Search Results - "Ghysels, An"

Permeability of membranes in the liquid ordered and liquid disordered phases by Ghysels, An, Krämer, Andreas, Venable, Richard M., Teague, Walter E., Lyman, Edward, Gawrisch, Klaus, Pastor, Richard W.

“…The functional significance of ordered nanodomains (or rafts) in cholesterol rich eukaryotic cell membranes has only begun to be explored. This study exploits…”
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An exact algorithm to find a maximum weight clique in a weighted undirected graph by Rozman, Kati, Ghysels, An, Janežič, Dušanka, Konc, Janez

“…We introduce a new algorithm MaxCliqueWeight for identifying a maximum weight clique in a weighted graph, and its variant MaxCliqueDynWeight with dynamically…”
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On the Thermodynamics of Framework Breathing: A Free Energy Model for Gas Adsorption in MIL-53 by Ghysels, An, Vanduyfhuys, Louis, Vandichel, Matthias, Waroquier, Michel, Van Speybroeck, Veronique, Smit, Berend

“…When adsorbing guest molecules, the porous metal–organic framework MIL-53(Cr) may vary its cell parameters drastically while retaining its crystallinity. A…”
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Shape-Selective Diffusion of Olefins in 8‑Ring Solid Acid Microporous Zeolites by Ghysels, An, Moors, Samuel L.C, Hemelsoet, Karen, De Wispelaere, Kristof, Waroquier, Michel, Sastre, German, Van Speybroeck, Veronique

“…The diffusion of olefins through 8-ring solid acid microporous zeolites is investigated using molecular dynamics simulations techniques and using a newly…”
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Membrane Permeability: Characteristic Times and Lengths for Oxygen and a Simulation-Based Test of the Inhomogeneous Solubility-Diffusion Model by De Vos, Oriana, Venable, Richard M, Van Hecke, Tanja, Hummer, Gerhard, Pastor, Richard W, Ghysels, An

“…The balance of normal and radial (lateral) diffusion of oxygen in phospholipid membranes is critical for biological function. Based on the Smoluchowski…”
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First Principle Kinetic Studies of Zeolite-Catalyzed Methylation Reactions by Van Speybroeck, Veronique, Van der Mynsbrugge, Jeroen, Vandichel, Matthias, Hemelsoet, Karen, Lesthaeghe, David, Ghysels, An, Marin, Guy B, Waroquier, Michel

“…Methylations of ethene, propene, and butene by methanol over the acidic microporous H-ZSM-5 catalyst are studied by means of state of the art computational…”
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Exact non-Markovian permeability from rare event simulations by Ghysels, An, Roet, Sander, Davoudi, Samaneh, van Erp, Titus S.

“…Permeation of compounds through membranes is important in biological and engineering processes, e.g., drug delivery through lipid bilayers, anesthetics, or…”
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The Importance of Cell Shape Sampling To Accurately Predict Flexibility in Metal–Organic Frameworks by Rogge, Sven M. J, Caroes, Senne, Demuynck, Ruben, Waroquier, Michel, Van Speybroeck, Veronique, Ghysels, An

“…In this work, the influence of cell shape sampling on the predicted stability of the different metastable phases in flexible metal–organic frameworks at finite…”
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Normal Mode Analysis in Zeolites: Toward an Efficient Calculation of Adsorption Entropies by De Moor, Bart A, Ghysels, An, Reyniers, Marie-Françoise, Van Speybroeck, Veronique, Waroquier, Michel, Marin, Guy B

“…An efficient procedure for normal-mode analysis of extended systems, such as zeolites, is developed and illustrated for the physisorption and chemisorption of…”
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Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit by Woodcock, H Lee, Zheng, Wenjun, Ghysels, An, Shao, Yihan, Kong, Jing, Brooks, Bernard R

“…A new vibrational subsystem analysis (VSA) method is presented for coupling global motion to a local subsystem while including the inertial effects of the…”
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Comparative study of various normal mode analysis techniques based on partial Hessians by Ghysels, An, Van Speybroeck, Veronique, Pauwels, Ewald, Catak, Saron, Brooks, Bernard R, Van Neck, Dimitri, Waroquier, Michel

“…Standard normal mode analysis becomes problematic for complex molecular systems, as a result of both the high computational cost and the excessive amount of…”
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Bringing hidden variables into the open unveils a barrier for lipid insertion into membranes by Ghysels, An

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Defining permeability of curved membranes in molecular dynamics simulations by Davoudi, Samaneh, Ghysels, An

“…Many phospholipid membranes in the cell have a high curvature; for instance, in caveolae, mitochondrial crystae, nanotubes, membrane pearls, small liposomes,…”
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Understanding Oxygen "Buffering" by Caveolae Using Coarse-Grained Molecular Dynamics Simulations by Davoudi, Samaneh, Ghysels, An

“…The "oxygen paradox" embodies the delicate interplay between two opposing biological processes involving oxygen (O ). O is indispensable for aerobic…”
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Inhomogeneous Solubility-Diffusion Model Gives Insight in Efficacy of Counting Crossings Method to Calculate the Membrane Permeability by Davoudi, Samaneh, Ghysels, An

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Conformational dynamics of α-1 acid glycoprotein (AGP) in cancer: A comparative study of glycosylated and unglycosylated AGP by Dixit, Bhawna, Vranken, Wim, Ghysels, An

“…α-1 acid glycoprotein (AGP) is one of the most abundant plasma proteins. It fulfills two important functions: immunomodulation, and binding to various drugs…”
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Oxygen Storage in Stacked Phospholipid Membranes Under an Oxygen Gradient as a Model for Myelin Sheaths by Vervust, Wouter, Ghysels, An

“…Axons in the brain and peripheral nervous system are enveloped by myelin sheaths, which are composed of stacked membrane bilayers containing large fractions of…”
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Capric Acid and Myristic Acid Permeability Enhancers in Curved Liposome Membranes by Davoudi, Samaneh, Raemdonck, Koen, Braeckmans, Kevin, Ghysels, An

“…Liposomes are considered as advanced drug delivery systems for cancer treatment. A generation of pH-sensitive liposomes is being developed that use fatty acids…”
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Counting permeant crossings to assess the effect of membrane curvature and composition on the permeability rate by Davoudi, Samaneh, Raemdonck, Koen, Braeckmans, Kevin, Ghysels, An

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Position-Dependent Diffusion Tensors in Anisotropic Media from Simulation: Oxygen Transport in and through Membranes by Ghysels, An, Venable, Richard M, Pastor, Richard W, Hummer, Gerhard

“…A Bayesian-based methodology is developed to estimate diffusion tensors from molecular dynamics simulations of permeants in anisotropic media, and is applied…”
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