Research Topics
| H QianSummaryAffiliation: University of Washington Country: USA Publications
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Detail Information
Publications
Open-system nonequilibrium steady state: statistical thermodynamics, fluctuations, and chemical oscillationsHong Qian
Department of Applied Mathematics, University of Washington, Seattle, Washington 98195, USA
J Phys Chem B 110:15063-74. 2006..The case studies illustrate an emerging theory for the isothermal nonequilibrium steady state of open systems...- Cooperativity in cellular biochemical processes: noise-enhanced sensitivity, fluctuating enzyme, bistability with nonlinear feedback, and other mechanisms for sigmoidal responsesHong Qian
Department of Applied Mathematics, University of Washington, Seattle, Washington 98195, USA
Annu Rev Biophys 41:179-204. 2012..The former gives rise to self-organized complexity, and the latter contains useful, albeit hidden, free energy that can be utilized for biological functions. There could be structures and energy in biochemical fluctuations... - Linear analysis near a steady-state of biochemical networks: control analysis, correlation metrics and circuit theoryWilliam J Heuett
Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
BMC Syst Biol 2:44. 2008..Here, we present a comprehensive theory of linear analysis for nonequilibrium steady-state (NESS) biochemical reaction networks that unites these disparate approaches in a common mathematical framework and thermodynamic basis... - Reducing intrinsic biochemical noise in cells and its thermodynamic limitHong Qian
Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA
J Mol Biol 362:387-92. 2006..We also study an optimal kinetic network design that is capable of approaching the thermodynamic limit... - Thermodynamic and kinetic analysis of sensitivity amplification in biological signal transductionHong Qian
Department of Applied Mathematics, University of Washington Seattle, WA 98195 2420, USA
Biophys Chem 105:585-93. 2003..Both utilize multiple kinetic cycles in time to gain temporal cooperativity, in contrast to allosteric cooperativity that utilizes multiple subunits in a protein... - Fluorescence correlation spectroscopy with high-order and dual-color correlation to probe nonequilibrium steady statesHong Qian
Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA
Proc Natl Acad Sci U S A 101:2828-33. 2004.... - Cooperativity and specificity in enzyme kinetics: a single-molecule time-based perspectiveHong Qian
Department of Applied Mathematics, University of Washington, Seattle, Washington, USA
Biophys J 95:10-7. 2008..The theory unifies dynamic cooperativity and Hopfield-Ninio's kinetic proofreading mechanism for specificity amplification... - Temporal cooperativity and sensitivity amplification in biological signal transductionHong Qian
Department of Applied Mathematics, University of Washington, Seattle, Washington 98195, USA
Biochemistry 47:2211-20. 2008..The theory is applicable to a wide range of processes in cell signaling including the specificity and sensitivity of T-cell activation... - An asymptotic comparative analysis of the thermodynamics of non-covalent associationH Qian
Department of Applied Mathematics, University of Washington, Seattle, WA 98195 2420, USA
J Math Biol 52:277-89. 2006..This work provides a mathematical basis for modeling non-covalent association processes in biology... - Phosphorylation energy hypothesis: open chemical systems and their biological functionsHong Qian
Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA
Annu Rev Phys Chem 58:113-42. 2007.... - Metabolic futile cycles and their functions: a systems analysis of energy and controlH Qian
Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA
Syst Biol (Stevenage) 153:192-200. 2006..The possibility of different roles for the two major mechanisms within cellular biochemical regulation, namely reversible chemical modifications via futile cycles and shifting equilibrium by macromolecular binding, are discussed... - Thermodynamics of stoichiometric biochemical networks in living systems far from equilibriumHong Qian
Departments of Applied Mathematics and Bioengineering, University of Washington, Seattle, 98195, USA
Biophys Chem 114:213-20. 2005..Energy conservation and the Second Law are established for steady-state and dynamic biochemical networks. The theory provides the physiochemical basis for analyzing large-scale metabolic networks in living organisms... - Hydrogen exchange kinetics of proteins in denaturants: a generalized two-process modelH Qian
Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA
J Mol Biol 286:607-16. 1999..This simple, minimalist's view of protein folding is consistent with various recent experimental observations on folding kinetics by HX... - Stochastic bifurcation, slow fluctuations, and bistability as an origin of biochemical complexityHong Qian
Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA
Phys Chem Chem Phys 11:4861-70. 2009..The implications of bistability to biochemical complexity are discussed... - Stoichiometric network theory for nonequilibrium biochemical systemsHong Qian
Department of Applied Mathematics and Bioengineering, University of Washington, Seattle, USA
Eur J Biochem 270:415-21. 2003..For sufficiently small flux a linear relationship between J and deltamu can be established as the linear flux-force relation in irreversible thermodynamics, analogous to Ohm's law in electrical circuits... - Quantitative study of polymer conformation and dynamics by single-particle trackingH Qian
Department of Applied Mathematics, University of Washington, Seattle, Washington 98195, USA
Biophys J 76:1598-605. 1999..Combining high precision measurements with the theoretical analysis presented here creates a powerful tool for studying conformational dynamics of biological and synthetic macromolecules at the single-molecule level... - Terminal twist induced continuous writhe of a circular rod with intrinsic curvatureH Qian
Department of Applied Mathematics, University of Washington, Seattle 98195, USA
J Biomol Struct Dyn 16:663-9. 1998..The implication of this result on elastic models of circular DNA is discussed... - Single-particle tracking: Brownian dynamics of viscoelastic materialsH Qian
Departments of Applied Mathematics and Bioengineering, University of Washington, Seattle, Washington 98195, USA
Biophys J 79:137-43. 2000.... - From discrete protein kinetics to continuous Brownian dynamics: a new perspectiveHong Qian
Department of Applied Mathematics, University of Washington, Seattle, Washington 98195 2420, USA
Protein Sci 11:1-5. 2002..A semiquantitative analysis based on Brownian dynamics in a continuous energy landscape offers a more comprehensive description for motions of biological macromolecules... - A mathematical analysis for the Brownian dynamics of a DNA tetherH Qian
Department of Applied Mathematics, University of Wahington, Seattle, WA 98195, USA
J Math Biol 41:331-40. 2000.... - Nonequilibrium thermodynamics and nonlinear kinetics in a cellular signaling switchHong Qian
Department of Applied Mathematics, University of Washington, Seattle, Washington 98195, USA
Phys Rev Lett 94:028101. 2005.... - Entropy demystified the "thermo"-dynamics of stochastically fluctuating systemsHong Qian
Department of Applied Mathematics, University of Washington, Seattle, Washington, USA
Methods Enzymol 467:111-34. 2009..Two examples from molecular biophysics, the efficiency of a motor protein ATPase and the substrate specificity of a phosphorylation-dephosphorylation cycle are discussed... - Stochastic bistability and bifurcation in a mesoscopic signaling system with autocatalytic kinaseLisa M Bishop
Department of Applied Mathematics, University of Washington, Seattle, Washington, USA
Biophys J 98:1-11. 2010..A previous reported noise-induced bistability in futile cycles is found to have originated from the kinase synchronization in a bistable system with slow transitions, as reported here... - Ultrasensitive dual phosphorylation dephosphorylation cycle kinetics exhibits canonical competition behaviorQingdao Huang
Department of Applied Mathematics, University of Washington, Seattle, Washington 98195, USA
Chaos 19:033109. 2009..A stochastic interpretation is also provided that further gives intuitive understanding of the bistable behavior inside the cells... - Stochastic dynamics and non-equilibrium thermodynamics of a bistable chemical system: the Schlögl model revisitedMelissa Vellela
Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA
J R Soc Interface 6:925-40. 2009..Finally, in the appendix section is an illustration of how the diffusion approximation of the chemical master equation can fail to represent correctly the mesoscopically interesting steady-state behaviour of the system... - Free-energy distribution of binary protein-protein binding suggests cross-species interactome differencesYi Y Shi
Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA
Proc Natl Acad Sci U S A 103:11527-32. 2006..This result is consistent with the evolution of increased protein unfoldedness and challenges the dogma that only specific protein-protein interactions can be biologically functional... - A stochastic model of oscillatory blood testosterone levelsWilliam J Heuett
Department of Applied Mathematics, University of Washington, Seattle, WA 98195 2420, USA
Bull Math Biol 68:1383-99. 2006..The Gillespie algorithm is used to simulate the hormone secretion model. Important parameters of the model are discussed and results from the model are compared to experimental observations... - Multiscale modeling of cardiac cellular energeticsJames B Bassingthwaighte
Bioengineering Department, University of Washington, Box 357962, Seattle, WA 98195 7962, USA
Ann N Y Acad Sci 1047:395-424. 2005..Currently there is to this end no established methodology from computational sciences... - Chromatin looping and the probability of transcriptionQiliang Li
Division of Medical Genetics, Department of Medicine, Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA
Trends Genet 22:197-202. 2006..This model can explain gene expression changes in the Hoxd gene cluster and the beta-globin locus... - Grand canonical Markov model: a stochastic theory for open nonequilibrium biochemical networksWilliam J Heuett
Department of Applied Mathematics, University of Washington, Seattle, Washington 98195, USA
J Chem Phys 124:044110. 2006..We are also able to suggest novel methods for experimentally determining reaction fluxes and biochemical affinities at nonequilibrium steady state as well as the overall network connectivity... - A quasistationary analysis of a stochastic chemical reaction: Keizer's paradoxMelissa Vellela
Department of Applied Mathematics, University of Washington Seattle, Seattle, WA 98195, USA
Bull Math Biol 69:1727-46. 2007..The appropriate system size that can be considered sufficiently large, an important parameter in numerical computation, is also discussed... - Energy balance for analysis of complex metabolic networksDaniel A Beard
Department of Bioengineering, University of Washington, Seattle, Washington 98915, USA
Biophys J 83:79-86. 2002..We show that EBA eliminates thermodynamically infeasible results associated with FBA... - A perturbation analysis of rate theory of self-regulating genes and signaling networksPei Zhe Shi
Department of Applied Mathematics, University of Washington, Seattle, Washington 98195, USA
J Chem Phys 134:065104. 2011..Generalization of the present approach can be included in multiple time-scale numerical computations for large biochemical networks... - Open-system thermodynamic analysis of DNA polymerase fidelityField Cady
Department of Applied Mathematics, University of Washington, Seattle, 98195, USA
Phys Biol 6:036011. 2009..The mechanism discussed in the present paper is not limited to DNA replication alone; it may be applicable to other biochemical systems... - Motor protein with nonequilibrium potential: Its thermodynamics and efficiencyHong Qian
Department of Applied Mathematics, University of Washington, Seattle, Washington 98195, USA
Phys Rev E Stat Nonlin Soft Matter Phys 69:012901. 2004..dS, representing the energy input. In terms of micro and h(d) the thermodynamic energy conservation in the mesoscopic stochastic system can be rigorously established and various types of motor efficiency are elucidated... - A stochastic analysis of a Brownian ratchet model for actin-based motilityHong Qian
Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA
Mech Chem Biosyst 1:267-78. 2004..For comparison, a continuous diffusion formalism of the BR model with great analytical simplicity is also studied... - Single-molecule enzymology: stochastic Michaelis-Menten kineticsHong Qian
Department of Applied Mathematics, University of Washington, WA Seattle 98195, USA
Biophys Chem 101:565-76. 2002..We suggest that in addition to fluctuating enzyme conformation, the stochastic nature of substrate concentration fluctuations is another possible source of the complex behavior of single-molecule enzyme kinetics... - A mechanism for SRC kinase-dependent signaling by noncatalytic receptorsJonathan A Cooper
Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
Biochemistry 47:5681-8. 2008..Other events that regulate signaling in specific cases may have evolved for fine-tuning of this basic mechanism... - Quantitative model for binary measurements of protein-protein interactionsYi Y Shi
Department of Applied Mathematics, University of Washington, Seattle, Washington 98195, USA
J Comput Biol 14:1011-23. 2007..It is also shown that not only the association constants but also the protein abundance could be a factor in producing the power-law degree distribution of protein-protein interaction networks... - Viscoelasticity of living materials: mechanics and chemistry of muscle as an active macromolecular systemHong Qian
Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA
Mol Cell Biomech 5:107-17. 2008..Some disparity between the mechanical and the chemical views of cross-bridges and motor proteins are noted, and a duality between force and energy in discrete states and transitions of macromolecular systems is discussed... - Clustering coefficients of protein-protein interaction networksGerald A Miller
Department of Physics, University of Washington Seattle, Seattle, WA 98195, USA
Phys Rev E Stat Nonlin Soft Matter Phys 75:051910. 2007..This shows that degree distributions are not sufficient to determine the properties of PINs... - DUX4, a candidate gene of facioscapulohumeral muscular dystrophy, encodes a transcriptional activator of PITX1Manjusha Dixit
Center for Genetic Medicine Research, Children s National Medical Center, Washington, DC 20010, USA
Proc Natl Acad Sci U S A 104:18157-62. 2007..Our results suggest that up-regulation of both DUX4 and PITX1 in FSHD muscles may play critical roles in the molecular mechanisms of the disease... - Sensitivity and specificity amplification in signal transductionGuangpu Li
Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
Cell Biochem Biophys 39:45-59. 2003..These studies have provided insights into the sensitivity and specificity amplification of biological signals in integrated systems... - Nonequilibrium steady state of a nanometric biochemical system: determining the thermodynamic driving force from single enzyme turnover time tracesWei Min
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
Nano Lett 5:2373-8. 2005..The statistical precisions of these three Deltamu estimators are analyzed and compared for experimental time traces with finite lengths... - Amplifying signal transduction specificity without multiple phosphorylationHong Qian
Biophys J 84:1410-1. 2003 - Kinetic timing: a novel mechanism that improves the accuracy of GTPase timers in endosome fusion and other biological processesGuangpu Li
Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, 940 SL Young Blvd, BMSB 853, Oklahoma City, OK 73104, USA
Traffic 3:249-55. 2002..It also explains the necessity for the existence of multiple GTP-bound intermediates identified by fluorescence spectroscopy and nuclear magnetic resonance studies... - Powering a burnt bridges Brownian ratchet: a model for an extracellular motor driven by proteolysis of collagenSaveez Saffarian
Cell Biology Department, Harvard Medical School/CBR, 200 Longwood Avenue, Boston, MA 02115, USA
Phys Rev E Stat Nonlin Soft Matter Phys 73:041909. 2006..1 pN stall force for individual collagenase molecules. A dimer, surprisingly, can generate a force in the range of 5 pN, suggesting that the motor can be of biological significance... - Thermodynamic-based computational profiling of cellular regulatory control in hepatocyte metabolismDaniel A Beard
Biotechnology and Bioengineering Center, Dept of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226, USA
Am J Physiol Endocrinol Metab 288:E633-44. 2005.... - Ab initio prediction of thermodynamically feasible reaction directions from biochemical network stoichiometryFeng Yang
Biotechnology and Bioengineering Center, Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
Metab Eng 7:251-9. 2005..We show that for a reaction network of 44 internal reactions representing energy metabolism, the computed linear inequality constraints represent necessary and sufficient conditions for thermodynamic feasibility... - Synchronized dynamics and non-equilibrium steady states in a stochastic yeast cell-cycle networkHao Ge
School of Mathematical Sciences, Peking University, Beijing, PR China
Math Biosci 211:132-52. 2008..Such a large separation in the magnitude of the circulations, between a dominant, main cycle and the rest, gives rise to the stochastic synchronization phenomenon... - Combining flux and energy balance analysis to model large-scale biochemical networksWilliam J Heuett
Department of Physics, University of Colorado, 390 UCB, Boulder, Colorado 80309 0390, USA
J Bioinform Comput Biol 4:1227-43. 2006..As a result, we suggest a novel optimization with respect to the heat dissipation rate of a system. We also emphasize the importance of incorporating interactions between a model network and its surroundings... - Thermodynamic constraints for biochemical networksDaniel A Beard
Biotechnology and Bioengineering Center, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
J Theor Biol 228:327-33. 2004.... - Oxygen-sensitive {delta}-opioid receptor-regulated survival and death signals: novel insights into neuronal preconditioning and protectionMing-Chieh Ma
Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
J Biol Chem 280:16208-18. 2005..Our findings demonstrate a novel mechanism of HPC neuroprotection (i.e. the intracellular up-regulation of DOR-regulated survival signals)... - Regional differences in rates of plant speciation and molecular evolution: a comparison between eastern Asia and eastern North AmericaQiu Yun Jenny Xiang
Department of Botany, North Carolina State University, Raleigh, North Carolina 27695 7612, USA
Evolution 58:2175-84. 2004..The close relationship between rates of ITS evolution and species richness further suggests that species production may be directly linked to rate of nucleotide substitution... - In vitro and in vivo activity of R547: a potent and selective cyclin-dependent kinase inhibitor currently in phase I clinical trialsWanda DePinto
Discovery Oncology, Hoffmann La Roche, Inc, 340 Kingsland Street, Nutley, NJ 07110, USA
Mol Cancer Ther 5:2644-58. 2006..R547 is currently being evaluated in phase I clinical trials... - Cytokines regulate postnatal hematopoietic stem cell expansion: opposing roles of thrombopoietin and LNKNatalija Buza-Vidas
Hematopoietic Stem Cell Laboratory, Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Lund University, Sweden
Genes Dev 20:2018-23. 2006..Lnk(-/-) HSC expansion is dependent on THPO, and 12-wk-old Lnk(-/-)Thpo(-/-) mice have 65-fold fewer LT-HSCs than Lnk(-/-) mice. Expansions of multiple myeloid, but not lymphoid, progenitors in Lnk(-/-) mice also proved THPO-dependent... - Molecular evidence for hierarchical transcriptional lineage priming in fetal and adult stem cells and multipotent progenitorsRobert Mansson
Hematopoietic Stem Cell Laboratory, Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Lund University, 221 84 Lund, Sweden
Immunity 26:407-19. 2007.... - Distinct roles of integrins alpha6 and alpha4 in homing of fetal liver hematopoietic stem and progenitor cellsHong Qian
Hematopoietic Stem Cell Laboratory, Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Lund University, Lund, Sweden
Blood 110:2399-407. 2007.... - A latitudinal gradient in large-scale beta diversity for vascular plants in North AmericaHong Qian
Research and Collections Center, Illinois State Museum, Springfield, IL 62703, USA
Ecol Lett 10:737-44. 2007..Therefore, decreasing beta diversity from south to north reflects decreasing climate differentiation within more northerly latitude zones, and primarily post-glacial dispersal limitation north of 50 degrees N... - Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray dataAgnes Baross
Genome Sciences Centre, BC Cancer Agency, British Columbia Cancer Agency, Suite 100, 570 West 7th Avenue, Vancouver, BC, V5Z 4S6, Canada
BMC Bioinformatics 8:368. 2007..The popularity of this technology and its associated open source data format have resulted in the development of an increasing number of software packages for the analysis of copy number changes using these SNP arrays... - Kit regulates maintenance of quiescent hematopoietic stem cellsLina A Thoren
Hematopoietic Stem Cell Laboratory, Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Lund University, Lund, Sweden
J Immunol 180:2045-53. 2008..Most notably, accelerated in vivo BrdU incorporation and cell cycle kinetics implicated a previously unrecognized role of Kit in maintaining quiescent HSCs in steady state adult hematopoiesis... - A global evaluation of metabolic theory as an explanation for terrestrial species richness gradientsBradford A Hawkins
Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA
Ecology 88:1877-88. 2007..We conclude that metabolic theory, as currently formulated, is a poor predictor of observed diversity gradients in most terrestrial systems...