70 research outputs found
Comparison of Dissipative Particle Dynamics and Langevin thermostats for out-of-equilibrium simulations of polymeric systems
In this work we compare and characterize the behavior of Langevin and
Dissipative Particle Dynamics (DPD) thermostats in a broad range of
non-equilibrium simulations of polymeric systems. Polymer brushes in relative
sliding motion, polymeric liquids in Poiseuille and Couette flows, and
brush-melt interfaces are used as model systems to analyze the efficiency and
limitations of different Langevin and DPD thermostat implementations. Widely
used coarse-grained bead-spring models under good and poor solvent conditions
are employed to assess the effects of the thermostats. We considered
equilibrium, transient, and steady state examples for testing the ability of
the thermostats to maintain constant temperature and to reproduce the
underlying physical phenomena in non-equilibrium situations. The common
practice of switching-off the Langevin thermostat in the flow direction is also
critically revisited. The efficiency of different weight functions for the DPD
thermostat is quantitatively analyzed as a function of the solvent quality and
the non-equilibrium situation.Comment: 12 pages, introduction improved, references added, to appear in Phys.
Rev.
Static and dynamic properties of the interface between a polymer brush and a melt of identical chains
Molecular dynamics simulations of a short-chain polymer melt between two
brush-covered surfaces under shear have been performed. The end-grafted
polymers which constitute the brush have the same chemical properties as the
free chains in the melt and provide a soft deformable substrate. Polymer chains
are described by a coarse-grained bead-spring model with Lennard-Jones
interactions between the beads and a FENE potential between nearest neighbors
along the backbone of the chains. The grafting density of the brush layer
offers a way of controlling the behavior of the surface without altering the
molecular interactions. We perform equilibrium and non-equilibrium Molecular
Dynamics simulations at constant temperature and volume using the Dissipative
Particle Dynamics thermostat. The equilibrium density profiles and the behavior
under shear are studied as well as the interdigitation of the melt into the
brush, the orientation on different length scales (bond vectors, radius of
gyration, and end-to-end vector) of free and grafted chains, and velocity
profiles. The viscosity and slippage at the interface are calculated as
functions of grafting density and shear velocity.Comment: 12 pages, submitted to J Chem Phy
Recommended from our members
Effect of crosslinking on the microtribological behavior of model polymer brushes
Polymer brushes in good solvents are known to exhibit excellent tribological properties. We have modeled polymer brushes and their gels using a multibead-spring model and studied their tribological behavior via nonequilibrium molecular-dynamics (MD) simulations. Simulations of brush- against-wall systems were performed using an implicit solvent-based approach. Polymer chains were modeled as linear chains, randomly grafted on a planar surface. Quantities extracted from the simulations are the normal stress, shear stress and concentration profiles. We find that while an increase in the degree of crosslinking leads to an increase in the coefficient of friction, an increase of the length of crosslinker chains does the opposite. Effect of crosslinking can be understood in two ways: (i) there are fewer polymer chains in the outer layer as the degree of crosslinking increases to take part in brush-assisted lubrication, and (ii) crosslinked polymer chains are more resistant to shear than non-crosslinked ones
Spinodal Decomposition in a Binary Polymer Mixture: Dynamic Self Consistent Field Theory and Monte Carlo Simulations
We investigate how the dynamics of a single chain influences the kinetics of
early stage phase separation in a symmetric binary polymer mixture. We consider
quenches from the disordered phase into the region of spinodal instability. On
a mean field level we approach this problem with two methods: a dynamical
extension of the self consistent field theory for Gaussian chains, with the
density variables evolving in time, and the method of the external potential
dynamics where the effective external fields are propagated in time. Different
wave vector dependencies of the kinetic coefficient are taken into account.
These early stages of spinodal decomposition are also studied through Monte
Carlo simulations employing the bond fluctuation model that maps the chains --
in our case with 64 effective segments -- on a coarse grained lattice. The
results obtained through self consistent field calculations and Monte Carlo
simulations can be compared because the time, length, and temperature scales
are mapped onto each other through the diffusion constant, the chain extension,
and the energy of mixing. The quantitative comparison of the relaxation rate of
the global structure factor shows that a kinetic coefficient according to the
Rouse model gives a much better agreement than a local, i.e. wave vector
independent, kinetic factor. Including fluctuations in the self consistent
field calculations leads to a shorter time span of spinodal behaviour and a
reduction of the relaxation rate for smaller wave vectors and prevents the
relaxation rate from becoming negative for larger values of the wave vector.
This is also in agreement with the simulation results.Comment: Phys.Rev.E in prin
Novel highly potent CD4bs bNAb with restricted pathway to HIV-1 escape
Purpose: Broadly HIV-1 neutralizing antibodies (bNAbs) can suppress viremia
in humans and represent a novel approach for effective immunotherapy.
However, bNAb monotherapy selects for antibody-resistant viral variants.
Thus, we focused on the identification of new antibody combinations and/or
novel bNAbs that restrict pathways of HIV-1 escape.
Methods: We screened HIV-1 positive patients for their neutralizing
capacities. Following, we performed single cell sorting and PCR of HIV-1
Env-reactive mature B cells of identified elite neutralizers. Found antibodies
were tested for neutralization and binding capacities in vitro. Further, their
antiviral activity was tested in an HIV-1 infected humanized mouse model.
Results: Here we report the isolation of antibody 1–18, a VH1–46-encoded
CD4 binding site (CD4bs) bNAb identified in an individual ranking among the
top 1% neutralizers of 2,274 HIV-1-infected subjects. Tested on a 119-virus
panel, 1–18 showed to be exceptionally broad and potent with a coverage of
97% and a mean IC50 of 0.048 lg/mL, exceeding the activity of most potent
CD4bs bNAbs described to-date. A 2.4 Å cryo-EM structure of 1–18 bound to a
native-like Env trimer revealed that it interacts with HIV-1 env similar to other
CD4bs bNAbs, but includes additional contacts to the V3 loop of the adjacent
protomer. Notably, in vitro, 1–18 maintained activity against viruses carrying
mutations associated with escape from VRC01-class bNAbs. Further, its HIV-1
env wide escape profile differed critically from other CD4bs bNAbs. In
humanized mice, monotherapy with 1–18 was sufficient to prevent the
development of viral escape variants that rapidly emerged during treatment
with other CD4bs bNAbs. Finally, 1–18 overcame classical HIV-1 mutations
that are driven by VRC01-like bNAbs in vivo.
Conclusion: 1–18 is a highly potent and broad bNAb that restricts escape and
overcomes frequent CD4bs escape pathways, providing new options for bNAb
combinations to prevent and treat HIV-1 infection
Scale-free static and dynamical correlations in melts of monodisperse and Flory-distributed homopolymers: A review of recent bond-fluctuation model studies
It has been assumed until very recently that all long-range correlations are
screened in three-dimensional melts of linear homopolymers on distances beyond
the correlation length characterizing the decay of the density
fluctuations. Summarizing simulation results obtained by means of a variant of
the bond-fluctuation model with finite monomer excluded volume interactions and
topology violating local and global Monte Carlo moves, we show that due to an
interplay of the chain connectivity and the incompressibility constraint, both
static and dynamical correlations arise on distances . These
correlations are scale-free and, surprisingly, do not depend explicitly on the
compressibility of the solution. Both monodisperse and (essentially)
Flory-distributed equilibrium polymers are considered.Comment: 60 pages, 49 figure
Cellular Differentiation of Human Monocytes Is Regulated by Time-Dependent Interleukin-4 Signaling and the Transcriptional Regulator NCOR2.
Human in vitro generated monocyte-derived dendritic cells (moDCs) and macrophages are used clinically, e.g., to induce immunity against cancer. However, their physiological counterparts, ontogeny, transcriptional regulation, and heterogeneity remains largely unknown, hampering their clinical use. High-dimensional techniques were used to elucidate transcriptional, phenotypic, and functional differences between human in vivo and in vitro generated mononuclear phagocytes to facilitate their full potential in the clinic. We demonstrate that monocytes differentiated by macrophage colony-stimulating factor (M-CSF) or granulocyte macrophage colony-stimulating factor (GM-CSF) resembled in vivo inflammatory macrophages, while moDCs resembled in vivo inflammatory DCs. Moreover, differentiated monocytes presented with profound transcriptomic, phenotypic, and functional differences. Monocytes integrated GM-CSF and IL-4 stimulation combinatorically and temporally, resulting in a mode- and time-dependent differentiation relying on NCOR2. Finally, moDCs are phenotypically heterogeneous and therefore necessitate the use of high-dimensional phenotyping to open new possibilities for better clinical tailoring of these cellular therapies
Forced-induced desorption of a polymer chain adsorbed on an attractive surface - Theory and Computer Experiment
We consider the properties of a self-avoiding polymer chain, adsorbed on a
solid attractive substrate which is attached with one end to a pulling force.
The conformational properties of such chain and its phase behavior are treated
within a Grand Canonical Ensemble (GCE) approach. We derive theoretical
expressions for the mean size of loops, trains, and tails of an adsorbed chain
under pulling as well as values for the universal exponents which describe
their probability distribution functions. A central result of the theoretical
analysis is the derivation of an expression for the crossover exponent ,
characterizing polymer adsorption at criticality, , which
relates the precise value of to the exponent , describing
polymer loop statistics. We demonstrate that , depending on the possibility of a single loop to interact with
neighboring loops in the adsorbed polymer. The universal surface loop exponent
and the Flory exponent .
We present the adsorption-desorption phase diagram of a polymer chain under
pulling and demonstrate that the relevant phase transformation becomes first
order whereas in the absence of external force it is known to be a continuous
one. The nature of this transformation turns to be dichotomic, i.e.,
coexistence of different phase states is not possible. These novel theoretical
predictions are verified by means of extensive Monte Carlo simulations.Comment: 24 pages, 14 figure
- …