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https://www.readbyqxmd.com/read/28641388/recognition-of-the-component-odors-in-mixtures
#1
Marion E Frank, Dane B Fletcher, Thomas P Hettinger
Natural olfactory stimuli are volatile-chemical mixtures in which relative perceptual saliencies determine which odor-components are identified. Odor identification also depends on rapid selective adaptation, as shown for 4 odor stimuli in an earlier experimental simulation of natural conditions. Adapt-test pairs of mixtures of water-soluble, distinct odor stimuli with chemical features in common were studied. Identification decreased for adapted components but increased for unadapted mixture-suppressed components, showing compound identities were retained, not degraded to individual molecular features...
June 21, 2017: Chemical Senses
https://www.readbyqxmd.com/read/28641267/a-cpu-mic-collaborated-parallel-framework-for-gromacs-on-tianhe-2-supercomputer
#2
Shaoliang Peng, Shunyun Yang, Wenhe Su, Xiaoyu Zhang, Tenglilang Zhang, Weiguo Liu, Xingming Zhao
Molecular Dynamics (MD) is the simulation of the dynamic behavior of atoms and molecules. As the most popular software for molecular dynamics, GROMACS cannot work on large-scale data because of limit computing resources. In this paper, we propose a CPU and Intel® Xeon Phi Many Integrated Core (MIC) collaborated parallel framework to accelerate GROMACS using the offload mode on a MIC coprocessor, with which the performance of GROMACS is improved significantly, especially with the utility of Tianhe-2 supercomputer...
June 16, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28641189/qualitative-and-quantitative-simulation-of-androgen-receptor-antagonists-a-case-study-of-polybrominated-diphenyl-ethers
#3
Yang Wu, Wei Shi, Pu Xia, Xiaowei Zhang, Hongxia Yu
Recently, great attention has been paid to the identification and prediction of the androgen disrupting potencies of polybrominated diphenyl ethers (PBDEs). However, few existing models can discriminate active and inactive compounds, which make the quantitative prediction process including the quantitative structure-activity relationship (QSAR) technique unreliable. In this study, different grouping methods were investigated and compared for qualitative identification, including molecular docking and molecular dynamics simulations (MD)...
June 19, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28641186/composition-of-dissolved-organic-matter-dom-from-periodically-submerged-soils-in-the-three-gorges-reservoir-areas-as-determined-by-elemental-and-optical-analysis-infrared-spectroscopy-pyrolysis-gc-ms-and-thermally-assisted-hydrolysis-and-methylation
#4
Tao Jiang, Joeri Kaal, Jian Liang, Yaoling Zhang, Shiqiang Wei, Dingyong Wang, Nelson W Green
Soil-derived dissolved organic matter (DOM) has a major influence in biogeochemical processes related to contaminant dynamics and greenhouse gas emissions, due to its reactivity and its bridging role between the soil and aquatic systems. Within the Three Gorges Reservoir (TGR, China) area, an extensive water-fluctuation zone periodically submerges the surrounding soils. Here we report a characterization study of soil-derived DOM across the TGR areas, using elemental and optical analysis, infrared spectroscopy (FTIR), pyrolysis-GC-MS (Py-GC-MS) and thermally assisted hydrolysis and methylation (THM-GC-MS)...
June 19, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28641174/new-insights-into-the-oleate-flotation-response-of-feldspar-particles-of-different-sizes-anisotropic-adsorption-model
#5
Longhua Xu, Jia Tian, Houqin Wu, Wei Deng, Yaohui Yang, Wei Sun, Zhiyong Gao, Yuehua Hu
The anisotropic adsorption of sodium oleate (NaOL) on feldspar surfaces was investigated to elucidate the different flotation properties of feldspar particles of four different size ranges. Microflotation experiments showed that the feldspar flotation recovery of particles with sizes spanning different ranges decreased in the order 0-19>19-38>45-75>38-45μm. Zeta potential and FTIR measurements showed that NaOL was chemically adsorbed on the Al sites of the feldspar surface. The anisotropic surface energies and broken bond densities estimated by density functional theory calculations showed that, although feldspar mostly exposed (010) and (001) surfaces, only the (001) surfaces contained the Al sites needed for NaOL adsorption...
June 8, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28641006/dft-simulation-of-structural-and-optical-properties-of-9-aminoacridine-half-sandwich-ru-ii-rh-iii-and-ir-iii-antitumoural-complexes-and-their-interaction-with-dna
#6
José Pedro Cerón-Carrasco, José Ruiz, Consuelo Vicente, Concepcion de Haro, Delia Bautista, Jose Zuniga, Alberto Requena
In this work, we use DFT-based methods to simulate the chemical structures, optical properties and interaction with DNA of a recently synthesized chelated CˆN 9-aminoacridine arene Ru (II) anticancer agent and two new closely related Rh(III) and Ir(III) complexes using DFT-based methods. Four chemical models and a number of theoretical approaches, which representatively include the PBE0, B97D, ωB97X, ωB97X-D, M06, and M06-L density functionals and the LANL2DZ, def2-SVP, def2- TZVP basis sets, are tested...
June 22, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28640963/a-truncated-molecular-star
#7
Soumyakanta Prusty, Kohei Yazaki, Michito Yoshizawa, Dillip Kumar Chand
Pentanuclear coordination complex assembled from palladium(II) component and non-chelating ligand(s) is hitherto unreported. The pentanuclear complex [Pd5(L1)5(L2)5](BF4)10, 1 that was prepared by the spontaneous complexation of [Pd(DMSO)4](BF4)2 with the non-chelating bidentate ligands 1,4-phenylenebis(methylene) diisonicotinate, L1 and 4,4'-bipyridine, L2 in one-pot at room temperature is reported here. The planar polycyclic complex 1 with outer diameters of ~3 nm is termed as a "molecular star" owing to its resemblance with "star pentagon" shape...
June 22, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28640952/label-free-dynamic-mass-redistribution-and-bio-impedance-methods-for-drug-discovery
#8
Manuel Grundmann
Label-free biosensors are increasingly employed in drug discovery. Cell-based biosensors provide valuable insights into the biological consequences of exposing cells and tissues to chemical agents and the underlying molecular mechanisms associated with these effects. Optical biosensors based on the detection of dynamic mass redistribution (DMR) and impedance biosensors using cellular dielectric spectroscopy (CDS) capture changes of the cytoskeleton of living cells in real time. Because signal transduction correlates with changes in cell morphology, DMR and CDS biosensors are exquisitely suited for recording integrated cell responses in an unbiased, yet pathway-specific manner without the use of labels that may interfere with cell function...
June 22, 2017: Current Protocols in Pharmacology
https://www.readbyqxmd.com/read/28640939/global-transcriptome-and-co-expression-network-analyses-reveal-cultivar-specific-molecular-signatures-associated-with-seed-development-and-seed-size-weight-determination-in-chickpea
#9
Rohini Garg, Vikash K Singh, Mohan Singh Rajkumar, Vinay Kumar, Mukesh Jain
Seed development is an intricate process regulated via a complex transcriptional regulatory network. To understand the molecular mechanisms governing seed development and seed size/weight in chickpea, we performed a comprehensive analysis of transcriptome dynamics during seed development in two cultivars with contrasting seed size/weight (small seeded, Himchana 1 and large-seeded, JGK 3). Our analysis identified stage-specific expression for a significant proportion (>13%) of the genes. About one-fourth of total genes exhibited significant differential expression in JGK 3 as compared to Himchana 1...
June 22, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28640852/differential-roles-of-3-hydroxyflavone-and-7-hydroxyflavone-against-nicotine-induced-oxidative-stress-in-rat-renal-proximal-tubule-cells
#10
Bidisha Sengupta, Mehdi Sahihi, Monireh Dehkhodaei, Darrian Kelly, Istvan Arany
Plant flavonoids are well known as antioxidants against oxidative stress induced by exposure to external pollutants. Nicotine (NIC) is one of those agents which increases renal oxidative stress, an important factor in the pathogenesis of renal epithelial injury in smokers. Although several studies had been conducted on flavonoids and oxidative stress, the mechanism of the protective pathways are not fully understood. Here, we present studies on antioxidant properties of two mono-hydroxyflavone isomers, 3-hydroxyflanove (3HF)- and 7-hydroxyflavone (7HF), against nicotine-associated oxidative stress and injury in cultured renal proximal tubule cells and correlate their antioxidant properties with their chemical structure...
2017: PloS One
https://www.readbyqxmd.com/read/28640851/ligand-mediated-and-tertiary-interactions-cooperatively-stabilize-the-p1-region-in-the-guanine-sensing-riboswitch
#11
Christian A Hanke, Holger Gohlke
Riboswitches are genetic regulatory elements that control gene expression depending on ligand binding. The guanine-sensing riboswitch (Gsw) binds ligands at a three-way junction formed by paired regions P1, P2, and P3. Loops L2 and L3 cap the P2 and P3 helices and form tertiary interactions. Part of P1 belongs to the switching sequence dictating the fate of the mRNA. Previous studies revealed an intricate relationship between ligand binding and presence of the tertiary interactions, and between ligand binding and influence on the P1 region...
2017: PloS One
https://www.readbyqxmd.com/read/28640814/a-novel-algorithm-identifies-stress-induced-alterations-in-mitochondrial-connectivity-and-inner-membrane-structure-from-confocal-images
#12
Mathieu Ouellet, Gérald Guillebaud, Valerie Gervais, David Lupien St-Pierre, Marc Germain
Mitochondria exist as a highly interconnected network that is exquisitely sensitive to variations in nutrient availability, as well as a large array of cellular stresses. Changes in length and connectivity of this network, as well as alterations in the mitochondrial inner membrane (cristae), regulate cell fate by controlling metabolism, proliferation, differentiation, and cell death. Given the key roles of mitochondrial dynamics, the process by which mitochondria constantly fuse and fragment, the measure of mitochondrial length and connectivity provides crucial information on the health and activity of various cell populations...
June 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28640808/transmembrane-helical-interactions-in-the-cftr-channel-pore
#13
Jhuma Das, Andrei A Aleksandrov, Liying Cui, Lihua He, John R Riordan, Nikolay V Dokholyan
Mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene affect CFTR protein biogenesis or its function as a chloride channel, resulting in dysregulation of epithelial fluid transport in the lung, pancreas and other organs in cystic fibrosis (CF). Development of pharmaceutical strategies to treat CF requires understanding of the mechanisms underlying channel function. However, incomplete 3D structural information on the unique ABC ion channel, CFTR, hinders elucidation of its functional mechanism and correction of cystic fibrosis causing mutants...
June 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28640604/parametrizaton-of-a-reactive-force-field-reaxff-for-molecular-dynamics-simulations-of-si-nanoparticles
#14
Giovanni Barcaro, Susanna Monti, Luca Sementa, Vincenzo Carravetta
A novel computational approach, based on classical reactive molecular dynamics simulations (RMD) and quantum chemistry (QC) global energy optimizations, is proposed for modelling large Si nanoparticles. The force field parameters, which can describe bond breaking and formation, are derived by reproducing energetic and structural properties of a set of Si clusters increasing in size. These reference models are obtained through a new protocol based on a joint high temperature RMD/low temperature Basin Hopping QC search...
June 22, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28640593/dna-condensation-induced-by-a-star-shaped-hexameric-cationic-surfactant
#15
Yaxun Fan, Hua Wang, Chengqian He, Fulin Qiao, Shu Wang, Yilin Wang
The interactions between a star-shaped hexameric cationic quaternary ammonium surfactant PAHB and calf thymus DNA and induced DNA condensation were investigated by ζ-potential, dynamic light scattering, atomic force microscopy, isothermal titration calorimetry, ethidium bromide exclusion assay, circular dichroism and cytotoxicity assay. With the addition of PAHB, long extended DNA molecules exhibit successive conformational transitions from elongated coil to partially condensed cluster-like aggregate, globules-on-a-string structure, and then to fully condensed globule until the saturation point of interaction between PAHB and DNA, which is slightly above their charge neutralization point...
June 22, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28640581/molecular-insight-of-water-desalination-across-multilayer-graphene-oxide-membranes
#16
Bo Chen, Haifeng Jiang, Xiang Liu, Xuejiao Hu
Transport of ionic solutions through graphene oxide (GO) membranes is a complicated issue because the complex and tortuous structure inside make it very hard to clarify. Using molecular dynamics (MD) simulations, we investigated the mechanism of water transport and ions movement across the multilayer graphene oxide. The significant flow rate is considerably influenced by the structural parameters of GO membranes. Due to the size effect on shrunken real flow area, there is disagreement between classical continuum model and nano-scaled flow...
June 22, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28637181/crosstalk-between-histone-modifications-indicates-that-inhibition-of-arginine-methyltransferase-carm1-activity-reverses-hiv-latency
#17
Zheng Zhang, Bryan C Nikolai, Leah A Gates, Sung Yun Jung, Edward B Siwak, Bin He, Andrew P Rice, Bert W O'Malley, Qin Feng
In eukaryotic cells, the gene expression status is strictly controlled by epigenetic modifications on chromatin. The repressive status of chromatin largely contributes to HIV latency. Studies have shown that modification of histone H3K27 acts as a key molecular switch for activation or suppression of many cellular genes. In this study, we found that K27-acetylated histone H3 specifically recruited Super Elongation Complex (SEC), the transcriptional elongation complex essential for HIV-1 long terminal repeat (LTR)-mediated and general cellular transcription...
June 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28636918/actin-filament-strain-promotes-severing-and-cofilin-dissociation
#18
Anthony C Schramm, Glen M Hocky, Gregory A Voth, Laurent Blanchoin, Jean-Louis Martiel, Enrique M De La Cruz
Computational and structural studies have been indispensable in investigating the molecular origins of actin filament mechanical properties and modulation by the regulatory severing protein cofilin. All-atom molecular dynamics simulations of cofilactin filament structures determined by electron cryomicroscopy reveal how cofilin enhances the bending and twisting compliance of actin filaments. Continuum mechanics models suggest that buckled cofilactin filaments localize elastic energy at boundaries between bare and cofilin-decorated segments because of their nonuniform elasticity, thereby accelerating filament severing...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636916/structural-behavior-of-the-peptaibol-harzianin-hk-vi-in-a-dmpc-bilayer-insights-from-md-simulations
#19
Marina Putzu, Sezgin Kara, Sergii Afonin, Stephan L Grage, Andrea Bordessa, Grégory Chaume, Thierry Brigaud, Anne S Ulrich, Tomáš Kubař
Microsecond molecular dynamics simulations of harzianin HK VI (HZ) interacting with a dimyristoylphosphatidylcholine bilayer were performed at the condition of low peptide-to-lipid ratio. Two orientations of HZ molecule in the bilayer were found and characterized. In the orientation perpendicular to the bilayer surface, HZ induces a local thinning of the bilayer. When inserted into the bilayer parallel to its surface, HZ is located nearly completely within the hydrophobic region of the bilayer. A combination of solid-state NMR and circular dichroism experiments found the latter orientation to be dominant...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636914/peptide-protein-binding-investigated-by-far-ir-spectroscopy-and-molecular-dynamics-simulations
#20
Yoann Cote, Yves Nominé, Juan Ramirez, Petra Hellwig, Roland H Stote
Molecular dynamics (MD) simulations and far-infrared (far-IR) spectroscopy were combined to study peptide binding by the second PDZ domain (PDZ1) of MAGI1, which has been identified as an important target for the Human Papilloma Virus. PDZ1 recognizes and binds to the C-terminal end of the E6 protein from high-risk Human Papilloma Virus. The far-IR spectra of two forms of the protein, an unbound APO form and a HOLO form (where the PDZ1 is bound to an 11-residue peptide derived from the C terminus of HPV16 E6), were obtained...
June 20, 2017: Biophysical Journal
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