Search results for "Biomolecules"

Non-equilibrium Markov state modeling of periodically driven biomolecules

2019

Molecular dynamics simulations allow to study the structure and dynamics of single biomolecules in microscopic detail. However, many processes occur on time scales beyond the reach of fully atomistic simulations and require coarse-grained multiscale models. While systematic approaches to construct such models have become available, these typically rely on microscopic dynamics that obey detailed balance. In vivo, however, biomolecules are constantly driven away from equilibrium in order to perform specific functions and thus break detailed balance. Here we introduce a method to construct Markov state models for systems that are driven through periodically changing one (or several) external p…

Infrared nanospectroscopic mapping of DNA molecules on mica surface

2022

Significant efforts have been done in last two decades to develop nanoscale spectroscopy techniques owning to their great potential for single-molecule structural detection and in addition, to resolve open questions in heterogeneous biological systems, such as protein-DNA complexes. Applying AFM-IR technique has become a powerful leverage for obtaining simultaneous absorption spectra with a nanoscale spatial resolution for studied proteins, however the IR-AFM investigation of DNA molecules on surface, as a benchmark for a nucleoprotein complexes nanocharacterization, has remained elusive. Herein, we demonstrate methodological approach for acquisition of IR-AFM mapping modalities with corres…

Monte Carlo Simulations in Polymer Science

2012

Monte Carlo methods are useful for computing the statistical properties of both single macromolecules of various chemical architectures and systems containing many polymers (solutions, melts, blends, etc.). Starting with simple models (lattice models such as the self-avoiding walk or the bond fluctuation model, as well as coarse-grained or chemically realistic models in the continuum) various algorithms exist to generate conformations typical for thermal equilibrium, but dynamic Monte Carlo methods can also model diffusion and relaxation processes (as described by the Rouse and the reptation models for polymer melt dynamics). Limitations of the method are explained, and also the measures to…

Shear Modulus of an Irreversible Diblock Copolymer Network from Self-Consistent Field Theory

2019

Using self-consistent field theory, we investigate the stretching-induced microphase separation in an irreversibly cross-linked polymer network composed of diblock copolymer chains and estimate its...

Computer Simulations for Polymer Dynamics

1991

In this paper we review recent work on the dynamics of polymeric systems using computer simulation methods. For a two-dimensional polymer melt, we show that the chains segregate and the dynamics can be described very well by the Rouse model. This simulation was carried out using the bond fluctuation Monte Carlo method. For three-dimensional (3d) melts and for the study of hydrodynamic effects, we use a molecular dynamics simulation. For 3d melts our results strongly support the concept of reptation. A detailed comparison to experiment shows that we can predict the time and length scales for the onset of reptation for a variety of polymeric liquids. For a single chain, we find the expected h…

Anomalous diffusion of polymers in supercooled melts near the glass transition

2007

Two coarse-grained models for polymer chains in dense melts near the glass transition are investigated: the bond fluctuation lattice model, where long bonds are energetically favored, is studied by dynamic Monte Carlo simulation, and an off-lattice bead-spring model with Lennard-Jones forces between the beads is treated by Molecular Dynamics. We compare the time-dependence of the mean square displacements of both models, and show that they become very similar on mesoscopic scales (i.e., displacements larger than a bond length). The slowing down of motions near the glass transition is discussed in terms of the mode coupling theory and other concepts.

Structure of diblock copolymers in supercritical carbon dioxide and critical micellization pressure

1999

This paper reports a small angle neutron scattering investigation of micelle formation by fluorocarbon-hydrocarbon block copolymers in supercritical ${\mathrm{CO}}_{2}{(\mathrm{s}\mathrm{c}\ensuremath{-}\mathrm{C}\mathrm{O}}_{2})$ at 65 \ifmmode^\circ\else\textdegree\fi{}C. A sharp unimer-micelle transition is obtained due to the tuning of the solvating ability of ${\mathrm{s}\mathrm{c}\ensuremath{-}\mathrm{C}\mathrm{O}}_{2}$ by profiling pressure, so that the block copolymer, in a semidilute solution, finds ${\mathrm{s}\mathrm{c}\ensuremath{-}\mathrm{C}\mathrm{O}}_{2}$ a good solvent at high pressure and a poor solvent at low pressure. At high pressure the copolymer is in a monomeric state…

1986

An osmotic pressure equation proposed over 50 years ago is found to be consistent with the des Cloizeaux scaling relation for semi-dilute polymer solutions in good solvents. With a physically plausible modification, the equation can also give a satisfactory representation of dilute solutions and of the cross-over to the semi-dilute regime.

Entropic Unmixing in Nematic Blends of Semiflexible Polymers

2020

Binary mixtures of semiflexible polymers with the same chain length but different persistence lengths separate into two coexisting different nematic phases when the osmotic pressure of the lyotropic solution is varied. Molecular Dynamics simulations and Density Functional Theory predict phase diagrams either with a triple point, where the isotropic phase coexists with two nematic phases, or a critical point of unmixing within the nematic mixture. The difference in locally preferred bond angles between the constituents drives this unmixing without any attractive interactions between monomers.

Phase Transitions and Relaxation Processes in Macromolecular Systems: The Case of Bottle-brush Polymers

2009

As an example for the interplay of structure, dynamics, and phase behavior of macromolecular systems, this article focuses on the problem of bottle-brush polymers with either rigid or flexible backbones. On a polymer with chain length $N_b$, side-chains with chain length $N$ are endgrafted with grafting density $\sigma$. Due to the multitude of characteristic length scales and the size of these polymers (typically these cylindrical macromolecules contain of the order of 10000 effective monomeric units) understanding of the structure is a challenge for experiment. But due to excessively large relaxation times (particularly under poor solvent conditions) such macromolecules also are a challen…