Search results for "Quantitative Biology"
showing 10 items of 1025 documents
Identifiability problem for recovering the mortality rate in an age-structured population dynamics model
2014
In this article is studied the identifiability of the age-dependent mortality rate of the Von Foerster–Mc Kendrick model, from the observation of a given age group of the population. In the case where there is no renewal for the population, translated by an additional homogeneous boundary condition to the Von Foerster equation, we give a necessary and sufficient condition on the initial density that ensures the mortality rate identifiability. In the inhomogeneous case, modelled by a non-local boundary condition, we make explicit a sufficient condition for the identifiability property, and give a condition for which the identifiability problem is ill-posed. We illustrate this latter case wit…
Simulation and theory of fluid demixing and interfacial tension of mixtures of colloids and nonideal polymers.
2005
An extension of the Asakura-Oosawa-Vrij model of hard sphere colloids and non-adsorbing polymers, that takes polymer non-ideality into account through a repulsive stepfunction pair potential between polymers, is studied with grand canonical Monte Carlo simulations and density functional theory. Simulation results validate previous theoretical findings for the shift of the bulk fluid demixing binodal upon increasing strength of polymer-polymer repulsion, promoting the tendency to mix. For increasing strength of the polymer-polymer repulsion, simulation and theory consistently predict the interfacial tension of the free colloidal liquid-gas interface to decrease significantly for fixed colloi…
Surface anchoring on liquid crystalline polymer brushes
2002
We present a Monte Carlo study of the surface anchoring of a nematic fluid on swollen layers of grafted liquid crystalline chain molecules. The liquid crystalline particles are modeled by soft repulsive ellipsoids, and the chains are made of the same particles. An appropriately modified version of the configurational bias Monte Carlo algorithm is introduced, which removes and redistributes chain bonds rather than whole monomers. With this algorithm, a wide range of grafting densities could be studied. The substrate is chosen such that it favors a planar orientation (parallel to the surface). Depending on the grafting density, we find three anchoring regimes: planar, tilted, and perpendicula…
Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates
2013
Conformational changes are known to be able to drive an enzyme through its catalytic cycle, allowing, for example, substrate binding or product release. However, the influence of protein motions on the chemical step is a controversial issue. One proposal is that the simple equilibrium fluctuations incorporated into transition-state theory are insufficient to account for the catalytic effect of enzymes and that protein motions should be treated dynamically. Here, we propose the use of free-energy surfaces, obtained as a function of both a chemical coordinate and an environmental coordinate, as an efficient way to elucidate the role of protein structure and motions during the reaction. We sho…
Calculation of the Phase Behavior of Lipids
1998
The self-assembly of monoacyl lipids in solution is studied employing a model in which the lipid's hydrocarbon tail is described within the Rotational Isomeric State framework and is attached to a simple hydrophilic head. Mean-field theory is employed, and the necessary partition function of a single lipid is obtained via a partial enumeration over a large sample of molecular conformations. The influence of the lipid architecture on the transition between the lamellar and inverted-hexagonal phases is calculated, and qualitative agreement with experiment is found.
Influence of polymer flexibility on nanoparticle dynamics in semidilute solutions
2018
The hierarchical structure and dynamics of polymer solutions control the transport of nanoparticles (NPs) through them. Here, we perform multi-particle collision dynamics simulations of solutions of semiflexible polymer chains with tunable persistence length lp to investigate the effect of chain stiffness on NP transport. The NPs exhibit two distinct dynamical regimes - subdiffusion on short time scales and diffusion on long time scales. The long-time NP diffusivities are compared with predictions from the Stokes-Einstein relation (SER), mode-coupling theory (MCT), and a recent polymer coupling theory (PCT). Increasing deviations from the SER as the polymer chains become more rigid (i.e. as…
Standard Definitions of Persistence Length Do Not Describe the Local “Intrinsic” Stiffness of Real Polymer Chains
2010
On the basis of extensive Monte Carlo simulations of lattice models for linear chains under good and Θ solvents conditions, and for bottle-brush polymers under good solvent conditions, different me...
Structure of bottle brush polymers on surfaces: weak versus strong adsorption.
2011
Large-scale Monte Carlo simulations are presented for a coarse-grained model of cylindrical molecular brushes adsorbed on a flat structureless substrate, varying both the chain length N of the side chains and the backbone chain length N(b). For the case of good solvent conditions, both the cases of weak adsorption (only 10 to 15% of the monomers being bound to the surface) and strong adsorption (~40% of the monomers being bound to the surface, forcing the bottle brush into an almost 2D conformation) are studied. We focus on the scaling of the total linear dimensions of the cylindrical brush with both chain lengths N and N(b), demonstrating a crossover from rod-like behavior (for not very la…
One- and two-component bottle-brush polymers: simulations compared to theoretical predictions
2007
Scaling predictions and results from self-consistent field calculations for bottle-brush polymers with a rigid backbone and flexible side chains under good solvent conditions are summarized and their validity and applicability is assessed by a comparison with Monte Carlo simulations of a simple lattice model. It is shown that under typical conditions, as they are also present in experiments, only a rather weak stretching of the side chains is realized, and then the scaling predictions based on the extension of the Daoud-Cotton blob picture are not applicable. Also two-component bottle brush polymers are considered, where two types (A,B) of side chains are grafted, assuming that monomers of …
Parity violation energy of biomolecules - III: RNA
2006
The energy of parity-violation associated with a typical DNA double helix is estimated with ab initio techniques. It is shown that weak-nuclear interactions do not favor the formation of the double helices found in nature. Possible implications regarding the potential effect of parity-violation interactions on the evolution of biological homochirality are discussed.