# Theoretical Biological Physics

The Group of Theoretical Biological Physics is led by Professor Erik Aurell.

## Research

Research projects within the group:

- Quantum Thermodynamics and heat in open quantum systems
- Non-equilibrium physics on the meso-scale
- Inverse statistical mechanics

## Contact

## Visiting Address

AlbaNova University Center

KTH Royal Institute of Technology

Roslagstullsbacken 11

SE-106 91 Stockholm, Sweden

## Publications in the KTH DiVA Database

[1]

C. Lacoux

*et al.*, "Dynamic insights on transcription initiation and RNA processing during bacterial adaptation,"*RNA : A publication of the RNA Society*, vol. 26, no. 4, pp. 382-395, 2020.
[2]

C.-Y. Gao

*et al.*, "DCA for genome-wide epistasis analysis : the statistical genetics perspective,"*Physical Biology*, vol. 16, no. 2, 2019.
[3]

E. Aurell and F. Montana,
"Thermal power of heat flow through a qubit,"

*Physical review. E*, vol. 99, no. 4, 2019.
[4]

E. Aurell,
"Global Estimates of Errors in Quantum Computation by the Feynman-Vernon Formalism,"

*Journal of statistical physics*, vol. 171, no. 5, pp. 745-767, 2018.
[5]

C.-Y. Gao, H.-J. Zhou and E. Aurell,
"Correlation-compressed direct-coupling analysis,"

*Physical review. E*, vol. 98, no. 3, 2018.
[6]

E. Aurell,
"Characteristic functions of quantum heat with baths at different temperatures,"

*Physical review. E*, vol. 97, no. 6, 2018.
[7]

E. Aurell

*et al.*, "Exploring the diluted ferromagnetic p-spin model with a cavity master equation,"*Physical review. E*, vol. 97, no. 5, 2018.
[8]

E. Aurell,
"Unified picture of strong-coupling stochastic thermodynamics and time reversals,"

*Physical review. E*, vol. 97, no. 4, 2018.
[9]

M. J. Skwark

*et al.*, "Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis,"*PLoS Genetics*, vol. 13, no. 2, 2017.
[10]

E. Aurell and S. Bo,
"Steady diffusion in a drift field : A comparison of large-deviation techniques and multiple-scale analysis,"

*Physical review. E*, vol. 96, no. 3, 2017.
[11]

E. Aurell and G. Del Ferraro,
"Causal analysis, Correlation-Response, and Dynamic cavity,"
in

*International Meeting on High-Dimensional Data-Driven Science (HD3-2015)*, 2016.
[12]

E. Aurell

*et al.*, "Diffusion of a Brownian ellipsoid in a force field,"*Europhysics letters*, vol. 114, no. 3, 2016.
[13]

R. Marino and E. Aurell,
"Advective-diffusive motion on large scales from small-scale dynamics with an internal symmetry,"

*PHYSICAL REVIEW E*, vol. 93, no. 6, 2016.
[14]

Q. Li

*et al.*, "Dynamics inside the cancer cell attractor reveal cell heterogeneity, limits of stability, and escape,"*Proceedings of the National Academy of Sciences of the United States of America*, vol. 113, no. 10, pp. 2672-2677, 2016.
[15]

[16]

E. Aurell, N. Innocenti and H.-J. Zhou,
"The bulk and the tail of minimal absent words in genome sequences,"

*Physical Biology*, vol. 13, no. 2, 2016.
[17]

G. Del Ferraro

*et al.*, "On one-step replica symmetry breaking in the Edwards-Anderson spin glass model,"*Journal of statistical physics*, 2016.
[18]

[19]

R. Marino, E. Aurell and R. Eichhorn,
"Entropy production of a Brownian ellipsoid in the overdamped limit,"

*PHYSICAL REVIEW E*, vol. 93, no. 012132, pp. 1-15, 2016.
[20]

[21]

E. Aurell, J. Zakrzewski and K. Zyczkowski,
"Time reversals of irreversible quantum maps,"

*Journal of Physics A : Mathematical and Theoretical*, vol. 48, no. 38, 2015.
[22]

Y. Lan and E. Aurell,
"The stochastic thermodynamics of a rotating Brownian particle in a gradient flow,"

*Scientific Reports*, vol. 5, 2015.
[23]

R. Lemoy, M. Alava and E. Aurell,
"Local search methods based on variable focusing for random K-satisfiability,"

*Physical Review E. Statistical, Nonlinear, and Soft Matter Physics*, vol. 91, no. 1, pp. 013305, 2015.
[24]

N. Innocenti

*et al.*, "Whole-genome mapping of 5′ RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis,"*RNA*, 2015.
[25]

N. Innocenti, F. Repoila and E. Aurell,
"Detection and quantitative estimation of spurious double stranded DNA formation during reverse transcription in bateria using tagRNA-seq,"

*RNA Biology*, 2015.
[26]

G. Del Ferraro and E. Aurell,
"Dynamic message-passing approach for kinetic spin models with reversible dynamics,"

*Physical Review E. Statistical, Nonlinear, and Soft Matter Physics*, vol. 92, no. 1, 2015.
[27]

E. Aurell and R. Eichhorn,
"On the von Neumann entropy of a bath linearly coupled to a driven quantum system,"

*New Journal of Physics*, vol. 17, 2015.
[28]

G. Del Ferraro and E. Aurell,
"Perturbative large deviation analysis of non-equilibrium dynamics,"

*Journal of the Physical Society of Japan*, vol. 83, no. 8, 2014.
[29]

R. Eichhorn and E. Aurell,
"Stochastic thermodynamics,"

*Physica Scripta*, vol. 89, no. 4, pp. 048001, 2014.
[30]

C. Feinauer

*et al.*, "Improving Contact Prediction along Three Dimensions,"*PloS Computational Biology*, vol. 10, no. 10, pp. e1003847, 2014.
[31]

M. Ekeberg, T. Hartonen and E. Aurell,
"Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences,"

*Journal of Computational Physics*, vol. 276, pp. 341-356, 2014.
[32]

S. Chatterjee

*et al.*, "SEK: Sparsity exploiting k-mer-based estimation of bacterial community composition,"*Bioinformatics*, vol. 30, no. 17, pp. 2423-2431, 2014.
[33]

E. Aurell,
"The physics of distributed information systems,"

*Journal of Physics, Conference Series*, vol. 473, no. 1, pp. 012017, 2013.
[34]

S. Bo

*et al.*, "Optimal stochastic transport in inhomogeneous thermal environments,"*Europhysics letters*, vol. 103, no. 1, pp. 10010, 2013.
[35]

N. Innocenti and E. Aurell,
"Lognormality and oscillations in the coverage of high-throughput transcriptomic data towards gene ends,"

*Journal of Statistical Mechanics : Theory and Experiment*, vol. 2013, no. 10, pp. P10013, 2013.
[36]

L.-L. Wu

*et al.*, "Witness of unsatisfiability for a random 3-satisfiability formula,"*Physical Review E. Statistical, Nonlinear, and Soft Matter Physics*, vol. 87, no. 5, pp. 052807, 2013.
[37]

M. Ekeberg

*et al.*, "Improved contact prediction in proteins : Using pseudolikelihoods to infer Potts models,"*Physical Review E. Statistical, Nonlinear, and Soft Matter Physics*, vol. 87, no. 1, pp. 012707, 2013.
[38]

H.-L. Zeng

*et al.*, "Maximum Likelihood Reconstruction for Ising Models with Asynchronous Updates,"*Physical Review Letters*, vol. 110, no. 21, pp. 210601, 2013.
[39]

M. Vehkaperä, Y. Kabashima and E. Aurell,
"Replica analysis of sparse l1-reconstruction with concatenated L-orthogonal basis,"
in

*Statistical Mechanics of Unsatisfiability and Glasses*, 2012.
[40]

M. Vehkaperä

*et al.*, "Analysis of Sparse Representations Using Bi-Orthogonal Dictionaries," in*Information Theory Workshop (ITW), 2012 IEEE*, 2012, pp. 647-651.
[41]

A. Celani

*et al.*, "Anomalous thermodynamics at the microscale,"*Physical Review Letters*, vol. 109, no. 26, pp. 260603, 2012.
[42]

E. Aurell

*et al.*, "Refined Second Law of Thermodynamics for Fast Random Processes,"*Journal of statistical physics*, vol. 147, no. 3, pp. 487-505, 2012.
[43]

E. Aurell and H. Mahmoudi,
"Dynamic mean-field and cavity methods for diluted Ising systems,"

*Physical Review E. Statistical, Nonlinear, and Soft Matter Physics*, vol. 85, no. 3, pp. 031119, 2012.
[44]

E. Aurell and M. Ekeberg,
"Inverse Ising Inference Using All the Data,"

*Physical Review Letters*, vol. 108, no. 9, pp. 090201, 2012.
[45]

E. Aurell, C. Mejia-Monasterio and P. Muratore-Ginanneschi,
"Boundary layers in stochastic thermodynamics,"

*Physical Review E. Statistical, Nonlinear, and Soft Matter Physics*, vol. 85, no. 2, pp. 020103, 2012.
[46]

J. X. Zhou

*et al.*, "Quasi-potential landscape in complex multi-stable systems,"*Journal of the Royal Society Interface*, vol. 9, no. 77, pp. 3539-3553, 2012.
[47]

E. Aurell and H. Mahmoudi,
"A message-passing scheme for non-equilibrium stationary states,"

*JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT*, pp. P04014, 2011.
[48]

H.-L. Zeng

*et al.*, "Network inference using asynchronously updated kinetic Ising model,"*Physical Review E*, vol. 83, no. 4, pp. 041135, 2011.
[49]

E. Aurell, C. Mejia-Monasterio and P. Muratore-Ginanneschi,
"Optimal Protocols and Optimal Transport in Stochastic Thermodynamics,"

*Physical Review Letters*, vol. 106, no. 25, pp. 250601, 2011.
[50]

A. Fouquier d'Hérouel

*et al.*, "A simple and efficient method to search for selected primary transcripts : non-coding and antisense RNAs in the human pathogen Enterococcus faecalis,"*Nucleic Acids Research*, vol. 39, no. 7, pp. E46, 2011.
[51]

E. Aurell and H. Mahmoudi,
"Three Lemmas on Dynamic Cavity Method,"

*Communications in Theoretical Physics*, vol. 56, no. 1, pp. 157-162, 2011.
[52]

V. Rathi

*et al.*, "Bounds on thresholds related to maximum satisfiability of regular random formulas," in*6th International Symposium on Turbo Codes and Iterative Information Processing (ISTC)*, 2010, pp. 107-111.
[53]

H. John

*et al.*, "Inferring network connectivity using kinetic Ising models," in*BMC Neuroscience*, 2010.
[54]

S. Krishnamurthy

*et al.*, "Brief Announcement: The Accuracy of Tree-based Counting in Dynamic Networks," in*PODC 2010 : PROCEEDINGS OF THE 2010 ACM SYMPOSIUM ON PRINCIPLES OF DISTRIBUTED COMPUTING*, 2010, pp. 291-292.
[55]

V. Rathi

*et al.*, "Bounds on Threshold of Regular Random k-SAT,"*Lecture Notes in Computer Science*, vol. 6175, pp. 264-277, 2010.
[56]

A. Göndör

*et al.*, "Window into the Complexities of Chromosome Interactomes,"*Cold Spring Harbor Symposia on Quantitative Biology*, vol. 75, pp. 493-500, 2010.
[57]

E. Aurell, C. Ollion and Y. Roudi,
"Dynamics and performance of susceptibility propagation on synthetic data,"

*European Physical Journal B : Condensed Matter Physics*, vol. 77, no. 4, pp. 587-595, 2010.
[58]

Y. Roudi, E. Aurell and J. A. Hertz,
"Statistical physics of pairwise probability models,"

*FRONTIERS IN COMPUTATIONAL NEUROSCIENCE*, vol. 3, pp. 22, 2009.
[59]

E. Aurell and R. Pfitzner,
"Gaussian belief with dynamic data and in dynamic network,"

*Europhysics letters*, vol. 87, no. 6, 2009.
[60]

M. Werner and E. Aurell,
"A computational study of lambda-lac mutants,"

*PHYS BIOL*, vol. 6, no. 4, 2009.
[61]

M. Alava

*et al.*, "Circumspect descent prevails in solving random constraint satisfaction problems,"*Proceedings of the National Academy of Sciences of the United States of America*, vol. 105, no. 40, pp. 15253-15257, 2008.
[62]

S. Krishnamurthy

*et al.*, "Comparing maintenance strategies for overlays," in*Proceedings of the 16th Euromicro Conference on Parallel, Distributed and Network-Based Processing, PDP 2008*, 2008, pp. 473-482.
[63]

S. Krishnamurthy

*et al.*, "An analytical study of a structured overlay in the presence of dynamic membership,"*IEEE/ACM Transactions on Networking*, vol. 16, no. 4, pp. 814-825, 2008.
[64]

M. Werner and E. Aurell,
"A computational systems biology study of the lambda-lac mutants,"
(Manuscript).

[65]

J. Ardelius, E. Aurell and S. Krishnamurthy,
"Clustering of solutions in hard satisfiability problems,"

*Journal of Statistical Mechanics: Theory and Experiment*, no. 10, pp. P10012, 2007.
[66]

M. Werner, L. Zhu and E. Aurell,
"Cooperative action in eukaryotic gene regulation : Physical properties of a viral example,"

*Physical Review E. Statistical, Nonlinear, and Soft Matter Physics : Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics*, vol. 76, no. 6, 2007.
[67]

E. Aurell

*et al.*, "Transcription factor concentrations versus binding site affinities in the yeast S. cerevisiae,"*Physical Biology*, vol. 4, no. 2, pp. 134-143, 2007.
[68]

M. Werner

*et al.*, "Epstein-Barr virus latency switch in human B-cells : a physico-chemical model,"*BMC SYST BIOL*, vol. 1, 2007.
[69]

J. Ardelius and E. Aurell,
"Behavior of heuristics on large and hard satisfiability problems,"

*Physical Review E. Statistical, Nonlinear, and Soft Matter Physics : Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics*, vol. 74, no. 3, pp. 037702, 2006.
[70]

E. Aurell and P. Muratore-Ginnaneschi,
"Optimal hedging of derivatives with transaction costs,"

*International Journal of Theoretical and Applied Finance*, vol. 9, no. 7, pp. 1051-1069, 2006.
[71]

A. Noullez

*et al.*, "Global picture of self-similar and non-self-similar decay in Burgers turbulence,"*Physical Review E*, vol. 71, no. 5, 2005.
[72]

U. Frisch, J. Bec and E. Aurell,
""Locally homogeneous turbulence" : Is it an inconsistent framework?,"

*Physics of fluids*, vol. 17, no. 8, 2005.
[73]

E. Aurell and S. El-Ansary,
"A physics-style approach to scalability of distributed systems,"

*Lecture Notes in Computer Science*, vol. 3267, pp. 266-272, 2005.
[74]

S. Krishnamurthy

*et al.*, "A statistical theory of Chord under churn,"*Lecture Notes in Computer Science*, vol. 3640, pp. 93-103, 2005.
[75]

S. El-Ansary, E. Aurell and S. Haridi,
"A physics-inspired performance evaluation of a structured peer-to-peer overlay network,"
in

*IASTED International Conference on Parallel and Distributed Computing and Networks, as part of the 23rd IASTED International Multi-Conference on Applied Informatics : Innsbruck: 15 February 2005 through 17 February 2005*, 2005, pp. 116-122.
[76]

E. Aurell, U. Gordon and S. Kirkpatrick,
"Comparing Beliefs, Surveys and Random Walks,"
in

*Advances in Neural Information Processing Systems 17 : proceedings of the 2004 conference*, 2005.
[77]

E. Aurell

*et al.*, "Non-linear regime of the gravitational instability," in*Proceedings of Frontiers of Nonlinear Physics*, 2005, pp. 619-629.
[78]

S. El-Ansary

*et al.*, "An Analytical Study of Consistency and Performance of DHTs under Churn," , SICS Technical Report, T2004:12, 2004.
[79]

S. El-Ansary

*et al.*, "Experience with a physics-style approach for the study of self properties in structured overlay networks," in*SELF-STAR : International Workshop on Self-* Properties in Complex Information Systems, May 2004, Bertinoro, Italy*, 2004.
[80]

E. Aurell and P. Muratore-Ginnaneschi,
"Growth-Optimal Strategies with Quadratic Friction Over Finite-Time Investment Horizons,"

*International Journal of Theoretical and Applied Finance*, vol. 7, no. 5, pp. 645-657, 2004.
[81]

A. Ameur

*et al.*, "Global gene expression analysis by combinatorial optimization,"*In Silico Biology*, vol. 4, no. 2, pp. 225-241, 2004.
[82]

G. Lacorata

*et al.*, "Evidence for a k(-5/3) spectrum from the EOLE Lagrangian balloons in the low stratosphere,"*Journal of Atmospheric Sciences*, vol. 61, no. 23, pp. 2936-2942, 2004.
[83]

A. Noullez, D. Fanelli and E. Aurell,
"A heap-based algorithm for the study of one-dimensional particle systems,"

*Journal of Computational Physics*, vol. 186, no. 2, pp. 697-703, 2003.
[84]

E. Aurell

*et al.*, "The inner structure of Zeldovich pancakes,"*Physica D : Non-linear phenomena*, vol. 186, no. 04-mar, pp. 171-184, 2003.
[85]

E. Aurell

*et al.*, "Stability puzzles in phage lambda,"*Physical Review E. Statistical, Nonlinear, and Soft Matter Physics : Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics*, vol. 65, no. 5, 2002.
[86]

E. Aurell and K. Sneppen,
"Epigenetics as a first exit problem,"

*Physical Review Letters*, vol. 88, no. 4, 2002.
[87]

A. K. Kozlov

*et al.*, "Mechanisms for lateral turns in lamprey in response to descending unilateral commands : a modeling study,"*Biological Cybernetics*, vol. 86, no. 1, pp. 1-14, 2002.
[88]

D. Fanelli and E. Aurell,
"Asymptotic behavior of a planar perturbation in a three dimensional expanding Universe,"

*Astronomy and Astrophysics*, vol. 395, no. 2, pp. 399-408, 2002.
[89]

A. K. Kozlov

*et al.*, "Turning behavior in lamprey in response to descending unilateral commands : Experiments and modeling,"*Neurocomputing*, vol. 38, pp. 1373-1378, 2001.
[90]

E. Aurell, D. Fanelli and P. Muratore-Ginanneschi,
"On the dynamics of a self-gravitating medium with random and non-random initial conditions,"

*Physica D : Non-linear phenomena*, vol. 148, no. 04-mar, pp. 272-288, 2001.
[91]

G. Lacorata, E. Aurell and A. Vulpiani,
"Drifter dispersion in the Adriatic Sea : Lagrangian data and chaotic model,"

*Annales Geophysicae*, vol. 19, no. 1, pp. 121-129, 2001.
[92]

A. K. Kozlov

*et al.*, "Modeling postural control in the lamprey,"*Biological Cybernetics*, vol. 84, no. 5, pp. 323-330, 2001.
[93]

A. Kozlov

*et al.*, "Modeling of substance P and 5-HT induced synaptic plasticity in the lamprey spinal CPG - consequences for network pattern generation,"*Journal of Computational Neuroscience*, vol. 11, no. 2, pp. 183-200, 2001.
[94]

A. Kozlov

*et al.*, "Modeling of substance P and 5-HT induced synaptic plasticity in the lamprey spinal CPG : Consequences for network pattern generation,"*Journal of Computational Neuroscience*, vol. 11, no. 2, pp. 183-200, 2001.
[95]

A. K. Kozlov

*et al.*, "Modeling control of roll-plane body orientation in lamprey,"*Neurocomputing*, vol. 32, pp. 871-877, 2000.
[96]

E. Aurell

*et al.*, "Growth optimal investment and pricing of derivatives,"*Physica A : Statistical Mechanics and its Applications*, vol. 280, no. 04-mar, pp. 505-521, 2000.
[97]

P. Fagerstedt

*et al.*, "computational modeling of turning behavior in lamprey," in*Soc. for Neurosci*, 2000.
[98]

A. Kozlov

*et al.*, "Modeling of plasticity of the synaptic connections in the lamprey spinal CPG - consequences for network behavior,"*Neurocomputing*, vol. 32, pp. 441-446, 2000.
[99]

A. Kozlov

*et al.*, "Modeling of plasticity of the synaptic connections in the lamprey spinal CPG - consequences for network behavior,"*Neurocomputing*, vol. 32-33, pp. 441-446, 2000.
[100]

A. Kozlov

*et al.*, "Turning behavior in lamprey in response to descending unilateral commands: experiments and modeling," in*9th Annual Computational Neuroscience Meeting (CNS*00)*, 2000.
[101]

A. Kozlov

*et al.*, "Modeling of metaplasticity of the synaptic connections in the lamprey spinal CPG---consequences for network behavior," in*Computational Neuroscience Meeting*, 1999.
[102]

A. Kozlov

*et al.*, "Modeling control of body orientation in the lamprey," in*8th Annual Computational Neurosciences Meeting (CNS 99)*, 1999.
[103]

M. Ullström

*et al.*, "Activity-dependent modulation of adaptation produces a constant burst proportion in a model of the lamprey spinal locomotor generator.,"*Biological Cybernetics*, vol. 79, no. 1, pp. 1-14, 1998.
[104]

E. Aurell and G. Del Ferraro,
"A Cavity Master Equation for the continuous time dynamics of discrete spins models,"
(Manuscript).

[105]

S. El-Ansary

*et al.*, "Analytical study of consistency and performance of DHTs under churn," (Manuscript).
[106]

S. El-Ansary, E. Aurell and S. Haridi,
"Physics-inspired performance evaluation of DHTs,"
(Manuscript).