Mobility and Diffusion of a Tagged Particle in a Driven Colloidal Suspension

We study numerically the influence of density and strain rate on the diffusion and mobility of a single tagged particle in a sheared colloidal suspension. We determine independently the time-dependent velocity autocorrelation functions and, through a novel method, the response functions with respect to a small force. While both the diffusion coefficient and the mobility depend on the strain rate the latter exhibits a rather weak dependency. Somewhat surprisingly, we find that the initial decay of response and correlation functions coincide, allowing for an interpretation in terms of an 'effective temperature'. Such a phenomenological effective temperature recovers the Einstein relation in nonequilibrium. We show that our data is well described by two expansions to lowest order in the strain rate.Comment: submitted to EP

Tagged particle in a sheared suspension: effective temperature determines density distribution in a slowly varying external potential beyond linear response

We consider a sheared colloidal suspension under the influence of an external potential that varies slowly in space in the plane perpendicular to the flow and acts on one selected (tagged) particle of the suspension. Using a Chapman-Enskog type expansion we derive a steady state equation for the tagged particle density distribution. We show that for potentials varying along one direction only, the tagged particle distribution is the same as the equilibrium distribution with the temperature equal to the effective temperature obtained from the violation of the Einstein relation between the self-diffusion and tagged particle mobility coefficients. We thus prove the usefulness of this effective temperature for the description of the tagged particle behavior beyond the realm of linear response. We illustrate our theoretical predictions with Brownian dynamics computer simulations.Comment: Accepted for publication in Europhys. Let

Effective Confinement as Origin of the Equivalence of Kinetic Temperature and Fluctuation-Dissipation Ratio in a Dense Shear Driven Suspension

We study response and velocity autocorrelation functions for a tagged particle in a shear driven suspension governed by underdamped stochastic dynamics. We follow the idea of an effective confinement in dense suspensions and exploit a time-scale separation between particle reorganization and vibrational motion. This allows us to approximately derive the fluctuation-dissipation theorem in a "hybrid" form involving the kinetic temperature as an effective temperature and an additive correction term. We show numerically that even in a moderately dense suspension the latter is negligible. We discuss similarities and differences with a simple toy model, a single trapped particle in shear flow

Modified Fluctuation-dissipation theorem for non-equilibrium steady-states and applications to molecular motors

We present a theoretical framework to understand a modified fluctuation-dissipation theorem valid for systems close to non-equilibrium steady-states and obeying markovian dynamics. We discuss the interpretation of this result in terms of trajectory entropy excess. The framework is illustrated on a simple pedagogical example of a molecular motor. We also derive in this context generalized Green-Kubo relations similar to the ones derived recently by Seifert., Phys. Rev. Lett., 104, 138101 (2010) for more general networks of biomolecular states.Comment: 6 pages, 2 figures, submitted in EP

Probing active forces via a fluctuation-dissipation relation: Application to living cells

We derive a new fluctuation-dissipation relation for non-equilibrium systems with long-term memory. We show how this relation allows one to access new experimental information regarding active forces in living cells that cannot otherwise be accessed. For a silica bead attached to the wall of a living cell, we identify a crossover time between thermally controlled fluctuations and those produced by the active forces. We show that the probe position is eventually slaved to the underlying random drive produced by the so-called active forces.Comment: 5 page

N‐Substituted Nipecotic Acids as (S )‐SNAP‐5114 Analogues with Modified Lipophilic Domains

Potential mGAT4 inhibitors derived from the lead substance (S )‐SNAP‐5114 have been synthesized and characterized for their inhibitory potency. Variations from the parent compound included the substitution of one of its aromatic 4‐methoxy and 4‐methoxyphenyl groups, respectively, with a more polar moiety, including a carboxylic acid, alcohol, nitrile, carboxamide, sulfonamide, aldehyde or ketone function, or amino acid partial structures. Furthermore, it was investigated how the substitution of more than one of the aromatic 4‐methoxy groups affects the potency and selectivity of the resulting compounds. Among the synthesized test substances (S )‐1‐{2‐[(4‐formylphenyl)bis(4‐methoxyphenyl)‐methoxy]ethyl}piperidine‐3‐carboxylic acid, that features a carbaldehyde function in place of one of the aromatic 4‐methoxy moieties of (S )‐SNAP‐5114, was found to have a pIC50 value of 5.89±0.07, hence constituting a slightly more potent mGAT4 inhibitor than the parent substance while showing comparable subtype selectivity

Entropy production for mechanically or chemically driven biomolecules

Entropy production along a single stochastic trajectory of a biomolecule is discussed for two different sources of non-equilibrium. For a molecule manipulated mechanically by an AFM or an optical tweezer, entropy production (or annihilation) occurs in the molecular conformation proper or in the surrounding medium. Within a Langevin dynamics, a unique identification of these two contributions is possible. The total entropy change obeys an integral fluctuation theorem and a class of further exact relations, which we prove for arbitrarily coupled slow degrees of freedom including hydrodynamic interactions. These theoretical results can therefore also be applied to driven colloidal systems. For transitions between different internal conformations of a biomolecule involving unbalanced chemical reactions, we provide a thermodynamically consistent formulation and identify again the two sources of entropy production, which obey similar exact relations. We clarify the particular role degenerate states have in such a description

EARL: Joint Entity and Relation Linking for Question Answering over Knowledge Graphs

Many question answering systems over knowledge graphs rely on entity and relation linking components in order to connect the natural language input to the underlying knowledge graph. Traditionally, entity linking and relation linking have been performed either as dependent sequential tasks or as independent parallel tasks. In this paper, we propose a framework called EARL, which performs entity linking and relation linking as a joint task. EARL implements two different solution strategies for which we provide a comparative analysis in this paper: The first strategy is a formalisation of the joint entity and relation linking tasks as an instance of the Generalised Travelling Salesman Problem (GTSP). In order to be computationally feasible, we employ approximate GTSP solvers. The second strategy uses machine learning in order to exploit the connection density between nodes in the knowledge graph. It relies on three base features and re-ranking steps in order to predict entities and relations. We compare the strategies and evaluate them on a dataset with 5000 questions. Both strategies significantly outperform the current state-of-the-art approaches for entity and relation linking.Comment: International Semantic Web Conference 201