Variance Reduction Result for a Projected Adaptive Biasing Force Method

This paper is committed to investigate an extension of the classical adaptive biasing force method, which is used to compute the free energy related to the Boltzmann-Gibbs measure and a reaction coordinate function. The issue of this technique is that the approximated gradient of the free energy, called biasing force, is not a gradient. The commitment to this field is to project the estimated biasing force on a gradient using the Helmholtz decomposition. The variance of the biasing force is reduced using this technique, which makes the algorithm more efficient than the standard ABF method. We prove exponential convergence to equilibrium of the estimated free energy, with a precise rate of convergence in function of Logarithmic Sobolev inequality constants

Efficiency of the Wang-Landau algorithm: a simple test case

We analyze the efficiency of the Wang-Landau algorithm to sample a multimodal distribution on a prototypical simple test case. We show that the exit time from a metastable state is much smaller for the Wang Landau dynamics than for the original standard Metropolis-Hastings algorithm, in some asymptotic regime. Our results are confirmed by numerical experiments on a more realistic test case

Etude des interactions protéine-protéine par double hybride bactérien : Applications en agro-alimentaire et en santé

Protein-protein interaction\u27s studies are a major challenge for current research. These interactions are highly specific and regulate all processes in cell, from metabolism to responses to external stimuli. So they are crucial targets for therapeutics. Many methods are available for study them, but only few allow discovering many protein complexes together, as two-hybrid can do. The goal of this work is to underscore new partners of p21 and STAT3, two major protein involved in tumour control, and on the other side is to define the function of MtSAP1 which is involved in Medicago truncatula seed germination and in abiotic stresses\u27 response. STAT3 and p21\u27s potential interacting partners analysis strongly suggest the existence of new tumour molecular mechanisms where STAT3 plays a role, and define new hypothesis for p21\u27s function when the cell enter in a specific process. A new protein complex, p21/prohibitin2, was chosen for a detailed study but its function was only supposed: it could be a transcriptional regulator and/or could be involved in p21 proteolysis. In parallel, MtSAP1 gene study and two-hybrid analysis strongly suggest the involvement of MtSAP1 during cell response to hypoxia: MtSAP1 would be induce in response to hypoxia and then could have an important role in plant detoxification and tolerance. This work, supported by literature, underscores a link between p21, STAT3 and MtSAP1 during human tumour cell response to hypoxia. The validation of this hypothesis will let to deepen cell protection mechanisms against hypoxia, in human tumour as well as during tolerance establishment in Medicago truncatula

Virtual gardening: Identifying problems and potential directions for 'ecological awareness' through soil management and plant recognition gaming

Games are increasingly proven to be effective learning tools through a multitude of methodologies and approaches and this is no different for issues relating to the environment and the place of humans within it. We collaborated with the Eden Project to create a mobile game addressing some concerns on the ecological awareness of visitors that they raised with us: a mobile garden management game with a plant recognition technology. Such a project proved a valuable opportunity to understand how a game for smart devices might promote short-term ecological awareness for a general audience. Using a research creation methodology, we analyse, document and run a limited empirical study through user experience testing on players to investigate if the game had an effect on their ecological awareness

Using nonequilibrium fluctuation theorems to understand and correct errors in equilibrium and nonequilibrium discrete Langevin dynamics simulations

Common algorithms for computationally simulating Langevin dynamics must discretize the stochastic differential equations of motion. These resulting finite time step integrators necessarily have several practical issues in common: Microscopic reversibility is violated, the sampled stationary distribution differs from the desired equilibrium distribution, and the work accumulated in nonequilibrium simulations is not directly usable in estimators based on nonequilibrium work theorems. Here, we show that even with a time-independent Hamiltonian, finite time step Langevin integrators can be thought of as a driven, nonequilibrium physical process. Once an appropriate work-like quantity is defined -- here called the shadow work -- recently developed nonequilibrium fluctuation theorems can be used to measure or correct for the errors introduced by the use of finite time steps. In particular, we demonstrate that amending estimators based on nonequilibrium work theorems to include this shadow work removes the time step dependent error from estimates of free energies. We also quantify, for the first time, the magnitude of deviations between the sampled stationary distribution and the desired equilibrium distribution for equilibrium Langevin simulations of solvated systems of varying size. While these deviations can be large, they can be eliminated altogether by Metropolization or greatly diminished by small reductions in the time step. Through this connection with driven processes, further developments in nonequilibrium fluctuation theorems can provide additional analytical tools for dealing with errors in finite time step integrators.Comment: 11 pages, 4 figure

Measurement of the neutron electric dipole moment via spin rotation in a non-centrosymmetric crystal

We have measured the neutron electric dipole moment using spin rotation in a non-centrosymmetric crystal. Our result is d_n = (2.5 +- 6.5(stat) +- 5.5(syst)) 10^{-24} e cm. The dominating contribution to the systematic uncertainty is statistical in nature and will reduce with improved statistics. The statistical sensitivity can be increased to 2 10^{-26} e cm in 100 days data taking with an improved setup. We state technical requirements for a systematic uncertainty at the same level.Comment: submitted to Phys. Lett.

Stochastic homogenization for a scalar viscoelastic model exhibiting stress–strain hysteresis

Motivated by rate-independent stress-strain hysteresis observed in filled rubber, this article considers a scalar viscoelastic model in which the constitutive law is random and varies on a lengthscale which is small relative to the overall size of the solid. Using stochastic two-scale convergence as introduced by Bourgeat, Mikelic and Wright, we obtain the homogenized limit of the evolution, and demonstrate that under certain hypotheses, the homogenized model exhibits hysteretic behaviour which persists under asymptotically slow loading. These results are illustrated by means of numerical simulations in a particular one-dimensional instance of the model

Extended skyrmion lattice scattering and long-time memory in the chiral magnet Fe1−x_{1-x}Cox_xSi

Small angle neutron scattering measurements on a bulk single crystal of the doped chiral magnet Fe$_{1-x}$Co$_x$Si with $x$=0.3 reveal a pronounced effect of the magnetic history and cooling rates on the magnetic phase diagram. The extracted phase diagrams are qualitatively different for zero and field cooling and reveal a metastable skyrmion lattice phase outside the A-phase for the latter case. These thermodynamically metastable skyrmion lattice correlations coexist with the conical phase and can be enhanced by increasing the cooling rate. They appear in a wide region of the phase diagram at temperatures below the $A$-phase but also at fields considerably smaller or higher than the fields required to stabilize the A-phase

Magnetic Fluctuations, Precursor Phenomena and Phase Transition in MnSi under Magnetic Field

The reference chiral helimagnet MnSi is the first system where skyrmion lattice correlations have been reported. At zero magnetic field the transition at $T_C$ to the helimagnetic state is of first order. Above $T_C$, in a region dominated by precursor phenomena, neutron scattering shows the build up of strong chiral fluctuating correlations over the surface of a sphere with radius $2\pi/\ell$, where $\ell$ is the pitch of the helix. It has been suggested that these fluctuating correlations drive the helical transition to first order following a scenario proposed by Brazovskii for liquid crystals. We present a comprehensive neutron scattering study under magnetic fields, which provides evidence that this is not the case. The sharp first order transition persists for magnetic fields up to 0.4 T whereas the fluctuating correlations weaken and start to concentrate along the field direction already above 0.2 T. Our results thus disconnect the first order nature of the transition from the precursor fluctuating correlations. They also show no indication for a tricritical point, where the first order transition crosses over to second order with increasing magnetic field. In this light, the nature of the first order helical transition and the precursor phenomena above $T_C$, both of general relevance to chiral magnetism, remain an open question

Overexpression of a Medicago truncatula stress-associated protein gene (MtSAP1) leads to nitric oxide accumulation and confers osmotic and salt stress tolerance in transgenic tobacco

The impact of Medicago truncatula stress-associated protein gene (MtSAP1) overexpression has been investigated in Nicotiana tabacum transgenic seedlings. Under optimal conditions, transgenic lines overexpressing MtSAP1 revealed better plant development and higher chlorophyll content as compared to wild type seedlings. Interestingly, transgenic lines showed a stronger accumulation of nitric oxide (NO), a signaling molecule involved in growth and development processes. This NO production seemed to be partially nitrate reductase dependent. Due to the fact that NO has been also reported to play a role in tolerance acquisition of plants to abiotic stresses, the responses of MtSAP1 overexpressors to osmotic and salt stress have been studied. Compared to the wild type, transgenic lines were less affected in their growth and development. Moreover, NO content in MtSAP1 overexpressors was always higher than that detected in wild seedlings under stress conditions. It seems that this better tolerance induced by MtSAP1 overexpression could be associated with this higher NO production that would enable seedlings to reach a high protection level to prepare them to cope with abiotic stresses