One of major challenges for post-genomic biology is to understand how molecules dynamically interact to form networks which facilitate sophisticated biological functions. Instead of analyzing individual molecules, systems biology is to study dynamical networks of interacting molecules which give rise to life. In recent years, many progress have been made in systematic approaches and high-throug...

There is a growing recognition of dynamical systems approaches and process oriented studies in clinical psychology and psychiatry. The new enthusiasm however risks turning into dissatisfaction when facing methodological obstacles in empirical research and mathematical modeling. Therefore graspable tools allowing a translation of current knowledge into meaningful dynamical models could be helpfu...

There is a growing recognition of dynamical systems approaches and process oriented studies in clinical psychology and psychiatry. The new enthusiasm however risks turning into dissatisfaction when facing methodological obstacles in empirical research and mathematical modeling. Therefore graspable tools allowing a translation of current knowledge into meaningful dynamical models could be helpfu...

The network of interacting regulatory signals within a cell comprises one of the most complex and powerful computational systems in biology. Gene regulatory networks (GRNs) play a key role in transforming the information encoded in a genome into morphological form. To achieve this feat, GRNs must respond to and integrate environmental signals with their internal dynamics in a robust and coordin...

Scientific analysis often relies on the ability to make accurate predictions of a system's dynamics. Mechanistic models, parameterized by a number of unknown parameters, are often used for this purpose. Accurate estimation of the model state and parameters prior to prediction is necessary, but may be complicated by issues such as noisy data and uncertainty in parameters and initial conditions. ...

We propose here a model to simulate the process of opinion formation, which accounts for the mutual affinity between interacting agents. Opinion and affinity evolve self-consistently, manifesting a highly nontrivial interplay. A continuous transition is found between single and multiple opinion states. Fractal dimension and signature of critical behavior are also reported. A rich phenomenology ...

Continuous Flash Suppression (CFS) is a technique in which a stationary image in one eye can be reliably suppressed by rapid presentation of different flashing images in the other. In this paper we address why flashing stimuli modulate the visibility of the stimuli. We determine, in particular, which type of neural network is sufficient for the modulation of the dominance duration, assuming tha...

The grand piano action is modeled as a set of four rigid bodies using Kane’s method. Computerized symbol manipulation is utilized to streamline the formulation of the equations of motion so that several models can be considered, each of increasing detail. Various methods for checking the dynamical model thus derived are explored. A computer animation driven by simulation of the equations of mot...

How can we model influence between individuals in a social system, even when the network of interactions is unknown? In this article, we review the literature on the “influence model,” which utilizes independent time series to estimate how much the state of one actor affects the state of another actor in the system. We extend this model to incorporate dynamical parameters that allow us to infer...

A key concept in template-based modeling (TBM) is the high correlation between sequence and structural divergence, with the practical consequence that homologous proteins that are similar at the sequence level will also be similar at the structural level. However, conformational diversity of the native state will reduce the correlation between structural and sequence divergence, because structu...