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High-content biological microscopy targets high-resolution imaging across large fields-of-view (FOVs). Recent works have demonstrated that computational imaging can provide efficient solutions for high-content microscopy. Here, we use…
This paper focuses on the Field Programmable Gate Array (FPGA) design and implementation of intelligent control system applications on a chip, specifically fuzzy logic and genetic algorithm processing units. Initially, an overview of the…
Given the ever-increasing advances of digital microfluidic biochips and their application in a wide range of areas including bio-chemistry experiments, diagnostics, and monitoring purposes like air and water quality control and etc.,…
CHIPP (Computing HTC in INAF Pilot Project) is an Italian project funded by the Italian Institute for Astrophysics (INAF) and promoted by the ICT office of INAF. The main purpose of the CHIPP project is to coordinate the use of, and access…
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…
ExaScale systems will be a key driver for simulations that are essential for advance of science and economic growth. We aim to present a new concept of microprocessor for floating-point computations useful for being a basic building block…
Correlative light-electron microscopy (CLEM) unifies the versatility of light microscopy (LM) with the high resolution of electron microscopy (EM), allowing one to zoom into the complex organization of cells. Most CLEM techniques use…
A new type of microfluidic system for biological cell manipulation, a CMOS/microfluidic hybrid, is demonstrated. The hybrid system starts with a custom-designed CMOS (complementary metal-oxide semiconductor) chip fabricated in a…
Cell spheroids are in vitro multicellular model systems that mimic the crowded micro-environment of biological tissues. Their mechanical characterization can provide valuable insights in how single-cell mechanics and cell-cell interactions…
The PySCF package has emerged as a powerful and flexible open-source platform for quantum chemistry simulations. However, the efficiency of electronic structure calculations can vary significantly depending on the choice of computational…
Molecular docking is a critical computational strategy in drug design and discovery, but the complex diversity of biomolecular structures and flexible binding conformations create an enormous search space that challenges conventional…
Fully Homomorphic Encryption (FHE) is a technique that allows arbitrary computations to be performed on encrypted data without the need for decryption, making it ideal for securing many emerging applications. However, FHE computation is…
Many cytoskeletal systems are now sufficiently well known to permit their precise quantitative modelling. Microtubule and actin filaments are well characterized, and the associated proteins are often known, as well as their abundance and…
Processing-in-memory (PIM) has shown extraordinary potential in accelerating neural networks. To evaluate the performance of PIM accelerators, we present an ISA-based simulation framework including a dedicated ISA targeting neural networks…
Automated and computerised control of scientific instrumentation is almost ubiquitous in the modern laboratory. Most instrumentation is controlled over decades old communication busses or is accessed via proprietary system libraries. This…
A modular, maintainable and extensible particle beam simulation architecture is presented. Design considerations for single particle, multi particle, and rms envelope simulations (in two and three dimensions) are outlined. Envelope…
We demonstrate a new computational illumination technique that achieves large space-bandwidth-time product, for quantitative phase imaging of unstained live samples in vitro. Microscope lenses can have either large field of view (FOV) or…
Animal cells are both encapsulated and subdivided by lipid bilayer membranes. Beyond just acting as boundaries, these membranes' shapes influence the function of cells and their compartments. Physically, membranes are two-dimensional fluids…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
Transshipment problem is one of the basic operational research problems. In this paper, our first work is to develop a biologically inspired mathematical model for a dynamical system, which is first used to solve minimum cost flow problem.…