This page lists the publications of the CCP group for the last 5 years.
For comprehensive lists, please visit the pages of Claudia Filippi and Wim Briels.
2018
- M. Dash, S. Moroni, A. Scemama, and C. Filippi
Perturbatively selected configuration-interaction wave functions for efficient geometry optimization in quantum Monte Carlo
submitted (2018). arXiv:1804.09610 - R. Putri, H. Zulfikri, J. Fredy, A. Juan Ruiz del Valle, P. Tananchayakul,
J. Cornelissen, M. Koay, C. Filippi, and N. Katsonis
Photo-programming allostery in the human serum albumin
Bioconjug. Chem. in press (2018). - I.M. Ilie, D. Nayar, W. K. den Otter, N. F. A. van der Vegt, and W. J. Briels
Intrinsic Conformational Preferences and Interactions in α-Synuclein Fibrils: Insights from Molecular Dynamics Simulations
J. Chem. Theory Comput. online (2018). DOI: 10.1021/acs.jctc.8b00183 - V. Metri, A. Louhichi, J. Yan, G. P. Baeza, K. Matyjaszewski, D. Vlassopoulos, and W. J. Briels
Physical networks from multifunctional telechelic star polymers: A rheological study by experiments and simulations
Macromolecules, 51, 2872–2886 (2018). DOI: 10.1021/acs.macromol.7b02613 - G. Villalobos
Brownian orientational lath model (BOLD): A computational model relating the self-assembly in a fluid of lath like particles with its rheology and gelation
PLoS ONE 13(2): e0191785 (2018). DOI: 10.1371/journal.pone.0191785 - V. R. Ahuja, J. van der Gucht and W. J. Briels
Hydrodynamically Coupled Brownian Dynamics: A coarse-grain particle-based Brownian Dynamics technique with hydrodynamic interactions for modeling self-developing flow of polymer solutions
J. Chem. Phys. 148, 034902 (2018). DOI: 10.1063/1.5006627
- B. W. Fitzgerald and W. J. Briels
A Mesoscopic Model with Vectorial Structure Parameter for Interacting Star Polymers
Macromol. Theory Simul. 1521-3919 (2017). DOI: 0.1002/mats.201700069 - R. Assaraf, S. Moroni, and C. Filippi
Optimizing the energy with quantum Monte Carlo: A lower numerical scaling for Jastrow-Slater expansions
J. Chem. Theory Comput. 13, 5273–5281 (2017). DOI: 10.1021/acs.jctc.7b00648 - J. Kullgren, M. J. Wolf, P. D. Mitev, K. Hermansson, and W. J. Briels
DFT-based Monte Carlo simulations of impurity clustering at CeO2(111). J. Phys. Chem. C 121, 1512-5134 (2017). DOI: 10.1021/acs.jpcc.7b00299 - M. Giani, W.K. den Otter, and W.J. Briels
Early stages of clathrin aggregation at a membrane in coarse-grained simulations
J. Chem. Phys. 145, 155102 (2017). DOI: 10.1063/1.4979985 - I. M. Ilie, W. K. den Otter and W. J. Briels
The attachment of α-synuclein to a fiber: A coarse-grain approach
J. Chem. Phys. 146, 115102 (2017). DOI: 10.1063/1.4978297
- V. R. Ahuja, J. van der Gucht and W. J. Briels
Coarse-grained simulations for flow of complex soft matter fluids in the bulk and in the presence of solid interfaces
J. Chem. Phys. 145, 194903 (2016). DOI: 10.1063/1.4967422 - 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 - 2016 JCP Editors' Choice
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
- 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
- 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
- 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
- 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