MacroMolecular Modeling (MaMoMo)

MacroMolecular Modeling (MaMoMo)

group of Dr. Peter Košovan
MacroMolecular Modeling (MaMoMo)

group of Dr. Peter Košovan

Molecular simulations and theoretical modeling of charged macromolecules - peptides, proteins or synthetic polymers. Combining modelling with accurate experiments to obtain physical insights

People of the Group

Raju Lunkad

Ph.D.,

Postdoc at University of Gottingen (next affiliation)

Pablo M. Blanco Andrés

Ph.D.

Assistant professor at University of Lleida (next affiliation)

Sebastian Pineda Pineda

Ph.D.

Postdoc at University of Lund, Sweden (next affiliation)

Research Topics

Modeling of polyelectrolytes

Polyelectrolyte solutions and gels
Coarse-grained simulations
Mean-field and Poisson-Boltzmann modeling
pH-dependent properties
Collaborators: Christian Holm (Stuttgart)

P eter Košovan

Polyelectrolyte complexes and coacervates

Coarse-grained simulations and phenomenological theories
Thermodynamic conditions of liquid-liquid phase separation and two-phase coexistence
Partitioning of low-molecular solutes
Acid-base equilibria
Collaborators: Roman Staňo (Vienna), Saskia Lindhoud (Twente)

P eter Košovan

Concentrated solutions of proteins and charged patchy colloids

Phase stability of protein and colloidal solutions at high concentrations
Donnan equilibrium
Charge distribution and charge patchiness
Charge regulation and acid-base equilibria
Collaborators: Pablo Blanco, Rita Dias (Trondheim)

P eter ...

Selected Publications

List of 28 publications

(5 currently shown)

S. P. Pineda, P. M. Blanco, R. Staňo and P. Košovan
Patchy Charge Distribution Affects the pH in Protein Solutions during Dialysis

Langmuir, 41(8), 2025

DOI, BibTeX

D. Beyer, P. M. Blanco, J. Landsgesell, P. Košovan and C. Holm
How To Correct Erroneous Symmetry-Breaking in Coarse-Grained Constant-pH Simulations

Journal of Chemical Theory and Computation, 21(3), 2025

DOI, BibTeX

P. M. Blanco and P. Košovan
The explicit bonding reaction ensemble Monte Carlo method

The Journal of Chemical Physics, 161(9), 2024

DOI, BibTeX

D. Beyer, P. B. Torres, S. P. Pineda, C. F. Narambuena, J.-N. Grad, P. Košovan and P. M. Blanco
pyMBE: The Python-based molecule builder for ESPResSo

The Journal of Chemical Physics, 161(2), 2024

DOI, BibTeX

S. P. Pineda, R. Staňo, A. Murmiliuk, P. M. Blanco, P. Montes, Z. Tošner, O. Groborz, J. Pánek et al.
Charge Regulation Triggers Condensation of Short Oligopeptides to Polyelectrolytes

JACS Au, 2024

DOI, BibTeX

P. Kosovan, J. Landsgesell, L. Nova, F. Uhlik, D. Beyer, P. M. Blanco, R. Stano and C. Holm
Reply to the ‘Comment on “Simulations of ionization equilibria in weak polyelectrolyte solutions and gels”’ by J. Landsgesell, L. Nová, O. Rud, F. Uhlík, D. Sean, P. Hebbeker, C. Holm and P. Košovan, Soft Matter, 2019, 15, 1155–1185

Soft Matter, 19, 2023

DOI, BibTeX

K. Fink, J. Cebula, Z. Tosner, M. Psurski, M. Uchman and T. M. Goszczyński
Cobalt bis(dicarbollide) is a DNA-neutral pharmacophore

Dalton Trans., 52, 2023

DOI, BibTeX

S. Das, S. Jana, M. Orsagh, K. Bys, J. Mishra, M. Uchman and V. Adyam
Building Sodium Metal Battery with Polyisoprene-Based Air-Stable Single-Ion Gel Polymer Electrolyte

ACS Applied Energy Materials, 6(10), 2023

DOI, BibTeX

B. Hleli, Z. Medos, P. Ogrin, Z. Tosner, S. Kereiche, M. Gradzielski, T. Urbic, M. Bester-Rogac et al.
Closo-dodecaborate-based dianionic surfactants with distorted classical morphology: Synthesis and atypical micellization in water

Journal of Colloid and Interface Science, 648, 2023

dodecaborate surfactants self-assembly micelles calorimetry simulations

DOI, BibTeX

S. Eldemrdash, G. Thalassinos, A. Alzahrani, Q. Sun, E. Walsh, E. Grant, H. Abe, T. L. Greaves et al.
Fluorescent HPHT nanodiamonds have disk- and rod-like shapes

Carbon, 206, 2023

DOI, BibTeX

J. Kozisek, M. Slouf and I. Sloufova
Factor analysis of the time series of SERS spectra reveals water arrangement and surface plasmon changes in Ag nanoparticle systems

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 293, 2023

DOI, BibTeX

E. Hlavatovicova, R. Fernandez-Alvarez, K. Bys, S. Kereiche, T. K. Mandal, L. I. Atanase, M. Stepanek and M. Uchman
Stimuli-Responsive Triblock Terpolymer Conversion into Multi-Stimuli-Responsive Micelles with Dynamic Covalent Bonds for Drug Delivery through a Quick and Controllable Post-Polymerization Reaction

Pharmaceutics, 15(1), 2023

BibTeX

J. Vavra, A. Sergunin, P. Pompach, D. Savchenko, J. Hranicek, I. Sloufova, T. Shimizu and M. Martinkova
Characterization of the interaction between the tumour suppressor p53 and heme and its role in the protein conformational dynamics studied by various spectroscopic techniques and hydrogen/deuterium exchange coupled with mass spectrometry

Journal of Inorganic Biochemistry, 243, 2023

DOI, BibTeX

M. Zurkova-Kokoskova, I. Sloufova, V. Gajdosova and B. Vlckova
Plasmon-catalysed decarboxylation of dicarboxybipyridine ligands in Ru(ii) complexes chemisorbed on Ag nanoparticles: conditions, proposed mechanism and role of Ag(0) adsorption sites

Phys. Chem. Chem. Phys., 24, 2022

DOI, BibTeX

R. Lunkad, P. Biehl, A. Murmiliuk, P. M. Blanco, P. Mons, M. Stepanek, F. H. Schacher and P. Kosovan
Simulations and Potentiometric Titrations Enable Reliable Determination of Effective pKa Values of Various Polyzwitterions

Macromolecules, 55(17), 2022

DOI, BibTeX

D. Beyer, J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Košovan and C. Holm
Correction to “Grand-Reaction Method for Simulations of Ionization Equilibria Coupled to Ion Partitioning”

Macromolecules, 55(3), 2022

DOI, BibTeX

J. Landsgesell, D. Beyer, P. Hebbeker, P. Košovan and C. Holm
The pH-Dependent Swelling of Weak Polyelectrolyte Hydrogels Modeled at Different Levels of Resolution

Macromolecules, 55(8), 2022

DOI, BibTeX

K. Prochazka, Z. Limpouchova, M. Stepanek, K. Sindelka and M. Lisal
DPD Modelling of the Self- and Co-Assembly of Polymers and Polyelectrolytes in Aqueous Media: Impact on Polymer Science

Polymers, 14(3), 2022

DOI, BibTeX

R. Lunkad, F. L. B. d. Silva and P. Kosovan
Both Charge-Regulation and Charge-Patch Distribution Can Drive Adsorption on the Wrong Side of the Isoelectric Point

Journal of the American Chemical Society, 144(4), 2022

DOI, BibTeX

K. Sindelka, Z. Limpouchova and K. Prochazka
Solubilization of Charged Porphyrins in Interpolyelectrolyte Complexes: A Computer Study

Polymers, 13(4), 2021

DOI, BibTeX

D. Vrbata, S. Kereiche, K. Kalíková and M. Uchman
Stimuli-responsive multifunctional micelles of ABC vs. ACB triblock terpolymers using reversible covalent bonding of phenylboronic acid: controlled synthesis, self-assembly and model drug release

Journal of Molecular Liquids, 335(1), 116528, 2021

DOI, BibTeX

O. V. Rud, J. Landsgesell, C. Holm and P. Košovan
Modeling of weak polyelectrolyte hydrogels under compression - Implications for water desalination

Desalination, 506, 2021

DOI, BibTeX

R. Staňo, P. Košovan, A. Tagliabue and C. Holm
Electrostatically Cross-Linked Reversible Gels—Effects of pH and Ionic Strength

Macromolecules, 54, 2021

DOI, BibTeX

R. Lunkad, A. Murmiliuk, Z. Tošner, M. Štěpánek and P. Košovan
Role of pKA in Charge Regulation and Conformation of Various Peptide Sequences

Polymers, 13(2), 214, 2021

DOI, BibTeX

D. Han, Q. Yuan, Z. Slanina, X. Tang, S. Yi, D.-Y. Zhou, F. Uhlik and L. Feng
Enhancing Built-In Electric Field and Defect Passivation through Gradient Doping in Inverted CsPbI 2 Br Perovskite Solar Cells

RRL Solar, 5(1), 2000629, 2021

DOI, BibTeX

R. Lunkad, A. Murmiliuk, P. Hebbeker, M. Boublík, Z. Tošner, M. Štěpánek and P. Košovan
Quantitative prediction of charge regulation in oligopeptides

Molecular Systems Design & Engineering, 6, 122-131, 2020

DOI, BibTeX

A. D. Kazakov, V. M. Prokacheva, F. Uhlík, P. Košovan and F. A. M. Leermakers
Computer modeling of polymer stars in variable solvent conditions: a comparison of MD simulations, self-consistent field (SCF) modeling and novel hybrid Monte Carlo SCF approach

Soft Matter, 17, 580-591, 2020

DOI, BibTeX

J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Košovan and C. Holm
Grand-Reaction Method for Simulations of Ionization Equilibria Coupled to Ion Partitioning

Macromolecules, 53(8), 2020

DOI, BibTeX

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