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The mechanical properties of cells are dominated by the cytoskeleton, an interconnected network of long elastic filaments. The connections between the filaments are provided by crosslinking proteins, which constitute, next to the filaments,…

Understanding the link between structure and function in proteins is fundamental in molecular biology and proteomics. A central question in this context is whether allostery - where the binding of a molecule at one site affects the activity…

In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…

The behaviour and stability of soft and biological matter depend significantly on electrostatic interactions, as particles such as proteins and colloids acquire a charge when dispersed in an electrolytic solution. A typical simplification…

Plastic deformation of metals involves the complex evolution of dislocations forming strongly connected dislocation networks. These dislocation networks are based on dislocation reactions, which can form junctions during the interactions of…

Elastic network models (ENM) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have…

This paper presents a half-analytical elastic solution convenient for parametric studies of 2D cracked pavements. The pavement structure is reduced to three elastic and homogeneous equivalent layers resting on a soil. In a similar way than…

Cellular energy production depends on electron transfer (ET) between proteins. In this theoretical study, we investigate the impact of structural and conformational variations on the electronic coupling between the redox proteins…

Link prediction is central to unraveling social network evolution and node relationships, as well as understanding the characteristic mechanisms of complex networks. Currently, research on link prediction for complex dynamic networks…

Phase separation has recently emerged as an important organizational principle in the dense and heterogeneous environment within living cells. Here, we use a synthetic system to show that compressive stresses in a polymer network suppress…

We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics (MD) simulations are suggested by single-molecule studies of protein-DNA…

The subject of this report is the dynamics of elastic system in conjunction with hydrogen bonds of the DNA. We draw attention to the draw-back of the familiar rod model of the DNA, and make a case of constructing models that could…

Network models are used as efficient representation of materials with complex, interconnected locally one-dimensional structures. They typically accurately capture the mechanical properties of a material, while substantially reducing…

Experiments have shown that elasticity of disordered filamentous networks with compliant crosslinks is very different from networks with rigid crosslinks. Here, we model and analyze filamentous networks as a collection of randomly oriented…

Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…

The time elapsed model describes the firing activity of an homogeneous assembly of neurons thanks to the distribution of times elapsed since the last discharge. It gives a mathematical description of the probability density of neurons…

The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…

Being able to describe accurately the dynamics and steady-states of driven and/or dissipative but quantum correlated lattice models is of fundamental importance in many areas of science: from quantum information to biology. An efficient…

In this article we address the question whether it is possible to learn the differential equations describing the physical properties of a dynamical system, subject to non-conservative forces, from observations of its realspace…

We present an efficient and robust numerical model for simulation of electrokinetic phenomena in porous networks over a wide range of applications including energy conversion, desalination, and lab-on-a-chip systems. Coupling between fluid…