A5049541847- Lipid Membrane Structure and Behavior
- Cell Image Analysis Techniques
- Protein Structure and Dynamics
- Surfactants and Colloidal Systems
- Force Microscopy Techniques and Applications
- Block Copolymer Self-Assembly
- Nuclear physics research studies
- RNA Research and Splicing
- Polymer Surface Interaction Studies
- Advanced Fluorescence Microscopy Techniques
- Topological and Geometric Data Analysis
- Neural dynamics and brain function
- Nanopore and Nanochannel Transport Studies
- Advanced Polymer Synthesis and Characterization
- Nuclear reactor physics and engineering
- Computational Drug Discovery Methods
- Pickering emulsions and particle stabilization
- Bacteriophages and microbial interactions
- Lipid metabolism and biosynthesis
- Advanced Memory and Neural Computing
- Optical Imaging and Spectroscopy Techniques
- Spectroscopy and Quantum Chemical Studies
- Markov Chains and Monte Carlo Methods
- Advanced Neuroimaging Techniques and Applications
- Cellular transport and secretion
École Polytechnique Fédérale de Lausanne
2015-2024
Charles Humbert 8
2020
University of Southern Denmark
2008-2011
Max Planck Institute of Colloids and Interfaces
1996-2009
Max Planck Society
1997-2009
University of Pennsylvania
2005-2006
Simon Fraser University
1986-1993
Michigan State University
1985
National Superconducting Cyclotron Laboratory
1985
The equilibrium structure and lateral stress profile of fluid bilayer membrane patches are investigated using the Dissipative Particle Dynamics simulation technique. Although there no attractive forces between model amphiphiles, they spontaneously aggregate into planar bilayers under suitable conditions concentration amphiphile architecture. Pure single-chain double-chain amphiphiles simulated, architecture interaction parameters varied. We find that a strong chain stiffness potential is...
A DPD model of PEO-based block copolymer vesicles in water is developed by introducing a new density based coarse graining and using experimental data for interfacial tension. Simulated as membrane patch, the excellent agreement with both area expansion modulus scaling hydrophobic core thickness molecular weight. Rupture simulations polymer vesicles, or "polymersomes", are presented to illustrate system sizes feasible DPD. The results should provide guidance theoretical derivations laws also...
DATA REPORT article Front. Neural Circuits, 08 October 2015 Volume 9 - | https://doi.org/10.3389/fncir.2015.00044
The bacterial Shiga toxin interacts with its cellular receptor, the glycosphingolipid globotriaosylceramide (Gb3 or CD77), as a first step to entering target cells. Previous studies have shown that molecules cluster on plasma membrane, despite apparent lack of direct interactions between them. precise mechanism by which this clustering occurs remains poorly defined. Here, we used vesicle and cell systems computer simulations show line tension due curvature, height, compositional mismatch,...
The bacterial Shiga toxin is composed of an enzymatically active A-subunit, and a receptor-binding homopentameric B-subunit (STxB) that mediates intracellular trafficking. Upon STxB-mediated binding to the glycolipid globotriaosylceramide (Gb3) at plasma membrane target cells, internalized by clathrin-dependent independent endocytosis. formation tubular invaginations essential step in clathrin-independent STxB uptake process. However, mechanism which induces these has remained unclear. Using...
The authors introduce a new parameterization for the dissipative particle dynamics simulations of lipid bilayers. In this parameterization, conservative pairwise forces between beads same type in two different hydrophobic chains are chosen to be less repulsive than water-water interaction, but intrachain bead interactions as interaction. For certain range parameters, bilayer can only stretched up 30% before it ruptures. Membrane tension, density profiles, and in-plane diffusion coefficient...
The dynamics of tension-induced fusion two vesicles is studied using dissipative particle (DPD) simulations. vesicle membranes use an improved DPD parameter set that results in their sustaining only a 10-30% relative area stretch before rupturing on the microsecond timescale Two distinct pathways are observed depending initial tensions. In pathway I, at low membrane tension, flattened adhesion zone formed between vesicles, and one subsequently ruptures this contact to form hemifusion state....
Biological membranes are examples of 'smart' materials whose properties and behaviour emerge from the propagation across many scales molecular characteristics their constituents. Artificial smart materials, such as drug delivery vehicles biosensors, often rely on modifying naturally occurring soft matter, polymers lipid vesicles, so that they possess useful behaviour. However, complexity natural membranes, both in static properties, exemplified phase behaviour, dynamic kinetics formation...
Biomolecular condensates play numerous roles in cells by selectively concentrating client proteins while excluding others. These functions are likely to be sensitive the spatial organization of scaffold forming condensate. We use coarse-grained molecular simulations show that model intrinsically-disordered phase separate into a heterogeneous, structured fluid characterized well-defined length scale. The modelled as semi-flexible polymers with punctate, multifunctional binding sites good...
The elastic properties of two-dimensional networks under tension are studied by the mean-field approximation and Monte Carlo simulation. characterized fixed (polymerized) connectivity either a square-well or Hooke's-law interaction among their components. Both self-avoiding phantom examined. at large equilibrium length found to be well represented model. All investigated show negative Poisson ratio over range tension. At finite tension, exhibit phase transition collapsed state.
Dissipative particle dynamics is used to extract the material parameters (bending and area stretch moduli) of a bilayer membrane patch. Some experiments indicate that modulus lipid vesicles varies little as chain length lipids composing increases. Here we show making interactions between hydrophilic head groups model amphiphiles proportional hydrophobic tail reproduces above result for modulus. We also bilayers composed with same number beads but asymmetric chains less than symmetric chains....
Amphiphilic vesicles are ubiquitous in living cells and industrially interesting as drug delivery vehicles. Vesicle self-assembly proceeds rapidly from nanometer to micrometer length scales is too fast image experimentally but slow for molecular dynamics simulations. Here, we use parallel dissipative particle (DPD) follow spontaneous vesicle up 445 μs with near-molecular resolution. The mean mass radius of gyration growing amphiphilic clusters obey power laws exponents 0.85 ± 0.03 0.41 0.02,...
Neuronal morphologies provide the foundation for electrical behavior of neurons, connectomes they form, and dynamical properties brain. Comprehensive neuron models are essential defining cell types, discerning their functional roles, investigating brain-disease-related dendritic alterations. However, a lack understanding principles underlying has hindered attempts to computationally synthesize decades. We introduce synthesis algorithm based on topological descriptor which enables rapid...
Lipid bilayer membranes below their main transition have two tilt order parameters, corresponding to the monolayers. These tilts may be strongly coupled membrane shape but only weakly each other. We discuss some implications of this observation for rippled and saddle phases, tubules, bicontinuous phases. Tilt difference introduces a length scale into elastic theory tilted fluid membranes. It can drive an instability flat phase; it also provides simple mechanism spontaneous breaking inversion...
The material parameters (area stretch modulus and bending rigidity) of two-component amphiphilic membranes are determined from dissipative particle dynamics simulations. preferred area per molecule for each species is varied so as to produce homogeneous mixtures or nonhomogeneous that form domains. If the latter composed amphiphiles with same tail length, but different areas molecule, their increase monotonically a function composition. By contrast, differ in both length exhibit smaller...
This work was produced as part of the activities FAPESP Research, Disseminations and Innovation Center for Neuromathematics (grant 2013/07699-0, S. Paulo Research Foundation). NLK is supported by a FAPESP postdoctoral fellowship (grant 2016/03855-5). ACR partially supported a CNPq 306251/2014-0).
The crowded interior of a living cell makes performing experiments on simpler in vitro systems attractive. Although these reveal interesting phenomena, their biological relevance can be questionable. A topical example is the phase separation intrinsically disordered proteins into biomolecular condensates, which proposed to underlie membrane-less compartmentalization many cellular functions. How reliably controls biochemical reactions compartments open compositionally-varying cytoplasm an...
The technique of nuclear interferometry is applied to proton and light fragment emission in intermediate energy heavy ion reactions. It shown that the source radii extracted by are consistently larger for correlations involving two deuterons than those with protons. time scale involved particle investigated places a rough upper bound few times ${10}^{\mathrm{\ensuremath{-}}22}$ sec on associated source. A cascade model formulated predict parameters, these found be at least qualitative...
The elastic properties of two-component bilayer membranes are studied using a coarse grain model for amphiphilic molecules. two species amphiphiles considered here differ only in their length. Molecular Dynamics simulations performed order to analyze the shape fluctuations and determine bending rigidity. Both rigidity its inverse found be nonmonotonic functions mole fraction $x_{\rm B}$ shorter B-amphiphiles and, thus, do not satisfy simple lever rule. intrinsic area also exhibits dependence...