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We use numerical simulations and an athermal quasi-static shear protocol to investigate the yielding of a model colloidal gel. Under increasing deformation, the elastic regime is followed by a significant stiffening before yielding takes…

The interaction between surface patches of proteins with different surface properties has a vital role to play driving conformational changes of proteins in different salt solutions. We demonstrate the existence of ion-specific attractive…

We present a comprehensive theoretical and computational model that explores the behavior of a thin hydrated film bonded to a non-hydrated / impermeable soft substrate in the context of surface and bulk elasticity coupled with surface…

This work proposes to model the space environment as a stochastic dynamic network where each node is a group of objects of a given class, or species, and their relationship is represented by stochastic links. A set of stochastic dynamic…

The osmotic virial coefficient $B_2$ of globular protein solutions is calculated as a function of added salt concentration at fixed pH by computer simulations of the ``primitive model''. The salt and counter-ions as well as a discrete…

Structural prediction of protein-protein interactions is important to understand the molecular basis of cellular interactions, but it still faces major challenges when significant conformational changes are present. We propose a generative…

We introduce a broad class of analytically solvable processes on networks. In the special case, they reduce to random walk and consensus process - two most basic processes on networks. Our class differs from previous models of interactions…

Large-scale atomistic calculations, using empirical potentials for modeling semiconductors, have been performed on a stressed system with linear surface defects like steps. Although the elastic limits of systems with surface defects remain…

The influence of structural constraints on the relaxation dynamics of three polyurea networks with varying degree of crosslinking, has been studied by means of a thorough analysis of broadband dielectric spectroscopy measurements. Two…

In physical networks trained using supervised learning, physical parameters are adjusted to produce desired responses to inputs. An example is electrical contrastive local learning networks of nodes connected by edges that are resistors…

Implicit solvent models are widely used to decrease the number of solvent degrees of freedom and enable the calculation of solvation energetics without water molecules. However, its accuracy often falls short compared to explicit models.…

Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…

The aggregation of protein-stabilised emulsions leads to the formation of emulsion gels. These soft solids are classically envisioned as droplet-filled matrices. Here however, it is assumed that protein-coated sub-micron droplets contribute…

The response function of a network of springs and masses, an elastodynamic network, is the matrix valued function $W(\omega)$, depending on the frequency $\omega$, mapping the displacements of some accessible or terminal nodes to the net…

We introduce a graph generating model aimed at representing the evolution of protein interaction networks. The model is based on the hypotesis of evolution by duplications and divergence of the genes which produce proteins. The obtained…

A novel energy landscape model, ELM, for proteins recently explained a collection of incoherent, elastic neutron scattering data from proteins. The ELM of proteins considers the elastic response of the proton and its environment to the…

Reactive chemistry of molecular hydrogen at surfaces, notably dissociative sticking and hydrogen evolution, plays a crucial role in energy storage and fuel cells. Theoretical studies can help to decipher underlying mechanisms and reaction…

An efficient numerical framework is presented for modeling viscoelasticity and permanent set of polymers. It is based on the hereditary integral form of transient network theory, in which polymer chains belong to distinct networks each with…

While operating communication networks adaptively may improve utilization and performance, frequent adjustments also introduce an algorithmic challenge: the re-optimization of traffic engineering solutions is time-consuming and may limit…

Polymer gels are comprised of a three-dimensional, cross-linked network that can typically withstand the mechanical deformation associated with both swelling and de-swelling. Thus, gels can be designed with smart behaviors that require both…