Related papers: Principles for optimal cooperativity in allosteric…

Allostery commonly refers to the mechanism that regulates protein activity through the binding of a molecule at a different, usually distal, site from the orthosteric site. The omnipresence of allosteric regulation in nature and its…

This paper presents a theory of optimization fabrics, second-order differential equations that encode nominal behaviors on a space and can be used to define the behavior of a smooth optimizer. Optimization fabrics can encode commonalities…

Here we present an approximate analytical theory for the relationship between a protein structure's contact matrix and the shape of its energy spectrum in amino acid sequence space. We demonstrate a dependence of the number of sequences of…

Many functional units in biology, such as enzymes or molecular motors, are composed of several subunits that can reversibly assemble and disassemble. This includes oligomeric proteins composed of several smaller monomers, as well as protein…

Fully pairing all elements of a set while attempting to maximize the total benefit is a combinatorically difficult problem. Such pairing problems naturally appear in various situations in science, technology, economics, and other fields. In…

Inspired by natural cellular materials such as trabecular bone, lattice structures have been developed as a new type of lightweight material. In this paper we present a novel method to design lattice structures that conform with both the…

Biological membranes are elastic media in which the presence of a transmembrane protein leads to local bilayer deformation. The energetics of deformation allow two membrane proteins in close proximity to influence each other's equilibrium…

Analyzing nonlinear conformational relaxation dynamics in elastic networks corresponding to two classical motor proteins, we find that they respond by well-defined internal mechanical motions to various initial deformations and that these…

Communication compression is an essential strategy for alleviating communication overhead by reducing the volume of information exchanged between computing nodes in large-scale distributed stochastic optimization. Although numerous…

We consider distributed optimization under communication constraints for training deep learning models. We propose a new algorithm, whose parameter updates rely on two forces: a regular gradient step, and a corrective direction dictated by…

Proteins perform their biological functions through three-dimensional structures encoded by amino acid sequences, and ligand-binding protein co-design requires models that generate sequence-structure compatible proteins under explicit…

The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and micro-clusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell…

Topology optimization is an important basis for the design of components. Here, the optimal structure is found within a design space subject to boundary conditions. Thereby, the specific material law has a strong impact on the final design.…

Collective communications, namely the patterns allgatherv, reduce_scatter, and allreduce in message-passing systems are optimised based on measurements at the installation time of the library. The algorithms used are set up in an…

Coherent propagation of two interacting particles in $1d$ weak random potential is considered. An accurate estimate of the matrix element of interaction in the basis of localized states leads to mapping onto the relevant matrix model. This…

A non-regenerative dual-hop wireless system based on a distributed space-time coding strategy is considered. It is assumed that each relay retransmits an appropriately scaled space-time coded version of its received signal. The main goal of…

In this study, we explore integrated sensing and communication (ISAC) networks to strike a more effective balance between sensing and communication (S&C) performance at the network scale. We leverage stochastic geometry to analyze the S&C…

Cooperative transmission of data fosters rapid accumulation of knowledge by efficiently combining experiences across learners. Although well studied in human learning and increasingly in machine learning, we lack formal frameworks through…

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…

Soft robots achieve functionality through tight coupling among geometry, material composition, and actuation. As a result, effective design optimization requires these three aspects to be considered jointly rather than in isolation. This…