Research

Nanomaterial interactions with biomembranes: Bridging the gap between soft matter models and biological context

Biointerphases 13, 028501 (2018); https://doi.org/10.1116/1.5022145
M. Werner, T. Auth, P. A. Beales, J. B. Fleury, F. Höök, H. Kress, R. C. Van Lehn, M. Müller, E. P. Petrov, L. Sarkisov, J.-U. Sommer and V. A. Baulin
Synthetic polymers, nanoparticles, and carbon-based materials have great potential in applications including drug delivery, gene transfection, in vitro and in vivo imaging, and […]

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Formation and Stabilization of Pores in Bilayer Membranes by Peptide-like Amphiphilic Polymers

Soft matter, 2018, DOI: 10.1039/C7SM02404E,
Ankush Checkervarty, Marco Werner, and Jens Uwe Sommer
We study pore formation in models of lipid-bilayer membranes interacting with amphiphilic copolymers mimicking anti-microbial peptides using Monte Carlo simulations and we rationalize our results by a simple brush-model for the fluid membrane. In our study a weak tension on the membrane is required […]

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Formation and Stabilization of Pores in Bilayer Membranes by Peptide-like Amphiphilic Polymers

Soft matter, 2018, DOI: 10.1039/C7SM02404E, Ankush Checkervarty, Marco Werner, and Jens Uwe Sommer. We study pore formation in models of lipid-bilayer membranes interacting with amphiphilic copolymers mimicking anti-microbial peptides using Monte Carlo simulations and we rationalize our results by a simple brush-model for the fluid membrane. In our study a weak tension on the membrane […]

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Subtle Variations in Surface Properties of Black Silicon Surfaces Influence the Degree of Bactericidal Efficiency

Nano-Micro Lett., 10, 36 (2018)
Chris M. Bhadra, Marco Werner, Vladimir A. Baulin, Vi Khanh Truong, Mohammad Al Kobaisi, Song Ha Nguyen, Armandas Balcytis, Saulius Juodkazis, James Y. Wang, David E. Mainwaring, Russell J. Crawford, Elena P. Ivanova
One of the major challenges faced by the biomedical industry is the development of robust synthetic surfaces that can resist […]

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Influence of a pH-sensitive polymer on the structure of monoolein cubosomes

Soft Matter, 13, 7571-7577 (2017)
Monika Kluzek, Arwen I. I. Tyler, Shiqi Wang, Rongjun Chen, Carlos M. Marques, Fabrice Thalmann, John M. Seddon, Marc Schmutz
Cubosomes consist in submicron size particles of lipid bicontinuous cubic phases stabilized by surfactant polymers. They provide an appealing road towards the practical use of lipid cubic phases for pharmaceutical and cosmetic […]

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Influence of Acyl Chain Saturation on the Membrane-Binding Activity of a Short Antimicrobial Peptide

ACS Omega, 2(11) 7482–7492 (2017)
Daniela Ciumac, Richard A. Campbell, Luke A. Clifton, Hai Xu∥ , Giovanna Fragneto, and Jian R. Lu
Different bacterial types and their living environments can lead to different saturations in the chains of their membrane lipids. Such structural differences may influence the efficacy of antibiotics that target bacterial membranes. In this work, […]

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The Effect of Coatings and Nerve Growth Factor on Attachment and Differentiation of Pheochromocytoma Cells

Materials, 11(1) 60 (2018)
Anna Orlowska, Pallale Tharushi Perera, Mohammad Al Kobaisi, Andre Dias,
Huu Khuong Duy Nguyen, Shahram Ghanaati, Vladimir A. Baulin, Russell J. Crawford, Elena P. Ivanova
Cellular attachment plays a vital role in the differentiation of pheochromocytoma (PC12) cells. PC12 cells are noradrenergic clonal cells isolated from the adrenal medulla of Rattus norvegicus and studied extensively […]

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Understanding the interactions between sebum triglycerides and water: a molecular dynamics simulation study

Phys. Chem. Chem. Phys., (2017)
Anna Sofia Tascini, Massimo Noro, Rongjun Chen, John Seddon and Fernando Bresme
In recent years, the sebum oil has been found to play a key role in the regulation of the hydration of the outermost layer of the skin, the stratum corneum. Understanding how a major component of the sebum oil, the triglyceride […]

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Sugar-based collagen membrane cross-linking increases barrier capacity of membranes

Clin. Oral Invest.,  (2017)
Po-ju Chia-LaiAnna OrlowskaSarah Al-MaawiAndre DiasYunxin ZhangXuejiu WangNiklas ZenderRobert SaderC. James KirkpatrickShahram Ghanaati
This study examines the permeability and barrier capacity of a sugar cross-linked resorbable collagen membrane ex vivo and in vivo. In an ex vivo study, injectable platelet-rich fibrin (i-PRF), a peripheral blood-derived human leukocyte-and-platelet-rich plasma was used to analyze membrane permeability. […]

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Reduction of the relative centrifugal force influences cell number and growth factor release within injectable PRF-based matrices

J Mater Sci: Mater Med, 28, 188 (2017)
Simon Wend, Alica Kubesch, Anna Orlowska, Sarah Al-Maawi, Niklas Zender, Andre Dias, Richard J. Miron, Robert Sader, Patrick Booms, C. James Kirkpatrick, Joseph Choukroun, Shahram Ghanaati
Platelet rich fibrin (PRF) is a blood concentrate system obtained by centrifugation of peripheral blood. First PRF matrices exhibited solid fibrin scaffold, more recently […]

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Bactericidal activity of self-assembled palmitic and stearic fatty acid crystals on highly ordered pyrolytic graphite

Acta Biomaterialia, 59, 148-157 (2017).
Elena P. Ivanova, Song Ha Nguyen, Yachong Guo, Vladimir A. Baulin, Hayden K. Webb, Vi Khanh Truong, Jason V. Wandiyanto, Christopher J. Garvey, Peter
J. Mahon, David E. Mainwaring, Russell J. Crawford
The wings of insects such as cicadas and dragonflies have been found to exhibit nanostructure arrays that are assembled from fatty acids, […]

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Nanoparticles of Various Degrees of Hydrophobicity Interacting with Lipid Membranes

J. Phys. Chem. Lett., 8, 4069–4076 (2017).
Chan-Fei Su, Holger Merlitz, Hauke Rabbel, and Jens-Uwe Sommer
Using coarse-grained molecular dynamics simulations, we study the passive translocation of nanoparticles with a size of about 1 nm and with tunable degrees of hydrophobicity through lipid bilayer membranes. We observe a window of translocation with a sharp maximum for nanoparticles […]

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In vivo cellular reactions to different biomaterials—Physiological and pathological aspects and their consequences

Seminars in Immunology, DOI: 10.1016/j.smim.2017.06.001 (2017).
Sarah Al-Maawi, Anna Orlowska, Robert Sader, C. James Kirkpatrick, Shahram Ghanaati
Biomaterials are widely used in guided bone regeneration (GBR) and guided tissue regeneration (GTR). After application, there is an interaction between the host immune system and the implanted biomaterial, leading to a biomaterial-specific cellular reaction. The present review focuses on […]

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Apatite nanoparticles strongly improve red blood cell cryopreservation by mediating trehalose delivery via enhanced membrane permeation

Biomaterials, 140, 138-149 (2017).
Martin Stefanic, Kevin Ward, Harvey Tawfik, Ralf Seemann, Vladimir Baulin, Yachong Guo, Jean-Baptiste Fleury, Christophe Drouet
Cryopreservation of red blood cells (RBC) is an important method for maintaining an inventory of rare RBC units and managing special transfusion circumstances. Currently, in a clinical setting, glycerol is used as cryoprotectant against freezing damage. After […]

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Implications of lipid monolayer charge characteristics on their selective interactions with a short antimicrobial peptide

Colloids and Surfaces B, 150, 308–316 (2017).
Daniela Ciumac, Richard A. Campbell, Hai Xu, Luke A. Clifton, Arwel V. Hughes, John R.P. Webster, Jian R. Lu
Many antimicrobial peptides (AMPs) target bacterial membranes and they kill bacteria by causing structural disruptions. One of the fundamental issues however lies in the selective responses of AMPs to different cell […]

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pH-Responsive, Lysine-Based, Hyperbranched Polymers Mimicking Endosomolytic Cell-Penetrating Peptides for Efficient Intracellular Delivery

Chem. Mater., DOI: 10.1021/acs.chemmater.7b00054 (2017).
Shiqi Wang and Rongjun Chen
The insufficient delivery of biomacromolecular therapeutic agents into the cytoplasm of mammalian cells remains a major barrier to their pharmaceutical applications. Cell-penetrating peptides (CPPs) are considered as potential carriers for cytoplasmic delivery of macromolecular drugs. However, due to the positive charge of most CPPs, strong non-specific cell […]

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GPU implementation of the Rosenbluth generation method for static Monte Carlo simulations

Computer Physics Communications, 216, 95–101(2017).
Yachong Guo, Vladimir A. Baulin
We present parallel version of Rosenbluth Self-Avoiding Walk generation method implemented on Graphics Processing Units (GPUs) using CUDA libraries. The method scales almost linearly with the number of CUDA cores and the method efficiency has only hardware limitations. The method is introduced in two realizations: on a […]

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The susceptibility of Staphylococcus aureus CIP 65.8 and Pseudomonas aeruginosa ATCC 9721 cells to the bactericidal action of nanostructured Calopteryx haemorrhoidalis damselfly wing surfaces

Appl Microbiol Biotechnol (2017). doi:10.1007/s00253-017-8205-9
Vi Khanh Truong, Nipuni Mahanamanam Geeganagamage, Vladimir A. Baulin, Jitraporn Vongsvivut, Mark J. Tobin, Pere Luque, Russell J. Crawford, Elena P. Ivanova
Nanostructured insect wing surfaces have been reported to possess the ability to resist bacterial colonization through the mechanical rupture of bacterial cells coming into contact with the surface. In this […]

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Dynamic studies of the interaction of a pH responsive, amphiphilic polymer with a DOPC lipid membrane

Soft Matter, 13, 3690-3700 (2017)
Sivaramakrishnan Ramadurai, Marco Werner, Nigel K.H. Slater, Aaron Martin, Vladimir A. Baulin, Tia Keyes
Deeper understanding of the molecular interactions between polymeric materials and the lipid membrane is important across a range of applications from permeation for drug delivery to encapsulation for immuno-evasion. Using highly fluidic microcavity supported lipid bilayers, we studied […]

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Membrane-Anchoring, Comb-Like Pseudopeptides for Efficient, pH-Mediated Membrane Destabilization and Intracellular Delivery

ACS Appl. Mater. Interfaces, Article ASAP (2017)
Siyuan Chen, Shiqi Wang, Michal Kopytynski, Marie Bachelet, and Rongjun Chen
Endosomal release has been identified as a rate-limiting step for intracellular delivery of therapeutic agents, in particular macromolecular drugs. Herein, we report a series of synthetic pH-responsive, membrane-anchoring polymers exhibiting dramatic endosomolytic activity for efficient intracellular delivery. The comb-like […]

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Thermal Tunneling of Homopolymers through Amphiphilic Membranes

ACS Macro Lett., 6, pp 247–251 (2017)
Marco Werner, Jasper Bathmann, Vladimir A. Baulin, and Jens-Uwe Sommer
We propose a theory to predict the passive translocation of flexible polymers through amphiphilic membranes. By using a generic model for the potential felt by a monomer across the membrane we calculate the free energy profile for homopolymers as a function […]

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Thermal transport across nanoparticle-fluid interfaces: the interplay of interfacial curvature and nanoparticle-fluid interactions

Phys. Chem. Chem. Phys. (2016)
Anna Sofia Tascini,   Jeff Armstrong,   Eliodoro Chiavazzo,   Matteo Fasano,   Pietro Asinari and    Fernando Bresme

We investigate the general dependence of the thermal transport across nanoparticle-fluid interfaces using molecular dynamics computations. We show that the thermal conductance depends strongly both on the wetting characteristics of the nanoparticle-fluid interface […]

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Direct proof of spontaneous translocation of lipid-covered hydrophobic nanoparticles through a phospholipid bilayer

Science Advances 2 (11), e1600261 (2016)
Yachong Guo, Emmanuel Terazzi, Ralf Seemann, Jean Baptiste Fleury and Vladimir A. Baulin

Hydrophobic nanoparticles introduced into living systems may lead to increased toxicity, can activate immune cells, or can be used as nanocarriers for drug or gene delivery. It is generally accepted that small hydrophobic nanoparticles are blocked by lipid bilayers and accumulate in the […]

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Pure Protein Bilayers and Vesicles from Native Fungal Hydrophobins

Advanced Materials: 10.1002/adma.201602888 (2016)
H. Hähl, J. Nabor Vargas, A. Griffo, P. Laaksonen, G. Szilvay, M. Lienemann, K. Jacobs, R. Seemann, J.-B. Fleury

Pure protein bilayers and vesicles are formed using the native, fungal hydrophobin HFBI. Bilayers with hydrophobic (red) and hydrophilic (blue) core are produced and, depending on the type of core, vesicles in water, oily […]

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Adsorption of Human Plasma Albumin and Fibronectin onto Nanostructured Black Silicon Surfaces

Langmuir: 10.1021/acs.langmuir.6b02601 (2016)
Duy H. K. Nguyen, Vy T. H. Pham, Mohammad Al Kobaisi, Chris M. Bhadra, Anna Orlowska, Shahram Ghanaati, Berardo Mario Manzi, Vladimir A Baulin, Saulius Juodkazis, Peter Kingshott, Russell J Crawford, and Elena P. Ivanova

The protein adsorption of two human plasma proteins, albumin (Alb) and fibronectin (Fn) onto synthetic nanostructured bactericidal material, black silicon […]

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“Race for the surface”: eukaryotic cells can win

ACS Appl. Mater. Interfaces: 8(34) 22025-22031 (2016)
Vy T. H. Pham, Vi Khanh Truong, Anna Orlowska, Shahram Ghanaati, Mike Barbeck, Patrick Booms, Alex James Fulcher, Chris M. Bhadra, Ricardas Buividas, Vladimir A Baulin, Charles James Kirkpatrick, Pauline Doran, David E. Mainwaring, Saulius Juodkazis, Russell J Crawford, and Elena P. Ivanova

With an aging population and the consequent […]

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The Bioeffects Resulting from Prokaryotic Cells and Yeast Being Exposed to an 18 GHz Electromagnetic Field

PLoS ONE 11(7): e0158135 (2016)
The Hong Phong Nguyen , Vy T. H. Pham , Song Ha Nguyen , Vladimir A. Baulin, Rodney J. Croft, Brian Phillips, Russell J. Crawford, Elena P. Ivanova

The mechanisms by which various biological effects are triggered by exposure to an electromagnetic field are not fully understood and have been the subject […]

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Amino Acid Based Hydrogels with Dual Responsiveness for Oral Drug Delivery

Macromol. Biosci. (2016)
Shiqi Wang, Xiaoxue Liu, Ignacio J. Villar-Garcia and Rongjun Chen

This study reports a series of novel amino acid based dual-responsive hydrogels. Prepared by a facile one-pot 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) coupling reaction, the solid content, structure, and mechanical behavior of hydrogels could be easily adjusted by changing the concentrations of the polymers and the crosslinkers. With pH-responsive anionic pseudo-peptides […]

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Peroxidised phospholipid bilayers: insight from Coarse-Grained Molecular Dynamics simulations

Soft Matter, 12, 263-271 (2016)
Yachong Guo, Vladimir Baulin and Fabrice Thalmann

An original coarse-grained model for peroxidised phospholipids is presented, based on the MARTINI lipid force field. This model results from a combination of thermodynamic modelling and structural information on the area per lipid, which have been made available recently. The resulting coarse-grained lipid molecules form stable bilayers, […]

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Self-organised nanoarchitecture of titanium surfaces influences the attachment of Staphylococcus aureus and Pseudomonas aeruginosa bacteria

Applied Microbiology and Biotechnology (2015) 99 (16), 6831-6840 DOI: 10.1007/s00253-015-6572-7
Vi K. Truong, Vy T. H. Pham, A. Medvedev, R. Lapovok, Y. Estrin, T. C. Lowe, V. Baulin, V. Boshkovikj, C. J. Fluke, R. J. Crawford, E. P. Ivanova

The surface nanotopography and architecture of medical implant devices are important factors that can control the extent of bacterial attachment. The ability to prevent bacterial attachment […]

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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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