MESA+ University of Twente
CCP Research Group

Publications


This page lists the publications of the CCP group for the last 5 years.

For comprehensive lists, please visit the pages of Claudia Filippi, Wim Briels and Wouter den Otter.



2016
  • R. Guareschi, O. Valsson, C. Curutchet, B. Mennucci, and C. Filippi
    Electrostatic versus resonance interactions in photoreceptor proteins: The case of rhodopsin
    J. Phys. Chem. Lett. 7, 4547 (2016). DOI: 10.1021/acs.jpclett.6b02043
  • M. Giani, W.K. den Otter, and W.J. Briels
    Clathrin Assembly Regulated by Adaptor Proteins in Coarse-Grained Models
    Biophys. J. 111, 222-235 (2016). DOI: 10.1016/j.bpj.2016.06.003
  • C. Filippi, R. Assaraf, and S. Moroni,
    Simple formalism for efficient derivatives and multi-determinant expansions in quantum Monte Carlo
    J. Chem. Phys. 144, 194105 (2016). DOI: 10.1063/1.4948778
  • I.M. Ilie, W.K. den Otter and W.J. Briels
    A coarse grained protein model with internal degrees of freedom. Application to α-synuclein aggregation
    J. Chem. Phys. 142, 085103 (2016). DOI: 10.1063/1.4942115
  • R. Guareschi, H. Zulfikri, C. Daday, F. M. Floris, C. Amovilli, B. Mennucci, and C. Filippi
    Introducing QMC/MMpol: Quantum Monte Carlo in polarizable force fields for excited states
    J. Chem. Theory Comput. 12, 1674 (2016). DOI: 10.1021/acs.jctc.6b00044
  • C.R.K. Windows-Yule, B.J. Scheper, W.K. den Otter, D.J. Parker and A.R. Thornton
    Modifying self-assembly and species separation in three-dimensional systems of shape-anisotropic particles
    Phys. Rev. E 93, 020901(R) (2016). DOI: 10.1103/PhysRevE.93.020901
  • H. Zulfikri, C. Amovilli, and C. Filippi
    Multiple-resonance local wave functions for accurate excited states in quantum Monte Carlo
    J. Chem. Theory Comput. 12, 1157 (2016). DOI: 10.1021/acs.jctc.5b01077
2015
  • C. Daday, C. Curutchet, A. Sinicropi, B. Mennucci, and C. Filippi
    Chromophore-protein coupling beyond non-polarizable models: Understanding absorption in green fluorescent protein
    J. Chem. Theory Comput. 11, 4825 (2015). DOI: 10.1021/acs.jctc.5b00650
  • I.M. Ilie, W.J. Briels and W.K. den Otter
    An elementary singularity-free Rotational Brownian Dynamics algorithm for anisotropic particles
    J. Chem. Phys. 141, 114103 (2015). DOI: 10.1063/1.4914322
  • O. Valsson, C. Filippi, and M. E. Casida
    Regarding the use and misuse of retinal protonated Schiff base photochemistry as a test case for time-dependent density-functional theory
    J. Chem. Phys. 142, 144104 (2015). DOI: 10.1063/1.4916354
2014
  • J. T. Padding and W. J. Briels
    Momentum conserving Brownian dynamics propagator for complex soft matter fluids
    J. Chem. Phys. 141, 244108 (2014). DOI: 10.1063/1.4904315
  • R. Guareschi, F. M. Floris, C. Amovilli, and C. Filippi
    Solvent effects on excited-state structures: A quantum Monte Carlo and density functional study
    J. Chem. Theory Comput. 10, 5528 (2014). DOI: 10.1021/ct500723s
  • F. Fracchia, C. Filippi, and C. Amovilli
    Multi-level quantum Monte Carlo wave functions for complex reactions: The decomposition of dimethylnitrosamine
    J. Comput. Chem. 35, 30 (2014). DOI: 10.1002/jcc.23461
  • C. Daday, C. Konig, J. Neugebauer, and C. Filippi
    Wavefunction-in-density functional theory embedding for excited states: Which wavefunctions, which densities?
    ChemPhysChem 15, 3205 (2014). DOI: 10.1002/cphc.201402459
  • M.M.H.D. Arntz, H.H. Beeftink, W.J. Briels, W.K. den Otter and R.H. Boom
    Segregation of granular particles by mass, radius and density in a horizontal rotating drum
    AIChE J. 60, 50-59 (2014). DOI: 10.1002/aic.14241
  • S. Moroni, S. Saccani, and C. Filippi
    Practical schemes for accurate forces in quantum Monte Carlo
    J. Chem. Theory Comput. 10, 4823 (2014). DOI: 10.1021/ct500780r
  • I.M. Ilie, W.K. den Otter and W.J. Briels
    Rotational Brownian Dynamics simulations of clathrin cage formation
    J. Chem. Phys. 141, 065101 (2014). DOI: 10.1063/1.4891306
  • L. Liu, W.K. den Otter and W.J. Briels
    Coarse grain forces in star polymer melts
    Soft Matter 10, 7874-7886 (2014). DOI: 10.1016/j.physa.2014.05.046
  • J. Kullgren, M.J. Wolf, C.W.M. Castleton, P. Mitev, W.J. Briels and K. Hermansson
    Oxygen vacancies versus fluorine at CeO2(111): a case of mistaken identity?
    Phys. Rev. Lett. 112, 156102 (2014). DOI: 10.1103/PhysRevLett.112.156102
  • D.A. Head, W.J. Briels and G. Gompper
    Nonequilibrium structure and dynamics in a microscopic model of thin-film active gels
    Phys. Rev. E 89, 032705 (2014). DOI: 10.1063/1.4867787
  • F. M. Floris, C. Filippi, and C. Amovilli
    Electronic excitations in a dielectric continuum solvent with quantum Monte Carlo: Acrolein in water
    J. Chem. Phys. 140, 034109 (2014). DOI: 10.1063/1.4861429
2013
  • R. Guareschi and C. Filippi
    Ground- and excited-state geometry optimization of small organic molecules with quantum Monte Carlo
    J. Chem. Theory Comput. 9, 5513 (2013). DOI: 10.1021/ct400876y
  • W.K. den Otter
    Revisiting the exact relation between potential of mean force and free-energy profile
    J. Chem. Theory Comput. 9, 3861 (2013). DOI: 10.1021/ct400134d
  • F. Fracchia, C. Filippi, and C. Amovilli
    Barrier heights in quantum Monte Carlo with linear-scaling generalized-valence-bond wave functions
    J. Chem. Theory Comput. 9, 3453 (2013). DOI: 10.1021/ct400395u
  • L. Liu, J.T. Padding, W.K. den Otter and W.J. Briels
    Coarse-grained simulations of moderately entangled star polyethylene melts
    J. Chem. Phys. 138, 244912 (2013). DOI: 10.1063/1.4811675
  • A. AlSunaidi, W.K. den Otter and J.H.R. Clarke
    Inducement by directional fields of rotational and translational phase ordering in polymer liquid-crystals
    J. Chem. Phys. 138, 154904 (2013). DOI: 10.1063/1.4798462
  • C. Daday, C. Konig, O. Valsson, J. Neugebauer, and C. Filippi
    State-specific embedding potentials for excitation-energy calculations
    J. Chem. Theory. Comput. 9, 2355 (2013). DOI: 10.1021/ct400086a
  • G.J. Schneider, K. Nusser, S. Neueder, M. Brodeck, L. Willner, B. Farago, O. Holderer, W. J. Briels and D. Richter
    Anomalous chain diffusion in unentangled model polymer nanocomposites
    Soft Matter 9, 4336 (2013). DOI: 10.1039/C3SM27886G
  • O. Valsson, P. Campomanes, I. Tavernelli, U. Rothlisberger, and C. Filippi
    Rhodopsin absorption from first principles: Bypassing common pitfalls
    J. Chem. Theory Comput. 9, 2441 (2013). DOI: 10.1021/ct3010408
  • S. Saccani, C. Filippi, and S. Moroni
    Minimum energy pathways via quantum Monte Carlo
    J. Chem. Phys. 138, 084109 (2013). DOI: 10.1063/1.4792717
  • I.S. Santos de Oliveira, W.K. den Otter and W.J. Briels
    Alignment and segregation of bidisperse colloids in a shear-thinning viscoelastic fluid under shear flow
    Europhys. Lett. 101, 28002 (2013). DOI: 10.1209/0295-5075/101/28002
  • M.M.H.D. Arntz, W.K. den Otter, H.H. Beeftink, R.M. Boom and W.J. Briels
    The influence of end walls on the segregation pattern in a horizontal rotating drum
    Granul. Matt. 15, 25 (2013). DOI: 10.1007/s10035-012-0386-4
  • T. Savin, W.J. Briels, H.C. Öttinger
    Thermodynamic formulation of flowing soft matter with transient forces
    Rheol. Acta 52, 23 (2013). DOI: 10.1007/s00397-012-0661-7
2012
  • I.S. Santos de Oliveria, W.K. den Otter and W.J. Briels
    The origin of flow-induced alignment of spherical colloids in shear-thinning viscoelastic fluids
    J. Chem. Phys. 137, 204908 (2012). DOI: 10.1063/1.4767721
  • S. de Beer, W.K. den Otter, D. van den Ende, W.J. Briels and F. Mugele
    Can confinement-induced variations in the viscous dissipation be measured?
    Tribol. Lett. 48, 1 (2012). DOI: 10.1007/s11249-011-9905-4
  • J.T. Padding, L.V. Mohite, D. Auhl, T. Schweizer, W.J. Briels and C. Bailly
    Quantitative mesoscale modeling of the oscillatory and transient shear rheology and the extensional rheology of pressure sensitive adhesives
    Soft Matter 8, 7967 (2012). DOI: 10.1039/C2SM07443E
  • S. de Beer, W.K. den Otter, D. van den Ende, W.J. Briels and F. Mugele
    Non-monotonic variation of viscous dissipation in confined liquid films: a reconciliation
    EPL 97, 46001 (2012). DOI: 10.1209/0295-5075/97/46001
  • C. Daday, S. Smart, G. Booth, A. Alavi, and C. Filippi
    Full Configuration Interaction excitations of ethene and butadiene: Resolution of an ancient question
    J. Chem. Theory Comput. 8, 4441 (2012). DOI: 10.1021/ct300486d
  • F. M. Floris, C. Filippi, and C. Amovilli
    A density functional and quantum Monte Carlo study of glutamic acid in vacuo and in a dielectric continuum medium
    J. Chem. Phys. 137, 075102 (2012). DOI: 10.1063/1.4746390
  • O. Valsson, C. Angeli, and C. Filippi
    Excitation energies of retinal chromophores: Critical role of the structural model
    Phys. Chem. Chem. Phys. 14, 11015 (2012). DOI: 10.1039/C2CP41387F
  • F. Fracchia, C. Filippi, and C. Amovilli
    Size-extensive wave functions for quantum Monte Carlo: A linear scaling generalized valence bond approach
    J. Chem. Theory Comput. 8, 1943 (2012). DOI: 10.1021/ct3001206
  • O. Valsson and C. Filippi
    Gas-phase retinal spectroscopy: Temperature effects are but a mirage
    J. Phys. Chem. Lett. 3, 908 (2012). DOI: 10.1021/jz300183g
  • C. Filippi, F. Buda, L. Guidoni, and A. Sinicropi
    Bathochormic shift in Green Fluorescent Protein: A puzzle for QM/MM approaches
    J. Chem. Theory Comput. 8, 112 (2012). DOI: 10.1021/ct200704k