Modeling biomembranes and red blood cells by coarse-grained particle methods

2017 ◽  
Vol 39 (1) ◽  
pp. 3-20 ◽  
Author(s):  
H. Li ◽  
H. Y. Chang ◽  
J. Yang ◽  
L. Lu ◽  
Y. H. Tang ◽  
...  
Keyword(s):  
Red Blood Cells ◽  
Blood Cells ◽  
Coarse Grained ◽  
Particle Methods

scholarly journals A new two-component approach in modeling red blood cells

2020 ◽  
Vol 11 (1) ◽  
pp. 55-71
Author(s):  
Luca Meacci ◽  
Gustavo C. Buscaglia ◽  
Fernando Mut ◽  
Roberto F. Ausas ◽  
Mario Primicerio
Keyword(s):  
Red Blood Cells ◽  
Blood Cells ◽  
Computational Modelling ◽  
Small Time ◽  
Discrete Models ◽  
Continuous Treatment ◽  
Particle Methods ◽  
Adhesion Forces ◽  
Component Approach ◽  
External Forces

Abstract This work consists in the presentation of a computational modelling approach to study normal and pathological behavior of red blood cells in slow transient processes that can not be accompanied by pure particle methods (which require very small time steps). The basic model, inspired by the best models currently available, considers the cytoskeleton as a discrete non-linear elastic structure. The novelty of the proposed work is to couple this skeleton with continuum models instead of the more common discrete models (molecular dynamics, particle methods) of the lipid bilayer. The interaction of the solid cytoskeleton with the bilayer, which is a two-dimensional fluid, will be done through adhesion forces adapting e cient solid-solid adhesion algorithms. The continuous treatment of the fluid parts is well justified by scale arguments and leads to much more stable and precise numerical problems when, as is the case, the size of the molecules (0.3 nm) is much smaller than the overall size (≃ 8000 nm). In this paper we display some numerical simulations that show how our approach can describe the interaction of an RBC with an exogenous body as well as the relaxation of the shape of an RBC toward its equilibrium configuration in absence of external forces.

scholarly journals Blood bank storage of red blood cells increases RBC cytoplasmic membrane order and bending rigidity

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259267
Author(s):  
Sebastian Himbert ◽  
Syed M. Qadri ◽  
William P. Sheffield ◽  
Peter Schubert ◽  
Angelo D’Alessandro ◽  
...  
Keyword(s):  
Red Blood Cells ◽  
Blood Cells ◽  
Storage Time ◽  
Cytoplasmic Membrane ◽  
Md Simulations ◽  
Coarse Grained ◽  
Small Contribution ◽  
Bending Rigidity ◽  
X Ray ◽  
Membrane Order

Blood banks around the world store blood components for several weeks ensuring its availability for transfusion medicine. Red blood cells (RBCs) are known to undergo compositional changes during storage, which may impact the cells’ function and eventually the recipients’ health. We extracted the RBC’s cytoplasmic membrane (RBCcm) to study the effect of storage on the membranes’ molecular structure and bending rigidity by a combination of X-ray diffraction (XRD), X-ray diffuse scattering (XDS) and coarse grained Molecular Dynamics (MD) simulations. Blood was stored in commercial blood bags for 2 and 5 weeks, respectively and compared to freshly drawn blood. Using mass spectrometry, we measured an increase of fatty acids together with a slight shift towards shorter tail lengths. We observe an increased fraction (6%) of liquid ordered (lo) domains in the RBCcms with storage time, and an increased lipid packing in these domains, leading to an increased membrane thickness and membrane order. The size of both, lo and liquid disordered (ld) lipid domains was found to decrease with increased storage time by up to 25%. XDS experiments reveal a storage dependent increase in the RBCcm’s bending modulus κ by a factor of 2.8, from 1.9 kBT to 5.3 kBT. MD simulations were conducted in the absence of proteins. The results show that the membrane composition has a small contribution to the increased bending rigidity and suggests additional protein-driven mechanisms.

Accurate Coarse-Grained Modeling of Red Blood Cells

2008 ◽  
Vol 101 (11) ◽  
Author(s):  
Igor V. Pivkin ◽  
George Em Karniadakis
Keyword(s):  
Red Blood Cells ◽  
Blood Cells ◽  
Coarse Grained

scholarly journals Rotational behaviour of red blood cells in suspension: a mesoscale simulation study

2011 ◽  
Vol 369 (1944) ◽  
pp. 2337-2344 ◽  
Author(s):  
F. Janoschek ◽  
F. Mancini ◽  
J. Harting ◽  
F. Toschi
Keyword(s):  
Red Blood Cells ◽  
Blood Cells ◽  
Coarse Grained ◽  
Soft Particle ◽  
Rotational Behaviour ◽  
Cell Orientation ◽  
Nematic Order ◽  
Rotation Periods ◽  
Boltzmann Method ◽  
Pronounced Peak

The nature of blood as a suspension of red blood cells makes computational haemodynamics a demanding task. Our coarse-grained blood model, which builds on a lattice Boltzmann method for soft particle suspensions, enables the study of the collective behaviour of the order of 10 6 cells in suspension. After demonstrating the viscosity measurement in Kolmogorov flow, we focus on the statistical analysis of the cell orientation and rotation in Couette flow. We quantify the average inclination with respect to the flow and the nematic order as a function of shear rate and haematocrit. We further record the distribution of rotation periods around the vorticity direction and find a pronounced peak in the vicinity of the theoretical value for free model cells, even though cell–cell interactions manifest themselves in a substantial width of the distribution.

Simulation of Red Blood Cell Mechanical Behavior in Optical Tweezers Experiment Based on a Particle Method

2010 ◽  
Author(s):  
M. T. Ahmadian ◽  
K. Firoozbakhsh ◽  
M. Hasanian
Keyword(s):  
Mechanical Behavior ◽  
Red Blood Cells ◽  
Optical Tweezers ◽  
Blood Cells ◽  
Experimental Studies ◽  
Particle Method ◽  
Living Cells ◽  
Discrete Models ◽  
Particle Methods ◽  
External Forces

Optical tweezers provide an accurate measurement technique for evaluating mechanical properties of the living cells and many experimental studies have been done to understand the behavior of cells due to external forces. Numerical studies such as finite element methods have been used in order to simulate mechanical behavior of the Red Blood Cells (RBCs). Recent studies have shown that the particle methods are useful tools to simulate the mechanical behavior of living cells. Since in microscopic scales, using discrete models are preferred than continuum methods, a particle-based method is used to simulate the deformation of RBC which is stretched by optical tweezers. The cytoplasm of RBC is modeled as a fluid and cell membrane is replaced by a set of discrete particles connected by springs. The results are comparable with previous observations of RBC optical tweezers experiments. It was observed that RBC viscoelastic characteristics are mainly associated with the cytoplasm fluidic properties. In order to understand the behavior and function of living red blood cells, this significant developed model could be implemented to RBC interaction within micocapillaries and constricted zones in blood flow.

Optical Tweezer Stretching of Miniature Coarse-Grained Red Blood Cells

2020 ◽  
Author(s):  
P. Appshaw ◽  
A. M. Seddon ◽  
S. Hanna
Keyword(s):  
Molecular Dynamics ◽  
Shear Modulus ◽  
Red Blood Cells ◽  
Blood Cells ◽  
Scale Invariance ◽  
Optical Tweezer ◽  
Coarse Grained ◽  
Whole Cell ◽  
Human Red Blood Cells

ABSTRACTDue to the high computational cost of full-cell coarse-grained molecular dynamics modelling, being able to simulate “miniature” cells that effectively represent their full-sized counterparts would be highly advantageous. To accurately represent the morphological and elastic properties of a human red blood cell in silico, such a model is employed utilising the molecular dynamics package LAMMPS. The scale invariance of the model is first tested qualitatively by following the shape evolution of red blood cells of various diameters, then quantitatively by evaluating the membrane shear modulus from simulations of optical tweezer-style stretching. Cells of physical diameter of at least 0.5µm were able to form the characteristic biconcave shape of human red blood cells, though smaller cells instead equilibrated to bowl-shaped stomatocytes. A positive correlation was found between the cell size and both magnitude of deformation from optical tweezer stretching and scaled shear modulus, indicating a lack of scale invariance in the models elastic response. However, the stable morphology and measured shear modulus of the 0.5 − 1.0µm diameter cells are deemed close enough to past in vitro studies on human red blood cells for them to still offer valuable use in making simplified predictions of whole-cell mechanics.SIGNIFICANCEThe study tests the invariance of a coarse-grained molecular dynamics red blood cell (RBC) model to system scale, asking whether it is qualitatively and quantitatively viable to perform whole-cell simulations in “miniature”. Simulating cells at a reduced scale greatly improves computational speed, making possible computational experiments that would otherwise be too computationally demanding. This facilitates the simulation of larger systems, both in number of whole-cells, and cells of greater structural complexity than the RBC. More generally, the accurate and efficient modelling of biological cells allows computational experimentation of real-world systems that would be very challenging or impossible to perform in vitro. Therefore, miniature-cell modelling could help both direct development in whole-cell modelling, and also developments in more widespread bio-physical studies.

Models For Optical Tweezer Stretching of Miniature Coarse-Grained Red Blood Cells

2021 ◽  
Author(s):  
Paul Appshaw ◽  
Annela M. Seddon ◽  
Simon Hanna
Keyword(s):  
Red Blood Cells ◽  
Blood Cells ◽  
Optical Tweezer ◽  
Coarse Grained

scholarly journals Scale-invariance in miniature coarse-grained red blood cells by fluctuation analysis

Soft Matter ◽  
2022 ◽  
Author(s):  
Paul Appshaw ◽  
Annela M. Seddon ◽  
Simon Hanna
Keyword(s):  
Molecular Dynamics ◽  
Blood Cell ◽  
Red Blood Cells ◽  
Red Blood Cell ◽  
Blood Cells ◽  
In Silico ◽  
Scale Invariance ◽  
Coarse Grained ◽  
Fluctuation Analysis ◽  
Dynamics Model

The scale-invariance of a coarse-grained molecular dynamics model of a red blood cell is investigated through fluctuation analysis, justifying the use of “miniature cells” in silico.

Sign in / Sign up

Export Citation Format

Share Document