Dynamics of the Neuropeptide Met-Enkephalin by Using Action-Derived Molecular Dynamics

김승연,In-Ho Lee 한국물리학회 2008 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.53 No.4

The brain neuropeptide Met-enkephalin, well known for its pain inhibition activities in the brain, is one of the most important biomolecules. It is composed of five amino acids with the sequence Tyr-Gly-Gly-Phe-Met. The folding dynamics of Met-enkephalin is investigated with all-atom resolution by using action-derived molecular dynamics. The AMBER all-atom force field and the GB/SA solvation potential implemented in the TINKER molecular design package are used to represent the Met-enkephalin with all-atom resolution. With only the inputs of the initial (extended) and the final (ground-state) conformations, the unknown dynamic pathways between the two given conformations of Met-enkephalin have been successfully obtained by using action-derived molecular dynamics. Also, the method of principal component analysis is introduced to analyze the dynamic pathways of Met-enkephalin in detail.

MOLECULAR DYNAMICS SIMULATION OF POPC AND POPE LIPID MEMBRANE BILAYERS ENFORCED BY AN INTERCALATED SINGLE-WALL CARBON NANOTUBE

SERGEY SHITYAKOV,THOMAS DANDEKAR 성균관대학교(자연과학캠퍼스) 성균나노과학기술원 2011 NANO Vol.6 No.1

Using classical all-atom molecular dynamics simulation, we investigated the molecular dynamics of palmitoyloleoylphosphatidylcholine and palmitoyloleoylphosphatidylethanolamine membrane bilayers enforced by a single-wall carbon nanotube. We postulated that an insertion of a single-wall carbon nanotube in the center of lipid membrane "strengthens" ambient lipids and prevents the whole system from further destabilization by high temperatures. We implemented root mean square deviation and root mean square fluctuation analyses of simulated structures from their initial states in order to emphasize the molecular dynamics behavior of these structures during 1000 ps simulation time at different temperatures. The data suggest that an intercalated carbon nanotube restrains the conformational freedom of adjacent lipids and hence has an impact on the membrane stabilization dynamics. On the other hand, different lipid membranes may have dissimilarities due to the differing abilities to create a bridge formation between the adherent lipid molecules. The results derived from this work may be of importance in developing stable nanosystems for construction of novel biomaterials and delivery of various biomolecules in the fields of biosensors, biomaterials, and biophysics.

Effects of density on flow in a nano channel using a molecular-continuum hybrid method

Kim, Youngjin,Jeong, Myunggeun,Zhou, Wenjing,Tao, Wen Quan,Ambrosia, Matthew Stanley,Ha, Man Yeong Elsevier 2017 Computers & fluids Vol.156 No.-

<P><B>Abstract</B></P> <P>A molecular-continuum hybrid method was developed to simulate micro- and nano-scale fluid flows that cannot be predicted using continuum fluidics. Molecular dynamics simulation was used near stationary solid surfaces, and Navier-Stokes equations were used in other regions. We carried out Couette flow simulation using this hybrid method and validated the results by comparing them with the analytical solution. We also studied the dependence of the velocity slip and slip length on the surface energy, liquid density, and roughness for a liquid channel flow with and without nano-structures on the solid surface. The behavior of the liquid near the solid wall changed with the surface energy as well as the liquid density. The variation of the velocity slip and slip length according to the surface energy also depended on the liquid density as well as the surface roughness. We compared the required computational time obtained from the molecular-continuum hybrid method with that obtained from full molecular dynamics simulation under the same computational condition, giving much shorter computational time for the case using the molecular-continuum hybrid method than that for full molecular dynamics simulation.</P> <P><B>Highlights</B></P> <P> <UL> <LI> The velocity slip and slip length decrease with increasing the surface energy. </LI> <LI> The locking boundary condition is enhanced with the structure. </LI> <LI> The trends of <I>u<SUB>s</SUB> </I> and <I>L<SUB>s</SUB> </I> at each liquid density are changed on the smooth surface. </LI> <LI> The trends at each liquid density differ between the rough and smooth surface. </LI> </UL> </P>

Molecular-dynamic simulation on the equilibrium and dynamical properties of fluids in a nano-channel

H. Hoang,S. Kang,Y. K. Suh 한국전산유체공학회 2008 한국전산유체공학회 학술대회논문집 Vol.2008 No.-

The equilibrium molecular-dynamic simulations have been performed to estimate the properties of the three kinds of fluids (the Lennard-Jones fluid, water and aqueous sodium-chloride solution) confined between two plates that are separated by 1.086 nm; included in the equilibrium properties are the density distribution and the static structure, and the diffusivity in the dynamic property. Three kinds of fluids considered in this study are. The water molecules are modeled by using the SPC/E model and the ions by the charged Lennard-Jones particle model. To treat the water molecules, we combined the quaternion coordinates with Euler angles. We also proposed a plausible algorithm to assign the initial position and direction of molecules. The influence of polarization of water molecules as well as the presence of ions in the solution on the properties will be addressed in this study. In addition, we performed the non-equilibrium molecular-dynamic simulation to compute the flow velocity for the case with the gravitational force acting on molecules.

A New Approach of Multi-Scale Simulation for Investigating Nano-Scale Material Deformation Behavior

Junyoung Park(박준영) 한국기계가공학회 2009 한국기계가공학회지 Vol.8 No.1

Recently, an approach for nano-scale material deformation has been developed that couples the atomistic and continuum approaches using Finite Element Method (FEM) and Molecular Dynamics (MD). However, this approach still has problems to connect two approaches because of the difference of basic assumptions, continuum and atomistic modeling. To solve this problem, an alternative way is developed that connects the QuasiMolecular Dynamics (QMD) and molecular dynamics. In this paper, we suggest the way to make and validate the MD-QMD coupled model.

Dynamics of a DNA minicircle: Poloidal rotation and in-plane circular vibration

Kim Minjung,Hong Chi Cheng,Lee Saeyeon,Kim Jun Soo 대한화학회 2022 Bulletin of the Korean Chemical Society Vol.43 No.4

We investigated the dynamics of a 90-base pair-long DNA minicircle with the sequence of (AT)45/(AT)45 using the all-atom molecular dynamics (MD) simulation. The simulation was run for a duration of 5 μs and the internal dynamics was analyzed in terms of the poloidal rotation and the in-plane circular vibration. The poloidal rotation was defined by the directional variation of each base pair relative to the plane of the DNA minicircle, and its correlation time was estimated to be 61 ns. The in-plane circular vibration was measured as the radial distance variation of each base pair from the center-of-mass of the DNA, and the correlation time was 6.3 ns. The characteristic time scales determined for the poloidal rotation and the radial fluctuation suggest that the internal motion of a small DNA minicircle is highly dynamic. This work provides a new set of dynamic information for small DNA minicircles, available for future applications.

Dynamic Structure-Based Pharmacophore Model Development: A New and Effective Addition in the Histone Deacetylase 8 (HDAC8) Inhibitor Discovery

Thangapandian, Sundarapandian,John, Shalini,Lee, Yuno,Kim, Songmi,Lee, Keun Woo Molecular Diversity Preservation International (MD 2011 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.12 No.12

<P>Histone deacetylase 8 (HDAC8) is an enzyme involved in deacetylating the amino groups of terminal lysine residues, thereby repressing the transcription of various genes including tumor suppressor gene. The over expression of HDAC8 was observed in many cancers and thus inhibition of this enzyme has emerged as an efficient cancer therapeutic strategy. In an effort to facilitate the future discovery of HDAC8 inhibitors, we developed two pharmacophore models containing six and five pharmacophoric features, respectively, using the representative structures from two molecular dynamic (MD) simulations performed in Gromacs 4.0.5 package. Various analyses of trajectories obtained from MD simulations have displayed the changes upon inhibitor binding. Thus utilization of the dynamically-responded protein structures in pharmacophore development has the added advantage of considering the conformational flexibility of protein. The MD trajectories were clustered based on single-linkage method and representative structures were taken to be used in the pharmacophore model development. Active site complimenting structure-based pharmacophore models were developed using Discovery Studio 2.5 program and validated using a dataset of known HDAC8 inhibitors. Virtual screening of chemical database coupled with drug-like filter has identified drug-like hit compounds that match the pharmacophore models. Molecular docking of these hits reduced the false positives and identified two potential compounds to be used in future HDAC8 inhibitor design.</P>

아스팔트 바인더의 상변화 온도 평가를 위한 분자동역학의 활용

윤태영 한국도로학회 2023 한국도로학회논문집 Vol.25 No.4

PURPOSES : In this study, we aimed to evaluate the transition temperature (Tt) of asphalt binders using molecular dynamics simulations, which can provide a more accurate assessment of the mechanical properties of a material at the molecular level and can be applied to material development and design. METHODS : Unlike conventional macro- or meso-level simulations, we utilized MD simulations to evaluate the Tg of asphalt binders based on material composition and aging degree as input variables. In this analysis, 11 temperatures ranging from 434 K to 233 K at 20 K intervals were utilized, and the bulk volume and density were calculated through MD simulations. RESULTS : The MD simulation successfully predicted the Tg of the asphalt binder, and the molecular-level properties and interactions determined in this study can be applied not only to material development but also to the determination of constitutive equations or contact models used in continuum mechanics or discrete element methods. The calculated Tg was slightly different depending on the aging of the asphalt binder; however, it was found to accurately reflect the transitional characteristics. CONCLUSIONS : This study demonstrated the potential of MD simulations as valuable tools for material development and design in the construction industry. The results indicate that the use of MD simulations can lead to more accurate and efficient material development and design by providing a more detailed understanding of material properties and interactions at the molecular level.

나노구조기판의 형상 및 온도변화에 따른 액체 클러스터의 거동에 대한 분자동역학적 연구

고선미 ( Sun Mi Ko ),정흥철 ( Heung Cheol Jeong ),최경민 ( Gyung Min Choi ),김덕줄 ( Duck Jool Kim ),( Masahiko Shibahara ) 한국액체미립화학회 2008 한국액체미립화학회지 Vol.13 No.1

Molecular dynamic simulations have been carried out to study the effect of the nano-structure substrate and its temperature on cluster laminating. The interaction between substrate molecules and liquid molecules was modeled in the molecular scale and simulated by the molecular dynamics method in order to understand behaviors of the liquid cluster on nano-structure substrate. In the present model, the Lennard-Jones potential is applied to mono-atomic molecules of argon as liquid and platinum as nano-structure substrate to perform simulations of molecular dynamics. The effect of wettability on a substrate was investigated for the various beta of Lennard-Jones potential. The behavior of the liquid cluster and nano-structure substrate depends on interface wettability and function of molecules force, such as attraction and repulsion, in the collision progress. Furthermore, nano-structure substrate temperature and beta of Lennard-Jones potential have effect on the accumulation ratio. These results of simulation will be the foundation of coating application technology for micro fabrication manufacturing.

Folding Dynamics of β-Hairpins: Molecular Dynamics Simulations

Lee, Jin-Hyuk,Jang, Soon-Min,Park, Young-Shang,Shin, Seok-Min Korean Chemical Society 2003 Bulletin of the Korean Chemical Society Vol.24 No.6

We have studied the folding mechanism of β-hairpins from proteins of 1GB1, 3AIT and 1A2P by unfolding simulations at high temperatures. The analysis of trajectories obtained from molecular dynamics simulations in explicit aqueous solution suggests that the three β-hairpin structures follow different mechanism of folding. The results of unfolding simulations showed that the positions of the hydrophobic core residues influence the folding dynamics. We discussed the characteristics of different mechanisms of β-hairpin folding based on the hydrogen-bond-centric and the hydrophobic-centric models.