2023 - Publications

Multilevel representations of isotropic Gaussian random fields on the sphere
Markus Bachmayr, Ana Djurdjevac
IMA J. Numerical Analysis 43, 1970-2000 (2023)
Link: https://doi.org/10.1093/imanum/drac034

Growth and aging in a few phase-separating active matter system
Florian Dittrich, Jiarul Midya, Peter Virnau, Subir K. Das
Physical Review E 108, 024609 (2023)
Link: https://doi.org/10.1103/PhysRevE.108.024609

Branching Brownian Motion with Self-Repulsion
Anton Bovier, Lisa Hartung
Annales Henri Poincaré 24, 931-956 (2023)
Link: https://doi.org/10.1007/s00023-022-01223-8

Can polymer helicity affect topological chirality of polymer knots?
Yani Zhao, Jan Rothörl, Pol Besenius, Peter Virnau, Kostas Ch. Daoulas
ACS Macro Letters 12, 234-240 (2023)
Link: https://doi.org/10.1021/acsmacrolett.2c00600

Thermodynamics, statistical mechanics and the vanishing pore width limit of confined fluids
W. Dong, T. Franosch, R. Schilling
Comm. Physics 6, 161 (2023)
Link: https://doi.org/10.1038/s42005-023-01255-4

Stability, Speed, and Constraints for Structural Coarse-Graining in VOTCA
Marvin P. Bernhardt, Martin Hanke, Nico F.A. van der Vegt
J. Chem. Theory Comput. 19, 580-595 (2023)
Link: https://doi.org/10.1021/acs.jctc.2c00665

A DZ white dwarf with a 30 MG magnetic field}
M.A. Hollands, S. Stopkowicz, M.-P. Kitsaras, F. Hampe, S. Blaschke, J.J. Hermes
Monthly Notices of the Royal Astonomical Society 520, 3560-3575 (2023)
Link: https://doi.org/10.1093/mnras/stad143

An ab initio method on large sized molecular aggregate system: Predicting absorption spectra of crystalline organic semiconducting films
Wenlan Liu, Denis Andrienko
The Journal of Chemical Physics 158, 094108 (2023)
Link: https://doi.org/10.1063/5.0138748

Another Torture Track for Quantum Chemistry: Reinvestigation of the Benzaldehyde Amidation by Nitrogen-Atom Transfer from Platinum(II) and Palladium(II) Metallonitrenes
H. Verplancke, M. Diefenbach, J.N. Lienert, M. Ugandi, M.-P. Kitsaras, M. Röhmelt, S. Stopkowicz, M.C. Holthausen
Israel J. Chemistry 63, e292399960 (2023)
Link: https://doi.org/10.1002/ijch.202300060

The speed of invasion in an advancing population
Anton Bovier, Lisa Hartung
J. Mathematical Biology 87, 56 (2023)
Link: https://doi.org/10.1007/s00285-023-01989-3

300-Times-Increased Diffusive Skyrmion Dynamics and Effective Pinning Reduction by Periodic Field Excitation
R. Gruber, M.A. Brems, J. Rothörl, T. Sparmann, M. Schmitt, I. Kononenko, F. Kammerbauer, M.-A. Syskaki, O. Farago, P. Virnau, M. Kläui
Advanced Materials 35, 2208922 (2023)
Link: https://doi.org/10.1002/adma.202208922

Local characteristic decomposition based central-upwind scheme
Alina Chertock, Shaoshuao Chu, Michael Herty, Alexander Kurganov, Mária Lukáčová-Medvid'ová
J. Comp. Phys. 473, 111718
Link: https://doi.org/10.1016/j.jcp.2022.111718

Perspective on unconventional computing using magnetic skyrmions
O. Lee, R. Msiska, M.A. Brems, M. Kläui, H. Kurebayashi, K. Everschor-Sitte
Applied Physics Letters 122, 260501 (2023)
Link: https://doi.org/10.1063/5.0148469

Micelle kinetics of photoswitchable surfactants: Self-assembly pathways and relaxation mechanisms
V.A. Bjørnestad, X. Li, C. Tribet, R. Lund, M. Cascella
J. Coll. Interf. Sci. 646, 883-899 (2023)
Link: https://doi.org/10.1016/j.jcis.2023.05.057

Constructing coarse-grained skyrmion potentials from experimental data with Iterative Boltzmann Inversion
Y. Ge, J. Rothörl, M.A. Brems, N. Kerber, R. Gruber, T. Dohi, M. Kläui, P. Virnau
Comm. Phys. 6, 30 (2023)
Link: https://doi.org/10.1038/s42005-023-01145-9

Electronic coarse-graining of long conjugated molecules: Case study of non-fullerene acceptors
Andriy Zhugyevych, Kun-Han Lin, Denis Andrienko
The Journal of Chemical Physics 159, 024107 (2023)
Link: https://doi.org/10.1063/5.0155488

Viscosity of flexible and semiflexible ring melts: Molecular origins and flow-induced segregation
Ranajay Datta, Fabian Berressem, Friederike Schmid, Arash Nikoubashman, Peter Virnau
Macromolecules 56, 7247-7255 (2023)
Link: https://doi.org/10.1021/acs.macromol.3c01046

Influence of ionic conditions on knotting in a coarse-grained model
Sarah Wettermann, Ranajay Datta, Peter Virnau
Frontiers in Chemistry 10, 1096014 (2023)
Link: https://doi.org/10.3389/fchem.2022.1096014

Cholesky decomposition of two-electron integrals in quantum-chemical calculations with perturbative or finite magnetic fields using gauge-including atomic orbitals
Jürgen Gauss, Simon Blaschke, Sophia Burger, Tommaso Nottoli, Filippo Lipparini, Stella Stopkowicz
Molecular Physics 121, 11-12 (2023)
Link: https://doi.org/10.1080/00268976.2022.2101562

HylleraasMD: A Domain Decomposition-Based Hybrid Particle-Field Software for Multiscale Simulations of Soft Matter
Morten Ledum, Samirah Sen, Xinmeng Li, Manuel Carrer, Yu Feng, Michele Cascella, Sibjørn Løland Bore
J. Chem. Theory Comput. 19, 2939-2952 (2023)
Link: https://doi.org/10.1021/acs.jctc.3c00134

On uniqueness and stable estimation of multiple parameters in the Cahn-Hilliard equation
Aaron Brunk, Herbert Egger, Oliver Habrich
Inverse Problems 39, 065002 (2023)
Link: https://doi.org/0.1088/1361-6420/acca44

Self-Solidifying Active Droplets Showing Memory-Induced Chirality
Kai Feng, Jose C.U. Marcos, Aritra K. Mukhopadhyay, Ran Niu, Qiang Zhao, Jinping Qu, Benno Liebchen
Adv. Scie. 10, 27 (2023)
Link: https://doi.org/10.1002/advs.202300866

SANS Spectra with PLUMED: Implementation and Application to Metainference
Henrique M. Cezar, Michele Cascella
J. Chem. Information Modelling 63, 4979-4985 (2023)
Link: https://doi.org/10.1021/acs.jcim.3c00724

Structural ensembles of disordered proteins from hierarchical chain growth and simulatio
Lisa M. Pietrek, Lukas Stelzl, Gerhard Hummer
Current Opinion in Structural Biology 78, 102501 (2023)
Link: https://doi.org/0.1016/j.sbi.2022.102501

Code modernization strategies for short-range non-bonded molecular dynamics simulations
James Vance, Zhen-Hao Xu, Nikita Tretyakov, Torsten Stuehn, Markus Rampp, Sebastian Eible, Christoph Junghans, Andre Brinkmann
Comp. Phys. Comm. 290, 108760 (2023)
Link: https://doi.org/10.1016/j.cpc.2023.108760

Stability of Branched Tubular Membrane Structures
Maike Jung, Gerhard Jung, Friederike Schmid
Physical Review Letters 130, 148401 (2023)
Link: https://doi.org/10.1103/PhysRevLett.130.148401

Soft Matter under Pressure: Pushing Particle-Field Molecular Dynamics to the Isobaric Ensemble
Samirah Sen, Morten Ledum, Sigbjørn Løland Bore, Michele Cascella
Journal of Chemical Information and Modeling 63, 2207-2217 (2023)
Link: https://doi.org/10.1021/acs.jcim.3c00186

On the equivalence of the hybrid particle-field and Gaussian core models
Morten Ledum, Samirah Sen, Sigbjørn Løland Bore, Michele Cascella
The Journal of Chemical Physics 158, 1194902 (2023)
Link: https://doi.org/10.1063/5.0145142

Error estimates of a finite volume method for the compressible Navier–Stokes–Fourier system
Danica Basarić, Hana Mizerová, Bangwei She, Yuhuan Yuan
Math.Comp. 92, 2543–2574 (2023)
Link: https://doi.org/10.1090/mcom/3852

Compressible Navier-Stokes equations with potential temperature transport: stability of the strong solution and nu-merical error estimates
M. Lukáčová-Medvid'ová, A. Schömer
Journal of Mathematical Fluid Mechanics 25, 1 (2023)
Link: https://doi.org/10.1007/s00021-022-00733-z

Computational approaches to lipid-based nucleic acid delivery systems
Giovanni Settanni
Eur. Phys. J. E 46, 127 (2023)
Link: https://doi.org/10.1140/epje/s10189-023-00385-5

Modeling of minimal systems based on ATP-Zn coordination for chemically fueled self-assembly
Emma Rossi, Alberta Ferrarini, Marialore Sulpizi
Physical Chemistry Chemical Physics 25, 6102-6111 (2023)
Link: https://doi.org/10.1039/d2cp05516c

Chilling alcohol on the computer: isothermal compressibility and the formation of hydrogen-bond clusters in liquid propan-1-ol
Luis A. Baptista, Mauricio Sevilla, Manfred Wagner, Kurt Kremer, Robinson Cortes-Huerto
Eur. Phys. J. E 46, 117 (2023)
Link: https://doi.org/10.1140/epje/s10189-023-00380-w

Anions and Cations Affect Amino Acid Dissociation Equilibria via Distinct Mechanisms
Varun Mandalaparthy, Madhusmita Tripathy, Nico F.A. van der Vegt
Journal of Physical Chemistry Letters 14, 9250-9256 (2023)
Link: https://doi.org/10.1021/acs.jpclett.3c02062

Finite-size excess-entropy scaling for simple liquids
Mauricio Sevilla, Atreyee Banerjee, Robinson Cortes-Huerto
The Journal of Chemical Physics 158, 204502 (2023)
Link: https://doi.org/10.1063/5.0142912

A novel coupled-cluster singles and doubles implementation that combines the exploitation of point-group symmetry and Cholesky decomposition of the two-electron integrals
Tommaso Nottoli, Jürgen Gauss, Filippo Lipparini
The Journal of Chemical Physics 159, 231101 (2023)
Link: https://doi.org/10.1063/5.0175956

Effective dynamics and fluctuations of a trapped probe moving in a fluid of active hard discs
Ashreya Jayaram, Thomas Speck
EPL 143, 17005 (2023)
Link: https://doi.org/10.1209/0295-5075/acdf1a

Exploiting compositional disorder in collectives of light-driven circle walkers
Frank Siebers, Ashreya Jayaram, Peter Blümler, Thomas Speck
Science Advances 9, eadf5443 (2023)
Link: https://doi.org/10.1126/sciadv.adf5443

Existence and weak-strong uniqueness for global weak solutions for the viscoelastic phase separation model in three space dimensions
Aaron Brunk
Discrete and continuous dynamics systems 43, 2120-2136 (2023)
Link: https://doi.org/10.3934/dcds.2023004

Monitoring the Charge-Carrier-Occupied Density of States in Disordered Organic Semiconductors under Nonequilibrium Conditions Using Thermally Stimulated Luminescence Spectroscopy
Andrei Stankevych, Rishabh Saxena, Alexander Vakhnin, Falk May, Naomi Kinaret, Denis Andrienko, Jan Genoe, Heinz Bässler, Anna Köhler, Andreh Kadashchuk
Physical Review Applied 19, 054007 (2023)
Link: https://doi.org/10.1103/PhysRevApplied.19.054007

Convergence of a stochastic collocation finite volume method for the compressible Navier–Stokes system.
E. Feireisl, M. Lukáčová-Medviďová
The Annals of Applied Probability, 33(6A), 4936-4963 (2023)
Link: https://doi.org/10.1214/23-AAP1937

Solvation Behavior of Elastin-like Polypeptides in Divalent Metal Salt Solutions
Yani Zhao, Swaminath Bharadwaj, Ryan L. Myers, Halil Okur, Pho T. Bui, Mengrui Cao, Lauren K. Welch, Tinglu Wang, Paul S. Cremer, Nico F.A. van der Vegt
Journal of Physical Chemistry Letters 14, 10113-10118 (2023)
Link: https://doi.org/10.1021/acs.jpclett.3c02476

Self-Solidifying Active Droplets Showing Memory-Induced Chirality
K. Feng, J.C. Ureña Marcos, A.K. Mukhopadhyay, R. Niu, Q. Zhao, J. Qu, B. Liebchen
Adv. Science 10, 2300866 (2023)
Link: https://doi.org/10.1002/advs.202300866

On the convergence of residual distribution schemes for the compressible Euler equations via dissipative weak solutions
Abgrall, R., Lukáčová-Medvid’ová, M. and Öffner, P.
Mathematical Models and Methods in Applied Sciences, 33(01), 139-173, (2023)
Link: https://doi.org/10.1142/S0218202523500057

Convergence of discontinuous Galerkin schemes for the Euler equations via dissipative weak solutions
Lukáčová-Medvid’ová, M. and Öffner, P.
Applied Mathematics and Computation, 436, 127508, (2023)
Link: https://doi.org/10.1016/j.amc.2022.127508

Statistical solutions for the Navier–Stokes–Fourier system
Feireisl, E., and Lukáčová-Medvid’ová, M.
Stochastics and Partial Differential Equations: Analysis and Computations, 1-25, (2023)
Link: https://doi.org/10.1007/s40072-023-00298-6

A second-order fully-balanced structure-preserving variational discretization scheme for the Cahn–Hilliard–Navier–Stokes system
Brunk, A., Egger, H., Habrich, O., and Lukáčová-Medviďová, M.
Mathematical Models and Methods in Applied Sciences, 33(12), 2587-2627, (2023)
Link: https://doi.org/10.1142/S0218202523500562

Stability and discretization error analysis for the Cahn–Hilliard system via relative energy estimates
Brunk, A., Egger, H., Habrich, O., and Lukáčová-Medviďová, M.
ESAIM: Mathematical Modelling and Numerical Analysis, 57(3), (2023)
Link: https://doi.org/10.1051/m2an/2023017

Relative energy and weak–strong uniqueness of a two-phase viscoelastic phase separation model
Aaron Brunk and Mária Lukáčová-Medviďová
ZAMM Z. Angew. Math. Mech. 103(7), Paper No. e202100240, 25 pp, (2023)
Link: https://doi.org/10.1002/zamm.202100240

Error estimates of a finite volume method for the compressible Navier–Stokes–Fourier system
Danica Basarić, Mária Lukáčová-Medviďová, Hana Mizerová, Bangwei She and Yuhuan Yuan
Math. Comp. 92 (2023), 2543-2574, (2023)
Link: https://doi.org/10.1090/mcom/3852

An all Mach number finite volume method for isentropic two-phase flow
Lukáčová-Medvid’ová, M., Puppo, G. and Thomann, A.
Journal of Numerical Mathematics, 31(3), 175-204, (2023)
Link: https://doi.org/10.1515/jnma-2022-0015

Dynamical coarse-grained models of molecular liquids and their ideal and non-ideal mixtures
Madhusmita Tripathy, Viktor Klippenstein and Nico van der Vegt
The Journal of Chemical Physics 2023, 159(9), (2023)
Link: https://doi.org/10.1063/5.0163097

Bottom-Up Informed and Iteratively Optimized Coarse-Grained Non-Markovian Water Models with Accurate Dynamics
Viktor Klippenstein and Nico van der Vegt
J. Chem. Theory Comput. 2023, 19(4), 1099-1110, (2023)
Link: https://doi.org/10.1021/acs.jctc.2c00871

Toward a structural identification of metastable molecular conformations
Simon Lemcke, Jörn H. Appeldorn, Michael Wand, Thomas Speck
The Journal of Chemical Physics 21 September 2023; 159 (11): 114105, (2023)
Link: https://doi.org/10.1063/5.0164145

Stabilizing α-Helicity of a Polypeptide in Aqueous Urea: Dipole Orientation or Hydrogen Bonding?
Luis A. Baptista, Yani Zhao, Kurt Kremer, Debashish Mukherji, and Robinson Cortes-Huerto
ACS Macro Letters 2023, 12, 841–847, (2023)
Link: https://doi.org/10.1021/acsmacrolett.3c00223

Enhanced Sampling Methods for Molecular Dynamics Simulations
Jérôme Hénin, Tony Lelièvre, Michael R. Shirts, Omar Valsson, and Lucie Delemotte
Living Journal of Computational Molecular Science, 4(1), 1583, (2023)
Link: https://doi.org/10.33011/livecoms.4.1.1583

Sampling rare event energy landscapes via birth-death augmented dynamics
Benjamin Pampel, Simon Holbach, Lisa Hartung, and Omar Valsson
Physical Review E 107, 024141 (2023)
Link: https://doi.org/10.1103/PhysRevE.107.024141

Molecular Structure and Dynamics in Wet Gecko beta-Keratin
H. Eslami, F. Müller-Plathe
ACS Biomaterials Sc. Engineering 9, 257 (2023)
Link: https://doi.org/10.1021/acsbiomaterials.2c01022

Molecular dynamics simulations of electrified interfaces including the metal polarisation
Samuel Ntim, Marialore Sulpizi
Physical Chemistry Chemical Physics 25, 22619-22625 (2023)
Link: https://doi.org/10.1039/d3cp01472j