Related papers: Temporal precision of regulated gene expression
The solution of high-dimensional inference and prediction problems in computational biology is almost always a compromise between mathematical theory and practical constraints such as limited computational resources. As time progresses,…
Gene regulation is a complex process involving the role of several genomic elements which work in concert to drive spatio-temporal expression. The experimental characterization of gene regulatory elements is a very complex and…
Neurons in the central nervous system are affected by complex and noisy signals due to fluctuations in their cellular environment and in the inputs they receive from many other cells 1,2. Such noise usually increases the probability that a…
Gene expression and its regulation is a nonequilibrium stochastic process. Different molecules are involved in several biochemical steps in this process with low copies. It is observed that the stochasticity in biochemical processes is…
Intercellular signaling has an important role in organism development, but not all communication occurs using the same mechanism. Here, we analyze the energy efficiency of intercellular signaling by two canonical mechanisms: diffusion of…
Genetic algorithms, as implemented in optimal control strategies, are currently successfully exploited in a wide range of problems in molecular physics. In this context, laser control of molecular alignment and orientation remains a very…
Microbiological systems evolve to fulfill their tasks with maximal efficiency. The immune system is a remarkable example, where self-non self distinction is accomplished by means of molecular interaction between self proteins and antigens,…
Precise spike timing as a means to encode information in neural networks is biologically supported, and is advantageous over frequency-based codes by processing input features on a much shorter time-scale. For these reasons, much recent…
Sperm swimming is crucial to fertilise the egg, in nature and in assisted reproductive technologies. Modelling the sperm dynamics involves elasticity, hydrodynamics, internal active forces, and out-of-equilibrium noise. Here we demonstrate…
Brain functions require both segregated processing of information in specialized circuits, as well as integration across circuits to perform high-level information processing. One possible way to implement these seemingly opposing demands…
A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these…
Cell size control is crucial for maintaining cellular function and homeostasis. In this study, we develop a first-order partial differential equation model to examine the effects of three key size control mechanisms: the sizer, timer, and…
Optical techniques for spatiotemporal control can produce laser pulses with custom amplitude, phase, or polarization structure. In nonlinear optics and plasma physics, the use of structured pulses typically follows a forward design…
Control synthesis from temporal logic specifications has gained popularity in recent years. In this paper, we use a model predictive approach to control discrete time linear systems with additive bounded disturbances subject to constraints…
When cells measure concentrations of chemical signals, they may average multiple measurements over time in order to reduce noise in their measurements. However, when cells are in a environment that changes over time, past measurements may…
Berg and Purcell [Biophys. J. 20, 193 (1977)] calculated how the accuracy of concentration sensing by single-celled organisms is limited by noise from the small number of counted molecules. Here we generalize their results to the sensing of…
Cells can utilize chemical communication to exchange information and coordinate their behavior in the presence of noise. Communication can reduce noise to shape a collective response, or amplify noise to generate distinct phenotypic…
Molecular circadian clocks, that are found in all nucleated cells of mammals, are known to dictate rhythms of approximately 24 hours (circa diem) to many physiological processes. This includes metabolism (e.g., temperature, hormonal blood…
We use conductance based neuron models and the mathematical modeling of Optogenetics to define controlled neuron models and we address the minimal time control of these affine systems for the first spike from equilibrium. We apply tools of…
Practice of a complex motor gesture involves exploration of motor space to attain a better match to target output, but little is known about the neural code for such exploration. Here, we examine spiking in an area of the songbird brain…