Search results for "multiscale model"

Multiscale modeling on biological systems

2018

Adversarial reverse mapping of equilibrated condensed-phase molecular structures

2020

A tight and consistent link between resolutions is crucial to further expand the impact of multiscale modeling for complex materials. We herein tackle the generation of condensed molecular structures as a refinement -- backmapping -- of a coarse-grained structure. Traditional schemes start from a rough coarse-to-fine mapping and perform further energy minimization and molecular dynamics simulations to equilibrate the system. In this study we introduce DeepBackmap: A deep neural network based approach to directly predict equilibrated molecular structures for condensed-phase systems. We use generative adversarial networks to learn the Boltzmann distribution from training data and realize reve…

Modeling of biomolecular machines in non-equilibrium steady states

2021

Numerical computations have become a pillar of all modern quantitative sciences. Any computation involves modeling--even if often this step is not made explicit--and any model has to neglect details while still being physically accurate. Equilibrium statistical mechanics guides both the development of models and numerical methods for dynamics obeying detailed balance. For systems driven away from thermal equilibrium such a universal theoretical framework is missing. For a restricted class of driven systems governed by Markov dynamics and local detailed balance, stochastic thermodynamics has evolved to fill this gap and to provide fundamental constraints and guiding principles. The next step…

Adversarial reverse mapping of condensed-phase molecular structures: Chemical transferability

2021

Switching between different levels of resolution is essential for multiscale modeling, but restoring details at higher resolution remains challenging. In our previous study we have introduced deepBackmap: a deep neural-network-based approach to reverse-map equilibrated molecular structures for condensed-phase systems. Our method combines data-driven and physics-based aspects, leading to high-quality reconstructed structures. In this work, we expand the scope of our model and examine its chemical transferability. To this end, we train deepBackmap solely on homogeneous molecular liquids of small molecules, and apply it to a more challenging polymer melt. We augment the generator's objective w…

Statistical Reconstruction of Microstructures Using Entropic Descriptors

2018

We report a multiscale approach of broad applicability to stochastic reconstruction of multiphase materials, including porous ones. The approach devised uses an optimization method, such as the simulated annealing (SA) and the so-called entropic descriptors (EDs). For a binary pattern, they quantify spatial inhomogeneity or statistical complexity at discrete length-scales. The EDs extract dissimilar structural information to that given by two-point correlation functions (CFs). Within the SA, we use an appropriate cost function consisting of EDs or comprised of EDs and CFs. It was found that the stochastic reconstruction is computationally efficient when we begin with a preliminary synthetic…

Multiscale modelling of structure formation of C$_{60}$ on insulating CaF$_2$ substrates

2021

Morphologies of adsorbed molecular films are of interest in a wide range of applications. To study the epitaxial growth of these systems in computer simulations requires access to long time and length scales, and one typically resorts to kinetic Monte Carlo (KMC) simulations. However, KMC simulations require as input transition rates and their dependence on external parameters (such as temperature). Experimental data allow only limited and indirect access to these rates, and models are often oversimplified. Here, we follow a bottom-up approach and aim at systematically constructing all relevant rates for an example system that has shown interesting properties in experiments, buckminsterfull…

The fractal model of non-local elasticity with long-range interactions

2010

The mechanically-based model of non-local elasticity with long-range interactions is framed, in this study, in a fractal mechanics context. Non-local interactions are modelled introducing long-range central body forces between non-adjacent volume elements of the elastic continuum. Such long-range interactions are modelled as proportional to the product of interacting volumes, to the relative displacements of the centroids and to a distance-decaying function that is monotonically-decreasing with the distance. The choice of the decaying function is a key aspect of the model and it has been proved that any continuous function, strictly positive, is thermodynamically consistent and it leads to …

DNA Photodamage and Repair: Computational Photobiology in Action

2020

DNA is constantly exposed to external and metabolic stress agents, including the solar radiation and in particular the UV portion of the electromagnetic spectrum. Such source of stress can induce photochemical modification of the structure of DNA and of its basic components, i.e. the nucleobases. DNA lesions may ultimately lead to genomic instability, mutations, and even to carcinogenesis. Hence, cells dispose of complex biochemical repair pathways in charge of remove the DNA lesions and avoid their accumulation. In this Chapter, we present the complexity of the DNA lesion chemical and structural space, also complicated by the intricate coupling with the biological relevant signaling pathwa…

Tracking Polariton Relaxation with Multiscale Molecular Dynamics Simulations

2019

When photoactive molecules interact strongly with confined light modes in optical cavities, new hybrid light–matter states form. They are known as polaritons and correspond to coherent superpositions of excitations of the molecules and of the cavity photon. The polariton energies and thus potential energy surfaces are changed with respect to the bare molecules, such that polariton formation is considered a promising paradigm for controlling photochemical reactions. To effectively manipulate photochemistry with confined light, the molecules need to remain in the polaritonic state long enough for the reaction on the modified potential energy surface to take place. To understand what determine…

Determination of lifetime probabilities of carbon fibre composite plates and pressure vessels for hydrogen storage

2011

International audience; It is shown that an analogy can be made between the failure of unidirectional carbon fibre reinforced epoxy plates and filament wound carbon fibre composite pressure vessels and that their strengths and failure probabilities can be determined. Fibres in filament wound composite structures are placed on geodesic paths around the mandrel, which becomes the liner; so that when the structure is pressurised the fibres are only subjected to tensile forces, as in a unidirectional composite. Multiscale modelling reveals that composite failure is controlled by fibre breakage and that clustering of fibre breaks determines ultimate reliability of the structure. Time dependent r…