Related papers: A Multi-Scale Simulation of Retinal Physiology
We present a bigraphical framework suited for modeling biological systems both at protein level and at membrane level. We characterize formally bigraphs corresponding to biologically meaningful systems, and bigraphic rewriting rules…
In many chemical and biological applications, systems of differential equations containing unknown parameters are used to explain empirical observations and experimental data. The DEs are typically nonlinear and difficult to analyze,…
To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit…
We review the approach to glasses based on the replica formalism. The replica approach presented here is a first principle's approach which aims at deriving the main glass properties from the microscopic Hamiltonian. In contrast to the old…
In this chapter we focus first on the theoretical methods and relevant computational approaches to calculate the electronic structure of atoms, molecules, and clusters containing heavy elements for which relativistic effects become…
A variety of models for the membrane-mediated interaction of particles in lipid membranes, mostly well-established in theoretical physics, is reviewed from a mathematical perspective. We provide mathematically consistent formulations in a…
There is currently limited understanding of the role played by haemodynamic forces on the processes governing vascular development. One of many obstacles to be overcome is being able to measure those forces, at the required resolution…
Realistic simulations of experiments at large scale photon facilities, such as optical laser laboratories, synchrotrons, and free electron lasers, are of vital importance for the successful preparation, execution, and analysis of these…
Single-particle cryo-EM has transformed structural biology but still faces challenges in resolving conformational heterogeneity at atomic resolution. Existing cryo-EM heterogeneity analysis methods either lack atomic details or tend to…
We extend the phase field crystal model to accommodate exact atomic configurations and vacancies by requiring the order parameter to be non-negative. The resulting theory dictates the number of atoms and describes the motion of each of…
A multi-timescale hybrid model is proposed to study microscopically the degraded performance of electronic devices, covering three individual stages of radiation effects studies, including ultrafast displacement cascade, intermediate defect…
Retinal Optical Coherence Tomography (OCT), a noninvasive cross-sectional scan of the eye with qualitative 3D visualization of the retinal anatomy is use to study the retinal structure and the presence of pathogens. The advent of the…
Optical coherence tomography (OCT) is a prevalent non-invasive imaging method which provides high resolution volumetric visualization of retina. However, its inherent defect, the speckle noise, can seriously deteriorate the tissue…
We develop a new and simple method to model baryonic effects at the field level relevant for weak lensing analyses. We analyze thousands of state-of-the-art hydrodynamic simulations from the CAMELS project, each with different cosmology and…
A distinguishing feature of a multicellular living system is that it operates at various scales, from the intracellular to organismal. Very little is known at present on how tissue level properties are related to cell and subcellular…
Interpretability is crucial to enhance trust in machine learning models for medical diagnostics. However, most state-of-the-art image classifiers based on neural networks are not interpretable. As a result, clinicians often resort to known…
The simulation of vibrational energy transport and quantum thermodynamics with trapped ions requires good methods for the estimation of temperatures. One valuable tool for this purpose is based on the fit of dark resonances in the…
In this paper we describe an adaptive and multi-scale algorithm for the parsimonious fit of the corneal surface data that allows to adapt the number of functions used in the reconstruction to the conditions of each cornea. The method…
Employing a recently developed method that is numerically accurate within a model space simulating the real-time dynamics of few-body systems interacting with macroscopic environmental quantum fields, we analyze the full dynamics of an…
Accurate segmentation of the optic disc from a retinal image is vital to extracting retinal features that may be highly correlated with retinal conditions such as glaucoma. In this paper, we propose a deep-learning based approach capable of…