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Detailed simulation of chemical reactions and the diffusion of ions through a neuronal membrane presents challenges due to the multiple scales at which this occurs, scales that require development and consolidation of a number of different simulation methodologies. In this paper, we describe Neuron Time Warp (NTW), a part of the NEURON project for...
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... human brain may be viewed as a sparsely connected network of neurons (Carnevale and Hines 2006) containing approximately 10 14 neurons. A typical neuron is displayed in figure 1. Each neuron receives inputs from thousands of synapses. ...
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... rates affect the probability of a particular type of chemical reaction occurring, thereby altering the state of the system. This motivated us to experiment with different values of the diffusion rate in the Y-Shaped geometry-we doubled the diffusion rate of both of the prey and the predator (Figures 12 and 13). ...
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Citations
... We describe a dynamic load balancing algorithm and a dynamic time window algorithm to improve the efficiency of NTW. (Patoary et al. 2014) made use of a model of a dendrite branch in order to evaluate NTWs performance and accuracy for a spatial Lotka-Volterra model (Schinazi 1997). (Patoary et al. 2017) describes a simulation of a Ca buffer and a Ca 2+ wave model. ...
... There are two main approaches for solving the synchronization problem-conservative and optimistic. Time Warp (TW) synchronization is a widely used optimistic synchronization protocol and is the one which we make use of in NTW (Patoary et al. 2014). ...
... The history queue (HQ) is an addition to the structure described in XTW (Xu and Tropper 2006). A more detailed description of NTW's architecture along with a detailed description of event processing is contained in (Patoary et al. 2014). ...
... We previously made use of a model of a dendrite branch on which to evaluate NTWs performance in [2]. We employed a spatial Lotka-Volterra model and verified the accuracy of the models. ...
... There are two main approaches for solving the synchronization problem-conservative and optimistic. Time Warp (TW) synchronization is a widely used optimistic synchronization protocol and is the one which we make use of in NTW [2]. ...
The intra-cellular calcium signaling pathways of a neuron depends on both biochemical reactions and diffusions. Some quasi-isolated compartments (e.g. spines) are so small and calcium concentrations are so low that one extra molecule diffusing in by chance can make a nontrivial difference in its concentration (percentage-wise). These rare events can affect dynamics discretely in such way that they cannot be evaluated by a deterministic simulation. Stochastic models of such a system provide a more detailed understanding of these systems than existing deterministic models because they capture their behavior at a molecular level. Our research focuses on the development of a high performance parallel discrete event simulation environment, Neuron Time Warp (NTW), which is intended for use in the parallel simulation of stochastic reaction-diffusion systems such as intra-calcium signaling. NTW is integrated with NEURON, a simulator which is widely used within the neuroscience community. We simulate two models, a calcium buffer and a calcium wave model. The calcium buffer model is employed in order to verify the correctness and performance of NTW by comparing it to a serial deterministic simulation in NEURON. We also derived a discrete event calcium wave model from a deterministic model using the stochastic IP3R structure.
... It is intended that our simulators will be integrated into NEURON. We previously developed a process based simulator, NTW [18], which makes use of a multi-level queue. We verified and examined its performance on a Calcium buffer model and a predator prey [21] model. ...
... We verified and examined its performance on a Calcium buffer model and a predator prey [21] model. The queueing structure described in this paper and the one in [18] are outgrowths of the multi-level queue described in XTW [27]. ...
... LP 16 has four pending events which would be stored in a queue. One may notice that it is not necessary to store and sort all four events in the TEQ-only event (18,14) needs to stay in the TEQ. There are several reasons for this: (1) some insertions in the TEQ can be omitted, decreasing the probability of contention. ...
This paper describes a parallel discrete event simulator, Neuron Time Warp-Multi Thread (NTW-MT), developed for the simulation of reaction diffusion models of neurons. The simulator was developed as part of the NEURON project and is intended to be included in NEURON. It relies upon a stochastic discrete event model developed for chemical reactions. NTW-MT is optimistic and thread-based, in which communication latency among threads within the same process is minimized by pointers. We investigate the performance of NTW-MT on a reaction-diffusion model for the transmission of calcium waves in a neuron. Calcium plays a fundamental role in the second messenger system of a neuron. However, the mechanism by which calcium waves are transmitted is not entirely understood. Stochastic models are more realistic than deterministic models for small populations of ions such as those found in apical dendrites. To be more precise, we simulate a stochastic discrete event model for calcium wave propagation on an unbranched apical dendrite of a hippocampal pyramidal neuron. We examine the performance of NTW-MT on this calcium wave model and compare it to the performance of a (1) process based optimistic simulator and (2) a threaded simulator which uses a single priority (SQ) queue for each thread. Our multithreaded simulator is shown to achieve superior performance to these simulators.
Chemical reactions and molecular diffusion in a neuron play an important role in the transmission of signals within a neuron. Discrete event stochastic simulation of the chemical reactions and diffusion provides a more detailed view of the molecular dynamics within a neuron than continuous simulation. As part of the NEURON project we developed a multi-threaded optimistic PDES simulator, Neuron Time Warp-Multi Thread, for these reaction-diffusion models. We used NTW-MT to simulate a calcium wave model due to its importance to the neuroscience community and representativeness of the types of reaction-diffusion problems which need to be solved in neuroscience. During the course of our experiments we observed a decided need for load balancing and window control to achieve large-scale runs. In this paper, we improved the Q-Learning and Simulated Annealing load balancing algorithm according to characteristics of reaction and diffusion model to address both of these issues. We evaluated the algorithms by various parameters in various scales, and our results showed that (1) the algorithm improves the execution time for small simulations by up to 31% (using Q-Learning) and 19% (using SA) and (2) the SA approach is more suitable for larger models, decreasing the execution time by 41%.
This paper describes a parallel discrete event simulator, Neuron Time Warp-Multi Thread (NTW-MT), developed for the simulation of reaction diffusion models of neurons. The simulator was developed as part of the NEURON project and is intended to be included in NEURON. It relies upon a stochastic discrete event model developed for chemical reactions. NTW-MT is optimistic and thread-based, in which communication latency among threads within the same process is minimized by pointers. We investigate the performance of NTW-MT on a reaction-diffusion model for the transmission of calcium waves in a neuron. Calcium plays a fundamental role in the second messenger system of a neuron. However, the mechanism by which calcium waves are transmitted is not entirely understood. Stochastic models are more realistic than deterministic models for small populations of ions such as those found in apical dendrites. To be more precise, we simulate a stochastic discrete event model for calcium wave propagation on an unbranched apical dendrite of a hippocampal pyramidal neuron. We examine the performance of NTW-MT on this calcium wave model and compare it to the performance of (1) a process based optimistic simulator and (2) a threaded simulator which uses a single priority (SQ) queue for each thread. Our multi-threaded simulator is shown to achieve superior performance to these simulators.
