Search Results - "de Leeuw, Simon W"

Dynamic Heterogeneity and Ionic Conduction in an Organic Ionic Plastic Crystal and the Role of Vacancies by Chen, Fangfang, de Leeuw, Simon W, Forsyth, Maria

“…Dynamic heterogeneity was investigated for the first time in a conductive organic ionic plastic crystal by molecular dynamics simulation. A minority fraction…”
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Local Field Controlled Switching in a One-Dimensional Dipolar Array by de Jonge, Jeroen J, Ratner, Mark A, de Leeuw, Simon W

“…We use computational Langevin dynamics simulations to show that the orientation of the dipolar rotors in a one-dimensional chain can be controlled using a…”
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Free Energy Calculations for Identifying Efficient Promoter Molecules of Binary sH Hydrogen Clathrates by Atamas, Alexander A, Koudriachova, Marina V, de Leeuw, Simon W, Cuppen, Herma M

“…To determine the stabilizing effect of different promoter molecules on the clathrate, the Gibbs free energy of fully occupied binary sH hydrogen clathrates…”
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Concentration Dependence of α-Synuclein Fibril Length Assessed by Quantitative Atomic Force Microscopy and Statistical-Mechanical Theory by van Raaij, Martijn E., van Gestel, Jeroen, Segers-Nolten, Ine M.J., de Leeuw, Simon W., Subramaniam, Vinod

“…The initial concentration of monomeric amyloidogenic proteins is a crucial factor in the in vitro formation of amyloid fibrils. We use quantitative atomic…”
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Monte Carlo Calculations of the Free Energy of Binary SII Hydrogen Clathrate Hydrates for Identifying Efficient Promoter Molecules by Atamas, Alexander A, Cuppen, Herma M, Koudriachova, Marina V, de Leeuw, Simon W

“…The thermodynamics of binary sII hydrogen clathrates with secondary guest molecules is studied with Monte Carlo simulations. The small cages of the sII unit…”
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Effect of diffusion on lithium intercalation in titanium dioxide by Koudriachova, M V, Harrison, N M, de Leeuw, S W

“…A new model of Li intercalation into rutile and anatase structured titania has been developed from first principles calculations. The model includes both…”
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Reordering Hydrogen Bonds Using Hamiltonian Replica Exchange Enhances Sampling of Conformational Changes in Biomolecular Systems by Vreede, Jocelyne, Wolf, Maarten G, de Leeuw, Simon W, Bolhuis, Peter G

“…Hydrogen bonds play an important role in stabilizing (meta-)stable states in protein folding. Hence, they can potentially be used as a way to bias these states…”
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Optimizing transport in nanostructured catalysts: A computational study by Wang, Gang, Johannessen, Eivind, Kleijn, Chris R., de Leeuw, Simon W., Coppens, Marc-Olivier

“…A continuum modeling approach is used to compare the yield of catalyst particles called monodisperse, and containing only nanopores (i.e., micropores or narrow…”
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A Statistical-Mechanical Theory of Fibril Formation in Dilute Protein Solutions by van Gestel, Jeroen, de Leeuw, Simon W.

“…We outline a theoretical treatment that describes fibril formation in dilute protein solutions. For this, we combine a theory describing self-assembly and…”
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Open circuit voltage profile for Li-intercalation in rutile and anatase from first principles by Koudriachova, Marina V, Harrison, Nicholas M, de Leeuw, Simon W

“…Ab initio calculations of lithium intercalation into rutile- and anatase structured titanium dioxide are presented. An analysis of self-ordering at different…”
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First principles predictions for intercalation behaviour by Koudriachova, Marina V., Harrison, Nicholas M., de Leeuw, Simon W.

“…Li-insertion into rutile and anatase structured TiO 2 has been studied using first principles calculations. It has been show that intercalation behaviour and…”
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Monte Carlo calculations of the free energy of ice-like structures using the self-referential method by Atamas, Alexander, Koudriachova, Marina V., de Leeuw, Simon W., Sweatman, Martin B.

“…The self-referential method is a recently developed technique to compute the free energy of molecular crystals. In this paper, the method is extended to…”
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Modeling amyloid fibril formation: a free-energy approach by Wolf, Maarten G, Gestel, Jeroen van, de Leeuw, Simon W

“…Amyloid fibrils are structures consisting of many proteins with a well-defined conformation. The formation of these fibrils has been the subject of intense…”
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Rapid Free Energy Calculation of Peptide Self-Assembly by REMD Umbrella Sampling by Wolf, Maarten G, Jongejan, Jaap A, Laman, Jon D, de Leeuw, Simon W

“…We extend umbrella sampling with replica exchange steps to calculate free energies that are important in the self-assembly of peptides. This leads to a more…”
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Quantitative Prediction of Amyloid Fibril Growth of Short Peptides from Simulations: Calculating Association Constants To Dissect Side Chain Importance by Wolf, Maarten G, Jongejan, Jaap A, Laman, Jon D, de Leeuw, Simon W

“…Quantitative prediction of the fibril growth properties of different peptides is conducted with a molecular dynamics approach. Association constants of small…”
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Computational study of ground-state chiral induction in small peptides: Comparison of the relative stability of selected amino acid dimers and oligomers in homochiral and heterochiral combinations by Zhou, Yu, Oostenbrink, Chris, Jongejan, Aldo, Van Gunsteren, Wilfred F., Hagen, Wilfred R., De Leeuw, Simon W., Jongejan, Jaap A.

“…The relative stabilities of homochiral and heterochiral forms of selected dipeptides, AA, AS, AC, AV, AF, AD, AK, tripeptides, AAA, AVA, and an…”
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Molecular Dynamics Simulation of Poly(p-xylylene):  Bulk Phase and a Single Molecule by Gotlib, Igor Yu, Piotrovskaya, Elena M, de Leeuw, Simon W

“…The bulk phase of poly(p-xylylene) (PPX) at 295−595 K and isolated PPX chains at 195−995 K have been simulated by molecular dynamics using TraPPE-UA model…”
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A new phase of lithiated titania predicted from first principles by Koudriachova, Marina V., de Leeuw, Simon W., Harrison, Nicholas M.

“…A new phase of Li-intercalated rutile-structured titania, Li x TiO 2 for x=0.75, is predicted on the basis of first principles calculations. The existence of…”
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Controlling the Energy Transfer in Dipole Chains by de Jonge, Jeroen J, Ratner, Mark A, de Leeuw, Simon W, Simonis, Richard O

“…Processing digital signals on the molecular scale is of great interest. In this paper, we discuss the control of pulselike energy propagation through…”
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Molecular dynamics of an excess electron in aqueous solutions by Drukker, Karen, de Leeuw, Simon W

“…We used the molecular dynamics with quantum transitions method to investigate the behavior of an excess electron injected into an excited state of an…”
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