Search results for "multiscale modeling"

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…

Multiscale modeling on biological systems

2018

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…

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…

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…

Multiscale modeling of polycrystalline materials: A boundary element approach to material degradation and fracture

2015

Abstract In this work, a two-scale approach to degradation and failure in polycrystalline materials is proposed. The formulation involves the engineering component level (macro-scale) and the material grain level (micro-scale). The macro-continuum is modeled using a three-dimensional boundary element formulation in which the presence of damage is formulated through an initial stress approach to account for the local softening in the neighborhood of points experiencing degradation at the micro-scale. The microscopic degradation is explicitly modeled by associating Representative Volume Elements (RVEs) to relevant points of the macro continuum, for representing the polycrystalline microstruct…

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…

Multiscale modeling of polymers at interfaces

2009

A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this process, degrees of freedom on smaller scales are eliminated to the favor of a model suitable for efficient study of the system behavior on larger length and time scales. We emphasize the need to distinguish between dynamic and static properties regarding the model validation. A model which accurately reproduces static properties may fail completely, when it comes to the dynamic behavior of the system. Furthermore, we comment on the use of Monte Carlo method i…

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…

An Early Stage Researcher's Primer on Systems Medicine Terminology

2021

Background: Systems Medicine is a novel approach to medicine, that is, an interdisciplinary field that considers the human body as a system, composed of multiple parts and of complex relationships at multiple levels, and further integrated into an environment. Exploring Systems Medicine implies understanding and combining concepts coming from diametral different fields, including medicine, biology, statistics, modeling and simulation, and data science. Such heterogeneity leads to semantic issues, which may slow down implementation and fruitful interaction between these highly diverse fields. Methods: In this review, we collect and explain more than100 terms related to Systems Medicine. Thes…