Related papers: The Information Capacity of Specific Interactions
Proteins must bind to specific other proteins in vivo in order to function. The proteins must bind only to one or a few other proteins of the of order a thousand proteins typically present in vivo. Using a simple model of a protein,…
Proteins need to selectively interact with specific targets among a multitude of similar molecules in the cell. But despite a firm physical understanding of binding interactions, we lack a general theory of how proteins evolve high…
This article reviews recent inverse statistical-mechanical methodologies that we have devised to optimize interaction potentials in soft matter systems that correspond to stable "target" structures. We are interested in finding the…
The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein-protein interactions is complicated by the fact that the…
We use inverse methods of statistical mechanics to explore trade-offs associated with designing interactions to stabilize self-assembled structures against changes in density or temperature. Specifically, we find isotropic,convex-repulsive…
The concept of optimal communication channels shapes our understanding of wave-based communication. Its analysis, however, always pertains to specific communication-domain geometries, without a general theory of scaling laws or fundamental…
We introduce a simple model to describe the interplay between specific and non-specific interactions. We study the influence of various physical factors on the static and dynamic properties of the specific interactions of our model and show…
A tight-binding model together with a novel statistical method are used to investigate the relation between the sequence-dependent electric transport properties and the sequences of protein-coding regions of complete genomes. A correlation…
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…
Features in product lines and highly configurable systems can interact in ways that are contrary to developers' intent. Current methods to identify such unanticipated feature interactions are costly and inadequate. To address this problem…
The vicinity of phase transitions selectively amplifies weak stimuli, yielding optimal sensitivity to distinguish external input. Along with this enhanced sensitivity, enhanced levels of fluctuations at criticality reduce the specificity of…
Context dependence is central to the description of complexity. Keying on the pairwise definition of "set complexity" we use an information theory approach to formulate general measures of systems complexity. We examine the properties of…
To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve…
Nanoparticles functionalized with multiple ligands can be programmed to bind biological targets depending on the receptors they express, providing a general mechanism exploited in various technologies, from selective drug-delivery to…
As few real systems comprise indistinguishable units, diversity is a hallmark of nature. Diversity among interacting units shapes properties of collective behavior such as synchronization and information transmission. However, the benefits…
In program synthesis, we transform a specification into a program that is guaranteed to satisfy the specification. In synthesis of reactive systems, the environment in which the program operates may behave nondeterministically, e.g., by…
DNA-coated particles are promising as building blocks for functional and finite-sized assemblies because they can be programmed with orthogonal interactions owing to the sequence-specific hybridization of DNA strands. To fully exploit this…
We use computer simulation to study crystal-forming model proteins equipped with interactions that are both orientationally specific and nonspecific. Distinct dynamical pathways of crystal formation can be selected by tuning the strengths…
We formulate statistical-mechanical inverse methods in order to determine optimized interparticle interactions that spontaneously produce target many-particle configurations. Motivated by advances that give experimentalists greater and…
Information capacity of a symbol sequence is a measure of the unexpectedness of a continuation of given string of symbols. Continuation of a string is determined through the maximum entropy of the reconstructed frequency dictionary; the…