COPASI's Use In Biophysics

Peterson KJ, Loew LM (2024) Using SpringSaLaD mesoscale simulations with COPASI ODE parameter optimization to model membrane-associated kinetics based on measured volumetric rate constants. Biophysical Journal 123:22a Biophysics Link

1 publication
Naumov VV, Trofimov AV, Fedorova GF, Yablonskaya OI, Vasil’ev RF (2023) Kinetic Intricacies of the Light Emission and Antiradical Influence of Exogenous Bioantioxidants Transformation Products in the Chemiluminescence Bioantioxidant Assay. International Journal of Molecular Sciences 24:8486 Biochemistry Biophysics Link
Šimek J (2023) Is there a difference between 14-3-3 homo- and heterodimer? Diploma Thesis, Masaryk University, Brno, Czech Republic Macromolecular Biochemistry Biophysics Link
Yuan AT, Korkola NC, Stillman MJ (2023) Apo-metallothionein-3 cooperatively forms tightly compact structures under physiological conditions. Journal of Biological Chemistry 299:102899 Biochemistry Biophysics Link

3 publications
Faraj SE, Valsecchi WM, Ferreira-Gomes MS, Centeno M, Saint Martin EM, Fedosova NU, Rossi JPFC, Montes MR, Rossi RC (2022) Measurements of Na+-occluded intermediates during the catalytic cycle of the Na+/K+-ATPase provide novel insights into the mechanism of Na+ transport. Journal of Biological Chemistry 299:102811 Biochemistry Biophysics Link
Irgen-Gioro S, Yoshida SR, Walling V, Chong S (2022) Fixation can change the appearance of phase separation in living cells. eLife 11:e79903 Cell Biology Biophysics Link
Orrico F, Lopez AC, Saliwonczyk D, Acosta C, Rodriguez-Grecco I, Mouro-Chanteloup I, Ostuni MA, Denicola A, Thomson L, Möller MN (2022) The permeability of human red blood cell membranes to hydrogen peroxide is independent of aquaporins. Journal of Biological Chemistry 298:101503 Biophysics Biochemistry Link
Toyoda R, Hoang NV, Moghaddam KG, Crespi S, Pooler DRS, Faraji S, Pshenichnikov MS, Feringa BL (2022) Synergistic interplay between photoisomerization and photoluminescence in a light-driven rotary molecular motor. Nature Communications 13:5765 Biophysics Link

4 publications
Haque MA, Morozova K, Lawrence N, Ferrentino G, Scampicchio M (2021) Radical Scavenging Activity of Antioxidants by Cyclic Voltammetry. Electroanalysis 33:23–28 Chemistry Biophysics Link
Long BM, Förster B, Pulsford SB, Price GD, Badger MR (2021) Rubisco proton production can drive the elevation of CO2 within condensates and carboxysomes. Proceedings of the National Academy of Sciences USA 118:e2014406118 Metabolism Biophysics Plant Biology Link
Rosenbloom AD, Kovar EW, Kovar DR, Loew LM, Pollard TD (2021) Mechanism of actin filament nucleation. Biophysical Journal 120:4399–4417 Macromolecular Biochemistry Biophysics Link
Sotnikov DV, Berlina AN, Zherdev AV, Dzantiev BB (2021) Theoretical limitations for aggregation methods of analysis based on affine interactions. AIP Conference Proceedings 2371:070001 Biophysics Link
Virtanen O, Khorobrykh S, Tyystjärvi E (2021) Acclimation of Chlamydomonas reinhardtii to extremely strong light. Photosynthesis Research 147:91–106 Biophysics Microbiology Link

5 publications
Garzon Dasgupta AK, Martyanov AA, Filkova AA, Panteleev MA, Sveshnikova AN (2020) Development of a Simple Kinetic Mathematical Model of Aggregation of Particles or Clustering of Receptors. Life 10:E97 Biophysics Link
Karakhim SO, Zhuk PF, Kosterin SO (2020) Kinetics simulation of transmembrane transport of ions and molecules through a semipermeable membrane. Journal of Bioenergetics and Biomembranes 52:47–60 Biophysics Link
Pakhomov AA, Frolova AY, Tabakmakher VM, Chugunov AO, Efremov RG, Martynov VI (2020) Impact of external amino acids on fluorescent protein chromophore biosynthesis revealed by molecular dynamics and mutagenesis studies. Journal of Photochemistry and Photobiology B: Biology 206:111853 Biophysics Link
Schmallegger M, Barbon A, Bortolus M, Chemelli A, Bilkis I, Gescheidt G, Weiner L (2020) Systematic Quantification of Electron Transfer in a Bare Phospholipid Membrane Using Nitroxide-Labeled Stearic Acids: Distance Dependence, Kinetics, and Activation Parameters. Langmuir 36:10429–10437 Biophysics Biochemistry Link

4 publications
Aguilera LU, Bergmann FT, Dalmasso G, Elmas S, Elsässer T, Großeholz R, Holzheu P, Kalra P, Kummer U, Sahle S, Veith N (2019) Robustness of frequency vs. amplitude coding of calcium oscillations during changing temperatures. Biophysical Chemistry 245:17–24 Signaling Biophysics Link
Bell M, Bartol T, Sejnowski T, Rangamani P (2019) Dendritic spine geometry and spine apparatus organization govern the spatiotemporal dynamics of calcium. Journal of General Physiology 151:1017–1034 Cell Biology Biophysics Signaling Link
Cababie LA, Incicco JJ, González-Lebrero RM, Roman EA, Gebhard LG, Gamarnik AV, Kaufman SB (2019) Thermodynamic study of the effect of ions on the interaction between dengue virus NS3 helicase and single stranded RNA. Scientific Reports 9:10569 Biophysics Macromolecular Biochemistry Link
Hetmanski JHR, de Belly H, Busnelli I, Waring T, Nair RV, Sokleva V, Dobre O, Cameron A, Gauthier N, Lamaze C, Swift J, del Campo A, Starborg T, Zech T, Goetz JG, Paluch EK, Schwartz J-M, Caswell PT (2019) Membrane Tension Orchestrates Rear Retraction in Matrix-Directed Cell Migration. Developmental Cell 51:460-475.e10 Cell Biology Biophysics Link
Sinica V, Zimova L, Barvikova K, Macikova L, Barvik I, Vlachova V (2019) Human and Mouse TRPA1 Are Heat and Cold Sensors Differentially Tuned by Voltage. Cells 9:57 Biophysics Link
Xie Y, Kazmierczyk M, Graham BP, Dutia MB, Stefan MI, Dutia MB (2019) A multi-scale model reveals cellular and physiological mechanisms underlying hyperpolarisation-gated synaptic plasticity. bioRxiv doi:10.1101/418228 Macromolecular Biochemistry Biophysics Link

6 publications
Li X, Holmes WR (2018) Biophysical attributes that affect CaMKII activation deduced with a novel spatial stochastic simulation approach. PLoS Computational Biology 14:e1005946 Biophysics Signaling Link
Schams A, Britt M, Rowe I, Cetiner U, Anishkin A, Sukharev S (2018) Dissecting the Fast Hypoosmotic Permeability Response in E. coli. Biophysical Journal 114:112a–113a Biophysics Link
Wei Y, Mayoral-Delgado I, Stewart NA, Dymond MK (2018) Macromolecular crowding and membrane binding proteins: the case of phospholipase A1. Chemistry and Physics of Lipids 218:91–102 Biochemistry Biophysics Link
Winter F, Bludszuweit-Philipp C, Wolkenhauer O (2018) Mathematical analysis of the influence of brain metabolism on the BOLD signal in Alzheimer’s disease. Journal of Cerebral Blood Flow & Metabolism 38:304–316 Physiology Metabolism Biophysics Link

4 publications
Chelushkin MA, Panteleev MA, Sveshnikova AN (2017) Activation of the contact pathway of blood coagulation on the circulating microparticles may explain blood plasma coagulation induced by dilution. Biochemistry (Moscow) 11:130–143 Biophysics Link
Houwman JA (2017) The ribosome regulates flavodoxin folding. Ph.D. Thesis, Wageningen University, The Netherlands. Biophysics Biochemistry Link
Seitter H (2017) Retinal function of the voltage-gated calcium channel subunit α2δ-3 / Light-dependent effects in α2δ-3 mutant and in wild type retina. Ph.D. Thesis, Universität Tübingen, Germany. Biochemistry Biophysics Physiology Link
Tikidji-Hamburyan A, Reinhard K, Storchi R, Dietter J, Seitter H, Davis KE, Idrees S, Mutter M, Walmsley L, Bedford RA, Ueffing M, Ala-Laurila P, Brown TM, Lucas RJ, Münch TA (2017) Rods progressively escape saturation to drive visual responses in daylight conditions. Nature Communications 8:1813 Biochemistry Biophysics Physiology Link
Torbensen K, Ristori S, Rossi F, Abou-Hassan A (2017) Tuning the Chemical Communication of Oscillating Microdroplets by Means of Membrane Composition. Journal of Physical Chemistry 121:13256–13264 Chemistry Biophysics Link

5 publications
Pletneva NV, Pletnev S, Pakhomov AA, Chertkova RV, Martynov VI, Muslinkina L, Dauter Z, Pletnev VZ (2016) Crystal structure of the fluorescent protein from Dendronephthya sp. in both green and photoconverted red forms. Acta Crystallographica D72:922-932 Biophysics Link
Podoplelova NA, Sveshnikova AN, Kurasawa JH, Sarafanov AG, Chambost H, Vasil’ev SA, Demina IA, Ataullakhanov FI, Alessi M-C, Panteleev MA (2016) Hysteresis-like binding of coagulation factors X/Xa to procoagulant activated platelets and phospholipids results from multistep association and membrane-dependent multimerization. Biochimica et Biophysica Acta 1858:1216–1227 Immunology Biochemistry Biophysics Link

2 publications
Terentyeva VA, Sveshnikova AN, Panteleev MA (2015) Kinetics and mechanisms of surface-dependent coagulation factor XII activation. Journal of Theoretical Biology 382:235–243 Physiology Biophysics Link

1 publication
Rodriguez Plaza JG, Morales-Nava R, Diener C, Schreiber G, Gonzalez ZD, Lara Ortiz MT, Ortega Blake I, Pantoja O, Volkmer R, Klipp E, Herrmann A, Del Rio G (2014) Cell penetrating peptides and cationic antibacterial peptides: two sides of the same coin. Journal of Biological Chemistry 289:14448–14457 Macromolecular Biochemistry Biophysics Microbiology Link
Sugiura M, Azami C, Koyama K, Rutherford AW, Rappaport F, Boussac A (2014) Modification of the pheophytin redox potential in Thermosynechococcus elongatus Photosystem II with PsbA3 as D1. Biochimica et Biophysica Acta 1837:139–148 Metabolism Microbiology Biophysics Link

2 publications

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Phelix CF, Villareal G, Perez-Cordova M, Hernandez S, Perry G, Colom L (2012) P3-395: Reanimating basal forebrain cholinergic neurons in electrophysiology biosimulations using COPASI software. Alzheimer’s & Dementia 8:P593–P594 Physiology Biophysics Link

1 publication
Matuszak Z (2011) Photodynamic therapy of melanoma. Monte Carlo modeling of light transport in human pigmented skin. Bio Algorithms Med Syst. 7:85–93 Biophysics Link

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