Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 4074

Search results for: single molecule

4074 Segmental Motion of Polymer Chain at Glass Transition Probed by Single Molecule Detection

Authors: Hiroyuki Aoki

Abstract:

The glass transition phenomenon has been extensively studied for a long time. The glass transition of polymer materials is assigned to the transition of the dynamics of the chain backbone segment. However, the detailed mechanism of the transition behavior of the segmental motion is still unclear. In the current work, the single molecule detection technique was employed to reveal the trajectory of the molecular motion of the single polymer chain. The center segment of poly(butyl methacrylate) chain was labeled by a perylenediimide dye molecule and observed by a highly sensitive fluorescence microscope in a defocus condition. The translational and rotational diffusion of the center segment in a single polymer chain was analyzed near the glass transition temperature. The direct observation of the individual polymer chains revealed the intermittent behavior of the segmental motion, indicating the spatial inhomogeneity.

Keywords: glass transition, molecular motion, polymer materials, single molecule

Procedia PDF Downloads 193
4073 Single-Molecule Analysis of Structure and Dynamics in Polymer Materials by Super-Resolution Technique

Authors: Hiroyuki Aoki

Abstract:

The physical properties of polymer materials are dependent on the conformation and molecular motion of a polymer chain. Therefore, the structure and dynamic behavior of the single polymer chain have been the most important concerns in the field of polymer physics. However, it has been impossible to directly observe the conformation of the single polymer chain in a bulk medium. In the current work, the novel techniques to study the conformation and dynamics of a single polymer chain are proposed. Since a fluorescence method is extremely sensitive, the fluorescence microscopy enables the direct detection of a single molecule. However, the structure of the polymer chain as large as 100 nm cannot be resolved by conventional fluorescence methods because of the diffraction limit of light. In order to observe the single chains, we developed the labeling method of polymer materials with a photo-switchable dye and the super-resolution microscopy. The real-space conformational analysis of single polymer chains with the spatial resolution of 15-20 nm was achieved. The super-resolution microscopy enables us to obtain the three-dimensional coordinates; therefore, we succeeded the conformational analysis in three dimensions. The direct observation by the nanometric optical microscopy would reveal the detailed information on the molecular processes in the various polymer systems.

Keywords: polymer materials, single molecule, super-resolution techniques, conformation

Procedia PDF Downloads 204
4072 Single-Molecule Optical Study of Cholesterol-Mediated Dimerization Process of EGFRs in Different Cell Lines

Authors: Chien Y. Lin, Jung Y. Huang, Leu-Wei Lo

Abstract:

A growing body of data reveals that the membrane cholesterol molecules can alter the signaling pathways of living cells. However, the understanding about how membrane cholesterol modulates receptor proteins is still lacking. Single-molecule tracking can effectively probe into the microscopic environments and thermal fluctuations of receptor proteins in a living cell. In this study we applies single-molecule optical tracking on ligand-induced dimerization process of EGFRs in the plasma membranes of two cancer cell lines (HeLa and A431) and one normal endothelial cell line (MCF12A). We tracked individual EGFR and dual receptors, diffusing in a correlated manner in the plasma membranes of live cells. We developed an energetic model by integrating the generalized Langevin equation with the Cahn-Hilliard equation to help extracting important information from single-molecule trajectories. From the study, we discovered that ligand-bound EGFRs move from non-raft areas into lipid raft domains. This ligand-induced motion is a common behavior in both cancer and normal cells. By manipulating the total amount of membrane cholesterol with methyl-β-cyclodextrin and the local concentration of membrane cholesterol with nystatin, we further found that the amount of cholesterol can affect the stability of EGFR dimers. The EGFR dimers in the plasma membrane of normal cells are more sensitive to the local concentration changes of cholesterol than EGFR dimers in the cancer cells. Our method successfully captures dynamic interactions of receptors at the single-molecule level and provides insight into the functional architecture of both the diffusing EGFR molecules and their local cellular environment.

Keywords: membrane proteins, single-molecule tracking, Cahn-Hilliard equation, EGFR dimers

Procedia PDF Downloads 347
4071 Simulation of Stretching and Fragmenting DNA by Microfluidic for Optimizing Microfluidic Devices

Authors: Shuyi Wu, Chuang Li, Quanshui Zheng, Luping Xu

Abstract:

Stretching and snipping DNA molecule by microfluidic has important application value in gene analysis by lab on a chip. Movement, deformation and fragmenting of DNA in microfluidic are typical fluid-solid coupling problems. An efficient and common simulation system for researching the movement, deformation and fragmenting of DNA by microfluidic has not been well developed. In our study, Brownian dynamics-finite element method (BD-FEM) is used to simulate the dynamic process of stretching and fragmenting DNA by contraction flow. The shape and parameters of micro-channels are changed to optimize the stretching and fragmenting properties of DNA. Our results indicate that strain rate, resulting from contraction microchannel, is the main control parameter for stretching and fragmenting DNA. There is good consistency between the simulation data and previous experimental result about the single DNA molecule behavior and averaged fragmenting properties in this study. BD-FEM method is an efficient calculating tool to research stretching and fragmenting behavior of single DNA molecule and optimize microfluidic devices for manipulating, stretching and fragmenting DNA.

Keywords: fragmenting, DNA, microfluidic, optimize.

Procedia PDF Downloads 221
4070 Synthesis, Characterization, and Properties Study of New Magnetic Materials

Authors: Messai Amel, Badis Zakaria, Benali-Cherif Nourredine, Dominique Luneaub

Abstract:

We are interested in molecular polymetallic species having high spin and nuclearities in relation to the field of so call single-molecule magnets (SMMs). The goal is to find a way to synthesis metal clusters which may have application in magnetism and nano sciences. With this purpose, we decided to investigate the coordination chemistry of the Schiff base. Along this way we were able to create cubane-like complexes and elaborate new Single Molecule-Magnets. The idea was to use Schiff base ligands and different metals to generate high nuclear complexes. Complexation of Shiff base with copper (II) has been investigated. Tetra nuclear complex with a cubane like core have been synthesized with (Sciff base), with the same base and cobalt (II) we obtain an other single magnetic complex completely different. In this presentation, we report the synthesis, crystal structure and magnetic properties of the tetranuclear compound (Cu4 L4), and the tetranuclear compound. (Co4L4)

Keywords: cluster-assembled materials, magnetic compounds, Sciff base, cupper, cobalt

Procedia PDF Downloads 356
4069 Study υ_4 Fundamental Band of 12 CD4 Molecule

Authors: Kaarour Abdelkrim, Ouardi Okkacha, Meskine Mohamed

Abstract:

In this study, the υ_4 fundamental band of 12CD4 molecule has been studied by infrared spectroscopy with high resolution. Using XTDS and SPEVIEW software and the tensor formalism developed by ICB (laboratoire interdisciplinaire de Bourgogne) to several lines have been assigned and fitted with a standard deviation acceptable. This analysis allowed us to calculate several parameters of the molecule 12 CD4.

Keywords: XTDS, SPEVIEW, tetrahedral tensorial formalism, rovibrational band

Procedia PDF Downloads 240
4068 The Transport of Radical Species to Single and Double Strand Breaks in the Liver’s DNA Molecule by a Hybrid Method of Type Monte Carlo - Diffusion Equation

Authors: H. Oudira, A. Saifi

Abstract:

The therapeutic utility of certain Auger emitters such as iodine-125 depends on their position within the cell nucleus . Or diagnostically, and to maintain as low as possible cell damage, it is preferable to have radionuclide localized outside the cell or at least the core. One solution to this problem is to consider markers capable of conveying anticancer drugs to the tumor site regardless of their location within the human body. The objective of this study is to simulate the impact of a complex such as bleomycin on single and double strand breaks in the DNA molecule. Indeed, this simulation consists of the following transactions: - Construction of BLM -Fe- DNA complex. - Simulation of the electron’s transport from the metastable state excitation of Fe 57 by the Monte Carlo method. - Treatment of chemical reactions in the considered environment by the diffusion equation. For physical, physico-chemical and finally chemical steps, the geometry of the complex is considered as a sphere of 50 nm centered on the binding site , and the mathematical method used is called step by step based on Monte Carlo codes.

Keywords: concentration, yield, radical species, bleomycin, excitation, DNA

Procedia PDF Downloads 384
4067 Segmental Dynamics of Poly(Alkyl Methacrylate) Chain in Ultra-Thin Spin-Cast Films

Authors: Hiroyuki Aoki

Abstract:

Polymeric materials are often used in a form of thin film such as food wrap and surface coating. In such the applications, polymer films thinner than 100 nm have been often used. The thickness of such the ultra-thin film is less than the unperturbed size of a polymer chain; therefore, the polymer chain in an ultra-thin film is strongly constrained. However, the details on the constrained dynamics of polymer molecules in ultra-thin films are still unclear. In the current study, the segmental dynamics of single polymer chain was directly investigated by fluorescence microscopy. The individual chains of poly(alkyl methacrylate) labeled by a perylenediimide dye molecule were observed by a highly sensitive fluorescence microscope in a defocus condition. The translational and rotational diffusion of the center segment in a single polymer chain was directly analyzed. The segmental motion in a thin film with a thickness of 10 nm was found to be suppressed compared to that in a bulk state. The detailed analysis of the molecular motion revealed that the diffusion rate of the in-plane rotation was similar to the thin film and the bulk; on the other hand, the out-of-plane motion was restricted in a thin film. This result indicates that the spatial restriction in an ultra-thin film thinner than the unperturbed chain dimension alters the dynamics of individual molecules in a polymer system.

Keywords: polymer materials, single molecule, molecular motion, fluorescence microscopy, super-resolution techniques

Procedia PDF Downloads 217
4066 Spectroscopic Constant Calculation of the BeF Molecule

Authors: Nayla El-Kork, Farah Korjieh, Ahmed Bentiba, Mahmoud Korek

Abstract:

Ab-initio calculations have been performed to investigate the spectroscopic constants for the diatomic compound BeF. Values of the internuclear distance Re, the harmonic frequency ωe, the rotational constants Be, the electronic transition energy with respect to the ground state Te, the eignvalues Ev, the abscissas of the turning points Rmin, Rmax, the rotational constants Bv and the centrifugal distortion constants Dv have been calculated for the molecule’s ground and excited electronic states. Results are in agreement with experimental data.

Keywords: spectroscopic constant, potential energy curve, diatomic molecule, spectral analysis

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4065 Spectroscopic, Molecular Structure and Electrostatic Potential, Polarizability, Hyperpolarizability, and HOMO–LUMO Analysis of Monomeric and Dimeric Structures of N-(2-Methylphenyl)-2-Nitrobenzenesulfonamide

Authors: A. Didaoui, N. Benhalima, M. Elkeurti, A. Chouaih, F. Hamzaoui

Abstract:

The monomer and dimer structures of the title molecule have been obtained from density functional theory (DFT) B3LYP method with 6-31G (d,p) as basis set calculations. The optimized geometrical parameters obtained by B3LYP/6-31G (d,p) method show good agreement with xperimental X-ray data. The polarizability and first order hyperpolarizabilty of the title molecule were calculated and interpreted. the intermolecular N–H•••O hydrogen bonds are discussed in dimer structure of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 03 set of quantum chemistry codes. The predicted frontier molecular orbital energies at B3LYP/6-31G(d,p) method set show that charge transfer occurs within the molecule. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the total static hyperpolarizability. The results also show that N-(2-Methylphenyl)-2-nitrobenzenesulfonamide molecule may have nonlinear optical (NLO) comportment with non-zero values.

Keywords: DFT, Gaussian 03, NLO, N-(2-Methylphenyl)-2-nitrobenzenesulfonamide

Procedia PDF Downloads 474
4064 The Spectroscopic, Molecular Structure and Electrostatic Potential, Polarizability Hyperpolarizability, and Homo–Lumo Analysis of Monomeric and Dimeric Structures of 2-Chloro-N-(2 Methylphenyl) Benzamide

Authors: N. Khelloul, N. Benhalima, A. Chouaih, F. Hamzaoui

Abstract:

The monomer and dimer structures of the title molecule have been obtained from density functional theory (DFT) B3LYP method with 6-31G (d,p) as basis set calculations. The optimized geometrical parameters obtained by B3LYP/6-31G (d,p) method shows good agreement with experimental X-ray data. The polarizability and first order hyperpolarizabilty of the title molecule were calculated and interpreted. The intermolecular N–H•••O hydrogen bonds are discussed in dimer structure of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 09 set of quantum chemistry codes. The predicted frontier molecular orbital energies at B3LYP/6-31G(d,p) method set show that charge transfer occurs within the molecule. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the total static hyperpolarizability. The results also show that 2-Chloro-N-(2-methylphenyl) benzamide 2 molecule may have nonlinear optical (NLO) comportment with non-zero values.

Keywords: DFT, HOMO, LUMO, NLO

Procedia PDF Downloads 256
4063 The Spectroscopic, Molecular Structure and Electrostatic Potential, Polarizability, Hyperpolarizability, and HOMO–LUMO Analysis of Monomeric and Dimeric Structures of N-(2-Methylphenyl)-2-Nitrobenzenesulfonamide

Authors: A. Didaoui, N. Benhalima, M. Elkeurti, A. Chouaih, F. Hamzaoui

Abstract:

The monomer and dimer structures of the title molecule have been obtained from density functional theory (DFT) B3LYP method with 6-31G(d,p) as basis set calculations. The optimized geometrical parameters obtained by B3LYP/6-31G(d,p) method show good agreement with experimental X-ray data. The polarizability and first order hyperpolarizability of the title molecule were calculated and interpreted. The intermolecular N–H•••O hydrogen bonds are discussed in dimer structure of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 03 set of quantum chemistry codes. The predicted frontier molecular orbital energies at B3LYP/6-31G(d,p) method set show that charge transfer occurs within the molecule. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the total static hyperpolarizability. The results also show that N-(2-Methylphenyl)-2-nitrobenzenesulfonamide molecule may have nonlinear optical (NLO) comportment with non-zero values.

Keywords: DFT, Gaussian 03, NLO, N-(2-Methylphenyl)-2-nitrobenzenesulfonamide, polarizability

Procedia PDF Downloads 251
4062 Ultrafast Ground State Recovery Dynamics of a Cyanine Dye Molecule in Heterogeneous Environment

Authors: Tapas Goswami, Debabrata Goswami

Abstract:

We have studied the changes in ground state recovery dynamics of IR 144 dye using degenerate transient absorption spectroscopy technique when going from homogeneous solution phase to heterogeneous partially miscible liquid/liquid interface. Towards this aim, we set up a partially miscible liquid/liquid interface in which dye is insoluble in one solvent carbon tetrachloride (CCl₄) layer and soluble in other solvent dimethyl sulphoxide (DMSO). A gradual increase in ground state recovery time of the dye molecule is observed from homogenous bulk solution to more heterogeneous environment interface layer. In the bulk solution charge distribution of dye molecule is in equilibrium with polar DMSO solvent molecule. Near the interface micro transportation of non-polar solvent, CCl₄ disturbs the solvent equilibrium in DMSO layer and it relaxes to a new equilibrium state corresponding to a new charge distribution of dye with a heterogeneous mixture of polar and non-polar solvent. In this experiment, we have measured the time required for the dye molecule to relax to the new equilibrium state in different heterogeneous environment. As a result, dye remains longer time in the excited state such that even it can populate more triplet state. The present study of ground state recovery dynamics of a cyanine dye molecule in different solvent environment provides the important characteristics of effect of solvation on excited life time of a dye molecule.

Keywords: excited state, ground state recovery, solvation, transient absorption

Procedia PDF Downloads 200
4061 Investigation of Atomic Adsorption on the Surface of BC3 Nanotubes

Authors: S. V. Boroznin, I. V. Zaporotskova, N. P. Polikarpova

Abstract:

Studing of nanotubes sorption properties is very important for researching. These processes for carbon and boron nanotubes described in the high number of papers. But the sorption properties of boron containing nanotubes, susch as BC3-nanotubes haven’t been studied sufficiently yet. In this paper we present the results of theoretical research into the mechanism of atomic surface adsorption on the two types of boron-carbon nanotubes (BCNTs) within the framework of an ionic-built covalent-cyclic cluster model and an appropriately modified MNDO quantum chemical scheme and DFT method using B3LYP functional with 6-31G basis. These methods are well-known and the results, obtained using them, were in good agreement with the experiment. Also we studied three position of atom location above the nanotube surface. These facts suggest us to use them for our research and quantum-chemical calculations. We studied the mechanism of sorption of Cl, O and F atoms on the external surface of single-walled BC3 arm-chair nanotubes. We defined the optimal geometry of the sorption complexes and obtained the values of the sorption energies. Analysis of the band structure suggests that the band gap is insensitive to adsorption process. The electron density is located near atoms of the surface of the tube. Also we compared our results with others, which have been obtained earlier for pure carbon and boron nanotubes. The most stable adsorption complex has been between boron-carbon nanotube and oxygen atom. So, it suggests us to make a research of oxygen molecule adsorption on the BC3 nanotube surface. We modeled five variants of molecule orientation above the nanotube surface. The most stable sorption complex has been defined between the oxygen molecule and nanotube when the oxygen molecule is located above the nanotube surface perpendicular to the axis of the tube.

Keywords: Boron-carbon nanotubes, nanostructures, nanolayers, quantum-chemical calculations, nanoengineering

Procedia PDF Downloads 239
4060 An Energy Transfer Fluorescent Probe System for Glucose Sensor at Biomimetic Membrane Surface

Authors: Hoa Thi Hoang, Stephan Sass, Michael U. Kumke

Abstract:

Concanavalin A (conA) is a protein has been widely used in sensor system based on its specific binding to α-D-Glucose or α-D-Manose. For glucose sensor using conA, either fluoresence based techniques with intensity based or lifetime based are used. In this research, liposomes made from phospholipids were used as a biomimetic membrane system. In a first step, novel building blocks containing perylene labeled glucose units were added to the system and used to decorate the surface of the liposomes. Upon the binding between rhodamine labeled con A to the glucose units at the biomimetic membrane surface, a Förster resonance energy transfer system can be formed which combines unique fluorescence properties of perylene (e.g., high fluorescence quantum yield, no triplet formation) and its high hydrophobicity for efficient anchoring in membranes to form a novel probe for the investigation of sugar-driven binding reactions at biomimetic surfaces. Two glucose-labeled perylene derivatives were synthesized with different spacer length between the perylene and glucose unit in order to probe the binding of conA. The binding interaction was fully characterized by using high-end fluorescence techniques. Steady-state and time-resolved fluorescence techniques (e.g., fluorescence depolarization) in combination with single-molecule fluorescence spectroscopy techniques (fluorescence correlation spectroscopy, FCS) were used to monitor the interaction with conA. Base on the fluorescence depolarization, the rotational correlation times and the alteration in the diffusion coefficient (determined by FCS) the binding of the conA to the liposomes carrying the probe was studied. Moreover, single pair FRET experiments using pulsed interleaved excitation are used to characterize in detail the binding of conA to the liposome on a single molecule level avoiding averaging out effects.

Keywords: concanavalin A, FRET, sensor, biomimetic membrane

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4059 Preparation and Characterization of Electrospun CdTe Quantum Dots / Nylon-6 Nanofiber Mat

Authors: Negar Mesgara, Laleh Maleknia

Abstract:

In this paper, electrospun CdTe quantum dot / nylon-6 nanofiber mats were successfully prepared. The nanofiber mats were characterized by FE-SEM, XRD and EDX analyses. The results revealed that fibers in different distinct sizes (nano and subnano scale) were obtained with the electrospinning parameters. The phenomenon of ‘on ‘ and ‘off ‘ luminescence intermittency (blinking) of CdTe QDs in nylon-6 was investigated by single-molecule optical microscopy, and we identified that the intermittencies of single QDs were correlated with the interaction of water molecules absorbed on the QD surface. The ‘off’ times, the interval between adjacent ‘on’ states, remained essentially unaffected with an increase in excitation intensity. In the case of ‘on’ time distribution, power law behavior with an exponential cutoff tail is observed at longer time scales. These observations indicate that the luminescence blinking statistics of water-soluble single CdTe QDs is significantly dependent on the aqueous environment, which is interpreted in terms of passivation of the surface trap states of QDs.

Keywords: electrospinning, CdTe quantum dots, Nylon-6, Nanocomposite

Procedia PDF Downloads 356
4058 The Effect of the Structural Arrangement of Binary Bisamide Organogelators on their Self-Assembly Behavior

Authors: Elmira Ghanbari, Jan Van Esch, Stephen J. Picken, Sahil Aggarwal

Abstract:

Low-molecular-weight organogelators form gels by self-assembly into the crystalline network which immobilizes the organic solvent. For single bisamide organogelator systems, the effect of the molecular structure on the molecular interaction and their self-assembly behavior has been explored. The spatial arrangement of bisamide molecules in the gel-state is driven by a combination of hydrogen bonding and Van der Waals interactions. The hydrogen-bonding pattern between the amide groups of bisamide molecules is regulated by the number of methylene spacers; the even number of methylene spacers between two amide groups, in even-spaced bisamides, leads to the antiparallel position of amide groups within a molecule. An even-spaced bisamide molecule with antiparallel amide groups can make two pairs of hydrogen bonding with the molecules on the same plane. The odd-spaced bisamide with a parallel directionality of amide groups can form four independent hydrogen bonds with four other bisamide molecules on different planes. The arrangement of bisamide molecules in the crystalline state and the interaction of these molecules depends on the molecular structure, particularly the parity of the spacer length between the amide groups in the bisamide molecule. In this study, the directionality of amide groups has been exploited as a structural characteristic to affect the arrangement of molecules in the crystalline state and produce different binary bisamide gelators with different degrees of crystallinities. Single odd- and even-spaced single bisamides were synthesized and blended to produce binary bisamide organogelators to be characterized in order to understand the effect of the different directionality of amide groups on the molecular interaction in the crystalline state. The pattern of molecular interactions between these blended molecules, mixing or phase separation, has been monitored via differential scanning calorimetry (DSC) and crystallography techniques; X-ray powder diffraction (XRD) and Small-angle X-ray scattering (SAXS). The formation of lamellar structures for odd- and even-spaced bisamide gelators was confirmed by using SAXS and XRD techniques. DSC results have shown that binary bisamide organogelators with different parity of methylene spacers (odd-even binary blends) have a higher tendency for phase separation compared to the binary bisamides with the same parity (odd-odd or even-even binary blends). Phase separation in binary odd-even bisamides was confirmed by the presence of individual (100) reflections of odd and even lamellar structures. The structural characteristic of bisamide organogelators, the parity of spacer length in binary systems, is a promising tool to control the arrangement of molecules and their crystalline structure.

Keywords: binary bisamide organogelators, crystalline structure, phase separation, self-assembly behavior

Procedia PDF Downloads 103
4057 Molecular Dynamic Simulation of CO2 Absorption into Mixed Aqueous Solutions MDEA/PZ

Authors: N. Harun, E. E. Masiren, W. H. W. Ibrahim, F. Adam

Abstract:

Amine absorption process is an approach for mitigation of CO2 from flue gas that produces from power plant. This process is the most common system used in chemical and oil industries for gas purification to remove acid gases. On the challenges of this process is high energy requirement for solvent regeneration to release CO2. In the past few years, mixed alkanolamines have received increasing attention. In most cases, the mixtures contain N-methyldiethanolamine (MDEA) as the base amine with the addition of one or two more reactive amines such as PZ. The reason for the application of such blend amine is to take advantage of high reaction rate of CO2 with the activator combined with the advantages of the low heat of regeneration of MDEA. Several experimental and simulation studies have been undertaken to understand this process using blend MDEA/PZ solvent. Despite those studies, the mechanism of CO2 absorption into the aqueous MDEA is not well understood and available knowledge within the open literature is limited. The aim of this study is to investigate the intermolecular interaction of the blend MDEA/PZ using Molecular Dynamics (MD) simulation. MD simulation was run under condition 313K and 1 atm using NVE ensemble at 200ps and NVT ensemble at 1ns. The results were interpreted in term of Radial Distribution Function (RDF) analysis through two system of interest i.e binary and tertiary. The binary system will explain the interaction between amine and water molecule while tertiary system used to determine the interaction between the amine and CO2 molecule. For the binary system, it was observed that the –OH group of MDEA is more attracted to water molecule compared to –NH group of MDEA. The –OH group of MDEA can form the hydrogen bond with water that will assist the solubility of MDEA in water. The intermolecular interaction probability of –OH and –NH group of MDEA with CO2 in blended MDEA/PZ is higher than using single MDEA. This findings show that PZ molecule act as an activator to promote the intermolecular interaction between MDEA and CO2.Thus, blend of MDEA with PZ is expecting to increase the absorption rate of CO2 and reduce the heat regeneration requirement.

Keywords: amine absorption process, blend MDEA/PZ, CO2 capture, molecular dynamic simulation, radial distribution function

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4056 Amyloid-β Fibrils Remodeling by an Organic Molecule: Insight from All-Atomic Molecular Dynamics Simulations

Authors: Nikhil Agrawal, Adam A. Skelton

Abstract:

Alzheimer’s disease (AD) is one of the most common forms of dementia, which is caused by misfolding and aggregation of amyloid beta (Aβ) peptides into amyloid-β fibrils (Aβ fibrils). To disrupt the remodeling of Aβ fibrils, a number of candidate molecules have been proposed. To study the molecular mechanisms of Aβ fibrils remodeling we performed a series of all-atom molecular dynamics simulations, a total time of 3µs, in explicit solvent. Several previously undiscovered candidate molecule-Aβ fibrils binding modes are unraveled; one of which shows the direct conformational change of the Aβ fibril by understanding the physicochemical factors responsible for binding and subsequent remodeling of Aβ fibrils by the candidate molecule, open avenues into structure-based drug design for AD can be opened.

Keywords: alzheimer’s disease, amyloid, MD simulations, misfolded protein

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4055 Single Valued Neutrosophic Hesitant Fuzzy Rough Set and Its Application

Authors: K. M. Alsager, N. O. Alshehri

Abstract:

In this paper, we proposed the notion of single valued neutrosophic hesitant fuzzy rough set, by combining single valued neutrosophic hesitant fuzzy set and rough set. The combination of single valued neutrosophic hesitant fuzzy set and rough set is a powerful tool for dealing with uncertainty, granularity and incompleteness of knowledge in information systems. We presented both definition and some basic properties of the proposed model. Finally, we gave a general approach which is applied to a decision making problem in disease diagnoses, and demonstrated the effectiveness of the approach by a numerical example.

Keywords: single valued neutrosophic fuzzy set, single valued neutrosophic fuzzy hesitant set, rough set, single valued neutrosophic hesitant fuzzy rough set

Procedia PDF Downloads 88
4054 Molecular Electrostatic Potential in Z-3N(2-Ethoxyphenyl), 2-N'(2-Ethoxyphenyl) Imino Thiazolidin-4-one Molecule by Ab Initio and DFT Methods

Authors: Manel Boulakoud, Abdelkader Chouaih, Fodil Hamzaoui

Abstract:

In the present work we are interested in the determination of the Molecular electrostatic potential (MEP) in Z-3N(2-Ethoxyphenyl), 2-N’(2-Ethoxyphenyl) imino thiazolidin-4-one molecule by ab initio and Density Functional Theory (DFT) in the ground state. The MEP is related to the electronic density and is a very useful descriptor in understanding sites for electrophilic attack and nucleophilic reactions as well as hydrogen bonding interactions. First, geometry optimization was carried out using Hartree–Fock (HF) and DFT methods with 6-311G(d,p) basis set. In order to get more information on the molecule, its stability has been analyzed by natural bond orbital (NBO) analysis. Mulliken population analyses have been calculated. Finally, the molecular electrostatic potential (MEP) and HOMO-LUMO energy levels have been performed. The calculated HOMO and LUMO energies show also the charge transfer within the molecule. The energy gap obtained is about 4 eV which explain the stability of the studied compound. The obtained molecular electrostatic potential from the two methods confirms the nature of the electron charge transfer at the molecular shell and locate the electropositive part and the electronegative part in molecular scale of the title compound.

Keywords: DFT, ab initio, HOMO-LUMO, organic compounds

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4053 Small Molecule Inhibitors of PD1-PDL1 Interaction

Authors: K. Żak, S. Przetocka, R. Kitel, K. Guzik, B. Musielak, S. Malicki, G. Dubin, T. A. Holak

Abstract:

Studies on tumor genesis revealed a number of factors that may potentially serve as molecular targets for immunotherapies. One of such promising targets are PD1 and PDL1 proteins. PD1 (Programmed cell death protein 1) is expressed by activated T cells and plays a critical role in modulation of the host's immune response. One of the PD1 ligands -PDL1- is expressed by macrophages, monocytes and cancer cells which exploit it to avoid immune attack. The notion of the mechanisms used by cancer cells to block the immune system response was utilized in the development of therapies blocking PD1-PDL1 interaction. Up to date, human PD1-PDL1 complex has not been crystallized and structure of the mouse-human complex does not provide a complete view of the molecular basis of PD1-PDL1 interactions. The purpose of this study is to obtain crystal structure of the human PD1-PDL1 complex which shall allow rational design of small molecule inhibitors of the interaction. In addition, the study presents results of binding small-molecules to PD1 and fragment docking towards PD1 protein which will facilitate the design and development of small–molecule inhibitors of PD1-PDL1 interaction.

Keywords: PD1, PDL1, cancer, small molecule, drug discovery

Procedia PDF Downloads 321
4052 An Evolutionary Perspective on the Role of Extrinsic Noise in Filtering Transcript Variability in Small RNA Regulation in Bacteria

Authors: Rinat Arbel-Goren, Joel Stavans

Abstract:

Cell-to-cell variations in transcript or protein abundance, called noise, may give rise to phenotypic variability between isogenic cells, enhancing the probability of survival under stress conditions. These variations may be introduced by post-transcriptional regulatory processes such as non-coding, small RNAs stoichiometric degradation of target transcripts in bacteria. We study the iron homeostasis network in Escherichia coli, in which the RyhB small RNA regulates the expression of various targets as a model system. Using fluorescence reporter genes to detect protein levels and single-molecule fluorescence in situ hybridization to monitor transcripts levels in individual cells, allows us to compare noise at both transcript and protein levels. The experimental results and computer simulations show that extrinsic noise buffers through a feed-forward loop configuration the increase in variability introduced at the transcript level by iron deprivation, illuminating the important role that extrinsic noise plays during stress. Surprisingly, extrinsic noise also decouples of fluctuations of two different targets, in spite of RyhB being a common upstream factor degrading both. Thus, phenotypic variability increases under stress conditions by the decoupling of target fluctuations in the same cell rather than by increasing the noise of each. We also present preliminary results on the adaptation of cells to prolonged iron deprivation in order to shed light on the evolutionary role of post-transcriptional downregulation by small RNAs.

Keywords: cell-to-cell variability, Escherichia coli, noise, single-molecule fluorescence in situ hybridization (smFISH), transcript

Procedia PDF Downloads 102
4051 Evaluation of Anti-Cancer Activities of Formononetin in Lung Cancer by in vitro Methods

Authors: Vishnu Varthan Vaithiyalingam Jagannathan, Lakshmi Karunanidhi Santhanalakshmi, Srividya Ammayappan Rajam

Abstract:

Formononetin is the O-Methoxy Flavonol that has many pharmacological activities, which belongs to the flavonoid family. In the current study, activity of this molecule was evaluated in lung cancer cell lines. In general, flavonoids possess certain anticancer mechanism. Being a flavonoid subfamily, this molecule was subjected to evaluate cytotoxicity assay by MTT ((3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide)) stain, mode of cell death assay stained by acridine orange and ethidium bromide and Evaluation of Apoptosis pathway (extrinsic or intrinsic) by Caspase 3/7 stain and Rhodamine-123 stain. From the results, we could able to confirm that the investigatory molecule formononetin has anticancer activity and in future, the study will propose to evaluate the formononetin action against genetic changes occurs during lung cancer progression.

Keywords: Caspase 3/7, formononetin, lung cancer, Rhodamine-123

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4050 Study of the Ambiguity of Effective Hamiltonian for the Fundamental Degenerate States V3 of the Molecule 12CD4

Authors: Ouardi Okkacha, Kaarour Abedlkrim, Meskine Mohamed

Abstract:

The effective Hamiltonians are widely used in molecular spectroscopy for the interpretation of the vibration-rotation spectra. Their construction is an ambiguous procedure due to the existence of unitary transformations that change the effective Hamiltonian but do not change its eigenvalues. As a consequence of this ambiguity, it may happen that some parameters of effective Hamiltonians cannot be recovered from experimental data in a unique way. The type of admissible transformations which keeps the operator form of the effective Hamiltonian unaltered and the number of empirically determinable parameters strongly depend on the symmetry type of a molecule (asymmetric top, spherical top, and so on) and on the degeneracy of the vibrational state. In this work, we report the study of the ambiguity of effective Hamiltonian for the fundamental degenerate states v3 of the Molecule 12CD4.

Keywords: 12CD4, high-resolution infrared spectra, tetrahedral tensorial formalism, vibrational states, rovibrational line position analysis, XTDS, SPVIEW

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4049 Thermal Stability of Hydrogen in ZnO Bulk and Thin Films: A Kinetic Monte Carlo Study

Authors: M. A. Lahmer, K. Guergouri

Abstract:

In this work, Kinetic Monte Carlo (KMC) method was applied to study the thermal stability of hydrogen in ZnO bulk and thin films. Our simulation includes different possible events such as interstitial hydrogen (Hi) jumps, substitutional hydrogen (HO) formation and dissociation, oxygen and zinc vacancies jumps, hydrogen-VZn complexes formation and dissociation, HO-Hi complex formation and hydrogen molecule (H2) formation and dissociation. The obtained results show that the hidden hydrogen formed during thermal annealing or at room temperature is constituted of both hydrogen molecule and substitutional hydrogen. The ratio of this constituants depends on the initial defects concentration as well as the annealing temperature. For annealing temperature below 300°C hidden hydrogen was found to be constituted from both substitutional hydrogen and hydrogen molecule, however, for higher temperature it is composed essentially from HO defects only because H2 was found to be unstable. In the other side, our results show that the remaining hydrogen amount in sample during thermal annealing depend greatly on the oxygen vacancies in the material. H2 molecule was found to be stable for thermal annealing up to 200°C, VZnHn complexes are stable up to 350°C and HO was found to be stable up to 450°C.

Keywords: ZnO, hydrogen, thermal annealing, kinetic Monte Carlo

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4048 Raman and FTIR Studies of Azobenzene: Experimental and Theoretical Approach

Authors: Gomti Devi

Abstract:

Photoisomerization has been attracting to researchers due to its wide range of applications in optical switches, polymeric chains, liquid-crystalline systems and bilayer membranes etc. Azobenzene is a photochromic molecule which exhibits a reversible isomerisation process between its trans and cis isomers of different stability. An investigation has been conducted of the effects of temperature on intensity and position of Raman band of N=N, C-N stretching modes of Azobenzene (AZBN). It was found that the N=N stretching mode of Raman band shape shifts to lower frequency region with the increase in temperature. The Raman intensity was also decreased with the increase of temperature. The change in bandwidth with the increase in temperature has been studied. The FTIR spectrum of the molecule is recorded so as to complement the Raman spectra. In order to investigate the possibility of undergoing dimerization and trimerization as well as the stability of this molecule, ab initio calculation for geometry optimization and vibrational wavenumber calculation have been performed. Theoretically calculated values are found in good agreement with the experimental results.

Keywords: azobenzene, temperature, ab-initio, frequency

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4047 Single Atom Manipulation with 4 Scanning Tunneling Microscope Technique

Authors: Jianshu Yang, Delphine Sordes, Marek Kolmer, Christian Joachim

Abstract:

Nanoelectronics, for example the calculating circuits integrating at molecule scale logic gates, atomic scale circuits, has been constructed and investigated recently. A major challenge is their functional properties characterization because of the connecting problem from atomic scale to micrometer scale. New experimental instruments and new processes have been proposed therefore. To satisfy a precisely measurement at atomic scale and then connecting micrometer scale electrical integration controller, the technique improvement is kept on going. Our new machine, a low temperature high vacuum four scanning tunneling microscope, as a customer required instrument constructed by Omicron GmbH, is expected to be scaling down to atomic scale characterization. Here, we will present our first testified results about the performance of this new instrument. The sample we selected is Au(111) surface. The measurements have been taken at 4.2 K. The atomic resolution surface structure was observed with each of four scanners with noise level better than 3 pm. With a tip-sample distance calibration by I-z spectra, the sample conductance has been derived from its atomic locally I-V spectra. Furthermore, the surface conductance measurement has been performed using two methods, (1) by landing two STM tips on the surface with sample floating; and (2) by sample floating and one of the landed tips turned to be grounding. In addition, single atom manipulation has been achieved with a modified tip design, which is comparable to a conventional LT-STM.

Keywords: low temperature ultra-high vacuum four scanning tunneling microscope, nanoelectronics, point contact, single atom manipulation, tunneling resistance

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4046 Influence of Moringa Leaves Extract on the Response of Hb Molecule to Dose Rates’ Changes: II. Relaxation Time and Its Thermodynamic Driven State Functions

Authors: Mohamed M. M. Elnasharty, Azhar M. Elwan

Abstract:

Irradiation deposits energy through ionisation changing the bio-system’s net dipole, allowing the use of dielectric parameters and thermodynamic state functions related to these parameters as biophysical detectors to electrical inhomogeneity within the biosystem. This part is concerned with the effect of Moringa leaves extract, natural supplement, on the response of the biosystem to two different dose rates of irradiation. Having Hb molecule as a representative to the biosystem to be least invasive to the biosystem, dielectric measurements were used to extract the relaxation time of certain process found in the Hb spectrum within the indicated frequency window and the interrelated thermodynamic state functions were calculated from the deduced relaxation time. The results showed that relaxation time was decreased for both dose rates indicating a strong influence of Moringa on the response of biosystem and consequently Hb molecule. This influence was presented in the relaxation time and other parameters as well.

Keywords: activation energy, DC conductivity, dielectric relaxation, enthalpy change, Moringa leaves extract, relaxation time

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4045 Photophysics of a Coumarin Molecule in Graphene Oxide Containing Reverse Micelle

Authors: Aloke Bapli, Debabrata Seth

Abstract:

Graphene oxide (GO) is the two-dimensional (2D) nanoscale allotrope of carbon having several physiochemical properties such as high mechanical strength, high surface area, strong thermal and electrical conductivity makes it an important candidate in various modern applications such as drug delivery, supercapacitors, sensors etc. GO has been used in the photothermal treatment of cancers and Alzheimer’s disease etc. The main idea to choose GO in our work is that it is a surface active molecule, it has a large number of hydrophilic functional groups such as carboxylic acid, hydroxyl, epoxide on its surface and in basal plane. So it can easily interact with organic fluorophores through hydrogen bonding or any other kind of interaction and easily modulate the photophysics of the probe molecules. We have used different spectroscopic techniques for our work. The Ground-state absorption spectra and steady-state fluorescence emission spectra were measured by using UV-Vis spectrophotometer from Shimadzu (model-UV-2550) and spectrofluorometer from Horiba Jobin Yvon (model-Fluoromax 4P) respectively. All the fluorescence lifetime and anisotropy decays were collected by using time-correlated single photon counting (TCSPC) setup from Edinburgh instrument (model: LifeSpec-II, U.K.). Herein, we described the photophysics of a hydrophilic molecule 7-(n,n׀-diethylamino) coumarin-3-carboxylic acid (7-DCCA) in the reverse micelles containing GO. It was observed that photophysics of dye is modulated in the presence of GO compared to photophysics of dye in the absence of GO inside the reverse micelles. Here we have reported the solvent relaxation and rotational relaxation time in GO containing reverse micelle and compare our work with normal reverse micelle system by using 7-DCCA molecule. Normal reverse micelle means reverse micelle in the absence of GO. The absorption maxima of 7-DCCA were blue shifted and emission maxima were red shifted in GO containing reverse micelle compared to normal reverse micelle. The rotational relaxation time in GO containing reverse micelle is always faster compare to normal reverse micelle. Solvent relaxation time, at lower w₀ values, is always slower in GO containing reverse micelle compare to normal reverse micelle and at higher w₀ solvent relaxation time of GO containing reverse micelle becomes almost equal to normal reverse micelle. Here emission maximum of 7-DCCA exhibit bathochromic shift in GO containing reverse micelles compared to that in normal reverse micelles because in presence of GO the polarity of the system increases, as polarity increases the emission maxima was red shifted an average decay time of GO containing reverse micelle is less than that of the normal reverse micelle. In GO containing reverse micelle quantum yield, decay time, rotational relaxation time, solvent relaxation time at λₑₓ=375 nm is always higher than λₑₓ=405 nm, shows the excitation wavelength dependent photophysics of 7-DCCA in GO containing reverse micelles.

Keywords: photophysics, reverse micelle, rotational relaxation, solvent relaxation

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