• Bulletin of the Korean Chemical Society
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• v.33 no.11
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• pp.3597-3600
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• 2012

Thrombin binding aptamter (TBA-15) is a 15-mer guanine-rich oligonucleotide. This DNA apamer specifically binds to the thrombin protein involved in blood coagulation. Using extensive umbrella sampling molecular dynamics simulation method at all atom level, we investigated the potential of mean force (PMF) upon pulling the DNA aptamer from the binding mode of aptamer/thrombin complex. From this calculation, the free energy cost for a full dissociation of this aptamer/protein complex is 17 kcal/mol, indicating a substantial binding affinity of TBA-15. Interestingly, this PMF reveals noticeable plateau regions along the pulling coordinate. Possible structural changes of this complex in the plateau were investigated in details.

• Proceedings of the KSME Conference
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• 2002.08a
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• pp.373-376
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• 2002

The drift force acting on a floating OWC chamber in waves is studied taking account of fluctuating air pressure in the air chamber. A velocity potential in the water due to the free surface oscillating pressure patch is added to the conventional radiation-diffraction potential problem. The potential problem inside the chamber is formulated by making use of the Green integral equation associated with the Rankine Green function while the outer problem with the Kelvin Green function. The drift forces as well as the chamber motions are calculated taking account of the air pressure in the chamber.

• International Journal of Naval Architecture and Ocean Engineering
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• v.12 no.1
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• pp.367-375
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• 2020

This paper presents an integrated analysis about dynamic performance of a Floating Offshore Wind Turbine (FOWT) OC4 DeepCwind with semi-submersible platform under real sea environment. The emphasis of this paper is to investigate how the wave mean drift force and slow-drift wave excitation load (Quadratic transfer function, namely QTF) influence the platform motions, mooring line tension and tower base bending moments. Second order potential theory is being used for computing linear and nonlinear wave effects, including first order wave force, mean drift force and slow-drift excitation loads. Morison model is utilized to account the viscous effect from fluid. This approach considers floating wind turbine as an integrated coupled system. Two time-domain solvers, SIMA (SIMO/RIFLEX/AERODYN) and FAST are being chosen to analyze the global response of the integrated coupled system under small, moderate and severe sea condition. Results show that second order mean drift force and slow-drift force will drift the floater away along wave propagation direction. At the same time, slow-drift force has larger effect than mean drift force. Also tension of the mooring line at fairlead and tower base loads are increased accordingly in all sea conditions under investigation.

• Journal of Ocean Engineering and Technology
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• v.24 no.6
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• pp.1-6
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• 2010

A far field approximate solution of the slowly varying force on a 3 dimensional offshore structure in gravity ocean waves is presented. The first order potential, or at least the far field form of the Kochin function, of each frequency wave is assumed to be known. The momentum flux of the fluid domain is formulated to find the time variant force acting on the floating body in bichromatic waves. The second order difference frequency force is identified and extracted from the time variant force. The final solution is expressed as the circular integration of the product of Kochin functions. The limiting form of the slowly varying force is identical to the mean drift force. It shows that the slowly varying force components caused by the body disturbance potential can be evaluated at the far field.

• Membrane Journal
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• v.28 no.6
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• pp.388-394
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• 2018

Carbon nanotube (CNT) based membranes are promising candidates for separation membranes by showing high water transport rate and ion rejection rate according to their radii. The ion selectivity is an important factor to discover the full potential of CNT membranes, and it is affected by the functionalization of CNTs. With multivalent/size ion mixtures, the ion selectivity is affected by not only ion-functional groups interaction but also ion-ion interactions and ion size exclusion in a complex manner. In this study, molecular dynamics simulations are performed to study the ion selectivity of functionalized carbon nanotubes when multivalent/size ions are contained. The permeation energy barriers are calculated by plotting potential of mean force profiles, and various factors, such as CNT size and partial charges, affecting ion selectivity are investigated. The results presented here will be useful for designing CNT membranes for ion separation, biomimetic ion channels, etc.

• Journal of Ocean Engineering and Technology
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• v.11 no.2
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• pp.91-99
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• 1997

This paper presents theoretical formulations and numerical computations for predicting first-and second-order hydrodynamic force on a ship advvancing in waves. The theoretical formulation leads to linearized radiation and diffration problems solving the three-dimensional Green function integral equations over the mean wetted body surface. Green function representing a translating and pulsating source potantial for infinite water depth is used. In order to solve integral equations for three dimentional flows using Green function efficiently, the Hoff's method is adopted for numerical calculation of the Green function. Based on the first-order solution, the mean seconder-order forces and moments are obtained by directly integrating second-order pressure over the mean wetted body surface. The calculated items are carried out for analyzing the seakeeping characteristics of Series 60. The calculated items are hydrodynamic coefficients, wave exciting forces, frequency response functions and addd resistance in waves.

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.911-916
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• 2012

Ion selectivity in a simple cyclic peptide nanotube, composed of four cyclo[-(D-Ala-Glu-D-Ala-Gln)$_2-$] units, is investigated by calculating the PMF profiles of $Na^+$, $K^+$, and $Cl^-$ ions permeating through the peptide nanotube in water. The final PMF profiles of the ions obtained from the umbrella sampling (US) method show an excellent agreement with those from the thermodynamic integration (TI) method. The PMF profiles of $Na^+$ and $K^+$ display free energy wells while the PMF curve of $Cl^-$ features free energy barriers, indicating the selectivity of the cyclic peptide nanotube to cations. Decomposition of the total mean force into the contribution from each component in the system is also accomplished by using the TI method. The mean force decomposition profiles of $Na^+$ and $K^+$ demonstrate that the dehydration free energy barriers by water molecules near the channel entrance and inside the channel are completely compensated for by attractive electrostatic interactions between the cations and carbonyl oxygens in the nanotube. In the case of $Cl^-$, the dehydration free energy barriers are not eliminated by an interaction between the anion and the peptide nanotube, leading to the high free energy barriers in the PMF profile. Calculations of the coordination numbers of the ions with oxygen atoms pertaining to either water molecules or carbonyl groups in the peptide nanotube reveal that the stabilization of the cations in the midplane regions of the nanotube arises from the favorable interaction of the cations with the negatively charged carbonyl oxygens.

• The Transactions of The Korean Institute of Electrical Engineers
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• v.56 no.3
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• pp.632-640
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• 2007

The low force estimation method of skeletal muscle was proposed by using ICA(independent component analysis) and neuro-transmission model. An EMG decomposition is the procedure by which the signal is classified into its constituent MUAP(motor unit action potential). The force index of electromyography was due to the generation of MUAP. To estimate low force, current analysis technique, such as RMS(root mean square) and MAV(mean absolute value), have not been shown to provide direct measures of the number and timing of motoneurons firing or their firing frequencies, but are used due to lack of other options. In this paper, the method based on ICA and chemical signal transmission mechanism from neuron to muscle was proposed. The force generation model consists of two linear, first-order low pass filters separated by a static non-linearity. The model takes a modulated IPI(inter pulse interval) as input and produces isometric force as output. Both the step and random train were applied to the neuro-transmission model. As a results, the ICA has shown remarkable enhancement by finding a hidden MAUP from the original superimposed EMG signal and estimating accurate IPI. And the proposed estimation technique shows good agreements with the low force measured comparing with RMS and MAV method to the input patterns.

• 한국기계연구소 소보
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• s.14
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• pp.135-144
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• 1985

A method is described to obtain the first order force and second order steady force on the fixed two dimensional submerged or semisubmerged cylinders at infinite depth of water due to regular waves. The first order diffraction wave velocity potential which describes the flow diffracted by a body is obtained numerically using source distribution method on the mean wetted surface. And a technique to remove the irregular frequency phenomena of the source distribution method is also applied. The second order steady force is calculates by means of direct integration of the pressures on the body as derived from the first order velocity potential and is also computed by means of reflection wave height derives from momentum conservation theory. The results are compared with those of published works, and show good agreement.

• Bulletin of the Society of Naval Architects of Korea
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• v.23 no.2
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• pp.1-13
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• 1986

The nonlinear hydrodynamic forces acting on a two-dimensional circular cylinder, oscillating with large amplitude in the free surface, are calculated by using the Semi-Lagrangian Time-Step-ping Method used by O.M. Faltinsen. In present calculation the position and the potential value of free surface are calculated using the exact kinematic and dynamic free surface boundary condition. At each time step an integral equation is solved to obtain the value of potential and normal velocity along the boundaries, consisting of both the body surface and the free surface. Some effort was devoted to the elimination of instability arising in the range of high frequency. Numerical simulations were performed up to the 3rd or 4th period which seems to be enough for the transient effect to die out. Each harmonic component and time-mean force are obtained by the Fourier transform of forces in time domain. The results are compared with others' experimental and theoretical results. Particularly, the calculation shows the tendency that the acceleration-phase 1st-harmonic component(added mass) increases as the motion amplitude increases and a reverse tendency in the velocity-phase 1st-harmonic component(damping coefficient). The Yamashita's experimental result also shows the same tendency. In general, the present result show relatively good agreement with the Yamashita's experimental result except for the time-mean force.