相关论文: From biophysical to integrate-and-fire modelling

Using the Dominant Reaction Pathways method, we perform an ab-initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of…

We propose and analyze a new way of using $\pi$ stacking to design molecular junctions that either enhance or suppress a phononic heat current, but at the same time remain conductors for an electric current. Such functionality is highly…

A simulation package employing a Particle in Cell (PIC) method is developed to study the high current beam transport and the dynamics of plasmas. This package includes subroutines those are suited for various planned projects at University…

Nonlinear dynamic models are widely used for characterizing functional forms of processes that govern complex biological pathway systems. Over the past decade, validation and further development of these models became possible due to data…

Motivated by experiments on cell segregation, we present a two-species model of interacting particles, aiming at a quantitative description of this phenomenon. Under precise scaling hypothesis, we derive from the microscopic model a…

Hybrid modeling provides an effective solution to cope with multiple time scales dynamics in systems biology. Among the applications of this method, one of the most important is the cell cycle regulation. The machinery of the cell cycle,…

Motivated by the fact that living cells use molecular circuits (i.e. a set of chemical reactions) for information processing, this paper investigates the problem of designing molecular circuits for demodulation. In our earlier work, we use…

In this article we address the study of ion charge transport in the biological channels separating the intra and extracellular regions of a cell. The focus of the investigation is devoted to including thermal driving forces in the…

In the fields of computation and neuroscience, much is still unknown about the underlying computations that enable key cognitive functions including learning, memory, abstraction and behavior. This paper proposes a mathematical and…

Noise in spiking neurons is commonly modeled by a noisy input current or by generating output spikes stochastically with a voltage-dependent hazard rate ("escape noise"). While input noise lends itself to modeling biophysical noise…

Ordinary differential equation models have become a standard tool for the mechanistic description of biochemical processes. If parameters are inferred from experimental data, such mechanistic models can provide accurate predictions about…

Understanding the dynamics of wildfire is crucial for developing management and intervention strategies. Mathematical and computational models can be used to improve our understanding of wildfire processes and dynamics. This paper presents…

We present multiscale models of cancer tumor invasion with components at the molecular, cellular, and tissue levels. We provide biological justifications for the model components, present computational results from the model, and discuss…

The dual-fermion approach offers a way to perform diagrammatic expansion around the dynamical mean-field theory. Using this formalism, the influence of antiferromagnetic fluctuations on the self-energy is taken into account through…

Given the large size and complexity of most biochemical regulation and signaling networks, there is a non-trivial relationship between the micro-level logic of component interactions and the observed macro-dynamics. Here we address this…

The construction of transfer functions in theoretical neuroscience plays an important role in determining the spiking rate behavior of neurons in networks. These functions can be obtained through various fitting methods, but the biological…

Long-time series of neuronal recordings are resulting from the activity of connected neuronal networks. Yet how neuronal properties can be extracted remains empirical. We review here the data analysis based on network models to recover…

The paper aims at demonstrating communication capabilities of IPT. For this data communication is performed between two modules using the concept of IPT. IPT was deemed to be the best solution to the system houses a multi parameter…

A theory of temperature dynamics in many-body systems driven by time-dependent external sources is introduced. The formalism based on the combination of the perturbation theory and the fluctuational-electrodynamics approach in many-body…

We study a recent model for calcium signal transduction. This model displays spiking, bursting and chaotic oscillations in accordance with experimental results. We calculate bifurcation diagrams and study the bursting behaviour in detail.…