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https://www.readbyqxmd.com/read/28107751/molecular-modeling-study-of-cp-690550-derivatives-as-jak3-kinase-inhibitors-through-combined-3d-qsar-molecular-docking-and-dynamics-simulation-techniques
#1
Jing Li Wang, Li Ping Cheng, Tian Chi Wang, Wei Deng, Fan Hong Wu
To develop more potent JAK3 kinase inhibitors, a series of CP-690550 derivatives were investigated using combined molecular modeling techniques, such as 3D-QSAR, molecular docking and molecular dynamics (MD). The leave-one-out correlation (q(2)) and non-cross-validated correlation coefficient (r(2)) of the best CoMFA model are 0.715 and 0.992, respectively. The q(2) and r(2) values of the best CoMSIA model are 0.739 and 0.995, respectively. The steric, electrostatic, and hydrophobic fields played important roles in determining the inhibitory activity of CP-690550 derivatives...
January 4, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28106833/influence-of-temperature-on-transdermal-penetration-enhancing-mechanism-of-borneol-a-multi-scale-study
#2
Qianqian Yin, Ran Wang, Shufang Yang, Zhimin Wu, Shujuan Guo, Xingxing Dai, Yanjiang Qiao, Xinyuan Shi
The influence of temperature on the transdermal permeation enhancing mechanism of borneol (BO) was investigated using a multi-scale method, containing a coarse-grained molecular dynamic (CG-MD) simulation, an in vitro permeation experiment, and a transmission electron microscope (TEM) study. The results showed that BO has the potential to be used as a transdermal penetration enhancer to help osthole (OST) penetrate into the bilayer. With the increasing temperature, the stratum corneum (SC) becomes more flexible, proving to be synergistic with the permeation enhancement of BO, and the lag time (TLag) of BO and OST are shortened...
January 19, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28106047/scale-dependent-diffusion-anisotropy-in-nanoporous-silicon
#3
Daria Kondrashova, Alexander Lauerer, Dirk Mehlhorn, Hervé Jobic, Armin Feldhoff, Matthias Thommes, Dipanjan Chakraborty, Cedric Gommes, Jovana Zecevic, Petra de Jongh, Armin Bunde, Jörg Kärger, Rustem Valiullin
Nanoporous silicon produced by electrochemical etching of highly B-doped p-type silicon wafers can be prepared with tubular pores imbedded in a silicon matrix. Such materials have found many technological applications and provide a useful model system for studying phase transitions under confinement. This paper reports a joint experimental and simulation study of diffusion in such materials, covering displacements from molecular dimensions up to tens of micrometers with carefully selected probe molecules. In addition to mass transfer through the channels, diffusion (at much smaller rates) is also found to occur in directions perpendicular to the channels, thus providing clear evidence of connectivity...
January 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28103664/relaxation-in-a-prototype-ionic-liquid-influence-of-water-on-the-dynamics
#4
David L Price, Oleg Borodin, Miguel A González, Maiko Kofu, Kaoru Shibata, Takeshi Yamada, Osamu Yamamuro, Marie-Louise Saboungi
The influence of water on the relaxation of a prototype ionic liquid (IL) C8mimBF4 is examined in the IL-rich regime combining quasi-elastic neutron scattering (QENS) and molecular dynamics (MD) simulations. The QENS and MD simulations results for relaxation of the IL and the equimolar mixture with water probed by the dynamics of the C8mim hydrogen atoms in the time range of 2 ps - 1 ns are in excellent agreement. The QENS data show that translational relaxation increases by a factor of 7 on addition of water, while rotational relaxation involving multiple processes fitted by a KWW function with low β values is speeded up by a factor of 3 on the timescale of QENS measurements...
January 20, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28103046/food-protein-based-core-shell-nanocarriers-for-oral-drug-delivery-effect-of-shell-composition-on-in-vitro-and-in-vivo-functional-performance-of-zein-nanocarriers
#5
Mohammed S Alqahtani, Md Saiful Islam, Satheesh Podaralla, Radhey S Kaushik, Joshua J Reineke, Tofuko Woyengo, Omathanu Perumal
The study was aimed at systematically investigating the influence of shell composition on the particle size, stability, release, cell uptake, permeability and in-vivo gastrointestinal distribution of food protein-based nanocarriers for oral delivery applications. Three different core-shell nanocarriers were prepared using food-grade biopolymers including zein-casein (ZC) nanoparticles, zein-lactoferrin (ZLF) nanoparticles and zein-PEG (ZPEG) micelles. Nile red was used as a model hydrophobic dye for in-vitro studies...
January 19, 2017: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/28102351/origins-of-ripples-in-cvd-grown-few-layered-mos2-structures-under-applied-strain-at-atomic-scales
#6
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
https://www.readbyqxmd.com/read/28102286/chelerythrine-down-regulates-expression-of-vegfa-bcl2-and-kras-by-arresting-g-quadruplex-structures-at-their-promoter-regions
#7
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
https://www.readbyqxmd.com/read/28101951/rigidity-and-flexibility-in-the-tetrasaccharide-linker-of-proteoglycans-from-atomic-resolution-molecular-simulation
#8
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
https://www.readbyqxmd.com/read/28100151/renin-inhibition-by-soyasaponin-i-a-potent-native-anti-hypertensive-compound
#9
Zeinab Tavassoli, Majid Taghdir, Bijan Ranjbar
One way to control hypertension is inactivation of the Renin- Angiotensin- Aldosterone System (RAAS). Inhibition of renin as a rate-limiting step of this system is an effective way to stop up RAAS. It has been proved that soyasaponin I, an herbal compound obtained from soybeans, has anti-hypertensive effect via renin inhibition, so it has the potential of being an anti-hypertensive drug. Herein, some theoretical approaches such as Docking Simulation, Molecular Dynamics (MD) Simulation and MMPBSA analysis have been used to study how soyasaponin I inhibits renin at the structural level...
January 19, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28100048/unanticipated-stickiness-of-%C3%AE-pinene
#10
Hilary M Chase, Junming Ho, Mary Alice Upshur, Regan J Thomson, Victor S Batista, Franz M Geiger
Hilary M. Chase1#, Junming Ho2#, Mary Alice Upshur1, Regan J. Thomson1, Victor S. Batista3, Franz M. Geiger1* 1Department of Chemistry, Northwestern University, Evanston, IL. 60208, United States; 2 Agency for Science, Technology and Research, Institute of High Performance Computing, 1 Fusionopolis Way #16-16 Connexis North, Singapore 138632; 3Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT. 06520, United States # These authors contributed equally to this work. *corresponding author: geigerf@chem...
January 19, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28099024/surface-interactions-and-confinement-of-methane-a-high-pressure-magic-angle-spinning-nmr-and-computational-chemistry-study
#11
Salim Ok, David W Hoyt, Amity Andersen, Julie Sheets, Susan A Welch, David R Cole, Karl Todd Mueller, Nancy M Washton
Characterization and modeling of the molecular-level behavior of simple hydrocarbon gases, such as methane, in the presence of both nonporous and nano-porous mineral matrices allows for predictive understanding of important processes in engineered and natural systems. In this study, changes in local electromagnetic environments of the carbon atoms in methane under conditions of high pressure (up to 130 bar) and moderate temperature (up to 346 K) were observed with 13C magic-angle spinning (MAS) NMR spectroscopy while the methane gas was mixed with two model solid substrates: a fumed non-porous, 12 nm particle size silica and a mesoporous silica with 200 nm particle size and 4 nm average pore diameter...
January 18, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28099023/computational-models-of-the-gastrointestinal-environment-1-the-effect-of-digestion-on-the-phase-behaviour-of-intestinal-fluids
#12
Woldeamanuel A Birru, Dallas B Warren, Stephen J Headey, Hassan Benameur, Christopher J H Porter, Colin W Pouton, David K Chalmers
Improved models of the gastrointestinal environment have great potential to assist the complex process of drug formulation. Molecular dynamics (MD) is a powerful method for investigating phase behaviour at a molecular level. In this study we use multiple MD simulations to calculate phase diagrams for bile before and after digestion. In these computational models, undigested bile is represented by mixtures of palmitoyl-oleoylphosphatidylcholine (POPC), sodium glycodeoxycholate (GDX) and water. Digested bile is modelled using a 1:1 mixture of oleic acid and palmitoylphosphatidylcholine (lyso-phosphatidylcholine, LPC), GDX and water...
January 18, 2017: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/28098999/dna-deformation-coupled-recognition-of-8-oxoguanine-conformational-kinetic-gating-in-human-dna-glycosylase
#13
Haoquan Li, Anton V Endutkin, Christina Bergonzo, Fu Lin, Arthur P Grollman, Dmitry O Zharkov, Carlos Simmerling
8-Oxoguanine (8-oxoG), a mutagenic DNA lesion generated under oxidative stress, differs from its precursor guanine by only two substitutions (O8 and H7). Human 8-oxoguanine glycosylase 1 (OGG1) can locate and remove 8-oxoG through extrusion and excision. To date, it remains unclear how OGG1 efficiently distinguishes 8-oxoG from a large excess of undamaged DNA bases. We recently showed that formamidopyrimidine-DNA glycosylase (Fpg), a bacterial functional analog of OGG1, can selectively facilitate eversion of oxoG by stabilizing several intermediate states, and it is intriguing whether OGG1 also employs a similar mechanism in lesion recognition...
January 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28098421/hexagonal-boron-nitride-h-bn-sheets-decorated-with-oli-ona-and-li2-f-molecules-for-enhanced-energy-storage
#14
Syeda Rabab Naqvi, Gollu Sankar Rao, Wei Luo, Rajeev Ahuja, Tanveer Hussain
First-principles electronic structure calculations were carried out on hexagonal boron nitride (h-BN) sheets functionalized with small molecules, such as OLi, ONa, and Li2 F, to study their hydrogen (H2 ) storage properties. We found that OLi and ONa strongly adsorb on h-BN sheets with reasonably large inter-adsorbent separations, which is desirable for H2 storage. Ab initio molecular dynamics (MD) simulations further confirmed the structural stability of OLi-BN and ONa-BN systems at 400 K. On the other hand, Li2 F molecules form clusters over the surface of h-BN at higher temperatures...
January 18, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28098313/the-glass-transition-and-interfacial-dynamics-of-single-strand-fibers-of-polymers
#15
Hyun Woo Cho, Bong June Sung
We investigate the glass transition and interfacial dynamics of single strand fibers of flexible polymers by employing molecular dynamics (MD) simulations along with a coarse grained model. While the polymer fiber has drawn significant attention due to its applicability in tissue engineering and stretchable electronics, its dynamic properties, especially the glass transition temperature (Tg), are yet to be understood at the molecular level. For example, there has been a controversy on the effect of the polymer fiber radius (R) on Tg: Tg decreased with a decrease in R for some polymer fibers, whereas Tg of other polymer fibers was not sensitive to R...
January 18, 2017: Soft Matter
https://www.readbyqxmd.com/read/28095341/effect-of-the-r119g-mutation-on-human-p5cr-structure-and-its-interactions-with-nad-insights-derived-from-molecular-dynamics-simulation-and-free-energy-analysis
#16
Peng Sang, Yue-Hui Xie, Lin-Hua Li, Yu-Jia Ye, Wei Hu, Jing Wang, Wen Wan, Rui Li, Long-Jun Li, Lin-Ling Ma, Zhi Li, Shu-Qun Liu, Zhao-Hui Meng
Pyrroline-5-carboxylate reductase (P5CR), an enzyme with conserved housekeeping roles, is involved in the etiology of cutis laxa. While previous work has shown that the R119G point mutation in the P5CR protein is involved, the structural mechanism behind the pathology remains to be elucidated. In order to probe the role of the R119G mutation in cutis laxa, we performed molecular dynamics (MD) simulations, essential dynamics (ED) analysis, and Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculations on wild type (WT) and mutant P5CR-NAD complex...
January 5, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28095026/self-regulation-of-driving-speed-among-distracted-drivers-an-application-of-driver-behavioural-adaptation-theory
#17
Oscar Oviedo-Trespalacios, Md Mazharul Haque, Mark King, Simon Washington
OBJECTIVE: The adaptive behaviour of mobile phone distracted drivers has been a topic of much discussion in the recent literature. Both simulator and naturalistic studies suggests that distracted drivers generally select lower driving speeds; however, speed adaptation is not observed among all drivers, and the mechanisms of speed selection are not well understood. The aim of this research was to apply a driver behavioural adaptation model to investigate the speed adaptation of mobile phone distracted drivers...
January 17, 2017: Traffic Injury Prevention
https://www.readbyqxmd.com/read/28094942/simulation-of-dbs-dbs-cooh-and-dbs-conhnh2-as-hydrogelators
#18
Dafna Knani, David Alperstein
The organic gelator 1,3(R):2,4(S)-dibenzylidene-D-sorbitol (DBS) self-organizes to form a 3-D network at relatively low concentrations in a variety of nonpolar organic solvents and polymer melt. DBS could be transformed into a hydrogelator by introduction of hydrophilic groups, which facilitate its self-assembly in aqueous medium. In this work, we have investigated the hydrogelators DBS-COOH and DBS-CONHNH2 and the organogelator DBS by molecular modeling. We have used quantum mechanics (QM) to elucidate the preferred geometry of one molecule and a dimer of each of the gelators, and molecular dynamics (MD) to simulate the pure gelators and their mixtures with water...
January 17, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28094512/a-combined-spectroscopic-molecular-dynamic-study-for-investigating-a-methyl-carboxylated-pei-as-a-potential-uranium-decorporation-agent
#19
Florian Lahrouch, Anne Christine Chamayou, Gaëlle Creff, Magali Duvail, Christoph Hennig, Marisol Janeth Lozano Rodriguez, Christophe Den Auwer, Christophe Di Giorgio
Natural uranium has a very limited radioactive dose impact, but its chemical toxicity due to chronic exposure is still a matter of debate. Once inside the human body, the soluble uranium, under its uranyl form (U(VI)), is quickly removed from the blood system, partially excreted from the body, and partially retained in targeted organs, that is, the kidneys and bone matrix essentially. It is then crucial to remove or prevent the incorporation of uranium in these organs to limit the long-term chronic exposure...
January 17, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28094372/theoretical-studies-on-fgfr-isoform-selectivity-of-fgfr1-fgfr4-inhibitors-by-molecular-dynamics-simulations-and-free-energy-calculations
#20
Weitao Fu, Lingfeng Chen, Zhe Wang, Yanting Kang, Chao Wu, Qinqin Xia, Zhiguo Liu, Jianmin Zhou, Guang Liang, Yuepiao Cai
The activation and overexpression of fibroblast growth factor receptors (FGFRs) are highly correlated with a variety of cancers. Most small molecule inhibitors of FGFRs selectively target FGFR1-3, but not FGFR4. Hence, designing highly selective inhibitors towards FGFR4 remains a great challenge because FGFR4 and FGFR1 have a high sequence identity. Recently, two small molecule inhibitors of FGFRs, ponatinib and AZD4547, have attracted huge attention. Ponatinib, a type II inhibitor, has high affinity towards FGFR1/4 isoforms, but AZD4547, a type I inhibitor of FGFR1, displays much reduced inhibition toward FGFR4...
January 17, 2017: Physical Chemistry Chemical Physics: PCCP
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