2022 - Publications
Refined Large Deviation Principle for Branching Brownian Motion Conditioned to Have a Low Maximum
Yanjia Bai, Lisa Hartung
ALEA - Latin American Journal of Probability and Mathematical Statistics 19, 8590880 (2022)
Link: https://doi.org/10.30757/ALEA.v19-34
Asymptotic properties of a class of linearly implicit schemes for weakly compressible Euler equations
V. Kucera, M. Lukáčová-Medvid'ová, S. Nölle, J. Schütz
Numerische Mathematik 150, 79-103 (2022)
Link: https://doi.org/10.1007/s00211-021-01240-5
Approximating viscosity solutions of the Euler system
E. Feireisl, M. Lukáčová-Medvid'ová, S. Scheiner, B. Whe
Mathematics of Computation 91, 2129-2164 (2022)
Link: https://doi.org/10.1090/mcom/3738
Data-based stochastic modeling reveals sources of activity bursts in single-cell TGF-β signaling
Niklas Kolbe, Lorenz Hexemer, Lukas-Malte Bammert, Alexander Löwer, Mária Lukáčová-Medvid'ová, Stefan Legewie
PLOS Comp. Biology 18, 31010266 (2022)
Link: https://doi.org/10.1371/journal.pcbi.1010266
Small-to-large length scale transition of TMAO interaction with hydrophobic solutes
Angelina Folberth, Swaminath Bharadwaj, Nico F.A. van der Vegt
Phys. Chem. Chem. Phys. 24, 2080-2087 (2022)
Link: https://doi.org/10.1039/d1cp05167a
Computation of NMR shieldings at the CASSCF level using gauge-including atomic orbitals and Cholesky decomposition
T. Nottoli, S. Burger, S. Stopkowicz, J. Gauss, F. Lipparini
The Journal of Chemical Physics 157, 084122 (2022)
Link: https://doi.org/10.1063/5.0101838
Cononsolvency of thermoresponsive polymers: where we are now and where we are going
S. Bharadwaj, B.-J. Niebuur, K. Nothdurft, W. Richtering, N.F.A. van der Vegt, C.M. Papadakis
Soft Matter 18, 2884-2909 (2022)
Link: https://doi.org/10.1039/d2sm00146b
Open-circuit voltage of organic solar cells: interfacial roughness makes the difference
C. Pölking, J. Benduhn, D. Spoltore, M. Schwarze, S. Roland, F. Piersimoni, D. Neher, K. Leo, K. Vandewal, D. Andrienko
Comm. Phys. 5, 307 (2022)
Link: https://doi.org/10.1038/s42005-022-01084-x
Error Estimates of the Godunov Method for the Multidimensional Compressible Euler System
Mária Lukáčová-Medvid'ová, Bangwei She, Yuhuan Yuan
J. Scientific Computing 91, 71 (2022)
Link: https://doi.org/10.1007/s10915-022-01843-6
Particle number conservation and block structures in matrix product states
Markus Bachmayr, Michael Götte, Max Pfeffer
CALCOLO 59, 24 (2022)
Link: https://doi.org/10.1007/s10092-022-00462-9
Lower degree of dissociation of pyruvic acid at water surfaces than in bulk
Dominika Lesnicki, Veronika Wank, Jenee D. Cyran, Ellen H.G. Backus, Marialore Sulpizi
Physical Chemistry Chemical Physics 24, 13510-13513 (2022)
Link: https://doi.org/10.1039/d2cp01293f
Substrate spectrum of PPM1D in the cellular response to DNA
double-strand breaks
Justus F. Gräf, Ivan Mikicic, Xiaofei Ping, Claudia Scalera, Katharina Mayr, Lukas S. Stelzl, Petera Beli, Sebastian A. Wagner
iScience 25, 104892 (2022)
Link: https://doi.org/10.1016/j.isci.2022.104892
Knot formation of dsDNA pushed inside a nannochannel
Jan Rothörl, Sarah Wettermann, Peter Virnau, Ankiet Bhattacharya
Scientific Reports 12, 5342 (2022)
Link: https://doi.org/10.1038/s41598-022-09242-5
Temporally Coherent Backmapping of Molecular Trajectories From Coarse-Grained to Atomistic Resolution
Kirill Shmilovich, Marc Stieffenhofer, Nichalas E. Charron, Moritz Hoffmann
The Journal of Physical Chemistry A 126, 9124-9139 (2022)
Link: https://doi.org/10.1021/acs.jpca.2c07716
Solvation shell thermodynamics of extended hydrophobic solutes in mixed solvents
Madhusmita Tripathy, Swaminath Bharadwaj, Nico F.A. van der Vegt
The Journal of Chemical Physics 156, 164901 (2022)
Link: https://doi.org/10.1063/5.0090646
A Relation between the Formation of a Hydrogen-Bond Network and a Time-Scale Separation of Translation and Rotation in Molecular Liquids
Manuel Becher, Robin Horstmann, Sebastian Kloth, Ernst A. Rössler, Michael Vogel
Journal of Physical Chemistry Letters 13, 4556-4562 (2022)
Link: https://doi.org/10.1021/acs.jpclett.2c00821
Structural and Dynamical Properties of Liquids in Confinements: A Review of Molecular Dynamics Simulation Studies
R. Horstmann, L. Hecht, S. Kloth, M. Vogel
Soft Matter 18, 2373-2382 (2022)
Link: https://doi.org/10.1021/acs.langmuir.2c00521
Finite-size scaling and thermodynamics of model supercooled liquids: long-range concentration fluctuations and the role of attractive interactions
Atreyee Banerjee, Mauricio Sevilla, Joseph F. Rudzinski, Robinson Cortes-Huerto
Soft Matter 18, 2373-2382 (2022)
Link: https://doi.org/10.1039/d2sm00089j
pH-Dependent Behavior of Ionizable Cationic Lipids in mRNA-Carrying Lipoplexes Investigated by Molecular Dynamics Simulations
Giovanni Settanni, Wolfgang Brill, Heinrich Haas, Friederike Schmid
Macromolecular rapid communications 43, 2100683 (2022)
Link: https://doi.org/10.1002/marc.202100683
Editorial: Multiscale simulation methods for soft matter systems
Friederike Schmid
J. Phys.: Cond. Matter 34, 160401 (2022)
Link: https://doi.org/10.1088/1361-648X/ac5071
Critical behavior of active Brownian particles: Connection to field theories
Thomas Speck
Physical Review E 105, 064601 (2022)
Link: https://doi.org/10.1103/PhysRevE.105.064601
Connecting density fluctuations and Kirkwood-Buff integrals for finite-size systems
Mauricio Sevilla, Robinson Cortes-Huerto
The Journal of Chemical Physics 156, 044502 (2022)
Link: https://doi.org/10.1063/5.0076744
A deterministic two-phase model for an active suspension with non-spherical active particles using the Eulerian spatial averaging theory
B. Deußen, Y. Wang, M. Oberlack
Phys. Fluids 34, 023302 (2022)
Link: https://doi.org/10.1063/5.0077735
Single-chain and condensed-state behavior of hnRNPA1 from molecular simulations
D.J. Bauer, L.S. Stelzl, A. Nikoubashman
The Journal of Chemical Physics 165, 044118 (2022)
Link: https://doi.org/10.1063/5.0105540
An adaptive stochastic Galerkin method based on multilevel expansions of random fields: Convergence and optimality
Markus Bachmayr, Igor Voulis
Esaim - Mathematical modelling and numerical analysis 56, 12955-1992 (2022)
Link: https://doi.org/10.1051/m2an/2022062
Benchmarking coarse-grained models of organic semiconductors via deep backmapping
Marc Stieffenhofer, Christoph Scherer, Falk May, Tristan Bereau, Denis Andrienko
Frontiers in Chemistry 10, 982757 (2022)
Link: https://doi.org/10.3389/fchem.2022.982757
Nonadditive ion effects on the coil-globule equilibrium of PNIPAM: a computer simulation study
Yani Zhao, Saminath Bharadwaj, Nico F.A. van der Vegt
Phys. Chem. Chem. Phys. 24, 10346-10355 (2022)
Link: https://doi.org/10.1039/d2cp00057a
Slow liquid dynamics near solid surfaces: Insights from site-resolved studies of ionic liquids in silica confinement
Robin Köster, Michael Vogel
The Journal of Chemical Physics 156, 074501 (2022)
Link: https://doi.org/10.1063/5.0079722
AlphaFold predicts the most complex protein knot and composite protein knots
Brems, Maarten A. and Runkel, Robert and Yeates, Todd O. and Virnau, Peter
Protein Science 31, e4380 (2022)
Link: https://doi.org/10.1002/pro.4380
On a Hybrid Continuum-Kinetic Model for Complex Fluids
A. Chertock, P. Degond, G. Dimarco, and M. Lukáčová-Medvid'ová
Partial Differ. Equ. Appl. 3, Paper No. 63, 28 pp. (2022)
Link: https://doi.org/10.1007/s42985-022-00198-9
Convergence and Error Analysis for Compressible Fluid Flows with Random Data: Monte Carlo Method
E. Feireisl, M. Lukáčová-Medvid'ová, B. She, B., Y. Yuan
Math. Mod. Meth. Appl. Sci. 32 (14), 2887-2925 (2022)
Link: https://doi.org/10.1142/S0218202522500671
Understanding and Modeling Polymers: The Challenge of Multiple Scales
F. Schmid
ACS Polymers Au 3, 28-58 (2022)
Link: https://doi.org/10.1021/acspolymersau.2c00049
Water Uptake by Gecko beta-Keratin and the Influence of the Relative Humidity on its Mechanical and Volumetric Properties
M. Khani, T. Materzok, H. Eslami, S. Gorb, and F. Müller-Plathe
J. R. Soc. Interface 19, 20220372 (2022)
Link: https://doi.org/10.1098/rsif.2022.0372
How Ethanolic Disinfectants Disintegrate Coronavirus Model Membranes: A Dissipative-Particle-Dynamics Simulation Study
T. Zhou, Z. Wu, S. Das, H. Eslami, and F. Müller-Plathe
Journal of Chemical Theory and Computation 18, 2597–2615 (2022)
Link: https://doi.org/10.1021/acs.jctc.1c01120
Self-Assembly of Model Triblock Janus Colloidal Particles in Two Dimensions
K. Bahri, H. Eslami, and Florian Müller-Plathe
Journal of Chemical Theory and Computation 18, 1870–1882 (2022)
Link: https://doi.org/10.1021/acs.jctc.1c01116
Mobility of polymer melts in a regular array of carbon nanotubes
S.A.N. Alberti, J. Schneider, and F. Müller-Plathe
Journal of Chemical Theory and Computation 18, 3285–3295 (2022)
Link: https://doi.org/10.1021/acs.jctc.1c01281
Boron-Modified Perhydropolysilazane Towards Facile and Economical Synthesis of Amorphous SiBN Ceramic with Excellent Thermal Stability
Y. Zhan, W. Li, T. Jiang, C. Fasel, E. Ricohermoso III, J. Bernauer, Z. Yu, Z. Wu, F. Müller-Plathe, L. Molina-Luna, R. Grottenmüller, and R. Riedel
Journal of Advanced Ceramics 11, 1104–1116 (2022)
Link: https://doi.org/10.1007/s40145-022-0597-z
Slip-Spring Hybrid Particle-Field Model for Coarse-Graining Branched Polymer Melts: Polystyrene Melts as an Example
Z. Wu and F. Müller-Plathe
Journal of Chemical Theory and Computation 18, 3814–3828 (2022)
Link: https://doi.org/10.1021/acs.jctc.2c00107
Roughness volumes: An improved RoughMob concept for predicting the increase of molecular mobility upon coarse-graining
M.K. Meinel and F. Müller-Plathe
The Journal of Physical Chemistry B 126, 3737−3747 (2022)
Link: https://doi.org/10.1021/acs.jpcb.2c00944
Passive probe particle in an active bath: can we tell it is out of equilibrium?
Jeanine Shea, Gerhard Jung, Friederike Schmid
Soft Matter, 2022,18, 6965-6973, (2022)
Link: https://doi.org/10.1039/d2sm00905f
Force Generation in Confined Active Fluids: The Role of Microstructure
Shuvojit Paul, Ashreya Jayaram, N Narinder, Thomas Speck, Clemens Bechinger
Physical Review Letters 129, 058001 (2022)
Link: https://doi.org/10.1103/PhysRevLett.129.058001
Penalization method for the Navier-Stokes-Fourier system
Danica Basarić, Eduard Feireisl, Mária Lukáčová-Medviďová, Hana Mizerová, Yuhuan Yuan
ESAIM: Mathematical Modelling and Numerical Analysis, (2022)
Link: https://doi.org/10.1051/m2an/2022063
Existence of Dissipative Solutions to the Compressible Navier-Stokes System with Potential Temperature Transport
M. Lukáčová-Medvid'ová, A. Schömer
Journal of Mathematical Fluid Mechanics 24, 82 (2022)
Link: https://doi.org/10.1007/s00021-022-00713-3
Global existence of weak solutions to viscoelastic phase separation: Part I Regular Case
Aaron Brunk, Mária Lukáčová-Medvid'ová
Nonlinearity 35, 3417-3458, (2022)
Link: https://doi.org/10.1088/1361-6544/ac5920
Global existence of weak solutions to viscoelastic phase separation: Part II Degenerate Case
A. Brunk, M. Lukáčová-Medvid'ová
Nonlinearity 35, 3459-3486, (2022)
Link: https://doi.org/10.1088/1361-6544/ac591e
A variational framework for the inverse Henderson problem of statistical mechanics
Fabio Frommer and Martin Hanke
Letters in Mathematical Physics 112, 71, (2022)
Link: https://doi.org/10.1007/s11005-022-01563-w
Employing Artificial Neural Networks to Identify Reaction Coordinates and Pathways for Self-Assembly
Jörn H. Appeldorn, Simon Lemcke, Thomas Speck, Arash Nikoubashman
The Journal of Physical Chemistry B 126 (27), 5007-5016, (2022)
Link: https://doi.org/10.1021/acs.jpcb.2c02232
Wavefunction-Based Electrostatic-Embedding QM/MM Using CFOUR through MiMiC
Till Kirsch, Jógvan Magnus Haugaard Olsen, Viacheslav Bolnykh, Simone Meloni, Emiliano Ippoliti, Ursula Rothlisberger, Michele Cascella, Jürgen Gauss
Journal of Chemical Theory and Computation 18 (1),13-24 (2022)
Link: https://doi.org/10.1021/acs.jctc.1c00878
Cross-correlation corrected friction in generalized Langevin models: Application to the continuous Asakura–Oosawa model
Viktor Klippenstein, Nico F. A. van der Vegt
The Journal of Chemical Physics 157, 044103 (2022)
Link: https://doi.org/10.1063/5.0093056
A multi-scale method for complex flows of non-Newtonian fluids
F. Tedeschi, G.G. Giusteri, L. Yelash, M. Lukáčová-Medvid’ova
Mathematics in Engineering 4, 6 (2022)
Link: https://doi.org/10.3934/mine.2022050
Existence, Regularity and Weak-Strong Uniqueness for Three-Dimensional Peterlin Viscoelastic Model
Brunk, A., Lu, Y., and Lukáčová-Medvid'ová, M.
Commun. Math. Sci. 20, 2022, 201-230 (2022)
Link: https://doi.org/10.4310/CMS.2022.v20.n1.a6
Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials
Benjamin Pampel and Omar Valsson
Journal of Chemical Theory and Computation 18, 7, 4127–4141 (2022)
Link: https://doi.org/10.1021/acs.jctc.2c00197
Where Lennard-Jones Potentials Fail: Iterative Optimization of Ion–Water Pair Potentials Based on Ab Initio Molecular Dynamics Data
Marvin P. Bernhardt, Yuki Nagata, Nico F.A. van der Vegt
Journal of Physical Chemistry Letters 13, 16, 3712–3717 (2022)
Link: https://doi.org/10.1021/acs.jpclett.2c00121