Related papers: Principles for optimal cooperativity in allosteric…

A novel scenario-adapted distributed signaling technique in the context of opportunistic communications is presented in this work. Each opportunistic user acquires locally sampled observations from the wireless environment to determine the…

The behaviour of many real-world phenomena can be modelled by nonlinear dynamical systems whereby a latent system state is observed through a filter. We are interested in interacting subsystems of this form, which we model by a set of…

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…

Soft materials capable of large inelastic deformation play an essential role in high-performance nacre-inspired architectured materials with a combination of stiffness, strength and toughness. The rigid "building blocks" made from glass or…

An optimization method for the design of multi-lattice structures satisfying local buckling constraints is proposed in this paper. First, the concept of free material optimization is introduced to find an optimal elastic tensor distribution…

Despite the recognized importance of the multi-scale spatio-temporal organization of proteins, most computational tools can only access a limited spectrum of time and spatial scales, thereby ignoring the effects on protein behavior of the…

A topology optimization method is presented for the design of periodic microstructured materials with prescribed homogenized nonlinear constitutive properties over finite strain ranges. The mechanical model assumes linear elastic isotropic…

We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…

Optimal structure of proteins is described by linear stochastic differential equation with mean decrease of free energy and volatility. Structure determining strategy is given by a twin of stochastic variables for which empirical conditions…

We present a distributed algorithm that enables a group of robots to collaboratively optimize the parameters of a deep neural network model while communicating over a mesh network. Each robot only has access to its own data and maintains…

The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…

Cooperation is commonly found in ecological and social systems even when it apparently seems that individuals can benefit from selfish behavior. We investigate how cooperation emerges with the spatial prisoner's dilemma played in a class of…

Allostery plays a fundament role in most biological processes. However, little theory is available to describe it outside of two-state models. Here we use a statistical mechanical approach to show that the allosteric coupling between two…

Plasticity is inherent to many engineering materials such as metals. While it can degrade the load-carrying capacity of structures via material yielding, it can also protect structures through plastic energy dissipation. To fully harness…

In this work, we study the numerical optimization of nearest-neighbor concurrence of bipartite one and two dimensional lattices, as well as non bipartite two dimensional lattices. These systems are described in the framework of a…

Machine-learning of atomic-scale properties amounts to extracting correlations between structure, composition and the quantity that one wants to predict. Representing the input structure in a way that best reflects such correlations makes…

Highly-optimized complex transport networks serve crucial functions in many man-made and natural systems such as power grids and plant or animal vasculature. Often, the relevant optimization functional is non-convex and characterized by…

While allostery is of paramount importance for protein regulation, the underlying dynamical process of ligand (un)binding at one site, resulting time evolution of the protein structure, and change of the binding affinity at a remote site is…

We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and…

Optimal growth of structures governed by spatially stochastic dynamics arises in many scientific settings, for example in processes such as solution-based crystallization and the formation of microbial biofilms on patterned substrates or…