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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

Group web pages

Contact

Erik Aurell
Erik Aurell professor

Google Scholar

Visiting Address

AlbaNova University Center
KTH Royal Institute of Technology
Roslagstullsbacken 11
SE-106 91 Stockholm, Sweden

Publications in the KTH DiVA Database 

[1]
E. Aurell, D. Machado Perez and R. Mulet, "A closure for the master equation starting from the dynamic cavity method," Journal of Physics A : Mathematical and Theoretical, vol. 56, no. 17, 2023.
[2]
V. Dichio, H.-L. Zeng and E. Aurell, "Statistical genetics in and out of quasi-linkage equilibrium," Reports on progress in physics (Print), vol. 86, no. 5, 2023.
[3]
E. Aurell, R. Mulet and J. Tuziemski, "Real-time dynamics in diluted quantum networks," Physical Review A: covering atomic, molecular, and optical physics and quantum information, vol. 105, no. 2, 2022.
[4]
E. Aurell, M. Eckstein and P. Horodecki, "Hawking radiation and the quantum marginal problem," Journal of Cosmology and Astroparticle Physics, no. 1, 2022.
[5]
H.-L. Zeng et al., "Inferring epistasis from genomic data with comparable mutation and outcrossing rate," Journal of Statistical Mechanics : Theory and Experiment, vol. 2021, no. 8, 2021.
[6]
G. Chiribella, E. Aurell and K. Zyczkowski, "Symmetries of quantum evolutions," Physical Review Research, vol. 3, no. 3, 2021.
[7]
E. Aurell, M. Eckstein and P. Horodecki, "Quantum Black Holes as Solvents," Foundations of physics, vol. 51, no. 2, 2021.
[8]
E. Rydving, E. Aurell and I. Pikovski, "Do Gedanken experiments compel quantization of gravity?," Physical Review D : covering particles, fields, gravitation, and cosmology, vol. 104, no. 8, 2021.
[9]
E. Aurell and J. Tuziemski, "Frohlich-coupled qubits interacting with fermionic baths," Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, vol. 102, no. 1, 2020.
[10]
H.-L. Zeng and E. Aurell, "Inferring genetic fitness from genomic data," Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, vol. 101, no. 5, 2020.
[11]
E. Aurell, R. Kawai and K. Goyal, "An operator derivation of the Feynman-Vernon theory, with applications to the generating function of bath energy changes and to an-harmonic baths," Journal of Physics A : Mathematical and Theoretical, vol. 53, no. 27, 2020.
[12]
E. Aurell, B. Donvil and K. Mallick, "Large deviations and fluctuation theorem for the quantum heat current in the spin-boson model," Physical review. E, vol. 101, no. 5, 2020.
[13]
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.
[14]
H.-L. Zeng et al., "Global analysis of more than 50,000 SARS-CoV-2 genomes reveals epistasis between eight viral genes," Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 49, pp. 31519-31526, 2020.
[15]
H.-L. Zeng and E. Aurell, "Inverse Ising techniques to infer underlying mechanisms from data," Chinese Physics B, vol. 29, no. 8, 2020.
[16]
C.-Y. Gao et al., "DCA for genome-wide epistasis analysis : the statistical genetics perspective," Physical Biology, vol. 16, no. 2, 2019.
[17]
E. Aurell and F. Montana, "Thermal power of heat flow through a qubit," Physical review. E, vol. 99, no. 4, 2019.
[18]
E. Aurell, "Characteristic functions of quantum heat with baths at different temperatures," Physical review. E, vol. 97, no. 6, 2018.
[19]
E. Aurell et al., "Exploring the diluted ferromagnetic p-spin model with a cavity master equation," Physical review. E, vol. 97, no. 5, 2018.
[20]
C.-Y. Gao, H.-J. Zhou and E. Aurell, "Correlation-compressed direct-coupling analysis," Physical review. E, vol. 98, no. 3, 2018.
[21]
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.
[22]
E. Aurell, "Unified picture of strong-coupling stochastic thermodynamics and time reversals," Physical review. E, vol. 97, no. 4, 2018.
[23]
E. Aurell et al., "Cavity master equation for the continuous time dynamics of discrete-spin models," Physical review. E, vol. 95, no. 5, 2017.
[24]
E. Aurell, "On Work and Heat in Time-Dependent Strong Coupling," Entropy, vol. 19, no. 11, 2017.
[25]
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.
[26]
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.
[27]
R. Marino, E. Aurell and R. Eichhorn, "Entropy production of a Brownian ellipsoid in the overdamped limit," Physical Review E. Statistical, Nonlinear, and Soft Matter Physics : Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, vol. 93, no. 012132, pp. 1-15, 2016.
[28]
E. Aurell et al., "Diffusion of a Brownian ellipsoid in a force field," Europhysics letters, vol. 114, no. 3, 2016.
[29]
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.
[30]
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.
[31]
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.
[32]
A. Maes et al., "Landscape of RNA polyadenylation in E. coli," Nucleic Acids Research, 2016.
[33]
G. Del Ferraro et al., "On one-step replica symmetry breaking in the Edwards-Anderson spin glass model," Journal of statistical physics, 2016.
[34]
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.
[35]
E. Aurell, "The Maximum Entropy Fallacy Redux?," PloS Computational Biology, vol. 12, no. 5, 2016.
[36]
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.
[37]
N. Innocenti et al., "Whole-genome mapping of 5′ RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis," RNA, 2015.
[38]
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.
[39]
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.
[40]
N. Innocenti et al., "An observation of circular RNAs in bacterial RNA-seq data.," (Manuscript).
[41]
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.
[42]
Y. Lan and E. Aurell, "The stochastic thermodynamics of a rotating Brownian particle in a gradient flow," Scientific Reports, vol. 5, 2015.
[43]
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.
[44]
S. Chatterjee et al., "SEK: Sparsity exploiting k-mer-based estimation of bacterial community composition," Bioinformatics, vol. 30, no. 17, pp. 2423-2431, 2014.
[45]
R. Eichhorn and E. Aurell, "Stochastic thermodynamics," Physica Scripta, vol. 89, no. 4, pp. 048001, 2014.
[46]
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.
[47]
C. Feinauer et al., "Improving Contact Prediction along Three Dimensions," PloS Computational Biology, vol. 10, no. 10, pp. e1003847, 2014.
[48]
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.
[49]
S. Bo et al., "Optimal stochastic transport in inhomogeneous thermal environments," Europhysics letters, vol. 103, no. 1, pp. 10010, 2013.
[50]
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.
[51]
H.-L. Zeng et al., "Maximum Likelihood Reconstruction for Ising Models with Asynchronous Updates," Physical Review Letters, vol. 110, no. 21, pp. 210601, 2013.
[52]
E. Aurell, "The physics of distributed information systems," Journal of Physics, Conference Series, vol. 473, no. 1, pp. 012017, 2013.
[53]
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.
[54]
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.
[55]
M. Vehkaperä et al., "Analysis of Sparse Representations Using Bi-Orthogonal Dictionaries," in Information Theory Workshop (ITW), 2012 IEEE, 2012, pp. 647-651.
[56]
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.
[57]
A. Celani et al., "Anomalous thermodynamics at the microscale," Physical Review Letters, vol. 109, no. 26, pp. 260603, 2012.
[58]
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.
[59]
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.
[60]
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.
[61]
E. Aurell and M. Ekeberg, "Inverse Ising Inference Using All the Data," Physical Review Letters, vol. 108, no. 9, pp. 090201, 2012.
[62]
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.
[63]
E. Aurell and H. Mahmoudi, "A message-passing scheme for non-equilibrium stationary states," JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, pp. P04014, 2011.
[64]
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.
[65]
H.-L. Zeng et al., "Network inference using asynchronously updated kinetic Ising model," Physical Review E, vol. 83, no. 4, pp. 041135, 2011.
[66]
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.
[67]
E. Aurell and H. Mahmoudi, "Three Lemmas on Dynamic Cavity Method," Communications in Theoretical Physics, vol. 56, no. 1, pp. 157-162, 2011.
[68]
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.
[69]
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.
[70]
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.
[71]
H. John et al., "Inferring network connectivity using kinetic Ising models," in BMC Neuroscience, 2010.
[72]
A. Göndör et al., "Window into the Complexities of Chromosome Interactomes," Cold Spring Harbor Symposia on Quantitative Biology, vol. 75, pp. 493-500, 2010.
[73]
V. Rathi et al., "Bounds on Threshold of Regular Random k-SAT," Lecture Notes in Computer Science, vol. 6175, pp. 264-277, 2010.
[74]
E. Aurell and R. Pfitzner, "Gaussian belief with dynamic data and in dynamic network," Europhysics letters, vol. 87, no. 6, 2009.
[75]
M. Werner and E. Aurell, "A computational study of lambda-lac mutants," PHYS BIOL, vol. 6, no. 4, 2009.
[76]
Y. Roudi, E. Aurell and J. A. Hertz, "Statistical physics of pairwise probability models," Frontiers in Computational Neuroscience, vol. 3, pp. 22, 2009.
[77]
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.
[78]
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.
[79]
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.
[80]
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.
[81]
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.
[82]
M. Werner and E. Aurell, "A computational systems biology study of the lambda-lac mutants," (Manuscript).
[83]
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.
[84]
M. Werner et al., "Epstein-Barr virus latency switch in human B-cells : a physico-chemical model," BMC Systems Biology, vol. 1, 2007.
[85]
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.
[86]
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.
[87]
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.
[88]
U. Frisch, J. Bec and E. Aurell, ""Locally homogeneous turbulence" : Is it an inconsistent framework?," Physics of fluids, vol. 17, no. 8, 2005.
[89]
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.
[90]
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.
[91]
E. Aurell et al., "Non-linear regime of the gravitational instability," in Proceedings of Frontiers of Nonlinear Physics, 2005, pp. 619-629.
[92]
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.
[93]
S. Krishnamurthy et al., "A statistical theory of Chord under churn," Lecture Notes in Computer Science, vol. 3640, pp. 93-103, 2005.
[94]
A. Ameur et al., "Global gene expression analysis by combinatorial optimization," In Silico Biology, vol. 4, no. 2, pp. 225-241, 2004.
[95]
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.
[96]
G. Lacorata et al., "Evidence for a k(-5/3) spectrum from the EOLE Lagrangian balloons in the low stratosphere," Journal of the Atmospheric Sciences, vol. 61, no. 23, pp. 2936-2942, 2004.
[97]
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.
[98]
S. El-Ansary et al., "An Analytical Study of Consistency and Performance of DHTs under Churn," , SICS Technical Report, T2004:12, 2004.
[99]
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.
[100]
E. Aurell et al., "The inner structure of Zeldovich pancakes," Physica D : Non-linear phenomena, vol. 186, no. 04-mar, pp. 171-184, 2003.
[101]
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.
[102]
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.
[103]
E. Aurell and K. Sneppen, "Epigenetics as a first exit problem," Physical Review Letters, vol. 88, no. 4, 2002.
[104]
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.
[105]
A. K. Kozlov et al., "Modeling postural control in the lamprey," Biological Cybernetics, vol. 84, no. 5, pp. 323-330, 2001.
[106]
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.
[107]
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.
[108]
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.
[109]
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.
[110]
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.
[111]
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, pp. 1373-1378.
[112]
P. Fagerstedt et al., "computational modeling of turning behavior in lamprey," in Soc. for Neurosci, 2000.
[113]
A. K. Kozlov et al., "Modeling control of roll-plane body orientation in lamprey," Neurocomputing, vol. 32, pp. 871-877, 2000.
[114]
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.
[115]
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.
[116]
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.
[117]
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.
[118]
E. Aurell and G. Del Ferraro, "A Cavity Master Equation for the continuous time dynamics of discrete spins models," (Manuscript).
[119]
S. El-Ansary et al., "Analytical study of consistency and performance of DHTs under churn," (Manuscript).
[120]
S. El-Ansary, E. Aurell and S. Haridi, "Physics-inspired performance evaluation of DHTs," (Manuscript).
Full list in the KTH publications portal