Browse by Projects

A

Azouz, Nurit P. and Klingler, Andrea M. and Callahan, Victoria and Akhrymuk, Ivan V. and Elez, Katarina and Raich, Lluís and Henry, Brandon M. and Benoit, Justin L. and Benoit, Stefanie W. and Noé, Frank and Kehn-Hall, Kylene and Rothenberg, Marc E. (2021) Alpha 1 Antitrypsin is an Inhibitor of the SARS-CoV-2–Priming Protease TMPRSS2. Pathogens and Immunity, 6 (1). pp. 55-74.

Agarwal, A. and Clementi, C. and Delle Site, L. (2017) Path Integral-GC-AdResS simulation of a large hydrophobic solute in water: A tool to investigate the interplay between local microscopic structures and quantum delocalization of atoms in space. Physical Chemistry Chemical Physics, 19 . pp. 13030-13037. ISSN 1463-9084

Agarwal, A. and Delle Site, L. (2015) Path Integral Molecular Dynamics within the Grand Canonical-like Adaptive Resolution Technique: Simulation of Liquid Water. Journal of Chemical Physics, 143 (9). ISSN 0021-9606

Agarwal, A. and Zhu, J. and Wang, H. and Hartmann, C. and Delle Site, L. (2015) Molecular dynamics in a Grand Ensemble: Bergmann-Lebowitz model and adaptive resolution simulation. New Journal of Physics, 17 (083042). ISSN 1367-2630

C

Cortes-Huerto, Robinson and Praprotnik, Matej and Kremer, Kurt and Delle Site, Luigi (2021) From Adaptive Resolution to Molecular Dynamics of Open Systems. The European Physical Journal B, 94 (189). pp. 1-22.

Ciccotti, G. and Delle Site, L. (2019) The physics of open systems for the simulation of complex molecular environments in soft matter. Soft Matter, 15 (10). pp. 2114-2124. ISSN 1744-683X, ESSN: 1744-6848

D

Delle Site, Luigi and Hartmann, Carsten (2024) Computationally feasible bounds for the free energy of nonequilibrium steady states, applied to simple models of heat conduction. Molecular Physics .

Delle Site, Luigi and Djurdjevac, Ana (2024) An effective Hamiltonian for the simulation of open quantum molecular systems. Journal of Physics A: Mathematical and Theoretical, 57 (25).

Delle Site, Luigi and Hartmann, Carsten (2024) Scaling law for the size dependence of a short-ranged quantum gas. Physical Review A, 109 .

Delle Site, Luigi and Hartmann, Carsten (2024) Scaling law for the size dependence of a finite-range quantum gas. Physical Review A, 109 (2).

Delle Site, Luigi (2021) Investigation of water-mediated intermolecular interactions with the adaptive resolution simulation technique. Journal of Physics: Condensed Matter, 34 (11). pp. 1-15.

Delle Site, L. and Klein, R. and Höfling, F. and Viand, R. E. (2020) Theory and simulation of open systems out of equilibrium. J. Chem. Phys. (2020);, 153 (10). pp. 1-7. ISSN 101102

Delle Site, L. and Klein, R. (2020) Liouville-type equations for the n-particle distribution functions of an open system. Journal of Mathematical Physics, 61 (8).

Delle Site, L. and Praprotnik, M. and Bell, John B. and Klein, R. (2020) "Particle-Continuum Coupling and its Scaling Regimes: Theory and Applications". Advanced Theory and Simulations, 3 (5).

Delle Site, L. and Praprotnik, M. and Bell, J. B. and Klein, R. (2020) Particle–Continuum Coupling and its Scaling Regimes: Theory and Applications. Advanced Theory and Simulation, 3, 1900232 (2020), 3 (190023). pp. 1-20.

Delle Site, L. and Krekeler, C. and Whittaker, J. and Agarwal, A. and Klein, R. and Höflling, F. (2019) Molecular dynamics of open systems: construction of a mean-field particle reservoir. Adv. Th. Simul, 2 (5).

Delle Site, L. and Ciccotti, G. and Hartmann, C. (2017) Partitioning a macroscopic system into independent subsystems. Journal of Statistical Mechanics: Theory and Experiment, 2017 . pp. 1-13.

Delle Site, L. and Praprotnik, M. (2017) Molecular systems with open boundaries: Theory and Simulation. Physics Reports, 693 . pp. 1-56. ISSN 0370-1573

Delle Site, L. (2016) Formulation of Liouville's theorem for grand ensemble molecular simulations. Physical Review E, 93 (022130).

Delle Site, L. and Agarwal, A. (2016) Grand-Canonical Adaptive Resolution Centroid Molecular Dynamics: Implementation and Application. Computer Physics Communications (206). pp. 26-34.

E

Enciso, M. and Schütte, Ch. and Delle Site, L. (2015) Influence of pH and sequence in peptide aggregation via molecular simulation. Journal of Chemical Physics, 143 (24). p. 243130. ISSN 0021-9606

G

Gholami, Abbas and Klein, R. and Delle Site, Luigi (2022) Simulation of a Particle Domain in a Continuum, Fluctuating Hydrodynamics Reservoir. Physical Review Letters, 129 (23).

Gholami, Abbas and Klein, R. and Delle Site, Luigi (2021) On the relation between Pressure and Coupling Potential in Adaptive Resolution Simulations of Open Systems in contact with a Reservoir. Advanced Theory and Simulations, 5 . pp. 1-8.

Gholami, A. and Höfling, Felix and Klein, R. and Delle Site, Luigi (2021) Thermodynamic Relations at the Coupling Boundary in Adaptive Resolution Simulations for Open Systems. Advanced Theory and Simulations, 4 . pp. 1-10.

H

Höfling, F. and Dietrich, S. (2020) Finite-size corrections for the static structure factor of a liquid slab with open boundaries. Journal of Chemical Physics, 153 (5). pp. 1-13.

Hartmann, C. and Delle Site, L. (2015) Scale Bridging in Molecular Simulation. The European Physical Journal Special Topics, 224 (12). pp. 2173-2176. ISSN 1951-6355

J

Junghans, C. and Agarwal, A. and Delle Site, L. (2017) Computational Efficiency and Amdahl's law for the Adaptive Resolution Simulation Technique. Computer Physics Communications, 215 . pp. 20-25. ISSN 0010-4655

K

Klein, R. and Delle Site, Luigi (2022) Derivation of Liouville-like equations for the n-state probability density of an open system with thermalized particle reservoirs and its link to molecular simulation. Journal of Physics A: Mathematical and Theoretical, 55 . pp. 1-18.

Klein, R. and Viand, R. E. and Höfling, Felix and Delle Site, Luigi (2021) Nonequilibrium Induced by Reservoirs: Physico-Mathematical Models and Numerical Tests. Advanced Theory and Simulations, 4 . pp. 1-10.

Krekeler, C. and Agarwal, A. and Junghans, C. and Praprotnik, M. and Delle Site, L. (2018) Adaptive Resolution Molecular Dynamics Technique: Down to the Essential. J. Chem. Phys., 149 . 024104. ISSN 0021-9606, ESSN: 1089-7690

Klein, R. (2015) Comments on "Open Boundary Molecular Dynamics " by R. Delgado-Buscalioni, J. Sablic, and M. Praprotnik. The European Physical Journal, 224 (12). pp. 2509-2510. ISSN Online: 1951-6401 Print: 1951-6355

Klein, R. (2015) Comments on "Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations" by K. Kreis, A.C. Fogarty, K. Kremer R. Potestio. The European Physical Journal, 224 (12). pp. 2503-2504. ISSN Online: 1951-6401 Print: 1951-6355

Klein, R. (2015) Comments on "Adaptive Resolution Simulation in Equilibrium and Beyond" by H. Wang and A. Agarwal. The European Physical Journal, 224 (12). pp. 2497-2499.

P

Panahian Jand, Sara and Nourbakhsh, Zahra and Delle Site, Luigi (2022) Nuclear Quantum Effects in Fullerene-Fullerene Aggregation in Water. Front. Chem., 10 . pp. 1-8.

Peters, J.H. and Gräser, C. and Klein, R. (2017) Membrane Deformation by N-BAR Proteins: Extraction of membrane geometry and protein diffusion characteristics from MD simulations. SFB 1114 Preprint in arXiv:1712.02666 . pp. 1-12. (Unpublished)

Peters, J.H. and Klein, R. and Delle Site, L. (2016) Simulation of macromolecular liquids with the adaptive resolution molecular dynamics technique. Phys. Rev. E, 94 (2). 023309.

R

Reible, Benedikt M. and Hille, Julian F. and Hartmann, Carsten and Delle Site, Luigi (2023) Finite-size effects and thermodynamic accuracy in many-particle systems. Physical Review Research, 5 (2).

Reible, Benedikt and Hartmann, Carsten and Delle Site, Luigi (2022) Two-sided Bogoliubov inequality to estimate finite size effects in quantum molecular simulations. Letters in Mathematical Physics, 112 (97).

S

Straube, Arthur V. and Kowalik, Bartosz G. and Netz, Roland R. and Höfling, Felix (2020) Rapid onset of molecular friction in liquids bridging between the atomistic and hydrodynamic pictures. Communications Physics, 3 (126). pp. 1-11.

Shadrack Jabes, B. and Delle Site, L. (2018) Nanoscale domains in Ionic Liquids: A statistical mechanics definition for molecular dynamics studies. J. Chem. Phys., 149 (18). p. 184502. ISSN 0021-9606, ESSN: 1089-7690

Shadrack Jabes, B. and Krekeler, C. and Klein, R. and Delle Site, L. (2018) Probing Spatial Locality in Ionic Liquids with the Grand Canonical Adaptive Resolution Molecular Dynamics Technique. The Journal of Chemical Physics, 148 (19). ISSN online: 1089-7690

Seshaditya, A. and Ghiringhelli, L. M. and Delle Site, L. (2017) Levy-Lieb-based Monte Carlo study of the dimensionality behaviour of the electronic kinetic functional. Computationa, 5 (2). pp. 1-10. ISSN 2079-3197

W

Whittaker, John and Delle Site, Luigi (2019) Investigation of the hydration shell of a membrane in an open system molecular dynamics simulation. Phys. Rev. Research, 1 (3).

Winkelmann, S. (2017) Markov Control with Rare State Observation: Average Optimality. Markov Processes and Related Fields, 23 . pp. 1-34. ISSN 1024-2953

Z

Zhu, J. and Klein, R. and Delle Site, L. (2016) Adaptive Molecular Resolution Approach in Hamiltonian Form: An Asymptotic Analysis. Physical Review E, 94 (043321).