Profile
Senior Lecturer.
Deciphering the life of a cell with physics. Loves crafting new ideas.
Publications
Nyberg, Markus; Ambjörnsson, Tobias; Stenberg, Per; Lizana, Ludvig Modeling protein target search in human chromosomes Journal Article Phys. Rev. Research, 3 , pp. 013055, 2021. @article{PhysRevResearch.3.013055, title = {Modeling protein target search in human chromosomes}, author = {Markus Nyberg and Tobias Ambjörnsson and Per Stenberg and Ludvig Lizana}, url = {https://link.aps.org/doi/10.1103/PhysRevResearch.3.013055}, doi = {10.1103/PhysRevResearch.3.013055}, year = {2021}, date = {2021-01-01}, journal = {Phys. Rev. Research}, volume = {3}, pages = {013055}, publisher = {American Physical Society}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lee, Sang Hoon; Kim, Yeonghoon; Lee, Sungmin; Durang, Xavier; Stenberg, Per; Jeon, Jae-Hyung; Lizana, Ludvig Mapping the spectrum of 3D communities in human chromosome conformation capture data Journal Article Scientific Reports, 9 , 2019. @article{Lee2018, title = {Mapping the spectrum of 3D communities in human chromosome conformation capture data}, author = {Sang Hoon Lee and Yeonghoon Kim and Sungmin Lee and Xavier Durang and Per Stenberg and Jae-Hyung Jeon and Ludvig Lizana}, doi = {https://doi.org/10.1038/s41598-019-42212-y}, year = {2019}, date = {2019-05-02}, journal = {Scientific Reports}, volume = {9}, abstract = {Several experiments show that the three dimensional (3D) organization of chromosomes affects genetic processes such as transcription and gene regulation. To better understand this connection, researchers developed the Hi-C method that is able to detect the pairwise physical contacts of all chromosomal loci. The Hi-C data shows that chromosomes are composed of 3D compartments that range over a variety of scales. However, it is challenging to systematically detect these cross-scale structures. Most studies have therefore designed methods for specific scales to study foremost topologically associated domains (TADs) and A/B compartments. To go beyond this limitation, we tailor a network community detection method that finds communities in compact fractal globule polymer systems. Our method allows us to continuously scan through all scales with a single resolution parameter. We found: (i) polymer segments belonging to the same 3D community do not have to be in consecutive order along the polymer chain. In other words, several TADs may belong to the same 3D community. (ii) CTCF proteins---a loop-stabilizing protein that is ascribed a big role in TAD formation---are correlated well with community borders only at one level of organization. (iii) TADs and A/B compartments are traditionally treated as two weakly related 3D structures and detected with different algorithms. With our method, we detect both by simply adjusting the resolution parameter. We therefore argue that they represent two specific levels of a continuous spectrum 3D communities, rather than seeing them as different structural entities.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Several experiments show that the three dimensional (3D) organization of chromosomes affects genetic processes such as transcription and gene regulation. To better understand this connection, researchers developed the Hi-C method that is able to detect the pairwise physical contacts of all chromosomal loci. The Hi-C data shows that chromosomes are composed of 3D compartments that range over a variety of scales. However, it is challenging to systematically detect these cross-scale structures. Most studies have therefore designed methods for specific scales to study foremost topologically associated domains (TADs) and A/B compartments. To go beyond this limitation, we tailor a network community detection method that finds communities in compact fractal globule polymer systems. Our method allows us to continuously scan through all scales with a single resolution parameter. We found: (i) polymer segments belonging to the same 3D community do not have to be in consecutive order along the polymer chain. In other words, several TADs may belong to the same 3D community. (ii) CTCF proteins---a loop-stabilizing protein that is ascribed a big role in TAD formation---are correlated well with community borders only at one level of organization. (iii) TADs and A/B compartments are traditionally treated as two weakly related 3D structures and detected with different algorithms. With our method, we detect both by simply adjusting the resolution parameter. We therefore argue that they represent two specific levels of a continuous spectrum 3D communities, rather than seeing them as different structural entities. |
Durang, Xavier; Lee, Sungmin; Lizana, Ludvig; Jeon, Jae-Hyung First-passage statistics under stochastic resetting in bounded domains Journal Article Journal of Physics A: Mathematical and Theoretical, 52 (22), pp. 224001, 2019. @article{Durang_2019, title = {First-passage statistics under stochastic resetting in bounded domains}, author = {Xavier Durang and Sungmin Lee and Ludvig Lizana and Jae-Hyung Jeon}, url = {https://doi.org/10.1088%2F1751-8121%2Fab15f5}, doi = {10.1088/1751-8121/ab15f5}, year = {2019}, date = {2019-04-01}, journal = {Journal of Physics A: Mathematical and Theoretical}, volume = {52}, number = {22}, pages = {224001}, publisher = {IOP Publishing}, abstract = {We investigate the first-passage problem where a diffusive searcher stochastically resets to a fixed position at a constant rate in a bounded domain. We put forward an analytical framework for this problem where the resetting rate r, the resetting position x r , the initial position x 0, the domain size L, and the particle’s diffusion constant D are independent variables. From this we obtain analytical expressions for the mean-first passage time, survival probability and the first-passage time density in Laplace space in terms of the above independent variables, and closed forms in time-domain expression in some cases. For the first-passage time distributions their full-time profiles in time-domain are numerically obtained and validated by Monte Carlo simulations. We show that for the general resetting condition the first-passage process has rich nontrivial features as it combines effects from resetting and the finiteness of the domain. A phase diagram showing the regions for resetting-enhanced and -suppressed first-passages is obtained analytically. Counter-intuitively, resetting facilitates the first-passage event even if the particle resets to a position that is further away from the target than where it started. Finally, we show that averaging over resetting positions, resetting never helps the search compared to a random search, unless the resetting position is displaced from the initial position.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We investigate the first-passage problem where a diffusive searcher stochastically resets to a fixed position at a constant rate in a bounded domain. We put forward an analytical framework for this problem where the resetting rate r, the resetting position x r , the initial position x 0, the domain size L, and the particle’s diffusion constant D are independent variables. From this we obtain analytical expressions for the mean-first passage time, survival probability and the first-passage time density in Laplace space in terms of the above independent variables, and closed forms in time-domain expression in some cases. For the first-passage time distributions their full-time profiles in time-domain are numerically obtained and validated by Monte Carlo simulations. We show that for the general resetting condition the first-passage process has rich nontrivial features as it combines effects from resetting and the finiteness of the domain. A phase diagram showing the regions for resetting-enhanced and -suppressed first-passages is obtained analytically. Counter-intuitively, resetting facilitates the first-passage event even if the particle resets to a position that is further away from the target than where it started. Finally, we show that averaging over resetting positions, resetting never helps the search compared to a random search, unless the resetting position is displaced from the initial position. |
Sobhy, Haitham; Kumar, Rajendra; Lewerentz, Jacob; Lizana, Ludvig; Stenberg, Per Highly interacting regions of the human genome are enriched with enhancers and bound by DNA repair proteins Journal Article Scientific Reports, 9 , 2019. @article{Sobhy2019, title = {Highly interacting regions of the human genome are enriched with enhancers and bound by DNA repair proteins}, author = {Haitham Sobhy and Rajendra Kumar and Jacob Lewerentz and Ludvig Lizana and Per Stenberg}, url = {https://www.nature.com/articles/s41598-019-40770-9}, doi = {https://doi.org/10.1038/s41598-019-40770-9}, year = {2019}, date = {2019-03-14}, journal = {Scientific Reports}, volume = {9}, abstract = {In specific cases, chromatin clearly forms long-range loops that place distant regulatory elements in close proximity to transcription start sites, but we have limited understanding of many loops identified by Chromosome Conformation Capture (such as Hi-C) analyses. In efforts to elucidate their characteristics and functions, we have identified highly interacting regions (HIRs) using intra-chromosomal Hi-C datasets with a new computational method based on looking at the eigenvector that corresponds to the smallest eigenvalue (here unity). Analysis of these regions using ENCODE data shows that they are in general enriched in bound factors involved in DNA damage repair and have actively transcribed genes. However, both highly transcribed regions as well as transcriptionally inactive regions can form HIRs. The results also indicate that enhancers and super-enhancers in particular form long-range interactions within the same chromosome. The accumulation of DNA repair factors in most identified HIRs suggests that protection from DNA damage in these regions is essential for avoidance of detrimental rearrangements.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In specific cases, chromatin clearly forms long-range loops that place distant regulatory elements in close proximity to transcription start sites, but we have limited understanding of many loops identified by Chromosome Conformation Capture (such as Hi-C) analyses. In efforts to elucidate their characteristics and functions, we have identified highly interacting regions (HIRs) using intra-chromosomal Hi-C datasets with a new computational method based on looking at the eigenvector that corresponds to the smallest eigenvalue (here unity). Analysis of these regions using ENCODE data shows that they are in general enriched in bound factors involved in DNA damage repair and have actively transcribed genes. However, both highly transcribed regions as well as transcriptionally inactive regions can form HIRs. The results also indicate that enhancers and super-enhancers in particular form long-range interactions within the same chromosome. The accumulation of DNA repair factors in most identified HIRs suggests that protection from DNA damage in these regions is essential for avoidance of detrimental rearrangements. |
Kumar, Rajendra; Lizana, Ludvig; Stenberg, Per Genomic 3D compartments emerge from unfolding mitotic chromosomes Journal Article Chromosoma, 128 , pp. 15-20, 2019, ISSN: 1432-0886. @article{Kumar2018, title = {Genomic 3D compartments emerge from unfolding mitotic chromosomes}, author = {Rajendra Kumar and Ludvig Lizana and Per Stenberg}, url = {https://doi.org/10.1007/s00412-018-0684-7}, doi = {10.1007/s00412-018-0684-7}, issn = {1432-0886}, year = {2019}, date = {2019-03-01}, journal = {Chromosoma}, volume = {128}, pages = {15-20}, abstract = {The 3D organisation of the genome in interphase cells is not a randomly folded polymer. Rather, experiments show that chromosomes arrange into a network of 3D compartments that correlate with biological processes, such as transcription, chromatin modifications and protein binding. However, these compartments do not exist during cell division when the DNA is condensed, and it is unclear how and when they emerge. In this paper, we focus on the early stages after cell division as the chromosomes start to decondense. We use a simple polymer model to understand the types of 3D structures that emerge from local unfolding of a compact initial state. From simulations, we recover 3D compartments, such as TADs and A/B compartments that are consistently detected in chromosome capture experiments across cell types and organisms. This suggests that the large-scale 3D organisation is a result of an inflation process.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The 3D organisation of the genome in interphase cells is not a randomly folded polymer. Rather, experiments show that chromosomes arrange into a network of 3D compartments that correlate with biological processes, such as transcription, chromatin modifications and protein binding. However, these compartments do not exist during cell division when the DNA is condensed, and it is unclear how and when they emerge. In this paper, we focus on the early stages after cell division as the chromosomes start to decondense. We use a simple polymer model to understand the types of 3D structures that emerge from local unfolding of a compact initial state. From simulations, we recover 3D compartments, such as TADs and A/B compartments that are consistently detected in chromosome capture experiments across cell types and organisms. This suggests that the large-scale 3D organisation is a result of an inflation process. |
Nyberg, Markus; Lizana, Ludvig Persistence of Non-Markovian Gaussian Stationary Processes in Discrete Time Journal Article Physical Review E, 97 (4), pp. 040101, 2018. @article{nyberg2018persistence, title = {Persistence of Non-Markovian Gaussian Stationary Processes in Discrete Time}, author = {Markus Nyberg and Ludvig Lizana}, doi = {10.1103/PhysRevE.97.040101}, year = {2018}, date = {2018-01-01}, journal = {Physical Review E}, volume = {97}, number = {4}, pages = {040101}, publisher = {APS doi=10.1103/PhysRevE.97.040101}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Nyberg, Markus; Lizana, Ludvig; Ambjörnsson, Tobias Zero-crossing statistics for non-Markovian time series Journal Article Physical Review E, 97 (3), pp. 032114, 2018. @article{nyberg2018zero, title = {Zero-crossing statistics for non-Markovian time series}, author = {Markus Nyberg and Ludvig Lizana and Tobias Ambjörnsson}, doi = {10.1103/PhysRevE.97.032114}, year = {2018}, date = {2018-01-01}, journal = {Physical Review E}, volume = {97}, number = {3}, pages = {032114}, publisher = {APS doi=10.1103/PhysRevE.97.032114}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Vasilyev, Oleg A; Lizana, Ludvig; Oshanin, Gleb Smoluchowski rate for diffusion-controlled reactions of molecules with antenna Journal Article Journal of Physics A: Mathematical and Theoretical, 50 (26), pp. 264004, 2017. @article{vasilyev2017smoluchowski, title = {Smoluchowski rate for diffusion-controlled reactions of molecules with antenna}, author = {Oleg A Vasilyev and Ludvig Lizana and Gleb Oshanin}, doi = {http://dx.doi.org/10.1088/1751-8121/aa7226}, year = {2017}, date = {2017-01-01}, journal = {Journal of Physics A: Mathematical and Theoretical}, volume = {50}, number = {26}, pages = {264004}, publisher = {IOP Publishing}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kumar, Rajendra; Sobhy, Haitham; Stenberg, Per; Lizana, Ludvig Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps Journal Article Nucleic acids research, 45 (17), pp. e152–e152, 2017. @article{kumar2017genome, title = {Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps}, author = {Rajendra Kumar and Haitham Sobhy and Per Stenberg and Ludvig Lizana}, doi = {10.1093/nar/gkx644}, year = {2017}, date = {2017-01-01}, journal = {Nucleic acids research}, volume = {45}, number = {17}, pages = {e152--e152}, publisher = {Oxford University Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Nyberg, Markus; Ambjörnsson, Tobias; Lizana, Ludvig A simple method to calculate first-passage time densities with arbitrary initial conditions Journal Article New Journal of Physics, 18 (6), pp. 063019, 2016. @article{nyberg2016simple, title = {A simple method to calculate first-passage time densities with arbitrary initial conditions}, author = {Markus Nyberg and Tobias Ambjörnsson and Ludvig Lizana}, doi = {10.1088/1367-2630/18/6/063019}, year = {2016}, date = {2016-01-01}, journal = {New Journal of Physics}, volume = {18}, number = {6}, pages = {063019}, publisher = {IOP Publishing doi=10.1088/1367-2630/18/6/063019}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lizana, Ludvig; Ambjörnsson, Tobias; Lomholt, Michael A Tracer particles in two-dimensional elastic networks diffuse logarithmically slow Journal Article Journal of Physics A: Mathematical and Theoretical, 50 (3), pp. 034001, 2016. @article{lizana2016tracer, title = {Tracer particles in two-dimensional elastic networks diffuse logarithmically slow}, author = {Ludvig Lizana and Tobias Ambjörnsson and Michael A Lomholt}, doi = {http://dx.doi.org/10.1088/1751-8121/50/3/034001}, year = {2016}, date = {2016-01-01}, journal = {Journal of Physics A: Mathematical and Theoretical}, volume = {50}, number = {3}, pages = {034001}, publisher = {IOP Publishing}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Ahlberg, Sebastian; Ambjörnsson, Tobias; Lizana, Ludvig Many-body effects on tracer particle diffusion with applications for single-protein dynamics on DNA Journal Article New Journal of Physics, 17 (4), pp. 043036, 2015. @article{ahlberg2015many, title = {Many-body effects on tracer particle diffusion with applications for single-protein dynamics on DNA}, author = {Sebastian Ahlberg and Tobias Ambjörnsson and Ludvig Lizana}, doi = {http://dx.doi.org/10.1088/1367-2630/17/4/043036}, year = {2015}, date = {2015-01-01}, journal = {New Journal of Physics}, volume = {17}, number = {4}, pages = {043036}, publisher = {IOP Publishing}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lizana, Ludvig; Lomholt, Michael A; Ambjörnsson, Tobias Single-file diffusion with non-thermal initial conditions Journal Article Physica A: Statistical Mechanics and its Applications, 395 , pp. 148–153, 2014. @article{lizana2014single, title = {Single-file diffusion with non-thermal initial conditions}, author = {Ludvig Lizana and Michael A Lomholt and Tobias Ambjörnsson}, doi = {http://dx.doi.org/10.1016/j.physa.2013.10.025}, year = {2014}, date = {2014-01-01}, journal = {Physica A: Statistical Mechanics and its Applications}, volume = {395}, pages = {148--153}, publisher = {North-Holland}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Sanders, Lloyd P; Lomholt, Michael A; Lizana, Ludvig; Fogelmark, Karl; Metzler, Ralf; Ambjörnsson, Tobias Severe slowing-down and universality of the dynamics in disordered interacting many-body systems: ageing and ultraslow diffusion Journal Article New Journal of Physics, 16 (11), pp. 113050, 2014. @article{sanders2014severe, title = {Severe slowing-down and universality of the dynamics in disordered interacting many-body systems: ageing and ultraslow diffusion}, author = {Lloyd P Sanders and Michael A Lomholt and Ludvig Lizana and Karl Fogelmark and Ralf Metzler and Tobias Ambjörnsson}, doi = {http://dx.doi.org/10.1088/1367-2630/16/11/113050}, year = {2014}, date = {2014-01-01}, journal = {New Journal of Physics}, volume = {16}, number = {11}, pages = {113050}, publisher = {IOP Publishing}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lizana, Ludvig; Grosberg, Alexander Y Exact expressions for the mobility and electrophoretic mobility of a weakly charged sphere in a simple electrolyte Journal Article EPL (Europhysics Letters), 104 (6), pp. 68004, 2014. @article{lizana2014exact, title = {Exact expressions for the mobility and electrophoretic mobility of a weakly charged sphere in a simple electrolyte}, author = {Ludvig Lizana and Alexander Y Grosberg}, doi = {http://dx.doi.org/10.1209/0295-5075/104/68004}, year = {2014}, date = {2014-01-01}, journal = {EPL (Europhysics Letters)}, volume = {104}, number = {6}, pages = {68004}, publisher = {IOP Publishing}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Forsling, Robin; Sanders, Lloyd P; Ambjörnsson, Tobias; Lizana, Ludvig Non-Markovian effects in the first-passage dynamics of obstructed tracer particle diffusion in one-dimensional systems Journal Article The Journal of chemical physics, 141 (9), pp. 094902, 2014. @article{forsling2014non, title = {Non-Markovian effects in the first-passage dynamics of obstructed tracer particle diffusion in one-dimensional systems}, author = {Robin Forsling and Lloyd P Sanders and Tobias Ambjörnsson and Ludvig Lizana}, doi = {http://dx.doi.org/10.1063/1.4894117}, year = {2014}, date = {2014-01-01}, journal = {The Journal of chemical physics}, volume = {141}, number = {9}, pages = {094902}, publisher = {AIP}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Metzler, Ralf; Sanders, Lloyd; Lomholt, Michael Andersen; Lizana, Ludvig; Fogelmark, Karl; Ambjörnsson, Tobias Ageing single file motion Journal Article The European Physical Journal Special Topics, 223 (14), pp. 3287–3293, 2014. @article{metzler2014ageing, title = {Ageing single file motion}, author = {Ralf Metzler and Lloyd Sanders and Michael Andersen Lomholt and Ludvig Lizana and Karl Fogelmark and Tobias Ambjörnsson}, doi = {http://dx.doi.org/10.1140/epjst/e2014-02333-5}, year = {2014}, date = {2014-01-01}, journal = {The European Physical Journal Special Topics}, volume = {223}, number = {14}, pages = {3287--3293}, publisher = {Springer Berlin Heidelberg}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Mirshahvalad, Atieh; Viamontes, Alcides; Lizana, Ludvig; Rosvall, Martin Dynamics of interacting information waves in networks Journal Article Physical Review E, 89 (1), 2014. @article{Mirshahvalad_2014, title = {Dynamics of interacting information waves in networks}, author = {Atieh Mirshahvalad and Alcides Viamontes and Ludvig Lizana and Martin Rosvall}, url = {https://doi.org/10.1103%2Fphysreve.89.012809}, doi = {10.1103/physreve.89.012809}, year = {2014}, date = {2014-01-01}, journal = {Physical Review E}, volume = {89}, number = {1}, publisher = {American Physical Society (APS)}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lund, Halvor; Lizana, Ludvig; Simonsen, Ingve Effects of city-size heterogeneity on epidemic spreading in a metapopulation: a reaction-diffusion approach Journal Article Journal of statistical physics, 151 (1-2), pp. 367–382, 2013. @article{lund2013effects, title = {Effects of city-size heterogeneity on epidemic spreading in a metapopulation: a reaction-diffusion approach}, author = {Halvor Lund and Ludvig Lizana and Ingve Simonsen}, doi = {http://dx.doi.org/10.1007/s10955-013-0690-3}, year = {2013}, date = {2013-01-01}, journal = {Journal of statistical physics}, volume = {151}, number = {1-2}, pages = {367--382}, publisher = {Springer US}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lomholt, Michael A; Lizana, Ludvig; Metzler, Ralf; Ambjörnsson, Tobias Microscopic origin of the logarithmic time evolution of aging processes in complex systems Journal Article Physical review letters, 110 (20), pp. 208301, 2013. @article{lomholt2013microscopic, title = {Microscopic origin of the logarithmic time evolution of aging processes in complex systems}, author = {Michael A Lomholt and Ludvig Lizana and Ralf Metzler and Tobias Ambjörnsson}, doi = {http://dx.doi.org/10.1103/PhysRevLett.110.208301}, year = {2013}, date = {2013-01-01}, journal = {Physical review letters}, volume = {110}, number = {20}, pages = {208301}, publisher = {American Physical Society}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Pigolotti, Simone; Lizana, Ludvig; Otzen, Daniel; Sneppen, Kim Quality control system response to stochastic growth of amyloid fibrils Journal Article FEBS letters, 587 (9), pp. 1405–1410, 2013. @article{pigolotti2013quality, title = {Quality control system response to stochastic growth of amyloid fibrils}, author = {Simone Pigolotti and Ludvig Lizana and Daniel Otzen and Kim Sneppen}, doi = {http://dx.doi.org/10.1016/j.febslet.2013.03.018}, year = {2013}, date = {2013-01-01}, journal = {FEBS letters}, volume = {587}, number = {9}, pages = {1405--1410}, publisher = {No longer published by Elsevier}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lomholt, Michael A; Lizana, Ludvig; Ambjörnsson, Tobias Dissimilar bouncy walkers Journal Article The Journal of chemical physics, 134 (4), pp. 01B625, 2011. @article{lomholt2011dissimilar, title = {Dissimilar bouncy walkers}, author = {Michael A Lomholt and Ludvig Lizana and Tobias Ambjörnsson}, doi = {http://dx.doi.org/10.1063/1.3526941}, year = {2011}, date = {2011-01-01}, journal = {The Journal of chemical physics}, volume = {134}, number = {4}, pages = {01B625}, publisher = {AIP}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lizana, Ludvig; Mitarai, Namiko; Sneppen, Kim; Nakanishi, Hiizu Modeling the spatial dynamics of culture spreading in the presence of cultural strongholds Journal Article Physical Review E, 83 (6), pp. 066116, 2011. @article{lizana2011modeling, title = {Modeling the spatial dynamics of culture spreading in the presence of cultural strongholds}, author = {Ludvig Lizana and Namiko Mitarai and Kim Sneppen and Hiizu Nakanishi}, doi = {http://dx.doi.org/10.1103/PhysRevE.83.066116}, year = {2011}, date = {2011-01-01}, journal = {Physical Review E}, volume = {83}, number = {6}, pages = {066116}, publisher = {APS}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Bernhardsson, Sebastian; Gerlee, Philip; Lizana, Ludvig Structural correlations in bacterial metabolic networks Journal Article BMC evolutionary biology, 11 (1), pp. 20, 2011. @article{bernhardsson2011structural, title = {Structural correlations in bacterial metabolic networks}, author = {Sebastian Bernhardsson and Philip Gerlee and Ludvig Lizana}, doi = {http://dx.doi.org/10.1186/1471-2148-11-20}, year = {2011}, date = {2011-01-01}, journal = {BMC evolutionary biology}, volume = {11}, number = {1}, pages = {20}, publisher = {BioMed Central}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lizana, Ludvig; Ambjörnsson, Tobias; Taloni, Alessandro; Barkai, Eli; Lomholt, Michael A Foundation of fractional Langevin equation: harmonization of a many-body problem Journal Article Physical Review E, 81 (5), pp. 051118, 2010. @article{lizana2010foundation, title = {Foundation of fractional Langevin equation: harmonization of a many-body problem}, author = {Ludvig Lizana and Tobias Ambjörnsson and Alessandro Taloni and Eli Barkai and Michael A Lomholt}, doi = {http://dx.doi.org/10.1103/PhysRevE.81.051118}, year = {2010}, date = {2010-01-01}, journal = {Physical Review E}, volume = {81}, number = {5}, pages = {051118}, publisher = {American Physical Society}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Jesorka, Aldo; Lizana, Ludvig; Konkoli, Zoran; Czolkos, Ilja; Orwar, Owe Controlling Chemistry in Dynamic Nanoscale Systems Incollection Single Molecule Spectroscopy in Chemistry, Physics and Biology, pp. 449–468, Springer, Berlin, Heidelberg, 2010. @incollection{jesorka2010controlling, title = {Controlling Chemistry in Dynamic Nanoscale Systems}, author = {Aldo Jesorka and Ludvig Lizana and Zoran Konkoli and Ilja Czolkos and Owe Orwar}, doi = {http://dx.doi.org/10.1007/978-3-642-02597-6_23}, year = {2010}, date = {2010-01-01}, booktitle = {Single Molecule Spectroscopy in Chemistry, Physics and Biology}, pages = {449--468}, publisher = {Springer, Berlin, Heidelberg}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
Lizana, Ludvig; Rosvall, Martin; Sneppen, Kim Time Walkers and Spatial Dynamics of Aging Information Journal Article Physical Review Letters, 104 (4), 2010. @article{Lizana_2010, title = {Time Walkers and Spatial Dynamics of Aging Information}, author = {Ludvig Lizana and Martin Rosvall and Kim Sneppen}, url = {https://doi.org/10.1103%2Fphysrevlett.104.040603}, doi = {10.1103/physrevlett.104.040603}, year = {2010}, date = {2010-01-01}, journal = {Physical Review Letters}, volume = {104}, number = {4}, publisher = {American Physical Society (APS)}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lizana, Ludvig; Konkoli, Zoran; Bauer, Brigitte; Jesorka, Aldo; Orwar, Owe Controlling chemistry by geometry in nanoscale systems Journal Article Annual review of physical chemistry, 60 , pp. 449–468, 2009. @article{lizana2009controlling, title = {Controlling chemistry by geometry in nanoscale systems}, author = {Ludvig Lizana and Zoran Konkoli and Brigitte Bauer and Aldo Jesorka and Owe Orwar}, doi = {http://dx.doi.org/10.1146/annurev.physchem.040808.090255}, year = {2009}, date = {2009-01-01}, journal = {Annual review of physical chemistry}, volume = {60}, pages = {449--468}, publisher = {Annual Reviews}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lizana, Ludvig; Ambjörnsson, Tobias Diffusion of finite-sized hard-core interacting particles in a one-dimensional box: Tagged particle dynamics Journal Article Physical Review E, 80 (5), pp. 051103, 2009. @article{lizana2009diffusion, title = {Diffusion of finite-sized hard-core interacting particles in a one-dimensional box: Tagged particle dynamics}, author = {Ludvig Lizana and Tobias Ambjörnsson}, doi = {http://dx.doi.org/10.1103/PhysRevE.80.051103}, year = {2009}, date = {2009-01-01}, journal = {Physical Review E}, volume = {80}, number = {5}, pages = {051103}, publisher = {American Physical Society}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Sneppen, Kim; Lizana, Ludvig; Jensen, Mogens H; Pigolotti, Simone; Otzen, Daniel Modeling proteasome dynamics in Parkinson's disease Journal Article Physical biology, 6 (3), pp. 036005, 2009. @article{sneppen2009modeling, title = {Modeling proteasome dynamics in Parkinson's disease}, author = {Kim Sneppen and Ludvig Lizana and Mogens H Jensen and Simone Pigolotti and Daniel Otzen}, year = {2009}, date = {2009-01-01}, journal = {Physical biology}, volume = {6}, number = {3}, pages = {036005}, publisher = {IOP Publishing doi=http://dx.doi.org/10.1088/1478-3975/6/3/036005}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Gerlee, Philip; Lizana, Ludvig; Sneppen, Kim Pathway identification by network pruning in the metabolic network of Escherichia coli Journal Article Bioinformatics, 25 (24), pp. 3282–3288, 2009. @article{gerlee2009pathway, title = {Pathway identification by network pruning in the metabolic network of Escherichia coli}, author = {Philip Gerlee and Ludvig Lizana and Kim Sneppen}, doi = {http://dx.doi.org/10.1093/bioinformatics/btp575}, year = {2009}, date = {2009-01-01}, journal = {Bioinformatics}, volume = {25}, number = {24}, pages = {3282--3288}, publisher = {Oxford University Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lizana, Ludvig; Ambjörnsson, Tobias Single-file diffusion in a box Journal Article Physical review letters, 100 (20), pp. 200601, 2008. @article{lizana2008single, title = {Single-file diffusion in a box}, author = {Ludvig Lizana and Tobias Ambjörnsson}, doi = {http://dx.doi.org/10.1103/PhysRevLett.100.200601}, year = {2008}, date = {2008-01-01}, journal = {Physical review letters}, volume = {100}, number = {20}, pages = {200601}, publisher = {APS}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lizana, Ludvig; Bauer, Brigitte; Orwar, Owe Controlling the rates of biochemical reactions and signaling networks by shape and volume changes Journal Article Proceedings of the National Academy of Sciences, 105 (11), pp. 4099–4104, 2008. @article{lizana2008controlling, title = {Controlling the rates of biochemical reactions and signaling networks by shape and volume changes}, author = {Ludvig Lizana and Brigitte Bauer and Owe Orwar}, doi = {http://dx.doi.org/10.1073/pnas.0709932105}, year = {2008}, date = {2008-01-01}, journal = {Proceedings of the National Academy of Sciences}, volume = {105}, number = {11}, pages = {4099--4104}, publisher = {National Acad Sciences}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Ambjörnsson, Tobias; Lizana, Ludvig; Lomholt, Michael A; Silbey, Robert J Single-file dynamics with different diffusion constants Journal Article The Journal of chemical physics, 129 (18), pp. 11B612, 2008. @article{ambjornsson2008single, title = {Single-file dynamics with different diffusion constants}, author = {Tobias Ambjörnsson and Ludvig Lizana and Michael A Lomholt and Robert J Silbey}, doi = {http://dx.doi.org/10.1063/1.3009853}, year = {2008}, date = {2008-01-01}, journal = {The Journal of chemical physics}, volume = {129}, number = {18}, pages = {11B612}, publisher = {AIP}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Markström, Martin; Lizana, Ludvig; Orwar, Owe; Jesorka, Aldo Thermoactuated diffusion control in soft matter nanofluidic devices Journal Article Langmuir, 24 (9), pp. 5166–5171, 2008. @article{markstrom2008thermoactuated, title = {Thermoactuated diffusion control in soft matter nanofluidic devices}, author = {Martin Markström and Ludvig Lizana and Owe Orwar and Aldo Jesorka}, year = {2008}, date = {2008-01-01}, journal = {Langmuir}, volume = {24}, number = {9}, pages = {5166--5171}, publisher = {ACS Publications}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lizana, Ludvig; Konkoli, Zoran; Orwar, Owe Tunable filtering of chemical signals in a simple nanoscale reaction-diffusion network Journal Article The Journal of Physical Chemistry B, 111 (22), pp. 6214–6219, 2007. @article{lizana2007tunable, title = {Tunable filtering of chemical signals in a simple nanoscale reaction-diffusion network}, author = {Ludvig Lizana and Zoran Konkoli and Owe Orwar}, year = {2007}, date = {2007-01-01}, journal = {The Journal of Physical Chemistry B}, volume = {111}, number = {22}, pages = {6214--6219}, publisher = {ACS Publications doi=http://dx.doi.org/10.1021/jp068313p}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Sott, Kristin; Lobovkina, Tatsiana; Lizana, Ludvig; Tokarz, Michal; Bauer, Brigitte; Konkoli, Zoran; Orwar, Owe Controlling enzymatic reactions by geometry in a biomimetic nanoscale network Journal Article Nano letters, 6 (2), pp. 209–214, 2006. @article{sott2006controlling, title = {Controlling enzymatic reactions by geometry in a biomimetic nanoscale network}, author = {Kristin Sott and Tatsiana Lobovkina and Ludvig Lizana and Michal Tokarz and Brigitte Bauer and Zoran Konkoli and Owe Orwar}, doi = {http://dx.doi.org/10.1021/nl052078p}, year = {2006}, date = {2006-01-01}, journal = {Nano letters}, volume = {6}, number = {2}, pages = {209--214}, publisher = {ACS Publications}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lizana, Ludvig; Konkoli, Zoran Diffusive transport in networks built of containers and tubes Journal Article Physical Review E, 72 (2), pp. 026305, 2005. @article{lizana2005diffusive, title = {Diffusive transport in networks built of containers and tubes}, author = {Ludvig Lizana and Zoran Konkoli}, doi = {http://dx.doi.org/10.1103/PhysRevE.72.026305}, year = {2005}, date = {2005-01-01}, journal = {Physical Review E}, volume = {72}, number = {2}, pages = {026305}, publisher = {APS}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Our genetic code has more characters than 850 bible books with about 20,000 genes and millions of regulatory elements. Stored in a two meter long polymer that is folded into a volume smaller than a fog water droplet, how is our DNA organised in 3D to promote important interactions, while avoiding entanglement that erroneously may change how genes turn on and off? Ludvig Lizana runs a research group that applies methods from theoretical physics to figure out how.
Before becoming an associate professor at the physics department in Umeå, and an icelab member, Ludvig worked as a postdoc together with prof. Alexander Grosberg at New York University. Starting out studying electrophoretic motion of large macromolecules (that is, dragging large molecules through a fluid with an electric field), such as DNA, Ludvig got to know about the DNA folding problem which today is a large part of his research. Before moving to New York, Ludvig was a postdoc in prof. Kim Sneppen’s lab, center for models of life, at the Niels Bohr institute (Copenhagen, Denmark). There he worked on various problems such as evolution of metabolic networks in bacteria, protein aggregation in cells, molecular crowding in one dimensional systems (such as protein diffusion along DNA or colloidal particles in nano-channels), and information spreading in social systems. Ludvig did his undergraduate and PhD studies at Chalmers University (Gothenburg, Sweden) where he modeled reaction-diffusion processes in nanofluidic networks.
Current Projects
Modelling the 3D organisation of DNA.
Ludvig Lizana (IceLab), Per Stenberg (UmU), Rajendra Kumar (UmU), Sanghoon-Lee (Korean Institute for Advanced Studies, Seoul, Korea), Negar Nahali (IceLab)
Modelling the epigenetic memory in Drosophila.
Ludvig Lizana, Yuri Schwartz (UmU)
Diffusion in crowded biological systems.
Ludvig Lizana, Jae-Hyung Jeon (POSTECH university, Pohang, Korea), Tobias Ambjörnsson (Lund University, Sweden)
Target search in biological systems.
Ludvig Lizana, Markus Nyberg (IceLab), Xavier Durang (Korean Institute for Advanced Study, Seoul, Korea), Sungmin-Lee (Korea University, Seoul)
Stochastic processes and statistical physics.
Ludvig Lizana, Markus Nyberg (IceLab), Tobias Ambjörnsson (Lund University, Sweden), Michael A. Lomholt (University of Southern Denmark, Odense, Denmark)
Are administrations too big?
Ludvig Lizana, Sebastian Långström (UmU), Rikard Eriksson (UmU)
The Latest Posts
Check out the latest updates by this IceLabber here
How long does it take a protein to find a target on our DNA?
How long does it take a protein to find a target on our DNA? The problem To get many different processes started in our nucleus, we [...]
Meet Florian Heyder and Alexander Lindström, Master’s students at IceLab
Florian Heyde and Alexander Lindström work on the projects supervised by Ludvig Lizana, senior lecturer at Department of Physics, IceLab. Here they tell us about their experiences. Florian Exchange Master’s student in Technical Physics, [...]
Hive Talk Board: Micro Loans and Crowdfunding in the Charity Space with Ludvig Lizana
Micro Loans and Crowdfunding in the Charity Space with Ludvig Lizana Hive Talk Snippet Ludvig began our season of hive talks with a presentation of the kiva loan data [www.kiva.org] [...]
The Genome Contact Map Explorer
The genome contact map explorer: a tool to find patterns in piles of DNA contact data The problem Every chromosome in our cells is a long polymer that is packaged [...]
What’s your message?
What’s your message? Public speaking with twice the impact, using half the effort. Author: Cam Barber This book debunks several myths about public speaking and gives handy tips on how to [...]