Publications


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Knoll, P, Kenny, B, Mirzaei, S, Koriska, K, Köhn, H & Neumann, M 2002, 'A (μ + λ) evolutionary algorithm for reconstruction of SPECT data' IEEE transactions on evolutionary computation, vol 6, no. 6, pp. 533-541. DOI: 10.1109/TEVC.2002.806743

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Coluzza, I 2011, 'A Coarse-Grained Approach to Protein Design: Learning from Design to Understand Folding' PLoS ONE, vol 6, no. 7, e20853. DOI: 10.1371/journal.pone.0020853

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Theodorakis, P, Dellago, C & Kahl, G 2013, 'A coarse-grained model for DNA-functionalized spherical colloids, revisited: Effective pair potential from parallel replica simulations' Journal of Chemical Physics, vol 138, no. 2, 025101. DOI: 10.1063/1.4773920

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Rovigatti, L, Sulc, P, Reguly, IZ & Romano, F 2015, 'A Comparison between Parallelization Approaches in Molecular Dynamics Simulations on GPUs' Journal of Computational Chemistry, vol 36, no. 1, pp. 1-8. DOI: 10.1002/jcc.23763

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Varga, S & Vesely, F 2009, 'A new generic model potential for mesogenic systems: Square well line potential of variable range' Journal of Chemical Physics, vol 131, 194506. DOI: 10.1063/1.3264109

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Köfinger, J, Hummer, G & Dellago, C 2009, 'A one-dimensional dipole lattice model for water in narrow nanopores' Journal of Chemical Physics, vol 130, 154110. DOI: 10.1063/1.3106223

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Leitold, C, Lechner, W & Dellago, C 2015, 'A string reaction coordinate for the folding of a polymer chain' Journal of Physics: Condensed Matter, vol 27, no. 19, 194126. DOI: 10.1088/0953-8984/27/19/194126

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Theodorakis, P & Fytas, G 2012, 'A study for the static properties of symmetric linear multiblock copolymers under poor solvent conditions' Journal of Chemical Physics, vol 136, no. 9, 094902. DOI: 10.1063/1.3689303

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Capone, B, Coluzza, I & Hansen, J-P 2011, 'A systematic coarse-graining strategy for semi-dilute copolymer solutions: from monomers to micelles' Journal of Physics: Condensed Matter, vol 23, no. 19, 194102. DOI: 10.1088/0953-8984/23/19/194102

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Geissler, PL, Dellago, C, Chandler, D, Hutter, J & Parrinello, MT 2000, 'Ab initio analysis of proton transfer dynamics in (H2O)3H+' Chemical Physics Letters, vol 321, no. 3-4, pp. 225-230. DOI: 10.1016/S0009-2614(00)00381-X

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Blaak, R, Capone, B, Likos, C & Rovigatti, L 2015, Accurate coarse-grained potentials for soft matter systems: Lecture Notes. in G Sutmann, J Grotendorst, G Gompper & D Marx (eds), Computational trends in solvation and transport in liquids. Schriften des Forschungszentrum Jülich, IAS Series, vol. 28, Jülich, pp. 209-258.

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Lechner, W & Dellago, C 2008, 'Accurate determination of crystal structures based on averaged local bond order parameters' Journal of Chemical Physics, vol 129, no. 11, 114707. DOI: 10.1063/1.2977970

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Poier, P, Likos, CN, Moreno, AJ & Blaak, R 2015, 'An Anisotropic Effective Model for the Simulation of Semiflexible Ring Polymers' Macromolecules, vol 48, no. 14, pp. 4983-4997. DOI: 10.1021/acs.macromol.5b00603

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Grünwald, M, Dellago, C & Geissler, PL 2007, 'An efficient transition path sampling algorithm for nanoparticles under pressure' Journal of Chemical Physics, vol 127, 154718. DOI: 10.1063/1.2790431

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Wirnsberger, P, Frenkel, D & Dellago, C 2015, 'An enhanced version of the heat exchange algorithm with excellent energy conservation properties' Journal of Chemical Physics, vol 143, no. 12, 124104. DOI: 10.1063/1.4931597

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Omasits, U, Knapp, B, Neumann, M, Steinhauser, O, Stockinger, H, Kobler, R & Schreiner, W 2008, 'Analysis of key parameters for molecular dynamics of pMHC molecules' Molecular Simulation, vol 34, no. 8, pp. 781-793. DOI: 10.1080/08927020802256298

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Theodorakis, P, Paul, W & Binder, K 2011, 'Analysis of the cluster formation in two-component cylindrical bottle-brush polymers under poor solvent conditions. A simulation study' European Physical Journal E. Soft Matter, vol 34, no. 5, 52. DOI: 10.1140/epje/i2011-11052-5

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Fytas, NG & Theodorakis, P 2011, 'Analysis of the static properties of cluster formations in symmetric linear multiblock copolymers' Journal of Physics: Condensed Matter, vol 23, no. 23, 235106. DOI: 10.1088/0953-8984/23/23/235106

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Coluzza, I, MacDonald, JT, Sadowski, MI, Taylor, WR & Goldstein, RA 2012, 'Analytic Markovian Rates for Generalized Protein Structure Evolution' PLoS ONE, vol 7, no. 5, e4228. DOI: 10.1371/journal.pone.0034228

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Donaldson, JG, Pyanzina, ES, Novak, EV & Kantorovich, SS 2015, 'Anisometric and anisotropic magnetic colloids: How to tune the response' Journal of Magnetism and Magnetic Materials, vol 383, pp. 267-271. DOI: 10.1016/j.jmmm.2014.11.013

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Poier, P, Bacova, P, Moreno, AJ, Likos, CN & Blaak, R 2016, 'Anisotropic effective interactions and stack formation in mixtures of semiflexible ring polymers' Soft Matter, vol 12, no. 21, pp. 4805-4820. DOI: 10.1039/c6sm00430j

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Narros González, A, Moreno, AJ & Likos, CN 2013, 'Architecture-induced size asymmetry and effective interactions of ring polymers: Simulation and theory' Macromolecules, vol 46, no. 23, pp. 9437-9445. DOI: 10.1021/ma4016483

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Dellago, C & Hoover, WG 2000, 'Are local Lyapunov exponents continuous in phase space?' Physics Letters. Section A: General, Atomic and Solid State Physics, vol 268, no. 4-6, pp. 330-334. DOI: 10.1016/S0375-9601(00)00218-8

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Holec, D, Zhou, L, Riedl, H, Koller, CM, Mayrhofer, PH, Friák, M, Šob, M, Körmann, F, Neugebauer, J, Music, D, Hartmann, MA & Fischer, FD 2017, 'Atomistic Modeling-Based Design of Novel Materials' Advanced Engineering Materials, vol 19, no. 4, 1600688. DOI: 10.1002/adem.201600688

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Sánchez, PA, Smiatek, J, Qiao, B, Sega, M & Holm, C 2016, Atomistic simulation of oligoelectrolyte multilayers growth. in WE Nagel, DH Kröner & MM Resch (eds), High Performance Computing in Science and Engineering '15: Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2015. Springer, pp. 215-228. DOI: 10.1007/978-3-319-24633-8_14

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Geissler, PL, Dellago, C, Chandler, D, Hutter, J & Parrinello, MT 2001, 'Autoionization in liquid water' Science, vol 291, no. 5511, pp. 2121-2124. DOI: 10.1126/science.1056991

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Borrero, EE & Dellago, C 2016, 'Avoiding traps in trajectory space: Metadynamics enhanced transition path sampling' European Physical Journal. Special Topics, vol 225, no. 8-9, pp. 1609-1620. DOI: 10.1140/epjst/e2016-60106-y

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Novak, EV, Pyanzina, ES & Kantorovich, SS 2015, 'Behaviour of magnetic Janus-like colloids' Journal of Physics: Condensed Matter, vol 27, no. 23, 234102. DOI: 10.1088/0953-8984/27/23/234102

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Köfinger, J & Dellago, C 2008, 'Biasing the center of charge in molecular dynamics simulations with empirical valence bond models: free energetics of an excess proton in a water droplet' The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, vol 112, no. 8, pp. 2349-2356. DOI: 10.1021/jp0736185

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Köfinger, J & Dellago, C 2008, 'Biasing the center of charge in molecular dynamics simulations with empirical valence bond models: Free energetics of an excess proton in a water droplet (vol 112, pg 2349, 2008)' The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, vol 112, no. 28, pp. 8425-8425. DOI: 10.1021/jp8048422

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Steinbach, G, Nissen, D, Albrecht, M, Novak, E, Sanchez, PA, Kantorovich, S, Gemming, S & Erbe, A 2016, 'Bistable self-assembly in homogeneous colloidal systems for flexible modular architectures' Soft Matter, vol 12, no. 10, pp. 2737-2743. DOI: 10.1039/C5SM02899J

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Mahynski, NA, Rovigatti, L, Likos, CN & Panagiotopoulos, AZ 2016, 'Bottom-Up Colloidal Crystal Assembly with a Twist' ACS Nano, vol 10, no. 5, pp. 5459-5467. DOI: 10.1021/acsnano.6b01854

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Nikoubashman, A & Likos, C 2010, 'Branched Polymers under Shear' Macromolecules, vol 43, no. 3, pp. 1610-1620. DOI: 10.1021/ma902212s

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Rovigatti, L, Kantorovich, S, Ivanov, AO, Tavares, JM & Sciortino, F 2013, 'Branching points in the low-temperature dipolar hard sphere fluid' Journal of Chemical Physics, vol 139, no. 13, 134901. DOI: 10.1063/1.4821935

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Vogler, C, Bruckner, F, Suess, D & Dellago, C 2015, 'Calculating thermal stability and attempt frequency of advanced recording structures without free parameters' Journal of Applied Physics, vol 117, no. 16, 163907. DOI: 10.1063/1.4918902

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Darvas, M, Jorge, M, Cordeiro, MNDS, Kantorovich, SS, Sega, M & Jedlovszky, P 2013, 'Calculation of the Intrinsic Solvation Free Energy Profile of an Ionic Penetrant Across a Liquid-Liquid Interface with Computer Simulations' The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, vol 117, no. 50, pp. 16148-16156. DOI: 10.1021/jp404699t

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Jungblut, S & Dellago, C 2015, 'Caveats of mean first-passage time methods applied to the crystallization transition: Effects of non-Markovianity' Journal of Chemical Physics, vol 142, no. 6, 064103. DOI: 10.1063/1.4907364

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Najafi, S, Tubiana, L, Podgornik, R & Potestio, R 2016, 'Chirality modifies the interaction between knots' Europhysics Letters, vol 114, no. 5, 50007. DOI: 10.1209/0295-5075/114/50007

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Jehser, M & Likos, C 2017, Closing a Gap -Polymer Ring Brushes pushed together: a DPD simulation study. in Conference Book. pp. 4.008, Liquids 2017, Ljubljana, Slovenia, 17-21 July.

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Pyanzina, ES, Gudkova, AV, Donaldson, JG & Kantorovich, SS 2017, 'Cluster analysis in systems of magnetic spheres and cubes' Journal of Magnetism and Magnetic Materials, vol 431, pp. 201-204. DOI: 10.1016/j.jmmm.2016.09.048

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Nikoubashman, A, Kahl, G & Likos, C 2011, 'Cluster Crystals under Shear' Physical Review Letters, vol 107, no. 6, 068302. DOI: 10.1103/PhysRevLett.107.068302

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Camargo, M, Egorov, SA & Likos, C 2012, 'Cluster formation in star-linear polymer mixtures: equilibrium and dynamical properties' Soft Matter, vol 8, no. 15, pp. 4177-4184. DOI: 10.1039/c2sm06849d

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Zakaria Slimani, M, Bacova, P, Bernabei, M, Narros, A, Likos, CN & Moreno, AJ 2014, 'Cluster Glasses of Semiflexible Ring Polymers' ACS Macro Letters, vol 3, no. 7, pp. 611-616. DOI: 10.1021/mz500117v

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Tröster, A 2007, 'Coarse grained free energies with gradient corrections from Monte Carlo simulations in Fourier space' Physical Review B (Condensed Matter and Materials Physics), vol 76, no. 1, 012402. DOI: 10.1103/PhysRevB.76.012402

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Marzi, D, Likos, C & Capone, B 2012, 'Coarse graining of star-polymer - colloid nanocomposites' Journal of Chemical Physics, vol 137, no. 1, 014902. DOI: 10.1063/1.4730751

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Capone, B 2013, 'Coarse graining polymers solutions in the semidilute regime' American Chemical Society. Abstracts of Papers (at the National Meeting), vol 246.

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Tröster, A & Dellago, C 2007, 'Coarse graining the phi 4 model: Landau-Ginzburg potentials from computer simulations' Ferroelectrics, vol 354, no. 1, pp. 225-237. DOI: 10.1080/00150190701454982

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Nikoubashman, A, Mahynski, NA, Capone, B, Panagiotopoulos, AZ & Likos, CN 2015, 'Coarse-graining and phase behavior of model star polymer-colloid mixtures in solvents of varying quality' Journal of Chemical Physics, vol 143, no. 24, 243108. DOI: 10.1063/1.4931410

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Riest, J, Mohanty, P, Schurtenberger, P & Likos, C 2012, 'Coarse-graining of ionic microgels: Theory and experiment' Zeitschrift für Physikalische Chemie / International Journal of Research in Physical Chemistry and Chemical Physics, vol 226, no. 7-8, pp. 711-735. DOI: 10.1524/zpch.2012.0258

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Kögel, A, Maretzki, R, Pyanzina, ES, Sánchez, PA, Kantorovich, S & Richter, R 2017, 'Coarsening dynamics of ferromagnetic networks --- experimental results and simulations' Soft Matter.
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