Search results for "molecular dynamics"
showing 10 items of 1075 documents
Phase behavior of flexible and semiflexible polymers in solvents of varying quality.
2019
The interplay of nematic order and phase separation in solutions of semiflexible polymers in solvents of variable quality is investigated by density functional theory (DFT) and molecular dynamics (MD) simulations. We studied coarse-grained models, with a bond-angle potential to control chain stiffness, for chain lengths comparable to the persistence length of the chains. We varied both the density of the monomeric units and the effective temperature that controls the quality of the implicit solvent. For very stiff chains, only a single transition from an isotropic fluid to a nematic is found, with a phase diagram of "swan-neck" topology. For less stiff chains, however, also unmixing between…
A new insight into the isotropic–nematic phase transition in lyotropic solutions of semiflexible polymers: density-functional theory tested by molecu…
2016
Semiflexible polymers in solution are studied for a wide range of both contour length L and persistence length lp as a function of monomer concentration under good solvent conditions. Both density-functional theory (DFT) and molecular dynamics (MD) simulation methods are used, and a very good agreement between both techniques is observed for rather stiff polymers. Evidence for a new mechanism of order parameter fluctuations in the nematic phase is presented, namely collective deformations of bundles of wormlike chains twisted around each other, and the typical wavelengths and amplitudes of these modes are estimated. These long wavelength fluctuations cause a reduction of the order parameter…
Semiflexible macromolecules in quasi-one-dimensional confinement: Discrete versus continuous bond angles
2015
The conformations of semiflexible polymers in two dimensions confined in a strip of width D are studied by computer simulations, investigating two different models for the mechanism by which chain stiffness is realized. One model (studied by molecular dynamics) is a bead-spring model in the continuum, where stiffness is controlled by a bond angle potential allowing for arbitrary bond angles. The other model (studied by Monte Carlo) is a self-avoiding walk chain on the square lattice, where only discrete bond angles (0° and ±90°) are possible, and the bond angle potential then controls the density of kinks along the chain contour. The first model is a crude description of DNA-like biopolymer…
Nematic order in solutions of semiflexible polymers: Hairpins, elastic constants, and the nematic-smectic transition
2018
Coarse-grained models of lyotropic solutions of semiflexible polymers are studied by both molecular dynamics simulations and density functional theory calculations, using an implicit solvent bead-spring model with a bond-angle potential. We systematically vary the monomer density, persistence length, and contour length over a wide range and explore the full range from the isotropic-nematic transition to the nematic-smectic transition. In the nematic regime, we span the entire regime from rigid-rod like polymers to thin wormlike chains, confined in effective straight tubes caused by the collective nematic effective ordering field. We show that the distribution of bond angles relative to the …
How does stiffness of polymer chains affect their adsorption transition?
2020
The adsorption transition and the structure of semiflexible adsorbed macromolecules are studied by a molecular dynamics simulation of a coarse-grained, bead-spring type model. Varying chain length N and stiffness κ (which is proportional to the persistence length lp in d = 3 dimensions) as well as the strength ϵwall of the adsorption potential, the adsorbed monomer fraction, orientational bond order parameter, and chain linear dimensions are studied. In the simulations, excluded volume interactions normally are included but can be “switched off,” and thus, the influence of excluded volume (leading to deviations from predictions of the wormlike chain model) can be identified. It is shown tha…
Semiflexible polymers under good solvent conditions interacting with repulsive walls.
2016
Solutions of semiflexible polymers confined by repulsive planar walls are studied by density functional theory and Molecular Dynamics simulations, to clarify the competition between the chain alignment favored by the wall and the depletion caused by the monomer-wall repulsion. A coarse-grained bead-spring model with bond bending potential is studied, varying both the contour length and the persistence length of the polymers, as well as the monomer concentration in the solution (good solvent conditions are assumed throughout, and solvent molecules are not included explicitly). The profiles of monomer density and pressure tensor components near the wall are studied, and the surface tension of…
Conformations and orientational ordering of semiflexible polymers in spherical confinement.
2017
Semiflexible polymers in lyotropic solution confined inside spherical nanoscopic “containers” with repulsive walls are studied by molecular dynamics simulations and density functional theory, as a first step to model confinement effects on stiff polymers inside of miniemulsions, vesicles, and cells. It is shown that the depletion effects caused by the monomer-wall repulsion depend distinctly on the radius R of the sphere. Further, nontrivial orientational effects occur when R, the persistence length ℓp, and the contour length L of the polymers are of similar magnitude. At intermediate densities, a “shell” of wall-attached chains is forming, such that the monomers belonging to those chains a…
Understanding the properties of liquid-crystalline polymers by computational modeling
2020
Abstract A topical review of recent theoretical work on the properties of lyotropic solutions and melts containing semiflexible polymers in thermal equilibrium is given, with a focus on the liquid-crystalline and smectic order of these systems in the bulk and under confinement. Starting with a discussion of single chain properties in terms of the Kratky-Porod worm-like chain model and its limitations, extensions along the lines of Onsager’s theory for the isotropic-nematic transition of solutions of hard rods are briefly reviewed. This discussion is followed by a review of recent Molecular Dynamics simulations and classical Density Functional Theory calculations. It is argued that, even in …
Deciphering the Potential of Pre and Pro-Vitamin D of Mushrooms against Mpro and PLpro Proteases of COVID-19: An In Silico Approach
2022
Vitamin D’s role in combating the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the virus causing COVID-19, has been established in unveiling viable inhibitors of COVID-19. The current study investigated the role of pre and pro-vitamin D bioactives from edible mushrooms against Mpro and PLpro proteases of SARS-CoV-2 by computational experiments. The bioactives of mushrooms, specifically ergosterol (provitamin D2), 7-dehydrocholesterol (provitamin-D3), 22,23-dihydroergocalciferol (provitamin-D4), cholecalciferol (vitamin-D3), and ergocalciferol (vitamin D2) were screened against Mpro and PLpro. Molecular docking analyses of the generated bioactive protease complexes unr…
Evaluation of the IKKβ Binding of Indicaxanthin by Induced-Fit Docking, Binding Pose Metadynamics, and Molecular Dynamics
2021
Background: Indicaxanthin, a betaxanthin belonging to the betalain class of compounds, has been recently demonstrated to exert significant antiproliferative effects inducing apoptosis of human melanoma cells through the inhibition of NF-κB as the predominant pathway. Specifically, Indicaxanthin inhibited IκBα degradation in A375 cells. In resting cells, NF-κB is arrested in the cytoplasm by binding to its inhibitor protein IκBα. Upon stimulation, IκBα is phosphorylated by the IKK complex, and degraded by the proteasome, liberating free NF-κB into the nucleus to initiate target gene transcription. Inhibition of the IKK complex leads to the arrest of the NF-κB pathway.Methods: To acquire deta…