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For: Andrews SS. Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface. Bioinformatics 2017;33:710-717. [PMID: 28365760 DOI: 10.1093/bioinformatics/btw700] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 11/03/2016] [Indexed: 12/17/2022]  Open
Number Cited by Other Article(s)
1
Guo S, Korolija N, Milfeld K, Jhaveri A, Sang M, Ying YM, Johnson ME. Parallelization of Particle-Based Reaction-Diffusion Simulations Using MPI. J Comput Chem 2025;46:e70132. [PMID: 40405327 DOI: 10.1002/jcc.70132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2024] [Revised: 04/22/2025] [Accepted: 05/02/2025] [Indexed: 05/24/2025]
2
Ruan S, He R, Liang Y, Zhang R, Yuan J. Phosphorylation-Dependent Dispersion of the Response Regulator in Bacterial Chemotaxis. J Mol Biol 2025;437:168920. [PMID: 39710331 DOI: 10.1016/j.jmb.2024.168920] [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: 07/29/2024] [Revised: 12/11/2024] [Accepted: 12/18/2024] [Indexed: 12/24/2024]
3
Dingwell DA, Cunningham CH. Particle-based MR modeling with diffusion, microstructure, and enzymatic reactions. Magn Reson Med 2025;93:369-383. [PMID: 39250417 DOI: 10.1002/mrm.30279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 07/21/2024] [Accepted: 08/14/2024] [Indexed: 09/11/2024]
4
Guo S, Korolija N, Milfeld K, Jhaveri A, Sang M, Ying YM, Johnson ME. Parallelization of particle-based reaction-diffusion simulations using MPI. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.06.627287. [PMID: 39713431 PMCID: PMC11661114 DOI: 10.1101/2024.12.06.627287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]
5
Ahmed YM, Brown LM, Varga K, Bowman GR. Phospho-signaling couples polar asymmetry and proteolysis within a membraneless microdomain in Caulobacter crescentus. Nat Commun 2024;15:9282. [PMID: 39468040 PMCID: PMC11519897 DOI: 10.1038/s41467-024-53395-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/09/2024] [Indexed: 10/30/2024]  Open
6
Liguori-Bills N, Blinov ML. bnglViz: online visualization of rule-based models. Bioinformatics 2024;40:btae351. [PMID: 38814806 PMCID: PMC11176710 DOI: 10.1093/bioinformatics/btae351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/01/2024] [Accepted: 05/29/2024] [Indexed: 06/01/2024]  Open
7
Losa J, Heinemann M. Contribution of different macromolecules to the diffusion of a 40 nm particle in Escherichia coli. Biophys J 2024;123:1211-1221. [PMID: 38555507 PMCID: PMC11140462 DOI: 10.1016/j.bpj.2024.03.040] [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: 01/19/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024]  Open
8
Husar A, Ordyan M, Garcia GC, Yancey JG, Saglam AS, Faeder JR, Bartol TM, Kennedy MB, Sejnowski TJ. MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface. PLoS Comput Biol 2024;20:e1011800. [PMID: 38656994 PMCID: PMC11073787 DOI: 10.1371/journal.pcbi.1011800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/06/2024] [Accepted: 01/03/2024] [Indexed: 04/26/2024]  Open
9
Chan D, Cromar GL, Taj B, Parkinson J. Cell4D: a general purpose spatial stochastic simulator for cellular pathways. BMC Bioinformatics 2024;25:121. [PMID: 38515063 PMCID: PMC10956314 DOI: 10.1186/s12859-024-05739-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/11/2024] [Indexed: 03/23/2024]  Open
10
Tran BM, Punter CM, Linnik D, Iyer A, Poolman B. Single-protein Diffusion in the Periplasm of Escherichia coli. J Mol Biol 2024;436:168420. [PMID: 38143021 DOI: 10.1016/j.jmb.2023.168420] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
11
Kaizu K, Takahashi K. Technologies for whole-cell modeling: Genome-wide reconstruction of a cell in silico. Dev Growth Differ 2023;65:554-564. [PMID: 37856476 PMCID: PMC11520977 DOI: 10.1111/dgd.12897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 09/06/2023] [Accepted: 10/14/2023] [Indexed: 10/21/2023]
12
Opalko H, Geng S, Hall AR, Vavylonis D, Moseley JB. Design principles of Cdr2 node patterns in fission yeast cells. Mol Biol Cell 2023;34:br18. [PMID: 37610834 PMCID: PMC10559309 DOI: 10.1091/mbc.e23-04-0135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/24/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023]  Open
13
Mantovanelli L, Linnik DS, Punter M, Kojakhmetov HJ, Śmigiel WM, Poolman B. Simulation-based Reconstructed Diffusion unveils the effect of aging on protein diffusion in Escherichia coli. PLoS Comput Biol 2023;19:e1011093. [PMID: 37695774 PMCID: PMC10513214 DOI: 10.1371/journal.pcbi.1011093] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/21/2023] [Accepted: 08/24/2023] [Indexed: 09/13/2023]  Open
14
Ahmed YM, Bowman GR. Phospho-signaling couples polar asymmetry and proteolysis within a membraneless microdomain in C. crescentus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.19.553945. [PMID: 37645878 PMCID: PMC10462113 DOI: 10.1101/2023.08.19.553945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
15
Opalko H, Geng S, Hall AR, Vavylonis D, Moseley JB. Design principles of Cdr2 node patterns in fission yeast cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537536. [PMID: 37131752 PMCID: PMC10153186 DOI: 10.1101/2023.04.19.537536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
16
Henning P, Köster T, Haack F, Burrage K, Uhrmacher AM. Implications of different membrane compartmentalization models in particle-based in silico studies. ROYAL SOCIETY OPEN SCIENCE 2023;10:221177. [PMID: 37416823 PMCID: PMC10320350 DOI: 10.1098/rsos.221177] [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: 09/08/2022] [Accepted: 06/12/2023] [Indexed: 07/08/2023]
17
Pradhan S, Rath R, Biswas M. GB1 Dimerization in Crowders: A Multiple Resolution Approach. J Chem Inf Model 2023;63:1570-1577. [PMID: 36858485 DOI: 10.1021/acs.jcim.3c00012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
18
Fullstone G. Rapid Particle-Based Simulations of Cellular Signalling with the FLAME-Accelerated Signalling Tool (FaST) and GPUs. Methods Mol Biol 2023;2634:191-212. [PMID: 37074580 DOI: 10.1007/978-1-0716-3008-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
19
Iwasa JH, Lyons B, Johnson GT. The dawn of interoperating spatial models in cell biology. Curr Opin Biotechnol 2022;78:102838. [PMID: 36402095 DOI: 10.1016/j.copbio.2022.102838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 06/01/2022] [Accepted: 10/07/2022] [Indexed: 11/18/2022]
20
Śmigiel WM, Mantovanelli L, Linnik DS, Punter M, Silberberg J, Xiang L, Xu K, Poolman B. Protein diffusion in Escherichia coli cytoplasm scales with the mass of the complexes and is location dependent. SCIENCE ADVANCES 2022;8:eabo5387. [PMID: 35960807 PMCID: PMC9374337 DOI: 10.1126/sciadv.abo5387] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/28/2022] [Indexed: 05/30/2023]
21
Stochastic model of ERK-mediated progesterone receptor translocation, clustering and transcriptional activity. Sci Rep 2022;12:11791. [PMID: 35821038 PMCID: PMC9276744 DOI: 10.1038/s41598-022-13821-x] [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: 10/14/2021] [Accepted: 05/27/2022] [Indexed: 11/26/2022]  Open
22
Zhang Y, Isaacson SA. Detailed balance for particle models of reversible reactions in bounded domains. J Chem Phys 2022;156:204105. [DOI: 10.1063/5.0085296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
23
Cholko T, Kaushik S, Wu KY, Montes R, Chang CEA. GeomBD3: Brownian Dynamics Simulation Software for Biological and Engineered Systems. J Chem Inf Model 2022;62:2257-2263. [PMID: 35549473 DOI: 10.1021/acs.jcim.1c01387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
24
Jayasinghe MK, Lee CY, Tran TTT, Tan R, Chew SM, Yeo BZJ, Loh WX, Pirisinu M, Le MTN. The Role of in silico Research in Developing Nanoparticle-Based Therapeutics. Front Digit Health 2022;4:838590. [PMID: 35373184 PMCID: PMC8965754 DOI: 10.3389/fdgth.2022.838590] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 02/16/2022] [Indexed: 12/12/2022]  Open
25
Simulation of receptor triggering by kinetic segregation shows role of oligomers and close-contacts. Biophys J 2022;121:1660-1674. [PMID: 35367423 PMCID: PMC9117938 DOI: 10.1016/j.bpj.2022.03.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/07/2022] [Accepted: 03/28/2022] [Indexed: 11/23/2022]  Open
26
Singh D, Andrews SS. Python interfaces for the Smoldyn simulator. Bioinformatics 2021;38:291-293. [PMID: 34293100 DOI: 10.1093/bioinformatics/btab530] [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: 12/15/2020] [Revised: 06/21/2021] [Accepted: 07/21/2021] [Indexed: 02/03/2023]  Open
27
Trapping or slowing the diffusion of T cell receptors at close contacts initiates T cell signaling. Proc Natl Acad Sci U S A 2021;118:2024250118. [PMID: 34526387 PMCID: PMC8488633 DOI: 10.1073/pnas.2024250118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2021] [Indexed: 12/27/2022]  Open
28
Lubbock AL, Lopez CF. Programmatic modeling for biological systems. CURRENT OPINION IN SYSTEMS BIOLOGY 2021;27:100343. [PMID: 34485764 PMCID: PMC8411905 DOI: 10.1016/j.coisb.2021.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
29
Kaushik S, Chang CEA. Molecular Mechanics Study of Flow and Surface Influence in Ligand-Protein Association. Front Mol Biosci 2021;8:659687. [PMID: 34041265 PMCID: PMC8142692 DOI: 10.3389/fmolb.2021.659687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022]  Open
30
Wu Y, Dhusia K, Su Z. Mechanistic dissection of spatial organization in NF-κB signaling pathways by hybrid simulations. Integr Biol (Camb) 2021;13:109-120. [PMID: 33893499 DOI: 10.1093/intbio/zyab006] [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] [Received: 11/12/2020] [Revised: 02/16/2021] [Accepted: 03/29/2021] [Indexed: 02/06/2023]
31
Clark-Cotton MR, Henderson NT, Pablo M, Ghose D, Elston TC, Lew DJ. Exploratory polarization facilitates mating partner selection in Saccharomyces cerevisiae. Mol Biol Cell 2021;32:1048-1063. [PMID: 33689470 PMCID: PMC8101489 DOI: 10.1091/mbc.e21-02-0068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
32
Johnson ME, Chen A, Faeder JR, Henning P, Moraru II, Meier-Schellersheim M, Murphy RF, Prüstel T, Theriot JA, Uhrmacher AM. Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry. Mol Biol Cell 2021;32:186-210. [PMID: 33237849 PMCID: PMC8120688 DOI: 10.1091/mbc.e20-08-0530] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/13/2020] [Accepted: 11/17/2020] [Indexed: 12/29/2022]  Open
33
Troják M, Šafránek D, Mertová L, Brim L. Executable biochemical space for specification and analysis of biochemical systems. PLoS One 2020;15:e0238838. [PMID: 32915842 PMCID: PMC7485897 DOI: 10.1371/journal.pone.0238838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 08/25/2020] [Indexed: 01/28/2023]  Open
34
Varga MJ, Fu Y, Loggia S, Yogurtcu ON, Johnson ME. NERDSS: A Nonequilibrium Simulator for Multibody Self-Assembly at the Cellular Scale. Biophys J 2020;118:3026-3040. [PMID: 32470324 DOI: 10.1016/j.bpj.2020.05.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 04/24/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022]  Open
35
Andrews SS. Effects of surfaces and macromolecular crowding on bimolecular reaction rates. Phys Biol 2020;17:045001. [DOI: 10.1088/1478-3975/ab7f51] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
36
Fullstone G, Guttà C, Beyer A, Rehm M. The FLAME-accelerated signalling tool (FaST) for facile parallelisation of flexible agent-based models of cell signalling. NPJ Syst Biol Appl 2020;6:10. [PMID: 32313030 PMCID: PMC7170865 DOI: 10.1038/s41540-020-0128-x] [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: 10/15/2019] [Accepted: 03/17/2020] [Indexed: 11/18/2022]  Open
37
Arjunan SNV, Miyauchi A, Iwamoto K, Takahashi K. pSpatiocyte: a high-performance simulator for intracellular reaction-diffusion systems. BMC Bioinformatics 2020;21:33. [PMID: 31996129 PMCID: PMC6990473 DOI: 10.1186/s12859-019-3338-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 12/30/2019] [Indexed: 12/19/2022]  Open
38
Köster T, Henning P, Uhrmacher AM. Potential based, spatial simulation of dynamically nested particles. BMC Bioinformatics 2019;20:607. [PMID: 31775608 PMCID: PMC6880518 DOI: 10.1186/s12859-019-3092-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 09/10/2019] [Indexed: 01/23/2023]  Open
39
Dibak M, Fröhner C, Noé F, Höfling F. Diffusion-influenced reaction rates in the presence of pair interactions. J Chem Phys 2019;151:164105. [PMID: 31675872 DOI: 10.1063/1.5124728] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
40
Henderson NT, Pablo M, Ghose D, Clark-Cotton MR, Zyla TR, Nolen J, Elston TC, Lew DJ. Ratiometric GPCR signaling enables directional sensing in yeast. PLoS Biol 2019;17:e3000484. [PMID: 31622333 PMCID: PMC6818790 DOI: 10.1371/journal.pbio.3000484] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/29/2019] [Accepted: 09/25/2019] [Indexed: 11/19/2022]  Open
41
Fu Y, Yogurtcu ON, Kothari R, Thorkelsdottir G, Sodt AJ, Johnson ME. An implicit lipid model for efficient reaction-diffusion simulations of protein binding to surfaces of arbitrary topology. J Chem Phys 2019;151:124115. [PMID: 31575182 DOI: 10.1063/1.5120516] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
42
Huber GA, McCammon JA. Brownian Dynamics Simulations of Biological Molecules. TRENDS IN CHEMISTRY 2019;1:727-738. [PMID: 32309795 DOI: 10.1016/j.trechm.2019.07.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
43
Rule-Based Modeling Using Wildcards in the Smoldyn Simulator. Methods Mol Biol 2019;1945:179-202. [PMID: 30945247 DOI: 10.1007/978-1-4939-9102-0_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
44
Chew WX, Kaizu K, Watabe M, Muniandy SV, Takahashi K, Arjunan SNV. Surface reaction-diffusion kinetics on lattice at the microscopic scale. Phys Rev E 2019;99:042411. [PMID: 31108654 DOI: 10.1103/physreve.99.042411] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Indexed: 01/06/2023]
45
Hoffmann M, Fröhner C, Noé F. ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics. PLoS Comput Biol 2019;15:e1006830. [PMID: 30818351 PMCID: PMC6413953 DOI: 10.1371/journal.pcbi.1006830] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 03/12/2019] [Accepted: 01/16/2019] [Indexed: 12/30/2022]  Open
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Murray SM, Howard M. Center Finding in E. coli and the Role of Mathematical Modeling: Past, Present and Future. J Mol Biol 2019;431:928-938. [PMID: 30664868 DOI: 10.1016/j.jmb.2019.01.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/09/2019] [Accepted: 01/14/2019] [Indexed: 10/27/2022]
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Hoffmann M, Fröhner C, Noé F. Reactive SINDy: Discovering governing reactions from concentration data. J Chem Phys 2019;150:025101. [DOI: 10.1063/1.5066099] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
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From membrane receptors to protein synthesis and actin cytoskeleton: Mechanisms underlying long lasting forms of synaptic plasticity. Semin Cell Dev Biol 2019;95:120-129. [PMID: 30634048 DOI: 10.1016/j.semcdb.2019.01.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 12/13/2022]
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The Interplay of Structural and Cellular Biophysics Controls Clustering of Multivalent Molecules. Biophys J 2019;116:560-572. [PMID: 30661665 DOI: 10.1016/j.bpj.2019.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/24/2018] [Accepted: 01/02/2019] [Indexed: 12/12/2022]  Open
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Tapia JJ, Saglam AS, Czech J, Kuczewski R, Bartol TM, Sejnowski TJ, Faeder JR. MCell-R: A Particle-Resolution Network-Free Spatial Modeling Framework. Methods Mol Biol 2019;1945:203-229. [PMID: 30945248 PMCID: PMC6580425 DOI: 10.1007/978-1-4939-9102-0_9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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