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Multirate method for co-simulation of electrical-chemical systems in multiscale modeling

components are different by several orders of magnitude, individual dynamics and Mikael Djurfeldt and Upinder S. Bhalla contributed equally to this work Jeanette Hellgren Kotaleski - mathematical

Bulbar Microcircuit Model Predicts Connectivity and Roles of Interneurons in Odor Coding

Stimulus encoding by primary sensory brain areas provides a data-rich context for understanding their circuit mechanisms. The vertebrate olfactory bulb is an input area having unusual two-layer dendro-dendritic connections whose roles in odor coding are unclear. To clarify these roles, we built a detailed compartmental model of the rat olfactory bulb that synthesizes a much wider...

NSDF: Neuroscience Simulation Data Format

, Tata institute of Fundamental Research , Bangalore , India 1 Daniel K. Wo ́jcik 2 Upinder S. Bhalla 3 Present address: National Institutes of Health , Bethesda, MD , USA 4 Nencki Institute of

Transcription Control Pathways Decode Patterned Synaptic Inputs into Diverse mRNA Expression Profiles

Synaptic plasticity requires transcription and translation to establish long-term changes that form the basis for long term memory. Diverse stimuli, such as synaptic activity and growth factors, trigger synthesis of mRNA to regulate changes at the synapse. The palette of possible mRNAs is vast, and a key question is how the cell selects which mRNAs to synthesize. To address this...

Theta Frequency Background Tunes Transmission but Not Summation of Spiking Responses

Hippocampal neurons are known to fire as a function of frequency and phase of spontaneous network rhythms, associated with the animal's behaviour. This dependence is believed to give rise to precise rate and temporal codes. However, it is not well understood how these periodic membrane potential fluctuations affect the integration of synaptic inputs. Here we used sinusoidal...

CA1 cell activity sequences emerge after reorganization of network correlation structure during associative learning

Animals can learn causal relationships between pairs of stimuli separated in time and this ability depends on the hippocampus. Such learning is believed to emerge from alterations in network connectivity, but large-scale connectivity is difficult to measure directly, especially during learning. Here, we show that area CA1 cells converge to time-locked firing sequences that bridge...

Biophysical model of odor representation and processing in the rat olfactory bulb

Aditya Gilra 0 Upinder S Bhalla 0 0 National Centre for Biological Sciences, Tata Institute of Fundamental Research , Bellary Road, Bangalore, 560065 , India Reference 1. Adil G. Khan, Mukund ... Thattai, Upinder S. Bhalla: Odor representations in the rat olfactory bulb change smoothly with morphing stimuli. Neuron 2008, 57(4):571-585. - Experimental findings from our lab [1] indicate that mitral

How To Record a Million Synaptic Weights in a Hippocampal Slice

A key step toward understanding the function of a brain circuit is to find its wiring diagram. New methods for optical stimulation and optical recording of neurons make it possible to map circuit connectivity on a very large scale. However, single synapses produce small responses that are difficult to measure on a large scale. Here I analyze how single synaptic responses may be...

Signaling Logic of Activity-Triggered Dendritic Protein Synthesis: An mTOR Gate But Not a Feedback Switch

Changes in synaptic efficacy are believed to form the cellular basis for memory. Protein synthesis in dendrites is needed to consolidate long-term synaptic changes. Many signals converge to regulate dendritic protein synthesis, including synaptic and cellular activity, and growth factors. The coordination of these multiple inputs is especially intriguing because the synthetic and...

Inferring ion channel densities from spike data

Oliver Muthmann 0 Matthias H Hennig Upinder S Bhalla 0 0 Department, National Centre for Biological Sciences, Tata Institute of Fundamental Research , Bangalore, 560065 , India In high density

Memory Switches in Chemical Reaction Space

Just as complex electronic circuits are built from simple Boolean gates, diverse biological functions, including signal transduction, differentiation, and stress response, frequently use biochemical switches as a functional module. A relatively small number of such switches have been described in the literature, and these exhibit considerable diversity in chemical topology. We...

Molecular Switches at the Synapse Emerge from Receptor and Kinase Traffic

Changes in the synaptic connection strengths between neurons are believed to play a role in memory formation. An important mechanism for changing synaptic strength is through movement of neurotransmitter receptors and regulatory proteins to and from the synapse. Several activity-triggered biochemical events control these movements. Here we use computer models to explore how these...

The chemical organization of signaling interactions

Upinder S. Bhalla 0 0 Neurobiology, National Centre for Biological Sciences , GKVK Campus, Bangalore 560065, India Motivation: Cellular chemical signaling pathways form complex networks that are

Adaptive stochastic-deterministic chemical kinetic simulations

Karan Vasudeva 0 Upinder S. Bhalla 0 0 National Centre for Biological Sciences , TIFR, GKVK Campus, Bangalore 560065 , India Motivation: Biochemical signaling pathways and genetic circuits often