17,604 research outputs found
Classical Time Crystals
We consider the possibility that classical dynamical systems display motion
in their lowest energy state, forming a time analogue of crystalline spatial
order. Challenges facing that idea are identified and overcome. We display
arbitrary orbits of an angular variable as lowest-energy trajectories for
nonsingular Lagrangian systems. Dynamics within orbits of broken symmetry
provide a natural arena for formation of time crystals. We exhibit models of
that kind, including a model with traveling density waves.Comment: 5 pages, 1 figur
Identifying influential spreaders and efficiently estimating infection numbers in epidemic models: a walk counting approach
We introduce a new method to efficiently approximate the number of infections
resulting from a given initially-infected node in a network of susceptible
individuals. Our approach is based on counting the number of possible infection
walks of various lengths to each other node in the network. We analytically
study the properties of our method, in particular demonstrating different forms
for SIS and SIR disease spreading (e.g. under the SIR model our method counts
self-avoiding walks). In comparison to existing methods to infer the spreading
efficiency of different nodes in the network (based on degree, k-shell
decomposition analysis and different centrality measures), our method directly
considers the spreading process and, as such, is unique in providing estimation
of actual numbers of infections. Crucially, in simulating infections on various
real-world networks with the SIR model, we show that our walks-based method
improves the inference of effectiveness of nodes over a wide range of infection
rates compared to existing methods. We also analyse the trade-off between
estimate accuracy and computational cost, showing that the better accuracy here
can still be obtained at a comparable computational cost to other methods.Comment: 6 page
Hydrodynamic flow patterns and synchronization of beating cilia
We calculate the hydrodynamic flow field generated far from a cilium which is
attached to a surface and beats periodically. In the case of two beating cilia,
hydrodynamic interactions can lead to synchronization of the cilia, which are
nonlinear oscillators. We present a state diagram where synchronized states
occur as a function of distance of cilia and the relative orientation of their
beat. Synchronized states occur with different relative phases. In addition,
asynchronous solutions exist. Our work could be relevant for the synchronized
motion of cilia generating hydrodynamic flows on the surface of cells.Comment: 5 pages, 4 figures, v2: minor correction
Thermal spin transport and spin-orbit interaction in ferromagnetic/non-magnetic metals
In this article we extend the currently established diffusion theory of
spin-dependent electrical conduction by including spin-dependent
thermoelectricity and thermal transport. Using this theory, we propose new
experiments aimed at demonstrating novel effects such as the spin-Peltier
effect, the reciprocal of the recently demonstrated thermally driven spin
injection, as well as the magnetic heat valve. We use finite-element methods to
model specific devices in literature to demonstrate our theory. Spin-orbit
effects such as anomalous-Hall, -Nernst, anisotropic magnetoresistance and
spin-Hall are also included in this model
DDGun: An untrained method for the prediction of protein stability changes upon single and multiple point variations
Background: Predicting the effect of single point variations on protein stability constitutes a crucial step toward understanding the relationship between protein structure and function. To this end, several methods have been developed to predict changes in the Gibbs free energy of unfolding (\u3b4\u3b4G) between wild type and variant proteins, using sequence and structure information. Most of the available methods however do not exhibit the anti-symmetric prediction property, which guarantees that the predicted \u3b4\u3b4G value for a variation is the exact opposite of that predicted for the reverse variation, i.e., \u3b4\u3b4G(A \u2192 B) = -\u3b4\u3b4G(B \u2192 A), where A and B are amino acids. Results: Here we introduce simple anti-symmetric features, based on evolutionary information, which are combined to define an untrained method, DDGun (DDG untrained). DDGun is a simple approach based on evolutionary information that predicts the \u3b4\u3b4G for single and multiple variations from sequence and structure information (DDGun3D). Our method achieves remarkable performance without any training on the experimental datasets, reaching Pearson correlation coefficients between predicted and measured \u3b4\u3b4G values of ~ 0.5 and ~ 0.4 for single and multiple site variations, respectively. Surprisingly, DDGun performances are comparable with those of state of the art methods. DDGun also naturally predicts multiple site variations, thereby defining a benchmark method for both single site and multiple site predictors. DDGun is anti-symmetric by construction predicting the value of the \u3b4\u3b4G of a reciprocal variation as almost equal (depending on the sequence profile) to -\u3b4\u3b4G of the direct variation. This is a valuable property that is missing in the majority of the methods. Conclusions: Evolutionary information alone combined in an untrained method can achieve remarkably high performances in the prediction of \u3b4\u3b4G upon protein mutation. Non-trained approaches like DDGun represent a valid benchmark both for scoring the predictive power of the individual features and for assessing the learning capability of supervised methods
Low-energy QCD: Chiral coefficients and the quark-quark interaction
A detailed investigation of the low-energy chiral expansion is presented
within a model truncation of QCD. The truncation allows for a phenomenological
description of the quark-quark interaction in a framework which maintains the
global symmetries of QCD and permits a expansion. The model dependence
of the chiral coefficients is tested for several forms of the quark-quark
interaction by varying the form of the running coupling, , in the
infrared region. The pattern in the coefficients that arises at tree level is
consistent with large QCD, and is related to the model truncation.Comment: 28 pages, Latex, 6 postscript figures available on request to
[email protected]
Riemann-Einstein Structure from Volume and Gauge Symmetry
It is shown how a metric structure can be induced in a simple way starting
with a gauge structure and a preferred volume, by spontaneous symmetry
breaking. A polynomial action, including coupling to matter, is constructed for
the symmetric phase. It is argued that assuming a preferred volume, in the
context of a metric theory, induces only a limited modification of the theory.Comment: LaTeX, 13 pages; Added additional reference in Reference
Non-universal equilibrium crystal shape results from sticky steps
The anisotropic surface free energy, Andreev surface free energy, and
equilibrium crystal shape (ECS) z=z(x,y) are calculated numerically using a
transfer matrix approach with the density matrix renormalization group (DMRG)
method. The adopted surface model is a restricted solid-on-solid (RSOS) model
with "sticky" steps, i.e., steps with a point-contact type attraction between
them (p-RSOS model). By analyzing the results, we obtain a first-order shape
transition on the ECS profile around the (111) facet; and on the curved surface
near the (001) facet edge, we obtain shape exponents having values different
from those of the universal Gruber-Mullins-Pokrovsky-Talapov (GMPT) class. In
order to elucidate the origin of the non-universal shape exponents, we
calculate the slope dependence of the mean step height of "step droplets"
(bound states of steps) using the Monte Carlo method, where p=(dz/dx,
dz/dy)$, and represents the thermal averag |p| dependence of , we
derive a |p|-expanded expression for the non-universal surface free energy
f_{eff}(p), which contains quadratic terms with respect to |p|. The first-order
shape transition and the non-universal shape exponents obtained by the DMRG
calculations are reproduced thermodynamically from the non-universal surface
free energy f_{eff}(p).Comment: 31 pages, 21 figure
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