Study of Ideal Gas Fluid Mechanics by Using One-Particle Simulations

이주련 한국물리학회 2008 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.53 No.6

Fluid mechanics concerns itself with the study of various properties of uids, where a fluid is regarded as a continuous medium. Although the dynamic equations for louids can be derived with various simplifying assumptions, it is difficult to obtain analytic solutions in general. In this work, a novel method for simulating a two-dimensional ideal gas is developed. The method is based on repetition of one-particle simulations, utilizing the fact that the particles forming an ideal gas are noninteracting by definition. As an example of a nontrivial application of the method, steady flow in a pipe with varying widths is simulated. The relation between the pressure and the fiuid velocity can be investigated. In particular, one can show that the velocity is increased and the pressure is decreased inside narrow regions, without deriving Bernoulli equation under the assumption of constant entropy per unit mass. If an explicit particle description is used instead of a continuous fluid, the origin of the low pressure at high velocity can be understood more intuitively. Fluid mechanics concerns itself with the study of various properties of uids, where a fluid is regarded as a continuous medium. Although the dynamic equations for louids can be derived with various simplifying assumptions, it is difficult to obtain analytic solutions in general. In this work, a novel method for simulating a two-dimensional ideal gas is developed. The method is based on repetition of one-particle simulations, utilizing the fact that the particles forming an ideal gas are noninteracting by definition. As an example of a nontrivial application of the method, steady flow in a pipe with varying widths is simulated. The relation between the pressure and the fiuid velocity can be investigated. In particular, one can show that the velocity is increased and the pressure is decreased inside narrow regions, without deriving Bernoulli equation under the assumption of constant entropy per unit mass. If an explicit particle description is used instead of a continuous fluid, the origin of the low pressure at high velocity can be understood more intuitively.

Analytic Form of the Phase Boundary for a Self-Regulatory Gene Circuit with Baseline Production

이주련 한국물리학회 2019 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.74 No.10

The feedback loop forms an important basic module of a genetic regulatory network. The dynamics of a gene regulatory network is described by a deterministic rate equation in the parameter region where the stochastic fluctuation can be neglected. In this work, I consider the deterministic rate equation for the simplest positive feedback loop with cooperative binding and baseline production and obtain an analytic expression for the phase boundary between the monostable and the bistable regions. The result is consistent with those in previous literature and puts them on a solid theoretical ground.

Protein Structure Prediction Using a Hybrid Energy Function and an Exact Enumeration

이주련,조광휘 한국물리학회 2008 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.53 No.2

We develop a protein structure prediction method that utilizes fragment assembly and a hybrid energy function. In a fragment assembly method, the local structure of the backbone is obtained from a structural database by using similarity of sequence features, in contrast to a pure physicsbased method in which all dihedral angles are allowed to vary continuously. Since the conformational space for the backbone is finite, we generate all possible conformations and vary only the side-chain dihedral angles for each of them. The conformations are scored using a hybrid energy function, where all the backbone atoms are described explicitly, but the side chain is modeled as a few interaction centers. We perform a test prediction on four proteins, 1l2y, 1e0l, 1bdd and 1bk2, to demonstrate the feasibility of protein structure prediction based on exact enumeration.

Real Value Prediction of Solvent Accessibility by Using the k-Nearest Neighbor Method

이주련 한국물리학회 2009 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.54 No.1

Prediction of a protein residue solvent accessibility gives useful guidance for the prediction of the full three-dimensional structure and function of a protein. Although solvent accessibility is a continuous quantity, it has been predicted mostly by assigning each residue into one of two or three classes by using various threshold values. Predictions of real values of solvent accessibility have been attempted only recently, but the k-nearest neighbor method has never been used. In this work, we apply a simple implementation of the k-nearest neighbor method to the real-value prediction of solvent accessibility, using PSI-BLAST profiles as feature vectors and obtain results comparable to those obtained by using other methods.

Analytic Model of the Schottky Anomaly and Phase Transition

이주련 한국물리학회 2015 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.67 No.7

The Schottky anomaly is a peak in the specific heat at low temperatures without divergence, in contrast to a phase transition which is characterized by a singularity of a physical quantity. A model with the analytic form of a density function, where both the phase transition and the Schottky anomaly appear depending on the limit of the model parameters, is presented. The model allows a unified analytic treatment of the phase transition and the Schottky anomaly.

조각 맞추기를 활용한 단백질 고리의 3차원 얼개 생성 알고리즘

이주련 한국물리학회 2010 새물리 Vol.60 No.2

Fragment assembly is a protein structure prediction method in which the local structure is extracted from a database by applying a pattern recognition algorithm to the protein sequence, and only the global structure is obtained by minimizing the free energy function. In order for the protein structure prediction based on fragment assembly to be successful, it should be possible to obtain native-like structure from fragment assembly. In this work, we attempted to generate native-like structures for 382 protein loop fragment whose lengths ranged from 3 to 12. First, in order to assess the ability of the method to generate native-like structures,we constructed a function quantifying the structural distance from the native structure and searched native-like structure by minimizing this function. We also found that the performance was the best when the fragment length was 7. In order to assess the performance for real predictions where the native structure is not known, we also stochastically generated 4000 conformations for each loop and found that the native-like conformation was included in the population. The results suggest that by employing an accurate free energy function, the structures of protein loops up to a length of 12 may be predicted with high accuracy. 조각 맞추기는 단백질의 3차원 얼개를 예측하기 위한 방법으로서,국소적인 얼개는 서열에 패턴식별 알고리즘을 적용하여데이타베이스로부터 추출하고 전체적인 얼개만 자유 에너지 함수를최소화하여 구하는 방법이다. 조각 맞추기 방법을 통해 단백질의 얼개를성공적으로 예측하기 위해서는 조각들을 짜맞추어서 고유 얼개에 충분히가까운 모형이 나와야 한다. 이 논문에서는 조각 맞추기 방법을 길이3-12인 단백질 고리의 382개의 얼개들을 생성하는 데에 적용하였다. 우선데이타베이스에서 얻은 조각들을 짜맞추어서 실제 고유 얼개와 얼마나가까운 모형 얼개를 얻을 수 있는지를 살펴보았는데, 이를 위해 실제고유 얼개와 모형 얼개와의 유사성을 함수로 만들어 최소화하였다. 조각길이는 7로 할 때 성능이 가장 뛰어나며, 고유 얼개와 거의 일치하는모형 얼개를 만들어낼 수 있었다. 고유 얼개를 모르는 상태에서 실제로단백질 얼개를 예측할 때의 성능을 검증해보기 위하여 각 고리마다4000개씩의 얼개들을 확률적으로 생성하여, 이 중에 실제 고유 얼개에가까운 것이 있는 것을 볼 수 있었다. 이러한 결과들을 통해, 정확한자유 에너지 함수를 활용한다면 조각 맞추기를 통해 최소한 길이12이하인 단백질 고리의 얼개는 상당한 정확도로 예측할 수 있다는 것을알게 되었다.

Finite-size Phase Diagram of the Wako-Saitˆo-Mu˜noz-Eaton -Helix Model

이주련 한국물리학회 2015 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.67 No.7

The folding transition of a Wako-Saitˆo-Mu˜noz-Eaton (WSME) -helix model is studied by using several methods. The transition temperature of a finite-size system is defined by using the extrapolation of partition function zeros, a microcanonical analysis, and the average fraction of unbroken native contacts, and the result is applied to a WSME -helix model. The analysis results in a phase diagram for the helix, whose boundaries depend on the method used for defining the transition temperature. However, the qualitative behaviors are quite similar for all of these methods, and any definition can lead to a reasonable phase diagram for a finite-size system.

Analysis of Precision and Accuracy in a Simple Model of Machine Learning

이주련 한국물리학회 2017 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.71 No.12

Machine learning is a procedure where a model for the world is constructed from a training set of examples. It is important that the model should capture relevant features of the training set, and at the same time make correct prediction for examples not included in the training set. I consider the polynomial regression, the simplest method of learning, and analyze the accuracy and precision for di®erent levels of the model complexity.

Low-temperature Behavior of the Finite-size One-dimensional Ising Model and the Partition Function Zeros

이주련 한국물리학회 2014 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.65 No.5

In contrast to an infinite chain, the low-temperature expansion of a one-dimensional free-fieldIsing model has a strong dependence on boundary conditions. I derive an explicit formula for theleading term of the expansion both under open and periodic boundary conditions and show thatthey are related to different distributions of the partition function zeros on the complex temperatureplane. In particular, when a periodic boundary condition is imposed, the leading coefficient of theexpansion grows with increasing size of the chain, due to the zeros approaching the origin.

제임스 조이스의 『젊은 예술가의 초상』에 나타난 조이스의 여성관 연구

이주련,강문순 한남대학교 교육연구소 2005 교육연구 Vol.12 No.2

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