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)$_n$(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