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# molecular dynamics

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#1
Di Zhang, Lijun Xue, Yongqiang Xu, Lijuan Song, Xinmei Liu
Mesoporous γ-Al2O3 supports with different pore structures were prepared by the cation-anion double hydrolysis method. Based on these samples, MoO3/γ-Al2O3 catalysts were made via impregnation. The adsorptions of 4,6-dimethyldibenzothiophene (4,6-DMDBT) and collidine over the supports and catalysts were studied by FT-IR. The supports or catalysts with larger pores can adsorb more 4,6-DMDBT. The methyl groups on adsorbate molecules are very close to the sulfur atom, resulting in apparent steric hindrance. Increasing the pore size can promote the interaction between the adsorbates and supports or catalysts, enhancing the CC bond and weakening the CS bond of 4,6-DMDBT...
January 10, 2017: Journal of Colloid and Interface Science
#2
Ramachandra Moorthy Bhaskara, Stephanie M Linker, Martin Vögele, Juergen Koefinger, Gerhard Hummer
The fusion of lipid membranes is opposed by high energetic barriers. In living organisms, complex protein machineries carry out this biologically essential process. Here we show that membrane-spanning carbon nanotubes (CNTs) can trigger spontaneous fusion of small lipid vesicles. In coarse-grained molecular dynamics simulations, we find that a CNT bridging between two vesicles locally perturbs their lipid structure. Their outer leaflets merge as the CNT pulls lipids out of the membranes, creating an hourglass-shaped fusion intermediate with still intact inner leaflets...
January 19, 2017: ACS Nano
#3
Dana D Medina, Michiel L Petrus, Askhat N Jumabekov, Johannes T Margraf, Simon Weinberger, Julian M Rotter, Timothy Clark, Thomas Bein
Charge carrier transport in oriented COF thin films is an important factor for realizing COF-based optoelectronic devices. We describe how highly oriented electron-donating BDT-COF thin films serve as a model system for a directed charge transport study. Oriented BDT-COF films were deposited on different electrodes with excellent control over film roughness and topology, allowing for high quality electrode-COF interfaces suitable for device fabrication. Hole-only devices were constructed to study the columnar hole-mobility of the BDT-COF films...
January 19, 2017: ACS Nano
#4
Xiaojuan Pang, Xueyan Cui, Deping Hu, Chenwei Jiang, Di Zhao, Zhenggang Lan, Fu-Li Li
Photoisomerization dynamics of a light-driven molecular rotary motor, 9-(2-methyl-2,3-dihydro-1H-cyclopenta[a]naphthalen-1-ylidene)-9H-fluorene, is investigated with trajectory surface-hopping dynamics at the semi-empirical OM2/MRCI level. The rapid population decay of the S1 excited state for the M isomer is observed, with two different decay timescales (500 fs and 1.0 ps). By weighting the contributions of fast and slow decay trajectories, the averaged lifetime of the S1 excited state is about 710 fs. The calculated quantum yield of the M-to-P photoisomerization of this molecular rotary motor is about 59...
January 19, 2017: Journal of Physical Chemistry. A
#5
Hanna Cho, Sandip Sengupta, Sean Sh Jeon, Wooyoung Hur, Hwan Geun Choi, Hong Seog Seo, Byung Joo Lee, Jeong Hun Kim, Minhwan Chung, Noo Li Jeon, Nam Doo Kim, Taebo Sim
We synthesized 1 (San78-130), a reversible version of L-783277, as a selective and potent ALK1 inhibitor. Our study showed that 1 possesses great kinase selectivity against a panel of 342 kinases and more potent activity against ALK1 than L-783277. Among the six ALK isotypes (ALK1-6), ALK1 is most significantly inhibited by compound 1. Compound 1 suppresses the BMP9-induced Smad1/5 pathway by mainly inhibiting ALK1 in C2C12 cells. Our molecular dynamics simulations suggest that H-bonding interaction between the C-4' hydroxyl group of 1 and Arg334 of ALK1 substantially contributes to the ALK1 inhibition...
January 19, 2017: Journal of Medicinal Chemistry
#6
Ichiro Inamoto, Gang Chen, Jumi A Shin
The molecular basis of protein-partner selection and DNA binding of the basic helix-loop-helix (bHLH) and basic region-leucine zipper (bZIP) superfamilies of dimeric transcription factors is fundamental toward understanding gene regulation. Because these families share structural similarities, we swapped the bHLH and leucine zipper (LZ) modules between families to uncover how individual modules influence protein-partnering and protein:DNA complexation. We previously described ArntFos, a bHLHZ-like hybrid of the bHLH domain from the bHLH/PAS protein Arnt and LZ from the bZIP protein c-Fos, binding to the Arnt E-box site (TCACGTGA) as a homodimer...
January 19, 2017: Molecular BioSystems
#7
Sebastiano Bernini, Francesco Puosi, Dino Leporini
We investigate by Molecular Dynamics simulations of a molecular liquid the thermodynamic scaling (TS) of the structural relaxation time $\tau_\alpha$ in terms of the quantity $T\rho^{-\gamma_{ts}}$ where T and rho are the temperature and the density, respectively. The liquid does not exhibit strong virial-energy correlations. We propose how to evaluate both the characteristic exponent $\gamma_{ts}$ and the TS master curve by resorting to experimentally accessible quantities characterising the anharmonic elasticity and no details about the microscopic interactions...
January 19, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
#8
Brian Kolb, Xuan Luo, Xueyao Zhou, Bin Jiang, Hua Guo
Ab initio molecular dynamics (AIMD) simulations of molecule-surface scattering allow first-principles characterization of the dynamics. However, the large number of density functional theory calculations along the trajectories are very costly, limiting simulations of long-time events. To avoid this computational bottleneck, we report here the development of a high-dimensional molecule-surface interaction potential energy surface (PES) with movable surface atoms, using a machine learning approach. With 60 degrees of freedom, this PES allows energy transfer between the impinging molecule and surface atoms...
January 19, 2017: Journal of Physical Chemistry Letters
#9
Jacob B J Chapman, Anna V Kimmel, Dorothy M Duffy
Exotic domain morphologies in ferroic materials are an exciting avenue for the development of novel nanoelectronics. In this work we have used large scale molecular dynamics to construct a strain-temperature phase diagram of the domain morphology of PbTiO3 ultrathin films. Sampling a wide interval of strain values over a temperature range up to the Curie temperature Tc, we found that epitaxial strain induces the formation of a variety of closure- and in-plane domain morphologies. The local strain and ferroelectric-antiferrodistortive coupling at the film surface vary for the strain mediated transition sequence and this could offer a route for experimental observation of the morphologies...
January 19, 2017: Physical Chemistry Chemical Physics: PCCP
#10
S D Feng, K C Chan, S H Chen, L Zhao, R P Liu
The varying degrees of configurational disorder in metallic glasses are investigated quantitatively by molecular dynamics studies. A parameter, the quasi-nearest atom, is used to characterize the configurational disorder in metallic glasses. Our observations suggest configurational disorder play a role in structural heterogeneity, plasticity and dynamic relaxations in metallic glasses. The broad configurational disorder regions distribution is the indicator of abundant potential deformation units and relaxations...
January 19, 2017: Scientific Reports
#11
Jin Wang, Raju R Namburu, Madan Dubey, Avinash M Dongare
The potential of the applicability of two-dimensional molybdenum disulfide (MoS2) structures, in various electronics, optoelectronics, and flexible devices requires a fundamental understanding of the effects of strain on the electronic, magnetic and optical properties. Particularly important is the recent capability to grow large flakes of few-layered structures using chemical vapor deposition (CVD) wherein the top layers are relatively smaller in size than the bottom layers, resulting in the presence of edges/steps across adjacent layers...
January 19, 2017: Scientific Reports
#12
Lu Huang, Yuyang Jiang, Yuzong Chen
Synergistic drug combinations enable enhanced therapeutics. Their discovery typically involves the measurement and assessment of drug combination index (CI), which can be facilitated by the development and applications of in-silico CI predictive tools. In this work, we developed and tested the ability of a mathematical model of drug-targeted EGFR-ERK pathway in predicting CIs and in analyzing multiple synergistic drug combinations against observations. Our mathematical model was validated against the literature reported signaling, drug response dynamics, and EGFR-MEK drug combination effect...
January 19, 2017: Scientific Reports
#13
Jagannath Jana, Soma Mondal, Payel Bhattacharjee, Pallabi Sengupta, Tanaya Roychowdhury, Pranay Saha, Pallob Kundu, Subhrangsu Chatterjee
A putative anticancer plant alkaloid, Chelerythrine binds to G-quadruplexes at promoters of VEGFA, BCL2 and KRAS genes and down regulates their expression. The association of Chelerythrine to G-quadruplex at the promoters of these oncogenes were monitored using UV absorption spectroscopy, fluorescence anisotropy, circular dichroism spectroscopy, CD melting, isothermal titration calorimetry, molecular dynamics simulation and quantitative RT-PCR technique. The pronounced hypochromism accompanied by red shifts in UV absorption spectroscopy in conjunction with ethidium bromide displacement assay indicates end stacking mode of interaction of Chelerythrine with the corresponding G-quadruplex structures...
January 19, 2017: Scientific Reports
#14
Henry C H Law, Samuel S W Szeto, Quan Quan, Yun Zhao, Zaijun Zhang, Olga Krakovska, Leong Ting Lui, Chengyou Zheng, Simon Ming Yuen Lee, K W Michael Siu, Yuqiang Wang, Ivan K Chu
Stroke is one of the main causes of mortality and long-term disability worldwide. The pathophysiological mechanisms underlying this disease are not well understood, particularly in the chronic phase after the initial ischemic episode. In this study, a Macaca fascicularis stroke model consisting of two sample groups, as determined by MRI-quantified infarct volumes as a measure of the stroke severity 28 days after the ischemic episode, was evaluated using qualitative and quantitative proteomics analyses. By using multiple online multidimensional liquid chromatography platforms, 8790 non-redundant proteins that condensed to 5223 protein groups at 1% global false discovery rate (FDR)...
January 19, 2017: Journal of Proteome Research
#15
Neharika G Chamachi, Suman Chakrabarty
The structural basis of misfolding pathways of a cellular Prion (PrP(C)) into the toxic scrapie form (PrP(SC)) and identification of possible intermediates (e.g. PrP(*)) still eludes us. In this work, we have used a cumulative ~65µs of Replica Exchange Molecular Dynamics simulation data to construct the conformational free energy landscapes and capture the structural and thermodynamic characteristics associated with various stages of the thermal denaturation process in human Prion protein. The temperature dependent free energy surfaces consist of multiple metastable states stabilized by non-native contacts and hydrogen bonds, thus rendering the protein prone towards misfolding...
January 19, 2017: Biochemistry
#16
Michael D Ward, Shivangi Nangia, Eric R May
The PACE force field presents an attractive model for conducting molecular dynamics simulations of membrane-protein systems. PACE is a hybrid model, in which lipids and solvents are coarse-grained consistent with the MARTINI mapping, while proteins are described by a united atom model. However, given PACE is linked to MARTINI, which is widely used to study membranes, the behavior of proteins interacting with membranes has only been limitedly examined in PACE. In this study, PACE is used to examine the behavior of several peptides in membrane environments, namely WALP peptides, melittin and influenza hemagglutinin fusion peptide (HAfp)...
January 19, 2017: Journal of Computational Chemistry
#17
You Xu, Alessandra Villa, Lennart Nilsson
Locked nucleic acid (LNA), a modified nucleoside which contains a bridging group across the ribose ring, improves the stability of DNA/RNA duplexes significantly, and therefore is of interest in biotechnology and gene therapy applications. In this study, we investigate the free energy change between LNA and DNA nucleosides. The transformation requires the breaking of the bridging group across the ribose ring, a problematic transformation in free energy calculations. To address this, we have developed a 3-step (easy to implement) and a 1-step protocol (more efficient, but more complicated to setup), for single and dual topologies in classical molecular dynamics simulations, using the Bennett Acceptance Ratio method to calculate the free energy...
January 19, 2017: Journal of Computational Chemistry
#18
Qi Huang, Jocelyn M Rodgers, Russell J Hemley, Toshiko Ichiye
A critical question about piezophilic (pressure-loving) microbes is how their constituent molecules maintain function under high pressure. Here, factors are examined that may lead to the increased activity under pressure in dihydrofolate reductase from the piezophilic Moritella profunda compared to the homologous enzyme from the mesophilic Escherichia coli. Molecular dynamics simulations are performed at various temperatures and pressures to examine how pressure affects the flexibility of the enzymes from these two microbes, since both stability and flexibility are necessary for enzyme activity...
January 19, 2017: Journal of Computational Chemistry
#19
Carlos E S Bernardes
Molecular Dynamic and Monte-Carlo simulations are widely used to investigate the structure and physical properties of solids and liquids at a molecular level. Tools to extract the most relevant information from the obtained results are, however, in considerable demand. One such tool, the program AGGREGATES, is described in this work. Based on distance criteria, the program searches trajectory files for the presence of molecular clusters and computes several statistical and shape properties for these structures...
January 19, 2017: Journal of Computational Chemistry
#20
Cathy Ng, Padmavathy Nandha Premnath, Olgun Guvench
Proteoglycans (PGs) are covalent conjugates between protein and carbohydrate (glycosaminoglycans). Certain classes of glycosaminoglycans such as chondroitin sulfate/dermatan sulfate and heparan sulfate utilize a specific tetrasaccharide linker for attachment to the protein component: GlcAβ1-3Galβ1-3Galβ1-4Xylβ1-O-Ser. Toward understanding the conformational preferences of this linker, the present work used all-atom explicit-solvent molecular dynamics (MD) simulations combined with Adaptive Biasing Force (ABF) sampling to determine high-resolution, high-precision conformational free energy maps ΔG(φ, ψ) for each glycosidic linkage between constituent disaccharides, including the variant where GlcA is substituted with IdoA...
January 19, 2017: Journal of Computational Chemistry
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