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Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…
Simplified, classical models of water are an integral part of atomistic molecular simulations, especially in biology and chemistry where hydration effects are critical. Yet, despite several decades of effort, these models are still far from…
In this paper we analyse a differential system related to a Glioblastoma growth. Using numerical simulations, we prove that model captures different kind of growth changing adequately the parameters of the model. Firstly, we make an…
In this paper, we present a dual representation of the influence functions, whose computational complexity scales with dataset size rather than model size. Both analytically and experimentally, we show that this representation can be an…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
Discovery of atomistic systems with desirable properties is a major challenge in chemistry and material science. Here we introduce a novel, autoregressive, convolutional deep neural network architecture that generates molecular equilibrium…
Computer models are commonly used to represent a wide range of real systems, but they often involve some unknown parameters. Estimating the parameters by collecting physical data becomes essential in many scientific fields, ranging from…
We address the problem of constructing varying-coefficient models based on basis expansions along with the technique of regularization. A crucial point in our modeling procedure is the selection of smoothing parameters in the regularization…
Due to the rapid growth of urban areas in the past decades, it has become increasingly important to model and monitor urban growth in mega cities. Although several researchers have proposed models for simulating urban growth, they have been…
Warm dense matter systems created in the laboratory are highly dynamical. In such cases electron dynamics is often needed to accurately simulate the evolution and properties of the system. Large systems force one to make simple…
Computer architecture design space is vast and complex. Tools are needed to explore new ideas and gain insights quickly, with low efforts and at a desired accuracy. We propose Calipers, a criticality-based framework to model key…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
In this paper, we analyse a model for the growth of three-dimensional walled cells. In this model the biomechanical expansion of the cell is coupled with the geometry of its wall. We consider that the density of building material depends on…
Background: Many mathematical models have now been employed across every area of systems biology. These models increasingly involve large numbers of unknown parameters, have complex structure which can result in substantial evaluation time…
Predicting the structure of multi-protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage pre-defined structural…
In the recent years, scientific workflows gained more and more popularity. In scientific workflows, tasks are typically treated as black boxes. Dealing with their complex interrelations to identify optimization potentials and bottlenecks is…
The use of spatially explicit land use and land cover (LULC) change models is widespread in environmental sciences and of interest in public decision-help. However, it appears that these models suffer from significant biases and…
Dynamic simulators model systems evolving over time. Often, it operates iteratively over fixed number of time-steps. The output of such simulator can be considered as time series or discrete functional outputs. Metamodeling is an e ective…
This paper is about models for a vector of probabilities whose elements must have a multiplicative structure and sum to 1 at the same time; in certain applications, as basket analysis, these models may be seen as a constrained version of…
Ball Mapper is an widely used tool in topological data analysis for summarizing the structure of high-dimensional data through metric-based coverings and graph representations. A central computational bottleneck in Ball Mapper is the…