size scaling. The form of the logarithmic correction to the scaling of the partition function zeros could also be obtained. The other locus does not show clear scaling behavior, but a supplementary analysis of the specific heat reveals a first-order-like pseudo-transition.

cond-mat.stat-mech↗
arXiv2011

Parallel Algorithm for Calculation of the Exact Partition Function of a Lattice Polymer

We develop a parallel algorithm that calculates the exact partition function of a lattice polymer, by enumerating the number of conformations for each energy level. An efficient parallelization of the calculation is achieved by classifying the conformations according to the shape of the box spanned by a conformation, and enumerating only those in a given box at a time. The calculation time for each box is reduced by preventing the conformations related by symmetries from being generated more than once. The algorithm is applied to study the collapse transition of a lattice homopolymer on a square lattice, by calculating the specific heat for chain lengths up to 36.

cond-mat.stat-mech↗
arXiv2011

Exact partition function zeros and the collapse transition of a two-dimensional lattice polymer

We study the collapse transition of the lattice homopolymer on a square lattice by calculating the exact partition function zeros. The exact partition function is obtained by enumerating the number of possible conformations for each energy value, and the exact distributions of the partition function zeros are found in the complex temperature plane by solving a polynomial equation. We observe that the locus of zeros closes in on the positive real axis as the chain length increases, providing the evidence for the onset of the collapse transition. By analyzing the scaling behavior of the first zero with the polymer length, we estimate the transition temperature and the crossover exponent.

cond-mat.stat-mech↗
arXiv2009

Yang-Lee Zeros of the Triangular Ising Antiferromagnets

Using both the exact enumeration method (microcanonical transfer matrix) for a small system (L = 9) and the Wang-Landau Monte Carlo algorithm for large systems to L = 30, we obtain the exact and approximate densities of states g(M,E), as a function of magnetization M and exchange energy E, for the triangular-lattice Ising model. Based on the density of states g(M,E), we investigate the phase transition properties of Yang-Lee zeros for the triangular Ising antiferromagnets and obtain the magnetic exponents at various temperatures.

cond-mat.stat-mech↗
arXiv2006

Density of Yang-Lee zeros for the Ising ferromagnet

The densities of Yang-Lee zeros for the Ising ferromagnet on the $L\times L$ square lattice are evaluated from the exact grand partition functions ($L=3\sim16$). The properties of the density of Yang-Lee zeros are discussed as a function of temperature $T$ and system size $L$. The three different classes of phase transitions for the Ising ferromagnet, first-order phase transition, second-order phase transition, and Yang-Lee edge singularity, are clearly distinguished by estimating the magnetic scaling exponent $y_h$ from the densities of zeros for finite-size systems. The divergence of the density of zeros at Yang-Lee edge in high temperatures (Yang-Lee edge singularity), which has been detected only by the series expansion until now for the square-lattice Ising ferromagnet, is obtained from the finite-size data. The identification of the orders of phase transitions in small systems is also discussed using the density of Yang-Lee zeros.

cond-mat.stat-mech↗
arXiv2003

Design of a Protein Potential Energy Landscape by Parameter Optimization

We propose an automated protocol for designing the energy landscape of a protein energy function by optimizing its parameters. The parameters are optimized so that not only the global minimum energy conformation becomes native-like, but also the conformations distinct from the native structure have higher energies than those close to the native one. We successfully apply our protocol to the parameter optimization of the UNRES potential energy, using the training set of betanova, 1fsd, the 36-residue subdomain of chicken villin headpiece (PDB ID 1vii), and the 10-55 residue fragment of staphylococcal protein A (PDB ID 1bdd). The new protocol of the parameter optimization shows better performance than earlier methods where only the difference between the lowest energies of native-like and non-native conformations was adjusted without considering various degrees of native-likeness of the conformations. We also perform jackknife tests on other proteins not included in the training set and obtain promising results. The results suggest that the parameters we obtained using the training set of the four proteins are transferable to other proteins to some extent.

cond-mat.soft↗
arXiv2003

Conformational space annealing and an off-lattice frustrated model protein

A global optimization method, conformational space annealing (CSA), is applied to study a 46-residue protein with the sequence B_9N_3(LB)_4N_3B_9N_3(LB)_5L, where B, L and N designate hydrophobic, hydrophilic, and neutral residues, respectively. The 46-residue BLN protein is folded into the native state of a four-stranded beta-barrel. It has been a challenging problem to locate the global minimum of the 46-residue BLN protein since the system is highly frustrated and consequently its energy landscape is quite rugged. The CSA successfully located the global minimum of the 46-mer for all 100 independent runs. The CPU time for CSA is about seventy times less than that for simulated annealing (SA), and its success rate (100 %) to find the global minimum is about eleven times higher. The amount of computational efforts used for CSA is also about ten times less than that of the best global optimization method yet applied to the 46-residue BLN protein, the quantum thermal annealing with renormalization. The 100 separate CSA runs produce the global minimum 100 times as well as other 5950 final conformations corresponding to a total of 2361 distinct local minima of the protein. Most of the final conformations have relatively small RMSD values from the global minimum, independent of their diverse energy values. Very close to the global minimum, there exist quasi-global-minima which are frequently obtained as one of the final answers from SA runs. We find that there exist two largest energy gaps between the quasi-global-minima and the other local minima. Once a SA run is trapped in one of these quasi-global-minima, it cannot be folded into the global minimum before crossing over the two large energy barriers, clearly demonstrating the reason for the poor success rate of SA.

cond-mat.stat-mech↗
arXiv2003

Folding Mechanism of Small Proteins

Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like conformations at appropriate temperatures. The results demonstrate that the folding mechanism is controlled not only by thermodynamic factors but also by kinetic factors: The way a protein folds into its native structure, is also determined by the convergence point of early folding trajectories, which cannot be obtained by the free energy surface.

cond-mat.stat-mech↗
arXiv2003

Yang-Lee zeros of the one-dimensional Q-state Potts model

The distributions of the Yang-Lee zeros of the ferromagnetic and antiferromagnetic Q-state Potts models in one dimension are studied for arbitrary Q and temperature. The Yang-Lee zeros of the Potts antiferromagnet have been fully investigated for the first time. The distributions of the Yang-Lee zeros show a variety of different shapes. Some of the Yang-Lee zeros lie on the positive real axis even for T>0. For the ferromagnetic model this happens only for Q<1, while there exist some zeros of the antiferromagnetic model on the positive real axis both for Q<1 and for Q>1.

cond-mat.stat-mech↗
arXiv2002

Partition function zeros of the Q-state Potts model on the simple-cubic lattice

The $Q$-state Potts model on the simple-cubic lattice is studied using the zeros of the exact partition function on a finite lattice. The critical behavior of the model in the ferromagnetic and antiferromagnetic phases is discussed based on the distribution of the zeros in the complex temperature plane. The characteristic exponents at complex-temperature singularities, which coexist with the physical critical points in the complex temperature plane for no magnetic field ($H_q=0$), are estimated using the low-temperature series expansion. We also study the partition function zeros of the Potts model for nonzero magnetic field. For $H_q>0$ the physical critical points disappear and the Fisher edge singularities appear in the complex temperature plane. The characteristic exponents at the Fisher edge singularities are calculated using the high-field, low-temperature series expansion. It seems that the Fisher edge singularity is related to the Yang-Lee edge singularity which appears in the complex magnetic-field plane for $T>T_c$.

cond-mat.stat-mech↗
arXiv2001

Density of states, Potts zeros, and Fisher zeros of the Q-state Potts model for continuous Q

The Q-state Potts model can be extended to noninteger and even complex Q in the FK representation. In the FK representation the partition function,Z(Q,a), is a polynomial in Q and v=a-1(a=e^-T) and the coefficients of this polynomial,Phi(b,c), are the number of graphs on the lattice consisting of b bonds and c connected clusters. We introduce the random-cluster transfer matrix to compute Phi exactly on finite square lattices. Given the FK representation of the partition function we begin by studying the critical Potts model Z_{CP}=Z(Q,a_c), where a_c=1+sqrt{Q}. We find a set of zeros in the complex w=sqrt{Q} plane that map to the Beraha numbers for real positive Q. We also identify tilde{Q}_c(L), the value of Q for a lattice of width L above which the locus of zeros in the complex p=v/sqrt{Q} plane lies on the unit circle. We find that 1/tilde{Q}_c->0 as 1/L->0. We then study zeros of the AF Potts model in the complex Q plane and determine Q_c(a), the largest value of Q for a fixed value of a below which there is AF order. We find excellent agreement with Q_c=(1-a)(a+3). We also investigate the locus of zeros of the FM Potts model in the complex Q plane and confirm that Q_c=(a-1)^2. We show that the edge singularity in the complex Q plane approaches Q_c as Q_c(L)~Q_c+AL^-y_q, and determine the scaling exponent y_q. Finally, by finite size scaling of the Fisher zeros near the AF critical point we determine the thermal exponent y_t as a function of Q in the range 2<Q<3. We find that y_t is a smooth function of Q and is well fit by y_t=(1+Au+Bu^2)/(C+Du) where u=u(Q). For Q=3 we find y_t~0.6; however if we include lattices up to L=12 we find y_t~0.50.

cond-mat.stat-mech↗
arXiv1999

Microcanonical Transfer Matrix and Yang-Lee Zeros of the Q-State Potts Model

The microcanonical transfer matrix and its extensions offer a new way of obtaining exact partition functions on finite two dimensional lattices. We show the density of the partition function zeros in the complex x- plane for the Ising model at $y=y_c$ and $y=0.5y_c$, and the density of the partition function zeros in the complex y-plane for the three-state Potts model.

cond-mat.stat-mech↗
arXiv1999

Exact results for the zeros of the partition function of the Potts model on finite lattices

The Yang-Lee zeros of the Q-state Potts model are investigated in 1, 2 and 3 dimensions. Analytical results derived from the transfer matrix for the one-dimensional model reveal a systematic behavior of the locus of zeros as a function of Q. For 1 2 they lie outside the unit circle for finite temperature. In the special case Q=2 the zeros lie exactly on the unit circle as proved by Lee and Yang. In two and three dimensions the zeros are calculated numerically and behave in the same way. Results are also presented for the critical line of the Potts model in an external field as determined from the zeros of the partition function in the complex temperature plane.

cond-mat.stat-mech↗
arXiv1999

Partition function zeros of the Q-state Potts model for non-integer Q

The distribution of the zeros of the partition function in the complex temperature plane (Fisher zeros) of the two-dimensional Q-state Potts model is studied for non-integer Q. On $L\times L$ self-dual lattices studied ($L\le8$), no Fisher zero lies on the unit circle $p_0=e^{iθ}$ in the complex $p=(e^{βJ}-1)/\sqrt{Q}$ plane for Q<1, while some of the Fisher zeros lie on the unit circle for Q>1 and the number of such zeros increases with increasing Q. The ferromagnetic and antiferromagnetic properties of the Potts model are investigated using the distribution of the Fisher zeros. For the Potts ferromagnet we verify the den Nijs formula for the thermal exponent $y_t$. For the Potts antiferromagnet we also verify the Baxter conjecture for the critical temperature and present new results for the thermal exponents in the range 0<Q<3.

cond-mat.stat-mech↗
arXiv1998

Microcanonical Transfer Matrix Study of the Q-state Potts Model

The microcanonical transfer matrix is used to study the zeros of the partition function of the Q-state Potts model. Results are presented for the Yang-Lee zeros of the 3-state model, the Fisher zeros of the 3-state model in an external field $H_q<0$, and the spontaneous magnetization of the 2-state model. In addition, we are able to calculate the ground-state entropy of the 3-state model and find $s_0=0.43153(3)$ in excellent agreement with the exact value, 0.43152...

cond-mat.stat-mech↗
arXiv1998

Yang-Lee zeros of the Q-state Potts model in the complex magnetic-field plane

The microcanonical transfer matrix is used to study the distribution of Yang-Lee zeros of the $Q$-state Potts model in the complex magnetic-field ($x=e^{βh}$) plane for the first time. Finite size scaling suggests that at (and below) the critical temperature the zeros lie close to, but not on, the unit circle with the two exceptions of the critical point $x=1$ ($h=0$) itself and the zeros in the limit T=0.

cond-mat.stat-mech↗