Related papers: Theory and simulations for crowding-induced change…
Experimental studies of systems containing active proteins that undergo conformational changes driven by catalytic chemical reactions have shown that the diffusion coefficients of passive tracer particles and active molecules are larger…
Collective behavior of proteins on biomembranes is usually studied within the spontaneous curvature model. Here we consider an alternative phenomenological approach, which accounts consistently for partial ordering of proteins as well as…
Experiments of particle-laden inclined film flow [Zhou, Dupuy, Bertozzi, and Hosoi, Phys. Rev. Lett. 94 (2005)] have displayed different settling behaviors depending on the particle concentration $\phi$ and angle of inclination $\theta$, in…
We investigate the conformations of DNA-like stiff chains, characterized by contour length ($L$) and persistence length ($l_p$), in a variety of crowded environments containing mono disperse soft spherical (SS) and spherocylindrical (SC)…
In the cell, proteins fold and perform complex functions through global structural rearrangements. Function requires a protein to be at the brink of stability to be susceptible to small environmental fluctuations, yet stable enough to…
One great challenge of modeling granular systems lies in capturing the rheologic dependencies on scale. For example, there are marked differences between quasi-static, intermediate, and rapid flow regimes. In this study, we demonstrate that…
Pan, Vekilov and Lubchenko[\textit{J. Phys. Chem. B}, 2010, \textbf{114}, 7620] have proposed that dense stable protein clusters appearing in weak protein solutions above the solubility curve are composed of protein oligomers. The…
Using the Ricci and scalar curvatures of the configuration manifold of gravitational N-body systems, we study the exponential instability in their trajectories. It is found that the exponentiation time-scale for isotropic Plummer spheres…
A putative powerlaw range of the probability density of velocity gradient in high-Reynolds-number forced Burgers turbulence is studied. In the absence of information about shock locations, elementary conservation and stationarity relations…
We investigate the influence of confinement on phase separation in colloid-polymer mixtures. To describe the particle interactions, the colloid-polymer model of Asakura and Oosawa [J. Chem. Phys. 22, 1255 (1954)] is used. Grand canonical…
Three-dimensional discrete numerical simulation is used to investigate the properties of close-packed frictionless granular assemblies as a function of particle polydispersity and shape. Unlike some experimental results, simulations show…
We examine by extensive computer simulations the self-diffusion of anisotropic star like particles in crowded two-dimensional solutions. We investigate the implications of the area coverage fraction $\phi$ of the crowders and the…
We derive a specific functional form for factor alpha decay -- hyperbolic decay alpha(t) = K/(1+lambda*t) -- from a game-theoretic equilibrium model, and test it against linear and exponential alternatives. Using eight Fama-French factors…
We show that the relative stability of the nematic tetratic phase with respect to the usual uniaxial nematic phase can be greatly enhanced by clustering effects. Two--dimensional rectangles of aspect ratio $\kappa$ interacting via hard…
When systems that can undergo phase separation between two coexisting phases in the bulk are confined in thin film geometry between parallel walls, the phase behavior can be profoundly modified. These phenomena shall be described and…
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…
Sphere packings in high dimensions interest mathematicians and physicists and have direct applications in communications theory. Remarkably, no one has been able to provide exponential improvement on a 100-year-old lower bound on the…
We study the thermodynamic and kinetic consequences of the competition between single-protein folding and protein-protein aggregation using a phenomenological model, in which the proteins can be in the unfolded (U), misfolded (M) or folded…
The stabilization of macromolecules is fundamental to developing biological formulations, such as vaccines and protein therapeutics. In this study, we employ coarse grained polymer models to investigate the impact of four sugars:…
The influence of crowding on the diffusion of tagged particles in a dense medium is investigated in the framework of a mean-field model, derived in the continuum limit from a microscopic stochastic process with exclusion. The probability…