• Coupled systems mechanics
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• v.6 no.3
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• pp.335-349
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• 2017

To cope with the demand on giant and durable buildings, reinforcement of concrete is a practical problem being extensively investigated in the civil engineering field. Among various reinforcing techniques, fiber-reinforced concrete (FRC) has been proven to be an effective approach. In practice, such fibers include steel fibers, polyvinyl alcohol (PVA) fibers, polyacrylonitrile (PAN) carbon fibers and asbestos fibers, with the length scale ranging from centimeters to micrometers. When advancing such technique down to the nanoscale, it is noticed that carbon nanotubes (CNTs) are stronger than other fibers and can provide a better reinforcement to concrete. In the last decade, CNT-reinforced concrete attracts a lot of attentions in research. Despite high cost of CNTs at present, the growing availability of carbon materials might push the usage of CNTs into practice in the near future, making the reinforcement technique of great potential. A review of existing research works may constitute a conclusive reference and facilitate further developments. In reference to the recent experimental works, this paper reports some key evaluations on CNT-reinforced cementitious materials, covering FRC mechanism, CNT dispersion, CNT-cement structures, mechanical properties and fire safety. Emphasis is placed on the interplay between CNTs and calcium silicate hydrate (C-S-H) at the nanoscale. The relationship between the CNTs-cement structures and the mechanical enhancement, especially at a high-temperature condition, is discussed based on molecular dynamics simulations. After concluding remarks, challenges to improve the CNTs reinforcement technique are proposed.

• Coupled systems mechanics
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• v.5 no.4
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• pp.355-369
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• 2016

Changes in chemical structure have profound effects on the physical properties of epoxy-based materials, and eventually affect the durability of the entire system. Microscopic structural voids generally existing in the epoxy cross-linked networks have a detrimental influence on the epoxy mechanical properties, but the relation remains elusive, which is hindered by the complex structure of epoxy-based materials. In this paper, we investigate the effect of structural voids on the epoxy-based materials by using our developed mesoscale model equipped with the concept of multiscale modeling, and SU-8 photoresist is used as a representative of epoxy-based materials. Developed from the results of full atomistic simulations, the mesoscopic model is validated against experimental measurements, which is suitable to describe the elastic deformation of epoxy-based materials over several orders of magnitude in time- and length scales. After that, a certain quantity of the structure voids is incorporated in the mesoscale model. It is found that the existence of structural voids reduces the tensile stiffness of the mesoscale epoxy network, when compared with the case without any voids in the model. In addition, it is noticed that a certain number of the structural voids have an insignificant effect on the epoxy elastic properties, and the mesoscale model containing structural voids is close to those found in real systems.

• Journal of Microbiology and Biotechnology
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• v.23 no.12
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• pp.1699-1707
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• 2013

During the fermentative production of 1,3-propanediol under high substrate concentrations, accumulation of intracellular 3-hydroxypropionaldehyde will cause premature cessation of cell growth and glycerol consumption. Discovery of oxidoreductases that can convert 3-hydroxypropionaldehyde to 1,3-propanediol using NADPH as cofactor could serve as a solution to this problem. In this paper, the yqhD gene from Klebsiella pneumoniae DSM2026, which was found encoding an aldehyde reductase (KpAR), was cloned and characterized. KpAR showed broad substrate specificity under physiological direction, whereas no catalytic activity was detected in the oxidation direction, and both NADPH and NADH can be utilized as cofactors. The cofactor binding mechanism was then investigated employing homology modeling and molecular dynamics simulations. Hydrogen-bond analysis showed that the hydrogen-bond interactions between KpAR and NADPH are much stronger than that for NADH. Free-energy decomposition dedicated that residues Gly37 to Val41 contribute most to the cofactor preference through polar interactions. In conclusion, this work provides a novel aldehyde reductase that has potential applications in the development of novel genetically engineered strains in the 1,3-propanediol industry, and gives a better understanding of the mechanisms involved in cofactor binding.

• Genomics & Informatics
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• v.12 no.4
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• pp.276-282
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• 2014

The disease tuberculosis, caused by Mycobacterium tuberculosis (MTB), remains a major cause of morbidity and mortality in developing countries. The evolution of drug-resistant tuberculosis causes a foremost threat to global health. Most drug-resistant MTB clinical strains are showing resistance to isoniazid and rifampicin (RIF), the frontline anti-tuberculosis drugs. Mutation in rpoB, the beta subunit of DNA-directed RNA polymerase of MTB, is reported to be a major cause of RIF resistance. Amongst mutations in the well-defined 81-base-pair central region of the rpoB gene, mutation at codon 450 (S450L) and 445 (H445Y) is mainly associated with RIF resistance. In this study, we modeled two resistant mutants of rpoB (S450L and H445Y) using Modeller9v10 and performed a docking analysis with RIF using AutoDock4.2 and compared the docking results of these mutants with the wild-type rpoB. The docking results revealed that RIF more effectively inhibited the wild-type rpoB with low binding energy than rpoB mutants. The rpoB mutants interacted with RIF with positive binding energy, revealing the incapableness of RIF inhibition and thus showing resistance. Subsequently, this was verified by molecular dynamics simulations. This in silico evidence may help us understand RIF resistance in rpoB mutant strains.

• Advances in nano research
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• v.1 no.3
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• pp.133-151
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• 2013

The availability of advanced nanotechnological methodologies (experimental and theoretical) has widened the investigation of biological/organic matter in interaction with substrates. Minerals are good candidates as substrates because they may present a wide variety of physico-chemical properties and surface nanostructures that can be used to actively condense and manipulate the biomolecules. Scanning Probe Microscopy (SPM) is one of the best suited techniques used to investigate at a single molecule level the surface interactions. In addition, the recent availability of high performance computing has increased the possibility to study quantum mechanically the interaction phenomena extending the number of atoms involved in the simulation. In the present paper, firstly we will briefly introduce new SPM technological developments and applications to investigate mineral surfaces and mineral-biomolecule interaction, then we will present results on the specific RNA-mineral interaction and recent basics and applicative achievements in the field of the interactions between other fundamental biological molecules and mineral surfaces from both an experimental and theoretical point of view.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.7 no.2
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• pp.168-174
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• 2006

We investigated field-effect ion-transport devices based on carbon nanotubes by using classical molecular dynamics simulations under applied external force fields, and we present model schematics that can be applied to the nanoscale data storage devices and unipolar ionic field-effect transistors. As the applied external force field is increased, potassium ions rapidly flow through the nanochannel. Under low external force fields, thermal fluctuations of the nanochannels affect tunneling of the potassium ions whereas the effects of thermal fluctuations are negligible under high external force fields. Since the electric current conductivity increases when potassium ions are inserted into fullerenes or carbon nanotubes, the field effect due to the gate, which can modify the position of the potassium ions, changes the tunneling current between the drain and the source.

• Journal of the Korean Vacuum Society
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• v.21 no.2
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• pp.86-92
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• 2012

We have studied the effect of speed of deposited atom on morphology evolution during Glancing Angle Deposition (GLAD). Using Kinetic Monte Carlo simulation that incorporate molecular dynamics simulations, we have shown that the rough surface morphology became smoother as the speed of deposited atom is increased. The growth exponent ${\beta}$ change from 0.97 to 0.67 as the speed increase from ${\upsilon}_0$ to $10{\upsilon}_0$ in the case of GLAD. We also examined the effect of speed of deposited atom for the case of chemical vapor deposition (CVD) simulation. Compared to GLAD, the variation in scaling exponent ${\beta}$ is small but the speed of deposited atom also have considerable effect on growth morpholgy in the case of CVD.

• Bulletin of the Korean Chemical Society
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• v.35 no.8
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• pp.2494-2504
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• 2014

P38 mitogen activated protein (MAP) kinase is an important anti-inflammatory drug target, which can be activated by responding to various stimuli such as stress and immune response. Based on the conformation of the conserved DFG loop (in or out), binding inhibitors are termed as type-I and II. Type-I inhibitors are ATP competitive, whereas type-II inhibitors bind in DFG-out conformation of allosteric pocket. It remains unclear that how these allosteric inhibitors stabilize the DFG-out conformation and interact. Organosilicon compounds provide unusual opportunity to enhance potency and diversity of drug molecules due to their low toxicity. However, very few examples have been reported to utilize this property. In this regard, we performed docking of an inhibitor (BIRB) and its silicon analog (Si-BIRB) in an allosteric binding pocket of p38. Further, molecular dynamics (MD) simulations were performed to study the dynamic behavior of the simulated complexes. The difference in the biological activity and mechanism of action of the simulated inhibitors could be explained based on the molecular mechanics/generalized Born surface area (MM/GBSA) binding free energy per residue decomposition. MM/GBSA showed that biological activities were related with calculated binding free energy of inhibitors. Analyses of the per-residue decomposed energy indicated that van der Waals and non-polar interactions were predominant in the ligand-protein interactions. Further, crucial residues identified for hydrogen bond, salt bridge and hydrophobic interactions were Tyr35, Lys53, Glu71, Leu74, Leu75, Ile84, Met109, Leu167, Asp168 and Phe169. Our results indicate that stronger hydrophobic interaction of Si-BIRB with the binding site residues could be responsible for its greater binding affinity compared with BIRB.

• The Bulletin of The Korean Astronomical Society
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• v.43 no.1
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• pp.43.1-43.1
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• 2018

Star formation in galaxies predominantly takes place in giant molecular clouds (GMCs). While it is widely believed that UV radiation feedback from young massive stars can destroy natal GMCs by exciting HII regions and driving their expansion, our understanding on how this actually occurs remains incomplete. To quantitatively assess the effect of UV radiation feedback on cloud disruption, we conduct a series of theoretical studies on the dynamics of HII regions and its role in controlling the star formation efficiency (SFE) and lifetime of GMCs in a wide range of star-forming environments. We first develop a semi-analytic model for the expansion of spherical dusty HII regions driven by the combination of gas and radiation pressures, finding that GMCs in normal disk galaxies are destroyed by gas-pressure driven expansion with SFE < 10%, while more dense and massive clouds with higher SFE are disrupted primarily by radiation pressure. Next, we turn to radiation hydrodynamic simulations of GMC dispersal to allow for self-consistent star formation as well as inhomogeneous density and velocity structures arising from supersonic turbulence. For this, we develop an efficient parallel algorithm for ray tracing method, which enables us to probe a range of cloud masses and sizes. Our parameter study shows that the net SFE, lifetime (measured in units of free-fall time), and the importance of radiation pressure (relative to photoionization) increase primarily with the initial surface density of the cloud. Unlike in the idealized spherical model, we find that the dominant mass loss mechanism is photoevaporation rather than dynamical ejection and that a significant fraction of radiation escapes through low optical-depth channels. We will discuss the astronomical.

• Journal of the Computational Structural Engineering Institute of Korea
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• v.26 no.6
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• pp.423-430
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• 2013

In this research, a paramteric study to account for the effect of interfacial strength and nanotube agglomeration on the elastoplastic behavior of carbon nanotube reinforced polypropylene composites is performed. At first, the elastoplastic behavior of nanocomposites is predicted from molecular dynamics(MD) simulations. By combining the MD simulation results with the nonlinear micromechanics model based on the Mori-Tanaka model, a two-step domain decomposition method is applied to inversely identify the elastoplastic behavior of adsorption interphase zone inside nanocomposites. In nonlinear micromechanics model, the secant moduli method combined with field fluctuation method is used to predict the elastoplastic behavior of nanocomposites. To account for the imperfect material interface between nanotube and matrix polymer, displacement discontinuity condition is applied to the micromechanics model. Using the elastoplastic behavior of the adsorption interphase zone obtained from the present study, stress-strain relation of nanocomposites at various interfacial bonding condition and local nanotube agglomeration is predicted from nonlinear micromechanics model with and without the adsorption interphase zone. As a result, it has been found that local nanotube agglomeration is the most important design factor to maximize reinforcing effect of nanotube in elastic and plastic behavior.