@misc{AgarwalWangSchuetteetal., author = {Agarwal, Animesh and Wang, Han and Sch{\"u}tte, Christof and Delle Site, Luigi}, title = {Chemical potential of liquids and mixtures via Adaptive Resolution Simulation}, issn = {1438-0064}, doi = {10.1063/1.4886807}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-50972}, abstract = {We employ the adaptive resolution approach AdResS, in its recently developed Grand Canonicallike version (GC-AdResS) [Wang et al. Phys.Rev.X 3, 011018 (2013)], to calculate the excess chemical potential, \$μ^{ex}\$, of various liquids and mixtures. We compare our results with those obtained from full atomistic simulations using the technique of thermodynamic integration and show a satisfactory agreement. In GC-AdResS the procedure to calculate \$μ^{ex}\$ corresponds to the process of standard initial equilibration of the system; this implies that, independently of the specific aim of the study, \$μ^{ex}\$, for each molecular species, is automatically calculated every time a GC-AdResS simulation is performed.}, language = {en} } @article{AgarwalWangSchuetteetal., author = {Agarwal, Animesh and Wang, Han and Sch{\"u}tte, Christof and Delle Site, Luigi}, title = {Chemical potential of liquids and mixtures via Adaptive Resolution Simulation}, series = {The Journal of Chemical Physics}, volume = {141}, journal = {The Journal of Chemical Physics}, doi = {10.1063/1.4886807}, pages = {034102}, language = {en} } @article{EncisoSchuetteDelleSite, author = {Enciso, Marta and Sch{\"u}tte, Christof and Delle Site, Luigi}, title = {pH-dependent Response of Coiled Coils: A Coarse-Grained Molecular Simulation Study}, series = {Molecular Physics}, volume = {111}, journal = {Molecular Physics}, number = {22-23}, doi = {10.1080/00268976.2013.827254}, pages = {3363 -- 3371}, language = {en} } @article{WangSchuetteCiccottietal., author = {Wang, Han and Sch{\"u}tte, Christof and Ciccotti, Giovanni and Delle Site, Luigi}, title = {Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation}, series = {Journal of Chemical Theory and Computation}, volume = {10}, journal = {Journal of Chemical Theory and Computation}, number = {4}, doi = {10.1186/s12859-017-1565-4}, pages = {1376 -- 1386}, language = {en} } @misc{EncisoSchuetteDelleSite, author = {Enciso, Marta and Sch{\"u}tte, Christof and Delle Site, Luigi}, title = {Influence of pH and sequence in peptide aggregation via molecular simulation}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-55805}, abstract = {We employ a recently developed coarse-grained model for peptides and proteins where the effect of pH is automatically included. We explore the effect of pH in the aggregation process of the amyloidogenic peptide KTVIIE and two related sequences, using three different pH environments. Simulations using large systems (24 peptides chains per box) allow us to correctly account for the formation of realistic peptide aggregates. We evaluate the thermodynamic and kinetic implications of changes in sequence and pH upon peptide aggregation, and we discuss how a minimalistic coarse- grained model can account for these details.}, language = {en} } @article{EncisoSchuetteDelleSite, author = {Enciso, Marta and Sch{\"u}tte, Christof and Delle Site, Luigi}, title = {Influence of pH and sequence in peptide aggregation via molecular simulation}, series = {Journal of Chemical Physics}, volume = {143}, journal = {Journal of Chemical Physics}, number = {24}, doi = {https://doi.org/10.1063/1.4935707}, language = {en} } @article{EncisoSchuetteDelleSite, author = {Enciso, Marta and Sch{\"u}tte, Christof and Delle Site, Luigi}, title = {A pH-dependent coarse-grained model for peptides}, series = {Soft Matter}, volume = {9}, journal = {Soft Matter}, number = {26}, doi = {10.1039/C3SM27893J}, pages = {6118 -- 6127}, abstract = {We propose the first, to our knowledge, coarse-grained modeling strategy for peptides where the effect of changes of the pH can be efficiently described. The idea is based on modeling the effects of the pH value on the main driving interactions. We use reference data from atomistic simulations and experimental databases and transfer their main physical features to the coarse-grained resolution according to the principle of "consistency across the scales". The coarse-grained model is refined by finding a set of parameters that, when applied to peptides with different sequences and experimental properties, reproduces the experimental and atomistic data of reference. We use such a parameterized model for performing several numerical tests to check its transferability to other systems and to prove the universality of the related modeling strategy. We have tried systems with rather different responses to pH variations, showing a highly satisfactory performance of the model.}, language = {en} } @article{EbrahimiViandHoeflingKleinetal., author = {Ebrahimi Viand, Roya and H{\"o}fling, Felix and Klein, Rupert and Delle Site, Luigi}, title = {Theory and simulation of open systems out of equilibrium}, series = {The Journal of Chemical Physics}, volume = {153}, journal = {The Journal of Chemical Physics}, doi = {10.1063/5.0014065}, pages = {101102}, abstract = {We consider the theoretical model of Bergmann and Lebowitz for open systems out of equilibrium and translate its principles in the adaptive resolution simulation molecular dynamics technique. We simulate Lennard-Jones fluids with open boundaries in a thermal gradient and find excellent agreement of the stationary responses with the results obtained from the simulation of a larger locally forced closed system. The encouraging results pave the way for a computational treatment of open systems far from equilibrium framed in a well-established theoretical model that avoids possible numerical artifacts and physical misinterpretations.}, language = {en} } @article{DelleSiteKrekelerWhittakeretal., author = {Delle Site, Luigi and Krekeler, Christian and Whittaker, John and Agarwal, Animesh and Klein, Rupert and H{\"o}fling, Felix}, title = {Molecular Dynamics of Open Systems: Construction of a Mean-Field Particle Reservoir}, series = {Advanced Theory and Simulations}, volume = {2}, journal = {Advanced Theory and Simulations}, doi = {10.1002/adts.201900014}, pages = {1900014}, abstract = {The simulation of open molecular systems requires explicit or implicit reservoirs of energy and particles. Whereas full atomistic resolution is desired in the region of interest, there is some freedom in the implementation of the reservoirs. Here, a combined, explicit reservoir is constructed by interfacing the atomistic region with regions of point-like, non-interacting particles (tracers) embedded in a thermodynamic mean field. The tracer molecules acquire atomistic resolution upon entering the atomistic region and equilibrate with this environment, while atomistic molecules become tracers governed by an effective mean-field potential after crossing the atomistic boundary. The approach is extensively tested on thermodynamic, structural, and dynamic properties of liquid water. Conceptual and numerical advantages of the procedure as well as new perspectives are highlighted and discussed.}, language = {en} } @article{KleinEbrahimiViandHoeflingetal., author = {Klein, Rupert and Ebrahimi Viand, Roya and H{\"o}fling, Felix and Delle Site, Luigi}, title = {Nonequilibrium induced by reservoirs: Physico-mathematical model and numerical tests}, series = {Advances Theory and Simulation}, volume = {4}, journal = {Advances Theory and Simulation}, doi = {10.1002/adts.202100071}, pages = {2100071}, language = {en} } @article{GholamiHoeflingKleinetal., author = {Gholami, Abbas and H{\"o}fling, Felix and Klein, Rupert and Delle Site, Luigi}, title = {Thermodynamic relations at the coupling boundary in adaptive resolution simulations for open systems}, series = {Advances Theory and Simulation}, volume = {4}, journal = {Advances Theory and Simulation}, doi = {10.1002/adts.202000303}, pages = {2000303}, language = {en} } @article{WangSchuetteSite2012, author = {Wang, Han and Sch{\"u}tte, Christof and Site, Luigi Delle}, title = {Adaptive Resolution Simulation (AdResS): A Smooth Thermodynamic and Structural Transition from Atomistic to Coarse Grained Resolution and Vice Versa in a Grand Canonical Fashion.}, series = {J. Chem. Theo. Comp.}, volume = {8}, journal = {J. Chem. Theo. Comp.}, number = {8}, doi = {10.1021/ct3003354}, pages = {2878 -- 2887}, year = {2012}, language = {en} } @article{EncisoSchuetteSite2012, author = {Enciso, Marta and Sch{\"u}tte, Christof and Site, Luigi Delle}, title = {A pH-dependent coarse-grained model of peptides}, series = {Soft Matter}, volume = {9}, journal = {Soft Matter}, number = {26}, doi = {10.1039/C3SM27893J}, pages = {6118 -- 6127}, year = {2012}, language = {en} } @article{WangHartmannSchuetteetal.2013, author = {Wang, Han and Hartmann, Carsten and Sch{\"u}tte, Christof and Site, Luigi Delle}, title = {Grand-canonical-like molecular-dynamics simulations by using an adaptive-resolution technique}, series = {Phys. Rev. X}, volume = {3}, journal = {Phys. Rev. X}, doi = {10.1103/PhysRevX.3.011018}, pages = {011018}, year = {2013}, language = {en} }