Research

Efficient and Stable Method to Solve Poisson–Boltzmann Equation with Steep Gradients

Computational Electrostatics for Biological Applications
2015, pp 111-119 DOI: 10.1007/978-3-319-12211-3_5
Beibei Huang and Vladimir A. Baulin

This work describes a method to solve Poisson–Boltzmann Equation (PBE) with steep gradients when common methods of solving non-linear equations do not converge or work inefficiently. This is particularly the case for relatively large boundary conditions leading to rapid changes of the solution in a narrow […]

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Mechanism of dynamic reorientation of cortical microtubules due to mechanical stress

Biophysical Chemistry, (2015) 207, 82–89 DOI: 10.1016/j.bpc.2015.09.004
Alexander Muratov and Vladimir A. Baulin
Directional growth caused by gravitropism and corresponding bending of plant cells has been explored since 19th century, however, many aspects of mechanisms underlying the perception of gravity at the molecular level are still not well known. Perception of gravity in root and shoot gravitropisms is usually attributed to gravisensitive […]

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Interactions of Amphiphilic Triblock Copolymers with Lipid Membranes: Modes of Interaction and Effect on Permeability Examined by Generic Monte Carlo Simulations

Soft Matter, DOI: 10.1021/acs.macromol.5b00720 (2015)
Hauke Rabbel, Marco Werner, and Jens-Uwe Sommer

We investigate interactions of linear amphiphilic ABA triblock copolymers with lipid bilayer membranes by means of Monte Carlo simulations in a generic coarse-grained model. The polymers have hydrophilic A-blocks and B-blocks of varying hydrophobicity. The effect of different conformational states of the polymer on the induced […]

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Graphene Induces Formation of Pores That Kill Spherical and Rod-Shaped Bacteria

ACS Nano, DOI: 10.1021/acsnano.5b03368 (2015)
Vy T. H. Pham, Vi Khanh Truong, Matthew D. J. Quinn, Shannon M. Notley, Yachong Guo, Vladimir A. Baulin, Mohammad Al Kobaisi, Russell J. Crawford, and Elena P. Ivanova

Pristine graphene, its derivatives, and composites have been widely reported to possess antibacterial properties. Most of the studies simulating the interaction between bacterial cell […]

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Translocation and Induced Permeability of Random Amphiphilic Copolymers Interacting with Lipid Bilayer Membranes

Biomacromolecules, (2014) Article ASAP DOI: 10.1021/bm501266x

Marco Werner  and Jens-Uwe Sommer
We investigate adsorption and passive translocation of random amphiphilic copolymers interacting with a self-assembled lipid bilayer membrane. By using the bond fluctuation model with explicit solvent, we consider random copolymers under variation of the fraction, H̅, of hydrophobic sites and chain length. Our results indicate a point of […]

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Mechanical properties of atomic force microscopy probes with deposited thin films

Thin Solid Films, (2014) 565, 267–270 DOI: 10.1016/j.tsf.2014.06.027

L. Sirghi, Daniela Ciumac, V. Tiron
Deposition of thin films on atomic force microscopy (AFM) probes is a common technique that is used to either improve the light reflectance of the back side of the probe cantilevers or to modify the surface properties of the probe tips. However, this technique also affects […]

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Interfacing Electrogenic Cells with 3D Nanoelectrodes: Position, Shape, and Size Matter

ACS Nano, 2014, 8 (7), pp 6713–6723 DOI: 10.1021/nn500393p

Francesca Santoro, Sabyasachi Dasgupta, Jan Schnitker, Thorsten Auth, Elmar Neumann, Gregory Panaitov, Gerhard Gompper, and Andreas Offenhaeusser

An in-depth understanding of the interface between cells and nanostructures is one of the key challenges for coupling electrically excitable cells and electronic devices. Recently, various 3D nanostructures have been introduced […]

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Fast membrane hemifusion via dewetting between lipid bilayers

Soft Matter, 2014, Advance Article DOI: 10.1039/C4SM01577K

Jose Nabor Vargas, Ralf Seemannab and Jean-Baptiste Fleury
The behavior of lipid bilayers is important to understand the functionality of cells like the trafficking of ions. Standard procedures to explore the properties of lipid bilayers and hemifused states typically use supported membranes or vesicles. Both techniques have several shortcomings in […]

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Membrane-Wrapping Contributions to Malaria Parasite Invasion of the Human Erythrocyte

Biophysical Journal, 2014, 107 (1), pp 43–54  http://dx.doi.org/10.1016/j.bpj.2014.05.024

Sabyasachi Dasgupta, Thorsten Auth, Nir S. Gov, Timothy J. Satchwell, Eric Hanssen, Elizabeth S. Zuccala, David T. Riglar, Ashley M. Toye, Timo Betz, Jake Baum, Gerhard Gompper

The blood stage malaria parasite, the merozoite, has a small window of opportunity during which it must successfully target and invade a human erythrocyte. The process of […]

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General model of phospholipid bilayers in fluid phase within the single chain mean field theory

J. Chem. Phys. 140, 174903 (2014)
Yachong Guo, Sergey Pogodin and Vladimir A. Baulin

Coarse-grained model for saturated phospholipids: 1,2-didecanoyl-sn-glycero-3-phosphocholine (DCPC), 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) and unsaturated phospholipids: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2- dioleoyl-sn-glycero-3-phosphocholine (DOPC) is introduced within the single chain mean field theory. A single set of parameters adjusted for DMPC bilayers gives an adequate description […]

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Nanotopography as a trigger for the microscale, autogenous and passive lysis of erythrocytes

J. Mater. Chem. B, 2 (19), 2785-2948 (2014)
Vy T. H. Pham, Vi Khanh Truong, David E. Mainwaring, Yachong Guo, Vladimir Baulin, Mohammad Al Kobaisi,   Gediminas Gervinskas, Saulius Juodkazis, Wendy R. Zeng, Pauline Doran, Russell J Crawford and Elena P. Ivanova

Microscale devices are increasingly being developed for diagnostic analysis although conventional lysis as an initial step presents […]

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Physical Damage on Giant Vesicles Membrane as a Result of Methylene Blue Photoirradiation

Biophys. J. 106 (1), 162-71 (2014)
Omar Mertins, Isabel O.L. Bacellar, Fabrice Thalmann, Carlos M. Marques, Maurício S. Baptista, Rosangela Itri
In this study we pursue a closer analysis of the photodamage promoted on giant unilamellar vesicles membranes made of dioleoyl-sn-glycero-3-phosphocholine (DOPC) or 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), by irradiating methylene blue present in the giant unilamellar vesicles solution. By means […]

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Shape and orientation matter for cellular uptake of non-spherical nanoparticles

Nano Lett., 2014, 14 (2), pp 687–693 DOI: 10.1021/nl403949h

Sabyasachi Dasgupta , Thorsten Auth , and Gerhard Gompper
Recent advances in nano-technology have made a whole zoo of particles of different shapes available for applications, but their interaction with biological cells and their toxicity is often not well understood. Experiments have shown that particle uptake by cells […]

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Lipid oxidation induces structural changes in biomimetic membranes

Soft Matter, 10, 4241-4247 (2014)
G. Weber, T. Charitat, M. S. Baptista, A. F. Uchoa, C. Pavani, H. C. Junqueira, Y. Guo, V. A. Baulin, R. Itri, C. M. Marques, A. P. Schroder

Oxidation can intimately influence and structurally compromise the levels of biological self-assembly embodied by intracellular and plasma membranes. Lipid peroxidation, a natural metabolic outcome of […]

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Bactericidal activity of black silicon

Nature Comm., 4, 2838 (2013)
E. P. Ivanova, J. Hasan, H. K. Webb, G. Gervinskas, S. Juodkazis, Vi K. Truong, A. H. F. Wu, R. N. Lamb, V. A. Baulin, G. S. Watson, J. A. Watson, D. E. Mainwaring, R. J. Crawford

 Black silicon is a synthetic nanomaterial that contains high aspect ratio nanoprotrusions on its surface, produced through a simple reactive-ion etching technique for use in photovoltaic applications. Surfaces with high […]

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Selective bactericidal activity of nanopatterned superhydrophobic cicada Psaltoda claripennis wing surfaces

Appl Microbiol Biotechnol., 97 (20), 9257-9262 (2013)
Jafar Hasan, Hayden K. Webb, Vi Khanh Truong, Sergey Pogodin, Vladimir A. Baulin, Gregory S. Watson, Jolanta A. Watson, Russell J. Crawford, Elena P. Ivanova
The nanopattern on the surface of Clanger cicada (Psaltoda claripennis) wings represents the first example of a new class of biomaterials that can kill bacteria on contact […]

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IPEC Solver: Numerical simulation tool to study inter-polyelectrolyte complexation

Comp. Phys. Comm., 184 (9), 2221–2229 (2013)
B. Huang and V.A. Baulin

IPEC Solver is a Windows program designed to analyze the stability of core–shell inter-polyelectrolyte complexes formed by complexation of oppositely charged block copolymers. The two-dimensional size distribution of the complexes composed by different numbers of positively or negatively charged polyelectrolytes is calculated based on the […]

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Bacterial attachment on sub-nanometrically smooth titanium substrata

Biofouling, 29 (2), 163-170 (2013)
H.K. Webb, V. Boshkovikj, C.J. Fluke, V.K. Truong, J. Hasan, V.A. Baulin, R. Lapovok, Y. Estrin, R.J. Crawford and E.P. Ivanova
Despite the volume of work that has been conducted on the topic, the role of surface topography in mediating bacterial cell adhesion is not well understood. The primary reason for this lack of […]

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The Capacitance and Electromechanical Coupling of Lipid Membranes Close to Transitions: The Effect of Electrostriction

Thomas Heimburg

Biophys. J., 103 (5), 918–929 (2012)

Biomembranes are thin capacitors with the unique feature of displaying phase transitions in a physiologically relevant regime. We investigate the voltage and lateral pressure dependence of their capacitance close to their chain melting transition. Because the gel and the fluid membrane have different area and thickness, the capacitance of […]

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Dual modes of antitumor action of an amphiphilic peptide A9K

Hai Xu, Cui Xia Chen, Jing Hua, Peng Zhou, Ping Zeng, Chang Hai Cao, Jian Ren Lu
Biomaterials, 34, 2731-2737 (2013)
Following our recent report of attractive antibacterial properties of a designed amphiphilic peptide, A9K, we have investigated its antitumor activities by examining the modes of its action against different mammalian cell types. The peptide strongly inhibited […]

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Wrapping of ellipsoidal nano-particles by fluid membranes

Sabyasachi Dasgupta, Thorsten Autha, Gerhard Gompper

Soft Matter, 9, 5473-5482 (2013)

Membrane budding and wrapping of particles, such as viruses and nano-particles, play a key role in intracellular transport and have been studied for a variety of biological and soft matter systems. We study nano-particle wrapping by numerical minimization of bending, surface tension, and adhesion energies. We […]

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Size- and coating-dependent uptake of polymer-coated gold nanoparticles in primary human dermal microvascular endothelial cells

Christian Freese, Matthew I. Gibso, Harm-Anton Klok, Ronald E. Unger, C. James Kirkpatrick

Biomacromolecules, 13 (5), pp 1533–1543 (2012)

A library-orientated approach is used to gain understanding of the interactions of well-defined nanoparticles with primary human endothelial cells, which are a key component of the vasculature. Fifteen sequentially modified gold nanoparticles (AuNPs) based on three different core […]

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Interactions of silica nanoparticles with lung epithelial cells and the association to flotillins

Jennifer Kasper, Maria I. Hermanns, Christoph Bantz, Olga Koshkina, Thomas Lang, Michael Maskos, Christine Pohl, Ronald E. Unger, C. James Kirkpatrick

Arch. Toxicol., 6 (2012)

Amorphous silica nanoparticles (aSNPs) gain increasing popularity for industrial and therapeutic claims. The lung with its surface area of 100–140 m2 displays an ideal target for therapeutic approaches, but it represents also […]

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Uptake and cytotoxicity of citrate-coated gold nanospheres: Comparative studies on human endothelial and epithelial cells

Christian Freese, Chiara Uboldi, Matthew I Gibson, Ronald E Unger, Babette B Weksler, Ignacio A Romero, Pierre-Olivier Couraud, C J Kirkpatrick

Part Fibre Toxicol., 9, 23 (2012)

BACKGROUND:
The use of gold nanoparticles (AuNPs) for diagnostic applications and for drug and gene-delivery is currently under intensive investigation. For such applications, biocompatibility and the absence of cytotoxicity of AuNPs […]

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Diblock copolymer–selective nanoparticle mixtures in the lamellar phase confined between two parallel walls: a mean field model

Lenin S. Shagolsem, Jens-Uwe Sommer
Soft Matter, 8, 11328-11335 (2012)
We present a mean field model for a mixture of AB diblock-copolymers and A-block selective nanoparticles confined between two identical non-selective walls. A horizontally symmetric lamellar structure of the nanocomposite is considered where nanoparticles are allowed to segregate between the polymer–wall interfaces. For a fixed value of […]

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Mechanisms of Vesicle Spreading on Surfaces: Coarse-Grained Simulations

Marc Fuhrmans, Marcus Müller

Langmuir, 29 (13), pp 4335–4349 (2013)

Exposition of unilamellar vesicles to attractive surfaces is a frequently used way to create supported lipid bilayers. Although this approach is known to produce continuous supported bilayer coatings, the mechanism of their formation and its dependence on factors like surface interaction and roughness or membrane tension as […]

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Exploring thermodynamic stability of the stalk fusion-intermediate with three-dimensional self-consistent field theory calculations

Kostas Ch. Daoulas, Marcus Müller

Soft Matter, 9, 4097-4102 (2013)

The prospects of compressible Self-Consistent Field (SCF) theory schemes for describing structures in amphiphilic membranes are illustrated by considering the thermodynamic stability of hourglass-shaped, hydrophobic connections (stalks) between apposed bilayers. The membranes are represented by a coarse-grained, solvent-free model. We represent the chain architecture […]

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Biophysical Model of Bacterial Cell Interactions with Nanopatterned Cicada Wing Surfaces

S. Pogodin, J. Hasan, V.A. Baulin, H.K. Webb, V.K. Truong, T.H.P. Nguyen, V. Boshkovikj, C.J. Fluke, G.S. Watson, J.A. Watson, R.J. Crawford and E.P. Ivanova

Biophys. J., 104 (4), 835-840 (2013)

The nanopattern on the surface of Clanger cicada (Psaltoda claripennis) wings represents the first example of a new class of biomaterials that can kill bacteria […]

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Nanoparticle-Induced Permeability of Lipid Membranes

Sergey Pogodin, Marco Werner, Jens-Uwe Sommer, Vladimir A. Baulin

ACS Nano, DOI: 10.1021/nn3028858 (2012)

Monte Carlo simulations using the bond fluctuation method with explicit solvent reveal the mechanism of enhanced permeability of lipid bilayers induced by the adsorption of nanoparticles with controlled hydrophobicity. Simulation results indicate an adsorption transition of nanoparticles on the bilayer in a […]

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Poly-ethylene glycol induced super-diffusivity in lipid bilayer membranes

Thibault Tabarin, Aaron Martin, Robert J. Forster and Tia E. Keyes

Soft Matter, 8, 8743-8751 (2012)

Fluorescence lifetime correlation spectroscopy (FLCS) has been used to probe the influence of PEG-8000 on the fluidity of fluorescently labeled planar supported lipid bilayers on ozone plasma treated glass. The lipid membrane compositions examined were; DOPC, DOPC/DOPS (80/20 mol/mol) […]

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Transition Path from Two Apposed Membranes to a Stalk Obtained by a Combination of Particle Simulations and String Method

Marcus Müller, Yuliya G. Smirnova, Giovanni Marelli, Marc Fuhrmans, and An-Chang Shi

Phys. Rev. Lett. 108, 228103 (2012)

The formation of an hourglass-shaped passage (stalk) connecting two apposed membranes is an essential initial step in membrane fusion. The most probable transition path from two separate membranes to a stalk, i.e., the minimum free-energy path (MFEP), is […]

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Line-Tension Controlled Mechanism for Influenza Fusion

Herre Jelger Risselada, Giovanni Marelli, Marc Fuhrmans, Yuliya G. Smirnova, Helmut Grubmüller, Siewert Jan Marrink, Marcus Müller

PLoS ONE 7(6): e38302 (2012)

Our molecular simulations reveal that wild-type influenza fusion peptides are able to stabilize a highly fusogenic pre-fusion structure, i.e. a peptide bundle formed by four or more trans-membrane arranged fusion peptides. We rationalize that the […]

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Homo-polymers with balanced hydrophobicity translocate through lipid bilayers and enhance local solvent permeability

Marco Werner, Jens-Uwe Sommer and Vladimir A. Baulin

Soft Matter, 8, 11708-11716 (2012)

Recent experimental studies indicate that polymeric structures with a well-adjusted balance of amphiphilic parts may translocate through self-assembled phospholipid bilayers and enhance the passive trans-membrane transport of smaller molecules. Using a coarse grained lattice Monte Carlo model with explicit solvent we investigate self-assembled lipid […]

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Molecular mechanisms of antibacterial and antitumor actions of designed surfactant-like peptides

Cuixia Chen, Jing Hu, Shengzhong Zhang, Peng Zhou, Xichen Zhao, Hai Xu, Xiubo Zhao, Mohammed Yaseen, Jian R. Lu

Biomaterials, 33 (2), 592–603 (2012)

Biomimicry of antimicrobial peptides secreted by innate immune systems represents a major strategy in developing novel antibacterial treatments. There are however emerging concerns over the possible compromise of host natural defenses by these […]

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Manipulation and sorting of membrane proteins using patterned diffusion-aided ratchets with AC fields in supported lipid bilayers

Matthew R. Cheetham, Jonathan P. Bramble, Duncan G. G. McMillan, Richard J. Bushby, Peter D. Olmsted, Lars J. C. Jeuken and Stephen D. Evans

Soft Matter, 2012,8, 5459-5465

We present ratchets capable of directing the movement of charged components within supported bilayer lipid membranes. These ratchets make use of asymmetrically patterned features […]

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Natural Bactericidal Surfaces: Mechanical Rupture of Pseudomonas aeruginosa Cells by Cicada Wings

Elena P. Ivanova, Jafar Hasan, Hayden K. Webb, Vi Khanh Truong, Gregory S. Watson, Jolanta A. Watson, Vladimir A. Baulin, Sergey Pogodin, James Y. Wang, Mark J. Tobin, Christian Löbbe, Russell J. Crawford

Small, 8 (16), 2489 – 2494 (2012)

Natural superhydrophobic surfaces are often thought to have antibiofouling potential due to their self-cleaning properties. However, when […]

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Self-assembly of spherical interpolyelectrolyte complexes from oppositely charged polymers

V. A. Baulin and E. Trizac
Soft Matter, 8 (25), 6755 – 6766 (2012)
The formation of inter-polyelectrolyte complexes from the association of oppositely charged polymers in an electrolyte is studied. The charged polymers are linear oppositely charged polyelectrolytes, with possibly a neutral block. This leads to complexes with a charged core, and a more dilute corona […]

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Critical adsorption controls translocation of polymer chain through lipid bilayers and permeation of solvent

J.-U. Sommer, M. Werner and V. A. Baulin

Europhysics Letters, 98, 18003 (2012)

Monte Carlo simulations using an explicit solvent model indicate a new pathway for translocation of a polymer chain through a lipid bilayer. We consider a polymer chain composed of repeat units with a given hydrophobicity and a coarse-grained model of a lipid bilayer in […]

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Degradation versus self-assembly of block copolymer micelles

A. Muratov and V. A. Baulin

Langmuir, 28, 3071-3076 (2012)

The stability of micelles self-assembled from block co-polymers can be altered by the degradation of the blocks. Slow degradation shifts the equilibrium size distribution of block co-polymer micelles and changes their properties. The quasi-equilibrium scaling theory shows that the degradation of hydrophobic blocks in the core of […]

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Biomolecule Surface Patterning May Enhance Membrane Association

S. Pogodin, N. K. H. Slater and V. A. Baulin

ACS Nano, 6(2), 1308-1313 (2012)

Under dehydration conditions, amphipathic late embryogenesis abundant proteins fold spontaneously from a random conformation into α-helical structures, and this transition is promoted by the presence of membranes. To gain insight into the thermodynamics of membrane association, we model the resulting α-helical structures […]

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