714 research outputs found
Non-conformal coarse-grained potentials for water
Water is a notoriously difficult substance to model both accurately and
efficiently. Here, we focus on descriptions with a single coarse-grained
particle per molecule using the so-called Approximate Non-Conformal (ANC) and
generalized Stockmayer potentials as the starting points. They are fitted using
the radial density function and the density of the atomistic SPC/E model by
downhill simplex optimization. We compare the results with monatomic water
(mW), ELBA, as well as with direct Iterative Boltzmann Inversion (IBI) of
SPC/E. The results show that symmetrical potentials result in non-transferable
models, that is, they need to be reparametrized for new state-points. This
indicates that transferability may require more complex models. Furthermore,
the results also show that the addition of a point dipole is not sufficient to
make the potentials accurate and transferable to different temperatures (300
K-500 K) and pressures without an appropriate choice of properties as targets
during model optimization
The physical observer I: Absolute and relative fields
Quantum Jet Theory (QJT) is a deformation of QFT where also the quantum
dynamics of the observer is taken into account. This is achieved by introducing
relative fields, labelled by locations measured by rods relative to the
observer's position. In the Hamiltonian formalism, the observer's momentum is
modified: p_i \to p_i - P_i, where P_i is the momentum carried by the field
quanta. The free scalar field, free electromagnetism and gravity are treated as
examples. Standard QFT results are recovered in the limit that the observer's
mass M \to \infty and its charge e \to 0. This limit is well defined except for
gravity, because e = M in that case (heavy mass equals inert mass). In a
companion paper we describe how QJT also leads to new observer-dependent gauge
and diff anomalies, which can not be formulated within QFT proper.Comment: 39 p
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
Instabilities and resistance fluctuations in thin accelerated superconducting rings
The non-equilibrium properties of a driven quasi-one dimensional
superconducting ring subjected to a constant electromotive force ({\it emf}) is
studied. The {\it emf} accelerates the superconducting electrons until the
critical current is reached and a dissipative phase slip occurs that lowers the
current. The phase slip phenomena is examined as a function of the strength of
the {\it emf}, thermal noise, and normal state resistivity. Numerical and
analytic methods are used to make detailed predictions for the magnitude of
phase slips and subsequent dissipation.Comment: Some movies are available here at http://www.lce.hut.fi/~karttune/S
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
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
- …