Coarse-Graining Auto-Encoders for Molecular Dynamics

Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and spatial scales involved in thermodynamic and kinetic phenomena in materials, atomistic simulations are often computationally unfeasible. Coarse-graining methods allow simulating larger systems, by reducing the dimensionality of the simulation, and propagating longer timesteps, by averaging out fast motions. Coarse-graining involves two coupled learning problems; defining the mapping from an all-atom to a reduced representation, and the parametrization of a Hamiltonian over coarse-grained coordinates. Multiple statistical mechanics approaches have addressed the latter, but the former is generally a hand-tuned process based on chemical intuition. Here we present Autograin, an optimization framework based on auto-encoders to learn both tasks simultaneously. Autograin is trained to learn the optimal mapping between all-atom and reduced representation, using the reconstruction loss to facilitate the learning of coarse-grained variables. In addition, a force-matching method is applied to variationally determine the coarse-grained potential energy function. This procedure is tested on a number of model systems including single-molecule and bulk-phase periodic simulations.Comment: 8 pages, 6 figure

Pre-big-bang black-hole remnants and the past low entropy

Dark matter could be composed by black-hole remnants formed before the big-bang era in a bouncing cosmology. This hypothetical scenario has major implications on the issue of the arrow of time: it would upset a common attribution of past low entropy to the state of the geometry, and provide a concrete realisation to the perspectival interpretation of past low entropy

Sharp and fuzzy observables on effect algebras

Observables on effect algebras and their fuzzy versions obtained by means of confidence measures (Markov kernels) are studied. It is shown that, on effect algebras with the (E)-property, given an observable and a confidence measure, there exists a fuzzy version of the observable. Ordering of observables according to their fuzzy properties is introduced, and some minimality conditions with respect to this ordering are found. Applications of some results of classical theory of experiments are considered.Comment: 23 page

Global coherence of quantum evolutions based on decoherent histories: theory and application to photosynthetic quantum energy transport

Assessing the role of interference in natural and artificial quantum dyanamical processes is a crucial task in quantum information theory. To this aim, an appopriate formalism is provided by the decoherent histories framework. While this approach has been deeply explored from different theoretical perspectives, it still lacks of a comprehensive set of tools able to concisely quantify the amount of coherence developed by a given dynamics. In this paper we introduce and test different measures of the (average) coherence present in dissipative (Markovian) quantum evolutions, at various time scales and for different levels of environmentally induced decoherence. In order to show the effectiveness of the introduced tools, we apply them to a paradigmatic quantum process where the role of coherence is being hotly debated: exciton transport in photosynthetic complexes. To spot out the essential features that may determine the performance of the transport we focus on a relevant trimeric subunit of the FMO complex and we use a simplified (Haken-Strobl) model for the system-bath interaction. Our analysis illustrates how the high efficiency of environmentally assisted transport can be traced back to a quantum recoil avoiding effect on the exciton dynamics, that preserves and sustains the benefits of the initial fast quantum delocalization of the exciton over the network. Indeed, for intermediate levels of decoherence, the bath is seen to selectively kill the negative interference between different exciton pathways, while retaining the initial positive one. The concepts and tools here developed show how the decoherent histories approach can be used to quantify the relation between coherence and efficiency in quantum dynamical processes.Comment: 13 papges, 9 figure

Asymmetry, abstraction and autonomy: justifying coarse-graining in statistical mechanics

Whilst the fundamental laws of physics are time-reversal invariant, most macroscopic processes are irreversible. Given that the fundamental laws are taken to underpin all other processes, how can the fundamental time-symmetry be reconciled with the asymmetry manifest elsewhere? In statistical mechanics, progress can be made with this question; what I dub the Zwanzig-Zeh-Wallace framework can be used to construct the irreversible equations of statistical mechanics from the underlying microdynamics. Yet this framework uses coarse-graining, a procedure that has faced much criticism. I focus on two objections in the literature: claims that coarse-graining makes time-asymmetry (i) `illusory' and (ii) `anthropocentric'. I argue that these objections arise from an unsatisfactory justi�fication of coarse-graining prevalent in the literature, rather than from coarse-graining itself. This justification relies on the idea of measurement imprecision. By considering the role that abstraction and autonomy play, I provide an alternative justi�fication and o�er replies to the illusory and anthropocentric objections. Finally I consider the broader consequences of this alternative justi�fication: the connection to debates about inter-theoretic reduction and further, the implication that the time-asymmetry in statistical mechanics is weakly emergent

Asymmetry, abstraction and autonomy: justifying coarse-graining in statistical mechanics

Whilst the fundamental laws of physics are time-reversal invariant, most macroscopic processes are irreversible. Given that the fundamental laws are taken to underpin all other processes, how can the fundamental time-symmetry be reconciled with the asymmetry manifest elsewhere? In statistical mechanics, progress can be made with this question; what I dub the Zwanzig-Zeh-Wallace framework can be used to construct the irreversible equations of statistical mechanics from the underlying microdynamics. Yet this framework uses coarse-graining, a procedure that has faced much criticism. I focus on two objections in the literature: claims that coarse-graining makes time-asymmetry (i) `illusory' and (ii) `anthropocentric'. I argue that these objections arise from an unsatisfactory justi�fication of coarse-graining prevalent in the literature, rather than from coarse-graining itself. This justification relies on the idea of measurement imprecision. By considering the role that abstraction and autonomy play, I provide an alternative justi�fication and o�er replies to the illusory and anthropocentric objections. Finally I consider the broader consequences of this alternative justi�fication: the connection to debates about inter-theoretic reduction and further, the implication that the time-asymmetry in statistical mechanics is weakly emergent