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Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
The determination of the isothermal adsorption curves represents a mechanism that allows ob-taining information on the process of adsorption of water in organic and inorganic materials. In addition, it is a measure to be considered when…
In recent years, progresses in nanotechnology have established the foundations for implementing nanomachines capable of carrying out simple but significant tasks. Under this stimulus, researchers have been proposing various solutions for…
Increasing the efficiency of materials design and discovery remains a significant challenge, especially given the prohibitively large size of chemical compound space. The use of a chemically transferable coarse-grained model enables…
Modeling of pores generation in 2-D with granular grains using molecular dynamics method is reported in this work. Grains with certain diameter distribution are let falling due to gravity. Three configurations (larger diameter on top,…
Molecular dynamics simulations are carried out to investigate mechanical properties and porous structure of binary glasses subjected to steady shear. The model vitreous systems were prepared via thermal quench at constant volume to a…
Biomolecular condensates govern essential cellular processes yet elude description by traditional equilibrium models. This roadmap, distilled from structured discussions at a workshop and reflecting the consensus of its participants,…
We have studied four complex organic molecules (COMs), methyl formate ($CH_3OCHO$), dimethyl ether ($CH_3OCH_3$), formamide ($NH_2CHO$), and ethyl cyanide ($C_2H_5CN$), towards a large sample of 39 high-mass star-forming regions…
In the 21st century, biosensors have gathered much wider attention than ever before, irrespective of the technology that promises to bring them forward. With the recent COVID-19 outbreak, the concern and efforts to restore global health and…
It is not common to consider the role of uncertainties in the rate coefficients used in interstellar gas-phase chemical models. In this paper, we report a new method to determine both the uncertainties in calculated molecular abundances and…
We propose an approach that links density functional theory (DFT) and molecular dynamics (MD) simulation to study fluid behavior in nanopores in contact with bulk (macropores). It consists of two principal steps. First, the theoretical…
This thesis is about the study of complex systems through simple models. Our work evidences the relevance of this kind of modeling in science, which provides us with a better understanding of nature at minimum cost. The fundamentals tools…
Having in mind as target audience beginner researchers working in the field of cultural heritage, we present succinctly the concept of two-scale modeling of reaction-diffusion problems as it fits to scenarios where the action of the…
Predictive dynamical models for marine ecosystems are used for a variety of needs. Due to sparse measurements and limited understanding of the myriad of ocean processes, there is however significant uncertainty. There is model uncertainty…
Quantifying the relationship between geometric descriptors of microstructure and effective properties like permeability is essential for understanding and improving the behavior of porous materials. In this paper, we employ a previously…
Advances in molecular technologies underlie an enormous growth in the size of data sets pertaining to biology and biomedicine. These advances parallel those in the deep learning subfield of machine learning. Components in the differentiable…
The past decade has witnessed the rapid progress in synthesizing nanoporous organic networks or polymer frameworks for various potential applications. Generally speaking, functionalization of porous networks to add extra properties and…
Porous materials are relevant for a broad range of technologies from catalysis and filtration, to tissue engineering and lightweight structures. Controlling the porosity of these materials over multiple length scales often leads to enticing…
A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural…
The understanding of morphogenesis in living organisms has been renewed by tremendous progressin experimental techniques that provide access to cell-scale, quantitative information both on theshapes of cells within tissues and on the genes…