Search Results - "Mark, Alan"

A Ring to Rule Them All: The Effect of Cyclopropane Fatty Acids on the Fluidity of Lipid Bilayers by Poger, David, Mark, Alan E

“…Cyclopropane fatty acids are widespread in bacteria. As their concentration increases on exposure to hostile environments, they have been proposed to protect…”
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Validating lipid force fields against experimental data: Progress, challenges and perspectives by Poger, David, Caron, Bertrand, Mark, Alan E.

“…Biological membranes display a great diversity in lipid composition and lateral structure that is crucial in a variety of cellular functions. Simulations of…”
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Automated Topology Builder Version 3.0: Prediction of Solvation Free Enthalpies in Water and Hexane by Stroet, Martin, Caron, Bertrand, Visscher, Koen M, Geerke, Daan P, Malde, Alpeshkumar K, Mark, Alan E

“…The ability of atomic interaction parameters generated using the Automated Topology Builder and Repository version 3.0 (ATB3.0) to predict experimental…”
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On the Validation of Molecular Dynamics Simulations of Saturated and cis-Monounsaturated Phosphatidylcholine Lipid Bilayers: A Comparison with Experiment by Poger, David, Mark, Alan E

“…Molecular dynamics simulations of fully hydrated pure bilayers of four widely studied phospholipids, 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC),…”
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Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies by Koziara, Katarzyna B., Stroet, Martin, Malde, Alpeshkumar K., Mark, Alan E.

“…To test and validate the Automated force field Topology Builder and Repository (ATB; http://compbio.biosci.uq.edu.au/atb/ ) the hydration free enthalpies for a…”
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Effect of Triclosan and Chloroxylenol on Bacterial Membranes by Poger, David, Mark, Alan E

“…Triclosan and chloroxylenol are broad-spectrum biocides used extensively in healthcare and consumer products. They have been suggested to perturb the structure…”
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Engineering Transferable Atomic Force Fields: Empirical Optimization of Hydrocarbon Lennard–Jones Interactions by Direct Mapping of Parameter Space by Zhou, Zihan, Mark, Alan E., Stroet, Martin

“…The utility of atomistic simulations depends on the accuracy of the force field used to represent the potential energy landscape, the consistency with which…”
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Effect of Methyl-Branched Fatty Acids on the Structure of Lipid Bilayers by Poger, David, Caron, Bertrand, Mark, Alan E

“…Methyl-branched fatty acids are widespread in prokaryotic membranes. Although anteiso and iso branching (that is on the antepenultimate and penultimate…”
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National Museum Wales and the scalar bureaucracies of institutional memory work by Rhodes II, Mark Alan

“…Museums form a core institutional foundation to the formation of national identities. They reflect, obfuscate, perform, and shape national narrative and…”
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An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0 by Malde, Alpeshkumar K, Zuo, Le, Breeze, Matthew, Stroet, Martin, Poger, David, Nair, Pramod C, Oostenbrink, Chris, Mark, Alan E

“…The Automated force field Topology Builder (ATB, http://compbio.biosci.uq.edu.au/atb) is a Web-accessible server that can provide topologies and parameters for…”
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Understanding the Effect of pH on the Solubility and Aggregation Extent of Humic Acid in Solution by Combining Simulation and the Experiment by Lan, Tu, Wu, Peng, Liu, Ziyi, Stroet, Martin, Liao, Jiali, Chai, Zhifang, Mark, Alan E, Liu, Ning, Wang, Dongqi

“…Molecular dynamics (MD) simulations were performed to investigate the dynamics of humic acid (HA) in an aqueous solution and the influence of pH, temperature,…”
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Can Machine Learning Algorithms Predict Which Patients Will Achieve Minimally Clinically Important Differences From Total Joint Arthroplasty? by Fontana, Mark Alan, Lyman, Stephen, Sarker, Gourab K, Padgett, Douglas E, MacLean, Catherine H

“…Identifying patients at risk of not achieving meaningful gains in long-term postsurgical patient-reported outcome measures (PROMs) is important for improving…”
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A new force field for simulating phosphatidylcholine bilayers by Poger, David, Van Gunsteren, Wilfred F., Mark, Alan E.

“…A new force field for the simulation of dipalmitoylphosphatidylcholine (DPPC) in the liquid‐crystalline, fluid phase at zero surface tension is presented. The…”
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Toroidal pores formed by antimicrobial peptides show significant disorder by Sengupta, Durba, Leontiadou, Hari, Mark, Alan E., Marrink, Siewert-Jan

“…A large variety of antimicrobial peptides have been shown to act, at least in vitro, by poration of the lipid membrane. The nanometre size of these pores,…”
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The reliability of molecular dynamics simulations of the multidrug transporter P-glycoprotein in a membrane environment by Condic-Jurkic, Karmen, Subramanian, Nandhitha, Mark, Alan E, O'Mara, Megan L

“…Despite decades of research, the mechanism of action of the ABC multidrug transporter P-glycoprotein (P-gp) remains elusive. Due to experimental limitations,…”
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Definition and testing of the GROMOS force-field versions 54A7 and 54B7 by Schmid, Nathan, Eichenberger, Andreas P., Choutko, Alexandra, Riniker, Sereina, Winger, Moritz, Mark, Alan E., van Gunsteren, Wilfred F.

“…New parameter sets of the GROMOS biomolecular force field, 54A7 and 54B7, are introduced. These parameter sets summarise some previously published force field…”
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Understanding the Activated Form of a Class-I Fusion Protein: Modeling the Interaction of the Ebola Virus Glycoprotein 2 with a Lipid Bilayer by Barfoot, Shelley, Poger, David, Mark, Alan E

“…The fusion of the viral and target cell membranes is a key step in the life cycle of all enveloped viruses. Here, a range of structural data is used to…”
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Validation of Molecular Simulation: An Overview of Issues by van Gunsteren, Wilfred F., Daura, Xavier, Hansen, Niels, Mark, Alan E., Oostenbrink, Chris, Riniker, Sereina, Smith, Lorna J.

“…Computer simulation of molecular systems enables structure–energy–function relationships of molecular processes to be described at the sub‐atomic, atomic,…”
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Basic ingredients of free energy calculations: A review by Christ, Clara D, Mark, Alan E, van Gunsteren, Wilfred F

“…Methods to compute free energy differences between different states of a molecular system are reviewed with the aim of identifying their basic ingredients and…”
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Lipid Bilayers: The Effect of Force Field on Ordering and Dynamics by Poger, David, Mark, Alan E

“…The sensitivity of the structure and dynamics of a fully hydrated pure bilayer of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) in molecular dynamics…”
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