Protein loop modeling by using fragment assembly and analytical loop closure

Lee, Julian,Lee, Dongseon,Park, Hahnbeom,Coutsias, Evangelos A.,Seok, Chaok Wiley Subscription Services, Inc., A Wiley Company 2010 Proteins Vol.78 No.16

<P><B>Abstract</B></P><P>Protein loops are often involved in important biological functions such as molecular recognition, signal transduction, or enzymatic action. The three dimensional structures of loops can provide essential information for understanding molecular mechanisms behind protein functions. In this article, we develop a novel method for protein loop modeling, where the loop conformations are generated by fragment assembly and analytical loop closure. The fragment assembly method reduces the conformational space drastically, and the analytical loop closure method finds the geometrically consistent loop conformations efficiently. We also derive an analytic formula for the gradient of any analytical function of dihedral angles in the space of closed loops. The gradient can be used to optimize various restraints derived from experiments or databases, for example restraints for preferential interactions between specific residues or for preferred backbone angles. We demonstrate that the current loop modeling method outperforms previous methods that employ residue‐based torsion angle maps or different loop closure strategies when tested on two sets of loop targets of lengths ranging from 4 to 12. Proteins 2010. © 2010 Wiley‐Liss, Inc.</P>

Segmented TMA T-loop spring에 의한 견치 후방이동시의 응력분포에 관한 광탄성법적 분석

유필식,윤영주,김광원 대한치과교정학회 2001 대한치과교정학회지 Vol.31 No.2

본 연구는 교정치료를 시행함에 있어 전치부 crowding을 해결하기 위한 견치의 단독견인 방법중 새로운 segmented TMA T-loop spring으로 견치 후방견인시 치근단과 그 주위 치조골에서의 응력상태를 알아보기 위해 시행되었다. PL-3 epoxy resin으로 광탄성 모형을 제작하여 B/L ratio가 0.25, 0.5, 0.75인 위치로 T-loop을 위치시키고 각 위치에서 5mm, 3mm, 1mm activation하였다. 이후 광탄성 응력 해석장치를 이용하여 견치견인시 치근단과 그 주위 치조골에서의 초기 응력 상태를 광탄성법으로 분석한 바, 다음과 같은 결론을 얻었다 1.T-loop 위치에 상관없이 activation량이 감소할수록 상악 1소구치 발치부위에 응력이 감소하였고 상악 1대구치의 함입응력은 증가하였다. 2.5mm activation시 T-loop위치가 구치부쪽으로 이동할수록 상악 1소구치 발치부위에 응력이 증가하였다. 3.3mm activation시 T-loop위치가 구치부쪽으로 이동할수록 상악 1소구치 발치부위와 상악 1대구치 협측 근심치근 근심면하방 1/2부위에 응력이 증가하였다. 4.1mm activation시 T-loop위치가 견치쪽으로 이동할수록 상악 견치의 근심치근면 상방과 치근첨 하방의 응력이 증가하였다. 5.B/L ratio가 0.25이고 3mm activation시 상악견치의 치체이동이 나타났다. 이상의 결과를 종합해볼 때 segmented T-loop spring의 근,원심 위치와 activation량을 조절하여 원하는 치아이동과 고정원 조절이 가능하다고 사료된다. The segmented TMA T-loop spring, used for reciprocal space closure and described by Burstone, was used to achievebodily movement of canine. Photoelastic analysis is a technique for the transformation of Internal stress into visiblelight patterns. The two-dimensional photoelastic stress analysis was performed, and stress distribution was recorded byphotography. The purpose of this study was to visualize photoelastically the distribution of forces transmitted to the alveolus and surrounding structures using new segmented TMA T-loop spring for canine retraction. The resuts were as follows: 1.Decreased activation produced decreased stress of upper 1st. premolar extraction site and increased intrusive stress of upper 1st. molar, regardless of T-loop position. 2.At 5mm activation, More posterior positioning of T-loop produced an increased stress in upper 1st. premolar extraction site. 3.At 3mm activation, More posterior positioning of T-loop produced an increased stress in upper 1st. premolar extraction site and menial lower half of upper 1st. molar mesio-buccal root. 4.At 1mm activation, More anterior positioning of T-loop produced an increased stress in upper menial and blew apex area of upper canine root. 5.0.25 B/L ratio and 3mm activation produced bodily movement of canine. To summarize, desired tooth movement and anchorage requirement is possible byaltering the activation and mesio-distal position of the T-loop spring.

변환요소에 따른 LOOPED WIRE의 탄성 변화에 관한 연구

나용인,김상철 대한치과교정학회 1995 대한치과교정학회지 Vol.25 No.3

Canine retraction spring과 같은 looped wire에서, 각 변환요소에 따라 변하는 탄성 정도를 알아보기 위하여, wire의 재료, 굵기, loop에 소요된 길이, loop의 모양, gabling의 여부 등 5가지의 변환요소를 설정하여, 각 wire activation시의 탄성을 range, force, stiffness등의 면에서 알아보고자 하였다. wire의 재료적인 면에서 Hi-T (Unitek Co.)와 blue Elgiloy (Rocky Mountain Orthodontics)를 선택하였으며, 굵기로는 .016˝x .022˝와 .018˝x .025˝를 선택하였다. loop 자체에 소요된 wire 길이를 15mm와 20mm의 두가지로, loop의 모양을 vertical open loop과 vertical closed loop의 두가지로, gabling의 양을 0˚와 30˚의 두가지로 하여 각각 제작하였다. 따라서 wire의 재료와 굵기, loop의 길이와 모양, gabling의 5가지 변환요소에 따라 32개군으로 구분되었으며, 각 군의 시료수는 8개씩으로, 총 256개의 시료를 대상으로 하였다. Instron(4202, Instron Co, USA)을 사용하여 각 시료의 하중변형곡선을 얻었으며 elastic limit에서의 하중과 변형을 계측하고, 그때의 stiffness(force/range)를 산출하여, ANOVA 등의 통계처리로 32개군 간의 상관성을 조사하였다. 그 결과 wire의 재료, 굵기, loop의 길이, 모양, gabling 모두가 looped wire의 하중 변형도에 유의한 영향을 미치는 것을 관찰할 수 있었으며, 탄성범위에서의 force는 Hi-T, .016˝x .022˝, loop 길이 20mm, open loop, non-gable군에서 가장 적었으며, blue Elgiloy, .018˝x .025˝, loop 길이 15mm, closed loop, non-gable군에서 가장 컸다. 탄성범위에서의 range는 Hi-T, .018˝x .025˝, loop 길이 15mm, open loop, non-gable군이 가장 적었으며, Hi-T, .016˝x .022˝, loop 길이 20mm, closed loop, gable군에서 가장 컸다. 또한 Looped wire의 탄성에 가장 큰 영향을 미치는 변환요소는 loop의 모양과 길이였으며, gabling의 영향이 가장 적었다. The purpose of this study was to evaluate and compare the effect of the variable factors of wire on the elastic properties of looped rectangular wire. Five variable factors were presented - material(Hi-T, blue Elgiloy), wire size(016˝x .022˝, .018˝x .025˝), loop length(15mm, 20mm), loop configuration(open loop, closed loop), gabling (non-gable, gable). So, the total 256 specimens were divided into 32 groups, and each of those was pulled on Instron testing machine. The load-deflection curve of each wire was obtained, from which force, range in elastic limit, and stiffness were computed and analyzed statistically. The results were obtained as follows : 1. All of the variable factors - wire material, size, loop length, loop configuration, and gabling - took a significant effect on load-deflection rate of looped wire. 2. The force at elastic limit was the smallest in the group of Hi-T, 016˝x.022˝, 20mm loop length, open loop, non-gable, and the largest in the group of blue Elgiloy, .018˝x.025˝, 15mm loop length, closed loop, non-gable. 3. The range at elastic limit was the smallest in the group of Hi-T, .018˝x.025˝, 15mm loop length, open loop, non-gable, and the largest in the group of HI-T, 016˝x.022˝, 20mm loop length, closed loop, gable. 4. Loop configuration and loop length were most effective factors on the elastic properties of looped wires, and gabling was the least effective.

Space closing loop에 의해 야기되는 상악 절치부 이동양상에 관한 역학적 연구

민상홍,윤영주,김광원 대한치과교정학회 1995 대한치과교정학회지 Vol.25 No.2

이 연구는 다양한 형태의 closing loops의 activation에 따른 치주조직에서의 응력분포를 평가하고 상악 절치의 이동 양상을 예측하기 위하여 3차원 유한요소법에 의하여 시행되었다. 동시에 상악 절치의 견인시 사용되는 bull loop, key-hole loop, T-loop, combination loop 그리고 asymmetrical T-loop도 3차원 유한요소법에 의해 분석되었다. 이 연구로부터 얻어진 결과는 다음과 같다. 1. 여러가지 형태의 공간폐쇄용 루프중 bull loop에서 가장 큰 수평력을 나타냈으며, key-hole, combination loop, T-loop 순이었다. 이들 모두 치아이동의 양상은 uncontrolled tipping을 나타냈다. 2. Asymmetrical TMA T-loop에서는 수령력이 현저히 감소하였으며, 절치부위에 함입력이 나타났다. 3. 절치부에서 torque의 증가에 따라 모멘트가 증가하였고, 선형적인 증가를 보였다. 4. 모멘트의 증가에 따라 치아의 초기 이동양상은 uncontrolled tipping에서 치근이동 양상으로 변화되었다. This study was performed, by Finite Element Method, to evaluate the stress distribution on the periodontal tissue according to activation of the various closing loops and to predict the pattern of movement of maxillary incisors. At the same time, bull loop, key-hole loop, T-loop, combination loop and asymmetrical T-loop which were used for retraction of maxillary incisors was analysed by Finite Element Method. The following results were obtained 1. Horizontal force was the greatest in bull loop, the followed by key-hole loop, combination loop, T-loop and initial tooth movement exhibited uncontrolled tipping. 2. Horizontal force in asymmetrical T-loop compared to other closing loops was remarkably decreased, and the intrusive force on the incisors occurred. 3. As torque was increased, the moment was increased as a linear increment. 4. As moment was increased, initial movement of tooth changed to root movement from uncontrolled tipping.

편리하게 사용할 수 있는 BOOST CONVERTER 제어기 설계 기법

박해찬,김일송 사단법인 인문사회과학기술융합학회 2016 예술인문사회융합멀티미디어논문지 Vol.6 No.9

This purpose of this paper is to design a block diagram of the Two-loop system controller using the MATLAB SISO TOOL. In this paper, Controllers are using PI Control method which is used in control methods. The PI Control decreases steady-state error of output respond and is easy. The block diagram of Boost Converter Controller consists of Two-loop system which is inner loop in outer loop. The inner loop is current controller and the outer loop is voltage controller. Generally, the gains of current controller and voltage controller designed each with a Single-loop. Even many difference between inner loop frequency and outer loop frequency, it is influence on a small scale to each other. The gain value can easily be obtained regardless z-conversion and s-domain using the MATLAB SISO TOOL. It does not need many calculation and can modify in possible realtime. This advantages using the MATLAB SISO TOOL are verified by computer simulation(PSIM). 본 연구는 Two-loop 시스템 제어기를 MATLAB SISO TOOL을 사용하여 설계기법을 제시한다. 부스트 컨버터는 inner loop와 outer loop로 구성된다. 전류제어기인 inner loop와 전압제어기인 outer loop의 제어기는 일반적으로 많이 사용하는 PI 제어를 사용한다. 일반적으로 전류제어기와 전압제어기의 게인 설계는 따로 설계한다. 주파수의 차이를 많이 주면 서로 영향을 많이 받지 않기 때문에 각각 Single-loop로 하여 설계하는 것이 대부분이다. 그러나 본 논문에서는 서로 영향 주는 부분까지 생각하여 boost converter의 제어기를 Single-loop로 설계하지 않고 MATLAB SISO TOOL을 사용하여 Two-loop로 설계하였다. MATLAB SISO TOOL은 많은 여러 장점이 있다. 많은 계산과정의 생략과 s-domain과 z-domain에서의 구분 없이 이용 가능하기 때문에 실제로 사용하기도 매우 편리고 정확하게 설계할 수 있고 리얼타임으로 실시간 수정이 가능하다는 장점이 있다. 본 논문에서는 MATLAB SISO TOOL을 사용방법과 이를 증명하기 위해 컴퓨터 시뮬레이션인 PSIM을 사용하여 증명하였다.

Loop형 스프링클러 설비의 수리계산 방법에 대한 제시

정기신 한국화재소방학회 2015 한국화재소방학회논문지 Vol.29 No.1

There are three kinds of design method of the fire sprinkler systems. Grid type is connected all branch as a trapezoid. Loop type is connected cross-mains like circle. The last one is a tree type most commonly used. Grid type needs computerprogram to calculate the friction loss and flow rate apart from very simple form. In loop type, manual calculation ispossible. Design engineer can draw up and calculate the demands without computer program. Because water supplies twodirection in loop type, friction loss is smaller than tree type. Water distribution in operation area is uniform because of thesmall differences of sprinklers discharge pressure. Loop type is superior to tree type in respect of total pressure and flowrate. Using the small diameter pipe, the labor and construction cost will be decreased in the end. Loop type sprinklerdesign is rarely laid out because design engineers don’t know the method. This paper is intended to inform that the looptype is better than the tree type in performance and economic point of view. And also this paper intend to use the looptype easily and widely. 스프링클러 설비의 설계방법은 크게 3가지로 분류한다. 가지관을 서로 연결하여 사다리형태로 배관을 설치하는 Grid형과 가지관은 연결하지 않고 교차배관만을 연결하는 Loop형 그리고 가장 일반적으로 사용되는 Tree형이 있다. 이 중Grid형은 아주 간단한 것을 제외하고는 컴퓨터프로그램으로 마찰손실을 계산하여야 하지만 Loop형의 경우는 프로그램의 도움 없이 설계자가 직접 계산하여 마찰손실에 따른 필요압력과 소요유량을 산출할 수 있다. Loop형 설비의 경우소화수 공급이 2방향으로 분리되어 마찰손실이 작아지고 헤드간 방출압력의 차이가 Tree형보다 작게 되어 살수분포가 우수하게 되며 작은 마찰손실에 의한 소구경의 배관을 사용하여 자재비와 인건비가 절감되므로 Loop형에 의한 스프링클러의 설계가 Tree형 설비에 비해 성능과 경제성에서 우수한 설계 방법이다. 하지만 Loop형 설비의 설계는 설계방법이잘 알려져 있지 않아 거의 이루어지지 않고 있다. 본 논문에서는 Tree형 보다 우수한 Loop형 설비의 설계방법을 설명하여 많은 설계자가 성능과 경제면에서 우수한 Loop형 설계를 쉽게, 널리 사용하게 하고자 하였다.

A Loop Transformation for Parallelism from Single Loops

Sam Jin Jeong 한국콘텐츠학회(IJOC) 2006 International Journal of Contents Vol.2 No.4

This paper describes several loop partitioning techniques such as loop splitting method by thresholds and Polychronopoulos' loop splitting method for exploiting parallelism from single loop which already developed. We propose improved loop splitting method for maximizing parallelism of single loops with non-constant dependence distances. By using the distance for the source of the first dependence, and by our defined theorems, we present generalized and optimal algorithms for single loops with non-uniform dependences. The algorithms generalize how to transform general single loops into parallel loops.

A Loop Transformation for Parallelism from Single Loops

Jeong, Sam-Jin The Korea Contents Association 2006 International Journal of Contents Vol.2 No.4

This paper describes several loop partitioning techniques such as loop splitting method by thresholds and Polychronopoulos' loop splitting method for exploiting parallelism from single loop which already developed. We propose improved loop splitting method for maximizing parallelism of single loops with non-constant dependence distances. By using the distance for the source of the first dependence, and by our defined theorems, we present generalized and optimal algorithms for single loops with non-uniform dependences. The algorithms generalize how to transform general single loops into parallel loops.

Iterative Design of the Reduced-order Controller for the H<SUB>∞</SUB> Loop-shaping Method under Open-loop Magnitude Constraints and Application to Gain-scheduling Control

Masashi Yamamoto,Kazuhiro Yubai,Junji Hirai 제어로봇시스템학회 2011 제어로봇시스템학회 국제학술대회 논문집 Vol.2011 No.10

The H∞ loop-shaping method is known to be an effective control method, however, it has two drawbacks. The first is that it is difficult to select appropriate loop-shaping weights, and the second is that the resulting controller is very complex. For the first drawback, Lanzon has proposed a suboptimal loop-shaping weight design method. It is formulated as a generalized eigenvalue minimization problem. This suboptimal loop-shaping weight design method provides high order weights, emphasizing the second drawback. To resolve these two drawbacks, a reduced-order loop-shaping weight and a stabilizing controller design methods are proposed in this paper. In the proposed method, the weight structure is first fixed, and the weight is decomposed into the frequency-dependent vector and the parameter matrices characterizing the loop-shaping weight. Since the open-loop constraints are represented as linear matrix inequalities with respect to the parameter matrices, the reduced-order loop-shaping weight design problem is formulated as a generalized eigenvalue minimization problem as well as the Lanzon’s suboptimal loop-shaping weight design method. Moreover, the stabilizing controller is first fixed to the initial stabilizing controller. The initial stabilizing controller is designed for the shaped plant obtained by the reduced-order weight design, by solving linear matrix inequalities. The proposed method can reduce the designer’s burden. The effectiveness of the proposed method is verified experimentally by the gain-scheduling control of a vertical-type inverted pendulum system.

칼만필터 기반의 통합 GPS 수신기 추적루프 설계

송종화(Jong-Hwa Song),지규인(Gyu-In Jee),김광훈(Kwang-Hoon Kim) 제어로봇시스템학회 2008 제어·로봇·시스템학회 논문지 Vol.14 No.9

The GPS tracking loop consists of three parts in general: discriminator, loop filter and DCO (Digitally Controlled Oscillator). The loop filter is the main part of the tracking loop designed to ensure a good tracking performance. Generally, the loop filter is designed using classical PI(Proportional Integral) control. Although the carrier Doppler and code Doppler are generated by the same relative movement between the satellite and the user, often, the loop filters for each tracking loop are designed separately and independently. Sometimes, they are used in a combined manner such as carrier aided code tracking, FLL assisted PLL, etc. For better GPS signal tracking, we need to design the FLL/PLL/DLL altogether optimally. The purpose of this paper is to design a GPS receiver tracking loop based on the Kalman filter in a combined manner. Also, the proposed GPS receiver tracking loop is compared with a conventional tracking loop in terms of the transfer function and the DCO input.. This paper shows that conventional tracking loop is equal to the Kalman filter based tracking loop.