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Post-doc position in Fluid flows shaping morphology

The Max Planck Institute for Dynamics and Self-Organization at Göttingen, Germany, is an international research institute. It performs both experimental and theoretical fundamental scientific research and currently employs about 300 people.
Project: We are looking for excellent, highly motivated early-career researchers to join our research team. We offer a highly international, interdisciplinary and collaborative environment in […]

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PhD in multiscale mechanisms of evolutionary dynamics in microbes

The Theoretical Biology Group at ETH Zurich is hiring a Ph.D. student to study multiscale mechanisms of evolutionary dynamics in microbes.  We will begin reviewing applications on November 15, 2018.  For more information on the position and how to apply, please follow the link:

https://www.ethz.ch/content/dam/ethz/special-interest/usys/ibz/theoreticalbiology/group/job_9-2018.pdf

Please feel free to pass this information along to others who may […]

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Kinetic evolution of DOPC lipid bilayers exposed to α-cyclodextrins

Soft Matter, , (2018)
Monika Kluzek, Marc Schmutz, Carlos M. Marques and Fabrice Thalmann
Cyclodextrins are cyclic oligosaccharides capable of forming inclusion complexes with a variety of molecules, and as such have been recognized as a pharmaceutical and biotechnological asset. Cyclodextrins are known to interact with the components of cell membranes, and this correlates with a significant […]

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Antioxidant modified amphiphilic polymer improves intracellular cryoprotectant delivery and alleviates oxidative stress in HeLa cells

Adv Mater Sci, DOI: 10.15761/AMS.1000131 (2017)
Alexander Chen, Sergio A Mercado, Nigel KH Slater
The design and synthesis of a dual-function, cell permeating polymer with an antioxidative property is described and its use for the intracellular delivery of the cryoprotectant trehalose into HeLa cells is demonstrated. The polymer, PVitE-25, was created by grafting the water insoluble hydrophobic […]

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DPPC Bilayers in Solutions of High Sucrose Content

Biophysical J, 114(9), 2165–2173 (2018)
Mattia I. Morandi, Mathieu Sommer, Monika Kluzek, Fabrice Thalmann, André P. Schroder, Carlos M. Marques
The properties of lipid bilayers in sucrose solutions have been intensely scrutinized over recent decades because of the importance of sugars in the field of biopreservation. However, a consensus has not yet been formed on the mechanisms […]

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Variable resolution algorithms for macromolecular simulations

Two postdoc positions are available in the framework of the ERC StG project VARIAMOLS – Variable resolution algorithms for macromolecular simulations. A postdoc researcher is sought for a 2-years long project involving deep neural network—based method development and applications in the context of macromolecular modelling and simulation. Candidates with background in physics, chemistry, biology, and […]

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Variable resolution algorithms for macromolecular simulations

TwoPhD positions are available in the framework of the ERC StG project VARIAMOLS – Variable resolution algorithms for macromolecular simulations. The successful candidates will work on the development and application of computational methods for the study of large macromolecules – e.g. proteins and DNA. The research projects aim at the design, implementation, and application of […]

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Microfluidic flow of biomimetic tissues

The University of Montpellier offers three PhD grants to carry on a PhD in Physics in the Laboratory of Charles Coulomb (L2C), starting on October 2018 and for a duration of three years.
Project description: 
During embryogenesis, tissues and organs develop through cell differentiation and reorganization. Individual and collective motion of cells leads to a flow tissue, […]

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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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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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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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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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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 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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Summer School in Roccalumera

With the sound of waves breaking on the sand, a new generation of scientists was learning, questioning, and interacting with their peers. Such a social experience is always fruitful because it helps people to understand each other and create unique moments which will be remembered.
The summer school in Roccalumera (Sicily, Italy) aimed to bring together […]

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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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Roccalumera: ITN SNAL Summer School on biomaterials, cell membranes and lipid bilayers 2015

ITN SNAL Summer School on biomaterials, cell membranes and lipid bilayers is organized within the scope of training events of Initial Training Network SNAL funded by European Union through Marie Skłodowska-Curie actions. The summer school will be held at the Main Palace Hotel, a 4-star superior hotel in Taormina, Sicily from 24 July to 2 […]

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Roccalumera: Soft Interaction in Bio-Nanostructures

From Modeling to Advanced Applications
Date: 23 July 2015
Location:  Main Palace Hotel, Roccalumera, Sicily (near Taormina) – Italy
Satellite Event of ITN-SNAL Summer School on Biomaterials, Cell Membranes and Bilayers 24 July – 2 August 2015

This workshop will bring together researchers working in different fields of Nanoscience and Biotechnology and is an opportunity to discuss the existing and novel approaches in Modeling, Fabrication, […]

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Fluoresce-Activated Cell Sorting (FACS)

Flow cytometry is a laser-based biophysical technology employed in cell counting, cell sorting, and biomarker detection. Cells or materials are suspended in a stream of fluid and passed through the electronic detection apparatus. The equipment allows simultaneous multiparametric analysis of physical and chemical characteristics up to thousands of particles per second.

Fluorescence-activated cell sorting (FACS) is […]

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Gel permeation chromatography/ Size exclusion chromatography

Gel permeation chromatography (GPC)/ Size exclusion chromatography (SEC) is a widely used technique for  measuring the molecular weight and molecular weight distribution of natural and synthetic polymers. It is based on  liquid chromatographic techniques that separate individual polymer chains on the basis of their size in solution and not on their chemical properties. The separation […]

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Association of polymers and small solute molecules with phospholipid membranes

Theoretical physics, theory in soft matter, computer simulations

Objectives
In many cases the properties of cell membranes are modified through biopolymers and small solute molecules such as anesthetics or neurotransmitters. They can associate to membranes and significantly alter their structure, either thermodynamic state or induce reorganization in form of pores. The project aims to describe the fundamental […]

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Monika Kluzek

Electron microscopy of vesicles interacting with nano-objects

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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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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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Advanced School in Soft Condensed Matter ‘Solutions in the Spring’ 2014

on

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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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ESR5-L: Synthesis and characterization of functional biomimetic polymers for intracellular delivery

Chemical synthesis, characterisation of polymers and nano-objects
Objectives
This project is focused on development of functional biomimetic polymers which can traverse across cellular membranes to deliver payloads into the cell interior.

Synthesis and characterization of pH-responsive, membrane-active polymers.
Preparation of therapeutic nanoparticles incorporating chemotherapeutic agents or biological molecules.
Understanding and controlling of the trafficking of polymers into a model cellular […]

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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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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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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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Jian Lu

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Self-consistent field theory of brushes of neutral water-soluble polymers

V.A. Baulin, E.B. Zhulina, A. Halperin
J. Chem. Phys., 119, 2874 (2003)
The self-consistent field theory of brushes of neutral water-soluble polymers described by two-state models is formulated in terms of the effective Flory interaction parameter χeff(T,ϕ) that depends on both temperature, T, and the monomer volume fraction, ϕ. The concentration profiles, distribution of free ends and […]

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Tension-Induced Translocation of Ultra-Short Carbon Nanotube through a Phospholipid Bilayer

ACS Nano, November (2018)
Yachong Guo, Marco Werner, Ralf Seemann, Vladimir A Baulin, and Jean-Baptiste Fleury
Increasing awareness of bioeffects and toxicity of nanomaterials interacting with cells puts in focus the mechanisms by which nanomaterials can cross lipid membranes. Apart from well-discussed energy-dependent endocytosis for large objects and passive diffusion through membranes by solute molecules, there can […]

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Master/PhD Position: Principles of Biofilm Architecture

We are hiring! You are a Master student? Attracted by interdisciplinary research? Fascinated by biological materials? Join us to study how bacteria design and build their cosy slimy home!
The topic: Biofilms are complex 3D structures, which form as bacteria get embedded in a matrix of self-produced fibers (amyloid and cellulose). Because biofilms are known to […]

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Postdoctoral position in Biological Physics

The BioModeling, BioInformatics & BioProcesses lab of the Free University of Brussels (ULB) invites applications for a postdoctoral research position in the field of biological physics.  The appointment will be initially for a period for 18 months starting between January and March 2019, financed by the FNRS Fund for Scientific Research, with the possibility of […]

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Postdoc position: simulation and modelling of shear-thickening suspensions in Université Grenoble-Alpes, Grenoble, France

We have an opening for a 18-month postdoctoral researcher, starting from February 2019, to work on the simulation and modelling of shear-thickening suspensions in Université Grenoble-Alpes, Grenoble, France. The work will be centered on understanding the emergence of instabilities and on modeling the transient interplay between dilation and pore pressure feedback as shear thickening occurs.
The position is funded by […]

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Bridging molecular simulation models and elastic theories for amphiphilic membranes

J. Chem. Phys., 149, 014902 (2018)
Adrien Berthault, Marco Werner, Vladimir A. Baulin
The Single Chain Mean Field theory is used to link coarse-grained models of amphiphilic molecules with analytical models for membrane elasticity, where phenomenological parameters are deduced from explicit molecular models and force fields. We estimate the elastic constants based on the free energy of […]

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