Related papers: Optimal flexibility for conformational transitions…
Conformational changes are observed in many enzymes, but their role in catalysis is highly controversial. Here we present a theoretical model that illustrates how rigid catalysts can be fundamentally limited and how a conformational change…
The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results…
Hydrophobic polyelectrolytes (HPE) can solubilize bilayer membranes, form micelles or can reversibly aggregate as a function of pH. The transitions are often remarkably sharp. We show that these cooperative transitions occur by a…
In intracellular transports, motor proteins transport macromolecules as cargos to desired locations by moving on biopolymers such as microtubules. Recent experiments suggest that cargos that can associate motor proteins during their…
The hopping model for cargo transport by molecular motors introduced in Refs. goldman1, goldman2, is extended here in order to incorporate the movement of cargo-motor complexes. In this context, hopping process expresses the possibility for…
We study the model of a molecular switch comprised of a molecule with a soft vibrational degree of freedom coupled to metallic leads. In the presence of strong electron-ion interaction, different charge states of the molecule correspond to…
Couplings play a central role in the analysis of Markov chain convergence and in the construction of novel Markov chain Monte Carlo estimators, diagnostics, and variance reduction techniques. The set of possible couplings is often…
The coil-globule transition of hetero-polymer chains is studied here. By means of extensive Molecular Dynamics simulations, we show that the transition is directly linked to the complexity of the chain, which depends on the number of…
Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
Chromatin and associated proteins constitute the highly folded structure of chromosomes. We consider a self-avoiding polymer model of the chromatin, segments of which may get cross-linked via protein binders that repel each other. The…
People organize in groups and contagions spread across them. A simple process, but complex to model due to dynamical correlations within groups and between groups. Groups can also change as agents join and leave them to avoid infection. To…
Microorganisms often perform chemotaxis, (i.e., sensing and moving toward a region with a higher concentration of an attractive chemical) by changing the rate of tumbling for random walk. We studied several models with internal adaptive…
We introduce a generic, purely mechanical model for environment sensitive motion of mammalian cells that is applicable to chemotaxis, haptotaxis, and durotaxis as modes of motility. It is able to theoretically explain all relevant…
Biomolecular machines transduce between different forms of energy. These machines make directed progress and increase their speed by consuming free energy, typically in the form of nonequilibrium chemical concentrations. Machine dynamics…
We study the Lagrangian dynamics of semi-flexible macromolecules in laminar as well as in homogeneous and isotropic turbulent flows by means of analytically solvable stochastic models and direct numerical simulations. The statistics of the…
We present molecular dynamics simulations of a binary Lennard-Jones mixture at temperatures below the kinetic glass transition. The ``mobility'' of a particle is characterized by the amplitude of its fluctuation around its average position.…
We show how dynamic heterogeneities (DH), a hallmark of glass-forming materials, depend on chain flexibility and chain length in polymers. For highly flexible polymers, a relatively large number of monomers ($N_c\sim500$) undergo correlated…
We present experimental confirmation of dynamic facilitation in monodisperse and bidisperse colloidal suspensions near the glass transition volume fraction. Correlations in particle dynamics are seen to exist not only in space (clusters and…
The ability to tune the microstructures formed by block copolymers using accessible physical approaches provides control for practical material applications. A common strategy involves the addition of homopolymers, which can induce…
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…