Search results for: natural molecular crowding
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 7400

Search results for: natural molecular crowding

7400 Effect of Natural Molecular Crowding on the Structure and Stability of DNA Duplex

Authors: Chaudhari S. G., Saxena, S.

Abstract:

We systematically and quantitatively investigated the effect of glucose as a model of natural molecular crowding agent on the structure and thermodynamics of Watson-Crick base paired three duplexes (named as D1, D2 and D3) of different base compositions and lengths. Structural analyses demonstrated that duplexes (D1 and D2) folded into B-form with different cations in the absence and presence of glucose while duplex (D3) folded into mixed A and B-form. Moreover, we demonstrated that the duplex was more stable in the absence of glucose, and marginally destabilized in its presence because glucose act as a weak structure breaker on the tetrahedral network of water. In the absence of glucose, the values of ΔG°25 for duplex (D1) were -13.56, -13.76, -12.46, and -12.36 kcal/mol, for duplex (D2) were -13.64, -12.93, -12.86, and -12.30 kcal/mol, for duplex (D3) were -10.05, -11.76, -9.91, -9.70 kcal/mol in the presence of Na+, K+, Na+ + Mg++ and K+ + Mg++ respectively. At high concentration of glucose (1:10000), there was increase in ΔG°25 for duplex (D1) -12.47, -12.37, -11.96, -11.55 kcal/mol, for duplex (D2) -12.37, -11.47, -11.98, -11.01 kcal/mol and for duplex (D3) -8.47, -9.17, -9.16, -8.66 kcal/mol. Our results provide the information that structure and stability of DNA duplex depends on the structure of molecular crowding agent present in its close vicinity. In this study, I have taken the hydration of simple sugar as an essential model for understanding interactions between hydrophilic groups and interfacial water molecules and its effect on hydrogen bonded DNA duplexes. On the basis of these relatively simple building blocks I hope to gain some insights for understanding more generally the properties of sugar–water–salt systems with DNA duplexes.

Keywords: natural molecular crowding, DNA Duplex, structure of DNA, bioengineering and life sciences

Procedia PDF Downloads 427
7399 Multi-Objective Random Drift Particle Swarm Optimization Algorithm Based on RDPSO and Crowding Distance Sorting

Authors: Yiqiong Yuan, Jun Sun, Dongmei Zhou, Jianan Sun

Abstract:

In this paper, we presented a Multi-Objective Random Drift Particle Swarm Optimization algorithm (MORDPSO-CD) based on RDPSO and crowding distance sorting to improve the convergence and distribution with less computation cost. MORDPSO-CD makes the most of RDPSO to approach the true Pareto optimal solutions fast. We adopt the crowding distance sorting technique to update and maintain the archived optimal solutions. Introducing the crowding distance technique into MORDPSO can make the leader particles find the true Pareto solution ultimately. The simulation results reveal that the proposed algorithm has better convergence and distribution

Keywords: multi-objective optimization, random drift particle swarm optimization, crowding distance sorting, pareto optimal solution

Procedia PDF Downloads 212
7398 Impact of Emergency Medicine Department Crowding on Mortality

Authors: Morteza Gharibi, Abdolghader Pakniat, Somayeh Bahrampouri

Abstract:

Introduction: Emergency department (E.R.) crowding is a serious widespread problem in hospitals that leads to irregularities, a slower rate of delivery of services to patients, and a long-term stay. In addition, the long-term stay in the E.D. reduces the possibility of providing services with appropriate quality to other patients who are undergoing medical emergencies, which leads to dissatisfaction among patients. This study aimed to determine the relationship between ED-crowding and the mortality rate of the patients referred to the E.D. In a retrospective cohort study, all patients who expired in first 24 hours of admission were enrolled in the study. Crowding index at the moment of admission was calculated using Edwin Score. The data including history and physical examination, time of arrival in the E.D., diagnosis (using ICD 10 code), time of death, cause of death, demographic information was recoded based on triage forms on admission and patients’ medical files. Data analysis was performed by using descriptive statistics and chi square test, ANOVA tests using SPSS ver. 19. The time of arrival in E.D. to death in crowded E.D. conditions, with an average of five hours and 25 minutes, was significantly higher than the average admission Time of arrival in E.D. to death in active and crowded E.D. conditions. More physicians and nurses can be employed during crowded times to reduce staff fatigue and improve their performance during these hours.

Keywords: mortality, emergency, department, crowding

Procedia PDF Downloads 60
7397 Ambient Factors in the Perception of Crowding in Public Transport

Authors: John Zacharias, Bin Wang

Abstract:

Travel comfort is increasingly seen as crucial to effecting the switch from private motorized modes to public transit. Surveys suggest that travel comfort is closely related to perceived crowding, that may involve lack of available seating, difficulty entering and exiting, jostling and other physical contacts with strangers. As found in studies on environmental stress, other factors may moderate perceptions of crowding–in this case, we hypothesize that the ambient environment may play a significant role. Travel comfort was measured by applying a structured survey to randomly selected passengers (n=369) on 3 lines of the Beijing metro on workdays. Respondents were standing with all seats occupied and with car occupancy at 14 levels. A second research assistant filmed the metro car while passengers were interviewed, to obtain the total number of passengers. Metro lines 4, 6 and 10 were selected that travel through the central city north-south, east-west and circumferentially. Respondents evaluated the following factors: crowding, noise, smell, air quality, temperature, illumination, vibration and perceived safety as they experienced them at the time of interview, and then were asked to rank these 8 factors according to their importance for their travel comfort. Evaluations were semantic differentials on a 7-point scale from highly unsatisfactory (-3) to highly satisfactory (+3). The control variables included age, sex, annual income and trip purpose. Crowding was assessed most negatively, with 41% of the scores between -3 and -2. Noise and air quality were also assessed negatively, with two-thirds of the evaluations below 0. Illumination was assessed most positively, followed by crime, vibration and temperature, all scoring at indifference (0) or slightly positive. Perception of crowding was linearly and positively related to the number of passengers in the car. Linear regression tested the impact of ambient environmental factors on perception of crowding. Noise intensity accounted for more than the actual number of individuals in the car in the perception of crowding, with smell also contributing. Other variables do not interact with the crowding variable although the evaluations are distinct. In all, only one-third of the perception of crowding (R2=.154) is explained by the number of people, with the other ambient environmental variables accounting for two-thirds of the variance (R2=.316). However, when ranking the factors by their importance to travel comfort, perceived crowding made up 69% of the first rank, followed by noise at 11%. At rank 2, smell dominates (25%), followed by noise and air quality (17%). Commuting to work induces significantly lower evaluations of travel comfort with shopping the most positive. Clearly, travel comfort is particularly important to commuters. Moreover, their perception of crowding while travelling on metro is highly conditioned by the ambient environment in the metro car. Focussing attention on the ambient environmental conditions of the metro is an effective way to address the primary concerns of travellers with overcrowding. In general, the strongly held opinions on travel comfort require more attention in the effort to induce ridership in public transit.

Keywords: ambient environment, mass rail transit, public transit, travel comfort

Procedia PDF Downloads 226
7396 The Success Rate of Anterior Crowding Orthodontic Treatment Using Removable Appliances

Authors: Belly Yordan

Abstract:

Orthodontic treatment can be done by using the fix and removable orthodontic appliance. The success of treatment depends on the patient’s age, the type of malocclusion, treatment of space discrepancy, patient’s oral hygiene, operator skills, and patient cooperation. This case report was aimed to show the success of orthodontic treatment in patients with skeletal class I relationship, class I angle dental malocclusion with anterior crowding and rotation by using a removable appliance with modification. The removable appliance used is standard with removable plate components such as passive clasp (Adam’s hook clasp) accompanied with some active clasps (labial bow, some springs, etc.). A button is used as an additional tool or combined with other tools to correct tooth in rotated position. The results obtained by the success of treatments which is shown in pre and post-treatment photos, the overjet was reduced, the arch form became normal, the tooth malposition became normal, and rotation was corrected. Facial profile appearance of the patient is getting better, and the dental coordination also became better. This case report is to prove that treatment with the removable appliance is quite successful with the robust wearing of appropriate retainers.

Keywords: success rate, anterior crowding, orthodontic treatment, removable appliances

Procedia PDF Downloads 134
7395 Preventing Neurodegenerative Diseases by Stabilization of Superoxide Dismutase by Natural Polyphenolic Compounds

Authors: Danish Idrees, Vijay Kumar, Samudrala Gourinath

Abstract:

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease caused by misfolding and aggregation of Cu, Zn superoxide dismutase (SOD1). The use of small molecules has been shown to stabilize the SOD1 dimer and preventing its dissociation and aggregation. In this study, we employed molecular docking, molecular dynamics simulation and surface plasmon resonance (SPR) to study the interactions between SOD1 and natural polyphenolic compounds. In order to explore the noncovalent interaction between SOD1 and natural polyphenolic compounds, molecular docking and molecular dynamic (MD) simulations were employed to gain insights into the binding modes and free energies of SOD1-polyphenolic compounds. MM/PBSA methods were used to calculate free energies from obtained MD trajectories. The compounds, Hesperidin, Ergosterol, and Rutin showed the excellent binding affinity in micromolar range with SOD1. Ergosterol and Hesperidin have the strongest binding affinity to SOD1 and was subjected to further characterization. Biophysical experiments using Circular Dichroism and Thioflavin T fluorescence spectroscopy results show that the binding of these two compounds can stabilize SOD1 dimer and inhibit the aggregation of SOD1. Molecular simulation results also suggest that these compounds reduce the dissociation of SOD1 dimers through direct interaction with the dimer interface. This study will be helpful to develop other drug-like molecules which may have the effect to reduce the aggregation of SOD1.

Keywords: amyotrophic lateral sclerosis, molecular dynamics simulation, surface plasmon resonance, superoxide dismutase

Procedia PDF Downloads 99
7394 First-Principles Study of Inter-Cage Interactions in Inorganic Molecular Crystals

Authors: Abdul Majid, Alia Jabeen, Nimra Zulifqar

Abstract:

The inorganic molecular crystal (IMCs) due to their unusual structure has grabbed a lot of attention due to anisotropy in crystal structure. The IMCs consist of the molecular structures joined together via weak forces. Therefore, a difference between the bonding between the inter-cage and intra-cage interactions exists. To look closely at the bonding and interactions, we investigated interactions between two cages of Sb2O3 structure. The interactions were characterized via Extended Transition State-Natural Orbital for Chemical Valence-method (ETS-NOCV), Natural Bond Orbitals (NBO) and Quantum Theory of Atoms in Molecules (QTAIM). The results revealed strong intra-cage covalent bonding while weak van der Waals (vdWs) interactions along inter-cages exits. This structure cannot be termed as layered material although they have anisotropy in bonding and presence of weak vdWs interactions but its bulk is termed as inorganic layered clusters. This is due to the fact that the free standing sheet/films with these materials are not possible. This type of structures may be the most feasible to be used for the system to deal with high pressures and stress bearing materials.

Keywords: inorganic molecular crystals, density functional theory, cages, interactions

Procedia PDF Downloads 51
7393 Naturally Occurring Chemicals in Biopesticides' Resistance Control through Molecular Topology

Authors: Riccardo Zanni, Maria Galvez-Llompart, Ramon Garcia-Domenech, Jorge Galvez

Abstract:

Biopesticides, such as naturally occurring chemicals, pheromones, fungi, bacteria and insect predators are often a winning choice in crop protection because of their environmental friendly profile. They are considered to have lower toxicity than traditional pesticides. After almost a century of pesticides use, resistances to traditional insecticides are wide spread, while those to bioinsecticides have raised less attention, and resistance management is frequently neglected. This seems to be a crucial mistake since resistances have already occurred for many marketed biopesticides. With an eye to the future, we present here a selection of new natural occurring chemicals as potential bioinsecticides. The molecules were selected using a consolidated mathematical paradigm called molecular topology. Several QSAR equations were depicted and subsequently applied for the virtual screening of hundred thousands molecules of natural origin, which resulted in the selection of new potential bioinsecticides. The most innovative aspect of this work does not only reside in the importance of the identification of new molecules overcoming biopesticides’ resistances, but on the possibility to promote shared knowledge in the field of green chemistry through this unique in silico discipline named molecular topology.

Keywords: green chemistry, QSAR, molecular topology, biopesticide

Procedia PDF Downloads 278
7392 Avoiding Gas Hydrate Problems in Qatar Oil and Gas Industry: Environmentally Friendly Solvents for Gas Hydrate Inhibition

Authors: Nabila Mohamed, Santiago Aparicio, Bahman Tohidi, Mert Atilhan

Abstract:

Qatar's one of the biggest problem in processing its natural resource, which is natural gas, is the often occurring blockage in the pipelines caused due to uncontrolled gas hydrate formation in the pipelines. Several millions of dollars are being spent at the process site to dehydrate the blockage safely by using chemical inhibitors. We aim to establish national database, which addresses the physical conditions that promotes Qatari natural gas to form gas hydrates in the pipelines. Moreover, we aim to design and test novel hydrate inhibitors that are suitable for Qatari natural gas and its processing facilities. From these perspectives we are aiming to provide more effective and sustainable reservoir utilization and processing of Qatari natural gas. In this work, we present the initial findings of a QNRF funded project, which deals with the natural gas hydrate formation characteristics of Qatari type gas in both experimental (PVTx) and computational (molecular simulations) methods. We present the data from the two fully automated apparatus: a gas hydrate autoclave and a rocking cell. Hydrate equilibrium curves including growth/dissociation conditions for multi-component systems for several gas mixtures that represent Qatari type natural gas with and without the presence of well known kinetic and thermodynamic hydrate inhibitors. Ionic liquids were designed and used for testing their inhibition performance and their DFT and molecular modeling simulation results were also obtained and compared with the experimental results. Results showed significant performance of ionic liquids with up to 0.5 % in volume with up to 2 to 4 0C inhibition at high pressures.

Keywords: gas hydrates, natural gas, ionic liquids, inhibition, thermodynamic inhibitors, kinetic inhibitors

Procedia PDF Downloads 1270
7391 Theoretical Study of Carbonic Anhydrase-Ii Inhibitors for Treatment of Glaucoma

Authors: F. Boukli Hacene, W. Soufi, S. Ghalem

Abstract:

Glaucoma disease is a progressive degenerative optic neuropathy, with irreversible visual field deficits and high eye pressure being one of the risk factors. Sulfonamides are carbonic anhydrase-II inhibitors that aim to decrease the secretion of aqueous humor by direct inhibition of this enzyme at the level of the ciliary processes. These drugs present undesirable effects that are difficult to accept by the patient. In our study, we are interested in the inhibition of carbonic anhydrase-II by different natural ligands (curcumin analogues) using molecular modeling methods using molecular operating environment (MOE) software to predict their interaction with this enzyme.

Keywords: carbonic anhydrase-II, curcumin analogues, drug research, molecular modeling

Procedia PDF Downloads 52
7390 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

Procedia PDF Downloads 490
7389 Reducing Ambulance Offload Delay: A Quality Improvement Project at Princess Royal University Hospital

Authors: Fergus Wade, Jasmine Makker, Matthew Jankinson, Aminah Qamar, Gemma Morrelli, Shayan Shah

Abstract:

Background: Ambulance offload delays (AODs) affect patient outcomes. At baseline, the average AOD at Princess Royal University Hospital (PRUH) was 41 minutes, in breach of the 15-minute target. Aims: By February 2023, we aimed to reduce: the average AOD to 30 minutes percentage of AOD >30 minutes (PA30) to 25% and >60 minutes (PA60) to 10% Methods: Following a root-cause analysis, we implemented 2 Plan, Do, Study, Act (PDSA) cycles. PDSA-1 ‘Drop-and-run’: ambulances waiting >15 minutes for a handover left the patients in the Emergency Department (ED) and returned to the community. PDSA-2: Booking in the patients before the handover, allowing direct updates to online records, eliminating the need for handwritten notes. Outcome measures: AOD, PA30, and PA60, and process measures: total ambulances and patients in the ED were recorded for 16 weeks. Results: In PDSA-1, all parameters increased slightly despite unvarying ED crowding. In PDSA-2, two shifts in data were seen: initially, a sharp increase in the outcome measures consistent with increased ED crowding, followed by a downward shift when crowding returned to baseline (p<0.01). Within this interval, the AOD reduced to 29.9 minutes, and PA30 and PA60 were 31.2% and 9.2% respectively. Discussion/conclusion: PDSA-1 didn’t result in any significant changes; lack of compliance was a key cause. The initial upward shift in PDSA-2 is likely associated with NHS staff strikes. However, during the second interval, the AOD and the PA60 met our targets of 30 minutes and 10%, respectively, improving patient flow in the ED. This was sustained without further input and if maintained, saves 2 paramedic shifts every 3 days.

Keywords: ambulance offload, district general hospital, handover, quality improvement

Procedia PDF Downloads 56
7388 In Silico Study of Alpha glucosidase Inhibitors by Flavonoids

Authors: Boukli Hacene Faiza, Soufi Wassila, Ghalem Said

Abstract:

The oral antidiabetics drugs such as alpha glucosidase inhibitors present undesirable effects like acarbose. Flavonoids are class of molecules widely distributed in plants, for this reason we are interested in our work to study the inhibition in silico of alpha glucosidase by natural ligands ( flavonoids analogues) using molecular modeling methods using MOE (Molecular Operating Environment) software to predict their interaction with this enzyme with score energy, ADME /T tests and druglikeness properties experiments. Two flavonoids Beicalein and Apigenin have high binding affinity with alpha glucosidase with lower IC50 supposed potent inhibitors.

Keywords: alpha glucosidase, flavonoides analogues, drug research, molecular modeling

Procedia PDF Downloads 60
7387 Clustering of Natural and Nature Derived Compounds for Cardiovascular Disease: Pharmacophore Modeling

Authors: S. Roy, R. Rekha, K. Sriram, G. Subhadra, R. Johana

Abstract:

Cardiovascular disease remains a leading cause of death in most industrialized countries. Many chemical drugs are available in the market which targets different receptor proteins related to cardiovascular diseases. Of late the traditional herbal drugs are safer when compared to chemical drugs because of its side effects. However, many herbal remedies used in treating cardiovascular diseases have not undergone scientific assessment to prove its pharmacological activities. There are many natural compounds, nature derived and Natural product mimic compounds are available which are in the market as approved drug. In the most of the cases drug activity at the molecular level are not known. Here we have categorized those compounds with our experimental compounds in different classes based on the structural similarity and physicochemical properties, using a tool, Chemmine and has attempted to understand the mechanism of the action of a experimental compound, which are clustered with Simvastatin, Lovastatin, Mevastatin and Pravastatin. Target protein molecule for Simvastatin, Lovastatin, Mevastatin and Pravastatin is HMG-CoA reductase, so we concluded that the experimental compound may be able to bind to the same target. Molecular docking and atomic interaction studies with simvastatin and our experimental compound were compared. A pharmacophore modeling was done based on the experimental compound and HMG-CoA reductase inhibitor.

Keywords: molecular docking, physicochemical properties, pharmacophore modeling structural similarity, pravastatin

Procedia PDF Downloads 283
7386 Molecular Interaction of Acetylcholinesterase with Flavonoids Involved in Neurodegenerative Diseases

Authors: W. Soufi, F. Boukli Hacene, S. Ghalem

Abstract:

Alzheimer's disease (AD) is a neurodegenerative disease that leads to a progressive and permanent deterioration of nerve cells. This disease is progressively accompanied by an intellectual deterioration leading to psychological manifestations and behavioral disorders that lead to a loss of autonomy. It is the most frequent of degenerative dementia. Alzheimer's disease (AD), which affects a growing number of people, has become a major public health problem in a few years. In the context of the study of the mechanisms governing the evolution of AD disease, we have found that natural flavonoids are good acetylcholinesterase inhibitors that reduce the rate of ßA secretion in neurons. This work is to study the inhibition of acetylcholinesterase (AChE) which is an enzyme involved in Alzheimer's disease, by methods of molecular modeling. These results will probably help in the development of an effective therapeutic tool in the fight against the development of Alzheimer's disease. Our goal of the research is to study the inhibition of acetylcholinesterase (AChE) by molecular modeling methods.

Keywords: Alzheimer's disease, acetylcholinesterase, flavonoids, molecular modeling

Procedia PDF Downloads 65
7385 Thick Disc Molecular Gas Fraction in NGC 6946

Authors: Narendra Nath Patra

Abstract:

Several recent studies reinforce the existence of a thick molecular disc in galaxies along with the dynamically cold thin disc. Assuming a two-component molecular disc, we model the disc of NGC 6946 as a four-component system consists of stars, HI, thin disc molecular gas, and thick disc molecular gas in vertical hydrostatic equilibrium. Following, we set up the joint Poisson-Boltzmann equation of hydrostatic equilibrium and solve it numerically to obtain a three-dimensional density distribution of different baryonic components. Using the density solutions and the observed rotation curve, we further build a three-dimensional dynamical model of the molecular disc and consecutively produce simulated CO spectral cube and spectral width profile. We find that the simulated spectral width profiles distinguishably differs for different assumed thick disc molecular gas fraction. Several CO spectral width profiles are then produced for different assumed thick disc molecular gas fractions and compared with the observed one to obtain the best fit thick disc molecular gas fraction profile. We find that the thick disc molecular gas fraction in NGC 6946 largely remains constant across its molecular disc with a mean value of 0.70 +/- 0.09. We also estimate the amount of extra-planar molecular gas in NGC 6946. We find 60% of the total molecular gas is extra-planar at the central region, whereas this fraction reduces to ~ 35% at the edge of the molecular disc. With our method, for the first time, we estimate the thick disc molecular gas fraction as a function of radius in an external galaxy with sub-kpc resolution.

Keywords: galaxies: kinematics and dynamic, galaxies: spiral, galaxies: structure , ISM: molecules, molecular data

Procedia PDF Downloads 95
7384 Molecular Clustering and Velocity Increase in Converging-Diverging Nozzle in Molecular Dynamics Simulation

Authors: Jeoungsu Na, Jaehawn Lee, Changil Hong, Suhee Kim

Abstract:

A molecular dynamics simulation in a converging-diverging nozzle was performed to study molecular collisions and their influence to average flow velocity according to a variety of vacuum levels. The static pressures and the dynamic pressure exerted by the molecule collision on the selected walls were compared to figure out the intensity variances of the directional flows. With pressure differences constant between the entrance and the exit of the nozzle, the numerical experiment was performed for molecular velocities and directional flows. The result shows that the velocities increased at the nozzle exit as the vacuum level gets higher in that area because less molecular collisions.

Keywords: cavitation, molecular collision, nozzle, vacuum, velocity increase

Procedia PDF Downloads 398
7383 Normal Coordinate Analysis, Molecular Structure, Vibrational, Electronic Spectra, and NMR Investigation of 4-Amino-3-Phenyl-1H-1,2,4-Triazole-5(4H)-Thione by Ab Initio HF and DFT Method

Authors: Khaled Bahgat

Abstract:

In the present work, the characterization of 4-Amino-3-phenyl-1H-1,2,4-triazole-5(4H)-thione (APTT) molecule was carried out by quantum chemical method and vibrational spectral techniques. The FT-IR (4000–400 cm_1) and FT-Raman (4000–100 cm_1) spectra of APTT were recorded in solid phase. The UV–Vis absorption spectrum of the APTT was recorded in the range of 200–400 nm. The molecular geometry, harmonic vibrational frequencies and bonding features of APTT in the ground state have been calculated by HF and DFT methods using 6-311++G(d,p) basis set. The complete vibrational frequency assignments were made by normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMF). The molecular stability and bond strength were investigated by applying the natural bond orbital analysis (NBO) and natural localized molecular orbital (NLMO) analysis. The electronic properties, such as excitation energies, absorption wavelength, HOMO and LUMO energies were performed by time depended DFT (TD-DFT) approach. The 1H and 13C nuclear magnetic resonance chemical shift of the molecule were calculated using the gauge-including atomic orbital (GIAO) method and compared with experimental results. Finally, the calculation results were analyzed to simulate infrared, FT-Raman and UV spectra of the title compound which shows better agreement with observed spectra.

Keywords: 4-amino-3-phenyl-1H-1, 2, 4-triazole-5(4H)-thione, vibrational assignments, normal coordinate analysis, quantum mechanical calculations

Procedia PDF Downloads 433
7382 Origin of Hydrogen Bonding: Natural Bond Orbital Electron Donor-Acceptor Interactions

Authors: Mohamed Ayoub

Abstract:

We perform computational investigation using density functional theory, B3LYP with aug-cc-pVTZ basis set followed by natural bond orbital analysis (NBO), which provides best single “natural Lewis structure” (NLS) representation of chosen wavefunction (Ψ) with natural resonance theory (NRT) to provide an analysis of molecular electron density in terms of resonance structures (RS) and weights (w). We selected for the study a wide range of gas phase dimers (B…HA), with hydrogen bond dissociation energies (ΔEB…H) that span more than two orders of magnitude. We demonstrate that charge transfer from a donor Lewis-type NBO (nB:) to an acceptor non-Lewis-type NBO (σHA*) is the primary cause for H-bonding not classical electrostatic (dipole-dipole or ionic). We provide a variety of structure, and spectroscopic descriptors to support the conclusion, such as IR frequency shift (ΔνHA), H-bond penetration distance (ΔRB..H), bond order (bB..H), charge-transfer (CTB→HA) and the corresponding donor-acceptor stabilization energy (ΔE(2)).

Keywords: natural bond orbital, hydrogen bonding, electron donor, electron acceptor

Procedia PDF Downloads 399
7381 The Fabrication of Stress Sensing Based on Artificial Antibodies to Cortisol by Molecular Imprinted Polymer

Authors: Supannika Klangphukhiew, Roongnapa Srichana, Rina Patramanon

Abstract:

Cortisol has been used as a well-known commercial stress biomarker. A homeostasis response to psychological stress is indicated by an increased level of cortisol produced in hypothalamus-pituitary-adrenal (HPA) axis. Chronic psychological stress contributing to the high level of cortisol relates to several health problems. In this study, the cortisol biosensor was fabricated that mimicked the natural receptors. The artificial antibodies were prepared using molecular imprinted polymer technique that can imitate the performance of natural anti-cortisol antibody with high stability. Cortisol-molecular imprinted polymer (cortisol-MIP) was obtained using the multi-step swelling and polymerization protocol with cortisol as a target molecule combining methacrylic acid:acrylamide (2:1) with bisacryloyl-1,2-dihydroxy-1,2-ethylenediamine and ethylenedioxy-N-methylamphetamine as cross-linkers. Cortisol-MIP was integrated to the sensor. It was coated on the disposable screen-printed carbon electrode (SPCE) for portable electrochemical analysis. The physical properties of Cortisol-MIP were characterized by means of electron microscope techniques. The binding characteristics were evaluated via covalent patterns changing in FTIR spectra which were related to voltammetry response. The performance of cortisol-MIP modified SPCE was investigated in terms of detection range, high selectivity with a detection limit of 1.28 ng/ml. The disposable cortisol biosensor represented an application of MIP technique to recognize steroids according to their structures with feasibility and cost-effectiveness that can be developed to use in point-of-care.

Keywords: stress biomarker, cortisol, molecular imprinted polymer, screen-printed carbon electrode

Procedia PDF Downloads 227
7380 Molecular Junctions between Graphene Strips: Electronic and Transport Properties

Authors: Adel Belayadi, Ahmed Mougari, Boualem Bourahla

Abstract:

Molecular junctions are currently considered a promising style in the miniaturization of electronic devices. In this contribution, we provide a tight-binding model to investigate the quantum transport properties across-molecular junctions sandwiched between 2D-graphene nanoribbons in the zigzag direction. We investigate, in particular, the effect of embedded atoms such as Gold and Silicon across the molecular junction. The results exhibit a resonance behavior in terms of incident Fermi levels, depending on the molecular junction type. Additionally, the transport properties under a perpendicular magnetic field exhibit an oscillation for the transmittance versus the magnetic field strength.

Keywords: molecular junction, 2D-graphene nanoribbons, quantum transport properties, magnetic field

Procedia PDF Downloads 53
7379 Application of Systems Engineering Tools and Methods to Improve Healthcare Delivery Inside the Emergency Department of a Mid-Size Hospital

Authors: Mohamed Elshal, Hazim El-Mounayri, Omar El-Mounayri

Abstract:

Emergency department (ED) is considered as a complex system of interacting entities: patients, human resources, software and hardware systems, interfaces, and other systems. This paper represents a research for implementing a detailed Systems Engineering (SE) approach in a mid-size hospital in central Indiana. This methodology will be applied by “The Initiative for Product Lifecycle Innovation (IPLI)” institution at Indiana University to study and solve the crowding problem with the aim of increasing throughput of patients and enhance their treatment experience; therefore, the nature of crowding problem needs to be investigated with all other problems that leads to it. The presented SE methods are workflow analysis and systems modeling where SE tools such as Microsoft Visio are used to construct a group of system-level diagrams that demonstrate: patient’s workflow, documentation and communication flow, data systems, human resources workflow and requirements, leadership involved, and integration between ER different systems. Finally, the ultimate goal will be managing the process through implementation of an executable model using commercialized software tools, which will identify bottlenecks, improve documentation flow, and help make the process faster.

Keywords: systems modeling, ED operation, workflow modeling, systems analysis

Procedia PDF Downloads 142
7378 Molecular Dynamics Simulation of Free Vibration of Graphene Sheets

Authors: Seyyed Feisal Asbaghian Namin, Reza Pilafkan, Mahmood Kaffash Irzarahimi

Abstract:

TThis paper considers vibration of single-layered graphene sheets using molecular dynamics (MD) and nonlocal elasticity theory. Based on the MD simulations, Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), an open source software, is used to obtain fundamental frequencies. On the other hand, governing equations are derived using nonlocal elasticity and first order shear deformation theory (FSDT) and solved using generalized differential quadrature method (GDQ). The small-scale effect is applied in governing equations of motion by nonlocal parameter. The effect of different side lengths, boundary conditions and nonlocal parameter are inspected for aforementioned methods. Results are obtained from MD simulations is compared with those of the nonlocal elasticity theory to calculate appropriate values for the nonlocal parameter. The nonlocal parameter value is suggested for graphene sheets with various boundary conditions. Furthermore, it is shown that the nonlocal elasticity approach using classical plate theory (CLPT) assumptions overestimates the natural frequencies.

Keywords: graphene sheets, molecular dynamics simulations, fundamental frequencies, nonlocal elasticity theory, nonlocal parameter

Procedia PDF Downloads 467
7377 Molecular Docking Assessment of Pesticides Binding to Bacterial Chitinases

Authors: Diana Larisa Vladoiu, Vasile Ostafe, Adriana Isvoran

Abstract:

Molecular docking calculations reveal that pesticides provide favorable interactions with the bacterial chitinases. Pesticides interact with both hydrophilic and aromatic residues involved in the active site of the enzymes, their positions partially overlapping the substrate and the inhibitors locations. Molecular docking outcomes, in correlation with experimental literature data, suggest that the pesticides may be degraded or having an inhibitor effect on the activity of these enzymes, depending of the application dose and rate.

Keywords: chitinases, inhibition, molecular docking, pesticides

Procedia PDF Downloads 504
7376 Assessment of Drug Delivery Systems from Molecular Dynamic Perspective

Authors: M. Rahimnejad, B. Vahidi, B. Ebrahimi Hoseinzadeh, F. Yazdian, P. Motamed Fath, R. Jamjah

Abstract:

In this study, we developed and simulated nano-drug delivery systems efficacy in compare to free drug prescription. Computational models can be utilized to accelerate experimental steps and control the experiments high cost. Molecular dynamics simulation (MDS), in particular NAMD was utilized to better understand the anti-cancer drug interaction with cell membrane model. Paclitaxel (PTX) and dipalmitoylphosphatidylcholine (DPPC) were selected for the drug molecule and as a natural phospholipid nanocarrier, respectively. This work focused on two important interaction parameters between molecules in terms of center of mass (COM) and van der Waals interaction energy. Furthermore, we compared the simulation results of the PTX interaction with the cell membrane and the interaction of DPPC as a nanocarrier loaded by the drug with the cell membrane. The molecular dynamic analysis resulted in low energy between the nanocarrier and the cell membrane as well as significant decrease of COM amount in the nanocarrier and the cell membrane system during the interaction. Thus, the drug vehicle showed notably better interaction with the cell membrane in compared to free drug interaction with the cell membrane.

Keywords: anti-cancer drug, center of mass, interaction energy, molecular dynamics simulation, nanocarrier

Procedia PDF Downloads 297
7375 Observation of Inverse Blech Length Effect during Electromigration of Cu Thin Film

Authors: Nalla Somaiah, Praveen Kumar

Abstract:

Scaling of transistors and, hence, interconnects is very important for the enhanced performance of microelectronic devices. Scaling of devices creates significant complexity, especially in the multilevel interconnect architectures, wherein current crowding occurs at the corners of interconnects. Such a current crowding creates hot-spots at the respective corners, resulting in non-uniform temperature distribution in the interconnect as well. This non-uniform temperature distribution, which is exuberated with continued scaling of devices, creates a temperature gradient in the interconnect. In particular, the increased current density at corners and the associated temperature rise due to Joule heating accelerate the electromigration induced failures in interconnects, especially at corners. This has been the classic reliability issue associated with metallic interconnects. Herein, it is generally understood that electromigration induced damages can be avoided if the length of interconnect is smaller than a critical length, often termed as Blech length. Interestingly, the effect of non-negligible temperature gradients generated at these corners in terms of thermomigration and electromigration-thermomigration coupling has not attracted enough attention. Accordingly, in this work, the interplay between the electromigration and temperature gradient induced mass transport was studied using standard Blech structure. In this particular sample structure, the majority of the current is forcefully directed into the low resistivity metallic film from a high resistivity underlayer film, resulting in current crowding at the edges of the metallic film. In this study, 150 nm thick Cu metallic film was deposited on 30 nm thick W underlayer film in the configuration of Blech structure. Series of Cu thin strips, with lengths of 10, 20, 50, 100, 150 and 200 μm, were fabricated. Current density of ≈ 4 × 1010 A/m² was passed through Cu and W films at a temperature of 250ºC. Herein, along with expected forward migration of Cu atoms from the cathode to the anode at the cathode end of the Cu film, backward migration from the anode towards the center of Cu film was also observed. Interestingly, smaller length samples consistently showed enhanced migration at the cathode end, thus indicating the existence of inverse Blech length effect in presence of temperature gradient. A finite element based model showing the interplay between electromigration and thermomigration driving forces has been developed to explain this observation.

Keywords: Blech structure, electromigration, temperature gradient, thin films

Procedia PDF Downloads 223
7374 Redefining Problems and Challenges of Natural Resource Management in Indonesia

Authors: Amalia Zuhra

Abstract:

Indonesia is very rich with its natural resources. Natural resource management becomes a challenge for Indonesia. Improper management will make the natural resources run out and future generations will not be able to enjoy the natural wealth. A good rule of law and proper implementation determines the success of the management of a country's natural resources. This paper examines the need to redefine problems and challenges in the management of natural resources in Indonesia in the context of law. The purpose of this article is to overview the latest issues and challenges in natural resource management and to redefine legal provisions related to environmental management and human rights protection so that the management of natural resources in the present and future will be more sustainable. This paper finds that sustainable management of natural resources is absolutely essential. The aspect of environmental protection and human rights must be elaborated more deeply so that the management of natural resources can be done maximally without harming not only people but also the environment.

Keywords: international environmental law, human rights law, natural resource management, sustainable development

Procedia PDF Downloads 226
7373 In-Vitro Dextran Synthesis and Characterization of an Intracellular Glucosyltransferase from Leuconostoc Mesenteroides AA1

Authors: Afsheen Aman, Shah Ali Ul Qader

Abstract:

Dextransucrase [EC 2.4.1.5] is a glucosyltransferase that catalysis the biosynthesis of a natural biopolymer called dextran. It can catalyze the transfer of D-glucopyranosyl residues from sucrose to the main chain of dextran. This unique biopolymer has multiple applications in several industries and the key utilization of dextran lies on its molecular weight and the type of branching. Extracellular dextransucrase from Leuconostoc mesenteroides is most extensively studied and characterized. Limited data is available regarding cell-bound or intracellular dextransucrase and on the characterization of dextran produced by in-vitro reaction of intracellular dextransucrase. L. mesenteroides AA1 is reported to produce extracellular dextransucrase that catalyzes biosynthesis of a high molecular weight dextran with only α-(1→6) linkage. Current study deals with the characterization of an intracellular dextransucrase and in vitro biosynthesis of low molecular weight dextran from L. mesenteroides AA1. Intracellular dextransucrase was extracted from cytoplasm and purified to homogeneity for characterization. Kinetic constants, molecular weight and N-terminal sequence analysis of intracellular dextransucrase reveal unique variation with previously reported extracellular dextransucrase from the same strain. In vitro synthesized biopolymer was characterized using NMR spectroscopic techniques. Intracellular dextransucrase exhibited Vmax and Km values of 130.8 DSU ml-1 hr-1 and 221.3 mM, respectively. Optimum catalytic activity was detected at 35°C in 0.15 M citrate phosphate buffer (pH-5.5) in 05 minutes. Molecular mass of purified intracellular dextransucrase is approximately 220.0 kDa on SDS-PAGE. N-terminal sequence of the intracellular enzyme is: GLPGYFGVN that showed no homology with previously reported sequence for the extracellular dextransucrase. This intracellular dextransucrase is capable of in vitro synthesis of dextran under specific conditions. This intracellular dextransucrase is capable of in vitro synthesis of dextran under specific conditions and this biopolymer can be hydrolyzed into different molecular weight fractions for various applications.

Keywords: characterization, dextran, dextransucrase, leuconostoc mesenteroides

Procedia PDF Downloads 352
7372 Effect of Plasticizer Additives on the Mechanical Properties of Cement Composite: A Molecular Dynamics Analysis

Authors: R. Mohan, V. Jadhav, A. Ahmed, J. Rivas, A. Kelkar

Abstract:

Cementitious materials are an excellent example of a composite material with complex hierarchical features and random features that range from nanometer (nm) to millimeter (mm) scale. Multi-scale modeling of complex material systems requires starting from fundamental building blocks to capture the scale relevant features through associated computational models. In this paper, molecular dynamics (MD) modeling is employed to predict the effect of plasticizer additive on the mechanical properties of key hydrated cement constituent calcium-silicate-hydrate (CSH) at the molecular, nanometer scale level. Due to complexity, still unknown molecular configuration of CSH, a representative configuration widely accepted in the field of mineral Jennite is employed. The effectiveness of the Molecular Dynamics modeling to understand the predictive influence of material chemistry changes based on molecular/nanoscale models is demonstrated.

Keywords: cement composite, mechanical properties, molecular dynamics, plasticizer additives

Procedia PDF Downloads 411
7371 Understanding Nanocarrier Efficacy in Drug Delivery Systems Using Molecular Dynamics

Authors: Maedeh Rahimnejad, Bahman Vahidi, Bahman Ebrahimi Hoseinzadeh, Fatemeh Yazdian, Puria Motamed Fath, Roghieh Jamjah

Abstract:

Introduction: The intensive labor and high cost of developing new vehicles for controlled drug delivery highlights the need for a change in their discovery process. Computational models can be used to accelerate experimental steps and control the high cost of experiments. Methods: In this work, to better understand the interaction of anti-cancer drug and the nanocarrier with the cell membrane, we have done molecular dynamics simulation using NAMD. We have chosen paclitaxel for the drug molecule and dipalmitoylphosphatidylcholine (DPPC) as a natural phospholipid nanocarrier. Results: Next, center of mass (COM) between molecules and the van der Waals interaction energy close to the cell membrane has been analyzed. Furthermore, the simulation results of the paclitaxel interaction with the cell membrane and the interaction of DPPC as a nanocarrier loaded by the drug with the cell membrane have been compared. Discussion: Analysis by molecular dynamics (MD) showed that not only the energy between the nanocarrier and the cell membrane is low, but also the center of mass amount decreases in the nanocarrier and the cell membrane system during the interaction; therefore they show significantly better interaction in comparison to the individual drug with the cell membrane.

Keywords: anti-cancer drug, center of mass, interaction energy, molecular dynamics simulation, nanocarrier

Procedia PDF Downloads 253