DANIEL BEARD

Summary

Affiliation: Medical College of Wisconsin
Country: USA

Publications

  1. pmc Linear analysis near a steady-state of biochemical networks: control analysis, correlation metrics and circuit theory
    William 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
  2. pmc Roles of the creatine kinase system and myoglobin in maintaining energetic state in the working heart
    Fan Wu
    Biotechnology and Bioengineering Center, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
    BMC Syst Biol 3:22. 2009
  3. pmc Generating rate equations for complex enzyme systems by a computer-assisted systematic method
    Feng Qi
    Biotechnology and Bioengineering Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
    BMC Bioinformatics 10:238. 2009
  4. pmc Understanding Guyton's venous return curves
    Daniel A Beard
    Department of Physiology, Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
    Am J Physiol Heart Circ Physiol 301:H629-33. 2011
  5. pmc Relationship between thermodynamic driving force and one-way fluxes in reversible processes
    Daniel A Beard
    Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
    PLoS ONE 2:e144. 2007
  6. pmc Detailed enzyme kinetics in terms of biochemical species: study of citrate synthase
    Daniel A Beard
    Biotechnology and Bioengineering Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
    PLoS ONE 3:e1825. 2008
  7. pmc A biophysical model of the mitochondrial respiratory system and oxidative phosphorylation
    Daniel A Beard
    Biotechnology and Bioengineering Center, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
    PLoS Comput Biol 1:e36. 2005
  8. pmc Modeling of oxygen transport and cellular energetics explains observations on in vivo cardiac energy metabolism
    Daniel A Beard
    Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
    PLoS Comput Biol 2:e107. 2006
  9. ncbi request reprint Thermodynamic-based computational profiling of cellular regulatory control in hepatocyte metabolism
    Daniel 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
  10. ncbi request reprint Thermodynamic constraints for biochemical networks
    Daniel A Beard
    Biotechnology and Bioengineering Center, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
    J Theor Biol 228:327-33. 2004

Detail Information

Publications45

  1. pmc Linear analysis near a steady-state of biochemical networks: control analysis, correlation metrics and circuit theory
    William 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...
  2. pmc Roles of the creatine kinase system and myoglobin in maintaining energetic state in the working heart
    Fan Wu
    Biotechnology and Bioengineering Center, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
    BMC Syst Biol 3:22. 2009
    ....
  3. pmc Generating rate equations for complex enzyme systems by a computer-assisted systematic method
    Feng Qi
    Biotechnology and Bioengineering Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
    BMC Bioinformatics 10:238. 2009
    ..Furthermore, none is freely available for download and use by the community...
  4. pmc Understanding Guyton's venous return curves
    Daniel A Beard
    Department of Physiology, Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
    Am J Physiol Heart Circ Physiol 301:H629-33. 2011
    ..Because Guyton's venous return curves have generated much confusion and little clarity, we suggest that the concept and previous interpretations of venous return be removed from educational materials...
  5. pmc Relationship between thermodynamic driving force and one-way fluxes in reversible processes
    Daniel A Beard
    Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
    PLoS ONE 2:e144. 2007
    ....
  6. pmc Detailed enzyme kinetics in terms of biochemical species: study of citrate synthase
    Daniel A Beard
    Biotechnology and Bioengineering Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
    PLoS ONE 3:e1825. 2008
    ..This analysis provides a mechanistic model that is consistent with the data that have been used support competing hypotheses regarding the catalytic mechanism of this enzyme...
  7. pmc A biophysical model of the mitochondrial respiratory system and oxidative phosphorylation
    Daniel A Beard
    Biotechnology and Bioengineering Center, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
    PLoS Comput Biol 1:e36. 2005
    ..The resulting validated and verified model provides a foundation for building larger and more complex systems models and investigating complex physiological and pathophysiological interactions in cardiac energetics...
  8. pmc Modeling of oxygen transport and cellular energetics explains observations on in vivo cardiac energy metabolism
    Daniel A Beard
    Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
    PLoS Comput Biol 2:e107. 2006
    ..In addition, the validated model provides quantitative predictions of changes in phosphate metabolites during cardiac ischemia...
  9. ncbi request reprint Thermodynamic-based computational profiling of cellular regulatory control in hepatocyte metabolism
    Daniel 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
    ....
  10. ncbi request reprint Thermodynamic constraints for biochemical networks
    Daniel A Beard
    Biotechnology and Bioengineering Center, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
    J Theor Biol 228:327-33. 2004
    ....
  11. doi request reprint Modeling of cellular metabolism and microcirculatory transport
    Daniel A Beard
    Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
    Microcirculation 15:777-93. 2008
    ..This tight integration between cellular metabolism and microcirculatory transport begs for integrative simulations that span the cell, tissue, and organ scales...
  12. pmc Apparent diffusivity and Taylor dispersion of water and solutes in capillary beds
    Daniel A Beard
    Department of Physiology, Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
    Bull Math Biol 71:1366-77. 2009
    ..Measurement of the ratio of axial to transverse diffusivity may be combined with an independent measurement of perfusion to provide an estimate of capillary vessel density in the tissue...
  13. pmc Creatine and phosphate pools are maintained at energetically optimal levels in the heart during hypertrophic remodeling and heart failure
    Daniel A Beard
    Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
    Conf Proc IEEE Eng Med Biol Soc 2009:4487-90. 2009
    ....
  14. ncbi request reprint Computer modeling of mitochondrial tricarboxylic acid cycle, oxidative phosphorylation, metabolite transport, and electrophysiology
    Fan Wu
    Biotechnology and Bioengineering Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
    J Biol Chem 282:24525-37. 2007
    ....
  15. pmc Phosphate metabolite concentrations and ATP hydrolysis potential in normal and ischaemic hearts
    Fan Wu
    Biotechnology and Bioengineering Center and Department of Physiology, Medical College of Wiscosin, Milwaukee, WI 53213, USA
    J Physiol 586:4193-208. 2008
    ..Due to the lack of precise quantification of P(i) in vivo, these hypotheses and associated model predictions remain to be carefully tested experimentally...
  16. pmc A biophysically based mathematical model for the kinetics of mitochondrial Na+-Ca2+ antiporter
    Ranjan K Pradhan
    Biotechnology and Bioengineering Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
    Biophys J 98:218-30. 2010
    ....
  17. pmc Mitochondrial free [Ca2+] increases during ATP/ADP antiport and ADP phosphorylation: exploration of mechanisms
    Johan Haumann
    Anesthesiology Research Laboratories, Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
    Biophys J 99:997-1006. 2010
    ..These data suggest that matrix ADP influx and subsequent phosphorylation increase [Ca2+](m) largely due to the interaction of matrix Ca2+ with ATP, ADP, P(i), and cation buffering proteins in the matrix...
  18. pmc Detailed kinetics and regulation of mammalian NAD-linked isocitrate dehydrogenase
    Feng Qi
    Biotechnology and Bioengineering Center and Department of Physiology, Medical College of Wisconsin, USA
    Biochim Biophys Acta 1784:1641-51. 2008
    ..In addition, the enzyme is highly sensitive to Mg(2+) concentration in the physiological range, pointing to a potential regulatory role of [Mg(2+)] in mitochondrial energy metabolism...
  19. ncbi request reprint Oxidative ATP synthesis in skeletal muscle is controlled by substrate feedback
    Fan Wu
    Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
    Am J Physiol Cell Physiol 292:C115-24. 2007
    ....
  20. pmc Kinetics and regulation of mammalian NADH-ubiquinone oxidoreductase (Complex I)
    Xuewen Chen
    Biotechnology and Bioengineering Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
    Biophys J 99:1426-36. 2010
    ..The overall kinetic analysis demonstrates a hybrid ping-pong rapid-equilibrium random bi-bi mechanism, consolidating the characteristics from previously reported kinetic mechanisms and data...
  21. pmc A biophysically based mathematical model for the kinetics of mitochondrial calcium uniporter
    Ranjan K Dash
    Biotechnology and Bioengineering Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
    Biophys J 96:1318-32. 2009
    ....
  22. pmc Design of experiments for identification of complex biochemical systems with applications to mitochondrial bioenergetics
    Kalyan C Vinnakota
    Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
    Conf Proc IEEE Eng Med Biol Soc 2009:4171-4. 2009
    ..Experimental perturbations and variables yielding the most number of parameters above a 5% sensitivity level are presented and discussed...
  23. pmc The role of theoretical modeling in microcirculation research
    Timothy W Secomb
    Department of Physiology, University of Arizona, Tucson, Arizona 85724, USA
    Microcirculation 15:693-8. 2008
    ..The concepts discussed are generally applicable to the theoretical modeling of biological systems and are illustrated by using examples of modeling in microcirculation research...
  24. pmc Experimentally observed phenomena on cardiac energetics in heart failure emerge from simulations of cardiac metabolism
    Fan Wu
    Biotechnology and Bioengineering Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
    Proc Natl Acad Sci U S A 106:7143-8. 2009
    ..Thus, both increases and decreases to the creatine pool are predicted to result in diminished energetic state unless accompanied by appropriate simultaneous changes in the other pools...
  25. ncbi request reprint Ab initio prediction of thermodynamically feasible reaction directions from biochemical network stoichiometry
    Feng 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...
  26. pmc Analysis of cardiac mitochondrial Na+-Ca2+ exchanger kinetics with a biophysical model of mitochondrial Ca2+ handling suggests a 3:1 stoichiometry
    Ranjan K Dash
    Biotechnology and Bioengineering Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226 6509, USA
    J Physiol 586:3267-85. 2008
    ..Based on these analyses, it is concluded that the mitochondrial NCE is electrogenic with a stoichiometry of 3:1...
  27. pmc Identifying physiological origins of baroreflex dysfunction in salt-sensitive hypertension in the Dahl SS rat
    Scott M Bugenhagen
    Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
    Physiol Genomics 42:23-41. 2010
    ....
  28. ncbi request reprint Thermodynamically based profiling of drug metabolism and drug-drug metabolic interactions: a case study of acetaminophen and ethanol toxic interaction
    Feng Yang
    Biotechnology and Bioengineering Center, Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, United States
    Biophys Chem 120:121-34. 2006
    ..These results point to the potential utility of thermodynamically based profiling of metabolic network interactions in screening of drug candidates and analysis of potential toxicity...
  29. ncbi request reprint Population-based analysis of methadone distribution and metabolism using an age-dependent physiologically based pharmacokinetic model
    Feng Yang
    Department of Physiology, Medical College of Wisconsin, Biotechnology and Bioengineering Center, Milwaukee, WI 53226, USA
    J Pharmacokinet Pharmacodyn 33:485-518. 2006
    ..In addition, it is shown that when doses are designed for individuals based on prior protein expression information, inter-individual variability in methadone kinetics may be greatly reduced...
  30. pmc Multiple ion binding equilibria, reaction kinetics, and thermodynamics in dynamic models of biochemical pathways
    Kalyan C Vinnakota
    Biotechnology and Bioengineering Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
    Methods Enzymol 454:29-68. 2009
    ..Several applications to physiological systems are demonstrated based on this coherent simulation framework...
  31. pmc Computational analyses of intravascular tracer washout reveal altered capillary-level flow distributions in obese Zucker rats
    Fan Wu
    Biotechnology and Bioengineering Centre and Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
    J Physiol 589:4527-43. 2011
    ....
  32. doi request reprint Differential expression of cardiac mitochondrial proteins
    Julia R Smith
    Biotechnology Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
    Proteomics 8:446-62. 2008
    ..Mathematical modeling of mitochondrial electron transport predicted that the observed change in ETFA expression may result in decreased activity of the electron transport chain...
  33. pmc The effects of reversibility and noise on stochastic phosphorylation cycles and cascades
    Clark A Miller
    Department of Chemical and Biological Engineering, University of Wisconsin Madison, USA
    Biophys J 95:2183-92. 2008
    ..Likewise, the variance in the response can be maximized or minimized by tuning the number of enzymes in the second cycle...
  34. pmc Energy balance for analysis of complex metabolic networks
    Daniel 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...
  35. ncbi request reprint Optical spectroscopy demonstrates elevated intracellular oxygenation in an endotoxic model of sepsis in the perfused heart
    Kenneth A Schenkman
    Departments of Pediatrics, University of Washington, Seattle, Washington, USA
    Shock 27:695-700. 2007
    ..Cellular dysfunction seen in sepsis may be caused by compromised oxygen use rather than insufficient oxygen delivery. Optical spectroscopy has the potential to noninvasively monitor patients and their responses to therapy...
  36. ncbi request reprint Myocardial oxygenation in isolated hearts predicted by an anatomically realistic microvascular transport model
    Daniel A Beard
    Department of Bioengineering, University of Washington, Box 352255, Seattle, WA 98195, USA
    Am J Physiol Heart Circ Physiol 285:H1826-36. 2003
    ..It is incorrect to assume that the usual buffer-perfused Langendorff heart preparation is adequately oxygenated for flows in the range of < or =10 ml. min-1. ml tissue-1...
  37. pmc Extreme pathways and Kirchhoff's second law
    Nathan D Price
    Biophys J 83:2879-82. 2002
  38. ncbi request reprint Computational modeling of physiological systems
    Daniel A Beard
    Physiol Genomics 23:1-3; discussion 4. 2005
  39. ncbi request reprint Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm
    Qing Zhang
    Department of Chemistry and Courant Institute of Mathematical Sciences, New York University and the Howard Hughes Medical Institute, 251 Mercer St, New York, New York 10012, USA
    J Comput Chem 24:2063-74. 2003
    ..DiSCO is generally applicable to other interesting macromolecular systems for which mesoscale models are appropriate, to yield a resolution between the all-atom representative and the polymer level...
  40. ncbi request reprint Myocardial oxygenation and adenosine release in isolated guinea pig hearts during changes in contractility
    J Chiaka Ejike
    Department of Pediatrics, University of Washington, Seattle, Washington 98105, USA
    Am J Physiol Heart Circ Physiol 288:H2062-7. 2005
    ....
  41. ncbi request reprint Stoichiometric network theory for nonequilibrium biochemical systems
    Hong 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...
  42. ncbi request reprint Comparison of buffer and red blood cell perfusion of guinea pig heart oxygenation
    Kenneth A Schenkman
    Anesthesia and Critical Care 9 G1, Children s Hospital and Regional Medical Center, 4800 Sand Point Way NE, Seattle, WA 98105, USA
    Am J Physiol Heart Circ Physiol 285:H1819-25. 2003
    ..These results suggest that caution should be used in extrapolating intracellular oxygen dynamics from buffer-perfused to blood-perfused hearts...
  43. pmc Unbiased rotational moves for rigid-body dynamics
    Daniel A Beard
    Department of Bioengineering, University of Washington, Seattle, Washington, USA
    Biophys J 85:2973-6. 2003
    ..Our algorithm should thus replace standard approaches to rotate local coordinate frames in Langevin and Brownian dynamics simulations...
  44. ncbi request reprint Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium
    Hong 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...
  45. ncbi request reprint Systems biology of the mitochondrion
    Daniel A Beard
    Am J Physiol Cell Physiol 291:C1101-3. 2006

Research Grants16

  1. Mechanisms of Metabolic Dysfunction in Heart Disease
    Daniel A Beard; Fiscal Year: 2010
    ..These data will be used in Aim 2 for model development, parameterization, and validation. Development and application of tissue-level modeling and simulation tools are pursued in Aim 3. ..
  2. Integrated Modeling of Cardiac Metabolism and Transport
    DANIEL BEARD; Fiscal Year: 2009
    ..In addition, our proposed tools for simulation of the pathophysiological operation of metabolic control mechanisms in heart disease may be used to guide clinical interventions aimed at modulation of cardiac energy metabolism. ..
  3. Mechanisms of Metabolic Dysfunction in Heart Disease
    DANIEL BEARD; Fiscal Year: 2009
    ..These data will be used in Aim 2 for model development, parameterization, and validation. Development and application of tissue-level modeling and simulation tools are pursued in Aim 3. ..
  4. Analysis of Large-Scale Biochemical Systems
    DANIEL BEARD; Fiscal Year: 2007
    ..In addition, the computational tools that are developed by this research program will be disseminated through a partnership with a software company. ..
  5. MSM Multiscale Modeling of the Heart in Cardiovascular
    DANIEL BEARD; Fiscal Year: 2007
    ..abstract_text> ..
  6. Integrated Modeling of Cardiac Metabolism and Transport
    DANIEL BEARD; Fiscal Year: 2007
    ..Further applications of the proposed integrated model include profiling physiological responses to several challenges, such as (1) exercise; (2) ischemia; and (3) myoglobin and adenylate kinase gene deletions. ..
  7. Integrated Modeling of Cardiac Metabolism and Transport
    Daniel A Beard; Fiscal Year: 2010
    ..In addition, our proposed tools for simulation of the pathophysiological operation of metabolic control mechanisms in heart disease may be used to guide clinical interventions aimed at modulation of cardiac energy metabolism. ..