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Wang P, Sheriff J, Zhang P, Deng Y, Bluestein D. A Multiscale Model for Shear-Mediated Platelet Adhesion Dynamics: Correlating In Silico with In Vitro Results. Ann Biomed Eng 2023; 51:1094-1105. [PMID: 37020171 DOI: 10.1007/s10439-023-03193-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/22/2023] [Indexed: 04/07/2023]
Abstract
Platelet adhesion to blood vessel walls is a key initial event in thrombus formation in both vascular disease processes and prosthetic cardiovascular devices. We extended a deformable multiscale model (MSM) of flowing platelets, incorporating Dissipative Particle Dynamics (DPD) and Coarse-Grained Molecular Dynamics (CGMD) describing molecular-scale intraplatelet constituents and their interaction with surrounding flow, to predict platelet adhesion dynamics under physiological flow shear stresses. Binding of platelet glycoprotein receptor Ibα (GPIbα) to von Willebrand factor (vWF) on the blood vessel wall was modeled by a molecular-level hybrid force field and validated with in vitro microchannel experiments of flowing platelets at 30 dyne/cm2. High frame rate videos of flipping platelets were analyzed with a Semi-Unsupervised Learning System (SULS) machine learning-guided imaging approach to segment platelet geometries and quantify adhesion dynamics parameters. In silico flipping dynamics followed in vitro measurements at 15 and 45 dyne/cm2 with high fidelity, predicting GPIbα-vWF bonding and debonding processes, distribution of bonds strength, and providing a biomechanical insight into initiation of the complex platelet adhesion process. The adhesion model and simulation framework can be further integrated with our established MSMs of platelet activation and aggregation to simulate initial mural thrombus formation on blood vessel walls.
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Affiliation(s)
- Peineng Wang
- Department of Biomedical Engineering, T08-50 Health Sciences Center, Stony Brook University, Stony Brook, NY, 11794-8084, USA
| | - Jawaad Sheriff
- Department of Biomedical Engineering, T08-50 Health Sciences Center, Stony Brook University, Stony Brook, NY, 11794-8084, USA
| | - Peng Zhang
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Yuefan Deng
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Danny Bluestein
- Department of Biomedical Engineering, T08-50 Health Sciences Center, Stony Brook University, Stony Brook, NY, 11794-8084, USA.
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Niu Z, Hasegawa K, Deng Y, Zhang Z, Rafailovich M, Simon M, Zhang P. Modeling of the thermal properties of SARS-CoV-2 S-protein. Front Mol Biosci 2022; 9:953064. [PMID: 36237574 PMCID: PMC9550926 DOI: 10.3389/fmolb.2022.953064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/26/2022] [Indexed: 11/24/2022] Open
Abstract
We calculate the thermal and conformational states of the spike glycoprotein (S-protein) of SARS-CoV-2 at seven temperatures ranging from 3°C to 95°C by all-atom molecular dynamics (MD) µs-scale simulations with the objectives to understand the structural variations on the temperatures and to determine the potential phase transition while trying to correlate such findings of the S-protein with the observed properties of the SARS-CoV2. Our simulations revealed the following thermal properties of the S-protein: 1) It is structurally stable at 3°C, agreeing with observations that the virus stays active for more than two weeks in the cold supply chain; 2) Its structure varies more significantly at temperature values of 60°C–80°C; 3) The sharpest structural variations occur near 60°C, signaling a plausible critical temperature nearby; 4) The maximum deviation of the receptor-binding domain at 37°C, corroborating the anecdotal observations that the virus is most infective at 37°C; 5) The in silico data agree with reported experiments of the SARS-CoV-2 survival times from weeks to seconds by our clustering approach analysis. Our MD simulations at µs scales demonstrated the S-protein’s thermodynamics of the critical states at around 60°C, and the stable and denatured states for temperatures below and above this value, respectively.
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Affiliation(s)
- Ziyuan Niu
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
| | - Karin Hasegawa
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
| | - Yuefan Deng
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
- Mathematics, Division of Science, New York University, Abu Dhabi, United Arab Emirates
| | - Ziji Zhang
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
| | - Miriam Rafailovich
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, NY, United States
| | - Marcia Simon
- Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, NY, United States
| | - Peng Zhang
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
- *Correspondence: Peng Zhang,
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Special Issue of the VPH2020 Conference: "Virtual Physiological Human: When Models, Methods and Experiments Meet the Clinic". Ann Biomed Eng 2022; 50:483-484. [PMID: 35334017 DOI: 10.1007/s10439-022-02943-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 11/01/2022]
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