Peter Salamon
San Diego State University, Mathematics and Statistics, Faculty Member
A theorem is proved establishing the equality of ‘‘lengths’’ calculated with the entropy-based metric ∂2S/∂Xi∂Xj used by Ruppeiner and with a metric based on the information–theoretic entropy max(−Σpj ln pj).
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... Communications 49 (1988) 423428 NorthHolland, Amsterdam SIMULATED ANNEALING WITH CONSTANT THERMODYNAMIC SPEED Peter SALAMON a James D. NULTON b John R. HARLAND ... Hoffmann, K. Mosegaard, J. Nulton, JM Pedersen and P. Salamon, J. de... more
... Communications 49 (1988) 423428 NorthHolland, Amsterdam SIMULATED ANNEALING WITH CONSTANT THERMODYNAMIC SPEED Peter SALAMON a James D. NULTON b John R. HARLAND ... Hoffmann, K. Mosegaard, J. Nulton, JM Pedersen and P. Salamon, J. de Phys. ...
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ABSTRACT We present a solution to the minimum time control problem for a classical harmonic oscillator to reach a target energy E T from a given initial state (q i , p i) by controlling its frequency ω, ω min ω ω max . A brief synopsis of... more
ABSTRACT We present a solution to the minimum time control problem for a classical harmonic oscillator to reach a target energy E T from a given initial state (q i , p i) by controlling its frequency ω, ω min ω ω max . A brief synopsis of optimal control theory is included and the solution for the harmonic oscillator problem is used to illustrate the theory.
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The proportionality between the square of the distance traversed as measured in thermodynamic length and the minimum associated dissipation of a process is established in a new context independent of dynamical laws. A quasistatic... more
The proportionality between the square of the distance traversed as measured in thermodynamic length and the minimum associated dissipation of a process is established in a new context independent of dynamical laws. A quasistatic thermodynamic process consisting of K steps, each equilibrating with an appropriate reservoir, is optimized with respect to the position of the steps and the allocation of the total time τ for the process among the steps. It is found that the steps should be of equal thermodynamic length. For large K the bounds based on thermodynamic length are recovered.
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... Bjarne Andresen (1), Karl Heinz Hoffmann (2), Klaus Mosegaard (3), Jim Nulton (4), Jacob Mørch Pedersen (1) and Peter Salamon (1) ... An important family of such problems involves minimization of a function on real m-space Rm. ...
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Research Interests: Probability Theory, Computer Science, Physics, Statistical Mechanics, Combinatorial Optimization, and 13 moreSimulated Annealing, Numerical Analysis, Medicine, Probabilistic Logic, Mathematical Sciences, Physical sciences, Physical, CHEMICAL SCIENCES, Heat Capacity, Schedule, Discrete random variable, Probabilistic Algorithm, and Relaxation Time
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For any given bacteriophage genome or phage sequences in metagenomic data sets, we are unable to assign a function to 50-90% of genes. Structural protein-encoding genes constitute a large fraction of the average phage genome and are among... more
For any given bacteriophage genome or phage sequences in metagenomic data sets, we are unable to assign a function to 50-90% of genes. Structural protein-encoding genes constitute a large fraction of the average phage genome and are among the most divergent and difficult-to-identify genes using homology-based methods. To understand the functions encoded by phages, their contributions to their environments, and to help gauge their utility as potential phage therapy agents, we have developed a new approach to classify phage ORFs into ten major classes of structural proteins or into an “other” category. The resulting tool is named PhANNs (Phage Artificial Neural Networks). We built a database of 538,213 manually curated phage protein sequences that we split into eleven subsets (10 for cross-validation, one for testing) using a novel clustering method that ensures there are no homologous proteins between sets yet maintains the maximum sequence diversity for training. An Artificial Neura...
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Microbial viruses can control host abundances via density-dependent lytic predator-prey dynamics. Less clear is how temperate viruses, which coexist and replicate with their host, influence microbial communities. Here we show that... more
Microbial viruses can control host abundances via density-dependent lytic predator-prey dynamics. Less clear is how temperate viruses, which coexist and replicate with their host, influence microbial communities. Here we show that virus-like particles are relatively less abundant at high host densities. This suggests suppressed lysis where established models predict lytic dynamics are favoured. Meta-analysis of published viral and microbial densities showed that this trend was widespread in diverse ecosystems ranging from soil to freshwater to human lungs. Experimental manipulations showed viral densities more consistent with temperate than lytic life cycles at increasing microbial abundance. An analysis of 24 coral reef viromes showed a relative increase in the abundance of hallmark genes encoded by temperate viruses with increased microbial abundance. Based on these four lines of evidence, we propose the Piggyback-the-Winner model wherein temperate dynamics become increasingly imp...
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This paper investigates the post-hoc calibration of confidence for “exploratory” machine learning classification problems. The difficulty in these problems stems from the continuing desire to push the boundaries of which categories have... more
This paper investigates the post-hoc calibration of confidence for “exploratory” machine learning classification problems. The difficulty in these problems stems from the continuing desire to push the boundaries of which categories have enough examples to generalize from when curating datasets, and confusion regarding the validity of those categories. We argue that for such problems the “one-versus-all” approach (top-label calibration) must be used rather than the “calibrate-the-full-response-matrix” approach advocated elsewhere in the literature. We introduce and test four new algorithms designed to handle the idiosyncrasies of category-specific confidence estimation using only the test set and the final model. Chief among these methods is the use of kernel density ratios for confidence calibration including a novel algorithm for choosing the bandwidth. We test our claims and explore the limits of calibration on a bioinformatics application (PhANNs) as well as the classic MNIST ben...
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Research Interests: Biophysics, Thermodynamics, Electron Microscopy, Structural Biology, Modeling, and 15 moreElectron Tomography, Biology, Scanning Electron Microscopy, Transmission Electron Microscopy, Mitochondria, Medicine, Structural, Animals, Three Dimensional Imaging, Three Dimensional, X ray Computed Tomography, Lipid Bilayer, Biochemistry and cell biology, Membrane topology, and Mitochondrial swelling
The dissipation in an irreversible step process is reduced when the number of steps is increased in any refinement of the steps in the process. This is a consequence of the ladder theorem, which states that, for any irreversible process... more
The dissipation in an irreversible step process is reduced when the number of steps is increased in any refinement of the steps in the process. This is a consequence of the ladder theorem, which states that, for any irreversible process proceeding by a sequence of relaxations, dividing any relaxation step into two will result in a new sequence that is more efficient than the original one. This results in a more-steps-the-better rule, even when the new sequence of steps is not reoptimized. This superiority of many steps is well established empirically in, e.g., insulation and separation applications. In particular, the fact that the division of any step into two steps improves the overall efficiency has interesting implications for biological evolution and emphasizes thermodynamic length as a central measure for dissipation.
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Finite-time thermodynamics was created 45 years ago as a slight modification of classical thermodynamics, by adding the constraint that the process in question goes to completion within a finite length of time [...]
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Incorporating time into thermodynamics allows addressing the tradeoff between efficiency and power. A qubit engine serves as a toy model to study this tradeoff from first principles, based on the quantum theory of open systems. We study... more
Incorporating time into thermodynamics allows addressing the tradeoff between efficiency and power. A qubit engine serves as a toy model to study this tradeoff from first principles, based on the quantum theory of open systems. We study the quantum origin of irreversibility, originating from heat transport, quantum friction and thermalization in the presence of external driving. We construct various finite-time engine cycles based on the Otto and Carnot templates. Our analysis highlights the role of coherence and the quantum origin of entropy production.
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The traditional connection between rate constants and free energy landscapes is extended to define effective free energy landscapes relevant on any chosen timescale. Although the Eyring–Polanyi transition state theory specifies a fixed... more
The traditional connection between rate constants and free energy landscapes is extended to define effective free energy landscapes relevant on any chosen timescale. Although the Eyring–Polanyi transition state theory specifies a fixed timescale of
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Consider a thermodynamic system brought along a particular sequence of equilibrium states via a sequence of relaxations. This is the classic quasistatic process that, in the limit, allows the dissipation to go to zero. At each point along... more
Consider a thermodynamic system brought along a particular sequence of equilibrium states via a sequence of relaxations. This is the classic quasistatic process that, in the limit, allows the dissipation to go to zero. At each point along the process, the system relaxes to a bath that is in a state just ahead of the current state of the system. In the quasistatic limit, the baths are only infinitesimally ahead and the time of the process goes to infinity. This situation is depicted in figure 1 Figure 1: A horse-carrot process. The system (horse) keeps trying to relax to the position of the carrot (environment). Consider an approximation to this process obtained by choosing K states of the system along the given process and using baths at these states for K successive relaxation processes of our system [1]. If K is large and the baths are well dispersed along the process, all of the relaxations are small. This is illustrated in Figure 2 below with the process being the heating of a c...
Substitution matrices are among the most widely used scoring techniques : BLAST, Mus- cle and other alignment packages, all use them. How- ever these matrices are general; they ignore organ- ism speciflc properties and do not provide... more
Substitution matrices are among the most widely used scoring techniques : BLAST, Mus- cle and other alignment packages, all use them. How- ever these matrices are general; they ignore organ- ism speciflc properties and do not provide customized scoring schemes. We present a 'hage-speciflc scoring matrix based on the abundances of aligned substitu- tions. These matrices use information from approx- imately flve and a half million similar protein align- ments from over flve hundred 'hage genomes. Our scoring matrix is difierent from the existing PAM and BLOSUM matrices. This indicates the need for simi- lar treatments for other groups of organisms.
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The first paper published as Finite-Time Thermodynamics is from 1977 [...]
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Incorporating time into thermodynamics allows for addressing the tradeoff between efficiency and power. A qubit engine serves as a toy model in order to study this tradeoff from first principles, based on the quantum theory of open... more
Incorporating time into thermodynamics allows for addressing the tradeoff between efficiency and power. A qubit engine serves as a toy model in order to study this tradeoff from first principles, based on the quantum theory of open systems. We study the quantum origin of irreversibility, originating from heat transport, quantum friction, and thermalization in the presence of external driving. We construct various finite-time engine cycles that are based on the Otto and Carnot templates. Our analysis highlights the role of coherence and the quantum origin of entropy production.
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An overall synthesis of biology and non-equilibrium thermodynamics remains a challenge at the interface between the physical and life sciences. Herein, theorems from finite-time and control thermodynamics are applied to biological... more
An overall synthesis of biology and non-equilibrium thermodynamics remains a challenge at the interface between the physical and life sciences. Herein, theorems from finite-time and control thermodynamics are applied to biological processes to indicate which biological strategies will succeed over different time scales. In general, living systems maximize power at the expense of efficiency during the early stages of their development while proceeding at slower rates to maximize efficiency over longer time scales. The exact combination of yield and power depends upon the constraints on the system, the degrees of freedom in question, and the time scales of the processes. It is emphasized that biological processes are not driven by entropy production but, rather, by informed exergy flow. The entropy production is the generalized friction that is minimized insofar as the constraints allow. Theorems concerning thermodynamic path length and entropy production show that there is a direct t...