L. Tsimring - Academia.edu (original) (raw)
Papers by L. Tsimring
Stochasticity inherent to biochemical reactions (intrinsic noise) and variability in cellular sta... more Stochasticity inherent to biochemical reactions (intrinsic noise) and variability in cellular states (extrinsic noise) degrade information transmitted through signaling networks. We analyzed the ability of temporal signal modulation--that is, dynamics--to reduce noise-induced information loss. In the extracellular signal-regulated kinase (ERK), calcium (Ca(2+)), and nuclear factor kappa-B (NF-κB) pathways, response dynamics resulted in significantly greater information transmission capacities compared to nondynamic responses. Theoretical analysis demonstrated that signaling dynamics has a key role in overcoming extrinsic noise. Experimental measurements of information transmission in the ERK network under varying signal-to-noise levels confirmed our predictions and showed that signaling dynamics mitigate, and can potentially eliminate, extrinsic noise-induced information loss. By curbing the information-degrading effects of cell-to-cell variability, dynamic responses substantially increase the accuracy of biochemical signaling networks.
Physical Review Letters, 1999
We present experimental study of a topological excitation, interface, in a vertically vibrated la... more We present experimental study of a topological excitation, interface, in a vertically vibrated layer of granular material. We show that these interfaces, separating regions of granular material oscillation with opposite phases, can be shifted and controlled by a very small amount of an additional subharmonic signal, mixed with the harmonic driving signal. The speed and the direction of interface motion depends sensitively on the phase and the amplitude of the subharmonic driving.
Physical Review Letters, 1995
Physical Review Letters, 1997
Population dynamics on a rugged landscape is studied analytically and numerically within a simple... more Population dynamics on a rugged landscape is studied analytically and numerically within a simple discrete model for evolution of N individuals in one-dimensional fitness space. We reduce the set of master equations to a single Fokker-Plank equation which allows us to describe the dynamics of the population in terms of thermo-activated Langevin diffusion of a single particle in a specific random potential. We found that the randomness in the mutation rate leads to pinning of the population and on average to a logarithmic slowdown of the evolution, resembling aging phenomenon in spin glass systems. In contrast, the randomness in the replication rate turns out to be irrelevant for evolution in the long-time limit as it is smoothed out by increasing "evolution temperature". The analytic results are in a good agreement with numerical simulations.
IEEE Communications Letters, 2000
In this letter we investigate a communication strategy for digital ultra-wide bandwidth impulse r... more In this letter we investigate a communication strategy for digital ultra-wide bandwidth impulse radio, where the separation between the adjacent pulses is chaotic arising from a dynamical system with irregular behavior. A pulse position method is used to modulate binary information onto the carrier. The receiver is synchronized to the chaotic pulse train, thus providing the time reference for information extraction. We characterize the performance of this scheme in terms of error probability versus 0 by numerically simulating its operation in the presence of noise and filtering.
Numerical simulation of the collapse of granular material over an horizontal plane using both con... more Numerical simulation of the collapse of granular material over an horizontal plane using both continuum and discrete element approach shows that continuum models based on the Long Wave Approximation (LWA) overestimate the driving forces involved during the collapse. This effect increases when the aspect ratio of the granular mass increases. Comparison between discrete and continuum simulations makes it possible to show that the assumption of hydrostatic normal stress is essentially responsible of the limits of the LWA when the aspect ratio increases. The vertical acceleration, neglected in the vertical momentum equation, is shown to play a significant role when the aspect ratio increases. As a result, numerical simulations of real geophysical flows using thin layer models will be significantly improved if a new asymptotic analysis is performed including the effects of the vertical acceleration.
Stochasticity inherent to biochemical reactions (intrinsic noise) and variability in cellular sta... more Stochasticity inherent to biochemical reactions (intrinsic noise) and variability in cellular states (extrinsic noise) degrade information transmitted through signaling networks. We analyzed the ability of temporal signal modulation--that is, dynamics--to reduce noise-induced information loss. In the extracellular signal-regulated kinase (ERK), calcium (Ca(2+)), and nuclear factor kappa-B (NF-κB) pathways, response dynamics resulted in significantly greater information transmission capacities compared to nondynamic responses. Theoretical analysis demonstrated that signaling dynamics has a key role in overcoming extrinsic noise. Experimental measurements of information transmission in the ERK network under varying signal-to-noise levels confirmed our predictions and showed that signaling dynamics mitigate, and can potentially eliminate, extrinsic noise-induced information loss. By curbing the information-degrading effects of cell-to-cell variability, dynamic responses substantially increase the accuracy of biochemical signaling networks.
Physical Review Letters, 1999
We present experimental study of a topological excitation, interface, in a vertically vibrated la... more We present experimental study of a topological excitation, interface, in a vertically vibrated layer of granular material. We show that these interfaces, separating regions of granular material oscillation with opposite phases, can be shifted and controlled by a very small amount of an additional subharmonic signal, mixed with the harmonic driving signal. The speed and the direction of interface motion depends sensitively on the phase and the amplitude of the subharmonic driving.
Physical Review Letters, 1995
Physical Review Letters, 1997
Population dynamics on a rugged landscape is studied analytically and numerically within a simple... more Population dynamics on a rugged landscape is studied analytically and numerically within a simple discrete model for evolution of N individuals in one-dimensional fitness space. We reduce the set of master equations to a single Fokker-Plank equation which allows us to describe the dynamics of the population in terms of thermo-activated Langevin diffusion of a single particle in a specific random potential. We found that the randomness in the mutation rate leads to pinning of the population and on average to a logarithmic slowdown of the evolution, resembling aging phenomenon in spin glass systems. In contrast, the randomness in the replication rate turns out to be irrelevant for evolution in the long-time limit as it is smoothed out by increasing "evolution temperature". The analytic results are in a good agreement with numerical simulations.
IEEE Communications Letters, 2000
In this letter we investigate a communication strategy for digital ultra-wide bandwidth impulse r... more In this letter we investigate a communication strategy for digital ultra-wide bandwidth impulse radio, where the separation between the adjacent pulses is chaotic arising from a dynamical system with irregular behavior. A pulse position method is used to modulate binary information onto the carrier. The receiver is synchronized to the chaotic pulse train, thus providing the time reference for information extraction. We characterize the performance of this scheme in terms of error probability versus 0 by numerically simulating its operation in the presence of noise and filtering.
Numerical simulation of the collapse of granular material over an horizontal plane using both con... more Numerical simulation of the collapse of granular material over an horizontal plane using both continuum and discrete element approach shows that continuum models based on the Long Wave Approximation (LWA) overestimate the driving forces involved during the collapse. This effect increases when the aspect ratio of the granular mass increases. Comparison between discrete and continuum simulations makes it possible to show that the assumption of hydrostatic normal stress is essentially responsible of the limits of the LWA when the aspect ratio increases. The vertical acceleration, neglected in the vertical momentum equation, is shown to play a significant role when the aspect ratio increases. As a result, numerical simulations of real geophysical flows using thin layer models will be significantly improved if a new asymptotic analysis is performed including the effects of the vertical acceleration.