Related papers: A computational framework for bioimaging simulatio…
Sample-induced image-degradation remains an intricate wave-optical problem in light-sheet microscopy. Here we present biobeam, an open-source software package that enables to simulate operational light-sheet microscopes by combining data…
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…
The mathematical models used to capture features of complex, biological systems are typically non-linear, meaning that there are no generally valid simple relationships between their outputs and the data that might be used to validate them.…
Simulations of biophysical systems inevitably include steps that correspond to time integrations of ordinary differential equations. These equations are often related to enzyme action in the synthesis and destruction of molecular species,…
Biological tissues are complex structures composed of many elements which make light-based tissue diagnostics challenging. Over the past decades, Monte Carlo technique has been used as a fundamental and versatile approach toward modeling…
We present and analyse a model for cell signalling processes in biological tissues. The model includes diffusion and nonlinear reactions on the cell surfaces, and both inter- and intracellular signalling. Using techniques from the theory of…
Understanding the causal effects of organ-specific features from medical imaging on clinical outcomes is essential for biomedical research and patient care. We propose a novel Functional Linear Structural Equation Model (FLSEM) to capture…
While high-resolution microscopic techniques are crucial for studying cellular structures in cell biology, obtaining such images from thick 3D engineered tissues remains challenging. In this review, we explore advancements in fluorescence…
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…
As the computer vision matures into a systems science and engineering discipline, there is a trend in leveraging latest advances in computer graphics simulations for performance evaluation, learning, and inference. However, there is an open…
Innovation in synthetic biology often still depends on large-scale experimental trial-and-error, domain expertise, and ingenuity. The application of rational design engineering methods promise to make this more efficient, faster, cheaper…
The network of biochemical reactions inside living organisms is characterized by an overwhelming complexity which stems from the sheer number of reactions and from the complicated topology of biochemical cycles. However the high speed of…
Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical…
With the proliferation of inexpensive CMOS cameras, medical imaging experiences a noticeable influx of new technologies. While anatomical imaging is based on well-established principles of photography, physiological optical imaging is a…
The nature of distributed computation has often been described in terms of the component operations of universal computation: information storage, transfer and modification. We review the first complete framework that quantifies each of…
Modelling of photonic devices traditionally involves solving the equations of light-matter interaction and light propagation, and it is restrained by their applicability. Here we demonstrate an alternative modelling methodology by creating…
Quantum simulators, in which well controlled quantum systems are used to reproduce the dynamics of less understood ones, have the potential to explore physics that is inaccessible to modeling with classical computers. However, checking the…
Nonlinear quantum photonics serves as a cornerstone in photonic quantum technologies, such as universal quantum computing and quantum communications. The emergence of integrated photonics platform not only offers the advantage of…
The physiological tradition of biological research analyzes biological systems using reduced descriptions much as an engineer uses a 'black box' description of an amplifier. Simple models have been used by physiologists for a very long…
Mathematical modelling is a cornerstone of computational biology. While mechanistic models might describe the interactions of interest of a system, they are often difficult to study. On the other hand, abstract models might capture key…