Publications

PUBLICATIONS - Peter Salamon

1. "Mathematical Analysis of Plant Growth", P. Salamon, A. List, and P. Grenetz, Plant Physiology, 51, 635, 1973.

2. "Thermodynamics in Finite Time I: The Step Carnot Cycle", B. Andresen, R. S. Berry, A. Nitzan, and P. Salamon, Physical Review A, 15, 2086-2093, 1977.

3. "Thermodynamics in Finite Time II: Potentials for Finite Time Processes", P. Salamon, B. Andresen and R. S. Berry, Physical Review A, 15, 2094-2102, 1977.

4. "Thermodynamics in Finite Time III: Extremals for Imperfect Heat Engines", B. Andresen, P. Salamon, and R. S. Berry, Journal of Chemical Physics, 66, 1571-1577, 1977.

5. "Optimization of Processes with Finite Time Thermodynamics", B. Andresen, R. S. Berry, and P. Salamon, Proceedings of the Conference on Energy Use Management, Tucson, AZ, October 1977, Pergamon Press, New York, 1977, Vol. II, p. 1.

6. "On a Relation between Thermodynamic and Economic Optima", R. S. Berry, P. Salamon, and G. Heal, Resources and Energy, 1, 125-137, 1978.

7. "The Thermodynamic Legendre Transformation or How to Observe the Inside of a Black Box", P. Salamon, PhD Thesis, Department of Chemistry, University of Chicago, March, 1978.

8. "Minimum Entropy Production and the Optimization of Heat Engines", P. Salamon, A. Nitzan, B. Andresen, and R.S. Berry, Physical Review A, 21, 2115-2129, 1980.

9. "Maximum Work Production from a Heated Gas in a Cylinder Equipped with a Piston", Y.B. Band, O. Kafri, and P. Salamon, Chemical Physics Letters, 72, 127, 1980.

10. "Interpretation of Weinhold's Metric", P. Salamon, B. Andresen, P. Gait, and R.S. Berry, Journal of Chemical Physics, 73, 1001-1002, 1980.

11. "Finite Time Optimizations of a Newtonís Law Carnot Cycle", P. Salamon and A. Nitzan, Journal of Chemical Physics, 74, 3546-3560, 1981.

12. "Optimal Heating of a Working Fluid in a Cylinder with a Moving Piston", Y.B. Band, O. Kafri, and P. Salamon, Journal of Applied Physics, 52, 3745-3749, 1981.

13. "Optimal Expansion of a Heated Working Fluid", Y.B. Band, O. Kafri, and P. Salamon, Journal of Applied Physics, 53, 8-28, 1982.

14. "Optimization of a Model External Combustion Engine", Y.B. Band, O. Kafri, and P. Salamon, Journal of Applied Physics, 53, 29-33, 1982.

15. "Maximum Power from a Cycling Working Fluid", P. Salamon, Y. B. Band, and O. Kafri, Journal of Applied Physics, 53, 197-202, 1982.

16. "Thermodynamic Length and Dissipated Availability", P. Salamon and R.S. Berry, Physical Review Letters, 51, 1127-1130, 1983.

17. "A Group of Coordinate Transformations Preserving the Metric of Weinhold", P. Salamon, E. Ihrig, and R.S. Berry, Journal of Mathematical Physics, 24, 2515, 1983.

18. "Thermodynamics in Finite Time", B. Andresen, P. Salamon, and R.S. Berry, Physics Today, September 1984.

19. "Thermodynamics for Processes in Finite Time", B. Andresen, R.S. Berry, M.J. Ondrechen, and P. Salamon, Accounts of Chemical Research, 17, 266-271, 1984.

20. "A Graph Theoretic Bound on the Permanent of a Nonnegative Matrix: I", J. Donald, J. Elwin, R. Hager, and P. Salamon, Linear Algebra and Its Applications, 61, 187, 1984.

21. "A Graph Theoretic Bound on the Permanent of a Nonnegative Matrix: II", J. Donald, J. Elwin, R. Hager, and P. Salamon, Linear Algebra and Its Applications, 61, 199, 1984.

22. "On the Relation between Energy and Entropy Versions of Thermodynamic Length", P. Salamon, J. Nulton, and E. Ihrig, Journal of Chemical Physics, 80, 436, 1984.

23. "Thermodynamics of Heat Engines in Finite Time", Proceedings of the Workshop on Solar Applications of Direct Energy Technology, S.E.R.I., Lakewood, CO, February, 1985.

24. "The Influence of Nonzero Diagonal on Minimum Feedback Vertex Sets", J. Donald, J. Elwin, R. Hager, and P. Salamon, IEEE Transactions on Circuits and Systems, CAS-32, 491, 1985.

25. "The Geometry of the Ideal Gas", J. Nulton and P. Salamon, Physical Review A, 31, 2520-2524, 1985.

26. "Length in Statistical Thermodynamics", P. Salamon, J.D. Nulton, and R.S. Berry, Journal of Chemical Physics, 82, 2433-2436, 1985.

27. "Quasistatic Processes as Step Equilibrations", J. Nulton, P. Salamon, B. Andresen, and Qi Anmin, Journal of Chemical Physics, 83, 334-338, 1985.

28. "Evaluation and Elaboration of Glucose Response To Exogenously Administered Nutrients", C. Farrer, D. Presley, A. Qi, J. Hoover-Plow, P. Crapo, and P. Salamon, Proceedings of the Conference on Mathematical Modeling in Nutrition, Athens, Ga., 1985.

29. "Thermodynamic Lengths and Intrinsic Time Scales in Molecular Relaxation," T. Feldmann, B. Andresen, Anmin Qi, and P. Salamon, Journal of Chemical Physics, 83, 5849-5853, 1985.

30. "A Geometric View of Consumer Surplus with Non-Instantaneous Adjustment", P. Salamon, J. Komlos, B. Andresen, and J.D. Nulton, Mathematical Social Sciences, 13, 2, 1986.

31. "On the Tensorial Formulation of Extended Nonequilibrium Thermodynamics of Lumped Systems", S. Sieniutycz and P. Salamon, Journal of Physical Chemistry, 90, 1396, 1986.

32. "A Geometrical Measure for Entropy Changes", R. D. Levine, T. Feldmann, and P. Salamon, Journal of Statistical Physics, 42, 1127, 1986.

33. "Finite Time Thermodynamics of a Porous Plug," G. Brown, S. Snow, B. Andresen, and P. Salamon, Physical Review A, 34, 4370-4379, 1986.

34. "Handle Bases and Bounds on the Number of Subgraphs", J. Donald, J. Elwin, R. Hager, and P. Salamon, Journal of Combinatorial Theory B, 42, 1, 1987.

35. "Lower Bounds on Dissipation in Composite Systems," K. H. Hoffmann and P. Salamon, Physical Review A, 35, 369-373 (1987).

36. "Metric Bounds on Losses in Adaptive Coding", J.D. Flick, P. Salamon, and B. Andresen, Information Sciences, 42, 239 (1987).

The Physics and Chemistry of Small Clusters

38. "The Solution to a Problem of Grünbaum", P. Salamon and P. Erdös, Canadian Mathematical Bulletin, 31, 129-138 (1988).

39. "Thermodynamic geometry and the metrics of Weinhold and Gilmore," B. Andresen, R. S. Berry, R. Gilmore, E. Ihrig, and P. Salamon, Physical Review A, 37, 845-848 (1988).

40. "Inducing Weinhold's Metric from Euclidean and Riemannian metrics." B. Andresen, R. S. Berry, E. Ihrig, and P. Salamon, Physical Review A, 37, 849-851 (1988).

41. "Simulated Annealing with Constant Thermodynamic Speed," P. Salamon, J. Nulton, J. Robinson, J. Pedersen, G. Ruppeiner, and L. Liao, Computer Physics Communications, 49, 423 (1988).

42. "Statistical Mechanics of Combinatorial Optimization," J. Nulton and P. Salamon, Physical Review A, 37, 1351-1356 (1988).

43. "Simulated Annealing: A Review of the Thermodynamic Approach," J. R. Harland and P. Salamon, Nuclear Physics B (Proc. Suppl.) 5A, 109 (1988).

44. "Glucose Infusion Rates from Various Complex Carbohydrates Estimated from Two Models", J. Hoover-Plow, C. Farrer, D. Presley, P. Crapo, and P. Salamon, Progress in Food and Nutrition Science, Pergamon Press, 1988.

45. "On Lumped Models for Thermodynamic Properties of Simulated Annealing Problems", B. Andresen, K. H. Hoffmann, K. Mosegaard, J. Nulton, J. M. Pedersen, P. Salamon, J. Phys. France, 49, 1485 (1988).

46. "The Shapes of First Stage Sinters," P. Salamon, J. Bernholcz, R. S. Berry, M. Carrera-Patiño, F. Amar, and J. Jellinek, Journal of Applied Physics, 65, 3219 (1989).

47. "Measures of Dissipation", Karl Heinz Hoffmann, Bjarne Andresen, and Peter Salamon, Physical Review A, 40, 3618-3630 (1989).

48. "An Information Theoretic Bound on the Performance of Simulated Annealing Algorithms", Peter Salamon, Karl Heinz Hoffmann, John Ro Harland, and James D. Nulton, Research Report IRC.89.2, Interdisciplinary Research Center, San Diego State University.

49. "The Wetted Solid - A Generalization of Plateau's Problem and Its Implications for Sintered Materials", P. Salamon, J. Bernholcz, R. S. Berry, M. Carrera-Patiño, and B. Andresen, Journal of Mathematical Physics, 31, 610 (1990).

50. "A Statistical Approach to the Geometric Structure of Thermodynamics", R. Mrugala, J. D. Nulton, J. C. Schön, and P. Salamon, Physical Review A, 41, 3156-3160 (1990).

51. "The Optimal Simulated Annealing Schedule for a Simple Model", Karl Heinz Hoffmann and Peter Salamon, Journal of Physics A, 23, 3511 (1990).

52. "Neural Network Ensembles", Lars Kai Hansen and Peter Salamon, I.E.E.E. Transactions on Pattern Analysis and Machine Intelligence, 12, 993-1001 (1990).

Advances in Thermodynamics 3: Nonequilibrium Theory and Extremum Principles

Advances in Thermodynamics 4: Finite-Time Thermodynamics and Thermoeconomics

Advances in Thermodynamics 3: Nonequilibrium Theory and Extremum Principles

57. "Optimal Ensemble Size for Parallel Implementations of Simulated Annealing", Karl Heinz Hoffmann, Paolo Sibani, Jacob M. Pedersen, and Peter Salamon, Applied Mathematics Letters, 3, 53-56 (1990).

58. "On collective Decisions by Neural Network Ensembles", Lars Kai Hansen and Peter Salamon, Proceedings of the Symposium in Applied Statistics, Copenhagen, Denmark, January 22-24, 1990. Editor Jannik Godt, UNIC, Danish Center for Scientific Computing.

59. "Monte Carlo dynamics of optimization problems, a scaling description", P. Sibani, J. M. Pedersen, K. H. Hoffmann, and P. Salamon, Physical Review A, 42, 7080-7086 (1990).

60. "Predicting the Performance of Neural Network Ensembles ", P. Salamon and L. K. Hansen to appear in, Proceedings of the 8th International Congress on Cybernetics and Systems, New York, June 1990, edited by Constantine Manikopoulos, (New Jersey Institute of Technology Press, Newark, 1990).

61. "The Disappearance of Grain Boundaries in Sintering," R. S. Berry, J. Bernholc, and P. Salamon, Applied Physics Letters, 58, 595-597 (1991).

Clusters and Clustering: From Atoms to Fractals

63. "Shapes of Wetted Solids and Sinters", P. Basa, J. C. Schön, R. S. Berry, J. Bernholc, J. Jellinek, and P. Salamon, Physical Review B, 43, 8113-8122 (1991).

64. "Modelling Early Stages in the Formation of Cluster-Assembled Materials," J. C. Schoen and P. Salamon, in Clusters and Cluster-Assembled Materials, edited by R. S. Averback, J. Bernholc, and D. L. Nelson, MRS Symp. Proc. vol 206, p. 521 (1991).

65. "Ensemble Approach to Simulated Annealing", George Ruppeiner, Jacob Mørch Pedersen, and Peter Salamon, J. Phys. I, 1, 455-470 (1991).

66. "Simulated Annealing Strategies for Molecular Dynamics", Jea-Yel Yi, Jerzy Bernholc, and Peter Salamon, Computer Physics Communications, 66, 177-180 (1991).

67. "Contact Transformations in Thermodynamics", R. Mrugala, J. D. Nulton, J. C. Schön, and P. Salamon, Reports on Mathematical Physics 29, 109-121 (1991).

68. "Simulated Annealing for Single Minimum Optimization Problems", Karl Heinz Hoffmann and Peter Salamon, International Journal of Computer Mathematics, 39, pp. 193-204 (1991).

69. "A Novel Euler-Lagrange Equation Arising in the Optimization of Photochemical Branching Ratios", David Tannor and Peter Salamon, Reports on Mathematical Physics, 30, 233 (1991).

Advances in Thermodynamics 6: Flow, Diffusion, and Rate Processes

Advances in Thermodynamics 7: Extended Thermodynamic Systems

Advances in Thermodynamics 6: Flow, Diffusion, and Rate Processes

74. "Workshop on Computational Molecular Biology," A. K. Konopka and P. Salamon, Human Genome News, p. 11, January 1992.

75. "The Demon Algorithm", T. Zimmermann and P. Salamon, International Journal of Computer Mathematics, 42, 21-32 (1992).

76. "On the Shapes of Completely Wetted Two-Dimensional Powder Compacts for Applications to Sintering", J. C. Schön, R. Frost, M. Chu, J. Lawson and P. Salamon, Journal of Applied Physics, 71, 3266 (1992).

77. "A Maximum Entropy Principle for Distribution of Local Complexity in Naturally Occurring Nucleotide Sequences," P. Salamon and A. K. Konopka, Computers and Chemistry, 16, 117-124 (1992).

Statistical Thermodynamics and Differential Geometry of Microstructured Material

79. "Ensemble Methods for Handwritten Digit Recognition," L. K. Hansen, C. Liisberg, and P. Salamon, in Neural Networks for Signal Processing II, Proceedings of the 1992 I.E.E.E.-S.P. Workshop, edited by S.Y. Kung, F. Fallside, J. Aa. Sorenson, and C.A. Kamm, Denmark 1992.

80. "Stochastic Dynamics of Supervised Learning," L.K. Hansen, R.K. Pathria, and Peter Salamon, Journal of Physics A: Math. Gen., 26, 63-71 (1993).

The Economics of Exhaustible Resources

82. "Emergent Hierarchical Structures in Complex System Dynamics," P. Sibani, J. C. Schoen, P. Salamon, and J. O. Andersson, Europhysics Letters, 22, 479-485 (1993).

83. "Simulation of Random Close Packed Discs and Spheres", R. Frost, J.C. Schon, P. Salamon, Computational Materials Science 1, 343-350 (1993).

84. "On the Robustness of Maximum Entropy Relationships for Complexity Distributions of Nucleotide Sequences," P. Salamon, J. Wootten, L.K. Hansen, and A. K. Konopka, Computers and Chemistry, 17, 135-148 (1993).

85. "Carnot-like Processes in Finite Time I:Theoretical Limits," J. D. Nulton, P. Salamon, and R. K. Pathria, American Journal of Physics, 61, 911-916 (1993).

86. "Carnot-like Processes in Finite Time II: Applications to Model Cycles," R. K. Pathria, J. D. Nulton, and P. Salamon, American Journal of Physics, 61, 916-924 (1993).

87. "The Creation of Composite Materials by Cluster Fusion: a Summary of the SDSU Sintering Project", P. Salamon, J. C. Schön, and R. Frost, Zeitschrift für Physik D, 26, 89-92 (1993).

88. R. Frost, N. Priebe and P. Salamon in An Ensemble-Based Simulated Annealing Library for Multiprocessors, in ISUG-93, St Louis, MO, 1993, edited by N. Branan (Intel Supercomputer Systems, Portland OR, 1993).

89. "Second International Workshop on Open Problems in Computational Molecular Biology," A.K. Konopka, and P. Salamon, Human Genome News, 5, May 1993.

90. "The Use of Delaunay Curves for the Wetting and Sintering of Axisymmetric Bodies," P. Basa, J. C. Schön and P. Salamon, Quarterly of Applied Mathematics, 52, 1-22 (1994).

91. "Variation in the Glucose Tolerance Curve for a Standard Meal in Non-Diabetic Subjects", J. Hoover-Plow, C. Farrer, and P. Salamon, Nutrition Research, 14, 485-498 (1994).

92. "Towards Automatic Semen Quality Assessment", C. Linneberg, P. Salamon, C. Svarer, L. K. Hansen, and J. Meyrowitsch in Neural Networks for Signal Processing IV, Proceedings of the IEEE Workshop, Eds. J. Vlontzos et al., IEEE Service Center, Piscataway NJ, pp. 509-511 (1994).

93. "Optimal Simulated Annealing Schedules in Self Similar Systems," K. Ergenzinger, K.H. Hoffmann, and P. Salamon, Journal of Applied Physics 77, 5501 (1995).

94. "Heat Engines in Finite Time Governed by Master Equations," T. Feldmann, E. Geva, R. Kosloff, and P. Salamon, American Journal of Physics, 64, 485-492 (1996).

95. "A Finite Time Heat Engine with Fixed Capacity Heat Transfers", R.K. Pathria, J.D. Nulton, and P. Salamon, Journal of Physics A, 29, 6925-6937 (1996).

96. "The Error-Reject Tradeoff", L.K. Hansen, C. Liisberg and P. Salamon, Open Systems and Information Dynamics, 4, 159-184 (1997).

97. "Ensemble Implementations in Simulated Annealing: A Modeling Approach", P. Salamon, J. M. Pedersen, P. Sibani, and K. H. Hoffmann, Mathematical Modelling and Scientific Computing, 7, 28-37 (1997).

98. "Optimal Operation of Finite Time Tricycles with Heat Conduction Losses", R.K. Pathria, P. Salamon and J. Nulton, Journal of Physics A, 31, 3171-3183 (1998).

Proceedings of Seminaire Eurotherm

Proceedings of ECOSí98

101. "Physics versus engineering of finite-time thermodynamic models and optimizations", Proceedings of the NATO Advanced Studies Institute on Thermodynamics and the Optimization of Complex Energy Systems, editors A. Bejan and E. Mamut, Neptun Romania July 1998.

102. "The Geometry of Separation Processes: The Horse-Carrot Theorem for Steady Flow Systems", P. Salamon and J. Nulton, Europhysics Letters, 42, 571-576 (1998).

103. "Maximum possibilities of thermomechanical systems. Processes with one source", S.A. Amelkin, B. Andresen, P. Salamon, A.M. Tsirlin, V.N. Yumaguzhina, Applied energy (Izvestiia Akademii nauk. Energetika), 36, 112 (1998).

104. S.A. Amelkin, B. Andresen, P. Salamon, A.M. Tsirlin, V.N. Yumaguzhina. Extreme efficiency of thermomechanical systems with several sources. Izvestija of Russian Academy of Sciences. Energetica, No.1, 152 (1999).

Global Aspects of the Environment,

Recent Advances in Finite-Time Thermodynamics

107. "Various Approaches to Thermodynamics", P. Salamon, Proceedings of ECOS99, edited by M. Ishida, Tokyo (1999).

pp. 286-318

Thermodynamics of Energy Conservation and Transport

pp. 319-331

Thermodynamics of Energy Conservation and Transport

110. "Optimal Distillation Calculated by Thermodynamic Geometry", B. Andresen and P. Salamon, Entropie, 36, 4-10 (2000).

Computer-Aided Chemical Engineering

Thermodynamic Optimization of Finite-Time Processes

113. "Thermodynamic geometry determines optimal temperature profile in distillation column", B. Andresen and P. Salamon in P. C. Hansen, B. H. Jacobsen, K. Mosegaard (eds.): Methods and applications of inversion (Springer Verlag, 2000), p. 15-30.

Editing Economics

115. "Comparison of Entropy Production Rate Minimization Methods for Binary Tray Distillation Columns", G. DeKoier, S. Kjelstrup, P. Salamon, G. Siragusa, M. Schaller, and K.H. Hoffmann, in Proceedings of ECOS2001, A. Öztürk editor.

116. "Principles of Control Thermodynamics", P. Salamon, J. D. Nulton, G. Siragusa, T. R. Andersen, and A. Limon, Energy, 26, 307-319 (2001).

117. "Optimized performance in diabatic distillation columns", M. Schaller, K.H. Hoffmann, G. Siragusa, P. Salamon, and B. Andresen, Computers & Chemical Engineering, 25, 1537-1548 (2001).

118. "What conditions make minimum entropy production equivalent to maximum power production?," Peter Salamon, Karl Heinz Hoffmann, Sven Schubert, R. Stephen Berry, and Bjarne Andresen, Journal of Non-Equilibrium Thermodynamics 26, 73-83 (2001).

119. "Best possible strategy for finding ground states", A. Franz, K. H. Hoffmann, and P. Salamon, Physical Review Letters, 86, 5219-5222 (2001).

, 271-288 (2002)

121. "A Simple Example of Control to Minimize Entropy Production", Peter Salamon, James D. Nulton, Gino Siragusa, Alfonso Limon, Dick Bedeaux, Signe Kjelstrup, Journal of Non-Equilibrium Thermodynamics, 27, 45-55 (2002).

Facts, Conjectures, and Improvements for Simulated Annealing

, 257-269 (2002).

138

, 137-144 (2002).

, 046706 (2002).

, 14250-14255 (2002).

128. "Diversity and Population Structure of a Nearshore Marine Sediment Viral Community", Mya Breitbart, Ben Felts, Scott Kelley, Joseph M. Mahaffy, James Nulton, Peter Salamon, Forest Rohwer, Proceedings of the Royal Society of London, 03pb0422 (2003).

129. "How to avoid overcooking: optimal yield of B from the consecutive chemical reactions A<=>B<=>C", Thor A. Bak, Bjarne Andresen, James D. Nulton, Benjamin Felts III, and Peter Salamon, Proceedings of ECOS 2003, editors N. Houbak, B. Elmegaard, B. Qvale, and M. Moran (IKON, Lyngby, Denmark, 2003).

130. "Simulation Based Optimization of a Diabatic Distillation Column", Edward Steven Jimenez, Peter Salamon, Ricardo Rivero, Consuelo Rendon, Karl Heinz Hoffmann and Markus Schaller, Proceedings of ECOS 2003, editors N. Houbak, B. Elmegaard, B. Qvale, and M. Moran (IKON, Lyngby, Denmark, 2003).

131. "Disordered systems on various time scales: a-Si3B3N7 and homogeneous sintering", J. C. Schoen, A. Hannemann, G. Sethi, M. Jansen, P. Salamon, R. Frost, L. Kjeldgaard, Proceedings of JENA 2002.

Physics Today

133. "Metagenomic Analyses of an Uncultured Viral Community from Human Feces", Mya Breitbart, Ian Hewson, Ben Felts, Joseph M. Mahaffy, James Nulton, Peter Salamon, and Forest Rohwer, Journal of Bacteriology,185, p. 62206223, 2003.

134. "Correlation structure of landscapes of NP-complete optimization problems at finite temperatures", Wolfgang Gehring, Peter Salamon, Roger E. Whitney and Paolo Sibani, Open Systems and Information Dynamics, 11: 177-184 (2004) (pdf).

135. "Optimal Allocation of Heat Exchanger Inventory in a Serial Type Diabatic Distillation Column", Edward Steven Jimenez, Peter Salamon, Ricardo Rivero, Consuelo Rendon, and Karl Heinz Hoffmann, Proceedings of ECOS 2004, editors R. Rivero, L. Monroy, R. Pulido, and G. Tsatsaronis, pp. 179-187 (IMP, Mexico, 2004) (pdf).

136. "Best possible probability distribution over extremal optimization ranks", F. Heilmann, K. H. Hoffmann and P. Salamon, Europhysics Letters, 66 pp. 305–310 (2004)(pdf)

137. "Optimization of a Diabatic Distillation Column with Sequential Heat Exchangers," E.S. Jimenez, P. Salamon, R. Rivero, C. Rendon, K.H. Hoffmann, M. Schaller, and B. Andresen, Ind. Eng. Chem. Res. 43, 7566-7571 (2004) (pdf).

138. "Fitness Threshold Accepting over Extremal Optimization Ranks," K.H. Hoffmann, F. Heilmann, and P. Salamon, Physical Review E, 70, 046704-1 -- 046704-6 (2004) (pdf).

139. "Modeling tubular shapes of mitochondrial membranes" A. Ponnuswamy, J. Nulton, J. Mahaffy, P. Salamon, T. Frey and A. R. C. Baljon, Physical Biology, 2 , 73-79 (2005). (pdf).

140. "Transport of O2 from arterioles," S. Bertuglia, A. Limon, B. Andresen, K.H. Hoffmann, C. Essex, and P. Salamon, Journal of Non-Equilibrium Thermodynamics, 30, pp.151-162 (2005) (pdf).

141. "PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information," F. Angly, B. Rodriguez-Brito, D. Bangor, P. McNairnie, M. Breitbart, P. Salamon, B. Felts, J. Nulton, J. Mahaffy, and F. Rohwer, BMC Bioinformatics, 6, 41 (2005). (pdf)

142. "The Structure of Marine Phage Populations" Karl Heinz Hoffmann, Beltran Rodriguez-Brito, Mya Breitbart, David Bangor, Florent Angly, Ben Felts, James Nulton, Forest Rohwer, and Peter Salamon, Proceedings of ECOS 2005, editors Signe Kjelstrup and Johan Einar Hustad (pdf).

143. "Cycling Co-Evolution Resulting from Genetic Adaptation in Two-Person Zero-Sum Games", David Salamon and Peter Salamon, Open Systems and Information Dynamics, 12, 265-271 (2005). (pdf).

144. "A Structural Diffusion Approach to Labeling Rows and Columns in an Irregular Array", P. Salamon, B. Felts, C. Hand, A. Limon, J. Rose and J. Torre-Bueno, Proceedings of the 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, editors F. Valafar, H. Valafar, and H.R. Arabnia, CSREA Press, p. 269-273 (2005). (pdf).

145. "Labeling Rows and Columns in an Irregular Array", P. Salamon, B. Felts, C. Hand, A. Limon, J. Rose and J. Torre-Bueno, Medical Image Analysis, 10, 150-161 (2006) (pdf).

146. "Oxygen Transport from the Outer Boundary of a Pulsating Wall of an Arteriole to the Surrounding Tissue," A. Limon, S. Bertuglia, A. Nadim, and P. Salamon, Mathematics and Computers in Simulation 73, 175-182 (2006) (pdf).

147. "Thermodynamics for Systems Biology", Peter Salamon, Anna Salamon, and Andrzej K. Konopka, in Systems Biology, ed. A.K. Konopka, (CRC, New York, 2006). (pdf)

148. "The mathematical structure of thermodynamics for systems biologists", Peter Salamon, Andrzej K. Konopka, James Nulton, and Bjarne Andresen, in Systems Biology, ed. A.K. Konopka, (CRC, New York, 2006). (pdf)

149. "The Marine Viromes of Four Oceanic Regions," F. Angly, B. Felts, M. Breitbart, P. Salamon, R. Edwards, C. Carlson, A. Chan, M. Haynes, S. Kelley, H. Liu, J. Mahaffy, J. Mueller, J. Nulton, R. Olson, R. Parsons, S. Rayhawk, C. Suttle, F. Rohwer, PLoS BIOLOGY, 4, e368 (2006) (pdf).

150. "Membrane Remodeling and Diffusion of Cytochrome C from a Geometrically Idealized Mitochondrial Crista," J.C. Manor, T. Frey, A. Baljon, J. Mahaffy J. Nulton, and P. Salamon in Proceedings of the 2006 International Conference on Bioinformatics & Computational Biology, H.R. Arabnia & H. Valafar editors, (CSREA Press, USA 2006).

151. "Power law rank-abundance relationships in marine phage populations," Karl Heinz Hoffmann, Beltran Rodriguez-Brito, Mya Breitbart, David Bangor, Florent Angly, Ben Felts, James Nulton, Forest Rohwer, and Peter Salamon, FEMS Microbiology Letters, 273, 224-228 (2007). (pdf)

152. "Metagenomic and small-subunit rRNA analyses of the genetic diversity of bacteria, archaea, fungi, and viruses in soil," N. Fierer, M. Breitbart, J. Nulton, P. Salamon, C. Lozupone, R. Jones, M. Robeson, R.A. Edwards, B. Felts, S. Rayhawk, R. Knight, F. Rohwer, R.B. Jackson, Applied and Environmental Microbiology 73, 7059-7066 (2007). (pdf)

153. "Direct measurements of heat output by marine microbial and phage communities," E. Djamali, P. Turner, J. Nulton, F. Rohwer, and P. Salamon CSRCR2008-18. (pdf)

154. "The Poverty of Growth with Interdependent Utility Functions," Komlos, John and Salamon, Peter, Journal of Socio-Economics, 37, 2242-2247 (2008) (pdf).

155. “An Interlacing Theorem for Markov Chains,” Robert Grone, Karl Heinz Hoffmann and Peter Salamon, Journal of Physics A: Mathematical and Theoretical, 41, 212002 (2008) (iop).

156. “Viral Diversity and Dynamics in an Infant’s Gut,” M. Breitbart, M. Haynes, S. Kelley, F. Angly, R. A. Edwards, B. Felts, J.M. Mahaffy, J. Mueller, J. Nulton, S. Rayhawk, B. Rodriguez-Brito, P. Salamon, F. Rohwer, Research in Microbiology, 159, 367-373 (2008). (pdf).

157. "Interactions between branched DNAs and peptide inhibitors of DNA repair", Kevin V. Kepple, Namita Patel, Peter Salamon and Anca M. Segall, doi:10.1093/nar/gkn512 (2008); Nucleic Acids Res. (html/pdf).

158. "Apparatus and method for labeling rows and columns in an irregular array", Jose De La Torre-Bueno and Peter Salamon, U.S. Patent number 7,457,481 (2008).

159. "Maximum Work in Minimum Time from a Conservative Quantum System", P.Salamon, K.H. Hoffmann, Y. Rezek, and R. Kosloff, Phys. Chem. Chem. Phys., 11, 1027–1032 (2009) (pdf).

160. "The Quantum Refrigerator: The quest for absolute zero", Yair Rezek, Peter Salamon, Karl Heinz Hoffmann, and Ronnie Kosloff, Europhysics Letters, 85, 30008 (2009) (pdf).

161. “Bounding the Lumping Error in Markov Chain Dynamics,” Karl Heinz Hoffmann and Peter Salamon, Applied Mathematics Letters, 22, 1471-1475 (2009). (pdf)

162. "Mitochondrial stereology from the statistics of sections", D.C. Flynn, J.D. Nulton, P. Salamon, T.G. Frey, A. Rabinovitch, and A.R.C. Baljon, Image Analysis and Stereology, 28, 11-22 (2009). (pdf).

163. "Deviations from ultrametricity in phage protein distances", Chad Wagner, Anna Salamon, Robert A. Edwards, Forest Rohwer and Peter Salamon, Open Systems and Information Dynamics, 16, 75-84 (2009). (pdf)

164. "Review of Entropy and the Time Evolution of Macroscopic Systems, by W. Grandy", P. Salamon, Physics Today, November 2009. (pdf)

165. "Viral and microbial community dynamics in four aquatic environments", B. Rodriguez-Brito, L. Li, L. Wegley, M. Furlan, F. Angly, M. Breitbart, J. Buchanan, C. Desnues, E. Dinsdale, R.A. Edwards, B Felts, M. Haynes, H. Liu, D. Lipson, J. Mahaffy, A. B. Martin-Cuadrado, A. Mira, J. Nulton, L. Pasic´, S. Rayhawk, J. Rodriguez-Mueller, F. Rodriguez-Valera, P. Salamon, S. Srinagesh, T.F. Thingstad, T. Tran, R.V. Thurber, D Willner, M. Youle and F.L. Rohwer, ISME Journal, 4, 739-751 (2010). (pdf)

166. "Tensile Forces and Shape Entropy Explain Observed Crista Structure in Mitochondria", M. Ghochani, J. D. Nulton, P. Salamon, T. G. Frey, A. Rabinovitch, and A. R. C. Baljon, Biophysical Journal, 99, 3244–3254 (2010). (pdf)

167. "Economic implications of software minds", Steven Kaas, Steve Rayhawk, Anna Salamon, Peter Salamon, pages 431-438 in Proceedings of ECAP 10, VIII European Conference of Computing and Philosophy, Klaus Mainzer editor, ISBN 978-3-86853-546-4, Verlag Dr. Hut, Munchen 2010. (pdf)

168. "Optimal control in a quantum cooling problem", P. Salamon, K. H. Hoffmann, and A. Tsirlin, Applied Mathematics Letters, doi:10.1016/j.aml.2011.11.020 (2011). (pdf)

169. "Time-optimal controls for frictionless cooling in harmonic traps", K. H. Hoffmann, P. Salamon, Y. Rezek and R. Kosloff, Europhysics Letters 96, 60015 (2011). (pdf)

170. "Change of State Variables in the Problems of Parametric Control of Oscillators", A.M. Tsirlin, P. Salamon, and K.H. Hoffmann, Automation and Remote Control, 72, 1627-1638 (2011). (pdf)

171. "Potent antimicrobial small molecules screened as inhibitors of tyrosine recombinases and Holliday junction-resolving enzymes", M.C. Rideout, J.L. Boldt, G. Vahi-Ferguson, P. Salamon, A. Nefzi, J.M. Ostresh, M. Giulianotti, C. Pinilla, A.M. Segall, Molecular Diversity, DOI: 10.1007/s11030-011-9333-2 (2011). (pdf)

172. "Accuracy of coarse grained Markovian dynamics", K. H. Hoffmann and P. Salamon, Physica A, 390, 3086-3094 (2011). (pdf)

173."Optimal Control of the Parametric Oscillator", B. Andresen, K. H. Hoffmann, J. Nulton, A. Tsirlin, P. Salamon, European Journal of Physics 32, 827-843 (2011). (pdf)

174. “Mucus Distribution Model in a Lung with Cystic Fibrosis,” Computational and Mathematical Methods in Medicine, Sara Zarei, Ali Mirtar, Forest Rohwer, Douglas J. Conrad, Rebecca J. Theilmann, and Peter Salamon, vol. 2012, Article ID 970809, 8 pages, 2012. doi:10.1155/2012/970809 (open access).

175. "Reference-independent comparative metagenomics using cross-assembly: crAss," Bas E. Dutilh; Robert Schmieder; Jim Nulton; Ben Felts; Peter Salamon; Robert A. Edwards; John L. Mokili, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts613 (open access).

176. "Evaluating Spirometric Trends in Cystic Fibrosis Patients," Zarei, S., Abouali, M., Mirtar, A., Salamon, P., Redfield, J., Palmer, D., and Conrad, D.,Proceedings of BIOCOMP’12, International Conference on Bioinformatics and Computational Biology, Las Vegas 2012.

177. "Evaluating Chronic Cystic Fibrosis Severity using Artificial Neural Networks," Redfield, J., Palmer, D., Conrad, D., and Salamon, P., Proceedings of ICIA '12, International Conference on Artificial Intelligence, Las Vegas 2012.

178. "Time optimal Processes for Interacting Spin Systems," F. Boldt, K.H. Hoffmann, P. Salamon, R. Kosloff, to appear, Europhysics Letters (2012).

179. "Assessing Coral Reefs on a Pacific-Wide Scale Using the Microbialization Score," T. McDole, J. Nulton, K.L. Barott, B. Felts, C. Hand, M. Hatay, H. Lee, M.O. Nadon, B. Nosrat, P. Salamon, B. Bailey, S.A. Sandin, B. Vargas-Angel, M. Youle, B.J. Zgliczynski, R.E. Brainard, F. Rohwer, PLoS ONE 7(9): e43233. doi:10.1371/journal.pone.0043233 (2012) (open access).

180. "Artificial Neural Networks Trained to Detect Viral and Phage Structural Proteins," Victor Seguritan, Nelson Alves Jr., Michael Arnoult, Amy Raymond, Don Lorimer, Alex B. Burgin Jr., Peter Salamon, Anca M. Segall. PLoS Comput Biol 8(8): e1002657. doi:10.1371/journal.pcbi.1002657 (2012) (open access).

181. "Heat output by marine microbial and viral communities", E. Djamali, J. Nulton, P. Turner, F. Rohwer and P. Salamon, J. Non-Equilibrium Thermodynamics, DOI: 101515/jnetdy-2011-0235 (2012) (pdf).

182. "Controllability on relaxation-free subspaces: On the relationship between adiabatic population transfer and optimal control", H. Yuan, C.P. Koch, P. Salamon and D.J. Tannor, Physical Review A 85, 033417 (2012). (pdf)