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1
Phougat M, Sahni NS, Choudhury D. Understanding the relationship between preferential interactions of peptides in water-acetonitrile mixtures with protein-solvent contact surface area. J Comput Aided Mol Des 2024;38:38. [PMID: 39537830 DOI: 10.1007/s10822-024-00579-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2024] [Accepted: 10/29/2024] [Indexed: 11/16/2024]
2
Roshal DS, Fedorenko KK, Martin M, Baghdiguian S, Rochal SB. Topological balance of cell distributions in plane monolayers. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2024;36:265101. [PMID: 38537291 DOI: 10.1088/1361-648x/ad387a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 03/27/2024] [Indexed: 04/06/2024]
3
Zhou Y, Isaksson P, Persson C. An improved trabecular bone model based on Voronoi tessellation. J Mech Behav Biomed Mater 2023;148:106172. [PMID: 37852087 DOI: 10.1016/j.jmbbm.2023.106172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/17/2023] [Accepted: 10/09/2023] [Indexed: 10/20/2023]
4
Olechnovič K, Venclovas Č. VoroIF-GNN: Voronoi tessellation-derived protein-protein interface assessment using a graph neural network. Proteins 2023;91:1879-1888. [PMID: 37482904 DOI: 10.1002/prot.26554] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/19/2023] [Accepted: 07/01/2023] [Indexed: 07/25/2023]
5
Báez-Yáñez MG, Siero JCW, Petridou N. A mechanistic computational framework to investigate the hemodynamic fingerprint of the blood oxygenation level-dependent signal. NMR IN BIOMEDICINE 2023;36:e5026. [PMID: 37643645 DOI: 10.1002/nbm.5026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 07/18/2023] [Accepted: 07/28/2023] [Indexed: 08/31/2023]
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Frenkel M, Shoval S, Bormashenko E. Shannon Entropy of Ramsey Graphs with up to Six Vertices. ENTROPY (BASEL, SWITZERLAND) 2023;25:1427. [PMID: 37895548 PMCID: PMC10606126 DOI: 10.3390/e25101427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/03/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023]
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Merighi A, Lossi L. Co-cultures of cerebellar slices from mice with different reelin genetic backgrounds as a model to study cortical lamination. F1000Res 2023;11:1183. [PMID: 37881513 PMCID: PMC10594056 DOI: 10.12688/f1000research.126787.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/07/2023] [Indexed: 10/27/2023]  Open
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Merighi A, Lossi L. Co-cultures of cerebellar slices from mice with different reelin genetic backgrounds as a model to study cortical lamination. F1000Res 2023;11:1183. [PMID: 37881513 PMCID: PMC10594056 DOI: 10.12688/f1000research.126787.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/07/2023] [Indexed: 10/27/2023]  Open
9
Gelléri M, Chen SY, Hübner B, Neumann J, Kröger O, Sadlo F, Imhoff J, Hendzel MJ, Cremer M, Cremer T, Strickfaden H, Cremer C. True-to-scale DNA-density maps correlate with major accessibility differences between active and inactive chromatin. Cell Rep 2023;42:112567. [PMID: 37243597 DOI: 10.1016/j.celrep.2023.112567] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 03/02/2023] [Accepted: 05/10/2023] [Indexed: 05/29/2023]  Open
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Bormashenko E, Legchenkova I, Frenkel M, Shvalb N, Shoval S. Voronoi Tessellations and the Shannon Entropy of the Pentagonal Tilings. ENTROPY (BASEL, SWITZERLAND) 2023;25:92. [PMID: 36673233 PMCID: PMC9857938 DOI: 10.3390/e25010092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
11
Simulation of Diffusion-Controlled Growth of Interdependent Nuclei under Potentiostatic Conditions. MATERIALS 2022;15:ma15103603. [PMID: 35629634 PMCID: PMC9147730 DOI: 10.3390/ma15103603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 12/10/2022]
12
Zou S, Gong H, Gao J. Additively Manufactured Multilevel Voronoi-Lattice Scaffolds with Bonelike Mechanical Properties. ACS Biomater Sci Eng 2022;8:3022-3037. [PMID: 35537212 DOI: 10.1021/acsbiomaterials.1c01482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
13
Boribayeva A, Iniyatova G, Uringaliyeva A, Golman B. Porous Structure of Cylindrical Particle Compacts. MICROMACHINES 2021;12:mi12121498. [PMID: 34945346 PMCID: PMC8706371 DOI: 10.3390/mi12121498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 11/16/2022]
14
Cooperative success in epithelial public goods games. J Theor Biol 2021;528:110838. [PMID: 34303702 DOI: 10.1016/j.jtbi.2021.110838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 07/06/2021] [Accepted: 07/19/2021] [Indexed: 11/23/2022]
15
Simulation of Leather Visco-Elastic Behavior Based on Collagen Fiber-Bundle Properties and a Meso-Structure Network Model. MATERIALS 2021;14:ma14081894. [PMID: 33920286 PMCID: PMC8070376 DOI: 10.3390/ma14081894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 11/17/2022]
16
Brehm M, Thomas M. Optimized Atomic Partial Charges and Radii Defined by Radical Voronoi Tessellation of Bulk Phase Simulations. Molecules 2021;26:1875. [PMID: 33810337 PMCID: PMC8036805 DOI: 10.3390/molecules26071875] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 12/05/2022]  Open
17
Zhang M, Shang J, Guo S, Hur B, Yue X. Numerical Investigation of Effective Thermal Conductivity of Strut-Based Cellular Structures Designed by Spatial Voronoi Tessellation. MATERIALS 2020;14:ma14010138. [PMID: 33396900 PMCID: PMC7795474 DOI: 10.3390/ma14010138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/18/2020] [Accepted: 12/28/2020] [Indexed: 02/04/2023]
18
Renton J, Page KM. Evolution of cooperation in an epithelium. J R Soc Interface 2020;16:20180918. [PMID: 30913980 PMCID: PMC6451401 DOI: 10.1098/rsif.2018.0918] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
19
Olechnovič K, Venclovas Č. Contact Area-Based Structural Analysis of Proteins and Their Complexes Using CAD-Score. Methods Mol Biol 2020;2112:75-90. [PMID: 32006279 DOI: 10.1007/978-1-0716-0270-6_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
20
Jenner AL, Frascoli F, Coster ACF, Kim PS. Enhancing oncolytic virotherapy: Observations from a Voronoi Cell-Based model. J Theor Biol 2019;485:110052. [PMID: 31626813 DOI: 10.1016/j.jtbi.2019.110052] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 09/13/2019] [Accepted: 10/14/2019] [Indexed: 02/07/2023]
21
Validation and Investigation on the Mechanical Behavior of Concrete Using a Novel 3D Mesoscale Method. MATERIALS 2019;12:ma12162647. [PMID: 31434332 PMCID: PMC6721098 DOI: 10.3390/ma12162647] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 11/30/2022]
22
Zufiria PJ, Hernández-Medina MÁ. A New Technique Based on Voronoi Tessellation to Assess the Space-Dependence of Categorical Variables. ENTROPY 2019;21:e21080774. [PMID: 33267486 PMCID: PMC7515304 DOI: 10.3390/e21080774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/02/2019] [Accepted: 08/02/2019] [Indexed: 11/20/2022]
23
Bormashenko E, Legchenkova I, Frenkel M. Symmetry and Shannon Measure of Ordering: Paradoxes of Voronoi Tessellation. ENTROPY 2019;21:e21050452. [PMID: 33267166 PMCID: PMC7514941 DOI: 10.3390/e21050452] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/28/2019] [Accepted: 04/29/2019] [Indexed: 11/17/2022]
24
Influence of Porosity on the Mechanical Behavior during Uniaxial Compressive Testing on Voronoi-Based Open-Cell Aluminium Foam. MATERIALS 2019;12:ma12071041. [PMID: 30934831 PMCID: PMC6480085 DOI: 10.3390/ma12071041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/18/2019] [Accepted: 03/25/2019] [Indexed: 11/17/2022]
25
Hummel MH, Yu B, Simmerling C, Coutsias EA. LAGUERRE-INTERSECTION METHOD FOR IMPLICIT SOLVATION. ACTA ACUST UNITED AC 2019;28:1-38. [PMID: 30853740 DOI: 10.1142/s0218195918500012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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