Instrumented activity and semiotic mediation: two frames to describe the conjecture construction process as curricular organizer

We document part of the process through which conjectures produced by students, with the aid of the dynamic geometry software Cabri, when they solve proposed geometric problems, become a curriculum organizer in the classroom. We first focus on characterizing students’ instrumented activity recurring to utilization schema (Rabardel, 1995, in Bartolini Bussi and Mariotti, 2008), and then describe the teacher’s content management through which the ideas produced by the students become key elements of knowledge construction

A simple asynchronous replica-exchange implementation

We discuss the possibility of implementing asynchronous replica-exchange (or parallel tempering) molecular dynamics. In our scheme, the exchange attempts are driven by asynchronous messages sent by one of the computing nodes, so that different replicas are allowed to perform a different number of time-steps between subsequent attempts. The implementation is simple and based on the message-passing interface (MPI). We illustrate the advantages of our scheme with respect to the standard synchronous algorithm and we benchmark it for a model Lennard-Jones liquid on an IBM-LS21 blade center cluster.Comment: Preprint of Proceeding for CSFI 200

A Lagrangian Neighbourhood Theorem for shifted symplectic derived schemes

Pantev, Toen, Vaqui\'e and Vezzosi arXiv:1111.3209 defined $k$-shifted symplectic derived schemes and stacks ${\bf X}$ for $k\in\mathbb Z$, and Lagrangians ${\bf f}:{\bf L}\to{\bf X}$ in them. They have important applications to Calabi-Yau geometry and quantization. Bussi, Brav and Joyce arXiv:1305.6302 proved a 'Darboux Theorem' giving explicit Zariski or \'etale local models for $k$-shifted symplectic derived schemes ${\bf X}$ for $k<0$ presenting them as twisted shifted cotangent bundles. We prove a 'Lagrangian Neighbourhood Theorem' giving explicit Zariski or etale local models for Lagrangians ${\bf f}:{\bf L}\to{\bf X}$ in $k$-shifted symplectic derived schemes ${\bf X}$ for $k<0$, relative to the Bussi-Brav-Joyce 'Darboux form' local models for ${\bf X}$. That is, locally such Lagrangians can be presented as twisted shifted conormal bundles. We also give a partial result when $k=0$. We expect our results will have future applications to $k$-shifted Poisson geometry (see arXiv:1506.03699), to defining 'Fukaya categories' of complex or algebraic symplectic manifolds, and to categorifying Donaldson-Thomas theory of Calabi-Yau 3-folds and 'Cohomological Hall algebras'.Comment: 68 page

Metadynamics with Discriminants: a Tool for Understanding Chemistry

We introduce an extension of a recently published method\cite{Mendels2018} to obtain low-dimensional collective variables for studying multiple states free energy processes in chemical reactions. The only information needed is a collection of simple statistics of the equilibrium properties of the reactants and product states. No information on the reaction mechanism has to be given. The method allows studying a large variety of chemical reactivity problems including multiple reaction pathways, isomerization, stereo- and regiospecificity. We applied the method to two fundamental organic chemical reactions. First we study the \ce{S_N2} nucleophilic substitution reaction of a \ce{Cl} in \ce{CH_2 Cl_2} leading to an understanding of the kinetic origin of the chirality inversion in such processes. Subsequently, we tackle the problem of regioselectivity in the hydrobromination of propene revealing that the nature of empirical observations such as the Markovinikov's rules lies in the chemical kinetics rather than the thermodynamic stability of the products

On the effect of the thermostat in non-equilibrium molecular dynamics simulations

The numerical investigation of the statics and dynamics of systems in nonequilibrium in general, and under shear flow in particular, has become more and more common. However, not all the numerical methods developed to simulate equilibrium systems can be successfully adapted to out-of-equilibrium cases. This is especially true for thermostats. Indeed, even though thermostats developed to work under equilibrium conditions sometimes display good agreement with rheology experiments, their performance rapidly degrades beyond weak dissipation and small shear rates. Here we focus on gauging the relative performances of three thermostats, Langevin, dissipative particle dynamics, and Bussi-Donadio-Parrinello under varying parameters and external conditions. We compare their effectiveness by looking at different observables and clearly demonstrate that choosing the right thermostat (and its parameters) requires a careful evaluation of, at least, temperature, density and velocity profiles. We also show that small modifications of the Langevin and DPD thermostats greatly enhance their performance in a wide range of parameters.Comment: 13 pages, 9 figure

A 'Darboux Theorem' for shifted symplectic structures on derived Artin stacks, with applications

This is the fifth in a series arXiv:1304.4508, arXiv:1305,6302, arXiv:1211.3259, arXiv:1305.6428 on the '$k$-shifted symplectic derived algebraic geometry' of Pantev, Toen, Vaquie and Vezzosi, arXiv:1111.3209. This paper extends the previous three from (derived) schemes to (derived) Artin stacks. We prove four main results: (a) If $(X,\omega)$ is a $k$-shifted symplectic derived Artin stack for $k<0$ in the sense of arXiv:1111.3209, then near each $x\in X$ we can find a 'minimal' smooth atlas $\varphi:U\to X$ with $U$ an affine derived scheme, such that $(U,\varphi^*(\omega))$ may be written explicitly in coordinates in a standard 'Darboux form'. (b) If $(X,\omega)$ is a $-1$-shifted symplectic derived Artin stack and $X'$ the underlying classical Artin stack, then $X'$ extends naturally to a 'd-critical stack' $(X',s)$ in the sense of arXiv:1304.4508. (c) If $(X,s)$ is an oriented d-critical stack, we can define a natural perverse sheaf $P^\bullet_{X,s}$ on $X$, such that whenever $T$ is a scheme and $t:T\to X$ is smooth of relative dimension $n$, then $T$ is locally modelled on a critical locus Crit$(f:U\to{\mathbb A}^1)$ for $U$ smooth, and $t^*(P^\bullet_{X,s})[n]$ is locally modelled on the perverse sheaf of vanishing cycles $PV_{U,f}^\bullet$ of $f$. (d) If $(X,s)$ is a finite type oriented d-critical stack, we can define a natural motive $MF_{X,s}$ in a ring of motives $\bar{\mathcal M}^{st,\hat\mu}_X$ on $X$, such that whenever $T$ is a finite type scheme and $t:T\to X$ is smooth of dimension $n$, then $T$ is locally modelled on a critical locus Crit$(f:U\to{\mathbb A}^1)$ for $U$ smooth, and ${\mathbb L}^{-n/2}\odot t^*(MF_{X,s})$ is locally modelled on the motivic vanishing cycle $MF^{mot,\phi}_{U,f}$ of $f$ in $\bar{\mathcal M}^{st,\hat\mu}_T$. Our results have applications to categorified and motivic extensions of Donaldson-Thomas theory of Calabi-Yau 3-foldsComment: (v2) 61 pages. Minor corrections, foundational material on perverse sheaves shortene