Search results for "Quantitative Biology::Biomolecules"
showing 10 items of 467 documents
Capillary Nematization of Semiflexible Polymers
2016
emiflexible polymers under good solvent conditions confined by two planar parallel repulsive walls are investigated for a wide range of monomer concentrations and distances between the walls, for a case where persistence length and contour length of the macromolecules are almost equal. Chain conformations and local nematic ordering near the walls are studied by both molecular dynamics methods and density functional theory, putting it in perspective with the recent work where the isotropic phase of semiflexible polymer solutions in the vicinity of a single repulsive wall in semi-infinite geometry is considered. Profiles of the total density of monomers as well as densities of end- and middle…
Coupling of Nanoparticle Dynamics to Polymer Center-of-Mass Motion in Semidilute Polymer Solutions
2017
We investigate the dynamics of nanoparticles in semidilute polymer solutions when the nanoparticles are comparably sized to the polymer coils using explicit- and implicit-solvent simulation methods. The nanoparticle dynamics are subdiffusive on short time scales before transitioning to diffusive motion on long time scales. The long-time diffusivities scale according to theoretical predictions based on full dynamic coupling to the polymer segmental relaxations. In agreement with our recent experiments, however, we observe that the nanoparticle subdiffusive exponents are significantly larger than predicted by the coupling theory over a broad range of polymer concentrations. We attribute this …
Equilibrium Dynamics and Shear Rheology of Semiflexible Polymers in Solution
2017
We study the structure and dynamics of semidilute solutions of semiflexible polymers at rest and under shear using hybrid molecular dynamics simulations that take hydrodynamic interactions into account. We show that the polymer center-of-mass diffusion coefficient significantly decreases with increasing chain stiffness at fixed monomer density. The zero-shear viscosity shows a corresponding increase due to the intermolecular interactions of stiffer chains. We apply steady shear flow to the polymer solutions and show that at high shear rates the flow properties become almost independent of polymer stiffness. We characterize the polymer conformations under shear and find that in this regime p…
Shear-Thinning in Oligomer Melts—Molecular Origins and Applications
2021
We investigate the molecular origin of shear-thinning in melts of flexible, semiflexible and rigid oligomers with coarse-grained simulations of a sheared melt. Entanglements, alignment, stretching and tumbling modes or suppression of the latter all contribute to understanding how macroscopic flow properties emerge from the molecular level. In particular, we identify the rise and decline of entanglements with increasing chain stiffness as the major cause for the non-monotonic behaviour of the viscosity in equilibrium and at low shear rates, even for rather small oligomeric systems. At higher shear rates, chains align and disentangle, contributing to shear-thinning. By performing simulations …
Spherical polymer brushes under good solvent conditions: molecular dynamics results compared to density functional theory.
2010
A coarse grained model for flexible polymers end-grafted to repulsive spherical nanoparticles is studied for various chain lengths and grafting densities under good solvent conditions, by Molecular Dynamics methods and density functional theory. With increasing chain length the monomer density profile exhibits a crossover to the star polymer limit. The distribution of polymer ends and the linear dimensions of individual polymer chains are obtained, while the inhomogeneous stretching of the chains is characterized by the local persistence lengths. The results on the structure factor of both single chain and full spherical brush as well as the range of applicability of the different theoretic…
Monte Carlo analysis of polymer translocation with deterministic and noisy electric fields
2012
AbstractPolymer translocation through the nanochannel is studied by means of a Monte Carlo approach, in the presence of a static or oscillating external electric voltage. The polymer is described as a chain molecule according to the two-dimensional “bond fluctuation model”. It moves through a piecewise linear channel, which mimics a nanopore in a biological membrane. The monomers of the chain interact with the walls of the channel, modelled as a reflecting barrier. We analyze the polymer dynamics, concentrating on the translocation time through the channel, when an external electric field is applied. By introducing a source of coloured noise, we analyze the effect of correlated random fluct…
Conformational Changes and Charge Transfer in Biomolecules Resolved Using Dynamic Enhanced Raman Correlation Spectroscopy
2019
International audience; In this contribution, we report that conforma-tional changes of molecules that are often buried in a wide-distributed Gaussian distribution can be discerned by analyzing the dynamics of specific Raman lines. We investigate the pertinence of the auto-and cross-correlation functions applied to the dynamics of three Raman lines of an amino acid, the tryptophan. The cross-correlation between intensity and the Raman band is an indicator of the charge transfer during the diffusion limited reaction of tryptophan and the gold surface. The Pećlet number Pe can provide a valuable indicator of the convective and/or diffusive features of each Raman band. Adsorption induced confo…
A DNA-nanoparticle actuator enabling optical monitoring of nanoscale movements induced by an electric field.
2018
Merging biological and non-biological matter to fabricate nanoscale assemblies with controllable motion and function is of great interest due to its potential application, for example, in diagnostics and biosensing. Here, we have constructed a DNA-based bionanoactuator that interfaces with biological and non-biological matter via an electric field in a reversibly controllable fashion. The read-out of the actuator is based on motion-induced changes in the plasmon resonance of a gold nanoparticle immobilized to a gold surface by single stranded DNA. The motion of the gold nanoparticle and thus the conformational changes of the DNA under varying electric field were analyzed by dark field spect…
Conformal invariance of the writhe of a knot
2008
We give a new proof of an old theorem by Banchoff and White 1975 that claims that the writhe of a knot is conformally invariant.
The Calder\'on problem for the conformal Laplacian
2016
We consider a conformally invariant version of the Calder\'on problem, where the objective is to determine the conformal class of a Riemannian manifold with boundary from the Dirichlet-to-Neumann map for the conformal Laplacian. The main result states that a locally conformally real-analytic manifold in dimensions $\geq 3$ can be determined in this way, giving a positive answer to an earlier conjecture by Lassas and Uhlmann (2001). The proof proceeds as in the standard Calder\'on problem on a real-analytic Riemannian manifold, but new features appear due to the conformal structure. In particular, we introduce a new coordinate system that replaces harmonic coordinates when determining the co…