Related papers: From biophysical to integrate-and-fire modelling
This paper presents a two-phase method for learning interaction kernels of stochastic many-particle systems. After transforming stochastic trajectories of every particle into the particle density function by the kernel density estimation…
We introduce a phase field approach for diffusion inside and outside a closed cell with damping and with source terms at the interface. The method is compared to exact solutions (where possible) and the more traditional finite element…
Cellular signaling is essential in information processing and decision making. Therefore, a variety of experimental approaches have been developed to study signaling on bulk and single-cell level. Single-cell measurements of signaling…
We review two examples where the linear response of a neuronal network submitted to an external stimulus can be derived explicitely, including network parameters dependence. This is done in a statistical physics-like approach where one…
The space of possible behaviors complex biological systems may exhibit is unimaginably vast, and these systems often appear to be stochastic, whether due to variable noisy environmental inputs or intrinsically generated chaos. The brain is…
The development of complex multicellular organisms from a single parent cell is a highly orchestrated process that cells conduct collectively without central guidance, creating intricate dynamic patterns essential for development and…
To survive in ever-changing environments, living organisms need to continuously combine the ongoing external inputs they receive, representing present conditions, with their dynamical internal state, which includes influences of past…
The flexible profile approach proposed earlier to create CTM (compact or reduced order thermal models) is extended to cover the area of conjugate heat transfer. The flexible profile approach is a methodology that allows building a highly…
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…
The reaction-diffusion models have been extensively applied to explain the mechanism of pattern formations in early embryogenesis based on geometrically confined microtissues consisting of human pluripotent stem cells. Recently, mechanical…
The biological cell exhibits a fantastic range of behaviors, but ultimately these are governed by a handful of physical and chemical principles. Here we explore simple theory, known for decades and based on the simple thermodynamics of…
In recent years, there has been increasing interest in developing models and tools to address the complex patterns of connectivity found in brain tissue. Specifically, this is due to a need to understand how emergent properties emerge from…
A new model for the electrical conductivity of dense plasmas with a mixture of ion species, containing no adjustable parameters, is presented. The model takes the temperature, mass density and relative abundances of the species as input. It…
Models of physical systems are used to explain and predict experimental results and observations. When students encounter discrepancies between the actual and expected behavior of a system, they revise their models to include the newly…
We propose a method to change the effective interaction between two fluids by modulation of their local density distributions with external periodic potentials, whereby the mixing properties can be controlled. This method is applied to a…
The concept of control is crucial for effectively understanding and applying biological network models. Key structural features relate to control functions through gene regulation, signaling, or metabolic mechanisms, and computational…
The concepts and methods of Systems Biology are being extended to neuropharmacology, to test and design drugs against neurological and psychiatric disorders. Computational modeling by integrating compartmental neural modeling technique and…
Constraining the many biological parameters that govern cortical dynamics is computationally and conceptually difficult because of the curse of dimensionality. This paper addresses these challenges by proposing (1) a novel data-informed…
This is the second component of a two-part paper dealing with a unification of characteristic mode decomposition. This second part addresses modal tracking and losses and presents several numerical examples for both surface- and…
Motivated by the phenomenology of transport through the Golgi apparatus of cells, we study a multi-species model with boundary injection of one species of particle, interconversion between the different species of particle, and driven…