Publications

2018

Kabelka, I.; Vácha, R.: Optimal Hydrophobicity and Reorientation of Amphiphilic Peptides Translocating Through Membrane. Biophysical Journal 2018, 115 (6), 1045-1054, link

Leber, R.; Pachler, M.; Kabelka, I.; Svoboda, I.; Koller, D.; Vácha, R.; Lohner, K.; Pabst, G.: Synergism of Antimicrobial Frog Peptides Couples to Membrane Intrinsic Curvature Strain. Biophysical Journal 2018, 114 (8), 1945-1954, link

Tesei, G.; Hellstrand, E.; Sanagavarapu, K.; Linse, S.; Sparr, E.; Vácha, R.; Lund, M.: Aggregate Size Dependence of Amyloid Adsorption onto Charged Interfaces. Langmuir 2018, 34 (4), 1266–1273, link

2017

Schubertová, V.; Martinez-Veracoechea, F.J.; Vácha, R.Design of Multivalent Inhibitors for Preventing Cellular Uptake. Scientific Reports 2017, 7, 11689, link
Jurásek, M.; Vácha, R.Self-assembled clusters of patchy rod-like molecules. Soft Matter 2017, 13, 7492 - 7497, link

2016

Amaro, M.; Sachl, R.; Aydogan, G.; Mikhalyov, I.I.; Vácha, R.; Hof, M.: GM1 Ganglioside Inhibits beta-Amyloid Oligomerization Induced by Sphingomyelin. Angewandte Chemie International Edition 2016, 55, 1-6, link

2015

Kabelka, I.; Vácha, R.: Optimal conditions for opening of membrane pore by amphiphilic peptides. The Journal of Chemical Physics 2015, 143, 243115, link
Schubertová, V.; Martinez-Veracoechea, F.J.; Vácha, R.Influence of ligand distribution on uptake efficiencySoft Matter 2015, 11, 2726-2730, link

2014

Vácha, R.; Linse, S.; Lund, M.: Surface Effects on Aggregation Kinetics of Amyloidogenic PeptidesJournal of American Chemical Society 2014, 136 (33), 11776-11782, link
Vácha, R.; Frenkel, D.: Stability of Bicelles: A Simulation StudyLangmuir 2014, 30 (15), 4229-4235, link
Vácha, R.; Frenkel, D.: Simulations Suggest Possible Novel Membrane Pore StructureLangmuir 2014, 30 (5), 1304-1310, link
Vácha, R.; Uhlig, F.; Jungwirth, P.: Charges at aqueous interfaces: development of computational approaches in direct contact with experimentAdvances in Chemical Physics 2014, 155, 69-95, link

2013

Shi, Q.; Bergquist, K.-E.; Huo, R.; Li, J.; Lund, M.; Vácha, R.; Sundin, A.; Butkus, E.; Orentas, E.; Warnmark, K.: Composition- and Size-Controlled Cyclic Self-Assembly by Solvent and C60-Responsive Self-Sorting. Journal of American Chemical Society 2013, 135 (40), 15263-15268, link
Stenqvist, B.; Thuresson, A.; Kurut, A.; Vácha, R.; Lund, M.: Faunus - a flexible framework for Monte Carlo simulationMolecular Simulation 2013, 39(14-15), 1233-1239, link

2012

Vácha, R.; Martinez-Veracoechea, F.J.; Frenkel, D.: Intracellular Release of Endocytosed Nanoparticles Upon a Change of Ligand-Receptor InteractionACS Nano 2012, 6 (12), 10598-10605, link
Bieler, N.S.; Knowles, T.P.J.; Frenkel, D.; Vácha, R.Connecting Macroscopic Observables and Microscopic Assembly Events in Amyloid Formation Using Coarse Grained SimulationsPLoS Computational Biology 2012, 8 (10), e1002692, link
Vácha, R.; Roke; S.: Sodium Dodecyl Sulfate at Water-Hydrophobic Interfaces: A Simulation Study. Journal of Physical Chemistry B 2012, 116 (39), 11936-11942, link
Vazdar, M.; Pluharová, E.; Mason, P.E.; Vácha, R.; Jungwirth, P.: Ions at Hydrophobic Aqueous Interfaces: Molecular Dynamics with Effective Polarization. Journal of Physical Chemistry Letters 2012, 3, 2087-2091, link
Berkowitz, M.L. and Vácha, R.Aqueous Solutions at the Interface with Phospholipid BilayersAccounts of Chemical Research 2012, 45 (1), 74-82, link
Vácha, R.; Marsalek, O.; Willard, A.P.; Bonthuis, D.J.; Netz, R.R.; Jungwirth, P.: Charge Transfer between Water Molecules As the Possible Origin of the Observed Charging at the Surface of Pure WaterJournal of Physical Chemistry Letters 2012, 3 (1), 107-111, link
Pospíšil, M.; Kovár, P.; Vácha, R.; Svoboda, M.: Study of the betulin molecule in a water environment; ab initio and molecular simulation calculations. Journal of Molecular Modeling 2012, 18(1), 367-376 link

2011

Vácha, R.; Martinez-Veracoechea, F.J.; Frenkel, D.: Receptor-Mediated Endocytosis of Nanoparticles of Various Shapes. Nano Letters 2011, 11 (12), 5391-5395, link
Vácha, R.; Frenkel, D.: Relation between Molecular Shape and the Morphology of Self-Assembling Aggregates: A Simulation Study. Biophysical Journal 2011, 101, 1432-1439, link
Vácha, R.; Rick, S.W.; Jungwirth, P.; de Beer, A.G.F.; de Aguiar, H.B.; Samson, J.-S.; Roke, S.: The Orientation and Charge of Water at the Hydrophobic Oil Droplet–Water Interface. Journal of American Chemical Society 2011, 133 (26), 10204-10210, link

2010

Wolff, W.; McKenna, J.; Vácha, R.; Zohrabi, M.; Gaire, B.; Carnesa, K.D.; Ben-Itzhak, I.: Three-dimensional energy profile measurement of a molecular ion beam by coincidence momentum imaging compared to a retarding field analyzer. Journal of Instrumentation 2010, P10006 link
Lund, M.; Jagoda-Cwiklik, B.; Woodward C.E.; Vácha, R.; Jungwirth, P.: Dielectric Interpretation of Specificity of Ion Pairing in WaterJournal of Physical Chemistry Letters 2010, 1 (1), 300-303, link
Vácha, R.; Horinek, D.; Buchner, R.; Winter, B.; Jungwirth, P.: Comment on "An explanation for the charge on water's surface" by A. Gray-Weale and J. K. Beattie, Phys. Chem. Chem. Phys., 2009, 11, 10994 Physical Chemistry Chemical Physics 2010, 12 (42), 14362-14363, link
Vácha, R.; Jurkiewicz, P.; Petrov, M.; Berkowitz, M.L.; Böckmann, R. A.; Barucha-Kraszewska, J.; Hof, M.; Jungwirth, P.: Mechanism of Interaction of Monovalent Ions with Phosphatidylcholine Lipid Membranes. Journal of Physical Chemistry B 2010, 114 (29), 9504-9509, link

2009

Ottosson, N.; Vácha, R.; Aziz, E. F.; Pokapanich, W.; Eberhardt, W.; Svensson, S.; Öhrwall, G.; Jungwirth, P.; Björneholm, O.; Winter, B.: Large variations in the propensity of aqueous oxychlorine anions for the solution/vapor interface. Journal of Chemical Physics 2009, 131, 124706 link
Winter, B.; Faubel, M.; Vácha, R.; Jungwirth, P.: Reply to comments on Frontiers Article 'Behavior of hydroxide at the water/vapor interface'. Chemical Physics Letters 2009, 481, 19-21 link
Winter, B.; Faubel, M.; Vácha, R.; Jungwirth, P.: Behavior of hydroxide at the water/vapor interface. Chemical Physics Letters 2009, 474, 241-247 link
Heyda, J.; Pokorna, J.; Vrbka, L.; Vácha, R.; Jagoda-Cwiklik, B.; Konvalinka, J.; Jungwirth, P.; Vondrasek, J.: Ion specific effects of sodium and potassium on the catalytic activity of HIV-1 proteasePhysical Chemistry Chemical Physics 2009, 11, 7599-7604 link
Vácha, R.; Berkowitz, M. L.; Jungwirth, P.: Molecular Model of a Cell Plasma Membrane with an Asymmetric Multicomponent Composition: Water Permeation and Ion EffectsBiophysical Journal 2009, 96(11), 4493-4501 link
Vácha, R.; Megyes, T.; Bako, I.; Pusztai, I.; Jungwirth, P.: Benchmarking polarizable molecular dynamics simulations of aqueous sodium hydroxide by diffraction measurementsJournal of Physical Chemistry A 2009, 113 (16), 4022-4027 link
Vácha, R.; Siu, S. W. I.; Petrov, M.; Bockmann, R. A.; Barucha-Kraszewska, J.; Jurkiewicz, P.; Hof. M.; Berkowitz, M. L.; Jungwirth, P.: Effects of alkali cations and halide anions on the DOPC lipid membraneJournal of Physical Chemistry B 2009, 113 (26), 7235-7243 link
Vlachy, N.; Jagoda-Cwiklik, B.; Vácha, R.; Touraud, D.; Jungwirth, P.; Kunz, W.: Hofmeister series and specific interactions of charged headgroups with aqueous ionsAdvances in Colloid and Interface Science 2009, 146, 42-47 link

2008

Aziz, E. F.; Ottosson, N.; Eisebitt, S.; Jagoda-Cwiklik, B.; Vácha, R.; Jungwirth, P.; Winter, B.: Cation-specific interactions with carboxylate in amino acid and acetate aqueous s olutions: X-ray absorption and ab initio calculations. Journal of Physical Chemistry B 2008, 112, 12567-12570 link
Vácha, R.; Buch, V.; Milet, A.; Devlin, J.P.; Jungwirth, P.: Response to Comment on Autoionization at the surface of neat water: is the top layer pH neutral, basic, or acidic? by J. K. Beattie, Phys. Chem. Chem. Phys., 2007, 9, DOI : 10.1039/b713702h Physical Chemistry Chemical Physics 2008, 10 (2), 332-333 link 
Vácha, R.; Horinek, D.; Berkowitz, M. L.; Jungwirth, P.: Hydronium and hydroxide at the interface between water and hydrophobic mediaPhysical Chemistry Chemical Physics 2008, 10, 4975-4980 link
Vácha, R.; Zangi, R.; Engberts, J. B. F. N.; Jungwirth, P.: Water Structuring and Hydroxide Ion Binding at the Interface between Water and Hydrophobic Walls of Varying Rigidity a nd van der Waals Interactions. Journal of Physical Chemistry C 2008, 112 (20), 7689-7692 link
Vácha, R.; Cwiklik, L.; Rezac, J.; Hobza, P.; Jungwirth, P.; Valsaraj, K.; Bahr, S.; Kempter, V.: Adsorption and Heterogeneous Reactions of Aromatic Hydrocarbons at Environmental Aqueous Surfaces. Journal of Physical Chemistry A 2008, 112 (22), 4942-4950 link
Siu, S. W. I; Vácha, R.; Jungwirth, P.; Bockmann, R. A.: Biomolecular simulations of membranes: Physical properties from different force fieldsJournal of Chemical Physics 2008, 128, 125103, link
Lund, M.; Vácha, R.; Jungwirth, P.: Specific Ion-Binding to Macromolecules: Effects of Hydrophobicity and Ion PairingLangmuir 2008, 24(7), 3387-3391 link

2007

Jagoda-Cwiklik, B.; Vácha, R.; Lund, M.; Srebro, M.; Jungwirth, P.: Ion pairing as a possible clue for discriminating between sodium and potassium in biological and other complex environmentsJournal of Physical Chemistry B 2007, 111, 14077-14079 link
Vácha, R.; Buch, V.; Milet, A.; Devlin J.P.; Jungwirth, P.: Autoionization at the surface of neat water: is the top layer pH neutral, basic, or acidic? Physical Chemistry Chemical Physics 2007, 34, 4736-4747 link
Buch, V.; Milet, A.; Vácha, R.; Jungwirth, P.; Devlin J.P.: Water surface is acidicProceedings of the National Academy of Sciences of the United States of America 2007, 107 (18), 7342-7347 link

2006

Vrbka, L.; Vondrasek, J.; Jagoda-Cwiklik, B.; Vácha, R.; Jungwirth, P.: Quantification and rationalization of the higher affinity of sodium over potassium to protein surfaces. Proceedings of the National Academy of Sciences of the United States of America 2006, 103 (42), 15440-15444 link
Vácha, R.; Jungwirth, P.; Chen, J.; Valsaraj, K.: Adsorption of polycyclic aromatic hydrocarbons at the air-water interface: Molecular dynamics simulations and experimental atmospheric observationsPhysical Chemistry Chemical Physics 2006, 8 (38), 4461-4467 link
Minofar, B.; Vácha, R.; Wahab, A.; Mahiuddin, S.; Kunz, W.; Jungwirth, P.: Propensity for the air/water interface and ion pairing in magnesium acetate vs magnesium nitrate solutions: Molecular dynamics simulations and surface tension measurementsJournal of Physical Chemistry B 2006, 110 (32), 15939-15944 link

2004

Vácha, R.; Slavicek, P.; Mucha, M.; Finlayson-Pitts, B. J.; Jungwirth, P.: Adsorption of atmospherically relevant gases at the air/water interface: Free energy profiles of aqueous solvation of N2, O2, O3, OH, H2O, HO2, and H2O2. Journal of Physical Chemistry A 2004, 108, 11573-11579 link