Related papers: Calculating Germinal Centre Reactions
Gaussian processes (GP) are widely used as a metamodel for emulating time-consuming computer codes. We focus on problems involving categorical inputs, with a potentially large number L of levels (typically several tens), partitioned in G <<…
Complex systems have interested researchers across a broad range of fields for many years and as computing has become more accesible and feasible, it is now possible to simulate aspects of these systems. A major point of research is how…
We present an overview of the role of generating functions in quantum mechanical contexts, mainly in the modern theory of polarization and in the study of quantum phase transitions. Generating functions enable the derivation of moments and…
Probabilistic Graphical Models are often used to understand dynamics of a system. They can model relationships between features (nodes) and the underlying distribution. Theoretically these models can represent very complex dependency…
A model of bit-strings, that uses the technique of multi-spin coding, was previously used to study the time evolution of B-cell clone repertoire, in a paper by Lagreca, Almeida and Santos. In this work we extend that simplified model to…
The metabolic processes complexity is at the heart of energy conversion in living organisms and forms a huge obstacle to develop tractable thermodynamic metabolism models. By raising our analysis to a higher level of abstraction, we develop…
Recurrent neural networks have been widely used to generate millions of de novo molecules in a known chemical space. These deep generative models are typically setup with LSTM or GRU units and trained with canonical SMILEs. In this study,…
This paper is devoted to the thermally activated dynamics of the capillary condensation. We present a simple model which enables us to identify the critical nucleus involved in the transition mechanism. This simple model is then applied to…
Myriad experiments have identified an important role for $\rm CD8^+$ T cell response mechanisms in determining recovery from influenza A virus infection. Animal models of influenza infection further implicate multiple elements of the immune…
In chemotaxis, cells are modulating their migration patterns in response to concentration gradients of a guiding substance. Immune cells are believed to use such chemotactic sensing for remotely detecting and homing in on pathogens.…
Generating functions, which are widely used in combinatorics and probability theory, encode function values into the coefficients of a polynomial. In this paper, we explore their use as a tractable probabilistic model, and propose…
We present a mathematical study for the development of Multiple Sclerosis in which a spatio-temporal kinetic { theory} model describes, at the mesoscopic level, the dynamics of a high number of interacting agents. We consider both…
We present a spatial hybrid discrete-continuum modelling framework for the interaction dynamics between tumour cells and cytotoxic T cells, which play a pivotal role in the immune response against tumours. In this framework, tumour cells…
The vertebrate immune system is a wonder of modern evolution. Occasionally, however, correlations within the immune system lead to inappropriate recruitment of preexisting T cells against novel viral diseases. We present a random energy…
Hematopoiesis is a complex biological process that leads to the production and regulation of blood cells. It is based upon differentiation of stem cells under the action of growth factors. A mathematical approach of this process is proposed…
Polymer models are a widely used tool to study the prebiotic formation of metabolism at the origins of life. Counts of the number of reactions in these models are often crucial in probabilistic arguments concerning the emergence of…
We consider the problem of predicting perturbation effects via causal models. In many applications, it is a priori unknown which mechanisms of a system are modified by an external perturbation, even though the features of the perturbation…
The predictions of the geometric collective model (GCM) for different sets of Hamiltonian parameter values are related by analytic scaling relations. For the quartic truncated form of the GCM -- which describes harmonic oscillator, rotor,…
The formation process, properties, and spatial distribution of galaxy groups and clusters are closely related to the background cosmological model. We use numerical simulations of variants of the CDM model with different cosmological…
This paper presents an overview of recent computer simulations of grain boundary (GB) diffusion focusing on atomistic understanding of diffusion mechanisms. At low temperatures when GB structure is ordered, diffusion is mediated by point…