Related papers: Collective Molecular Dynamics in Proteins and Memb…
Living cells are soft bodies of a characteristic form, but endowed with a capacity for a steady turnover of their structures. Both of these material properties, i.e. recovery of the shape after an external stress has been imposed and…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical…
The macroscopic properties of polymeric fluids are inherited from the material properties of the fibers embedded in the solvent. The behavior of such passive fibers in flow has been of interest in a wide range of systems, including cellular…
Integral membrane proteins deform the surrounding bilayer creating long-ranged forces that influence distant proteins. These forces can be attractive or repulsive, depending on the proteins' shape, height, contact angle with the bilayer, as…
The precise measurement of neutrino properties is among the highest priorities in fundamental particle physics, involving many experiments worldwide. Since the experiments rely on the interactions of neutrinos with bound nucleons inside…
This study explores the dynamics of finite-size fibers suspended freely in a viscoelastic turbulent flow. For a fiber suspended in Newtonian flows, two different flapping regimes were identified previously by Rosti et al (2018). Here we…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
The dynamics of a tracer molecule near a fluid membrane is investigated, with particular emphasis given to the interplay between the instantaneous position of the particle and membrane fluctuations. It is found that hydrodynamic…
The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that…
Membrane proteins often need to be inserted into or attached on the cell membrane to perform their functions. Understanding their transmembrane topology and conformational dynamics during insertion is crucial for elucidating their roles.…
Whether live cell membranes show miscibility phase transitions (MPTs), and if so, how they fluctuate near the transitions remain outstanding unresolved issues in physics and biology alike. Motivated by these questions we construct a generic…
The internal dynamics of active gels, both in artificial (in-vitro) model systems and inside the cytoskeleton of living cells, has been extensively studied by experiments of recent years. These dynamics are probed using tracer particles…
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered…
Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…
Polymers are a primary building block in many biomaterials, often interacting with anisotropic backgrounds. While previous studies have considered polymer dynamics within nematic solvents, rarely are the the effects of anisotropic viscosity…
Molecular dynamics simulation is now a widespread approach for understanding complex systems on the atomistic scale. It finds applications from physics and chemistry to engineering, life and medical science. In the last decade, the approach…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
We determine both the in-plane and out-of-plane dynamics of viscoelastic membranes separating two viscous fluids in order to understand microrheological studies of such membranes. We demonstrate the general viscoelastic signatures in the…