Publications

RECENT PUBLICATIONS - Peter Salamon

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)

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. (pdf).

161. “Bounding the Lumping Error in Markov Chain Dynamics,” Karl Heinz Hoffmann and Peter Salamon, Applied Mathematics Letters, 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).

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).

2008

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).

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).

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).

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).

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

2007

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)

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)

2006

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).

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).

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)

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)

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).

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).

2005

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).

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).

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).

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)

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).

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).

2004

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).

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).

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)

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).

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).

2003

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. 6220–6223, 2003 (pdf).

132. Review of "A Matter of Degrees: What Temperature Reveals about the Past and Future of Our Species, Planet, and Universe" by Gino Segre, Physics Today, p. 59, June 2003 (pdf).

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 (pdf).

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) (pdf).

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) (pdf).

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) (pdf).

2002

127. "Genomic analysis of an uncultured marine viral community", Mya Breitbart, Peter Salamon, Bjarne Andresen, Joseph M. Mahaffy, Anca M. Segall, David Mead, Farooq Azam, Forest Rohwer, Proceedings of the National Academy of Sciences, 99, 14250-14255 (2002) (pdf).

126. "Optimal behavior of consecutive chemical reactions", Thor A. Bak, Peter Salamon, Bjarne Andresen, Journal of Physical Chemistry A, 106, 10961-10964 (2002) (pdf).

125. "The structure of best possible strategies for finding ground states", Karl Heinz Hoffmann, Astrid Franz, Peter Salamon, Physical Review E. 66, 046706 (2002) (pdf).

124. "A thermodynamic model describing the nature of the crista junction; a structural motif in the mitochondrion.", Christian Renken, Gino Siragusa, Guy Perkins, Lance Washington, Jim Nulton, Peter Salamon, and Terrence G. Frey, Journal of Structural Biology. 138, 137-144 (2002) (pdf).

123. "The Influence of Heat Transfer Irreversibilities on the Optimal Performance of Diabatic Distillation Columns.", Markus Schaller, Karl Heinz Hoffmann, Ricardo Rivero, Bjarne Andresen, Peter Salamon, Journal of Non-Equilibrium Thermodynamics, 27, 257-269 (2002) (pdf).

122. Facts, Conjectures, and Improvements for Simulated Annealing, P. Salamon, P. Sibani, and R. Frost, SIAM Monographs on Mathematical Modeling and Engineering (2002) (SIAM).

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) (pdf).

120. "Optimality in Multi-stage Operations with Asymptotically Vanishing Cost", James D. Nulton and Peter Salamon, Journal of Non-Equilibrium Thermodynamics, 27, 271-288 (2002) (pdf).

2001

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

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). (pdf)

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). (pdf)

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

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. Ozturk editor. (pdf)

114. "Growth and Social Welfare with Interdependent Utility Functions", J. Komlos and P. Salamon, in Editing Economics, edited by H. Lim, K. Park, and G.C. Harcourt, Taylor and Francis (2001).

2000

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.

112. Review of Thermodynamic Optimization of Finite-Time Processes, P. Salamon, Chemical Engineering Journal, 81, 340-341 (2000). (pdf)

111. "Energy Efficient Distillation by Optimal Distribution of Heating and Cooling Requirements", Torben Ravn Andersen, Gino Siragusa, Bjarne Andresen, Peter Salamon and Sten Bay Joergensen in Proceedings of ESCAPE-10, pp. 709-715 edited by Sauro Pierucci, published as part of series in European Symposium on Computer Aided Process Engineering, (Elsevier, Pisa, 2000). (pdf)

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

109. "Optimal Distillation Using Thermodynamic Geometry" Bjarne Andresen and Peter Salamon, pp. 319-331 in Thermodynamics of Energy Conservation and Transport, editors A. DeVos and S. Sieniutycz, Springer Verlag (2000). (pdf)

108. "From Statistical Distances to Minimally Dissipative Processes", Lajos Diosi and Peter Salamon, pp. 286-318 in Thermodynamics of Energy Conservation and Transport, editors A. DeVos and S. Sieniutycz, Springer Verlag (2000). (pdf)

1999

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

106. "A Contrast Between the Physical and the Engineering Approaches to Finite-time Thermodynamic Models and Optimizations", P. Salamon, in Recent Advances in Finite-Time Thermodynamics, edited by Chih Wu, Lingen Chen and Jincan Chen, Nova Science Publishers, Inc. (1999). (pdf)

105. "On the Relation between Economic and Thermodynamic Optima",R. S. Berry, P. Salamon, and G. Heal in Global Aspects of the Environment, edited by R. Ayres, K.J. Button, and P. Nijkamp, Edward Elgar Publishing Ltd., Cheltenham U.K. (1999). (pdf)

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. Energetika, No.1, 152 (1999).

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).

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). (pdf)

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. (pdf)

100. "Finite-time Thermodynamic Analysis of Controlled Heat Integration", James D. Nulton and Peter Salamon, Proceedings of ECOS98 (Efficiency, Cost, Optimization, Simulation, and Environmental Aspects of Energy Systems and Processes), editors A. Bejan, M. Feidt, M.J. Moran, and G. Tsatsaronis, Nancy France July 1998. (pdf)

99. "Some Issues in Finite-Time Thermodynamics", P. Salamon, Proceedings of Seminaire Eurotherm No59, editors H. Auracher, M. Feidt, and G. Tsatsaronis, Nancy France July 1998. (pdf)

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). (pdf)