Related papers: The atomic-level mechanism underlying the function…
Motor-proteins are responsible for transport inside cells. Harnessing their activity is key towards developing new nano-technologies, or functional biomaterials. Cytoskeleton-like networks, recently tailored in vitro, result from the…
Based on recent studies on hydrophobic interactions, it is devoted to investigate the directional nature of hydrophobic interactions. It means that the hydrophobic interactions are dependent on the relative orientations as the solutes tend…
Cells accomplish diverse functions using the same molecular building blocks, from setting up cytoplasmic flows to generating mechanical forces. In particular, transitions between these non-equilibrium states are triggered by regulating the…
Functionalization of nanoparticles or colloids is increasingly being used to develop customizable "atoms". Functionalization by attaching single strands of DNA allows for direct control of the binding between nanoparticles, since…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single stranded DNA molecule that forms hairpin structure and calculate the properties…
Cells make use of semi-flexible biopolymers such as actin or intermediate filaments to control their local viscoelastic response by dynamically adjusting the concentration and type of cross-linker molecules. The microstructure of the…
The folding of the cholesterol trapping apolipoprotein A1 in aqueous solution at increasing ionic strength is studied using atomically detailed molecular dynamics simulations. We calculate various structural properties to characterize the…
We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a…
With molecular simulation for water and a tunable hydrophobic substrate, we apply the instantaneous interface construction [A. P. Willard and D. Chandler, J. Phys. Chem. B, 114, 1954 (2010)] to examine the similarity between a water-vapor…
We investigate the translocation of a stiff polymer consisting of M monomers through a nanopore in a membrane, in the presence of binding particles (chaperones) that bind onto the polymer, and partially prevent backsliding of the polymer…
We use numerical simulations to investigate the hydrodynamic behavior of the interface between nematic (N) and isotropic (I) phases of a confined active liquid crystal. At low activities, a stable interface with constant shape and velocity…
Understanding protein motion within the cell is crucial for predicting reaction rates and macromolecular transport in the cytoplasm. A key question is how crowded environments affect protein dynamics through hydrodynamic and direct…
We have investigated the dynamics of water confined in mesostructured porous silicas (SBA-15, MCM-41) and four periodic mesoporous organosilicas (PMOs) by dielectric relaxation spectroscopy. The influence of water-surface interaction has…
In living organisms, information is processed in interconnected symphonies of ionic currents spiking through protein ion channels. As a result of dynamically switching their conductive states, ion channels exhibit a variety of…
Rotors are common in nature - from rotating membrane-proteins to superfluid-vortices. Yet, little is known about the collective dynamics of heterogeneous populations of rotors. Here, we show experimentally, numerically, and analytically…
Protein-protein interactions comprise both transport and reaction steps. During the transport step, anisotropy of proteins and their complexes is important both for hydrodynamic diffusion and accessibility of the binding site. Using a…
The function of membrane-embedded proteins such as ion channels depends crucially on their conformation. We demonstrate how conformational changes in asymmetric membrane proteins may be inferred from measurements of their diffusion. Such…
Ubiquitin, discovered less than 50 years ago, tags thousands of diseased proteins for destruction. It is small (only 76 amino acids), and is found unchanged in mammals, birds, fish and even worms. Key features of its functionality are…
Understanding the stabilities of proteins in nanopores requires a quantitative description of confinement induced interactions between amino acid side chains. We use molecular dynamics simulations to study the nature of interactions between…
Hydrophobic interactions are central to biological self-assembly and soft matter organization, yet their microscopic origins remain debated. A key hallmark is the strengthening of attraction between hydrophobic solutes with increasing…