Search results for "Multiscale modeling"
showing 10 items of 13 documents
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…
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…
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…
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…
Modelización computacional cardiaca
2020
Resumen Las enfermedades cardiovasculares tienen en la actualidad un gran impacto social y economico y constituyen una de las principales causas de mortalidad y morbilidad. Los modelos computacionales personalizados del corazon estan demostrando ser utiles tanto para ayudar a comprender los mecanismos subyacentes a las patologias cardiacas como para optimizar su tratamiento prediciendo la respuesta del paciente. En este contexto, se ha puesto en marcha la Red Espanola de Investigacion en Modelizacion Computacional Cardiaca (V-Heart SN). El objetivo general de V-Heart SN es el desarrollo de un modelo computacional multifisico y multiescala integrado del corazon. Este objetivo general se abor…
Limits of lateral expansion in two-dimensional materials with line defects
2021
The flexibility of two-dimensional (2D) materials enables static and dynamic ripples that are known to cause lateral contraction, shrinking of the material boundary. However, the limits of 2D materials' \emph{lateral expansion} are unknown. Therefore, here we discuss the limits of intrinsic lateral expansion of 2D materials that are modified by compressive line defects. Using thin sheet elasticity theory and sequential multiscale modeling, we find that the lateral expansion is inevitably limited by the onset of rippling. The maximum lateral expansion $\chi_{max}\approx 2.1\cdot t^2\sigma_d$, governed by the elastic thickness $t$ and the defect density $\sigma_d$, remains typically well belo…