Plunkett, Claire E.; Lawley, Sean D. Bimolecular binding rates for pairs of spherical molecules with small binding sites. (English) Zbl 1458.35430 Multiscale Model. Simul. 19, No. 1, 148-183 (2021). MSC: 35Q92 35B25 35C20 35J05 92C05 92C40 60J65 81V55 82D60 82M31 PDFBibTeX XMLCite \textit{C. E. Plunkett} and \textit{S. D. Lawley}, Multiscale Model. Simul. 19, No. 1, 148--183 (2021; Zbl 1458.35430) Full Text: DOI arXiv
Miles, Christopher E.; Lawley, Sean D.; Keener, James P. Analysis of nonprocessive molecular motor transport using renewal reward theory. (English) Zbl 1397.92038 SIAM J. Appl. Math. 78, No. 5, 2511-2532 (2018). MSC: 92C05 60K20 60J28 60H10 PDFBibTeX XMLCite \textit{C. E. Miles} et al., SIAM J. Appl. Math. 78, No. 5, 2511--2532 (2018; Zbl 1397.92038) Full Text: DOI arXiv
Boronovsky, S. E.; Nartsissov, Y. R. Computer simulator of glycine receptor activity: a new window into a virtual world. (English) Zbl 1361.92008 Bull. Math. Biol. 78, No. 7, 1380-1393 (2016). MSC: 92C05 92C40 60J70 PDFBibTeX XMLCite \textit{S. E. Boronovsky} and \textit{Y. R. Nartsissov}, Bull. Math. Biol. 78, No. 7, 1380--1393 (2016; Zbl 1361.92008) Full Text: DOI
Bernstein, Jason; Fricks, John Analysis of single particle diffusion with transient binding using particle filtering. (English) Zbl 1343.92143 J. Theor. Biol. 401, 109-121 (2016). MSC: 92C40 92C05 60J70 PDFBibTeX XMLCite \textit{J. Bernstein} and \textit{J. Fricks}, J. Theor. Biol. 401, 109--121 (2016; Zbl 1343.92143) Full Text: DOI
Simpson, D. J. W. Book review of: Z. Schuss, Brownian dynamics at boundaries and interfaces. In physics, chemistry, and biology. (English) Zbl 1306.00024 SIAM Rev. 56, No. 4, 72-723 (2014). MSC: 00A17 60-02 60-08 60H10 60J60 35Q84 92E20 92C05 92C20 92C40 PDFBibTeX XMLCite \textit{D. J. W. Simpson}, SIAM Rev. 56, No. 4, 72--723 (2014; Zbl 1306.00024) Full Text: DOI
Santillán, Moisés Chemical kinetics, stochastic processes, and irreversible thermodynamics. (English) Zbl 1295.92003 Lecture Notes on Mathematical Modelling in the Life Sciences. Cham: Springer (ISBN 978-3-319-06688-2/pbk; 978-3-319-06689-9/ebook). xiii, 126 p. (2014). Reviewer: Nina Shokina (Freiburg) MSC: 92-01 92-02 92C40 92C45 92C05 80A30 82C31 60H35 PDFBibTeX XMLCite \textit{M. Santillán}, Chemical kinetics, stochastic processes, and irreversible thermodynamics. Cham: Springer (2014; Zbl 1295.92003) Full Text: DOI
Plante, Ianik; Devroye, Luc; Cucinotta, Francis A. Random sampling of the Green’s functions for reversible reactions with an intermediate state. (English) Zbl 1301.82030 J. Comput. Phys. 242, 531-543 (2013). MSC: 82B80 65C05 82-08 60J65 81V55 92C05 PDFBibTeX XMLCite \textit{I. Plante} et al., J. Comput. Phys. 242, 531--543 (2013; Zbl 1301.82030) Full Text: DOI
Schuss, Zeev Brownian dynamics at boundaries and interfaces. In physics, chemistry, and biology. (English) Zbl 1305.60006 Applied Mathematical Sciences 186. New York, NY: Springer (ISBN 978-1-4614-7686-3/hbk; 978-1-4614-7687-0/ebook). xx, 322 p. (2013). Reviewer: P. R. C. Ruffino (Campinas) MSC: 60-02 60-08 60H10 60J60 35Q84 92E20 92C05 92C20 92C40 PDFBibTeX XMLCite \textit{Z. Schuss}, Brownian dynamics at boundaries and interfaces. In physics, chemistry, and biology. New York, NY: Springer (2013; Zbl 1305.60006) Full Text: DOI
Hughes, John; Hancock, William O.; Fricks, John Kinesins with extended neck linkers: A chemomechanical model for variable-length stepping. (English) Zbl 1251.92002 Bull. Math. Biol. 74, No. 5, 1066-1097 (2012). MSC: 92C05 92C40 60J20 92-08 92C37 60K10 PDFBibTeX XMLCite \textit{J. Hughes} et al., Bull. Math. Biol. 74, No. 5, 1066--1097 (2012; Zbl 1251.92002) Full Text: DOI Link
Shtylla, Blerta; Keener, James P. A mathematical model for force generation at the kinetochore-microtubule interface. (English) Zbl 1230.92009 SIAM J. Appl. Math. 71, No. 5, 1821-1848 (2011). MSC: 92C05 92C40 65C20 60J99 PDFBibTeX XMLCite \textit{B. Shtylla} and \textit{J. P. Keener}, SIAM J. Appl. Math. 71, No. 5, 1821--1848 (2011; Zbl 1230.92009) Full Text: DOI Link
Newby, Jay M.; Keener, James P. An asymptotic analysis of the spatially inhomogeneous velocity-jump process. (English) Zbl 1236.60079 Multiscale Model. Simul. 9, No. 2, 735-765 (2011). Reviewer: A. Świerniak (Gliwice) MSC: 60J75 35B25 60F10 92C05 92C40 60H35 60H15 35C20 PDFBibTeX XMLCite \textit{J. M. Newby} and \textit{J. P. Keener}, Multiscale Model. Simul. 9, No. 2, 735--765 (2011; Zbl 1236.60079) Full Text: DOI
Ben-Ari, Iddo; Boushaba, Khalid; Matzavinos, Anastasios; Roitershtein, Alexander Stochastic analysis of the motion of DNA nanomechanical bipeds. (English) Zbl 1220.92005 Bull. Math. Biol. 73, No. 8, 1932-1951 (2011). MSC: 92C05 92C40 60G50 60F17 60F15 PDFBibTeX XMLCite \textit{I. Ben-Ari} et al., Bull. Math. Biol. 73, No. 8, 1932--1951 (2011; Zbl 1220.92005) Full Text: DOI
Newby, Jay M.; Bressloff, Paul C. Quasi-steady state reduction of molecular motor-based models of directed intermittent search. (English) Zbl 1203.92006 Bull. Math. Biol. 72, No. 7, 1840-1866 (2010). MSC: 92C05 65C05 60K99 PDFBibTeX XMLCite \textit{J. M. Newby} and \textit{P. C. Bressloff}, Bull. Math. Biol. 72, No. 7, 1840--1866 (2010; Zbl 1203.92006) Full Text: DOI Link
Sergienko, I. V.; Ryazanov, V. V.; Biletskyy, B. A.; Byts, A. V.; Gupal, A. M.; Rzhepeskyy, S. S. Methods to predict protein spatial structure. (English. Russian original) Zbl 1204.92035 Cybern. Syst. Anal. 46, No. 1, 34-50 (2010); translation from Kibern. Sist. Anal. 2010, No. 1, 38-58 (2010). MSC: 92C40 92C05 60J20 05C90 PDFBibTeX XMLCite \textit{I. V. Sergienko} et al., Cybern. Syst. Anal. 46, No. 1, 34--50 (2010; Zbl 1204.92035); translation from Kibern. Sist. Anal. 2010, No. 1, 38--58 (2010) Full Text: DOI
Kramer, Peter R.; Latorre, Juan C.; Khan, Adnan A. Two coarse-graining studies of stochastic models in molecular biology. (English) Zbl 1195.92020 Commun. Math. Sci. 8, No. 2, 481-517 (2010). MSC: 92C40 92C05 60J20 60J70 PDFBibTeX XMLCite \textit{P. R. Kramer} et al., Commun. Math. Sci. 8, No. 2, 481--517 (2010; Zbl 1195.92020) Full Text: DOI Euclid
Avetisov, V. A.; Bikulov, A. Kh. Ultrametricity of fluctuation dynamic mobility of protein molecules. (English. Russian original) Zbl 1179.92007 Proc. Steklov Inst. Math. 265, 75-81 (2009); translation from Tr. Mat. Inst. Steklova 265, 82-89 (2009). MSC: 92C05 92C40 60J70 54E35 PDFBibTeX XMLCite \textit{V. A. Avetisov} and \textit{A. Kh. Bikulov}, Proc. Steklov Inst. Math. 265, 75--81 (2009; Zbl 1179.92007); translation from Tr. Mat. Inst. Steklova 265, 82--89 (2009) Full Text: DOI
Arsuaga, J.; Borgo, B.; Diao, Y.; Scharein, R. The growth of the mean average crossing number of equilateral polygons in confinement. (English) Zbl 1182.92026 J. Phys. A, Math. Theor. 42, No. 46, Article ID 465202, 9 p. (2009). MSC: 92C40 92C05 57M25 60D05 PDFBibTeX XMLCite \textit{J. Arsuaga} et al., J. Phys. A, Math. Theor. 42, No. 46, Article ID 465202, 9 p. (2009; Zbl 1182.92026) Full Text: DOI Link
Hendricks, Adam G.; Epureanu, Bogdan I.; Meyhöfer, Edgar Mechanistic mathematical model of kinesin under time and space fluctuating loads. (English) Zbl 1172.92003 Nonlinear Dyn. 53, No. 4, 303-320 (2008). MSC: 92C05 92C40 60J65 65C05 PDFBibTeX XMLCite \textit{A. G. Hendricks} et al., Nonlinear Dyn. 53, No. 4, 303--320 (2008; Zbl 1172.92003) Full Text: DOI
Ando, Tadashi Brownian dynamics simulation for protein folding and binding. (English) Zbl 1177.92009 García, Julio César (ed.) et al., Quantum probability and related topics. Proceedings of the 28th conference, CIMAT-Guanajuato, Mexico, 2–8 September 2007. Hackensack, NJ: World Scientific (ISBN 978-981-283-526-0/hbk). QP-PQ: Quantum Probability and White Noise Analysis 23, 11-22 (2008). MSC: 92C40 60J70 92C05 PDFBibTeX XMLCite \textit{T. Ando}, in: Quantum probability and related topics. Proceedings of the 28th conference, CIMAT-Guanajuato, Mexico, 2--8 September 2007. Hackensack, NJ: World Scientific. 11--22 (2008; Zbl 1177.92009)
Chowdhury, Debashish; Garai, Ashok; Greulich, Philip; Nishinari, Katsuhiro; Schadschneider, Andreas; Tripathi, Tripti; Wang, Jian-Sheng From CA to gene expression: Machines and mechanisms. (English) Zbl 1159.92301 Umeo, Hiroshi (ed.) et al., Cellular automata. 8th international conference on cellular automata for research and industry, ACRI 2008, Yokohama, Japan, September 23–26, 2008. Proceedings. Berlin: Springer (ISBN 978-3-540-79991-7/pbk). Lecture Notes in Computer Science 5191, 1-10 (2008). MSC: 92C05 92C40 60K35 PDFBibTeX XMLCite \textit{D. Chowdhury} et al., Lect. Notes Comput. Sci. 5191, 1--10 (2008; Zbl 1159.92301) Full Text: DOI
Deville, R. E. Lee; Vanden-Eijnden, Eric Regularity and synchrony in motor proteins. (English) Zbl 1139.92014 Bull. Math. Biol. 70, No. 2, 484-516 (2008). MSC: 92C40 92C05 60G35 92C30 PDFBibTeX XMLCite \textit{R. E. L. Deville} and \textit{E. Vanden-Eijnden}, Bull. Math. Biol. 70, No. 2, 484--516 (2008; Zbl 1139.92014) Full Text: DOI
Lipowsky, Reinhard; Liepelt, Steffen Chemomechanical coupling of molecular motors: thermodynamics, network representations, and balance conditions. (English) Zbl 1134.82043 J. Stat. Phys. 130, No. 1, 39-67 (2008). MSC: 82C41 60J25 92C40 92C05 PDFBibTeX XMLCite \textit{R. Lipowsky} and \textit{S. Liepelt}, J. Stat. Phys. 130, No. 1, 39--67 (2008; Zbl 1134.82043) Full Text: DOI
Harada, Takahiro; Sasa, Shin-Ichi Fluctuations, responses and energetics of molecular motors. (English) Zbl 1117.92003 Math. Biosci. 207, No. 2, 365-386 (2007). MSC: 92C05 92C50 60J65 60J60 PDFBibTeX XMLCite \textit{T. Harada} and \textit{S.-I. Sasa}, Math. Biosci. 207, No. 2, 365--386 (2007; Zbl 1117.92003) Full Text: DOI arXiv
Krstić, Vladimir; Maglica, Željka; Paljetak, Hana Čipčić; Podobnik, Boris; Pavin, Nenad Min-protein oscillations in E. coli : three-dimensional off-lattice stochastic reaction-diffusion model. (English) Zbl 1118.92002 J. Stat. Phys. 128, No. 1-2, 5-20 (2007). MSC: 92C05 92C40 60H30 82D60 PDFBibTeX XMLCite \textit{V. Krstić} et al., J. Stat. Phys. 128, No. 1--2, 5--20 (2007; Zbl 1118.92002) Full Text: DOI
Yang, Xiao-Dong; Melnik, Roderick V. N. Effect of internal viscosity on Brownian dynamics of DNA molecules in shear flow. (English) Zbl 1124.92004 Comput. Biol. Chem. 31, No. 2, 110-114 (2007). MSC: 92C05 92C40 60J65 PDFBibTeX XMLCite \textit{X.-D. Yang} and \textit{R. V. N. Melnik}, Comput. Biol. Chem. 31, No. 2, 110--114 (2007; Zbl 1124.92004) Full Text: DOI arXiv
Chodera, John D.; Swope, William C.; Pitera, Jed W.; Dill, Ken A. Long-time protein folding dynamics from short-time molecular dynamics simulations. (English) Zbl 1133.92011 Multiscale Model. Simul. 5, No. 4, 1214-1226 (2006). Reviewer: Marius Iosifescu (Bucureşti) MSC: 92C40 60J20 92C05 74A25 PDFBibTeX XMLCite \textit{J. D. Chodera} et al., Multiscale Model. Simul. 5, No. 4, 1214--1226 (2006; Zbl 1133.92011) Full Text: DOI
Aerts, Diederik; Czachor, Marek Abstract DNA-type systems. (English) Zbl 1084.92016 Nonlinearity 19, No. 3, 575-589 (2006). MSC: 92C40 37N25 92C05 92C45 60K35 PDFBibTeX XMLCite \textit{D. Aerts} and \textit{M. Czachor}, Nonlinearity 19, No. 3, 575--589 (2006; Zbl 1084.92016) Full Text: DOI arXiv
Buša, Ján; Džurina, Jozef; Hayryan, Edik; Hayryan, Shura; Hu, Chin-Kun; Plavka, Ján; Pokorný, Imrich; Skřivánek, Jaroslav; Wu, Ming-Chya ARVO: A Fortran package for computing the solvent accessible surface area and the excluded volume of overlapping spheres via analytic equations. (English) Zbl 1196.92001 Comput. Phys. Commun. 165, No. 1, 59-96 (2005). MSC: 92-04 92C05 92C40 60K35 92-08 PDFBibTeX XMLCite \textit{J. Buša} et al., Comput. Phys. Commun. 165, No. 1, 59--96 (2005; Zbl 1196.92001) Full Text: DOI
Hanke, Andreas; Metzler, Ralf Bubble dynamics in DNA. (English) Zbl 1073.92502 J. Phys. A, Math. Gen. 36, No. 36, L473-L480 (2003). MSC: 92C05 92C40 60J70 PDFBibTeX XMLCite \textit{A. Hanke} and \textit{R. Metzler}, J. Phys. A, Math. Gen. 36, No. 36, L473--L480 (2003; Zbl 1073.92502) Full Text: DOI arXiv
Lachal, Aimé Some probability distributions in modeling DNA replication. (English) Zbl 1043.92010 Ann. Appl. Probab. 13, No. 3, 1207-1230 (2003). Reviewer: P. R. Parthasarathy (Chennai) MSC: 92C40 92C05 60K05 34K60 PDFBibTeX XMLCite \textit{A. Lachal}, Ann. Appl. Probab. 13, No. 3, 1207--1230 (2003; Zbl 1043.92010) Full Text: DOI
Chipot, Michel; Kinderlehrer, David; Kowalczyk, Michal A variational principle for molecular motors. (English) Zbl 1032.92005 Meccanica 38, No. 5, 505-518 (2003). MSC: 92C05 92C37 60J70 PDFBibTeX XMLCite \textit{M. Chipot} et al., Meccanica 38, No. 5, 505--518 (2003; Zbl 1032.92005) Full Text: DOI
Maes, Christian; van Wieren, Maarten H. A Markov model for kinesin. (English) Zbl 1016.92010 J. Stat. Phys. 112, No. 1-2, 329-355 (2003). MSC: 92C40 60J20 92C05 82C10 PDFBibTeX XMLCite \textit{C. Maes} and \textit{M. H. van Wieren}, J. Stat. Phys. 112, No. 1--2, 329--355 (2003; Zbl 1016.92010) Full Text: DOI
Baumann, Gerd; Kleinschmidtt, Siglinde; Kleinschmidt, Albrecht K. A headful of T4 coliphage DNA: dynamical modelling. (English) Zbl 1134.92306 Losa, Gabriele A. (ed.) et al., Fractals in biology and medicine. Vol. 3. 3rd international symposium, Centro Seminariale Monte Verità, Ascona, Switzerland, March 8–11, 2000. Basel: Birkhäuser (ISBN 3-7643-6474-2). 287-309 (2002). MSC: 92C05 60J70 92C40 PDFBibTeX XMLCite \textit{G. Baumann} et al., in: Fractals in biology and medicine. Vol. 3. 3rd international symposium, Centro Seminariale Monte Verità, Ascona, Switzerland, March 8--11, 2000. Basel: Birkhäuser. 287--309 (2002; Zbl 1134.92306)
Resendis-Antonio, O. A Fokker-Planck framework in the PolyC:PolyG denaturation. (English) Zbl 0998.92002 Physica A 312, No. 3-4, 307-314 (2002). MSC: 92C05 60J70 92C40 PDFBibTeX XMLCite \textit{O. Resendis-Antonio}, Physica A 312, No. 3--4, 307--314 (2002; Zbl 0998.92002) Full Text: DOI
Carlini, P.; Bizzarri, A. R.; Cannistraro, S. Temporal fluctuations in the potential energy of proteins: \(1/f^{\alpha}\) noise and diffusion. (English) Zbl 1001.92008 Physica D 165, No. 3-4, 242-250 (2002). MSC: 92C05 92C40 60J70 PDFBibTeX XMLCite \textit{P. Carlini} et al., Physica D 165, No. 3--4, 242--250 (2002; Zbl 1001.92008) Full Text: DOI
Tsironis, G. P. Noise in molecular systems. (English) Zbl 1026.92019 Christiansen, P. L. (ed.) et al., Nonlinear science at the dawn of the 21st century. Berlin: Springer. Lect. Notes Phys. 542, 357-370 (2000). MSC: 92C40 92C05 60J70 PDFBibTeX XMLCite \textit{G. P. Tsironis}, Lect. Notes Phys. 542, 357--370 (2000; Zbl 1026.92019)
Tüzel, Erkan; Erzan, Ayşe Dissipative dynamics and the statistics of energy states of a Hookean model for protein folding. (English) Zbl 1002.92508 J. Stat. Phys. 100, No. 1-2, 405-422 (2000). MSC: 92C05 92C40 60J70 PDFBibTeX XMLCite \textit{E. Tüzel} and \textit{A. Erzan}, J. Stat. Phys. 100, No. 1--2, 405--422 (2000; Zbl 1002.92508) Full Text: DOI arXiv
Duan, Jinqiao Probabilistic structural dynamics of protein folding. (English) Zbl 1017.92015 Appl. Math. Comput. 113, No. 1, 97-100 (2000). MSC: 92C40 92C05 60J70 92D20 PDFBibTeX XMLCite \textit{J. Duan}, Appl. Math. Comput. 113, No. 1, 97--100 (2000; Zbl 1017.92015) Full Text: DOI
Elston, Timothy C.; You, Dwight; Peskin, Charles S. Protein flexibility and the correlation ratchet. (English) Zbl 1038.92004 SIAM J. Appl. Math. 61, No. 3, 776-791 (2000). MSC: 92C05 92C40 60J70 PDFBibTeX XMLCite \textit{T. C. Elston} et al., SIAM J. Appl. Math. 61, No. 3, 776--791 (2000; Zbl 1038.92004) Full Text: DOI
Elston, Timothy C.; Peskin, Charles S. The role of protein flexibility in molecular motor function: Coupled diffusion in a tilted periodic potential. (English) Zbl 1008.92004 SIAM J. Appl. Math. 60, No. 3, 842-867 (2000). MSC: 92C05 60J70 92C40 PDFBibTeX XMLCite \textit{T. C. Elston} and \textit{C. S. Peskin}, SIAM J. Appl. Math. 60, No. 3, 842--867 (2000; Zbl 1008.92004) Full Text: DOI
Sachs, Rainer K.; Ponomarev, Artem L.; Hahnfeldt, Philip; Hlatky, Lynn R. Locations of radiation-produced DNA double strand breaks along chromosomes: A stochastic cluster process formalism. (English) Zbl 0977.92001 Math. Biosci. 159, No. 2, 165-187 (1999). MSC: 92C05 92C40 92C50 60G35 PDFBibTeX XMLCite \textit{R. K. Sachs} et al., Math. Biosci. 159, No. 2, 165--187 (1999; Zbl 0977.92001) Full Text: DOI
Fernández, Ariel Searching for the underlying action principle that governs biopolymer folding. (English) Zbl 0876.92010 Fernández Stacco, Edgardo L. (ed.) et al., Proceedings of the 3rd conference of mathematics “Dr. Antonio A. R. Monteiro”, Bahía Blanca, Argentina, April 26-28, 1995. Bahía Blanca: Universidad Nacional del Sur, Dept. de Matemática, 107-120 (1996). MSC: 92C40 60K35 92C05 82D60 60K40 PDFBibTeX XMLCite \textit{A. Fernández}, in: Actas del tercer congreso de matemática ``Dr. Antonio A. R. Monteiro'', Bahía Blanca, Argentina, abril 26-28, 1995. Bahía Blanca: Universidad Nacional del Sur, Dept. de Matemática. 107--120 (1996; Zbl 0876.92010)
Dickinson, Richard B.; Tranquillo, Robert T. A stochastic model for adhesion-mediated cell random motility and haptotaxis. (English) Zbl 0811.92003 J. Math. Biol. 31, No. 6, 563-600 (1993). MSC: 92C05 92C30 60H30 60H15 92C40 PDFBibTeX XMLCite \textit{R. B. Dickinson} and \textit{R. T. Tranquillo}, J. Math. Biol. 31, No. 6, 563--600 (1993; Zbl 0811.92003) Full Text: DOI
Dankov, G. Yu. Mathematical models in radiobiology. (Matematicheskie modeli v radiobiologii.) (Russian) Zbl 0791.92014 Moskva: Izdatel’stvo Moskovskogo Universiteta. 199 p. (1992). Reviewer: A.Balint (Timişoara) MSC: 92C50 92-02 60J99 60K99 PDFBibTeX XMLCite \textit{G. Yu. Dankov}, Matematicheskie modeli v radiobiologii (Russian). Moskva: Izdatel'stvo Moskovskogo Universiteta (1992; Zbl 0791.92014)