LIST OF PUBLICATIONS

Loss of percolation transition
for a pushy random walker

2025

Sagi Meir; Tommer D. Keidar; Shlomi Reuveni; Barak Hirshberg (2025). First-Passage Approach to Optimizing Perturbations for Improved Training of Machine Learning Models. arXiv:2502.04121.
Divya Singh; Michael Urbakh; Shlomi Reuveni (2025). Inferring binding rates from enzymatic turnover time statistics. bioRxiv 2025.02.04.636412.
Tommer David Keidar; Shlomi Reuveni (2025). Universal Linear Response of the Mean First-Passage Time. arXiv:2410.16129.
Tommer David Keidar; Ofir Blumer; Barak Hirshberg; Shlomi Reuveni (2025). Adaptive resetting for informed search strategies and the design of non-equilibrium steady-states. arXiv:2409.14419.
Divya Singh; Tal Robin; Michael Urbakh; Shlomi Reuveni (2025). High-order Michaelis-Menten equations allow inference of hidden kinetic parameters in enzyme catalysis. Nat. Commun., 15, 240.
Ofek Lauber Bonomo; Uri Yechiali; Shlomi Reuveni (2025). Queues with service resetting. Eur. J. Oper. Res. 322, 3, 1 2025.
Jonathan Church; Ofir Blumer; Tommer David Keidar; Leo Ploutno; Shlomi Reuveni; Barak Hirshberg (2025). Accelerating molecular dynamics through informed resetting. J. Chem. Theory Comput. 21, 2, 605–613.
Ofir Tal-Friedman; Tommer David Keidar; Shlomi Reuveni; Yael Roichman (2025). Smart resetting: an energy-efficient strategy for stochastic search processes. Phys. Rev. Research 7 , 013033.

2023

Yuval Scher; Shlomi Reuveni; Denis S. Grebenkov (2023). Escape of a sticky particle. Phys. Rev. Research 5, 043196.
Ofek Lauber Bonomo; Shlomi Reuveni (2023). Loss of percolation transition in the presence of simple tracer-media interactions. Phys. Rev. Research 5, L042015. [YouTube Talk ]
Aanjaneya Kumar; Yuval Scher; Shlomi Reuveni; M. S. Santhanam (2023). Inference from gated first-passage times. Phys. Rev. Research 5, L032043.
Yuval Scher; Ofek Lauber Bonomo; Arnab Pal; Shlomi Reuveni (2023). Microscopic theory of adsorption kinetics. J. Chem. Phys. 158, 094107.
Iddo Eliazar; Shlomi Reuveni (2023). Diversity of sharp restart. J. Phys. A: Math. Theor. 56 , 024003.
Iddo Eliazar; Shlomi Reuveni (2023). Entropy of sharp restart. J. Phys. A: Math. Theor. 56 , 024002.

2024

Ofir Blumer; Shlomi Reuveni; Barak Hirshberg (2024). Inference of non-exponential kinetics through stochastic resetting. J. Chem. Phys. 161, 224104.
Yuval Scher; Aanjaneya Kumar; M. S. Santhanam; Shlomi Reuveni (2024). Continuous gated first-passage processes. Rep. Prog. Phys. 87, 108101.
Ofek Lauber Bonomo; Itamar Shitrit; Shlomi Reuveni (2024). Sokoban percolation on the Bethe lattice. J. Phys. A: Math. Theor. 57, 33LT01.
Amy Altshuler; Ofek Lauber Bonomo; Nicole Gorohovsky; Shany Marchini; Eran Rosen; Ofir Tal-Friedman; Shlomi Reuveni; Yael Roichman (2024). Environmental memory facilitates search with home returns. Phys. Rev. Research 6, 023255.
Yuval Scher; Shlomi Reuveni; Denis S. Grebenkov (2024). Escape from textured adsorbing surfaces. J. Chem. Phys. 160, 184105.
Ofir Blumer; Shlomi Reuveni; Barak Hirshberg (2024). Short-time infrequent Metadynamics for improved kinetics inference. J. Chem. Theory Comput. 20, 9, 3484.
Omri Shelef, Tal Kopp, Rozan Tannous, Moriah Jospe-Kaufman, Maxence Arutkin, Shlomi Reuveni, Doron Shabat, and Micha Fridman (2024). Enzymatic activity profiling using an ultra-sensitive array of chemiluminescent probes for bacterial classification and characterization. J. Am. Chem. Soc. 146, 8, 5263.
Maxence Arutkin; Shlomi Reuveni (2024). Doubly stochastic continuous time random walk. Phys. Rev. Research 6, L012033.
Anupam Kundu; Shlomi Reuveni (2024). Preface: stochastic resetting—theory and applications. J. Phys. A. 57, 060301.
Ofir Blumer; Shlomi Reuveni; Barak Hirshberg (2024). Combining stochastic resetting with Metadynamics to speed-up molecular dynamics simulations. Nat. Commun., 15, 240. [Behind the Paper ] [Yet Coverage] [YouTube Talk ]

2022

Ofir Blumer; Shlomi Reuveni, Barak Hirshberg (2022). Stochastic resetting for enhanced sampling. J. Phys. Chem. Lett. 13, 11230. [YouTube Talk ]
Ofir Tal-Friedman; Yael Roichman; Shlomi Reuveni (2022). Diffusion with partial resetting. Phys. Rev. E 106, 054116.
Ofek Lauber Bonomo; Arnab Pal; Shlomi Reuveni (2022). Mitigating long queues and waiting times with service resetting. PNAS Nexus 1, 3. [YouTube Talk ]
Arnab Pal; Sarah Kostinski; Shlomi Reuveni (2022). The inspection paradox in stochastic resetting. J. Phys. A: Math. Theor. 55, 021001. [YouTube Talk ]

2021

Yuval Scher; Shlomi Reuveni (2021). Gated reactions in discrete time and space. J. Chem. Phys. 155, 234112.
Arnab Pal; Shlomi Reuveni; Saar Rahav (2021). Thermodynamic uncertainty relation for first-passage times on markov chains. Phys. Rev. Research 3, L032034.
Iddo Eliazar; Shlomi Reuveni (2021). Mean-performance of sharp restart II: inequality roadmap. J. Phys. A: Math. Theor. 54, 355001.
Somrita Ray; Shlomi Reuveni (2021). Resetting transition is governed by an interplay between thermal and potential energy. J. Chem. Phys. 154, 171103.
Yuval Scher; Shlomi Reuveni (2021). Unified approach to gated reactions on networks. Phys. Rev. Lett. 127, 018301. [YouTube Talk ]
Asaf Miron; Shlomi Reuveni (2021). Diffusion with local resetting and exclusion. Phys. Rev. Research 3, L012023.
Iddo Eliazar; Shlomi Reuveni (2021). Tail-behavior roadmap for sharp restart. J. Phys. A: Math. Theor. 54 125001.
Arnab Pal; Shlomi Reuveni; Saar Rahav (2021). Thermodynamic uncertainty relation for systems with unidirectional transitions. Phys. Rev. Research 3, 013273.
Sarah Kostinski; Shlomi Reuveni (2021). Growth-laws and invariants from ribosome biogenesis in lower Eukarya. Phys. Rev. Research 3, 013020.

2020

Arnab Pal; Łukasz Kuśmierz; Shlomi Reuveni (2020). Search with home returns provides advantage under high uncertainty. Phys. Rev. Research 2 (4), 043174.
Iddo Eliazar; Shlomi Reuveni (2020). Mean-performance of sharp restart I: statistical roadmap. J. Phys. A: Math. Theor. 53 405004.
Ofir Tal-Friedman; Arnab Pal; Amandeep Sekhon; Shlomi Reuveni; Yael Roichman (2020). Experimental realization of diffusion with stochastic resetting. J. Phys. Chem. Lett. 11, 7350. [Yet Coverage]
Sarah Kostinski; Shlomi Reuveni (2020). Ribosome composition maximizes cellular growth rates in E. coli. Phys. Rev. Lett. 125, 028103. [Viewpoint in Physics: Speed Limit for Cell Growth]
Somrita Ray; Shlomi Reuveni (2020). Diffusion with resetting in a logarithmic potential. J. Chem. Phys. 152, 234110.
Yuval Scher; Shlomi Reuveni; Yoram Cohen (2020). Constant gradient FEXSY: a time-efficient method for measuring exchange. J. Magn. Reson., 311, 106667.

2019

Arnab Pal; Łukasz Kuśmierz; Shlomi Reuveni (2019). Invariants of motion with stochastic resetting and space-time coupled returns. New J. Phys. 21, 113024.
Arnab Pal; Łukasz Kuśmierz; Shlomi Reuveni (2019). Time-dependent density of diffusion with stochastic resetting is invariant to return speed. Phys. Rev. E 100, 040101(R).
Ofek Lauber Bonomo; Shlomi Reuveni (2019). Occupancy correlations in the asymmetric simple inclusion process. Phys. Rev. E 100, 042109.
Elizabeth A. Libby; Shlomi Reuveni; Jonathan Dworkin (2019). Multisite phosphorylation drives phenotypic variation in (p)ppGpp synthetase-dependent antibiotic tolerance. Nat. Commun., 10, 5133.
Iddo Eliazar; Ralf Metzler; Shlomi Reuveni (2019). Gumbel central limit theorem for max-min and min-max. Phys. Rev. E 100, 020104(R).
Iddo Eliazar; Ralf Metzler; Shlomi Reuveni (2019). Poisson-process limit-laws yield Gumbel max-min and min-max. Phys. Rev. E 100, 022129.
Ella Borberg; Marina Zverzhinetsky; Adva Krivitsky; Alon Kosloff; Omri Heifler; Gal Degabli; Hagit Peretz Soroka; Ronit Satchi-Fainaro; Larisa Burstein; Shiomi Reuveni; Haim Diamant; Vadim Krivitsky; Fernando Patolsky (2019). Light-controlled selective collection-and-release of biomolecules by an on-chip nanostructured device. Nano Lett. 19, 9, 5868.
Arnab Pal; Rakesh Chatterjee; Shlomi Reuveni; Anupam Kundu (2019). Local time of diffusion with stochastic resetting. J. Phys. A. 52, 264002.
Somrita Ray; Debasish Mondal; Shlomi Reuveni (2019). Péclet number governs transition to acceleratory restart in drift-diffusion. J. Phys. A. 52, 255002.
Arnab Pal; Iddo Eliazar; Shlomi Reuveni (2019). First passage under restart with branching. Phys. Rev. Lett. 122, 020602.

2018

Tal Robin; Shlomi Reuveni; Michael Urbakh (2018). Single-molecule theory of enzymatic inhibition. Nat. Commun. 9(1), 779.

2017

Shlomi Reuveni; Måns Ehrenberg; Johan Paulsson (2017). Ribosomes are optimized for autocatalytic production. Nature 547 (7663), 293.
Arnab Pal; Shlomi Reuveni (2017). First passage under restart. Phys. Rev. Lett. 118, 030603.

2016

Shlomi Reuveni (2016). Optimal stochastic restart renders fluctuations in first passage times universal. Phys. Rev. Lett. 116, 170601.

2015

Tal Robin; Shlomi Reuveni; Michael Urbakh (2015). Michaelis-Menten reaction scheme as a unified approach towards the optimal restart problem. Phys. Rev. E 92, 060101(R).

2014

Shlomi Reuveni; Michael Urbakh; Joseph Klafter (2014). Role of substrate unbinding in Michaelis–Menten enzymatic reactions. Proc. Natl. Acad. Sci. 111 (12), 4391.
Shlomi Reuveni (2014). Catalan's trapezoids. Probab. Eng. Inf. Sci., 28 (03), 353.
Shlomi Reuveni; Ori Hirschberg; Iddo Eliazar; Uri Yechiali (2014). Occupation probabilities and fluctuations in the asymmetric simple inclusion process. Phys. Rev. E 89, 042109.

2012

Shlomi Reuveni; Iddo Eliazar; Uri Yechiali (2012). Limit laws for the asymmetric inclusion process. Phys. Rev. E 86, 061133.
Shlomi Reuveni; Iddo Eliazar; Uri Yechiali (2012). Asymmetric inclusion process as a showcase of complexity. Phys. Rev. Lett. 109, 020603.
Shlomi Reuveni; Joseph Klafter; Rony Granek (2012). Dynamic structure factor of vibrating fractals: proteins as a case study. Phys. Rev. E 85, 011906.
Shlomi Reuveni; Joseph Klafter; Rony Granek (2012). Dynamic structure factor of vibrating fractals. Phys. Rev. Lett. 108, 068101.

2011

Shlomi Reuveni; Iddo Eliazar; Uri Yechiali (2011). Asymmetric inclusion process, Phys. Rev. E 84, 041101.
Shlomi Reuveni; Isaac Meilijson; Martin Kupiec; Eytan Ruppin; Tamir Tuller (2011). Genome-scale analysis of translation elongation with a ribosome flow model. PLOS Comput. Biol. 7(9).

2010

Shlomi Reuveni; Rony Granek; Joseph Klafter (2010). General mapping between random walks and thermal vibrations in elastic networks: fractal networks as a case study. Phys. Rev. E 82, 041132.
Shlomi Reuveni; Rony Granek; Joseph Klafter (2010). Anomalies in the vibrational dynamics of proteins are a consequence of fractal like structure. Proc. Natl. Acad. Sci. 107 (31), 13696.
Shlomi Reuveni; Rony Granek; Joseph Klafter (2010). Vibrational shortcut to the mean-first-passage-time problem. Phys. Rev. E 81, 040103(R).

2009

Marina de Leeuw; Shlomi Reuveni; Joseph Klafter; Rony Granek (2009). Coexistence of flexibility and stability of proteins: an equation of state. PLOS ONE 4(10).

2008

Shlomi Reuveni; Rony Granek; Joseph Klafter (2008). Proteins: coexistence of stability and flexibility. Phys. Rev. Lett. 100, 208101.

DISSERTATIONS

Shlomi Reuveni, Tandem stochastic systems: the asymmetric simple inclusion process, Ph.D. Thesis, School of Mathematical Sciences, Tel Aviv University, (2014).
Shlomi Reuveni, The fractal-like nature of proteins: foundations, applications and ramifications, Ph.D. Thesis, School of Chemistry, Tel Aviv University, (2013).
Shlomi Reuveni, Proteins: unraveling universality in a realm of specificity, M.Sc. Thesis, School of Chemistry, Tel Aviv University, (2007).

LIST OF PUBLICATIONS

Loss of percolation transition for a pushy random walker

2025

​

​

2023

​

​2024​​

​

2022

​

​

2021

​

​

2020

​

Yuval Scher; Shlomi Reuveni; Yoram Cohen (2020). Constant gradient FEXSY: a time-efficient method for measuring exchange. J. Magn. Reson., 311, 106667.

​

2019

​

Arnab Pal; Łukasz Kuśmierz; Shlomi Reuveni (2019). Invariants of motion with stochastic resetting and space-time coupled returns. New J. Phys. 21, 113024.

Arnab Pal; Łukasz Kuśmierz; Shlomi Reuveni (2019). Time-dependent density of diffusion with stochastic resetting is invariant to return speed. Phys. Rev. E 100, 040101(R).

Ofek Lauber Bonomo; Shlomi Reuveni (2019). Occupancy correlations in the asymmetric simple inclusion process. Phys. Rev. E 100, 042109.

Elizabeth A. Libby; Shlomi Reuveni; Jonathan Dworkin (2019). Multisite phosphorylation drives phenotypic variation in (p)ppGpp synthetase-dependent antibiotic tolerance. Nat. Commun., 10, 5133.

Iddo Eliazar; Ralf Metzler; Shlomi Reuveni (2019). Gumbel central limit theorem for max-min and min-max. Phys. Rev. E 100, 020104(R).

Iddo Eliazar; Ralf Metzler; Shlomi Reuveni (2019). Poisson-process limit-laws yield Gumbel max-min and min-max. Phys. Rev. E 100, 022129.

Arnab Pal; Rakesh Chatterjee; Shlomi Reuveni; Anupam Kundu (2019). Local time of diffusion with stochastic resetting. J. Phys. A. 52, 264002.

Somrita Ray; Debasish Mondal; Shlomi Reuveni (2019). Péclet number governs transition to acceleratory restart in drift-diffusion. J. Phys. A. 52, 255002.

Arnab Pal; Iddo Eliazar; Shlomi Reuveni (2019). First passage under restart with branching. Phys. Rev. Lett. 122, 020602.

​

2018

​

Tal Robin; Shlomi Reuveni; Michael Urbakh (2018). Single-molecule theory of enzymatic inhibition. Nat. Commun. 9(1), 779.

​

2017

​

Shlomi Reuveni; Måns Ehrenberg; Johan Paulsson (2017). Ribosomes are optimized for autocatalytic production. Nature 547 (7663), 293.

Arnab Pal; Shlomi Reuveni (2017). First passage under restart. Phys. Rev. Lett. 118, 030603.

​

2016

​

Shlomi Reuveni (2016). Optimal stochastic restart renders fluctuations in first passage times universal. Phys. Rev. Lett. 116, 170601.

​

2015

​

Tal Robin; Shlomi Reuveni; Michael Urbakh (2015). Michaelis-Menten reaction scheme as a unified approach towards the optimal restart problem. Phys. Rev. E 92, 060101(R).

​

2014

​

Shlomi Reuveni; Michael Urbakh; Joseph Klafter (2014). Role of substrate unbinding in Michaelis–Menten enzymatic reactions. Proc. Natl. Acad. Sci. 111 (12), 4391.

Shlomi Reuveni (2014). Catalan's trapezoids. Probab. Eng. Inf. Sci., 28 (03), 353.

Shlomi Reuveni; Ori Hirschberg; Iddo Eliazar; Uri Yechiali (2014). Occupation probabilities and fluctuations in the asymmetric simple inclusion process. Phys. Rev. E 89, 042109.

​

2012

​

Shlomi Reuveni; Iddo Eliazar; Uri Yechiali (2012). Limit laws for the asymmetric inclusion process. Phys. Rev. E 86, 061133.

Shlomi Reuveni; Iddo Eliazar; Uri Yechiali (2012). Asymmetric inclusion process as a showcase of complexity. Phys. Rev. Lett. 109, 020603.

Shlomi Reuveni; Joseph Klafter; Rony Granek (2012). Dynamic structure factor of vibrating fractals: proteins as a case study. Phys. Rev. E 85, 011906.

Shlomi Reuveni; Joseph Klafter; Rony Granek (2012). Dynamic structure factor of vibrating fractals. Phys. Rev. Lett. 108, 068101.

2011

​

Shlomi Reuveni; Iddo Eliazar; Uri Yechiali (2011). Asymmetric inclusion process, Phys. Rev. E 84, 041101.

Shlomi Reuveni; Isaac Meilijson; Martin Kupiec; Eytan Ruppin; Tamir Tuller (2011). Genome-scale analysis of translation elongation with a ribosome flow model. PLOS Comput. Biol. 7(9).

​

2010

​

Shlomi Reuveni; Rony Granek; Joseph Klafter (2010). General mapping between random walks and thermal vibrations in elastic networks: fractal networks as a case study. Phys. Rev. E 82, 041132.

Shlomi Reuveni; Rony Granek; Joseph Klafter (2010). Anomalies in the vibrational dynamics of proteins are a consequence of fractal like structure. Proc. Natl. Acad. Sci. 107 (31), 13696.

Shlomi Reuveni; Rony Granek; Joseph Klafter (2010). Vibrational shortcut to the mean-first-passage-time problem. Phys. Rev. E 81, 040103(R).

​

2009

​

Marina de Leeuw; Shlomi Reuveni; Joseph Klafter; Rony Granek (2009). Coexistence of flexibility and stability of proteins: an equation of state. PLOS ONE 4(10).

​

2008

​

Shlomi Reuveni; Rony Granek; Joseph Klafter (2008). Proteins: coexistence of stability and flexibility. Phys. Rev. Lett. 100, 208101.

​

DISSERTATIONS

Loss of percolation transition
for a pushy random walker

2024