31 research outputs found
Co-non-solvency: Mean-field polymer theory does not describe polymer collapse transition in a mixture of two competing good solvents
Smart polymers are a modern class of polymeric materials that often exhibit
unpredictable behavior in mixtures of solvents. One such phenomenon is
co-non-solvency. Co-non-solvency occurs when two (perfectly) miscible and
competing good solvents, for a given polymer, are mixed together. As a result,
the same polymer collapses into a compact globule within intermediate mixing
ratios. More interestingly, polymer collapses when the solvent quality remains
good and even gets increasingly better by the addition of the better cosolvent.
This is a puzzling phenomenon that is driven by strong local concentration
fluctuations. Because of the discrete particle based nature of the
interactions, Flory-Huggins type mean field arguments become unsuitable. In
this work, we extend the analysis of the co-non-solvency effect presented
earlier [Nature Communications 5, 4882 (2014)]. We explain why co-non-solvency
is a generic phenomenon that can be understood by the thermodynamic treatment
of the competitive displacement of (co)solvent components. This competition can
result in a polymer collapse upon improvement of the solvent quality. Specific
chemical details are not required to understand these complex conformational
transitions. Therefore, a broad range of polymers are expected to exhibit
similar reentrant coil-globule-coil transitions in competing good solvents
IBI: Targeting cumulative coordination within an iterative protocol to derive coarse-grained models of (multi-component) complex fluids
We present a coarse-graining strategy that we test for aqueous mixtures. The
method uses pair-wise cumulative coordination as a target function within an
iterative Boltzmann inversion (IBI) like protocol. We name this method
coordination iterative Boltzmann inversion (IBI). While the
underlying coarse-grained model is still structure based and, thus, preserves
pair-wise solution structure, our method also reproduces solvation
thermodynamics of binary and/or ternary mixtures. Additionally, we observe much
faster convergence within IBI compared to IBI. To validate the
robustness, we apply IBI to study test cases of solvation
thermodynamics of aqueous urea and a triglycine solvation in aqueous urea
Thermal conductivity of bottle-brush polymers
Using molecular dynamics (MD) simulations of a generic model, we investigate
heat propagation in bottle--brush polymers (BBP). An architecture is referred
to as a BBP when a linear (backbone) polymer is grafted with the side chains of
different length and grafting density , which control
the bending stiffness of a backbone. A BBP is of particular interest due to two
competing mechanics: increased backbone stiffness, via and
, increases the thermal transport coefficient , while the
presence of side chains provides additional pathways for heat leakage. We show
how a delicate competition between these two effects controls . These
results reveal that going from a weakly grafting () to a
highly grafting () regime, changes
non--monotonically that is independent of . The effect of side chain
mass on and heat flow in the BBP melts are also discussed
Dynamic instability of microtubules: effect of catastrophe-suppressing drugs
Microtubules are stiff filamentary proteins that constitute an important
component of the cytoskeleton of cells. These are known to exhibit a dynamic
instability. A steadily growing microtubule can suddenly start depolymerizing
very rapidly; this phenomenon is known as ``catastrophe''. However, often a
shrinking microtubule is ``rescued'' and starts polymerizing again. Here we
develope a model for the polymerization-depolymerization dynamics of
microtubules in the presence of {\it catastrophe-suppressing drugs}. Solving
the dynamical equations in the steady-state, we derive exact analytical
expressions for the length distributions of the microtubules tipped with
drug-bound tubulin subunits as well as those of the microtubules, in the
growing and shrinking phases, tipped with drug-free pure tubulin subunits. We
also examine the stability of the steady-state solutions.Comment: Minor corrections; final published versio
Why Do Elastin-Like Polypeptides Possibly Have Different Solvation Behaviors in Water-Ethanol and Water-Urea Mixtures?
The solvent quality determines the collapsed or the expanded state of a
polymer. For example, a polymer dissolved in a poor solvent collapses, whereas
in a good solvent it opens up. While this standard understanding is generally
valid, there are examples when a polymer collapses even in a mixture of two
good solvents. This phenomenon, commonly known as co-non-solvency, is usually
associated with smart polymers. Moreover, recent experiments have shown that
the elastin-like polypeptides (ELPs) show co-non-solvency behavior in
aqueous-ethanol mixtures. In this study, we investigate the phase behavior of
ELPs in aqueous binary mixtures using molecular dynamics simulations of
all-atom and complementary explicit solvent generic models. The model is
parameterized by mapping the solvation free energy obtained from the all-atom
simulations onto the generic interaction parameters. For this purpose, we
derive segment based generic parameters for four different peptides, namely
proline (P), valine (V), glycine (G) and alanine (A). Here we compare the
conformational behavior of two ELP sequences, namely VPGGG and VPGVG, in
aqueous-ethanol and -urea mixtures. Consistent with recent experiments, we find
that ELPs show co-non-solvency in aqueous-ethanol mixtures. Ethanol molecules
have preferential binding with all ELP residues and thus driving the
coil-to-globule transition. On the contrary, ELP conformations show weak
variation in aqueous-urea mixtures. Our simulations suggest that the glycine
residues dictate the overall behavior of ELPs in aqueous-urea, where urea
molecules have a rather weak preferential binding with glycine, i.e., less than
kT. While the validation of the latter findings will require more detailed
experimental investigation, the results presented here may provide a new twist
to the present understanding of cosolvent interactions with peptides and
proteins.Comment: Accepted for publication in Macromolecule
Tuning the thermal conductivity of silicon nanowires by surface passivation
Using large scale molecular dynamics simulations, we study the thermal
conductivity of bare and surface passivated silicon nanowires (SiNWs). For the
smaller cross-sectional widths , SiNWs become unstable because of the
surface amorphousization and even evaporation of a certain fraction of Si atoms
when nm. Our results suggest that the surface (in--)stability is
related to a large excess energy of the surface Si atoms with respect
to the bulk Si. This is because the surface Si atoms being less coordinated and
having dangling bonds. As a first step of our study, we propose a practically
relevant method that uses as a guiding tool to passivate these
dangling bonds and thus stabilizes SiNWs. The surface stabilization is achieved
by passivation of Si atoms by hydrogen or oxygen. These passivated SiNWs are
then used for the calculation of the thermal conductivity coefficient .
While the expected trend of is observed for all SiNWs,
surface passivation provides an added flexibility of tuning with the
surface coverage concentration of passivated atoms. Analyzing the phonon
band structures via spectral energy density, we discuss separate contributions
from the surface and the core to . The effect of passivation on SiNW
stiffness is also discussed