Related papers: Maximum entropy models for antibody diversity
The immune response to a pathogen has two basic features. The first is the expansion of a few pathogen-specific cells to form a population large enough to control the pathogen. The second is the process of differentiation of cells from an…
A pattern of a sequence is a sequence of integer indices with each index describing the order of first occurrence of the respective symbol in the original sequence. In a recent paper, tight general bounds on the block entropy of patterns of…
Some natural proteins display recurrent structural patterns. Despite being highly similar at the tertiary structure level, repetitions within a single repeat protein can be extremely variable at the sequence level. We propose a mathematical…
The design and optimization of antibodies requires an intricate balance across multiple properties. Protein inverse folding models, capable of generating diverse sequences folding into the same structure, are promising tools for maintaining…
Nowadays we are often faced with huge databases resulting from the rapid growth of data storage technologies. This is particularly true when dealing with music databases. In this context, it is essential to have techniques and tools able to…
In this work we propose a physical model of organismal evolution, where phenotype, organism life expectancy, is directly related to genotype i.e. the stability of its proteins which can be determined exactly in the model. Simulating the…
The growth dynamics of complex systems often exhibit statistical regularities involving power-law relationships. For real finite complex systems formed by countable tokens (animals, words) as instances of distinct types (species, dictionary…
Food webs are complex ecological networks whose structure is both ecologically and statistically constrained, with many network properties being correlated with each other. Despite the recognition of these invariable relationships in food…
The metaphor of a potential epigenetic differentiation landscape broadly suggests that during differentiation a stem cell follows the steepest descending gradient toward a stable equilibrium state which represents the final cell type. It…
Genomic evolution can be viewed as string-editing processes driven by mutations. An understanding of the statistical properties resulting from these mutation processes is of value in a variety of tasks related to biological sequence data,…
Complex network states are characterized by the interplay between system's structure and dynamics. One way to represent such states is by means of network density matrices, whose von Neumann entropy characterizes the number of distinct…
This contribution is devoted to a new model of HIV multiplication motivated by the patent of one of the authors. We take into account the antigenic diversity through what we define "antigenicity", whether of the virus or of the adapted…
The consistency of the species abundance distribution across diverse communities has attracted widespread attention. In this paper, I argue that the consistency of pattern arises because diverse ecological mechanisms share a common symmetry…
Maximum entropy methods provide a principled path connecting measurements of neural activity directly to statistical physics models, and this approach has been successful for populations of $N\sim 100$ neurons. As $N$ increases in new…
Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is…
Information has an entropic character which can be analyzed within the Statistical Theory in molecular systems. R. Landauer and C.H. Bennett showed that a logical copy can be carried out in the limit of no dissipation if the computation is…
We show that statistical criticality, i.e. the occurrence of power law frequency distributions, arises in samples that are maximally informative about the underlying generating process. In order to reach this conclusion, we first identify…
Graphs are widely used for describing systems made up of many interacting components and for understanding the structure of their interactions. Various statistical models exist, which describe this structure as the result of a combination…
Maximum diversity problems arise in many practical settings from facility location to social networks, and constitute an important class of NP-hard problems in combinatorial optimization. There has been a growing interest in these problems…
We investigate a model where idiotypes (characterizing B-lymphocytes and antibodies of an immune system) and anti-idiotypes are represented by complementary bitstrings of a given length d allowing for a number of mismatches (matching…