相关论文: Thermodynamic Capacity of a Protein
The primate heteromodal cortex presents an evident functional modularity at a mesoscopic level, with physiological and anatomical evidence pointing to it as likely substrate of long-term memory. In order to investigate some of its…
The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed…
Dense Associative Memories or Modern Hopfield Networks have many appealing properties of associative memory. They can do pattern completion, store a large number of memories, and can be described using a recurrent neural network with a…
The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure, or of wider and sometimes highly elaborated motions. Coarse-grained elastic-network descriptions are…
We present a Hopfield-like autoassociative network for memories representing examples of concepts. Each memory is encoded by two activity patterns with complementary properties. The first is dense and correlated across examples within…
Humans can learn individual episodes and generalizable rules and also successfully retain both kinds of acquired knowledge over time. In the cognitive science literature, (1) learning individual episodes and rules and (2) learning and…
In this Communication we present statistical analysis of conservation profiles in families of homologous sequences for nine proteins whose folding nucleus was determined by protein engineering methods. We show that in all but one protein…
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…
We review the recent progress in computational approaches to protein design which builds on advances in statistical-mechanical protein folding theory. In particular, we evaluate the degeneracy of the protein code (i.e. how many sequences…
Biological flow networks adapt their network morphology to optimise flow while being exposed to external stimuli from different spatial locations in their environment. These adaptive flow networks retain a memory of the stimulus location in…
Computational protein design is experiencing a transformation driven by AI/ML. However, the range of potential protein sequences and structures is astronomically vast, even for moderately sized proteins. Hence, achieving convergence between…
To confer high specificity and affinity in binding, contacts at interfaces between two interacting macromolecules are expected to exhibit pair preferences for types of atoms or residues. Here we quantify these preferences by measuring the…
The binding affinity between the T-cell receptors (TCRs) and antigenic peptides mainly determines immunological recognition. It is not a trivial task that T cells identify the digital sequences of peptide amino acids by simply relying on…
Protein structures in nature often exhibit a high degree of regularity (secondary structures, tertiary symmetries, etc.) absent in random compact conformations. We demonstrate in a simple lattice model of protein folding that structural…
Phase-separated biomolecular condensates exhibit a wide range of dynamical properties, which depend on the sequences of the constituent proteins and RNAs. However, it is unclear to what extent condensate dynamics can be tuned without also…
A rigorous thermodynamic expression is derived for the total biological information capacity per unit length of a DNA molecule. The total information includes the usual four letter coding sequence information plus that excess information…
It has been shown that a neural network model recently proposed to describe basic memory performance is based on a ternary/binary coding/decoding algorithm which leads to a new neural network assembly memory model (NNAMM) providing…
We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…
By exact computer enumeration and combinatorial methods, we have calculated the designability of proteins in a simple lattice H-P model for the protein folding problem. We show that if the strength of the non-additive part of the…
The majority of mammalian genomic transcripts do not directly code for proteins and it is currently believed that most of these are not under evolutionary constraint. However given the abundance non-coding RNA (ncRNA) and its strong…