Home About us Contact
|
Home About us Contact | ||
|
|
||
Dynamics Study (dynamics + study)
Kinds of Dynamics Study Selected AbstractsThermal Behavior of Tetrahydropyran-Intercalated VOPO4: Structural and Dynamics StudyEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 3 2007Klára Melánová Abstract The thermal behavior of tetrahydropyran-(THP-)intercalated VOPO4 was probed by an extensive combination of experimental methods (XRD, DSC, FTIR, solid-state NMR) and quantum chemical calculations. Two temperature-induced transitions were detected and all polymorphs exhibit a high degree of molecular order and tight packing of THP in VOPO4. The first reversible thermal transition at around 100 °C was attributed to boat/chair conformation changes of the THP molecules. Most probably, a low-temperature boat conformation of the guest molecules present in the interlayer space of VOPO4 changes to a high-temperature chair conformation. This rearrangement of the THP molecules was confirmed by variable-temperature 13C CP/MAS NMR spectroscopy. Quantum chemical calculations using a B3LYP functional and 6-31G(d) basis set also support this idea. The second change at around 140 °C is probably caused by a weakening of the donor,acceptor bond between the oxygen molecule of THP and the vanadium atom of the host and the formation of a disorder in packing of the THP molecules. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source] An Ab Initio Molecular Dynamics Study of Bioactive Phosphate Glasses,ADVANCED ENGINEERING MATERIALS, Issue 7 2010Emilia Tang First principles molecular dynamics simulations of ternary phosphate-based glasses P2O5CaONa2O (PBGs) have been carried out in order to provide an accurate description of the local structure and properties of these important materials for biomedical applications. The structures of PBGs with compositions (P2O5)0.45(CaO)x(Na2O)0.55,,,x (x,=,0.30, 0.35, and 0.40) were generated using a full ab initio molecular dynamics melt-and-quench procedure. The analysis of the structure of the glasses at 300,K shows the prevalence of the metaphosphate Q2 and pyrophosphate Q1 species, whereas the number of Q3 units, which constitute the three-dimensional phosphate network, significantly decreases with the increase in calcium content in the glass. Calculation of the pair and angular distribution functions suggests that the rigidity of the phosphate tetrahedral glass network increases with the concentration of calcium, an observation which is interpreted in terms of the tendency of Ca2+ to be a stronger coordinator than sodium. [source] Informal Caregiving Time and Costs for Urinary Incontinence in Older Individuals in the United StatesJOURNAL OF AMERICAN GERIATRICS SOCIETY, Issue 4 2002Kenneth M. Langa MD OBJECTIVES: To obtain nationally representative estimates of the additional time, and related cost, of informal caregiving associated with urinary incontinence in older individuals. DESIGN: Multivariate regression models using data from the 1993 Asset and Health Dynamics Study, a nationally representative survey of people aged 70 and older (N = 7,443). SETTING: Community-dwelling older people. PARTICIPANTS: National population-based sample of community-dwelling older people. MEASUREMENTS: Weekly hours of informal caregiving, and imputed cost of caregiver time, for community-dwelling older people who reported (1) no unintended urine loss, (2) incontinence that did not require the use of absorbent pads, and (3) incontinence that required the use of absorbent pads. RESULTS: Thirteen percent of men and 24% of women reported incontinence. After adjusting for sociodemographics, living situation, and comorbidities, continent men received 7.4 hours per week of care, incontinent men who did not use pads received 11.3 hours, and incontinent men who used pads received 16.6 hours (P < .001). Women in these groups received 5.9, 7.6, and 10.7 hours (P < .001), respectively. The additional yearly cost of informal care associated with incontinence was $1,700 and $4,000 for incontinent men who did not and did use pads, respectively, whereas, for women in these groups, the additional yearly cost was $700 and $2,000. Overall, this represents a national annual cost of more than $6 billion for incontinence-related informal care. CONCLUSIONS: The quantity of informal caregiving for older people with incontinence and its associated economic cost are substantial. Future analyses of the costs of incontinence, and the cost-effectiveness of interventions to prevent or treat incontinence, should consider the significant informal caregiving costs associated with this condition. [source] The Impact of Aortic/Subclavian Outflow Cannulation for Cardiopulmonary Bypass and Cardiac Support: A Computational Fluid Dynamics StudyARTIFICIAL ORGANS, Issue 9 2009Tim A.S. Kaufmann Abstract Approximately 100 000 cases of oxygen deficiency in the brain occur during cardiopulmonary bypass (CPB) procedures each year. In particular, perfusion of the carotid and vertebral arteries is affected. The position of the outflow cannula influences the blood flow to the cardiovascular system and thus end organ perfusion. Traditionally, the cannula returns blood into the ascending aorta. But some surgeons prefer cannulation to the right subclavian artery. A computational fluid dynamics study was initially undertaken for both approaches. The vessel model was created from real computed tomography/magnetic resonance imaging data of young healthy patients. The simulations were run with usual CPB conditions. The flow distribution for different cannula positions in the aorta was studied, as well as the impact of the cannula tip distance to vertebral artery for the subclavian position. The study presents a fast method of analyzing the flow distribution in the cardiovascular system, and can be adapted for other applications such as ventricular assist device support. It revealed that two effects cause the loss of perfusion seen clinically: a vortex under the brachiocephalic trunk and low pressure regions near the cannula jet. The results suggest that cannulation to the subclavian artery is preferred if the cannula tip is sufficiently far away from the branch of the vertebral artery. For the aortic positions, however, the cannula should be injected from the left body side. [source] ChemInform Abstract: Hydrated Electron Production by Reaction of Hydrogen Atoms with Hydroxide Ions: A First-Principles Molecular Dynamics Study.CHEMINFORM, Issue 44 2008Jean Philippe Renault Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] ChemInform Abstract: Molecular Dynamics Study of the Stabilization of the Silica Hexamer Si6O156- in Aqueous and Methanolic Solutions.CHEMINFORM, Issue 17 2008S. Caratzoulas Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] Molecular Dynamics Study of the Thermodynamic Properties of Calcium Apatites.CHEMINFORM, Issue 28 2006Part 2. Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF. [source] Water Permeation Through MCM-41 Channels: A Molecular Dynamics Study.CHEMINFORM, Issue 21 2006Kourosh Malek Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF. [source] A Molecular Dynamics Study of Thorium NitrideCHEMINFORM, Issue 30 2005Jun Adachi Abstract For Abstract see ChemInform Abstract in Full Text. [source] Thermal Fluctuations of the Unusually Symmetric and Stable Superoxide Tetrahydrate Complex: An ab initio Molecular Dynamics Study.CHEMINFORM, Issue 5 2003I-Feng W. Kuo No abstract is available for this article. [source] Importance of Interfacial Adsorption in the Biphasic Hydroformylation of Higher Olefins Promoted by Cyclodextrins: A Molecular Dynamics Study at the Decene/Water InterfaceCHEMISTRY - A EUROPEAN JOURNAL, Issue 7 2007Nicolas Sieffert Abstract We report herein a molecular dynamics study of the main species involved in the hydroformylation of higher olefins promoted by cyclodextrins in 1-decene/water biphasic systems at a temperature of 350,K. The two liquids form a well-defined sharp interface of approximately 7,Å width in the absence of solute; the decene molecules are generally oriented "parallel" to the interface where they display transient contacts with water. We first focused on rhodium complexes bearing water-soluble TPPTS3, ligands (where TPPTS3, represents tris(m -sulfonatophenyl)phosphine) involved in the early steps of the reaction. The most important finding concerned the surface activity of the "active" form of the catalyst [RhH(CO)(TPPTS)2]6,, the [RhH(CO)2(TPPTS)2]6, complex, and the key reaction intermediate [RhH(CO)(TPPTS)2(decene)]6, (with the olefin ,-coordinated to the metal center) which are adsorbed at the water side of the interface in spite of their ,6 charge. The free TPPTS3, ligands themselves are also surface-active, whereas the ,9 charged catalyst precursor [RhH(CO)(TPPTS)3]9, prefers to be solubilized in water. The role of cyclodextrins was then investigated by performing simulations on 2,6-dimethyl-,-cyclodextrin ("CD") and its inclusion complexes with the reactant (1-decene), a reaction product (undecanal), and the corresponding key reaction intermediate [RhH(CO)(TPPTS)2(decene)]6, as guests; they were all shown to be surface-active and prefer the interface over the bulk aqueous phase. These results suggest that the biphasic hydroformylation of higher olefins takes place "right" at the interface and that the CDs promote the "meeting" of the olefin and the catalyst in this peculiar region of the solution by forming inclusion complexes "preorganized" for the reaction. Our results thus point to the importance of adsorption at the liquid/liquid interface in this important phase-transfer-catalyzed reaction. [source] Car,Parrinello Molecular Dynamics Study of the Blue-Shifted F3CH,,,FCD3 System in Liquid N2CHEMPHYSCHEM, Issue 6 2006Pawel Rodziewicz Dr. Abstract Fluoroform, as confirmed by both experimental and theoretical studies, can participate in improper H-bond formation, which is characterized by a noticeable increase in the fundamental stretching frequency ,(CH) (so-called blue frequency shift), an irregular change of its integral intensity, and a CH bond contraction. A Car,Parrinello molecular dynamics simulation was performed for a complex formed by fluoroform (F3CH) and deuterated methyl fluoride (FCD3) in liquid nitrogen. Vibrational analysis based on the Fourier transform of the dipole moment autocorrelation function reproduces the blue shift of the fundamental stretching frequency ,(CH) and the decrease in the integral intensity. The dynamic contraction of the CH bond is also predicted. The stoichiometry of the solvated, blue-shifted complexes and their residence times are examined. [source] Density and Temperature Dependence of Proton Diffusion in Water: A First-Principles Molecular Dynamics StudyCHEMPHYSCHEM, Issue 9 2005Mauro Boero Prof. New insights into proton propagation: The authors present a detailed report on the diffusion of a proton in different thermodynamic states of water. At high temperature and intermediate density, the proton,which spends more time as an Eigen complex than as a Zundel complex (see figure),is destabilized, its migration is faster, and an incomplete Eigen complex acts as an acid with high chemical reactivity. [source] Car,Parrinello Molecular Dynamics Study of DCl Hydrate Crystals,CHEMPHYSCHEM, Issue 9 2005Atte Sillanpää Dr. Abstract Three DCl hydrates have been studied using Car,Parrinello (CP) molecular dynamics. The structural results at low temperatures (T<350 K) agree with experiment and previously published CP results. The monohydrate has been shown to be built from D3O+and Cl,ions. The dihydrate is built exclusively from D5O2+and Cl,ions. The trihydrate consists of D2O, D5O2+, and Cl,ions. Thus, the DCl hydrates are excellent systems for studying ideal D3O+and D5O2+ions. The data from these ideal structures can be compared to high-concentration acid,liquid simulations. [ClD,,,Cl],ions were detected at amorphous and fluid conditions after melting the di- and trihydrate crystals. The experimentally observed spectral continuum can be explained by combining the Eigen and Zundel spectra, and interpolating between the shared deuterium frequencies of the latter and the stretching band of the former. [source] Comparison of Properties of Aib-Rich Peptides in Crystal and Solution: A Molecular Dynamics StudyCHEMPHYSCHEM, Issue 5 2004Haibo Yu Abstract In order to study the differences of the structural properties of Aib-rich peptides in solution and in the crystalline state, molecular dynamics (MD) simulations of the Aib-containing peptide II (pBrBz-(Aib)5 -Leu-(Aib)2 -OMe) were performed in the crystalline state, starting from two different conformers obtained experimentally by X-ray diffraction. The structural properties as derived from X-ray crystallography (e.g., torsional angles and hydrogen bonds) are well-reproduced in both constant-volume and constant-pressure simulations, although the force-field parameters used result in a too-high density of the crystals. Through comparison with the results from previous MD and nuclear magnetic resonance (NMR) studies of the very similar peptide I (Z-(Aib)5 -Leu-(Aib)2 -OMe) in dimethylsulfoxide (DMSO) solution, it is found that, in the crystal simulation, the conformational distribution of peptide II is much narrower than that in the solution simulation of peptide I. This leads to a significant difference in 3J(HN, HC,) coupling constant values, in agreement with experimental data, whereas the NOE intensities or proton,proton distance bounds appear insensitive to the difference in conformational distribution. For small peptides the differences between their conformational distribution in the crystalline form and in solution may be much larger than for proteins, a fact which should be kept in mind when interpretating molecular properties in the solution state by using X-ray crystallographic data. [source] P - and S -wave reflectors in D, beneath southeast AsiaGEOPHYSICAL JOURNAL INTERNATIONAL, Issue 2 2009Jeremy W. Chaloner SUMMARY Earthquakes from the South Pacific region recorded at the Kyrgyz Seismic Network (KNET) and the GHENGIS network (both part of the Tien Shan Continental Dynamics study) have been analysed to search for evidence of reflections from the D, region. The reflection points of this source,receiver combination are in a seismically fast area beneath Southeast Asia. Employing several array methods, we find evidence for reflections from a D, reflector in both P and S waves. The reflector depth generally agrees for both wave types. There is some evidence for a second, deeper reflector in this region; migrating the data suggests a lower-seismic reflector beneath the northeastern end of the study region. The waveforms of P and S waves imply that the upper reflector has a negative impedance contrast for P but a positive impedance contrast for S. Several possibilities are discussed for generating the observed reflector(s), with the post-perovskite phase transition in combination with a cold slab being the preferred explanation. [source] Electrophoretic collision of a DNA molecule with a small elliptical obstacleELECTROPHORESIS, Issue 5 2010Jaeseol Cho Abstract We present a Brownian dynamics study of the collision and unhooking of a ,-DNA molecule with an elliptical obstacle. The semi-major and semi-minor axes of the obstacle are comparable to the radius of gyration of the DNA, and the field is sufficiently strong to cause frequent hairpin formation upon collision. We focus on how the dynamics of a head-on collision (impact parameter of zero) are affected by the angle between the major axis of the ellipse and the direction of the electric field far from the elliptical surface. When this orientation angle breaks the symmetry of the system, we find that the collision dynamics are considerably more complicated than the cylindrical obstacle case. In particular, a higher strain rate at the stagnation point on an elliptical surface does not always lead to a higher hooking probability. As a result, elliptical obstacles should be less effective than cylindrical obstacles for DNA separations based on hairpin formation. [source] Binding of ciprofloxacin by humic substances: A molecular dynamics studyENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 1 2010Ludmilla Aristilde Abstract A comprehensive assessment of the potential impacts of antimicrobials released into the environment requires an understanding of their sequestration by natural particles. Of particular interest are the strong interactions of antimicrobials with natural organic matter (NOM), which are believed to reduce their bioavailability, retard their abiotic and biotic degradation, and facilitate their persistence in soils and aquatic sediments. Molecular dynamics (MD) relaxation studies of a widely used fluoroquinolone antibiotic, ciprofloxacin (Cipro), interacting with a model humic substance (HS) in a hydrated environment, were performed to elucidate the mechanisms of these interactions. Specifically, a zwitterionic Cipro molecule, the predominant species at circumneutral pH, was reacted either with protonated HS or deprotonated HS bearing Ca, Mg, or Fe(II) cations. The HS underwent conformational changes through rearrangements of its hydrophobic and hydrophilic regions and disruption of its intramolecular H-bonds to facilitate favorable intermolecular H-bonding interactions with Cipro. Complexation of the metal cations with HS carboxylates appeared to impede binding of the positively charged amino group of Cipro with these negatively charged HS complexation sites. On the other hand, an outer-sphere complex between Cipro and the HS-bound cation led to ternary Cipro,metal,HS complexes in the case of Mg,HS and Fe(II),HS, but no such bridging interaction occurred with Ca,HS. The results suggested that the ionic potential (valence/ionic radius) of the divalent cation may be a determining factor in the formation of the ternary complex, with high ionic potential favoring the bridging interaction. Environ. Toxicol. Chem. 2010;29:90,98. © 2009 SETAC [source] Formation of 2,4,D complexes on montmorillonites , an ab initio molecular dynamics studyEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 3 2007D. Tunega Summary Sorption of the anionic form of the pesticide 2,4,D (2,4,dichlorophenoxyacetic acid) on the surface of the clay mineral montmorillonite was investigated using a short-time ab initio molecular dynamics (MD) simulation at room temperature. Three different situations were modelled: sorption on a dry surface, on a hydrated surface and an intercalation between montmorillonite layers. In all three cases, the calcium cation compensates the excess negative charge of the montmorillonite layer and the negative charge of the 2,4,D anion. It was found that in all models with direct contact of the Ca2+ cation with the montmorillonite layer, the most stable position of Ca2+ is above the ditrigonal hole of the mineral layer. While in the case of a dry surface very stable bidentate binding is created between the 2,4,D anion and the Ca2+ cation, the formation of the monodentate complexes is preferred in all models that include water molecules. Hydrogen bonds formed between water molecules and the 2,4,D anion make a considerable contribution to the formation of the monodentate complexes. Tetrahedral substitutions in the montmorillonite layer have a significant effect on the formation of the complexes of any type. However, the MD simulations did not support the role of Ca2+ as a cation bridge in the adsorption mechanism. Calculations showed that hydrated 2,4,D···Ca2+ complexes are thermodynamically more stable than complexes in which the Ca2+ cation acts as a bridge to the surface. On the other hand, it is possible that phyllosilicates with a greater concentration of isomorphic substitutions (e.g. mica) will be able to form stable surface complexes with a cation bridge mechanism. [source] Molecular dynamics study for dissociation phenomena of a gas molecule on a metal surfaceHEAT TRANSFER - ASIAN RESEARCH (FORMERLY HEAT TRANSFER-JAPANESE RESEARCH), Issue 8 2008Takashi Tokumasu Abstract The dissociation phenomena of a gas molecule on a metal surface were analyzed by the molecular dynamics method. A platinum (111) surface and hydrogen were chosen as the metal surface and the gas molecule, respectively. The embedded atom method was used as the interaction between atoms in order to express the dependence of electron density. The parameters were determined so that the results such as the electron density, adsorption energy of an H atom on a Pt(111) surface, and the interaction between H atoms of an H2 molecule obtained by the EAM method were consistent with those obtained by the density functional theory or empirical function. Collisions between a hydrogen molecule and the platinum surface were simulated by the molecular dynamics method, and the dissociation probability was obtained. Using these results, the effect of the motion of the surface atoms or the hydrogen molecule on the dissociation probability was analyzed. © 2008 Wiley Periodicals, Inc. Heat Trans Asian Res; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/htj.20222 [source] Molecular dynamics study on effects of surface structures in nanometer scale on energy transfer from fluid to surfaceHEAT TRANSFER - ASIAN RESEARCH (FORMERLY HEAT TRANSFER-JAPANESE RESEARCH), Issue 3 2005Masahiko Shibahara Abstract Energy transfer from fluid to surface was calculated numerically by using the classical molecular dynamics method in order to investigate the effects of surface structures from 0.1 nm to 10 nm on surface energy transfer. Surface structures on a constant surface area were composed of several hundred atoms having various potential energy parameters, in other words, thermal properties. The upper region in the calculation domain was controlled at a constant temperature and one of the solid atomic layers at the lower region in the calculation domain was controlled at another constant temperature to create a temperature gradient in the calculation system. Energy transfer to the surface was very dependent on surface nanometer scale structures in that affected the static structure and the dynamic behaviors of fluid molecules in the vicinity of the surface. © 2005 Wiley Periodicals, Inc. Heat Trans Asian Res, 34(3): 171,179, 2005; Published online in Wiley InterScience (www.interscience. wiley.com). DOI 10.1002/htj.20055 [source] Combination therapy with lamivudine and famciclovir for chronic hepatitis B,infected Chinese patients: A viral dynamics studyHEPATOLOGY, Issue 2 2000George Ka Lau M.D. In vitro studies have shown that lamivudine and penciclovir (the active metabolite of famciclovir) act synergistically to inhibit hepatitis B virus (HBV) replication. We compared the effectiveness of HBV viral suppression by lamivudine monotherapy versus lamivudine plus famciclovir combination therapy in Chinese patients with chronic HBV infection. Twenty-one Chinese hepatitis B e antigen (HBeAg)-positive patients, with detectable HBV DNA (Digene Hybrid Capture II), were randomized to receive either lamivudine 150 mg/d orally (group 1, 9 patients) or lamivudine 150 mg/d plus famciclovir 500 mg 3 times a day orally (group 2, 12 patients) for 12 weeks, with a follow-up period of at least 16 weeks. Serial serum HBV-DNA levels were determined and a mathematical model with provision for incomplete inhibition of virus production during therapy was applied to analyze the dynamics of viral clearance. The mean antiviral efficacy was significantly greater in group 2 than in group 1 (0.988 ± 0.012 vs. 0.94 ± 0.03, P = .0012). HBV DNA returned to pretreatment level within 16 weeks after the end of initial treatment in 4 patients (66.7%) in group 1 and none in group 2 (P = .08), who remained HBeAg positive and received no further treatment after week 12. Hence, in Chinese chronic HBeAg-positive patients, combination therapy using lamivudine and famciclovir was superior to lamivudine monotherapy in inhibiting HBV replication. Further studies of longer duration are needed to define whether combination therapy will increase the HBeAg seroconversion rate and decrease the rate of emergence of lamivudine-resistant variants. [source] A simple approach for improving the hybrid MMVB force field: Application to the photoisomerization of s - cis butadieneJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2003Marco Garavelli Abstract MMVB is a QM/MM hybrid method, consisting of a molecular mechanics force field coupled to a valence bond Heisenberg Hamiltonian parametrized from ab initio CASSCF calculations on several prototype molecules. The Heisenberg Hamiltonian matrix elements Qij and Kij, whose expressions are partitioned here into a primary contribution and second-order correction terms, are calculated analytically in MMVB. When the original MMVB force field fails to produce potential energy surfaces accurate enough for dynamics calculations, we show that significant improvements can be made by refitting the second-order correction terms for the particular molecule(s) being studied. This "local" reparametrization is based on values of Kij extracted (using effective Hamiltonian techniques) from CASSCF calculations on the same molecule(s). The method is demonstrated for the photoisomerization of s - cis butadiene, and we explain how the correction terms that enabled a successful MMVB dynamics study [Garavelli, M.; Bernardi, F.; Olivucci, M.; Bearpark, M. J.; Klein, S.; Robb, M. A. J Phys Chem A 2001, 105, 11496] were refitted. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1357,1363, 2003 [source] Characterization of Taylor vortex flow in a short liquid columnAICHE JOURNAL, Issue 12 2009Rensheng Deng Abstract We present a study on Taylor vortex flow in the annulus between a rotating inner cylinder and a stationary outer cylinder, featured with a wide gap (radius ratio is 0.613) and a short column (aspect ratio is 5.17). A particle image velocimetry (PIV) system was used to determine the position, shape, and velocity distribution of the vortices, by which the flow was also confirmed to lie in the nonwavy Taylor vortex regime for all operating conditions explored in this study. Our results suggest that end boundary effects are important, in which the vortex number decreases with decreasing column length. For a system with an aspect ratio of 5.17, six vortices appear in the gap with their position, size, and shape varying at different Reynolds numbers. The fluid velocities show an asymmetric feature with respect to the vortex centers, while the maximum axial and radial velocities increase almost linearly with the increasing reduced Reynolds number (Re , Rec). In addition, computational fluid dynamics study was employed under the same conditions, and its results agree well with the PIV measurements. Overall, this study provides a quantitative understanding of the formation of Taylor vortices in a constrained space. © 2009 American Institute of Chemical Engineers AIChE J, 2009 [source] A molecular dynamics study on binding recognition between several 4,5 and 4,6-linked aminoglycosides with A-site RNAJOURNAL OF MOLECULAR RECOGNITION, Issue 5 2010Shih-Yuan Chen Abstract A molecular dynamics (MD) simulation has been performed for two sets of aminoglycoside antibiotics bound with an RNA duplex corresponding to the aminoacyl-tRNA decoding site of the 16S rRNA to characterize the energetics and dynamics of binding for several aminoglycosides. The binding free energy, essential dynamics and hydration analysis have been conducted to characterize the dynamics' properties associated with the binding recognition between each set of antibiotics and the RNA duplex. We have built several dynamic models with reasonable binding free energies showing good correlation with the experimental data. We have also conducted a hydration analysis on some long residency water molecules detected as W8 and W49 sites around the U1406,·,U1495 pair and which are found to be important in binding recognition and in causing some apparent stretch variations of this pair during the dynamic studies. In addition, we also find that the hydration sites with long residence time identified between the ring III of two 4,6-linked antibiotics (tobramycin and kanamycin) and phosphate oxygen atoms of G1405/U1406 may be worthy of further exploration for rational drug design. Copyright © 2009 John Wiley & Sons, Ltd. [source] Analysis of interactions responsible for vasopressin binding to human neurohypophyseal hormone receptors,molecular dynamics study of the activated receptor,vasopressin,G, systemsJOURNAL OF PEPTIDE SCIENCE, Issue 3 2006Magdalena J., lusarz Abstract Vasopressin (CYFQNCPRG-NH2, AVP) is a semicyclic endogenous peptide, which exerts a variety of biological effects in mammals. The main physiological roles of AVP are the regulation of water balance and the control of blood pressure and adrenocorticotropin hormone (ACTH) secretion, mediated via three different subtypes of vasopressin receptors: V1a, V1b and V2 receptors (V1aR, V1bR and V2R, respectively). They are the members of the class A, G-protein-coupled receptors (GPCRs). AVP also modulates several behavioral and social functions. In this study, the interactions responsible for AVP binding to vasopressin V1a and V2 receptors versus the closely related oxytocin ([I3,L8]AVP, OT) receptor (OTR) have been investigated. Three-dimensional models of the activated receptors were constructed using multiple sequence alignment, followed by homology modeling using the complex of activated rhodopsin with Gt,C -terminal peptide of transducin MII-Gt(338-350) prototype as a template. AVP was docked into the receptor-G, systems. The three lowest-energy pairs of receptor-AVP-G, (two complexes per each receptor) were selected. The 1-ns unconstrained molecular dynamics (MD) of complexes embedded into the fully hydrated 1-palmitoyl-2-oleoyl- sn -glycero-3-phosphatidylcholine (POPC) lipid bilayer was conducted in the AMBER 7.0 force field. Six relaxed receptor-AVP-G, models were obtained. The residues responsible for AVP binding to vasopressin receptors have been identified and a different mechanism of AVP binding to V2R than to V1aR has been proposed. Copyright © 2005 European Peptide Society and John Wiley & Sons, Ltd. [source] Functionalization and molecular dynamics study of carboxy-terminated poly(1-vinylpyrrolidin-2-one): A potential soluble carrier of biomoleculesJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 5 2008Clara Baldoli Abstract The reactivity of carboxy-terminated poly(1-vinylpyrrolidin-2-one) (PVP-COOH) 40-mers 1 with various small bi-functionalized molecules has been investigated. A number of new differently functionalized PVP 3,11 have been successfully obtained demonstrating that the presence of the bulky PVP chain did not hamper the reactivity of the carboxy group. This would imply that in solution the carboxyl group is not buried inside the coil, but well exposed to the solvent, as further confirmed by a molecular dynamics conformational study. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 1683,1698, 2008 [source] Change of the unbinding mechanism upon a mutation: A molecular dynamics study of an antibody,hapten complexPROTEIN SCIENCE, Issue 10 2005Raffaele Curcio Abstract We study forced unbinding of fluorescein from the wild type (WT) and a mutant [H(H58)A] of the single-chain variable-fragment (scFv) anti-fluorescein antibody FITC-E2 by molecular dynamics simulations using various pulling techniques. A large number of long simulations were needed to obtain statistically meaningful results as both the wild type and the H(H58)A mutant unbinding occurs through multiple pathways, often with metastable intermediates. For the wild type, the rate-limiting step in the unbinding process corresponds to the breaking of the non-native interactions characteristic of a specific intermediate. The H(H58)A mutation disfavors the occurrence of this intermediate. Two events where the hapten partially unbinds in the absence of pulling force are observed in extensive equilibrium simulations of the wild type, and their analysis indicates that forced unbinding and spontaneous unbinding proceed along similar pathways. The different unbinding mechanisms observed in the simulations suggest a possible reason for the difference in the experimental off-rate between the two antibodies. We predict mutations that are expected to modulate the occurrence of the unbinding intermediate. For two such new mutants [H(H58)A and S(H52)A], our predictions are validated in silico by additional simulations. The accompanying paper in this issue by Honegger et al. reports the X-ray structure of FITC-E2 with a derivative of fluorescein, which was used as the starting conformation for the work presented here. [source] Ligand diffusion in the catalase from Proteus mirabilis: A molecular dynamics studyPROTEIN SCIENCE, Issue 10 2001Patricia Amara Abstract The role of the channels and cavities present in the catalase from Proteus mirabilis (PMC) was investigated using molecular dynamics (MD) simulations. The reactant and products of the reaction, H2O2 ,1/2 O2 + H2O, catalyzed by the enzyme were allowed to diffuse to and from the active site. Dynamic fluctuations in the structure are found necessary for the opening of the major channel, ideied in the X-ray model, which allows access to the active site. This channel is the only pathway to the active site observed during the dynamics, and both the products and reactant use it. H2O and O2 are also detected in a cavity defined by the heme and Ser196, which could play an important role during the reaction. Free energy profiles of the ligands diffusing through the major channel indicate that the barriers to ligand diffusion are less than 20 kJ mol,1 for each of the species. It is not clear from our study that minor channels play a role for access to the protein active site or to the protein surface. [source] The Impact of Aortic/Subclavian Outflow Cannulation for Cardiopulmonary Bypass and Cardiac Support: A Computational Fluid Dynamics StudyARTIFICIAL ORGANS, Issue 9 2009Tim A.S. Kaufmann Abstract Approximately 100 000 cases of oxygen deficiency in the brain occur during cardiopulmonary bypass (CPB) procedures each year. In particular, perfusion of the carotid and vertebral arteries is affected. The position of the outflow cannula influences the blood flow to the cardiovascular system and thus end organ perfusion. Traditionally, the cannula returns blood into the ascending aorta. But some surgeons prefer cannulation to the right subclavian artery. A computational fluid dynamics study was initially undertaken for both approaches. The vessel model was created from real computed tomography/magnetic resonance imaging data of young healthy patients. The simulations were run with usual CPB conditions. The flow distribution for different cannula positions in the aorta was studied, as well as the impact of the cannula tip distance to vertebral artery for the subclavian position. The study presents a fast method of analyzing the flow distribution in the cardiovascular system, and can be adapted for other applications such as ventricular assist device support. It revealed that two effects cause the loss of perfusion seen clinically: a vortex under the brachiocephalic trunk and low pressure regions near the cannula jet. The results suggest that cannulation to the subclavian artery is preferred if the cannula tip is sufficiently far away from the branch of the vertebral artery. For the aortic positions, however, the cannula should be injected from the left body side. [source] | ||||||||||||||||||||||