1
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Babaki M, Fedosov DA, Gholivand A, Opdam J, Tuinier R, Lettinga MP. Competition between deformation and free volume quantified by 3D image analysis of red blood cell. Biophys J 2023; 122:1646-1658. [PMID: 36964658 PMCID: PMC10183325 DOI: 10.1016/j.bpj.2023.03.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/14/2023] [Accepted: 03/21/2023] [Indexed: 03/26/2023] Open
Abstract
Cells in living organisms are subjected to mechanical strains caused by external forces like overcrowding, resulting in strong deformations that affect cell function. We study the interplay between deformation and crowding of red blood cells (RBCs) in dispersions of nonabsorbing rod-like viruses. We identify a sequence of configurational transitions of RBC doublets, including configurations that can only be induced by long-ranged attraction: highly fluctuating T-shaped and face-to-face configurations at low, and doublets approaching a complete spherical configuration at high, rod concentrations. Complementary simulations are used to explore different energy contributions to deformation as well as the stability of RBC doublet configurations. Our advanced analysis of 3D reconstructed confocal images of RBC doublets quantifies the depletion interaction and the resulting deformation energy. Thus, we introduce a noninvasive, high-throughput platform that is generally applicable to investigate the mechanical response of biological cells to external forces and characterize their mechanical properties.
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Affiliation(s)
- Mehrnaz Babaki
- Institute of Biological Information Processing IBI-4, Forschungszentrum Jülich, Jülich, Germany; Laboratory for Soft Matter and Biophysics, KU Leuven, Leuven, Belgium
| | - Dmitry A Fedosov
- Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, Jülich, Germany
| | - Amirreza Gholivand
- Institute of Biological Information Processing IBI-4, Forschungszentrum Jülich, Jülich, Germany; Laboratory for Soft Matter and Biophysics, KU Leuven, Leuven, Belgium
| | - Joeri Opdam
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry, and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Remco Tuinier
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry, and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Minne Paul Lettinga
- Institute of Biological Information Processing IBI-4, Forschungszentrum Jülich, Jülich, Germany; Laboratory for Soft Matter and Biophysics, KU Leuven, Leuven, Belgium.
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2
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Han K, Ma S, Sun J, Xu M, Qi X, Wang S, Li L, Li X. In silico modeling of patient-specific blood rheology in type 2 diabetes mellitus. Biophys J 2023; 122:1445-1458. [PMID: 36905122 PMCID: PMC10147843 DOI: 10.1016/j.bpj.2023.03.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/16/2022] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
Increased blood viscosity in type 2 diabetes mellitus (T2DM) is a risk factor for the development of insulin resistance and diabetes-related vascular complications; however, individuals with T2DM exhibit heterogeneous hemorheological properties, including cell deformation and aggregation. Using a multiscale red blood cell (RBC) model with key parameters derived from patient-specific data, we present a computational study of the rheological properties of blood from individual patients with T2DM. Specifically, one key model parameter, which determines the shear stiffness of the RBC membrane (μ) is informed by the high-shear-rate blood viscosity of patients with T2DM. At the same time, the other, which contributes to the strength of the RBC aggregation interaction (D0), is derived from the low-shear-rate blood viscosity of patients with T2DM. The T2DM RBC suspensions are simulated at different shear rates, and the predicted blood viscosity is compared with clinical laboratory-measured data. The results show that the blood viscosity obtained from clinical laboratories and computational simulations are in agreement at both low and high shear rates. These quantitative simulation results demonstrate that the patient-specific model has truly learned the rheological behavior of T2DM blood by unifying the mechanical and aggregation factors of the RBCs, which provides an effective way to extract quantitative predictions of the rheological properties of the blood of individual patients with T2DM.
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Affiliation(s)
- Keqin Han
- State Key Laboratory of Fluid Power and Mechatronic Systems, Department of Engineering Mechanics, and Center for X-Mechanics, Zhejiang University, Hangzhou, China
| | - Shuhao Ma
- State Key Laboratory of Fluid Power and Mechatronic Systems, Department of Engineering Mechanics, and Center for X-Mechanics, Zhejiang University, Hangzhou, China
| | - Jiehui Sun
- Department of Endocrinology and Metabolism, Ningbo First Hospital, Ningbo, China
| | - Miao Xu
- Department of Endocrinology and Metabolism, Ningbo First Hospital, Ningbo, China
| | - Xiaojing Qi
- State Key Laboratory of Fluid Power and Mechatronic Systems, Department of Engineering Mechanics, and Center for X-Mechanics, Zhejiang University, Hangzhou, China
| | - Shuo Wang
- State Key Laboratory of Fluid Power and Mechatronic Systems, Department of Engineering Mechanics, and Center for X-Mechanics, Zhejiang University, Hangzhou, China
| | - Li Li
- Department of Endocrinology and Metabolism, Ningbo First Hospital, Ningbo, China.
| | - Xuejin Li
- State Key Laboratory of Fluid Power and Mechatronic Systems, Department of Engineering Mechanics, and Center for X-Mechanics, Zhejiang University, Hangzhou, China; The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China.
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3
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Jung M, Jung G, Schmid F. Stability of Branched Tubular Membrane Structures. PHYSICAL REVIEW LETTERS 2023; 130:148401. [PMID: 37084449 DOI: 10.1103/physrevlett.130.148401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 02/15/2023] [Indexed: 05/03/2023]
Abstract
We study the energetics and stability of branched tubular membrane structures by computer simulations of a triangulated network model. We find that triple (Y) junctions can be created and stabilized by applying mechanical forces, if the angle between branches is 120°. The same holds for tetrahedral junctions with tetraeder angles. If the wrong angles are enforced, the branches coalesce to a linear structure, a pure tube. After releasing the mechanical force, Y-branched structures remain metastable if one constrains the enclosed volume and the average curvature (the area difference) to a fixed value; tetrahedral junctions however split up into two Y junctions. Somewhat counterintuitively, the energy cost of adding a Y branch is negative in structures with fixed surface area and tube diameter, even if one accounts for the positive contribution of the additional branch end. For fixed average curvature, however, adding a branch also enforces a thinning of tubes, therefore the overall curvature energy cost is positive. Possible implications for the stability of branched networks structures in cells are discussed.
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Affiliation(s)
- Maike Jung
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, 55128 Mainz, Germany
| | - Gerhard Jung
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS, 34095 Montpellier, France
| | - Friederike Schmid
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, 55128 Mainz, Germany
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4
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Midya J, Auth T, Gompper G. Membrane-Mediated Interactions Between Nonspherical Elastic Particles. ACS NANO 2023; 17:1935-1945. [PMID: 36669092 PMCID: PMC9933614 DOI: 10.1021/acsnano.2c05801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
The transport of particles across lipid-bilayer membranes is important for biological cells to exchange information and material with their environment. Large particles often get wrapped by membranes, a process which has been intensively investigated in the case of hard particles. However, many particles in vivo and in vitro are deformable, e.g., vesicles, filamentous viruses, macromolecular condensates, polymer-grafted nanoparticles, and microgels. Vesicles may serve as a generic model system for deformable particles. Here, we study nonspherical vesicles with various sizes, shapes, and elastic properties at initially planar lipid-bilayer membranes. Using the Helfrich Hamiltonian, triangulated membranes, and energy minimization, we predict the interplay of vesicle shapes and wrapping states. Increasing particle softness enhances the stability of shallow-wrapped and deep-wrapped states over nonwrapped and complete-wrapped states. The free membrane mediates an interaction between partial-wrapped vesicles. For the pair interaction between deep-wrapped vesicles, we predict repulsion. For shallow-wrapped vesicles, we predict attraction for tip-to-tip orientation and repulsion for side-by-side orientation. Our predictions may guide the design and fabrication of deformable particles for efficient use in medical applications, such as targeted drug delivery.
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Affiliation(s)
- Jiarul Midya
- Theoretical Physics of Living Matter,
Institute for Biological Information Processing and Institute for
Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Thorsten Auth
- Theoretical Physics of Living Matter,
Institute for Biological Information Processing and Institute for
Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Gerhard Gompper
- Theoretical Physics of Living Matter,
Institute for Biological Information Processing and Institute for
Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany
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5
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Merlo A, Losserand S, Yaya F, Connes P, Faivre M, Lorthois S, Minetti C, Nader E, Podgorski T, Renoux C, Coupier G, Franceschini E. Influence of storage and buffer composition on the mechanical behavior of flowing red blood cells. Biophys J 2023; 122:360-373. [PMID: 36476993 PMCID: PMC9892622 DOI: 10.1016/j.bpj.2022.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/17/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
On-chip study of blood flow has emerged as a powerful tool to assess the contribution of each component of blood to its overall function. Blood has indeed many functions, from gas and nutrient transport to immune response and thermal regulation. Red blood cells play a central role therein, in particular through their specific mechanical properties, which directly influence pressure regulation, oxygen perfusion, or platelet and white cell segregation toward endothelial walls. As the bloom of in-vitro studies has led to the apparition of various storage and sample preparation protocols, we address the question of the robustness of the results involving cell mechanical behavior against this diversity. The effects of three conservation media (EDTA, citrate, and glucose-albumin-sodium-phosphate) and storage time on the red blood cell mechanical behavior are assessed under different flow conditions: cell deformability by ektacytometry, shape recovery of cells flowing out of a microfluidic constriction, and cell-flipping dynamics under shear flow. The impact of buffer solutions (phosphate-buffered saline and density-matched suspension using iodixanol/Optiprep) are also studied by investigating individual cell-flipping dynamics, relative viscosity of cell suspensions, and cell structuration under Poiseuille flow. Our results reveal that storing blood samples up to 7 days after withdrawal and suspending them in adequate density-matched buffer solutions has, in most experiments, a moderate effect on the overall mechanical response, with a possible rapid evolution in the first 3 days after sample collection.
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Affiliation(s)
- Adlan Merlo
- GDR MECABIO, France; Institut de Mécanique des Fluides de Toulouse (IMFT), Université de Toulouse, CNRS, Toulouse, France; Biomechanics and Bioengineering Laboratory (UMR 7338), Université de Technologie de Compiègne - CNRS, Compiègne, France
| | - Sylvain Losserand
- GDR MECABIO, France; Université Grenoble Alpes, CNRS, LIPhy, Grenoble, France
| | - François Yaya
- GDR MECABIO, France; Université Grenoble Alpes, CNRS, LIPhy, Grenoble, France
| | - Philippe Connes
- GDR MECABIO, France; Team 'Vascular Biology and Red Blood Cell', Laboratoire Interuniversitaire de Biologie de la Motricité (LIBM) EA7424, Université Claude Bernard Lyon 1, Université de Lyon, Villeurbanne, France; Laboratoire d'Excellence du Globule Rouge (Labex GR-Ex), PRES Sorbonne, Paris, France
| | - Magalie Faivre
- GDR MECABIO, France; University Lyon, CNRS, INSA Lyon, Ecole Centrale de Lyon, Université Claude Bernard Lyon 1, CPE Lyon, INL, UMR5270, Villeurbanne, France
| | - Sylvie Lorthois
- GDR MECABIO, France; Institut de Mécanique des Fluides de Toulouse (IMFT), Université de Toulouse, CNRS, Toulouse, France
| | - Christophe Minetti
- Aero Thermo Mechanics CP 165/43, Université libre de Bruxelles, Brussels, Belgium
| | - Elie Nader
- GDR MECABIO, France; Team 'Vascular Biology and Red Blood Cell', Laboratoire Interuniversitaire de Biologie de la Motricité (LIBM) EA7424, Université Claude Bernard Lyon 1, Université de Lyon, Villeurbanne, France; Laboratoire d'Excellence du Globule Rouge (Labex GR-Ex), PRES Sorbonne, Paris, France
| | - Thomas Podgorski
- GDR MECABIO, France; Université Grenoble Alpes, CNRS, LIPhy, Grenoble, France; Université Grenoble Alpes, CNRS, Grenoble INP, LRP, Grenoble, France
| | - Céline Renoux
- GDR MECABIO, France; Team 'Vascular Biology and Red Blood Cell', Laboratoire Interuniversitaire de Biologie de la Motricité (LIBM) EA7424, Université Claude Bernard Lyon 1, Université de Lyon, Villeurbanne, France; Laboratoire d'Excellence du Globule Rouge (Labex GR-Ex), PRES Sorbonne, Paris, France; Service de biochimie et biologie moléculaire, Hospices Civils de Lyon, Lyon, France
| | - Gwennou Coupier
- GDR MECABIO, France; Université Grenoble Alpes, CNRS, LIPhy, Grenoble, France.
| | - Emilie Franceschini
- GDR MECABIO, France; Aix-Marseille University, CNRS, Centrale Marseille, LMA, Turing Center for Living Systems, Marseille, France.
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6
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Semenov AN, Gvozdev DA, Moysenovich AM, Zlenko DV, Parshina EY, Baizhumanov AA, Budylin GS, Maksimov EG. Probing Red Blood Cell Membrane Microviscosity Using Fluorescence Anisotropy Decay Curves of the Lipophilic Dye PKH26. Int J Mol Sci 2022; 23:ijms232415767. [PMID: 36555408 PMCID: PMC9781149 DOI: 10.3390/ijms232415767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/01/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022] Open
Abstract
Red blood cell (RBC) aggregation and deformation are governed by the molecular processes occurring on the membrane. Since several social important diseases are accompanied by alterations in RBC aggregation and deformability, it is important to develop a diagnostic parameter of RBC membrane structural integrity and stability. In this work, we propose membrane microviscosity assessed by time-resolved fluorescence anisotropy of the lipophilic PKH26 fluorescent probe as a diagnostic parameter. We measured the fluorescence decay curves of the PKH26 probe in the RBC membrane to establish the optimal parameters of the developed fluorescence assay. We observed a complex biphasic profile of the fluorescence anisotropy decay characterized by two correlation times corresponding to the rotational diffusion of free PKH26, and membrane-bounded molecules of the probe. The developed assay allowed us to estimate membrane microviscosity ηm in the range of 100-500 cP depending on the temperature, which paves the way for assessing RBC membrane properties in clinical applications as predictors of blood microrheological abnormalities.
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Affiliation(s)
- Alexey N. Semenov
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory Str., 119991 Moscow, Russia
| | - Daniil A. Gvozdev
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory Str., 119991 Moscow, Russia
| | - Anastasia M. Moysenovich
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory Str., 119991 Moscow, Russia
| | - Dmitry V. Zlenko
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory Str., 119991 Moscow, Russia
| | - Evgenia Yu. Parshina
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory Str., 119991 Moscow, Russia
| | - Adil A. Baizhumanov
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory Str., 119991 Moscow, Russia
| | - Gleb S. Budylin
- Laboratory of Clinical Biophotonics, Biomedical Science and Technology Park, I.M. Sechenov First Moscow State Medical University, 8-2 Trubetskaya Str., 119991 Moscow, Russia
| | - Eugene G. Maksimov
- Interdisciplinary Scientific and Educational School, Molecular Technologies of the Living Systems and Synthetic Biology, M.V. Lomonosov Moscow State University, 1 Leninskie Gory Str., 119991 Moscow, Russia
- Correspondence:
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7
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Deng YX, Chang HY, Li H. Recent Advances in Computational Modeling of Biomechanics and Biorheology of Red Blood Cells in Diabetes. Biomimetics (Basel) 2022; 7:15. [PMID: 35076493 PMCID: PMC8788472 DOI: 10.3390/biomimetics7010015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/01/2022] [Accepted: 01/08/2022] [Indexed: 02/06/2023] Open
Abstract
Diabetes mellitus, a metabolic disease characterized by chronically elevated blood glucose levels, affects about 29 million Americans and more than 422 million adults all over the world. Particularly, type 2 diabetes mellitus (T2DM) accounts for 90-95% of the cases of vascular disease and its prevalence is increasing due to the rising obesity rates in modern societies. Although multiple factors associated with diabetes, such as reduced red blood cell (RBC) deformability, enhanced RBC aggregation and adhesion to the endothelium, as well as elevated blood viscosity are thought to contribute to the hemodynamic impairment and vascular occlusion, clinical or experimental studies cannot directly quantify the contributions of these factors to the abnormal hematology in T2DM. Recently, computational modeling has been employed to dissect the impacts of the aberrant biomechanics of diabetic RBCs and their adverse effects on microcirculation. In this review, we summarize the recent advances in the developments and applications of computational models in investigating the abnormal properties of diabetic blood from the cellular level to the vascular level. We expect that this review will motivate and steer the development of new models in this area and shift the attention of the community from conventional laboratory studies to combined experimental and computational investigations, aiming to provide new inspirations for the development of advanced tools to improve our understanding of the pathogenesis and pathology of T2DM.
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Affiliation(s)
- Yi-Xiang Deng
- School of Engineering, Brown University, Providence, RI 02912, USA;
| | - Hung-Yu Chang
- Division of Applied Mathematics, Brown University, Providence, RI 02912, USA;
| | - He Li
- Center for Biomedical Engineering, Brown University, Providence, RI 02912, USA
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8
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Khan MI, Ferdous SF, Adnan A. Mechanical behavior of actin and spectrin subjected to high strain rate: A molecular dynamics simulation study. Comput Struct Biotechnol J 2021; 19:1738-1749. [PMID: 33897978 PMCID: PMC8050423 DOI: 10.1016/j.csbj.2021.03.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/21/2021] [Accepted: 03/23/2021] [Indexed: 11/16/2022] Open
Abstract
Recent nanoscopy and super-resolution microscopy studies have substantiated the structural contribution of periodic actin-spectrin lattice to the axonal cytoskeleton of neuron. However, sufficient mechanical insight is not present for spectrin and actin-spectrin network, especially in high strain rate scenario. To quantify the mechanical behavior of actin-spectrin cytoskeleton in such conditions, this study determines individual stretching characteristics of actin and spectrin at high strain rate by molecular dynamics (MD) simulation. The actin-spectrin separation criteria are also determined. It is found that both actin and spectrin have high stiffness when susceptible to high strain rate and show strong dependence on applied strain rate. The stretching stiffness of actin and forced unfolding mechanism of spectrin are in harmony with the current literature. Actin-spectrin model provides novel insight into their interaction and separation stretch. It is shown that the region vulnerable to failure is the actin-spectrin interface at lower strain rate, while it is the inter-repeat region of spectrin at higher strain rate.
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Affiliation(s)
- Md Ishak Khan
- Department of Mechanical and Aerospace Engineering, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Sheikh Fahad Ferdous
- Department of Applied Engineering and Technology Management, Indiana State University, Terre Haute, IN 47809, USA
| | - Ashfaq Adnan
- Department of Mechanical and Aerospace Engineering, University of Texas at Arlington, Arlington, TX 76019, USA
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9
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Emanuel MD, Cherstvy AG, Metzler R, Gompper G. Buckling transitions and soft-phase invasion of two-component icosahedral shells. Phys Rev E 2021; 102:062104. [PMID: 33465945 DOI: 10.1103/physreve.102.062104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 11/11/2020] [Indexed: 12/18/2022]
Abstract
What is the optimal distribution of two types of crystalline phases on the surface of icosahedral shells, such as of many viral capsids? We here investigate the distribution of a thin layer of soft material on a crystalline convex icosahedral shell. We demonstrate how the shapes of spherical viruses can be understood from the perspective of elasticity theory of thin two-component shells. We develop a theory of shape transformations of an icosahedral shell upon addition of a softer, but still crystalline, material onto its surface. We show how the soft component "invades" the regions with the highest elastic energy and stress imposed by the 12 topological defects on the surface. We explore the phase diagram as a function of the surface fraction of the soft material, the shell size, and the incommensurability of the elastic moduli of the rigid and soft phases. We find that, as expected, progressive filling of the rigid shell by the soft phase starts from the most deformed regions of the icosahedron. With a progressively increasing soft-phase coverage, the spherical segments of domes are filled first (12 vertices of the shell), then the cylindrical segments connecting the domes (30 edges) are invaded, and, ultimately, the 20 flat faces of the icosahedral shell tend to be occupied by the soft material. We present a detailed theoretical investigation of the first two stages of this invasion process and develop a model of morphological changes of the cone structure that permits noncircular cross sections. In conclusion, we discuss the biological relevance of some structures predicted from our calculations, in particular for the shape of viral capsids.
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Affiliation(s)
- Marc D Emanuel
- Theoretical Physics of Living Matter, Institute of Biological Information Processing, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Kavli Institute for Nanoscience, Technical University Delft, 2628 CJ Delft, Netherlands
| | - Andrey G Cherstvy
- Theoretical Physics of Living Matter, Institute of Biological Information Processing, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Ralf Metzler
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Gerhard Gompper
- Theoretical Physics of Living Matter, Institute of Biological Information Processing, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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10
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Chan C, Du S, Dong Y, Cheng X. Computational and Experimental Approaches to Investigate Lipid Nanoparticles as Drug and Gene Delivery Systems. Curr Top Med Chem 2021; 21:92-114. [PMID: 33243123 PMCID: PMC8191596 DOI: 10.2174/1568026620666201126162945] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/16/2020] [Accepted: 10/22/2020] [Indexed: 02/06/2023]
Abstract
Lipid nanoparticles (LNPs) have been widely applied in drug and gene delivery. More than twenty years ago, DoxilTM was the first LNPs-based drug approved by the US Food and Drug Administration (FDA). Since then, with decades of research and development, more and more LNP-based therapeutics have been used to treat diverse diseases, which often offer the benefits of reduced toxicity and/or enhanced efficacy compared to the active ingredients alone. Here, we provide a review of recent advances in the development of efficient and robust LNPs for drug/gene delivery. We emphasize the importance of rationally combining experimental and computational approaches, especially those providing multiscale structural and functional information of LNPs, to the design of novel and powerful LNP-based delivery systems.
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Affiliation(s)
- Chun Chan
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Shi Du
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Yizhou Dong
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
- Department of Biomedical Engineering; The Center for Clinical and Translational Science; The Comprehensive Cancer Center; Dorothy M. Davis Heart & Lung Research Institute; Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
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11
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Murakami K, Ebihara R, Kono T, Chiba T, Sakuma Y, Ziherl P, Imai M. Morphologies of Vesicle Doublets: Competition among Bending Elasticity, Surface Tension, and Adhesion. Biophys J 2020; 119:1735-1748. [PMID: 33080225 DOI: 10.1016/j.bpj.2020.09.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/20/2020] [Accepted: 09/25/2020] [Indexed: 11/20/2022] Open
Abstract
To study the mechanical laws governing the form of multicellular organisms, we examine the morphology of adhering vesicle doublets as the simplest model system. We monitor the morphological transformations of doublets induced by changes of adhesion strength and volume/area ratio, which are controlled by intermembrane interactions and thermal area expansion, respectively. When we increase the temperature in the weak adhesion regime, a dumbbell flat-contact doublet is transformed to a parallel-prolate doublet, whereas in the strong adhesion regime, heating transforms the dumbbell flat-contact doublet into a spherical sigmoid-contact doublet. We reproduce the observed doublet morphologies by numerically minimizing the total energy, including the contact-potential adhesion term as well as the surface and bending terms, using the Surface Evolver package. From the reproduced morphologies, we extract the adhesion strength, the surface tension, and the volume/area ratio of the vesicles, which reveals the detailed mechanisms of the morphological transitions in doublets.
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Affiliation(s)
- Kei Murakami
- Department of Physics, Tohoku University, Aoba, Sendai, Japan
| | - Ryuta Ebihara
- Department of Physics, Tohoku University, Aoba, Sendai, Japan
| | - Takuma Kono
- Department of Physics, Tohoku University, Aoba, Sendai, Japan
| | - Toshikaze Chiba
- Department of Physics, Tohoku University, Aoba, Sendai, Japan
| | - Yuka Sakuma
- Department of Physics, Tohoku University, Aoba, Sendai, Japan
| | - Primož Ziherl
- Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia; Jožef Stefan Institute, Ljubljana, Slovenia
| | - Masayuki Imai
- Department of Physics, Tohoku University, Aoba, Sendai, Japan.
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Deng Y, Papageorgiou DP, Li X, Perakakis N, Mantzoros CS, Dao M, Karniadakis GE. Quantifying Fibrinogen-Dependent Aggregation of Red Blood Cells in Type 2 Diabetes Mellitus. Biophys J 2020; 119:900-912. [PMID: 32814061 PMCID: PMC7474208 DOI: 10.1016/j.bpj.2020.07.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/12/2020] [Accepted: 07/28/2020] [Indexed: 01/08/2023] Open
Abstract
Fibrinogen is regarded as the main glycoprotein in the aggregation of red blood cells (RBCs), a normally occurring phenomenon that has a major impact on blood rheology and hemodynamics, especially under pathological conditions, including type 2 diabetes mellitus (T2DM). In this study, we investigate the fibrinogen-dependent aggregation dynamics of T2DM RBCs through patient-specific predictive computational simulations that invoke key parameters derived from microfluidic experiments. We first calibrate our model parameters at the doublet (a rouleau consisting of two aggregated RBCs) level for healthy blood samples by matching the detaching force required to fully separate RBC doublets with measurements using atomic force microscopy and optical tweezers. Using results from companion microfluidic experiments that also provide in vitro quantitative information on cell-cell adhesive dynamics, we then quantify the rouleau dissociation dynamics at the doublet and multiplet (a rouleau consisting of three or more aggregated RBCs) levels for obese patients with or without T2DM. Specifically, we examine the rouleau breakup rate when it passes through microgates at doublet level and investigate the effect of rouleau alignment in altering its breakup pattern at multiplet level. This study seamlessly integrates in vitro experiments and simulations and consequently enhances our understanding of the complex cell-cell interaction, highlighting the importance of the aggregation and disaggregation dynamics of RBCs in patients at increased risk of microvascular complications.
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Affiliation(s)
- Yixiang Deng
- Division of Applied Mathematics, Brown University, Providence, Rhode Island; School of Engineering, Brown University, Providence, Rhode Island
| | - Dimitrios P Papageorgiou
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Xuejin Li
- Department of Engineering Mechanics and Center for X-Mechanics, Zhejiang University, Hangzhou, People's Republic of China
| | - Nikolaos Perakakis
- Division of Endocrinology, Diabetes and Metabolism, Department of Internal Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Christos S Mantzoros
- Division of Endocrinology, Diabetes and Metabolism, Department of Internal Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts; Boston VA Healthcare System, Boston, Massachusetts
| | - Ming Dao
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
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Pezeshkian W, König M, Wassenaar TA, Marrink SJ. Backmapping triangulated surfaces to coarse-grained membrane models. Nat Commun 2020; 11:2296. [PMID: 32385270 PMCID: PMC7210967 DOI: 10.1038/s41467-020-16094-y] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/07/2020] [Indexed: 12/14/2022] Open
Abstract
Many biological processes involve large-scale changes in membrane shape. Computer simulations of these processes are challenging since they occur across a wide range of spatiotemporal scales that cannot be investigated in full by any single current simulation technique. A potential solution is to combine different levels of resolution through a multiscale scheme. Here, we present a multiscale algorithm that backmaps a continuum membrane model represented as a dynamically triangulated surface (DTS) to its corresponding molecular model based on the coarse-grained (CG) Martini force field. Thus, we can use DTS simulations to equilibrate slow large-scale membrane conformational changes and then explore the local properties at CG resolution. We demonstrate the power of our method by backmapping a vesicular bud induced by binding of Shiga toxin and by transforming the membranes of an entire mitochondrion to near-atomic resolution. Our approach opens the way to whole cell simulations at molecular detail. Computer simulations of large-scale changes in membrane shape are challenging since they occur across a wide range of spatiotemporal scales. Here, authors present a multiscale algorithm that backmaps a continuum membrane model represented as a dynamically triangulated surface to its corresponding molecular model based on the coarse-grained Martini force field.
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Affiliation(s)
- Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands.
| | - Melanie König
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Tsjerk A Wassenaar
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands.
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Bachratý H, Bachratá K, Chovanec M, Jančigová I, Smiešková M, Kovalčíková K. Applications of machine learning for simulations of red blood cells in microfluidic devices. BMC Bioinformatics 2020; 21:90. [PMID: 32164547 PMCID: PMC7068868 DOI: 10.1186/s12859-020-3357-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background For optimization of microfluidic devices for the analysis of blood samples, it is useful to simulate blood cells as elastic objects in flow of blood plasma. In such numerical models, we primarily need to take into consideration the movement and behavior of the dominant component of the blood, the red blood cells. This can be done quite precisely in small channels and within a short timeframe. However, larger volumes or timescales require different approaches. Instead of simplifying the simulation, we use a neural network to predict the movement of the red blood cells. Results The neural network uses data from the numerical simulation for learning, however, the simulation needs only be run once. Alternatively, the data could come from video processing of a recording of a biological experiment. Afterwards, the network is able to predict the movement of the red blood cells because it is a system of bases that gives an approximate cell velocity at each point of the simulation channel as a linear combination of bases.In a simple box geometry, the neural network gives results comparable to predictions using fluid streamlines, however in a channel with obstacles forming slits, the neural network is about five times more accurate.The network can also be used as a discriminator between different situations. We observe about two-fold increase in mean relative error when a network trained on one geometry is used to predict trajectories in a modified geometry. Even larger increase was observed when it was used to predict trajectories of cells with different elastic properties. Conclusions While for uncomplicated box channels there is no advantage in using a system of bases instead of a simple prediction using fluid streamlines, in a more complicated geometry, the neural network is significantly more accurate. Another application of this system of bases is using it as a comparison tool for different modeled situations. This has a significant future potential when applied to processing data from videos of microfluidic flows.
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Affiliation(s)
- Hynek Bachratý
- Department of Software Technologies, Faculty of Management Science and Informatics, University of žilina, Cell-in-fluid Research Group, žilina, Slovakia
| | - Katarína Bachratá
- Department of Software Technologies, Faculty of Management Science and Informatics, University of žilina, Cell-in-fluid Research Group, žilina, Slovakia
| | - Michal Chovanec
- Department of Technical Cybernetics, Faculty of Management Science and Informatics, University of žilina, žilina, Slovakia
| | - Iveta Jančigová
- Department of Software Technologies, Faculty of Management Science and Informatics, University of žilina, Cell-in-fluid Research Group, žilina, Slovakia
| | - Monika Smiešková
- Department of Software Technologies, Faculty of Management Science and Informatics, University of žilina, Cell-in-fluid Research Group, žilina, Slovakia
| | - Kristína Kovalčíková
- Department of Software Technologies, Faculty of Management Science and Informatics, University of žilina, Cell-in-fluid Research Group, žilina, Slovakia
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