579 research outputs found
Coarse-Grained Model for Phospholipid/Cholesterol Bilayer
We construct a coarse-grained (CG) model for dipalmitoylphosphatidylcholine
(DPPC)/cholesterol bilayers and apply it to large-scale simulation studies of
lipid membranes. Our CG model is a two-dimensional representation of the
membrane, where the individual lipid and sterol molecules are described by
point-like particles. The effective intermolecular interactions used in the
model are systematically derived from detailed atomic-scale molecular dynamics
simulations using the Inverse Monte Carlo technique, which guarantees that the
radial distribution properties of the CG model are consistent with those given
by the corresponding atomistic system. We find that the coarse-grained model
for the DPPC/cholesterol bilayer is substantially more efficient than atomistic
models, providing a speed-up of approximately eight orders of magnitude. The
results are in favor of formation of cholesterol-rich and cholesterol-poor
domains at intermediate cholesterol concentrations, in agreement with the
experimental phase diagram of the system. We also explore the limits of the
novel coarse-grained model, and discuss the general validity and applicability
of the present approach
Molecular Dynamics Study of Charged Dendrimers in Salt-Free Solution: Effect of Counterions
Polyamidoamine (PAMAM) dendrimers, being protonated under physiological
conditions, represent a promising class of nonviral, nano-sized vectors for
drug and gene delivery. We performed extensive molecular dynamics simulations
of a generic model dendrimer in a salt-free solution with dendrimer's terminal
beads positively charged. Solvent molecules as well as counterions were
explicitly included as interacting beads. We find that the size of the charged
dendrimer depends non-monotonically on the strength of electrostatic
interactions demonstrating a maximum when the Bjerrum length equals the
diameter of a bead. Many other structural and dynamic characteristics of
charged dendrimers are also found to follow this pattern. We address such a
behavior to the interplay between repulsive interactions of the charged
terminal beads and their attractive interactions with oppositely charged
counterions. The former favors swelling at small Bjerrum lengths and the latter
promotes counterion condensation. Thus, counterions can have a dramatic effect
on the structure and dynamics of charged dendrimers and, under certain
conditions, cannot be treated implicitly
Folding and insertion thermodynamics of the transmembrane WALP peptide
The anchor of most integral membrane proteins consists of one or several
helices spanning the lipid bilayer. The WALP peptide, GWW(LA)(L)WWA, is a
common model helix to study the fundamentals of protein insertion and folding,
as well as helix-helix association in the membrane. Its structural properties
have been illuminated in a large number of experimental and simulation studies.
In this combined coarse-grained and atomistic simulation study, we probe the
thermodynamics of a single WALP peptide, focusing on both the insertion across
the water-membrane interface, as well as folding in both water and a membrane.
The potential of mean force characterizing the peptide's insertion into the
membrane shows qualitatively similar behavior across peptides and three force
fields. However, the Martini force field exhibits a pronounced secondary
minimum for an adsorbed interfacial state, which may even become the global
minimum---in contrast to both atomistic simulations and the alternative PLUM
force field. Even though the two coarse-grained models reproduce the free
energy of insertion of individual amino acids side chains, they both
underestimate its corresponding value for the full peptide (as compared with
atomistic simulations), hinting at cooperative physics beyond the residue
level. Folding of WALP in the two environments indicates the helix as the most
stable structure, though with different relative stabilities and chain-length
dependence.Comment: 12 pages, 5 figure
Enhanced dielectrophoresis of nanocolloids by dimer formation
We investigate the dielectrophoretic motion of charge-neutral, polarizable
nanocolloids through molecular dynamics simulations. Comparison to analytical
results derived for continuum systems shows that the discrete charge
distributions on the nanocolloids have a significant impact on their coupling
to the external field. Aggregation of nanocolloids leads to enhanced
dielectrophoretic transport, provided that increase in the dipole moment upon
aggregation can overcome the related increase in friction. The dimer
orientation and the exact structure of the nanocolloid charge distribution are
shown to be important in the enhanced transport
Phase Diagram and Commensurate-Incommensurate Transitions in the Phase Field Crystal Model with an External Pinning Potential
We study the phase diagram and the commensurate-incommensurate transitions in
a phase field model of a two-dimensional crystal lattice in the presence of an
external pinning potential. The model allows for both elastic and plastic
deformations and provides a continuum description of lattice systems, such as
for adsorbed atomic layers or two-dimensional vortex lattices. Analytically, a
mode expansion analysis is used to determine the ground states and the
commensurate-incommensurate transitions in the model as a function of the
strength of the pinning potential and the lattice mismatch parameter. Numerical
minimization of the corresponding free energy shows good agreement with the
analytical predictions and provides details on the topological defects in the
transition region. We find that for small mismatch the transition is of
first-order, and it remains so for the largest values of mismatch studied here.
Our results are consistent with results of simulations for atomistic models of
adsorbed overlayers
Compiling Linguistic Constraints into Finite State Automata
International audienceThis paper deals with linguistic constraints encoded in the form of (binary) tables, generally called lexicon-grammar tables. We describe a unified method to compile sets of tables of linguistic constraints into Finite State Automata. This method has been practically implemented in the linguistic platform Unitex
Key Role of Defects in Thermoelectric Performance of TiMSn (M = Ni, Pd, and Pt) Half-Heusler Alloys
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Size-Exclusion Chromatography Separation Reveals That Vesicular and Non-Vesicular Small RNA Profiles Differ in Cell Free Urine.
Urinary extracellular vesicles (EVs) and their RNA cargo are a novel source of biomarkers for various diseases. We aimed to identify the optimal method for isolating small (<200 nm) EVs from human urine prior to small RNA analysis. EVs from filtered healthy volunteer urine were concentrated using three methods: ultracentrifugation (UC); a precipitation-based kit (PR); and ultrafiltration (UF). EVs were further purified by size-exclusion chromatography (SEC). EV preparations were analysed with transmission electron microscopy (TEM), Western blotting, nanoparticle tracking analysis (NTA) and an Agilent Bioanalyzer Small RNA kit. UF yielded the highest number of particles both before and after SEC. Small RNA analysis from UF-concentrated urine identified two major peaks at 10-40 nucleotides (nt) and 40-80 nt. In contrast, EV preparations obtained after UC, PR or SEC combined with any concentrating method, contained predominantly 40-80 nt sized small RNA. Protein fractions from UF+SEC contained small RNA of 10-40 nt in size (consistent with miRNAs). These data indicate that most of the microRNA-sized RNAs in filtered urine are not associated with small-sized EVs, and highlights the importance of removing non-vesicular proteins and RNA from urine EV preparations prior to small RNA analysis
Phase diagram of pinned lattices in the phase field crystal model
We study the phase diagram and the commensurate-incommensurate phase transitions of a two-dimensional phase field crystal model for adsorbed layers. The model allows for both elastic and plastic deformations on atomic and diffusive time-scales, and provides a continuum description of lattice systems, such as adsorbed atomic layers or two-dimensional vortex lattices. Analytically, mode expansion analysis and numerical minimization of the free energy are used to determine the ground states as a function of the pinning potential and lattice mismatch parameter. The results show a rich phase diagram with several different types of commensurate and incommensurate phases.Peer reviewe
Dielectrophoresis of nanocolloids: a molecular dynamics study
Dielectrophoresis (DEP), the motion of polarizable particles in non-uniform
electric fields, has become an important tool for the transport, separation,
and characterization of microparticles in biomedical and nanoelectronics
research. In this article we present, to our knowledge, the first molecular
dynamics simulations of DEP of nanometer-sized colloidal particles. We
introduce a simplified model for polarizable nanoparticles, consisting of a
large charged macroion and oppositely charged microions, in an explicit
solvent. The model is then used to study DEP motion of the particle at
different combinations of temperature and electric field strength. In accord
with linear response theory, the particle drift velocities are shown to be
proportional to the DEP force. Analysis of the colloid DEP mobility shows a
clear time dependence, demonstrating the variation of friction under
non-equilibrium. The time dependence of the mobility further results in an
apparent weak variation of the DEP displacements with temperature
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