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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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) […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]