Quantum Mechanics of Consecutive Measurements (2009)
I analyze consecutive projective measurements in quantum mechanics in terms of quantum information theory and a no-collapse picture of measurement. I show that the entropy of all detectors that...
Impact of Epistasis on Evolutionary Adaptation (2009)
Ostman, Bjorn, Hintze, Arend, Adami, Christoph
We investigate the impact of epistasis on adaptive evolution in a multiplicative NK model, by evolving a population of asexual haploid organisms with circular binary genomes of length N, where each...
Modularity and anti-modularity in networks with arbitrary degree distribution (2009)
Hintze, Arend, Adami, Christoph
Networks describing the interaction of the elements that constitute a complex system grow and develop via a number of different mechanisms, such as the addition and deletion of nodes, the addition...
84 R EPORTS Adaptive Radiation from Resource Competition in Digital Organisms (2008)
Stephanie S. Chow, Claus O. Wilke, Charles Ofria, Richard E. Lenski, Christoph Adami
Species richness often peaks at intermediate productivity and decreases as resources become more or less abundant. The mechanisms that produce this pattern are not completely known, but several...
Evolution of Virtual Catapults (2008)
Nicolas Chaumont, Richard Egli, Christoph Adami
We describe the re-implementation of a system to evolve the morphology and behavior of artificial creatures, originally due to Karl Sims. The new implementation is fast, flexible, and allows for the...
Evolution of Complex Modular Biological Networks (2008)
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of...
Evolution of complex modular biological networks (2007)
Hintze, Arend, Adami, Christoph
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of...
DOI: 10.1126/science.1135929 (2006)
The following resources related to this article are available online at
Why highly expressed proteins evolve slowly (2005)
Drummond, D. Allan, Bloom, Jesse D., Adami, Christoph, Wilke, Claus O., Arnold, Frances H.
Much recent work has explored molecular and population-genetic constraints on the rate of protein sequence evolution. The best predictor of evolutionary rate is expression level, for reasons that...
Quasispecies can exist under neutral drift at finite population sizes (2005)
Forster, Robert, Adami, Christoph, Wilke, Claus O.
We investigate the evolutionary dynamics of a finite population of RNA sequences adapting to a neutral fitness landscape. Despite the lack of differential fitness between viable sequences, we observe...
Why highly expressed proteins evolve slowly (2005)
Drummond, D. Allan, Bloom, Jesse D., Adami, Christoph, Wilke, Claus O., Arnold, Frances H.
Much recent work has explored molecular and population-genetic constraints on the rate of protein sequence evolution. The best predictor of evolutionary rate is expression level, for reasons which...
Random matrix model of adiabatic quantum computing (2005)
Mitchell, David R., Adami, Christoph, Lue, Waynn, Williams, Colin P.
We present an analysis of the quantum adiabatic algorithm for solving hard instances of 3-SAT (an NP-complete problem) in terms of random matrix theory (RMT). We determine the global regularity of...
Thermodynamic prediction of protein neutrality (2005)
Bloom, Jesse D., Silberg, Jonathan J., Wilke, Claus O., Drummond, D. Allan, Adami, Christoph, Arnold, Frances H.
We present a simple theory that uses thermodynamic parameters to predict the probability that a protein retains the wild-type structure after one or more random amino acid substitutions. Our theory...
A Random Matrix Model of Adiabatic Quantum Computing (2004)
Mitchell, David R., Adami, Christoph, Lue, Waynn, Williams, Colin P.
We present an analysis of the quantum adiabatic algorithm for solving hard instances of 3-SAT (an NP-complete problem) in terms of Random Matrix Theory (RMT). We determine the global regularity of...
Thermodynamic Prediction of Protein Neutrality (2004)
Bloom, Jesse D., Silberg, Jonathan J., Wilke, Claus O., Drummond, D. Allan, Adami, Christoph, Arnold, Frances H.
We present a simple theory that uses thermodynamic parameters to predict the probability that a protein retains the wildtype structure after one or more random amino acid substitutions. Our theory...
Black holes conserve information in curved-space quantum field theory (2004)
Adami, Christoph, Steeg, Greg L. Ver
We show that black hole formation and evaporation in curved-space quantum field theory can be described in a unitary manner consistent with previous results that take scattering and stimulated...
Bloom, Jesse D., Adami, Christoph
A response to Fraser HB, Hirsh AE: Evolutionary rate depends on number of protein-protein interactions independently of gene expression level. BMC Evol Biol 2004, 4:13
Bloom, Jesse D, Adami, Christoph
Abstract A response to Fraser HB, Hirsh AE: Evolutionary rate depends on number of protein-protein interactions independently of gene expression level. BMC Evol Biol 2004, 4: 13
Information theory in molecular biology (2004)
This article introduces the physics of information in the context of molecular biology and genomics. Entropy and information, the two central concepts of Shannon's theory of information and...
The Physics of Information (2004)
Information theory is a statistical theory concerned with the relative state of detectors and physical systems. As a consequence, the classical framework of Shannon needs to be extended to deal with...
Evolution of robustness in digital organisms (2004)
Edlund, Jeffrey A., Adami, Christoph
We study the evolution of robustness in digital organisms adapting to a high mutation rate. As genomes adjust to the harsh mutational environment, the mean effect of single Imitations decreases, up...
Influence of chance, history, and adaptation on digital evolution (2004)
Wagenaar, Daniel A., Adami, Christoph
We evolved multiple clones of populations of digital organisms to study the effects of chance, history, and adaptation in evolution. We show that clones adapted to a specific environment can adapt to...
Bifurcation into functional niches in adaptation (2004)
White, Justin S., Adami, Christoph
One of the central questions in evolutionary biology concerns the dynamics of adaptation and diversification. This issue can be addressed experimentally if replicate populations adapting to identical...
Stability and the Evolvability of Function in a Model Protein (2004)
Bloom, Jesse D, Wilke, Claus O, Arnold, Frances H, Adami, Christoph
Functional proteins must fold with some minimal stability to a structure that can perform a biochemical task. Here we use a simple model to investigate the relationship between the stability...
Experiments in Digital Evolution (Editors’ Introduction to the Special Issue) (2004)
Adami, Christoph, Wilke, Claus O.
[No abstract]
Towards photostatistics from photon-number discriminating detectors (2003)
Lee, Hwang, Yurtsever, Ulvi H., Kok, Pieter, Hockney, George M., Adami, Christoph, Braunstein, Samuel L., ...
We study the properties of a photodetector that has a number-resolving capability. In the absence of dark counts, due to its finite quantum efficiency, photodetection with such a detector can only...
Bloom, Jesse D., Adami, Christoph
Background: Several studies have suggested that proteins that interact with more partners evolve more slowly. The strength and validity of this association has been called into question. Here we...
Bloom, Jesse D, Adami, Christoph
Abstract Background Several studies have suggested that proteins that interact with more partners evolve more slowly. The strength and validity of this association has been called into question. Here...
Modeling stochastic clonal interference (2003)
Campos, Paulo R. A., Adami, Christoph, Wilke, Claus O.
We study the competition between several advantageous mutants in an asexual population (clonal interference) as a function of the time between the appearance of the mutants, their selective...
Wilke, Claus O, Lenski, Richard E, Adami, Christoph
Background: The rate at which fitness declines as an organism's genome accumulates random mutations is an important variable in several evolutionary theories. At an intuitive level, it might seem...
Entangled Light in Moving Frames (2003)
Bergou, Attila J., Gingrich, Robert M., Adami, Christoph
We calculate the entanglement between a pair of polarization-entangled photon beams as a function of the reference frame, in a fully relativistic framework. We find the transformation law for...
Wilke, Claus O., Lenski, Richard E., Adami, Christoph
Background: The rate at which fitness declines as an organism's genome accumulates random mutations is an important variable in several evolutionary theories. At an intuitive level, it might seem...
Wilke, Claus O, Lenski, Richard E, Adami, Christoph
Background The rate at which fitness declines as an organism's genome accumulates random mutations is an important variable in several evolutionary theories. At an intuitive level, it might seem...
Selective pressures on genomes in molecular evolution (2003)
Ofria, Charles, Adami, Christoph, Collier, Travis C.
We describe the evolution of macromolecules as an information transmission process and apply tools from Shannon information theory to it. This allows us to isolate three independent, competing...
Charles Ofria, Christoph Adami, Travis C. Collier
We describe the evolution of macromolecules as an information transmission process and apply tools from Shannon information theory to it. This allows us to isolate three independent, competing...
Kamp, Christel, Wilke, Claus O., Adami, Christoph, Bornholdt, Stefan
Based on a recent model of evolving viruses competing with an adapting immune system [1], we study the conditions under which a viral quasispecies can maximize its growth rate. The range of mutation...
Critical and near-critical branching processes (2002)
Scale-free dynamics in physical and biological systems can arise from a variety of causes. Here, we explore a branching process which leads to such dynamics. We find conditions for the appearance of...
Quantum Entanglement of Moving Bodies (2002)
Gingrich, Robert M., Adami, Christoph
We study the properties of quantum information and quantum entanglement in moving frames. We show that the entanglement between the spins and the momenta of two particles can be interchanged under a...
Optimal adaptive performance and delocalization in NK fitness landscapes (2001)
Campos, Paulo R. A., Adami, Christoph, Wilke, Claus O.
We investigate the evolutionary dynamics of a finite population of sequences adapting to NK fitness landscapes. We find that, unlike in the case of an infinite population, the average fitness in a...
Interaction between directional epistasis and average mutational effects (2000)
Wilke, Claus O., Adami, Christoph
We investigate the relationship between the average fitness decay due to single mutations and the strength of epistatic interactions in genetic sequences. We observe that epistatic interactions...
Evolution of Biological Complexity (2000)
Adami, Christoph, Ofria, Charles, Collier, Travis C.
In order to make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic...
Evolution of differentiated expression patterns in digital organisms (2000)
Ofria, Charles, Adami, Christoph, Collier, Travis C., Hsu, Grace K.
We investigate the evolutionary processes behind the development and optimization of multiple threads of execution in digital organisms using the avida platform, a software package that implements...
Evolution of biological complexity (2000)
Christoph Adami, Charles Ofria, Travis C. Collier
In order to make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic...
Evolution of genetic organization in digital organisms (1999)
Ofria, Charles, Adami, Christoph
We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed...
Critical and Near-Critical Branching Processes (1999)
Scale-free dynamics in physical and biological systems can arise from a variety of causes. Here, we explore a branching process which leads to such dynamics. We find conditions for the appearance of...
Zugl.: Dortmund, Universiẗat, Diss., 1998.
Evolution of Genetic Organization in Digital Organisms (1999)
Charles Ofria, Christoph Adami
. We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed...
Development and Evolution of Neural Networks in an Artificial Chemistry (1998)
Astor, Jens C., Adami, Christoph
We present a model of decentralized growth for Artificial Neural Networks (ANNs) inspired by the development and the physiology of real nervous systems. In this model, each individual artificial...
Development and Evolution of Neural Networks in an Artificial Chemistry (1998)
Jens C. Astor, Christoph Adami
We present a model of decentralized growth for Artificial Neural Networks (ANNs) inspired by the development and the physiology of real nervous systems. In this model, each individual artificial...
Aspects of matter under extreme conditions / (1991)
Thesis (Ph. D.)--State University of New York at Stony Brook, 1991.
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of...
Evolution of biological complexity
Adami, Christoph, Ofria, Charles, Collier, Travis C.
To make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic (but...
A simple explanation for taxon abundance patterns
For taxonomic levels higher than species, the abundance distributions of the number of subtaxa per taxon tend to approximate power laws but often show strong deviations from such laws. Previously,...
Thermodynamic prediction of protein neutrality
Bloom, Jesse D., Silberg, Jonathan J., Wilke, Claus O., Drummond, D. Allan, Adami, Christoph, Arnold, Frances H.
We present a simple theory that uses thermodynamic parameters to predict the probability that a protein retains the wild-type structure after one or more random amino acid substitutions. Our theory...
Stability and the Evolvability of Function in a Model Protein
Bloom, Jesse D., Wilke, Claus O., Arnold, Frances H., Adami, Christoph
Functional proteins must fold with some minimal stability to a structure that can perform a biochemical task. Here we use a simple model to investigate the relationship between the stability...
Why highly expressed proteins evolve slowly
Drummond, D. Allan, Bloom, Jesse D., Adami, Christoph, Wilke, Claus O., Arnold, Frances H.
Much recent work has explored molecular and population-genetic constraints on the rate of protein sequence evolution. The best predictor of evolutionary rate is expression level, for reasons that...
Evolution of biological complexity
Adami, Christoph, Ofria, Charles, Collier, Travis C.
To make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic (but...
A simple explanation for taxon abundance patterns
For taxonomic levels higher than species, the abundance distributions of the number of subtaxa per taxon tend to approximate power laws but often show strong deviations from such laws. Previously,...
Thermodynamic prediction of protein neutrality
Bloom, Jesse D., Silberg, Jonathan J., Wilke, Claus O., Drummond, D. Allan, Adami, Christoph, Arnold, Frances H.
We present a simple theory that uses thermodynamic parameters to predict the probability that a protein retains the wild-type structure after one or more random amino acid substitutions. Our theory...
Why highly expressed proteins evolve slowly
Drummond, D. Allan, Bloom, Jesse D., Adami, Christoph, Wilke, Claus O., Arnold, Frances H.
Much recent work has explored molecular and population-genetic constraints on the rate of protein sequence evolution. The best predictor of evolutionary rate is expression level, for reasons that...
Stability and the Evolvability of Function in a Model Protein
Bloom, Jesse D., Wilke, Claus O., Arnold, Frances H., Adami, Christoph
Functional proteins must fold with some minimal stability to a structure that can perform a biochemical task. Here we use a simple model to investigate the relationship between the stability...
Evolution of Complex Modular Biological Networks
Hintze, Arend, Adami, Christoph
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of...
Evolution of Differentiated Expression Patterns in Digital Organisms
Charles Ofria, Christoph Adami, Travis C. Collier, Grace K. Hsu
We investigate the evolutionary processes behind the development and optimization of multiple threads of execution in digital organisms using the Avida platform, a software package that implements...