arXiv subjects

Shlomi Reuveni

Publications and source records attributed to Shlomi Reuveni.

60 records · Page 4Linked to original sources

arXiv2018

First passage under restart with branching

First passage under restart with branching is proposed as a generalization of first passage under restart. Strong motivation to study this generalization comes from the observation that restart with branching can expedite the completion of processes that cannot be expedited with simple restart; yet a sharp and quantitative formulation of this statement is still lacking. We develop a comprehensive theory of first passage under restart with branching. This reveals that two widely applied measures of statistical dispersion---the coefficient of variation and the Gini index---come together to determine how restart with branching affects the mean completion time of an arbitrary stochastic process. The universality of this result is demonstrated and its connection to extreme value theory is also pointed out and explored.

cond-mat.stat-mech↗

arXiv2017

Single-molecule theory of enzymatic inhibition predicts the emergence of inhibitor-activator duality

The classical theory of enzymatic inhibition aims to quantitatively describe the effect of certain molecules -- called inhibitors -- on the progression of enzymatic reactions, but growing signs indicate that it must be revised to keep pace with the single-molecule revolution that is sweeping through the sciences. Here, we take the single enzyme perspective and rebuild the theory of enzymatic inhibition from the bottom up. We find that accounting for multi-conformational enzyme structure and intrinsic randomness cannot undermine the validity of classical results in the case of competitive inhibition; but that it should strongly change our view on the uncompetitive and mixed modes of inhibition. There, stochastic fluctuations on the single-enzyme level could give rise to inhibitor-activator duality -- a phenomenon in which, under some conditions, the introduction of a molecule whose binding shuts down enzymatic catalysis will counter intuitively work to facilitate product formation. We state -- in terms of experimentally measurable quantities -- a mathematical condition for the emergence of inhibitor-activator duality, and propose that it could explain why certain molecules that act as inhibitors when substrate concentrations are high elicit a non-monotonic dose response when substrate concentrations are low. The fundamental and practical implications of our findings are thoroughly discussed.

q-bio.QM↗

arXiv2016

First Passage Under Restart

First passage under restart has recently emerged as a conceptual framework suitable for the description of a wide range of phenomena, but the endless variety of ways in which restart mechanisms and first passage processes mix and match hindered the identification of unifying principles and general truths. Hope that these exist came from a recently discovered universality displayed by processes under optimal, constant rate, restart---but extensions and generalizations proved challenging as they marry arbitrarily complex processes and restart mechanisms. To address this challenge, we develop a generic approach to first passage under restart. Key features of diffusion under restart---the ultimate poster boy for this wide and diverse class of problems---are then shown to be completely universal.

cond-mat.stat-mech↗

arXiv2015

Optimal stochastic restart renders fluctuations in first passage times universal

Stochastic restart may drastically reduce the expected run time of a computer algorithm, expedite the completion of a complex search process, or increase the turnover rate of an enzymatic reaction. These diverse first-passage-time (FPT) processes seem to have very little in common but it is actually quite the other way around. Here we show that the relative standard deviation associated with the FPT of an optimally restarted process, i.e., one that is restarted at a (non-zero) rate which brings the mean FPT to a minimum, is always unity. We interpret, further generalize, and discuss this finding and the implications arising from it.

cond-mat.stat-mech↗

arXiv2015

The Michaelis-Menten reaction scheme as a unified approach towards the optimal restart problem

We study the effect of restart, and retry, on the mean completion time of a generic process. The need to do so arises in various branches of the sciences and we show that it can naturally be addressed by taking advantage of the classical reaction scheme of Michaelis and Menten. Stopping a process in its midst, only to start it all over again, may prolong, leave unchanged, or even shorten the time taken for its completion. Here we are interested in the optimal restart problem, i.e., in finding a restart rate which brings the mean completion time of a process to a minimum. We derive the governing equation for this problem and show that it is exactly solvable in cases of particular interest. We then continue to discover regimes at which solutions to the problem take on universal, details independent, forms which further give rise to optimal scaling laws. The formalism we develop, and the results obtained, can be utilized when optimizing stochastic search processes and randomized computer algorithms. An immediate connection with kinetic proofreading is also noted and discussed.

cond-mat.stat-mech↗

arXiv2013

Occupation Probabilities and Fluctuations in the Asymmetric Simple Inclusion Process

The Asymmetric Simple Inclusion Process (ASIP), a lattice-gas model of unidirectional transport and aggregation, was recently proposed as an `inclusion' counterpart of the Asymmetric Simple Exclusion Process (ASEP). In this paper we present an exact closed-form expression for the probability that a given number of particles occupies a given set of consecutive lattice sites. Our results are expressed in terms of the entries of Catalan's trapezoids --- number arrays which generalize Catalan's numbers and Catalan's triangle. We further prove that the ASIP is asymptotically governed by: (i) an inverse square root law of occupation; (ii) a square root law of fluctuation; and (iii) a Rayleigh law for the distribution of inter-exit times. The universality of these results is discussed.

cond-mat.stat-mech↗